Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012257.1 Corchorus capsularis cultivar CVL-1 contig12278, 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: 41290
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:8872 original size:33 final size:33
Alignment explanation
Indices: 8830--8910 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 33
8820 GTGTTTTAGA
** *
8830 TGTTGTTTGCGATGATGCTAAACCTAATTTGAG
1 TGTTGTTTGCGATGACACTAAACCTAATTTAAG
* * **
8863 TGTTGTTTGCAATGACACTAAATCTTTTTTAAG
1 TGTTGTTTGCGATGACACTAAACCTAATTTAAG
*
8896 TGTTGTTTGTGATGA
1 TGTTGTTTGCGATGA
8911 AAATAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGCGATGACACTAAACCTAATTTAAG
Found at i:12731 original size:42 final size:42
Alignment explanation
Indices: 12654--12734 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
12644 GGATCGAATG
*
12654 GCCGGTTGTGGCCGGATGGCGCATGCGTTGGCCCGTGCGATT
1 GCCGGTTGTGGCCGGATGGCGCATGCGATGGCCCGTGCGATT
*** *
12696 GCCGGTTGTGGCCGGATGGCTTGTGCGATGTCCCGTGCG
1 GCCGGTTGTGGCCGGATGGCGCATGCGATGGCCCGTGCG
12735 GCGTCCCATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.06, C:0.26, G:0.43, T:0.25
Consensus pattern (42 bp):
GCCGGTTGTGGCCGGATGGCGCATGCGATGGCCCGTGCGATT
Found at i:12740 original size:12 final size:12
Alignment explanation
Indices: 12725--12758 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12715 CTTGTGCGAT
*
12725 GTCCCGTGCGGC
1 GTCCCATGCGGC
*
12737 GTCCCATGAGGC
1 GTCCCATGCGGC
12749 GTCCCATGCG
1 GTCCCATGCG
12759 TTGGCCGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.38, G:0.35, T:0.18
Consensus pattern (12 bp):
GTCCCATGCGGC
Found at i:13260 original size:33 final size:33
Alignment explanation
Indices: 13223--13285 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
13213 GAAAACAAAC
* *
13223 CTGTTGTGGTTGATCATAGCATTGCAAATAATT
1 CTGTTGTGGTTGATCATAGCACTGAAAATAATT
*
13256 CTGTTTTGGTTGATCATAGCACTGAAAATA
1 CTGTTGTGGTTGATCATAGCACTGAAAATA
13286 GGACTGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.38
Consensus pattern (33 bp):
CTGTTGTGGTTGATCATAGCACTGAAAATAATT
Found at i:13293 original size:33 final size:33
Alignment explanation
Indices: 13223--13297 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
13213 GAAAACAAAC
* * * **
13223 CTGTTGTGGTTGATCATAGCATTGCAAATAATT
1 CTGTTTTGGTTGATCATAGCACTGAAAATAAGA
*
13256 CTGTTTTGGTTGATCATAGCACTGAAAATAGGA
1 CTGTTTTGGTTGATCATAGCACTGAAAATAAGA
13289 CTGTTTTGG
1 CTGTTTTGG
13298 GTAAAAAGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (33 bp):
CTGTTTTGGTTGATCATAGCACTGAAAATAAGA
Found at i:16367 original size:33 final size:32
Alignment explanation
Indices: 16270--16374 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
16260 TTGAAAAGAG
* *
16270 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGAAACTAAATC
* * * *
16303 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGAAACTAAATC
* *
16336 TGTTTTAAGTGTTATTTGTGATGAAACTAAATC
1 TGTTTT-AGTGTTGTTTGCGATGAAACTAAATC
16369 TGTTTT
1 TGTTTT
16375 GGATGCTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 3 0.05
33 51 0.86
34 5 0.08
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.45
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGAAACTAAATC
Found at i:16391 original size:33 final size:34
