Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018145.1 Corchorus olitorius cultivar O-4 contig18178, 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: 96938
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4653 original size:19 final size:21
Alignment explanation
Indices: 4629--4668 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
4619 CCTGACATGA
4629 TATGTG-AAA-CATACACAAG
1 TATGTGAAAACCATACACAAG
4648 TATGTGTAAAACCATACACAA
1 TATGTG-AAAACCATACACAA
4669 TAAGCATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.23
Consensus pattern (21 bp):
TATGTGAAAACCATACACAAG
Found at i:21661 original size:23 final size:23
Alignment explanation
Indices: 21635--21678 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
21625 GGTATTTTTT
21635 TAAAAAA-AATTACATTATTTACC
1 TAAAAAAGAATTACATT-TTTACC
*
21658 TAAAAAAGGATTACATTTTTA
1 TAAAAAAGAATTACATTTTTA
21679 TTTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (23 bp):
TAAAAAAGAATTACATTTTTACC
Found at i:23245 original size:21 final size:22
Alignment explanation
Indices: 23206--23255 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
23196 CACCTCCACT
*
23206 AACTACTCATTTAAAAAAAAAA
1 AACTACCCATTTAAAAAAAAAA
23228 AACTACCCATTT-AAAAAAAAA
1 AACTACCCATTTAAAAAAAAAA
23249 AACTACC
1 AACTACC
23256 ACAAACTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (22 bp):
AACTACCCATTTAAAAAAAAAA
Found at i:33060 original size:5 final size:5
Alignment explanation
Indices: 33050--33080 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
33040 GAGAAGAGGA
33050 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
33081 TGAATTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:46818 original size:80 final size:80
Alignment explanation
Indices: 46708--46876 Score: 275
Period size: 80 Copynumber: 2.1 Consensus size: 80
46698 AATTACAAAC
* * *
46708 TTTATCATTCGGTTGAGTGGTTATTGCATGATCGATAAGATTTAAACCTTATTTGTTCATAAAAT
1 TTTATCATTCGATTGAATGGTTATTACATGATCGATAAGATTTAAACCTTATTTGTTCATAAAAT
46773 ACCGTTGTTAGCATA
66 ACCGTTGTTAGCATA
* *
46788 TTTATCATTCGATTGAATGGTTATTACATGATCGATAAGATTTGAATCTTATTTGTTCATAAAAT
1 TTTATCATTCGATTGAATGGTTATTACATGATCGATAAGATTTAAACCTTATTTGTTCATAAAAT
**
46853 ATGGTTGTTAGCATA
66 ACCGTTGTTAGCATA
46868 TTTATCATT
1 TTTATCATT
46877 AGTTATATAC
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.44
Consensus pattern (80 bp):
TTTATCATTCGATTGAATGGTTATTACATGATCGATAAGATTTAAACCTTATTTGTTCATAAAAT
ACCGTTGTTAGCATA
Found at i:51513 original size:39 final size:39
Alignment explanation
Indices: 51455--51538 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
51445 ATGTAAGTTG
51455 AGGG-TAGCTTTTCCCAATCTGCTCTATCATTTCAACGT
1 AGGGATAGCTTTTCCCAATCTGCTCTATCATTTCAACGT
51493 AGGGATAGCTTTTCCCAATCTGCTCTATCATTTCAACGT
1 AGGGATAGCTTTTCCCAATCTGCTCTATCATTTCAACGT
51532 AGGGATA
1 AGGGATA
51539 TCTCGGATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 4 0.09
39 41 0.91
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (39 bp):
AGGGATAGCTTTTCCCAATCTGCTCTATCATTTCAACGT
Found at i:52043 original size:27 final size:27
Alignment explanation
Indices: 52013--52066 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
52003 ATCTTGCTAT
*
52013 CCAAGTCTTCCCATCTTCTTAAACCCA
1 CCAAGTATTCCCATCTTCTTAAACCCA
52040 CCAAGTATTCCCATCTTCTTAAACCCA
1 CCAAGTATTCCCATCTTCTTAAACCCA
52067 TCCGGGCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.39, G:0.04, T:0.30
Consensus pattern (27 bp):
CCAAGTATTCCCATCTTCTTAAACCCA
Found at i:53411 original size:30 final size:31
Alignment explanation
Indices: 53375--53434 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
53365 TTGGGCCGCA
53375 CGGGGGAGA-GATGAGGACTCACATGTGAAT
1 CGGGGGAGATGATGAGGACTCACATGTGAAT
* *
53405 CGGGGGAGATTGTTGAGGATTCACATGTGA
1 CGGGGGAGA-TGATGAGGACTCACATGTGA
53435 GGGAACATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 9 0.35
32 17 0.65
ACGTcount: A:0.27, C:0.12, G:0.40, T:0.22
Consensus pattern (31 bp):
CGGGGGAGATGATGAGGACTCACATGTGAAT
Found at i:54209 original size:11 final size:11
Alignment explanation
Indices: 54193--54237 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
54183 CGTGAGGTTG
54193 GATAGTTGTTA
1 GATAGTTGTTA
