Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012915.1 Corchorus capsularis cultivar CVL-1 contig12936, 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: 4282
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Found at i:21 original size:15 final size:15
Alignment explanation
Indices: 1--33 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1 ACTGATTACCT-TTTT
1 ACTGATTA-CTATTTT
16 ACTGATTACTATTTT
1 ACTGATTACTATTTT
31 ACT
1 ACT
34 CTTTGCTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (15 bp):
ACTGATTACTATTTT
Found at i:61 original size:36 final size:36
Alignment explanation
Indices: 1--127 Score: 155
Period size: 36 Copynumber: 3.3 Consensus size: 36
*
1 ACTGATTACCTTTTTACTGATTACTATTTTACTCTTT
1 ACTGATTACC-TTCTACTGATTACTATTTTACTCTTT
*
38 GCTGATTACCTTCTACTGATTACTATTTTACTCTTT
1 ACTGATTACCTTCTACTGATTACTATTTTACTCTTT
74 ACTGATTACCTTCTTACTTTTTATTGATTACTATTTTACTCTTT
1 ACTGATTACCTTC-TAC-------TGATTACTATTTTACTCTTT
118 ACTGATTACC
1 ACTGATTACC
128 ATTTTGCTCT
Statistics
Matches: 79, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
36 37 0.47
37 12 0.15
44 30 0.38
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.52
Consensus pattern (36 bp):
ACTGATTACCTTCTACTGATTACTATTTTACTCTTT
Found at i:68 original size:22 final size:22
Alignment explanation
Indices: 43--188 Score: 110
Period size: 22 Copynumber: 6.8 Consensus size: 22
33 TCTTTGCTGA
43 TTACCTTCTACTGATTACTATT
1 TTACCTTCTACTGATTACTATT
*
65 TTACTCTT-TACTGATTACCT-TC
1 TTAC-CTTCTACTGATTA-CTATT
* * *
87 TTACTTTTTATTGATTACTATT
1 TTACCTTCTACTGATTACTATT
*
109 TTACTCTT-TACTGATTACCATT
1 TTAC-CTTCTACTGATTACTATT
* * *
131 TT-GC-TCTCATTGATTACCA-T
1 TTACCTTCT-ACTGATTACTATT
151 TTA-C-TCTTACTGATTACTATT
1 TTACCTTC-TACTGATTACTATT
*
172 TTACCTTTTACTGATTA
1 TTACCTTCTACTGATTA
189 TCATTACTTT
Statistics
Matches: 100, Mismatches: 12, Indels: 24
0.74 0.09 0.18
Matches are distributed among these distances:
19 1 0.01
20 17 0.17
21 19 0.19
22 55 0.55
23 8 0.08
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.52
Consensus pattern (22 bp):
TTACCTTCTACTGATTACTATT
Found at i:214 original size:35 final size:34
Alignment explanation
Indices: 172--279 Score: 128
Period size: 35 Copynumber: 3.1 Consensus size: 34
162 GATTACTATT
* ** *
172 TTACCTTTTACTGATTATCATTACTT-TTTACTGA
1 TTACCCTTTACTCTTTACCATT-CTTCTTTACTGA
206 TTACCCTTTACTCTTTACCATTCTTCCTTTACTGA
1 TTACCCTTTACTCTTTACCATTCTT-CTTTACTGA
* *
241 TTACTCTTTACTTTTTACCATTCTTCTTCTACTGA
1 TTACCCTTTACTCTTTACCATTCTTCTT-TACTGA
276 TTAC
1 TTAC
280 TCTCTACTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
33 3 0.05
34 21 0.32
35 41 0.63
ACGTcount: A:0.19, C:0.25, G:0.04, T:0.52
Consensus pattern (34 bp):
TTACCCTTTACTCTTTACCATTCTTCTTTACTGA
Found at i:280 original size:35 final size:35
Alignment explanation
Indices: 198--289 Score: 141
Period size: 35 Copynumber: 2.6 Consensus size: 35
188 ATCATTACTT
* *
198 TTTACTGATTACCCTTTACTCTTTACCATTCTTCC
1 TTTACTGATTACTCTTTACTTTTTACCATTCTTCC
233 TTTACTGATTACTCTTTACTTTTTACCATTCTT-C
1 TTTACTGATTACTCTTTACTTTTTACCATTCTTCC
*
267 TTCTACTGATTACTCTCTACTTT
1 TT-TACTGATTACTCTTTACTTT
290 CTATCATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
34 3 0.06
35 50 0.94
ACGTcount: A:0.17, C:0.27, G:0.03, T:0.52
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTTTTTACCATTCTTCC
Found at i:336 original size:14 final size:14
Alignment explanation
Indices: 299--337 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
289 TCTATCATTT
299 TACTCTTTACTAAC
1 TACTCTTTACTAAC
* *
313 TACTCCTTACTAAT
1 TACTCTTTACTAAC
*
327 TATTCTTTACT
1 TACTCTTTACT
338 CTTTACCATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (14 bp):
TACTCTTTACTAAC
Found at i:364 original size:21 final size:21
Alignment explanation
Indices: 331--370 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
321 ACTAATTATT
*
331 CTTTACTCTTTACCATTTTTC
1 CTTTACTCATTACCATTTTTC
* *
352 CTTTACTGATTACTATTTT
1 CTTTACTCATTACCATTTT
371 ACTCTCTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.57
Consensus pattern (21 bp):
CTTTACTCATTACCATTTTTC
Found at i:437 original size:16 final size:17
Alignment explanation
Indices: 413--447 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
403 ACTGATTACC
413 TTTTACTCTTTACC-AT
1 TTTTACTCTTTACCGAT
*
429 TTTTGCTCTTTACCGAT
1 TTTTACTCTTTACCGAT
446 TT
1 TT
448 ACTGATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.14, C:0.23, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTTACTCTTTACCGAT
Found at i:482 original size:40 final size:39
Alignment explanation
Indices: 438--544 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 39
428 TTTTTGCTCT
438 TTACCGATTTACTGATTACTTCTTTTACTCCT-ACTCTTAA
1 TTACC-ATTTACTGATTACTTCTTTTACT-CTGACTCTTAA
*
478 TTACCATTTTACTGATTACTTCTTTTACTTTGACTCTTAA
1 TTACCA-TTTACTGATTACTTCTTTTACTCTGACTCTTAA
* * *
518 TTATCAAATTACTGATTAATCTCTTTT
1 TTA-CCATTTACTGATTACT-TCTTTT
545 TACTTAATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
39 2 0.03
40 49 0.83
41 8 0.14
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (39 bp):
TTACCATTTACTGATTACTTCTTTTACTCTGACTCTTAA
Found at i:793 original size:38 final size:40
Alignment explanation
Indices: 728--802 Score: 91
Period size: 38 Copynumber: 1.9 Consensus size: 40
718 CTCATTGCTG
* * * *
728 CTTTTACTTCCTCTCTTAGTTATCAATTTACTAATTAATC
1 CTTTTACTTCCTCTCTTAATCACCAATTGACTAATTAATC
*
768 CTTTTACTT-C-CTCTTAATCACCAATTGACTGATTA
1 CTTTTACTTCCTCTCTTAATCACCAATTGACTAATTA
803 CTACTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 20 0.67
39 1 0.03
40 9 0.30
ACGTcount: A:0.25, C:0.24, G:0.04, T:0.47
Consensus pattern (40 bp):
CTTTTACTTCCTCTCTTAATCACCAATTGACTAATTAATC
Done.