Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006952.1 Corchorus capsularis cultivar CVL-1 contig06973, 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: 79376
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:305 original size:51 final size:51
Alignment explanation
Indices: 245--367 Score: 165
Period size: 51 Copynumber: 2.4 Consensus size: 51
235 GATCACAGAA
* * ** *
245 TCAAACTCCTGCCCCGATTCCTGCACCAAATGCTGCTAGAATTTCCAGTCC
1 TCAAACTCCTGCCCCGAGTACAACACCAAATGATGCTAGAATTTCCAGTCC
* * * *
296 TCAAACTCCTGCCCTGAGTACAACACCAAATGATGCTGGCATTTCCCGTCC
1 TCAAACTCCTGCCCCGAGTACAACACCAAATGATGCTAGAATTTCCAGTCC
347 TCAAACTCCTGCCCCGAGTAC
1 TCAAACTCCTGCCCCGAGTAC
368 TGCAGCAAGC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (51 bp):
TCAAACTCCTGCCCCGAGTACAACACCAAATGATGCTAGAATTTCCAGTCC
Found at i:386 original size:51 final size:51
Alignment explanation
Indices: 331--527 Score: 277
Period size: 51 Copynumber: 3.9 Consensus size: 51
321 CCAAATGATG
*
331 CTGGCATTTCCCGTCCTCAAACTCCTGCCCCGAGTACTGCAGCAAGCCTCC
1 CTGGCATTTCCCATCCTCAAACTCCTGCCCCGAGTACTGCAGCAAGCCTCC
* * *
382 CTGGCATTTCCCGTCCTCAAACTCCTGCCTCGAGTACTGCAGCAACCCTCC
1 CTGGCATTTCCCATCCTCAAACTCCTGCCCCGAGTACTGCAGCAAGCCTCC
* * * * *
433 CTGGCATTTCTCATCCTCCAAGTCCTGCTCTGAGTACTGCAGCAAGCCTCC
1 CTGGCATTTCCCATCCTCAAACTCCTGCCCCGAGTACTGCAGCAAGCCTCC
* * * *
484 CTGGCATTTCCCATCCTCCAAGTCCTTCTCCGAGTACTGCAGCA
1 CTGGCATTTCCCATCCTCAAACTCCTGCCCCGAGTACTGCAGCA
528 CCGTTTAGGG
Statistics
Matches: 133, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 133 1.00
ACGTcount: A:0.18, C:0.41, G:0.17, T:0.25
Consensus pattern (51 bp):
CTGGCATTTCCCATCCTCAAACTCCTGCCCCGAGTACTGCAGCAAGCCTCC
Found at i:3633 original size:32 final size:32
Alignment explanation
Indices: 3592--3691 Score: 139
Period size: 32 Copynumber: 3.1 Consensus size: 32
3582 CATATATTGC
*
3592 GGCGACTTCTGAAGCAAACGCCGTGATATAGA
1 GGCGACTTCTGAAGCAAACGCCGTGATATAGG
* *
3624 GGCGTCTTCTGAAG-AAATCGTCGTGATATAGG
1 GGCGACTTCTGAAGCAAA-CGCCGTGATATAGG
* *
3656 GGCAACTTATGAAGCAAACGCCGTGATATAGG
1 GGCGACTTCTGAAGCAAACGCCGTGATATAGG
3688 GGCG
1 GGCG
3692 CCTTTAGAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.05
32 52 0.90
33 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (32 bp):
GGCGACTTCTGAAGCAAACGCCGTGATATAGG
Found at i:3855 original size:34 final size:33
Alignment explanation
Indices: 3817--3897 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 33
3807 ACTATATAGG
* ** *
3817 GGCGTTTCTTTAAGGGGAAACGCTGCCATATGAC
1 GGCGTTTCTTTAA-GAGAAACGCCACCATATCAC
* * *
3851 GGCGTTTGTTTCAATATAAACGCCACCATATCAC
1 GGCGTTTCTTT-AAGAGAAACGCCACCATATCAC
3885 GGCGTTTCTTTAA
1 GGCGTTTCTTTAA
3898 TAAAAATGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
33 2 0.05
34 34 0.89
35 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (33 bp):
GGCGTTTCTTTAAGAGAAACGCCACCATATCAC
Found at i:8523 original size:6 final size:6
Alignment explanation
Indices: 8509--8544 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
8499 GAATATCAAT
*
8509 CCCTCC CCCTAC CCCTAC CCCTAC CCCTAC CCCTAC
1 CCCTAC CCCTAC CCCTAC CCCTAC CCCTAC CCCTAC
8545 ACCCAAGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.69, G:0.00, T:0.17
Consensus pattern (6 bp):
CCCTAC
Found at i:10522 original size:168 final size:163
Alignment explanation
Indices: 10230--10561 Score: 540
Period size: 168 Copynumber: 2.0 Consensus size: 163
10220 GATGAGAATT
10230 TGGGTCAATCATGTCCGCCATGCCTAATAGTTTTGGAGTAGTCACCACTTGATATTTTACCACTA
1 TGGGTCAATCATGTCCGCCATGCCTAATAGTTTTGGAGTAGTCACCACTTGATATTTTACCACTA
* * *
10295 TTGGAGCAGGATGAATGATAAGTTTCTTTATTAGAGTTTAATTGATATTGTCAACATCTTATGTA
66 TTGGAGCAGGATGAATGATAAATTTCTTTATTAGAATTTAATTGATACTGTCAACATCTTATGTA
10360 T-AAAAAATGTCAAATAGGAGTATTATTTAATAGTACAA
