[Bioperl-guts-l] bioperl-live/t/data Glimmer2.out, NONE, 1.1 Glimmer3.detail, NONE, 1.1 Glimmer3.predict, NONE, 1.1 GlimmerHMM.out, NONE, 1.1 GlimmerM.out, NONE, 1.1
Torsten Seemann
tseemann at dev.open-bio.org
Tue Sep 19 20:44:33 EDT 2006
Update of /home/repository/bioperl/bioperl-live/t/data
In directory dev.open-bio.org:/tmp/cvs-serv3026
Added Files:
Glimmer2.out Glimmer3.detail Glimmer3.predict GlimmerHMM.out
GlimmerM.out
Log Message:
Output file examples for four Glimmer flavours: 2.x 3.x HMM M
--- NEW FILE: Glimmer3.predict ---
>BCTDNA
orf00001 29263 9 +1 9.60
orf00002 298 1623 +1 8.09
orf00003 1856 2098 +2 3.34
orf00004 2349 2230 -1 2.72
orf00005 3279 4400 +3 9.99
orf00006 5062 6159 +1 9.87
orf00007 6156 6620 +3 12.71
orf00008 6686 8605 +2 12.31
orf00009 8624 11128 +2 12.75
orf00010 11133 12122 +3 11.50
orf00012 12273 12473 +3 8.92
orf00013 12715 13452 +1 11.15
orf00015 14781 13804 -1 5.51
orf00017 15776 15216 -3 11.26
orf00018 15948 17462 +3 9.28
orf00020 19407 18319 -1 7.45
orf00021 19980 20195 +3 3.15
orf00022 20749 20186 -2 9.01
orf00023 20810 21706 +2 11.68
orf00024 21851 22354 +2 10.53
orf00025 22359 23102 +3 13.70
orf00026 23118 23726 +3 11.50
orf00028 24216 25898 +3 11.23
orf00029 26103 26219 +3 2.08
orf00030 26593 26474 -2 3.57
orf00031 27090 26728 -1 10.84
orf00035 28185 29198 +3 6.81
--- NEW FILE: GlimmerM.out ---
GlimmerM (Version 3.0)
Sequence name: gi|23613028|ref|NC_004326.1|
Sequence length: 69930 bp
Predicted genes/exons
Gene Exon Strand Exon Exon Range Exon
# # Type Length
1 1 - Single 461 523 63
2 1 + Initial 1095 1103 9
2 2 + Internal 1167 1208 42
2 3 + Terminal 1404 1445 42
3 1 - Single 7055 7162 108
4 1 + Initial 7273 7356 84
4 2 + Internal 7434 7598 165
4 3 + Internal 7861 7898 38
4 4 + Terminal 7957 7975 19
5 1 + Initial 20929 23815 2887
5 2 + Terminal 23910 23956 47
6 1 + Initial 24046 26310 2265
6 2 + Internal 27215 28399 1185
6 3 + Internal 28848 28855 8
6 4 + Internal 29246 29309 64
6 5 + Terminal 29502 29516 15
7 2 - Terminal 29593 29600 8
7 1 - Initial 29919 30636 718
8 8 - Terminal 30737 30744 8
8 7 - Internal 31124 31150 27
8 6 - Internal 31814 31883 70
8 5 - Internal 32469 32515 47
8 4 - Internal 33199 34126 928
8 3 - Internal 34647 34688 42
8 2 - Internal 35216 35334 119
8 1 - Initial 36613 36853 241
9 1 + Initial 36912 37101 190
9 2 + Internal 37285 37300 16
9 3 + Terminal 37999 38005 7
10 5 - Terminal 42047 42104 58
10 4 - Internal 42781 42795 15
10 3 - Internal 42864 42888 25
10 2 - Internal 43211 43217 7
10 1 - Initial 43372 46329 2958
--- NEW FILE: GlimmerHMM.out ---
GlimmerHMM
Sequence name: gi|23613028|ref|NC_004326.1|
Sequence length: 69930 bp
Predicted genes/exons
Gene Exon Strand Exon Exon Range Exon
# # Type Length
1 1 + Terminal 2235 2284 50
2 1 - Terminal 2324 2340 17
2 2 - Initial 2413 2434 22
3 1 + Initial 2461 2667 207
3 2 + Internal 2937 2989 53
3 3 + Internal 4203 4216 14
3 4 + Terminal 4587 4627 41
4 1 + Initial 4628 4669 42
4 2 + Terminal 5063 5083 21
5 1 - Terminal 5095 5102 8
5 2 - Initial 5108 5129 22
6 1 - Single 5138 5152 15
7 1 - Single 5158 5205 48
8 1 + Single 5214 5252 39
9 1 + Initial 5262 5469 208
9 2 + Terminal 5538 5647 110
10 1 + Initial 5663 5665 3
10 2 + Terminal 5712 5942 231
11 1 + Initial 5952 6159 208
11 2 + Terminal 6228 6337 110
12 1 + Initial 6353 6355 3
12 2 + Internal 6402 6431 30
12 3 + Internal 6463 6489 27
12 4 + Internal 6563 6707 145
12 5 + Internal 6911 6960 50
12 6 + Internal 7252 7399 148
12 7 + Internal 7672 7860 189
12 8 + Internal 7915 7967 53
12 9 + Internal 8030 8198 169
12 10 + Terminal 8204 8322 119
13 1 + Initial 8329 8385 57
13 2 + Internal 8721 8748 28
13 3 + Internal 8820 8976 157
13 4 + Terminal 11310 11361 52
14 1 - Single 11364 11375 12
