Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014236.1 Corchorus capsularis cultivar CVL-1 contig14257, 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: 22419
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:1934 original size:15 final size:16
Alignment explanation
Indices: 1901--1934 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1891 TATTCCTTTG
*
1901 TTTTCATGTTTTTCAA
1 TTTTCATGTTTTGCAA
1917 TTTTCATG-TTTGCAA
1 TTTTCATGTTTTGCAA
1932 TTT
1 TTT
1935 AGTTTTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.62
Consensus pattern (16 bp):
TTTTCATGTTTTGCAA
Found at i:12076 original size:20 final size:20
Alignment explanation
Indices: 12051--12093 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12041 CCAAGGAATA
12051 ATTACGTCTGTAAGTTATAT
1 ATTACGTCTGTAAGTTATAT
12071 ATTACGTCTGTAAGTTATAT
1 ATTACGTCTGTAAGTTATAT
12091 ATT
1 ATT
12094 TTTCATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (20 bp):
ATTACGTCTGTAAGTTATAT
Found at i:16297 original size:68 final size:68
Alignment explanation
Indices: 16219--16416 Score: 378
Period size: 68 Copynumber: 2.9 Consensus size: 68
16209 AATCAAATAT
*
16219 TAAACATATATCAATTTAATTATAAGTCAAAGTATCCAATTATTGAAACGTAACCGTGTCTACGA
1 TAAACATATATCAATTTCATTATAAGTCAAAGTATCCAATTATTGAAACGTAACCGTGTCTACGA
16284 TAG
66 TAG
16287 TAAACATATATCAATTTCATTATAAGTCAAAGTATCCAATTATTGAAACGTAACCGTGTCTACGA
1 TAAACATATATCAATTTCATTATAAGTCAAAGTATCCAATTATTGAAACGTAACCGTGTCTACGA
16352 TAG
66 TAG
*
16355 TAAACATATATCAATTTCATTATAAGTCAAAGTAACCAATTATTGAAACGTAACCGTGTCTA
1 TAAACATATATCAATTTCATTATAAGTCAAAGTATCCAATTATTGAAACGTAACCGTGTCTA
16417 TGAAAGTAGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 128 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (68 bp):
TAAACATATATCAATTTCATTATAAGTCAAAGTATCCAATTATTGAAACGTAACCGTGTCTACGA
TAG
Found at i:16481 original size:2 final size:2
Alignment explanation
Indices: 16474--16500 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16464 TTGACTTCTT
16474 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 T
16501 TTTGATCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18144 original size:20 final size:20
Alignment explanation
Indices: 18103--18145 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
18093 CTCTCACAAG
*
18103 TTTCTAGCCGTTGAAGCTCT
1 TTTCTAGCCGTTGAAGCACT
18123 TTTCTAGCCGTT-ATAGCACT
1 TTTCTAGCCGTTGA-AGCACT
18143 TTT
1 TTT
18146 TCCACCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTGAAGCACT
Found at i:18439 original size:104 final size:105
Alignment explanation
Indices: 18204--18439 Score: 330
Period size: 105 Copynumber: 2.3 Consensus size: 105
18194 CTGTCAGAAA
* *
18204 AGTATTAGTCGATGAAAACTCAAGTTTTAATTCCAGTGTTAATCGACTAAAACTCCAAGTCTCCA
1 AGTATTAATCGATGAAAACTCAAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAGTCTCCA
* * **
18269 CTTTTAAAAAAGTGGCAGTGTTGACAGTGAGCCCGGAGGT
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * ** *
18309 AGTATTAATCGATGAAAACTCCAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
1 AGTATTAATCGATGAAAACTCAAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAGTCTCCA
*
18374 C-TTTAAAAAAGTGGCAGTGTTGACAGCGAACCTGGAGCC
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * *
18413 AGTATTAATTGATGAATACTTAAGTTT
1 AGTATTAATCGATGAAAACTCAAGTTT
18440 CATGTTTCAA
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
104 56 0.49
105 59 0.51
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (105 bp):
AGTATTAATCGATGAAAACTCAAGTTTTAATTCCAGTATTAATCGACTAAAACTCCAAGTCTCCA
CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
Found at i:18465 original size:105 final size:105
Alignment explanation
Indices: 18204--18467 Score: 305
Period size: 105 Copynumber: 2.5 Consensus size: 105
18194 CTGTCAGAAA
* * * * ***
18204 AGTATTAGTCGATGAAAACTCAAGTTTTAATTCCAGTGTTAATCGACTAAAACTCCAAGTCTCCA
1 AGTATTAATCGATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTCCA
* * **
18269 CTTTTAAAAAAGTGGCAGTGTTGACAGTGAGCCCGGAGGT
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * * ** *
18309 AGTATTAATCGATGAAAACTCCAGTTTTAGTTTTAGTATTAATCGACTAAAACTCCAAGTCTTCA
1 AGTATTAATCGATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTCCA
*
18374 C-TTTAAAAAAGTGGCAGTGTTGACAGCGAACCTGGAGCC
66 CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
* * * * *
18413 AGTATTAATTGATGAATACTTAAGTTTCATGTTTCAACATTCATCGATTAAAACT
1 AGTATTAATCGATGAAAACTCAAGTTTCA-GTTTCAACATTAATCGACTAAAACT
18468 TTCTTTAATT
Statistics
Matches: 136, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
104 57 0.42
105 79 0.58
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (105 bp):
AGTATTAATCGATGAAAACTCAAGTTTCAGTTTCAACATTAATCGACTAAAACTCCAAGTCTCCA
CTTTTAAAAAAGTGGCAGTGTTGACAGCGAACCCGGAGCC
Found at i:19016 original size:22 final size:22
Alignment explanation
Indices: 18991--19036 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
18981 TTCATTTGAA
*
18991 ATAACACAAAATAAATTATTTC
1 ATAACACAAAAGAAATTATTTC
19013 ATAACACAAAAGAAATTATTTC
1 ATAACACAAAAGAAATTATTTC
19035 AT
1 AT
19037 GGCACCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAACACAAAAGAAATTATTTC
Done.