Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013442.1 Corchorus capsularis cultivar CVL-1 contig13463, 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: 8438
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Found at i:953 original size:38 final size:38
Alignment explanation
Indices: 921--1243 Score: 237
Period size: 38 Copynumber: 8.6 Consensus size: 38
911 AATTAAGGAC
* *
921 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
*
959 CAAAGTAAGAATAATCAGTAAAATTGATAATTACGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
*
997 --AA-T-AG--TAATCAGTGAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
*
1029 CAAAGTAAGAATAATCAGTAAAATTGATAATCAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
** *
1067 CAAAGTAACG-GCAATCAGT-AAA-TCAGTAATTAAGTAG-
1 CAAAGTAA-GAATAATCAGTAAAATTGA-TAATTAAG-AGT
* * * *
1104 -AAAG--GGATTAATCAGT--AATTCGGTAATCAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATT-GATAATTAAGAGT
* * ** * *
1138 CAAGGTAATAGATTAATCAGCGAAATCGGTAATTAAAGAGT
1 CAAAGT-A-AGAATAATCAGTAAAATTGATAATT-AAGAGT
*
1179 CAAAGTAAAAGAAGTAATCAGTAAAA-TGGTAATTAAGAGT
1 CAAAGT--AAGAA-TAATCAGTAAAATTGATAATTAAGAGT
*
1219 AAAAGTAAAAGAAGTAATCAGTAAA
1 CAAAGT--AAGAA-TAATCAGTAAA
1244 TCGGTAAAGA
Statistics
Matches: 234, Mismatches: 28, Indels: 44
0.76 0.09 0.14
Matches are distributed among these distances:
32 25 0.11
33 5 0.02
34 19 0.08
35 5 0.02
36 10 0.04
37 10 0.04
38 77 0.33
39 11 0.05
40 36 0.15
41 24 0.10
42 12 0.05
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (38 bp):
CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
Found at i:1005 original size:70 final size:70
Alignment explanation
Indices: 924--1059 Score: 263
Period size: 70 Copynumber: 1.9 Consensus size: 70
914 TAAGGACCAA
924 AGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAA
1 AGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAA
989 TTACG
66 TTACG
*
994 AGTAATAGTAATCAGTGAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAA
1 AGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAA
1059 T
66 T
1060 CAAGAGTCAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (70 bp):
AGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAA
TTACG
Found at i:1224 original size:40 final size:41
Alignment explanation
Indices: 1112--1250 Score: 169
Period size: 40 Copynumber: 3.5 Consensus size: 41
1102 AGAAAGGGAT
* * * * *
1112 TAATCAGT-AATTCGGTAATCAAGAGTCAAGGTAATAG-AT
1 TAATCAGTAAAATCGGTAATTAAGAGTCAAAGTAAAAGAAG
**
1151 TAATCAGCGAAATCGGTAATTAAAGAGTCAAAGTAAAAGAAG
1 TAATCAGTAAAATCGGTAATT-AAGAGTCAAAGTAAAAGAAG
*
1193 TAATCAGTAAAAT-GGTAATTAAGAGTAAAAGTAAAAGAAG
1 TAATCAGTAAAATCGGTAATTAAGAGTCAAAGTAAAAGAAG
1233 TAATCAGT-AAATCGGTAA
1 TAATCAGTAAAATCGGTAA
1251 AGAGTAAAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
39 11 0.13
40 42 0.48
41 22 0.25
42 12 0.14
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (41 bp):
TAATCAGTAAAATCGGTAATTAAGAGTCAAAGTAAAAGAAG
Found at i:1267 original size:16 final size:17
Alignment explanation
Indices: 1241--1275 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1231 AGTAATCAGT
*
1241 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
1258 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAAAGTAA
1274 AA
1 AA
1276 GGGTAATCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:1301 original size:21 final size:21
Alignment explanation
Indices: 1272--1481 Score: 124
Period size: 22 Copynumber: 9.8 Consensus size: 21
1262 GGTAAAAAGT
* *
1272 AAAAGGGTAATCGGTAAGAGC
1 AAAATGGTAATCAGTAAGAGC
* *
1293 AAAATGGTAACCAGTAAAGAGT
1 AAAATGGTAATCAGT-AAGAGC
* *
1315 AAAATAGTAATCAGTAAAAGC
1 AAAATGGTAATCAGTAAGAGC
* * *
1336 AAAATGGGAACCAGTAAAGAGT
1 AAAATGGTAATCAGT-AAGAGC
* *
1358 AAAATAGTAATCAGTAAAAGC
1 AAAATGGTAATCAGTAAGAGC
