Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012483.1 Corchorus olitorius cultivar O-4 contig12516, 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: 24514
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:643 original size:40 final size:39
Alignment explanation
Indices: 607--1646 Score: 1303
Period size: 40 Copynumber: 26.3 Consensus size: 39
597 GGTCCTGAAT
* * **
607 AGGATTTTTGAAATTAA-CTGATAAAACAAGGATCCTGAAT
1 AGGA-TTTTGAAATTAATTTGATAAAA-AATGATCCTGAGC
* * * * *
647 AGGATTCTGAAATTGA-CTGAT---AAA-GACCCTGAAC
1 AGGATTTTGAAATTAATTTGATAAAAAATGATCCTGAGC
*
681 AGGATTCTGAAATTAATTTGAT----AATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAAATGATCCTGAGC
* * *
716 AGGGTTTTGAAATAAATTTGATAAAGCAATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGC
756 A-GAGTTTTGAAATTAATTTGATAAAAAGATGATCCTGAGC
1 AGGA-TTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
* *
796 AGGATTTTGAGATTAATTTGATAAAACAATGATTCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAA-AATGATCCTGAGC
* *
836 AGGGTTTTGAAATTAATTTGATAAAAAGATGATCCTGAAC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
*
876 AGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
* *
916 AGGATTCTGAAATTAATTTGATAAAAAGATGATCTTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
*
956 AGGATTTTGAGATTAATTTGATAAAAAGATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
*
996 AGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGC
* *
1036 AGGGTTTTGAAATTAATTTAATAAAAACATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
* * *
1076 CGGATTCTGAAATTAACTTGATAAAAAGATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
* * *
1116 AGGATTTTGAAATTAATTTGATAAAGCAATTATCTTGAGC
1 AGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGC
* *
1156 AGGGTTTTGAAATTAATTTGATAAAAGATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAAATGATCCTGAGC
*
1195 AGGATTTTGAAATTAACTTGATAAAAAGATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
*
1235 AGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
1275 AGGATTTTGAAATTAATTTGATAAAAAGATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
* *
1315 AGGATTTTGAAATTAATTTGATAAAGCAATGATCCTGAGT
1 AGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGC
*
1355 AGGGTTTTGAAATTAATTTGATAAAAAGATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
* * *
1395 AGGATTCTGAAATTAATTTGATAAAGCAATTATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGC
* *
1435 AGGGTTTTGAAATTAATTTGATGAAAAGATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGAT-AAAAAATGATCCTGAGC
* * *
1475 AGGATTTTGAAATTAACTTGATAAAGCAATGATCCTGAGT
1 AGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGC
* * *
1515 AGGGTTTTGAAATTAACTTGATAAAGCAATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGC
*
1555 AGGGTTTTGAAATTAATTTGATAAAAAGATGATCCTGAGC
1 AGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGC
* *
1595 AGGGTTTTGAAATTAATTTG-TAAAGAAATGATCCTGAGT
1 AGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGC
*
1634 AGGATTCTGAAAT
1 AGGATTTTGAAAT
1647 CGACTAATAA
Statistics
Matches: 896, Mismatches: 81, Indels: 47
0.88 0.08 0.05
Matches are distributed among these distances:
34 25 0.03
35 33 0.04
36 1 0.00
39 84 0.09
40 743 0.83
41 10 0.01
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (39 bp):
AGGATTTTGAAATTAATTTGATAAAAAATGATCCTGAGC
Found at i:2106 original size:143 final size:142
Alignment explanation
Indices: 1783--2294 Score: 824
Period size: 139 Copynumber: 3.6 Consensus size: 142
1773 ATATGGAATG
* * * * *
1783 CCCGGAGGACTTGTCAGAATTAATATCCAGAGGTTTCTGAAATTGTGCCCGAAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
*
