Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014612.1 Corchorus capsularis cultivar CVL-1 contig14633, 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: 19978
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:807 original size:27 final size:26
Alignment explanation
Indices: 769--979 Score: 232
Period size: 26 Copynumber: 8.0 Consensus size: 26
759 ATAGTAAATT
* *
769 AGTAATCAGTAAAAAAGAGTAGGAAAC
1 AGTATTCAGT-AAAAAGAGTAAGAAAC
796 AGTATTCAGTAAAAAGAGTAAGAAA-
1 AGTATTCAGTAAAAAGAGTAAGAAAC
*
821 AGAATCATCAGTAAAAAGAGTAAGAAACC
1 AGTAT--TCAGTAAAAAGAGTAAGAAA-C
*
850 A-TATTCAGTAAAAAGAGTAAGAAAAG
1 AGTATTCAGTAAAAAGAGTAAG-AAAC
*
876 AGCCA-TCAGTAAAAAGAGTAAGAAAC
1 AG-TATTCAGTAAAAAGAGTAAGAAAC
* *
902 AGTATTCAGTAAGAAGAGTAAGAAAAG
1 AGTATTCAGTAAAAAGAGTAAG-AAAC
* *
929 AGTCA-TAAGTAAAAAGAGTAGGAAAC
1 AGT-ATTCAGTAAAAAGAGTAAGAAAC
*
955 AATATTCAGTAAAAAGAGTAAGAAA
1 AGTATTCAGTAAAAAGAGTAAGAAA
980 AGCGCAATAG
Statistics
Matches: 156, Mismatches: 17, Indels: 23
0.80 0.09 0.12
Matches are distributed among these distances:
25 6 0.04
26 76 0.49
27 69 0.44
28 4 0.03
29 1 0.01
ACGTcount: A:0.55, C:0.08, G:0.20, T:0.17
Consensus pattern (26 bp):
AGTATTCAGTAAAAAGAGTAAGAAAC
Found at i:848 original size:53 final size:53
Alignment explanation
Indices: 773--981 Score: 330
Period size: 53 Copynumber: 3.9 Consensus size: 53
763 TAAATTAGTA
* *
773 ATCAGTAAAAAAGAGTAGGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAATC
1 ATCAGT-AAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAGTC
*
827 ATCAGTAAAAAGAGTAAGAAACCA-TATTCAGTAAAAAGAGTAAGAAAAGAGCC
1 ATCAGTAAAAAGAGTAAGAAA-CAGTATTCAGTAAAAAGAGTAAGAAAAGAGTC
*
880 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAGAAGAGTAAGAAAAGAGTC
1 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAGTC
* * *
933 ATAAGTAAAAAGAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
1 ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAG
982 CGCAATAGTA
Statistics
Matches: 144, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
52 2 0.01
53 134 0.93
54 8 0.06
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.16
Consensus pattern (53 bp):
ATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAGTC
Found at i:1130 original size:37 final size:36
Alignment explanation
Indices: 1059--1148 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
1049 AAAGGCAATC
*
1059 AGTAAAGAGTAATCAGT--GAAGAAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAGAAAAAAAATGGTAAAG
1093 AGTAAAGAGTAATCAGTAAAGAAAAAAAATGGTAAAG
1 AGTAAAGAGTAATCAGT-AAGAAAAAAAATGGTAAAG
* * *
1130 AATGAAGAGTAATTAGTAA
1 AGTAAAGAGTAATCAGTAA
1149 CATGGTACAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 17 0.35
36 2 0.04
37 30 0.61
ACGTcount: A:0.56, C:0.02, G:0.23, T:0.19
Consensus pattern (36 bp):
AGTAAAGAGTAATCAGTAAGAAAAAAAATGGTAAAG
Found at i:1189 original size:26 final size:25
Alignment explanation
Indices: 1159--1222 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
1149 CATGGTACAG