15 1 - Single 11378 11386 9
16 1 - Terminal 11411 11413 3
16 2 - Initial 11522 11533 12
17 1 + Initial 11541 11595 55
17 2 + Internal 11926 11967 42
17 3 + Internal 12472 12483 12
17 4 + Terminal 12641 12921 281
18 1 + Initial 12928 13035 108
18 2 + Internal 13334 13350 17
18 3 + Internal 13376 13383 8
18 4 + Internal 13397 13455 59
18 5 + Internal 13481 13497 17
18 6 + Internal 13502 13530 29
18 7 + Internal 13603 13615 13
18 8 + Internal 13649 13656 8
18 9 + Internal 13776 13960 185
18 10 + Internal 13965 13972 8
18 11 + Internal 14173 14189 17
18 12 + Internal 14236 14252 17
18 13 + Internal 14277 14293 17
18 14 + Internal 14487 14515 29
18 15 + Internal 14844 14860 17
18 16 + Internal 15281 15309 29
18 17 + Internal 15470 15477 8
18 18 + Internal 15743 15750 8
18 19 + Internal 15764 15771 8
18 20 + Internal 15785 15792 8
18 21 + Internal 16122 16128 7
18 22 + Internal 16478 16506 29
18 23 + Terminal 17424 17662 239
19 1 + Initial 17669 17741 73
19 2 + Internal 17907 18091 185
19 3 + Internal 18139 18146 8
19 4 + Internal 18159 18237 79
19 5 + Internal 18275 18292 18
19 6 + Internal 18431 18532 102
19 7 + Internal 18813 18839 27
19 8 + Internal 18933 18943 11
19 9 + Internal 19248 19269 22
19 10 + Internal 19423 19486 64
19 11 + Internal 19520 19551 32
19 12 + Internal 19671 19744 74
19 13 + Internal 19799 19944 146
19 14 + Internal 20356 20421 66
19 15 + Internal 20912 26376 5465
19 16 + Internal 27215 28172 958
19 17 + Internal 28378 28381 4
19 18 + Internal 28440 28617 178
19 19 + Internal 28980 29244 265
19 20 + Internal 29259 29330 72
19 21 + Internal 30135 30187 53
19 22 + Terminal 30442 30486 45
20 1 - Terminal 30483 30503 21
20 2 - Initial 30573 30587 15
21 1 + Single 30600 30701 102
22 1 - Single 30707 30715 9
23 1 + Initial 30723 30768 46
23 2 + Internal 30950 30951 2
23 3 + Internal 31436 31516 81
23 4 + Internal 31862 31887 26
23 5 + Internal 31902 31915 14
23 6 + Internal 32005 32075 71
23 7 + Terminal 32357 32401 45
24 1 - Single 32408 32413 6
25 1 - Single 32450 32470 21
26 1 + Initial 32485 32526 42
26 2 + Internal 32809 32817 9
26 3 + Internal 33416 33470 55
26 4 + Terminal 33601 33956 356
27 1 + Initial 33967 34133 167
27 2 + Internal 34240 34252 13
27 3 + Internal 34368 34389 22
27 4 + Internal 34917 34929 13
27 5 + Internal 35211 35289 79
27 6 + Internal 35408 35416 9
27 7 + Internal 35421 35516 96
27 8 + Internal 35827 35964 138
27 9 + Internal 36797 36800 4
27 10 + Internal 36871 36886 16
27 11 + Internal 37250 37352 103
27 12 + Internal 38015 38087 73
27 13 + Internal 38193 38242 50
27 14 + Internal 38538 38540 3
27 15 + Internal 38865 38911 47
27 16 + Internal 38966 38992 27
27 17 + Internal 39553 39567 15
27 18 + Internal 39607 39728 122
27 19 + Internal 39785 39797 13
27 20 + Internal 40060 40090 31
27 21 + Internal 40686 40694 9
27 22 + Internal 41048 41114 67
27 23 + Terminal 41274 41317 44
28 1 + Initial 41321 41383 63
28 2 + Internal 41895 41924 30
28 3 + Internal 42145 42158 14
28 4 + Terminal 42273 42366 94
29 1 + Initial 42378 42407 30
29 2 + Terminal 43154 43186 33
30 1 - Single 43188 43208 21
31 1 - Terminal 43211 43217 7
31 2 - Initial 43239 43255 17
32 1 - Terminal 43260 43358 99
32 2 - Initial 43372 43650 279
33 1 + Initial 43659 43669 11
33 2 + Internal 43827 44543 717
33 3 + Internal 45352 45895 544
33 4 + Internal 47453 47470 18
33 5 + Internal 47477 47501 25
33 6 + Internal 47897 47903 7
33 7 + Internal 48413 48433 21
33 8 + Internal 48698 48711 14
33 9 + Internal 49405 49430 26
33 10 + Internal 49635 49678 44
33 11 + Internal 50184 50212 29
33 12 + Internal 50480 50504 25
33 13 + Internal 50871 50875 5
33 14 + Internal 51003 51079 77
33 15 + Internal 51396 51416 21
