Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006405.1 Corchorus capsularis cultivar CVL-1 contig06426, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21229
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Found at i:609 original size:27 final size:28
Alignment explanation
Indices: 547--620 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 28
537 AAATTGAAGG
* **
547 TGACTAAAATGCCCCTAAGTGCAAAAAA
1 TGACCAAAATGCCCCTGGGTGCAAAAAA
*
575 TGACCAAAATGCCCCTGGGTGC-GAAAA
1 TGACCAAAATGCCCCTGGGTGCAAAAAA
* *
602 TGACCAAAATACCCTTGGG
1 TGACCAAAATGCCCCTGGG
621 CGACCTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (28 bp):
TGACCAAAATGCCCCTGGGTGCAAAAAA
Found at i:3098 original size:121 final size:120
Alignment explanation
Indices: 2952--3249 Score: 372
Period size: 119 Copynumber: 2.5 Consensus size: 120
2942 TTCAAACTTA
* * * * * * * *
2952 TCAAATTCAACTAATGTTTTACTTAAATCTTAAAAGAATTACGAAAGTTTCCAAAAAGTTTATT-
1 TCAAATTCAATTAAAGATTCACTTAAATCTTAAATGAATTATGAAAATTACC--AAAGTTT-TTA
* * * * *
3016 TACTAAAACTTTTAAACACTTAATTAAACC-TAAGTTTTAGGTTACTTAACCTTTATT
63 GACTAAAACTTGTAAACACTTAATTAAACCTTAAGTCTTAGGTCACTTAACCTTAATT
3073 TCAAATTCAATTAAAGATTCACTTAAATCTTAAATGAATTATGAAAATTACCAAAGTTTTTAGAC
1 TCAAATTCAATTAAAGATTCACTTAAATCTTAAATGAATTATGAAAATTACCAAAGTTTTTAGAC
** **
3138 TAAAGGTTGTAATTACTTAATTAAACCTTAAGTCTTAGGTCACTTAACCTTAATT
66 TAAAACTTGTAAACACTTAATTAAACCTTAAGTCTTAGGTCACTTAACCTTAATT
*
3193 TCAAATCCAATTAAA-ATTCACTTAAATCTTAAATGAATTATGAAAA-TA-CAAAGTTTT
1 TCAAATTCAATTAAAGATTCACTTAAATCTTAAATGAATTATGAAAATTACCAAAGTTTT
3250 AATTCATTTC
Statistics
Matches: 157, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
117 9 0.06
118 4 0.03
119 62 0.39
120 38 0.24
121 44 0.28
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.38
Consensus pattern (120 bp):
TCAAATTCAATTAAAGATTCACTTAAATCTTAAATGAATTATGAAAATTACCAAAGTTTTTAGAC
TAAAACTTGTAAACACTTAATTAAACCTTAAGTCTTAGGTCACTTAACCTTAATT
Found at i:9386 original size:25 final size:25
Alignment explanation
Indices: 9358--9407 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
9348 GTCCCATCCA
9358 TTTT-CATTTTCTCATTAGTCCTATT
1 TTTTGCATTTTCTCATTAGT-CTATT
*
9383 TTTTGCATTTTCTCATTGGTCTATT
1 TTTTGCATTTTCTCATTAGTCTATT
9408 AGTCATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.14, C:0.18, G:0.08, T:0.60
Consensus pattern (25 bp):
TTTTGCATTTTCTCATTAGTCTATT
Found at i:13007 original size:20 final size:20
Alignment explanation
Indices: 12966--13441 Score: 137
Period size: 20 Copynumber: 24.4 Consensus size: 20
12956 AATAAACATA
* * *
12966 AAGAGTAAAAGATGATTAGT
1 AAGAGTAAAAGGTAATCAGT
*
12986 AAGAGTAAAAGGTAATCGGT
1 AAGAGTAAAAGGTAATCAGT
*
13006 AAGAGTAAGAGGTAATCAGT
1 AAGAGTAAAAGGTAATCAGT
*
13026 -A-AG---AAGATAATCAGT
1 AAGAGTAAAAGGTAATCAGT
* *
13041 AAGAGCAAAAAGTAATCAGT
