Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021648.1 Corchorus olitorius cultivar O-4 contig21681, 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: 12519
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Found at i:1376 original size:36 final size:35
Alignment explanation
Indices: 1330--1724 Score: 205
Period size: 36 Copynumber: 11.3 Consensus size: 35
1320 TAACTGAAAT
*
1330 AAACTAAAGAACAACCACCCTCGATCATTCCGGCAC
1 AAACTGAAGAACAACCACCCTCGATCATTCCGG-AC
*
1366 AAACTGAAGAA-AGACCA-CC-C--T-A----GGTC
1 AAACTGAAGAACA-ACCACCCTCGATCATTCCGGAC
* * *
1392 -AACTGAAAAACGACCACCCTCAATCATTCCGGAC
1 AAACTGAAGAACAACCACCCTCGATCATTCCGGAC
* *
1426 TAAACTAAAGAACAACCACCCTCGATCATTCCGAATC
1 -AAACTGAAGAACAACCACCCTCGATCATTCCGGA-C
* * * *
1463 AAGCTGCAGAA-AGACCACCCTAGGTCATTCCGGAC
1 AAACTGAAGAACA-ACCACCCTCGATCATTCCGGAC
* *
1498 TGAACTGAAGAACAACCACCCTCGACCATTCC-GACTC
1 -AAACTGAAGAACAACCACCCTCGATCATTCCGGA--C
* * * * * * * * *
1535 AAACTGAATAA-AGACTACCCTGGGTTA-ACTGAAAT
1 AAACTGAAGAACA-ACCACCCTCGATCATTCCG-GAC
* * *
1570 AAAATGAAGAACGACCACCCTCGATCATTCCAGAC
1 AAACTGAAGAACAACCACCCTCGATCATTCCGGAC
* *
1605 TAAACTAAAGAACAACCACCCTCGATCATT-CAGACTC
1 -AAACTGAAGAACAACCACCCTCGATCATTCCGGA--C
* * * * *
1642 AAGCTGCAGAA-AGACCACCCTGGGTCATCCCGGAC
1 AAACTGAAGAACA-ACCACCCTCGATCATTCCGGAC
* *
1677 TGAACTGAAGAACAACCACCCTCGATCATT-CTGACTC
1 -AAACTGAAGAACAACCACCCTCGATCATTCCGGA--C
1714 AAACTGAAGAA
1 AAACTGAAGAA
1725 AAAAAATCAC
Statistics
Matches: 263, Mismatches: 63, Indels: 66
0.67 0.16 0.17
Matches are distributed among these distances:
25 13 0.05
26 3 0.01
27 3 0.01
29 1 0.00
30 1 0.00
31 1 0.00
32 1 0.00
34 4 0.02
35 38 0.14
36 188 0.71
37 10 0.04
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.16
Consensus pattern (35 bp):
AAACTGAAGAACAACCACCCTCGATCATTCCGGAC
Found at i:1520 original size:72 final size:72
Alignment explanation
Indices: 1392--1635 Score: 228
Period size: 72 Copynumber: 3.4 Consensus size: 72
1382 ACCCTAGGTC
* *
1392 AACTGAA-AAACGACCACCCTCA-ATCATTCCGGACTAAACTAAAGAACAACCACCCTCGATCAT
1 AACTGAAGAAA-GACCACCCT-AGGTCATTCCGGACTAAACTGAAGAACAACCACCCTCGATCAT
1455 TCCGAATCA
64 TCCGAATCA
* * * *
1464 AGCTGCAGAAAGACCACCCTAGGTCATTCCGGACTGAACTGAAGAACAACCACCCTCGACCATTC
1 AACTGAAGAAAGACCACCCTAGGTCATTCCGGACTAAACTGAAGAACAACCACCCTCGATCATTC
*
1529 CGACTCA
66 CGAATCA
* * * * * * * * * *
1536 AACTGAATAAAGACTACCCTGGGTTA-ACTGAAATAAAATGAAGAACGACCACCCTCGATCATTC
1 AACTGAAGAAAGACCACCCTAGGTCATTCCGGACTAAACTGAAGAACAACCACCCTCGATCATTC
*
1600 CAGACT-A
66 C-GAATCA
* * *
1607 AACTAAAGAACA-ACCACCCTCGATCATTC
1 AACTGAAGAA-AGACCACCCTAGGTCATTC
1636 AGACTCAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
71 51 0.37
72 85 0.61
