CDS complement (370 - 483)
  /gene="1"
  /product="gp1"
  /function="hypothetical protein"
  /locus tag="RunningBrook_1"
    /note=Original Glimmer call @bp 483 has strength 2.76
    /note=SSC: 483-370 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein SEA_MUSETTA_2 [Microbacterium phage Musetta] ],,NCBI, q1:s16 100.0% 1.54685E-17 GAP: 334 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.33, -4.2236164172743695, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MUSETTA_2 [Microbacterium phage Musetta] ],,AXH50162,71.1538,1.54685E-17 SIF-HHPRED:  SIF-Syn: DustyDino, Yuma, Musetta
    /note=GeneMark does not include all coding potential. Starterator only shows one other member who proposed the same start site as ours. Blast is similar but not 1 to 1 with other members. Third highest z score and second least negative overall score.
    /note=HHpred had no hit.

CDS complement (818 - 1114)
  /gene="2"
  /product="gp2"
  /function="hypothetical protein"
  /locus tag="RunningBrook_2"
    /note=Original Glimmer call @bp 1114 has strength 3.78; Genemark calls start at 1114
    /note=SSC: 1114-818 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_4 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 8.98687E-65 GAP: 212 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.12, -4.394706008439538, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_4 [Microbacterium phage DustyDino] ],,URM87409,100.0,8.98687E-65 SIF-HHPRED:  SIF-Syn: DustyDino and Necrophoxinus
    /note=GeneMark includes all coding potential. Starterator shows DustyDino chose same start site. Blast is 1 to 1 with DustyDino. Second highest z score and least negative overall score.
    /note=HHpred had high probability but bad e-value.

CDS complement (1327 - 1629)
  /gene="3"
  /product="gp3"
  /function="hypothetical protein"
  /locus tag="RunningBrook_3"
    /note=Original Glimmer call @bp 1605 has strength 1.92; Genemark calls start at 1629
    /note=SSC: 1629-1327 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_5 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.55359E-66 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.752, -5.443606692405957, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_5 [Microbacterium phage DustyDino] ],,URM87410,100.0,1.55359E-66 SIF-HHPRED:  SIF-Syn: DustyDino, Yuma, Fork, and Necrophoxinus
    /note=All GeneMark Coding Potential, Blast is 1:1 with DustyDino and others, Starterator matches with DustyDino and others. No best RBS values.

CDS complement (1629 - 2225)
  /gene="4"
  /product="gp4"
  /function="hypothetical protein"
  /locus tag="RunningBrook_4"
    /note=Original Glimmer call @bp 2225 has strength 13.57; Genemark calls start at 2225
    /note=SSC: 2225-1629 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_6 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.71473E-145 GAP: 80 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.758, -5.080915947802713, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_6 [Microbacterium phage DustyDino] ],,URM87411,100.0,1.71473E-145 SIF-HHPRED:  SIF-Syn: DustyDino and Necrophoxinus
    /note=GeneMark includes all coding potential. Starterator shows almost every other member chose same start site. Blast is 1 to 1 with DustyDino and similar to other members. 5th highest z score and 4th least negative score.

CDS complement (2306 - 2692)
  /gene="5"
  /product="gp5"
  /function="hypothetical protein"
  /locus tag="RunningBrook_5"
    /note=Original Glimmer call @bp 2692 has strength 16.03; Genemark calls start at 2692
    /note=SSC: 2692-2306 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_7 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.00791E-86 GAP: 27 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.934, -5.058605177999316, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_7 [Microbacterium phage DustyDino] ],,URM87412,100.0,1.00791E-86 SIF-HHPRED:  SIF-Syn: DustyDino, Musetta, and Necrophoxinus
    /note=GeneMark includes all coding potential. Starterator shows all other members except 1. Blast is 1 to 1 with DustyDino and very close to other members. 2nd lowest z score and 3rd least negative overall score.
    /note=
    /note=HHpred had probability of 89.4% but bad e-value.

CDS complement (2720 - 3067)
  /gene="6"
  /product="gp6"
  /function="hypothetical protein"
  /locus tag="RunningBrook_6"
    /note=Original Glimmer call @bp 3067 has strength 15.6; Genemark calls start at 3067
    /note=SSC: 3067-2720 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_8 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.10407E-76 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.951, -2.5594668560256912, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_8 [Microbacterium phage DustyDino] ],,URM87413,100.0,1.10407E-76 SIF-HHPRED:  SIF-Syn: DustyDino, Necrophoxinus, and Musetta
    /note=GeneMark includes all coding potential. Starterator shows DustyDino and other members chose same start site. Blast is 1 to 1 with DustyDino. Highest z score and least negative overall score.
    /note=
    /note=HHpred had good probability and e-value for PF12098.11

CDS complement (3134 - 3412)
  /gene="7"
  /product="gp7"
  /function="hypothetical protein"
  /locus tag="RunningBrook_7"
    /note=Original Glimmer call @bp 3274 has strength 4.59; Genemark calls start at 3412
    /note=SSC: 3412-3134 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_9 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.21931E-59 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.951, -2.5594668560256912, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_9 [Microbacterium phage DustyDino] ],,URM87414,100.0,1.21931E-59 SIF-HHPRED:  SIF-Syn: DustyDino and Welcome
    /note=GeneMark includes all coding potential. Starterator is not informative. Blast is 1 to 1 with DustyDino and similar to others. Highest z score and least negative overall score.

CDS complement (3423 - 3578)
  /gene="8"
  /product="gp8"
  /function="hypothetical protein"
  /locus tag="RunningBrook_8"
    /note=Original Glimmer call @bp 3578 has strength 4.12; Genemark calls start at 3578
    /note=SSC: 3578-3423 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MUSETTA_123 [Microbacterium phage Musetta] ],,NCBI, q1:s1 100.0% 7.28713E-27 GAP: 646 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.829, -2.8793565916978188, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MUSETTA_123 [Microbacterium phage Musetta] ],,AXH50170,100.0,7.28713E-27 SIF-HHPRED:  SIF-Syn: DustyDino, Musetta, and Yuma
    /note=GeneMark includes all coding potential. Starterator shows DustyDino and other members chose same start site. Blast is 1 to 1 with 4 other members. Highest z score and least negative overall score.

CDS 4225 - 4386
  /gene="9"
  /product="gp9"
  /function="hypothetical protein"
  /locus tag="RunningBrook_9"
    /note=Original Glimmer call @bp 4225 has strength 14.78; Genemark calls start at 4225
    /note=SSC: 4225-4386 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_11 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 6.46982E-27 GAP: 646 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.085, -2.356391881054909, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_11 [Microbacterium phage DustyDino]],,URM87416,100.0,6.46982E-27 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Musetta
    /note=GeneMark algorithm includes all coding potential.  Starterator shows that other members, including Dusty_dino which has a genome similar to ours, has the same start as ours.  Blast showed that gene 11 was 1 to 1 with dusty_dino.  The RBS had least negative score and highest z value.
    /note=
    /note=HHpred has 82.7% probability for 5ET3_B, but low e-value

CDS 4379 - 4678
  /gene="10"
  /product="gp10"
  /function="hypothetical protein"
  /locus tag="RunningBrook_10"
    /note=Original Glimmer call @bp 4379 has strength 8.03; Genemark calls start at 4379
    /note=SSC: 4379-4678 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_12 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 4.89489E-65 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.38, -4.293682540785866, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_12 [Microbacterium phage Lyell] ],,AXC36119,100.0,4.89489E-65 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Necrophoxinus
    /note=GeneMark includes all coding potential.  Starterator shows other members had this same start codon approved.  Blast showed 1 to 1 connection with another member who had the same start in starterator.  RBS had a high z score and a low negative score, but not the best in each category.
    /note=
    /note=HHpred shows 82.6% hit for 6JSX_A, but bad e-value

CDS 4681 - 5079
  /gene="11"
  /product="gp11"
  /function="hypothetical protein"
  /locus tag="RunningBrook_11"
    /note=Original Glimmer call @bp 4681 has strength 8.34; Genemark calls start at 4681
    /note=SSC: 4681-5079 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_13 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 6.36278E-92 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.445, -3.6907860541164537, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_13 [Microbacterium phage DustyDino]],,URM87418,100.0,6.36278E-92 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Necrophoxinus
    /note=GeneMark includes all of the coding capacity.  Starterator shows other closely related members had same start site.  Blast was 1 to 1 with other closely related member, DustyDino.  RBS had low score and high overall z score, but not the best in each.

CDS 5076 - 5228
  /gene="12"
  /product="gp12"
  /function="hypothetical protein"
  /locus tag="RunningBrook_12"
    /note=Original Glimmer call @bp 5076 has strength 8.46; Genemark calls start at 5076
    /note=SSC: 5076-5228 CP: yes SCS: both ST: NI BLAST-Start: [DNA binding protein [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 9.64132E-28 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.425, -3.75071250087134, no F: hypothetical protein SIF-BLAST: ,,[DNA binding protein [Microbacterium phage DustyDino]],,URM87419,100.0,9.64132E-28 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Lyell
    /note=GeneMark includes all coding potential.  Other members in starterator chose the same start.  Blast is 1 to 1 with other member.  Has highest z score and second least negative overall score.
    /note=
    /note=DustyDino picked DNA binding protein because of synteny, but the phages that it mentioned did not have a known function in the same gene. HHPRED shows very high probability and good e-value for a metal binding protein, but not enough evidence to call it.

CDS 5225 - 5473
  /gene="13"
  /product="gp13"
  /function="hypothetical protein"
  /locus tag="RunningBrook_13"
    /note=Original Glimmer call @bp 5195 has strength 10.64; Genemark calls start at 5228
    /note=SSC: 5225-5473 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_15 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 4.49688E-52 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.46, -3.6776057178969577, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_15 [Microbacterium phage DustyDino]],,URM87420,100.0,4.49688E-52 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Welcome
    /note=GeneMark includes all coding potential.  Starterator shows DustyDino had same start.  Blast is 1 to 1 with DustyDino.  Not the highest z score nor the lowest negative score, but still has good values.  The two start sites before have excessive overlap with previous gene.
    /note=
    /note=High probability but bad e-value for cd15485.

CDS 5470 - 5712
  /gene="14"
  /product="gp14"
  /function="hypothetical protein"
  /locus tag="RunningBrook_14"
    /note=Original Glimmer call @bp 5473 has strength 6.06; Genemark calls start at 5473
    /note=SSC: 5470-5712 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_16 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 2.25828E-51 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.085, -2.356391881054909, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_16 [Microbacterium phage DustyDino]],,URM87421,100.0,2.25828E-51 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Fork
    /note=GeneMark includes all coding potential.  Starterator showed other close member, DustyDino, had same start.  Some other members had the third start picked, but DustyDino was the most recently approved.  Blast is 1 to 1 with said member.  Tied for highest z score, but second best overall score.  This start has slight overlap with previous gene (4 bp).

CDS 5846 - 6226
  /gene="15"
  /product="gp15"
  /function="hypothetical protein"
  /locus tag="RunningBrook_15"
    /note=Original Glimmer call @bp 5846 has strength 11.76; Genemark calls start at 5846
    /note=SSC: 5846-6226 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_17 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 5.67182E-86 GAP: 133 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.085, -2.338663114094478, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_17 [Microbacterium phage DustyDino]],,URM87422,100.0,5.67182E-86 SIF-HHPRED:  SIF-Syn: DustyDino, Necrophoxinus, and Musetta
    /note=GeneMark includes all coding potential.  Starterator shows that nearly every other member chose the same start site.  Blast is 1 to 1 with DustyDino.  Lowest negative score and highest z score.
    /note=
    /note=Almost 89.8% probability for 7OF0_V, but bad e-value

CDS 6226 - 6465
  /gene="16"
  /product="gp16"
  /function="hypothetical protein"
  /locus tag="RunningBrook_16"
    /note=Original Glimmer call @bp 6226 has strength 3.61; Genemark calls start at 6226
    /note=SSC: 6226-6465 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_18 [Microbacterium phage DustyDino]],,NCBI, q1:s2 100.0% 8.13744E-51 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.13, -4.294054598558697, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_18 [Microbacterium phage DustyDino]],,URM87423,98.75,8.13744E-51 SIF-HHPRED:  SIF-Syn: DustyDino, Necrophoxinus, and Lyell
    /note=GeneMark includes all coding potential.  Starterator showed DustyDino picked same start site.  Blast is 1 to 1 with DustyDino.  High z score and good overall score.

CDS 6462 - 6662
  /gene="17"
  /product="gp17"
  /function="hypothetical protein"
  /locus tag="RunningBrook_17"
    /note=Original Glimmer call @bp 6462 has strength 10.16; Genemark calls start at 6474
    /note=SSC: 6462-6662 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_19 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 2.35553E-39 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.854, -2.8454123590742793, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_19 [Microbacterium phage DustyDino]],,URM87424,100.0,2.35553E-39 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Necrophoxinus
    /note=GeneMark includes all coding potential.  Starterator showed many other members have same start site.  Blast is 1 to 1 with DustyDino.  The z value was the highest and the total score was the least negative.

