Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007696.1 Corchorus capsularis cultivar CVL-1 contig07717, 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: 52457
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:4805 original size:37 final size:34
Alignment explanation
Indices: 4684--4817 Score: 115
Period size: 37 Copynumber: 3.6 Consensus size: 34
4674 TGCTGTGGAG
* *
4684 GGGAACTTTCCCATTTTGAAAACTGAAACCTGAAACT
1 GGGAACTTTCCCAATTTGAAAACTAAAACCTG--A-T
* *
4721 GACGGGAACTTTCCCTAAATTGAAAACTAAAACCTGGT
1 ---GGGAACTTTCCC-AATTTGAAAACTAAAACCTGAT
* *
4759 GGGAACTTTCCCAATTTGAAAACTTTGACAACTTGAT
1 GGGAACTTTCCCAATTTGAAAAC--T-AAAACCTGAT
*
4796 GGGAACTTTCCCACTTTGAAAA
1 GGGAACTTTCCCAATTTGAAAA
4818 ACTTGGAGAA
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
34 10 0.12
35 12 0.15
36 1 0.01
37 28 0.35
38 1 0.01
40 12 0.15
41 17 0.21
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (34 bp):
GGGAACTTTCCCAATTTGAAAACTAAAACCTGAT
Found at i:14357 original size:29 final size:29
Alignment explanation
Indices: 14315--14372 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
14305 GGGTGGGGTT
14315 CTGTTAGTACTAACTAGGAAAAGGAACAA
1 CTGTTAGTACTAACTAGGAAAAGGAACAA
14344 CTGTTAGTACTAACTAGGAAAAGGAACAA
1 CTGTTAGTACTAACTAGGAAAAGGAACAA
14373 AGAAATCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (29 bp):
CTGTTAGTACTAACTAGGAAAAGGAACAA
Found at i:15680 original size:14 final size:14
Alignment explanation
Indices: 15661--15688 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15651 GCATATTAAC
15661 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
15675 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
15689 ATTACTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:15901 original size:20 final size:20
Alignment explanation
Indices: 15876--15914 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
15866 AAATACAAGG
15876 CATTTGATTTACAAATTGGA
1 CATTTGATTTACAAATTGGA
*
15896 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
15915 TGCTCCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:16483 original size:19 final size:19
Alignment explanation
Indices: 16459--16497 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
16449 ACTTTGCAGC
16459 ATGGATTTTACAATAGGAG
1 ATGGATTTTACAATAGGAG
16478 ATGGATTTTACAATAGGAG
1 ATGGATTTTACAATAGGAG
16497 A
1 A
16498 ATTTTATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (19 bp):
ATGGATTTTACAATAGGAG
Found at i:16503 original size:16 final size:17
Alignment explanation
Indices: 16462--16503 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
16452 TTGCAGCATG
16462 GATTTTACAATAGGAGA
1 GATTTTACAATAGGAGA
16479 TGGATTTTACAATAGGAGA
1 --GATTTTACAATAGGAGA
16498 -ATTTTA
1 GATTTTA
16504 TTCAAAGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
19 17 0.74
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (17 bp):
GATTTTACAATAGGAGA
Found at i:17127 original size:20 final size:19
Alignment explanation
Indices: 17088--17127 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17078 CCTGGAGGAT
*
17088 TCATTGAATCATTTTACTC
1 TCATTGAATCATTCTACTC
*
17107 TCATTGATTCATCTCTACTC
1 TCATTGAATCAT-TCTACTC
17127 T
1 T
17128 TCCCTCACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.23, C:0.25, G:0.05, T:0.47
Consensus pattern (19 bp):
TCATTGAATCATTCTACTC
Found at i:19159 original size:16 final size:17
Alignment explanation
Indices: 19140--19172 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19130 GTCAAGATTT
*
19140 GGAAGAA-AGAAGAAAA
1 GGAAGAAGAAAAGAAAA
19156 GGAAGAAGAAAAGAAAA
1 GGAAGAAGAAAAGAAAA
19173 TCCAAAAAAA
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:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
GGAAGAAGAAAAGAAAA
Found at i:20091 original size:14 final size:14
Alignment explanation
Indices: 20067--20099 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20057 TGTGCCTATC
20067 TAATG-AAAATGCT
1 TAATGCAAAATGCT
*
20080 TAATGCAAAATGTT
1 TAATGCAAAATGCT
20094 TAATGC
1 TAATGC
20100 TTGAACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (14 bp):
TAATGCAAAATGCT
Found at i:20626 original size:30 final size:30
Alignment explanation
Indices: 20591--20671 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 30