33 16 + Internal 51762 51808 47
33 17 + Internal 52597 52652 56
33 18 + Internal 52671 52672 2
33 19 + Internal 53093 53095 3
33 20 + Internal 53262 53308 47
33 21 + Internal 53469 53531 63
33 22 + Internal 55819 56055 237
33 23 + Internal 57050 57132 83
33 24 + Terminal 57138 57181 44
34 1 + Single 57193 57207 15
35 1 + Single 57208 57216 9
36 1 + Initial 57240 57338 99
36 2 + Internal 57510 57543 34
36 3 + Internal 57950 58055 106
36 4 + Terminal 58384 58390 7
37 1 + Initial 58406 58463 58
37 2 + Internal 58550 58656 107
37 3 + Internal 59051 59123 73
37 4 + Internal 59168 59226 59
37 5 + Internal 59407 59451 45
37 6 + Internal 59627 59649 23
37 7 + Internal 59680 59705 26
37 8 + Internal 59968 59977 10
37 9 + Internal 60747 60750 4
37 10 + Internal 60942 60947 6
37 11 + Internal 61442 61464 23
37 12 + Internal 61991 62137 147
37 13 + Internal 62413 62425 13
37 14 + Internal 62508 62522 15
37 15 + Terminal 62830 62838 9
38 1 + Initial 62839 62850 12
38 2 + Internal 63403 63410 8
38 3 + Internal 63916 63931 16
38 4 + Terminal 63992 64009 18
39 1 - Single 64040 64066 27
40 1 + Single 64123 64137 15
41 1 + Initial 64145 64179 35
41 2 + Internal 64194 64266 73
41 3 + Internal 64332 65390 1059
41 4 + Internal 65945 65955 11
41 5 + Internal 66065 66070 6
41 6 + Internal 66469 66485 17
41 7 + Terminal 66697 66704 8
42 1 + Initial 66704 66716 13
42 2 + Internal 66964 67005 42
42 3 + Internal 68146 68190 45
42 4 + Internal 68458 68600 143
42 5 + Terminal 68895 68924 30
43 1 + Initial 68930 69670 741
43 2 + Terminal 69839 69868 30
44 1 - Terminal 69866 69929 64
--- NEW FILE: Glimmer3.detail ---
Command: /bio/sw/glimmer3/bin/glimmer3 -o 50 -g 110 -t 30 ../BCTDNA Glimmer3.icm Glimmer3
Sequence file = ../BCTDNA
ICM model file = Glimmer3.icm
Excluded regions file = none
List of orfs file = none
Truncated orfs = false
Circular genome = true
Minimum gene length = 110 bp
Maximum overlap bases = 50
Input is NOT separate orfs
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
>BCTDNA
Sequence length = 29940
GC percentage = 33.3%
Ignore independent score on orfs longer than 482
----- Start ----- --- Length ---- ------------- Scores -------------
ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 NC
0001 +1 29263 29263 9 684 684 9.68 99 99 - - - - - 0 1.00
-1 984 894 769 213 123 -9.85 0 99 - - 0 - - 0 1.00
0002 +1 292 298 1623 1329 1323 8.26 99 99 - - - - - 0 1.00
+2 1592 1706 1840 246 132 -5.10 0 - 0 - - - - 99 1.00
+3 1860 1881 2003 141 120 -2.68 0 - 75 0 - 0 - 23 1.00
0003 +2 1841 1949 2098 255 147 6.59 99 - 99 - - 0 - 0 1.00
-2 2152 1993 1862 288 129 -3.37 0 - 44 0 - 0 - 55 1.00
+3 2004 2040 2177 171 135 -1.77 0 - - 0 - - - 99 1.00
0004 -1 2385 2349 2230 153 117 4.69 97 - - - 97 - - 2 1.00
-2 3253 3235 3095 156 138 -9.03 0 - - 0 - 0 - 99 1.00
+3 3087 3126 3257 168 129 -9.09 0 - - 0 - 0 - 99 1.00
-2 3463 3439 3320 141 117 7.18 1 - - 98 - 1 - 0 1.00
+1 3550 3589 3702 150 111 -0.25 0 0 - 99 - - - 0 1.00
-1 4038 4026 3913 123 111 -10.13 0 - - 99 0 - - 0 1.00
+1 4171 4192 4314 141 120 -8.48 0 0 - 99 - 0 0 0 1.00
0005 +3 3258 3279 4400 1140 1119 10.20 99 - - 99 - - - 0 1.00
-2 4405 4300 4181 222 117 -0.45 0 0 - 99 - 0 0 0 1.00
-3 4481 4436 4320 159 114 -12.02 0 - - - - - 0 99 1.00
-1 5025 4962 4798 225 162 -6.25 0 - 0 - 0 - - 99 1.00
+2 4790 4913 5029 237 114 -7.57 0 - 0 - 0 - - 99 1.00
0006 +1 5038 5062 6159 1119 1095 9.92 99 99 - - - - - 0 1.00
-3 6386 6368 6213 171 153 -1.23 0 0 - 99 - - 0 0 1.00
+1 6217 6295 6435 216 138 -7.86 0 0 - 99 - - - 0 1.00
-2 6487 6469 6335 150 132 2.90 0 - - 99 - 0 - 0 1.00
0007 +3 6105 6156 6620 513 462 12.86 99 - - 99 - - - 0 1.00
-2 6880 6856 6740 138 114 -9.49 0 - 99 0 - 0 - 0 1.00
+3 7062 7062 7190 126 126 -3.41 0 - 99 0 - 0 0 0 1.00
