Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005041.1 Corchorus capsularis cultivar CVL-1 contig05059, 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: 2606
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:1369 original size:660 final size:661
Alignment explanation
Indices: 98--1702 Score: 2451
Period size: 660 Copynumber: 2.4 Consensus size: 661
88 CACATCAATC
* *
98 TTTTTGGCTAAAAATGAGTTCCGGTGCTCCCGTTCAGTTTTGCATGATTTTTTGCGCCAGGACTC
1 TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGTTCAGTTTTGCATGATTTTTTGCGCCAGGACTC
*
163 ATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACTATGGATTGAAGGATTTGATTTGTGG
66 ATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACTATGGATTTAAGGATTTGATTTG-GG
* * *
228 G-GTATCAGAATCATGTCTGATTTAATGAGAAATTAACTT-GGAAAAATATAGGAAAATCGATAT
130 GAGCATCAGAATCATATCT-CTTTAATGAGAAATTAA-TTCGGAAAAATATAGGAAAATCGATAT
* * * *
291 TAGAAGCGTGAAATGCTCATCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGA
193 TAGAAGCGTGAAAAGCCCATCATTCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGG
* * *
356 CAAAAAATTGT-GAAAAAATTTTTGGGTCAATTTTTGCAATATTTTAACCCAAATCGTGTACTAA
258 CCAAAAATTGTGGAAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAACCCAAATCGTGTACTAA
* * ** *
420 CCATCATGTTTTTTGTCTAAAAATGCGTTCCAGTGCTCCGGTTAAGTTTTCCATGATTTTTGCGC
323 CCATAACGGCTTTTGTCTAAAAATGCGTTCCAGTACTCCGGTTAAGTTTTCCATGATTTTTGCGC
* *
485 CAAGACACATTAAAAAATCTATACTCATCTAACCAAATATCAGCCACTATGGATTTAATGATTTG
388 CAAGACACATTAAAAAATCTATACTCATCTAACCAAATATCAGCCACTATGGATTGAAGGATTTG
* * *
550 ATTTGTGGAGCATCAGAATCATCTCTCGGTTAATGAGAAATTAATTCTGAAAAATTTAGGAAAAT
453 ATTTGTGGAGCATCAGAATCATCTCTCGGTTAATGAGAAATTAACTCGGAAAAATATAGGAAAAT
615 CGATATTAGAAGCGTGAAATGCCCATCAATCTTTTTGGCATTGAATTATATATTTCTTATGAGTA
518 CGATATTAGAAGCGTGAAATGCCCATCAATCTTTTTGGCATTGAATTATATATTTCTTATGAGTA
*
680 TTCTGGCCAAAAATTGTGGAAAAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
583 TTCTGGCCAAAAAATGTGG-AAAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
745 TACTAACCATCACGG
647 TACTAACCATCACGG
* * *
760 TTTTTAGCAAAAAATGCGTTCCGGTGCTCCGGTTCAGTTTTGCATGATTTTTTGCGTCAGGACTC
1 TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGTTCAGTTTTGCATGATTTTTTGCGCCAGGACTC
*
825 ATTGAAATATCTATATTTATCTAACCAAATCTCAGCCACTATGGATTTAAGGATTTGATTTGGGG
66 ATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACTATGGATTTAAGGATTTGATTTGGGG
* * *
890 AGCATCATAATCATATCTCTTTAATAAGAAATTAATTCGG-AAAATACAGG-AAATCGATATTAG
131 AGCATCAGAATCATATCTCTTTAATGAGAAATTAATTCGGAAAAATATAGGAAAATCGATATTAG
*
953 AAGCGTGAAAAGCCCATCATTCTTTTTGGCATTGAATTTTATATTTTTTATGAGTATTCTGGCCA
196 AAGCGTGAAAAGCCCATCATTCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGGCCA
*
1018 AAAATTGTGGAAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAGCCCAAATCGTGTACTAACCA
