Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011562.1 Corchorus capsularis cultivar CVL-1 contig11583, 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: 6994
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Found at i:582 original size:33 final size:33
Alignment explanation
Indices: 540--648 Score: 148
Period size: 33 Copynumber: 3.3 Consensus size: 33
530 GTCATTTAGA
540 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
1 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
* * * * * *
573 TGTTGTTTGCAATGACATTAAATCT-GTTTTAG
1 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
605 ATGTTGTTTGCGATGATACTAAACCTAATTTGAG
1 -TGTTGTTTGCGATGATACTAAACCTAATTTGAG
639 TGTTGTTTGC
1 TGTTGTTTGC
649 AATAAAACTA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
32 5 0.08
33 52 0.84
34 5 0.08
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (33 bp):
TGTTGTTTGCGATGATACTAAACCTAATTTGAG
Found at i:616 original size:66 final size:66
Alignment explanation
Indices: 534--673 Score: 244
Period size: 66 Copynumber: 2.1 Consensus size: 66
524 CAAAGAGTCA
* * *
534 TTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATGACATTAAATCTG
1 TTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAATCTG
599 T
66 T
600 TTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAATCTG
1 TTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAATCTG
665 T
66 T
*
666 TTTGGATG
1 TTTAGATG
674 CTAATTGTGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (66 bp):
TTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGCAATAAAACTAAATCTG
T
Found at i:727 original size:33 final size:33
Alignment explanation
Indices: 685--806 Score: 154
Period size: 33 Copynumber: 3.7 Consensus size: 33
675 TAATTGTGAT
*
685 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTG
*
718 AAAACAATTCTGTTTTGGTTGATCATAGCATTG
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTG
* * * * **
751 CAAATAACTCTGTTTTGGTTGATCATAATATTG
1 AAAACAATTCTGTTTTGGTTGAACATAGCATTG
* *
784 AAAATAATTCTGTTTTGGGTGAA
1 AAAACAATTCTGTTTTGGTTGAA
807 GAGAAAGAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (33 bp):
AAAACAATTCTGTTTTGGTTGAACATAGCATTG
Found at i:2457 original size:667 final size:666
Alignment explanation
Indices: 1184--2516 Score: 2450
Period size: 667 Copynumber: 2.0 Consensus size: 666
1174 GGGGAGGGAA
* *
1184 TGATGCGCCCAAGGCTTATCATGGAAGGAATTATGCGCCAAGGACTTATTATAGACTTGAAGACA
1 TGATGCGCCCAAGGCTTATCATGGAAGGAATGATGCGCCAAGGACTTACTATAGACTTGAAGACA
*
1249 AGCATGGAGAGCATGGAAAGGATGATCAAGGGCTGCAAGGAAGCATGGACAAGCTTAAAGGAGAG
66 AGCATGGAGAGCATGGAAAGGATGATCAAGGGCTGCAAAGAAGCATGGACAAGCTTAAAGGAGAG
* *
1314 GATGGAATCGTAAATCACCAAGAAGATGCCATTAAGATGCCATTTGATCCTTTGAAGATGCCATT