1379 AAAATGGTAAAAT-AGTAA-A--
1 AAAATGGT--AATCAGTAAGAGC
* * * *
1398 AAATGATGATAATCCGTAAAAGGT
1 AAA--ATGGTAATCAGTAAGA-GC
* *
1422 AAGATGGTAATCAGTGAGAGC
1 AAAATGGTAATCAGTAAGAGC
* * *
1443 AAAATAGTAATCAGTAAAAGGT
1 AAAATGGTAATCAGTAAGA-GC
1465 AAGAA-GGTAATCAGTAA
1 AA-AATGGTAATCAGTAA
1482 AGAATAACAT
Statistics
Matches: 143, Mismatches: 33, Indels: 25
0.71 0.16 0.12
Matches are distributed among these distances:
19 6 0.04
20 4 0.03
21 61 0.43
22 65 0.45
23 5 0.03
24 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.19
Consensus pattern (21 bp):
AAAATGGTAATCAGTAAGAGC
Found at i:1317 original size:43 final size:43
Alignment explanation
Indices: 1263--1496 Score: 201
Period size: 43 Copynumber: 5.4 Consensus size: 43
1253 AGTAAAAATG
* ** * *
1263 GTAAAAAGTAAAAGGGTAATCGGTAAGAGCAAAATGGTAACCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAACCA
*
1306 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGGAACCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAACCA
**
1349 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAAAATA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGT-AACCA
* * * * *
1393 GTAAA-A--AATGAT-GATAATCCGTAAAAGGTAAGATGGTAATCA
1 GTAAAGAGTAA-AATAG-TAATCAGTAAAA-GCAAAATGGTAACCA
* * * *
1435 GT-GAGAGCAAAATAGTAATCAGTAAAAGGTAAGAA-GGTAATCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAA-GCAA-AATGGTAACCA
* *
1478 GTAAAGAATAACATAGTAA
1 GTAAAGAGTAAAATAGTAA
1497 AAAGTGATGA
Statistics
Matches: 158, Mismatches: 23, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
41 4 0.03
42 19 0.12
43 111 0.70
44 24 0.15
ACGTcount: A:0.52, C:0.07, G:0.22, T:0.19
Consensus pattern (43 bp):
GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAACCA
Found at i:1517 original size:100 final size:100
Alignment explanation
Indices: 1304--1581 Score: 292
Period size: 100 Copynumber: 2.7 Consensus size: 100
1294 AAATGGTAAC
* * * * * * *
1304 CAGT-AAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGGAACCAGTAAAGAGTAAAATA-GTA
1 CAGTAAAAG-GTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAATAAAGAGCAAAA-AGGTA
* *
1367 ATCAGTAAAAGCAAAATGGTAAAATAGTAAAAAATGATGATAAT
64 ATCAGT-AAAG---AA---TAACATAGTAAAAAATGATGACAAT
* * * * * *
1411 CCGTAAAAGGTAAGATGGTAATCAGTGAGAGCAAAATAGTAATCAGTAAA-AGGTAAGAAGGTAA
1 CAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAATAAAGA-GCAAAAAGGTAA
*
1475 TCAGTAAAGAATAACATAGTAAAAAGTGATGACAAT
65 TCAGTAAAGAATAACATAGTAAAAAATGATGACAAT
*
1511 CAGTAAAAGGTAAAATGGTAATCAGTAAGAGCGAAATAGTAATCAATAAAGAGCAAAAAGGTAAT
1 CAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAATAAAGAGCAAAAAGGTAAT
1576 CAGTAA
66 CAGTAA
1582 GAACAAAATG
Statistics
Matches: 148, Mismatches: 19, Indels: 15
0.81 0.10 0.08
Matches are distributed among these distances:
100 84 0.57
101 1 0.01
103 2 0.01
106 6 0.04
107 51 0.34
108 4 0.03
ACGTcount: A:0.52, C:0.08, G:0.21, T:0.19
Consensus pattern (100 bp):
CAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAATAAAGAGCAAAAAGGTAAT
CAGTAAAGAATAACATAGTAAAAAATGATGACAAT
Found at i:1552 original size:21 final size:22
Alignment explanation
Indices: 1508--1660 Score: 138
Period size: 22 Copynumber: 7.1 Consensus size: 22
1498 AAGTGATGAC
* *
1508 AATCAGTAAA-AGGTAAAATGGT
1 AATCAGTAAAGA-GCAAAATAGT
*
1530 AATCAGT-AAGAGCGAAATAGT
1 AATCAGTAAAGAGCAAAATAGT
*
1551 AATCAATAAAGAGCAAAA-AGGT
1 AATCAGTAAAGAGCAAAATA-GT
* *
1573 AATCAGT-AAGAACAAAATGGT
1 AATCAGTAAAGAGCAAAATAGT
*
1594 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGCAAAATAGT
* * *
1616 AATCAG-AAAAAGTAAGA-AGAT
1 AATCAGTAAAGAGCAAAATAG-T
*
1637 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAGAGCAAAATAGT
1659 AA
1 AA
1661 AAAGTAATCA
Statistics
Matches: 108, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
20 2 0.02
21 50 0.46
22 54 0.50
23 2 0.02
