Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022498.1 Corchorus olitorius cultivar O-4 contig22531, 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: 12466
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:900 original size:31 final size:31
Alignment explanation
Indices: 849--940 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
839 ACTTTTTGAA
849 ACACATGATCACTTTTTTGGTACACATGGCGTG
1 ACACATG-TCAC-TTTTTGGTACACATGGCGTG
* ** *
882 ATATGTGTCACTTTTTGGTATACATGGCGTG
1 ACACATGTCACTTTTTGGTACACATGGCGTG
* * *
913 CCACATGTCGCTTTTTGGTACACGTGGC
1 ACACATGTCACTTTTTGGTACACATGGC
941 ATGCCATCGT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
31 40 0.83
32 4 0.08
33 4 0.08
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (31 bp):
ACACATGTCACTTTTTGGTACACATGGCGTG
Found at i:1150 original size:2 final size:2
Alignment explanation
Indices: 1143--1180 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1133 TCAGAATATG
1143 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1181 TTTGAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5005 original size:16 final size:17
Alignment explanation
Indices: 4984--5027 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
4974 AATTCTTTTG
*
4984 TTTTTTTTTTTA-ATTC
1 TTTTTTATTTTATATTC
*
5000 TTTTTTATTTTATTTTC
1 TTTTTTATTTTATATTC
*
5017 TTTTTAATTTT
1 TTTTTTATTTT
5028 TGTAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTATTTTATATTC
Found at i:5010 original size:17 final size:18
Alignment explanation
Indices: 4984--5028 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
4974 AATTCTTTTG
4984 TTTTTT-TTTTTA-ATTC
1 TTTTTTATTTTTATATTC
*
5000 TTTTTTA-TTTTATTTTC
1 TTTTTTATTTTTATATTC
*
5017 TTTTTAATTTTT
1 TTTTTTATTTTT
5029 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTATTTTTATATTC
Found at i:5010 original size:21 final size:21
Alignment explanation
Indices: 4974--5015 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4964 CGGCGTCGAC
*
4974 AATTCTTTTGTTTTTTTTTTT
1 AATTCTTTTGTTTTTTATTTT
4995 AATTCTTTT-TTATTTTATTTT
1 AATTCTTTTGTT-TTTTATTTT
5016 CTTTTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (21 bp):
AATTCTTTTGTTTTTTATTTT
Found at i:5608 original size:46 final size:46
Alignment explanation
Indices: 5541--5634 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
5531 GAAGAGTACA
*
5541 CCGCTACATGATTAGCTATAATACCGAAATGCTAATCTATGACCTT
1 CCGCTACATGATTAGCTATAATACCAAAATGCTAATCTATGACCTT
5587 CCGCTACATGATTAGCTATAATACCAAAATGCTAATCTATGACCTT
1 CCGCTACATGATTAGCTATAATACCAAAATGCTAATCTATGACCTT
5633 CC
1 CC
5635 CCAACAAACA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (46 bp):
CCGCTACATGATTAGCTATAATACCAAAATGCTAATCTATGACCTT
Found at i:5871 original size:23 final size:23
Alignment explanation
Indices: 5807--5888 Score: 96
Period size: 23 Copynumber: 3.5 Consensus size: 23
5797 TGGTAATAAA
*
5807 ATAGTGATAAAATTAACTTTAAC
1 ATAGTAATAAAATTAACTTTAAC
*
5830 -T-TTAAATTTATAAATTAACTTTAAC
1 ATAGT-AA--TA-AAATTAACTTTAAC
5855 ATAGTAATAAAATTAACTTTAAC
1 ATAGTAATAAAATTAACTTTAAC
5878 ATAGTAATAAA
1 ATAGTAATAAA
5889 TGGTGAAGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
21 1 0.02
22 2 0.04
23 25 0.50
24 4 0.08
25 14 0.28
26 3 0.06
27 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (23 bp):
ATAGTAATAAAATTAACTTTAAC
Found at i:8660 original size:19 final size:19
Alignment explanation
Indices: 8636--8694 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
8626 CTGTTTAGCA
8636 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
*
8655 ACTGTACAGATTAGATTAGAT
1 ACTGTACAGATGAGATT--AT
* *
8676 ATTGTACATATGAGATTAT
1 ACTGTACAGATGAGATTAT
8695 TAGAACAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAT
Found at i:8683 original size:21 final size:20
Alignment explanation
Indices: 8636--8693 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
8626 CTGTTTAGCA
8636 ACTGTACAGATGAGATT-AT
1 ACTGTACAGATGAGATTAAT
*
8655 ACTGTACAGATTAGATTAGAT
1 ACTGTACAGATGAGATTA-AT
* *
8676 ATTGTACATATGAGATTA
1 ACTGTACAGATGAGATTA
8694 TTAGAACAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAAT
Found at i:9940 original size:20 final size:20
Alignment explanation
Indices: 9912--9953 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
9902 CCGACAATAA
9912 CACTCAGCAGTATCATTGAT
1 CACTCAGCAGTATCATTGAT
*
9932 CACTTAGCAGTATCATTGAT
1 CACTCAGCAGTATCATTGAT
9952 CA
1 CA
9954 TCAACAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (20 bp):
CACTCAGCAGTATCATTGAT
Found at i:10010 original size:51 final size:55
Alignment explanation
Indices: 9951--10057 Score: 159
Period size: 56 Copynumber: 2.0 Consensus size: 55
9941 GTATCATTGA
*
9951 TCATCAACAACATACTCATTTT-G-CTG-AAA-AGTTTTGAAGATTGGGAGCCAT
1 TCATCAACAACATACTCATTTTGGACGGTAAAGAGTTTTGAAGATTGGGAGCCAT
*
10002 TCATCAACAGCATACTCATTTTGGTACGGTAAAGAGTTTTGAAGATTGGGAGCCAT
1 TCATCAACAACATACTCATTTTGG-ACGGTAAAGAGTTTTGAAGATTGGGAGCCAT
10058 ACTCCAAGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
51 21 0.43
52 1 0.02
54 2 0.04
55 3 0.06
56 22 0.45
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (55 bp):
TCATCAACAACATACTCATTTTGGACGGTAAAGAGTTTTGAAGATTGGGAGCCAT
Found at i:10804 original size:22 final size:22
Alignment explanation
Indices: 10776--10819 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10766 GTTGCCGTGA
**
10776 TTCGTTTTTGATCGGTGTCATT
1 TTCGTTTAAGATCGGTGTCATT
10798 TTCGTTTAAGATCGGTGTCATT
1 TTCGTTTAAGATCGGTGTCATT
10820 CGTTTCTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (22 bp):
TTCGTTTAAGATCGGTGTCATT
Found at i:10830 original size:20 final size:20
Alignment explanation
Indices: 10775--10830 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
10765 TGTTGCCGTG
*
10775 ATTCGTTTTTGATCGGTGTC
1 ATTCGTTTATGATCGGTGTC
*
10795 ATTTTCGTTTAAGATCGGTGTC
1 A--TTCGTTTATGATCGGTGTC
*
10817 ATTCGTTTCTGATC
1 ATTCGTTTATGATC
10831 CATATTGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.48
Consensus pattern (20 bp):
ATTCGTTTATGATCGGTGTC
Done.