Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014525.1 Corchorus olitorius cultivar O-4 contig14558, 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: 52745
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4076 original size:19 final size:19
Alignment explanation
Indices: 4041--4078 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4031 TTTCTCTTCT
*
4041 CAAATTCCCATATTCAATC
1 CAAATTCCCAAATTCAATC
4060 CAAATT-CCAAATCTCAATC
1 CAAATTCCCAAAT-TCAATC
4079 TTCAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (19 bp):
CAAATTCCCAAATTCAATC
Found at i:5054 original size:21 final size:21
Alignment explanation
Indices: 5030--5071 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5020 GTTGAAGATG
5030 CCTTTGATCCTGGTTTTGATT
1 CCTTTGATCCTGGTTTTGATT
**
5051 CCTTTGATTGTGGTTTTGATT
1 CCTTTGATCCTGGTTTTGATT
5072 TCTAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.14, G:0.21, T:0.55
Consensus pattern (21 bp):
CCTTTGATCCTGGTTTTGATT
Found at i:6125 original size:2 final size:2
Alignment explanation
Indices: 6118--6172 Score: 58
Period size: 2 Copynumber: 25.5 Consensus size: 2
6108 ATGGGCCATC
6118 AT AT AT AT AT AT AT ACT A- AT AT AT AT ACT AT AT ACT AT AT ACT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT A-T AT AT A-T
6161 AT AT ACT AT AT A
1 AT AT A-T AT AT A
6173 CCATAAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
1 1 0.02
2 36 0.77
3 10 0.21
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6151 original size:7 final size:7
Alignment explanation
Indices: 6121--6173 Score: 85
Period size: 7 Copynumber: 8.0 Consensus size: 7
6111 GGCCATCATA
6121 TATATA-
1 TATATAC
6127 TATATAC
1 TATATAC
6134 TA-ATA-
1 TATATAC
6139 TATATAC
1 TATATAC
6146 TATATAC
1 TATATAC
6153 TATATAC
1 TATATAC
6160 TATATAC
1 TATATAC
6167 TATATAC
1 TATATAC
6174 CATAAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
5 2 0.05
6 12 0.27
7 30 0.68
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (7 bp):
TATATAC
Found at i:11751 original size:37 final size:37
Alignment explanation
Indices: 11701--11776 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
11691 TCTTCTTTTT
*
11701 ATTTTCTCCATATCTCTAAATATTTCCGTGTGTATTA
1 ATTTTCTCCATATCTCTAAATATTTCCCTGTGTATTA
*
11738 ATTTTCTCCATATCTCTCAATATTTCCCTGTGTATTA
1 ATTTTCTCCATATCTCTAAATATTTCCCTGTGTATTA
11775 AT
1 AT
11777 GGTTTTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.49
Consensus pattern (37 bp):
ATTTTCTCCATATCTCTAAATATTTCCCTGTGTATTA
Found at i:14037 original size:62 final size:62
Alignment explanation
Indices: 13958--14080 Score: 192
Period size: 62 Copynumber: 2.0 Consensus size: 62
13948 TTTCAAAAGA
* * *
13958 TTTTAAGTTTATTGTATGGTTTGGATTTGGTTTCTAGTTCTCCTATGAACTACTACTTATGG
1 TTTTAAGTTTATGGTATGATTTGGATTTGGTTTCTAGTTCTCCTATGAACCACTACTTATGG
* * *
14020 TTTTAATTTTATGGTATGATTTGGATTTGGTTTTTAGTTCTCCTATGAACCACTGCTTATG
1 TTTTAAGTTTATGGTATGATTTGGATTTGGTTTCTAGTTCTCCTATGAACCACTACTTATG
14081 ATCTAATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (62 bp):
TTTTAAGTTTATGGTATGATTTGGATTTGGTTTCTAGTTCTCCTATGAACCACTACTTATGG
Found at i:17307 original size:27 final size:27
