Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006701.1 Corchorus capsularis cultivar CVL-1 contig06722, 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: 52424
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:215 original size:21 final size:22
Alignment explanation
Indices: 184--229 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
174 CAAAAATTAT
**
184 AAAAGGGGGGGCGGTATTTAGC
1 AAAAGGGGGGGCGGTAAATAGC
206 AAAA-GGGGGGCGGTAAATAGC
1 AAAAGGGGGGGCGGTAAATAGC
227 AAA
1 AAA
230 CCCCTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.37, C:0.09, G:0.41, T:0.13
Consensus pattern (22 bp):
AAAAGGGGGGGCGGTAAATAGC
Found at i:2099 original size:6 final size:6
Alignment explanation
Indices: 2090--2158 Score: 63
Period size: 6 Copynumber: 11.5 Consensus size: 6
2080 TTCGGGTTTT
**
2090 TTCGGG TTCGGG TATTTCGGG TTCGGG TT--TT TTCGGG TTCGGG TTCGGG
1 TTCGGG TTCGGG ---TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
*
2139 TCCGGG -TCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTC
2159 ACTTTCGATA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
4 2 0.04
5 4 0.08
6 39 0.76
9 6 0.12
ACGTcount: A:0.01, C:0.17, G:0.43, T:0.38
Consensus pattern (6 bp):
TTCGGG
Found at i:2111 original size:31 final size:31
Alignment explanation
Indices: 2044--2133 Score: 153
Period size: 31 Copynumber: 2.9 Consensus size: 31
2034 GGCAATTGGG
* *
2044 CGGGTTCGGGTATTTTCGGGTTCGGGATTTTT
1 CGGGTTCGGGTTTTTTCGGGTTCGGG-TATTT
2076 CGGGTTCGGGTTTTTTCGGGTTCGGGTATTT
1 CGGGTTCGGGTTTTTTCGGGTTCGGGTATTT
2107 CGGGTTCGGGTTTTTTCGGGTTCGGGT
1 CGGGTTCGGGTTTTTTCGGGTTCGGGT
2134 TCGGGTCCGG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
31 31 0.55
32 25 0.45
ACGTcount: A:0.03, C:0.13, G:0.40, T:0.43
Consensus pattern (31 bp):
CGGGTTCGGGTTTTTTCGGGTTCGGGTATTT
Found at i:2134 original size:16 final size:16
Alignment explanation
Indices: 2044--2134 Score: 148
Period size: 16 Copynumber: 5.8 Consensus size: 16
2034 GGCAATTGGG
*
2044 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTTTTTT
*
2060 CGGGTTCGGGATTTTT
1 CGGGTTCGGGTTTTTT
2076 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTTTTTT
*
2092 CGGGTTCGGG-TATTT
1 CGGGTTCGGGTTTTTT
2107 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTTTTTT
2123 CGGGTTCGGGTT
1 CGGGTTCGGGTT
2135 CGGGTCCGGG
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
15 14 0.20
16 55 0.80
ACGTcount: A:0.03, C:0.13, G:0.40, T:0.44
Consensus pattern (16 bp):
CGGGTTCGGGTTTTTT
Found at i:2150 original size:17 final size:18
Alignment explanation
Indices: 2123--2156 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2113 CGGGTTTTTT
2123 CGGGTTCGGGTTCGGGTC
1 CGGGTTCGGGTTCGGGTC
2141 CGGG-TCGGGTTCGGGT
1 CGGGTTCGGGTTCGGGT
2157 TCACTTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.00, C:0.21, G:0.53, T:0.26
Consensus pattern (18 bp):
CGGGTTCGGGTTCGGGTC
Found at i:2933 original size:17 final size:17
Alignment explanation
Indices: 2907--2950 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
2897 TATTTTGATC
*
2907 TCGGGCTCGGG-TCGGG
1 TCGGGTTCGGGTTCGGG
2923 TTCGGGTTCGGGTTCGGG
1 -TCGGGTTCGGGTTCGGG
2941 -CGGGTTCGGG
1 TCGGGTTCGGG
2951 ACGTTGACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 10 0.40
17 10 0.40
18 5 0.20
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (17 bp):
TCGGGTTCGGGTTCGGG
Found at i:2950 original size:6 final size:6
