Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015086.1 Corchorus capsularis cultivar CVL-1 contig15107, 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: 47105
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:239 original size:33 final size:33
Alignment explanation
Indices: 144--245 Score: 138
Period size: 33 Copynumber: 3.2 Consensus size: 33
134 ATCAGATTTA
* *
144 TTTTCAATGC--T-ATCAACCAAAACAGGATTA
1 TTTTCAATGCTATGATCAACCAAAACAGAATTG
*
174 TTTGCAATGCTATGATCAACCAAAACAGAATTG
1 TTTTCAATGCTATGATCAACCAAAACAGAATTG
* *
207 TTTTTAATGCTATGTTCAACCAAAACAGAATTG
1 TTTTCAATGCTATGATCAACCAAAACAGAATTG
240 TTTTCA
1 TTTTCA
246 TCACAATTAG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
30 9 0.15
32 1 0.02
33 52 0.84
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (33 bp):
TTTTCAATGCTATGATCAACCAAAACAGAATTG
Found at i:306 original size:33 final size:33
Alignment explanation
Indices: 281--389 Score: 139
Period size: 33 Copynumber: 3.3 Consensus size: 33
271 TAGTTTTATT
*
281 GCAAACAACACTCAAGTTAGGTTTAGTATCATC
1 GCAAACAACACTCAAATTAGGTTTAGTATCATC
** * * *
314 GCAAACAACA-TCTAAAACAGATTTAGTGTCATT
1 GCAAACAACACTC-AAATTAGGTTTAGTATCATC
*
347 GCAAACAACACTCAATTTAGGTTTAGTATCATC
1 GCAAACAACACTCAAATTAGGTTTAGTATCATC
380 GCAAACAACA
1 GCAAACAACA
390 TCTAAAAGAC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
32 2 0.03
33 58 0.94
34 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (33 bp):
GCAAACAACACTCAAATTAGGTTTAGTATCATC
Found at i:313 original size:66 final size:66
Alignment explanation
Indices: 256--396 Score: 210
Period size: 66 Copynumber: 2.1 Consensus size: 66
246 TCACAATTAG
* * * *
256 CATCCAAAACGGATTTAGTTTTATTGCAAACAACACTCAAGTTAGGTTTAGTATCATCGCAAACA
1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAGTTAGGTTTAGTATCATCACAAACA
321 A
66 A
* * *
322 CATCTAAAACAGATTTAGTGTCATTGCAAACAACACTCAATTTAGGTTTAGTATCATCGCAAACA
1 CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAGTTAGGTTTAGTATCATCACAAACA
387 A
66 A
*
388 CATCTAAAA
1 CATCCAAAA
397 GACTCTTTTC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (66 bp):
CATCCAAAACAGATTTAGTGTCATTGCAAACAACACTCAAGTTAGGTTTAGTATCATCACAAACA
A
Found at i:1906 original size:8 final size:8
Alignment explanation
Indices: 1878--1911 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1868 GAATCGGCTA
1878 TGAATTTT
1 TGAATTTT
*
1886 TGAAGTTTC
1 TGAA-TTTT
1895 TGAATTTT
1 TGAATTTT
1903 TGAATTTT
1 TGAATTTT
1911 T
1 T
1912 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:3929 original size:26 final size:27
Alignment explanation
Indices: 3882--3932 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
3872 TACAGAGAGT
*
3882 TTGAGAGAAAAGCGCGGAGCTTGAAAA
1 TTGAGAGAAAAGCACGGAGCTTGAAAA
3909 TTGAGAG-AAAGCACAGG-GCTTGAA
1 TTGAGAGAAAAGCAC-GGAGCTTGAA
3933 GTTTTGCACG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.39, C:0.12, G:0.33, T:0.16
Consensus pattern (27 bp):
TTGAGAGAAAAGCACGGAGCTTGAAAA
Found at i:7079 original size:2 final size:2
Alignment explanation
Indices: 7072--7100 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7062 ACTAAATACA
7072 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 A
7101 AAGGGGGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10776 original size:40 final size:39
Alignment explanation