Alignment explanation
Indices: 17267--17325 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
17257 AGCAATAATT
*
17267 TTTTACAACTAGTGGAAATTGTCCCAA
1 TTTTACAACCAGTGGAAATTGTCCCAA
* *
17294 TTTTACGACCAGTGGAAATTGTCCCGA
1 TTTTACAACCAGTGGAAATTGTCCCAA
17321 TTTTA
1 TTTTA
17326 ATTAGGGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (27 bp):
TTTTACAACCAGTGGAAATTGTCCCAA
Found at i:17350 original size:27 final size:27
Alignment explanation
Indices: 17320--17374 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
17310 AATTGTCCCG
17320 ATTTTAATTAGGGAGAGGATCCTCTCC
1 ATTTTAATTAGGGAGAGGATCCTCTCC
17347 ATTTTAATTAGGGAGAGGATCCTCTCC
1 ATTTTAATTAGGGAGAGGATCCTCTCC
17374 A
1 A
17375 CTGGAGAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (27 bp):
ATTTTAATTAGGGAGAGGATCCTCTCC
Found at i:18248 original size:71 final size:71
Alignment explanation
Indices: 18127--18328 Score: 280
Period size: 71 Copynumber: 2.7 Consensus size: 71
18117 GAAATCATCT
*
18127 TCGGTAAAAACATGTTAGTAAATGCAAGTGGAAAACTTCAGAAACTCATTCTCATTATTCAGGAA
1 TCGGTAAAAACATGTTAGTAAATGCAAGTGGAAAATTTCAGAAACTCATTCTCATTATTCAGGAA
18192 AACTGG
66 AACTGG
*
18198 TCGGTAAAAACATGTTAGTAAATGCAAGTGGAAAATTTCAGAAACACATTCTCATTATTCAGGAA
1 TCGGTAAAAACATGTTAGTAAATGCAAGTGGAAAATTTCAGAAACTCATTCTCATTATTCAGGAA
18263 AACTGG
66 AACTGG
* **
18269 TAGGATAAAATGTATAAACA-AATAGTAAATGCAAGTGGAAAATTTCAGAAACTCATTCTC
1 TCGG-T---A---A-AAACATGTTAGTAAATGCAAGTGGAAAATTTCAGAAACTCATTCTC
18329 TGTATAAACA
Statistics
Matches: 117, Mismatches: 6, Indels: 9
0.89 0.05 0.07
Matches are distributed among these distances:
71 72 0.62
72 1 0.01
75 1 0.01
78 38 0.32
79 5 0.04
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (71 bp):
TCGGTAAAAACATGTTAGTAAATGCAAGTGGAAAATTTCAGAAACTCATTCTCATTATTCAGGAA
AACTGG
Found at i:18337 original size:50 final size:50
Alignment explanation
Indices: 18279--18379 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
18269 TAGGATAAAA
18279 TGTATAAACAAATAGTAAATGCAAGTGGAAAATTTCAGAAACTCATTCTC
1 TGTATAAACAAATAGTAAATGCAAGTGGAAAATTTCAGAAACTCATTCTC
18329 TGTATAAACAAATAGTAAATGCAAGTGGAAAATTTCAGAAACTCATTCTC
1 TGTATAAACAAATAGTAAATGCAAGTGGAAAATTTCAGAAACTCATTCTC
18379 T
1 T
18380 TTATTCAGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (50 bp):
TGTATAAACAAATAGTAAATGCAAGTGGAAAATTTCAGAAACTCATTCTC
Found at i:19854 original size:23 final size:22
Alignment explanation
Indices: 19828--19888 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
19818 CAAGTTAGCC
19828 ACTTTCTACCCTAAAATTCACAA
1 ACTTTC-ACCCTAAAATTCACAA
*
19851 ACTTTCAACCTCAAAATTCACAA
1 ACTTTCACCCT-AAAATTCACAA
*
19874 ATTTTCACCC-AAAAT
1 ACTTTCACCCTAAAAT
19889 CTATATTCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.15
22 4 0.12
23 25 0.74
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.30
Consensus pattern (22 bp):
ACTTTCACCCTAAAATTCACAA
Found at i:19936 original size:17 final size:17
Alignment explanation
Indices: 19916--19949 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19906 ATTCACATAC
19916 TTTCACTTAAATAAACA
1 TTTCACTTAAATAAACA
19933 TTTCACTTAAATAAACA
1 TTTCACTTAAATAAACA