73 3 0.02
ACGTcount: A:0.38, C:0.31, G:0.14, T:0.17
Consensus pattern (72 bp):
AACTGAAGAAAGACCACCCTAGGTCATTCCGGACTAAACTGAAGAACAACCACCCTCGATCATTC
CGAATCA
Found at i:1621 original size:107 final size:108
Alignment explanation
Indices: 1392--1724 Score: 298
Period size: 107 Copynumber: 3.1 Consensus size: 108
1382 ACCCTAGGTC
* * * * * * * *
1392 AACTGAAAAACGACCACCCTCAATCATTCCGGACT-AAACTAAAGAACA-ACCACCCTCGATCAT
1 AACTGAAGAACAACCACCCTCGACCATT-CAGACTCAAACTGAAGAA-AGACCACCCTGGGTCAT
* ** * * * * * *
1455 TCCG-AATCAAGCTGCAGAAAGACCACCCTAGGTCATTCCGGACTG
64 ACCGAAAT-AAAATGAAGAACGACCACCCTCGATCATTCCAGACTA
* * * *
1500 AACTGAAGAACAACCACCCTCGACCATTCCGACTCAAACTGAATAAAGACTACCCTGGGTTA-AC
1 AACTGAAGAACAACCACCCTCGACCATTCAGACTCAAACTGAAGAAAGACCACCCTGGGTCATAC
*
1564 TGAAATAAAATGAAGAACGACCACCCTCGATCATTCCAGACTA
66 CGAAATAAAATGAAGAACGACCACCCTCGATCATTCCAGACTA
* * * * *
1607 AACTAAAGAACAACCACCCTCGATCATTCAGACTCAAGCTGCAGAAAGACCACCCTGGGTCATCC
1 AACTGAAGAACAACCACCCTCGACCATTCAGACTCAAACTGAAGAAAGACCACCCTGGGTCATAC
* * * * * *
1672 CGGACTGAACTGAAGAACAACCACCCTCGATCATT-CTGACTCA
66 CGAAATAAAATGAAGAACGACCACCCTCGATCATTCCAGACT-A
1715 AACTGAAGAA
1 AACTGAAGAA
1725 AAAAAATCAC
Statistics
Matches: 182, Mismatches: 38, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
107 96 0.53
108 86 0.47
ACGTcount: A:0.37, C:0.31, G:0.15, T:0.17
Consensus pattern (108 bp):
AACTGAAGAACAACCACCCTCGACCATTCAGACTCAAACTGAAGAAAGACCACCCTGGGTCATAC
CGAAATAAAATGAAGAACGACCACCCTCGATCATTCCAGACTA
Found at i:1623 original size:179 final size:179
Alignment explanation
Indices: 1395--1721 Score: 573
Period size: 179 Copynumber: 1.8 Consensus size: 179
1385 CTAGGTCAAC
* *
1395 TGAAAAACGACCACCCTCAATCATTCCGGACTAAACTAAAGAACAACCACCCTCGATCATTCCGA
1 TGAAAAACGACCACCCTCAATCATTCCAGACTAAACTAAAGAACAACCACCCTCGATCATTCAGA
*
1460 ATCAAGCTGCAGAAAGACCACCCTAGGTCATTCCGGACTGAACTGAAGAACAACCACCCTCGACC
66 ATCAAGCTGCAGAAAGACCACCCTAGGTCATCCCGGACTGAACTGAAGAACAACCACCCTCGACC
1525 ATTCCGACTCAAACTGAATAAAGACTACCCTGGGTTAACTGAAATAAAA
131 ATTCCGACTCAAACTGAATAAAGACTACCCTGGGTTAACTGAAATAAAA
* *
1574 TGAAGAACGACCACCCTCGATCATTCCAGACTAAACTAAAGAACAACCACCCTCGATCATTCAGA
1 TGAAAAACGACCACCCTCAATCATTCCAGACTAAACTAAAGAACAACCACCCTCGATCATTCAGA
* * *
1639 CTCAAGCTGCAGAAAGACCACCCTGGGTCATCCCGGACTGAACTGAAGAACAACCACCCTCGATC
66 ATCAAGCTGCAGAAAGACCACCCTAGGTCATCCCGGACTGAACTGAAGAACAACCACCCTCGACC
*
1704 ATTCTGACTCAAACTGAA
131 ATTCCGACTCAAACTGAA
1722 GAAAAAAAAT
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
179 139 1.00
ACGTcount: A:0.37, C:0.31, G:0.15, T:0.17
Consensus pattern (179 bp):
TGAAAAACGACCACCCTCAATCATTCCAGACTAAACTAAAGAACAACCACCCTCGATCATTCAGA
ATCAAGCTGCAGAAAGACCACCCTAGGTCATCCCGGACTGAACTGAAGAACAACCACCCTCGACC
