Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014175.1 Corchorus olitorius cultivar O-4 contig14208, 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: 26948
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:2719 original size:22 final size:22
Alignment explanation
Indices: 2692--2734 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2682 AGGCAAGTGC
* *
2692 AAATGTGAGATAAATCTGCAAA
1 AAATGTAAGATAAATATGCAAA
*
2714 AAATGTAATATAAATATGCAA
1 AAATGTAAGATAAATATGCAA
2735 GAGAACATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (22 bp):
AAATGTAAGATAAATATGCAAA
Found at i:2894 original size:28 final size:26
Alignment explanation
Indices: 2832--2896 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 26
2822 AAGCTAGTAA
*
2832 TGAAGTACAAAAGACCAAAGTGCCCC
1 TGAAGTACAAAAGACCAAAATGCCCC
*
2858 TGAAATACAAAAGACCAAAATGCCCCCC
1 TGAAGTACAAAAGACCAAAATG--CCCC
2886 TGAAGTACAAA
1 TGAAGTACAAA
2897 TGAATCAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 20 0.59
28 14 0.41
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.12
Consensus pattern (26 bp):
TGAAGTACAAAAGACCAAAATGCCCC
Found at i:9946 original size:19 final size:19
Alignment explanation
Indices: 9922--9958 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
9912 CATTGTTTTA
9922 ATATTAAATTTTTACTTAT
1 ATATTAAATTTTTACTTAT
9941 ATATTAAATTTTTACTTA
1 ATATTAAATTTTTACTTA
9959 AAAATTACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTAAATTTTTACTTAT
Found at i:9965 original size:19 final size:19
Alignment explanation
Indices: 9924--9965 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
9914 TTGTTTTAAT
* *
9924 ATTAAATTTTTACTTATAT
1 ATTAAATTTTTACTTAAAA
9943 ATTAAATTTTTACTTAAAA
1 ATTAAATTTTTACTTAAAA
9962 ATTA
1 ATTA
9966 CTCATAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTAAATTTTTACTTAAAA
Found at i:11516 original size:42 final size:43
Alignment explanation
Indices: 11465--11558 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
11455 AGTGCATTAC
* * *
11465 CTAA-ATTCTA-CTGCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTAATCAAAATAAAG
11506 CTAATATTCTACTCCTCCATCTCTAGATAATTAATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTAATCAAAATAAAG
11551 CTAATATT
1 CTAATATT
11559 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTAATCAAAATAAAG
Found at i:12388 original size:2 final size:2
Alignment explanation
Indices: 12375--12419 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
12365 ACTAAAAGTA
12375 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12417 AT A
1 AT A
12420 AAATTAGAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12494 original size:18 final size:17
Alignment explanation
Indices: 12452--12499 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
12442 TGAATCAATA
12452 TTCTTCAATAATTACAT
1 TTCTTCAATAATTACAT
* *
12469 TT-TATCAATATTCTGCAT
1 TTCT-TCAATAAT-TACAT
12487 TTCTTCAATAATT
1 TTCTTCAATAATT
12500 GCTTAAGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
16 1 0.04
17 10 0.40
18 13 0.52
19 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.02, T:0.50
Consensus pattern (17 bp):
TTCTTCAATAATTACAT
Found at i:14082 original size:2 final size:2
Alignment explanation
Indices: 14075--14107 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14065 TTAACTTGTA
14075 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14108 ACCATAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14651 original size:2 final size:2
Alignment explanation
Indices: 14644--14687 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
14634 TTTTATAGGA
* *
14644 AT AT AT AT AT TT AT AGG A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
14686 AT
1 AT
14688 GTTTCTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14658 original size:18 final size:18
Alignment explanation
Indices: 14635--14676 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
14625 TATAATAGTT
14635 TTTATAGGAATATATATA
1 TTTATAGGAATATATATA
14653 TTTATAGGAATATATATA
1 TTTATAGGAATATATATA
*
14671 TATATA
1 TTTATA
14677 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (18 bp):
TTTATAGGAATATATATA
Found at i:15332 original size:49 final size:48
Alignment explanation
Indices: 15220--15348 Score: 138
Period size: 49 Copynumber: 2.7 Consensus size: 48
15210 AGCGTGTCAA
* * *
15220 TCAATTTTGTATAAAAATTGATAATAA-GTGCAATGAAAAGTAAATGC
1 TCAATTTTGTATAAAAATTGAGAAAAAGGTGCAATGAAAAGTAAAGGC
* * * * *
15267 TCAATTTTATCTTAAAAATTGAGAAAAAGGTGCGA-GTAAAATTAAAGGT
1 TCAATTTTGT-ATAAAAATTGAGAAAAAGGTGCAATG-AAAAGTAAAGGC
15316 TCAATTTTGTAGTAAAAATTGAGAAAAA-GTGCA
1 TCAATTTTGTA-TAAAAATTGAGAAAAAGGTGCA
15349 GGAAATGTAA
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
47 9 0.13
48 19 0.28
49 39 0.58
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (48 bp):
TCAATTTTGTATAAAAATTGAGAAAAAGGTGCAATGAAAAGTAAAGGC
Done.