Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011111.1 Corchorus capsularis cultivar CVL-1 contig11132, 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: 87384
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1605 original size:11 final size:12
Alignment explanation
Indices: 1575--1604 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1565 AGCTTTCTTT
1575 AAAAAAAGAAAA
1 AAAAAAAGAAAA
1587 AAAAAAAGAAAA
1 AAAAAAAGAAAA
1599 AAAAAA
1 AAAAAA
1605 GCTATTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:5050 original size:51 final size:51
Alignment explanation
Indices: 4994--5137 Score: 216
Period size: 51 Copynumber: 2.8 Consensus size: 51
4984 CCCCCGCACT
* *
4994 CTCTTAAACCCCGGTGACTCTATGGCGAGGGGCACACATGTGAGTCCTGTG
1 CTCTTAAACCCCGGTGACTCCATGGCGAGGGGCACACCTGTGAGTCCTGTG
** * *
5045 CTCTTAAACCCTAGTGACTCCATAGTGAGGGGCACACCTGTGAGTCCTGTG
1 CTCTTAAACCCCGGTGACTCCATGGCGAGGGGCACACCTGTGAGTCCTGTG
* *
5096 CTTTTAAACCCCGGTAACTCCATGGCGAGGGGCACACCTGTG
1 CTCTTAAACCCCGGTGACTCCATGGCGAGGGGCACACCTGTG
5138 GGTTCTATGG
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.21, C:0.28, G:0.27, T:0.24
Consensus pattern (51 bp):
CTCTTAAACCCCGGTGACTCCATGGCGAGGGGCACACCTGTGAGTCCTGTG
Found at i:5184 original size:55 final size:55
Alignment explanation
Indices: 5111--5222 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
5101 AAACCCCGGT
*
5111 AACTCCATGGCGAGGGGCACACCTGTGGGTTCTATGGGTAGTAGTGGAACGTGCC
1 AACTCCATGGCGAAGGGCACACCTGTGGGTTCTATGGGTAGTAGTGGAACGTGCC
*
5166 AACTCCATGGCGAAGGGCACACCTGTGGGTTCTATGGGTAGTAGTGGGACGTGCC
1 AACTCCATGGCGAAGGGCACACCTGTGGGTTCTATGGGTAGTAGTGGAACGTGCC
5221 AA
1 AA
5223 GAGTGCATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (55 bp):
AACTCCATGGCGAAGGGCACACCTGTGGGTTCTATGGGTAGTAGTGGAACGTGCC
Found at i:24229 original size:94 final size:92
Alignment explanation
Indices: 24084--24262 Score: 238
Period size: 93 Copynumber: 1.9 Consensus size: 92
24074 GGAGCAGAAG
* * * *
24084 CTCCTCTCTTAACATGATATGTATTTTATACATGAATCCAATAGAATTTTGCCACTTAA-CTTTT
1 CTCCTCTATTAACATAATATGTATTTTATACATGAATCCAAGAGAATTTTGCAAC-TAAGCTTTT
24148 AAGAAAAGTTCTGCCAACCAGTGATTCTA
65 AAG-AAAGTTCTGCCAACCAGTGATTCTA
* *
24177 CTCCTCTATTGACATAATAATGTATTTTCAATA-A-GAATCTAAGAGAATTTTGCAACTAAGCTT
1 CTCCTCTATTAACATAAT-ATGTATTTT--ATACATGAATCCAAGAGAATTTTGCAACTAAGCTT
24240 TTAAGAAAGTTCTGCCAACCAGT
63 TTAAGAAAGTTCTGCCAACCAGT
24263 AGCTAGTCAT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
93 36 0.47
94 36 0.47
95 1 0.01
96 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (92 bp):
CTCCTCTATTAACATAATATGTATTTTATACATGAATCCAAGAGAATTTTGCAACTAAGCTTTTA
AGAAAGTTCTGCCAACCAGTGATTCTA
Found at i:43202 original size:2 final size:2
Alignment explanation
Indices: 43195--43219 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43185 TAAATCTACT
43195 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
43220 TACGTAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66872 original size:2 final size:2
Alignment explanation
Indices: 66865--66895 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
66855 CACTCACAAA
66865 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
66896 GCACCTCTCA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:68451 original size:18 final size:18
Alignment explanation
Indices: 68418--68452 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
68408 TGAGGAGGCA
*
68418 GCAGAGGAGACGGAGGAC
1 GCAGAGGAGACAGAGGAC
*
68436 GCAGAGGAGGCAGAGGA
1 GCAGAGGAGACAGAGGA
68453 AACTAGCATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.51, T:0.00
Consensus pattern (18 bp):
GCAGAGGAGACAGAGGAC
Done.