131 TAAAAAAATG-----T-GGAGTATTATTTAATAGTACAA
*
10398 TGGGTCAATCATGTCCGCCATGCCTAATAGTTTTGGAGTAGTCACCACTTGATATTTTACCATTA
1 TGGGTCAATCATGTCCGCCATGCCTAATAGTTTTGGAGTAGTCACCACTTGATATTTTACCACTA
* * *
10463 TTGGAGCAGGATGAATGATAAATTTCTTTATTAGAATTTAGTTGATGCTGTCGACATCTTATGTA
66 TTGGAGCAGGATGAATGATAAATTTCTTTATTAGAATTTAATTGATACTGTCAACATCTTATGTA
10528 TAAAAAAATGTGGAGTATTATTTAATAGTACAA
131 TAAAAAAATGTGGAGTATTATTTAATAGTACAA
10561 T
1 T
10562 ATTACTTGAA
Statistics
Matches: 156, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
163 23 0.15
164 1 0.01
168 124 0.79
169 8 0.05
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (163 bp):
TGGGTCAATCATGTCCGCCATGCCTAATAGTTTTGGAGTAGTCACCACTTGATATTTTACCACTA
TTGGAGCAGGATGAATGATAAATTTCTTTATTAGAATTTAATTGATACTGTCAACATCTTATGTA
TAAAAAAATGTGGAGTATTATTTAATAGTACAA
Found at i:15398 original size:6 final size:7
Alignment explanation
Indices: 15380--15405 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
15370 GGAGGCAAGG
15380 GAAAAAT
1 GAAAAAT
15387 GAAAAAT
1 GAAAAAT
15394 GAAAAAT
1 GAAAAAT
15401 GAAAA
1 GAAAA
15406 CGAAGATTTA
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:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
GAAAAAT
Found at i:22094 original size:18 final size:18
Alignment explanation
Indices: 22057--22095 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
22047 GTTGTGTTTG
* *
22057 ACACGATTAAGACACGAA
1 ACACGATTAAAACACAAA
*
22075 ACACGATTAAAAGACAAA
1 ACACGATTAAAACACAAA
22093 ACA
1 ACA
22096 TGTTAAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.21, G:0.13, T:0.10
Consensus pattern (18 bp):
ACACGATTAAAACACAAA
Found at i:30293 original size:13 final size:13
Alignment explanation
Indices: 30275--30299 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30265 GCTTGTACCC
30275 AAAAAAAAAAATG
1 AAAAAAAAAAATG
30288 AAAAAAAAAAAT
1 AAAAAAAAAAAT
30300 CCTTTCTCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.04, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAAATG
Found at i:31828 original size:19 final size:19
Alignment explanation
Indices: 31804--31845 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
31794 TCAAGAAATG
31804 AGATTTTACTGTGAATATA
1 AGATTTTACTGTGAATATA
31823 AGATTTTACTGTGAATATA
1 AGATTTTACTGTGAATATA
31842 AGAT
1 AGAT
31846 GCAACACCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (19 bp):
AGATTTTACTGTGAATATA
Found at i:32615 original size:22 final size:21
Alignment explanation
Indices: 32574--32622 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
32564 TCGAGCTCGG
32574 CTCGAA-TTTTCCGAGCCGAA
1 CTCGAATTTTTCCGAGCCGAA
*
32594 CTCGAATTTTTCTCGAGTCGAA
1 CTCGAATTTTTC-CGAGCCGAA
*
32616 CCCGAAT
1 CTCGAAT
32623 AGTTCGCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.24
21 5 0.20
22 14 0.56
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (21 bp):
CTCGAATTTTTCCGAGCCGAA
Found at i:36963 original size:33 final size:33
Alignment explanation
Indices: 36921--36988 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
36911 AAATTATGTC
36921 ATAGTTATTGATCTTGATACATGAGGGTATTAG
1 ATAGTTATTGATCTTGATACATGAGGGTATTAG
*
36954 ATAGTTATTGATCTTGATAGATGAGGGTATTAG
1 ATAGTTATTGATCTTGATACATGAGGGTATTAG
36987 AT
1 AT
36989 TCGATTGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.04, G:0.25, T:0.40
Consensus pattern (33 bp):
ATAGTTATTGATCTTGATACATGAGGGTATTAG
Found at i:59194 original size:6 final size:6
Alignment explanation
Indices: 59183--59207 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
59173 GGCAGATATG
59183 GCAGAA GCAGAA GCAGAA GCAGAA G
1 GCAGAA GCAGAA GCAGAA GCAGAA G
59208 GCTTTTGATG
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:0.48, C:0.16, G:0.36, T:0.00
Consensus pattern (6 bp):
GCAGAA
Done.