ATTCCGACTCAAACTGAATAAAGACTACCCTGGGTTAACTGAAATAAAA
Found at i:2116 original size:36 final size:36
Alignment explanation
Indices: 2079--2146 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
2069 ATCGACTTGA
*
2079 AAAC-AACTGAAGAAAGACCGCCCTGGGTCAATGTG
1 AAACTAACTGAAGAAAGACCACCCTGGGTCAATGTG
* *
2114 AAACTAACTGAATAGAGACCACCCTGGGTCAAT
1 AAACTAACTGAAGAAAGACCACCCTGGGTCAAT
2147 CATGATTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 4 0.14
36 25 0.86
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (36 bp):
AAACTAACTGAAGAAAGACCACCCTGGGTCAATGTG
Found at i:2169 original size:35 final size:35
Alignment explanation
Indices: 2083--2171 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 35
2073 ACTTGAAAAC
* *
2083 AACTGAAGAAAGACCGCCCTGGGTCAATGTGAAACT
1 AACTGAAGAAAGACCACCCTGGGTCAATATG-AACT
* * *
2119 AACTGAATAGAGACCACCCTGGGTCAATCATG-ATT
1 AACTGAAGAAAGACCACCCTGGGTCAAT-ATGAACT
2154 AACTGAA-AAATGACCACC
1 AACTGAAGAAA-GACCACC
2172 TGTAGACACC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
34 2 0.04
35 16 0.36
36 25 0.56
37 2 0.04
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (35 bp):
AACTGAAGAAAGACCACCCTGGGTCAATATGAACT
Found at i:2503 original size:12 final size:13
Alignment explanation
Indices: 2470--2507 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2460 TACTAATTGG
2470 GCTGGTAGAAATA
1 GCTGGTAGAAATA
2483 GCTGGTAGAAATA
1 GCTGGTAGAAATA
2496 GC-GGTAGAAATA
1 GCTGGTAGAAATA
2508 AAATTTGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.39, C:0.08, G:0.32, T:0.21
Consensus pattern (13 bp):
GCTGGTAGAAATA
Found at i:2523 original size:19 final size:19
Alignment explanation
Indices: 2499--2536 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2489 AGAAATAGCG
2499 GTAGAAATAAAATTTGCAT
1 GTAGAAATAAAATTTGCAT
*
2518 GTAGAAATAGAATTTGCAT
1 GTAGAAATAAAATTTGCAT
2537 TGGCATGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (19 bp):
GTAGAAATAAAATTTGCAT
Found at i:10066 original size:31 final size:30
Alignment explanation
Indices: 10031--10088 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
10021 CAATGATCCT
*
10031 AAAATAAAGCAATGATCCTAAATCAGGATTA
1 AAAAT-AAGCAATGATCCTAAACCAGGATTA
*
10062 AAAATAAGCAATGATCCTCAACCAGGA
1 AAAATAAGCAATGATCCTAAACCAGGA
10089 CTAAGACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (30 bp):
AAAATAAGCAATGATCCTAAACCAGGATTA
Found at i:10326 original size:91 final size:91
Alignment explanation
Indices: 10203--10422 Score: 248
Period size: 91 Copynumber: 2.4 Consensus size: 91
10193 ATAATCTATT
* *
10203 TTTCAAGTTAATTTTAATCTAAAAATCAAACCTTTAAATCAAAAACTAAATTTTCAAATTACA-A
1 TTTCAAGTTAATTTTAATCCAAAAATCAAACCTTTAAATCAAAAACTAAATTTTCAAATCA-AGA