20581 TATGATATCC
20591 TAATGCATGTATGCAATGTTAAAATTGAAG
1 TAATGCATGTATGCAATGTTAAAATTGAAG
20621 TAATGCTAATGCAAGTATGCAATGTTAAAATTGAAG
1 TAATGC--AT----GTATGCAATGTTAAAATTGAAG
*
20657 TAATGCA-GTACGCAA
1 TAATGCATGTATGCAA
20672 AATGCAAGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
29 7 0.16
30 6 0.14
32 2 0.05
34 1 0.02
36 28 0.64
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.30
Consensus pattern (30 bp):
TAATGCATGTATGCAATGTTAAAATTGAAG
Found at i:20630 original size:36 final size:36
Alignment explanation
Indices: 20590--20662 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
20580 GTATGATATC
*
20590 CTAATGCATGTATGCAATGTTAAAATTGAAGTAATG
1 CTAATGCAAGTATGCAATGTTAAAATTGAAGTAATG
20626 CTAATGCAAGTATGCAATGTTAAAATTGAAGTAATG
1 CTAATGCAAGTATGCAATGTTAAAATTGAAGTAATG
20662 C
1 C
20663 AGTACGCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (36 bp):
CTAATGCAAGTATGCAATGTTAAAATTGAAGTAATG
Found at i:20677 original size:36 final size:36
Alignment explanation
Indices: 20601--20678 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
20591 TAATGCATGT
* *
20601 ATGCAATGTTAAAATTGAAGTAATGCTAATGCAAGT
1 ATGCAATGTTAAAATTGAAGTAATGCTAACGCAAGA
20637 ATGCAATGTTAAAATTGAAGTAATGC-AGTACGCAA-A
1 ATGCAATGTTAAAATTGAAGTAATGCTA--ACGCAAGA
20673 ATGCAA
1 ATGCAA
20679 GCTATGAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
35 1 0.03
36 32 0.84
37 5 0.13
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (36 bp):
ATGCAATGTTAAAATTGAAGTAATGCTAACGCAAGA
Found at i:41654 original size:21 final size:21
Alignment explanation
Indices: 41628--41671 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
41618 AAAAACTAGA
* *
41628 TTGCTAAACACCGCCCCCCTT
1 TTGCTAAACACCACCCCCATT
*
41649 TTGCTAAATACCACCCCCATT
1 TTGCTAAACACCACCCCCATT
41670 TT
1 TT
41672 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.41, G:0.07, T:0.30
Consensus pattern (21 bp):
TTGCTAAACACCACCCCCATT
Found at i:41793 original size:22 final size:22
Alignment explanation
Indices: 41765--41811 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
41755 TAACAACTTC
*
41765 TTCTAAC-TTCTTCAAACTTCAT
1 TTCTAACAATCTTCAAA-TTCAT
41787 TTCTAACAAATCTTCAAATTCAT
1 TTCTAAC-AATCTTCAAATTCAT
41810 TT
1 TT
41812 TCCTTCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 7 0.32
24 8 0.36
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (22 bp):
TTCTAACAATCTTCAAATTCAT
Found at i:41850 original size:26 final size:26
Alignment explanation
Indices: 41821--41888 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
41811 TTCCTTCATT
41821 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
41847 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
41873 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
41889 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:42201 original size:21 final size:22
Alignment explanation
Indices: 42172--42217 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
42162 AAAAATTATA
**
42172 AAAATGGGGGGCGGTATTTAGC
1 AAAATGGGGGGCGGTAAATAGC
42194 AAAA-GGGGGGCGGTAAATAGC
1 AAAATGGGGGGCGGTAAATAGC
42215 AAA
1 AAA
42218 CCCCTTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.37, C:0.09, G:0.39, T:0.15
Consensus pattern (22 bp):
AAAATGGGGGGCGGTAAATAGC
Found at i:42618 original size:2 final size:2
Alignment explanation
Indices: 42611--42635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42601 ATCTATAGTG
42611 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
42636 TATGTGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45831 original size:12 final size:12
Alignment explanation
Indices: 45814--45841 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
45804 GGAAGCTCAG
45814 AAAAAAAGAAAA
1 AAAAAAAGAAAA
45826 AAAAAAAGAAAA
1 AAAAAAAGAAAA
45838 AAAA
1 AAAA
45842 GTGAGGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:51897 original size:18 final size:18
Alignment explanation
Indices: 51863--51897 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51853 ATATCAATAA
*
51863 TAGTGCTGGATTGGTTAG
1 TAGTGCTGGATTAGTTAG
*
51881 TAGTGCTGGGTTAGTTA
1 TAGTGCTGGATTAGTTA
51898 CGAATATTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.06, G:0.37, T:0.40
Consensus pattern (18 bp):
TAGTGCTGGATTAGTTAG
Done.