Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019966.1 Corchorus olitorius cultivar O-4 contig19999, 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: 49782
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:6607 original size:50 final size:50
Alignment explanation
Indices: 6548--6642 Score: 172
Period size: 50 Copynumber: 1.9 Consensus size: 50
6538 TTACTGAACC
* *
6548 AAGGGTCAATGGTACTTGGAAAGTAAAAGGAAGCCATTTGAAGCAGAATT
1 AAGGGTCAATGGTACTTGGAAAGGAAAAGGAAGCAATTTGAAGCAGAATT
6598 AAGGGTCAATGGTACTTGGAAAGGAAAAGGAAGCAATTTGAAGCA
1 AAGGGTCAATGGTACTTGGAAAGGAAAAGGAAGCAATTTGAAGCA
6643 AAAAAGATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.41, C:0.09, G:0.29, T:0.20
Consensus pattern (50 bp):
AAGGGTCAATGGTACTTGGAAAGGAAAAGGAAGCAATTTGAAGCAGAATT
Found at i:11032 original size:30 final size:29
Alignment explanation
Indices: 10997--11080 Score: 107
Period size: 29 Copynumber: 2.8 Consensus size: 29
10987 AAATGCTTCC
10997 AAATTGCAAGTTTAGGGGGCAAAACATCCA
1 AAATTGCAAGTTTAGGGGGCAAAACAT-CA
*
11027 AAATTG-AAGTTTAGGGGGTAAAACATCA
1 AAATTGCAAGTTTAGGGGGCAAAACATCA
* *
11055 AAATCATACAGGTTTAGGGGGCAAAA
1 AAAT--TGCAAGTTTAGGGGGCAAAA
11081 AGGGCATTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 6 0.13
29 19 0.40
30 7 0.15
31 15 0.32
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (29 bp):
AAATTGCAAGTTTAGGGGGCAAAACATCA
Found at i:13628 original size:59 final size:58
Alignment explanation
Indices: 13529--13639 Score: 177
Period size: 59 Copynumber: 1.9 Consensus size: 58
13519 ATTAATCAAA
*
13529 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
* * *
13587 TATCAAGTGACATGTTTTTTTATTAGATGCCTTAAAAAAGACGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACC
13640 GAGGCATGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
58 14 0.29
59 34 0.71
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
Found at i:14950 original size:36 final size:36
Alignment explanation
Indices: 14903--14972 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
14893 TTCAATAACC
*
14903 TTACATCTTTTGTGATTTTTG-TTATCATATTTCTTA
1 TTACATCTTTTGT-AATTTTGATTATCATATTTCTTA
*
14939 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
14973 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.61
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:16017 original size:25 final size:24
Alignment explanation
Indices: 15983--16029 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
15973 ACGTTTGCAC
15983 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
16008 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
16030 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:16075 original size:39 final size:40
Alignment explanation
Indices: 16020--16100 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
16010 ATACCTAAGA
*
16020 ATTTAATTAATGTAAGTATTTCAGTTATTA-TAATATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATTAATATTAC
* *
16059 ATTTAATTAATATAAGTATTTTAGTTATTATTTATATTAC
1 ATTTAATTAATATAAGTATTTCAGTTATTATTAATATTAC
16099 AT
1 AT
16101 CAGAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 28 0.74
40 10 0.26
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (40 bp):
ATTTAATTAATATAAGTATTTCAGTTATTATTAATATTAC
