Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022003.1 Corchorus olitorius cultivar O-4 contig22036, 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: 5346
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Found at i:2594 original size:26 final size:26
Alignment explanation
Indices: 2565--2629 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
2555 GGAAAGAAAA
*
2565 AAAAAGAAAA-ATGAAGAAAAGAA-TTG
1 AAAAAGAAAAGA-AAAG-AAAGAAGTTG
2591 AAAAAGAAAAGAAAAGAAAGAAGTTG
1 AAAAAGAAAAGAAAAGAAAGAAGTTG
2617 AAAAAGCAAAAGA
1 AAAAAG-AAAAGA
2630 TGGAGGAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 6 0.17
26 22 0.63
27 7 0.20
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.08
Consensus pattern (26 bp):
AAAAAGAAAAGAAAAGAAAGAAGTTG
Found at i:2895 original size:41 final size:41
Alignment explanation
Indices: 2818--2895 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
2808 ATATTTTCTC
** ** *
2818 CAAAGTGTGATCTTTTCAAAAGAAAAAGGTTTTTTTTTCCT
1 CAAAGTGCAATCTTTTCAAAAGAAAAAGAATGTTTTTTCCT
2859 CAAAGTGCAATCTTTTCAAAAGAGAAAA-AATGTTTTT
1 CAAAGTGCAATCTTTTCAAAAGA-AAAAGAATGTTTTT
2896 CAAAAAGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 27 0.87
42 4 0.13
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (41 bp):
CAAAGTGCAATCTTTTCAAAAGAAAAAGAATGTTTTTTCCT
Found at i:4043 original size:54 final size:54
Alignment explanation
Indices: 3956--4099 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
3946 GTACAAGTGT
* *
3956 TTAAAATGACCTAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAACAGATC
1 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAACAGATC
4010 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAACAGATC
1 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAACAGATC
* *
4064 TTAAGATGACTC-GATATGGTCTTTCATAGAAGTTTT
1 TTAAGATGACCCAG-TGTGGTCTTTCATAGAAGTTTT
4100 TTTAATGATC
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
53 1 0.01
54 84 0.99
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (54 bp):
TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAACAGATC
Found at i:4190 original size:35 final size:35
Alignment explanation
Indices: 4085--4447 Score: 372
Period size: 35 Copynumber: 9.9 Consensus size: 35
4075 CGATATGGTC
* *
4085 TTTCATAGAAGTTTTTTTAATGATCAGAGTTGATCTCG
1 TTTCA-AGAAG-TTTTCT-ATGATCAGAGTTGATCTCA
* *
4123 TTTCAAGAAGTTTTTTTTTAATGATCAGAGTTGATCTCG
1 TTTCAAGAAG---TTTTCT-ATGATCAGAGTTGATCTCA
** *
4162 TTTCAAGAAGTTTTCGGTGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCTATGATCAGAGTTGATCTCA
* *
4197 TTTCAGGAAGTTTTTTATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCTATGATCAGAGTTGATCTCA
* *
4232 TTTTCAAGATGTTTT-TATGGTCAGAGTTGATCTCA
1 -TTTCAAGAAGTTTTCTATGATCAGAGTTGATCTCA
* * *
4267 TTTCAAGAAGTTTTCGATGATCATAGTTGATCTCG
1 TTTCAAGAAGTTTTCTATGATCAGAGTTGATCTCA
4302 TTTCAA-AGAGTTTTC-ATTGATCAGAGTTGATCTCA
1 TTTCAAGA-AGTTTTCTA-TGATCAGAGTTGATCTCA
* * *
4337 TTTCAAGAAGTTTTTTATATGGTCAGAGTTGATCTCC
1 TTTCAAGAAG--TTTTCTATGATCAGAGTTGATCTCA
*
4374 TTTCAAGAAGTTTTTTTTTTTTATGATCAGAGTTGATCTCA
1 TTTCAAGAAG------TTTTCTATGATCAGAGTTGATCTCA
*
4415 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
1 TTTCAAGAAGTTTTCTATGATCAGAGTTGATCT
4448 TCACATTGAT
Statistics
Matches: 284, Mismatches: 27, Indels: 31
0.83 0.08 0.09
Matches are distributed among these distances:
34 15 0.05
35 140 0.49
36 17 0.06
37 35 0.12
38 6 0.02
39 37 0.13
41 34 0.12
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.43
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCTATGATCAGAGTTGATCTCA
Done.