Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010125.1 Corchorus capsularis cultivar CVL-1 contig10146, 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: 24564
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:9298 original size:89 final size:89
Alignment explanation
Indices: 9147--9324 Score: 338
Period size: 89 Copynumber: 2.0 Consensus size: 89
9137 TAGACCTGAC
*
9147 AATGTGTAACTTCAAAGAACAAATATAAATTGTTCACAAAAAATCAATCCCATAGCAAAATAGCT
1 AATGTGTAACTTCAAAGAACAAATACAAATTGTTCACAAAAAATCAATCCCATAGCAAAATAGCT
9212 AACATATCCTATAGCTAACATAAA
66 AACATATCCTATAGCTAACATAAA
*
9236 AATGTGTAACTTCAAAGCACAAATACAAATTGTTCACAAAAAATCAATCCCATAGCAAAATAGCT
1 AATGTGTAACTTCAAAGAACAAATACAAATTGTTCACAAAAAATCAATCCCATAGCAAAATAGCT
9301 AACATATCCTATAGCTAACATAAA
66 AACATATCCTATAGCTAACATAAA
9325 TAGTTCATTA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (89 bp):
AATGTGTAACTTCAAAGAACAAATACAAATTGTTCACAAAAAATCAATCCCATAGCAAAATAGCT
AACATATCCTATAGCTAACATAAA
Found at i:10481 original size:26 final size:26
Alignment explanation
Indices: 10431--10482 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
10421 TTAGTAGAAT
*
10431 AATTGTAAAAGTTTATTTCTAAAAAA
1 AATTGTAAAAGTATATTTCTAAAAAA
10457 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
10483 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 6 0.26
28 6 0.26
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (26 bp):
AATTGTAAAAGTATATTTCTAAAAAA
Found at i:15561 original size:17 final size:18
Alignment explanation
Indices: 15541--15575 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
15531 GAGACAATAG
*
15541 ATATGGAGAA-GAAGAAA
1 ATATGAAGAATGAAGAAA
15558 ATATGAAGAATGAAGAAA
1 ATATGAAGAATGAAGAAA
15576 TTATTCTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (18 bp):
ATATGAAGAATGAAGAAA
Found at i:16231 original size:22 final size:22
Alignment explanation
Indices: 16190--16252 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
16180 ATAACGATAC
* ** *
16190 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGTTAACCTTCT
*
16212 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGTTAACCTTCT
16234 TATGAAATTTTGTTAACCT
1 TATGAAATTTTGTTAACCT
16253 CTCTAAGGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 3 0.09
22 27 0.82
23 3 0.09
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (22 bp):
TATGAAATTTTGTTAACCTTCT
Found at i:16328 original size:22 final size:22
Alignment explanation
Indices: 16300--16353 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
16290 CATTGAAATT
*
16300 TTGATAACCA-CACTATGAGATG
1 TTGATAACCACCA-TATGAGATA
* *
16322 TTGATAACCTCCATATGATATA
1 TTGATAACCACCATATGAGATA
16344 TTGATAACCA
1 TTGATAACCA
16354 TGTTATGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (22 bp):
TTGATAACCACCATATGAGATA
Found at i:16464 original size:23 final size:23
Alignment explanation
Indices: 16416--16513 Score: 76
Period size: 23 Copynumber: 4.3 Consensus size: 23
16406 GATAATCACT
*
16416 CTATGAAATTGTAATAACC-TCG
1 CTATGAAATTTTAATAACCTTCG
16438 CTATGAAATTTTAATAAACCTTC-
1 CTATGAAATTTTAAT-AACCTTCG
* * *
16461 CTATAAAATTTTGATAAACCTCTCT
1 CTATGAAATTTTAAT-AACCT-TCG
* * * *
16486 ATATAAAATTTTGATAACC-TCC
1 CTATGAAATTTTAATAACCTTCG
16508 CTATGA
1 CTATGA
16514 TTTTTCGATT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
22 20 0.31
23 23 0.35
24 8 0.12
25 14 0.22
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (23 bp):
CTATGAAATTTTAATAACCTTCG
Found at i:16511 original size:24 final size:25
Alignment explanation
Indices: 16443--16511 Score: 90
Period size: 23 Copynumber: 2.9 Consensus size: 25
16433 CCTCGCTATG
* *
16443 AAATTTTAATAAACCTTCC--TATA
1 AAATTTTGATAAACCTCCCTATATA
*
16466 AAATTTTGATAAACCTCTCTATATA
1 AAATTTTGATAAACCTCCCTATATA
16491 AAATTTTGAT-AACCTCCCTAT
1 AAATTTTGATAAACCTCCCTAT
16512 GATTTTTCGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 16 0.40
24 10 0.25
25 14 0.35
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (25 bp):
AAATTTTGATAAACCTCCCTATATA
Found at i:16978 original size:22 final size:22
Alignment explanation
Indices: 16953--17182 Score: 148
Period size: 22 Copynumber: 10.5 Consensus size: 22
16943 AATCACATTT
* *
16953 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
16975 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
16997 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
17019 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* *
17041 TGTAATTTTGATAACCT-TGCTT
1 TGAAATTTTGATAACCTCT-CTA
** **
17063 TGAAATTTTGATAACAACAATA
1 TGAAATTTTGATAACCTCTCTA
* * *
17085 TAAAATTTCGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
*
17107 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTCTCTA
* * *
17131 TGAAATTCTGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
17153 TGAGA-TTTGATTACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
*
17173 TCAAATTTTG
1 TGAAATTTTG
17183 GTACTCCTTA
Statistics
Matches: 155, Mismatches: 42, Indels: 23
0.70 0.19 0.10
Matches are distributed among these distances:
