Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013241.1 Corchorus olitorius cultivar O-4 contig13274, 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: 22814
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:659 original size:14 final size:14
Alignment explanation
Indices: 640--671 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
630 TAAGTTGTTT
*
640 TTTTATTTTTTACA
1 TTTTATTTTTTAAA
654 TTTTATTTTTTAAA
1 TTTTATTTTTTAAA
668 TTTT
1 TTTT
672 TGATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTTTAAA
Found at i:1388 original size:53 final size:55
Alignment explanation
Indices: 1325--1431 Score: 155
Period size: 53 Copynumber: 2.0 Consensus size: 55
1315 CAGTCATACG
** *
1325 TATCTTGCTTGTGATGCAAGATTTAAAAGGCAT-AAGCCCTG-AAAATAGCTCTT
1 TATCTTGCTTGCAATGCAAGATTTAAAAGGCATGAAGCACTGTAAAATAGCTCTT
* *
1378 TATCTTGCTTGCAATGCAAGCTTTAAAAGGCATGAAGCATTGTAAAATAGCTCT
1 TATCTTGCTTGCAATGCAAGATTTAAAAGGCATGAAGCACTGTAAAATAGCTCT
1432 CATCAATGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 30 0.64
54 6 0.13
55 11 0.23
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (55 bp):
TATCTTGCTTGCAATGCAAGATTTAAAAGGCATGAAGCACTGTAAAATAGCTCTT
Found at i:8421 original size:17 final size:17
Alignment explanation
Indices: 8399--8432 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
8389 GTTTGGTTGA
8399 AGGGGTA-GAGAGGGGTG
1 AGGGGTAGGA-AGGGGTG
8416 AGGGGTAGGAAGGGGTG
1 AGGGGTAGGAAGGGGTG
8433 CTTGCTACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.24, C:0.00, G:0.65, T:0.12
Consensus pattern (17 bp):
AGGGGTAGGAAGGGGTG
Found at i:9153 original size:2 final size:2
Alignment explanation
Indices: 9142--9173 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9132 AAATGCACAT
9142 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9174 TTGAAAGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14009 original size:22 final size:23
Alignment explanation
Indices: 13983--14025 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
13973 GGATTTCTGG
*
13983 AAAATTAATTT-TATTAAAATAA
1 AAAATTAATTTAAATTAAAATAA
14005 AAAATTAATTTAAATTAAAAT
1 AAAATTAATTTAAATTAAAAT
14026 TTAAAAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATTAATTTAAATTAAAATAA
Found at i:19023 original size:17 final size:17
Alignment explanation
Indices: 18980--19024 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
18970 CTAAACAAAT
* *
18980 AAAAGAAAACATGCAGG
1 AAAAGAAAACATGAAAG
18997 AAAA-AGAAACATGAAAG
1 AAAAGA-AAACATGAAAG
19014 AAAAGAAAACA
1 AAAAGAAAACA
19025 AAGCAGAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.69, C:0.09, G:0.18, T:0.04
Consensus pattern (17 bp):
AAAAGAAAACATGAAAG
Found at i:19831 original size:28 final size:29
Alignment explanation
Indices: 19764--19852 Score: 144
Period size: 29 Copynumber: 3.1 Consensus size: 29
19754 TAGGGTCACT
19764 CATCCAGGGGCATTTTGGTCATTTTTGCA
1 CATCCAGGGGCATTTTGGTCATTTTTGCA
* *
19793 TATCCATGGGCATTTTGGTCA-TTTTGCA
1 CATCCAGGGGCATTTTGGTCATTTTTGCA
*
19821 CATCTAGGGGCATTTTGGTCATTTTTGCA
1 CATCCAGGGGCATTTTGGTCATTTTTGCA
19850 CAT
1 CAT
19853 TTAGGGGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
28 25 0.46
29 29 0.54
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.40
Consensus pattern (29 bp):
CATCCAGGGGCATTTTGGTCATTTTTGCA
Found at i:19857 original size:29 final size:29
Alignment explanation
Indices: 19764--19864 Score: 141
Period size: 29 Copynumber: 3.5 Consensus size: 29
19754 TAGGGTCACT
*
19764 CATCCAGGGGCATTTTGGTCATTTTTGCA
1 CATCTAGGGGCATTTTGGTCATTTTTGCA
* * *
19793 TATCCATGGGCATTTTGGTCA-TTTTGCA
1 CATCTAGGGGCATTTTGGTCATTTTTGCA
19821 CATCTAGGGGCATTTTGGTCATTTTTGCA
1 CATCTAGGGGCATTTTGGTCATTTTTGCA
* *
19850 CATTTAGGGGTATTT
1 CATCTAGGGGCATTT
19865 CAGTCACTTC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
28 25 0.39
29 39 0.61
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (29 bp):
CATCTAGGGGCATTTTGGTCATTTTTGCA
Done.