User:James Estevez/Notebook/Spring 2011: Bdellovibrio Independent Study/2011/01/30/Bdellovibrio strain W glimmer3.detail
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Command: glimmer3 /home/james/Data/bdcost/b_strain_w/bdw.contigs.seq /home/james/Data/bdcost/bd100.icm bdw
Sequence file = /home/james/Data/bdcost/b_strain_w/bdw.contigs.seq
Number of sequences = 561
ICM model file = /home/james/Data/bdcost/bd100.icm
Excluded regions file = none
List of orfs file = none
Input is NOT separate orfs
Independent (non-coding) scores are used
Circular genome = true
Truncated orfs = false
Minimum gene length = 100 bp
Maximum overlap bases = 30
Threshold score = 30
Use first start codon = false
Start codons = atg,gtg,ttg
Start probs = 0.600,0.300,0.100
Stop codons = taa,tag,tga
GC percentage = 49.7%
Ignore score on orfs longer than 725
>bdw.fasta.screen.Contig1
Sequence length = 1001
----- Start ----- --- Length ---- ------------- Scores -------------
ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 NC
+1 957 100 387 429 285 -7.17 0 0 - - 0 - - 99
-2 481 451 332 147 117 -23.76 0 - - 0 0 0 - 99
+1 412 514 624 210 108 -15.35 0 0 - 0 - - 0 99
+3 264 501 662 396 159 -16.85 0 - - 0 - - 0 99
-3 662 617 363 297 252 -18.34 0 - - 0 - - 0 99
-1 924 654 541 381 111 -14.50 0 - - 0 0 - 0 99
+3 663 681 956 291 273 -10.71 0 - - 0 - - - 99
-2 985 976 851 132 123 -14.39 0 0 - - - 0 - 99
-2 362 113 986 375 126 -17.61 0 - - 0 0 0 0 99
-3 528 120 957 570 162 -18.76 0 - - 0 0 - 0 99
-1 163 88 925 237 162 -16.78 0 - - - 0 - - 99
>bdw.fasta.screen.Contig2
Sequence length = 2651
----- Start ----- --- Length ---- ------------- Scores -------------
ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 NC
+2 2497 2506 19 171 162 -21.87 0 - 0 - - 0 - 99
+3 2648 78 221 222 141 -8.99 0 - - 0 0 - - 99
+3 330 441 572 240 129 -17.43 0 - - 0 0 - - 99
+2 494 509 637 141 126 -11.66 0 - 0 - 0 - - 99
-3 986 923 801 183 120 -11.84 0 - - - 0 - 0 99
+1 868 871 990 120 117 -18.35 0 0 - - 0 - 0 99
+1 1003 1048 1236 231 186 -20.39 0 0 - - 0 - - 99
+2 1166 1223 1366 198 141 -19.64 0 - 0 - 0 0 - 99
-3 1748 1742 1617 129 123 -11.47 0 - - - 0 - 0 99
+2 1646 1814 1954 306 138 -14.14 0 - 0 - 0 - - 99
-3 2024 2003 1899 123 102 -6.68 0 0 - 0 0 - 0 99
+3 2046 2055 2168 120 111 -6.20 0 0 - 0 0 - - 99
+1 2059 2062 2184 123 120 -22.11 0 0 - - 0 - - 99
+2 2180 2228 2371 189 141 -22.98 0 - 0 - 0 - - 99
+1 2317 2368 2496 177 126 -34.11 0 0 - - 0 - - 99
+2 2510 2543 2647 135 102 -10.31 0 0 0 - 0 - - 99
0001 -1 37 7 40 2646 2616 -15.52 0 - - - 0 - - 99
Full report at: b_strain_w.detail
- James Estevez 07:55, 31 January 2011 (EST):