1 AAGAGTAAAAGGTAATCAGT
*
13061 AAAAGTAAAAGGTAATCAGCT
1 AAGAGTAAAAGGTAATCAG-T
* *
13082 ---AGT---GGGTAATCAAT
1 AAGAGTAAAAGGTAATCAGT
13096 AAGAGTAAAAGGTAATCAGT
1 AAGAGTAAAAGGTAATCAGT
13116 AAGAG-----GGTAATCAGT
1 AAGAGTAAAAGGTAATCAGT
* *
13131 AAGAGCAAAGGGGTAAT---T
1 AAGAGTAAA-AGGTAATCAGT
13149 -AGCA--AAAA--TAATCAGT
1 AAG-AGTAAAAGGTAATCAGT
* * *
13165 AAGAGTGAAAGGTGACCAGT
1 AAGAGTAAAAGGTAATCAGT
13185 AAGAGT-AAAGGATAATCAGT
1 AAGAGTAAAAGG-TAATCAGT
13205 AA-AGTAAATCA-GTAAAAT-AGT
1 AAGAGTAAA--AGGT--AATCAGT
* **
13226 AATCAGTAAAA-AAAAT-A-T
1 AA-GAGTAAAAGGTAATCAGT
*
13244 -A-A-T-AATGGTAATCAGT
1 AAGAGTAAAAGGTAATCAGT
*
13260 AAAAGGTAAAATGGTAATCAGT
1 AAGA-GTAAAA-GGTAATCAGT
* *
13282 AAAAGGTAAAATGGTAATTAGT
1 AAGA-GTAAAA-GGTAATCAGT
* * *
13304 AAAAAGCAATATGGTAATCAGT
1 -AAGAGTAA-AAGGTAATCAGT
* **
13326 AAGAAGT-AATGACAATCAGT
1 AAG-AGTAAAAGGTAATCAGT
* *
13346 AAAAAAGTAAAAAGGTAGTCAGT
1 --AAGAGT-AAAAGGTAATCAGT
* * *
13369 AATGGGTACAATGGTAATTAGT
1 AA-GAGTA-AAAGGTAATCAGT
13391 ATAGAGT-AAAGTGATAATCAGT
1 A-AGAGTAAAAG-G-TAATCAGT
* *
13413 AAAGAGTAATAGG-AATCAAT
1 -AAGAGTAAAAGGTAATCAGT
13433 AAGAGTAAA
1 AAGAGTAAA
13442 GTAGTAATTA
Statistics
Matches: 345, Mismatches: 53, Indels: 117
0.67 0.10 0.23
Matches are distributed among these distances:
13 6 0.02
14 5 0.01
15 35 0.10
16 7 0.02
17 11 0.03
18 12 0.03
19 21 0.06
20 117 0.34
21 26 0.08
22 80 0.23
23 25 0.07
ACGTcount: A:0.50, C:0.06, G:0.23, T:0.22
Consensus pattern (20 bp):
AAGAGTAAAAGGTAATCAGT
Found at i:13037 original size:35 final size:34
Alignment explanation
Indices: 12989--13065 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 34
12979 GATTAGTAAG
* * * * *
12989 AGTAAAAGGTAATCGGTAAGAGTAAGAGGTAATC
1 AGTAAAAGATAATCAGTAAGAGCAAAAAGTAATC
13023 AGTAAGAAGATAATCAGTAAGAGCAAAAAGTAATC
1 AGTAA-AAGATAATCAGTAAGAGCAAAAAGTAATC
13058 AGTAAAAG
1 AGTAAAAG
13066 TAAAAGGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 8 0.22
35 29 0.78
ACGTcount: A:0.51, C:0.06, G:0.25, T:0.18
Consensus pattern (34 bp):
AGTAAAAGATAATCAGTAAGAGCAAAAAGTAATC
Found at i:13038 original size:15 final size:15
Alignment explanation
Indices: 13009--13044 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12999 AATCGGTAAG
*
13009 AGTAAG-AGGTAATC
1 AGTAAGAAGATAATC
13023 AGTAAGAAGATAATC
1 AGTAAGAAGATAATC
13038 AGTAAGA
1 AGTAAGA
13045 GCAAAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (15 bp):
AGTAAGAAGATAATC
Found at i:13042 original size:55 final size:55
Alignment explanation
Indices: 12969--13120 Score: 182
Period size: 55 Copynumber: 2.8 Consensus size: 55
12959 AAACATAAAG
* * * *
12969 AGTAA-AAGATGATTAGTAAGAGTAAAAGGTAATCGGTAAGAGTAAGAGGTAATC
1 AGTAAGAAGATAATCAGTAAGAGTAAAAGGTAATCAGTAAGAGTAAAAGGTAATC
* * *
13023 AGTAAGAAGATAATCAGTAAGAGCAAAAAGTAATCAGTAAAAGTAAAAGGTAATC
