Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006458.1 Corchorus capsularis cultivar CVL-1 contig06479, 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: 3054
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Found at i:1419 original size:33 final size:33
Alignment explanation
Indices: 1377--1441 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1367 CCAGCCATGC
*
1377 GACTTGGAGAAGCCCGGCCAACACCGGCCACGT
1 GACTCGGAGAAGCCCGGCCAACACCGGCCACGT
*
1410 GACTCGGAGATGCCCGGCCAACACCGGCCACG
1 GACTCGGAGAAGCCCGGCCAACACCGGCCACG
1442 CGACATGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (33 bp):
GACTCGGAGAAGCCCGGCCAACACCGGCCACGT
Found at i:1460 original size:33 final size:33
Alignment explanation
Indices: 1370--1472 Score: 111
Period size: 33 Copynumber: 3.1 Consensus size: 33
1360 CTAGTGACCA
* * * *
1370 GCCATGCGACTTGGAGAAGCCCGGCCAACACCG
1 GCCACGCGACTCGGACATGCCCGGCCAACACCG
* *
1403 GCCACGTGACTCGGAGATGCCCGGCCAACACCG
1 GCCACGCGACTCGGACATGCCCGGCCAACACCG
*
1436 GCCACGCGACAT-GGACATGTCCGGCC-ACAACCG
1 GCCACGCGAC-TCGGACATGCCCGGCCAAC-ACCG
1469 GCCA
1 GCCA
1473 TCGCTTAGCG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
32 2 0.03
33 58 0.95
34 1 0.02
ACGTcount: A:0.23, C:0.39, G:0.29, T:0.09
Consensus pattern (33 bp):
GCCACGCGACTCGGACATGCCCGGCCAACACCG
Found at i:2390 original size:153 final size:153
Alignment explanation
Indices: 2058--3054 Score: 1389
Period size: 153 Copynumber: 6.5 Consensus size: 153
2048 TCGATTTCTT
* * * *
2058 AAAATAATTATAGTTAGGCCAGAAATAATGGAAAGAAAAGCTTTATGGTTTGCCAAATCA-AAGA
1 AAAATAATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAAT-AGAAGA
* * *
2122 CGATTTAAAACAGCACTAATGGGCCCCGAAAGTACCCGAAATAACAAGTGTTCTGAATGAGCT-T
65 CGATTCAAAACAGCACTAATGGGCCCC-AAAG-GCCCGAAATAACAAGTGTTCTGAATGAGCTAA
* *
2186 TAACTTGACAATGGACTAATCTCATC
128 AAACTTCACAATGGACTAATCTCATC
* * * **
2212 AAAATAATTATAGCTAGG-TAGAAACAAAGGAAAGAAAAGCTTTGTGGTTTGCCAAATAGAAGAC
1 AAAATAATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATAGAAGAC
*
2276 GATTCAAAACAGCACTAATGGGCCCCAAAGGCCCGAAATAAAAAGTGTTCTGAATGAGCTAAAAA
66 GATTCAAAACAGCACTAATGGGCCCCAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA
2341 CTTCACAATGGACTAATCTCATC
131 CTTCACAATGGACTAATCTCATC
* *
2364 AAAATAATTATAGTTAGGCCATAAACAATTGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
1 AAAATAATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATAGAAGAC
* * *
2429 GATTCAAAACAGCACTAATGAGCCCCAAATGGCCCGAAAATAACAAGCGTTCTGAATGAGTTAAA
66 GATTCAAAACAGCACTAATGGGCCCCAAA-GGCCCG-AAATAACAAGTGTTCTGAATGAGCTAAA
*
2494 AACTTCACAATGGACTAATTTCATAC
129 AACTTCACAATGGACTAATCTCAT-C
* * * *
2520 AAAATAATTATGGTTGGGACCATAAACAATTGAAACAAAAGCTTTGTGGTTTGCCAAATCA-AGG
1 AAAATAATTATAGTTAGG-CCATAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAAT-AGAAG
* *