Indices: 10721--10824 Score: 163
Period size: 40 Copynumber: 2.6 Consensus size: 39
10711 CTATTTAAGC
* *
10721 AATTCCAATAGAAGACTTTTGGAAAATAAATGTTTTTAG
1 AATTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTTAG
*
10760 TAATTCCAAGAGAAGACTTTTGGAAAATAAAAGTTTTTAG
1 -AATTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTTAG
*
10800 AAATCCAAAAGAAGACTTTTGGAAA
1 AATTCCAAAAGAAGACTTTTGGAAA
10825 TTAATAAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 23 0.38
40 37 0.62
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (39 bp):
AATTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTTAG
Found at i:22976 original size:437 final size:437
Alignment explanation
Indices: 22277--23382 Score: 1804
Period size: 437 Copynumber: 2.5 Consensus size: 437
22267 TTTTTTATTG
* * * * * *
22277 AAACATAAAAATTGGCTTTTGAGTGCTTAATGAAAGTTGTAGATCATGAAATCACCTTTTAATAG
1 AAACATTAAAATTGACTTCTGAGTCCTTAATGGAAGTTGTAGATCATGAAATTACCTTTTAATAG
* * * * * * *
22342 GCACTTGAATCACCTTAATCGGACAAACATGACAAAAAAATAAAAGAATTAAAGTCGAAACGTTA
66 ACACTTGAATCACCTTGATCGGACAAGCA--A-AAAAAAATAAAAGAATCAAAGCCAAAACGTTC
* * * * *
22407 AATCGTCCAACCTAGAATTTTGTGAGGGATTAAATAGCATAAAGCATAAACGTATGAGGATCA-T
128 AGTCGTCCAACCCAGAA-ATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTATGAGGATCATT
22471 TGAATAAATAATCCAGCAAAAAAATATTTGTTTATGGAGACAAAACATAAAAATTCCCTCTCGAA
192 TG-ATAAATAATCCAGCAAAAAAATATTTGTTTATGGAGACAAAACATAAAAATTCCCTCTCGAA
* *
22536 CCCTCCACGAAACTCATCAATCAAATTCAGCTTTCAGGCCCTTAACGAAAGTAGTAGATTATACA
256 CCCTCCACGAAACTCATCAATCAAATTCAGCTTTCAGGCCCTTAACGAAAGTAGTAGATCACACA
**
22601 ATAACCTTTTAACCGACACTTGAACAATCTCAATCGGACAAGTGGACCGAAAATTATACAATATT
321 ATAAAATTTTAACCGACACTTGAACAATCTCAATCGGACAAGTGGACCGAAAATTATACAATATT
22666 AGAGAGACCGGCAATCGAGACCACAAAATTTCAGAAGCAATTTTTACAATCA
386 AGAGAGACCGGCAATCGAGACCACAAAATTTCAGAAGCAATTTTTACAATCA
22718 AAACATTAAAATTGACTTCTGAGTCCTTAATGGAAGTTGTAGATCATGAAATTACCTTTTAATAG
1 AAACATTAAAATTGACTTCTGAGTCCTTAATGGAAGTTGTAGATCATGAAATTACCTTTTAATAG
22783 ACACTTGAATCACCTTGATCGGACAAGC-AAAAAAAATAAAAGAATCAAAGCCAAAACGTTCAGT
66 ACACTTGAATCACCTTGATCGGACAAGCAAAAAAAAATAAAAGAATCAAAGCCAAAACGTTCAGT
*
22847 CGTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAACATAAAAGTATGAGGATCATTTGAT
131 CGTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTATGAGGATCATTTGAT
* *
22912 AAATAATCCAGCAAAAAAAATATTTGTTTATGGAGACCAAACATAGAAATTCCCTCTCGAACCCT
196 AAATAATCCAGC-AAAAAAATATTTGTTTATGGAGACAAAACATAAAAATTCCCTCTCGAACCCT
* ** *
22977 CCACGAAACTCATTAATCAAATTCAGCTTTCAGGCCCTTAACGAAAGTCTTAGATCACATAATAA
260 CCACGAAACTCATCAATCAAATTCAGCTTTCAGGCCCTTAACGAAAGTAGTAGATCACACAATAA
23042 AATTTTAACCGACACTTGAACAATCTCAATCGGACAAGTGGACCGAAAATTATACAATATTAGAG
325 AATTTTAACCGACACTTGAACAATCTCAATCGGACAAGTGGACCGAAAATTATACAATATTAGAG
*
23107 AGACCGGCAATCGAGACCACAAAATTTCAGAAGCAATTTTTAGAATCA
390 AGACCGGCAATCGAGACCACAAAATTTCAGAAGCAATTTTTACAATCA
* *
23155 AAACATTAAAACTGACTTCTGAGTCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAG
1 AAACATTAAAATTGACTTCTGAGTCCTTAATGGAAGTTGTAGATCATGAAATTACCTTTTAATAG
23220 ACACTTGAATCACCTTGATCGGACAAGCAAAACAAAAAATAAAAGAATCAAAGCCAAAACGTTCA
66 ACACTTGAATCACCTTGATCGGACAAGC-AAA-AAAAAATAAAAGAATCAAAGCCAAAACGTTCA
23285 GTCGTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTAT-AGGGATCATTT
129 GTCGTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTATGA-GGATCATTT
