Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005181.1 Corchorus capsularis cultivar CVL-1 contig05199, 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: 14329
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Found at i:1596 original size:440 final size:440
Alignment explanation
Indices: 910--2018 Score: 1397
Period size: 440 Copynumber: 2.5 Consensus size: 440
900 TGAAGCATTT
* * * * * *
910 TCAAATCATC-AAATTGGCTTTCGAGTTCTTTATGAAAGTTGTAAATCATTAAATTACCTTTCAA
1 TCAAAACATCAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAAATCATGAAATTACCTTTAAA
* * *
974 TAGACACTTGAATCACCTTGATCCGACAAATAG-AACAAAAAATACAAA-AATAAAAGTCGATAT
66 TAGACACTTGAATCACCTTGATCGGACAAATAGAAACAAAAAATA-AAAGAATAAAAGCCGAAAT
* * *
1037 GTTAAATCATCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGGGGGTCA
130 GTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGAGGATCA
* * * *
1102 TTTGATAAATAATCCAGGGACAAAAAT-ATTTGTTTATGAAGACCAAGCATAAAAATTACCTCTT
195 TTTGATAAATAATCCA-GCAAAAAAATGATTTGTTTATGAAGACCAAACATAAAAATTACCTCTC
* ** * *
1166 GAA-CTCTCCACGAAACTCATTAATCAAATTCAACTTTCAGGCCCTTGGCGAAAGTCGTAGATAA
259 GAATC-CTCCACGAAACTCATTAATCAAATTCAACTTTCAGACCCTTAACGAAAGTCATAAATAA
* * * * **
1230 TATAATAACCTTTCAACCGACACTTGAACAATCTCAATCGGACAAGTGGGCTGAAAATTATAC-C
323 CACAATAACCTTTCAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCAAAAATTATACGC
* * *
1294 ATATTAGATAGAACGACAATCGAGACCACAAAATTTTAGAAGCATTTTTTAGAA
388 ATATCAGAGAGAACGACAATCGAGACCACAAAATTTCAGAAGCATTTTTT-GAA
* * * *
1348 TCAAAACATCAAAATTGGCTTTTGAGTCCTTCATGAAAATTGTAGACCATGGAATTACCTTTAAA
1 TCAAAACATCAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAAATCATGAAATTACCTTTAAA
** * * * *
1413 TAGACACCCGAATCACCTTGATCGGTCAAATAGAAAAAAAAAATAAAAGAATTAAAGCCGAAATA
66 TAGACACTTGAATCACCTTGATCGGACAAATAGAAACAAAAAATAAAAGAATAAAAGCCGAAATG
* * * **
1478 TTTAATTGTCGAACCCATAATTGTAAAGGATTAAATAGCATAAATTATAAAAGTATGAGGATCAT
131 TTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGAGGATCAT
* * * *
1543 TTAATAAATAATCCAACAAAAAAATGATTTGTTTATGGAGACCAAACATAAAAATTCCCTCTCGA
196 TTGATAAATAATCCAGCAAAAAAATGATTTGTTTATGAAGACCAAACATAAAAATTACCTCTCGA
* * *
1608 ATCCTCCACGAAACTCATTAATCAAATTCAGCTTTTAGACCCTTAACGAAAGTCATAAATCACAC
261 ATCCTCCACGAAACTCATTAATCAAATTCAACTTTCAGACCCTTAACGAAAGTCATAAATAACAC
* * * *
1673 AATAACCTTTTAATCGACACTTGAACAACCTCAATCGGACAAGTTGACCAAAAATTATACGGATA
326 AATAACCTTTCAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCAAAAATTATACGCATA
* * * *
1738 TCAGAGAGACCGGCAATTGAGACCATAAAATTTCAGAAGCATTTTTTGAA
391 TCAGAGAGAACGACAATCGAGACCACAAAATTTCAGAAGCATTTTTTGAA
* * * *
1788 TCAAAACATTAAAATTGACTTTTGAGTCCTTCATGGAAGTTGTAAATCATGAAATTACCTTTTAA
1 TCAAAACATCAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAAATCATGAAATTACCTTTAAA
* * ** * *
1853 TAGATACTTGAATCACCTTGATTGGACAAGCA-AAACAAAAAATAAAAGAATCAAAGCCGAAACG
66 TAGACACTTGAATCACCTTGATCGGACAAATAGAAACAAAAAATAAAAGAATAAAAGCCGAAATG
* * * * * * * *
1917 TTCAGTCGTCCAACCCAGAAATTGTGAGGGACTAAATAACATAGAGCATAAAAGTAT-AGGGATC
131 TTAAATCGTCCAACCCA-TAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGA-GGATC
*
1981 ATTTGATAAATAAACCAGCAAAAAAATGATTTGTTTAT
194 ATTTGATAAATAATCCAGCAAAAAAATGATTTGTTTAT
2019 TATACGCGGG
Statistics
Matches: 569, Mismatches: 94, Indels: 14
0.84 0.14 0.02
Matches are distributed among these distances:
438 9 0.02
439 126 0.22
440 390 0.69
441 44 0.08
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (440 bp):
TCAAAACATCAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAAATCATGAAATTACCTTTAAA
TAGACACTTGAATCACCTTGATCGGACAAATAGAAACAAAAAATAAAAGAATAAAAGCCGAAATG
TTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATGAGGATCAT
TTGATAAATAATCCAGCAAAAAAATGATTTGTTTATGAAGACCAAACATAAAAATTACCTCTCGA
ATCCTCCACGAAACTCATTAATCAAATTCAACTTTCAGACCCTTAACGAAAGTCATAAATAACAC
AATAACCTTTCAACCGACACTTGAACAACCTCAATCGGACAAGTGGACCAAAAATTATACGCATA
TCAGAGAGAACGACAATCGAGACCACAAAATTTCAGAAGCATTTTTTGAA
Found at i:9874 original size:69 final size:69
Alignment explanation
Indices: 9795--9933 Score: 244
