Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012678.1 Corchorus capsularis cultivar CVL-1 contig12699, 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: 61195
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:260 original size:11 final size:11
Alignment explanation
Indices: 236--270 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
226 TTGACAGCGT
236 AACAAAAACAA
1 AACAAAAACAA
* *
247 AACGAAAACGA
1 AACAAAAACAA
258 AACAAAAACAA
1 AACAAAAACAA
269 AA
1 AA
271 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:1105 original size:16 final size:17
Alignment explanation
Indices: 1074--1106 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1064 TGAGCTGTGG
1074 ATATGCCTAGGGTATTT
1 ATATGCCTAGGGTATTT
*
1091 ATATGGCTA-GGTATTT
1 ATATGCCTAGGGTATTT
1107 CACTTGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (17 bp):
ATATGCCTAGGGTATTT
Found at i:2975 original size:26 final size:26
Alignment explanation
Indices: 2946--2995 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2936 CAATGAATAT
*
2946 ACATGTTTTAAAAATGAATATCACCA
1 ACATGTATTAAAAATGAATATCACCA
*
2972 ACATGTATTAAAAGTGAATATCAC
1 ACATGTATTAAAAATGAATATCAC
2996 ATTACAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (26 bp):
ACATGTATTAAAAATGAATATCACCA
Found at i:5143 original size:17 final size:18
Alignment explanation
Indices: 5117--5151 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5107 TTTTTCTACC
*
5117 TTTCTTTAG-TTTAGGTT
1 TTTCTCTAGTTTTAGGTT
5134 TTTCTCTAGTTTTAGGTT
1 TTTCTCTAGTTTTAGGTT
5152 AAGGGTGTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.63
Consensus pattern (18 bp):
TTTCTCTAGTTTTAGGTT
Found at i:6237 original size:23 final size:23
Alignment explanation
Indices: 6155--6239 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
6145 CTTTTTCCGT
6155 TTTTTCTA-AAAAAAAAATTGCG
1 TTTTTCTATAAAAAAAAATTGCG
*
6177 TTTTTCTAAAAAAAAAAATTTAG-G
1 TTTTTCTATAAAAAAAAA-TT-GCG
* * * *
6201 GTTTGCGATTAAAAAAAATTGCG
1 TTTTTCTATAAAAAAAAATTGCG
*
6224 TTTTTCTCTAAAAAAA
1 TTTTTCTATAAAAAAA
6240 TTTATCTTCT
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
22 9 0.18
23 23 0.47
24 16 0.33
25 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (23 bp):
TTTTTCTATAAAAAAAAATTGCG
Found at i:9926 original size:17 final size:18
Alignment explanation
Indices: 9900--9934 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9890 TTTTTCTACC
*
9900 TTTCTTTAG-TTTAGGTT
1 TTTCTCTAGTTTTAGGTT
9917 TTTCTCTAGTTTTAGGTT
1 TTTCTCTAGTTTTAGGTT
9935 AAGGGTGTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.63
Consensus pattern (18 bp):
TTTCTCTAGTTTTAGGTT
Found at i:13037 original size:10 final size:10
Alignment explanation
Indices: 13024--13049 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13014 AAATCTCGAT
13024 ATATCCGTAA
1 ATATCCGTAA
13034 ATATCCGTAA
1 ATATCCGTAA
13044 ATATCC
1 ATATCC
13050 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:14358 original size:11 final size:12
Alignment explanation
Indices: 14326--14379 Score: 74
Period size: 12 Copynumber: 4.5 Consensus size: 12
14316 CATCAATACC
14326 TCGATATATCCG
1 TCGATATATCCG
14338 TCGATATATCCG
