Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007727.1 Corchorus capsularis cultivar CVL-1 contig07748, 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: 53876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3621 original size:55 final size:57
Alignment explanation
Indices: 3532--3698 Score: 248
Period size: 55 Copynumber: 2.9 Consensus size: 57
3522 GTAGACTGAT
* * *
3532 CATTCTGCCCTCTACGGTTGTCCACGACTTGTTCTGTTTTTGGTGTTTGTTCTGAACC
1 CATTCTG-CCTATACGGTTGTCCACGACTTGTTCTGTTTTGGGTGTTTGTTCCGAACC
* *
3590 CGTTCTG-C-ATACGGTTGTCCACGACTTGTTCTGTTTTGGGTGTTTGTTCCGGACC
1 CATTCTGCCTATACGGTTGTCCACGACTTGTTCTGTTTTGGGTGTTTGTTCCGAACC
*
3645 CATTCTGCCCTATACGGTTGTCCACGACTTATTCTGTTTTGGGTGTTTGTTCCG
1 CATTCTG-CCTATACGGTTGTCCACGACTTGTTCTGTTTTGGGTGTTTGTTCCG
3699 GACTACATGT
Statistics
Matches: 99, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
55 49 0.49
56 1 0.01
57 1 0.01
58 48 0.48
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (57 bp):
CATTCTGCCTATACGGTTGTCCACGACTTGTTCTGTTTTGGGTGTTTGTTCCGAACC
Found at i:3681 original size:58 final size:58
Alignment explanation
Indices: 3532--3701 Score: 265
Period size: 58 Copynumber: 3.0 Consensus size: 58
3522 GTAGACTGAT
* * * *
3532 CATTCTGCCCTCTACGGTTGTCCACGACTTGTTCTGTTTTTGGTGTTTGTTCTGAACC
1 CATTCTGCCCTATACGGTTGTCCACGACTTGTTCTGTTTTGGGTGTTTGTTCCGGACC
*
3590 CGTTCTG--C-ATACGGTTGTCCACGACTTGTTCTGTTTTGGGTGTTTGTTCCGGACC
1 CATTCTGCCCTATACGGTTGTCCACGACTTGTTCTGTTTTGGGTGTTTGTTCCGGACC
*
3645 CATTCTGCCCTATACGGTTGTCCACGACTTATTCTGTTTTGGGTGTTTGTTCCGGAC
1 CATTCTGCCCTATACGGTTGTCCACGACTTGTTCTGTTTTGGGTGTTTGTTCCGGAC
3702 TACATGTGAG
Statistics
Matches: 102, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
55 49 0.48
56 1 0.01
57 1 0.01
58 51 0.50
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.41
Consensus pattern (58 bp):
CATTCTGCCCTATACGGTTGTCCACGACTTGTTCTGTTTTGGGTGTTTGTTCCGGACC
Found at i:4018 original size:2 final size:2
Alignment explanation
Indices: 4013--4040 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4003 CTCAGAGCAA
4013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4041 GCACGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4512 original size:3 final size:3
Alignment explanation
Indices: 4504--4532 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4494 GAGTCTTTTT
4504 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4533 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4539 original size:3 final size:3
Alignment explanation
Indices: 4533--4570 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4523 AATAATAATA
4533 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4571 AAATAAATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:11003 original size:12 final size:11
Alignment explanation
Indices: 10976--11005 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10966 TTGATGCATG
10976 CAAAAATGTGA
1 CAAAAATGTGA
*
10987 CAAAAATGTTA
1 CAAAAATGTGA
10998 CAAAAATG
1 CAAAAATG
11006 GCCATACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (11 bp):
CAAAAATGTGA
Found at i:11643 original size:68 final size:68
Alignment explanation
Indices: 11529--11664 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 68
11519 ATCCTCTCGG
* * * * * *
11529 TTATTTAGTAGCCATGTTGGGTCATGATTAATCGAGAGTGAAGTTGTATCGAACCTCAAACAGAA
1 TTATCTAGTAGCCATATTGGATCATAATTAATCGAGAGTGAAGTTGTATCAAACCCCAAACAGAA
11594 GGA
66 GGA
* * *
11597 TTATCTAGTAGCCATATTGGATCCTAATTAATCGAGAGTGAAGTTGTGTCAAACCCCAAATAGAA
1 TTATCTAGTAGCCATATTGGATCATAATTAATCGAGAGTGAAGTTGTATCAAACCCCAAACAGAA
11662 GGA
66 GGA
11665 AGTTCTCCCA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (68 bp):