Found at i:19557 original size:19 final size:20
Alignment explanation
Indices: 19527--19590 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
19517 TTGACACTGT
19527 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
*
19548 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAGA
* *
19567 TTAGGTACTGTACAGATGAAA
1 TTA-GCACTGTACAGATGAGA
19588 TTA
1 TTA
19591 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:19590 original size:21 final size:19
Alignment explanation
Indices: 19533--19590 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
19523 CTGTTTAGCA
19533 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
19552 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
*
19573 ACTGTACAGATGAAATTA
1 ACTGTACAGATGAGATTA
19591 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:34004 original size:14 final size:15
Alignment explanation
Indices: 33980--34011 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
33970 AATAAAAACA
33980 TTGACAAGCTTAACC
1 TTGACAAGCTTAACC
33995 TTGA-AAGCTTAACC
1 TTGACAAGCTTAACC
34009 TTG
1 TTG
34012 TTGTTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (15 bp):
TTGACAAGCTTAACC
Found at i:40882 original size:59 final size:62
Alignment explanation
Indices: 40819--40935 Score: 177
Period size: 59 Copynumber: 1.9 Consensus size: 62
40809 TGTTAATACC
*
40819 TTTTCCGTAGAATATGCCTGATTATGGATTCTATT-GTT-TA-AATTGTACTTTGTTGCTTT
1 TTTTCCCTAGAATATGCCTGATTATGGATTCTATTGGTTATAGAATTGTACTTTGTTGCTTT
* * *
40878 TTTTCCCTAGAATATGCCTGCTTATGGATTCTTTTGGTTATAGTATTGTACTTTGTTG
1 TTTTCCCTAGAATATGCCTGATTATGGATTCTATTGGTTATAGAATTGTACTTTGTTG
40936 GTTTCTTAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 32 0.63
60 3 0.06
61 2 0.04
62 14 0.27
ACGTcount: A:0.19, C:0.13, G:0.18, T:0.50
Consensus pattern (62 bp):
TTTTCCCTAGAATATGCCTGATTATGGATTCTATTGGTTATAGAATTGTACTTTGTTGCTTT
Found at i:47811 original size:13 final size:13
Alignment explanation
Indices: 47793--47817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47783 GTTATCAAAT
47793 TTACAGTAATTAG
1 TTACAGTAATTAG
47806 TTACAGTAATTA
1 TTACAGTAATTA
47818 TCAAATTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TTACAGTAATTAG
Found at i:48112 original size:38 final size:38
Alignment explanation
Indices: 48069--48141 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
48059 TTTACAATAC
* *
48069 TTAATTACTCAAAAAGTTATAACGGTTATGAAAAAAAG
1 TTAATTACTCAAAAAGCTATAACAGTTATGAAAAAAAG
48107 TTAATTACTCAAAAAGCTATAACAGTTATGAAAAA
1 TTAATTACTCAAAAAGCTATAACAGTTATGAAAAA
48142 GGTTATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.29
Consensus pattern (38 bp):
TTAATTACTCAAAAAGCTATAACAGTTATGAAAAAAAG
Found at i:48729 original size:70 final size:70
Alignment explanation
Indices: 48616--48760 Score: 263
Period size: 70 Copynumber: 2.1 Consensus size: 70
48606 TAACTTTGAA
*
48616 ACACAACATATGAGCATTAATTACACAAATAACACATTCGAAATAAATATTTTCTCCAAAACAAC
1 ACACAACATATGAGCATTAATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
48681 GTTCT
66 GTTCT
* *
48686 ACACAACATATGAGCATTGATTACATAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
1 ACACAACATATGAGCATTAATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
48751 GTTCT
66 GTTCT
48756 ACACA
1 ACACA
