Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015069.1 Corchorus capsularis cultivar CVL-1 contig15090, 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: 43016
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1550 original size:31 final size:32
Alignment explanation
Indices: 1494--1569 Score: 111
Period size: 31 Copynumber: 2.4 Consensus size: 32
1484 GTGGACTTGG
1494 ACGGGTCTTGGACAAACCCTTTTTTTATTTGA
1 ACGGGTCTTGGACAAACCCTTTTTTTATTTGA
* * *
1526 ACGGGTCTTAGACAAA-GCTTTTTTTATTTGG
1 ACGGGTCTTGGACAAACCCTTTTTTTATTTGA
1557 ACGGG-CTTGGACA
1 ACGGGTCTTGGACA
1570 TACGTAGAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 7 0.17
31 18 0.45
32 15 0.38
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (32 bp):
ACGGGTCTTGGACAAACCCTTTTTTTATTTGA
Found at i:2890 original size:70 final size:70
Alignment explanation
Indices: 2777--2922 Score: 265
Period size: 70 Copynumber: 2.1 Consensus size: 70
2767 GATTTAGGCT
*
2777 TGGTTTAGGACTGAGTTTGGAGATAAAAAAAAAAATACTTTTCACCTTAAACACAATGCCAAATA
1 TGGTTTAGGACTGAGTTTGGAGATAAAAAAAAAAATACTTTTCACCTCAAACACAATGCCAAATA
2842 AGTCA
66 AGTCA
* *
2847 TGGTTTAGGACTGAGTTTGGAGATAAAAAAAAAACTACTTTTCACCTCAAACACAATGTCAAATA
1 TGGTTTAGGACTGAGTTTGGAGATAAAAAAAAAAATACTTTTCACCTCAAACACAATGCCAAATA
2912 AGTCA
66 AGTCA
2917 TGGTTT
1 TGGTTT
2923 GTATCAAAAG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.29
Consensus pattern (70 bp):
TGGTTTAGGACTGAGTTTGGAGATAAAAAAAAAAATACTTTTCACCTCAAACACAATGCCAAATA
AGTCA
Found at i:4210 original size:32 final size:32
Alignment explanation
Indices: 4164--4262 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
4154 TTGAATCAGG
*
4164 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
1 TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
* *
4196 TCGGGTTAAGTTTGGATCAGGTTGATTCGGAT
1 TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
* * * *
4228 TCGAGTCAATTTTGGATCAGG-TAATTTCGGGT
1 TCGGGTTAAATTTGGATCAGGTTGA-TTCGGGT
4260 TCG
1 TCG
4263 AGTTTGGGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 2 0.03
32 56 0.97
ACGTcount: A:0.18, C:0.11, G:0.33, T:0.37
Consensus pattern (32 bp):
TCGGGTTAAATTTGGATCAGGTTGATTCGGGT
Found at i:4476 original size:22 final size:22
Alignment explanation
Indices: 4446--4487 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4436 TTAGTATTGA
*
4446 ATTCAAGTTTTTTCAAATTTGG
1 ATTCAAGTTTTATCAAATTTGG
* *
4468 ATTCGAGTTTTATCAGATTT
1 ATTCAAGTTTTATCAAATTT
4488 TAGATTTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (22 bp):
ATTCAAGTTTTATCAAATTTGG
Found at i:16142 original size:60 final size:60
Alignment explanation
Indices: 16070--16188 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
16060 TTTTTTTAAT
*
16070 AAAAAAATTCAGATGAGAAAATGAAGAATATATACACAAGCTCATCAAATAGCAAAAAAA
1 AAAAAAAATCAGATGAGAAAATGAAGAATATATACACAAGCTCATCAAATAGCAAAAAAA
16130 AAAAAAAATCAGATGAGAAAATGAAGAATATATACACAAGCTCATCAAATAGCAAAAAA
1 AAAAAAAATCAGATGAGAAAATGAAGAATATATACACAAGCTCATCAAATAGCAAAAAA
16189 GGGAGATTCA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.16
Consensus pattern (60 bp):
AAAAAAAATCAGATGAGAAAATGAAGAATATATACACAAGCTCATCAAATAGCAAAAAAA
Found at i:17880 original size:6 final size:6
Alignment explanation
Indices: 17871--17895 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17861 CTTTTTTAAA
17871 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
17896 AATTGATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:20726 original size:46 final size:46
Alignment explanation
Indices: 20675--20765 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
20665 AGTATATATA
20675 TATATATATATATAATATTAATGTAAAATATCTTCATAAAACTCCT
1 TATATATATATATAATATTAATGTAAAATATCTTCATAAAACTCCT
20721 TATATATATATATAATATTAATGTAAAATATCTTCATAAAACTCC
1 TATATATATATATAATATTAATGTAAAATATCTTCATAAAACTCC
20766 AATTAAGGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (46 bp):
TATATATATATATAATATTAATGTAAAATATCTTCATAAAACTCCT
Found at i:22028 original size:40 final size:40
Alignment explanation
Indices: 21983--22106 Score: 96
Period size: 40 Copynumber: 3.1 Consensus size: 40
21973 GTAAATTGGT