Period size: 69 Copynumber: 2.0 Consensus size: 69
9785 TGTCAATCAC
*
9795 AATAATCTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAA-ACTTGAATTTAATTAAATG
1 AATAACCTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAATA-TTGAATTTAATTAAATG
9859 AAAAT
65 AAAAT
*
9864 AATAACCTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAGTTAAATGA
1 AATAACCTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGA
9929 AAAT
66 AAAT
9933 A
1 A
9934 GAGTTTTTGG
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 66 0.99
70 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (69 bp):
AATAACCTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGA
AAAT
Found at i:10189 original size:4 final size:4
Alignment explanation
Indices: 10177--10216 Score: 71
Period size: 4 Copynumber: 9.8 Consensus size: 4
10167 ACTTTTATAT
10177 ATAG TATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG -ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
10217 AATTCAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 31 0.89
5 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.28
Consensus pattern (4 bp):
ATAG
Found at i:11964 original size:20 final size:21
Alignment explanation
Indices: 11939--11977 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11929 TTGTTGCTAT
*
11939 TTATTT-ATTTTCAATATTTA
1 TTATTTAATTTACAATATTTA
11959 TTATTTAATTTACAATATT
1 TTATTTAATTTACAATATT
11978 AACCTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTTAATTTACAATATTTA
Found at i:12386 original size:3 final size:3
Alignment explanation
Indices: 12380--12426 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
12370 TTTTATTATG
12380 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12427 GATGTAATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:13073 original size:211 final size:211
Alignment explanation
Indices: 12700--13121 Score: 747
Period size: 211 Copynumber: 2.0 Consensus size: 211
12690 TTTGTAAATG
* * *
12700 GTTTGGCTGAGTGGTCTATTTAACGTTATATAATTTTTGCTATGGATATCCGATCAAGGTGATTC
1 GTTTGGCTAAGTGGTCTATTTAACATTATATAATTTTTGCTATGGATATCCAATCAAGGTGATTC
12765 AAGTGTCTATTAAAAGGTTGTTCCATGATCTACGAATTTCAAGAAGGAATCGAAAACTAAATTTA
66 AAGTGTCTATTAAAAGGTTGTTCCATGATCTACGAATTTCAAGAAGGAATCGAAAACTAAATTTA
**
12830 ATGTTTCAAGTATCGAAAATGCTTCCGAAAAATTAGTTGTTTCGATTAATAGGAATGGACGATCC
131 ATGTTTCAAGTATCGAAAATGCTTCCGAAAAATTAGTTGTTTCGATTAATAGGAACAGACGATCC
*
12895 ACTTAATGTTACATAA
196 ACTTAATATTACATAA
12911 GTTTGGCTAAGTGGTCTATTTAACATTATATAATTTTTGCTCA-GGATATCCAATCAAGGTGATT
1 GTTTGGCTAAGTGGTCTATTTAACATTATATAATTTTTGCT-ATGGATATCCAATCAAGGTGATT
*
12975 CAAGTGTCTATTAAAAGGTTGTTCCATGATCTACGAATTTCACGAAGGAATCGAAAACTAAATTT
65 CAAGTGTCTATTAAAAGGTTGTTCCATGATCTACGAATTTCAAGAAGGAATCGAAAACTAAATTT
* *
13040 AATGTTTCAAGTATCGAAAATGTTTCTGAAAAATTAGTTGTTTCGATTAATAGGAACAGACGATC
130 AATGTTTCAAGTATCGAAAATGCTTCCGAAAAATTAGTTGTTTCGATTAATAGGAACAGACGATC
13105 CACTTAATATTACATAA
195 CACTTAATATTACATAA
13122 CTTTTACTCC
Statistics
Matches: 201, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
211 200 1.00
212 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (211 bp):
GTTTGGCTAAGTGGTCTATTTAACATTATATAATTTTTGCTATGGATATCCAATCAAGGTGATTC
AAGTGTCTATTAAAAGGTTGTTCCATGATCTACGAATTTCAAGAAGGAATCGAAAACTAAATTTA
ATGTTTCAAGTATCGAAAATGCTTCCGAAAAATTAGTTGTTTCGATTAATAGGAACAGACGATCC
ACTTAATATTACATAA
Found at i:13915 original size:19 final size:19
Alignment explanation
Indices: 13897--13933 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
13887 TATTAATTAT
13897 TTTA-ATATTATACTTTTA
1 TTTATATATTATACTTTTA
*
13915 TTTATATATTATATTTTTA
1 TTTATATATTATACTTTTA
13934 CTTAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTATACTTTTA
Found at i:14066 original size:13 final size:13
Alignment explanation
Indices: 14048--14074 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14038 AAATATAATA
14048 AATATGATTTATG
1 AATATGATTTATG
14061 AATATGATTTATG
1 AATATGATTTATG
14074 A
1 A
14075 GGTTATAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
AATATGATTTATG
Done.