Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005785.1 Corchorus capsularis cultivar CVL-1 contig05803, 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: 2740
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Found at i:94 original size:55 final size:55
Alignment explanation
Indices: 33--141 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
23 ACTAATTAAT
*
33 CTCTTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTAA
1 CTCTTTTTACTTAATTACCAATTTACTGACTACTATTACCTTGACTCTTAACTAA
* * *
88 CTCTTTTTACTTACTTACTAATTTACTGATTACTATTACCTTGACTCTTAACTA
1 CTCTTTTTACTTAATTACCAATTTACTGACTACTATTACCTTGACTCTTAACTA
142 TCAATTTACT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.46
Consensus pattern (55 bp):
CTCTTTTTACTTAATTACCAATTTACTGACTACTATTACCTTGACTCTTAACTAA
Found at i:161 original size:18 final size:18
Alignment explanation
Indices: 107--197 Score: 62
Period size: 18 Copynumber: 5.0 Consensus size: 18
97 CTTACTTACT
*
107 AATTTACTGATTACTATT
1 AATTTACTGATTACTATC
* * *
125 ACCTTGACT-CTTAACTATC
1 A-ATTTACTGATT-ACTATC
144 AATTTACTGATTACTATC
1 AATTTACTGATTACTATC
* **
162 -TTTTGA-TTCTTAACTATC
1 AATTT-ACTGATT-ACTATC
180 AATTTACTGATTACTATC
1 AATTTACTGATTACTATC
198 TTTTTACTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 14
0.66 0.16 0.17
Matches are distributed among these distances:
17 6 0.11
18 28 0.53
19 19 0.36
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (18 bp):
AATTTACTGATTACTATC
Found at i:180 original size:36 final size:36
Alignment explanation
Indices: 107--257 Score: 154
Period size: 36 Copynumber: 4.2 Consensus size: 36
97 CTTACTTACT
*
107 AATTTACTGATTACTAT-TACCTTGACTCTTAACTATC
1 AATTTACTGATTACTATCT--TTTGACTCTTAACTATC
*
144 AATTTACTGATTACTATCTTTTGATTCTTAACTATC
1 AATTTACTGATTACTATCTTTTGACTCTTAACTATC
*
180 AATTTACTGATTACTATCTTTTTA--CTTAA-T-TGC
1 AATTTACTGATTACTATCTTTTGACTCTTAACTAT-C
* *
213 TGATTTACTGATTACTA-CTTTT-ACTCCCTTAATTATC
1 -AATTTACTGATTACTATCTTTTGACT--CTTAACTATC
250 AATTTACT
1 AATTTACT
258 TAATTAATCT
Statistics
Matches: 100, Mismatches: 5, Indels: 19
0.81 0.04 0.15
Matches are distributed among these distances:
32 2 0.02
33 7 0.07
34 20 0.20
36 50 0.50
37 19 0.19
38 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48
Consensus pattern (36 bp):
AATTTACTGATTACTATCTTTTGACTCTTAACTATC
Found at i:203 original size:18 final size:18
Alignment explanation
Indices: 146--205 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
136 TAACTATCAA
146 TTTACTGATTACTATCTT
1 TTTACTGATTACTATCTT
* ** **
164 TTGA-TTCTTAACTATCAA
1 TTTACTGATT-ACTATCTT
182 TTTACTGATTACTATCTT
1 TTTACTGATTACTATCTT
200 TTTACT
1 TTTACT
206 TAATTGCTGA
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTACTGATTACTATCTT
Found at i:226 original size:70 final size:70
Alignment explanation
Indices: 145--299 Score: 210
Period size: 69 Copynumber: 2.2 Consensus size: 70
135 TTAACTATCA
* *
145 ATTTACTGATTACTATCTTTTGA-T-TCTTAACTATCAATTTAC-TGATTACTATCTTTTTACTT
1 ATTTACTGATTACTATCTTTT-ACTCCCTTAACTATCAATTTACTTAATTA--ATCTTTTTACTT
*
207 AATTGCTG
63 AATTACTG
* *
215 ATTTACTGATTACTA-CTTTTACTCCCTTAATTATCAATTTACTTAATTAATCTTTTTACTTTAT
1 ATTTACTGATTACTATCTTTTACTCCCTTAACTATCAATTTACTTAATTAATCTTTTTACTTAAT
279 TACTG
66 TACTG
284 ATTTACTGATTACTAT
1 ATTTACTGATTACTAT
300 TTCCTTGACT
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
68 1 0.01
69 39 0.51
70 31 0.41
71 5 0.07
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.52
Consensus pattern (70 bp):
ATTTACTGATTACTATCTTTTACTCCCTTAACTATCAATTTACTTAATTAATCTTTTTACTTAAT
TACTG
Found at i:336 original size:55 final size:54
Alignment explanation
Indices: 265--421 Score: 260
Period size: 55 Copynumber: 2.9 Consensus size: 54
255 ACTTAATTAA
*
265 TCTTTTTACTTTATTACTGATTTACTGATTACTATTTCCTTGACTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACTCT-ATTAATC
320 TCTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACTCATATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACTC-TATTAATC
* * *
375 TCTTTTTACTTAATTCCTGATTTACTGATTACTATTACTTTGACTCT
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACTCT
422 TAATTACTTA
Statistics
Matches: 97, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
54 1 0.01
55 95 0.98
56 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.06, T:0.52
Consensus pattern (54 bp):
TCTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACTCTATTAATC
Found at i:424 original size:37 final size:37
Alignment explanation
Indices: 383--463 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
373 TCTCTTTTTA
* * *
383 CTTAATTCCTGATTTACTGATTACTATTACTTTGACT
1 CTTAATTACTGAATTACTGATTACCATTACTTTGACT
* * *
420 CTTAATTACTTAATTACTTATTACCGTTACTTTGACT
1 CTTAATTACTGAATTACTGATTACCATTACTTTGACT
*
457 CCTAATT
1 CTTAATT
464 TATTGGAGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (37 bp):
CTTAATTACTGAATTACTGATTACCATTACTTTGACT
Done.