CDS 6655 - 6819
  /gene="18"
  /product="gp18"
  /function="hypothetical protein"
  /locus tag="RunningBrook_18"
    /note=Original Glimmer call @bp 6655 has strength 7.58; Genemark calls start at 6655
    /note=SSC: 6655-6819 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_20 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 1.84226E-28 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.006, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_20 [Microbacterium phage Lyell] ],,AXC36127,100.0,1.84226E-28 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Necrophoxinus
    /note=GeneMark includes all coding potential.  Starterator shows that all other members chose the same start site.  Blast was 1 to 1 with multiple members.  Has highest z score and lowest negative score.

CDS 6828 - 7094
  /gene="19"
  /product="gp19"
  /function="hypothetical protein"
  /locus tag="RunningBrook_19"
    /note=Original Glimmer call @bp 6828 has strength 8.48; Genemark calls start at 6828
    /note=SSC: 6828-7094 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_21 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 3.79673E-56 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.347, -3.9166971242758706, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_21 [Microbacterium phage DustyDino]],,URM87426,100.0,3.79673E-56 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Lyell
    /note=GeneMark includes all coding potential.  All other members chose the same start site on starterator.  Blast is 1 to 1 with multiple members who chose the same start site.  Not the highest z score, but the least negative overall score.

CDS 7091 - 7345
  /gene="20"
  /product="gp20"
  /function="hypothetical protein"
  /locus tag="RunningBrook_20"
    /note=Original Glimmer call @bp 7094 has strength 15.12; Genemark calls start at 7094
    /note=SSC: 7091-7345 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_22 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 1.77156E-51 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.598, -3.83326386801984, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_22 [Microbacterium phage DustyDino]],,URM87427,100.0,1.77156E-51 SIF-HHPRED:  SIF-Syn: DustyDino, Necrophoxinus, and Fork
    /note=GeneMark includes all coding potential.  Starterator shows DustyDino and another member chose the same start site.  Blast is 1 to 1 with both of these members.  Second highest z score and lowest overall score.
    /note=
    /note=84.3% probability for 3KFU_J but bad e-value.

CDS 7345 - 7518
  /gene="21"
  /product="gp21"
  /function="hypothetical protein"
  /locus tag="RunningBrook_21"
    /note=Original Glimmer call @bp 7345 has strength 8.36; Genemark calls start at 7345
    /note=SSC: 7345-7518 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_NECROPHOXINUS_23 [Microbacterium phage Necrophoxinus] ],,NCBI, q1:s1 100.0% 2.59897E-33 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.758, -3.108788982793736, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NECROPHOXINUS_23 [Microbacterium phage Necrophoxinus] ],,QWS69389,100.0,2.59897E-33 SIF-HHPRED:  SIF-Syn: DustyDino, Necrophoxinus, and Fork
    /note=GeneMark includes all coding potential.  Starterator shows DustyDino and another member chose the same start site.  Blast is 1 to 1 with both of these members.  Second highest z score and lowest overall score.

CDS 7750 - 7914
  /gene="22"
  /product="gp22"
  /function="hypothetical protein"
  /locus tag="RunningBrook_22"
    /note=Original Glimmer call @bp 7750 has strength 13.2; Genemark calls start at 7822
    /note=SSC: 7750-7914 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_23 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 4.29869E-30 GAP: 231 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.283, -4.879056974934018, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_23 [Microbacterium phage Lyell] ],,AXC36130,100.0,4.29869E-30 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Musetta
    /note=GeneMark does not include all coding potential.  Starterator shows other members chose the same start site.  Blast is 1 to 1 with other members.  Highest z score, second lowest overall score.  Might have to recheck.

CDS 7914 - 8234
  /gene="23"
  /product="gp23"
  /function="hypothetical protein"
  /locus tag="RunningBrook_23"
    /note=Original Glimmer call @bp 7914 has strength 11.07; Genemark calls start at 7914
    /note=SSC: 7914-8234 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_24 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 1.46916E-70 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.989, -2.8298788511194775, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_24 [Microbacterium phage Lyell] ],,AXC36131,100.0,1.46916E-70 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Musetta
    /note=Prediction of 7914 to 8234 correct based on GeneMark, Starterator matches with other approved start codons, translation BLAST was 1 to 1 with Lyell_24 other approved phage, Best- least negative Z score.

CDS 8236 - 8439
  /gene="24"
  /product="gp24"
  /function="hypothetical protein"
  /locus tag="RunningBrook_24"
    /note=Original Glimmer call @bp 8278 has strength 1.96; Genemark calls start at 8236
    /note=SSC: 8236-8439 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_27 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 9.67706E-42 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.658, -4.085313187509542, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_27 [Microbacterium phage DustyDino]],,URM87431,100.0,9.67706E-42 SIF-HHPRED:  SIF-Syn: DustyDino, Necrophoxinus, and Fork
    /note=Change in predicted start codon site based on Glimmer and Genemark beginning at 8236 not 8278. . Starterator evidence from approved codon sites from Dusty Dino and others. BLAST compared to approved others was 1 to 1. Had the BEST most least negative final score from RBS. Close to the better, higher z score.

tRNA 8538 - 8594
  /gene="25"
  /product="tRNA-Asn(gtt)"
  /locus tag="RUNNINGBROOK_25"
    /note=tRNA-Asn(gtt)

tRNA 8678 - 8747
  /gene="26"
  /product="tRNA-Gly(tcc)"
  /locus tag="RUNNINGBROOK_26"
    /note=tRNA-Gly(tcc)

tRNA 8842 - 8907
  /gene="27"
  /product="tRNA-Thr(agt)"
  /locus tag="RUNNINGBROOK_27"
    /note=tRNA-Thr(agt)

CDS 9201 - 9506
  /gene="28"
  /product="gp28"
  /function="hypothetical protein"
  /locus tag="RunningBrook_28"
    /note=Original Glimmer call @bp 9201 has strength 10.57; Genemark calls start at 9201
    /note=SSC: 9201-9506 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_32 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 1.60321E-65 GAP: 761 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.085, -2.2763497933341483, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_32 [Microbacterium phage DustyDino]],,URM87432,100.0,1.60321E-65 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Musetta
    /note=Agree with predicted start codon from 9201 to 9506 according to Genemark, Starterator agreed with DustyDino_32 and other approved phage, BLAST has 1:1 with DustyDino_32 and others, RBS has best= highest Z score and final score.

CDS 9503 - 9766
  /gene="29"
  /product="gp29"
  /function="hypothetical protein"
  /locus tag="RunningBrook_29"
    /note=Original Glimmer call @bp 9503 has strength 4.85; Genemark calls start at 9503
    /note=SSC: 9503-9766 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_33 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 2.26798E-57 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.601, -5.491506094349139, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_33 [Microbacterium phage DustyDino]],,URM87433,100.0,2.26798E-57 SIF-HHPRED:  SIF-Syn: DustyDino,  Lyell, and Necrophoxinus
    /note=Agree with start codon prediction 9503 to 9766 due to matching GeneMark, Starterator aligns with approved DustDino_32 and others, BLAST has 1:1 match with DustyDino_32 and others, RBS has best- least negative Z score and Final score.

CDS 9797 - 10087
  /gene="30"
  /product="gp30"
  /function="hypothetical protein"
  /locus tag="RunningBrook_30"
    /note=Original Glimmer call @bp 9797 has strength 11.1; Genemark calls start at 9797
    /note=SSC: 9797-10087 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_34 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 3.26862E-61 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_34 [Microbacterium phage DustyDino]],,URM87434,100.0,3.26862E-61 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Necrophoxinus
    /note=Predicted start codon from 9797 to 10087 is correct due to match in GeneMark, Starterator agrees with approved DustyDino_32 and others. Blast of 1:1 in DustyDino_32 and others, RBS has best= least negative Z score and final score.

CDS 10084 - 10350
  /gene="31"
  /product="gp31"
  /function="hypothetical protein"
  /locus tag="RunningBrook_31"
    /note=Original Glimmer call @bp 10084 has strength 8.16; Genemark calls start at 10084
    /note=SSC: 10084-10350 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_35 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 7.80971E-57 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.513, -4.3934175870462076, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_35 [Microbacterium phage DustyDino]],,URM87435,100.0,7.80971E-57 SIF-HHPRED:  SIF-Syn: DustyDino
    /note=Predicted start from 10084 to 10350 is correct based on evidence from GeneMark which matches, Starterator matches with approved DustyDino_36, Blast sequence aligns 1:1 with DustyDino_32 and others, and the RBS score showed it had the best = least negative Z value and final score.

CDS 10347 - 10574
  /gene="32"
  /product="gp32"
  /function="hypothetical protein"
  /locus tag="RunningBrook_32"
    /note=Original Glimmer call @bp 10347 has strength 8.7; Genemark calls start at 10347
    /note=SSC: 10347-10574 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_36 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 1.1925E-46 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.8, -5.643396235448333, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_36 [Microbacterium phage DustyDino]],,URM87436,100.0,1.1925E-46 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Necrophoxinus
    /note=Prediction of start from 10347 to 10574 due to evidence matching with GeneMark, Starterator matched with approved phage DustyDino_36 and others, BLAST showed 1:1 match with DustyDino_36 and others, RBS however showed none of the best= least negative values.
    /note=
    /note=HHPRED shows 98.5% probability for PF06288.16 but bad e-value.

CDS 10571 - 10822
  /gene="33"
  /product="gp33"
  /function="hypothetical protein"
  /locus tag="RunningBrook_33"
    /note=Original Glimmer call @bp 10571 has strength 12.13; Genemark calls start at 10571
    /note=SSC: 10571-10822 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_37 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 1.28702E-52 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.12, -4.394706008439538, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_37 [Microbacterium phage DustyDino]],,URM87437,100.0,1.28702E-52 SIF-HHPRED:  SIF-Syn: DustyDino, Musetta, and Necrophoxinus
    /note=Prediction that start is 10571 to 10822 is correct due to match in GeneMark, Starterator shows matching start site to approved phage DustyDino_36 and others, BLAST shows 1:1 with approved DustyDino_36 and others, RBS do not have the best= highest however most accurate sequence of region.
    /note=
    /note=HHPRED shows 91.2% probability for PF20035.2 but bad e-value

CDS 10938 - 11192
  /gene="34"
  /product="gp34"
  /function="NrdH-like glutaredoxin"
  /locus tag="RunningBrook_34"
    /note=Original Glimmer call @bp 10938 has strength 8.51; Genemark calls start at 10938
    /note=SSC: 10938-11192 CP: yes SCS: both ST: NI BLAST-Start: [NrdH-like glutaredoxin [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 3.64811E-51 GAP: 115 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.006, -2.970161406017234, yes F: NrdH-like glutaredoxin SIF-BLAST: ,,[NrdH-like glutaredoxin [Microbacterium phage DustyDino]],,URM87438,100.0,3.64811E-51 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Necrophoxinus
    /note=Predicted start 10938 to 11192 confirmed with matching GM, Starterator matched with approved DustyDino_36 and others, BLAST 1:1 match with DustyDino_36 and others, RBS had best= highest Z value and final score.
    /note=
    /note=HHPRED shows many hits with good probability and e-values, but their functions do not coincide with what other phages under synteny called.

CDS 11348 - 12682
  /gene="35"
  /product="gp35"
  /function="phosphoesterase"
  /locus tag="RunningBrook_35"
    /note=Original Glimmer call @bp 11348 has strength 9.05; Genemark calls start at 11396
    /note=SSC: 11348-12682 CP: yes SCS: both-gl ST: NI BLAST-Start: [phosphoesterase [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 0.0 GAP: 155 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.523003374675015, yes F: phosphoesterase SIF-BLAST: ,,[phosphoesterase [Microbacterium phage DustyDino]],,URM87439,100.0,0.0 SIF-HHPRED: DNA double-strand break repair protein mre11; DNA repair, Calcineurin-like phosphoesterase, ABC transporter ATPase domain-like, DNA double-strand break repair, HerA-NurA complex, Nbs1 in; HET: IPA, GOL, AGS; 3.1A {Methanocaldococcus jannaschii},,,3AV0_A,63.0631,99.6 SIF-Syn: DustyDino
    /note=Predicted start from 11348 to 12682 because GM includes all coding potential, Starterator showed match with approved phage DustyDino_36 and others with BLAST 1:1 with others, RBS best= highest Z value and final score.
    /note=
    /note=HHPRED shows 99.6% for 3AV0_A and good e-value.

CDS 12687 - 13172
  /gene="36"
  /product="gp36"
  /function="hypothetical protein"
  /locus tag="RunningBrook_36"
    /note=Original Glimmer call @bp 12687 has strength 1.63; Genemark calls start at 12687
    /note=SSC: 12687-13172 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_40 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 7.72738E-114 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.425, -4.322809268821859, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_40 [Microbacterium phage DustyDino]],,URM87440,98.7578,7.72738E-114 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Lyell
    /note=Prediction start from 12687 to 13172 correct due to GM all coding potential, Starterator match with other approved phage ex: DustyDino, BLAST showed 1:1 match with DustyDino and other, RBS has the best/ least negative Z and final score.
    /note=
    /note=Several HHPRED hits with good probability and e-values, but no other evidence for it.