*
23349 GATAAATAAACCAGCAAAAAAATGATTTGTTTAT
193 GATAAATAATCCAGCAAAAAAAT-ATTTGTTTAT
23383 TATAAGCGGG
Statistics
Matches: 624, Mismatches: 34, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
436 55 0.09
437 356 0.57
438 1 0.00
439 11 0.02
440 117 0.19
441 84 0.13
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (437 bp):
AAACATTAAAATTGACTTCTGAGTCCTTAATGGAAGTTGTAGATCATGAAATTACCTTTTAATAG
ACACTTGAATCACCTTGATCGGACAAGCAAAAAAAAATAAAAGAATCAAAGCCAAAACGTTCAGT
CGTCCAACCCAGAAATTGTGAGGGACTAAATAGCATAAAGCATAAAAGTATGAGGATCATTTGAT
AAATAATCCAGCAAAAAAATATTTGTTTATGGAGACAAAACATAAAAATTCCCTCTCGAACCCTC
CACGAAACTCATCAATCAAATTCAGCTTTCAGGCCCTTAACGAAAGTAGTAGATCACACAATAAA
ATTTTAACCGACACTTGAACAATCTCAATCGGACAAGTGGACCGAAAATTATACAATATTAGAGA
GACCGGCAATCGAGACCACAAAATTTCAGAAGCAATTTTTACAATCA
Found at i:24460 original size:167 final size:166
Alignment explanation
Indices: 24080--24483 Score: 540
Period size: 166 Copynumber: 2.4 Consensus size: 166
24070 TGAGTCATTT
*
24080 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAACGTTAGGACAT
* * * * * * * ** * *
24145 TTAAGTAATTTGCCAAGTAAGTAAAGACGAAAAAGATTACTTCTCTAGCTCATCATCAATCCTTG
66 TTAAGTAATCTACAAAGTAAGAAAAGACGAAAAAAATAACTTCTCTAACTCAAAAGCAAGCCTTG
* * * *
24210 ATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
131 ATAGGGACCTTTTAGTAATTCCACTACTCTATTAAA
* * * * * *
24246 TTCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCGCTCAAGAATCAAACGTTTGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAACGTTAGGACAT
* *
24311 TTAAGTAATCTACAAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCTT
66 TTAAGTAATCTACAAAGTAAGAAAAGACGAAAAAAATAACTTCTCTAACT-CAAAAGCAAGCCTT
* *
24376 GGTAGGGACCTTTTAGTAATTCCACTACTTTATTAAA
130 GATAGGGACCTTTTAGTAATTCCACTACTCTATTAAA
*
24413 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATTAAAAC-TTAGGACA
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAA-TCAAACGTTAGGACA
24477 TTTAAGT
65 TTTAAGT
24484 TTAAACTCTA
Statistics
Matches: 203, Mismatches: 33, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
166 99 0.49
167 99 0.49
168 5 0.02
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAACGTTAGGACAT
TTAAGTAATCTACAAAGTAAGAAAAGACGAAAAAAATAACTTCTCTAACTCAAAAGCAAGCCTTG
ATAGGGACCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:24867 original size:45 final size:45
Alignment explanation
Indices: 24796--24881 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
24786 ACTTCTCCAG
*
24796 CTCATCATTAATTCGGAGTAGAGATCTTTTAGTAATTCCACCCAA
1 CTCATCATTAACTCGGAGTAGAGATCTTTTAGTAATTCCACCCAA
*
24841 CTCATCATTAACTC-GAGGTAGGGATCTTTTAGTAATTCCAC
1 CTCATCATTAACTCGGA-GTAGAGATCTTTTAGTAATTCCAC
24882 TACTTTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 2 0.05
45 36 0.95
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (45 bp):
CTCATCATTAACTCGGAGTAGAGATCTTTTAGTAATTCCACCCAA
Found at i:25483 original size:26 final size:27
Alignment explanation
Indices: 25420--25486 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
25410 TCATCTCTAC
** *
25420 ATACATTTTATCTCT-TCTATATTCCA
1 ATACATTTTATCTCTAGATACATTCCA
* *
25446 ATA-ATATCATCTCTAGATACATT-CA
1 ATACATTTTATCTCTAGATACATTCCA
25471 ATACATTTTATCTCTA
1 ATACATTTTATCTCTA
25487 AAATTTACGT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.33, C:0.21, G:0.01, T:0.45
