Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020742.1 Corchorus olitorius cultivar O-4 contig20775, 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: 66421
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1186 original size:31 final size:31
Alignment explanation
Indices: 1138--1216 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
1128 ATTTATGGCC
*
1138 ATCAATTTGAAG-CTAAACCTTTCA-AAAGTAG
1 ATCAATTTG-AGTCTAAACCTTCCAGAAA-TAG
* * *
1169 GTCAATTTGAGTTTAAACCTTCCAGAAATTG
1 ATCAATTTGAGTCTAAACCTTCCAGAAATAG
1200 ATCAATTTGAGTCTAAA
1 ATCAATTTGAGTCTAAA
1217 AAACTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 2 0.05
31 35 0.88
32 3 0.08
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (31 bp):
ATCAATTTGAGTCTAAACCTTCCAGAAATAG
Found at i:5713 original size:21 final size:19
Alignment explanation
Indices: 5668--5725 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
5658 CTGTTTAGTA
5668 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
5687 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
5708 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
5726 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:16578 original size:86 final size:86
Alignment explanation
Indices: 16486--16654 Score: 311
Period size: 86 Copynumber: 2.0 Consensus size: 86
16476 TGTTTTGGTA
* *
16486 TATGGTAATCCCCGCTCTGTCCCGTATATATTAATAATAATATTTTTAAAATTCATTTTTTATAT
1 TATGGTAATCCCCGCTCCGTCCCGTATATATTAATAATAATATTTTTAAAATTCATTTTTAATAT
16551 ATTTTAAAGATGTTTAAGCAG
66 ATTTTAAAGATGTTTAAGCAG
*
16572 TATGGTAATCTCCGCTCCGTCCCGTATATATTAATAATAATATTTTTAAAATTCATTTTTAATAT
1 TATGGTAATCCCCGCTCCGTCCCGTATATATTAATAATAATATTTTTAAAATTCATTTTTAATAT
16637 ATTTTAAAGATGTTTAAG
66 ATTTTAAAGATGTTTAAG
16655 TAGTTAAATA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (86 bp):
TATGGTAATCCCCGCTCCGTCCCGTATATATTAATAATAATATTTTTAAAATTCATTTTTAATAT
ATTTTAAAGATGTTTAAGCAG
Found at i:25262 original size:4 final size:4
Alignment explanation
Indices: 25255--25281 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
25245 TATAGTTAGC
25255 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
25282 CTTGATCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:40051 original size:15 final size:15
Alignment explanation
Indices: 40031--40067 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
40021 TTGACATTCT
40031 TGGTTTGGTTTGCCA
1 TGGTTTGGTTTGCCA
40046 TGGTTTGGTTTGCCA
1 TGGTTTGGTTTGCCA
40061 T-GTTTGG
1 TGGTTTGG
40068 GCTAAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.05, C:0.11, G:0.35, T:0.49
Consensus pattern (15 bp):
TGGTTTGGTTTGCCA
Found at i:40702 original size:22 final size:20
Alignment explanation
Indices: 40655--40702 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
40645 GTCATTCTTC
*
40655 TCTCTCCCCCCCATTAACTC
1 TCTCTCCCCCCCATTAACTA
* *
40675 TTTCTCCTCCTCCCATTCACTA
1 TCTCTCC-CC-CCCATTAACTA
40697 TCTCTC
1 TCTCTC
40703 TTTATAAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.27
21 2 0.09
22 14 0.64
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (20 bp):
TCTCTCCCCCCCATTAACTA
Found at i:50474 original size:18 final size:18
Alignment explanation
Indices: 50451--50485 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
50441 TGTATTATTG
*
50451 TTTATATTTAATCATCAC
1 TTTATACTTAATCATCAC
*
50469 TTTATACTTAATGATCA
1 TTTATACTTAATCATCA
50486 AATATTGAAT
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:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (18 bp):
TTTATACTTAATCATCAC
Found at i:51778 original size:14 final size:14
Alignment explanation
Indices: 51744--51781 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
51734 ATATACTCCC
*
51744 TCTGTCCCATATTA
1 TCTGTCTCATATTA
51758 TCTGTCTCATATTA
1 TCTGTCTCATATTA
51772 TCTGTCTCAT
1 TCTGTCTCAT
51782 TTGGGTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.18, C:0.26, G:0.08, T:0.47
Consensus pattern (14 bp):
TCTGTCTCATATTA
Found at i:54003 original size:2 final size:2
Alignment explanation
Indices: 53996--54024 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
53986 CTTGCTTGCG
53996 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
54025 CTTTTCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:55747 original size:158 final size:157
Alignment explanation
Indices: 55477--55809 Score: 479
Period size: 158 Copynumber: 2.1 Consensus size: 157
55467 GCCCTGTTAT
* * * ** *
55477 CGCCTTTGTCGCTATGTTAGTTGTTCAAAATTATTGGATTCCGCAGATGCCGGATGTATAACGTG
1 CGCCTTTGTCGTTATGTTAGTTCTTCAAAATGATTAAATTCCGCAGATGCCGGATGCATAACGTG
*
55542 CTGAATGCACTACTCTAATACTATCAAAATCCAACAAGAATTTGCTTTTTATGCTTCCGAAATCC
66 CTGAATGCACTACTCTAATACTATCAAAATCCAACAAGAATTTGCTTTTTATGCTTCCAAAATCC
**
55607 CAACAGTTCTTGTTTTCTCCCTGACAC
131 CAACAGTTCTTGACTTCTCCCTGACAC
** *
55634 CGCCTTTGTCGTTATGTTAGTTCTTCAGGATGATTAAAGTTCCGCAGATGCCGGATGCATCACGT
1 CGCCTTTGTCGTTATGTTAGTTCTTCAAAATGATTAAA-TTCCGCAGATGCCGGATGCATAACGT
* * *
55699 GTTTAATGCACTACTCTAATA-TGATCAAAATCCAACAGGAATTTGCTTTTTATGCTTCCAAAAT
65 GCTGAATGCACTACTCTAATACT-ATCAAAATCCAACAAGAATTTGCTTTTTATGCTTCCAAAAT
* * *
55763 CCTAACCGTTCTTGACTTCTCCCTGCCAC
129 CCCAACAGTTCTTGACTTCTCCCTGACAC
55792 CGCCTTTGTCGTTATGTT
1 CGCCTTTGTCGTTATGTT
55810 TCTATGATTC
Statistics
Matches: 156, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
157 32 0.21
158 124 0.79
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (157 bp):
CGCCTTTGTCGTTATGTTAGTTCTTCAAAATGATTAAATTCCGCAGATGCCGGATGCATAACGTG
CTGAATGCACTACTCTAATACTATCAAAATCCAACAAGAATTTGCTTTTTATGCTTCCAAAATCC
CAACAGTTCTTGACTTCTCCCTGACAC
Done.