Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011297.1 Corchorus capsularis cultivar CVL-1 contig11318, 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: 31037
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3447 original size:84 final size:84
Alignment explanation
Indices: 3306--3464 Score: 221
Period size: 84 Copynumber: 1.9 Consensus size: 84
3296 AATAACCATA
* * * * *
3306 TTGGTAGGCGATCTGTAAGTCCACAAAATTTACAAGTGAATGTCCAATGAATTCGTAAATTT-TC
1 TTGGTAGGCGATCTGTAAGTCCAAAAAATTAACAAGTAAAAGTCCAATGAATCCGTAAATTTCT-
3370 AAAAAGGTTGGTGGTTTGGT
65 AAAAAGGTTGGTGGTTTGGT
* * * *
3390 TTGGTAGGCGATCTGTAAGTCTAAAAAATTAATAAGTAAAAGTCCAATGGATCCGTAAATTTCTG
1 TTGGTAGGCGATCTGTAAGTCCAAAAAATTAACAAGTAAAAGTCCAATGAATCCGTAAATTTCTA
3455 AAAAGGTTGG
66 AAAAGGTTGG
3465 CAGTTTACTC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
84 64 0.98
85 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (84 bp):
TTGGTAGGCGATCTGTAAGTCCAAAAAATTAACAAGTAAAAGTCCAATGAATCCGTAAATTTCTA
AAAAGGTTGGTGGTTTGGT
Found at i:9650 original size:2 final size:2
Alignment explanation
Indices: 9643--9669 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9633 AGGTAGACGG
9643 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9670 ATTGAAGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11038 original size:12 final size:12
Alignment explanation
Indices: 11021--11047 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11011 AAATGTAGGC
11021 AAATTCAAAAAG
1 AAATTCAAAAAG
11033 AAATTCAAAAAG
1 AAATTCAAAAAG
11045 AAA
1 AAA
11048 AGGGCCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (12 bp):
AAATTCAAAAAG
Found at i:20421 original size:9 final size:9
Alignment explanation
Indices: 20407--20432 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
20397 TAAGGGTAAA
20407 GATATTTAT
1 GATATTTAT
20416 GATATTTAT
1 GATATTTAT
20425 GATATTTA
1 GATATTTA
20433 CTCGGATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (9 bp):
GATATTTAT
Found at i:21585 original size:15 final size:15
Alignment explanation
Indices: 21567--21595 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21557 CAGACCCATC
21567 AAGAGAATGAGGAAG
1 AAGAGAATGAGGAAG
21582 AAGAGAATGAGGAA
1 AAGAGAATGAGGAA
21596 AGTAGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (15 bp):
AAGAGAATGAGGAAG
Found at i:22034 original size:12 final size:14
Alignment explanation
Indices: 22006--22037 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
21996 ACATAAATTC
22006 AATGTTATAACATA
1 AATGTTATAACATA
22020 AATGTTAT-A-ATA
1 AATGTTATAACATA
22032 AATGTT
1 AATGTT
22038 CTAGAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (14 bp):
AATGTTATAACATA
Found at i:22793 original size:2 final size:2
Alignment explanation
Indices: 22786--22825 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
22776 ATTGATCTTT
22786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22826 CTTGACCACG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29362 original size:33 final size:33
Alignment explanation
Indices: 29290--29363 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
29280 AAACCATGGG
* *
29290 TATACATGTAAAAACTTGGGTACTAAATATAGT
1 TATACATGTAAAAACTTGGGAAATAAATATAGT
* * *
29323 TTTACATGTAGAAATTTGGGAAATAAATATA-T
1 TATACATGTAAAAACTTGGGAAATAAATATAGT
29355 TAATACATG
1 T-ATACATG
29364 ATTGGTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (33 bp):
TATACATGTAAAAACTTGGGAAATAAATATAGT
Done.