Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016222.1 Corchorus capsularis cultivar CVL-1 contig16243, 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: 33049
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Found at i:6268 original size:144 final size:144
Alignment explanation
Indices: 6008--6286 Score: 549
Period size: 144 Copynumber: 1.9 Consensus size: 144
5998 CTTGCCCTAA
6008 CTATTTGTCATTGGTTTGTGGGGATTTATCTTGTGATTTGTTCAACGACCGAGCACTTACTTCTC
1 CTATTTGTCATTGGTTTGTGGGGATTTATCTTGTGATTTGTTCAACGACCGAGCACTTACTTCTC
6073 TTGATTTTTCTTAATTTTCCTTAATTTCACTGAATTAGGACTTACTTTTCTTAACTTTCCTTAAT
66 TTGATTTTTCTTAATTTTCCTTAATTTCACTGAATTAGGACTTACTTTTCTTAACTTTCCTTAAT
6138 CTTACCTTTCTTAG
131 CTTACCTTTCTTAG
*
6152 CTATTTGTTATTGGTTTGTGGGGATTTATCTTGTGATTTGTTCAACGACCGAGCACTTACTTCTC
1 CTATTTGTCATTGGTTTGTGGGGATTTATCTTGTGATTTGTTCAACGACCGAGCACTTACTTCTC
6217 TTGATTTTTCTTAATTTTCCTTAATTTCACTGAATTAGGACTTACTTTTCTTAACTTTCCTTAAT
66 TTGATTTTTCTTAATTTTCCTTAATTTCACTGAATTAGGACTTACTTTTCTTAACTTTCCTTAAT
6282 CTTAC
131 CTTAC
6287 TGAATTAGAG
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 134 1.00
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (144 bp):
CTATTTGTCATTGGTTTGTGGGGATTTATCTTGTGATTTGTTCAACGACCGAGCACTTACTTCTC
TTGATTTTTCTTAATTTTCCTTAATTTCACTGAATTAGGACTTACTTTTCTTAACTTTCCTTAAT
CTTACCTTTCTTAG
Found at i:10576 original size:13 final size:13
Alignment explanation
Indices: 10558--10583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10548 ATCATGCACC
10558 CAAAACATTTTAT
1 CAAAACATTTTAT
10571 CAAAACATTTTAT
1 CAAAACATTTTAT
10584 AAAGCGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
CAAAACATTTTAT
Found at i:10803 original size:13 final size:13
Alignment explanation
Indices: 10785--10827 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
10775 GTATCATAAT
*
10785 CAAAGTCATAAAC
1 CAAAGTAATAAAC
10798 CAAAGTAATAAAC
1 CAAAGTAATAAAC
*
10811 CAGAA-TAATAGAC
1 CA-AAGTAATAAAC
10824 CAAA
1 CAAA
10828 ACAGTCAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 2 0.07
13 23 0.85
14 2 0.07
ACGTcount: A:0.58, C:0.19, G:0.09, T:0.14
Consensus pattern (13 bp):
CAAAGTAATAAAC
Found at i:13064 original size:12 final size:12
Alignment explanation
Indices: 13047--13080 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13037 GTGACAATGC
13047 CCAAACCAGAGA
1 CCAAACCAGAGA
*
13059 CCAAACCGGAGA
1 CCAAACCAGAGA
*
13071 CTAAACCAGA
1 CCAAACCAGA
13081 AACTCAACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.32, G:0.18, T:0.03
Consensus pattern (12 bp):
CCAAACCAGAGA
Found at i:14869 original size:26 final size:26
Alignment explanation
Indices: 14839--14890 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
14829 GTCTTATAAA
14839 AATACCTATTAAACTTTATGTCTATG
1 AATACCTATTAAACTTTATGTCTATG
14865 AATACCTATTAAACTTTATGTCTATG
1 AATACCTATTAAACTTTATGTCTATG
14891 TGTGCTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (26 bp):
AATACCTATTAAACTTTATGTCTATG
Found at i:19767 original size:48 final size:48
Alignment explanation
Indices: 19696--19803 Score: 207
Period size: 48 Copynumber: 2.2 Consensus size: 48
19686 TAATTTGACT
*