1 AGTAAGAAGATAATCAGTAAGAGTAAAAGGTAATCAGTAAGAGTAAAAGGTAATC
** * *
13078 AGCT-AGTGGGTAATCAATAAGAGTAAAAGGTAATCAGTAAGAG
1 AG-TAAGAAGATAATCAGTAAGAGTAAAAGGTAATCAGTAAGAG
13121 GGTAATCAGT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
54 5 0.06
55 76 0.93
56 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.25, T:0.20
Consensus pattern (55 bp):
AGTAAGAAGATAATCAGTAAGAGTAAAAGGTAATCAGTAAGAGTAAAAGGTAATC
Found at i:13126 original size:15 final size:15
Alignment explanation
Indices: 13106--13135 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13096 AAGAGTAAAA
13106 GGTAATCAGTAAGAG
1 GGTAATCAGTAAGAG
13121 GGTAATCAGTAAGAG
1 GGTAATCAGTAAGAG
13136 CAAAGGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (15 bp):
GGTAATCAGTAAGAG
Found at i:13134 original size:35 final size:35
Alignment explanation
Indices: 13052--13189 Score: 129
Period size: 35 Copynumber: 4.0 Consensus size: 35
13042 AGAGCAAAAA
* *
13052 GTAATCAGTAAAAGTAAAAGGTAATCAGCT-AGTGG
1 GTAATCAGTAAGAGTAAAAGGTAATCAG-TAAGAGG
*
13087 GTAATCAATAAGAGTAAAAGGTAATCAGTAAGAGG
1 GTAATCAGTAAGAGTAAAAGGTAATCAGTAAGAGG
* * * * *
13122 GTAATCAGTAAGAGCAAAGGGGTAATTAGCAA-A-A
1 GTAATCAGTAAGAGTAAA-AGGTAATCAGTAAGAGG
* * * *
13156 ATAATCAGTAAGAGTGAAAGGTGACCAGTAAGAG
1 GTAATCAGTAAGAGTAAAAGGTAATCAGTAAGAG
13190 TAAAGGATAA
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
33 8 0.10
34 17 0.21
35 47 0.57
36 10 0.12
ACGTcount: A:0.46, C:0.08, G:0.27, T:0.20
Consensus pattern (35 bp):
GTAATCAGTAAGAGTAAAAGGTAATCAGTAAGAGG
Found at i:13216 original size:13 final size:14
Alignment explanation
Indices: 13188--13235 Score: 62
Period size: 13 Copynumber: 3.4 Consensus size: 14
13178 GACCAGTAAG
*
13188 AGTAAAGGATAATC
1 AGTAAAGTATAATC
13202 AGTAAAGTA-AATC
1 AGTAAAGTATAATC
*
13215 AGTAAAATAGTAATC
1 AGTAAAGTA-TAATC
13230 AGTAAA
1 AGTAAA
13236 AAAAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 12 0.40
14 8 0.27
15 10 0.33
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (14 bp):
AGTAAAGTATAATC
Found at i:13262 original size:27 final size:28
Alignment explanation
Indices: 13197--13263 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
13187 GAGTAAAGGA
**
13197 TAATCAGTAAAGTAAATCAGTAAAATAG
1 TAATCAGTAAAAAAAATCAGTAAAATAG
*
13225 TAATCAGTAAAAAAAAT-A-TAATAATGG
1 TAATCAGTAAAAAAAATCAGTAA-AATAG
13252 TAATCAGTAAAA
1 TAATCAGTAAAA
13264 GGTAAAATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 3 0.09
27 17 0.49
28 15 0.43
ACGTcount: A:0.57, C:0.06, G:0.12, T:0.25
Consensus pattern (28 bp):
TAATCAGTAAAAAAAATCAGTAAAATAG
Found at i:13272 original size:22 final size:22
Alignment explanation
Indices: 13247--13415 Score: 139
Period size: 22 Copynumber: 7.7 Consensus size: 22
13237 AAAATATAAT
13247 AATGGTAATCAGTAAAAGGTAA
1 AATGGTAATCAGTAAAAGGTAA
13269 AATGGTAATCAGTAAAAGGTAA