Alignment explanation
Indices: 2907--2950 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
2897 TATTTTGATC
*
2907 TCGGGC TCGGG- TCGGGT TCGGGT TCGGGT TCGGG- -CGGGT TCGGG
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGG
2951 ACGTTGACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.11
5 5 0.14
6 26 0.74
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (6 bp):
TCGGGT
Found at i:4674 original size:69 final size:69
Alignment explanation
Indices: 4592--4724 Score: 221
Period size: 69 Copynumber: 1.9 Consensus size: 69
4582 GATATCCGTA
* *
4592 CTCGAGTGAAATTTTGCCAGCTACAATAATATGTTTCTTTAAGATAAAATTAGTAGTATGCTTAC
1 CTCGAGTGAAATTTTGCCAGCTACAATAATAGGTTTCTTTAAGATAAAATTAGTAGTATACTTAC
4657 CCGG
66 CCGG
* * *
4661 CTCGAGTGAAATTTTGTCAGCTATACTAATAGGTTTCTTTAAGATAAAATTAGTAGTATACTTA
1 CTCGAGTGAAATTTTGCCAGCTACAATAATAGGTTTCTTTAAGATAAAATTAGTAGTATACTTA
4725 AGATTTTAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (69 bp):
CTCGAGTGAAATTTTGCCAGCTACAATAATAGGTTTCTTTAAGATAAAATTAGTAGTATACTTAC
CCGG
Found at i:4990 original size:21 final size:21
Alignment explanation
Indices: 4931--4990 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
4921 CACTGTTTAG
4931 GTACTGTACAGATGAGATT-A
1 GTACTGTACAGATGAGATTAA
* * *
4951 -CACTGTACAGATCAAATTAA
1 GTACTGTACAGATGAGATTAA
4971 GTACTGTACAGATGAGATTA
1 GTACTGTACAGATGAGATTA
4991 TTAGAATAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 15 0.47
20 1 0.03
21 16 0.50
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (21 bp):
GTACTGTACAGATGAGATTAA
Found at i:5285 original size:13 final size:13
Alignment explanation
Indices: 5266--5299 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5256 GCAACGACAA
5266 ATTTTTTTCTTTT
1 ATTTTTTTCTTTT
* *
5279 CTTTTTTTTTTTT
1 ATTTTTTTCTTTT
5292 ATTTTTTT
1 ATTTTTTT
5300 AACTCTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (13 bp):
ATTTTTTTCTTTT
Found at i:5438 original size:25 final size:25
Alignment explanation
Indices: 5410--5459 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5400 TTTTTAATAA
5410 TTATATATGAAAATGGGGTTAAATT
1 TTATATATGAAAATGGGGTTAAATT
5435 TTATATATGAAAATGGGGTTAAATT
1 TTATATATGAAAATGGGGTTAAATT
5460 GTAAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (25 bp):
TTATATATGAAAATGGGGTTAAATT
Found at i:16779 original size:39 final size:39
Alignment explanation
Indices: 16717--17355 Score: 689
Period size: 39 Copynumber: 16.4 Consensus size: 39
16707 TGGCTGGAAC
** * *
16717 CAACAAAAGTCAG-TGGAAGATTCACAAGTTTGGGGCTCC
1 CAACAAAAGTCAGCT-GAACCTTCACAAGGTTGGGGCTCA
* * * * *
16756 CAACATAATTCAGC-GGACCATTCACCAGGTTGGGGCTCC
1 CAACAAAAGTCAGCTGAACC-TTCACAAGGTTGGGGCTCA
* *
16795 CAACAAAAGTCAGCT-AACCGTTCACAAGGTTGGGACTCC
1 CAACAAAAGTCAGCTGAACC-TTCACAAGGTTGGGGCTCA
** * ** ** * *
16834 CAA-AAGAAGTCAGAGGACCCTTTGCCGGGTTGGGGGTCC
1 CAACAA-AAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
* * ** * *
16873 CAAAAAAAGTCAG-TGGACCGTTCACAAGACTGGGACTCG
1 CAACAAAAGTCAGCTGAACC-TTCACAAGGTTGGGGCTCA
* * ** *** * *
16912 CACCAAAAGTCACCAAAACAGACACAAGGCTGGGGCTCT
1 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
* * * *
16951 CAA-AAGAAGTCA-ATGGACCATTCACAAGGTGGGGGCTTA
1 CAACAA-AAGTCAGCTGAACC-TTCACAAGGTTGGGGCTCA
* * *
16990 CAAGAAAAGTCACCTGAACCTTCACAAGGTTGGGGCTCT
1 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
*
17029 CAACAAAAGTCACCTGAACCTTCACAAGGTTGGGGCTCA
