Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001829.1 Corchorus capsularis cultivar CVL-1 contig01830, 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: 2265
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Found at i:510 original size:181 final size:179
Alignment explanation
Indices: 185--547 Score: 559
Period size: 183 Copynumber: 2.0 Consensus size: 179
175 AAATAACATG
* * * * * * *
185 TTACCCTTATTTTTTATTATATTTCTTAAATGTCATTGTTTAAATTTTTATAGTTTTATTAAATT
1 TTACCCTTATTTTTAAATATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTAAATT
*
250 AAAAACTCTATTTTTATTTAATTTAATATCTAATATATTTATAAATATTTTATTTTTATCATTAC
66 AAAAACTCTATTTTTATTTAATTCAATATCTAATATATTTATAAATATTTTATTTTTATCATTAC
315 ACTATTTTAATTAAAAAAACTTAGATATATTAGAATTTTTTAAATATATTTC
131 ACTATTTTAATT--AAAAA-TTAGATATATTAGAATTTTTTAAATATATTTC
* *
367 TTACCCTTATTTTTCAAATATATTTCTTAAATGCCGTTGTTTAAACTTTTACAATTTTACTCAAT
1 TTACCCTTATTTTT-AAATATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTAAAT
* *
432 TAAAAACTCTATTTTTATTTAA-TCAA-ATCTAATATATTTATAACTATTTTATTTTTATCATTT
65 TAAAAACTCTATTTTTATTTAATTCAATATCTAATATATTTATAAATATTTTATTTTTATCATTA
*
495 TACTATTTTAATTAAAAATTAGATATATTAGAATTTTTTAAATATATTTC
130 CACTATTTTAATTAAAAATTAGATATATTAGAATTTTTTAAATATATTTC
545 TTA
1 TTA
548 AATGACATTA
Statistics
Matches: 167, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
178 35 0.21
179 5 0.03
181 47 0.28
182 17 0.10
183 63 0.38
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (179 bp):
TTACCCTTATTTTTAAATATATTTCTTAAATGCCATTGTTTAAACTTTTACAATTTTACTAAATT
AAAAACTCTATTTTTATTTAATTCAATATCTAATATATTTATAAATATTTTATTTTTATCATTAC
ACTATTTTAATTAAAAATTAGATATATTAGAATTTTTTAAATATATTTC
Found at i:740 original size:6 final size:7
Alignment explanation
Indices: 722--749 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
712 AGAGTTTTTG
722 GAAAAAA
1 GAAAAAA
729 GAAAAAA
1 GAAAAAA
736 GAAAAAA
1 GAAAAAA
743 GAAAAAA
1 GAAAAAA
750 AATCAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:865 original size:32 final size:32
Alignment explanation
Indices: 803--887 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 32
793 AAAACAATTT
*
803 CTTATGTTTTTCTTTTGTGAC-AAAAAAATCC
1 CTTATGTTTTTCTTTTGGGACAAAAAAAATCC
834 CTTATGTTTTTCTTTTGGGACAAAAAAAATCC
1 CTTATGTTTTTCTTTTGGGACAAAAAAAATCC
*
866 CTTAT-ATTTT-TTTTGGGACAAA
1 CTTATGTTTTTCTTTTGGGACAAA
888 CTAGTCCGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
30 12 0.24
31 24 0.47
32 15 0.29
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (32 bp):
CTTATGTTTTTCTTTTGGGACAAAAAAAATCC
Found at i:1018 original size:29 final size:30
Alignment explanation
Indices: 976--1043 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
966 CTCATTTTTG
* *
976 AAACGTAAGGGATTAATTTGTTCCAAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAAGA
*
1005 AAACATAAGGGATTATTTTGTCCCAAAAGTA
1 AAACATAAGGGATTAATTTGTCCCAAAAG-A
1036 AAACATAA
1 AAACATAA
1044 CAGATTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 25 0.74
31 9 0.26
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAAGA
Found at i:1055 original size:31 final size:29
Alignment explanation
Indices: 986--1055 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
976 AAACGTAAGG
* * **
986 GATTAATTTGTTCCAAAAAAAACATAAGG
1 GATTATTTTGTCCCAAAAAAAACATAACA
1015 GATTATTTTGTCCCAAAAGTAAAACATAACA
1 GATTATTTTGTCCCAAAA--AAAACATAACA
*
1046 GATTTTTTTG
1 GATTATTTTG
1056 GGTATTTAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 16 0.47
31 18 0.53
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.34
Consensus pattern (29 bp):
GATTATTTTGTCCCAAAAAAAACATAACA
Done.