Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012215.1 Corchorus capsularis cultivar CVL-1 contig12236, 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: 13652
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:210 original size:21 final size:21
Alignment explanation
Indices: 184--228 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
174 TTAAGCTAAA
184 TTGTTAAACACCGCCCCATTT
1 TTGTTAAACACCGCCCCATTT
** *
205 TTGTTATTCACCGCCTCATTT
1 TTGTTAAACACCGCCCCATTT
226 TTG
1 TTG
229 ACCTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (21 bp):
TTGTTAAACACCGCCCCATTT
Found at i:556 original size:32 final size:32
Alignment explanation
Indices: 460--561 Score: 116
Period size: 32 Copynumber: 3.1 Consensus size: 32
450 CCACTTGGGA
* *
460 GGCTTCGCCACGGCAAGCCGCCCTC-ATGGGGC
1 GGCTTCGCCACGGCAGGCCGCCC-CGGTGGGGC
* * *
492 GGCTTCACCATGGGCAGGCCCGTCCCGGTGGGGC
1 GGCTTCGCCA-CGGCAGG-CCGCCCCGGTGGGGC
*
526 GGCTTCGCCACGGCAGGCTGCCCCGGTGGGGC
1 GGCTTCGCCACGGCAGGCCGCCCCGGTGGGGC
558 GGCT
1 GGCT
562 CGACTATTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
32 26 0.45
33 12 0.21
34 20 0.34
ACGTcount: A:0.09, C:0.37, G:0.40, T:0.14
Consensus pattern (32 bp):
GGCTTCGCCACGGCAGGCCGCCCCGGTGGGGC
Found at i:677 original size:33 final size:31
Alignment explanation
Indices: 627--742 Score: 96
Period size: 33 Copynumber: 3.5 Consensus size: 31
617 CCCCACCGGT
627 GCCGTCCC-CCTGGGGCGGCTGAGCCATGGCCAA
1 GCCG-CCCTCCTGGGGCGGCT-A-CCATGGCCAA
*
660 GCCGCCCTCCTGGGGCGGCACTACCATGGCCAG
1 GCCGCCCTCCTGGGGCGG--CTACCATGGCCAA
693 GCCG-CCTCCTTGGGGCGGCCCTACCATGG--ATA
1 GCCGCCCTCC-TGGGGCGG--CTACCATGGCCA-A
*
725 GACCGCCCCCCTGGGGCG
1 G-CCGCCCTCCTGGGGCG
743 ACACCGGTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
31 1 0.01
32 9 0.12
33 55 0.76
34 5 0.07
35 2 0.03
ACGTcount: A:0.11, C:0.41, G:0.34, T:0.13
Consensus pattern (31 bp):
GCCGCCCTCCTGGGGCGGCTACCATGGCCAA
Found at i:923 original size:32 final size:32
Alignment explanation
Indices: 811--914 Score: 190
Period size: 32 Copynumber: 3.2 Consensus size: 32
801 AAAAGCCTTA
*
811 GGGCGGCTAGCCATGGCAGAGCCGTCCTAGTG
1 GGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTG
843 GGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTG
1 GGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTG
875 GGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTG
1 GGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTG
*
907 GGGAGGCT
1 GGGCGGCT
915 CCGCGTGGCT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.13, C:0.27, G:0.44, T:0.15
Consensus pattern (32 bp):
GGGCGGCTAGCCGTGGCAGAGCCGTCCTAGTG
Found at i:1387 original size:46 final size:46
Alignment explanation
Indices: 1301--1391 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
1291 AAATTATACA
** *
1301 AATATGAGTAGGAGAAGAGTTAAATGCCGAATATGAAGAATAACCG
1 AATATGAGTAGGAGAAGAGTTAAACACCGAACATGAAGAATAACCG
* * *
1347 AATATGAGTAGGAGAAGAGTTGAACACTGAACATGGAGAATAACC
1 AATATGAGTAGGAGAAGAGTTAAACACCGAACATGAAGAATAACC
1392 CAATGTTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (46 bp):
AATATGAGTAGGAGAAGAGTTAAACACCGAACATGAAGAATAACCG
Found at i:3023 original size:58 final size:61
Alignment explanation
Indices: 2956--3071 Score: 166
Period size: 58 Copynumber: 1.9 Consensus size: 61
2946 CGGCGTCTTG
* *
2956 ACGCCGCTATTTATAGATTTTCAAAAAAAA-AA-TTTT-AATTGCATATAGCGGCGTCCAA