2584 ACGATAT-AAAACAGCACTAATGGGCCTCGAACGGCCCGAAATAACAAGTGTTCTG-ATGAGCTA
64 ACGAT-TCAAAACAGCACTAATGGGCC-CCAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTA
2647 AAAACTTCACAATGGACTAATCTCATC
127 AAAACTTCACAATGGACTAATCTCATC
* * * *
2674 AAAATAATTATGGTTGGGCCATAAACAATTGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
1 AAAATAATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATAGAAGAC
* *
2739 GATTCAAAACAGCACTAATGAGACCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAA
66 GATTCAAAACAGCACTAATG-GGCCCCAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAA
*
2804 ACTTCACAATGGACTAATCTCACC
130 ACTTCACAATGGACTAATCTCATC
* * * * * *
2828 AAAATGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGCTTTGTTGG-TTG-CAAATTGAAGC
1 AAAATAATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCTTTG-TGGTTTGCCAAATAGAAGA
* * *
2891 CGATTCAAAACAGCTCTAATGGGCCTCTAAAGGCCCGAAATAACAAGTGTTCTGAACGAGCTAAA
65 CGATTCAAAACAGCACTAATGGGCC-CCAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAA
2956 AACTTCACAATGGACTAATCTCATC
129 AACTTCACAATGGACTAATCTCATC
* * * * *
2981 AAAATAATTATAGGTAGGCCAGAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAGTCGAAGAC
1 AAAATAATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATAGAAGAC
3046 GATTCAAAA
66 GATTCAAAA
Statistics
Matches: 764, Mismatches: 61, Indels: 36
0.89 0.07 0.04
Matches are distributed among these distances:
151 28 0.04
152 53 0.07
153 354 0.46
154 138 0.18
155 83 0.11
156 33 0.04
157 71 0.09
158 4 0.01
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (153 bp):
AAAATAATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCTTTGTGGTTTGCCAAATAGAAGAC
GATTCAAAACAGCACTAATGGGCCCCAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAAA
CTTCACAATGGACTAATCTCATC
Found at i:2696 original size:310 final size:304
Alignment explanation
Indices: 2058--3054 Score: 1423
Period size: 310 Copynumber: 3.2 Consensus size: 304
2048 TCGATTTCTT
* * * *
2058 AAAATAATTATAGTTAGGCCAGAAATAATGGAAAGAAAAGCTTTATGGTTTGCCAAATCAAAGAC
1 AAAATAATTATAGTTAGGCCAGAAACAATGGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
* * *
2123 GATTTAAAACAGCACTAATGGGCCCCGAAAGTACCCGAAATAACAAGTGTTCTGAATGAGCTT--
66 GATTCAAAACAGCACTAATGAGCCCC-AAAG-GCCCGAAATAACAAGTGTTCTGAATGAG-TTAA
* * * * **
2186 TAACTTGACAATGGACTAATCTCATCAAAATAATTATAGCTAGGTAGAAACAAAGGAAAGAAAAG
128 AAACTTCACAATGGACTAATCTCATCAAAATAATTATAGCTAGGCATAAACAATTGAAAGAAAAG
2251 CTTTGTGGTTTGCCAAATAGAAGACGATTCAAAACAGCACTAATGGGCC-CCAAAGGCCCGAAAT
193 CTTTGTGGTTTGCCAAAT--AAGACGATTCAAAACAGCACTAATGGGCCTCCAAAGGCCCGAAAT
*
2315 AAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
256 AACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
* *
2364 AAAATAATTATAGTTAGGCCATAAACAATTGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