1 AATGGTAATCAGTAAAAGGTAA
* * *
13291 AATGGTAATTAGTAAAAAGCAA
1 AATGGTAATCAGTAAAAGGTAA
*
13313 TATGGTAATCAGTAAGAA-GT--
1 AATGGTAATCAGTAA-AAGGTAA
** *
13333 AATGACAATCAGTAAAAAAGTAA
1 AATGGTAATCAGT-AAAAGGTAA
* * ** *
13356 AAAGGTAGTCAGTAATGGGTAC
1 AATGGTAATCAGTAAAAGGTAA
* *
13378 AATGGTAATTAGT-ATAGAGTAA
1 AATGGTAATCAGTAAAAG-GTAA
* *
13400 AGTGATAATCAGTAAA
1 AATGGTAATCAGTAAA
13416 GAGTAATAGG
Statistics
Matches: 114, Mismatches: 26, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
20 12 0.11
21 7 0.06
22 83 0.73
23 12 0.11
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (22 bp):
AATGGTAATCAGTAAAAGGTAA
Found at i:13400 original size:109 final size:110
Alignment explanation
Indices: 13226--13440 Score: 242
Period size: 109 Copynumber: 2.0 Consensus size: 110
13216 GTAAAATAGT
13226 AATCAGTAAAAAAAATATAATAATGGTAATCAGTAAAAGGTAAAATGGTAATCAGTAAAAGGTAA
1 AATCAGTAAAAAAAATATAATAATGGTAATCAGTAAAAGGTAAAATGGTAATCAGTAAAAGGTAA
* * *
13291 AATGGTAATTAGTAAAAAGCAATATGGTAATCAGTAAGAAGTAATGAC
66 AATGATAATCAGTAAAAAGCAATA-GG-AATCAATAAG-AGTAATGAC
* * ** * * *
13339 AATCAGT-AAAAAAGTA-AA-AA-GGTAGTCAGTAATGGGTACAATGGTAATTAGT-ATAGAGTA
1 AATCAGTAAAAAAAATATAATAATGGTAATCAGTAAAAGGTAAAATGGTAATCAGTAAAAG-GTA
* * *
13399 AAGTGATAATCAGTAAAGAGTAATAGGAATCAATAAGAGTAA
65 AAATGATAATCAGTAAAAAGCAATAGGAATCAATAAGAGTAA
13441 AGTAGTAATT
Statistics
Matches: 88, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
106 5 0.06
107 9 0.10
108 5 0.06
109 50 0.57
110 2 0.02
111 2 0.02
112 8 0.09
113 7 0.08
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (110 bp):
AATCAGTAAAAAAAATATAATAATGGTAATCAGTAAAAGGTAAAATGGTAATCAGTAAAAGGTAA
AATGATAATCAGTAAAAAGCAATAGGAATCAATAAGAGTAATGAC
Found at i:13418 original size:22 final size:22
Alignment explanation
Indices: 13247--13500 Score: 114
Period size: 22 Copynumber: 11.7 Consensus size: 22
13237 AAAATATAAT
*
13247 AATGGTAATCAGTAAA-AGGTAA
1 AATGATAATCAGTAAAGA-GTAA
*
13269 AATGGTAATCAGTAAA-AGGTAA
1 AATGATAATCAGTAAAGA-GTAA
* * * *
13291 AATGGTAATTAGTAAAAAGCAA
1 AATGATAATCAGTAAAGAGTAA
* *
13313 TATGGTAATCAGT-AAGAAGT--
1 AATGATAATCAGTAAAG-AGTAA
* *
13333 AATGACAATCAGTAAAAAAGTAA
1 AATGATAATCAGT-AAAGAGTAA
* * * * * *
13356 AAAGGTAGTCAGTAATGGGTAC
1 AATGATAATCAGTAAAGAGTAA
* * *
13378 AATGGTAATTAGTATAGAGTAA
1 AATGATAATCAGTAAAGAGTAA
*
13400 AGTGATAATCAGTAAAGAGTAA
1 AATGATAATCAGTAAAGAGTAA
* * *
13422 TA-G-GAATCAAT-AAGAGTAA
1 AATGATAATCAGTAAAGAGTAA
* * * *
13441 AGT-AGTAATTAATAAAAAAGT-A
1 AATGA-TAATCAGT-AAAGAGTAA
*
13463 AAGGAATAATCAGTAAAGAGTAA
1 AATG-ATAATCAGTAAAGAGTAA
*
13486 AATGATAGTCAGTAA
1 AATGATAATCAGTAA
13501 TTAAGTTCAA
Statistics
Matches: 173, Mismatches: 45, Indels: 28
0.70 0.18 0.11
Matches are distributed among these distances:
19 8 0.05
20 16 0.09
21 12 0.07
22 111 0.64
23 25 0.14