1 ACGCCGCTATCTATAGATTTTCAAAAAAAATAATTTTTAAATTACATATAGCGGCGTCCAA
* *
3014 ACGCTGCTATCTGTAGATTTTCAAAAAAAATAATTTTTTAAATTACATATAGCGGCGT
1 ACGCCGCTATCTATAGATTTTCAAAAAAAATAA-TTTTTAAATTACATATAGCGGCGT
3072 ATACACGTCG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 27 0.54
59 2 0.04
61 4 0.08
62 17 0.34
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (61 bp):
ACGCCGCTATCTATAGATTTTCAAAAAAAATAATTTTTAAATTACATATAGCGGCGTCCAA
Found at i:4728 original size:17 final size:17
Alignment explanation
Indices: 4703--4737 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4693 TGTATAATGT
4703 TAATATACCAACAAGAA
1 TAATATACCAACAAGAA
*
4720 TAATGTACCAACAAGAA
1 TAATATACCAACAAGAA
4737 T
1 T
4738 GCACATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (17 bp):
TAATATACCAACAAGAA
Found at i:5591 original size:27 final size:27
Alignment explanation
Indices: 5553--5652 Score: 155
Period size: 27 Copynumber: 3.7 Consensus size: 27
5543 CGACCCGAGG
5553 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
* *
5580 CGAAGTGGGAGGATCCATTGTTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
* * *
5607 CGAAGTAGGAGGATCCTCTACTGGGGT
1 CGAAGTGGGAGGATCCACTGCTGGGGT
5634 CGAAGTGGGAGGATCCACT
1 CGAAGTGGGAGGATCCACT
5653 ACGGCAACAG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.21, C:0.17, G:0.41, T:0.21
Consensus pattern (27 bp):
CGAAGTGGGAGGATCCACTGCTGGGGT
Found at i:10225 original size:131 final size:133
Alignment explanation
Indices: 9964--10225 Score: 320
Period size: 131 Copynumber: 2.0 Consensus size: 133
9954 GACGCCGCTA
* * * *
9964 TATATTATAGGCGTGTAGTTGTAAACTTTTCTTTGTTTTAGGGGGAGGGAGTTTTTCACTCCAAA
1 TATATTATAGGCGTGTAGTTGGAAAC-TTTCTTTGTTTTAGGGGGAGAGAATTTTTCACTCAAAA
* * * * *
10029 AAAAAGGAAAAAGAATTTCTCCCTCCATATATTAAAATAGCGGCGTTTCTGGATGTAGACGCCAC
65 AAAAAGGAAAAAGAATATCTCCCTCCACATATTAAAATAGCGGCGTTTCTGGATCTAAACACCAC
10094 TCTT
130 TCTT
*
10098 TATATTATAGGCGTAG-AGTTGGAGAA-TTTCTTTGTTTTA-GGGGAGAGAATTTTTCCCTCAAA
1 TATATTATAGGCGT-GTAGTTGGA-AACTTTCTTTGTTTTAGGGGGAGAGAATTTTTCACTC-AA
* * *
10160 AAAAAAAGG-AAAA-AATATCTCCCTCCACATATTAATATGGCGGCGTCTTCT-TATCTAAACAC
63 AAAAAAAGGAAAAAGAATATCTCCCTCCACATATTAAAATAGCGGCGT-TTCTGGATCTAAACAC
10222 CACT
127 CACT
10226 AAATAACGGC
Statistics
Matches: 111, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
131 40 0.36
132 25 0.23
133 23 0.21
134 20 0.18
135 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (133 bp):
TATATTATAGGCGTGTAGTTGGAAACTTTCTTTGTTTTAGGGGGAGAGAATTTTTCACTCAAAAA
AAAAGGAAAAAGAATATCTCCCTCCACATATTAAAATAGCGGCGTTTCTGGATCTAAACACCACT
CTT
Found at i:13136 original size:13 final size:13
Alignment explanation
Indices: 13118--13149 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
13108 TGACACGTTA
13118 GGAGGGACAAATT
1 GGAGGGACAAATT
*
13131 GGAGGGACAAGTT
1 GGAGGGACAAATT
13144 GGAGGG
1 GGAGGG
13150 TCATGTAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.50, T:0.12
Consensus pattern (13 bp):
GGAGGGACAAATT
Found at i:13619 original size:15 final size:16
Alignment explanation
Indices: 13589--13624 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
13579 CTTTCATAAG
*
13589 AAAGTGTTTTCTTATA
1 AAAGTGTTTTCCTATA
13605 AAAGT-TTTTCCTATA
1 AAAGTGTTTTCCTATA
13620 AAAGT
1 AAAGT
13625 CTTTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (16 bp):
AAAGTGTTTTCCTATA
Done.