Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024779.1 Corchorus olitorius cultivar O-4 contig24812, 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: 29206
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:218 original size:31 final size:31
Alignment explanation
Indices: 153--220 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
143 TAAATAACGA
* *
153 TCAATTTAGGCCATGTACTCATAAGATTGGG
1 TCAATTTAGGCCATGTACTCACAAGATTGAG
* *
184 TCAATTTAGTCCTTGTACTCACAAGGA-TGAG
1 TCAATTTAGGCCATGTACTCACAA-GATTGAG
215 TCAATT
1 TCAATT
221 GAGTTCTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (31 bp):
TCAATTTAGGCCATGTACTCACAAGATTGAG
Found at i:282 original size:31 final size:31
Alignment explanation
Indices: 247--320 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
237 TTTATTGATT
*
247 GGACTCAATTGACCCAATCTTATGAGTATAG
1 GGACTAAATTGACCCAATCTTATGAGTATAG
278 GGACTAAATTGACCCAATCTTATGAGTATAG
1 GGACTAAATTGACCCAATCTTATGAGTATAG
309 GGACTAAATTGA
1 GGACTAAATTGA
321 TCGTTTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (31 bp):
GGACTAAATTGACCCAATCTTATGAGTATAG
Found at i:356 original size:29 final size:29
Alignment explanation
Indices: 302--357 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
292 CAATCTTATG
* * *
302 AGTATAGGGACTAAATTGATCGTTTTTTT
1 AGTATAGGGACTAAATTAAACATTTTTTT
331 AGTATAGGGA-TGAAATTAAACATTTTT
1 AGTATAGGGACT-AAATTAAACATTTTT
358 GTACGGTGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.04
29 22 0.96
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (29 bp):
AGTATAGGGACTAAATTAAACATTTTTTT
Found at i:7889 original size:22 final size:22
Alignment explanation
Indices: 7852--7914 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
7842 TGAAGTTGAA
7852 AAGAATGCA--TGTTGATTTAT
1 AAGAATGCATGTGTTGATTTAT
7872 AAGAATGCATGTGTTGATTTAT
1 AAGAATGCATGTGTTGATTTAT
7894 AAGAATGCATGTGTTGATTTA
1 AAGAATGCATGTGTTGATTTA
7915 AGTGAACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.22
22 32 0.78
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (22 bp):
AAGAATGCATGTGTTGATTTAT
Found at i:9024 original size:31 final size:31
Alignment explanation
Indices: 8992--9136 Score: 166
Period size: 31 Copynumber: 4.7 Consensus size: 31
8982 GCATATCACG
* * *
8992 TGTACCAAAAAGTGACATGTGGCACGCTACG
1 TGTACCAAAAAGTGACACGTGGCACGCCACA
* * *
9023 TGTATCAAAAAGCGATACGTGGCACGCCACA
1 TGTACCAAAAAGTGACACGTGGCACGCCACA
* ** *
9054 TGTACCAAAAAGCGACACGTGATACACCACA
1 TGTACCAAAAAGTGACACGTGGCACGCCACA
* * *
9085 TG-GCCAAAAAGTGACACGTGTCACGCCATA
1 TGTACCAAAAAGTGACACGTGGCACGCCACA
9115 TGTACCAAAAAGTGACACGTGG
1 TGTACCAAAAAGTGACACGTGG
9137 TATGCCTCGT
Statistics
Matches: 94, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
30 24 0.26
31 70 0.74
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.17
Consensus pattern (31 bp):
TGTACCAAAAAGTGACACGTGGCACGCCACA
Found at i:9154 original size:61 final size:60
Alignment explanation
Indices: 8992--9161 Score: 173
Period size: 61 Copynumber: 2.8 Consensus size: 60
8982 GCATATCACG
* * * *
8992 TGTACCAAAAAGTGACATGTGGCACG-CTACGTGTATCAAAAAGCGATACGTGGCACGCCACA
1 TGTACCAAAAAGTGACACGTGGTACGCCT-CGTGCA-CAAAAAG-GACACGTGGCACGCCACA
* * * * * * *
9054 TGTACCAAAAAGCGACACGTGATACACCACATGGC-CAAAAAGTGACACGTGTCACGCCATA
1 TGTACCAAAAAGTGACACGTGGTACGCCTCGT-GCACAAAAAG-GACACGTGGCACGCCACA
*
9115 TGTACCAAAAAGTGACACGTGGTATGCCTCGTGCACAAAAAGGACAC
1 TGTACCAAAAAGTGACACGTGGTACGCCTCGTGCACAAAAAGGACAC
9162 ATGACCGATT
Statistics
Matches: 87, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
60 7 0.08
61 55 0.63
62 23 0.26
63 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (60 bp):
TGTACCAAAAAGTGACACGTGGTACGCCTCGTGCACAAAAAGGACACGTGGCACGCCACA
Found at i:10144 original size:11 final size:11
Alignment explanation
Indices: 10128--10162 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
10118 TTTTCCTGTT
10128 TTTTGTTTTTG
1 TTTTGTTTTTG
*
10139 TTTTGTTTTCG
1 TTTTGTTTTTG
10150 TTTTGTTTTTG
1 TTTTGTTTTTG
10161 TT
1 TT
10163 GTATTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:20569 original size:28 final size:28
Alignment explanation
Indices: 20518--20572 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
20508 AGCATTAAAC
**
20518 TAAATTAGTGTTTTATTGCCAAAAAAAG
1 TAAATTAGTGTTTTACGGCCAAAAAAAG
20546 TAAATTAGTGTTTT-CGGCCTAAAAAAA
1 TAAATTAGTGTTTTACGGCC-AAAAAAA
