Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019269.1 Corchorus olitorius cultivar O-4 contig19302, 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: 8160
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:663 original size:113 final size:115
Alignment explanation
Indices: 461--687 Score: 377
Period size: 113 Copynumber: 2.0 Consensus size: 115
451 ATATCGACAA
* *
461 TTGCTAACTACTATAACCCGTTAGCAGGGCTTTAAGCTAACTATTATAACCCATTAGCAGGGCCG
1 TTGCTAACTACTATAACCCGTTAGCAGGGCCTTAA-C-AACAATTATAACCCATTAGCAGGGCCG
*
526 TTTTCCAATTACTATAACCCACTGGCCATGGCCGATAGAACATGTTCTCAAT
64 TTTTCCAATTACTATAACCCACTGGCCAGGGCCGATAGAACATGTTCTCAAT
*
578 TTGCTAACTACTATAACCCGTTAGCAGGGCCTT-A-AACAATTATAACCCGTTAGCAGGGCCGTT
1 TTGCTAACTACTATAACCCGTTAGCAGGGCCTTAACAACAATTATAACCCATTAGCAGGGCCGTT
*
641 TTCCAGTTACTATAACCCACTGGCCAGGGCCGATAGAACATGTTCTC
66 TTCCAATTACTATAACCCACTGGCCAGGGCCGATAGAACATGTTCTC
688 TGTCGATCAT
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
113 72 0.69
116 1 0.01
117 32 0.30
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (115 bp):
TTGCTAACTACTATAACCCGTTAGCAGGGCCTTAACAACAATTATAACCCATTAGCAGGGCCGTT
TTCCAATTACTATAACCCACTGGCCAGGGCCGATAGAACATGTTCTCAAT
Found at i:4564 original size:22 final size:22
Alignment explanation
Indices: 4500--4695 Score: 86
Period size: 22 Copynumber: 9.0 Consensus size: 22
4490 TGATGACAAT
* *
4500 ACTGTGAAAGTTTGATAACCTT
1 ACTGTGAAAATTTGATAACCTC
* * *
4522 ATTATG-AAATGGTCGATAACCTC
1 ACTGTGAAAAT--TTGATAACCTC
* *
4545 CCTGTGAAAATTTGATAACCAC
1 ACTGTGAAAATTTGATAACCTC
* * *
4567 ACGGTG-AAATCTTAATAACCAC
1 ACTGTGAAAAT-TTGATAACCTC
* *
4589 ACGGTG-AAATCTTAATAACCTC
1 ACTGTGAAAAT-TTGATAACCTC
* * *
4611 ATTGTGAAATTTTGATAATCTC
1 ACTGTGAAAATTTGATAACCTC
* *
4633 CCTAT-AAAATTTTGATAACCTC
1 ACTGTGAAAA-TTTGATAACCTC
*
4655 A---T-AAAATTTTGATAACCAC
1 ACTGTGAAAA-TTTGATAACCTC
**
4674 ACCATG-AAATTTAGATAACCTC
1 ACTGTGAAAATTT-GATAACCTC
4696 CCTATGAGAA
Statistics
Matches: 136, Mismatches: 27, Indels: 22
0.74 0.15 0.12
Matches are distributed among these distances:
19 18 0.13
21 13 0.10
22 86 0.63
23 15 0.11
24 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (22 bp):
ACTGTGAAAATTTGATAACCTC
Found at i:4660 original size:19 final size:20
Alignment explanation
Indices: 4617--4671 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 20
4607 CCTCATTGTG
4617 AAATTTTGATAATCTCCCTATA
1 AAATTTTGATAA-C-CCCTATA
*
4639 AAATTTTGATAACCTC-ATA
1 AAATTTTGATAACCCCTATA
4658 AAATTTTGATAACC
1 AAATTTTGATAACC
4672 ACACCATGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 17 0.53
20 2 0.06
21 1 0.03
22 12 0.38
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.38
Consensus pattern (20 bp):
AAATTTTGATAACCCCTATA
Found at i:4667 original size:41 final size:41
Alignment explanation
Indices: 4617--4695 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
4607 CCTCATTGTG
* * *
4617 AAATTTTGATAATCTC-CCTATAAAATTTTGATAACCTCATA
1 AAATTTTGATAACCACACC-ATAAAATTTAGATAACCTCATA
*
4658 AAATTTTGATAACCACACCATGAAATTTAGATAACCTC
1 AAATTTTGATAACCACACCATAAAATTTAGATAACCTC
4696 CCTATGAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 31 0.94
42 2 0.06
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (41 bp):
AAATTTTGATAACCACACCATAAAATTTAGATAACCTCATA
Found at i:4999 original size:22 final size:22
Alignment explanation
Indices: 4734--5002 Score: 144
Period size: 22 Copynumber: 12.3 Consensus size: 22
4724 TGATCTATAT
*
4734 AATTTTGATAACC-TCTCTATAA
1 AATTTTGATAACCTTCT-TATGA
* * *
4756 AATTTTTATAACCTCCCTATGA
1 AATTTTGATAACCTTCTTATGA
* *
4778 AATTTTGTTAACCTTCTTAGGA
1 AATTTTGATAACCTTCTTATGA
* * *
4800 AATTTTAATAA---GC--A-CA
1 AATTTTGATAACCTTCTTATGA
4816 AATTTTGATAACCTTCCTCCCTATGA
1 AATTTTGATAACCTT-CT---TATGA
* * *
4842 AATTTTGTTAGCCTTCTTATTA
1 AATTTTGATAACCTTCTTATGA
* * *
4864 AATTTTGATAA-CTACACTATAA
1 AATTTTGATAACCTTC-TTATGA
*
4886 AATTTCGATAACCTT-TGTATGA
1 AATTTTGATAACCTTCT-TATGA
* * ** * *
4908 TATTTTGTTAACCACCCTAAGA
1 AATTTTGATAACCTTCTTATGA
*
4930 AATTTTGATAACCTTTTTATGA
1 AATTTTGATAACCTTCTTATGA
* *
4952 AATTTTGGTAATC-TCTGTATGA
1 AATTTTGATAACCTTCT-TATGA
* * *
4974 AATTTTGCTAACCTTCTCATGT
1 AATTTTGATAACCTTCTTATGA
4996 AATTTTG
1 AATTTTG
5003 GTTTGATTGT
Statistics
Matches: 181, Mismatches: 49, Indels: 34
0.69 0.19 0.13
Matches are distributed among these distances:
16 11 0.06
17 1 0.01
19 1 0.01
20 1 0.01
21 5 0.03
22 139 0.77
23 6 0.03
25 3 0.02
26 14 0.08
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (22 bp):
AATTTTGATAACCTTCTTATGA
Done.