CDS 13277 - 13807
  /gene="37"
  /product="gp37"
  /function="hypothetical protein"
  /locus tag="RunningBrook_37"
    /note=Original Glimmer call @bp 13277 has strength 9.89; Genemark calls start at 13277
    /note=SSC: 13277-13807 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_38 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 2.21422E-124 GAP: 104 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.049, -4.465043966605421, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_38 [Microbacterium phage Lyell] ],,AXC36142,100.0,2.21422E-124 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Lyell
    /note=Agree with predicted start site from 13277 to 13807 because GM has all coding potential, Starterator matched with approved StevieWelch and others. BLAST has 1:1 match with Yuma and others, does not have the best= least negative Final and Z scores.
    /note=
    /note=HHPRED has a 88.7% probability for 3MZY_A but bad e-value

CDS 13804 - 15549
  /gene="38"
  /product="gp38"
  /function="terminase"
  /locus tag="RunningBrook_38"
    /note=Original Glimmer call @bp 13804 has strength 13.57; Genemark calls start at 13804
    /note=SSC: 13804-15549 CP: yes SCS: both ST: NI BLAST-Start: [terminase [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.523003374675015, yes F: terminase SIF-BLAST: ,,[terminase [Microbacterium phage DustyDino]],,URM87442,100.0,0.0 SIF-HHPRED: Gene 2 protein; DNA packaging, terminase, ATPase, nuclease, ATP binding, Magnesium binding, VIRAL PROTEIN; 1.69A {Shigella phage Sf6},,,4IDH_A,88.1239,100.0 SIF-Syn: DustyDino, Fork, and Musetta
    /note=Agree with prediction start 13804 to 15549 because all GM coding potential, Starterator matches with approved StevieWelch and others, Blast is 1:1 with Dusty Dino and others. RBS has best= least negative Z score and final score.
    /note=
    /note=HHPRED shows multiple good hits for terminase genes.

CDS 15611 - 17131
  /gene="39"
  /product="gp39"
  /function="portal protein"
  /locus tag="RunningBrook_39"
    /note=Original Glimmer call @bp 15611 has strength 8.7; Genemark calls start at 15611
    /note=SSC: 15611-17131 CP: yes SCS: both ST: NI BLAST-Start: [portal protein [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 0.0 GAP: 61 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.572, -4.268618610724321, no F: portal protein SIF-BLAST: ,,[portal protein [Microbacterium phage DustyDino]],,URM87443,100.0,0.0 SIF-HHPRED: Phage_portal_2 ; Phage portal protein, lambda family,,,PF05136.16,66.6008,99.9 SIF-Syn: DustyDino, Fork, and Necrophoxinus
    /note=Agree with predicted 15611 to 17131 because has GM all coding potential, Starterator matches with approved Musette and others, BLAST 1:1 match with Dusty Dino and others, RBS does not have best=least negative values.
    /note=
    /note=HHPRED has multiple good hits for portal proteins.

CDS 17199 - 18140
  /gene="40"
  /product="gp40"
  /function="capsid maturation protease"
  /locus tag="RunningBrook_40"
    /note=Original Glimmer call @bp 17199 has strength 6.17; Genemark calls start at 17199
    /note=SSC: 17199-18140 CP: yes SCS: both ST: NI BLAST-Start: [capsid maturation protease [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 0.0 GAP: 67 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.314, -6.018071631562228, no F: capsid maturation protease SIF-BLAST: ,,[capsid maturation protease [Microbacterium phage DustyDino]],,URM87444,100.0,0.0 SIF-HHPRED: Peptidase_S77 ; Prohead core protein serine protease,,,PF03420.16,43.4505,99.7 SIF-Syn: DustyDino, Necrophoxinus, and Fork
    /note=Has the most GeneMark potential. Starterator agrees with multiple verified Genes such as  DustyDino_44, Erenyeager_40, Necrophoxinus_43, and more. During Protein Blast everything lined up suchDustyDino_44, Necrophoxinus_43, Yuma_40, and more. Finale score was close to the best Finale Score and Z value was close to the best possible score.
    /note=
    /note=HHPRED shows multiple good hits for capsid maturation protease.

CDS 18143 - 18595
  /gene="41"
  /product="gp41"
  /function="hypothetical protein"
  /locus tag="RunningBrook_41"
    /note=Original Glimmer call @bp 18143 has strength 6.74; Genemark calls start at 18143
    /note=SSC: 18143-18595 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_NECROPHOXINUS_44 [Microbacterium phage Necrophoxinus] ],,NCBI, q1:s1 100.0% 3.08316E-98 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.744, -3.649124603923531, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NECROPHOXINUS_44 [Microbacterium phage Necrophoxinus] ],,QWS69407,100.0,3.08316E-98 SIF-HHPRED:  SIF-Syn: DustyDino and Necrophoxinus
    /note=Maximum potential of start codon shown on GeneMark. Starterator shows exact same codon start points used for DustyDino_46, Erenyeager_41, and , Yuma_41. Protein Blast shows one to one ratio with the following: Yuma_41, Welcome_43, Necrophoxinus_44, and more. Finale score is close to the least negative scores and Z value is close to the highest score.
    /note=
    /note=HHPRED shows very good hit for PF09956.12, but no other evidence.

CDS 18588 - 19790
  /gene="42"
  /product="gp42"
  /function="major capsid protein"
  /locus tag="RunningBrook_42"
    /note=Original Glimmer call @bp 18588 has strength 8.97; Genemark calls start at 18588
    /note=SSC: 18588-19790 CP: yes SCS: both ST: NI BLAST-Start: [major capsid protein [Microbacterium phage Musetta] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.928, -4.72126161785304, no F: major capsid protein SIF-BLAST: ,,[major capsid protein [Microbacterium phage Musetta] ],,AXH50199,100.0,0.0 SIF-HHPRED: Mu-like_gpT ; Mu-like prophage major head subunit gpT,,,PF10124.12,51.0,99.9 SIF-Syn: DustyDino, Musetta, and Necrophoxinus
    /note=GeneMark shows that all of coding potential is being used. Starterator shows same coding potential show in DustyDino_46 and  ASegato_39. ProteinBlast shows one to one ratios with the following: Musetta_43, DustyDino_46, Yuma_42, and more verified genes. RBS finale score is very close to the least negative score and the Z value is close to the best highest value.

CDS 19985 - 20500
  /gene="43"
  /product="gp43"
  /function="hypothetical protein"
  /locus tag="RunningBrook_43"
    /note=Original Glimmer call @bp 20033 has strength 6.59; Genemark calls start at 19976
    /note=SSC: 19985-20500 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_44 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 3.98994E-119 GAP: 194 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.723, -3.869197702737806, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_44 [Microbacterium phage Lyell] ],,AXC36148,100.0,3.98994E-119 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, and Necrophoxinus
    /note=GeneMarks shows that all of potential coding is being used at this codon. Other verified genes such as DustyDino_47, Welcome_45, and Necrophoxinus_46 show this codon as a starting point. ProteinBlast shows one to one ratios with this codon for the following verified genes: Necrophoxinus_46, DustyDino_47, Fork_40, and more. For the RBS reader, the finale score is pretty negative and the Z value is close to the best possible score.

CDS 20500 - 20847
  /gene="44"
  /product="gp44"
  /function="minor tail protein"
  /locus tag="RunningBrook_44"
    /note=Original Glimmer call @bp 20500 has strength 9.91; Genemark calls start at 20500
    /note=SSC: 20500-20847 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_45 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 1.13442E-78 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.588, -3.9797067239234645, yes F: minor tail protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_45 [Microbacterium phage Lyell] ],,AXC36149,100.0,1.13442E-78 SIF-HHPRED:  SIF-Syn: DustyDino
    /note=GeneMarks shows all of coding potential is being used. Staraterator displays other genes such as, Lyell_45, Necrophoxinus_47, Fork_41 that use the same start codon. ProteinBlast shows one to one ratio with the following verified genes: Welcome_46, Necrophoxinus_47, Lyell_45, and more. Codon has the best final score and the best highest Z value.
    /note=
    /note=HHPRED shows multiple good hits for fibre proteins, which are related.

CDS 20847 - 21458
  /gene="45"
  /product="gp45"
  /function="hypothetical protein"
  /locus tag="RunningBrook_45"
    /note=Original Glimmer call @bp 20847 has strength 5.51; Genemark calls start at 20847
    /note=SSC: 20847-21458 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_46 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 1.30804E-136 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.723, -3.103280908771174, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_46 [Microbacterium phage Lyell] ],,AXC36150,100.0,1.30804E-136 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Lyell
    /note=GeneMarks shows all of coding potential is being used. Starterator showed other verified genes such as DustyDino_49, Welcome_47, and Lyell_46 using this start codon. ProteinBlast showed that the following codons had one to one rations: Yuma_45, Necrophoxinus_48, Lyell_46, and more. On RBS reader, the finale score was close to the best score and the z value was the highest and best score.

CDS 21455 - 23215
  /gene="46"
  /product="gp46"
  /function="minor tail protein"
  /locus tag="RunningBrook_46"
    /note=Original Glimmer call @bp 21455 has strength 6.25; Genemark calls start at 21461
    /note=SSC: 21455-23215 CP: yes SCS: both-gl ST: NI BLAST-Start: [minor tail protein [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.454, -4.137199935798589, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage DustyDino]],,URM87450,100.0,0.0 SIF-HHPRED:  SIF-Syn: DustyDino
    /note=GeneMarks shows that all of coding potential is being used. Starterator shows identical sequence to  DustyDino_50 and similar starts to other genes such as Yuma_46,  Necrophoxinus_49, and more. ProteinBlast shows one to one ratios with the following verified genes: DustyDino_50, Fork_43, Yuma_46, and more.  On RBS reader, it has the best finale score and z score.
    /note=
    /note=More recently approved DustyDIno is assumed to be correct.

CDS 23328 - 23777
  /gene="47"
  /product="gp47"
  /function="head-to-tail stopper"
  /locus tag="RunningBrook_47"
    /note=Original Glimmer call @bp 23328 has strength 8.0; Genemark calls start at 23328
    /note=SSC: 23328-23777 CP: yes SCS: both ST: NI BLAST-Start: [head-to-tail stopper [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 2.83961E-106 GAP: 112 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.163, -2.1123791669543204, yes F: head-to-tail stopper SIF-BLAST: ,,[head-to-tail stopper [Microbacterium phage DustyDino]],,URM87451,100.0,2.83961E-106 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Lyell
    /note=GeneMarks show that all coding potential is being used. Starterator shows multiple verified genes such as Yuma_49, Fork_46, and others that use the same start codon. Blast results show that multiple verified genes such as Musetta_50, DustyDino_53, and others have one to one ratios with this codon. RBS scores show that this codon has the best finale score and z score.
    /note=
    /note=Strong hit and e-value for PF19586.2, but it has no know function as well.

CDS 23770 - 24219
  /gene="48"
  /product="gp48"
  /function="hypothetical protein"
  /locus tag="RunningBrook_48"
    /note=Original Glimmer call @bp 23770 has strength 5.66; Genemark calls start at 23770
    /note=SSC: 23770-24219 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_FORK_45 [Microbacterium phage Fork] ],,NCBI, q1:s1 100.0% 9.67133E-103 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.083, -4.534089041695007, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FORK_45 [Microbacterium phage Fork] ],,AXC36271,100.0,9.67133E-103 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Musetta
    /note=GeneMarks shows that all of coding potential is being used. Starterator shows that multiple verified genes such as DustyDino_52,  Necrophoxinus_51, and others use this starting codon. Blast results show one to one ratios with multiple verified genes such as Yuma_48, Welcome_50, Musetta_49, and others. RBS scores show that both the finale and z score is close to the best scores possible
    /note=
    /note=HHPRED has good hits for minor capsid proteins, but no other evidence is provided.

CDS 24219 - 24686
  /gene="49"
  /product="gp49"
  /function="tail terminator"
  /locus tag="RunningBrook_49"
    /note=Original Glimmer call @bp 24219 has strength 11.48; Genemark calls start at 24219
    /note=SSC: 24219-24686 CP: yes SCS: both ST: NI BLAST-Start: [tail terminator [Microbacterium phage Fork] ],,NCBI, q1:s1 100.0% 3.64551E-109 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.91, -2.6453814847322845, yes F: tail terminator SIF-BLAST: ,,[tail terminator [Microbacterium phage Fork] ],,AXC36272,100.0,3.64551E-109 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Musetta
    /note=GeneMarks show that all of the coding potential is being used. Starterator shows multiple verified genes such as DustyDino_52, Lyell_49, and others that use that same start codon. Blast results show one to one ratios with other verified genes such as DustyDino_52, Necrophoxinus_51, and others. RBS score shows the finale score is close to the best score and that the z score is close to the best score.

CDS 24710 - 24925
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="RunningBrook_50"
    /note=Original Glimmer call @bp 24710 has strength 8.5; Genemark calls start at 24710
    /note=SSC: 24710-24925 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_FORK_47 [Microbacterium phage Fork] ],,NCBI, q1:s1 100.0% 4.28034E-43 GAP: 23 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.295, -4.853679090582491, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FORK_47 [Microbacterium phage Fork] ],,AXC36273,100.0,4.28034E-43 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, and Musetta
    /note=GeneMarks show all of coding potential is used. Starterator shows multiple verified genes such as Yuma_50, Fork_47, Musetta_51, Welcome_52 and more using the same start codon. Blast shows one to one ratios with multiple verified such as Fork_47, DustyDino_54, Necrophoxinus_53, and more. RBS finale score has the best score and the z score also has the best score.