1848 GCAATCTCAACCTTGAGCAAGGTTTTGATTTTGAAATTTAAACGCAACTTTGATTAAAACTTGAT
66 GCAAACTCAACCTTGAGCAAGGTTTTGA--TTGAAATTTAAACGCAACTTTGATTAAAACTTGAT
1913 G----AAA-TGATA
129 GAAATAAAGTGATA
*
1922 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTTCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
* * *
1987 GCAAACTCAAACTTGAGCAAGGTTTTGATTGAAATTTAAACGCAAATTTGATTAAAAACTTGTTG
66 GCAAACTCAACCTTGAGCAAGGTTTTGATTGAAATTTAAACGCAACTTTGATT-AAAACTTGATG
2052 AAATAAAGTGATA
130 AAATAAAGTGATA
2065 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
2130 GCAAACTCAACCTTGAGCAAGG-TTT--TTGAAATTTAAACGCAACTTTGATTAAAACTTGATGA
66 GCAAACTCAACCTTGAGCAAGGTTTTGATTGAAATTTAAACGCAACTTTGATTAAAACTTGATGA
*
2192 AATAAAGAGATA
131 AATAAAGTGATA
*
2204 CCCGGAGGATTTATCAGAATTAATACCCGGAGATTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
*
2269 GCGAACTCAACCTTGAGCAAGGTTTT
66 GCAAACTCAACCTTGAGCAAGGTTTT
2295 TAAACTTAAA
Statistics
Matches: 349, Mismatches: 17, Indels: 13
0.92 0.04 0.03
Matches are distributed among these distances:
137 24 0.07
138 10 0.03
139 192 0.55
140 27 0.08
142 6 0.02
143 90 0.26
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (142 bp):
CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
GCAAACTCAACCTTGAGCAAGGTTTTGATTGAAATTTAAACGCAACTTTGATTAAAACTTGATGA
AATAAAGTGATA
Found at i:2287 original size:282 final size:279
Alignment explanation
Indices: 1783--2294 Score: 848
Period size: 282 Copynumber: 1.8 Consensus size: 279
1773 ATATGGAATG
* *
1783 CCCGGAGGACTTGTCAGAATTAATATCCAGAGGTTTCTGAAATTGTGCCCGAAGGTCTTACAAAT
1 CCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAAATTGTGCCCGAAGGTCTTACAAAT
*
1848 GCAATCTCAACCTTGAGCAAGGTTTTGATTTTGAAATTTAAACGCAACTTTGATTAAAACTTGAT
66 GCAAACTCAACCTTGAGCAAGG--TT-ATTTTGAAATTTAAACGCAACTTTGATTAAAACTTGAT
* *
1913 GAAATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTTCCCGGAGGT
128 GAAATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGATTTCTGAAATTGTGCCCGGAGGT
1978 CTTACAAATGCAAACTCAAACTTGAGCAAGGTTTTGATTGAAATTTAAACGCAAATTTGATTAAA
193 CTTACAAATGCAAACTCAAACTTGAGCAAGGTTTTGATTGAAATTTAAACGCAAATTTGATTAAA
2043 AACTTGTTGAAATAAAGTGATA
258 AACTTGTTGAAATAAAGTGATA
* * *
2065 CCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAAT
1 CCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAAATTGTGCCCGAAGGTCTTACAAAT
2130 GCAAACTCAACCTTGAGCAAGG-T-TTTTGAAATTTAAACGCAACTTTGATTAAAACTTGATGAA
66 GCAAACTCAACCTTGAGCAAGGTTATTTTGAAATTTAAACGCAACTTTGATTAAAACTTGATGAA
2193 ATAAAGAGATACCCGGAGGATTTATCAGAATTAATACCCGGAGATTTCTGAAATTGTGCCCGGAG
131 AT-----GATACCCGGAGGATTTATCAGAATTAATACCCGGAGATTTCTGAAATTGTGCCCGGAG
* *
2258 GTCTTACAAATGCGAACTCAACCTTGAGCAAGGTTTT
191 GTCTTACAAATGCAAACTCAAACTTGAGCAAGGTTTT
2295 TAAACTTAAA
Statistics
Matches: 215, Mismatches: 10, Indels: 10
0.91 0.04 0.04
Matches are distributed among these distances:
277 42 0.20
279 1 0.00
282 172 0.80
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (279 bp):
CCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAAATTGTGCCCGAAGGTCTTACAAAT
GCAAACTCAACCTTGAGCAAGGTTATTTTGAAATTTAAACGCAACTTTGATTAAAACTTGATGAA
ATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGATTTCTGAAATTGTGCCCGGAGGTCTT
ACAAATGCAAACTCAAACTTGAGCAAGGTTTTGATTGAAATTTAAACGCAAATTTGATTAAAAAC
TTGTTGAAATAAAGTGATA
Found at i:10127 original size:25 final size:25
Alignment explanation
Indices: 10099--10160 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
10089 ATCCTCTCTT
10099 TTTTTTGAATTATCAACCCCCTCGG
1 TTTTTTGAATTATCAACCCCCTCGG
* * *
10124 TTTTTTGTATTATGAACCCTCTCGG
1 TTTTTTGAATTATCAACCCCCTCGG
*
10149 TTCTTTTTAATT
1 TT-TTTTGAATT
10161 TTGAAGTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 24 0.77