131 AATGGAATCGCAAATCACCAAGAAGATGCCATTAAGATGCCATTTGATCCTTTGAAGATGCCATT
1379 AGGTCCGATGACAAGAGCAAGAGCTAAAAGATTCAAGGATGCACTCATGGGCATTGTTCGAACTC
196 AGGTCCGATGACAAGAGCAAGAGCTAAAAGATTCAAGGATGCACTCATGGGCATTGTTCGAACTC
1444 ATCTTGAAGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGAAA
261 ATCTTGAAGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGAAA
1509 TTACAAATCAATTACAAGTTCATCACATTGCTTGCAATTGATTCTAGATGGCCGGATTGACATCA
326 TTACAAATCAATTACAAGTTCATCACATTGCTTGCAATTGATTCTAGATGGCCGGATTGACATCA
1574 TGGCATGAGCCCATTAGCATTAGTTTGCTTTGTTTGGGCTTAATTATATCTTAAATTAGCTTATT
391 TGGCATGAGCCCATTAGCATTAGTTTGCTTTGTTTGGGCTTAATTATATCTTAAATTAGCTTATT
1639 TTTAAGTTTGGACCTTATTTGGATTGGGCCTTGGTTGACTAAGTCCAATCCTTGTTTAATTATGT
456 TTTAAGTTTGGACCTTATTTGGATTGGGCCTTGGTTGACTAAGTCCAATCCTTGTTTAATTATGT
1704 CTTTATTTCCTTTTCCTAGTTGGGCAAGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAA
521 CTTTATTTCCTTTTCCTAGTTGGGCAAGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAA
1769 TTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATACCTCTTCTAA
586 TTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATACCTCTTCTAA
1834 AAGTGGAAGTTGAGTTG
651 AAGT-GAAGTTGAGTTG
* *
1851 TGATGCGCCCAAGGCTTATTATGGAAGGAATGATGCGCCAAGGACTTACTATGGACTTGAAGACA
1 TGATGCGCCCAAGGCTTATCATGGAAGGAATGATGCGCCAAGGACTTACTATAGACTTGAAGACA
* ** *
1916 AGCATGGAGAGCATGGAAAGGGTGATCAAGGGCTGCAAAGAAGTGTGGACAAGTTTAAAGGAGAG
66 AGCATGGAGAGCATGGAAAGGATGATCAAGGGCTGCAAAGAAGCATGGACAAGCTTAAAGGAGAG
*
1981 AATGGAATCGCAATTCACCAAGAAGATGCCATTAAGATGCCATTTGATCCTTTGAAGATGCCATT
131 AATGGAATCGCAAATCACCAAGAAGATGCCATTAAGATGCCATTTGATCCTTTGAAGATGCCATT
* * * *
2046 AGGTCCGATGACAAGAGCAAGAGCTAAAAGGTTCAAGGTTGCACTCATGTGCCTTGTTCGAACTC
196 AGGTCCGATGACAAGAGCAAGAGCTAAAAGATTCAAGGATGCACTCATGGGCATTGTTCGAACTC
*
2111 ATCTTGAAGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGAAG
261 ATCTTGAAGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGAAA
*
2176 TTACAAATCAATTACAAGTTCATCACATTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCA
326 TTACAAATCAATTACAAGTTCATCACATTGCTTGCAATTGATTCTAGATGGCCGGATTGACATCA
* * *
2241 TGGCATGAGCCCATTAGCTTTAGTTTGCTTTGTTTGGGCTTAATTCTATCTTAGATTAGCTTATT
391 TGGCATGAGCCCATTAGCATTAGTTTGCTTTGTTTGGGCTTAATTATATCTTAAATTAGCTTATT
2306 TTTAAGTTTGGACCTTATTTGGATTGGGCCTTGGTTGACTAAGTCCAATCCTTGTTTAATTATGT
456 TTTAAGTTTGGACCTTATTTGGATTGGGCCTTGGTTGACTAAGTCCAATCCTTGTTTAATTATGT
2371 CTTTATTTCCTTTTCCTAGTTGGGCAAGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAA
521 CTTTATTTCCTTTTCCTAGTTGGGCAAGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAA
* *
2436 TTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATCTCTTGTAA
586 TTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATACCTCTTCTAA
2501 AAGTGAAGTTGAGTTG
651 AAGTGAAGTTGAGTTG
2517 ATTAATAAAG