TTATCTAGTAGCCATATTGGATCATAATTAATCGAGAGTGAAGTTGTATCAAACCCCAAACAGAA
GGA
Found at i:11756 original size:49 final size:49
Alignment explanation
Indices: 11684--11799 Score: 214
Period size: 49 Copynumber: 2.4 Consensus size: 49
11674 AAGTCCCAAT
*
11684 GCATATATTTTTCCATTTATTATAAAATTCGAATTTAAGACTTTTAAAG
1 GCATATATTTTTCCATTTATTATAAAATTCGAATTTAAGACTTTTAAAA
11733 GCATATATTTTTCCATTTATTATAAAATTCGAATTTAAGACTTTTAAAA
1 GCATATATTTTTCCATTTATTATAAAATTCGAATTTAAGACTTTTAAAA
*
11782 GCATATATTTTTTCATTT
1 GCATATATTTTTCCATTT
11800 TATAACTTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (49 bp):
GCATATATTTTTCCATTTATTATAAAATTCGAATTTAAGACTTTTAAAA
Found at i:17410 original size:13 final size:12
Alignment explanation
Indices: 17392--17424 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
17382 TCATAATTAC
17392 AAAGAAAAAGAAA
1 AAAGAAAAA-AAA
17405 AAAGAAAAAAAA
1 AAAGAAAAAAAA
17417 AAA-AAAAA
1 AAAGAAAAA
17425 CTATATCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 6 0.30
13 9 0.45
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:25891 original size:2 final size:2
Alignment explanation
Indices: 25884--25909 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25874 TAAACCCTTA
25884 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25910 TAATAGCCAA
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):
AT
Found at i:28233 original size:82 final size:83
Alignment explanation
Indices: 28120--28281 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 83
28110 GATTTTTTTA
28120 TGAAGTACTTGAAGTTTTGTCCGAAATTGAACCATCA-CAAGTTC-TCTTAAG-TACATAAGATG
1 TGAAGTACTTGAAGTTTTGTCCGAAATTGAA-CAT-AGCAAGTTCTTC-TAAGATACATAAGATG
28182 ATAAACTAATTTAACTTTGTT
63 ATAAACTAATTTAACTTTGTT
*
28203 TGAAGTACTTGAAG-TTTGTCCGAAATTGAACGTAGTCAAGTTCTTCTAAGTATACATAAGATGA
1 TGAAGTACTTGAAGTTTTGTCCGAAATTGAACATAG-CAAGTTCTTCTAAG-ATACATAAGATGA
28267 TAAACTAATTTAACT
64 TAAACTAATTTAACT
28282 CAGACTACAC
Statistics
Matches: 73, Mismatches: 1, Indels: 9
0.88 0.01 0.11
Matches are distributed among these distances:
80 1 0.01
81 2 0.03
82 27 0.37
83 16 0.22
84 27 0.37
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (83 bp):
TGAAGTACTTGAAGTTTTGTCCGAAATTGAACATAGCAAGTTCTTCTAAGATACATAAGATGATA
AACTAATTTAACTTTGTT
Found at i:29493 original size:12 final size:12
Alignment explanation
Indices: 29476--29500 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29466 GCTAGAAATG
29476 TTTAATTAGGAT
1 TTTAATTAGGAT
29488 TTTAATTAGGAT
1 TTTAATTAGGAT
29500 T
1 T
29501 AGAAAGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTTAATTAGGAT
Found at i:31114 original size:156 final size:156
Alignment explanation
Indices: 30744--31114 Score: 389
Period size: 156 Copynumber: 2.4 Consensus size: 156
30734 TCATCTCAAA
* * **
30744 CAGACTTAGTATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAATTTGAGGTGTCAAACCAAC
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAAACCAAC
* * * * * *
30809 TTCTCTATGCTAGAGAGTTCGGTTTTACTTAGATTTTTCCCCATAGATTTATGGTGATAATCTAA
66 TTCACCATGCAAGAGAGGTCGGTTTTACTTAGATTTTTCCCCATAGATTTATGGAGATAATATAA
* *
30874 GTCTCCTGGTGGAAAATCAGCCTCGTT
131 GTCTCC-GATGGAAAATCAGCCTCATT
* * * * *
30901 -GGACTTAGAATGAAAAACTAATACTAGTTTTTCATTTAAGGACAATTT-AGGGAGAGAAACCTA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGA-GGTGAGAAACCAA
* * * *
30964 GTTCACCAT-CAAGAGAAGGTCGGTTTTACTTGGAATTTTT-TCCATAG-TCTTATGGAGATAGT
65 CTTCACCATGCAAGAG-AGGTCGGTTTTACTTAG-ATTTTTCCCCATAGAT-TTATGGAGATAAT
31026 ATAAGTCT-C-ATGGAAAAGTTTCAG-CTCATT
127 ATAAGTCTCCGATGGAAAA---TCAGCCTCATT
** **
31056 CAGACTTAGAATGGGAAACTTATGCTAGTTTTTCATTTAAGGACGGTTTGAGGTGAGAA