261 AAAATTGTGGAAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAACCCAAATCGTGTACTAACCA
* * * * *
1083 TAACGGCTTTTG-CTAAAAATGTGTTCCGGTACTCCGGTTCAGTTTTGCATGATTTTTTGCGGCA
326 TAACGGCTTTTGTCTAAAAATGCGTTCCAGTACTCCGGTTAAGTTTTCCATGA-TTTTTGCGCCA
* * * * *
1147 AGACTCATTGAAATATCTATATTCATCTAACCAAATATCAGTCACTATGGATTGAAGGATTTGAT
390 AGACACATTAAAAAATCTATACTCATCTAACCAAATATCAGCCACTATGGATTGAAGGATTTGAT
* * * *
1212 TTGTGGAGTATCAGAATCATGTCTCGATTTAATGAGAAATTAACTCGGAGAAATATAGGAAAATC
455 TTGTGGAGCATCAGAATCATCTCTCG-GTTAATGAGAAATTAACTCGGAAAAATATAGGAAAATC
* *
1277 GATATTAGAAGCGTGAAATGCTCATCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTAT
519 GATATTAGAAGCGTGAAATGCCCATCAATCTTTTTGGCATTGAATTATATATTTCTTATGAGTAT
* *
1342 TCTGGCCAAAAAAATGTGG-AAAATTTTTGGGTCAATTTTTGCAATATTTTAGCTGAAATCGTGT
584 TCTGGCC-AAAAAATGTGGAAAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
1406 ACTAACCATCACGG
648 ACTAACCATCACGG
* *
1420 TTTTTGGCTAAAAATGCGTTCC-GTGCTCTGGTTCAGTTTCT-CATGATTTTTTTGCGCCAAGAC
1 TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGTTCAGTTT-TGCATGA-TTTTTTGCGCCAGGAC
* *
1483 TCATTGAAATATCTATATTCATCTAACCAAATTTCAGCCACTATGGATTTAAGGATTTGATTTGA
64 TCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACTATGGATTTAAGGATTTGATTTGG
* * * *
1548 CGAGCATCAGATTCATATGTCGATTTAATGAGAAATTAATTCGGAAAAATATAGGAAAATCAATA
129 GGAGCATCAGAATCATATCTC--TTTAATGAGAAATTAATTCGGAAAAATATAGGAAAATCGATA
*
1613 TTAGAAGCGTGAAAAGCCCATCAATT-TTTTT-GCGGTTGAATTATATATTTTTTATGAGTATTC
192 TTAGAAGCGTGAAAAGCCCATC-ATTCTTTTTGGC-ATTGAATTATATATTTTTTATGAGTATTC
* *
1676 TCGCCTAAAATTGTGG-AAAAAATTTTG
255 TGGCCAAAAATTGTGGAAAAAAATTTTG
1703 AGTTTCTTGC
Statistics
Matches: 859, Mismatches: 70, Indels: 27
0.90 0.07 0.03
Matches are distributed among these distances:
659 136 0.16
660 335 0.39
661 123 0.14
662 164 0.19
663 22 0.03
664 76 0.09
665 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (661 bp):
TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGTTCAGTTTTGCATGATTTTTTGCGCCAGGACTC
ATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACTATGGATTTAAGGATTTGATTTGGGG
AGCATCAGAATCATATCTCTTTAATGAGAAATTAATTCGGAAAAATATAGGAAAATCGATATTAG
AAGCGTGAAAAGCCCATCATTCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGGCCA
AAAATTGTGGAAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAACCCAAATCGTGTACTAACCA
TAACGGCTTTTGTCTAAAAATGCGTTCCAGTACTCCGGTTAAGTTTTCCATGATTTTTGCGCCAA
GACACATTAAAAAATCTATACTCATCTAACCAAATATCAGCCACTATGGATTGAAGGATTTGATT
TGTGGAGCATCAGAATCATCTCTCGGTTAATGAGAAATTAACTCGGAAAAATATAGGAAAATCGA
TATTAGAAGCGTGAAATGCCCATCAATCTTTTTGGCATTGAATTATATATTTCTTATGAGTATTC
TGGCCAAAAAATGTGGAAAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
AACCATCACGG
Found at i:1473 original size:332 final size:331
Alignment explanation
Indices: 98--1695 Score: 2365
Period size: 332 Copynumber: 4.8 Consensus size: 331
88 CACATCAATC
* * *