Alignment explanation
Indices: 16323--16409 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 34
16313 GTTGTTTGCA
* * * * *
16323 ATGACACTAAATCTGTTTT-AAGTGTTATTTGTG
1 ATGAAACTAAATCTGTTTTGGAGTGCTAATTATG
16356 ATGAAACTAAATCTGTTTTGGA-TGCTAATTATG
1 ATGAAACTAAATCTGTTTTGGAGTGCTAATTATG
*
16389 ATGAAAAC-AATTCTGTTTTGG
1 ATG-AAACTAAATCTGTTTTGG
16410 TTGAACATAG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
33 41 0.89
34 5 0.11
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.41
Consensus pattern (34 bp):
ATGAAACTAAATCTGTTTTGGAGTGCTAATTATG
Found at i:16439 original size:33 final size:33
Alignment explanation
Indices: 16392--16505 Score: 126
Period size: 33 Copynumber: 3.5 Consensus size: 33
16382 AATTATGATG
*
16392 AAAACAATTCTGTTTTGGTTGAACATAGCATTA
1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA
* * *
16425 AAAATAATTTTGTTTTGGTTGATCATAGCATTG
1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA
* * * *
16458 CAAATAATCCTGTTTTGGTTG---ATGGCATTG
1 AAAATAATTCTGTTTTGGTTGAACATAGCATTA
*
16488 AAAATAAATCTGTTTTGG
1 AAAATAATTCTGTTTTGG
16506 GTGACGAGAA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
30 23 0.33
33 47 0.67
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (33 bp):
AAAATAATTCTGTTTTGGTTGAACATAGCATTA
Found at i:22267 original size:433 final size:431
Alignment explanation
Indices: 21440--22304 Score: 1444
Period size: 433 Copynumber: 2.0 Consensus size: 431
21430 CTTAGAATCA
*
21440 AGCATGGAAAGTAAGACATACCTCCTTGATAAAGCATCGGCTACCACATTCTCCTTACCTTGTTT
1 AGCATGGAAAGTAAGACATACCTCCTTGATAAAGCATCGGCTACAACATTCTCCTTACCTTGTTT
* * *
21505 GTATCGCACAACATAAGGAAAAGACTCAATGAACTCGCTCCACTTAGCATCTCTCTTGTTCAACT
66 GTATCGCACAACATAAGGAAAAGACTCAATGAACTCACTCCACATAGCATCTCTCTTCTTCAACT
* *
21570 TTTGTTGGCCTCTTAATTACTTCAAGCTCTCATGATCCGTATGAATCACAAATTCCTTAGGGCAT
131 TTTGTTGGCCTCTTAAATACTTCAAGCTCTCATGATCCGTATGAATCACAAATTCCTTAGGCCAT
** * *
21635 AGGTAGTGTTGCCAAGTTTGCAACGCCCTCACAAGAGCATAAAACTCTTTGTCATAGGTTAGATT
196 AAATAGTGTTGCCAAGTTTGCAACGCCCTCACAAGAGCATAAAACTCTTTGTCATAAGTTAGATA
* *
21700 GTTCAATGCTGCCCCATTCAATTTCTCACTAAAATATGCGACGGGCTTCCCACCTTGCATCAAAA
261 ATTCAATGCAGCCCCATTCAATTTCTCACTAAAATATGCGACGGGCTTCCCACCTTGCATCAAAA
*
21765 CAACTCTAATTCCAACCCCTGATGCATCACATTCAATCTCAAAAGTATTGTTAAAGTTAGGTAAA
326 CAACTCCAATTCCAACCCCTGATGCATCACATTCAATCTCAAAAGTATTGTTAAAGTTAGGTAAA
21830 ACAAGCAAAGGAGCATTAGTAAGTTTTTCCTTCAACGTCTC
391 ACAAGCAAAGGAGCATTAGTAAGTTTTTCCTTCAACGTCTC
21871 AGCATGGAAAGTAAGACATACCTCTCCTTGATAAAGCATCGGCTACAACATTCTCCTTACCTTGT
1 AGCATGGAAAGTAAGACATA-C-CTCCTTGATAAAGCATCGGCTACAACATTCTCCTTACCTTGT
* * * *
21936 TTGTATCGCACAACATAAGG-AAAGCTCTCTATGAACTCACTCCACATAGCATGTCTCTTCTTTA
64 TTGTATCGCACAACATAAGGAAAAG-ACTCAATGAACTCACTCCACATAGCATCTCTCTTCTTCA
*
22000 GCTTTTGTTGGCCTCTTAAATACTTCAAGCTCTCATGATCCGTATGAATCACAAATTCCTTAGGC
128 ACTTTTGTTGGCCTCTTAAATACTTCAAGCTCTCATGATCCGTATGAATCACAAATTCCTTAGGC
* *
22065 CATAAATAGTGTTGCCAAGTTTGCAACGCCCTCACAAGAGCATACAACTCTTTGTCATAAGTTGG
193 CATAAATAGTGTTGCCAAGTTTGCAACGCCCTCACAAGAGCATAAAACTCTTTGTCATAAGTTAG
* *
22130 ATAATTCAATGCAGCCCCATTCAATTTCTCAGTAAAATATGCGACGGGCTTCCCACCTTGCATTA
258 ATAATTCAATGCAGCCCCATTCAATTTCTCACTAAAATATGCGACGGGCTTCCCACCTTGCATCA
* * *
22195 AAAGAGCTCCAATTCCAACCCCTGATGCATCACATTCAATCTCAAAAGTATTTTTAAAGTTAGGT