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.19
Consensus pattern (22 bp):
AATCAGTAAAGAGCAAAATAGT
Found at i:1574 original size:43 final size:43
Alignment explanation
Indices: 1522--1621 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 43
1512 AGTAAAAGGT
* * *
1522 AAAATGGTAATCAGTAAGAGCGAAATAGTAATCAATAAAGAGC
1 AAAAAGGTAATCAGTAAGAACAAAATAGTAATCAATAAAGAGC
* * *
1565 AAAAAGGTAATCAGTAAGAACAAAATGGTAATCAGTAAAGAGT
1 AAAAAGGTAATCAGTAAGAACAAAATAGTAATCAATAAAGAGC
1608 AAAATA-GTAATCAG
1 AAAA-AGGTAATCAG
1622 AAAAAGTAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
43 49 0.98
44 1 0.02
ACGTcount: A:0.53, C:0.08, G:0.20, T:0.19
Consensus pattern (43 bp):
AAAAAGGTAATCAGTAAGAACAAAATAGTAATCAATAAAGAGC
Found at i:1640 original size:64 final size:64
Alignment explanation
Indices: 1522--1645 Score: 171
Period size: 64 Copynumber: 1.9 Consensus size: 64
1512 AGTAAAAGGT
* *
1522 AAAATGGTAATCAGTAAGAGCGAAATAGTAATCAATAAAGAGCAAAAAGGTAATCAGTAAGAAC
1 AAAATGGTAATCAGTAAGAGCAAAATAGTAATCAATAAAGAGCAAAAAGATAATCAGTAAGAAC
* * *
1586 AAAATGGTAATCAGTAAAGAGTAAAATAGTAATCAGA-AAA-AGTAAGAAGATAATCAGTAA
1 AAAATGGTAATCAGT-AAGAGCAAAATAGTAATCA-ATAAAGAGCAAAAAGATAATCAGTAA
1646 AGAGTAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
64 32 0.60
65 20 0.38
66 1 0.02
ACGTcount: A:0.55, C:0.07, G:0.19, T:0.19
Consensus pattern (64 bp):
AAAATGGTAATCAGTAAGAGCAAAATAGTAATCAATAAAGAGCAAAAAGATAATCAGTAAGAAC
Found at i:1653 original size:7 final size:7
Alignment explanation
Indices: 1598--1689 Score: 51
Period size: 7 Copynumber: 12.7 Consensus size: 7
1588 AATGGTAATC
*
1598 AGTAAAG
1 AGTAAAA
1605 AGTAAAA
1 AGTAAAA
**
1612 TAGTAATC
1 -AGTAAAA
1620 AG-AAAA
1 AGTAAAA
*
1626 AGTAAGA
1 AGTAAAA
**
1633 AGATAATC
1 AG-TAAAA
*
1641 AGTAAAG
1 AGTAAAA
1648 AGTAAAA
1 AGTAAAA
1655 TAGTAAAA
1 -AGTAAAA
**
1663 AGTAATC
1 AGTAAAA
1670 AGTAAAA
1 AGTAAAA
*
1677 GGTAAAA
1 AGTAAAA
1684 TAGTAA
1 -AGTAA
1690 TCAGTAGGAG
Statistics
Matches: 63, Mismatches: 17, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
6 4 0.06
7 38 0.60
8 21 0.33
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.20
Consensus pattern (7 bp):
AGTAAAA
Found at i:1667 original size:86 final size:86
Alignment explanation
Indices: 1508--1667 Score: 184
Period size: 86 Copynumber: 1.9 Consensus size: 86
1498 AAGTGATGAC
* * *
1508 AATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCGAAATAGTAATCAATAAAGAGCAAAAAGGT
1 AATCAGTAAAAGGTAAAATAGTAATCAGAAAAAGCGAAATAGTAATCAATAAAGAGCAAAAAGGT
**
1573 AATCAGTAAGAACAAAATGGT
66 AAAAAGTAAGAACAAAATGGT
* * *
1594 AATCAGT-AAAGAGTAAAATAGTAATCAGAAAAAG-TAAGA-AGATAATCAGTAAAGAGTAAAAT
1 AATCAGTAAAAG-GTAAAATAGTAATCAGAAAAAGCGAA-ATAG-TAATCAATAAAGAGCAAAA-
1656 A-GTAAAAAGTAA
62 AGGTAAAAAGTAA
1668 TCAGTAAAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
85 8 0.13
86 53 0.85
87 1 0.02
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (86 bp):
AATCAGTAAAAGGTAAAATAGTAATCAGAAAAAGCGAAATAGTAATCAATAAAGAGCAAAAAGGT
AAAAAGTAAGAACAAAATGGT
Found at i:1669 original size:29 final size:30
Alignment explanation
Indices: 1622--1689 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
1612 TAGTAATCAG
*
1622 AAAA-AGTAAGAAGATAATCAGT-AAAGAGT
1 AAAATAGTAAAAAGATAATCAGTAAAAG-GT
1651 AAAATAGTAAAAAG-TAATCAGTAAAAGGT
1 AAAATAGTAAAAAGATAATCAGTAAAAGGT
1680 AAAATAGTAA
1 AAAATAGTAA
1690 TCAGTAGGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.60, C:0.03, G:0.18, T:0.19
Consensus pattern (30 bp):
AAAATAGTAAAAAGATAATCAGTAAAAGGT
Found at i:8397 original size:2 final size:2
Alignment explanation
Indices: 8390--8430 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
8380 GTGAAATAGG
8390 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
8431 TAGTAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.