1 TCGATATATCCG
*
14350 TC-CTATATCCG
1 TCGATATATCCG
*
14361 TTCGATATATCCA
1 -TCGATATATCCG
14374 TCGATA
1 TCGATA
14380 CCTGTATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
11 8 0.22
12 22 0.59
13 7 0.19
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:16333 original size:10 final size:10
Alignment explanation
Indices: 16315--16349 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
16305 CTAGTCGAAA
16315 TTTTTTTAT-
1 TTTTTTTATG
16324 TTTCTTTTATG
1 TTT-TTTTATG
16335 TTTTTTTATG
1 TTTTTTTATG
16345 TTTTT
1 TTTTT
16350 CGATATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 3 0.12
10 18 0.75
11 3 0.12
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.83
Consensus pattern (10 bp):
TTTTTTTATG
Found at i:17423 original size:30 final size:31
Alignment explanation
Indices: 17387--17454 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
17377 TGCCCTGTCT
* *
17387 TGTGCGATTAGC-CCATGCCATGGCCGGTCA
1 TGTGCGATTACCTCCATGCAATGGCCGGTCA
* *
17417 TGTGCGA-TCCCTCCATGCAATGGCCGGTCT
1 TGTGCGATTACCTCCATGCAATGGCCGGTCA
17447 TGTGCGAT
1 TGTGCGAT
17455 GGCATCCTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.26
Consensus pattern (31 bp):
TGTGCGATTACCTCCATGCAATGGCCGGTCA
Found at i:23463 original size:94 final size:95
Alignment explanation
Indices: 23302--23494 Score: 370
Period size: 94 Copynumber: 2.0 Consensus size: 95
23292 AATTACCATA
23302 ATATCCATCTCAATAGTAACCAATTCAATGAGCATCAACCTTTAGACCGGTTTTGAAGTAATTTC
1 ATATCCATCTCAATAGTAACCAATTCAATGAGCATCAACCTTTAGACCGGTTTTGAAGTAATTTC
23367 ACTTCTTAATCTTATTATTTTTTATAAT-T
66 ACTTCTTAATCTTATTATTTTTTATAATAT
23396 ATATCCATCTCAATAGTAACCAATTCAATGAGCATCAACCTTTAGACCGGTTTTGAAGTAATTTC
1 ATATCCATCTCAATAGTAACCAATTCAATGAGCATCAACCTTTAGACCGGTTTTGAAGTAATTTC
*
23461 ACTTCTTAATCTTATTGTTTTTTATAATAT
66 ACTTCTTAATCTTATTATTTTTTATAATAT
23491 ATAT
1 ATAT
23495 ATATTCTTAA
Statistics
Matches: 97, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 92 0.95
95 5 0.05
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (95 bp):
ATATCCATCTCAATAGTAACCAATTCAATGAGCATCAACCTTTAGACCGGTTTTGAAGTAATTTC
ACTTCTTAATCTTATTATTTTTTATAATAT
Found at i:37319 original size:33 final size:33
Alignment explanation
Indices: 37282--37353 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
37272 ATTTGCATCC
* *
37282 AAAACAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * *
37315 AAAACAGATTTAGTGTCATTGCAAACAATATCT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
37348 AAAACA
1 AAAACA
37354 CTCTTTGCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:39839 original size:21 final size:21
Alignment explanation
Indices: 39805--39847 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39795 TTCAACAGAC
* *
39805 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGAGCAGGACTTGT
*
39826 CAAGTTCTGAGCAGGACTTGT
1 CAAGTCCTGAGCAGGACTTGT
39847 C
1 C
39848 CTGTTTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (21 bp):
CAAGTCCTGAGCAGGACTTGT
Found at i:50752 original size:26 final size:26
Alignment explanation
Indices: 50721--50772 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
50711 TTCCGTTCGG
50721 TTTGATGTTTGCGGTTCATTCAACAA