98 TTTTTGGCTAAAAATGAGTTCCGGTGCTCCCGTTCAGTTTTGCATGATTTTTTGCGCCAGGACTC
1 TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGTTCAGTTTTGCATGATTTTTTGCGCCAAGACTC
* *
163 ATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACTATGGATTGAAGGATTTGATTTGTGG
66 ATTGAAATATCTATATTCATCTAACCAAATATCAGCCACTATGGATTTAAGGATTTGATTTGTGG
* * *
228 GGTATCAGAATCATGTCT-GATTTAATGAGAAATTAACTT-GGAAAAATATAGGAAAATCGATAT
131 AGCATCAGAATCATATCTCGATTTAATGAGAAATTAA-TTCGGAAAAATATAGGAAAATCGATAT
* *
291 TAGAAGCGTGAAATGCTCATCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGA
195 TAGAAGCGTGAAATGCCCATCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGG
* * * *
356 CAAAAAATTGTGAAAAAATTTTTGGGTCAATTTTTGCAATATTTTAACCCAAATCGTGTACTAAC
260 CCAAAAATTGTG-GAAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCCAAATCGTGTACTAAC
* *
421 CATCATGT
324 CATCACGG
* * * * *
429 TTTTTGTCTAAAAATGCGTTCCAGTGCTCCGGTTAAGTTTTCCATGA-TTTTTGCGCCAAGACAC
1 TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGTTCAGTTTTGCATGATTTTTTGCGCCAAGACTC
* * * *
493 ATTAAAAAATCTATACTCATCTAACCAAATATCAGCCACTATGGATTTAATGATTTGATTTGTGG
66 ATTGAAATATCTATATTCATCTAACCAAATATCAGCCACTATGGATTTAAGGATTTGATTTGTGG
* * * *
558 AGCATCAGAATCATCTCTCG-GTTAATGAGAAATTAATTCTGAAAAATTTAGGAAAATCGATATT
131 AGCATCAGAATCATATCTCGATTTAATGAGAAATTAATTCGGAAAAATATAGGAAAATCGATATT
*
622 AGAAGCGTGAAATGCCCATCAATCTTTTTGGCATTGAATTATATATTTCTTATGAGTATTCTGGC
196 AGAAGCGTGAAATGCCCATCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGGC
*
687 CAAAAATTGTGGAAAAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC
261 CAAAAATTGTGG--AAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCCAAATCGTGTACTAAC
752 CATCACGG
324 CATCACGG
* * * *
760 TTTTTAGCAAAAAATGCGTTCCGGTGCTCCGGTTCAGTTTTGCATGATTTTTTGCGTCAGGACTC
1 TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGTTCAGTTTTGCATGATTTTTTGCGCCAAGACTC
* * *
825 ATTGAAATATCTATATTTATCTAACCAAATCTCAGCCACTATGGATTTAAGGATTTGATTTGGGG
66 ATTGAAATATCTATATTCATCTAACCAAATATCAGCCACTATGGATTTAAGGATTTGATTTGTGG
* * *
890 AGCATCATAATCATATCTC--TTTAATAAGAAATTAATTCGG-AAAATACAGG-AAATCGATATT
131 AGCATCAGAATCATATCTCGATTTAATGAGAAATTAATTCGGAAAAATATAGGAAAATCGATATT
* * *
951 AGAAGCGTGAAAAGCCCATCATTCTTTTTGGCATTGAATTTTATATTTTTTATGAGTATTCTGGC
196 AGAAGCGTGAAATGCCCATCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGGC
*
1016 CAAAAATTGTGGAAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAGCCCAAATCGTGTACTAAC
261 CAAAAATTGTGG--AAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCCAAATCGTGTACTAAC
*
1081 CATAACGG
324 CATCACGG
* * * *
1089 CTTTT-GCTAAAAATGTGTTCCGGTACTCCGGTTCAGTTTTGCATGATTTTTTGCGGCAAGACTC
1 TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGTTCAGTTTTGCATGATTTTTTGCGCCAAGACTC
* *
1153 ATTGAAATATCTATATTCATCTAACCAAATATCAGTCACTATGGATTGAAGGATTTGATTTGTGG
66 ATTGAAATATCTATATTCATCTAACCAAATATCAGCCACTATGGATTTAAGGATTTGATTTGTGG