24 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (22 bp):
AATGATAATCAGTAAAGAGTAA
Found at i:13430 original size:87 final size:86
Alignment explanation
Indices: 13253--13422 Score: 209
Period size: 87 Copynumber: 2.0 Consensus size: 86
13243 TAATAATGGT
* * *
13253 AATCAGTAAAAGGTAAAATGGTAATCAGTAAAAGGTAAAATGGTAATTAGTAAAAAGCAATATGG
1 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAGGTAAAATGGTAATTAGTAAAAAGCAATATGA
13318 TAATCAGTAAGAAGTAATGAC
66 TAATCAGTAAGAAGTAATGAC
* ** * * * *
13339 AATCAGTAAAAAAGTAAAAAGGTAGTCAGTAATGGGTACAATGGTAATTAGTATAGAGTAA-AGT
1 AATCAGT-AAAAAGTAAAAAGGTAATCAGTAAAAGGTAAAATGGTAATTAGTAAAAAGCAATA-T
13403 GATAATCAGTAA-AGAGTAAT
64 GATAATCAGTAAGA-AGTAAT
13423 AGGAATCAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
86 9 0.13
87 62 0.87
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (86 bp):
AATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAGGTAAAATGGTAATTAGTAAAAAGCAATATGA
TAATCAGTAAGAAGTAATGAC
Found at i:13652 original size:21 final size:20
Alignment explanation
Indices: 13592--13653 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
13582 AAAGTATTGG
* *
13592 TAATCAGTAAAAGTGAAATAG
1 TAATCAGTAAAAGT-AAAAAA
*
13613 TAATCAATAAAAAAGTAAAAAA
1 TAATCAGT--AAAAGTAAAAAA
13635 TAATCAGTAAAGAGTAAAA
1 TAATCAGTAAA-AGTAAAA
13654 TGATAGTCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.09
21 14 0.41
22 11 0.32
23 6 0.18
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (20 bp):
TAATCAGTAAAAGTAAAAAA
Found at i:13742 original size:27 final size:26
Alignment explanation
Indices: 13702--13869 Score: 144
Period size: 26 Copynumber: 6.2 Consensus size: 26
13692 CAGTAAAAAG
*
13702 AGTAAGAAATGAGTAAAAAGTGGTGATT
1 AGTAA-AAA-GAGTAAAAAGTGGTAATT
13730 AGTAATAAAGAGTAAGAAA-TGGTAATT
1 AGTAA-AAAGAGTAA-AAAGTGGTAATT
* *
13757 AAATAAAAAGAGTAAAAAGTGAT-ATT
1 -AGTAAAAAGAGTAAAAAGTGGTAATT
* * *
13783 CAGTAAAAACAGTAAGAAAAGGGGTAATC
1 -AGTAAAAAGAGT-A-AAAAGTGGTAATT
*
13812 AGTAAAAAAGAGTAAAATA-TGGTAATC
1 AGT-AAAAAGAGTAAAA-AGTGGTAATT
* *
13839 AGTACAAAGAGTAAAAAATGGTAATT
1 AGTAAAAAGAGTAAAAAGTGGTAATT
13865 AGTAA
1 AGTAA
13870 TCAAGAAATA
Statistics
Matches: 116, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
25 1 0.01
26 39 0.34
27 39 0.34
28 27 0.23
29 10 0.09
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.22
Consensus pattern (26 bp):
AGTAAAAAGAGTAAAAAGTGGTAATT
Found at i:13841 original size:55 final size:53
Alignment explanation
Indices: 13702--13869 Score: 133
Period size: 55 Copynumber: 3.1 Consensus size: 53
13692 CAGTAAAAAG
* * * * * * * *
13702 AGTAAGAAATGAGTAAAAAGTGGTGATTAGTAATAAAGAGTAAGAAATGGTAATT
1 AGTAA-AAAAGAGTAAAAAGTGATAATCAGTAA-AAACAGTAAAAAAGGGTAATC
* *
13757 A-AATAAAAAGAGTAAAAAGTGATATTCAGTAAAAACAGTAAGAAAAGGGGTAATC
1 AGTA-AAAAAGAGTAAAAAGTGATAATCAGTAAAAACAGTAA-AAAA-GGGTAATC
