Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006645.1 Corchorus capsularis cultivar CVL-1 contig06666, 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, 660
Length: 1101
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Found at i:464 original size:154 final size:154
Alignment explanation
Indices: 1--1101 Score: 1814
Period size: 154 Copynumber: 7.1 Consensus size: 154
* * * *
1 TCGGGCCTTTCGGGACCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAAGCGCAAAGCTT
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCACAAAGCTT
*
66 TTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
66 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
131 AGCTCATTCAGAACACTTGTTATT
131 AGCTCATTCAGAACACTTGTTATT
*
155 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGACTTCGATTTGGGAAACCATAAAGC-
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGG-CTTCGATTTGGGAAACCACAAAGCT
219 TTTC-TTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
65 TTTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTT
283 TAGCTCATTCAGAACACTTGTTATT
130 TAGCTCATTCAGAACACTTGTTATT
* *
308 TCGGTCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCATAAAGCTT
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCACAAAGCTT
373 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
66 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
*
438 CGCTCATTCAGAACACTTGTTATT
131 AGCTCATTCAGAACACTTGTTATT
* * * *
462 TCGGGTCTTTCGGGACCCGTTAGTGCTGTTTTGAATCGGCTTCGATTTGGCAAACCACAAAGCTT
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCACAAAGCTT
* *
527 TTCTTTTAATTGTTTACGACCTAACTATAATCATTTTGGTGAGATTAGTCCA-TCGTGAAGTTTT
66 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT-GTGAAGTTTT
*
591 TAGCTCATTCAGAACACTTGTTTTT
130 TAGCTCATTCAGAACACTTGTTATT
* *
616 TCGGACCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCATAAAGCTT
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCACAAAGCTT
* *
681 TTCTTTCAATTGTTTACGGCCTAACTATTATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTT
66 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
746 AGCTCATTCAGAACACTTGTTATT
131 AGCTCATTCAGAACACTTGTTATT
* * * * *
770 TCGGGCCATTC-GGGCCCATTAGTGCTGTTTTCAATCAGCTTCGATTTGGCAAACCACATAGCTT
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCACAAAGCTT
* * *
834 TTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGGTGAGATTAGTCCATTGTGAAGTTTTT
66 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
*
899 AGCTCATTCAGAACACTTGTTTTT
131 AGCTCATTCAGAACACTTGTTATT
* * *
923 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAAGCACAATGCTT
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCACAAAGCTT
*
988 TTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTCGAGATTAGTCCACTGTGAAGTTTT
66 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGT-GAGATTAGTCCACTGTGAAG-TTT
*
1053 TTCGCTCATTCAGAACACTTGTTATT
129 TTAGCTCATTCAGAACACTTGTTATT
* *
1079 TCGGGTCTTTCGGGGCCCGTTAG
1 TCGGGCCTTTCGGGGCCCATTAG
Statistics
Matches: 884, Mismatches: 55, Indels: 14
0.93 0.06 0.01
Matches are distributed among these distances:
152 24 0.03
153 270 0.31
154 502 0.57
155 40 0.05
156 48 0.05
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (154 bp):
TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCACAAAGCTT
TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
AGCTCATTCAGAACACTTGTTATT
Found at i:872 original size:461 final size:461
Alignment explanation
Indices: 1--1101 Score: 1866
Period size: 461 Copynumber: 2.4 Consensus size: 461
*
1 TCGGGCCTTTCGGGACCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAAGCGCAAAGCTT
1 TCGGGCCTTTCGGGACCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAAGCACAAAGCTT
66 TTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
66 TTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
131 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGAC
131 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGAC
196 TTCGATTTGGGAAACCATAAAGCTTTCTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGA
196 TTCGATTTGGGAAACCATAAAGCTTTCTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGA
* *
261 GATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGTCCTTTCGGGGCCC
261 GATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCATTCGGGGCCC
* * * *
326 ATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCATAAAGCTTTTCTTTCAATTGTTTACG
326 ATTAGTGCTGTTTTCAATCAGCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACG
* *
391 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTCGCTCATTCAGAACACTT
391 ACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTT
456 GTTATT
456 GTTATT
* * * * *
462 TCGGGTCTTTCGGGACCCGTTAGTGCTGTTTTGAATCGGCTTCGATTTGGCAAACCACAAAGCTT
1 TCGGGCCTTTCGGGACCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAAGCACAAAGCTT
* * *
527 TTCTTTTAATTGTTTACGACCTAACTATAATCATTTTGGTGAGATTAGTCCA-TCGTGAAGTTTT
66 TTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT-GTGAAGTTTT
* *
591 TAGCTCATTCAGAACACTTGTTTTTTCGGACCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGG-
130 TAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGA
*
655 CTTCGATTTGGGAAACCATAAAGCTTTTCTTTCAATTGTTTACGGCCTAACTATTATCATTTTGG
195 CTTCGATTTGGGAAACCATAAAGC-TTTC-TTCAATTGTTTACGGCCTAACTATAATCATTTTGG
*
720 TGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCATTC-GGG
258 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCATTCGGGG
*
784 CCCATTAGTGCTGTTTTCAATCAGCTTCGATTTGGCAAACCACATAGCTTTTCTTTCAATTGTTT
323 CCCATTAGTGCTGTTTTCAATCAGCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTT
* *
849 ACGACCTAACTATAATTATTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACA
388 ACGACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACA
*
914 CTTGTTTTT
453 CTTGTTATT
* *
923 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAAGCACAATGCTT
1 TCGGGCCTTTCGGGACCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAAGCACAAAGCTT
988 TTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTCGAGATTAGTCCACTGTGAAGTTTT
66 TTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGT-GAGATTAGTCCACTGTGAAG-TTT
* * *
1053 TTCGCTCATTCAGAACACTTGTTATTTCGGGTCTTTCGGGGCCCGTTAG
129 TTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAG
Statistics
Matches: 594, Mismatches: 40, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
460 25 0.04
461 411 0.69
462 110 0.19
463 48 0.08
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (461 bp):
TCGGGCCTTTCGGGACCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAAGCACAAAGCTT
TTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGAC
TTCGATTTGGGAAACCATAAAGCTTTCTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGA
GATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTCGGGCCATTCGGGGCCC
ATTAGTGCTGTTTTCAATCAGCTTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACG
ACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTT
GTTATT
Found at i:949 original size:307 final size:308
Alignment explanation
Indices: 1--1101 Score: 1848
Period size: 307 Copynumber: 3.6 Consensus size: 308
* * *
1 TCGGGCCTTTCGGGACCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAAGCGCAAAGCTT
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAACCACAAAGCTT
*
66 TTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
66 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
131 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGAC
131 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGG-C
* * *
196 TTCGATTTGGGAAACCATAAAGC-TTTC-TTCAATTGTTTACGGCCTAACTATAATCATTTTGGT
195 TTCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGGT
* *
259 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATT
260 GAGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTTTT
* * *
308 TCGGTCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCATAAAGCTT
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAACCACAAAGCTT
373 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
66 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* * * *
438 CGCTCATTCAGAACACTTGTTATTTCGGGTCTTTCGGGACCCGTTAGTGCTGTTTTGAATCGGCT
131 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCT
*
503 TCGATTTGGCAAACCACAAAGCTTTTCTTTTAATTGTTTACGACCTAACTATAATCATTTTGGTG
196 TCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGGTG
*
568 AGATTAGTCCATCGTGAAGTTTTTAGCTCATTCAGAACACTTGTTTTT
261 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTTTT
* * *
616 TCGGACCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGATTTGGGAAACCATAAAGCTT
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAACCACAAAGCTT
* *
681 TTCTTTCAATTGTTTACGGCCTAACTATTATCATTTTGGTGAGATTAGTCCATTGTGAAGTTTTT
66 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
* * *
746 AGCTCATTCAGAACACTTGTTATTTCGGGCCATTC-GGGCCCATTAGTGCTGTTTTCAATCAGCT
131 AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCT
* *
810 TCGATTTGGCAAACCACATAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATTATTTTGGTG
196 TCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGGTG
875 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTTTT
261 AGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTTTT
* *
923 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAAGCACAATGCTT
1 TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAACCACAAAGCTT
*
988 TTCTTTCAATTTTTTACGGCCTAACTATAATCATTTTGGTCGAGATTAGTCCACTGTGAAGTTTT
66 TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGT-GAGATTAGTCCACTGTGAAG-TTT
* * *
1053 TTCGCTCATTCAGAACACTTGTTATTTCGGGTCTTTCGGGGCCCGTTAG
129 TTAGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAG
Statistics
Matches: 745, Mismatches: 44, Indels: 7
0.94 0.06 0.01
Matches are distributed among these distances:
306 22 0.03
307 418 0.56
308 258 0.35
309 37 0.05
310 10 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (308 bp):
TCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCTTCGAGTTGGGAAACCACAAAGCTT
TTCTTTCAATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
AGCTCATTCAGAACACTTGTTATTTCGGGCCTTTCGGGGCCCATTAGTGCTGTTTTGAATCGGCT
TCGATTTGGCAAACCACAAAGCTTTTCTTTCAATTGTTTACGACCTAACTATAATCATTTTGGTG
AGATTAGTCCATTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTTTT
Done.