-2 7267 7162 7034 231 126 -8.57 0 - 99 - - 0 0 0 1.00
+3 7299 7299 7418 117 117 -2.08 0 - 99 0 - - - 0 1.00
-2 7525 7468 7334 189 132 -0.14 0 - 99 - - 0 - 0 1.00
+3 7896 7920 8039 141 117 -7.88 0 - 99 0 - 0 0 0 1.00
-3 8147 8069 7872 273 195 -0.71 0 - 99 - - - 0 0 1.00
-2 8305 8293 8120 183 171 -10.93 0 - 99 - - 0 - 0 1.00
0008 +2 6674 6686 8605 1929 1917 12.34 99 - 99 - - - - 0 1.00
-2 8986 8929 8816 168 111 -9.33 0 - 99 - - 0 - 0 1.00
+3 9003 9084 9200 195 114 -11.31 0 - 99 0 - - - 0 1.00
-2 10417 10315 10196 219 117 -9.22 0 - 99 - - 0 - 0 1.00
-2 10576 10576 10418 156 156 -7.32 0 - 99 - - 0 - 0 1.00
-1 10851 10728 10573 276 153 1.00 0 - 99 - 0 - - 0 1.00
0009 +2 8606 8624 11128 2520 2502 12.77 99 - 99 - - - - 0 1.00
-3 11399 11345 11202 195 141 -9.23 0 - - 99 - - 0 0 1.00
-2 11584 11536 11393 189 141 -3.32 0 - - 99 - 0 - 0 1.00
0010 +3 11118 11133 12122 1002 987 11.55 99 - - 99 - - - 0 1.00
+1 11974 11974 12132 156 156 -4.16 0 0 - - - 54 - 45 1.00
0011 -2 12142 12130 11918 222 210 2.27 92 - - - - 92 - 7 1.00
-3 12149 12143 12009 138 132 -5.42 0 - - - - 56 0 43 1.00
-2 12469 12355 12164 303 189 -7.16 0 - - 20 - 0 - 79 1.00
0012 +3 12123 12273 12473 348 198 10.08 99 - - 99 - 0 - 0 1.00
-3 12494 12470 12306 186 162 -4.46 0 - - 99 - 0 0 0 1.00
+3 12477 12507 12665 186 156 -5.68 0 - - 0 - - - 99 1.00
-3 13169 13166 12969 198 195 2.54 0 99 - - - - 0 0 1.00
0013 +1 12670 12715 13452 780 735 11.22 99 99 - - - - - 0 1.00
-1 13470 13449 13291 177 156 -7.69 0 99 - - 0 - - 0 1.00
0014 +3 13656 13722 13841 183 117 4.01 92 - - 92 - - - 7 1.00
-3 13889 13871 13737 150 132 -1.62 1 - - - - - 1 98 1.00
+1 13762 13774 13920 156 144 -3.79 0 0 - - - - - 99 1.00
+2 13928 13949 14077 147 126 3.00 0 0 0 - 99 - - 0 1.00
+1 13921 13963 14091 168 126 -10.74 0 0 - - 99 - - 0 1.00
+3 14103 14142 14333 228 189 -3.47 0 - - 0 99 - - 0 1.00
-3 14603 14594 14436 165 156 -3.77 0 - - - 99 - 0 0 1.00
0015 -1 14847 14805 13804 1041 999 5.49 99 - - - 99 - - 0 1.00
-2 15682 15676 15527 153 147 -1.39 0 - - 0 - 0 99 0 1.00
0016 +3 15210 15219 15749 537 528 -12.48 0 0 - 0 - - 99 0 1.00
0017 -3 15791 15776 15216 573 558 11.35 99 - - - - - 99 0 1.00
+2 17198 17207 17338 138 129 -3.68 0 - 0 99 0 - - 0 1.00
-1 17370 17271 17155 213 114 3.30 0 - - 99 0 - - 0 1.00
0018 +3 15849 15948 17462 1611 1512 9.36 99 - - 99 - - - 0 1.00
-2 17677 17623 17480 195 141 -1.26 1 - - 34 - 1 - 64 1.00
0019 +3 17463 17484 18377 912 891 6.43 99 - - 99 - - - 0 1.00
-3 18620 18554 18435 183 117 -5.09 0 0 - - 99 - 0 0 1.00
-3 19040 18995 18882 156 111 -2.90 0 - - - 99 - 0 0 1.00
+3 18978 19014 19127 147 111 1.67 0 - - 0 99 - - 0 1.00
-3 19235 19211 19041 192 168 1.29 0 - - - 99 - 0 0 1.00
-2 19357 19357 19208 147 147 -3.27 0 - - 0 99 0 - 0 1.00
+3 19188 19269 19394 204 123 -2.25 0 - - 0 98 - - 1 1.00
0020 -1 19449 19407 18319 1128 1086 7.49 99 - - - 99 - - 0 1.00
-2 19873 19843 19715 156 126 -8.77 0 - - 0 - 0 - 99 1.00
+3 19719 19740 19898 177 156 -7.39 0 - - 0 - - - 99 1.00
-2 20185 20110 19973 210 135 -0.77 0 - - 98 - 0 - 1 1.00
0021 +3 19977 19980 20195 216 213 3.39 99 - - 99 - - - 0 1.00
-1 20445 20418 20302 141 114 -3.04 0 - 0 - 0 99 - 0 1.00
+2 20261 20309 20449 186 138 -4.98 0 - 0 - 0 99 - 0 1.00
+1 20404 20413 20604 198 189 -5.81 0 0 - - - 99 - 0 1.00
+3 20469 20583 20759 288 174 2.71 0 - - 0 - 99 - 0 1.00
0022 -2 20824 20749 20186 636 561 9.10 99 - - - - 99 - 0 1.00
+1 20752 20773 20913 159 138 -3.20 0 0 0 - - - - 99 1.00
-1 21078 21039 20839 237 198 4.53 0 - 99 - 0 - - 0 1.00
+3 21063 21069 21215 150 144 -2.93 0 - 99 0 - - - 0 1.00
0023 +2 20765 20810 21706 939 894 11.73 99 - 99 - - - - 0 1.00
-2 22108 22051 21911 195 138 -4.96 0 - 99 - - 0 - 0 1.00
