Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014528.1 Corchorus capsularis cultivar CVL-1 contig14549, 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: 13007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1680 original size:16 final size:14
Alignment explanation
Indices: 1651--1677 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1641 TTATTAGATT
1651 ATATATAAATTTTA
1 ATATATAAATTTTA
1665 ATATATAAATTTT
1 ATATATAAATTTT
1678 TTATTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATAAATTTTA
Found at i:1681 original size:29 final size:27
Alignment explanation
Indices: 1649--1708 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
1639 TGTTATTAGA
*
1649 TTATATATAAATTTTAATATATAAATT-TT
1 TTATATA-AAAATTTAAT-TAT-AATTATT
*
1678 TTATTTAAAAATTTAATTATAATTATT
1 TTATATAAAAATTTAATTATAATTATT
1705 TTAT
1 TTAT
1709 TTTAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 9 0.32
28 9 0.32
29 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTATATAAAAATTTAATTATAATTATT
Found at i:1698 original size:27 final size:29
Alignment explanation
Indices: 1661--1716 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1651 ATATATAAAT
1661 TTTAATATATAAATT-TTTTA-TTTAAAAA
1 TTTAATATAT-AATTATTTTATTTTAAAAA
1689 TTTAAT-TATAATTATTTTATTTTAAAAA
1 TTTAATATATAATTATTTTATTTTAAAAA
1717 ATAAATATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 4 0.15
27 8 0.31
28 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTAATATATAATTATTTTATTTTAAAAA
Found at i:2037 original size:31 final size:31
Alignment explanation
Indices: 1968--2121 Score: 128
Period size: 31 Copynumber: 5.3 Consensus size: 31
1958 TCCTTTTATG
* * **
1968 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
1999 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * *
2030 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
2061 CA--T-G--TGGCAC--G--ACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * * *
2083 CATGTGGCGTGCCACATGTCACTTTTTGGCA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
2114 CACGTGGC
1 CACGTGGC
2122 GTGTTACGTC
Statistics
Matches: 100, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
22 13 0.13
24 2 0.02
25 1 0.01
26 4 0.04
27 5 0.05
28 1 0.01
29 2 0.02
31 72 0.72
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:2081 original size:53 final size:53
Alignment explanation
Indices: 2019--2121 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
2009 GCCACGTGTC
** * *
2019 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGCACACGTGGCACG
* *
2072 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGCACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGCACACGTGGC
2122 GTGTTACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGCACACGTGGCACG
Found at i:6300 original size:502 final size:502
Alignment explanation
Indices: 5358--6360 Score: 1819
Period size: 502 Copynumber: 2.0 Consensus size: 502
5348 TTTTTTTTGT
* * * *
5358 GTGTAGACTTCAGCGTTTTCGTTGTGATACTCCCACTTTTGGATGTGACGCTCCTAACGATTTTT
