Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015746.1 Corchorus capsularis cultivar CVL-1 contig15767, 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: 57267
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--46 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC
1 TC TC
47 AACATTTCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:21303 original size:2 final size:2
Alignment explanation
Indices: 21296--21328 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21286 ATTTCAAATA
21296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21329 CTAGGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22262 original size:20 final size:20
Alignment explanation
Indices: 22224--22264 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
22214 TGATTCTCAA
22224 ATTAAGCTCTACATGAAAAT
1 ATTAAGCTCTACATGAAAAT
22244 ATTAGAGCTCTACAT-AAAAT
1 ATTA-AGCTCTACATGAAAAT
22264 A
1 A
22265 CTTGACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (20 bp):
ATTAAGCTCTACATGAAAAT
Found at i:27057 original size:246 final size:241
Alignment explanation
Indices: 26725--27213 Score: 852
Period size: 246 Copynumber: 2.0 Consensus size: 241
26715 TTTCAAGAGG
*
26725 GACAATACTTCCGCATCCCATGCCTCTTATCCTCTTTCCAAGGGTTACTAACTCCTTTTGTTAAA
1 GACAATACTTCCGCATCCCATGCCTCTTATCCTCTTTCCAAGAGTTACTAACTCCTTTTGTTAAA
* *
26790 GAAAATAGTGACAACAATGGAAAAGGTTTTTTTTTTAAGCAGAAATACCTCTTCTCCTCTTTTCA
66 GAAAAGAGTGACAACAATGGAAAAGGTTGTTTTTTTAAGCAGAAATACCTCTTCTCCTCTTTTCA
26855 TGAAAACACTTCTTTTTTTAAAAAGATTTTAGCTACCCTTCACACCCCCACACTTTGTCTTTGAC
131 TGAAAACACTTC--TTTTT---AAGATTTTAGCTACCCTTCACACCCCCACACTTTGTCTTTGAC
* *
26920 ATATCCATGACATACTTCTATAAATGTACACAAGATTCAACACATGTTTTA
191 ATATCCATGACATACTTCTATAAATGTACACAAGATTCAACACAAGTTCTA
*
26971 GACAATACTTCCGCATTCCATGCCTCTTATCCTCTTTCCAAGAGTTACTAACTCCTTTTGTTAAA
1 GACAATACTTCCGCATCCCATGCCTCTTATCCTCTTTCCAAGAGTTACTAACTCCTTTTGTTAAA
* * *
27036 GAAAAGCGTGACAACAATGGAAAATGTTGTTTTTTTAAGCAGAAATACCTTTTCTCCTCTTTTCA
66 GAAAAGAGTGACAACAATGGAAAAGGTTGTTTTTTTAAGCAGAAATACCTCTTCTCCTCTTTTCA
27101 TGAAAACACTTCTTTTTAAGATTTTAGCTACCCTTCACACCCCCACACTTTGTCTTTGACATATC
131 TGAAAACACTTCTTTTTAAGATTTTAGCTACCCTTCACACCCCCACACTTTGTCTTTGACATATC
27166 CATGACATACTTCTATAAATGTACACAAGATTCAACACAAGTTCTA
196 CATGACATACTTCTATAAATGTACACAAGATTCAACACAAGTTCTA
27212 GA
1 GA
27214 AGTAATACAC
Statistics
Matches: 234, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
241 94 0.40
244 5 0.02
246 135 0.58
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.35
Consensus pattern (241 bp):
GACAATACTTCCGCATCCCATGCCTCTTATCCTCTTTCCAAGAGTTACTAACTCCTTTTGTTAAA
GAAAAGAGTGACAACAATGGAAAAGGTTGTTTTTTTAAGCAGAAATACCTCTTCTCCTCTTTTCA
TGAAAACACTTCTTTTTAAGATTTTAGCTACCCTTCACACCCCCACACTTTGTCTTTGACATATC
CATGACATACTTCTATAAATGTACACAAGATTCAACACAAGTTCTA
Found at i:27881 original size:19 final size:19
Alignment explanation
Indices: 27857--27896 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
27847 CAATGTCATG
*
27857 ATAAAATGCAAAACATATA
1 ATAAAATGCAAAACACATA
27876 ATAAAATGCAAAACACATA