+3 21918 21945 22112 192 165 -9.58 0 - 99 0 - 0 - 0 1.00
+3 22113 22116 22241 126 123 -1.18 0 - 99 0 0 - 0 0 1.00
-3 22277 22187 22017 258 168 3.69 0 - 99 - - - 0 0 1.00
-1 22320 22194 22078 240 114 8.28 0 - 99 - 0 - 0 0 1.00
0024 +2 21845 21851 22354 507 501 10.64 99 - 99 - - - - 0 1.00
-2 22465 22462 22238 225 222 -1.02 1 - - - - 1 - 98 1.00
+1 22402 22420 22557 153 135 0.60 0 0 - 99 - - - 0 1.00
-2 22720 22681 22544 174 135 5.32 0 - - 99 - 0 - 0 1.00
+1 22657 22663 22779 120 114 -5.87 0 0 - 99 - - 0 0 1.00
0025 +3 22332 22359 23102 768 741 14.02 99 - - 99 - - - 0 1.00
-3 23501 23432 23268 231 162 -6.68 0 - - 99 - - 0 0 1.00
0026 +3 23112 23118 23726 612 606 11.58 99 - - 99 - - - 0 1.00
+1 23920 23920 24036 114 114 -9.23 0 0 - - - - - 99 1.00
0027 -2 24673 24670 24545 126 123 9.42 38 0 - 61 - 38 - 0 1.00
+1 24496 24586 24726 228 138 -4.39 0 0 - 99 - - - 0 1.00
-1 25095 25089 24964 129 123 -11.50 0 - - 99 0 - - 0 1.00
-3 25343 25304 25182 159 120 -19.97 0 - - 99 - - 0 0 1.00
+2 25208 25331 25447 237 114 -11.98 0 - 0 99 - - - 0 1.00
0028 +3 24150 24216 25898 1746 1680 11.26 99 - - 99 - - - 0 1.00
-2 26158 26125 25967 189 156 -6.07 0 - - - - 0 - 99 1.00
0029 +3 26055 26103 26219 162 114 2.53 65 - - 65 - - - 34 1.00
-3 26309 26249 26130 177 117 -1.20 3 - - - - - 3 96 1.00
-1 26370 26328 26209 159 117 -2.70 0 - - - 0 - - 99 1.00
0030 -2 26698 26593 26474 222 117 4.01 91 - - 0 - 91 - 8 1.00
-1 26703 26697 26554 147 141 -3.06 0 - - - 0 6 - 93 1.00
+2 26672 26684 26893 219 207 -1.12 1 - 1 - - - - 98 1.00
+2 26945 26954 27070 123 114 6.59 0 - 0 - 99 - - 0 1.00
0031 -1 27117 27090 26728 387 360 10.98 99 - - - 99 - - 0 1.00
+1 27904 27952 28095 189 141 -0.69 4 4 - - - - - 95 1.00
0032 +2 28001 28025 28144 141 117 1.77 53 - 53 - - - - 46 1.00
0033 -1 28272 28203 28078 192 123 1.32 35 - - - 35 - - 64 1.00
+1 28240 28240 28365 123 123 -9.11 0 0 - 99 - 0 - 0 1.00
0034 -2 28390 28276 28151 237 123 6.20 93 - - 5 - 93 - 0 1.00
-3 28544 28502 28380 162 120 -5.88 0 - - 99 - - 0 0 1.00
+1 28387 28417 28551 162 132 -3.22 0 0 - 71 - - - 28 1.00
+1 28591 28663 28794 201 129 -6.01 0 0 - 99 - - 0 0 1.00
-3 28988 28940 28809 177 129 -9.43 0 - - 99 - 0 0 0 1.00
-2 29005 28885 28763 240 120 4.66 0 - - 99 - 0 - 0 1.00
0035 +3 28155 28188 29198 1041 1008 7.00 99 - - 99 - - - 0 1.00
+1 28987 29119 29247 258 126 -7.99 0 0 - - - - - 99 1.00
-3 29579 29561 29427 150 132 3.22 0 99 - - - - 0 0 1.00
-2 29866 29836 29699 165 135 0.42 0 99 - 0 - 0 0 0 1.00
--- NEW FILE: Glimmer2.out ---
GC Proportion = 33.3%
Minimum gene length = 90
Minimum overlap length = 30
Minimum overlap percent = 10.0%
Threshold score = 90
Use independent scores = True
Ignore independent score on orfs longer than 481
Use strict independent model = True
Use first start codon = True
Orf Gene Lengths Gene -- Frame Scores - Indep
ID# Fr Start Start End Orf Gene Score F1 F2 F3 R1 R2 R3 Score
F3 654 681 779 126 99 0 99 _ 0 _ _ _ 0 0 -1.452
R1 984 957 772 213 186 0 99 _ _ 0 _ _ 0 0 -1.383
F2 917 917 1009 93 93 0 99 0 _ _ _ _ 0 0 -1.335
1 F1 292 292 1620 1329 1329 99 99 _ _ _ _ _ 0 396 -1.219
R2 1631 1607 1515 117 93 0 99 _ _ _ 0 _ 0 0 -1.331
F2 1592 1706 1837 246 132 0 _ 0 _ _ _ _ 99 0 -1.346
R2 1844 1829 1737 108 93 0 _ 0 _ _ 0 _ 99 0 -1.351
F3 1860 1881 2000 141 120 2 _ 7 2 _ _ 21 68 2 -1.372
F2 1841 1856 2095 255 240 0 _ 0 _ _ _ _ 99 7 -1.373
R3 2152 2017 1865 288 153 0 _ 8 _ _ _ 0 90 21 -1.397
F3 2004 2028 2174 171 147 0 _ _ 0 _ _ _ 99 0 -1.385
2 R1 2385 2349 2233 153 117 99 _ _ _ 99 _ _ 0 99 -1.208
R1 3039 3033 2944 96 90 14 _ _ _ 14 _ _ 85 14 -1.262
R3 3253 3235 3098 156 138 0 _ _ 0 _ _ 0 99 0 -1.356
F3 3087 3105 3254 168 150 0 _ _ 0 _ _ 0 99 0 -1.336
R3 3463 3439 3323 141 117 1 _ _ 98 _ _ 1 0 1 -1.235
