Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013634.1 Corchorus capsularis cultivar CVL-1 contig13655, 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: 5507
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Found at i:645 original size:159 final size:159
Alignment explanation
Indices: 356--1375 Score: 1445
Period size: 159 Copynumber: 6.4 Consensus size: 159
346 CGTTCTTATC
* * * * * *
356 GAAGCATTTTTTGTGCAAGGAGTGCTGAAAAGTCTTGTATCGGTGTGAGAAGAGCTTGTTGGACA
1 GAAGCATTTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACA
421 GCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACATTGCGCGTTTGTGTGCAAA
66 GCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACATTGCGCGTTTGTGTGCAAA
* * * *
486 ATAT-GTTTCTTATTGAAATGCTCATTCCG
131 ACATCG-TTCTTATCGAAAGGCTCATTCCA
515 GAAGCGA-TTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGAC
1 GAAGC-ATTTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGAC
* * * **
579 AGCCCTGCGCAAAAACAAAACTCTCCTTGAAGCCCAAATCCTCTGCATTGCGCGTTTGTGTGCAA
65 AGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACATTGCGCGTTTGTGTGCAA
* *
644 AACATCGTTCTTAGCGAAAGGCTCATTCTA
130 AACATCGTTCTTATCGAAAGGCTCATTCCA
*
674 GAAGCATTTTTTGTGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACA
1 GAAGCATTTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACA
* * *
739 GCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAGCATTGTGCGTTCGTGTGCAAA
66 GCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACATTGCGCGTTTGTGTGCAAA
* *
804 ACATTGTTCTTATCGAAATGCTCATTCCA
131 ACATCGTTCTTATCGAAAGGCTCATTCCA
** ** *
833 GAAGCATTTTTTGCGCAACGAGTGCTCAAAACCCTTGTGTCAAAGTGAGATGAGCTTGTTGGATA
1 GAAGCATTTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACA
* *
898 GCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAATCCTCTACATTGCGCGTTTGTGTGCAAA
66 GCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACATTGCGCGTTTGTGTGCAAA
963 ACATCGTTCTTATCGAAAGGCTCATTCCA
131 ACATCGTTCTTATCGAAAGGCTCATTCCA
* * * ** * * *
992 GAAGTATGTTTTGTGCAACGAGTGCTCAAAAGTCTTGCATCAGAGTGAGAAGAGCTTTTTGGACA
1 GAAGCATTTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACA
* **
1057 GCCCTGTGCAAAAACAAAGCTCTTCTTGAAGCCCGGAGCCTCAACATTGCGCGTTTGTGTGCAAA
66 GCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACATTGCGCGTTTGTGTGCAAA
* * *
1122 ACATGGTTCATT-TCGAAATGCTCATTCCG
131 ACATCGTTC-TTATCGAAAGGCTCATTCCA
* * * * * * *
1151 GAAGTGA-TTTTTGCGCAACGAGTGCTCAGAAGCCTTTTGTTGGAGTAAGATGAGCTTGTTTGAC
1 GAAG-CATTTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGAC
* * * ** * *
1215 AGCCTTGTGCAAAAACAAAGCTCTCCTTGAAGCCAAAATCCTCAACATTGCATGTTTCTATGCAA
65 AGCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACATTGCGCGTTTGTGTGCAA
*
1280 AACATCGTTCTTAGCGAAAGGCTCATTCCA
130 AACATCGTTCTTATCGAAAGGCTCATTCCA
1310 GAAGCATTTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACA
1 GAAGCATTTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACA
1375 G
66 G
1376 TGATCGAGCC
Statistics
Matches: 759, Mismatches: 95, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
158 4 0.01
159 750 0.99
160 5 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (159 bp):
GAAGCATTTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACA
GCCCTGTGCAAAAACAAAGCTCTCCTTGAAGCCCAAAGCCTCAACATTGCGCGTTTGTGTGCAAA
ACATCGTTCTTATCGAAAGGCTCATTCCA
Found at i:3213 original size:5 final size:6
Alignment explanation
Indices: 3180--3211 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
3170 GGAGATTGTG
3180 TTCTATT TTCTTT TTCTTT TTCTTT TTCTTT T
1 TTCT-TT TTCTTT TTCTTT TTCTTT TTCTTT T
3212 CTATCAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:3766 original size:159 final size:159
Alignment explanation
Indices: 3505--5293 Score: 2392
Period size: 159 Copynumber: 11.3 Consensus size: 159
3495 GTCCTTCAAG
* *
3505 CCTCAGCATTGCGCGTTTGTGTGCAAAACATTGTTCTTATCGAAAGGCTCATTCCAGAAGCATTT
1 CCTCAACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTT
* * ** *
3570 TTTGCACAACGAGTGCTCAAAAGCCTTGTGTTAGAGTGAGATGAGCTTGTTGGACAACCCTGTGC
66 TTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTGC
*
3635 AAAAACAAAGCTCTCCTTTAAGCCCAAAT
131 AAAAACAAAGCTCTCCTTGAAGCCCAAAT
** * * *
3664 CCTCTGCATAGCGCGTTTGTGTGCAAAACATCGTTATTATCGAAAGGCTCATTTCAGAAGCATTT
1 CCTCAACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTT
* * * * * * *
3729 TTTGTGCAATGAGTGCTGAAAAGTGTTGTATCGGAGTGAGAAGAGCTTGTTGGACAGCCCTATGC
66 TTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTGC
*
3794 AAAAACAAAGCTCTCCTTGAAGCCCAAAG
131 AAAAACAAAGCTCTCCTTGAAGCCCAAAT
* * *
3823 CCTCAACATTTCGCGTTTGTGTGCAAAACAT-GTTTCTTATCGAAATGCTCATTCCGGAAGCGA-
1 CCTCAACATTGCGCGTTTGTGTGCAAAACATCG-TTCTTATCGAAAGGCTCATTCCAGAAGC-AT
*
3886 TTTTTGCGCAACGAGTTCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGT
64 TTTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGT
* *
3951 GCAAAAACAAAGCTCTCCTTGAAGCCTAAAG
129 GCAAAAACAAAGCTCTCCTTGAAGCCCAAAT
* * * *
3982 CCTCAACATTGCGCGTTTGTGTGCAAAACATGGTTCTTTTCGAAATGCTCATTCCGGAAGCGA-T
1 CCTCAACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGC-ATT
* * * * * * * * *
4046 TTTTGCGCAACGAGTGCTCAGAAGCCTTTTGTTGAAGTAAGATGAGCTTGTTTGACAGCCTTTTG
65 TTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTG
* * *
4111 CAAAAACAAACCTCTCCTTGAGGCCAAAAT
130 CAAAAACAAAGCTCTCCTTGAAGCCCAAAT
** * * ** *
4141 CCTCAACATTGCATGTTTCTATGCAAAACATCGTTCTTAGAGAAAGGCTCATTCCAGAAGCATTA
1 CCTCAACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTT
* * *
4206 TTTGCGCAACGAGTGCTCAAAACTCTTGTGTCGGAGTGAGATGAGGTTATTGGACAGCCCTGTGC
66 TTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTGC
*
4271 AAAAACAAAGCTCTCCTTCAAGCCCAAAT
131 AAAAACAAAGCTCTCCTTGAAGCCCAAAT
* *
4300 CCTCAACATTGCGCGTTTGTGTGCAAAAAAAT-TTTCTTATCGAAAGGCTCATTCCAGAAGCA-T
1 CCTCAACATTGCGCGTTTGTGTGC-AAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATT
* * *
4363 TTTTGCACAACGAGTGCTCAAAAGCCTTGTGTCAGAGTGAGATGAGCTTGTTGGACAGCCCTGTG
65 TTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTG
*
4428 CAAAAACAAAGCTCTCCTTGAAGCCAAAAT
130 CAAAAACAAAGCTCTCCTTGAAGCCCAAAT
* ** * * *
4458 CCTCAACATTACATGTTAGTGTGCAAAACATCGTCCTTATCGAAAGGCTCATTCCAGAAGAATTT
1 CCTCAACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTT
* * * * *
4523 TTT-TGCAACGAGTGCTCAAAAGTCTTGTATCTGAGTGAGAAGAGCTTGTTGGATAGCCCTGTGC
66 TTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTGC
* *
4587 AAAAACAAAGCTCTCATTGAAGCCCAAAA
131 AAAAACAAAGCTCTCCTTGAAGCCCAAAT