CDS 24925 - 25485
  /gene="51"
  /product="gp51"
  /function="major tail protein"
  /locus tag="RunningBrook_51"
    /note=Original Glimmer call @bp 24925 has strength 10.69; Genemark calls start at 24925
    /note=SSC: 24925-25485 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MUSETTA_52 [Microbacterium phage Musetta] ],,NCBI, q1:s1 100.0% 1.56144E-132 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.529, -3.5316035464369326, yes F: major tail protein SIF-BLAST: ,,[hypothetical protein SEA_MUSETTA_52 [Microbacterium phage Musetta] ],,AXH50208,100.0,1.56144E-132 SIF-HHPRED:  SIF-Syn: DustyDino, Musetta, and Welcome
    /note=GeneMarks shows all of coding potential is being used. Starterator displays multiple verified genes such as DustyDino_55, Musetta_52, Welcome_53, and others that use this start codon. Blast shows multiple genes having one to one ratios such as Musetta_52, DustyDino_55, and others. RBS shows that the finale score is the best and the z score is also the best score possible. Other past genomes call NKF but DustyDino_55 was recently verified and called for tail protein. Probability is lower but close to 90 and the e score was good.

CDS 25504 - 26289
  /gene="52"
  /product="gp52"
  /function="major tail protein"
  /locus tag="RunningBrook_52"
    /note=Original Glimmer call @bp 25504 has strength 8.15; Genemark calls start at 25504
    /note=SSC: 25504-26289 CP: yes SCS: both ST: NI BLAST-Start: [major tail protein [Microbacterium phage Necrophoxinus] ],,NCBI, q1:s1 100.0% 0.0 GAP: 18 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.5052746077145835, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Microbacterium phage Necrophoxinus] ],,QWS69418,100.0,0.0 SIF-HHPRED:  SIF-Syn: DustyDino_55, Necrophoxinus, and Musetta
    /note=GeneMark shows that all coding potential is being used. Starterator displays other verified genes such as  Musetta_53, DustyDino_56, and others that use the same start codon. Blast shows multiple one to one ratios with other verified genes such as Necrophoxinus_55, DustyDino_56, Welcome_54, and others. RBS shows that the finale score and the z score have the best scores. Good Probability in HHPRED but poor e score for 6P3E_G. DB Blast shows DustyDino_55 has a good e score.

CDS 26354 - 26965
  /gene="53"
  /product="gp53"
  /function="tail assembly chaperone"
  /locus tag="RunningBrook_53"
    /note=Original Glimmer call @bp 26354 has strength 10.79; Genemark calls start at 26354
    /note=SSC: 26354-26965 CP: yes SCS: both ST: NI BLAST-Start: [tail assembly chaperone [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 1.93874E-144 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.231, -4.989254565642423, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage DustyDino]],,URM87457,100.0,1.93874E-144 SIF-HHPRED:  SIF-Syn: DustyDino_55, Lyell, and Fork
    /note=GM; all coding potential, starterator agrees with Erenyeager and others, BLAST; Lines up one to one with DustyDino and others, RBS; Close to best final score, close to best Z value. 2OB9_A has a probability close to 90 but has poor e score. DustyDino has a good e score on DB Blast.

CDS 26986 - 27501
  /gene="54"
  /product="gp54"
  /function="tail assembly chaperone"
  /locus tag="RunningBrook_54"
    /note=Original Glimmer call @bp 26986 has strength 4.3; Genemark calls start at 26986
    /note=SSC: 26986-27501 CP: no SCS: both ST: NI BLAST-Start: [tail assembly chaperone [Microbacterium phage Welcome]],,NCBI, q1:s212 100.0% 2.02234E-118 GAP: 20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.083, -7.608323496372297, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Welcome]],,QYC54174,44.7644,2.02234E-118 SIF-HHPRED:  SIF-Syn: DustyDino
    /note=Ribosomal slippage
    /note=CDS join (26354. .26953;26953. .27501)
    /note=
    /note=-1 frameshift

CDS 27525 - 31031
  /gene="55"
  /product="gp55"
  /function="tape measure protein"
  /locus tag="RunningBrook_55"
    /note=Original Glimmer call @bp 27525 has strength 7.24; Genemark calls start at 27525
    /note=SSC: 27525-31031 CP: yes SCS: both ST: NI BLAST-Start: [tape measure protein [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 0.0 GAP: 23 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.173, -2.1518296047551457, yes F: tape measure protein SIF-BLAST: ,,[tape measure protein [Microbacterium phage DustyDino]],,URM87459,100.0,0.0 SIF-HHPRED:  SIF-Syn: DustyDino_55, Necrophoxinus, and Yuma
    /note=GM; All coding potential, startertor agrees with Yuma and others, BLAST; Lines up one to one with DustyDino and others, RBS; best final score, best Z value. URM87459 on NCBI Blast shows a good e score for function. DustyDino and Necrophoxinus show good e scores as well on phages DB Blast. 	6V8I_AF on HHPRED shows a good probability but poor e score.

CDS 31031 - 31909
  /gene="56"
  /product="gp56"
  /function="minor tail protein"
  /locus tag="RunningBrook_56"
    /note=Original Glimmer call @bp 31082 has strength 4.78; Genemark calls start at 31031
    /note=SSC: 31031-31909 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_57 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.427, -3.8079208184165134, no F: minor tail protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_57 [Microbacterium phage Lyell] ],,AXC36161,100.0,0.0 SIF-HHPRED:  SIF-Syn: DustyDino, Welcome, Yuma
    /note=GM; all coding potential, starterator agrees with Roman and many others, BLAST; Lines up one to one with Yuma and others, RBS; best final score, close to the best Z value. HHPRED high probabilities such as 6TEH_B and PF05939.16 but e values are not good but likely due to domains. BD Blast shows high proabilities with good e values.

CDS 31900 - 33525
  /gene="57"
  /product="gp57"
  /function="minor tail protein"
  /locus tag="RunningBrook_57"
    /note=Original Glimmer call @bp 31900 has strength 10.63; Genemark calls start at 31900
    /note=SSC: 31900-33525 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Microbacterium phage Musetta] ],,NCBI, q1:s1 100.0% 0.0 GAP: -10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.657, -3.2616920228519697, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Musetta] ],,AXH50214,100.0,0.0 SIF-HHPRED:  SIF-Syn: DustyDino, Musetta, Welcome
    /note=GM; all coding potential, starterator agrees with Erenyeager and others, BLAST; Lines up one to one with DustyDino and others, RBS; Best final score, Best Z value. DB Blast shows e value of 0 for function from other verified genes. HHPRED shows high probability with 3CDD_C but poor E-value.

CDS 33522 - 34094
  /gene="58"
  /product="gp58"
  /function="hypothetical protein"
  /locus tag="RunningBrook_58"
    /note=Original Glimmer call @bp 33522 has strength 5.82; Genemark calls start at 33618
    /note=SSC: 33522-34094 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_59 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 9.07513E-135 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.502, -3.588526034455651, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_59 [Microbacterium phage Lyell] ],,AXC36163,100.0,9.07513E-135 SIF-HHPRED:  SIF-Syn: Fork, Lyell, Musetta
    /note=GM; all coding potetial, starterator agrees with Erenyeager and others, BLAST; Lines up one to one with StevieWelch and others, RBS; Best final score, Best Z value. HHPRED shoes poor probability and E value for  	4OUS_A. DB Blast shows that DustyDino is assigned a function but looking in the general area of genome on pecaan shows that synteny has functions but db last for this gene shows phages with unknown function.

CDS 34091 - 34708
  /gene="59"
  /product="gp59"
  /function="hypothetical protein"
  /locus tag="RunningBrook_59"
    /note=Original Glimmer call @bp 34091 has strength 10.68; Genemark calls start at 34091
    /note=SSC: 34091-34708 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_60 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 2.13615E-145 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.187, -4.236379132697792, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_60 [Microbacterium phage Lyell] ],,AXC36164,100.0,2.13615E-145 SIF-HHPRED:  SIF-Syn: DustyDno, Lyell, Fork
    /note=GM; All coding potential, sarterator agrees with OlinDD and many others, BLAST; Lines up one to one with StevieWelch and many others, RBS; Best final score, Close to best Z value. HHPRED shows poor probability and e value. DB Blast shows verified genes with NKF

CDS 34746 - 35312
  /gene="60"
  /product="gp60"
  /function="hypothetical protein"
  /locus tag="RunningBrook_60"
    /note=Original Glimmer call @bp 34746 has strength 5.73; Genemark calls start at 34746
    /note=SSC: 34746-35312 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_61 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 5.68595E-133 GAP: 37 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.357, -3.8137921535956054, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_61 [Microbacterium phage Lyell] ],,AXC36165,100.0,5.68595E-133 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, Lyell
    /note=GM; All coding potential, starterator agrees with Erenyeager, BLAST; Lines up one to one with Yuma and others, RBS; Close to best final score, close to best Z value. HHPRED shows high probability with a very poor e value. DB blast shows multiple verified genes with NKF

CDS 35309 - 36241
  /gene="61"
  /product="gp61"
  /function="endolysin"
  /locus tag="RunningBrook_61"
    /note=Original Glimmer call @bp 35309 has strength 6.25; Genemark calls start at 35309
    /note=SSC: 35309-36241 CP: yes SCS: both ST: NI BLAST-Start: [lysin A [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.991, -6.764086808685657, no F: endolysin SIF-BLAST: ,,[lysin A [Microbacterium phage Lyell] ],,AXC36166,100.0,0.0 SIF-HHPRED: D-alanyl-D-alanine carboxypeptidase; Vancomycin resistance, peptidase, metallopeptidase family M15, HYDROLASE; HET: PG4, MSE, GOL; 1.65A {Enterococcus faecalis V583},,,5ZHF_B,40.3226,99.3 SIF-Syn: DustyDino
    /note=GM; all coding potntial, starterator agrees with Yuma and others, BLAST; lines up one to one with Yuma and many others, RBS; Close to best final score, close to best Z value. High hits with HHPRED with D-alanyl-D-alanine carboxypeptidase. Other similar phages called lysin A.  But unless we find lysin B, this should be endolysin.

CDS 36241 - 36519
  /gene="62"
  /product="gp62"
  /function="tail needle protein"
  /locus tag="RunningBrook_62"
    /note=Original Glimmer call @bp 36241 has strength 5.36; Genemark calls start at 36241
    /note=SSC: 36241-36519 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_63 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 4.16616E-59 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.824, -7.134041170973121, no F: tail needle protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_63 [Microbacterium phage Lyell] ],,AXC36167,100.0,4.16616E-59 SIF-HHPRED:  SIF-Syn: DustyDino, Welcome, Yuma
    /note=GM; All coding potential, starterator agrees with Erenyeager and many others, BLAST; Lines up one to one with Yuma and many others, RBS; Close to best final score, close to best Z value
    /note=
    /note=HHPRED has high probability but poor e value and coverage suggesting a domain is shared in-between those. BD blast shows good e values

CDS 36531 - 36770
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="RunningBrook_63"
    /note=Original Glimmer call @bp 36531 has strength 8.97; Genemark calls start at 36531
    /note=SSC: 36531-36770 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_64 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 9.63303E-48 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.248, -1.993391246735709, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_64 [Microbacterium phage Lyell] ],,AXC36168,100.0,9.63303E-48 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, Lyell
    /note=GM; All coding potential, starterator agrees with Necrophoxinus and many others, BLAST; Lines up one to one with Yuma and many others, RBS; Best final score, best Z value. HHPRED shows poor probability and e values. DB Blast shows good e values for multiple verified genes.

CDS complement (37178 - 37633)
  /gene="64"
  /product="gp64"
  /function="RuvC-like resolvase"
  /locus tag="RunningBrook_64"
    /note=Original Glimmer call @bp 37633 has strength 3.33; Genemark calls start at 37633
    /note=SSC: 37633-37178 CP: yes SCS: both ST: NI BLAST-Start: [RuvC-like resolvase [Microbacterium phage Yuma]],,NCBI, q1:s1 98.0132% 3.91307E-102 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.956, -4.723615450753023, no F: RuvC-like resolvase SIF-BLAST: ,,[RuvC-like resolvase [Microbacterium phage Yuma]],,UVK62479,99.3243,3.91307E-102 SIF-HHPRED:  SIF-Syn: Yuma, DustyDino, and Fork
    /note=GeneMark includes all coding potential. Starterator shows some other members chose same start site. Blast is 1 to 1 with DustyDino. 3rd highest z score and second highest negative z score. Good HHPRED probabilities and e values like UVK62479, SCOP_d1hjra_, and more. DB Blast shows good probabilities and e values with multiple verified genes.

CDS complement (37620 - 38201)
  /gene="65"
  /product="gp65"
  /function="hypothetical protein"
  /locus tag="RunningBrook_65"
    /note=Original Glimmer call @bp 38201 has strength 8.81; Genemark calls start at 38201
    /note=SSC: 38201-37620 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_WELCOME_67 [Microbacterium phage Welcome] ],,NCBI, q1:s1 100.0% 6.39281E-140 GAP: 25 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.085, -2.627458653341447, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_WELCOME_67 [Microbacterium phage Welcome] ],,QYC54185,100.0,6.39281E-140 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, Welcome
    /note=GeneMark includes all coding potential. Starterator shows other members chose same start site. Blast is 1 to 1 with other members who chose same start site. Second highest z score, least negative overall score. Poor e value and probability in HHPRED. DB blast shows good e values with other verified genes.