F1 3550 3589 3699 150 111 0 0 _ 99 _ _ _ 0 0 -1.281
R3 3727 3712 3611 117 102 0 _ _ 99 _ _ 0 0 0 -1.247
R1 4038 4026 3916 123 111 0 _ _ 99 0 _ _ 0 0 -1.376
R2 4097 4091 3999 99 93 0 _ _ 99 _ 0 _ 0 0 -1.296
F1 4009 4009 4110 102 102 0 0 _ 99 _ _ _ 0 0 -1.341
F1 4171 4189 4311 141 123 0 0 _ 99 _ 0 0 0 0 -1.416
3 F3 3258 3279 4397 1140 1119 99 _ _ 99 _ _ _ 0 791 -1.201
R3 4405 4300 4184 222 117 0 0 _ 99 _ 0 0 0 0 -1.360
R2 4481 4436 4323 159 114 0 _ _ _ _ 0 _ 99 0 -1.359
F2 4454 4460 4549 96 90 0 _ 0 _ _ _ _ 99 0 -1.348
R1 5025 4962 4801 225 162 0 _ 0 _ 0 _ _ 99 0 -1.394
F2 4790 4811 5026 237 216 0 _ 0 _ 0 _ _ 99 0 -1.350
4 F1 5038 5062 6156 1119 1095 99 99 _ _ _ _ _ 0 99 -1.184
R2 6386 6383 6216 171 168 0 0 _ 99 _ 0 _ 0 0 -1.345
F1 6217 6292 6432 216 141 0 0 _ 99 _ _ _ 0 0 -1.391
R3 6487 6469 6338 150 132 1 _ _ 98 _ _ 1 0 1 -1.268
5 F3 6105 6156 6617 513 462 99 _ _ 99 _ _ _ 0 395 -1.205
R2 6722 6704 6600 123 105 0 0 _ _ _ 0 _ 99 0 -1.380
F1 6601 6628 6723 123 96 0 0 _ _ _ 0 0 99 0 -1.504
R3 6880 6856 6743 138 114 0 _ 99 0 _ _ 0 0 0 -1.541
R3 7033 6988 6884 150 105 0 _ 99 _ _ _ 0 0 0 -1.423
F3 7062 7062 7187 126 126 0 _ 99 0 _ 0 0 0 0 -1.379
R2 7196 7067 6975 222 93 0 _ 99 _ _ 0 _ 0 0 -1.504
R3 7267 7237 7037 231 201 0 _ 99 _ _ _ 0 0 0 -1.426
F3 7299 7299 7415 117 117 0 _ 99 0 _ _ _ 0 0 -1.388
R2 7502 7481 7389 114 93 0 _ 99 _ _ 0 0 0 0 -1.329
F3 7419 7425 7514 96 90 0 _ 98 0 1 _ 0 0 0 -1.341
R3 7525 7468 7337 189 132 0 _ 99 _ _ _ 0 0 0 -1.333
R1 7683 7524 7423 261 102 0 _ 96 _ 0 _ 0 2 1 -1.288
F3 7896 7899 8036 141 138 0 _ 99 0 _ 0 0 0 0 -1.479
R3 8050 8002 7895 156 108 0 _ 99 0 _ 0 0 0 0 -1.540
R2 8147 8069 7875 273 195 0 _ 99 _ _ 0 _ 0 0 -1.384
R3 8305 8293 8123 183 171 0 _ 99 _ _ _ 0 0 0 -1.399
6 F2 6674 6686 8602 1929 1917 99 _ 99 _ _ _ _ 0 1481 -1.218
R3 8986 8935 8819 168 117 0 _ 99 _ _ _ 0 0 0 -1.463
F3 9003 9003 9197 195 195 0 _ 99 0 _ _ _ 0 0 -1.421
R1 9246 9240 9142 105 99 0 _ 99 _ 0 _ _ 0 0 -1.309
R3 10417 10360 10199 219 162 0 _ 99 _ _ _ 0 0 0 -1.428
R3 10576 10576 10421 156 156 0 _ 99 _ _ _ 0 0 0 -1.380
R1 10851 10809 10576 276 234 0 _ 99 _ 0 _ _ 0 0 -1.340
R1 11097 11088 10999 99 90 0 _ 99 _ 0 _ _ 0 0 -1.362
7 F2 8606 8624 11125 2520 2502 99 _ 99 _ _ _ _ 0 792 -1.206
R2 11399 11345 11205 195 141 0 _ _ 99 _ 0 _ 0 0 -1.459
R3 11584 11536 11396 189 141 0 _ _ 99 _ _ 0 0 0 -1.375
R1 11742 11724 11635 108 90 0 _ 0 99 0 0 _ 0 0 -1.396
8 F3 11118 11133 12119 1002 987 99 _ _ 99 _ _ _ 0 396 -1.229
F1 11974 11974 12129 156 156 0 0 _ _ _ _ 81 18 0 -1.379
9 R3 12142 12130 11921 222 210 94 _ _ _ _ _ 94 5 175 -1.287
R2 12149 12146 12012 138 135 0 _ _ _ _ 0 _ 99 0 -1.381
R3 12469 12355 12167 303 189 0 _ _ 0 _ _ 0 99 0 -1.466
F3 12123 12129 12470 348 342 6 _ _ 6 _ _ _ 93 6 -1.391
R2 12494 12494 12309 186 186 0 _ _ _ _ 0 _ 99 0 -1.454
F2 12422 12473 12565 144 93 6 _ 6 _ _ _ _ 93 6 -1.318
R1 12651 12636 12541 111 96 0 _ _ 1 0 _ _ 98 0 -1.441
F3 12477 12489 12662 186 174 0 _ _ 0 _ _ _ 99 1 -1.389
R3 13084 13069 12977 108 93 0 99 _ _ _ 0 0 0 0 -1.347
R2 13169 13166 12972 198 195 0 99 _ _ _ 0 _ 0 0 -1.282
F3 13176 13218 13313 138 96 0 99 _ 0 _ _ _ 0 0 -1.296
10 F1 12670 12715 13449 780 735 99 99 _ _ _ _ _ 0 396 -1.211
R1 13470 13449 13294 177 156 0 99 _ _ 0 _ _ 0 0 -1.444
R3 13627 13624 13535 93 90 0 _ _ _ _ _ 0 99 0 -1.409
R2 13691 13688 13593 99 96 0 _ _ _ _ 0 _ 99 0 -1.364
11 F3 13656 13671 13838 183 168 99 _ _ 99 _ _ _ 0 99 -1.293
R2 13889 13871 13740 150 132 4 _ _ _ _ 4 _ 95 4 -1.327
F1 13762 13774 13917 156 144 0 0 _ _ _ _ _ 99 0 -1.376
F2 13928 13949 14074 147 126 1 0 1 _ 98 _ _ 0 1 -1.301
F1 13921 13963 14088 168 126 0 0 _ _ 99 _ _ 0 0 -1.425
R2 14222 14192 14091 132 102 0 _ _ _ 84 0 _ 15 0 -1.473
F1 14128 14128 14223 96 96 0 0 _ 0 98 0 _ 1 0 -1.481