21983 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
1 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
* * ** * * * * * *
22023 AAAATAGAGTTTTTAGTTGAGTAAAATAG---TAA-AATGGT-
1 AAAATATAATAGTTA--TAAGGATATTAGATTTAATTAT-ATA
22061 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
1 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
22101 AAAATA
1 AAAATA
22107 GAGTTTTTAG
Statistics
Matches: 56, Mismatches: 20, Indels: 16
0.61 0.22 0.17
Matches are distributed among these distances:
36 8 0.14
38 13 0.23
39 8 0.14
40 19 0.34
42 8 0.14
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (40 bp):
AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
Found at i:22051 original size:78 final size:78
Alignment explanation
Indices: 21966--22212 Score: 415
Period size: 78 Copynumber: 3.2 Consensus size: 78
21956 AGTTTTTAAT
*
21966 TAAAATAGTAAATTGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
22031 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
22044 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
22109 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * ** * *
22122 TAAAATAGTAAAAAGGTAAAATAAAATAGTTATAAATATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
22187 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
22200 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
22213 ACCTAAACAA
Statistics
Matches: 161, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
78 159 0.99
79 2 0.01
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.36
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:23079 original size:146 final size:146
Alignment explanation
Indices: 22815--23107 Score: 541
Period size: 146 Copynumber: 2.0 Consensus size: 146
22805 AATATACTAC
22815 ATATTATTTTTGTAGCAACATGAAATTACTTAACAGTCCTTCCAACTTTTAATCTGGTGAGACCT
1 ATATTATTTTTGTAGCAACATGAAATTACTTAACAGTCCTTCCAACTTTTAATCTGGTGAGACCT
*
22880 TATCGCCCCGTTTTAGTAATTTTTTACAAACCCTTAATTAACACTTAATTAAAAGAGTTATAAAA
66 TATCGCCCCGTTTTAGTAATTTTTTACAAACCATTAATTAACACTTAATTAAAAGAGTTATAAAA
22945 CCAAACCATTAACTCG
131 CCAAACCATTAACTCG
* * *
22961 ATATTATTTTTGTAGCAATATGAAATTACTTAACGGTCCTTCTAACTTTTAATCTGGTGAGACCT
1 ATATTATTTTTGTAGCAACATGAAATTACTTAACAGTCCTTCCAACTTTTAATCTGGTGAGACCT
*
23026 TATCGCCCCGTTTTATTAATTTTTTACAAACCATTAATTAACACTTAATTAAAAGAGTTATAAAA
66 TATCGCCCCGTTTTAGTAATTTTTTACAAACCATTAATTAACACTTAATTAAAAGAGTTATAAAA
23091 CCAAACCATTAACTCG
131 CCAAACCATTAACTCG
23107 A
1 A
23108 AATAAAATCA
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
146 142 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (146 bp):
ATATTATTTTTGTAGCAACATGAAATTACTTAACAGTCCTTCCAACTTTTAATCTGGTGAGACCT
TATCGCCCCGTTTTAGTAATTTTTTACAAACCATTAATTAACACTTAATTAAAAGAGTTATAAAA
CCAAACCATTAACTCG
Found at i:24821 original size:15 final size:16
Alignment explanation
Indices: 24794--24831 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
24784 TTTAAATTAT
24794 ATAA-ATAAAATTTAA
1 ATAATATAAAATTTAA
*
24809 AT-ATATAACATTTAA
1 ATAATATAAAATTTAA
24824 ATAATATA
1 ATAATATA
24832 TTTATCCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 14 0.70
16 5 0.25
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATATAAAATTTAA
Found at i:26322 original size:22 final size:22
Alignment explanation
Indices: 26292--26338 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
26282 TATCCTTATA
* * *
26292 ACTATTTTATTTTTACCATTTT
1 ACTAATTTACTTTTACAATTTT
*
26314 ACTAATTTACTTTTATAATTTT
1 ACTAATTTACTTTTACAATTTT
26336 ACT
1 ACT
26339 CAACTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.60
Consensus pattern (22 bp):
ACTAATTTACTTTTACAATTTT
Found at i:26393 original size:92 final size:92
Alignment explanation
Indices: 26230--26414 Score: 327
Period size: 92 Copynumber: 2.0 Consensus size: 92
26220 CATTGTTTAA
*
26230 ACTTTTATATTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACT
1 ACTTTTATATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACT
*
26295 ATTTTATTTTTACCATTTTACTAATTT
66 ATTTTATTTTTACCATATTACTAATTT
*
26322 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATT-AATCTAATATCCTTATACC