48761 CAAACATGCA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (70 bp):
ACACAACATATGAGCATTAATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
GTTCT
Found at i:49211 original size:22 final size:22
Alignment explanation
Indices: 49177--49640 Score: 167
Period size: 22 Copynumber: 20.9 Consensus size: 22
49167 TTTCGATAAG
* *
49177 CTATGAAAATTTGAT-ACACGCA
1 CTATGAAATTTTGATAAC-CACA
*
49199 CTGTGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
* * *
49221 CTATGAAATTTTGATAATCTCC
1 CTATGAAATTTTGATAACCACA
*
49243 CTATGAAATTTTGATAATCACA
1 CTATGAAATTTTGATAACCACA
* * *
49265 CTAT-AAA-ATTGGTAACCGCA
1 CTATGAAATTTTGATAACCACA
*
49285 TTATGAAAATTTTGATAACCACA
1 CTATG-AAATTTTGATAACCACA
* * *** * *
49308 CCATGAAGTTTCCCT-TCCTATGA
1 CTATGAAATTTTGATAACC-A-CA
** * * * *
49331 GAATGAAACTTTGATATCCTCT
1 CTATGAAATTTTGATAACCACA
* **
49353 TTATTTAATTTTGATAA-CATC-
1 CTATGAAATTTTGATAACCA-CA
* * *
49374 TTCATAAAATTTTTG-TAACCTTC-
1 CT-ATGAAA-TTTTGATAACC-ACA
* * *
49397 CTATGAAATTTTGTTAACCTCC
1 CTATGAAATTTTGATAACCACA
* * * * *
49419 CTAGGAAACTTTGATAGCCTCCCTCC
1 CTATGAAATTTTGATA----ACCACA
49445 CTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
*
49467 CTAT-AAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* * * *
49488 GTATAAAATTTTGTTAACGACACT
1 CTATGAAATTTTGATAAC--CACA
***
49512 CTATGAAATTTTGATAACCTTT
1 CTATGAAATTTTGATAACCACA
* * * ** *
49534 TTATAAAATTTTGGTAACGTCT
1 CTATGAAATTTTGATAACCACA
* * *
49556 GTATGGAATTTTGATAACTACA
1 CTATGAAATTTTGATAACCACA
** *
49578 CTATGACGTTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
*
49599 CATATGAAATTTTAATAACCACA
1 C-TATGAAATTTTGATAACCACA
*
49622 CTATGAAAATTTGATAACC
1 CTATGAAATTTTGATAACC
49641 TTCCTATGTA
Statistics
Matches: 328, Mismatches: 89, Indels: 50
0.70 0.19 0.11
Matches are distributed among these distances:
20 12 0.04
21 33 0.10
22 211 0.64
23 34 0.10
24 19 0.06
26 19 0.06
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:49529 original size:46 final size:45
Alignment explanation
Indices: 49450--49573 Score: 146
Period size: 46 Copynumber: 2.8 Consensus size: 45
49440 CCTCCCTATG
*
49450 AAATTTTGATAAC-CACACTAT-AAATTTTGATAACCTTCGTATA
1 AAATTTTGATAACGCACTCTATGAAATTTTGATAACCTTCGTATA
* **
49493 AAATTTTGTTAACGACACTCTATGAAATTTTGATAACCTTTTTATA
1 AAATTTTGATAACG-CACTCTATGAAATTTTGATAACCTTCGTATA
* * * *
49539 AAATTTTGGTAACG-TCTGTATGGAATTTTGATAAC
1 AAATTTTGATAACGCACTCTATGAAATTTTGATAAC
49574 TACACTATGA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
43 12 0.17
44 18 0.26
45 7 0.10
46 33 0.47
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAACGCACTCTATGAAATTTTGATAACCTTCGTATA
Found at i:49590 original size:44 final size:44
Alignment explanation
Indices: 49557--49655 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
49547 GTAACGTCTG
* * *
49557 TATGGAATTTTGATAACTACACTATGACGTTTTGATAACCTCCA
1 TATGAAATTTTAATAACCACACTATGACGTTTTGATAACCTCCA
***
49601 TATGAAATTTTAATAACCACACTATGAAAATTTGATAACCTTCC-
1 TATGAAATTTTAATAACCACACTATGACGTTTTGATAACC-TCCA
*
49645 TATGTAATTTT
1 TATGAAATTTT
49656 GGTTTGATTG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 44 0.94
45 3 0.06
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTAATAACCACACTATGACGTTTTGATAACCTCCA
Done.