Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022149.1 Corchorus olitorius cultivar O-4 contig22182, 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: 13809
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:614 original size:23 final size:23
Alignment explanation
Indices: 568--630 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
558 GGAACTAAAT
* *
568 CCAAAGTATAAACTAGAATCTAAG
1 CCAAAGCAT-AACTAAAATCTAAG
* * *
592 CCCAAGCCTAACTAAAATTTAAG
1 CCAAAGCATAACTAAAATCTAAG
*
615 CCAAAGTATAACTAAA
1 CCAAAGCATAACTAAA
631 GTTCAAAGGC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (23 bp):
CCAAAGCATAACTAAAATCTAAG
Found at i:3101 original size:17 final size:17
Alignment explanation
Indices: 3060--3103 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3050 TTTTGAGGAG
*
3060 CTAATAAGGGAATGGGCT
1 CTAA-AAGGAAATGGGCT
*
3078 TTAAAAGGAAATGGGCT
1 CTAAAAGGAAATGGGCT
*
3095 CTGAAAGGA
1 CTAAAAGGA
3104 TTAAAGCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.39, C:0.09, G:0.32, T:0.20
Consensus pattern (17 bp):
CTAAAAGGAAATGGGCT
Found at i:4709 original size:14 final size:14
Alignment explanation
Indices: 4692--4719 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4682 ATTTACTGAA
4692 ATAATAATTATTAT
1 ATAATAATTATTAT
4706 ATAATAATTATTAT
1 ATAATAATTATTAT
4720 TATCCAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATAATTATTAT
Found at i:4728 original size:17 final size:17
Alignment explanation
Indices: 4691--4730 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4681 TATTTACTGA
*
4691 AATAATAATTATTATAT
1 AATAATAATTATTATAC
* *
4708 AATAATTATTATTATCC
1 AATAATAATTATTATAC
4725 AATAAT
1 AATAAT
4731 GTTACTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAATAATTATTATAC
Found at i:4989 original size:19 final size:19
Alignment explanation
Indices: 4965--5013 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
4955 AACAGTTTTT
4965 TTTTTTTAAATA-GGTATAG
1 TTTTTTTAAATATGG-ATAG
* *
4984 TTTTTTTAAAAATGGGTAG
1 TTTTTTTAAATATGGATAG
5003 TTTTTTTAAAT
1 TTTTTTTAAAT
5014 GATATTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 24 0.92
20 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (19 bp):
TTTTTTTAAATATGGATAG
Found at i:7085 original size:20 final size:21
Alignment explanation
Indices: 7047--7087 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
7037 ACCGAATTCA
7047 TGCAAAGGTTGCTTCTCCAAC
1 TGCAAAGGTTGCTTCTCCAAC
* *
7068 TGCAAA-GTTGGTTTTCCAAC
1 TGCAAAGGTTGCTTCTCCAAC
7088 ATCATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (21 bp):
TGCAAAGGTTGCTTCTCCAAC
Found at i:7317 original size:64 final size:64
Alignment explanation
Indices: 7216--7386 Score: 252
Period size: 64 Copynumber: 2.7 Consensus size: 64
7206 TTTTTTTTTT
* *
7216 GCGATCCAACTTTCCCAGAGTTCACATCGCAATAGGAATCCATACGACAGCTTGATCCCACGCG
1 GCGATCCAACTTTCCCAGAGTTCACGTCGCAGTAGGAATCCATACGACAGCTTGATCCCACGCG
* * *
7280 GCGATCCAGCTTTCCCAGAGTTCACGTCGCAGTAGGAATCCATGCGGCAGCTTGATCCCACGCG
1 GCGATCCAACTTTCCCAGAGTTCACGTCGCAGTAGGAATCCATACGACAGCTTGATCCCACGCG
* * * * *
7344 GAGATCCAACTTTCCCAAAGTTCACGCCACAGTTGGAATCCAT
1 GCGATCCAACTTTCCCAGAGTTCACGTCGCAGTAGGAATCCAT
7387 GTGGCAATCC
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 96 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (64 bp):
GCGATCCAACTTTCCCAGAGTTCACGTCGCAGTAGGAATCCATACGACAGCTTGATCCCACGCG
Found at i:7795 original size:14 final size:15
Alignment explanation
Indices: 7778--7815 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
7768 ACTTATTATT
7778 TATTAT-TTAAAATA
1 TATTATATTAAAATA
*
7792 TATT-TATTAATATA
1 TATTATATTAAAATA
7806 TATTATATTA
1 TATTATATTA
7816 TATCTAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 15 0.71
15 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATATTAAAATA
Found at i:7795 original size:18 final size:19
Alignment explanation
Indices: 7750--7800 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
7740 AAAAAAATGC
7750 AATATTTATTTATT-TTTAA
1 AATA-TTATTTATTATTTAA
**
7769 CTTATTATTTATTATTTAA
1 AATATTATTTATTATTTAA
7788 AATA-TATTTATTA
1 AATATTATTTATTA
7801 ATATATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
AATATTATTTATTATTTAA
Found at i:9902 original size:2 final size:2
Alignment explanation
Indices: 9897--9940 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
9887 TTTAGAAGAA
9897 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9939 AG
1 AG
9941 TATTAGTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13361 original size:2 final size:2
Alignment explanation
Indices: 13354--13392 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
13344 CTATTAAAAT
13354 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
13393 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13783 original size:2 final size:2
Alignment explanation
Indices: 13776--13806 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13766 ACTTAGAATG
13776 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 A
13807 GTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.