1 AAAATAATTATAGTTAGGCCAGAAACAATGGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
*
2429 GATTCAAAACAGCACTAATGAGCCCCAAATGGCCCGAAAATAACAAGCGTTCTGAATGAGTTAAA
66 GATTCAAAACAGCACTAATGAGCCCCAAA-GGCCCG-AAATAACAAGTGTTCTGAATGAGTTAAA
* * * * *
2494 AACTTCACAATGGACTAATTTCATACAAAATAATTATGGTTGGGACCATAAACAATTGAAACAAA
129 AACTTCACAATGGACTAATCTCAT-CAAAATAATTATAGCTAGG--CATAAACAATTGAAAGAAA
* *
2559 AGCTTTGTGGTTTGCCAAATCAAGGACGATAT-AAAACAGCACTAATGGGCCTCGAACGGCCCGA
191 AGCTTTGTGGTTTGCCAAAT-AA-GACGAT-TCAAAACAGCACTAATGGGCCTCCAAAGGCCCGA
2623 AATAACAAGTGTTCTG-ATGAGCTAAAAACTTCACAATGGACTAATCTCATC
253 AATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
* * * *
2674 AAAATAATTATGGTTGGGCCATAAACAATTGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
1 AAAATAATTATAGTTAGGCCAGAAACAATGGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
* *
2739 GATTCAAAACAGCACTAATGAGACCCGAAAGGCCCGAAATAACAAGTGTTCTGAATGAGCTAAAA
66 GATTCAAAACAGCACTAATGAG-CCCCAAAGGCCCGAAATAACAAGTGTTCTGAATGAGTTAAAA
* * *
2804 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGCTAGGTCGTAAACAATTGAAAGAAAAGC
130 ACTTCACAATGGACTAATCTCATCAAAATAATTATAGCTAGG-CATAAACAATTGAAAGAAAAGC
* * *
2869 TTTGTTGG-TTG-CAAATTGAAGCCGATTCAAAACAGCTCTAATGGGCCTCTAAAGGCCCGAAAT
194 TTTG-TGGTTTGCCAAA-T-AAGACGATTCAAAACAGCACTAATGGGCCTCCAAAGGCCCGAAAT
*
2932 AACAAGTGTTCTGAACGAGCTAAAAACTTCACAATGGACTAATCTCATC
256 AACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
* * *
2981 AAAATAATTATAGGTAGGCCAGAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAGTCGAAGAC
1 AAAATAATTATAGTTAGGCCAGAAACAATGGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
3046 GATTCAAAA
66 GATTCAAAA
Statistics
Matches: 624, Mismatches: 52, Indels: 29
0.89 0.07 0.04
Matches are distributed among these distances:
305 10 0.02
306 160 0.26
307 153 0.25
308 34 0.05
309 50 0.08
310 185 0.30
311 32 0.05
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (304 bp):
AAAATAATTATAGTTAGGCCAGAAACAATGGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGAC
GATTCAAAACAGCACTAATGAGCCCCAAAGGCCCGAAATAACAAGTGTTCTGAATGAGTTAAAAA
CTTCACAATGGACTAATCTCATCAAAATAATTATAGCTAGGCATAAACAATTGAAAGAAAAGCTT
TGTGGTTTGCCAAATAAGACGATTCAAAACAGCACTAATGGGCCTCCAAAGGCCCGAAATAACAA
GTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATC
Found at i:2928 original size:463 final size:460
Alignment explanation
Indices: 2058--3048 Score: 1463
Period size: 463 Copynumber: 2.1 Consensus size: 460
2048 TCGATTTCTT
* * *
2058 AAAATAATTATAGTTAGGCCAGAAATAATGGAAAGAAAAGCTTTATGGTTTGCCAAATCAAAGAC
1 AAAATAATTATGGTTAGGCCAGAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCAAAGAC
* **
2123 GATTTAAAACAGCACTAATGGGCCCCGAAAGTACCCGAAATAACAAGTGTTCTGAATGAGCTTTA
66 GATATAAAACAGCACTAATGGGCCCCGAAAGTACCCGAAATAACAAGTGTTCTGAATGAGCTAAA
* * *
2188 ACTTGACAATGGACTAATCTCATCAAAATAATTATAGCTAGGTAGAAACAAAGGAAAGAAAAGCT