CDS complement (38227 - 38601)
  /gene="66"
  /product="gp66"
  /function="hypothetical protein"
  /locus tag="RunningBrook_66"
    /note=Original Glimmer call @bp 38601 has strength 8.09; Genemark calls start at 38601
    /note=SSC: 38601-38227 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_70 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 1.63853E-84 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.248, -2.838489286749966, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_70 [Microbacterium phage DustyDino]],,URM87470,100.0,1.63853E-84 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, Yuma
    /note=GeneMark includes all coding potential. Starterator shows other close members in same track chose the same start site. Blast is 1 to 1 with other members as well. Highest z score, least negative overall score. HHPRED shows poor probabilities and e values. DB blast shows good e values with other verified genes.

CDS complement (38591 - 38800)
  /gene="67"
  /product="gp67"
  /function="hypothetical protein"
  /locus tag="RunningBrook_67"
    /note=Original Glimmer call @bp 38800 has strength 6.42; Genemark calls start at 38797
    /note=SSC: 38800-38591 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_71 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.74988E-42 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.706, -5.269767271831238, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_71 [Microbacterium phage DustyDino] ],,URM87471,100.0,1.74988E-42 SIF-HHPRED:  SIF-Syn: DustyDino, Fork, Yuma
    /note=GeneMark includes all coding potential. Starterator shows all other members in same track chose the start site. Blast 1 to 1 with both other members who chose the same start site. 5th highest z score and 4th least negative overall score. HHPRED shows high probabilities but really poor e values. DB blast shows good e values with other verified genes.

CDS complement (38797 - 39195)
  /gene="68"
  /product="gp68"
  /function="hypothetical protein"
  /locus tag="RunningBrook_68"
    /note=Original Glimmer call @bp 39195 has strength 10.39; Genemark calls start at 39210
    /note=SSC: 39195-38797 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_72 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 1.18957E-91 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.325, -4.232316027061245, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_72 [Microbacterium phage DustyDino]],,URM87472,100.0,1.18957E-91 SIF-HHPRED: DUF3310 ; Protein of unknwon function (DUF3310),,,PF11753.11,41.6667,99.7 SIF-Syn: DustyDino, Yuma, Fork
    /note=GeneMark includes all coding potential. Starterator shows other members chose same start site. Blast is 1 to 1 with DustyDino, other member is 98%. Highest z score, least negative score. 	HHPRED shows high probability and e value with PF11753.11 for unkown function. DB blast shows good e values for NKF

CDS complement (39192 - 41723)
  /gene="69"
  /product="gp69"
  /function="DNA primase/polymerase"
  /locus tag="RunningBrook_69"
    /note=Original Glimmer call @bp 41723 has strength 7.86; Genemark calls start at 41723
    /note=SSC: 41723-39192 CP: yes SCS: both ST: NI BLAST-Start: [DNA primase/polymerase [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 0.0 GAP: 110 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.085, -3.326428657677466, yes F: DNA primase/polymerase SIF-BLAST: ,,[DNA primase/polymerase [Microbacterium phage DustyDino]],,URM87473,100.0,0.0 SIF-HHPRED: DNA primase; Helicase, DNA binding, AMPPNP, REPLICATION; HET: ANP; 3.1A {Staphylococcus aureus},,,7OM0_B,27.9953,99.7 SIF-Syn: DustyDino, Yuma, Lyell
    /note=GeneMark includes all coding potential. Starterator shows DustyDino chose same start site. Blast has a value of 0 with other members, seems to be a DNA primase/polymerase. Not the highest z score nor the least negative overall score. HHPRED shows good probabilities and e values in relation to the primase/dna polymerase. Examples: 7OM0_B, 1RO2_A and more. DB Blast shows good results with good e values.

CDS complement (41834 - 41986)
  /gene="70"
  /product="gp70"
  /function="hypothetical protein"
  /locus tag="RunningBrook_70"
    /note=Original Glimmer call @bp 41971 has strength 1.45
    /note=SSC: 41986-41834 CP: no SCS: glimmer-cs ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_71 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 2.74696E-28 GAP: 65 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.049, -4.992814376408644, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_71 [Microbacterium phage Lyell] ],,AXC36175,100.0,2.74696E-28 SIF-HHPRED:  SIF-Syn: DustyDino and Lyell also had UKF.
    /note=GeneMark does not include any coding potential. Starterator shows other members chose same start site. Blast is 1 to 1 with same members. Highest z score and least negative overall score.

CDS complement (42052 - 42669)
  /gene="71"
  /product="gp71"
  /function="hypothetical protein"
  /locus tag="RunningBrook_71"
    /note=Original Glimmer call @bp 42669 has strength 12.01; Genemark calls start at 42669
    /note=SSC: 42669-42052 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_72 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 1.81196E-145 GAP: 13 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.006, -2.970161406017234, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_72 [Microbacterium phage Lyell] ],,AXC36176,100.0,1.81196E-145 SIF-HHPRED: DUF669 ; Protein of unknown function (DUF669),,,PF05037.16,56.0976,99.7 SIF-Syn: DustyDino, Fork, Lyell
    /note=GeneMarks show all coding potential is being used. Starterator shows that multiple verified genes use the same start codon such as Welcome_74, Fork_68, Yuma_71, Musetta_72, and more. ProteinBlast shows one to one ratios with multiple verified genes such as Yuma_71,Welcome_74, Lyell_72, DustyDino_76, and more. RBS reader show that both the finale and z scores are the best possible scores available. HHPRED shows PF05037.16 has good probability and e value. DB Blast shows multiple verified genes with good e values.

CDS complement (42683 - 42868)
  /gene="72"
  /product="gp72"
  /function="hypothetical protein"
  /locus tag="RunningBrook_72"
    /note=Original Glimmer call @bp 42868 has strength 7.8; Genemark calls start at 42868
    /note=SSC: 42868-42683 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_73 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 7.03949E-36 GAP: -23 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.758, -3.0478325568523097, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_73 [Microbacterium phage Lyell] ],,AXC36177,100.0,7.03949E-36 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, Necrophoxinus
    /note=GeneMark shows all coding potential is being used. Starterator shows multiple verified genes using the same start codon such as Lyell_73, Fork_69, Yuma_72, and more. ProteinBlast shows multiple one to one ratios with other verified genes such as Yuma_72, Necrophoxinus_75, Lyell_73, DustyDino_77, and more. RBS reader show that the finale score is the best possible score and that the z score is close to the best possible answer. HHPRED shows no good matches. DB Blast shows good e values with multiple verified genes.

CDS complement (42846 - 43706)
  /gene="73"
  /product="gp73"
  /function="Cas4 exonuclease"
  /locus tag="RunningBrook_73"
    /note=Original Glimmer call @bp 43706 has strength 9.31; Genemark calls start at 43706
    /note=SSC: 43706-42846 CP: yes SCS: both ST: NI BLAST-Start: [Cas4 family exonuclease [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.19, -4.308385737595809, no F: Cas4 exonuclease SIF-BLAST: ,,[Cas4 family exonuclease [Microbacterium phage DustyDino] ],,URM87477,100.0,0.0 SIF-HHPRED:  SIF-Syn: DustyDino, Necrophoxinus
    /note=GeneMark shows all coding potential is being used. Starterator show multiple verified genes using the same start codon such as Lyell_74, Fork_70, Musetta_74, and more. ProteinBlast show one to one ratios with multiple verified genes such as Yuma_73, DustyDino_78, Welcome_76, Lyell_74, and many more. RBS reader shows that both the finale and z scores are close to the best possible score. Several HHPRED hits  in general are performing exonuclease functions. DB Blast shows good e values. DustyDino has shown many similarities with RunningBrook which is why its been chosen to declare same function.

CDS complement (43709 - 44413)
  /gene="74"
  /product="gp74"
  /function="ERF family DNA pairing protein"
  /locus tag="RunningBrook_74"
    /note=Original Glimmer call @bp 44413 has strength 13.96; Genemark calls start at 44413
    /note=SSC: 44413-43709 CP: yes SCS: both ST: NI BLAST-Start: [ERF family ssDNA binding protein [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.10773E-168 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.583959800616441, yes F: ERF family DNA pairing protein SIF-BLAST: ,,[ERF family ssDNA binding protein [Microbacterium phage DustyDino] ],,URM87478,100.0,1.10773E-168 SIF-HHPRED: ERF ; ERF superfamily,,,PF04404.15,58.1197,99.9 SIF-Syn: DustyDino, Welcome
    /note=GeneMarks show that all coding potential is being used. Starterator shows that multiple verified genes use the same start codon such as , DustyDino_79, Musetta_75, Yuma_74, and more. ProteinBlast show one to one ratios with multiple verified genes such as Yuma_74, DustyDino_79, Welcome_77, Musetta_75, and many more. RBS reader show that both the z and finale score are the best scores. HHPRED shows high probability and good e value with PF04404.15. DB Blast shows good e values with multiple verified genes.

CDS complement (44410 - 44739)
  /gene="75"
  /product="gp75"
  /function="hypothetical protein"
  /locus tag="RunningBrook_75"
    /note=Original Glimmer call @bp 44739 has strength 10.0; Genemark calls start at 44739
    /note=SSC: 44739-44410 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_WELCOME_78 [Microbacterium phage Welcome] ],,NCBI, q1:s1 100.0% 5.72386E-71 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_WELCOME_78 [Microbacterium phage Welcome] ],,QYC54195,100.0,5.72386E-71 SIF-HHPRED:  SIF-Syn: DustyDino, Yuma, Welcome
    /note=GeneMarks show all coding potential is being used. Starterator show that multipler verified genes use the same codon such as Lyell_76, Fork_72, Welcome_78, and many more. ProteinBlast show one to one ratios with multiple verified genes such as Yuma_75, Welcome_78, DustyDino_80, and many more. RBS reader show that both the finale and z scores have the best possible score. HHPRED shows poor probabilities and e values. DB Blast shows good e values.

CDS complement (44736 - 45467)
  /gene="76"
  /product="gp76"
  /function="DnaQ-like (DNA polymerase III subunit)"
  /locus tag="RunningBrook_76"
    /note=Original Glimmer call @bp 45467 has strength 7.22; Genemark calls start at 45467
    /note=SSC: 45467-44736 CP: yes SCS: both ST: NI BLAST-Start: [exonuclease [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 2.56966E-180 GAP: 60 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.085, -2.356391881054909, yes F: DnaQ-like (DNA polymerase III subunit) SIF-BLAST: ,,[exonuclease [Microbacterium phage Lyell] ],,AXC36181,100.0,2.56966E-180 SIF-HHPRED: DNA polymerase III subunit epsilon; DNA editing Proofreading Exonuclease Polymerase, DNA Binding protein; 6.7A {Escherichia coli K12},,,5M1S_D,75.7202,99.8 SIF-Syn: DustyDino, Necrophoxinus
    /note=GeneMarks shows all coding potential is being used. Starterator shows that multiple verified genes use the same start codon such as Necrophoxinus_79, Yuma_76, DustyDino_81, and more. ProteinBlast shows one to one ratios with multiple verified genes such as Yuma_76, Necrophoxinus_79, Lyell_77, and many more. RBS reader shows that both the finale and z scores are the best possible answers. HHPRED shows good probabilities and e values examples include 5M1S_D and 2GUI_A. DB Blast shows good hits.

CDS complement (45528 - 45689)
  /gene="77"
  /product="gp77"
  /function="hypothetical protein"
  /locus tag="RunningBrook_77"
    /note=Original Glimmer call @bp 45689 has strength 9.15; Genemark calls start at 45689
    /note=SSC: 45689-45528 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_78 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 1.92244E-28 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.25, -4.119687612794143, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_78 [Microbacterium phage Lyell] ],,AXC36182,100.0,1.92244E-28 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, Necrophoxinus
    /note=GeneMarks show all coding potential is being used. Starterator shows other verified genes using the same codon such as Fork_74, Yuma_77,DustyDino_82, and more. ProteinBlast shows one to one ratios with other verified genes such as Yuma_77, Necrophoxinus_80, Lyell_78, and more. RBS reader shows that the finale and z scores are the best possible scores. HHPRED shows poor hits. DB Blast shows good e values with multiple verified genes.

CDS complement (45682 - 46005)
  /gene="78"
  /product="gp78"
  /function="hypothetical protein"
  /locus tag="RunningBrook_78"
    /note=Original Glimmer call @bp 46005 has strength 8.91; Genemark calls start at 46005
    /note=SSC: 46005-45682 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_83 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 8.34042E-72 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.085, -2.417348306996335, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_83 [Microbacterium phage DustyDino] ],,URM87482,100.0,8.34042E-72 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, Yuma
    /note=GeneMarks show that all coding potential is being used. Starterater shows other verified genes using the same codon such as DustyDino_83, Yuma_78, and more. ProteinBlast shows one to one ratios with other genes such as Yuma_78, DustyDino_83, Lyell_79, and more. RBS reader shows that both the finale and z scores are the best possible scores. HHPRED shows poor hits. DB Blast shows good e values.