* ** * * * *
4616 CTTCAACATTGTTCGTTTGTGTGCAAAACATGGTTCTTATCGAAATGTTCATTCCGGAAGCGA-T
1 CCTCAACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGC-ATT
* * * *
4680 GTTTGCGCAACGAGTGCTTAAAAGTCTTGTGTCTGAGTGAGATGAGCTTGTTGGACAGCCCAGTG
65 TTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTG
* * *
4745 CAAAAACAAAGGTCACCTTCAAGCCCAAA-
130 CAAAAACAAAGCTCTCCTTGAAGCCCAAAT
* * * *
4774 CATCAGCATTGCGCGTTTGTGTGCAAAACATTGTTCTTATCGAAAGGCTCATTCCAAAAGCATTT
1 CCTCAACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTT
* * * *
4839 TTTGCGCAACGAATGCTCAAAAGCCTTGTGTCAGAGTGAGATGAGCTTGTTGGATAGCCCTGTGC
66 TTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTGC
4904 AAAAACAAAGCTCTCCTTGAAGCCCAAAT
131 AAAAACAAAGCTCTCCTTGAAGCCCAAAT
** *
4933 CCTCTGCATTGCGCGTTTGTGTGCAAAACATCATTCTTATCGAAAGGCTCATTCCAGAAGCATTT
1 CCTCAACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTT
* * * * *
4998 TTTGTGCAACGAGTGCTCAAAAGTTTTGTATCGGAGTGAGAAGAGCTTGTTGGATAGCCCTGTGC
66 TTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTGC
*
5063 AAAAACAAAGCTCTCCTTGAAGCCCAAAA
131 AAAAACAAAGCTCTCCTTGAAGCCCAAAT
* ** *
5092 CCTCAACATTGCGCGTTTGTGTGCAAAACATGGTTCTTATCGAAATTCTCATTCCGGAAGCGA-T
1 CCTCAACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGC-ATT
** ** *
5156 TTTTGCGCAACGAGTGCTCAAAACCCTTGTGTCAAAGTGAGATGAGCTTGTTGGATAGCCCTGTG
65 TTTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTG
*
5221 CAAATACAAAGCTCTCCTTGAAGCCCAAAT
130 CAAAAACAAAGCTCTCCTTGAAGCCCAAAT
* * *
5251 ACT-ATGCGTTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGA
1 CCTCA-ACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGA
5294 TGTGCAACGA
Statistics
Matches: 1427, Mismatches: 190, Indels: 26
0.87 0.12 0.02
Matches are distributed among these distances:
157 7 0.00
158 407 0.29
159 1004 0.70
160 9 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (159 bp):
CCTCAACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATCGAAAGGCTCATTCCAGAAGCATTT
TTTGCGCAACGAGTGCTCAAAAGTCTTGTGTCGGAGTGAGATGAGCTTGTTGGACAGCCCTGTGC
AAAAACAAAGCTCTCCTTGAAGCCCAAAT
Found at i:5404 original size:135 final size:135
Alignment explanation
Indices: 5162--5428 Score: 338
Period size: 135 Copynumber: 2.0 Consensus size: 135
5152 CGATTTTTGC
** * * * *
5162 GCAACGAGTGCTCAAAACCCTTGTGTCAAAGTGAGATGAGCTTGTTGGATAGCCCTGTGCAAATA
1 GCAACGAGTGCTCAAAACCCTTGCATCAAAGGGAGAAGAGCTTGTTGGACAGCCCTGTGCAAACA
* * *
5227 CAAAGCTCTCCTTGAAGCCCAAATACTATGCGTTGCGCGTTTGTGTGCAAAACATCGTTCTTATC
66 CAAAGCTCTCCTTGAAGCCCAAAGACTATACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATC
5292 GATGT
131 GATGT
** * * * * *
5297 GCAACGAGTGCTCAAAAGTCTTGCATCAGAGGGAGAAGAGCTTTTTGGACGGTCTTGTGCAAACA
1 GCAACGAGTGCTCAAAACCCTTGCATCAAAGGGAGAAGAGCTTGTTGGACAGCCCTGTGCAAACA
* * * *
5362 CAAAGCTCTCCTTGAAGCCTAAAGCCTCA-ACATTGCGCGTTTGTGTGCAAAACATGGTTCTTTT
66 CAAAGCTCTCCTTGAAGCCCAAAGACT-ATACATTGCGCGTTTGTGTGCAAAACATCGTTCTTAT
5426 CGA
130 CGA
5429 AATGCTCATT
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
135 110 0.99
136 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (135 bp):
GCAACGAGTGCTCAAAACCCTTGCATCAAAGGGAGAAGAGCTTGTTGGACAGCCCTGTGCAAACA
CAAAGCTCTCCTTGAAGCCCAAAGACTATACATTGCGCGTTTGTGTGCAAAACATCGTTCTTATC
GATGT
Done.