1 ATAAAATGCAAAACACATA
27895 AT
1 AT
27897 CCTAAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.20
Consensus pattern (19 bp):
ATAAAATGCAAAACACATA
Found at i:34457 original size:36 final size:36
Alignment explanation
Indices: 34408--34478 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
34398 TCCAAGAATT
**
34408 AGTTTTTGTTTTTTCCGTTTTTTCTAAAAAAAAAAA
1 AGTTTTTCCTTTTTCCGTTTTTTCTAAAAAAAAAAA
34444 AGTTTTTCCTTTTTCCGTTTTTTCTAAAAAAAAAA
1 AGTTTTTCCTTTTTCCGTTTTTTCTAAAAAAAAAA
34479 GTTTGCGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.49
Consensus pattern (36 bp):
AGTTTTTCCTTTTTCCGTTTTTTCTAAAAAAAAAAA
Found at i:51004 original size:68 final size:68
Alignment explanation
Indices: 50930--51123 Score: 248
Period size: 68 Copynumber: 2.9 Consensus size: 68
50920 AGCAAGATCC
*
50930 AAAACTTAATCTCACAGGAATTAAGTGAATTATCAAAGACATAATTTCACAAGAGTTAAGCAAGT
1 AAAACTTAATCTCACAAGAATTAAGTGAATTATCAAAGACATAATTTCACAAGAGTTAAGCAAGT
50995 TAA
66 TAA
* * * *
50998 AAAACTTAATCTCACAAGAATTAAGTGAATCATCAAAGACATAATTTCATATGAGATAAGCAAGT
1 AAAACTTAATCTCACAAGAATTAAGTGAATTATCAAAGACATAATTTCACAAGAGTTAAGCAAGT
*
51063 TCA
66 TAA
** * * * * * *
51066 AAGTCTTAATTTCACAAGAATTAA--GAATTAGCAAAGGCTTAATTCCACAAGAATTAAG
1 AAAACTTAATCTCACAAGAATTAAGTGAATTATCAAAGACATAATTTCACAAGAGTTAAG
51124 TAAAGTCAGC
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 25 0.23
68 83 0.77
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (68 bp):
AAAACTTAATCTCACAAGAATTAAGTGAATTATCAAAGACATAATTTCACAAGAGTTAAGCAAGT
TAA
Found at i:51015 original size:33 final size:34
Alignment explanation
Indices: 50930--51124 Score: 109
Period size: 33 Copynumber: 5.8 Consensus size: 34
50920 AGCAAGATCC
* *
50930 AAAACTTAATCTCACAGGAATTAAGTGAATTATCA
1 AAAACTTAATCTCACAAGAATTAAGTCAATTA-CA
* * * *
50965 AAGACATAATTTCACAAGAGTTAAG-CAAGTTA-A
1 AAAACTTAATCTCACAAGAATTAAGTCAA-TTACA
* *
50998 AAAACTTAATCTCACAAGAATTAAGTGAATCATCA
1 AAAACTTAATCTCACAAGAATTAAGTCAATTA-CA
* * * * *
51033 AAGACATAATTTCATATGAGA-TAAG-CAAGTT-CA
1 AAAACTTAATCTCACAAGA-ATTAAGTCAA-TTACA
** *
51066 AAGTCTTAATTTCACAAGAATTAAG--AATTAGCA
1 AAAACTTAATCTCACAAGAATTAAGTCAATTA-CA
**
51099 AAGGCTTAAT-TCCACAAGAATTAAGT
1 AAAACTTAATCT-CACAAGAATTAAGT
51125 AAAGTCAGCA
Statistics
Matches: 125, Mismatches: 24, Indels: 23
0.73 0.14 0.13
Matches are distributed among these distances:
31 2 0.02
32 4 0.03
33 69 0.55
34 6 0.05
35 43 0.34
36 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (34 bp):
AAAACTTAATCTCACAAGAATTAAGTCAATTACA
Found at i:51379 original size:11 final size:11
Alignment explanation
Indices: 51363--51516 Score: 139
Period size: 11 Copynumber: 14.0 Consensus size: 11
51353 TTAGGCAAAG
51363 TTAGACTGAAA
1 TTAGACTGAAA
*
51374 TTAGACTGATA
1 TTAGACTGAAA
** *
51385 GAAGACTAAAA
1 TTAGACTGAAA
51396 TTAGACTGAAA
1 TTAGACTGAAA
*
51407 TTAGACTGATA
1 TTAGACTGAAA
* *
51418 TAAGACTGATA
1 TTAGACTGAAA
*
51429 TTATACTGAAA
1 TTAGACTGAAA
51440 TTAGACTGAAA
1 TTAGACTGAAA
** *
51451 AAAGACTGATA
1 TTAGACTGAAA
*
51462 TTAGACTAAAA
1 TTAGACTGAAA
*
51473 TTAGACT-AGTA
