Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009343.1 Corchorus capsularis cultivar CVL-1 contig09364, 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: 38463
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:3448 original size:5 final size:5
Alignment explanation
Indices: 3438--3479 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
3428 TATCTATATG
*
3438 AATTT AATTT AATTT AATTT AATTT AATTT AAATT AATTT AA
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AA
3480 CAGTCACGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:4307 original size:12 final size:12
Alignment explanation
Indices: 4274--4314 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
4264 GGTGGTGAAA
4274 AGGAATTTGTAT
1 AGGAATTTGTAT
*
4286 AGGATTATTTATAT
1 AGGA--ATTTGTAT
4300 AGGAATTTGTAT
1 AGGAATTTGTAT
4312 AGG
1 AGG
4315 TTATCGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 14 0.56
14 11 0.44
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (12 bp):
AGGAATTTGTAT
Found at i:5062 original size:2 final size:2
Alignment explanation
Indices: 5055--5080 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5045 CACAAGCTGG
5055 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5081 CATAATATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11889 original size:18 final size:18
Alignment explanation
Indices: 11866--11900 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11856 TTGACTTAGT
*
11866 CGGGTAATTATCGGGTAA
1 CGGGTAATTAACGGGTAA
*
11884 CGGGTAGTTAACGGGTA
1 CGGGTAATTAACGGGTA
11901 GTGTAAATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.37, T:0.26
Consensus pattern (18 bp):
CGGGTAATTAACGGGTAA
Found at i:12083 original size:25 final size:25
Alignment explanation
Indices: 12055--12116 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
12045 ACACGAACAT
12055 GAGACCTGTTTATAAACGTGTACAC
1 GAGACCTGTTTATAAACGTGTACAC
*
12080 GAGACCTATTTATAAACGTGTACAC
1 GAGACCTGTTTATAAACGTGTACAC
12105 GAGACCTGTTTA
1 GAGACCTGTTTA
12117 CATGATTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (25 bp):
GAGACCTGTTTATAAACGTGTACAC
Found at i:15005 original size:18 final size:18
Alignment explanation
Indices: 14982--15018 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
14972 ATCAGGGTGG
14982 AAATGAGGGTGGCAATGC
1 AAATGAGGGTGGCAATGC
15000 AAATGAGGGTGGCAATGC
1 AAATGAGGGTGGCAATGC
15018 A
1 A
15019 GGTGGCCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.38, T:0.16
Consensus pattern (18 bp):
AAATGAGGGTGGCAATGC
Found at i:15882 original size:24 final size:23
Alignment explanation
Indices: 15824--15870 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
15814 AAGACAAATA
*
15824 AGCAAAATAGCAGCATTTTCAAC
1 AGCAAAATAGAAGCATTTTCAAC
*
15847 AGCAAAACAGAAGCATTTTCAAC
1 AGCAAAATAGAAGCATTTTCAAC
15870 A
1 A
15871 TAGAAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (23 bp):
AGCAAAATAGAAGCATTTTCAAC
Found at i:16668 original size:11 final size:10
Alignment explanation
Indices: 16651--16684 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
16641 GAAATTCGTG
16651 TTTGAAGATT
1 TTTGAAGATT
16661 TCTTGAAGATAT
1 T-TTGAAGAT-T
16673 TTTGAAGATT
1 TTTGAAGATT
16683 TT
1 TT
16685 AAGACAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTGAAGATT
Found at i:18153 original size:31 final size:32
Alignment explanation
Indices: 18097--18156 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
18087 TAAGAGTGTA
* * *
18097 AAATGACCATTAGGTCTTTTAACATAAAAATT
1 AAATGACCATTAAGTATATTAACATAAAAATT
18129 AAATGACCA-TAAGTATATTAACATAAAA
1 AAATGACCATTAAGTATATTAACATAAAA
18157 TTATTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (32 bp):
AAATGACCATTAAGTATATTAACATAAAAATT
Found at i:20518 original size:3 final size:3
Alignment explanation
Indices: 20510--20534 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20500 TTCCTCAACT
20510 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
