Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014056.1 Corchorus capsularis cultivar CVL-1 contig14077, 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: 31080
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--29 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1 TA TA 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 TA TA T
30 GCTTTTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10042 original size:23 final size:24
Alignment explanation
Indices: 9974--10044 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 24
9964 ATTCCTTTGC
9974 AGATCCTTTGAGTCCCATCTGTTTGA
1 AGATCCTTTGAGTCCCATCTG--TGA
* *
10000 AGATCACTTT-A-TAGCAATCTG-GA
1 AGATC-CTTTGAGT-CCCATCTGTGA
10023 AGATCCTTTGAGTCCCATCTGT
1 AGATCCTTTGAGTCCCATCTGT
10045 TTCTAGCCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
22 4 0.11
23 14 0.39
24 1 0.03
25 1 0.03
26 12 0.33
27 4 0.11
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (24 bp):
AGATCCTTTGAGTCCCATCTGTGA
Found at i:27360 original size:27 final size:27
Alignment explanation
Indices: 27322--27401 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 27
27312 ATTAATTGTG
27322 TGAGAGACGATTTGTTCTAAATAAATT
1 TGAGAGACGATTTGTTCTAAATAAATT
** ** *
27349 TGAGAGACGA-TTAAT-T-AAT-TGTG
1 TGAGAGACGATTTGTTCTAAATAAATT
27372 TGAGAGACGATTTGTTCTAAATAAATT
1 TGAGAGACGATTTGTTCTAAATAAATT
27399 TGA
1 TGA
27402 ACATATAATG
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
23 11 0.28
24 6 0.15
25 2 0.05
26 6 0.15
27 14 0.36
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (27 bp):
TGAGAGACGATTTGTTCTAAATAAATT
Found at i:27375 original size:23 final size:23
Alignment explanation
Indices: 27308--27383 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
27298 AGAATTAACA
27308 ATTAATTAATTGTGTGAGAGACG
1 ATTAATTAATTGTGTGAGAGACG
** ** *
27331 ATTTGTTCTAAATAAATTTGAGAGACG
1 A-TTAAT-T-AAT-TGTGTGAGAGACG
27358 ATTAATTAATTGTGTGAGAGACG
1 ATTAATTAATTGTGTGAGAGACG
27381 ATT
1 ATT
27384 TGTTCTAAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
23 14 0.36
24 6 0.15
25 2 0.05
26 6 0.15
27 11 0.28
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (23 bp):
ATTAATTAATTGTGTGAGAGACG
Found at i:29613 original size:31 final size:31
Alignment explanation
Indices: 29565--29623 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
29555 AGTTTTGAGA
* * *
29565 AACTTTTGAAATGCCTATTGTATCCTTATTT
1 AACTTTTAAAATACCTATTATATCCTTATTT
29596 AACTTTTAAAATACCTATTATATCCTTA
1 AACTTTTAAAATACCTATTATATCCTTA
29624 CTTATCTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (31 bp):
AACTTTTAAAATACCTATTATATCCTTATTT
Found at i:29992 original size:248 final size:248
Alignment explanation
Indices: 29554--30051 Score: 978
Period size: 248 Copynumber: 2.0 Consensus size: 248
29544 ATAAAAGTAC
29554 GAGTTTTGAGAAACTTTTGAAATGCCTATTGTATCCTTATTTAACTTTTAAAATACCTATTATAT
1 GAGTTTTGAGAAACTTTTGAAATGCCTATTGTATCCTTATTTAACTTTTAAAATACCTATTATAT
29619 CCTTACTTATCTAACATATTTCTAAAAACTGCCATTATGCAATTAATTTTTAATTTTGTTAATTT
66 CCTTACTTATCTAACATATTTCTAAAAACTGCCATTATGCAATTAATTTTTAATTTTGTTAATTT
29684 GCATTTAACCTAACCCATAGCCTTAATATGAATTTAGTTAAAATTACTATTAAATAAATAATCTC
131 GCATTTAACCTAACCCATAGCCTTAATATGAATTTAGTTAAAATTACTATTAAATAAATAATCTC
29749 ACCATTTGGATTTGATTAAAGTTTTGGATTTGTAAACAAATAATATCACATTT
196 ACCATTTGGATTTGATTAAAGTTTTGGATTTGTAAACAAATAATATCACATTT
*
29802 GAGTTTTGAGAAACTTTTGAAATGCCTATTGTATCTTTATTTAACTTTTAAAATACCTATTATAT
1 GAGTTTTGAGAAACTTTTGAAATGCCTATTGTATCCTTATTTAACTTTTAAAATACCTATTATAT
*
29867 CCTTACTTATCTAACATATTTCTAAAAATTGCCATTATGCAATTAATTTTTAATTTTGTTAATTT
66 CCTTACTTATCTAACATATTTCTAAAAACTGCCATTATGCAATTAATTTTTAATTTTGTTAATTT
29932 GCATTTAACCTAACCCATAGCCTTAATATGAATTTAGTTAAAATTACTATTAAATAAATAATCTC
131 GCATTTAACCTAACCCATAGCCTTAATATGAATTTAGTTAAAATTACTATTAAATAAATAATCTC
29997 ACCATTTGGATTTGATTAAAGTTTTGGATTTGTAAACAAATAATATCACATTT
196 ACCATTTGGATTTGATTAAAGTTTTGGATTTGTAAACAAATAATATCACATTT
30050 GA
1 GA
30052 TTAAAGTTTT
Statistics
Matches: 248, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
248 248 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (248 bp):
GAGTTTTGAGAAACTTTTGAAATGCCTATTGTATCCTTATTTAACTTTTAAAATACCTATTATAT
CCTTACTTATCTAACATATTTCTAAAAACTGCCATTATGCAATTAATTTTTAATTTTGTTAATTT
GCATTTAACCTAACCCATAGCCTTAATATGAATTTAGTTAAAATTACTATTAAATAAATAATCTC
ACCATTTGGATTTGATTAAAGTTTTGGATTTGTAAACAAATAATATCACATTT
Found at i:30050 original size:40 final size:40
Alignment explanation
Indices: 30006--30085 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
29996 CACCATTTGG
30006 ATTTGATTAAAGTTTTGGATTTGTAAACAAATAATATCAC
1 ATTTGATTAAAGTTTTGGATTTGTAAACAAATAATATCAC
30046 ATTTGATTAAAGTTTTGGATTTGTAAACAAATAATATCAC
1 ATTTGATTAAAGTTTTGGATTTGTAAACAAATAATATCAC
30086 TGTAGATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (40 bp):
ATTTGATTAAAGTTTTGGATTTGTAAACAAATAATATCAC
Done.