Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006204.1 Corchorus capsularis cultivar CVL-1 contig06223, 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: 3117
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Found at i:615 original size:18 final size:18
Alignment explanation
Indices: 594--631 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
584 GTTGAAGTCA
594 AGTTAATCAATAAAGTTG
1 AGTTAATCAATAAAGTTG
* *
612 AGTTGATTAATAAAGTTG
1 AGTTAATCAATAAAGTTG
630 AG
1 AG
632 GATTATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (18 bp):
AGTTAATCAATAAAGTTG
Found at i:1998 original size:154 final size:154
Alignment explanation
Indices: 1521--3117 Score: 2406
Period size: 154 Copynumber: 10.4 Consensus size: 154
1511 GAGGCCTCAT
* *
1521 TTCTGAATGAGCTAAAATCTTCACAATGGACTAAACTCATCAAAATAATTATAGTTAGGCCATAA
1 TTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAA
* *
1586 ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTGTAATGGTCC
66 ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGCC
*
1651 CCGAAAGGCCCGATATAACAAGTG
131 CCGAAAGGCCCGAAATAACAAGTG
*
1675 TTCTGAATGAGCTAAAAACTAT-ACAATGGACTAATCTCATCAAAATAATTATAGTTAGCCCATA
1 TTCTGAATGAGCTAAAAACT-TCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATA
* * * ** * *
1739 AAGAATGGAAAGAAAAGCATTATGGTTTTGTC-AAATCGAAGTCGATTCAAAACAGCACTAATGG
65 AACAATGGAAAGAAAAGCTTTGTGG-TTTG-CAAAATCGAAAACGATTCAAAGCAGCTCTAATGG
* *
1803 GCCCCGAAAGGCCCAAAATAACAAGTA
128 GCCCCGAAAGGCCCGAAATAACAAGTG
* * *
1830 TTCTGAATGAGCTAAAATCTTCACAATGGACTAAACTCATCAAAATAATTATATTTAGGCCATAA
1 TTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAA
* * * *
1895 ACAATGGAATGAAAAGCTTTGTGGATTGCAAAATCGAAAACGATTCAAAGCAGCACTAAGGGGCC
66 ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGCC
1960 CCGAAAGGCCCGAAATAACAAGTG
131 CCGAAAGGCCCGAAATAACAAGTG
* *
1984 TTCTGAATGAGCTAAAATCTTCACAATGGACTAATCTCTTC-AAATAATTATAGTTAGGCCATAA
1 TTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAA
*
2048 ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTTTAATGGG-C
66 ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGCC
*
2112 CCGAAAGGCCAGAAATAACAAGTG
131 CCGAAAGGCCCGAAATAACAAGTG
* * *
2136 GTCTGAATGAGCTAAAAACTAT-ACAATGGACTAATCTCACCAAAATAATTATAGTTAGGCCAAA
1 TTCTGAATGAGCTAAAAACT-TCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATA
* *
2200 AACAATGG-AAGAAAAGCTTTGTGATTTGCAAAATCGAAAACGATTCAAAGCAGCTCTGATGGGC
65 AACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGC
*
2264 CCCGAAAGGCCCGAAATATCAAGTG
130 CCCGAAAGGCCCGAAATAACAAGTG
*
2289 TTCTGAATGTGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAA
1 TTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAA
* ** * *
2354 ACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCC
66 ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGCC
2419 CCGAAAGGCCCGAAATAACAAGTG
131 CCGAAAGGCCCGAAATAACAAGTG
* *
2443 TTATGAATGAGACT-AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGCCCATA
1 TTCTGAATGAG-CTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATA
* ** * ** * *
2507 AAGAATACAAAGAAAAGCATTGTGGTTTTGTC-AAATCGAAGCCGATTCAAAACAGCACTAATGG
65 AACAATGGAAAGAAAAGCTTTGTGG-TTTG-CAAAATCGAAAACGATTCAAAGCAGCTCTAATGG
* *
2571 GTCCCGAAAGACCCGAAATAACAAGTG
128 GCCCCGAAAGGCCCGAAATAACAAGTG
*
2598 TTCGGAATGAGCTAAAAATCTTCACAATGGACTAATCTCATC-AAATAATTATAGTTAGGCCATA
1 TTCTGAATGAGCTAAAAA-CTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATA
*
2662 AACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAACTCTAATGGGC
65 AACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGC
*
2727 CCCGAAATGCCCGAAATAACAAGTG
130 CCCGAAAGGCCCGAAATAACAAGTG
* *
2752 ATCTGAATGAGCTAAAAACTAT-ACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCAAA
1 TTCTGAATGAGCTAAAAACT-TCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATA
* *
2816 AACAATGGAAAGAAAAGCTTTGTGATTTGCAAAATCGAAAATGATTCAAAGCAGCTCTAATGGGC
65 AACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGC
*
2881 CCCGATAGGCCCGAAATAACAAGTG
130 CCCGAAAGGCCCGAAATAACAAGTG
* *
2906 ATCTGAATGAGCTAAAAACTAT-ACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCAAA
1 TTCTGAATGAGCTAAAAACT-TCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATA
* * *
2970 AACAATGGAAAGAAAAGCATTGTGGTTTGCAAAATCGAAAATGATTCAAAGCAGCTTTAATGGGC
65 AACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGC
* *
3035 TCCGAACGGCCCGAAATAACAAGTG
130 CCCGAAAGGCCCGAAATAACAAGTG
* *
3060 TTCTAAATGTGCTAAAAAACTTCACAAGTGGACTAATCTCATCAAAATAATTATAGTT
1 TTCTGAATGAGCT-AAAAACTTCACAA-TGGACTAATCTCATCAAAATAATTATAGTT
Statistics
Matches: 1320, Mismatches: 102, Indels: 40
0.90 0.07 0.03
Matches are distributed among these distances:
152 112 0.08
153 222 0.17
154 668 0.51
155 263 0.20
156 55 0.04