CDS complement (46002 - 47312)
  /gene="79"
  /product="gp79"
  /function="RNA ligase"
  /locus tag="RunningBrook_79"
    /note=Original Glimmer call @bp 47312 has strength 10.34; Genemark calls start at 47312
    /note=SSC: 47312-46002 CP: yes SCS: both ST: NI BLAST-Start: [RNA ligase [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 0.0 GAP: 16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.523003374675015, yes F: RNA ligase SIF-BLAST: ,,[RNA ligase [Microbacterium phage DustyDino] ],,URM87483,100.0,0.0 SIF-HHPRED: RNA ligase; RNA repair, adenylyltransferase, LIGASE; HET: ATP; 1.547A {Naegleria gruberi},,,6VTB_A,94.7248,100.0 SIF-Syn: DustyDino, Necrophoxinus, Yuma
    /note=GeneMarks show all coding potential is being used. Starterator shows other genes using the same codon such as  DustyDino_84, Yuma_79, and more. ProteinBlast shows one to one ratios with other genes such as Yuma_79, DustyDino_84, Necrophoxinus_82, and more. RBS reader shows that the z and finale scores are the best possible scores. HHPRED shows good probability and e value with 6VTB_A.

CDS complement (47329 - 48252)
  /gene="80"
  /product="gp80"
  /function="polynucleotide kinase"
  /locus tag="RunningBrook_80"
    /note=Original Glimmer call @bp 48252 has strength 9.55; Genemark calls start at 48252
    /note=SSC: 48252-47329 CP: yes SCS: both ST: NI BLAST-Start: [polynucleotide kinase [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.854, -2.8454123590742793, yes F: polynucleotide kinase SIF-BLAST: ,,[polynucleotide kinase [Microbacterium phage DustyDino] ],,URM87484,100.0,0.0 SIF-HHPRED: Pnkp1; RNA repair, kinase, phosphatase, methyltransferase, ligase, PROTEIN BINDING; HET: GOL, PO4, SO4; 3.3A {Capnocytophaga gingivalis},,,4XRP_A,98.6971,100.0 SIF-Syn: DustyDino, Yuma, Lyell
    /note=GeneMarks show all coding potential is being used. Starterator shows other genes using the same codon such as DustyDino_85, Yuma_80, and more. ProteinBlast shows one to one ratios with other genes such as Yuma_80, DustyDino_85, Lyell_81, Necrophoxinus_83, and more. RBS reader show that the finale and z scores are the best possible scores. HHPRED shows many good hits such as 4XRP_A and 1LTQ_A. DB Blast shows good e values for verified genes.

CDS complement (48249 - 48914)
  /gene="81"
  /product="gp81"
  /function="hypothetical protein"
  /locus tag="RunningBrook_81"
    /note=Original Glimmer call @bp 48914 has strength 8.3; Genemark calls start at 48914
    /note=SSC: 48914-48249 CP: yes SCS: both ST: NI BLAST-Start: [oxidoreductase [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.39841E-163 GAP: 26 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[oxidoreductase [Microbacterium phage DustyDino] ],,URM87485,100.0,1.39841E-163 SIF-HHPRED:  SIF-Syn: Welcome, Yuma, Lyell
    /note=GeneMarks show all coding potential is being used. Starterator shows other genes using the same codon such as DustyDino_86, Yuma_81, and more. ProteinBlast shows one to one ratios with other genes such as Yuma_81, DustyDino_86, and Musetta_82. RBS reader shows that the finale and z scores are the best possible scores.
    /note=HHPRED shows good probabilities but very poor e values. DustyDino called for a function but their HHPRED scores show really poor e values. DB Blast shows other verified genes with really good e values.

CDS complement (48941 - 49273)
  /gene="82"
  /product="gp82"
  /function="hypothetical protein"
  /locus tag="RunningBrook_82"
    /note=Original Glimmer call @bp 49273 has strength 7.34; Genemark calls start at 49273
    /note=SSC: 49273-48941 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_87 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.56063E-75 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.829, -2.8970853586582503, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_87 [Microbacterium phage DustyDino] ],,URM87486,100.0,1.56063E-75 SIF-HHPRED:  SIF-Syn: DustyDino, Yuma, Fork
    /note=GeneMarks show all coding potential is being used. Starterator shows other genes using the same codon such as Yuma_82, Fork_79, DustyDino_87, and more. ProteinBlast shows one to one ratios with other genes such as Yuma_82, DustyDino_87, Fork_79, Necrophoxinus_85, and more. RBS reader shows that the codon has the best finale score and a z score that is close to the best possible answer. HHPRED shows no good hits. DB Blast shows good e values

CDS complement (49270 - 50790)
  /gene="83"
  /product="gp83"
  /function="DNA helicase"
  /locus tag="RunningBrook_83"
    /note=Original Glimmer call @bp 50790 has strength 10.76; Genemark calls start at 50790
    /note=SSC: 50790-49270 CP: yes SCS: both ST: NI BLAST-Start: [DNA helicase [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.918, -4.803592052135256, no F: DNA helicase SIF-BLAST: ,,[DNA helicase [Microbacterium phage DustyDino]],,URM87487,100.0,0.0 SIF-HHPRED: Nuclear protein STH1/NPS1; Chromatin remodeling, Nucleosome, Gene Regulation, MOTOR PROTEIN; HET: ATP, ADP, MG, BEF; 3.9A {Xenopus laevis},,,6VZ4_K,98.2213,100.0 SIF-Syn: DustyDino, Lyell, Musetta
    /note=GeneMarks show all coding potential is being used. Starterator shows other genes using the same codon such as DustyDino_88, Yuma_83, and more. ProteinBlast shows one to one ratios with other genes such as DustyDino_88, Musetta_83, Lyell_84, and more. RBS reader shows that the z and finale scores are not the best possible scores provided. HHPRED shows many good hits such as 6VZ4_K, 6PWF_K, and more. DB Blast shows many good e values with verified genes.

CDS complement (50787 - 51038)
  /gene="84"
  /product="gp84"
  /function="hypothetical protein"
  /locus tag="RunningBrook_84"
    /note=Original Glimmer call @bp 51038 has strength 8.3; Genemark calls start at 51038
    /note=SSC: 51038-50787 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MUSETTA_84 [Microbacterium phage Musetta] ],,NCBI, q1:s1 100.0% 3.6661E-54 GAP: 44 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.691, -3.1085431521568267, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MUSETTA_84 [Microbacterium phage Musetta] ],,AXH50239,100.0,3.6661E-54 SIF-HHPRED:  SIF-Syn: DustyDino, Musetta, Welcome
    /note=GeneMarks show all coding potential is being used. Starterator show other genes using the same codon such as Welcome_87, DustyDino_89, Yuma_84, and more. ProteinBlast shows one to one ratios with other genes such as Yuma_84, Welcome_87, Musetta_84, and more. RBS reader shows best possible z and finale score for this codon. HHPRED shows poor hits. DB Blast shows many good e values with many verified genes.

CDS complement (51083 - 51262)
  /gene="85"
  /product="gp85"
  /function="hypothetical protein"
  /locus tag="RunningBrook_85"
    /note=Original Glimmer call @bp 51262 has strength 15.1; Genemark calls start at 51262
    /note=SSC: 51262-51083 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_86 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 1.95918E-31 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.794070146961553, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_86 [Microbacterium phage Lyell] ],,AXC36190,100.0,1.95918E-31 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, Welcome
    /note=GeneMarks show all coding potential is being used. Starterator shows othe genes using the same codon such as Necrophoxinus_88, Welcome_88, DustyDino_90, and more. ProteinBlast shows one to one ratios with other genes such as Yuma_85, Welcome_88, Lyell_86, and more. RBS reader shows that this codon has the best finale and z scores. HHPRED sows no good hits. DB Blast shows good e values for many verified genes.

CDS complement (51278 - 51475)
  /gene="86"
  /product="gp86"
  /function="hypothetical protein"
  /locus tag="RunningBrook_86"
    /note=Original Glimmer call @bp 51475 has strength 8.63; Genemark calls start at 51475
    /note=SSC: 51475-51278 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_87 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 8.06677E-38 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.854, -2.9063687850157054, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_87 [Microbacterium phage Lyell] ],,AXC36191,100.0,8.06677E-38 SIF-HHPRED:  SIF-Syn: DustyDino, Lyell, Fork
    /note=GeneMark includes all coding potential. Starterator shows many other members chose same start site. Blast is 1 to 1 with DustyDino and is close to other members. 3rd highest z score and 2nd least negative overall score. HHPRED shows no good hits. DB Blast shows good e values with many verified genes.

CDS complement (51475 - 51636)
  /gene="87"
  /product="gp87"
  /function="hypothetical protein"
  /locus tag="RunningBrook_87"
    /note=Original Glimmer call @bp 51636 has strength 16.87; Genemark calls start at 51636
    /note=SSC: 51636-51475 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_92 [Microbacterium phage DustyDino]],,NCBI, q1:s1 100.0% 1.81071E-29 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.425, -3.75071250087134, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_92 [Microbacterium phage DustyDino]],,URM87491,100.0,1.81071E-29 SIF-HHPRED:  SIF-Syn: DustyDino, Musetta, Fork
    /note=GM; All coding potential, starterator agrees with DustyDino and others, BLAST; Lines up one to one with StevieWelch and many others, RBS; Best final score, Best z value. HHPRED shows no good hits. DB Blast shows good e values with many verified genes.

CDS complement (51633 - 51848)
  /gene="88"
  /product="gp88"
  /function="hypothetical protein"
  /locus tag="RunningBrook_88"
    /note=Original Glimmer call @bp 51848 has strength 12.61; Genemark calls start at 51848
    /note=SSC: 51848-51633 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MUSETTA_88 [Microbacterium phage Musetta] ],,NCBI, q1:s1 100.0% 3.03235E-44 GAP: 74 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.598, -3.3060637489568596, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MUSETTA_88 [Microbacterium phage Musetta] ],,AXH50243,100.0,3.03235E-44 SIF-HHPRED:  SIF-Syn: DustyDino, Musetta, Yuma
    /note=GeneMark includes all coding potential. Starterator shows all other members chose same start site. Blast is 1 to 1 with 5 other members. Highest z score and least negative overall score. HHPRED shows good probability but poor e value. DB Blast shows good e values for many verified genes.

CDS complement (51923 - 52270)
  /gene="89"
  /product="gp89"
  /function="hypothetical protein"
  /locus tag="RunningBrook_89"
    /note=Original Glimmer call @bp 52270 has strength 10.93; Genemark calls start at 52270
    /note=SSC: 52270-51923 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_NECROPHOXINUS_92 [Microbacterium phage Necrophoxinus] ],,NCBI, q1:s1 100.0% 6.64386E-78 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.006, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NECROPHOXINUS_92 [Microbacterium phage Necrophoxinus] ],,QWS69454,100.0,6.64386E-78 SIF-HHPRED: DUF1523 ; Protein of unknown function (DUF1523),,,PF07509.14,95.6522,100.0 SIF-Syn: DustyDino, Necrophoxinus, Yuma
    /note=GeneMark shows all coding potential is being used. Starterator shows multiple verified genes such as Musetta_89, Lyell_90, Yuma_89, and more that use this start codon. Blast shows one to one ratios with multiple verified genes such as Yuma_89, Necrophoxinus_92, DustyDino_94, and more. RBS shows the finale and z score has the best scores. HHPRED shows a good hit with PF07509.14. DB Blast shows good e values for verified genes.

CDS complement (52267 - 52491)
  /gene="90"
  /product="gp90"
  /function="hypothetical protein"
  /locus tag="RunningBrook_90"
    /note=Original Glimmer call @bp 52491 has strength 4.57; Genemark calls start at 52503
    /note=SSC: 52491-52267 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_NECROPHOXINUS_93 [Microbacterium phage Necrophoxinus] ],,NCBI, q1:s1 100.0% 5.83903E-43 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.971, -4.629584883725491, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NECROPHOXINUS_93 [Microbacterium phage Necrophoxinus] ],,QWS69455,100.0,5.83903E-43 SIF-HHPRED:  SIF-Syn: DustyDino, Necrophoxinus, Yuma
    /note=GeneMark show all coding potential is being used. Starterator displays multiple verified genes such as DustyDino_95, Lyell_91, and others using this start codon. Blast shows one to one ratios with verified genes such as Yuma_90, Necrophoxinus_93, DustyDino_95, and more. RBS shows finale score and z score have the best scores. HHPRED shows poor hits. DB Blast shows good verified genes.

