Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015571.1 Corchorus capsularis cultivar CVL-1 contig15592, 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: 37809
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:737 original size:58 final size:57
Alignment explanation
Indices: 667--852 Score: 224
Period size: 60 Copynumber: 3.3 Consensus size: 57
657 CCCAATAATT
*
667 AAAGTCCTCAAACACATGGGTATTTATAAGTCCCTAAACACAGAGGCAATTCTATATC
1 AAAGTCCTCAAACACAAGGGTATTTATAAGTCCCTAAACACAGAGGC-ATTCTATATC
* *
725 AAAGTCCTCAAACACAAGGGTA--T-TCA-TCCCTAAACACAGAGGCATT-TACATC
1 AAAGTCCTCAAACACAAGGGTATTTATAAGTCCCTAAACACAGAGGCATTCTATATC
*
777 AAAGTCCTCAAACACAAGGGCATCTATATTAAAGTCCCTAAACACAGAGGCA-TCTATA-C
1 AAAGTCCTCAAACACAAGGGTAT-T-TA-T-AAGTCCCTAAACACAGAGGCATTCTATATC
*
836 TAAAGTCCCCAAACACA
1 -AAAGTCCTCAAACACA
853 TGTAACACAG
Statistics
Matches: 111, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
52 26 0.23
53 3 0.03
54 17 0.15
55 2 0.02
56 2 0.02
58 22 0.20
59 3 0.03
60 36 0.32
ACGTcount: A:0.40, C:0.26, G:0.13, T:0.22
Consensus pattern (57 bp):
AAAGTCCTCAAACACAAGGGTATTTATAAGTCCCTAAACACAGAGGCATTCTATATC
Found at i:792 original size:30 final size:28
Alignment explanation
Indices: 751--852 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 28
741 AGGGTATTCA
751 TCCCTAAACACAGAGGCATTTACATCAAAG
1 TCCC-AAACACAGAGGCATTTACAT-AAAG
* *
781 TCCTCAAACACA-AGGGCATCTATATTAAAG
1 TCC-CAAACACAGA-GGCATTTACA-TAAAG
811 TCCCTAAACACAGAGGCATCTATAC-TAAAG
1 TCCC-AAACACAGAGGCAT-T-TACATAAAG
841 TCCCCAAACACA
1 T-CCCAAACACA
853 TGTAACACAG
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
29 2 0.03
30 50 0.83
31 6 0.10
32 2 0.03
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (28 bp):
TCCCAAACACAGAGGCATTTACATAAAG
Found at i:1738 original size:19 final size:19
Alignment explanation
Indices: 1701--1739 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1691 CATGAACATC
*
1701 CATCACTTCATACAGGAAT
1 CATCACTTCATACAAGAAT
1720 CATCATCTTCAT-CAAGAAT
1 CATCA-CTTCATACAAGAAT
1739 C
1 C
1740 TCTCAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (19 bp):
CATCACTTCATACAAGAAT
Found at i:2771 original size:2 final size:2
Alignment explanation
Indices: 2764--2788 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2754 GAGGTAACAT
2764 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 T
2789 TGCAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3542 original size:2 final size:2
Alignment explanation
Indices: 3535--3561 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3525 ATAATGTAAT
3535 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
3562 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4791 original size:2 final size:2
Alignment explanation
Indices: 4780--4809 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4770 GAGGTAACAT
4780 TA TA TA -A 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 TA TA T
4810 TGCAAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5514 original size:5 final size:5
Alignment explanation
Indices: 5504--5541 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
5494 AAAAATTAAT
*
5504 ATATA ATATA ATATA ATATA ATACA ATAT- ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT
5542 TCCATGTCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:8027 original size:18 final size:18
Alignment explanation
Indices: 8004--8041 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
7994 AAGGTATTTT
8004 AAGCTGTATTTCTTTTAG
1 AAGCTGTATTTCTTTTAG
8022 AAGCTGTATTTCTTTTAG
1 AAGCTGTATTTCTTTTAG
8040 AA
1 AA
8042 TTACTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (18 bp):
AAGCTGTATTTCTTTTAG
Found at i:10703 original size:6 final size:6
Alignment explanation
Indices: 10694--10732 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
10684 GGGAGTGGAC
* *
10694 ATGGTG ATGGTC ATGGTG ATGGTG ATGGTG CTGGTG ATG
1 ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG ATGGTG ATG
10733 ACGAATCTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.15, C:0.05, G:0.46, T:0.33