1 GTGTAGACTTCAGCGCTCTCGTTGTGATACTCCCACTTTTGGATGTGACGCTCCCAACGATTTCT
* * *
5423 GACCATTGGGTTTAATATCTAATTTCCTTACCGTCCGATAAAATAAGTTTTTAACTTGCTAAATA
66 GACCATTGGATTCAATATCTAATTTCCTTACCGTCCGATAAAATAAGTTTTTAACTTGCTAAACA
* * *
5488 GGTTTTAAAAACCTTTTGGACTGAATTCGTATGTGATTGTCCTCGTGATAGATTTTTACACCTTT
131 AGTTTTAAAAACCTTTTGGACTGAATCCGTATGTGATTGTCCTCGTGATAGATTTTTACACATTT
*
5553 TTTATTCCACCCGTTGATATCAACTACAATTTTTTTCTTGATTTATTATTTTTTTCTTTAACTTT
196 TTTATTCCACCCATTGATATCAACTACAATTTTTTTCTTGATTTATTATTTTTTTCTTTAACTTT
5618 TTTACGTTAAAGATCATTTGCAAGAGTTTCGGGAAAATATGATTTTAATAATTGGGGGTGTATTA
261 TTTACGTTAAAGATCATTTGCAAGAGTTTCGGGAAAATATGATTTTAATAATTGGGGGTGTATTA
*
5683 TTTGGTGTTGAGGATAACTGTGAAGATTGGGATTTGGAATTGGAGGAAGAGTTAGTTTCATATTT
326 TTTGGTGTTGAGGACAACTGTGAAGATTGGGATTTGGAATTGGAGGAAGAGTTAGTTTCATATTT
*
5748 GAAGACACTATTATCATCTCGAGAGAATGGGTAAGTAAATTGAAATTAAAATTATATTAGATGAT
391 GAAGACACTATTATCATCCCGAGAGAATGGGTAAGTAAATTGAAATTAAAATTATATTAGATGAT
5813 GTTTAGTTATGTTTATTTAATTTTATTGTTTAATTTAATTCTGAATG
456 GTTTAGTTATGTTTATTTAATTTTATTGTTTAATTTAATTCTGAATG
* * *
5860 GTGTAGACTTTAGCGCTCTCGTTGTGATATTCTCACTTTTGGATGTGACGCTCCCAACGATTTCT
1 GTGTAGACTTCAGCGCTCTCGTTGTGATACTCCCACTTTTGGATGTGACGCTCCCAACGATTTCT
*
5925 GACCATTGGATTCAATATCTAATTTCCTTACCGTCCGATACAATAAG-TTTTAACTTGCTAAACA
66 GACCATTGGATTCAATATCTAATTTCCTTACCGTCCGATAAAATAAGTTTTTAACTTGCTAAACA
*
5989 AGTTTTAAAAACCTTTTGGACTGAATCCGTATGTGGTTGTCCTCGTGATAGATTTTTACACATTT
131 AGTTTTAAAAACCTTTTGGACTGAATCCGTATGTGATTGTCCTCGTGATAGATTTTTACACATTT
6054 TTTATTCCACCCATTGATATCAACTACAATTTTTTTCTTGATTTATTATTTTTTTTCTTTAACTT
196 TTTATTCCACCCATTGATATCAACTACAATTTTTTTCTTGATTTATTA-TTTTTTTCTTTAACTT
6119 TTTTACGTTAAAGATCATTTGCAAGAGTTTCGGGAAAATATGATTTTAATAATTGGGGGTGTATT
260 TTTTACGTTAAAGATCATTTGCAAGAGTTTCGGGAAAATATGATTTTAATAATTGGGGGTGTATT
6184 ATTTGGTGTTGAGGACAACTGTGAAGATTGGGATTTGGAATTGGAGGAAGAGTTAGTTTCATATT
325 ATTTGGTGTTGAGGACAACTGTGAAGATTGGGATTTGGAATTGGAGGAAGAGTTAGTTTCATATT
*
6249 TGAAGGCACTATTATCATCCCGAGAGAATGGGTAAGTAAATTGAAATTAAAATTATATTAGATGA
390 TGAAGACACTATTATCATCCCGAGAGAATGGGTAAGTAAATTGAAATTAAAATTATATTAGATGA
6314 TGTTTAGTTATGTTTATTTAATTTTATTGTTTAATTTAATTCTGAAT
455 TGTTTAGTTATGTTTATTTAATTTTATTGTTTAATTTAATTCTGAAT
6361 ATACTTTTTG
Statistics
Matches: 481, Mismatches: 19, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
501 124 0.26
502 357 0.74
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (502 bp):
GTGTAGACTTCAGCGCTCTCGTTGTGATACTCCCACTTTTGGATGTGACGCTCCCAACGATTTCT
GACCATTGGATTCAATATCTAATTTCCTTACCGTCCGATAAAATAAGTTTTTAACTTGCTAAACA
AGTTTTAAAAACCTTTTGGACTGAATCCGTATGTGATTGTCCTCGTGATAGATTTTTACACATTT
TTTATTCCACCCATTGATATCAACTACAATTTTTTTCTTGATTTATTATTTTTTTCTTTAACTTT
TTTACGTTAAAGATCATTTGCAAGAGTTTCGGGAAAATATGATTTTAATAATTGGGGGTGTATTA
TTTGGTGTTGAGGACAACTGTGAAGATTGGGATTTGGAATTGGAGGAAGAGTTAGTTTCATATTT
GAAGACACTATTATCATCCCGAGAGAATGGGTAAGTAAATTGAAATTAAAATTATATTAGATGAT
GTTTAGTTATGTTTATTTAATTTTATTGTTTAATTTAATTCTGAATG
Found at i:12695 original size:333 final size:334