CDS complement (52488 - 52568)
  /gene="91"
  /product="gp91"
  /function="hypothetical protein"
  /locus tag="RunningBrook_91"
    /note=Original Glimmer call @bp 52610 has strength 3.01
    /note=SSC: 52568-52488 CP: yes SCS: glimmer-cs ST: NI BLAST-Start: [hypothetical protein SEA_WELCOME_94 [Microbacterium phage Welcome] ],,NCBI, q1:s1 100.0% 7.44316E-7 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.445, -3.708514821076885, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_WELCOME_94 [Microbacterium phage Welcome] ],,QYC54211,100.0,7.44316E-7 SIF-HHPRED:  SIF-Syn: DustyDino 
Yuma
    /note=GeneMarks shows all coding potential is being used. Starterator is not informative. 
    /note=ProteinBlast shows more verified one to one ratios with this starting codons, examples include: Welcome_94, DustyDino_96, Lyell_92, and Fork_88. Has the best finale and z score on RBS reader.
    /note=
    /note=HHPRED= poor
    /note=NCBI= Hypothetical Protein

CDS complement (52565 - 52768)
  /gene="92"
  /product="gp92"
  /function="hypothetical protein"
  /locus tag="RunningBrook_92"
    /note=Original Glimmer call @bp 52768 has strength 4.63; Genemark calls start at 52768
    /note=SSC: 52768-52565 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_NECROPHOXINUS_95 [Microbacterium phage Necrophoxinus] ],,NCBI, q1:s1 100.0% 4.95893E-43 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.452, -6.078801327161882, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_NECROPHOXINUS_95 [Microbacterium phage Necrophoxinus] ],,QWS69457,100.0,4.95893E-43 SIF-HHPRED:  SIF-Syn: DustyDino 
Necrophoxinus 
Yuma
    /note=GeneMarks shows all coding potential is being used. Starterator is showing hits with other verified genes such as : DustyDino_97, Lyell_93, and more. ProteinBlast shows one to one ratios with other verified genes such as Yuma_92, Necrophoxinus_95, Welcome_95, and more. RBS reader shows z score and finale score are not the best.
    /note=
    /note=HHPRED= poor
    /note=NCBI= Hypothetical protein

CDS complement (52774 - 52890)
  /gene="93"
  /product="gp93"
  /function="hypothetical protein"
  /locus tag="RunningBrook_93"
    /note=Original Glimmer call @bp 52890 has strength 5.83; Genemark calls start at 52890
    /note=SSC: 52890-52774 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_94 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 4.19411E-14 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.871, -7.095031720982019, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_94 [Microbacterium phage Lyell] ],,AXC36197,100.0,4.19411E-14 SIF-HHPRED:  SIF-Syn: DustyDino
Lyell
Musetta
Necrophoxinus
Fork
    /note=GeneMarks shows all coding potential is being used. Starterator shows verified genes using the same start codon such as DustyDino_98, Yuma_93, and Necrophoxinus_96. ProteinBlast shows other verified genes have one to one ratios such as Musetta_93, Necrophoxinus_96, Yuma_93, and more. RBS scores are not informative.
    /note=
    /note=HHPRED= poor
    /note=NCBI= Hypothetical Protein

CDS complement (52890 - 53030)
  /gene="94"
  /product="gp94"
  /function="hypothetical protein"
  /locus tag="RunningBrook_94"
    /note=Original Glimmer call @bp 53030 has strength 12.71; Genemark calls start at 53030
    /note=SSC: 53030-52890 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MUSETTA_94 [Microbacterium phage Musetta] ],,NCBI, q1:s1 100.0% 3.46311E-22 GAP: 84 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MUSETTA_94 [Microbacterium phage Musetta] ],,AXH50249,100.0,3.46311E-22 SIF-HHPRED:  SIF-Syn: DustyDino
Musetta
Necrophoxinus 
Yuma 
Welcome
    /note=GeneMarks show all coding potential is being used. Starterator shows multple verified genes using the same codon such as : Necrophoxinus_97, DustyDino_99, and Welcome_97. ProteinBlast shows one to one ratios with multiple verified genes such as Yuma_94, Welcome_97, Musetta_94 and more. RBS readers show that the z score and the finale score have the best scores overall.
    /note=
    /note=HHPRED = poor
    /note=NCBI= Hypothetical Protein

CDS complement (53115 - 53288)
  /gene="95"
  /product="gp95"
  /function="hypothetical protein"
  /locus tag="RunningBrook_95"
    /note=Original Glimmer call @bp 53276 has strength 6.37; Genemark calls start at 53288
    /note=SSC: 53288-53115 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_MUSETTA_95 [Microbacterium phage Musetta] ],,NCBI, q1:s1 100.0% 3.00393E-32 GAP: 33 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.006, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MUSETTA_95 [Microbacterium phage Musetta] ],,AXH50250,100.0,3.00393E-32 SIF-HHPRED:  SIF-Syn: DustyDino 
Musetta
Mecrophoxinus
Yuma
    /note=GeneMark shows all coding potential is being used. Starterator shows other verified genes use start codon such as Lyell_96, Welcome_98, and more. ProteinBlast shows one to one ratios with multiple verified genes such as Yuma_95, Necrophoxinus_98, Musetta_95, and more. RBS reader shows the z score and finale score are the best and top scores.
    /note=
    /note=HHPRED= Poor
    /note=NCBI= Hypothetical Protein

CDS complement (53322 - 53651)
  /gene="96"
  /product="gp96"
  /function="hypothetical protein"
  /locus tag="RunningBrook_96"
    /note=Original Glimmer call @bp 53651 has strength 3.66; Genemark calls start at 53651
    /note=SSC: 53651-53322 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_101 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 2.28039E-74 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.657, -3.3226484487933954, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_101 [Microbacterium phage DustyDino] ],,URM87500,100.0,2.28039E-74 SIF-HHPRED:  SIF-Syn: DustyDino 
Yuma
Musetta
Necrophoxinus
    /note=GeneMarks show that all coding potential is being used. Starterator shows other verified genes using the same start codon such as DustyDino_101 and Yuma_96. ProteinBlast shows one to one ratios with verified genes such as Welcome_99, DustyDino_101, Yuma_96, Welcome_99, and more. RBS reader shows z value and finale score both have the best possible scores.
    /note=
    /note=HHPRED= poor
    /note=NCBI= Hypothetical Protein

CDS complement (53654 - 53776)
  /gene="97"
  /product="gp97"
  /function="hypothetical protein"
  /locus tag="RunningBrook_97"
    /note=Original Glimmer call @bp 53776 has strength 6.12; Genemark calls start at 53770
    /note=SSC: 53776-53654 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_102 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 5.39692E-19 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.376, -3.914968956777623, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_102 [Microbacterium phage DustyDino] ],,URM87501,100.0,5.39692E-19 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma
    /note=GeneMarks show all coding potential is being used. Starterator shows other verified genes using the same start codon such as Yuma_97 and DustyDino_102. ProteinBlast shows one to one ratios with multiple verified genes such as Yuma_97, DustyDino_102, Musetta_97, Welcome_100, and more. RBS reader shows it has the best finale score and that the z score is close to the best score shown.
    /note=
    /note=HHPRED= bad values
    /note=Blast= hypothetical Protein

CDS complement (53773 - 53979)
  /gene="98"
  /product="gp98"
  /function="hypothetical protein"
  /locus tag="RunningBrook_98"
    /note=Original Glimmer call @bp 53979 has strength 7.98; Genemark calls start at 53979
    /note=SSC: 53979-53773 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_99 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 2.03013E-37 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.598, -3.4470622626190464, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_99 [Microbacterium phage Lyell] ],,AXC36202,100.0,2.03013E-37 SIF-HHPRED:  SIF-Syn: 
    /note=GeneMarks show all coding potential is being used. Starterator show verified genes using the same start codon such as DustyDino_103, Yuma_98, Lyell_99, Necrophoxinus_101, and more. ProteinBlast shows one to one ratios with multiple verified genes such as Yuma_98, Necrophoxinus_101, Lyell_99, DustyDino_103, Fork_95, and more. RBS reader shows that the finale score and the z score are not the best scores possible.
    /note=
    /note=DustyDino
    /note=Lyell
    /note=Yuma
    /note=Necrophoxinus
    /note=Fork

CDS complement (53976 - 54236)
  /gene="99"
  /product="gp99"
  /function="hypothetical protein"
  /locus tag="RunningBrook_99"
    /note=Original Glimmer call @bp 54236 has strength 11.55; Genemark calls start at 54236
    /note=SSC: 54236-53976 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_100 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 1.33496E-53 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.248, -2.45827804503836, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_100 [Microbacterium phage Lyell] ],,AXC36203,100.0,1.33496E-53 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma 
Lyell
Necrophoxinus
    /note=GeneMarks show all coding potential is being used. Starterator shows multiple verified genes using the same start codon such as , Lyell_100, Yuma_99, DustyDino_104, and Necrophoxinus_102. ProteinBlast shows one to one ratios with other verified genes such as Yuma_99, Necrophoxinus_102, Fork_96, Welcome_102, and more. RBS reader show that both the finale and z scores have the best possible answer provided.

CDS complement (54245 - 54805)
  /gene="100"
  /product="gp100"
  /function="DNA binding protein"
  /locus tag="RunningBrook_100"
    /note=Original Glimmer call @bp 54805 has strength 10.11; Genemark calls start at 54805
    /note=SSC: 54805-54245 CP: yes SCS: both ST: NI BLAST-Start: [DNA binding domain protein [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.21072E-133 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.502, -4.4158953075094765, yes F: DNA binding protein SIF-BLAST: ,,[DNA binding domain protein [Microbacterium phage DustyDino] ],,URM87504,100.0,1.21072E-133 SIF-HHPRED:  SIF-Syn: DustyDino
    /note=GeneMarks show all coding potential is being used. Starterator show multiple verified genes using the same codon such as Yuma_100, Musetta_100, DustyDino_105, and more. ProteinBlast shows one to one ratios with multiple verified genes such as Yuma_100, DustyDino_105, Welcome_103, Necrophoxinus_103, and more. RBS reader show that the finale score is close to the best score and that the z score is the best score.
    /note=
    /note=HHPRED > 90 but does not meet e value requirment
    /note=BLAST DustyDiny= 100% match to DNA binding protein.

CDS complement (54805 - 54993)
  /gene="101"
  /product="gp101"
  /function="hypothetical protein"
  /locus tag="RunningBrook_101"
    /note=Original Glimmer call @bp 54993 has strength 6.94; Genemark calls start at 54993
    /note=SSC: 54993-54805 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_106 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 5.7943E-36 GAP: 34 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.357, -3.8761054743559344, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_106 [Microbacterium phage DustyDino] ],,URM87505,100.0,5.7943E-36 SIF-HHPRED:  SIF-Syn: DustyDino 
Yuma
Musetta
    /note=GeneMarks show all coding potential is being used. Starterator shows other verified genes using the same codon such as  Lyell_102, Yuma_101,  DustyDino_106, Musetta_101, and more. ProteinBlast show one to one ratios with other verified genes such as Yuma_101, DustyDino_106, Musetta_101, Welcome_104, and more. RBS reader show that both the finale and z scores and close to the best possible answers available.
    /note=
    /note=No HHPRED 
    /note=NCBI= Hypothetical Protein

CDS complement (55028 - 55282)
  /gene="102"
  /product="gp102"
  /function="hypothetical protein"
  /locus tag="RunningBrook_102"
    /note=Original Glimmer call @bp 55282 has strength 6.3; Genemark calls start at 55282
    /note=SSC: 55282-55028 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_107 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 3.00506E-53 GAP: 82 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.754, -3.116480142619113, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_107 [Microbacterium phage DustyDino] ],,URM87506,100.0,3.00506E-53 SIF-HHPRED:  SIF-Syn: DustyDino
Lyell
Yuma
Fork
    /note=GeneMarks show all coding potential is being used. Starterator shows multiple verified genes using the same codon such as Fork_100, Yuma_102, Welcome_106, Lyell_103, and more. ProteinBlast showed one to one ratios with multiple verified genes such as Yuma_102, DustyDino_107, Lyell_103, and more. RBS reader shows that both the finale and z scores are the best possible scores.
    /note=
    /note=No HHPRED 
    /note=NCBI Blast hypothetical protein

CDS complement (55365 - 56189)
  /gene="103"
  /product="gp103"
  /function="hypothetical protein"
  /locus tag="RunningBrook_103"
    /note=Original Glimmer call @bp 56189 has strength 6.63; Genemark calls start at 56189
    /note=SSC: 56189-55365 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_108 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 0.0 GAP: 54 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.669, -3.296037457437639, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_108 [Microbacterium phage DustyDino] ],,URM87507,100.0,0.0 SIF-HHPRED:  SIF-Syn: Lyell
Fork
DustyDino
    /note=GeneMarsks show all coding potential is being used. Starterator show multiple verified genes using the same codon such as Yuma_103, DustyDino_108, and more. ProteinBlast show one to one ratios with multiple verified genes such as Yuma_103, DustyDino_108, Fork_101, Welcome_107, and more. RBS reader shows that both the finale and z scores are the best possible scores.
    /note=
    /note=Blast= DustyDino/Lyell/Musetta 100% match to hypothetical protein.

CDS complement (56244 - 56453)
  /gene="104"
  /product="gp104"
  /function="hypothetical protein"
  /locus tag="RunningBrook_104"
    /note=Original Glimmer call @bp 56453 has strength 4.88; Genemark calls start at 56453
    /note=SSC: 56453-56244 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_105 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 6.51088E-43 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.277, -4.1237215507168505, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_105 [Microbacterium phage Lyell] ],,AXC36208,100.0,6.51088E-43 SIF-HHPRED:  SIF-Syn: Lyell
DustyDino 
Musetta
    /note=GeneMarks show all coding potential is being used. Starterator show multiple verified genes are using the same codon such as Lyell_105, Yuma_104, Musetta_104, and more. ProteinBlast show multiple verified genes having one to one ratios such as Yuma_104, Musetta_104, Lyell_105, DustyDino_109, and more. RBS reader show that the finale score is the best possible score and the z score is close to the best score.
    /note=
    /note=Blast= DustyDino/Lyell/Musetta 100% match to hypothetical protein.