Consensus pattern (6 bp):
ATGGTG
Found at i:11121 original size:30 final size:29
Alignment explanation
Indices: 11085--11154 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 29
11075 AATGTTATGT
* *
11085 AGTACTGATTTTAACTATTATCATGCATGC
1 AGTACTGATTTTAACTATAAGCAT-CATGC
* *
11115 AGTACTGATTTTAACTATAAGCATTATGT
1 AGTACTGATTTTAACTATAAGCATCATGC
11144 AGTACTGATTT
1 AGTACTGATTT
11155 AGTACTGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 14 0.39
30 22 0.61
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (29 bp):
AGTACTGATTTTAACTATAAGCATCATGC
Found at i:11273 original size:54 final size:55
Alignment explanation
Indices: 11208--11317 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
11198 TTGACAAGGC
11208 AATAATGGAAATGTT-AAAAAATTATACACGATTGAAATTGCTTGTCTTCGGTAA
1 AATAATGGAAATGTTAAAAAAATTATACACGATTGAAATTGCTTGTCTTCGGTAA
* *
11262 AATAATTGAAATGTTAAAAAAATTATACACGATTGAAATTGCTTGTCTTGGGTAA
1 AATAATGGAAATGTTAAAAAAATTATACACGATTGAAATTGCTTGTCTTCGGTAA
11317 A
1 A
11318 GTACAAAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
54 14 0.26
55 39 0.74
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (55 bp):
AATAATGGAAATGTTAAAAAAATTATACACGATTGAAATTGCTTGTCTTCGGTAA
Found at i:22589 original size:23 final size:23
Alignment explanation
Indices: 22563--22614 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
22553 GTTTCGATTG
22563 AAAGTTTGGAAATGACTTTCATA
1 AAAGTTTGGAAATGACTTTCATA
* *
22586 AAAGTTTGGGAGTGACTTTCATA
1 AAAGTTTGGAAATGACTTTCATA
22609 AAAGTT
1 AAAGTT
22615 CATGAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.35
Consensus pattern (23 bp):
AAAGTTTGGAAATGACTTTCATA
Found at i:23668 original size:18 final size:18
Alignment explanation
Indices: 23637--23671 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23627 GGTGAAATGG
*
23637 GTCGGTTGAGTCGGTTTT
1 GTCGGGTGAGTCGGTTTT
*
23655 GTCGGGTGATTCGGTTT
1 GTCGGGTGAGTCGGTTT
23672 GTGAAGTCGG
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:0.06, C:0.11, G:0.40, T:0.43
Consensus pattern (18 bp):
GTCGGGTGAGTCGGTTTT
Found at i:23909 original size:40 final size:41
Alignment explanation
Indices: 23844--23944 Score: 111
Period size: 40 Copynumber: 2.5 Consensus size: 41
23834 AAATCATTTT
*
23844 TATT-TTAATATGTAAAATATTTTATTAAATA-AGAATATA
1 TATTATTAATATGTAAAATATTTTATTAAATATAGAATACA
* * *
23883 TA-TATATATATATGTAAGA-ATTTTATTTAATATATAATACA
1 TATTAT-TA-ATATGTAAAATATTTTATTAAATATAGAATACA
*
23924 TATTATTAATATGTAATATAT
1 TATTATTAATATGTAAAATAT
23945 ATATATGTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
38 1 0.02
39 3 0.06
40 23 0.45
41 21 0.41
42 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.48
Consensus pattern (41 bp):
TATTATTAATATGTAAAATATTTTATTAAATATAGAATACA
Found at i:23932 original size:20 final size:20
Alignment explanation
Indices: 23909--23946 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23899 AGAATTTTAT
23909 TTAATATATAATACATATTA
1 TTAATATATAATACATATTA
* *
23929 TTAATATGTAATATATAT
1 TTAATATATAATACATAT
23947 ATATGTGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
TTAATATATAATACATATTA
Found at i:27126 original size:17 final size:18
Alignment explanation
Indices: 27106--27142 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
27096 AAAGAGGAAG
*
27106 GAGAAGAAGAAA-AAAAA
1 GAGAAGAAAAAAGAAAAA
27123 GAGAAGAAAAAAGAAAAA
1 GAGAAGAAAAAAGAAAAA
27141 GA
1 GA
27143 AACGGATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
GAGAAGAAAAAAGAAAAA
Found at i:37069 original size:14 final size:15
Alignment explanation
Indices: 37045--37088 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
37035 CGTTCCACTT
*
37045 TTTACACTTTTGCCC
1 TTTACACTTTTACCC
37060 TTTA-ACTTTTACCC
1 TTTACACTTTTACCC
37074 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
37089 ACTGAGCCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 9 0.36
15 4 0.16
16 4 0.16
17 8 0.32
ACGTcount: A:0.18, C:0.27, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTACACTTTTACCC
Done.