Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010505.1 Corchorus capsularis cultivar CVL-1 contig10526, 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: 53272
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2902 original size:25 final size:25
Alignment explanation
Indices: 2868--2945 Score: 156
Period size: 25 Copynumber: 3.1 Consensus size: 25
2858 TGATTTCTGT
2868 TTTATTAATGCCTTATGCCTGGCCA
1 TTTATTAATGCCTTATGCCTGGCCA
2893 TTTATTAATGCCTTATGCCTGGCCA
1 TTTATTAATGCCTTATGCCTGGCCA
2918 TTTATTAATGCCTTATGCCTGGCCA
1 TTTATTAATGCCTTATGCCTGGCCA
2943 TTT
1 TTT
2946 TTATATATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (25 bp):
TTTATTAATGCCTTATGCCTGGCCA
Found at i:12018 original size:16 final size:17
Alignment explanation
Indices: 11999--12036 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
11989 TTTTTATTTG
11999 AGTTTG-TTTTTGAGTC
1 AGTTTGTTTTTTGAGTC
*
12015 AGTTTGTTTTTTTAGTC
1 AGTTTGTTTTTTGAGTC
12032 AGTTT
1 AGTTT
12037 CGAGTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.13, C:0.05, G:0.21, T:0.61
Consensus pattern (17 bp):
AGTTTGTTTTTTGAGTC
Found at i:13427 original size:16 final size:16
Alignment explanation
Indices: 13403--13433 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13393 TTCAGATTAA
13403 AAAAAAAAATGAAAAC
1 AAAAAAAAATGAAAAC
*
13419 AAAAGAAAATGAAAA
1 AAAAAAAAATGAAAA
13434 TGAAAATCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.03, G:0.10, T:0.06
Consensus pattern (16 bp):
AAAAAAAAATGAAAAC
Found at i:13781 original size:16 final size:16
Alignment explanation
Indices: 13757--13793 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
13747 CGGGTAAGTT
* *
13757 CTTTTCTTTTCCTTTC
1 CTTTCCTTTTCCTCTC
13773 CTTTCCTTTTCCTCTC
1 CTTTCCTTTTCCTCTC
13789 CTTTC
1 CTTTC
13794 TGTTCTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCCTTTTCCTCTC
Found at i:20554 original size:14 final size:14
Alignment explanation
Indices: 20518--20552 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20508 CGTTTTTCAG
*
20518 TTTCTGTTCTTTCT
1 TTTCTTTTCTTTCT
20532 TTTCTTTTCTTT-T
1 TTTCTTTTCTTTCT
20545 TTTCTTTT
1 TTTCTTTT
20553 TCCTGTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:21735 original size:35 final size:35
Alignment explanation
Indices: 21695--21768 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
21685 TTTGCTTTAA
21695 CTAGGTACCACTTTAGCTTTAATTACTATACATTT
1 CTAGGTACCACTTTAGCTTTAATTACTATACATTT
21730 CTAGGTACCACTTTAGCTTTAATTACTATACATTT
1 CTAGGTACCACTTTAGCTTTAATTACTATACATTT
21765 CTAG
1 CTAG
21769 CGACAACAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.42
Consensus pattern (35 bp):
CTAGGTACCACTTTAGCTTTAATTACTATACATTT
Found at i:40402 original size:21 final size:20
Alignment explanation
Indices: 40364--40403 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40354 TTATCTTTCT
* *
40364 TTTTTTTCTTTTGTCAATTA
1 TTTTCTTCTTTTGCCAATTA
40384 TTTTCTTCTTTTGGCCAATT
1 TTTTCTTCTTTT-GCCAATT
40404 CTGAAACTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.12, C:0.15, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTCTTCTTTTGCCAATTA
Found at i:51155 original size:107 final size:106
Alignment explanation
Indices: 50964--51219 Score: 325
Period size: 107 Copynumber: 2.4 Consensus size: 106
50954 ATAAAAAGTG
* * * * *
50964 CTAAAGGTGAAATGATATGTATTAGAATTAATTTTCGACATATTGCACAATGAGAATACAATGAT
1 CTAAAGGTGAAATGACATG-ATCAGAAATAATTTTTGAC--ATTGCACAATGAGAATACAAGGAT
* * ** *
51029 TGATTAGTTTACATGGTTTGACATTTGTTTCCTTACAAAAACTT
63 TCATTAGTTTAAATGGTTTGACACCTGTTTCCTTACAAAAACTC
*
51073 CTAAAGGTGAAATGACATGAATCAGAAATAATTTTTGACATTGTACAATGAGAATACAAGGATTC
1 CTAAAGGTGAAATGACATG-ATCAGAAATAATTTTTGACATTGCACAATGAGAATACAAGGATTC
* *
51138 ATTAGTTTAAATGGTTTGACACCTGTTTCCTTATAAAAAGTC
65 ATTAGTTTAAATGGTTTGACACCTGTTTCCTTACAAAAACTC
*
51180 CTAAAGGTGAAATGACATG-TCTTGAAATTAATTTTTGACA
1 CTAAAGGTGAAATGACATGATC-AGAAA-TAATTTTTGACA
51220 AATTTTTGTA
Statistics
Matches: 130, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
105 2 0.02
106 4 0.03
107 90 0.69
109 34 0.26
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (106 bp):
CTAAAGGTGAAATGACATGATCAGAAATAATTTTTGACATTGCACAATGAGAATACAAGGATTCA
TTAGTTTAAATGGTTTGACACCTGTTTCCTTACAAAAACTC
Found at i:52980 original size:29 final size:29
Alignment explanation
Indices: 52931--53004 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
52921 GGGTTGAGGA
52931 GGCAAAACGTCTCAAAATTGAAGTTAAAGG
1 GGCAAAACGTC-CAAAATTGAAGTTAAAGG
* * * *
52961 GGCAAAATGTCCTAAATTGAAGTTCATGG
1 GGCAAAACGTCCAAAATTGAAGTTAAAGG
52990 GGCAAAACGTCCAAA
1 GGCAAAACGTCCAAA
53005 CGCTACAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
29 28 0.74
30 10 0.26
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (29 bp):
GGCAAAACGTCCAAAATTGAAGTTAAAGG
Done.