Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012811.1 Corchorus olitorius cultivar O-4 contig12844, 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: 11151
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Found at i:2569 original size:45 final size:45
Alignment explanation
Indices: 2505--2633 Score: 204
Period size: 45 Copynumber: 2.9 Consensus size: 45
2495 TGCAACAATT
*
2505 AATATTAACTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
* * * *
2550 AATATTAGCTTTATTTTGATGAATTACGTAGAGATAGATGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
*
2595 AGTATTAGCTTTATTTTGATGAATTACCTAGAGATGGAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAG
2634 TAGAATTTAG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Found at i:3600 original size:23 final size:23
Alignment explanation
Indices: 3574--3617 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3564 ATTATTCTAC
3574 TAAAAAC-TCTATTTTTATAAAAT
1 TAAAAACAT-TATTTTTATAAAAT
**
3597 TAAATTCATTATTTTTATAAA
1 TAAAAACATTATTTTTATAAA
3618 TATTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAAAACATTATTTTTATAAAAT
Found at i:3710 original size:31 final size:31
Alignment explanation
Indices: 3672--3733 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3662 AGTTTTGTAA
3672 AACTTTTGAAACACCTATTATACCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
*
3703 AACTTTTGAATCACCTATTATACCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
3734 TTTGAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.44
Consensus pattern (31 bp):
AACTTTTGAAACACCTATTATACCCTTATTT
Found at i:3847 original size:14 final size:14
Alignment explanation
Indices: 3828--3866 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
3818 TATCTTTATA
*
3828 ACTATTTTATTTTT
1 ACTATTTTACTTTT
3842 ACTATTTTACTTTT
1 ACTATTTTACTTTT
3856 A-TAGTTTTACT
1 ACTA-TTTTACT
3867 CAACTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (14 bp):
ACTATTTTACTTTT
Found at i:3861 original size:84 final size:85
Alignment explanation
Indices: 3759--3937 Score: 279
Period size: 85 Copynumber: 2.1 Consensus size: 85
3749 TAAATATCAT
* * *
3759 TATTTATATTTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTA-TTAATTAAATCTAATATCT
1 TATTT-TACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCC
*
3823 TTATAACTATTTTATTTTTAC
65 TTATAACTATTTTATTCTTAC
3844 TATTTTACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCT
1 TATTTTACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCT
*
3909 TATACCTATTTTATTCTTAC
66 TATAACTATTTTATTCTTAC
* *
3929 GATATTACT
1 TATTTTACT
3938 AATTTAATCA
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 37 0.43
85 49 0.57
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (85 bp):
TATTTTACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCT
TATAACTATTTTATTCTTAC
Found at i:5542 original size:16 final size:16
Alignment explanation
Indices: 5517--5564 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
5507 TACCCATCTC
5517 AATTATAATATAAACT
1 AATTATAATATAAACT
*
5533 AATT-TGAATA-AAA-A
1 AATTAT-AATATAAACT
5547 AATTATAATATAAACT
1 AATTATAATATAAACT
5563 AA
1 AA
5565 CAAAAATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 8 0.31
15 8 0.31
16 10 0.38
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (16 bp):
AATTATAATATAAACT
Found at i:5556 original size:14 final size:16
Alignment explanation
Indices: 5517--5561 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
5507 TACCCATCTC
*
5517 AATTATAATATAAACT
1 AATTATAATATAAACA
5533 AATT-TGAATA-AAA-A
1 AATTAT-AATATAAACA
5547 AATTATAATATAAAC
1 AATTATAATATAAAC
5562 TAACAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
14 8 0.33
15 8 0.33
16 8 0.33
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (16 bp):
AATTATAATATAAACA
Found at i:5926 original size:31 final size:31
Alignment explanation
Indices: 5869--5927 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
5859 TTCGACTCAT
* *
5869 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
*
5900 CTGGATTTAGGGTCATGCAGGT-TCGGGT
1 CTGGATTCA-GGTCATGCAGGTCTCGGGT
5928 TTTGGCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
Found at i:8649 original size:130 final size:131
Alignment explanation
Indices: 8495--8746 Score: 416
Period size: 130 Copynumber: 1.9 Consensus size: 131
8485 TTGTTTAGAC
8495 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
* * * *
8560 TTTAATTTTTACCATTTTACTATTTTAATTAAAAAAATTATATATATTATAATTTTTTTAATATG
66 TTTAATTTTTACCAATTTACTAATTTAATTAAAAAAATTAAATATATTAAAATTTTTTTAATATG
8625 T
131 T
* *
8626 TTTTATAG-TTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
* * *
8690 TTTTATTTTTATCAATTTACTAATTTAATTAAAAAACTTAAATATATTAAAATTTTT
66 TTTAATTTTTACCAATTTACTAATTTAATTAAAAAAATTAAATATATTAAAATTTTT
8747 AAAATATATT
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
130 104 0.93
131 8 0.07
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (131 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTAATTTTTACCAATTTACTAATTTAATTAAAAAAATTAAATATATTAAAATTTTTTTAATATG
T
Found at i:9857 original size:30 final size:30
Alignment explanation
Indices: 9821--9881 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
9811 ATTAAAAAGT
9821 ACGTTCACTTGTAAAACTTTTGAATTGCCC
1 ACGTTCACTTGTAAAACTTTTGAATTGCCC
9851 ACGTTCACTTGTAAAACTTTTGAATTGCCC
1 ACGTTCACTTGTAAAACTTTTGAATTGCCC
9881 A
1 A
9882 TTATACCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (30 bp):
ACGTTCACTTGTAAAACTTTTGAATTGCCC
Found at i:10830 original size:20 final size:21
Alignment explanation
Indices: 10805--10843 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
10795 GCCCAATTTT
*
10805 AAAGAAAAG-TAAAAGAAATA
1 AAAGAAAAGAGAAAAGAAATA
10825 AAAGAAAAGAGAAAAGAAA
1 AAAGAAAAGAGAAAAGAAA
10844 AGAAAGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (21 bp):
AAAGAAAAGAGAAAAGAAATA
Done.