F3 14103 14133 14330 228 198 0 _ _ 0 99 _ _ 0 0 -1.405
F2 14216 14270 14362 147 93 38 0 38 _ 50 _ _ 11 38 -1.336
F1 14248 14296 14397 150 102 0 0 _ _ 96 _ _ 3 0 -1.454
R2 14603 14594 14439 165 156 0 _ _ _ 99 0 _ 0 0 -1.305
12 R1 14847 14805 13807 1041 999 99 _ _ _ 99 _ _ 0 822 -1.279
F2 15419 15440 15544 126 105 0 _ 0 0 _ 94 _ 5 0 -1.496
R3 15682 15682 15530 153 153 0 _ _ 0 _ 99 0 0 0 -1.381
F2 15584 15599 15688 105 90 0 0 0 0 _ 99 _ 0 0 -1.518
F3 15210 15219 15746 537 528 0 _ _ 0 _ 99 _ 0 0 -1.512
13 R2 15791 15776 15219 573 558 99 _ _ _ _ 99 _ 0 490 -1.295
F1 16213 16219 16326 114 108 0 0 _ 99 _ _ _ 0 0 -1.297
F2 16253 16268 16369 117 102 0 _ 0 99 _ _ _ 0 0 -1.351
R3 17203 17101 17006 198 96 0 _ _ 98 _ _ 0 0 0 -1.297
F2 17198 17207 17335 138 129 0 _ 0 99 0 _ _ 0 0 -1.393
R1 17370 17349 17158 213 192 0 _ _ 99 0 _ _ 0 0 -1.339
14 F3 15849 15855 17459 1611 1605 99 _ _ 99 _ _ _ 0 593 -1.232
R3 17677 17623 17483 195 141 0 _ _ 99 _ _ 0 0 0 -1.339
R2 18242 18137 18045 198 93 0 _ _ 99 _ 0 _ 0 0 -1.320
15 F3 17463 17484 18374 912 891 99 _ _ 99 _ _ _ 0 297 -1.206
R2 18620 18554 18438 183 117 0 0 _ _ 99 0 _ 0 0 -1.344
F1 18439 18535 18633 195 99 0 0 _ _ 99 _ _ 0 0 -1.318
F2 18677 18719 18811 135 93 4 _ 4 _ 95 _ 0 0 4 -1.188
F1 18808 18835 18927 120 93 0 0 _ _ 99 _ _ 0 0 -1.497
R2 19040 18995 18885 156 111 0 _ _ _ 99 0 _ 0 0 -1.367
F3 18978 18981 19124 147 144 0 _ _ 0 99 _ _ 0 0 -1.309
R2 19235 19232 19044 192 189 0 _ _ _ 99 0 _ 0 0 -1.301
R3 19357 19357 19211 147 147 0 _ _ 0 99 _ 0 0 0 -1.360
F3 19188 19269 19391 204 123 0 _ _ 0 99 _ _ 0 0 -1.269
16 R1 19449 19407 18322 1128 1086 99 _ _ _ 99 _ _ 0 986 -1.187
F3 19443 19473 19571 129 99 0 _ _ 0 _ _ _ 99 0 -1.312
R2 19631 19628 19527 105 102 23 _ _ _ _ 23 _ 76 23 -1.268
F2 19610 19616 19720 111 105 42 _ 42 _ _ _ _ 57 42 -1.247
R3 19873 19843 19718 156 126 0 _ _ 0 _ _ 0 99 0 -1.478
F3 19719 19740 19895 177 156 0 _ _ 0 _ _ _ 99 0 -1.482
F1 20041 20068 20175 135 108 0 0 _ 70 _ _ 28 1 0 -1.444
R3 20185 20110 19976 210 135 0 _ _ 99 _ _ 0 0 28 -1.372
17 F3 19977 19980 20192 216 213 99 _ _ 99 _ _ _ 0 268 -1.320
F1 20179 20266 20364 186 99 0 0 0 _ _ _ 99 0 0 -1.365
R1 20445 20418 20305 141 114 0 _ 0 _ 0 _ 99 0 0 -1.318
F2 20261 20288 20446 186 159 0 _ 0 _ _ _ 99 0 0 -1.376
F1 20404 20413 20601 198 189 0 0 _ _ _ _ 99 0 0 -1.361
F3 20469 20583 20756 288 174 0 _ _ 0 _ _ 99 0 0 -1.274
18 R3 20824 20749 20189 636 561 99 _ _ _ _ _ 99 0 594 -1.215
F1 20752 20773 20910 159 138 4 4 2 _ _ _ _ 92 4 -1.340
R1 21078 21039 20842 237 198 0 _ 99 _ 0 _ _ 0 0 -1.243
F3 21063 21069 21212 150 144 0 _ 99 0 _ _ _ 0 0 -1.350
R1 21597 21585 21496 102 90 0 _ 99 _ 0 0 _ 0 0 -1.313
F1 21508 21520 21624 117 105 0 0 99 _ _ 0 _ 0 0 -1.361
19 F2 20765 20801 21703 939 903 99 _ 99 _ _ _ _ 0 497 -1.192
R3 22108 22078 21914 195 165 0 _ 99 _ _ _ 0 0 0 -1.325
F3 21918 21945 22109 192 165 0 _ 99 0 _ _ 0 0 0 -1.374
F3 22113 22116 22238 126 123 0 _ 99 0 0 0 _ 0 0 -1.273
R2 22277 22232 22020 258 213 0 _ 99 _ _ 0 _ 0 0 -1.294
R1 22320 22194 22081 240 114 0 _ 99 _ 0 0 _ 0 0 -1.237
20 F2 21845 21851 22351 507 501 99 _ 99 _ _ _ _ 0 594 -1.193
R3 22465 22462 22241 225 222 0 _ _ _ _ _ 0 99 0 -1.358
R2 22490 22487 22398 93 90 0 _ _ 99 _ 0 _ 0 0 -1.415
F1 22402 22420 22554 153 135 0 0 _ 99 _ _ _ 0 0 -1.354
R2 22598 22592 22494 105 99 0 _ _ 99 _ 0 _ 0 0 -1.425
R3 22720 22681 22547 174 135 0 _ _ 99 _ _ 0 0 0 -1.269
F1 22657 22663 22776 120 114 0 0 _ 99 _ 0 _ 0 0 -1.353
21 F3 22332 22359 23099 768 741 99 _ _ 99 _ _ _ 0 594 -1.221
R2 23501 23471 23271 231 201 0 _ _ 99 _ 0 _ 0 0 -1.351
22 F3 23112 23118 23723 612 606 99 _ _ 99 _ _ _ 0 198 -1.186
R2 24008 24008 23910 99 99 0 _ _ _ _ 0 _ 99 0 -1.382
F1 23920 23920 24033 114 114 0 0 _ _ _ _ _ 99 0 -1.364
