Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008076.1 Corchorus capsularis cultivar CVL-1 contig08097, 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: 35281
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3729 original size:16 final size:16
Alignment explanation
Indices: 3708--3738 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3698 AATTATTCCC
*
3708 AATTTCGAATTTCTTG
1 AATTTCAAATTTCTTG
3724 AATTTCAAATTTCTT
1 AATTTCAAATTTCTT
3739 ATTCTTTGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (16 bp):
AATTTCAAATTTCTTG
Found at i:3808 original size:32 final size:33
Alignment explanation
Indices: 3758--3832 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 33
3748 GGAGAAGTTC
*
3758 TTGTAATTTTTTGTAAATTATATTCT-GTTCTTA
1 TTGTAATTTTTTGCAAATTATATT-TGGTTCTTA
3791 TTGTAATTTTTT-CAAATTATATTTGGTTCTTA
1 TTGTAATTTTTTGCAAATTATATTTGGTTCTTA
3823 TTG--ATTTTTT
1 TTGTAATTTTTT
3833 ACTTTATTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
30 7 0.17
31 1 0.03
32 20 0.50
33 12 0.30
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.63
Consensus pattern (33 bp):
TTGTAATTTTTTGCAAATTATATTTGGTTCTTA
Found at i:4589 original size:12 final size:12
Alignment explanation
Indices: 4572--4600 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4562 TCCATTAGCT
4572 AATGGTGATGCC
1 AATGGTGATGCC
4584 AATGGTGATGCC
1 AATGGTGATGCC
4596 AATGG
1 AATGG
4601 CGAAGAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (12 bp):
AATGGTGATGCC
Found at i:11543 original size:21 final size:21
Alignment explanation
Indices: 11519--11562 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
11509 GCAGACTTTA
11519 AGAAGAA-TG-GAAGCTAAAAGG
1 AGAAGAAGTGAGAAGC--AAAGG
11540 AGAAGAAGTGAGAAGCAAAGG
1 AGAAGAAGTGAGAAGCAAAGG
11561 AG
1 AG
11563 TTCAAGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 14 0.67
22 2 0.10
23 5 0.24
ACGTcount: A:0.52, C:0.05, G:0.36, T:0.07
Consensus pattern (21 bp):
AGAAGAAGTGAGAAGCAAAGG
Found at i:12715 original size:201 final size:201
Alignment explanation
Indices: 12370--12771 Score: 804
Period size: 201 Copynumber: 2.0 Consensus size: 201
12360 TTATGAAATG
12370 GTAACTACTACTCAAATATAGAATTCTATGAAGAATTGGCATTTAGTTTTGATCTGAGGCTTTTT
1 GTAACTACTACTCAAATATAGAATTCTATGAAGAATTGGCATTTAGTTTTGATCTGAGGCTTTTT
12435 TGCTCTGAATGTAAATCACATGAAACTGGAGATTTTCAGTTTAAGCATAGGCTGGTTCCCAGTTG
66 TGCTCTGAATGTAAATCACATGAAACTGGAGATTTTCAGTTTAAGCATAGGCTGGTTCCCAGTTG
12500 TATGATAGATGGTATTAAAATCATCATAATTAATCCCTGTTAGTATTGGAAATTCAAAGATGAAT
131 TATGATAGATGGTATTAAAATCATCATAATTAATCCCTGTTAGTATTGGAAATTCAAAGATGAAT
12565 GATATT
196 GATATT
12571 GTAACTACTACTCAAATATAGAATTCTATGAAGAATTGGCATTTAGTTTTGATCTGAGGCTTTTT
1 GTAACTACTACTCAAATATAGAATTCTATGAAGAATTGGCATTTAGTTTTGATCTGAGGCTTTTT
12636 TGCTCTGAATGTAAATCACATGAAACTGGAGATTTTCAGTTTAAGCATAGGCTGGTTCCCAGTTG
66 TGCTCTGAATGTAAATCACATGAAACTGGAGATTTTCAGTTTAAGCATAGGCTGGTTCCCAGTTG
12701 TATGATAGATGGTATTAAAATCATCATAATTAATCCCTGTTAGTATTGGAAATTCAAAGATGAAT
131 TATGATAGATGGTATTAAAATCATCATAATTAATCCCTGTTAGTATTGGAAATTCAAAGATGAAT
12766 GATATT
196 GATATT
12772 TGGATTTGGG
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 201 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (201 bp):
GTAACTACTACTCAAATATAGAATTCTATGAAGAATTGGCATTTAGTTTTGATCTGAGGCTTTTT
TGCTCTGAATGTAAATCACATGAAACTGGAGATTTTCAGTTTAAGCATAGGCTGGTTCCCAGTTG
TATGATAGATGGTATTAAAATCATCATAATTAATCCCTGTTAGTATTGGAAATTCAAAGATGAAT
GATATT
Found at i:24993 original size:30 final size:30
Alignment explanation
Indices: 24957--25022 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
24947 AAGGTGTCTT
** *
24957 CTTGAATACTTACTGCTTTCA-CTCTCCTCA
1 CTTGAATACCCACTGCTTCCACCTC-CCTCA
*
24987 CTTGAATGCCCACTGCTTCCACCTCCCTCA
1 CTTGAATACCCACTGCTTCCACCTCCCTCA
25017 CTTGAA
1 CTTGAA
25023 AGCCTCCCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.20, C:0.38, G:0.09, T:0.33
Consensus pattern (30 bp):
CTTGAATACCCACTGCTTCCACCTCCCTCA
Found at i:30129 original size:13 final size:13
Alignment explanation
Indices: 30111--30135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30101 ATTCTCGAGC
30111 TTACACTATTTAT
1 TTACACTATTTAT
30124 TTACACTATTTA
1 TTACACTATTTA
30136 CAAAATTACT
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (13 bp):
TTACACTATTTAT
Done.