* * * * *
13812 AGTAAAAAAGAGTAAAATA-TGGTAATCAGTACAAAGAGTAAAAAATGGTAATT
1 AGTAAAAAAGAGTAAAA-AGTGATAATCAGTAAAAACAGTAAAAAAGGGTAATC
13865 AGTAA
1 AGTAA
13870 TCAAGAAATA
Statistics
Matches: 91, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
53 19 0.21
54 30 0.33
55 40 0.44
56 2 0.02
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.22
Consensus pattern (53 bp):
AGTAAAAAAGAGTAAAAAGTGATAATCAGTAAAAACAGTAAAAAAGGGTAATC
Found at i:13875 original size:27 final size:26
Alignment explanation
Indices: 13702--13869 Score: 149
Period size: 27 Copynumber: 6.2 Consensus size: 26
13692 CAGTAAAAAG
* *
13702 AGTAAGAAATGAGTAAAAAGTGGTGATT
1 AGTAA-AAA-GAGTAAAAAATGGTAATT
*
13730 AGTAATAAAGAGTAAGAAATGGTAATT
1 AGTAA-AAAGAGTAAAAAATGGTAATT
* * *
13757 AAATAAAAAGAGTAAAAAGTGAT-ATT
1 -AGTAAAAAGAGTAAAAAATGGTAATT
* * *
13783 CAGTAAAAACAGTAAGAAAAGGGGTAATC
1 -AGTAAAAAGAGTAA-AAAA-TGGTAATT
* *
13812 AGTAAAAAAGAGTAAAATATGGTAATC
1 AGT-AAAAAGAGTAAAAAATGGTAATT
*
13839 AGTACAAAGAGTAAAAAATGGTAATT
1 AGTAAAAAGAGTAAAAAATGGTAATT
13865 AGTAA
1 AGTAA
13870 TCAAGAAATA
Statistics
Matches: 113, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
26 39 0.35
27 42 0.37
28 20 0.18
29 12 0.11
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.22
Consensus pattern (26 bp):
AGTAAAAAGAGTAAAAAATGGTAATT
Found at i:17879 original size:35 final size:34
Alignment explanation
Indices: 17839--18211 Score: 431
Period size: 35 Copynumber: 10.9 Consensus size: 34
17829 GTGAGTCAGT
*
17839 AGTAATCAACTTAATTCAGGGTAATTAAGTGAATC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTGAGTC
17874 AGTAATCAACTTAATTCAGGGTAATTAAGT-AGTTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTGAG-TC
*
17909 AGTAATCAACTTAATTCAGGGTAATTAAGTGGGTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTGAGTC
*
17944 AGTAATCAGCTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAAT-AACTTAATTCAGGGTAATTAAGTGAGTC
*
17979 AGTGAATAACTTAATTCAGGGTAATTAAGTCAGT-
1 AGT-AATAACTTAATTCAGGGTAATTAAGTGAGTC
* *
18013 A--AATAGCTTAATTCAGGGTAATTAATTGAGTC
1 AGTAATAACTTAATTCAGGGTAATTAAGTGAGTC
* *
18045 AGTTAATGACTTAATTCAGGATAATT-A---AGTC
1 AG-TAATAACTTAATTCAGGGTAATTAAGTGAGTC
* *
18076 AGTAAGTAGCTTAATTCAGGGTAATTAAGTGAATC
1 AGTAA-TAACTTAATTCAGGGTAATTAAGTGAGTC
*
18111 AGTAATCAACTTTAATTCAGGGTAATTAAGTGAGTT
1 AGTAAT-AAC-TTAATTCAGGGTAATTAAGTGAGTC
* *
18147 AATGAAAAACTTAATTCAGGGTAATTAAGT-AGTTC
1 AGT-AATAACTTAATTCAGGGTAATTAAGTGAG-TC
* *
18182 AATAAGTAACTTAATTCATGGTAATTAAGT
1 AGTAA-TAACTTAATTCAGGGTAATTAAGT
18212 TTAGTGAGCA
Statistics
Matches: 297, Mismatches: 24, Indels: 34
0.84 0.07 0.10
Matches are distributed among these distances:
30 3 0.01
31 50 0.17
32 2 0.01
34 8 0.03
35 200 0.67
36 32 0.11
37 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (34 bp):
AGTAATAACTTAATTCAGGGTAATTAAGTGAGTC
Done.