Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014699.1 Corchorus capsularis cultivar CVL-1 contig14720, 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: 24712
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:121 original size:50 final size:50
Alignment explanation
Indices: 1--424 Score: 518
Period size: 50 Copynumber: 8.6 Consensus size: 50
* * *
1 AAAATGCCCCTTCCCAGTCGGAAGGTCCCTGTTTTCTTTGTTT-ATT-CC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC
* *
49 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTATTTTCTTTATTCGTTTCCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC
* ** * * * *
99 AAAATGCCCCTTCCCGGACGGAAGGTTACAGTTTTCTTCT-CTT-ATTCCA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTT-TATTTGTTTCCC
* * * *
148 AAAATGCCCCTTCCCGGTCGGAAGATCCCTGTCTTCTCTATTTGTTTCCA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC
* * * * *
198 AAAATGCCCCTTCTCGGTCGGAAGGTCCTTATTTTATGTATTTTGTTTCCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTA-TTTGTTTCCC
* * *
249 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTGCTTTGTTTGTTTCCA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC
* * *
299 AAAATGCTCCTTCCCGGTCGGAAGGTCCCTGTTTACTTTGTTTGTTT-CC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC
* *
348 AAAATGCCCCTTCCCGGTCGAAAGGTCCCTGTTCTCTTTATTTGTTTCCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC
*
398 AAAATG-CCCTTCCCAGTCGGAAGGTCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCC
425 AACTTTCTCT
Statistics
Matches: 320, Mismatches: 49, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
48 40 0.12
49 101 0.32
50 136 0.43
51 43 0.13
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.35
Consensus pattern (50 bp):
AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTATTTGTTTCCC
Found at i:210 original size:99 final size:98
Alignment explanation
Indices: 1--424 Score: 509
Period size: 99 Copynumber: 4.3 Consensus size: 98
* *
1 AAAATGCCCCTTCCCAGTCGGAAGGTCCCTGTTTTCTTTGTTT-ATTCCAAAATGCCCCTTCCCG
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCTTTGTTTGATTCCAAAATGCCCCTTCCCG
* * *
65 GTCGGAAGGTCCCTATTTTCTTTATTCGTTTCCC
66 GTCGGAAGGTCCCT-GTTTCTTTATTTGTTTCCA
* ** *
99 AAAATGCCCCTTCCCGGACGGAAGGTTACAGTTTTCTTCT-CTT-ATTCCAAAAATGCCCCTTCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCTT-TGTTTGATTCC-AAAATGCCCCTTCC
* *
162 CGGTCGGAAGATCCCTGTCTTCTCTATTTGTTTCCA
64 CGGTCGGAAGGTCCCTGT-TTCTTTATTTGTTTCCA
* * * *
198 AAAATGCCCCTTCTCGGTCGGAAGGTCCTTA-TTTTATGTAT-TTTGTTTCCCAAAATGCCCCTT
1 AAAATGCCCCTTCCCGGTCGGAAGGTCC-CAGTTTTCT-T-TGTTTGATT-CCAAAATGCCCCTT
*
261 CCCGGTCGGAAGGTCCCTGTTTGCTTTGTTTGTTTCCA
62 CCCGGTCGGAAGGTCCCTGTTT-CTTTATTTGTTTCCA
* * * *
299 AAAATGCTCCTTCCCGGTCGGAAGGTCCCTGTTTACTTTGTTTGTTTCCAAAATGCCCCTTCCCG
1 AAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCTTTGTTTGATTCCAAAATGCCCCTTCCCG
* *
364 GTCGAAAGGTCCCTGTTCTCTTTATTTGTTTCCC
66 GTCGGAAGGTCCCTGTT-TCTTTATTTGTTTCCA
*
398 AAAATG-CCCTTCCCAGTCGGAAGGTCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCC
425 AACTTTCTCT
Statistics
Matches: 281, Mismatches: 34, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
98 60 0.21
99 127 0.45
100 16 0.06
101 76 0.27
102 2 0.01
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.35
Consensus pattern (98 bp):
AAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTCTTTGTTTGATTCCAAAATGCCCCTTCCCG
GTCGGAAGGTCCCTGTTTCTTTATTTGTTTCCA
Found at i:4845 original size:2 final size:2
Alignment explanation
Indices: 4840--4873 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4830 CTCTCTCTCA
* *
