Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013754.1 Corchorus capsularis cultivar CVL-1 contig13775, 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: 34481
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:10665 original size:5 final size:5
Alignment explanation
Indices: 10655--10681 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
10645 ATATAGTTTG
10655 CTGTT CTGTT CTGTT CTGTT CTGTT CT
1 CTGTT CTGTT CTGTT CTGTT CTGTT CT
10682 TTATGTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.19, T:0.59
Consensus pattern (5 bp):
CTGTT
Found at i:10970 original size:47 final size:47
Alignment explanation
Indices: 10874--10970 Score: 151
Period size: 47 Copynumber: 2.1 Consensus size: 47
10864 ATCTAATATA
* *
10874 ATAGGATGATCATGTTCCTAATCTAAGTTAAACTCTTAAATCTGTCT
1 ATAGGATGATCATATTCCTAATCTAAGTTAAACTCTTAAATCTGGCT
*
10921 ATAGGATGATCATATTCCTAATCTAATTTAAACTCTTAAAT-TAGGCT
1 ATAGGATGATCATATTCCTAATCTAAGTTAAACTCTTAAATCT-GGCT
10968 ATA
1 ATA
10971 AAAAGGGAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 1 0.02
47 45 0.98
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (47 bp):
ATAGGATGATCATATTCCTAATCTAAGTTAAACTCTTAAATCTGGCT
Found at i:11026 original size:26 final size:26
Alignment explanation
Indices: 10990--11043 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
10980 GGCTTGGTAT
10990 AGGCTTTCACATATTTCAAAAGAAAA
1 AGGCTTTCACATATTTCAAAAGAAAA
11016 AGGCTTTCACATATTTCAAAAGAAAA
1 AGGCTTTCACATATTTCAAAAGAAAA
11042 AG
1 AG
11044 AAATCGATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (26 bp):
AGGCTTTCACATATTTCAAAAGAAAA
Found at i:15175 original size:31 final size:31
Alignment explanation
Indices: 15110--15271 Score: 146
Period size: 31 Copynumber: 5.5 Consensus size: 31
15100 TCCTTTTGTG
* * *
15110 CACGTGGCATGCCACGTGCCA-TTTTTTGTC
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
15140 CACGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* ** * *
15171 CACGTGGCGTGATATGTGTCACTTTTTAGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
15202 CA--T-G--TGGCAC--G--ACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* *
15224 CATGTGGCATGCCACATGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
15255 CACGTGGCGTGCCACGT
1 CACGTGGCATGCCACGT
15272 CGGACACCGT
Statistics
Matches: 106, Mismatches: 16, Indels: 19
0.75 0.11 0.13
Matches are distributed among these distances:
22 12 0.11
24 2 0.02
25 1 0.01
26 3 0.03
27 5 0.05
28 1 0.01
29 2 0.02
30 20 0.19
31 60 0.57
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:15217 original size:22 final size:22
Alignment explanation
Indices: 15191--15232 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
15181 GATATGTGTC
15191 ACTTTTTAGTACATGTGGCACG
1 ACTTTTTAGTACATGTGGCACG
*
15213 ACTTTTTGGTACATGTGGCA
1 ACTTTTTAGTACATGTGGCA
15233 TGCCACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (22 bp):
ACTTTTTAGTACATGTGGCACG
Found at i:15244 original size:53 final size:53
Alignment explanation
Indices: 15160--15262 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
15150 GCCACGTGTC
* * ** *
15160 ACTTTTTGGTACACGTGGCGTGATATGTGTCACTTTTTAGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTAGTACACGTGGCACG
* * *
15213 ACTTTTTGGTACATGTGGCATGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTAGTACACGTGGC
15263 GTGCCACGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCATGACACATGTCACTTTTTAGTACACGTGGCACG
Found at i:21732 original size:45 final size:45
Alignment explanation
Indices: 21683--21774 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
21673 CTTACTGTTG
21683 GAATCGTAATTATTTGGTTTAGTAGCTGTTAAGTTTCTGATTGGA
1 GAATCGTAATTATTTGGTTTAGTAGCTGTTAAGTTTCTGATTGGA
21728 GAATCGTAATTATTTGGTTTAGTAGCTGTTAAGTTTCTGATTGGA
1 GAATCGTAATTATTTGGTTTAGTAGCTGTTAAGTTTCTGATTGGA
21773 GA
1 GA
21775 TTGGAGGGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (45 bp):
GAATCGTAATTATTTGGTTTAGTAGCTGTTAAGTTTCTGATTGGA
Found at i:22909 original size:31 final size:30
Alignment explanation
Indices: 22814--22913 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 30
22804 AAAAATCGAG
* * *
22814 CCCTTATTTAAGCATTTTGGTAAATGTTAGG
1 CCCTTATTTGAGCATTTTAGTAAA-GTTAGA
** *
22845 CCCTTATTTG-GTCAAATTA-T-AAGATCAGA
1 CCCTTATTTGAG-CATTTTAGTAAAG-TTAGA
22874 CCCTTATTTGAGCATTTTAGTAAACGTTAGA
1 CCCTTATTTGAGCATTTTAGTAAA-GTTAGA
22905 CCCTTATTT
1 CCCTTATTT
22914 AAGGCTCCTC
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 1 0.02
29 20 0.37
30 4 0.07
31 28 0.52
32 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTAGTAAAGTTAGA
Found at i:33383 original size:6 final size:7
Alignment explanation
Indices: 33356--33381 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
33346 TCCTTATTTG
33356 TTTTTTC
1 TTTTTTC
33363 TTTTTTC
1 TTTTTTC
33370 TTTTTTC
1 TTTTTTC
33377 TTTTT
1 TTTTT
33382 CTCTAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Done.