Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013586.1 Corchorus olitorius cultivar O-4 contig13619, 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: 12543
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Found at i:10680 original size:24 final size:24
Alignment explanation
Indices: 10653--10738 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
10643 ATTATAGGCT
*
10653 TCCAGATCTTCATCGTCCTT-AGAA
1 TCCAGATCTTCATCAT-CTTCAGAA
10677 TCCAGATCTTCATCATCTTCAGAA
1 TCCAGATCTTCATCATCTTCAGAA
*
10701 TCCAAATCTTCATCATCTTCAGAA
1 TCCAGATCTTCATCATCTTCAGAA
*
10725 TCCAGATCGTCATC
1 TCCAGATCTTCATC
10739 TTCTGGAACT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
23 3 0.05
24 54 0.95
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (24 bp):
TCCAGATCTTCATCATCTTCAGAA
Found at i:11523 original size:39 final size:39
Alignment explanation
Indices: 11436--11515 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
11426 AATAATTACC
* *
11436 AAAACAAATACACTACAATTCATCAATATTTAAACCCAA
1 AAAACAAATACACTACAATACATCAACATTTAAACCCAA
*
11475 AAAACAAATACAGTACAATACATCAACATTTAAACCCAA
1 AAAACAAATACACTACAATACATCAACATTTAAACCCAA
11514 AA
1 AA
11516 CCCAAATAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.56, C:0.23, G:0.01, T:0.20
Consensus pattern (39 bp):
AAAACAAATACACTACAATACATCAACATTTAAACCCAA
Found at i:11828 original size:7 final size:7
Alignment explanation
Indices: 11818--11862 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
11808 TTAATGATTA
11818 AAAAAAC
1 AAAAAAC
11825 AAAAAA-
1 AAAAAAC
**
11831 AAGCAA-
1 AAAAAAC
11837 AAAAAAC
1 AAAAAAC
11844 -AAAAAC
1 AAAAAAC
11850 AAAAAAC
1 AAAAAAC
11857 AAAAAA
1 AAAAAA
11863 AAGGAGGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 14 0.44
7 18 0.56
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:11860 original size:19 final size:18
Alignment explanation
Indices: 11817--11861 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
11807 TTTAATGATT
11817 AAAAAAACAAAAAAAAGCA
1 AAAAAAACAAAAAAAA-CA
11836 AAAAAAACAAAAACAAA-A
1 AAAAAAACAAAAA-AAACA
11854 AACAAAAA
1 AA-AAAAA
11862 AAAGGAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.12
19 18 0.75
20 3 0.12
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAAACA
Found at i:12442 original size:29 final size:28
Alignment explanation
Indices: 12398--12453 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
12388 TTCTTCAAAC
*
12398 TTTCTAATTTCAAGAACGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
12426 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
12454 GTGGAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Done.