Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008764.1 Corchorus capsularis cultivar CVL-1 contig08785, 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: 2781
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Found at i:2266 original size:640 final size:643
Alignment explanation
Indices: 796--2745 Score: 3132
Period size: 640 Copynumber: 3.0 Consensus size: 643
786 AAAAAATTTA
* *
796 TTAGCCGAAATCGTGTACTAACCATTACGGTATTGGGGCT--AAACGCGTTTCAGGGTCTCGGCT
1 TTAGCCGAAATCGTGTACTAACCATTACGGTTTTGGGGCTAAAAACGCGTTTCAGGGTCCCGGCT
* *
859 CTGTTTTGCATGATTTTTTCCAAAAAAACTCATTGGAATATCAATATTCATCTAACAAAATCTCA
66 CTGGTTTGCATGATTTTTTCCAGAAAAACTCATTGGAATATCAATATTCATCTAACAAAATCTCA
* *
924 GCCGCGTTGGATTT-AGGTATTTGTTTTTCCGAGCATCTCAATCTTGTTTCGTTTTAATTAGAAA
131 GCCACGTTGGATTTAAGG-ATTTGTTTTTCCGAGCATCTGAATCTTGTTTCGTTTTAATTAGAAA
*
988 TAAATTCGGTCAAAAAATGGGAAAACGATATTAGAAACGTGGAAAACCCTTAAACTTTTTTGGGT
195 TAAATTCGGACAAAAAATGGGAAAACGATATTAGAAACGTGGAAAACCCTTAAACTTTTTTGGGT
*
1053 TCAATTATATACTTTTTCTGACTATTGTGGCAAAAAAATTGAGTTAAACTTTTTTCGGGTCAGTG
260 TCAATTATATAATTTTTCTGACTATTGTGGCAAAAAAATTGAGTTAAAC-TTTTTCGGGTCAGTG
*
1118 ATTTCAACATTTTAGCCGATATCGTGTACTAACCATCACGGTGTTTTTTGCTAAAAACGCGTTCT
324 ATTTCAACATTTTAGCCGAAATCGTGTACTAACCATCACGGT-TTTTTTGCTAAAAA------CT
1183 GGGCCCTGACTCAGTTTTGCATGATTTTTGGCATAAAGACTTCTTGAAATATCTATATTCATCAA
382 --G-CCTGACTCAGTTTTGCATGATTTTTGGCATAAAGACTTCTTGAAATATCTATATTCATCAA
* *
1248 ACCAAATCTGAGGCACAATAGAAATAAATATTTTTTTTACGAGCATCTGAATATTGTATTGATTC
444 ACCAAATCTGAGGCACATTAGAAATAAATATTTTTTTTACGAGCATCTGAATATTGTTTTGATTC
* * * *
1313 AATTAGAAATTAATTCAGAAAAAATATGAAAAAACGATATTAGAAACATGAAAAACCCATCAATA
509 AATTAGAAATTAATTCAGAAAAAACATGAAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATA
*
1378 TTTTTTTAGATGAATTATGTATTTTTTTTATTTTTGTGGCAAAAAAATTTATGAAAAATTTTTCG
574 TTTTTTTAGATGAATTATGTA---TTTTTATTTTTGTGGC-AAAAAATTTATTAAAAATTTTTCG
*
1443 AGTCAGTTT
635 AGTCAGTTC
* * *
1452 TTAACCGAAATCGTCTACTAACCATTACTGTTTTGGGGCTAAAAACGCGTTTCAGGGTCCCGGCT
1 TTAGCCGAAATCGTGTACTAACCATTACGGTTTTGGGGCTAAAAACGCGTTTCAGGGTCCCGGCT
*
1517 CT-GTTTGGCATGGTTTTTTCCAGAAAAACTCATTGGAATATCAATATTCATCTAACAAAATCTC
66 CTGGTTT-GCATGATTTTTTCCAGAAAAACTCATTGGAATATCAATATTCATCTAACAAAATCTC
*
1581 AGCCACGTTGGATTTAAGGATTTGTTTTTCCGAGTATCTGAATCTTGTTTCGTTTTAATTAGAAA
130 AGCCACGTTGGATTTAAGGATTTGTTTTTCCGAGCATCTGAATCTTGTTTCGTTTTAATTAGAAA
1646 TAAATTCGGACAAAAAATGGGAAAACGATATTAGAAACGTGGAAAACCCTTAAACTTTTTTGGGT
195 TAAATTCGGACAAAAAATGGGAAAACGATATTAGAAACGTGGAAAACCCTTAAACTTTTTTGGGT
* *
1711 TCAATTATATAATTTTTATGACTATTGTGGCAAAAAAATTGAGTCAAACTTTTTCGGGTCAGTGA
260 TCAATTATATAATTTTTCTGACTATTGTGGCAAAAAAATTGAGTTAAACTTTTTCGGGTCAGTGA
1776 TTTCAACATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTTTTGCTAAAAA-T-CCTGA
325 TTTCAACATTTTAGCCGAAATCGTGTACTAACCATCACGG--TTTTTTTGCTAAAAACTGCCTGA
*
1839 CTCAGTTTTGCATGATTTTTGGCATAAAGACTGCTTGAAATATCTATATTCATCAAACCAAATCT
388 CTCAGTTTTGCATGATTTTTGGCATAAAGACTTCTTGAAATATCTATATTCATCAAACCAAATCT
*
1904 GAGGCACATTAGAAATAAATATTTTTTTTACGAGAATCTGAATATTGTTTTGATTCAATTAGAAA