131 ACTTCACAATGGACTAATCTCATCAAAATAATTATAGCTAGGCAGAAACAAAGGAAACAAAAGCT
*
2253 TTGTGGTTTGCCAAATAGAAGACGATTCAAAACAGCACTAATGGGCCCCAAAGGCCCGAAATAAA
196 TTGTGGTTTGCCAAATAGAAGACGATTCAAAACAGCACTAATGGACCCCAAAGGCCCGAAATAAA
* *
2318 AAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCATCAAAATAATTATAGTTAGGC
261 AAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATAATTATAGCTAGGC
2383 CATAAACAATTGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAAT
326 CATAAACAATTGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAAT
* *
2448 GAGCCCCAAATGGCCCGAAAATAACAAGCGTTCTGAATGAGTTAAAAACTTCACAATGGACTAAT
391 GAGCCCCAAATGGCCCG-AAATAACAAGCGTTCTGAACGAGCTAAAAACTTCACAATGGACTAAT
*
2513 TTCATAC
455 CTCAT-C
* * * * *
2520 AAAATAATTATGGTTGGGACCATAAACAATTGAAACAAAAGCTTTGTGGTTTGCCAAATCAAGGA
1 AAAATAATTATGGTTAGG-CCAGAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCAAAGA
* * *
2585 CGATATAAAACAGCACTAATGGGCCTCGAACG-GCCCGAAATAACAAGTGTTCTG-ATGAGCTAA
65 CGATATAAAACAGCACTAATGGGCCCCGAAAGTACCCGAAATAACAAGTGTTCTGAATGAGCT-A
* * * * **
2648 AAACTTCACAATGGACTAATCTCATCAAAATAATTATGGTTGGGCCATAAACAATTGAAACAAAA
129 AAACTTCACAATGGACTAATCTCATCAAAATAATTATAGCTAGG-CAGAAACAAAGGAAACAAAA
* *
2713 GCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAATGAGACCCGAAAGGCCCGAAA
193 GCTTTGTGGTTTGCCAAATAGAAGACGATTCAAAACAGCACTAATG-GACCCCAAAGGCCCGAAA
* *
2778 TAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGCT
257 TAAAAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATAATTATAGCT
* * * * * *
2843 AGGTCGTAAACAATTGAAAGAAAAGCTTTGTTGG-TTG-CAAATTGAAGCCGATTCAAAACAGCT
322 AGGCCATAAACAATTGAAACAAAAGCTTTG-TGGTTTGCCAAATCGAAGACGATTCAAAACAGCA
* * *
2906 CTAATGGGCCTCTAAA-GGCCCGAAATAACAAGTGTTCTGAACGAGCTAAAAACTTCACAATGGA
386 CTAATGAGCC-CCAAATGGCCCGAAATAACAAGCGTTCTGAACGAGCTAAAAACTTCACAATGGA
2970 CTAATCTCATC
450 CTAATCTCATC
* *
2981 AAAATAATTATAGG-TAGGCCAGAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAGTCGAAGA
1 AAAATAATTAT-GGTTAGGCCAGAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCAAAGA
3045 CGAT
65 CGAT
3049 TCAAAA
Statistics
Matches: 473, Mismatches: 49, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
460 44 0.09
461 22 0.05
462 126 0.27
463 167 0.35
464 111 0.23
465 3 0.01
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (460 bp):
AAAATAATTATGGTTAGGCCAGAAACAATGGAAAGAAAAGCTTTGTGGTTTGCCAAATCAAAGAC
GATATAAAACAGCACTAATGGGCCCCGAAAGTACCCGAAATAACAAGTGTTCTGAATGAGCTAAA
ACTTCACAATGGACTAATCTCATCAAAATAATTATAGCTAGGCAGAAACAAAGGAAACAAAAGCT
TTGTGGTTTGCCAAATAGAAGACGATTCAAAACAGCACTAATGGACCCCAAAGGCCCGAAATAAA
AAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATAATTATAGCTAGGC
CATAAACAATTGAAACAAAAGCTTTGTGGTTTGCCAAATCGAAGACGATTCAAAACAGCACTAAT
GAGCCCCAAATGGCCCGAAATAACAAGCGTTCTGAACGAGCTAAAAACTTCACAATGGACTAATC
TCATC
Done.