Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016266.1 Corchorus olitorius cultivar O-4 contig16299, 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: 6419
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:366 original size:50 final size:48
Alignment explanation
Indices: 265--407 Score: 164
Period size: 49 Copynumber: 3.0 Consensus size: 48
255 CAAGCAATCA
* * ** *
265 TTTACTTTTCACTGCACTTTTTATCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTATCAATTTTTAAGACAAAATTGATCT
* *
313 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTATCAATTTTT-AAGACAAAATTGATCT
* *
363 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGAT
1 TTTAATTTTCATTGCACTTTTTATCAATTTTTAAGACAAAATTGAT
408 TGGCACGCTC
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
47 17 0.21
48 7 0.09
49 30 0.38
50 20 0.25
51 6 0.08
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (48 bp):
TTTAATTTTCATTGCACTTTTTATCAATTTTTAAGACAAAATTGATCT
Found at i:1883 original size:14 final size:14
Alignment explanation
Indices: 1866--1903 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
1856 ACTAAAACTA
1866 GAAGAGAAAAAGAG
1 GAAGAGAAAAAGAG
1880 GAAGAGAAAAAGAG
1 GAAGAGAAAAAGAG
1894 GAAGAGAAAA
1 GAAGAGAAAA
1904 TTATCTAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
GAAGAGAAAAAGAG
Found at i:2537 original size:19 final size:18
Alignment explanation
Indices: 2504--2539 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2494 TGGAAATAAT
2504 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
2522 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
2540 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:3782 original size:33 final size:33
Alignment explanation
Indices: 3745--3810 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
3735 CAAAAATTGG
3745 GGAAATTAAGATCAATCAAAAACAATCAAATTC
1 GGAAATTAAGATCAATCAAAAACAATCAAATTC
3778 GGAAATTAAGATCAATCAAAAACAATCAAATTC
1 GGAAATTAAGATCAATCAAAAACAATCAAATTC
3811 TATCCTAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (33 bp):
GGAAATTAAGATCAATCAAAAACAATCAAATTC
Found at i:4128 original size:30 final size:29
Alignment explanation
Indices: 4089--4145 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
4079 GTTTATTAAT
4089 GAAACTTGAAAATTAAAGACATAAGATAAAG
1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG
4120 GAAA-TTGAAAATTAAAGCATAAATAA
1 GAAACTTGAAAATTAAAGCATAAATAA
4146 CTAATCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (29 bp):
GAAACTTGAAAATTAAAGCATAAATAAAG
Found at i:5137 original size:6 final size:6
Alignment explanation
Indices: 5126--5158 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
5116 GATTAGTGTA
5126 AAAATT AAAATT AAAATT AAAATT AAAATT AAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAA
5159 TATGCAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Done.