Statistics
Matches: 643, Mismatches: 23, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
666 12 0.02
667 631 0.98
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (666 bp):
TGATGCGCCCAAGGCTTATCATGGAAGGAATGATGCGCCAAGGACTTACTATAGACTTGAAGACA
AGCATGGAGAGCATGGAAAGGATGATCAAGGGCTGCAAAGAAGCATGGACAAGCTTAAAGGAGAG
AATGGAATCGCAAATCACCAAGAAGATGCCATTAAGATGCCATTTGATCCTTTGAAGATGCCATT
AGGTCCGATGACAAGAGCAAGAGCTAAAAGATTCAAGGATGCACTCATGGGCATTGTTCGAACTC
ATCTTGAAGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGAAA
TTACAAATCAATTACAAGTTCATCACATTGCTTGCAATTGATTCTAGATGGCCGGATTGACATCA
TGGCATGAGCCCATTAGCATTAGTTTGCTTTGTTTGGGCTTAATTATATCTTAAATTAGCTTATT
TTTAAGTTTGGACCTTATTTGGATTGGGCCTTGGTTGACTAAGTCCAATCCTTGTTTAATTATGT
CTTTATTTCCTTTTCCTAGTTGGGCAAGGACTAGTTTTTCCCTAGCCCTTATATTTGGACGAAAA
TTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATACCTCTTCTAA
AAGTGAAGTTGAGTTG
Found at i:3061 original size:9 final size:9
Alignment explanation
Indices: 3043--3076 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3033 AGTTATATCG
*
3043 AAAAATATA
1 AAAAAAATA
3052 AAAAAAATA
1 AAAAAAATA
3061 AAATAAAATA
1 AAA-AAAATA
3071 AAAAAA
1 AAAAAA
3077 GTTTCGACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAAATA
Found at i:4631 original size:33 final size:33
Alignment explanation
Indices: 4536--4640 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
4526 TTGCAAAGAG
* * * *
4536 TGTTTTAGATGTTGCTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
* * * *
4569 TGATTT-GAGTGTTGTTTGCAATTACACTAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC
*
4602 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
4635 TGTTTT
1 TGTTTT
4641 GGATACTAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 1 0.02
33 56 0.97
34 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
Found at i:4703 original size:33 final size:33
Alignment explanation
Indices: 4666--4774 Score: 191
Period size: 33 Copynumber: 3.3 Consensus size: 33
4656 TGAAAACAAA
4666 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
4699 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
* * *
4732 TCTATTTTGGTTGATCATAACATTGAAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
4765 TCTGTTTTGG
1 TCTGTTTTGG
4775 GTGAAAAGAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:5188 original size:30 final size:30
Alignment explanation
Indices: 5152--5210 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5142 CAAGGGGGAG
*
5152 GGAATGATGCGCCCAAGG-CTTATTATGGAA
1 GGAATGATGCG-CCAAGGACTTACTATGGAA
5182 GGAATGATGCGCCAAGGACTTACTATGGA
1 GGAATGATGCGCCAAGGACTTACTATGGA
5211 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTACTATGGAA
Found at i:6350 original size:317 final size:315
Alignment explanation
