Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005746.1 Corchorus capsularis cultivar CVL-1 contig05764, 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: 22691
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:31 original size:21 final size:22
Alignment explanation
Indices: 1--43 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
*
1 ATTTGGGGTTTGA-CCATTACG
1 ATTTGAGGTTTGACCCATTACG
22 ATTTGAGGTTTGATCCCATTAC
1 ATTTGAGGTTTGA-CCCATTAC
44 TAGTAGGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (22 bp):
ATTTGAGGTTTGACCCATTACG
Found at i:153 original size:88 final size:87
Alignment explanation
Indices: 1--197 Score: 272
Period size: 88 Copynumber: 2.2 Consensus size: 87
*
1 ATTTGGGGTTTGACCATTACGATTTGAGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCAT
1 ATTTGGGGTTTGACCATTACGATTTGAGGTTTGATCCCATTACTACTAGGGGTTTGCCTAATCAT
*
66 GCTTTATAGTTTCACCATACATG
66 GCTTTA-AATTTCACCATACATG
* * *
89 ATTTGAGGTTTGACCATTAC-ACTTT-AGGGTTTGATCTCATTACTACTAGGGGTTTGCCTTATC
1 ATTTGGGGTTTGACCATTACGA-TTTGA-GGTTTGATCCCATTACTACTAGGGGTTTGCCTAATC
**
152 ATGCTTTAAATTTCATTATACATG
64 ATGCTTTAAATTTCACCATACATG
176 ATTTGGGGTTTGATCTCATTAC
1 ATTTGGGGTTTGA-C-CATTAC
198 TAGTAAGGGT
Statistics
Matches: 97, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
87 27 0.28
88 64 0.66
89 6 0.06
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (87 bp):
ATTTGGGGTTTGACCATTACGATTTGAGGTTTGATCCCATTACTACTAGGGGTTTGCCTAATCAT
GCTTTAAATTTCACCATACATG
Found at i:221 original size:66 final size:66
Alignment explanation
Indices: 115--261 Score: 244
Period size: 66 Copynumber: 2.3 Consensus size: 66
105 TTACACTTTA
* * *
115 GGGTTTGATCTCATTACTACTAGGGGTTTGCCTTATCATGCTTTAAATTTCATTATACATGATTT
1 GGGTTTGATCTCATTACTACTAAGGGTTTGCCTAATCATGCTTTAAATTTCACTATACATGATTT
180 G
66 G
*
181 GGGTTTGATCTCATTACTAGTAAGGGTTTGCCTAATCATGCTTTAAATTTCACTATACATGATTT
1 GGGTTTGATCTCATTACTACTAAGGGTTTGCCTAATCATGCTTTAAATTTCACTATACATGATTT
246 G
66 G
247 GGGTTTGA-C-CATTAC
1 GGGTTTGATCTCATTAC
262 GATTTGAGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
64 6 0.08
65 1 0.01
66 70 0.91
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (66 bp):
GGGTTTGATCTCATTACTACTAAGGGTTTGCCTAATCATGCTTTAAATTTCACTATACATGATTT
G
Found at i:266 original size:87 final size:88
Alignment explanation
Indices: 175--361 Score: 234
Period size: 87 Copynumber: 2.1 Consensus size: 88
165 CATTATACAT
** * *
175 GATTTGGGGTTTGATCTC-ATTACTAGTAAGGGTTTGCCTAATCATGCTTTA-AATTTCACTATA
1 GATTTGGGGTTTGATC-CAATTACTAGTAAGGGTTACCCTAATCATACTTTACAATTTCACCATA
* *
238 CATGATTTGGGGTTTGACCATTAC
65 CATGATTTGGAGTTTGACCATTAA
* * * * *
262 GATTTGAGATTTGATCCAATTACTAGTAGGGGTTACCCTAATCATACTTTACAGTTTGACCATAC
1 GATTTGGGGTTTGATCCAATTACTAGTAAGGGTTACCCTAATCATACTTTACAATTTCACCATAC
* *
327 ATTATTTGTAGTTTGACCATTAA
66 ATGATTTGGAGTTTGACCATTAA
350 GATTTGGGGTTT
1 GATTTGGGGTTT
362 CACAATGGAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
86 1 0.01
87 43 0.52
88 39 0.47
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (88 bp):
GATTTGGGGTTTGATCCAATTACTAGTAAGGGTTACCCTAATCATACTTTACAATTTCACCATAC
