Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006890.1 Corchorus capsularis cultivar CVL-1 contig06911, 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: 23305
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3885 original size:27 final size:28
Alignment explanation
Indices: 3851--3914 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
3841 TAGGGAACTG
* *
3851 ACTTTGAATGGGA-AATTGTTTTGACTA
1 ACTTTGAATGGGAGAACTGTCTTGACTA
*
3878 GCTTTGAAT-GGAGAACTGTCTTGACTA
1 ACTTTGAATGGGAGAACTGTCTTGACTA
*
3905 ACTTGGAATG
1 ACTTTGAATG
3915 AGAGTCTGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 3 0.10
27 27 0.90
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (28 bp):
ACTTTGAATGGGAGAACTGTCTTGACTA
Found at i:8389 original size:27 final size:27
Alignment explanation
Indices: 8356--8407 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
8346 GGGAACTGAC
*
8356 TTTGAATGG-GAAACTGTTTTGACTAGT
1 TTTGAATGGAG-AACTGTCTTGACTAGT
8383 TTTGAATGGAGAACTGTCTTGACTA
1 TTTGAATGGAGAACTGTCTTGACTA
8408 ACTTGAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (27 bp):
TTTGAATGGAGAACTGTCTTGACTAGT
Found at i:11080 original size:29 final size:32
Alignment explanation
Indices: 11041--11128 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 32
11031 AAAAAAATAC
11041 ATTATAATGTTAATTATGATATATTGAA-A-T-
1 ATTATAATGTTAATTATGATATATT-AACATTA
11071 A-TATAATGTTAATTATGATATAATTAACATTA
1 ATTATAATGTTAATTATGATAT-ATTAACATTA
*
11103 CATTATAATGTTAATTACGATATATT
1 -ATTATAATGTTAATTATGATATATT
11129 CTCTAATTAG
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
29 22 0.43
30 5 0.10
31 1 0.02
33 4 0.08
34 19 0.37
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (32 bp):
ATTATAATGTTAATTATGATATATTAACATTA
Found at i:11093 original size:17 final size:17
Alignment explanation
Indices: 11043--11126 Score: 65
Period size: 17 Copynumber: 5.2 Consensus size: 17
11033 AAAAATACAT
11043 TATAATGTTAATTATGA
1 TATAATGTTAATTATGA
*
11060 TAT-AT-TGAA--AT-A
1 TATAATGTTAATTATGA
11072 TATAATGTTAATTATGA
1 TATAATGTTAATTATGA
* *
11089 TATAAT-TAACATTA-CA
1 TATAATGTTA-ATTATGA
*
11105 TTATAATGTTAATTACGA
1 -TATAATGTTAATTATGA
11123 TATA
1 TATA
11127 TTCTCTAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
12 4 0.08
13 4 0.08
14 3 0.06
15 3 0.06
16 7 0.13
17 28 0.54
18 3 0.06
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (17 bp):
TATAATGTTAATTATGA
Found at i:15273 original size:22 final size:21
Alignment explanation
Indices: 15238--15278 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
15228 ACACCGGGAA
15238 GAAATTTTTTAAAAATGCTGT
1 GAAATTTTTTAAAAATGCTGT
15259 GAAATTTTTTAAAAATGCTG
1 GAAATTTTTTAAAAATGCTG
15279 GTTCAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (21 bp):
GAAATTTTTTAAAAATGCTGT
Found at i:15729 original size:18 final size:18
Alignment explanation
Indices: 15708--15748 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
15698 TATCTTTTAA
15708 TTTTCT-AATTTTTCCATT
1 TTTTCTCAATTTTTCC-TT
*
15726 TTTT-TCCATTTTTCCTT
1 TTTTCTCAATTTTTCCTT
15743 TTTTCT
1 TTTTCT
15749 TTTCATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTCTCAATTTTTCCTT
Found at i:19754 original size:15 final size:16
Alignment explanation
Indices: 19731--19765 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
19721 CACTAAAATA
*
19731 TTTTTTCTTCTT-TTC
1 TTTTCTCTTCTTCTTC
19746 TTTTCTCTTCTTCTTC
1 TTTTCTCTTCTTCTTC
19762 TTTT
1 TTTT
19766 TTTTCTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTCTTCTTCTTC
Found at i:19761 original size:21 final size:20
Alignment explanation
Indices: 19735--19775 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
19725 AAAATATTTT
19735 TTCTTCTTTTCTTTTCTCTTC
1 TTCTTCTTTT-TTTTCTCTTC
19756 TTCTTCTTTTTTTTCTCTTC
1 TTCTTCTTTTTTTTCTCTTC
19776 AGAATGCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TTCTTCTTTTTTTTCTCTTC
Found at i:19866 original size:27 final size:27
Alignment explanation
Indices: 19832--19903 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
19822 AAGTGTACTT
19832 AAAATGACCAAAATGCCCCTGGATGTAC
1 AAAATGACCAAAATGCCCCTGGA-GTAC
* * **
19860 -AAATGACCCAAAT-ACCCTTTAGTAC
1 AAAATGACCAAAATGCCCCTGGAGTAC
19885 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
19904 GATGTGATCC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
25 4 0.11
26 17 0.47
27 15 0.42
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGGAGTAC
Found at i:22056 original size:26 final size:26
Alignment explanation
Indices: 22027--22104 Score: 140
Period size: 26 Copynumber: 3.0 Consensus size: 26
22017 CAAATTATCC
22027 GTTAACGTTGATCTCTTTCCATGTTT
1 GTTAACGTTGATCTCTTTCCATGTTT
22053 GTTAACGTTGATCTCTTTCCATGTTT
1 GTTAACGTTGATCTCTTTCCATGTTT
22079 GTTAACGTTGATCTCTTGT-CATGTTT
1 GTTAACGTTGATCTCTT-TCCATGTTT
22105 AGTCTACATC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
26 50 0.98
27 1 0.02
ACGTcount: A:0.15, C:0.18, G:0.17, T:0.50
Consensus pattern (26 bp):
GTTAACGTTGATCTCTTTCCATGTTT
Found at i:22472 original size:6 final size:7
Alignment explanation
Indices: 22446--22471 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
22436 TAAAACCAGA
22446 AAAAAAG
1 AAAAAAG
22453 AAAAAAG
1 AAAAAAG
22460 AAAAAAG
1 AAAAAAG
22467 AAAAA
1 AAAAA
22472 GCAAATGAAA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Done.