19696 AAATTATGAAGCGCTAAAACATTAGCCTGAAAATTAGGAAATAGATTC
1 AAATTGTGAAGCGCTAAAACATTAGCCTGAAAATTAGGAAATAGATTC
19744 AAATTGTGAAGCGCTAAAACATTAGCCTGAAAATTAGGAAATAGATTC
1 AAATTGTGAAGCGCTAAAACATTAGCCTGAAAATTAGGAAATAGATTC
19792 AAATTGTGAAGC
1 AAATTGTGAAGC
19804 TAGGGCCAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (48 bp):
AAATTGTGAAGCGCTAAAACATTAGCCTGAAAATTAGGAAATAGATTC
Found at i:20405 original size:3 final size:3
Alignment explanation
Indices: 20397--20444 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
20387 AACATGATAG
*
20397 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20445 CTTAATTACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:30217 original size:2 final size:2
Alignment explanation
Indices: 30210--30239 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30200 TTATTTTACC
30210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30240 TGATTTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31268 original size:178 final size:178
Alignment explanation
Indices: 30898--31284 Score: 485
Period size: 178 Copynumber: 2.2 Consensus size: 178
30888 TTCCACCATA
* * * *
30898 AGCACAAA-TTATGTAATATTAAGTAGACCGTGTATTTCCGTTAACCGAAACAACTAATTCTTTG
1 AGCA-AAAGTTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTG
* * *
30962 AAAGCATTTTTTATACCTTGAATATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCA
65 AAAGCATTTTTGATACCTCGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCA
* * * *
31027 TGAAACAACCTTTGAAGAAACACTTGAATCATGTCAATCAGACATCTGT
130 TGAAACAACCTTTGAAGAAACACTTAAATCATCTCAATCAGACAACTGG
* *
31076 AGCAAAAGTTATATAATATTATGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCG
1 AGCAAAAGTTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTT-G
*
31140 GAAGCATTTTTGATA-CTCGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATC
65 AAAGCATTTTTGATACCTCG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATC
* * * * * * * *
31204 ATGAAGCAATCTTTTAATAGACACTTAAATCATCTTAATCGGATAACTGG
129 ATGAAACAACCTTTGAAGAAACACTTAAATCATCTCAATCAGACAACTGG
* * *
31254 AG-AGAAATTTATATAATGTTAAATAGACCGT
1 AGCA-AAAGTTATATAATATTAAGTAGACCGT
31285 TTAGCCAAAC
Statistics
Matches: 178, Mismatches: 27, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
177 10 0.06
178 168 0.94
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (178 bp):
AGCAAAAGTTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGA
AAGCATTTTTGATACCTCGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCAT
GAAACAACCTTTGAAGAAACACTTAAATCATCTCAATCAGACAACTGG
Found at i:32390 original size:435 final size:434
Alignment explanation
Indices: 31726--32528 Score: 1019
Period size: 435 Copynumber: 1.8 Consensus size: 434
31716 GAATTTGTAA
* ** * * * *
31726 TCATTTGATAACTAATTTAAATAAGAAAATATTTTGTAATAGATATTTTAAAACATAAAATTTAG
1 TCATTTGATAAATAATCCAAATAAGAAAATATTGTGTAATAGAGATCTTAAAACATAAAATTCAG
* * *
31791 CTTTTGAACCTTCATGAAACTTGTAGATCAAATTAACTTTCGGGTTCTTTCTGAAAGTCGTAGAT
66 CTTTTGAACCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTCCTTTCTGAAAGTCGTAAAT
* * * * * *
31856 CATATAGTAACCTTTTAACCGACACTTGAATAACTTTAATCAGACATGTGGATCGAAAATTATAT
131 CATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCAGACATGTGGAACAAAAATTATAT
* * * * *
31921 GGTATTAAATAGACCAACAATCGAAACGACAAAA-TTAGAAAGCATTTTTTTTTGAATTAAAACA
196 GATATTAAATAGACCAACAATCAAAACCACAAAATTTAGAAAGCA--TTTTTTAGAATCAAAACA
* * * *
31985 TAAAAATTTACTTTCGAATAATTCCTGAAAGTTGTAGATCATGAAATTACCTTTTAATA-ACACA
259 TAAAAATTGACTTTCGAATAATTCATGAAAATTGTAGATCATGAAATTACCCTTTAATAGACACA
**
32049 TGAATCAACTTAATTGGACAAAT-AAAAAAAATAAAAAAATAAATCTTAAACATTAGATTAAGAT
324 TGAATCAACTTAATCAGACAAATAAAAAAAAATAAAAAAATAAATCTTAAACATTAGATTAAGAT
32113 AGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGG
389 AGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGG
* *
32159 TCATTTGATAAATAATCCAAATAAGAAAATGCTTGT-TAATAGAGATCTTAAAGCATAAGAATTC
1 TCATTTGATAAATAATCCAAATAAGAAAAT-ATTGTGTAATAGAGATCTTAAAACATAA-AATTC
* *
32223 A-TTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGGTCC-TTCTTGAAAGTCG
64 AGCTTTTGAA-CCTTCATGAAACTCGTAGATCAAA-TTAACTTTCGGGTCCTTTC-TGAAAGTCG
* *
32286 TAAATCATGCAATAGCCTTTT-ACCTGACACTTCAATAACTTCAATCAGACATGT-GAACAAAAA
126 TAAATCATACAATAACCTTTTAACC-GACACTTCAATAACTTCAATCAGACATGTGGAAC-AAAA
* ** * *
32349 ATTATATGATATTAAATTGACCGGCAATCAAAACCACAAAATTTTGGAAGCATTTTTTAGAATCA
189 ATTATATGATATTAAATAGACCAACAATCAAAACCACAAAATTTAGAAAGCATTTTTTAGAATCA
* * * * * ** *
32414 TAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAATTACCCTTTAGTAG
254 AAACATAAAAATTGACTTTCGAATAATTCATGAAAATTGTAGATCATGAAATTACCCTTTAATAG
* * *
32479 ACACTTGAATCACCTTAATCAGACAAATAGAAAAAAAATACAAAAATAAA
319 ACACATGAATCAACTTAATCAGACAAATA-AAAAAAAATAAAAAAATAAA
32529 AGCCAACGCG
Statistics
Matches: 310, Mismatches: 49, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
433 53 0.17
434 103 0.33
435 127 0.41
436 8 0.03
437 19 0.06
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (434 bp):
TCATTTGATAAATAATCCAAATAAGAAAATATTGTGTAATAGAGATCTTAAAACATAAAATTCAG
CTTTTGAACCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTCCTTTCTGAAAGTCGTAAAT
CATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCAGACATGTGGAACAAAAATTATAT
GATATTAAATAGACCAACAATCAAAACCACAAAATTTAGAAAGCATTTTTTAGAATCAAAACATA
AAAATTGACTTTCGAATAATTCATGAAAATTGTAGATCATGAAATTACCCTTTAATAGACACATG
AATCAACTTAATCAGACAAATAAAAAAAAATAAAAAAATAAATCTTAAACATTAGATTAAGATAG
AATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGG
Found at i:32853 original size:39 final size:39
Alignment explanation
Indices: 32799--32877 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
32789 GGTTTCTAGG
32799 TAATTTCACTTTCTATTATTATTTTTGTTTTTCAAGTCA
1 TAATTTCACTTTCTATTATTATTTTTGTTTTTCAAGTCA
32838 TAATTTCACTTTCTATTATTATTTTTGTTTTTCAAGTCA
1 TAATTTCACTTTCTATTATTATTTTTGTTTTTCAAGTCA
32877 T
1 T
32878 GAGAAGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (39 bp):
TAATTTCACTTTCTATTATTATTTTTGTTTTTCAAGTCA
Found at i:33002 original size:10 final size:10
Alignment explanation
Indices: 33001--33042 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
32991 TTAGTATTTG
33001 TTATTTGTTA
1 TTATTTGTTA
*
33011 TTATATTATTA
1 TTAT-TTGTTA
*
33022 TTGTTTGTTA
1 TTATTTGTTA
33032 TTATTTGTTA
1 TTATTTGTTA
33042 T
1 T
33043 AATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (10 bp):
TTATTTGTTA
Done.