20573 AAAAAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (28 bp):
TAAATTAGTGTTTTACGGCCAAAAAAAG
Found at i:22980 original size:30 final size:30
Alignment explanation
Indices: 22941--23133 Score: 264
Period size: 30 Copynumber: 6.5 Consensus size: 30
22931 CTATTCAAAG
*
22941 CAGAAGTTGTCATGCTCCTGCAATTGACGC
1 CAGAAGTTGTCATGCTCCTGCAATTGACAC
* *
22971 CAAAAGTTGTCATGCTCCTGCAATTGGCAC
1 CAGAAGTTGTCATGCTCCTGCAATTGACAC
*
23001 CAGAAGTTGTCATGCTTCTGCAATTGACAC
1 CAGAAGTTGTCATGCTCCTGCAATTGACAC
*
23031 CCGAAGTTGTCATGCTCCTGCAATTGACAC
1 CAGAAGTTGTCATGCTCCTGCAATTGACAC
* * *
23061 CAGAAGTTGTCATGATCTTACAATTGACAC
1 CAGAAGTTGTCATGCTCCTGCAATTGACAC
* * *
23091 CAGAAGTTGTCAATGGTCTTACAATTG--AC
1 CAGAAGTTGTC-ATGCTCCTGCAATTGACAC
23120 CAGAAGTTGTCATG
1 CAGAAGTTGTCATG
23134 ATAAATTTCC
Statistics
Matches: 149, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
28 3 0.02
29 13 0.09
30 119 0.80
31 14 0.09
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (30 bp):
CAGAAGTTGTCATGCTCCTGCAATTGACAC
Found at i:23178 original size:27 final size:27
Alignment explanation
Indices: 23155--23219 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
23145 ATAGACACTT
23155 GAAGATGTCATAATTCAATTGACACCA
1 GAAGATGTCATAATTCAATTGACACCA
* *
23182 GAAGTTGTCATAATTCAAATGACACCA
1 GAAGATGTCATAATTCAATTGACACCA
*
23209 GAAGTTGTCAT
1 GAAGATGTCAT
23220 GATTTTACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (27 bp):
GAAGATGTCATAATTCAATTGACACCA
Found at i:27361 original size:24 final size:21
Alignment explanation
Indices: 27321--27373 Score: 52
Period size: 24 Copynumber: 2.3 Consensus size: 21
27311 CTGACTAGAT
* *
27321 ATTATCAAGTGATAAAGGGAAAG
1 ATTATC-AGAGATAAAGAG-AAG
27344 AATTATCAGAGATAAAAGAGAAG
1 -ATTATCAGAGAT-AAAGAGAAG
27367 ATTATCA
1 ATTATCA
27374 ACAACATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.27
23 8 0.31
24 11 0.42
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.23
Consensus pattern (21 bp):
ATTATCAGAGATAAAGAGAAG
Found at i:27987 original size:19 final size:19
Alignment explanation
Indices: 27963--28022 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
27953 TGTGCAAAAG
*
27963 TTGAAATATTTCACTGATT
1 TTGAAATATTTCACTAATT
* * **
27982 TTGAAAGATTGCA--AAAG
1 TTGAAATATTTCACTAATT
*
27999 TTGAAATATTTCACTTATT
1 TTGAAATATTTCACTAATT
28018 TTGAA
1 TTGAA
28023 TGGGAGAGAG
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
17 12 0.41
19 17 0.59
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (19 bp):
TTGAAATATTTCACTAATT
Found at i:28408 original size:18 final size:18
Alignment explanation
Indices: 28385--28419 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28375 ACAAAAATTG
28385 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
28403 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
28420 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:28568 original size:16 final size:16
Alignment explanation
Indices: 28547--28578 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28537 TTTATAATTT
28547 TTATTAATAATATATA
1 TTATTAATAATATATA
*
28563 TTATTATTAATATATA
1 TTATTAATAATATATA
28579 AATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:28571 original size:19 final size:19
Alignment explanation
Indices: 28547--28594 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
28537 TTTATAATTT
* *
28547 TTATTAATAATATATATTA
1 TTATTAATAATATAAATAA
28566 TTATTAAT-ATATAAATAA
1 TTATTAATAATATAAATAA
28584 TTATATAATAA
1 TTAT-TAATAA
28595 ATGAACGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.48
19 12 0.48
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATAAATAA
Found at i:28659 original size:35 final size:35
Alignment explanation
Indices: 28620--28694 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
28610 TTATATAAAC
* *
28620 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCAT
28655 GAACACTTAAATGAACAATAAACGAGCCTGTTCAT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCAT
28690 GAACA
1 GAACA
28695 TAAACGAGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCAT
Found at i:29170 original size:2 final size:2
Alignment explanation
Indices: 29163--29206 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
29153 AATTAGGCTT
29163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29205 TA
1 TA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.