CDS complement (56450 - 56887)
  /gene="105"
  /product="gp105"
  /function="hypothetical protein"
  /locus tag="RunningBrook_105"
    /note=Original Glimmer call @bp 56887 has strength 8.86; Genemark calls start at 56887
    /note=SSC: 56887-56450 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_106 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 4.28883E-101 GAP: 50 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.854, -2.7653702713535186, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_106 [Microbacterium phage Lyell] ],,AXC36209,100.0,4.28883E-101 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma
Lyell
Necrophoxinus
Fork
Welcome
    /note=GeneMarks show all coding potential is being used. Starterator shows that multiple verified genes are using the same codon such as Yuma_105, DustyDino_110, Fork_103, Welcome_109, and more. ProteinBlast shows one to one ratios with multiple verified genes such as Yuma_105, Musetta_105,Lyell_106, and more. RBS reader shows that the finale score is the best possible score and that the z score is close to the best possible score.
    /note=
    /note=Blast= DustyDino/Yuma 100% match to hypothetical protein.

CDS complement (56938 - 57330)
  /gene="106"
  /product="gp106"
  /function="hypothetical protein"
  /locus tag="RunningBrook_106"
    /note=Original Glimmer call @bp 57330 has strength 9.18; Genemark calls start at 57330
    /note=SSC: 57330-56938 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_111 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 3.01831E-89 GAP: 50 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.677, -3.219494343057515, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_111 [Microbacterium phage DustyDino] ],,URM87510,100.0,3.01831E-89 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma
Lyell
    /note=GeneMarks show that all coding potential is being used. Starterator shows that multiple verified genes are using the same codon such as Lyell_107, Yuma_106, Musetta_106, and more. ProteinBlast shows one to one ratios with multiple verified genes such as Yuma_106, DustyDino_111, Welcome_110, and more. RBS reader show that the Z and final scores are close to the best possible scores.
    /note=
    /note=Blast= DustyDino/Yuma 100% match to hypothetical protein.

CDS complement (57381 - 57494)
  /gene="107"
  /product="gp107"
  /function="hypothetical protein"
  /locus tag="RunningBrook_107"
    /note=Original Glimmer call @bp 57494 has strength 7.89; Genemark calls start at 57494
    /note=SSC: 57494-57381 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_112 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.75744E-17 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.851, -4.963787326180191, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_112 [Microbacterium phage DustyDino] ],,URM87511,100.0,1.75744E-17 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma
Lyell
    /note=GeneMarsks show all coding potential is being used. Starterator shows multiple verified genes using the same codon such as Welcome_111, Yuma_107, DustyDino_112, and more. ProteinBlast shows one to one ratios with multiple verified genes such as Yuma_107, DustyDino_112, Lyell_108, and Fork_105. RBS reader show that both the z and finale scores are close to the best possible answers.
    /note=
    /note=Blast= DustyDino/Yuma 100% match to hypothetical protein.
    /note=HHPRED>90 but poor e value

CDS complement (57491 - 57736)
  /gene="108"
  /product="gp108"
  /function="hypothetical protein"
  /locus tag="RunningBrook_108"
    /note=Original Glimmer call @bp 57736 has strength 8.78; Genemark calls start at 57736
    /note=SSC: 57736-57491 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_113 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.28633E-49 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.578, -3.4283035164720754, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_113 [Microbacterium phage DustyDino] ],,URM87512,100.0,1.28633E-49 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma
Lyell
    /note=GeneMarks show that all coding potential is being used. Starterator shows that multiple verified genes are using the same codon such as Yuma_108, DustyDino_113, and more. ProteinBlast shows one to one ratios with multiple genes such as Yuma_108, DustyDino_113, Musetta_107, and more. RBS reader shows that both the finale and z scores are the best posible scores.

CDS complement (57733 - 58143)
  /gene="109"
  /product="gp109"
  /function="hypothetical protein"
  /locus tag="RunningBrook_109"
    /note=Original Glimmer call @bp 58107 has strength 9.7; Genemark calls start at 58143
    /note=SSC: 58143-57733 CP: no SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_114 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.5468E-96 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.723, -4.346318957457468, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_114 [Microbacterium phage DustyDino] ],,URM87513,100.0,1.5468E-96 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma
Fork
    /note=Reject prediction of start 57733 to 58107. Genemark states more coding potential is listed with end at 58143. Blast for this is 1:1 with Dusty Dino and others, Starterator matches with Dusty Dino and others. RBS does not have the best= least negative results for any value.
    /note=
    /note=Blast= DustyDino/Yuma 100% match to hypothetical protein.

CDS complement (58140 - 58592)
  /gene="110"
  /product="gp110"
  /function="hypothetical protein"
  /locus tag="RunningBrook_110"
    /note=Original Glimmer call @bp 58592 has strength 8.8; Genemark calls start at 58592
    /note=SSC: 58592-58140 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_115 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 3.51077E-104 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.096, -2.253486910374644, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_115 [Microbacterium phage DustyDino] ],,URM87514,100.0,3.51077E-104 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma
Welcome
    /note=Correct start 58140 to 58592. Genemark has all coding potential, Blast 1:1 with DustyDino and others, starterator matches with DustyDino and others. RBS has best= least negative final and Z value.
    /note=
    /note=BLAST= 100%  DustyDino match to hypothetical protein.

CDS complement (58623 - 59123)
  /gene="111"
  /product="gp111"
  /function="hypothetical protein"
  /locus tag="RunningBrook_111"
    /note=Original Glimmer call @bp 59123 has strength 12.04; Genemark calls start at 59123
    /note=SSC: 59123-58623 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_116 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 4.00133E-117 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.598, -3.3060637489568596, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_116 [Microbacterium phage DustyDino] ],,URM87515,100.0,4.00133E-117 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma
Welcome
    /note=Confirm start: 58623 to 59123 with GeneMark all coding potential, Blast is 1:1 with DustyDino and others, Starterator matches with DustyDino and others. RBS does not have best=least negative values.
    /note=
    /note=Blast= DustyDino 100% match to hypothetical protein.
    /note=A few HHPRED>90 but poor e value.

CDS complement (59120 - 59422)
  /gene="112"
  /product="gp112"
  /function="hypothetical protein"
  /locus tag="RunningBrook_112"
    /note=Original Glimmer call @bp 59422 has strength 3.97; Genemark calls start at 59422
    /note=SSC: 59422-59120 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_117 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 3.32472E-68 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.238, -2.0949393225970705, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_117 [Microbacterium phage DustyDino] ],,URM87516,100.0,3.32472E-68 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma
Musetta
    /note=Confirm 59120 to 59422: Genemark has All coding potential, starterator matches with Dusty Dino and others, BLAST is 1:1 with DustyDino and others. RBS has best=least negative Z and final values.
    /note=
    /note=Poor HHPRED
    /note=Good e-value for synteny.

CDS complement (59419 - 59760)
  /gene="113"
  /product="gp113"
  /function="hypothetical protein"
  /locus tag="RunningBrook_113"
    /note=Original Glimmer call @bp 59760 has strength 7.08; Genemark calls start at 59760
    /note=SSC: 59760-59419 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_LYELL_115 [Microbacterium phage Lyell] ],,NCBI, q1:s1 100.0% 3.48732E-75 GAP: 1147 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.688, -5.309117108752867, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYELL_115 [Microbacterium phage Lyell] ],,AXC36218,100.0,3.48732E-75 SIF-HHPRED:  SIF-Syn: DustyDino
Lyell
Musetta
    /note=112 reverse: confirm 59419 to 59760: GeneMark has all coding potential, BLAST is 1:1 with Welcome, Starterator matched with DustyDino and others. RBS has least negative=best z and final values.
    /note=
    /note=Poor HHPRED score

CDS complement (60908 - 61204)
  /gene="114"
  /product="gp114"
  /function="hypothetical protein"
  /locus tag="RunningBrook_114"
    /note=Original Glimmer call @bp 61204 has strength 3.78; Genemark calls start at 61204
    /note=SSC: 61204-60908 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_4 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 8.98687E-65 GAP: 212 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.12, -4.394706008439538, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_4 [Microbacterium phage DustyDino] ],,URM87409,100.0,8.98687E-65 SIF-HHPRED:  SIF-Syn: DustyDino
Necrophoxius
Lyell
    /note=Yes to 60908 to 61204 because GeneMark has all coding potential, starterator matches with approved DustyDino and others, Blast is 1:1 with DustyDino and others, RBS has best = least negative final score.
    /note=
    /note=HHPRED > 90 bad e score
    /note=NCBI: hypothetical DustyDino Protein

CDS complement (61417 - 61719)
  /gene="115"
  /product="gp115"
  /function="hypothetical protein"
  /locus tag="RunningBrook_115"
    /note=Original Glimmer call @bp 61695 has strength 1.92; Genemark calls start at 61719
    /note=SSC: 61719-61417 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_5 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.55359E-66 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.752, -5.443606692405957, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_5 [Microbacterium phage DustyDino] ],,URM87410,100.0,1.55359E-66 SIF-HHPRED:  SIF-Syn: DustyDino
Yuma 
Fork
    /note=Change to 61417 to 61719 because includes GeneMark potential, Blast matches 1:1 with DustyDino and others. Starterator has capability to have same start site as DustyDino. None of best = least negative RBS scores.
    /note=
    /note=Bad HHPRED score
    /note=NCBI: Hypothetical DustyDino protein

CDS complement (61719 - 62315)
  /gene="116"
  /product="gp116"
  /function="hypothetical protein"
  /locus tag="RunningBrook_116"
    /note=Original Glimmer call @bp 62315 has strength 13.57; Genemark calls start at 62315
    /note=SSC: 62315-61719 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_6 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.71473E-145 GAP: 80 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.758, -5.080915947802713, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_6 [Microbacterium phage DustyDino] ],,URM87411,100.0,1.71473E-145 SIF-HHPRED:  SIF-Syn: DustyDino
Necrophoxinus
    /note=Yes to 62315 to 61719, has all GeneMark coding potential, BLAST is 1:1 with DustyDino and others, Starterator matches with DustyDino and others. No best = least equal RBS values.
    /note=
    /note=Bad HHPRED score
    /note=NCBI: Hypothetical Protein

CDS complement (62396 - 62782)
  /gene="117"
  /product="gp117"
  /function="hypothetical protein"
  /locus tag="RunningBrook_117"
    /note=Original Glimmer call @bp 62782 has strength 16.03; Genemark calls start at 62782
    /note=SSC: 62782-62396 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_7 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.00791E-86 GAP: 27 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.934, -5.058605177999316, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_7 [Microbacterium phage DustyDino] ],,URM87412,100.0,1.00791E-86 SIF-HHPRED:  SIF-Syn: DustyDino
Musetta
Necrophoxinus
    /note=Yes to 62396 to 62782, All GeneMark coding potential, BLAST is 1:1 with approved DustyDino and others, starterator matches with DustyDino and others. No best= least negative RBS values
    /note=
    /note=NCBI hypothetical protein
    /note=Bad HHPRED scores

CDS complement (62810 - 63157)
  /gene="118"
  /product="gp118"
  /function="hypothetical protein"
  /locus tag="RunningBrook_118"
    /note=Original Glimmer call @bp 63157 has strength 15.6; Genemark calls start at 63157
    /note=SSC: 63157-62810 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_8 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.10407E-76 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.951, -2.5594668560256912, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_8 [Microbacterium phage DustyDino] ],,URM87413,100.0,1.10407E-76 SIF-HHPRED: DUF3574 ; Protein of unknown function (DUF3574),,,PF12098.11,85.2174,99.9 SIF-Syn: DustyDino
Musetta
Necrophoxinus
    /note=Yes to 63157 to 62810 all GeneMark coding potential, Blast is 1:1 with DustyDino and others, starterator matches with approved DustyDino, has all best = least negative RBS values.
    /note=
    /note=Good HHPRED Probability + E-value: PF12098.11

CDS complement (63224 - 63502)
  /gene="119"
  /product="gp119"
  /function="hypothetical protein"
  /locus tag="RunningBrook_119"
    /note=Original Glimmer call @bp 63364 has strength 4.59; Genemark calls start at 63502
    /note=SSC: 63502-63224 CP: yes SCS: both-gm ST: NI BLAST-Start: [hypothetical protein SEA_DUSTYDINO_9 [Microbacterium phage DustyDino] ],,NCBI, q1:s1 100.0% 1.21931E-59 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.951, -2.5594668560256912, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DUSTYDINO_9 [Microbacterium phage DustyDino] ],,URM87414,100.0,1.21931E-59 SIF-HHPRED:  SIF-Syn: DustyDino: NKF
Welcome: NKF
    /note=Change to 63224 to 63502, GeneMark has all coding potential, Blast is 1:1 with DustyDino and others, Starterator NI, best = least negative RBS values.
    /note=
    /note=Prob < 90
    /note=synteny NKF
    /note=NCBI hypothetical

CDS complement (63513 - 63668)
  /gene="120"
  /product="gp120"
  /function="hypothetical protein"
  /locus tag="RunningBrook_120"
    /note=Original Glimmer call @bp 63668 has strength 4.12; Genemark calls start at 63668
    /note=SSC: 63668-63513 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_MUSETTA_123 [Microbacterium phage Musetta] ],,NCBI, q1:s1 100.0% 7.28713E-27 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.829, -2.8793565916978188, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_MUSETTA_123 [Microbacterium phage Musetta] ],,AXH50170,100.0,7.28713E-27 SIF-HHPRED:  SIF-Syn: DustyDino: NKF
Yuma: NKF
Musetta: NKF
    /note=Yes 63513 to 63668, all GeneMark potential, Blast is 1:1 with DustyDino and others, Starterator matches DustyDino and others. All best= least negative RBS values.
    /note=
    /note=NCBI: hypothetical protein