1 TTAGACTGA-AA
* *
51484 TAAGACTGATA
1 TTAGACTGAAA
*
51495 TTAAACTGAAA
1 TTAGACTGAAA
*
51506 TCAGACTGAAA
1 TTAGACTGAAA
51517 GAATACTGAA
Statistics
Matches: 113, Mismatches: 28, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
10 1 0.01
11 111 0.98
12 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.27
Consensus pattern (11 bp):
TTAGACTGAAA
Found at i:51405 original size:33 final size:33
Alignment explanation
Indices: 51363--51525 Score: 202
Period size: 33 Copynumber: 4.9 Consensus size: 33
51353 TTAGGCAAAG
* *
51363 TTAGACTGAAATTAGACTGATAGAAGACTAAAA
1 TTAGACTGAAATTAGACTGATAGAAGACTGATA
*
51396 TTAGACTGAAATTAGACTGATATAAGACTGATA
1 TTAGACTGAAATTAGACTGATAGAAGACTGATA
* * *
51429 TTATACTGAAATTAGACTGAAAAAAGACTGATA
1 TTAGACTGAAATTAGACTGATAGAAGACTGATA
* *
51462 TTAGACTAAAATTAGACT-AGTATAAGACTGATA
1 TTAGACTGAAATTAGACTGA-TAGAAGACTGATA
* * * *
51495 TTAAACTGAAATCAGACTGAAAGAATACTGA
1 TTAGACTGAAATTAGACTGATAGAAGACTGA
51526 AAGAAGACTA
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
32 1 0.01
33 110 0.98
34 1 0.01
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.27
Consensus pattern (33 bp):
TTAGACTGAAATTAGACTGATAGAAGACTGATA
Found at i:51590 original size:36 final size:36
Alignment explanation
Indices: 51534--51632 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
51524 GAAAGAAGAC
51534 TAAA-AAAAGAACTGGCTTAGTTTCAAGAAAACTAGG
1 TAAAGAAAAG-ACTGGCTTAGTTTCAAGAAAACTAGG
*
51570 TAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGG
1 TAAAGAAAAGACTGGCTTAGTTTCAAGAAAACTAGG
* *
51606 TAAAGGAAAGACTGGCTTAATTTCAAG
1 TAAAGAAAAGACTGGCTTAGTTTCAAG
51633 GAAATTAAGT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 54 0.92
37 5 0.08
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.23
Consensus pattern (36 bp):
TAAAGAAAAGACTGGCTTAGTTTCAAGAAAACTAGG
Found at i:51633 original size:36 final size:35
Alignment explanation
Indices: 51534--51670 Score: 152
Period size: 36 Copynumber: 3.9 Consensus size: 35
51524 GAAAGAAGAC
* * *
51534 TAAAAAAAGAACTGGCTTAGTTTCAAGAAAACTAGG
1 TAAAGAAAG-ACTGGCTTAATTTCAAGGAAACTAGG
*
51570 TAAAGAAAAGACTGGCTTAGTTTCAAGGAAACTAGG
1 TAAAG-AAAGACTGGCTTAATTTCAAGGAAACTAGG
* *
51606 TAAAGGAAAGACTGGCTTAATTTCAAGGAAATTAAG
1 TAAA-GAAAGACTGGCTTAATTTCAAGGAAACTAGG
* *
51642 TAAA-AAGACACAGGCTTAATTTC-AGGAAA
1 TAAAGAA-AGACTGGCTTAATTTCAAGGAAA
51671 GGAAATTAAG
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
34 8 0.09
35 14 0.15
36 64 0.70
37 5 0.05
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (35 bp):
TAAAGAAAGACTGGCTTAATTTCAAGGAAACTAGG
Found at i:51766 original size:36 final size:32
Alignment explanation
Indices: 51669--51745 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
51659 AATTTCAGGA
* *
51669 AAGGAAATTAAGTAAAATAAAGAACTTAATTC
1 AAGGTAATTAAGTAGAATAAAGAACTTAATTC
*
51701 AGGGTAATTAAGTAGAATAAAGAACTTAATTC
1 AAGGTAATTAAGTAGAATAAAGAACTTAATTC
51733 AAGGTAATTAAGT
1 AAGGTAATTAAGT
51746 GAAGTTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (32 bp):
AAGGTAATTAAGTAGAATAAAGAACTTAATTC
Done.