20535 GTATCGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:20774 original size:22 final size:22
Alignment explanation
Indices: 20749--20795 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
20739 CTACCATTAT
*
20749 TCAATTCTAAAATAGTGTTGTA
1 TCAATTCTAAAATAGTGTTCTA
* *
20771 TCAATTCTGAAATATTGTTCTA
1 TCAATTCTAAAATAGTGTTCTA
20793 TCA
1 TCA
20796 TCTTAATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (22 bp):
TCAATTCTAAAATAGTGTTCTA
Found at i:28713 original size:72 final size:72
Alignment explanation
Indices: 28595--28816 Score: 408
Period size: 72 Copynumber: 3.1 Consensus size: 72
28585 GTGTGGGTTG
* *
28595 TTGTTCCATATGTTATGTCCCAAGAATTATAATCCATGTGGATGGCTTCCAACCTATTAATGGTT
1 TTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
28660 ATACAAT
66 ATACAAT
*
28667 CTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
1 TTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
28732 ATACAAT
66 ATACAAT
*
28739 TTGTTCCATATGTTATGTCCCAAGTAATATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
1 TTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
28804 ATACAAT
66 ATACAAT
28811 TTGTTC
1 TTGTTC
28817 ATAACCAATT
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 145 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (72 bp):
TTGTTCCATATGTTATGTCCCAAGTATTATAATCCATGTGGATGGCTTCCACCCTATTAATGGTT
ATACAAT
Found at i:30624 original size:72 final size:72
Alignment explanation
Indices: 30502--30641 Score: 208
Period size: 72 Copynumber: 1.9 Consensus size: 72
30492 GCTTCTTCAT
* * *
30502 TTAGAGACAAAAATGTTCATGTTTGTCACCTTGGCTTGACCCATTACATTCTATCAATTTCTTTT
1 TTAGAAACAAAAATGCTCATGTTTGTCACCTTGGCTTGACCCATGACATTCTATCAATTTCTTTT
30567 ATTAATA
66 ATTAATA
* * * * *
30574 TTAGAAACAAAAATGCTCATGTTTGTCACCTTGGCTTGGCCCGTGGCATTCTTTTAATTTCTTTT
1 TTAGAAACAAAAATGCTCATGTTTGTCACCTTGGCTTGACCCATGACATTCTATCAATTTCTTTT
30639 ATT
66 ATT
30642 CATAAACATT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (72 bp):
TTAGAAACAAAAATGCTCATGTTTGTCACCTTGGCTTGACCCATGACATTCTATCAATTTCTTTT
ATTAATA
Found at i:32520 original size:79 final size:79
Alignment explanation
Indices: 32427--32584 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
32417 AAGAGTAAGA
32427 GAGGGAGAACTTTTTCTGCTGTGTGGAAGGAATGAAGATAGCAGATTTCTAAGAAAAATAACCAT
1 GAGGGAGAACTTTTTCTGCTGTGTGGAAGGAATGAAGATAGCAGATTTCTAAGAAAAATAACCAT
32492 GTATTAAAAATTGC
66 GTATTAAAAATTGC
32506 GAGGGAGAACTTTTTCTGCTGTGTGGAAGGAATGAAGATAGCAGATTTCTAAGAAAAATAACCAT
1 GAGGGAGAACTTTTTCTGCTGTGTGGAAGGAATGAAGATAGCAGATTTCTAAGAAAAATAACCAT
*
32571 GTATTGAAAATTGC
66 GTATTAAAAATTGC
32585 TATTGATACT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (79 bp):
GAGGGAGAACTTTTTCTGCTGTGTGGAAGGAATGAAGATAGCAGATTTCTAAGAAAAATAACCAT
GTATTAAAAATTGC
Found at i:34487 original size:6 final size:6
Alignment explanation
Indices: 34476--34500 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34466 TACACACACG
34476 CGCACA CGCACA CGCACA CGCACA C
1 CGCACA CGCACA CGCACA CGCACA C
34501 ATATACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CGCACA
Found at i:37529 original size:3 final size:3
Alignment explanation
Indices: 37523--37548 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
37513 ACCACCACCT
37523 CCG CCG CCG CCG CCG CCG CCG CCG CC
1 CCG CCG CCG CCG CCG CCG CCG CCG CC
37549 AGCACCACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.69, G:0.31, T:0.00
Consensus pattern (3 bp):
CCG
Found at i:38109 original size:10 final size:9
Alignment explanation
Indices: 38094--38128 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
38084 CTAATTTGAG
38094 TTTTTTTTC
1 TTTTTTTTC
38103 TTTTTTTTC
1 TTTTTTTTC
38112 TTTTTTTT-
1 TTTTTTTTC
38120 TTTGTTTTT
1 TTT-TTTTT
38129 ACTTGTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 3 0.12
9 22 0.88
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (9 bp):
TTTTTTTTC
Done.