F1 24220 24241 24330 111 90 0 0 _ 16 _ _ _ 83 0 -1.424
F2 24320 24365 24454 135 90 0 _ 0 19 _ _ _ 79 0 -1.403
R1 24507 24507 24412 96 96 0 _ _ 99 0 _ _ 0 0 -1.387
F2 24467 24536 24637 171 102 0 0 0 99 _ _ _ 0 0 -1.483
R3 24673 24670 24548 126 123 5 0 _ 94 _ _ 5 0 5 -1.270
F1 24496 24562 24723 228 162 0 0 _ 99 _ _ _ 0 0 -1.385
R1 25095 25089 24967 129 123 0 _ _ 99 0 _ _ 0 0 -1.450
R2 25343 25304 25185 159 120 0 _ _ 99 _ 0 _ 0 0 -1.591
F1 25225 25267 25362 138 96 0 0 0 99 _ _ _ 0 0 -1.484
F2 25208 25331 25444 237 114 0 _ 0 99 _ _ _ 0 0 -1.501
F1 25774 25774 25863 90 90 0 0 0 99 0 _ _ 0 0 -1.385
23 F3 24150 24216 25895 1746 1680 99 _ _ 99 _ _ _ 0 1020 -1.261
R3 26158 26125 25970 189 156 0 _ _ _ _ _ 0 99 0 -1.368
F3 26055 26064 26216 162 153 83 _ _ 83 _ _ _ 16 83 -1.262
R2 26309 26285 26133 177 153 1 _ _ _ _ 1 _ 98 1 -1.294
R1 26370 26328 26212 159 117 0 _ _ _ 0 _ _ 99 0 -1.327
F3 26463 26592 26684 222 93 19 _ _ 19 14 _ 7 59 19 -1.301
R3 26698 26647 26477 222 171 84 _ _ 0 _ _ 84 14 91 -1.290
R1 26703 26697 26557 147 141 0 _ _ _ 0 _ 92 7 14 -1.342
F2 26672 26684 26890 219 207 0 _ 0 _ _ _ _ 99 0 -1.325
F2 26945 26954 27067 123 114 2 _ 2 _ 97 _ _ 0 2 -1.253
24 R1 27117 27090 26731 387 360 99 _ _ _ 99 _ _ 0 196 -1.219
R1 27276 27231 27142 135 90 0 _ _ _ 0 _ _ 99 0 -1.239
R1 27405 27375 27280 126 96 4 _ _ _ 4 _ _ 95 4 -1.307
R2 27743 27743 27654 90 90 0 _ _ _ _ 0 _ 99 0 -1.310
F2 27833 27836 27934 102 99 0 _ 0 _ _ _ _ 99 0 -1.427
F1 27904 27952 28092 189 141 7 7 _ _ _ _ _ 92 7 -1.317
25 F2 28001 28025 28141 141 117 95 _ 95 _ _ _ _ 4 95 -1.284
R1 28272 28203 28081 192 123 70 _ _ _ 70 _ _ 29 70 -1.319
F1 28240 28240 28362 123 123 0 0 _ 99 _ _ 0 0 0 -1.434
R3 28390 28375 28154 237 222 0 _ _ 99 _ _ 0 0 0 -1.331
R2 28544 28544 28383 162 162 0 _ _ 99 _ 0 _ 0 0 -1.403
F1 28387 28417 28548 162 132 0 0 _ 99 _ _ _ 0 0 -1.393
F1 28591 28663 28791 201 129 0 0 _ 99 _ 0 _ 0 0 -1.460
R2 28988 28940 28812 177 129 0 _ _ 99 _ 0 0 0 0 -1.442
R3 29005 28885 28766 240 120 0 _ _ 99 _ _ 0 0 0 -1.343
R1 29019 28977 28885 135 93 0 _ _ 99 0 0 0 0 0 -1.354
26 F3 28155 28185 29195 1041 1011 99 _ _ 99 _ _ _ 0 891 -1.249
F1 28987 28993 29244 258 252 0 0 _ _ _ _ _ 99 0 -1.434
R2 29579 29561 29430 150 132 0 99 _ _ _ 0 _ 0 0 -1.207
R1 29622 29616 29521 102 96 0 98 _ _ 0 _ _ 1 0 -1.321
R3 29866 29836 29702 165 135 0 99 _ 0 _ 0 0 0 0 -1.290
27 F1 29263 29263 29946 684 684 99 99 _ _ _ _ _ 0 395 -1.187
End = 29940
Original Genes = 27
Potential Genes = 27
Avg Olaps = 0.1
Potential Changes = 2
Potential Rejects = 2
Sure Rejects = 2
Original Genes = 27
Potential Genes = 25
Avg Olaps = 0.0
Potential Changes = 0
Potential Rejects = 0
Sure Rejects = 0
Original Genes = 27
Potential Genes = 25
Avg Olaps = 0.0
Potential Changes = 0
Potential Rejects = 0
Sure Rejects = 0
Putative Genes:
1 292 1620 [+1 L=1329 r=-1.219]
2 2349 2233 [-1 L= 117 r=-1.208]
3 3279 4397 [+3 L=1119 r=-1.201]
4 5062 6156 [+1 L=1095 r=-1.184]
5 6156 6617 [+3 L= 462 r=-1.205]
6 6686 8602 [+2 L=1917 r=-1.218]
7 8624 11125 [+2 L=2502 r=-1.206]
8 11133 12119 [+3 L= 987 r=-1.229]
10 12715 13449 [+1 L= 735 r=-1.211]
12 14805 13807 [-1 L= 999 r=-1.279]
13 15776 15219 [-3 L= 558 r=-1.295]
14 15855 17459 [+3 L=1605 r=-1.232]
15 17484 18374 [+3 L= 891 r=-1.206]
16 19407 18322 [-1 L=1086 r=-1.187]
17 19980 20192 [+3 L= 213 r=-1.320]
18 20749 20189 [-2 L= 561 r=-1.215]
19 20801 21703 [+2 L= 903 r=-1.192]
20 21851 22351 [+2 L= 501 r=-1.193]
21 22359 23099 [+3 L= 741 r=-1.221]
22 23118 23723 [+3 L= 606 r=-1.186]
23 24216 25895 [+3 L=1680 r=-1.261]
24 27090 26731 [-1 L= 360 r=-1.219]
25 28025 28141 [+2 L= 117 r=-1.284]
26 28185 29195 [+3 L=1011 r=-1.249]
27 29263 6 [+1 L= 684 r=-1.187]
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