323 AAACAACTCCAATTCCAACCCCTGATGCATCACATTCAATCTCAAAAGTATTGTTAAAGTTAGGT
* * *
22260 AAAACAAGCAAAGTAGCATTAGTTAGTTTTTCCTTCAAGGTCTC
388 AAAACAAGCAAAGGAGCATTAGTAAGTTTTTCCTTCAACGTCTC
22304 A
1 A
22305 AATGCTTCTT
Statistics
Matches: 403, Mismatches: 28, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
431 20 0.05
432 5 0.01
433 378 0.94
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (431 bp):
AGCATGGAAAGTAAGACATACCTCCTTGATAAAGCATCGGCTACAACATTCTCCTTACCTTGTTT
GTATCGCACAACATAAGGAAAAGACTCAATGAACTCACTCCACATAGCATCTCTCTTCTTCAACT
TTTGTTGGCCTCTTAAATACTTCAAGCTCTCATGATCCGTATGAATCACAAATTCCTTAGGCCAT
AAATAGTGTTGCCAAGTTTGCAACGCCCTCACAAGAGCATAAAACTCTTTGTCATAAGTTAGATA
ATTCAATGCAGCCCCATTCAATTTCTCACTAAAATATGCGACGGGCTTCCCACCTTGCATCAAAA
CAACTCCAATTCCAACCCCTGATGCATCACATTCAATCTCAAAAGTATTGTTAAAGTTAGGTAAA
ACAAGCAAAGGAGCATTAGTAAGTTTTTCCTTCAACGTCTC
Found at i:28231 original size:41 final size:42
Alignment explanation
Indices: 28143--28314 Score: 140
Period size: 41 Copynumber: 4.1 Consensus size: 42
28133 CAACCTCAAT
* *
28143 GTGACAACTTC-CAGTGTCAATA-ATAA-TTTAAT-TTACCAGA
1 GTGACAACTTCTTA-TGTCAA-AGATAATTTTAATCTTACCAAA
** * *
28183 GCAACAACTTCTTTTGTCAACAG-TAATTTTAA-CTTACCAAG
1 GTGACAACTTCTTATGTCAA-AGATAATTTTAATCTTACCAAA
* *
28224 GTGACAACTTCTGATGTCAAAGATAATTTTAATTTTTACCAAA
1 GTGACAACTTCTTATGTCAAAGATAATTTTAA-TCTTACCAAA
* * * *
28267 GTGACAACTTCTTGTGTCAATGGTAGATTTTAATTTTTACCAAA
1 GTGACAACTTCTTATGTCAAAGATA-ATTTTAA-TCTTACCAAA
28311 GTGA
1 GTGA
28315 TAACATCTGG
Statistics
Matches: 107, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
40 21 0.20
41 36 0.34
43 28 0.26
44 22 0.21
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (42 bp):
GTGACAACTTCTTATGTCAAAGATAATTTTAATCTTACCAAA
Found at i:28276 original size:43 final size:41
Alignment explanation
Indices: 28143--28330 Score: 152
Period size: 44 Copynumber: 4.5 Consensus size: 41
28133 CAACCTCAAT
* * *
28143 GTGACAACTTCCAGTGTCAATAATAA-TTTAA--TTTACCAGA
1 GTGACAACTT-CTGTGTCAA-AGTAATTTTAATTTTTACCAAA
** * * *
28183 GCAACAACTTCTTTTGTCAACAGTAATTTTAA--CTTACCAAG
1 GTGACAACTTC-TGTGTCAA-AGTAATTTTAATTTTTACCAAA
28224 GTGACAACTTCTGATGTCAAAGATAATTTTAATTTTTACCAAA
1 GTGACAACTTCTG-TGTCAAAG-TAATTTTAATTTTTACCAAA
*
28267 GTGACAACTTCTTGTGTCAATGGTAGATTTTAATTTTTACCAAA
1 GTGACAACTTC-TGTGTCAA-AGTA-ATTTTAATTTTTACCAAA
* *
28311 GTGATAACATCTGGTGTCAA
1 GTGACAACTTCT-GTGTCAA
28331 CGGTAAAGCT
Statistics
Matches: 121, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
39 1 0.01
40 21 0.17
41 35 0.29
43 27 0.22
44 37 0.31
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (41 bp):
GTGACAACTTCTGTGTCAAAGTAATTTTAATTTTTACCAAA
Found at i:28310 original size:44 final size:43
Alignment explanation
Indices: 28186--28336 Score: 173
Period size: 44 Copynumber: 3.5 Consensus size: 43
28176 TACCAGAGCA
* * * *
28186 ACAACTTCTTTTGTCAACAGTAATTTTAA--CTTACCAAGGTG
1 ACAACTTCTTGTGTCAACGGTAATTTTAATTTTTACCAAAGTG
* *
28227 ACAACTTC-TGATGTCAAAGATAATTTTAATTTTTACCAAAGTG
1 ACAACTTCTTG-TGTCAACGGTAATTTTAATTTTTACCAAAGTG
*
28270 ACAACTTCTTGTGTCAATGGTAGATTTTAATTTTTACCAAAGTG
1 ACAACTTCTTGTGTCAACGGTA-ATTTTAATTTTTACCAAAGTG
* * *
28314 ATAACATCTGGTGTCAACGGTAA
1 ACAACTTCTTGTGTCAACGGTAA
28337 AGCTATCGTG
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.01
