Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006739.1 Corchorus capsularis cultivar CVL-1 contig06760, 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: 18446
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:3824 original size:30 final size:30
Alignment explanation
Indices: 3781--3856 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
3771 TGGAGGCTGT
* *
3781 GGATCAAACTCCTCATCAGGATCCTCATCCA
1 GGATCAAAATCCTCATCAGGATCATCAT-CA
* *
3812 GG-TCAAAATCCTCGTCAGGATCATCATCT
1 GGATCAAAATCCTCATCAGGATCATCATCA
*
3841 GGATCAAAATCATCAT
1 GGATCAAAATCCTCAT
3857 TTGGGTCAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 3 0.08
30 33 0.87
31 2 0.05
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (30 bp):
GGATCAAAATCCTCATCAGGATCATCATCA
Found at i:3854 original size:18 final size:18
Alignment explanation
Indices: 3831--3890 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
3821 CCTCGTCAGG
* *
3831 ATCATCATCTGGATCAAA
1 ATCATCATCTGGGTCAAC
*
3849 ATCATCATTTGGGTCAAC
1 ATCATCATCTGGGTCAAC
*
3867 ACCATCATCTGGGTCAAC
1 ATCATCATCTGGGTCAAC
3885 ATCATC
1 ATCATC
3891 CTCTAAATCC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (18 bp):
ATCATCATCTGGGTCAAC
Found at i:6225 original size:15 final size:15
Alignment explanation
Indices: 6205--6264 Score: 93
Period size: 15 Copynumber: 4.0 Consensus size: 15
6195 GCTTTCCATG
6205 GGAGAGTGATTCCCA
1 GGAGAGTGATTCCCA
**
6220 GGAGAGTGATTCCTG
1 GGAGAGTGATTCCCA
*
6235 GGAGAGTGATTCCCG
1 GGAGAGTGATTCCCA
6250 GGAGAGTGATTCCCA
1 GGAGAGTGATTCCCA
6265 AGAAAGTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (15 bp):
GGAGAGTGATTCCCA
Found at i:6239 original size:30 final size:31
Alignment explanation
Indices: 6198--6262 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
6188 GTTTGTTGCT
6198 TTCCATGGGAGAGTGATTCCCAGGAGAGTGA
1 TTCCATGGGAGAGTGATTCCCAGGAGAGTGA
*
6229 TTCC-TGGGAGAGTGATTCCCGGGAGAGTGA
1 TTCCATGGGAGAGTGATTCCCAGGAGAGTGA
6259 TTCC
1 TTCC
6263 CAAGAAAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (31 bp):
TTCCATGGGAGAGTGATTCCCAGGAGAGTGA
Found at i:8955 original size:19 final size:19
Alignment explanation
Indices: 8931--8974 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
8921 TTTGCGCAAG
8931 AATGGAAACGG-AATGGAGA
1 AATGGAAA-GGAAATGGAGA
8950 AATGG-AAGGCAAATGGAGA
1 AATGGAAAGG-AAATGGAGA
8969 AATGGA
1 AATGGA
8975 GAGCACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 18 0.82
ACGTcount: A:0.48, C:0.05, G:0.36, T:0.11
Consensus pattern (19 bp):
AATGGAAAGGAAATGGAGA
Found at i:8985 original size:21 final size:20
Alignment explanation
Indices: 8942--8996 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
8932 ATGGAAACGG
*
8942 AATGGAGAAATGGA-AGGCA
1 AATGGAGAAATGGAGAGACA
8961 AATGGAGAAATGGAGAGCACA
1 AATGGAGAAATGGAGAG-ACA
*
8982 AATGGAGGAATGGAG
1 AATGGAGAAATGGAG
8997 TAAGCGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 14 0.44
20 2 0.06
21 16 0.50
ACGTcount: A:0.45, C:0.05, G:0.38, T:0.11
Consensus pattern (20 bp):
AATGGAGAAATGGAGAGACA
Found at i:11693 original size:20 final size:19
Alignment explanation
Indices: 11646--11693 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
11636 TTAAAACAAA
*
11646 AGAAAAGAG-ATTAATTAT
1 AGAATAGAGAATTAATTAT
*
11664 AGAATTGAGAATTATATTAT
1 AGAATAGAGAATTA-ATTAT
*
11684 ATAATAGAGA
1 AGAATAGAGA
11694 TAGTTGGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 7 0.29
19 4 0.17
20 13 0.54
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (19 bp):
AGAATAGAGAATTAATTAT
Found at i:12392 original size:20 final size:19
Alignment explanation
Indices: 12349--12403 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
12339 GAAAACTATT
* * *
12349 ATTTATAGGATTTTTGTTT
1 ATTTAAAGGATTTTTGGTC
*
12368 TTTTAGAAGGATTTTTGGTC
1 ATTTA-AAGGATTTTTGGTC
*
12388 ATTTAAAGTATTTTTG
1 ATTTAAAGGATTTTTG
12404 AAAAGTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.24, C:0.02, G:0.18, T:0.56
Consensus pattern (19 bp):
ATTTAAAGGATTTTTGGTC
Found at i:18259 original size:2 final size:2
Alignment explanation
Indices: 18252--18288 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18242 TAAATTCGTG
18252 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
18289 GCCTCTAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.