1 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
*
17068 CAACAAAAGTCACCTGAACCTTCACAAGGTTGGGGCTCA
1 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
*
17107 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCT
1 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
*
17146 CAACAAAAGTCAGCTGAACCTTCACAAGGTCGGGGCTCA
1 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
* *
17185 CAACAAAAGTCACCTGAACCTTCACAAGGTTGGGGCTCT
1 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
17224 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
1 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
* *
17263 CAACAAAAGTCACCTGAACCTTCACAAGGTTGGGGCTCT
1 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
* * *
17302 CAACAAAAGTCACCTGAACCTTCACAAGGTTGGGGTTCT
1 CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
17341 CAACAAAAGTCAGCT
1 CAACAAAAGTCAGCT
17356 TGGGGATCCC
Statistics
Matches: 510, Mismatches: 78, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
38 11 0.02
39 485 0.95
40 14 0.03
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.18
Consensus pattern (39 bp):
CAACAAAAGTCAGCTGAACCTTCACAAGGTTGGGGCTCA
Found at i:21476 original size:18 final size:19
Alignment explanation
Indices: 21453--21488 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21443 TTTAGCGGCA
*
21453 ATTGA-TTTGAGATTCTTG
1 ATTGATTTTGACATTCTTG
21471 ATTGATTTTGACATTCTT
1 ATTGATTTTGACATTCTT
21489 TTATTCATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.22, C:0.08, G:0.17, T:0.53
Consensus pattern (19 bp):
ATTGATTTTGACATTCTTG
Found at i:33589 original size:16 final size:15
Alignment explanation
Indices: 33566--33600 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
33556 CATTTAATTA
33566 AATTTAATATTTTAT
1 AATTTAATATTTTAT
33581 AATTCTAATATTTTAT
1 AATT-TAATATTTTAT
33597 AATT
1 AATT
33601 ATTTTATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTAATATTTTAT
Found at i:42055 original size:6 final size:6
Alignment explanation
Indices: 42039--42075 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
42029 CTAAGCAAAG
42039 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA
42076 TAGCAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:43424 original size:11 final size:11
Alignment explanation
Indices: 43407--43438 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
43397 ATAGTCTTCA
43407 AATCTTCAAAT
1 AATCTTCAAAT
*
43418 TATCTTCAAAT
1 AATCTTCAAAT
43429 AATCTTCAAA
1 AATCTTCAAA
43439 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:45745 original size:54 final size:54
Alignment explanation
Indices: 45663--45770 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
45653 TATTTCTTTC
45663 TGATGGAAAAGGCTTAATTTTTGTGTTTGCCGTAAAACCTAATGAGTAGAGGGA
1 TGATGGAAAAGGCTTAATTTTTGTGTTTGCCGTAAAACCTAATGAGTAGAGGGA
45717 TGATGGAAAAGGCTTAATTTTTGTGTTTGCCGTAAAACCTAATGAGTAGAGGGA
1 TGATGGAAAAGGCTTAATTTTTGTGTTTGCCGTAAAACCTAATGAGTAGAGGGA
45771 GGACCAATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.31
Consensus pattern (54 bp):
TGATGGAAAAGGCTTAATTTTTGTGTTTGCCGTAAAACCTAATGAGTAGAGGGA
Found at i:46773 original size:2 final size:2
Alignment explanation
Indices: 46766--46800 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
46756 AAAGATAACA
*
46766 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46801 CAACACAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.