1159 AGTAAAAAGTAAA-GTAAAGAG-AGA
1 AGTAAAAAGTAAAGGTAAAGAGTA-A
*
1183 TCAGTAAAAAGAAAATGGTAAAGAGTAA
1 --AGTAAAAAGTAAA-GGTAAAGAGTAA
1211 AGTAAAAAGTAA
1 AGTAAAAAGTAA
1223 TCAGTAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 23 0.70
28 9 0.27
29 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.22, T:0.16
Consensus pattern (25 bp):
AGTAAAAAGTAAAGGTAAAGAGTAA
Found at i:1210 original size:40 final size:39
Alignment explanation
Indices: 1160--1274 Score: 115
Period size: 40 Copynumber: 2.8 Consensus size: 39
1150 ATGGTACAGA
*
1160 GTAAAAAGTAAAGTAAAGAG-AGATCAGTAAAAAGAAAATG
1 GTAAAAAGTAAAGTAAAAAGTA-ATCAGTAAAAAG-AAATG
* * *
1200 GTAAAGAGTAAAGTAAAAAGTAATCAGTAAGAAGTAATG
1 GTAAAAAGTAAAGTAAAAAGTAATCAGTAAAAAGAAATG
** *
1239 GTAATCAGTAAAAAGTAAAAAGGTAATCACTAAAAA
1 GTAAAAAGT--AAAGTAAAAA-GTAATCAGTAAAAA
1275 AGTAAAAAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 11 0.17
40 29 0.46
41 11 0.17
42 12 0.19
ACGTcount: A:0.57, C:0.04, G:0.20, T:0.18
Consensus pattern (39 bp):
GTAAAAAGTAAAGTAAAAAGTAATCAGTAAAAAGAAATG
Found at i:1228 original size:14 final size:13
Alignment explanation
Indices: 1159--1290 Score: 63
Period size: 14 Copynumber: 9.7 Consensus size: 13
1149 CATGGTACAG
1159 AGTAAAAAGTAA-
1 AGTAAAAAGTAAT
*
1171 AGTAAAGAG-AGAT
1 AGTAAAAAGTA-AT
*
1184 CAGTAAAAAGAAAAT
1 -AGTAAAAAG-TAAT
* *
1199 GGTAAAGAGTAA-
1 AGTAAAAAGTAAT
1211 AGTAAAAAGTAAT
1 AGTAAAAAGTAAT
*
1224 CAGTAAGAAGTAAT
1 -AGTAAAAAGTAAT
* ** *
1238 GGTAATCAGTAAAA
1 AGTAAAAAGT-AAT
1252 AGTAAAAAGGTAAT
1 AGTAAAAA-GTAAT
* *
1266 CACTAAAAAAGTAAAA
1 -AGT-AAAAAGT-AAT
1282 AGTAAAAAG
1 AGTAAAAAG
1291 GTATATGTAA
Statistics
Matches: 89, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
11 1 0.01
12 19 0.21
13 9 0.10
14 42 0.47
15 10 0.11
16 8 0.09
ACGTcount: A:0.59, C:0.04, G:0.20, T:0.17
Consensus pattern (13 bp):
AGTAAAAAGTAAT
Found at i:1272 original size:15 final size:15
Alignment explanation
Indices: 1246--1293 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1236 ATGGTAATCA
*
1246 GTAAAAAGTAAAAAG
1 GTAAAAACTAAAAAG
** *
1261 GTAATCACTAAAAAA
1 GTAAAAACTAAAAAG
*
1276 GTAAAAAGTAAAAAG
1 GTAAAAACTAAAAAG
1291 GTA
1 GTA
1294 TATGTAAAGG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.62, C:0.04, G:0.17, T:0.17
Consensus pattern (15 bp):
GTAAAAACTAAAAAG
Found at i:1286 original size:22 final size:21
Alignment explanation
Indices: 1209--1286 Score: 95
Period size: 20 Copynumber: 3.7 Consensus size: 21
1199 GGTAAAGAGT
1209 AAAGTAAAAAGTAATCAGTAA
1 AAAGTAAAAAGTAATCAGTAA
* **
1230 GAAGT-AATGGTAATCAGTAA
1 AAAGTAAAAAGTAATCAGTAA
*
1250 AAAGTAAAAAGGTAATCACTAAA
1 AAAGTAAAAA-GTAATCAGT-AA
1273 AAAGTAAAAAGTAA
1 AAAGTAAAAAGTAA
1287 AAAGGTATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 17 0.36
21 6 0.13
22 12 0.26
23 12 0.26
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.19
Consensus pattern (21 bp):
AAAGTAAAAAGTAATCAGTAA
Found at i:1329 original size:21 final size:21
Alignment explanation