26 7 0.23
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (25 bp):
TTTTTTGAATTATCAACCCCCTCGG
Found at i:12704 original size:25 final size:25
Alignment explanation
Indices: 12676--12724 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
12666 TGTTAGTTTG
12676 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
12701 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
12725 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:13050 original size:19 final size:19
Alignment explanation
Indices: 13026--13062 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
13016 TAGTCCAAAC
13026 TTGTGATATGGTTCGTCAA
1 TTGTGATATGGTTCGTCAA
13045 TTGTGATATGGTTCGTCA
1 TTGTGATATGGTTCGTCA
13063 GATTTGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.27, T:0.43
Consensus pattern (19 bp):
TTGTGATATGGTTCGTCAA
Found at i:13591 original size:25 final size:25
Alignment explanation
Indices: 13563--13611 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
13553 TGTTAGTTTG
*
13563 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGAACGAGCGAGAGTGCTCAAA
13588 TAGAGAACGAGCGAGAGTGCTCAA
1 TAGAGAACGAGCGAGAGTGCTCAA
13612 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGAACGAGCGAGAGTGCTCAAA
Found at i:13951 original size:165 final size:165
Alignment explanation
Indices: 13679--14010 Score: 637
Period size: 165 Copynumber: 2.0 Consensus size: 165
13669 GTTATTGAAA
*
13679 ATTATGTGTTGATGTAATTTTCTGTAACTAGTGGATTTCTCTTCTCCTCCGTGGATGTAGGCAAG
1 ATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTCTTCTCCTCCGTGGATGTAGGCAAG
*
13744 TTCAGTGTCGAACCACGTAAATTCTTTTGTCTTGTGTGGATGATTATTATTTTAGTTGCTTCCGC
66 TTCAGTGCCGAACCACGTAAATTCTTTTGTCTTGTGTGGATGATTATTATTTTAGTTGCTTCCGC
13809 TTGCATGATTAATTTGGTAGATTATGGTTTGGGAT
131 TTGCATGATTAATTTGGTAGATTATGGTTTGGGAT
13844 ATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTCTTCTCCTCCGTGGATGTAGGCAAG
1 ATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTCTTCTCCTCCGTGGATGTAGGCAAG
*
13909 TTCAGTGCCGAACCACGTAAATTCTTTTGTCTTTTGTGGATGATTATTATTTTAGTTGCTTCCGC
66 TTCAGTGCCGAACCACGTAAATTCTTTTGTCTTGTGTGGATGATTATTATTTTAGTTGCTTCCGC
13974 TTGCATGATTAATTTGGTAGATTATGGTTTGGGAT
131 TTGCATGATTAATTTGGTAGATTATGGTTTGGGAT
14009 AT
1 AT
14011 CCAGGTTACA
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 164 1.00
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (165 bp):
ATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTTCTCTTCTCCTCCGTGGATGTAGGCAAG
TTCAGTGCCGAACCACGTAAATTCTTTTGTCTTGTGTGGATGATTATTATTTTAGTTGCTTCCGC
TTGCATGATTAATTTGGTAGATTATGGTTTGGGAT
Found at i:20217 original size:20 final size:18
Alignment explanation
Indices: 20179--20218 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
20169 CTGCAAACAT
*
20179 AAGAAAAACACAAAAACG
1 AAGAAAAAAACAAAAACG
20197 AAGAACAAAAACAAAATACG
1 AAGAA-AAAAACAAAA-ACG
20217 AA
1 AA
20219 ATAAAACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.72, C:0.15, G:0.10, T:0.03
Consensus pattern (18 bp):
AAGAAAAAAACAAAAACG
Found at i:24514 original size:33 final size:33
Alignment explanation
Indices: 24396--24502 Score: 187
Period size: 33 Copynumber: 3.2 Consensus size: 33
24386 AAATGGTCGG
*
24396 TGCCGCCCTTGGTGGGCGGCATGGCCATGGGGA
1 TGCCGCCCTCGGTGGGCGGCATGGCCATGGGGA
24429 TGCCGCCCTCGGTGGGCGGCATGGCCATGGGGA
1 TGCCGCCCTCGGTGGGCGGCATGGCCATGGGGA
**
24462 TGCCGCCCTCGGTGGGCGGCATGGCCATGGTCA
1 TGCCGCCCTCGGTGGGCGGCATGGCCATGGGGA
24495 TGCCGCCC
1 TGCCGCCC
24503 AAGGAGGGCG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.08, C:0.33, G:0.42, T:0.17
Consensus pattern (33 bp):
TGCCGCCCTCGGTGGGCGGCATGGCCATGGGGA
Done.