19950 ACAACAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTCACTTAAATAAACA
Found at i:21479 original size:77 final size:75
Alignment explanation
Indices: 21329--21480 Score: 207
Period size: 77 Copynumber: 2.0 Consensus size: 75
21319 ACTAATTACT
*
21329 GGGACCCAAAGTCACACCAATCTCAAACTCAGTCCCGACTACTAATTAACCACCGGATTTCTCGG
1 GGGACCCAAAGTCACACCAATCTCAAACTCAGTCCCGACTACTAATTAACCACCGGATTTCAC-G
*
21394 TTATTGATTATC
65 -TACTGATTATC
* * *
21406 GGGACCCAAAGTCACACCAATCTCAAGCTCAGTCCCGGCTACTAATTAATCACCGGACTCATTCA
1 GGGACCCAAAGTCACACCAATCTCAAACTCAGTCCCGACTACTAATTAACCACCGGA-T--TTCA
21471 C-TACTGATTA
63 CGTACTGATTA
21481 ACCACCAGAC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
77 62 0.93
78 1 0.01
80 4 0.06
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.24
Consensus pattern (75 bp):
GGGACCCAAAGTCACACCAATCTCAAACTCAGTCCCGACTACTAATTAACCACCGGATTTCACGT
ACTGATTATC
Found at i:21515 original size:34 final size:34
Alignment explanation
Indices: 21471--21566 Score: 106
Period size: 35 Copynumber: 2.8 Consensus size: 34
21461 GACTCATTCA
* * *
21471 CTACTGATTAACCACCAGACTCAATC-AGTC-CCGG
1 CTACTAATTAACCACCGGACTCAA-CGACTCACC-G
* *
21505 CTACTAATTAACCACCGGATTCAACGACTCATTCG
1 CTACTAATTAACCACCGGACTCAACGACTCA-CCG
21540 CTACTAATTAACCACCGGACTCAACGA
1 CTACTAATTAACCACCGGACTCAACGA
21567 ATGAGGGCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
33 1 0.02
34 24 0.45
35 27 0.51
36 1 0.02
ACGTcount: A:0.32, C:0.33, G:0.12, T:0.22
Consensus pattern (34 bp):
CTACTAATTAACCACCGGACTCAACGACTCACCG
Found at i:35946 original size:16 final size:16
Alignment explanation
Indices: 35925--35955 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35915 TACAAGACAT
*
35925 AAAAAAATAAAATTAA
1 AAAAAAAAAAAATTAA
35941 AAAAAAAAAAAATTA
1 AAAAAAAAAAAATTA
35956 GTTGAATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAAAAAAAATTAA
Found at i:40764 original size:19 final size:19
Alignment explanation
Indices: 40740--40781 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
40730 GGATATTATT
40740 ATTGAAGCAAAATTAGGAA
1 ATTGAAGCAAAATTAGGAA
*
40759 ATTGAAGCAAGATTAGGAA
1 ATTGAAGCAAAATTAGGAA
40778 ATTG
1 ATTG
40782 TGGTTCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
ATTGAAGCAAAATTAGGAA
Found at i:42119 original size:30 final size:31
Alignment explanation
Indices: 42071--42129 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 31
42061 ATATAAATAT
42071 AATTTTAGTTATGAAATTT-CAATTCCAAAGA
1 AATTTTAGTTATGAAATTTACAA-TCCAAAGA
42102 AATTTT-G-TATGTAAATTTACAATCCAAA
1 AATTTTAGTTATG-AAATTTACAATCCAAA
42130 CTGAAGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 4 0.15
30 13 0.50
31 9 0.35
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (31 bp):
AATTTTAGTTATGAAATTTACAATCCAAAGA
Found at i:46872 original size:10 final size:10
Alignment explanation
Indices: 46856--46887 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
46846 CAGATAGTAA
46856 AAAACAGAGC
1 AAAACAGAGC
*
46866 GAAACAGAGC
1 AAAACAGAGC
46876 AAAACAGAGC
1 AAAACAGAGC
46886 AA
1 AA
46888 CTCAACTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.59, C:0.19, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAACAGAGC
Done.