Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015460.1 Corchorus olitorius cultivar O-4 contig15493, 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: 80660
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:17986 original size:19 final size:21
Alignment explanation
Indices: 17960--18017 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 21
17950 CTGTTTGGCA
17960 ACTGTACAGATAAGATTACA-
1 ACTGTACAGATAAGATTACAT
* * *
17980 A-TGTACATATTAGATTAGAT
1 ACTGTACAGATAAGATTACAT
*
18000 ACTGTACAGATGAGATTA
1 ACTGTACAGATAAGATTA
18018 TTAGAACAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 15 0.48
20 2 0.06
21 14 0.45
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (21 bp):
ACTGTACAGATAAGATTACAT
Found at i:38468 original size:2 final size:2
Alignment explanation
Indices: 38463--38488 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38453 CACAATATGA
38463 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
38489 GATGGTCAAA
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:42463 original size:12 final size:12
Alignment explanation
Indices: 42445--42475 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42435 ATATCTTAGG
42445 AAAAAAGATAAA
1 AAAAAAGATAAA
*
42457 GAAAAAGATAAA
1 AAAAAAGATAAA
42469 AAAAAAG
1 AAAAAAG
42476 TATATCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (12 bp):
AAAAAAGATAAA
Found at i:42715 original size:16 final size:16
Alignment explanation
Indices: 42694--42724 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42684 CTCTCTCTGA
*
42694 AAAAGAAAAGAAGAAG
1 AAAAGAAAAAAAGAAG
42710 AAAAGAAAAAAAGAA
1 AAAAGAAAAAAAGAA
42725 ACAACAATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAGAAG
Found at i:47369 original size:54 final size:54
Alignment explanation
Indices: 47303--47413 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
47293 GGATTTGACC
47303 CGCGTCGCGCACCTGGTTATGGTGGGTGAATCTCCCAACAGGGGCAGCTGCGTA
1 CGCGTCGCGCACCTGGTTATGGTGGGTGAATCTCCCAACAGGGGCAGCTGCGTA
* *
47357 CGCGTCGTGCACCTGGTTATGGTGGGTGAGTCTCCCAACAGGGGCAGCTGCGTA
1 CGCGTCGCGCACCTGGTTATGGTGGGTGAATCTCCCAACAGGGGCAGCTGCGTA
47411 CGC
1 CGC
47414 AAGGTCTCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.21
Consensus pattern (54 bp):
CGCGTCGCGCACCTGGTTATGGTGGGTGAATCTCCCAACAGGGGCAGCTGCGTA
Found at i:58530 original size:32 final size:32
Alignment explanation
Indices: 58489--58553 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
58479 CATGTAATGG
58489 TTTTTTTTTTGGCCGAAGAACAAAATCTTTGT
1 TTTTTTTTTTGGCCGAAGAACAAAATCTTTGT
58521 TTTTTTTTTTGGCCGAAGAACAAAATCTTTGT
1 TTTTTTTTTTGGCCGAAGAACAAAATCTTTGT
58553 T
1 T
58554 GTCTTAGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (32 bp):
TTTTTTTTTTGGCCGAAGAACAAAATCTTTGT
Found at i:61134 original size:29 final size:28
Alignment explanation
Indices: 61100--61155 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
61090 GTTATTCCAC
* * *
61100 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAACGTTCTT-AAAATTAGAAAT
61129 GTTCTTGAACGTTCTTAAAATTAGAAA
1 GTTCTTGAACGTTCTTAAAATTAGAAA
61156 GTTTGAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (28 bp):
GTTCTTGAACGTTCTTAAAATTAGAAAT
Found at i:69121 original size:2 final size:2
Alignment explanation
Indices: 69114--69145 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
69104 GAGTAATAAC
69114 AT AT AT 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 AT AT AT
69146 GAAAAGCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69272 original size:54 final size:56
Alignment explanation
Indices: 69190--69300 Score: 154
Period size: 54 Copynumber: 2.0 Consensus size: 56
69180 ATTTTGGCAG
* * *
69190 TTCCCTTGCTGCCTTTTGGTGACTAGGATCA-ACT-GCTGGTTGTTGATGATGATC
1 TTCCCTTGCTGCCTCTTGGCGACCAGGATCACACTAGCTGGTTGTTGATGATGATC
* *
69244 TTCCCTTGCTGCCTCTTGGCGACCAGGATGATCAGTAGCTGGTTGTTGATGATGATC
1 TTCCCTTGCTGCCTCTTGGCGACCAGGATCA-CACTAGCTGGTTGTTGATGATGATC
69301 CGAGTTATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
54 27 0.55
56 2 0.04
57 20 0.41
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.36
Consensus pattern (56 bp):
TTCCCTTGCTGCCTCTTGGCGACCAGGATCACACTAGCTGGTTGTTGATGATGATC
Found at i:70389 original size:2 final size:2
Alignment explanation
Indices: 70382--70415 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
70372 GTTTAGGTAC
70382 AT AT AT AT 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 AT AT AT AT
70416 GCACAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73085 original size:6 final size:6
Alignment explanation
Indices: 73074--73116 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
73064 GTAGAAAGAA
* *
73074 TTTTCC TTTTCC TTTTCC CTTTCC TTTTCC TTCTCC TTTTCC T
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC T
73117 GATCCTTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (6 bp):
TTTTCC
Found at i:73122 original size:24 final size:24
Alignment explanation
Indices: 73074--73138 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
73064 GTAGAAAGAA
* *
73074 TTTTCCTTTTCCTTTTCCCTTTCC
1 TTTTCCTTCTCCTTTTCCCTATCC
73098 TTTTCCTTCTCCTTTT-CCTGATCC
1 TTTTCCTTCTCCTTTTCCCT-ATCC
* *
73122 TTATCCTGCTTCCTTTT
1 TTTTCCTTC-TCCTTTT
73139 TGTTTGGGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.09
24 25 0.71
25 7 0.20
ACGTcount: A:0.03, C:0.35, G:0.03, T:0.58
Consensus pattern (24 bp):
TTTTCCTTCTCCTTTTCCCTATCC
Found at i:73315 original size:2 final size:2
Alignment explanation
Indices: 73310--73337 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
73300 ATAACAAATA
73310 AT 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 AT
73338 GAAAGCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.