Alignment explanation
Indices: 11133--13006 Score: 1898
Period size: 333 Copynumber: 5.6 Consensus size: 334
11123 TCGTATACTA
* * * * * * * * * *
11133 ACCATCACAGTTTTTGGCTAAAAATGTGTTT-TGGGACCTGGCGCAGTTTTTCGTGATTTATGGC
1 ACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC
* * * **
11197 -CCAGAGACTACTTCAAATATCTACATTCATCTAATAAAATCTTAGCCACATTAAATTTAAGGAT
66 GCC-GAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGTATTTAAGGAT
* * **
11261 TTGTTTTTACGAGCATCTGAATCTTATTTCCATTTAATCGGAAACTAATTCAGAAAAAATATAAA
130 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAACTAATTCAGAAAAAATATAAA
*
11326 AAATGATATTAAAAACGGTAAAAGTCCCCCAAT-TGTTTTAGAGTGAA--AT-TATATATAT-T-
195 AAATGATATTAAAAACGGTAAAAGTCCTCCAATCT-TTTTAGAGTGAATTATATATATATATATA
* * ** *
11385 TTAGGAGTACTTTTATCCAAAAATTGAGGAAAAATTTTCCAAGTCATTTTTCGCAAAAAATTTAG
259 TTAGGATTAC-TTTATCCAAAAATTGAGGAAAAATTTTTCGGGTCATTTTTCGC-AAAATTTTAG
11450 CAAAAAT-CGTGTACT
322 CAAAAATCCGTG---T
* * *
11465 AACCATCACAGTTTTTTTTTGGCTAAAAACGCGTTTTGGGGCCCCGACTCAATTTTGTATGATTT
1 -ACCATCACAG----TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTT
* * *
11530 TTGGCGCCAAGACTCTTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAA
61 TTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGTATTTAA
* * *
11595 GGATTT-TCTTTTACGAGCATATTATATCTTGTTTCGATTTAATGAGAAACTAATTCAG-AAAAA
126 GGATTTGT-TTTTACGAGCATCTGA-ATCTTGTTTCGATTTAATTAGAAACTAATTCAGAAAAAA
**
11658 TATAAAAAATGATATTAAAAAAAGTAAAAGTCC-CCTAATCTTTTTAGAGTGAAATTATATATAT
189 TATAAAAAATGATATTAAAAACGGTAAAAGTCCTCC-AATCTTTTTAGAGTG--A--AT-TATAT
* * * * * *
11722 ATATATATATATTAGGATTTCTTTATCCAAAGATTGATGAAAAAATTTTCGGATTATTTTTCGCA
248 ATATATATATATTAGGATTACTTTATCCAAAAATTGAGGAAAAATTTTTCGGGTCATTTTTCGCA
11787 AAATTTTAGC-AAAATCCGTGT
313 AAATTTTAGCAAAAATCCGTGT
* * * * * *
11808 ACTAATCATCATAGTTTTTGGCTAAAAACGCATTTCGGCGCTCTGACTTAGTTTTGCATGATTTT
1 AC----CATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTT
* * *
11873 TGGCGCCGAGACTCCTTGAAATATTTATATTCATCTAATAAAGTCTTAGCCACATTGCATTTAAG
62 TGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGTATTTAAG
* * * * *
11938 GATTTATTTTTACGAGCACCTAAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAAATAT
127 GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAACTAATTCAGAAAAAATAT
* * * * * * * * * *
12003 GAAAAACGATATTAAAAGCGTGGAAAA-ACTTTCAATGTTTTT-G-GCG--TTAAAT-TATATAT
192 AAAAAATGATATTAAAAACG-GTAAAAGTCCTCCAATCTTTTTAGAGTGAATTATATATATATAT
* * ** * * *
12062 ATATTAGGAGTAATTTATGAAAAAAATTGAGTAAAATATTTTTGGGGTCATTTTTTGCAAAATTT
256 ATATTAGGATTACTTTAT-CCAAAAATTGAGGAAAA-ATTTTTCGGGTCATTTTTCGCAAAATTT
12127 TAGC-AAAATCCGTGT
319 TAGCAAAAATCCGTGT
* * * ** * * * * *
12142 ACTAACCATCAGTTTTTGGCTAAAAACACGTTT-TTGACACCGGCTCAGTTTTACGTGATTTTTG
1 AC-CATCA-CAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTG
* ** * *
12206 GCACATAGGCTACTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATT-TCATTTAAGG
64 GCGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGT-ATTTAAGG