ATGATTTGGAGTTTGACCATTAA
Found at i:306 original size:153 final size:154
Alignment explanation
Indices: 21--312 Score: 421
Period size: 153 Copynumber: 1.9 Consensus size: 154
11 TGACCATTAC
* *
21 GATTTGAGGTTTGATCCCATTACTAGTAGGGGTTTGCCTAATCATGCTTTATAGTTTCACCATAC
1 GATTTGAGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTATAATTTCACCATAC
* ** *
86 ATGATTTGAGGTTTGACCATTACACTTTAGGGTTTGATCTCATTACTACTAGGGGTTTGCCTTAT
66 ATGATTTGAGGTTTGACCATTACACTTTAGGATTTGATCTCATTACTACTAGGGGTTACCCTAAT
*
151 CATGCTTTAAATTTCATTATACAT
131 CATACTTTAAATTTCATTATACAT
* * *
175 GATTTGGGGTTTGATCTCATTACTAGTAAGGGTTTGCCTAATCATGCTTTA-AATTTCACTATAC
1 GATTTGAGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTATAATTTCACCATAC
* *
239 ATGATTTGGGGTTTGACCATTACGA-TTT-GAGATTTGATC-CAATTACTAGTAGGGGTTACCCT
66 ATGATTTGAGGTTTGACCATTAC-ACTTTAG-GATTTGATCTC-ATTACTACTAGGGGTTACCCT
301 AATCATACTTTA
128 AATCATACTTTA
313 CAGTTTGACC
Statistics
Matches: 123, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
152 2 0.02
153 72 0.59
154 49 0.40
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (154 bp):
GATTTGAGGTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTATAATTTCACCATAC
ATGATTTGAGGTTTGACCATTACACTTTAGGATTTGATCTCATTACTACTAGGGGTTACCCTAAT
CATACTTTAAATTTCATTATACAT
Found at i:361 original size:21 final size:21
Alignment explanation
Indices: 337--398 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
327 ATTATTTGTA
337 GTTTGACCATTAAGATTTGGG
1 GTTTGACCATTAAGATTTGGG
* * * * *
358 GTTTCACAATGGATGCTTTGGG
1 GTTTGACCAT-TAAGATTTGGG
*
380 GTTTGACCATTAATATTTG
1 GTTTGACCATTAAGATTTG
399 AGCAAGTTGT
Statistics
Matches: 29, Mismatches: 11, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (21 bp):
GTTTGACCATTAAGATTTGGG
Found at i:2228 original size:19 final size:19
Alignment explanation
Indices: 2206--2242 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2196 ACCCTCCCTC
2206 CCATTTTATTCCCTTTTAG
1 CCATTTTATTCCCTTTTAG
*
2225 CCATTTTATTCCTTTTTA
1 CCATTTTATTCCCTTTTA
2243 TCTTTTTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (19 bp):
CCATTTTATTCCCTTTTAG
Found at i:3951 original size:21 final size:21
Alignment explanation
Indices: 3907--3951 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3897 TGTCGACATG
* **
3907 TTTAAATTAAATTAATTTTTT
1 TTTAAATTAAATTAAATTAAT
3928 TTTAAATTAAATTAAATTAAT
1 TTTAAATTAAATTAAATTAAT
3949 TTT
1 TTT
3952 TTAGAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAAATTAAATTAAATTAAT
Found at i:4721 original size:84 final size:82
Alignment explanation
Indices: 4563--4736 Score: 312
Period size: 82 Copynumber: 2.1 Consensus size: 82
4553 CGATTCTTGA
*
4563 CCGATCCGTTGACTTCCGATCCCATATATGTGACGGAATCGGATTAGTCCGATTCCGAGTTGAAC
1 CCGATCCGTTGACTTCCGATCCCATATATGTGACGGAACCGGATTAGTCCGATTCCGAGTTGAAC
4628 TAGTTCAACCGACCGGT
66 TAGTTCAACCGACCGGT
*
4645 CCGATCCGTTGACTTCCGATCCCATATATGTGACGGAACCGGATTAGTGTCTGATTCCGAGTTGA
1 CCGATCCGTTGACTTCCGATCCCATATATGTGACGGAACCGGATTA--GTCCGATTCCGAGTTGA
4710 ACTAGTTCAACCGACCGGT
64 ACTAGTTCAACCGACCGGT
4729 CCGATCCG
1 CCGATCCG