* **
10267 TTAACT-CAAAGAGA-TCAAATGGTCAA
65 TTAACTCCAAAAAGATTCAAA-AATCAA
* * * * * *
10293 TTTCAAAGTTAATTTTAATCCAAAAATCAAACCTTTAATTGAAAGAGTTAATTTTTAAATCAAGA
1 TTTC-AAGTTAATTTTAATCCAAAAATCAAACCTTTAAATCAAAAACTAAATTTTCAAATCAAGA
10358 TTAACTCCAAAAAGATTCAAAAATCAA
65 TTAACTCCAAAAAGATTCAAAAATCAA
* * * *
10385 TTTTTAAGTTGATTTTAATTCAAAAATCAACCCTTTAA
1 -TTTCAAGTTAATTTTAATCCAAAAATCAAACCTTTAA
10423 TTTAAAGTTT
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
90 5 0.05
91 56 0.51
92 41 0.37
93 8 0.07
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.35
Consensus pattern (91 bp):
TTTCAAGTTAATTTTAATCCAAAAATCAAACCTTTAAATCAAAAACTAAATTTTCAAATCAAGAT
TAACTCCAAAAAGATTCAAAAATCAA
Found at i:10450 original size:92 final size:91
Alignment explanation
Indices: 10139--10451 Score: 312
Period size: 92 Copynumber: 3.4 Consensus size: 91
10129 GAAATAAAAC
* * * * * *
10139 AACCTTTAA-TCAAAGTTTAAATTTTCAAAATTAAAACTAACTTAAAGAGATTCAATAATCTATT
1 AACCTTTAATTCAAAGATTAAATTTTC-AAATTAAGATTAACTCAAAGAGATTCAAAAATCAATT
10203 TTTCAAGTTAATTTTAA-TCTAAAAATCA
65 TTT-AAGTTAATTTTAATTC-AAAAATCA
* * * **
10231 AACCTTTAAATCAAAAACTAAATTTTCAAATTACA-ATTAACTCAAAGAGA-TCAAATGGTCAAT
1 AACCTTTAATTCAAAGATTAAATTTTCAAATTA-AGATTAACTCAAAGAGATTCAAA-AATCAAT
** *
10294 TTCAAAGTTAATTTTAATCCAAAAATCA
64 TTTTAAGTTAATTTTAATTCAAAAATCA
* * * *
10322 AACCTTTAATTGAAAGAGTT-AATTTTTAAATCAAGATTAACTCCAAAAAGATTCAAAAATCAAT
1 AACCTTTAATTCAAAGA-TTAAATTTTCAAATTAAGATTAACT-CAAAGAGATTCAAAAATCAAT
*
10386 TTTTAAGTTGATTTTAATTCAAAAATCA
64 TTTTAAGTTAATTTTAATTCAAAAATCA
* * * * *
10414 ACCCTTTAATTTAAAGTTTTAATTTTCCAATTAAGATT
1 AACCTTTAATTCAAAGATTAAATTTTCAAATTAAGATT
10452 GTCTTAACAC
Statistics
Matches: 181, Mismatches: 31, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
90 1 0.01
91 59 0.33
92 101 0.56
93 20 0.11
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (91 bp):
AACCTTTAATTCAAAGATTAAATTTTCAAATTAAGATTAACTCAAAGAGATTCAAAAATCAATTT
TTAAGTTAATTTTAATTCAAAAATCA
Found at i:10911 original size:73 final size:73
Alignment explanation
Indices: 10792--10941 Score: 255
Period size: 73 Copynumber: 2.1 Consensus size: 73
10782 CCCTTTTTCC
*
10792 CCCCCTAAATTGTGAAAATCCACTGAAAAAGTCCTATAACGGCGTTTAGTAATAATGAACGCCGT
1 CCCCCTAAATTGTGAAAATCCACTGAAAAAGTCCTAAAACGGCGTTTAGTAATAATGAACGCCGT
10857 TATAGGTT
66 TATAGGTT
* * * *
10865 CCCCCTAAATTGTGAAAATCCACTGAAAAAGTCCTAAAACTGCGTTTATTAGTAATGAACGTCGT
1 CCCCCTAAATTGTGAAAATCCACTGAAAAAGTCCTAAAACGGCGTTTAGTAATAATGAACGCCGT
10930 TATAGGTT
66 TATAGGTT
10938 CCCC
1 CCCC
10942 ACGTGACATA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (73 bp):
CCCCCTAAATTGTGAAAATCCACTGAAAAAGTCCTAAAACGGCGTTTAGTAATAATGAACGCCGT
TATAGGTT
Done.