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (154 bp):
TTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAA
ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGCC
CCGAAAGGCCCGAAATAACAAGTG
Found at i:2667 original size:309 final size:308
Alignment explanation
Indices: 1521--3117 Score: 2406
Period size: 309 Copynumber: 5.2 Consensus size: 308
1511 GAGGCCTCAT
* *
1521 TTCTGAATGAGCTAAAATCTTCACAATGGACTAAACTCATCAAAATAATTATAGTTAGGCCATAA
1 TTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAA
* *
1586 ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTGTAATGGTCC
66 ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGCC
*
1651 CCGAAAGGCCCGATATAACAAGTGTTCTGAATGAGCTAAAAACTAT-ACAATGGACTAATCTCAT
131 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACT-TCACAATGGACTAATCTCAT
* * * *
1715 CAAAATAATTATAGTTAGCCCATAAAGAATGGAAAGAAAAGCATTATGGTTTTGTC-AAATCGAA
195 CAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGG-TTTG-CAAAATCGAA
** * * * *
1779 GTCGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTA
258 AACGATTCAAAGCAGCTCTAATGGGCCCCGAAAGGCCCGAAATAACAAGTG
* * *
1830 TTCTGAATGAGCTAAAATCTTCACAATGGACTAAACTCATCAAAATAATTATATTTAGGCCATAA
1 TTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAA
* * * *
1895 ACAATGGAATGAAAAGCTTTGTGGATTGCAAAATCGAAAACGATTCAAAGCAGCACTAAGGGGCC
66 ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGCC
* *
1960 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAATCTTCACAATGGACTAATCTCTTC
131 CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
2025 -AAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAAC
196 AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAAC
* *
2089 GATTCAAAGCAGCTTTAATGGG-CCCGAAAGGCCAGAAATAACAAGTG
261 GATTCAAAGCAGCTCTAATGGGCCCCGAAAGGCCCGAAATAACAAGTG
* * *
2136 GTCTGAATGAGCTAAAAACTAT-ACAATGGACTAATCTCACCAAAATAATTATAGTTAGGCCAAA
1 TTCTGAATGAGCTAAAAACT-TCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATA
* *
2200 AACAATGG-AAGAAAAGCTTTGTGATTTGCAAAATCGAAAACGATTCAAAGCAGCTCTGATGGGC
65 AACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGC
* *
2264 CCCGAAAGGCCCGAAATATCAAGTGTTCTGAATGTGCTAAAAACTTCACAATGGACTAATCTCAT
130 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCAT
* **
2329 CAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGC
195 CAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAA
* *
2394 CGATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAATAACAAGTG
260 CGATTCAAAGCAGCTCTAATGGGCCCCGAAAGGCCCGAAATAACAAGTG
* *
2443 TTATGAATGAGACT-AAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGCCCATA
1 TTCTGAATGAG-CTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATA
* ** * ** * *
2507 AAGAATACAAAGAAAAGCATTGTGGTTTTGTC-AAATCGAAGCCGATTCAAAACAGCACTAATGG
65 AACAATGGAAAGAAAAGCTTTGTGG-TTTG-CAAAATCGAAAACGATTCAAAGCAGCTCTAATGG
* * *
2571 GTCCCGAAAGACCCGAAATAACAAGTGTTCGGAATGAGCTAAAAATCTTCACAATGGACTAATCT
128 GCCCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA-CTTCACAATGGACTAATCT
2636 CATC-AAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGA
192 CATCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGA
* *
2700 AAACGATTCAAAGCAACTCTAATGGGCCCCGAAATGCCCGAAATAACAAGTG
257 AAACGATTCAAAGCAGCTCTAATGGGCCCCGAAAGGCCCGAAATAACAAGTG
* *
2752 ATCTGAATGAGCTAAAAACTAT-ACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCAAA
1 TTCTGAATGAGCTAAAAACT-TCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATA
* *
2816 AACAATGGAAAGAAAAGCTTTGTGATTTGCAAAATCGAAAATGATTCAAAGCAGCTCTAATGGGC
65 AACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGC
* *
2881 CCCGATAGGCCCGAAATAACAAGTGATCTGAATGAGCTAAAAACTAT-ACAATGGACTAATCTCA
130 CCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACT-TCACAATGGACTAATCTCA
* *
2945 TCAAAATAATTATAGTTAGGCCAAAAACAATGGAAAGAAAAGCATTGTGGTTTGCAAAATCGAAA
194 TCAAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAA
* * * *
3010 ATGATTCAAAGCAGCTTTAATGGGCTCCGAACGGCCCGAAATAACAAGTG
259 ACGATTCAAAGCAGCTCTAATGGGCCCCGAAAGGCCCGAAATAACAAGTG
* *
3060 TTCTAAATGTGCTAAAAAACTTCACAAGTGGACTAATCTCATCAAAATAATTATAGTT
1 TTCTGAATGAGCT-AAAAACTTCACAA-TGGACTAATCTCATCAAAATAATTATAGTT
Statistics
Matches: 1167, Mismatches: 102, Indels: 37
0.89 0.08 0.03
Matches are distributed among these distances:
305 112 0.10
306 168 0.14
307 138 0.12
308 249 0.21
309 445 0.38
310 55 0.05
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (308 bp):
TTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGCCATAA
ACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAACGATTCAAAGCAGCTCTAATGGGCC
CCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
AAAATAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGTGGTTTGCAAAATCGAAAAC
GATTCAAAGCAGCTCTAATGGGCCCCGAAAGGCCCGAAATAACAAGTG
Done.