4737 ATTCCGTCAA
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
82 45 0.51
84 43 0.49
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (82 bp):
CCGATCCGTTGACTTCCGATCCCATATATGTGACGGAACCGGATTAGTCCGATTCCGAGTTGAAC
TAGTTCAACCGACCGGT
Found at i:5973 original size:11 final size:11
Alignment explanation
Indices: 5936--5973 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5926 TTCCTATATA
*
5936 AAATAAATTAT
1 AAATTAATTAT
5947 CAAA-TAATTAT
1 -AAATTAATTAT
5958 AAATTAATTAT
1 AAATTAATTAT
5969 AAATT
1 AAATT
5974 TGTTAAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:6377 original size:2 final size:2
Alignment explanation
Indices: 6370--6396 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6360 TTCTAGAATA
6370 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 A
6397 AGATAAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7775 original size:178 final size:178
Alignment explanation
Indices: 7498--7830 Score: 442
Period size: 178 Copynumber: 1.9 Consensus size: 178
7488 TTGATTATCC
* *
7498 GATTAAGATGATTTAAGTGTCTATTAGAAGATTGTTTCATAATCTACAACTTTCATGAAGGACTC
1 GATTAAGATGATTCAAGTGTCTATTAGAAGATTGTTCCATAATCTACAACTTTCATGAAGGACTC
* *** * *
7563 GAAAACTTGCTTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTAT-GATTAA
66 AAAAACTAAATTTAATGTTTCAAGTATAAAAAATGCTTCC-AAAGAATTAGTTGTT-TCGATTAA
7626 CAGG-AATAGACGGTCCACTTAATATTATATAACTTTTTCTCCAGATGTCT
129 C-GGAAATAGACGGTCCACTTAATATTATATAACTTTTTCTCCAGATGTCT
* * * * * *
7676 GATTGAGATGATTCAAGTGTCTCTT-GAGAGGTTGTTCCATGATGTACAACTTTTATGAAGGACT
1 GATTAAGATGATTCAAGTGTCTATTAGA-AGATTGTTCCATAATCTACAACTTTCATGAAGGACT
*
7740 CAAAAACTAAATTTAATG-TTCAAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAA
65 CAAAAACTAAATTTAATGTTTC-AAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGATTAA
*
7804 CGGAAATAGACGGTCTACTTAATATTA
129 CGGAAATAGACGGTCCACTTAATATTA
7831 CCTAATTTGT
Statistics
Matches: 134, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
177 11 0.08
178 123 0.92
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (178 bp):
GATTAAGATGATTCAAGTGTCTATTAGAAGATTGTTCCATAATCTACAACTTTCATGAAGGACTC
AAAAACTAAATTTAATGTTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGATTAACG
GAAATAGACGGTCCACTTAATATTATATAACTTTTTCTCCAGATGTCT
Found at i:14424 original size:2 final size:2
Alignment explanation
Indices: 14419--14447 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14409 TTGGCAGGCT
14419 TA TA 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 T
14448 TTCCAGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17110 original size:168 final size:166
Alignment explanation
Indices: 16738--17184 Score: 587
Period size: 168 Copynumber: 2.7 Consensus size: 166
16728 TGAGTCATTT
*
16738 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAAT-CCTCTCAAGAATCAAAAGTTAGGACA
1 GTCAATTGAGAAATGACCAAAAA-ATTAGTTATTTAATCCCT-TCAAGAATCAAAAGTTAGGACA
* ** ** * *
16802 TTTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAAAATTAGTTCTCTAGTTCATCATCAATCAT
64 TTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCAT
* * * *
