Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013765.1 Corchorus olitorius cultivar O-4 contig13798, 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: 25931
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:490 original size:36 final size:35
Alignment explanation
Indices: 437--505 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
427 TTCAATAACC
* *
437 TTACATTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATTTTTGTAATTTTGATTATCATATTTCTTA
472 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACA-TTTTTGTAATTTTGATTATCATATTTCT
506 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.61
Consensus pattern (35 bp):
TTACATTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:4146 original size:23 final size:24
Alignment explanation
Indices: 4120--4168 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
4110 AGATTTAACT
4120 AAATAAAA-ATAA-AGTTTTAAGTA
1 AAATAAAACATAATAG-TTTAAGTA
4143 AAATAAAACTATAATAGTTTAAGTA
1 AAATAAAAC-ATAATAGTTTAAGTA
4168 A
1 A
4169 TGACATTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.35
25 13 0.57
26 2 0.09
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (24 bp):
AAATAAAACATAATAGTTTAAGTA
Found at i:14213 original size:13 final size:13
Alignment explanation
Indices: 14195--14222 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
14185 CTATAACCTC
14195 ATAAATCATATTT
1 ATAAATCATATTT
14208 ATAAATCATATTT
1 ATAAATCATATTT
14221 AT
1 AT
14223 TATATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAAATCATATTT
Found at i:14362 original size:19 final size:18
Alignment explanation
Indices: 14333--14374 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
14323 TGAGTAGTTT
* *
14333 TTAAGTAAAAATGTAATA
1 TTAAATAAAAATATAATA
14351 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
14370 TTAAA
1 TTAAA
14375 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:14378 original size:19 final size:19
Alignment explanation
Indices: 14338--14374 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
14328 AGTTTTTAAG
*
14338 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
14357 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
14375 ATAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:25875 original size:2 final size:2
Alignment explanation
Indices: 25868--25921 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
25858 AATTTGGTGT
25868 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25910 AG AG AG AG AG AG
1 AG AG AG AG AG AG
25922 TAGTAGTAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.