Indices: 1305--1346 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1295 ATGTAAAGGG
* *
1305 TAAAATGGTAATTAGTAAAGA
1 TAAAATGATAATCAGTAAAGA
*
1326 TAAAGTGATAATCAGTAAAGA
1 TAAAATGATAATCAGTAAAGA
1347 GTAATAGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.19, T:0.26
Consensus pattern (21 bp):
TAAAATGATAATCAGTAAAGA
Found at i:1363 original size:20 final size:21
Alignment explanation
Indices: 1338--1384 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
1328 AAGTGATAAT
*
1338 CAGTAAAG-AGTAATAGTAAC
1 CAGTAAAGAAGTAATAGTAAA
1358 CAGT-AAGAAGTAATAGTAAA
1 CAGTAAAGAAGTAATAGTAAA
1378 CAGTAAA
1 CAGTAAA
1385 AATAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 19 0.79
21 2 0.08
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (21 bp):
CAGTAAAGAAGTAATAGTAAA
Found at i:1562 original size:39 final size:37
Alignment explanation
Indices: 1502--1585 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 37
1492 AAGTAAATTC
* *
1502 AAAGAGT-AAAATGGTAGTCAGTAAAAGAGAAAAAGA
1 AAAGAGTAAAAATGGTAATCAGTAAAAAAGAAAAAGA
**
1538 AGAAGAGTAAAAAGTGGTAATCAGTAAAAAAGAGTAAGA
1 A-AAGAGTAAAAA-TGGTAATCAGTAAAAAAGAAAAAGA
1577 AAAGAGTAA
1 AAAGAGTAA
1586 TCAGTAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.02
37 6 0.15
38 12 0.29
39 22 0.54
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.14
Consensus pattern (37 bp):
AAAGAGTAAAAATGGTAATCAGTAAAAAAGAAAAAGA
Found at i:1631 original size:65 final size:64
Alignment explanation
Indices: 1502--1672 Score: 193
Period size: 65 Copynumber: 2.6 Consensus size: 64
1492 AAGTAAATTC
* * ** * * *
1502 AAAGAGT-AAAATG-GTAGTCAGTAAAAGAGAAAAAGAAGAAGAGTAAAAAGTGGTAATCAGTAA
1 AAAGAGTAAAAAAGAGTAATCAGTAAAA-AGAGTAAGAA-ATGAGCAAAAAATGGTAATCAGTAA
1565 A
64 A
*
1566 AAAGAGTAAGAAAAGAGTAATCAGTAAAAAGAGTAAGAAATGAGCAAAAAATGGTGATCAGTAAA
1 AAAGAGTAA-AAAAGAGTAATCAGTAAAAAGAGTAAGAAATGAGCAAAAAATGGTAATCAGTAAA
** *
1631 AAAGAGTAAAAGGGAGTAATTAGTAATAAAGAGTAAGAAATG
1 AAAGAGTAAAAAAGAGTAATCAGTAA-AAAGAGTAAGAAATG
1673 GTGATCAGTA
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
64 21 0.23
65 47 0.51
66 12 0.13
67 12 0.13
ACGTcount: A:0.56, C:0.03, G:0.25, T:0.16
Consensus pattern (64 bp):
AAAGAGTAAAAAAGAGTAATCAGTAAAAAGAGTAAGAAATGAGCAAAAAATGGTAATCAGTAAA
Found at i:1682 original size:27 final size:26
Alignment explanation
Indices: 1612--1695 Score: 96
Period size: 27 Copynumber: 3.2 Consensus size: 26
1602 GAAATGAGCA
1612 AAAAATGGTGATCAGTAAAAAAGAGT
1 AAAAATGGTGATCAGTAAAAAAGAGT
** * * *
1638 AAAAGGGAGTAATTAGTAATAAAGAGT
1 AAAAATG-GTGATCAGTAAAAAAGAGT
*
1665 AAGAAATGGTGATCAGTAAGAAAGAGT
1 AA-AAATGGTGATCAGTAAAAAAGAGT
1692 AAAA
1 AAAA
1696 TGTGGCATTC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
26 7 0.15
27 36 0.78
28 3 0.07
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.19
Consensus pattern (26 bp):
AAAAATGGTGATCAGTAAAAAAGAGT
Found at i:1751 original size:28 final size:26
Alignment explanation
Indices: 1718--1777 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
