Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022241.1 Corchorus olitorius cultivar O-4 contig22274, 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: 90699
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:755 original size:51 final size:50
Alignment explanation
Indices: 654--756 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
644 GTTCTTCATA
** *
654 TTTTTCTTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
* * * *
704 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
755 TT
1 TT
757 CTCTTTCAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 4 0.09
51 39 0.89
52 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGT
Found at i:4454 original size:21 final size:21
Alignment explanation
Indices: 4416--4455 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4406 GGTGCCCACA
* *
4416 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAACACCCATG
*
4437 TGGTTTGCCTGATCACCCA
1 TGGTTTGCCTGAACACCCA
4456 GGTAGGCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TGGTTTGCCTGAACACCCATG
Found at i:9000 original size:21 final size:21
Alignment explanation
Indices: 8967--9006 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8957 CTCCAAGCAA
*
8967 AAACATCTTTGAATTCTCTTAG
1 AAACATCTGTGAATT-TCTTAG
8989 AAAC-TCTGTGAATTTCTT
1 AAACATCTGTGAATTTCTT
9007 TTTTTCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (21 bp):
AAACATCTGTGAATTTCTTAG
Found at i:25114 original size:16 final size:16
Alignment explanation
Indices: 25093--25125 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
25083 TACTTTTGAG
25093 TAGTTATTGATAAGAA
1 TAGTTATTGATAAGAA
25109 TAGTTATTGATAAGAA
1 TAGTTATTGATAAGAA
25125 T
1 T
25126 TGGAAAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (16 bp):
TAGTTATTGATAAGAA
Found at i:26170 original size:30 final size:30
Alignment explanation
Indices: 26070--26172 Score: 127
Period size: 30 Copynumber: 3.5 Consensus size: 30
26060 TTCAGATTCT
*
26070 GAGGATGA-TTTGACCCGGATGAGGATCCC
1 GAGGAGGATTTTGACCCGGATGAGGATCCC
* * *
26099 AAGGAGGATTTCGACCCGGACGAGGATCCC
1 GAGGAGGATTTTGACCCGGATGAGGATCCC
* * *
26129 GAAGAGGATTTTGACCCAGATTAGGATCCC
1 GAGGAGGATTTTGACCCGGATGAGGATCCC
*
26159 GAGGAAGATTTTGA
1 GAGGAGGATTTTGA
26173 AGTGTCAGCC
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
29 6 0.10
30 55 0.90
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.20
Consensus pattern (30 bp):
GAGGAGGATTTTGACCCGGATGAGGATCCC
Found at i:53772 original size:14 final size:13
Alignment explanation
Indices: 53752--53784 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
53742 TTGAAGAACA
53752 ATGGTAGTGTGAC
1 ATGGTAGTGTGAC
53765 ATTGGTAGTGTGAC
1 A-TGGTAGTGTGAC
53779 ATGGTA
1 ATGGTA
53785 TATTCCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.24, C:0.06, G:0.36, T:0.33
Consensus pattern (13 bp):
ATGGTAGTGTGAC
Found at i:65805 original size:2 final size:2
Alignment explanation
Indices: 65798--65823 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65788 CATTATTTTC
65798 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
65824 TCCCACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73330 original size:20 final size:20
Alignment explanation
Indices: 73305--73382 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
73295 CAACAATCAA
*
73305 AAGAAATTTGAGAGAGATAG
1 AAGAAATTTGAGAGAGACAG
* * * *
73325 AAGAAAATAGAGAGAGAGAA
1 AAGAAATTTGAGAGAGACAG
*
73345 AAGAAATTTGAGAGAGACGG
1 AAGAAATTTGAGAGAGACAG
*
73365 AAGAAATTCGAGAGAGAC
1 AAGAAATTTGAGAGAGAC
73383 GAGATCAGAG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.53, C:0.04, G:0.31, T:0.13
Consensus pattern (20 bp):
AAGAAATTTGAGAGAGACAG
Found at i:73358 original size:40 final size:40
Alignment explanation
Indices: 73303--73381 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
73293 TTCAACAATC
*
73303 AAAAGAAATTTGAGAGAGATAGAAGAAAATAGAGAGAGAG
1 AAAAGAAATTTGAGAGAGACAGAAGAAAATAGAGAGAGAG
* * *
73343 AAAAGAAATTTGAGAGAGACGGAAGAAATTCGAGAGAGA
1 AAAAGAAATTTGAGAGAGACAGAAGAAAATAGAGAGAGA
73382 CGAGATCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.54, C:0.03, G:0.30, T:0.13
Consensus pattern (40 bp):
AAAAGAAATTTGAGAGAGACAGAAGAAAATAGAGAGAGAG
Found at i:75107 original size:13 final size:13
Alignment explanation
Indices: 75089--75114 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
75079 CACATTCAAA
75089 ATTCATTCATTAC
1 ATTCATTCATTAC
75102 ATTCATTCATTAC
1 ATTCATTCATTAC
75115 TTTCCATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTCATTCATTAC
Found at i:78157 original size:75 final size:76
Alignment explanation
Indices: 78078--78224 Score: 217
Period size: 75 Copynumber: 1.9 Consensus size: 76
78068 AAACCTCTAT
* * *
78078 AAATTAATAATATTGGGA-TCATGAAAAATTATTAATTTAGAGATGTTATTAATTTATC-AGTGC
1 AAATTAATAATATTGGGACT-ATGAAAAATTATTAATTTAGAAAGGTTATTAATTTATCGAGTAC
78141 TAATTTATATGG
65 TAATTTATATGG
* * *
78153 AAATTAATAATGTTGGGACTATGAAAAATTATTAATTTGGAAAGGTTATTAATTTATCGAGTATT
1 AAATTAATAATATTGGGACTATGAAAAATTATTAATTTAGAAAGGTTATTAATTTATCGAGTACT
78218 AATTTAT
66 AATTTAT
78225 GGAGGTTATA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 52 0.81
76 12 0.19
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.41
Consensus pattern (76 bp):
AAATTAATAATATTGGGACTATGAAAAATTATTAATTTAGAAAGGTTATTAATTTATCGAGTACT
AATTTATATGG
Done.