16867 TGATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
129 TGATAGGGATCTTTGAGTAATTCCACTACTCTATTAAA
* * *
16905 GTCCATTGAGAATTGACCAAAAAAATTACTTATTTAATCCCTTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACC-AAAAAATTAGTTATTTAATCCCTTCAAGAATCAAAAGTTAGGACAT
* * *
16970 TTAAGTAATCTACCAAGTAGGAAAAGACGAAAAAAAATAAGTTCTCTAACTCTAAAAGCAAGCCT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAATTAGTTCTCTAACTC-AAAAGCAAGCAT
* *
17035 TGGTAGGGATCTTTGAGTAATTCCACTACTTTATTAAA
129 TGATAGGGATCTTTGAGTAATTCCACTACTCTATTAAA
17073 GTCAATTGAGAAATGACCAAAAAATCTAGTTATTTAATCACC-TCAAGAATCAAAAGTTAAGG-C
1 GTCAATTGAGAAATGACCAAAAAAT-TAGTTATTTAATC-CCTTCAAGAATCAAAAGTT-AGGAC
* * *
17136 ATTTAAGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTTAGTTCTCT
63 ATTTAAGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAAATTAGTTCTCT
17185 CGCTCCTCAT
Statistics
Matches: 245, Mismatches: 28, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
167 106 0.43
168 134 0.55
169 5 0.02
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAATTAGTTATTTAATCCCTTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCATTG
ATAGGGATCTTTGAGTAATTCCACTACTCTATTAAA
Found at i:17257 original size:2 final size:2
Alignment explanation
Indices: 17244--17293 Score: 61
Period size: 2 Copynumber: 25.5 Consensus size: 2
17234 TATTCAAATA
17244 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT A- AT AT AT GAT A- AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
17286 A- AT AT AT A
1 AT AT AT AT A
17294 ATCATCATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.07
2 36 0.84
3 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:17275 original size:30 final size:26
Alignment explanation
Indices: 17244--17293 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
17234 TATTCAAATA
*
17244 ATATATAGTATAT-AT-AT-ATATAT
1 ATATATAATATATGATAATAATATAT
17267 ATATATAATATATGATAATAATATAT
1 ATATATAATATATGATAATAATATAT
17293 A
1 A
17294 ATCATCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 2 0.09
25 2 0.09
26 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
ATATATAATATATGATAATAATATAT
Found at i:21256 original size:28 final size:28
Alignment explanation
Indices: 21224--21277 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
21214 TGATTTCTAT
21224 TAAAGTCATTATTATAAATTTATAACGG
1 TAAAGTCATTATTATAAATTTATAACGG
21252 TAAAGTCATTATTATAAATTTATAAC
1 TAAAGTCATTATTATAAATTTATAAC
21278 AATTAATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (28 bp):
TAAAGTCATTATTATAAATTTATAACGG
Found at i:22623 original size:35 final size:34
Alignment explanation
Indices: 22584--22651 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
22574 CCAAAGATTC
22584 TACAAAACAAAT-AAATATGCAATTTCAGAATTATT
1 TACAAAACAAATCAAA-ATGCAA-TTCAGAATTATT
* *
22619 TACAAAACAAATCAAAATGTAATTCTGAATTAT
1 TACAAAACAAATCAAAATGCAATTCAGAATTAT
22652 CCTACGGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 10 0.33
35 17 0.57
36 3 0.10
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (34 bp):
TACAAAACAAATCAAAATGCAATTCAGAATTATT
Done.