Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010664.1 Corchorus capsularis cultivar CVL-1 contig10685, 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: 2675
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Found at i:1086 original size:154 final size:154
Alignment explanation
Indices: 2--1917 Score: 2898
Period size: 154 Copynumber: 12.4 Consensus size: 154
1 C
2 TTAGGCCATAAACAATGGAAAGAAAAGCTTTAGTGGTTTGCCAAATCGAAGACGATTCAAAACAG
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTT-GTGGTTTGCCAAATCGAAGACGATTCAAAACAG
* *
67 CACTAATGGGCCCCGAAAGGCCCGAAACAAAAAGGGTTCTGAATGAGCTAAAAACTTCACAATGG
65 CACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
132 ACTAATCTCATCAAAATAA-TATAG
130 ACTAATCTCATCAAAATAATTATAG
* *
156 TTAGGCCATAAACAATGGAAAGAAAAGCTTTCTGGTTTGCCAAATCGAAGACGATTCAAAAGAGC
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGC
*
221 ACTAATGGGCCCCGAAAGGGACCGAAATAAAAAGTAGTTACTGAATGAGCTAAAAACTTCAACAA
66 ACTAATGGGCCCCGAAA-GGCCCGAAATAAAAAGT-GTT-CTGAATGAGCTAAAAACTTC-ACAA
*
286 TGGACTAATCTCATCAATATAATTATAG
127 TGGACTAATCTCATCAAAATAATTATAG
* * * *
314 TTAGGCCATAAACAATGGAAAG-AAGGCTTTGTGGTTTGTCATATCGAAGACGATACAAAACAGC
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGC
* * *
378 ACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTGTTCCGAATGAGCTAAAAGCTTCACAATGGA
66 ACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGA
443 CTAATCTCATCAAAATAATTATAG
131 CTAATCTCATCAAAATAATTATAG
* * * * *
467 TTAGGCCATAAACAATGGAAAGAAAAGCATTCGCGGTTTGTCATATCGAAGACGATACAAAACAG
1 TTAGGCCATAAACAATGGAAAGAAAAGC-TTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAG
* ** * * *
532 CACTAATGCGCCCCGAAAGGCTTGAAATAACAAGTGTTCTGAATGAGCTAAAAACCTCACAGTGG
65 CACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
* *
597 ACTAATCTCA-CCAAATGATTATAG
130 ACTAATCTCATCAAAATAATTATAG
* * * * *
621 TTATGCCATAAACAATGGAAAGAAAAGCTTTGCGGTTTGTCATATCGAAGACGATACAAAACAGC
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGC
*
686 ACTAATGCGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGA
66 ACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGA
751 CTAATCTCATCAAAATAATTATAG
131 CTAATCTCATCAAAATAATTATAG
* * * * *
775 TTAGGCCATAAAGAATGG-AAGAAAAGTTTTGTAGATTGCCAAATCGAAGACGATTCAAAAAAGC
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGC
839 ACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTTC-CAATGG
66 ACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAAC-TTCACAATGG
903 ACTAATCTCATCAAAATAATTATAG
130 ACTAATCTCATCAAAATAATTATAG
* * * * * * *
928 TTAGGTCGTAAACAATTGAAAGGAAAGCTTTGTTGG-TTGCCAAATTGAAGCCGATTTAAAACAG
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTG-TGGTTTGCCAAATCGAAGACGATTCAAAACAG
* *
992 CACTTATAGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
65 CACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
*
1057 ACTAATCTCATCAAAATAATTATAT
130 ACTAATCTCATCAAAATAATTATAG
*
1082 TTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACATC
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGC
*
1147 ACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTCAAAACTTCACAATGGA
66 ACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGA
1212 CTAATCTCATCAAAATAATTATAG
131 CTAATCTCATCAAAATAATTATAG
* * **
1236 TTAGGCCATAAACAATGGAAAGAAAAGTTTTGTAGTTTGCCAAATCGAAGACGATTCAAAGTAGC
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGC
* *
1301 ACTAATGGGCCCCGAAAGGGCCGAAATAAAAAGTGTACTGAATGAGCTAAAAACTTCACAATGGA
66 ACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGA
*
1366 CTAATCTCATCAATATAATTATAG
131 CTAATCTCATCAAAATAATTATAG
** * *
1390 GCAGGCCATAAACAACGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAGACGATTCAAAACAGC
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAG-
*
1455 CACTAATGGGCCCCGTAAAGGCCCGAAATAAAAAGTAGTTCTGAATGAGCTAAAAACTTACGCAA
65 CACTAATGGGCCCCG-AAAGGCCCGAAATAAAAAGT-GTTCTGAATGAGCTAAAAACTT-CACAA
*
1520 TGGACTAATCTCATC-AAATAATTATAT
127 TGGACTAATCTCATCAAAATAATTATAG
* * * * *
1547 TTAGGCCATAAACAATTGAAAGGAAAGCTTTGTTGG-TTGCCAAATTGAAGCCGATTTAAAACAG
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTG-TGGTTTGCCAAATCGAAGACGATTCAAAACAG
*
1611 CACTAATGGGCCCCGAAAGGCCCAAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
65 CACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGG
1676 ACTAATCTCATCAAAATAATTATAG
130 ACTAATCTCATCAAAATAATTATAG
* *
1701 TTAGGCCATAAACAATGGAAAGAAAACCTTTGTGGTTTTCCAAATCGAA-ACGATTCAAAACAGC
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGC
* * * *
1765 ACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTATTCTGAATAAGATAAAAACTTTACAATGGA
66 ACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGA
* *
1830 CTAATCTCACCAAAATGATTATAG
131 CTAATCTCATCAAAATAATTATAG
* * * * * *
1854 TTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTGG-TTGCCAAATTGAAGCCGATTTAAAACAG
1 TTAGGCCATAAACAATGGAAAGAAAAGCTTTG-TGGTTTGCCAAATCGAAGACGATTCAAAACAG
1918 GCTTTAGCTT
Statistics
Matches: 1609, Mismatches: 131, Indels: 44
0.90 0.07 0.02
Matches are distributed among these distances:
153 505 0.31
154 682 0.42
155 144 0.09
156 69 0.04
157 160 0.10
158 49 0.03
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (154 bp):
TTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGC
ACTAATGGGCCCCGAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGA
CTAATCTCATCAAAATAATTATAG
Done.