1708 TAAGAAAAGG
*
1718 GGTAATCAGTAAAAAAGAGTAAAGATAT
1 GGTAATCAGT-AAAAAGAGTAAA-AAAT
*
1746 GGTAATCAGTACAAAGAGTAAAAAAT
1 GGTAATCAGTAAAAAGAGTAAAAAAT
1772 GGTAAT
1 GGTAAT
1778 AAAGAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 9 0.30
27 11 0.37
28 10 0.33
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.22
Consensus pattern (26 bp):
GGTAATCAGTAAAAAGAGTAAAAAAT
Found at i:12982 original size:30 final size:30
Alignment explanation
Indices: 12955--13013 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
12945 CTGCCTGTTA
* *
12955 ATGCTTATGTGGCTTTCTGATGACCTGTAC
1 ATGCTTATGTGGATCTCTGATGACCTGTAC
* * *
12985 TTGTTTATGTGGATCTCTGATGACATGTA
1 ATGCTTATGTGGATCTCTGATGACCTGTA
13014 TTTCTGATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (30 bp):
ATGCTTATGTGGATCTCTGATGACCTGTAC
Found at i:14311 original size:23 final size:24
Alignment explanation
Indices: 14285--14337 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
14275 AAGAATTTGT
14285 TATATAAAATTAAAATTAAA-AAA
1 TATATAAAATTAAAATTAAATAAA
* *
14308 TATATAAAGTTAAAATTAAATATA
1 TATATAAAATTAAAATTAAATAAA
14332 TATATA
1 TATATA
14338 TATATTAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
TATATAAAATTAAAATTAAATAAA
Found at i:15131 original size:21 final size:21
Alignment explanation
Indices: 15105--15151 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
15095 TTAATTTAAT
15105 TTTTTTCCACTTGAAAGATAC
1 TTTTTTCCACTTGAAAGATAC
* *
15126 TTTTTTCCTCTTGAAAGCTAC
1 TTTTTTCCACTTGAAAGATAC
15147 TTTTT
1 TTTTT
15152 GTAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTTTTCCACTTGAAAGATAC
Found at i:18679 original size:24 final size:24
Alignment explanation
Indices: 18643--18689 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
18633 TTAATCGGGA
* *
18643 GAGCCATGTAAGTGCCACATAAAC
1 GAGCCATGCAAGTGCCAAATAAAC
18667 GAGCCATGCAAGTGCCAAATAAA
1 GAGCCATGCAAGTGCCAAATAAA
18690 AAGTAGTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.15
Consensus pattern (24 bp):
GAGCCATGCAAGTGCCAAATAAAC
Found at i:19273 original size:26 final size:25
Alignment explanation
Indices: 19244--19293 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
19234 TTGATTGCCA
*
19244 ATTACCATTTTTTACTCTTTGTACTG
1 ATTACCATATTTTACTCTTT-TACTG
19270 ATTACCATATTTTACTCTTTTACT
1 ATTACCATATTTTACTCTTTTACT
19294 TTAATTACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.54
Consensus pattern (25 bp):
ATTACCATATTTTACTCTTTTACTG
Found at i:19308 original size:26 final size:25
Alignment explanation
Indices: 19243--19308 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 25
19233 TTTGATTGCC
19243 AATTACCATTTTTTACTCTTTGTACT
1 AATTACCA-TTTTTACTCTTTGTACT
*
19269 GATTACCATATTTTACTCTTT-TACTTT
1 AATTACCAT-TTTTACTCTTTGTAC--T
*
19296 AATTACCCTTTTT
1 AATTACCATTTTT
19309 TTACTCCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 4 0.12
26 22 0.65
27 8 0.24
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.55
Consensus pattern (25 bp):
AATTACCATTTTTACTCTTTGTACT
Done.