Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006316.1 Corchorus capsularis cultivar CVL-1 contig06337, 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: 39843
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:11413 original size:25 final size:25
Alignment explanation
Indices: 11385--11438 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
11375 AGTACCGGTC
11385 ATCACCATGCCACCACCGGTCACCT
1 ATCACCATGCCACCACCGGTCACCT
* *
11410 ATCACCATGCCACCACTGGTTACCT
1 ATCACCATGCCACCACCGGTCACCT
11435 ATCA
1 ATCA
11439 ACGTGCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.26, C:0.43, G:0.11, T:0.20
Consensus pattern (25 bp):
ATCACCATGCCACCACCGGTCACCT
Found at i:11445 original size:25 final size:25
Alignment explanation
Indices: 11385--11446 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
11375 AGTACCGGTC
*
11385 ATCACCATGCCACCACCGGTCACCT
1 ATCAACATGCCACCACCGGTCACCT
* * *
11410 ATCACCATGCCACCACTGGTTACCT
1 ATCAACATGCCACCACCGGTCACCT
*
11435 ATCAACGTGCCA
1 ATCAACATGCCA
11447 TAACCAGTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.26, C:0.42, G:0.13, T:0.19
Consensus pattern (25 bp):
ATCAACATGCCACCACCGGTCACCT
Found at i:11670 original size:66 final size:66
Alignment explanation
Indices: 11564--11704 Score: 273
Period size: 66 Copynumber: 2.1 Consensus size: 66
11554 AGTGATTATA
11564 GCTTTGATTGATTGTCTATTCCATAATTTGAATTAGTTGCTTGAATTTCTTTTCTATGTTTTCTA
1 GCTTTGATTGATTGTCTATTCCATAATTTGAATTAGTTGCTTGAATTTCTTTTCTATGTTTTCTA
11629 T
66 T
*
11630 GCTTTGATTGATTGTCTATTCCTTAATTTGAATTAGTTGCTTGAATTTCTTTTCTATGTTTTCTA
1 GCTTTGATTGATTGTCTATTCCATAATTTGAATTAGTTGCTTGAATTTCTTTTCTATGTTTTCTA
11695 T
66 T
11696 GCTTTGATT
1 GCTTTGATT
11705 TAGATCTTAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.55
Consensus pattern (66 bp):
GCTTTGATTGATTGTCTATTCCATAATTTGAATTAGTTGCTTGAATTTCTTTTCTATGTTTTCTA
T
Found at i:11954 original size:11 final size:11
Alignment explanation
Indices: 11938--11968 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
11928 TAGAATCCAT
11938 GAAAATTTTTC
1 GAAAATTTTTC
11949 GAAAATTTTTC
1 GAAAATTTTTC
11960 GAAAATTTT
1 GAAAATTTT
11969 GATTTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (11 bp):
GAAAATTTTTC
Found at i:13365 original size:11 final size:12
Alignment explanation
Indices: 13349--13380 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
13339 GGAGTTCGTG
13349 TTTGAAGATTA-
1 TTTGAAGATTAT
13360 TTTGAAGA-TAT
1 TTTGAAGATTAT
13371 TTTGAAGATT
1 TTTGAAGATT
13381 TGAAGACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (12 bp):
TTTGAAGATTAT
Found at i:15313 original size:21 final size:21
Alignment explanation
Indices: 15289--15343 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
15279 CCAGCAGTAA
15289 TGCCCAAGCACCCAGGTTCAG
1 TGCCCAAGCACCCAGGTTCAG
15310 TGCCCAAGCACCCAGGTTCAG
1 TGCCCAAGCACCCAGGTTCAG
15331 TGCCCAAGCACCC
1 TGCCCAAGCACCC
15344 TTCCACTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.42, G:0.22, T:0.13
Consensus pattern (21 bp):
TGCCCAAGCACCCAGGTTCAG
Found at i:15637 original size:5 final size:5
Alignment explanation
Indices: 15621--15663 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
15611 TCGAGTCTTC
* * *
15621 AAACA AAGCA AAACA AAGCC AAA-A AAACA AAACA AAACA AAAC
1 AAACA AAACA AAACA AAACA AAACA AAACA AAACA AAACA AAAC
15664 CATATGGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
4 3 0.10
5 28 0.90
ACGTcount: A:0.74, C:0.21, G:0.05, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:19758 original size:6 final size:6
Alignment explanation
Indices: 19691--19741 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
19681 TATAATCTGC
19691 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA
19739 TTT
1 TTT
19742 GCTTTGCTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (6 bp):
TTTAGA
Found at i:29402 original size:31 final size:30
Alignment explanation
Indices: 29343--29449 Score: 196
Period size: 30 Copynumber: 3.5 Consensus size: 30
29333 GCAGTAATTG
*
29343 GATTAAGCATAGATTCCAGCCAAAAAAAAA
1 GATTAAGCATAGATTCCGGCCAAAAAAAAA
29373 GATTAAGCATAGATTCCGGCCAAAAAAAAAA
1 GATTAAGCATAGATTCCGGCC-AAAAAAAAA
29404 GATTAAGCATAGATTCCGGCCAAAAAAAAA
1 GATTAAGCATAGATTCCGGCCAAAAAAAAA
29434 GATTAAGCATAGATTC
1 GATTAAGCATAGATTC
29450 AAAATGATCT
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
30 45 0.60
31 30 0.40
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (30 bp):
GATTAAGCATAGATTCCGGCCAAAAAAAAA
Found at i:36072 original size:1 final size:1
Alignment explanation
Indices: 36066--36093 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
36056 AAGTAGTTAT
36066 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
36094 TTAAGTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:36707 original size:17 final size:18
Alignment explanation
Indices: 36675--36709 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36665 TACGAGAGTA
36675 GGGGCTTTTTAGTTTTTT
1 GGGGCTTTTTAGTTTTTT
*
36693 GGGGTTTTTTA-TTTTTT
1 GGGGCTTTTTAGTTTTTT
36710 ATTTATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.06, C:0.03, G:0.26, T:0.66
Consensus pattern (18 bp):
GGGGCTTTTTAGTTTTTT
Done.