4840 AT AT AT AT AT AA AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4874 TGGAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6056 original size:18 final size:18
Alignment explanation
Indices: 6033--6079 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
6023 TTCCTTTCTG
6033 CAGAGATCGGGATTATGA
1 CAGAGATCGGGATTATGA
* *
6051 CAGAGATAGAGATTATGA
1 CAGAGATCGGGATTATGA
* *
6069 TAGAGAACGGG
1 CAGAGATCGGG
6080 GACGTGGTCG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.34, T:0.19
Consensus pattern (18 bp):
CAGAGATCGGGATTATGA
Found at i:6165 original size:6 final size:6
Alignment explanation
Indices: 6091--6164 Score: 121
Period size: 6 Copynumber: 12.3 Consensus size: 6
6081 ACGTGGTCGT
* *
6091 GACAGA GACAAG GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG
1 GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG
*
6139 GACAGG GACAGG GACAGG GATAGG GA
1 GACAGG GACAGG GACAGG GACAGG GA
6165 TTGTTATCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.36, C:0.15, G:0.47, T:0.01
Consensus pattern (6 bp):
GACAGG
Found at i:7104 original size:15 final size:15
Alignment explanation
Indices: 7081--7111 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7071 GAAGGAGTAC
7081 TTGTCAACATGATAT
1 TTGTCAACATGATAT
*
7096 TTGTGAACATGATAT
1 TTGTCAACATGATAT
7111 T
1 T
7112 GAAATATTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (15 bp):
TTGTCAACATGATAT
Found at i:14194 original size:28 final size:28
Alignment explanation
Indices: 14154--14211 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
14144 TTTCAGAAAT
14154 CAACAGCATATGAACATATTGTGTAGTA
1 CAACAGCATATGAACATATTGTGTAGTA
14182 CAACAGCATATGAACATATTGTGTAGTA
1 CAACAGCATATGAACATATTGTGTAGTA
14210 CA
1 CA
14212 TGCAGTTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (28 bp):
CAACAGCATATGAACATATTGTGTAGTA
Found at i:16981 original size:19 final size:20
Alignment explanation
Indices: 16948--16993 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
16938 GATGAAATGA
16948 AGAAAGAAAATAAAGAAAGAG
1 AGAAA-AAAATAAAGAAAGAG
*
16969 AGAAAAAAA-AAAGAGAGAG
1 AGAAAAAAATAAAGAAAGAG
16988 AGAAAA
1 AGAAAA
16994 CGGAAAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 15 0.62
20 4 0.17
21 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
AGAAAAAAATAAAGAAAGAG
Found at i:16987 original size:17 final size:20
Alignment explanation
Indices: 16952--16993 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 20
16942 AAATGAAGAA
16952 AGAAAATAAAGAA-AGAGAG
1 AGAAAATAAAGAAGAGAGAG
16971 A-AAAA-AAA-AAGAGAGAG
1 AGAAAATAAAGAAGAGAGAG
16988 AGAAAA
1 AGAAAA
16994 CGGAAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.10
17 10 0.48
18 8 0.38
19 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
AGAAAATAAAGAAGAGAGAG
Found at i:16993 original size:15 final size:15
Alignment explanation
Indices: 16947--16986 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
16937 GGATGAAATG
*
16947 AAGAAAGAAAATAAAGA
1 AAGAGAGAAAA-AAA-A
16964 AAGAGAGAAAAAAAA
1 AAGAGAGAAAAAAAA
16979 AAGAGAGA
1 AAGAGAGA
16987 GAGAAAACGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 3 0.14
17 10 0.45
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
AAGAGAGAAAAAAAA
Found at i:23687 original size:2 final size:2
Alignment explanation
Indices: 23680--23726 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
23670 TTTTATCCAT
* *
23680 TA TA TA TA TA TA AA TA TA TA TA TA TA TA GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23722 TA TA T
1 TA TA T
23727 TTCAAACGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Done.