41 23 0.25
43 28 0.30
44 41 0.44
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (43 bp):
ACAACTTCTTGTGTCAACGGTAATTTTAATTTTTACCAAAGTG
Found at i:30443 original size:2 final size:2
Alignment explanation
Indices: 30387--30426 Score: 55
Period size: 2 Copynumber: 19.5 Consensus size: 2
30377 TTCTCATGTT
30387 TA TA CTA TA CTA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30427 TGAATTAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 30 0.86
3 4 0.11
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:30945 original size:60 final size:62
Alignment explanation
Indices: 30872--30996 Score: 227
Period size: 60 Copynumber: 2.0 Consensus size: 62
30862 CAGAATAAGT
30872 TACTGAGCTGTTGAGTTTGATTTTCTTGAAAAACACTGTCACTGT-ATATTCTTAT-TTGCG
1 TACTGAGCTGTTGAGTTTGATTTTCTTGAAAAACACTGTCACTGTAATATTCTTATATTGCG
30932 TACTGAGCTGTTGAGTTTGATTTTCTTGAAAAACACTGTCACTGTACATATTCTTATATTGCG
1 TACTGAGCTGTTGAGTTTGATTTTCTTGAAAAACACTGTCACTGTA-ATATTCTTATATTGCG
30995 TA
1 TA
30997 GATTCTAATA
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
60 45 0.73
62 10 0.16
63 7 0.11
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (62 bp):
TACTGAGCTGTTGAGTTTGATTTTCTTGAAAAACACTGTCACTGTAATATTCTTATATTGCG
Found at i:36829 original size:2 final size:2
Alignment explanation
Indices: 36822--36849 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36812 AATGAAGATT
36822 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
36850 ATGTGTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38489 original size:53 final size:54
Alignment explanation
Indices: 38405--38520 Score: 148
Period size: 53 Copynumber: 2.2 Consensus size: 54
38395 TCTTAGGGTG
* * * *
38405 CGTTTGGTTGGAGGATCACCTCTGGTGATCTTGGGTGGTGGTCTCAGATCACC-
1 CGTTTGGTTGGAGGATCACCTCTGGTGATCTTCGATAGTGATCTCAGATCACCT
*
38458 CTGTTTGGTT-G-GGATCACCTATTGGTGATCTTCGATAGTGATCTCAGATCACCT
1 C-GTTTGGTTGGAGGATCACCT-CTGGTGATCTTCGATAGTGATCTCAGATCACCT
38512 CGTTTGGTT
1 CGTTTGGTT
38521 ATACCTTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
52 9 0.16
53 37 0.67
54 9 0.16
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (54 bp):
CGTTTGGTTGGAGGATCACCTCTGGTGATCTTCGATAGTGATCTCAGATCACCT
Found at i:40798 original size:30 final size:30
Alignment explanation
Indices: 40749--40806 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
40739 GTCTTCAAGT
*
40749 CCATAGTAAGTCCTTGGCGCATCATTCCTG
1 CCATAATAAGTCCTTGGCGCATCATTCCTG
40779 CCATAATAAG-CCTTGGGCGCATCATTCC
1 CCATAATAAGTCCTT-GGCGCATCATTCC
40807 CTCCCCCTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (30 bp):
CCATAATAAGTCCTTGGCGCATCATTCCTG
Found at i:41268 original size:33 final size:33
Alignment explanation
Indices: 41187--41290 Score: 163
Period size: 33 Copynumber: 3.1 Consensus size: 33
41177 CTTTTCACCT
* * *
41187 AAAACAGAATTATTTTCAATGTTATGATCAATCT
1 AAAACAGAATTATTTGCAATGCTATGATCAA-CC
*
41221 AAAATAGAATTATTTGCAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
41254 AAAACAGAATTATTTGCAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
41287 AAAA
1 AAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
33 37 0.57
34 28 0.43
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (33 bp):
AAAACAGAATTATTTGCAATGCTATGATCAACC
Done.