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAA
31115 GTCTAGTTTA
Statistics
Matches: 176, Mismatches: 29, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
153 7 0.04
155 13 0.07
156 149 0.85
157 7 0.04
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (156 bp):
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGAGGTGAGAAACCAAC
TTCACCATGCAAGAGAGGTCGGTTTTACTTAGATTTTTCCCCATAGATTTATGGAGATAATATAA
GTCTCCGATGGAAAATCAGCCTCATT
Found at i:32110 original size:34 final size:34
Alignment explanation
Indices: 32056--32138 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 34
32046 AAATCGCTCT
* *
32056 GATCTTTTAA--T-CTGCTGCTACGTGCACCTCA
1 GATCTTTTAATCTGCTGCTGCTACGCGCACCCCA
32087 GATCTTTTAATCTGCTGCTGCTACGCGCACCCCA
1 GATCTTTTAATCTGCTGCTGCTACGCGCACCCCA
32121 GATCTTTTAATCTGCTGC
1 GATCTTTTAATCTGCTGC
32139 GCTTTCACCA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
31 10 0.21
33 1 0.02
34 36 0.77
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (34 bp):
GATCTTTTAATCTGCTGCTGCTACGCGCACCCCA
Found at i:35017 original size:10 final size:10
Alignment explanation
Indices: 35002--35037 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
34992 AAATTAATAT
35002 GGATATTTAC
1 GGATATTTAC
35012 GGATATTTAC
1 GGATATTTAC
*
35022 AGATATTTAC
1 GGATATTTAC
35032 GGATAT
1 GGATAT
35038 ATCGAGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (10 bp):
GGATATTTAC
Found at i:35059 original size:18 final size:18
Alignment explanation
Indices: 35036--35070 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35026 ATTTACGGAT
*
35036 ATATCGAGACATATCGAG
1 ATATCGAGAAATATCGAG
*
35054 ATATCGATAAATATCGA
1 ATATCGAGAAATATCGA
35071 CGGATATACG
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:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (18 bp):
ATATCGAGAAATATCGAG
Found at i:35076 original size:20 final size:19
Alignment explanation
Indices: 35036--35098 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
35026 ATTTACGGAT
*
35036 ATATCGAGACATATCGA--G
1 ATATCGATA-ATATCGACGG
35054 ATATCGATAAATATCGACGG
1 ATATCGAT-AATATCGACGG
35074 ATATACGGAT-ATATCGACGG
1 ATAT-C-GATAATATCGACGG
35094 ATATC
1 ATATC
35099 CGGTGACATT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 14 0.36
19 2 0.05
20 19 0.49
21 1 0.03
22 3 0.08
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (19 bp):
ATATCGATAATATCGACGG
Found at i:36356 original size:31 final size:31
Alignment explanation
Indices: 36321--36414 Score: 116
Period size: 31 Copynumber: 3.0 Consensus size: 31
36311 GCGTGTCACA
* *
36321 TGTCACTTTTTGGTACACGTGGCGTGACATG
1 TGTCACTTTTTGGTACACGTGGCATGCCATG
* ** **
36352 TGTCACTTTTTGGTATATATGGCATGCCACA
1 TGTCACTTTTTGGTACACGTGGCATGCCATG
*
36383 TGTCACTTTTTGGTACACGTGGCCTGCCATG
1 TGTCACTTTTTGGTACACGTGGCATGCCATG
36414 T
1 T
36415 CGGACACCGT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.37
Consensus pattern (31 bp):
TGTCACTTTTTGGTACACGTGGCATGCCATG
Found at i:47391 original size:6 final size:7
Alignment explanation
Indices: 47374--47399 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
47364 GACTTACCTT
47374 TTTTTTG
1 TTTTTTG
47381 TTTTTTG
1 TTTTTTG
47388 TTTTTTG
1 TTTTTTG
47395 TTTTT
1 TTTTT
47400 ACTTTAATCT
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTTG
Found at i:52914 original size:12 final size:12
Alignment explanation
Indices: 52897--52924 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
52887 TTACTGATAA
52897 TAATCTACTTTT
1 TAATCTACTTTT
52909 TAATCTACTTTT
1 TAATCTACTTTT
52921 TAAT
1 TAAT
52925 TTATTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (12 bp):
TAATCTACTTTT
Done.