Indices: 5745--6378 Score: 813
Period size: 317 Copynumber: 2.0 Consensus size: 315
5735 AGTGAAGTTG
5745 AGTTGATTAATAAAGTTGAGGATTATTTTCCCAAATTGATTATCTTAGCTTCATTGTTCTAGTTT
1 AGTTGATTAATAAAGTTGAGGATTATTTTCCCAAATTGATTATCTTAGCTTCATTGTTCTAGTTT
* ** *
5810 GAGCAAACTTAGGGTTCTTCATCTTGTAGAGTCCTAGAAAACAATTAAGTTGTGATTGCTTGGTT
66 GAGCAAACTTAGGGTTCTTCATCTTGTAGAGTCCTAGAAAACAATTAAGTTGAGATAACTTAGTT
** * *
5875 GTTTGTGAAATCTTGTGATCTTAGGTGTTCAAGTGCAGGTCGACTTGGAGGTCTAAGGCCGACGA
131 GTTTGTGAAATCTTGTGATCTTAGGAATTCAAGTGCAGGTCGAATTGAAGGTCTAAGGCCGACGA
* * * **
5940 ACGAAGGAAGATTTATCAAGTGAAGATTGTCGACATACACATCTAGAAGTTTGGTGATTCAAGTT
196 AAGAAGGAAGA-TTAGCAAGTGAAGATTATCGACATACACATCTAGAAGTTTGAAGATTCAAGTT
* * *
6005 GATCTTAGGCGGGTCTCTAAGGTGGATTTGGA-CCAATTACAACTAGATTCGTATCA
260 GATCTTAGGCGGATCTCAAAGGTGGATTTGAATCCAA-TACAACTAGATTCGTATCA
6061 AGTTGATTAATAAAGTTGAGGATTATTTTTCCCAAATTGATTATCTTAGCTTCATTGTTCTAGTT
1 AGTTGATTAATAAAGTTGAGGATTA-TTTTCCCAAATTGATTATCTTAGCTTCATTGTTCTAGTT
* * *
6126 TGAGCAAACTTAGGGTTCTTCATCTTGTAGAGTCCTAGCAAGCAATTAGGTTGAGATAACTTAGT
65 TGAGCAAACTTAGGGTTCTTCATCTTGTAGAGTCCTAGAAAACAATTAAGTTGAGATAACTTAGT
* *
6191 TGTTTGTG-AATCTTGTGATCTT-GAGAATTCAATTGCAGGTCTAATT-AA-GTGCTTAAGGCCG
130 TGTTTGTGAAATCTTGTGATCTTAG-GAATTCAAGTGCAGGTCGAATTGAAGGT-C-TAAGGCCG
* ** *
6252 ACGAAAG-AGGAGGGA-TAGCTTTGTGAAGATTATCGACATACA-AGTCTAGGAG-TTGAAGAAG
192 ACGAAAGAAGGA-AGATTAGC-AAGTGAAGATTATCGACATACACA-TCTAGAAGTTTGAAG-A-
* * *
6313 TTCAAGTTGAGT-TT-GGTGGATATTCAAAGGTTGGATTTGAATCTAATACAACTAGATTCGTAT
252 TTCAAGTTGA-TCTTAGGCGGAT-CTCAAAGG-TGGATTTGAATCCAATACAACTAGATTCGTAT
6376 CA
314 CA
6378 A
1 A
6379 TTGGTAATCA
Statistics
Matches: 277, Mismatches: 28, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
314 10 0.04
315 39 0.14
316 90 0.32
317 135 0.49
318 3 0.01
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (315 bp):
AGTTGATTAATAAAGTTGAGGATTATTTTCCCAAATTGATTATCTTAGCTTCATTGTTCTAGTTT
GAGCAAACTTAGGGTTCTTCATCTTGTAGAGTCCTAGAAAACAATTAAGTTGAGATAACTTAGTT
GTTTGTGAAATCTTGTGATCTTAGGAATTCAAGTGCAGGTCGAATTGAAGGTCTAAGGCCGACGA
AAGAAGGAAGATTAGCAAGTGAAGATTATCGACATACACATCTAGAAGTTTGAAGATTCAAGTTG
ATCTTAGGCGGATCTCAAAGGTGGATTTGAATCCAATACAACTAGATTCGTATCA
Found at i:6555 original size:30 final size:31
Alignment explanation
Indices: 6492--6573 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 31
6482 CACCACCTTC
* *
6492 TTGAAAACAATTCTGTTTTGGTTGATTATAGCA
1 TTGAAAATAAATCTGTTTTGGTTG--TATAGCA
*
6525 TTGCAAAT-AATCCTGTTTTGGTTG-ATAGCA
1 TTGAAAATAAAT-CTGTTTTGGTTGTATAGCA
6555 TTGAAAATAAATCTGTTTT
1 TTGAAAATAAATCTGTTTT
6574 AGGTGACAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 20 0.47
31 3 0.07
32 2 0.05
33 18 0.42
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (31 bp):
TTGAAAATAAATCTGTTTTGGTTGTATAGCA
Done.