1 TTTGATGTTTGCGGTTCATTCAACAA
**
50747 TTTGATGTTTGTTGTTCATTCAACAA
1 TTTGATGTTTGCGGTTCATTCAACAA
50773 GGGAAGCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.46
Consensus pattern (26 bp):
TTTGATGTTTGCGGTTCATTCAACAA
Found at i:51408 original size:20 final size:20
Alignment explanation
Indices: 51383--51431 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
51373 ATTTTTCTTT
* *
51383 TTCTTTTTCCTTATCTTCTA
1 TTCTTTCTCATTATCTTCTA
* *
51403 TTCTTTCTCATTTTCTTCTT
1 TTCTTTCTCATTATCTTCTA
51423 TTCTTTCTC
1 TTCTTTCTC
51432 TTTTCTACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTTTCTCATTATCTTCTA
Found at i:54148 original size:16 final size:16
Alignment explanation
Indices: 54129--54181 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
54119 CCCGAAGCCA
*
54129 AAAAAACCCGAACCCG
1 AAAAAACCCAAACCCG
* * *
54145 AAAAAGCTCAAACCTG
1 AAAAAACCCAAACCCG
* *
54161 AAAAAATCAAAACCCG
1 AAAAAACCCAAACCCG
54177 AAAAA
1 AAAAA
54182 TCTGAAACCC
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.58, C:0.26, G:0.09, T:0.06
Consensus pattern (16 bp):
AAAAAACCCAAACCCG
Found at i:54165 original size:32 final size:32
Alignment explanation
Indices: 54129--54190 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
54119 CCCGAAGCCA
**
54129 AAAAAACCCGAACCCGAAAAAGCTCAAACCTG
1 AAAAAACCAAAACCCGAAAAAGCTCAAACCTG
* * *
54161 AAAAAATCAAAACCCGAAAAATCTGAAACC
1 AAAAAACCAAAACCCGAAAAAGCTCAAACC
54191 CGAACCCGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.55, C:0.27, G:0.10, T:0.08
Consensus pattern (32 bp):
AAAAAACCAAAACCCGAAAAAGCTCAAACCTG
Found at i:54189 original size:16 final size:16
Alignment explanation
Indices: 54139--54194 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
54129 AAAAAACCCG
* *
54139 AACCCGAAAAAGCTCA
1 AACCCGAAAAATCTAA
*
54155 AACCTGAAAAAATC-AA
1 AACCCG-AAAAATCTAA
*
54171 AACCCGAAAAATCTGA
1 AACCCGAAAAATCTAA
54187 AACCCGAA
1 AACCCGAA
54195 CCCGAACCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 7 0.21
16 20 0.61
17 6 0.18
ACGTcount: A:0.54, C:0.27, G:0.11, T:0.09
Consensus pattern (16 bp):
AACCCGAAAAATCTAA
Found at i:54458 original size:32 final size:32
Alignment explanation
Indices: 54414--54503 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
54404 AAGCCGAACT
* *
54414 AACCTGATCCAAAATTAACCTGAACCCGAATC
1 AACCTGACCCAAATTTAACCTGAACCCGAATC
*
54446 AAGCTGACCCAAATTTAA-CTCGAACCCGAATC
1 AACCTGACCCAAATTTAACCT-GAACCCGAATC
** *
54478 AACCCAACCCAAATTTAACCCGAACC
1 AACCTGACCCAAATTTAACCTGAACC
54504 GGACTTAAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
31 2 0.04
32 46 0.94
33 1 0.02
ACGTcount: A:0.40, C:0.34, G:0.09, T:0.17
Consensus pattern (32 bp):
AACCTGACCCAAATTTAACCTGAACCCGAATC
Found at i:56963 original size:22 final size:22
Alignment explanation
Indices: 56932--56974 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
56922 GAAATACAGG
**
56932 ACAAGACCTGGGCAGGAGTTGA
1 ACAAGACCTGCCCAGGAGTTGA
*
56954 ACAAGCCCTGCCCAGGAGTTG
1 ACAAGACCTGCCCAGGAGTTG
56975 TTGTGGGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.26, G:0.33, T:0.14
Consensus pattern (22 bp):
ACAAGACCTGCCCAGGAGTTGA
Done.