1 ACTTTTAT-ATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
26386 TATTTTATTTTTACCATATTACTAATTT
65 TATTTTATTTTTACCATATTACTAATTT
26414 A
1 A
26415 ATTAAAAAGT
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
92 54 0.61
93 35 0.39
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.51
Consensus pattern (92 bp):
ACTTTTATATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACT
ATTTTATTTTTACCATATTACTAATTT
Found at i:27009 original size:15 final size:16
Alignment explanation
Indices: 26986--27018 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
26976 GGATTTCGGC
26986 TCATCTGGGT-TCAGG
1 TCATCTGGGTCTCAGG
*
27001 TCATTTGGGTCTCAGG
1 TCATCTGGGTCTCAGG
27017 TC
1 TC
27019 TGCTGAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.12, C:0.21, G:0.30, T:0.36
Consensus pattern (16 bp):
TCATCTGGGTCTCAGG
Found at i:30271 original size:30 final size:29
Alignment explanation
Indices: 30220--30280 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
30210 TATAAATAGT
* * *
30220 ATAATATAATTAAATCATTATATTTATAC
1 ATAATAAAATTAAATAATTATATGTATAC
*
30249 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTAAATAA-TTATATGTATAC
30279 AT
1 AT
30281 TGATTAGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (29 bp):
ATAATAAAATTAAATAATTATATGTATAC
Found at i:30404 original size:26 final size:25
Alignment explanation
Indices: 30365--30432 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
30355 TTATATATAA
*
30365 ATTTT-AAAGTTTAAATTTTATTTT
1 ATTTTAAAAATTTAAATTTTATTTT
30389 -TTATTAAAAAATTT-AATTATTATTTT
1 ATT-TT-AAAAATTTAAATT-TTATTTT
30415 ATTTTAAAAA-TTAAATTT
1 ATTTTAAAAATTTAAATTT
30433 GGGCGTGCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
23 2 0.05
24 5 0.14
25 13 0.35
26 15 0.41
27 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (25 bp):
ATTTTAAAAATTTAAATTTTATTTT
Found at i:30414 original size:24 final size:24
Alignment explanation
Indices: 30382--30431 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
30372 AGTTTAAATT
*
30382 TTATTTTTTA-TTAAAAAATTTAA
1 TTATTTTTTATTTAAAAAATTAAA
*
30405 TTATTATTTTATTTTAAAAATTAAA
1 TTATT-TTTTATTTAAAAAATTAAA
30430 TT
1 TT
30432 TGGGCGTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 5 0.22
25 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTTTTTATTTAAAAAATTAAA
Found at i:39385 original size:21 final size:22
Alignment explanation
Indices: 39350--39390 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
39340 CCATGTCAAA
**
39350 TTTTTGAAATTAAAA-AATATT
1 TTTTTGAAAAAAAAAGAATATT
39371 TTTTTGAAAAAAAAAGAATA
1 TTTTTGAAAAAAAAAGAATA
39391 GAAATAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (22 bp):
TTTTTGAAAAAAAAAGAATATT
Found at i:41556 original size:13 final size:13
Alignment explanation
Indices: 41533--41575 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 13
41523 TAAATACAGG
41533 TATCG-ACGGATA
1 TATCGAACGGATA
41545 TATCGAACGGATA
1 TATCGAACGGATA
*
41558 TATC-AACGAATA
1 TATCGAACGGATA
41570 TATCGA
1 TATCGA
41576 GGTATCGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 16 0.57
13 12 0.43
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (13 bp):
TATCGAACGGATA
Found at i:42623 original size:10 final size:10
Alignment explanation
Indices: 42608--42643 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
42598 AATTTAATAT
42608 GGATATTTAC
1 GGATATTTAC
*
42618 GGATATTTAT
1 GGATATTTAC
42628 GGATATTTAC
1 GGATATTTAC
42638 GGATAT
1 GGATAT
42644 ATCGAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:42630 original size:20 final size:20
Alignment explanation
Indices: 42605--42643 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
42595 TTTAATTTAA
42605 TATGGATATTTACGGATATT
1 TATGGATATTTACGGATATT
42625 TATGGATATTTACGGATAT
1 TATGGATATTTACGGATAT
42644 ATCGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (20 bp):
TATGGATATTTACGGATATT
Found at i:42993 original size:2 final size:2
Alignment explanation
Indices: 42986--43016 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42976 CTGTTAGTGC
42986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.