Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016219.1 Corchorus capsularis cultivar CVL-1 contig16240, 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: 6628
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Found at i:602 original size:39 final size:38
Alignment explanation
Indices: 531--760 Score: 300
Period size: 39 Copynumber: 6.0 Consensus size: 38
521 ATTAAGGAAG
*
531 TAGTAATCAGT-AAATCAATAATTAAGAGTCAAAGTAA
1 TAGTAATCAGTAAAATTAATAATTAAGAGTCAAAGTAA
*
568 TAGTAATCAGTAAAATTAATAAATTAAGAGTCAAAATAA
1 TAGTAATCAGTAAAATTAAT-AATTAAGAGTCAAAGTAA
* *
607 TAGTAATCATTAAAATTGATAATTAAGAGTCAAAGTAA
1 TAGTAATCAGTAAAATTAATAATTAAGAGTCAAAGTAA
* *
645 TAGTAATCAGTAAAATTAATAAATTAAGAGTGAAAATAA
1 TAGTAATCAGTAAAATTAAT-AATTAAGAGTCAAAGTAA
* * * *
684 TAGTAATCATTAAAATTGATAATTAAGGAGTCAAGGTAT
1 TAGTAATCAGTAAAATTAATAATTAA-GAGTCAAAGTAA
* * * *
723 TAGTAATCAGTAGAATTGATAATCAAGAGTCAAGGTAA
1 TAGTAATCAGTAAAATTAATAATTAAGAGTCAAAGTAA
761 AAAAACAGTA
Statistics
Matches: 170, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
37 11 0.06
38 59 0.35
39 100 0.59
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (38 bp):
TAGTAATCAGTAAAATTAATAATTAAGAGTCAAAGTAA
Found at i:633 original size:77 final size:77
Alignment explanation
Indices: 531--755 Score: 346
Period size: 77 Copynumber: 2.9 Consensus size: 77
521 ATTAAGGAAG
* **
531 TAGTAATCAGT-AAATCAATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAATAAATTAA
1 TAGTAATCATTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAATAAATTAA
595 GAGTCAAAATAA
66 GAGTCAAAATAA
607 TAGTAATCATTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAATAAATTAA
1 TAGTAATCATTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAATAAATTAA
*
672 GAGTGAAAATAA
66 GAGTCAAAATAA
* * * * *
684 TAGTAATCATTAAAATTGATAATTAAGGAGTCAAGGTATTAGTAATCAGTAGAATTGAT-AATCA
1 TAGTAATCATTAAAATTGATAATTAA-GAGTCAAAGTAATAGTAATCAGTAAAATTAATAAATTA
748 AGAGTCAA
65 AGAGTCAA
756 GGTAAAAAAA
Statistics
Matches: 137, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
76 10 0.07
77 99 0.72
78 28 0.20
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (77 bp):
TAGTAATCATTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAATAAATTAA
GAGTCAAAATAA
Found at i:674 original size:116 final size:114
Alignment explanation
Indices: 531--798 Score: 322
Period size: 116 Copynumber: 2.3 Consensus size: 114
521 ATTAAGGAAG
*
531 TAGTAATCAGTAAATCAATAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTAATAAATTAA-
1 TAGTAATCAGTAAATCAATAATTAAGAGTCAAAATAATAGTAATCAGTAAAATTAAT-AATTAAG
* *
595 GAGTCAAAATAATAGTAATCATTAAAATTGATAATTAAGAGTCAAAGTAA
65 GAGTCAAAATAATAGTAATCAGTAAAATTGATAATCAAGAGTCAAAGTAA
* * * *
645 TAGTAATCAGTAAAATTAATAAATTAAGAGTGAAAATAATAGTAATCATTAAAATTGATAATTAA
1 TAGTAATCAGT-AAATCAAT-AATTAAGAGTCAAAATAATAGTAATCAGTAAAATTAATAATTAA
** * * *
710 GGAGTCAAGGTATTAGTAATCAGTAGAATTGATAATCAAGAGTCAAGGTAAAAAAA
64 GGAGTCAAAATAATAGTAATCAGTAAAATTGATAATCAAGAGTCAAAGT-----AA
* *
766 CAGTAAATCAGTAAATCAGTAATTAAGAGTCAA
1 TAGT-AATCAGTAAATCAATAATTAAGAGTCAA
799 GGGATTAATC
Statistics
Matches: 129, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
114 11 0.09
115 13 0.10
116 75 0.58
120 12 0.09
121 11 0.09
122 7 0.05
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (114 bp):
TAGTAATCAGTAAATCAATAATTAAGAGTCAAAATAATAGTAATCAGTAAAATTAATAATTAAGG
AGTCAAAATAATAGTAATCAGTAAAATTGATAATCAAGAGTCAAAGTAA
Found at i:1158 original size:14 final size:14
Alignment explanation
Indices: 1135--1236 Score: 79
Period size: 14 Copynumber: 7.3 Consensus size: 14
1125 CAGTAAAAAG
1135 GTAAAG-GTAATCA
1 GTAAAGAGTAATCA
1148 GTAAAGAGTAATCA
1 GTAAAGAGTAATCA
* *
1162 GTAAAAAGTAA-AA
1 GTAAAGAGTAATCA
*
1175 GTGGCAAAGAGTAGT-A
1 GT---AAAGAGTAATCA
**
1191 AAAAAG-GTAATCA