Consensus pattern (27 bp):
ATACATTTTATCTCTAGATACATTCCA
Found at i:27184 original size:2 final size:2
Alignment explanation
Indices: 27177--27202 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27167 TGCTTTTTAT
27177 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
27203 CACACACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27398 original size:31 final size:30
Alignment explanation
Indices: 27314--27401 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 30
27304 ACAGAAATAT
* **
27314 TCAATTTCGTTCATGTACTCTA-AA-AGCGA
1 TCAATTTAGTTCATGTACTC-ACAAGATTGA
* ** *
27343 TCAATTTAGTTCTTAAACTTACAAGATTGA
1 TCAATTTAGTTCATGTACTCACAAGATTGA
27373 GTCAATTTAGTTCATGTACTCACAAGATT
1 -TCAATTTAGTTCATGTACTCACAAGATT
27402 TGGTTAATTG
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
28 1 0.02
29 17 0.38
30 3 0.07
31 24 0.53
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (30 bp):
TCAATTTAGTTCATGTACTCACAAGATTGA
Found at i:27506 original size:31 final size:30
Alignment explanation
Indices: 27458--27530 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
27448 TTATTGATTA
* * *
27458 GACTCAATTGAACCAATCTTGTTAGTAGATG
1 GACTAAATTG-ACCAATCTTATGAGTAGATG
*
27489 GACTAAATTGACTCAATCTTATGAGTATATG
1 GACTAAATTGAC-CAATCTTATGAGTAGATG
*
27520 TACTAAATTGA
1 GACTAAATTGA
27531 TCGCCTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 2 0.06
31 34 0.94
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (30 bp):
GACTAAATTGACCAATCTTATGAGTAGATG
Found at i:31629 original size:33 final size:33
Alignment explanation
Indices: 31587--31651 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
31577 GTGCATACGG
*
31587 GACTCCTTGTGAGAGCTTTTGTATTGTCTTTGA
1 GACTCCTTGTGAGAACTTTTGTATTGTCTTTGA
31620 GACTCCTTGTGAGAACTTTTGTATTGTCTTTG
1 GACTCCTTGTGAGAACTTTTGTATTGTCTTTG
31652 TACAATCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (33 bp):
GACTCCTTGTGAGAACTTTTGTATTGTCTTTGA
Found at i:39603 original size:21 final size:21
Alignment explanation
Indices: 39554--39607 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
39544 AGCACTGGAG
*
39554 CACATGGGGCGCGAGGCAAAC
1 CACATGGGGCGCCAGGCAAAC
** **
39575 CAGGTGGGGCGCCAGGCTTAC
1 CACATGGGGCGCCAGGCAAAC
39596 CACAT-GGGCGCC
1 CACATGGGGCGCC
39608 CAGCGCCAGT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.20, C:0.31, G:0.39, T:0.09
Consensus pattern (21 bp):
CACATGGGGCGCCAGGCAAAC
Found at i:41270 original size:6 final size:6
Alignment explanation
Indices: 41261--41330 Score: 95
Period size: 6 Copynumber: 11.5 Consensus size: 6
41251 TTTTTCGTTA
* *
41261 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTATAT TTATAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
41309 TTATAT TTATAT TTTTCAT TTT
1 TTTTAT TTTTAT TTTT-AT TTT
41331 AGTGCTAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
6 56 0.92
7 5 0.08
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:44814 original size:26 final size:25
Alignment explanation
Indices: 44781--44829 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
44771 TCCCTCTTTG
* *
44781 AAAAAAAATGAGTGTTAGTAACCTC
1 AAAAAAAAAGAGCGTTAGTAACCTC
*
44806 AAAAGAAAAAGGGCGTTAGTAACC
1 AAAA-AAAAAGAGCGTTAGTAACC
44830 CCTAAATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.18
Consensus pattern (25 bp):
AAAAAAAAAGAGCGTTAGTAACCTC
Done.