* * *
12270 ATTTG-TTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGGAACTAATTTAGAAAAAATATA
128 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAACTAATTCAGAAAAAATATA
*
12334 AAAAATGATATTAAAAGCGGTAAAAGTCCTCCAATCTTTTTAGAGTGAAATTATATATATATATA
193 AAAAATGATATTAAAAACGGTAAAAGTCCTCCAATCTTTTTAGAGTG-AATTATATATATATATA
* ** * *
12399 TATTAGAATTACTTTATCCAAAAAAGGAGGAAAATTTTTTCGGGTCATTTTTTGCAAAATTTTAG
257 TATTAGGATTACTTTATCCAAAAATTGAGGAAAAATTTTTCGGGTCATTTTTCGCAAAATTTTAG
12464 CAAAAAT-CGTGT
322 CAAAAATCCGTGT
* *
12476 ACCATCACAGTTTTTAGG-TAAAAACGCGTTTCAGGGCCCCGACTCAGTTTTGCATGATTTTTGA
1 ACCATCACAGTTTTT-GGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGG
** * * *
12540 CGCCGAGACTCCTTGAAATATCTATATTCATAAAATAAAATCTCAACCACAATGTATTTAAGGAT
65 CGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGTATTTAAGGAT
* ** * * *
12605 TTGTTTCTACGAGCAAATGAATCTTGTTTCGATTTAATTATAAACTACTTCAG-AAAAATTTAAA
130 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAACTAATTCAGAAAAAATATAAA
* * *
12669 AAATGATATTAAAAATGGTGAAAGTCCTCCAATCTTTTAAGAGT-AATTATATATATATATATAT
195 AAATGATATTAAAAACGGTAAAAGTCCTCCAATCTTTTTAGAGTGAATTATATATATATATATAT
** * * * ** *
12733 ATATATATTAGGAGCAATTAATCCAAAAATGGAAGAAGCATTTTTCGGGTCATTTTTCGTAAAAT
260 -TA-GGATT---A-C--TTTATCCAAAAATTGAGGAAAAATTTTTCGGGTCATTTTTCGCAAAAT
* ** *
12798 TTTTGCAAAAATTATGTACT
317 TTTAGCAAAAA-TCCGT-GT
* * * * * *
12818 AACCATCACAGTTTTTGGCTAAAAACGCGTTTTGGGTGCCCTG-TTTAGTTTTGCTTGATTTTTT
1 -ACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGG-GCCCCGACTCAGTTTTGCATGATTTTTG
* * *
12882 GCGCTGAGACTCCTTGAAATATCTATATTCATTTAATAAAATATTAGCCACATTGTATTTAAGGA
64 GCGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGTATTTAAGGA
* * * *
12947 TTTCG-TTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTAATAAAAAA
129 TTT-GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAACTAATTCAGAAAAAA
13007 A
Statistics
Matches: 1279, Mismatches: 201, Indels: 111
0.80 0.13 0.07
Matches are distributed among these distances:
329 5 0.00
330 82 0.06
331 105 0.08
332 67 0.05
333 164 0.13
334 120 0.09
335 22 0.02
336 23 0.02
337 23 0.02
338 142 0.11
339 82 0.06
340 4 0.00
341 33 0.03
342 160 0.13
343 155 0.12
344 11 0.01
345 7 0.01
346 30 0.02
347 36 0.03
348 8 0.01
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (334 bp):
ACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC
GCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGTATTTAAGGATT
TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAACTAATTCAGAAAAAATATAAAA
AATGATATTAAAAACGGTAAAAGTCCTCCAATCTTTTTAGAGTGAATTATATATATATATATATT
AGGATTACTTTATCCAAAAATTGAGGAAAAATTTTTCGGGTCATTTTTCGCAAAATTTTAGCAAA
AATCCGTGT
Found at i:12723 original size:2 final size:2
Alignment explanation
Indices: 12716--12740 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12706 TAAGAGTAAT
12716 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 T
12741 TAGGAGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.