1 GTAAAGAGTAATCA
1204 GGTAAA-AGTAATCA
1 -GTAAAGAGTAATCA
1218 GTAAAGAAGTAATCA
1 GTAAAG-AGTAATCA
1233 GTAA
1 GTAA
1237 GAAGGTCAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
12 4 0.06
13 19 0.27
14 27 0.39
15 12 0.17
16 8 0.11
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.20
Consensus pattern (14 bp):
GTAAAGAGTAATCA
Found at i:1278 original size:42 final size:42
Alignment explanation
Indices: 1232--1401 Score: 159
Period size: 42 Copynumber: 4.0 Consensus size: 42
1222 AGAAGTAATC
* * *
1232 AGTAAGAAGGTCAAAGATGGTATCAAGTGAAATATGGTATTG
1 AGTAAGAAGGTCAAAGATGGTATCAAGTAAAAAATGGTATTA
* *
1274 AGTAAGAAGGTCAAAAATGGTGT-AGAGTAAAAAATGGTATTA
1 AGTAAGAAGGTCAAAGATGGTATCA-AGTAAAAAATGGTATTA
* * *
1316 AGTAA-AAGAGT-AAAGAATGGTATTAATTAAAAAAATGGTGTTA
1 AGTAAGAAG-GTCAAAG-ATGGTATCAAGT-AAAAAATGGTATTA
* * * *
1359 AGTAAAAAGGTCCAAA-ATGGTATCCAGTAAGAGATGGTATTA
1 AGTAAGAAGGT-CAAAGATGGTATCAAGTAAAAAATGGTATTA
1401 A
1 A
1402 ACAAAAATGG
Statistics
Matches: 105, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
41 7 0.07
42 62 0.59
43 30 0.29
44 3 0.03
45 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.25, T:0.25
Consensus pattern (42 bp):
AGTAAGAAGGTCAAAGATGGTATCAAGTAAAAAATGGTATTA
Found at i:1325 original size:25 final size:25
Alignment explanation
Indices: 1297--1347 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1287 AAAATGGTGT
1297 AGAGTAAAAAATGGTATTAAGTAAA
1 AGAGTAAAAAATGGTATTAAGTAAA
* *
1322 AGAGTAAAGAATGGTATTAATTAAA
1 AGAGTAAAAAATGGTATTAAGTAAA
1347 A
1 A
1348 AAATGGTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (25 bp):
AGAGTAAAAAATGGTATTAAGTAAA
Found at i:1354 original size:18 final size:18
Alignment explanation
Indices: 1331--1366 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1321 AAGAGTAAAG
*
1331 AATGGTATTAATTAAAAA
1 AATGGTATTAAGTAAAAA
*
1349 AATGGTGTTAAGTAAAAA
1 AATGGTATTAAGTAAAAA
1367 GGTCCAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
AATGGTATTAAGTAAAAA
Found at i:1365 original size:17 final size:17
Alignment explanation
Indices: 1324--1366 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1314 TAAGTAAAAG
*
1324 AGTAAAGAATGGTATTA
1 AGTAAAAAATGGTATTA
* *
1341 ATTAAAAAAATGGTGTTA
1 AGT-AAAAAATGGTATTA
1359 AGTAAAAA
1 AGTAAAAA
1367 GGTCCAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (17 bp):
AGTAAAAAATGGTATTA
Found at i:1423 original size:16 final size:16
Alignment explanation
Indices: 1372--1453 Score: 57
Period size: 15 Copynumber: 5.4 Consensus size: 16
1362 AAAAAGGTCC
**
1372 AAAATGGTATCCAGTA
1 AAAATGGTATTAAGTA
* **
1388 AGAGATGGTATTAAACA
1 A-AAATGGTATTAAGTA
1405 AAAATGGTATTAAGT-
1 AAAATGGTATTAAGTA
*
1420 AAAA--GTAGTAAG-A
1 AAAATGGTATTAAGTA
*
1433 AAAATGGTA-AAAGTA
1 AAAATGGTATTAAGTA
1448 AAAATG
1 AAAATG
1454 ATAAAAGTAG
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
13 11 0.22
14 3 0.06
15 14 0.27
16 12 0.24
17 11 0.22
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.23
Consensus pattern (16 bp):
AAAATGGTATTAAGTA
Found at i:1452 original size:15 final size:15
Alignment explanation
Indices: 1432--1462 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1422 AAGTAGTAAG
*
1432 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
1447 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
1462 A
1 A
1463 GCAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Found at i:6512 original size:16 final size:16
Alignment explanation
Indices: 6491--6524 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6481 TCTAAAATAT
6491 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
6507 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
6523 TT
1 TT
6525 TCTGAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (16 bp):
TTCAGAGCTTTTCTGC
Done.