20 8 0.05
21 22 0.14
22 107 0.69
23 1 0.01
24 5 0.03
25 12 0.08
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:17048 original size:44 final size:43
Alignment explanation
Indices: 16928--17121 Score: 124
Period size: 44 Copynumber: 4.4 Consensus size: 43
16918 AAAAATACCA
* * * * * *
16928 CTATGAAAATTAGGTAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGAT-ACCCCT
* * * * *
16972 TTATGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGAT-ACCCCT
* * *
17016 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATACCCCT
* * * * ** *
17059 GCTTTGAAATTTTGATAA-CAACAATATAAAATTTCGATAATCTT
1 -CTATGAAATTTTGATAATC-ACATTATGAAATTTTGATACCCCT
17103 CCTAT-AAATTTTGATAATC
1 -CTATGAAATTTTGATAATC
17122 TGATCTCTAT
Statistics
Matches: 117, Mismatches: 28, Indels: 10
0.75 0.18 0.06
Matches are distributed among these distances:
43 18 0.15
44 98 0.84
45 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (43 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATACCCCT
Found at i:17087 original size:88 final size:88
Alignment explanation
Indices: 16928--17092 Score: 208
Period size: 88 Copynumber: 1.9 Consensus size: 88
16918 AAAAATACCA
* * **
16928 CTATGAAAATTAGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAAATTAGATAATCACATTATGAAAATTTGATAACCTCTTTATGAAATTTTGATAACAAC
**
16993 TCTATAAAATTTTGTTGACCCCT
66 AATATAAAATTTTGTTGACCCCT
* * * *
17016 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCT-TGCTT-TGAAATTTTGATAACA
1 CTATGAAAATTAGATAATCACATTATGAAAATTTGATAACCTCT--TTATGAAATTTTGATAACA
17079 ACAATATAAAATTT
64 ACAATATAAAATTT
17093 CGATAATCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
87 1 0.02
88 62 0.95
89 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (88 bp):
CTATGAAAATTAGATAATCACATTATGAAAATTTGATAACCTCTTTATGAAATTTTGATAACAAC
AATATAAAATTTTGTTGACCCCT
Found at i:17136 original size:25 final size:21
Alignment explanation
Indices: 17087--17146 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
17077 CAACAATATA
*
17087 AAATTTCGATAATCTTCCTAT
1 AAATTTTGATAATCTTCCTAT
17108 AAATTTTGATAATCTGATCTCTAT
1 AAATTTTGATAATCT--TC-CTAT
*
17132 GAAATTCTGATAATC
1 -AAATTTTGATAATC
17147 ACTCTATGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.42
23 2 0.06
24 4 0.12
25 13 0.39
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (21 bp):
AAATTTTGATAATCTTCCTAT
Found at i:17234 original size:22 final size:22
Alignment explanation
Indices: 17223--17263 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17213 CCTTCATAAG
17223 AAAA-TTTGATAACCACACTAA
1 AAAATTTTGATAACCACACTAA
17244 AAAATTTTGATAACCACACT
1 AAAATTTTGATAACCACACT
17264 GAAATTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.27
Consensus pattern (22 bp):
AAAATTTTGATAACCACACTAA
Found at i:17270 original size:20 final size:21
Alignment explanation
Indices: 17221--17270 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
17211 AACCTTCATA
*
17221 AGAAAATTTGATAACCACACT
1 AGAAATTTTGATAACCACACT
*
17242 AAAAAATTTTGATAACCACACT
1 -AGAAATTTTGATAACCACACT
17264 -GAAATTT
1 AGAAATTT
17271 CAATAACCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.24
22 19 0.76
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (21 bp):
AGAAATTTTGATAACCACACT
Found at i:19338 original size:22 final size:21
Alignment explanation
Indices: 19313--19398 Score: 82
Period size: 22 Copynumber: 4.0 Consensus size: 21
19303 TCAACTTTCA
*
19313 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCAC-C
* * *
19335 TATGGAATTTTGATAATCTCC
1 TATGAAATTTTGATAACCACC
* * *
19356 TCATGAAATTATAATAACCATCT
1 T-ATGAAATTTTGATAACCA-CC
19379 TATGAAATTTTGATAACCAC
1 TATGAAATTTTGATAACCAC
19399 GAAGAGACAA
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
21 3 0.06
22 45 0.90
23 2 0.04
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (21 bp):
TATGAAATTTTGATAACCACC
Found at i:20461 original size:29 final size:31
Alignment explanation
Indices: 20428--20491 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
20418 TGGCAATTTA
*
20428 GAAATATGCTTT-AAAA-AAGGGTACAATTG
1 GAAATATGCTTTGAAAATAAGGGTACAATCG
* *
20457 GAAATATGTTTTGAAAATAAGGGTAGAATCG
1 GAAATATGCTTTGAAAATAAGGGTACAATCG
20488 GAAA
1 GAAA
20492 ACATTAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 11 0.37
30 4 0.13
31 15 0.50
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (31 bp):
GAAATATGCTTTGAAAATAAGGGTACAATCG
Found at i:23016 original size:27 final size:28
Alignment explanation
Indices: 22960--23039 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
22950 TCTTATTTTT
22960 AAAAGTTAAGGGGCCAATTTGTCCCAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAA
* *
22988 AAAAGTTAAGGGGTCAATTTGTCCTAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAA
* *
23016 ATGGATAGTTAAGGGGCTAATTTG
1 A---AAAGTTAAGGGGCCAATTTG
23040 GGTATTAAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 27 0.61
31 17 0.39
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (28 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAA
Done.