453 GAGGCACATTAGAAATAAATATTTTTTTTACGAGCATCTGAATATTGTTTTGATTCAATTAGAAA
*
1969 TTAATTCAGAAAAAACATGAAAAAACGATATTTGAAGCGTGAAAAGCCCATCAAT-TTTTTTTAG
518 TTAATTCAGAAAAAACATGAAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATATTTTTTTAG
2033 ATGAATTATGTA-TTTT-TTTTTGTGGCAAAAAATTTATTAAAAATTTTTCGAGTCAGTTC
583 ATGAATTATGTATTTTTATTTTTGTGGCAAAAAATTTATTAAAAATTTTTCGAGTCAGTTC
*
2092 TTAGCCGAAATCGTGTACTAACCATCACGGTTTTGGGGCTAAAAACGCGTTTCAGGGTCCCGGCT
1 TTAGCCGAAATCGTGTACTAACCATTACGGTTTTGGGGCTAAAAACGCGTTTCAGGGTCCCGGCT
*
2157 CTGGTTTGCATGATTTTTTCCAGAAAAACTCATTGGAATATAAATATTCATCTAACAAAATCTCA
66 CTGGTTTGCATGATTTTTTCCAGAAAAACTCATTGGAATATCAATATTCATCTAACAAAATCTCA
* * *
2222 GTCACGTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
131 GCCACGTTGGATTTAAGGATTTGTTTTTCCGAGCATCTGAATCTTGTTTCGTTTTAATTAGAAAT
* * * * *
2287 ATATTCAGACAAAAAACGAGAAAACGATATTAGAAGCGTGGAAAACCCTTAAACTTTTTTGGGTT
196 AAATTCGGACAAAAAATGGGAAAACGATATTAGAAACGTGGAAAACCCTTAAACTTTTTTGGGTT
*
2352 CAATTATATATTTTTTCTGACTATTGTGGCAAAAAAAATTGAGTTAAACTTTTTCGGGTCAGTGA
261 CAATTATATAATTTTTCTGACTATTGTGGC-AAAAAAATTGAGTTAAACTTTTTCGGGTCAGTGA
2417 TTTCAACATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTTGCTAAAAACGCGTTCTAG
325 TTTCAACATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTTGCTAAAAA------CT--
2481 GCCCTGACTCAGTTTTGCATGATTTTTGGCATAAAGACTTCTTGAAATATCTATATTCATCAAAC
382 G-CCTGACTCAGTTTTGCATGATTTTTGGCATAAAGACTTCTTGAAATATCTATATTCATCAAAC
* *
2546 CAAATCTGAGGCACATTAGAGATACATA-TTTTTTTACGAGCATCTGAATATTGTTTTGATTCAA
446 CAAATCTGAGGCACATTAGAAATAAATATTTTTTTTACGAGCATCTGAATATTGTTTTGATTCAA
*
2610 TTAGAAATTAATTCAGAAAAAACATG-AAAAACGATATTAGAAGAGTGAAAAGCCCATCAATATT
511 TTAGAAATTAATTCAGAAAAAACATGAAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATATT
*
2674 TTTTTAGATGAATTATGTATTTTTTTTTTATTTTTGTGGCAAAAAATTTATTAAAAATTTTTCTA
576 TTTTTAGATGAATTATGTA-----TTTTTATTTTTGTGGCAAAAAATTTATTAAAAATTTTTCGA
2739 GTCAGTT
636 GTCAGTT
2746 TGTACTAACC
Statistics
Matches: 1215, Mismatches: 52, Indels: 55
0.92 0.04 0.04
Matches are distributed among these distances:
638 14 0.01
640 299 0.25
641 87 0.07
642 4 0.00
645 1 0.00
646 21 0.02
647 214 0.18
648 82 0.07
649 88 0.07
651 1 0.00
654 4 0.00
655 41 0.03
656 36 0.03
657 58 0.05
658 261 0.21
659 4 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (643 bp):
TTAGCCGAAATCGTGTACTAACCATTACGGTTTTGGGGCTAAAAACGCGTTTCAGGGTCCCGGCT
CTGGTTTGCATGATTTTTTCCAGAAAAACTCATTGGAATATCAATATTCATCTAACAAAATCTCA
GCCACGTTGGATTTAAGGATTTGTTTTTCCGAGCATCTGAATCTTGTTTCGTTTTAATTAGAAAT
AAATTCGGACAAAAAATGGGAAAACGATATTAGAAACGTGGAAAACCCTTAAACTTTTTTGGGTT
CAATTATATAATTTTTCTGACTATTGTGGCAAAAAAATTGAGTTAAACTTTTTCGGGTCAGTGAT
TTCAACATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTTGCTAAAAACTGCCTGACTC
AGTTTTGCATGATTTTTGGCATAAAGACTTCTTGAAATATCTATATTCATCAAACCAAATCTGAG
GCACATTAGAAATAAATATTTTTTTTACGAGCATCTGAATATTGTTTTGATTCAATTAGAAATTA
ATTCAGAAAAAACATGAAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATATTTTTTTAGATG
AATTATGTATTTTTATTTTTGTGGCAAAAAATTTATTAAAAATTTTTCGAGTCAGTTC
Done.