* * * *
1218 AGTATCAGAATCATGTCTCGATTTAATGAGAAATTAACTCGGAGAAATATAGGAAAATCGATATT
131 AGCATCAGAATCATATCTCGATTTAATGAGAAATTAATTCGGAAAAATATAGGAAAATCGATATT
*
1283 AGAAGCGTGAAATGCTCATCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGGC
196 AGAAGCGTGAAATGCCCATCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGGC
* * **
1348 CAAAAAAATGTGGAAAATTTTTGGGTCAATTTTTGCAATATTTTAGCTGAAATCGTGTACTAACC
261 C-AAAAATTGTGGAAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCCAAATCGTGTACTAACC
1413 ATCACGG
325 ATCACGG
*
1420 TTTTTGGCTAAAAATGCGTTCC-GTGCTCTGGTTCAGTTTCT-CATGATTTTTTTGCGCCAAGAC
1 TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGTTCAGTTT-TGCATGA-TTTTTTGCGCCAAGAC
* *
1483 TCATTGAAATATCTATATTCATCTAACCAAATTTCAGCCACTATGGATTTAAGGATTTGATTTGA
64 TCATTGAAATATCTATATTCATCTAACCAAATATCAGCCACTATGGATTTAAGGATTTGATTTGT
* * * *
1548 CGAGCATCAGATTCATATGTCGATTTAATGAGAAATTAATTCGGAAAAATATAGGAAAATCAATA
129 GGAGCATCAGAATCATATCTCGATTTAATGAGAAATTAATTCGGAAAAATATAGGAAAATCGATA
* * *
1613 TTAGAAGCGTGAAAAGCCCATCAAT-TTTTTTGCGGTTGAATTATATATTTTTTATGAGTATTCT
194 TTAGAAGCGTGAAATGCCCATCAATCTTTTTGGC-ATTGAATTATATATTTTTTATGAGTATTCT
* *
1677 CGCCTAAAATTGTGGAAAA
258 GGCCAAAAATTGTGGAAAA
1696 AATTTTGAGT
Statistics
Matches: 1141, Mismatches: 112, Indels: 28
0.89 0.09 0.02
Matches are distributed among these distances:
328 130 0.11
329 148 0.13
330 226 0.20
331 261 0.23
332 366 0.32
333 10 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (331 bp):
TTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGTTCAGTTTTGCATGATTTTTTGCGCCAAGACTC
ATTGAAATATCTATATTCATCTAACCAAATATCAGCCACTATGGATTTAAGGATTTGATTTGTGG
AGCATCAGAATCATATCTCGATTTAATGAGAAATTAATTCGGAAAAATATAGGAAAATCGATATT
AGAAGCGTGAAATGCCCATCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTCTGGC
CAAAAATTGTGGAAAATTTTTGGGTCAATTTTTGCAAAATTTTAGCCCAAATCGTGTACTAACCA
TCACGG
Found at i:1872 original size:24 final size:26
Alignment explanation
Indices: 1825--1880 Score: 89
Period size: 24 Copynumber: 2.2 Consensus size: 26
1815 CTCCAAAATT
1825 ATTTTTAAAAAAATAGAAAAAAACGG
1 ATTTTTAAAAAAATAGAAAAAAACGG
1851 ATTTTT-AAAAAATAG-AAAAAACGG
1 ATTTTTAAAAAAATAGAAAAAAACGG
*
1875 TTTTTT
1 ATTTTT
1881 CCGATGTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.48
25 9 0.31
26 6 0.21
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.32
Consensus pattern (26 bp):
ATTTTTAAAAAAATAGAAAAAAACGG
Found at i:2370 original size:20 final size:20
Alignment explanation
Indices: 2345--2382 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2335 ATAATGTGAA
2345 TTACTAAATACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
**
2365 TTACTAGCTACCGCCCCC
1 TTACTAAATACCGCCCCC
2383 CTCTTGGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.45, G:0.08, T:0.26
Consensus pattern (20 bp):
TTACTAAATACCGCCCCCTT
Done.