54204 GATAGTTGTGTA
1 GATAGTTGT-TA
*
54216 GTTGTAGTTGTTA
1 G--ATAGTTGTTA
54229 GATAGTTGT
1 GATAGTTGT
54238 GTAGTTGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 16 0.55
12 3 0.10
13 3 0.10
14 7 0.24
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (11 bp):
GATAGTTGTTA
Found at i:54225 original size:25 final size:25
Alignment explanation
Indices: 54195--54253 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
54185 TGAGGTTGGA
54195 TAGTTGTTAGATAGTTGTGTAGTTG
1 TAGTTGTTAGATAGTTGTGTAGTTG
54220 TAGTTGTTAGATAGTTGTGTAGTTG
1 TAGTTGTTAGATAGTTGTGTAGTTG
54245 TAGTT-TTAG
1 TAGTTGTTAG
54254 TATGGGGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.12
25 30 0.88
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (25 bp):
TAGTTGTTAGATAGTTGTGTAGTTG
Found at i:54410 original size:41 final size:42
Alignment explanation
Indices: 54332--54414 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 42
54322 CTGGTTCCCG
* *
54332 CCCTCTTTAATGTTGTTCATTACTAGTTATGACAAACTTGAT
1 CCCTCATTAATGTTGTTCATCACTAGTTATGACAAACTTGAT
54374 CCCTCATTAATGTTGTTCA-CACTAGTTATGACAAACTTGAT
1 CCCTCATTAATGTTGTTCATCACTAGTTATGACAAACTTGAT
54415 ATATTGATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 21 0.54
42 18 0.46
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (42 bp):
CCCTCATTAATGTTGTTCATCACTAGTTATGACAAACTTGAT
Found at i:55891 original size:12 final size:12
Alignment explanation
Indices: 55874--55905 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
55864 ACCTGGCAAT
55874 TCGTGTTTCGTG
1 TCGTGTTTCGTG
55886 TCGTGTTTCGTG
1 TCGTGTTTCGTG
55898 TCGTGTTT
1 TCGTGTTT
55906 ACATAGGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.31, T:0.53
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:56421 original size:5 final size:5
Alignment explanation
Indices: 56411--56440 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
56401 TATCTCGTTC
*
56411 CGTGT CGTGT CGTGT CGTAT CGTGT CGTGT
1 CGTGT CGTGT CGTGT CGTGT CGTGT CGTGT
56441 TAAGACCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.20, G:0.37, T:0.40
Consensus pattern (5 bp):
CGTGT
Found at i:57372 original size:36 final size:36
Alignment explanation
Indices: 57322--57394 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
57312 AGGCCTGAAC
*
57322 CTGAAAATCGGAGGCTCAAACCCAAAATTCCTGGAA
1 CTGAAAATCAGAGGCTCAAACCCAAAATTCCTGGAA
* *
57358 CTGAAAATCAGAGGCTCAAACCCGAAATTCTTGGAA
1 CTGAAAATCAGAGGCTCAAACCCAAAATTCCTGGAA
57394 C
1 C
57395 CATATAATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (36 bp):
CTGAAAATCAGAGGCTCAAACCCAAAATTCCTGGAA
Found at i:64248 original size:2 final size:2
Alignment explanation
Indices: 64230--64282 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
64220 AAAAGCAGAT
* * * * **
64230 TA TA AA TA TA CA TA TA TA TA TA TA TA CA TA TA GA GC 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
64272 TA TA TA TA TA T
1 TA TA TA TA TA T
64283 TTCTGACCTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (2 bp):
TA
Found at i:79991 original size:14 final size:14
Alignment explanation
Indices: 79972--80003 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
79962 TTGTATTACT
79972 CAAAGCATAAGGAA
1 CAAAGCATAAGGAA
79986 CAAAGCATAAGGAA
1 CAAAGCATAAGGAA
80000 CAAA
1 CAAA
80004 CAAAATCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.16, G:0.19, T:0.06
Consensus pattern (14 bp):
CAAAGCATAAGGAA
Found at i:95815 original size:87 final size:87
Alignment explanation
Indices: 95667--95836 Score: 295
Period size: 87 Copynumber: 2.0 Consensus size: 87
95657 ACTTCTCATG
*
95667 AAAGATATCTATTAAATATGAAAAAGTAGTTTTTAGAAGTTGAGATTTAATCAAAAAGTCTCTAA
1 AAAGATATCTATTAAATATGAAAAAGAAGTTTTTAGAAGTTGAGATTTAATCAAAAAGTCTCTAA
* *
95732 CTGAAAAATGCTATAGGACTTA
66 CCGAAAAATACTATAGGACTTA
* *
95754 AAAGATATCTATTAAATATGAAAATGAAGTTTTTAGAAGTTGAGATTTAATCAAAAGGTCTCTAA
1 AAAGATATCTATTAAATATGAAAAAGAAGTTTTTAGAAGTTGAGATTTAATCAAAAAGTCTCTAA
95819 CCGAAAAATACTATAGGA
66 CCGAAAAATACTATAGGA
95837 AATTTAAAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.31
Consensus pattern (87 bp):
AAAGATATCTATTAAATATGAAAAAGAAGTTTTTAGAAGTTGAGATTTAATCAAAAAGTCTCTAA
CCGAAAAATACTATAGGACTTA
Done.