Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018520.1 Corchorus olitorius cultivar O-4 contig18553, 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: 27489
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:625 original size:22 final size:23
Alignment explanation
Indices: 597--654 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
587 TATTTTTATG
* *
597 AAATTTTGATAACTATCCTAT-T
1 AAATTTTGATAACCATCCTATAA
*
619 AAATTTTGATAACCATGCTATGAA
1 AAATTTTGATAACCATCCTAT-AA
643 AAATTTTGATAA
1 AAATTTTGATAA
655 TTACCTAGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 19 0.61
24 12 0.39
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (23 bp):
AAATTTTGATAACCATCCTATAA
Found at i:725 original size:22 final size:23
Alignment explanation
Indices: 700--742 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
690 TAACCTAACA
700 ATGAAATTTTG-TAACCTTCCCT
1 ATGAAATTTTGTTAACCTTCCCT
*
722 ATGAAATTTTGTTAATCTTCC
1 ATGAAATTTTGTTAACCTTCC
743 TATAACTTTT
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:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (23 bp):
ATGAAATTTTGTTAACCTTCCCT
Found at i:3771 original size:9 final size:9
Alignment explanation
Indices: 3757--3782 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3747 TTGAGCTTTA
3757 GATTATATG
1 GATTATATG
3766 GATTATATG
1 GATTATATG
3775 GATTATAT
1 GATTATAT
3783 AGTAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (9 bp):
GATTATATG
Found at i:5427 original size:32 final size:32
Alignment explanation
Indices: 5391--5496 Score: 203
Period size: 32 Copynumber: 3.3 Consensus size: 32
5381 AACGACGACC
5391 ATATCTGACTATATGAAGAAACATAAGATGCA
1 ATATCTGACTATATGAAGAAACATAAGATGCA
*
5423 ATATCTGAATATATGAAGAAACATAAGATGCA
1 ATATCTGACTATATGAAGAAACATAAGATGCA
5455 ATATCTGACTATATGAAGAAACATAAGATGCA
1 ATATCTGACTATATGAAGAAACATAAGATGCA
5487 ATATCTGACT
1 ATATCTGACT
5497 TGGATATGTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.26
Consensus pattern (32 bp):
ATATCTGACTATATGAAGAAACATAAGATGCA
Found at i:9111 original size:16 final size:16
Alignment explanation
Indices: 9090--9129 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
9080 TGTTAAGAAA
*
9090 ATTAAAATATTAGTCC
1 ATTAAAATATTAATCC
9106 ATTAAAATATTAATCC
1 ATTAAAATATTAATCC
*
9122 ATTCAAAT
1 ATTAAAAT
9130 GAAGATCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (16 bp):
ATTAAAATATTAATCC
Found at i:12389 original size:34 final size:34
Alignment explanation
Indices: 12351--12426 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
12341 TTTCCCTGAA
* *
12351 TTGAAAACCAAAACTTGATGGGAGCTTTCCCAAT
1 TTGAAAACCAAAACCTGATGGGAACTTTCCCAAT
* * *
12385 TTGAAAACTAAACCCTGGTGGGAACTTTCCCAAT
1 TTGAAAACCAAAACCTGATGGGAACTTTCCCAAT
*
12419 TTTAAAAC
1 TTGAAAAC
12427 TATGAAGACT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (34 bp):
TTGAAAACCAAAACCTGATGGGAACTTTCCCAAT
Found at i:14157 original size:29 final size:29
Alignment explanation
Indices: 14125--14207 Score: 148
Period size: 29 Copynumber: 2.9 Consensus size: 29
14115 GGATCACCTG
*
14125 GGGGCATTTTGGTCATTTTTGCATGTCCA
1 GGGGCATTTTGGTCATTTTTGCATATCCA
14154 GGGGCATTTTGGTCATTTTTGCATATCCA
1 GGGGCATTTTGGTCATTTTTGCATATCCA
*
14183 GGGGCATTTTGGTCATTATTGCATA
1 GGGGCATTTTGGTCATTTTTGCATA
14208 CTCTGGGTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.41
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTTGCATATCCA
Found at i:15818 original size:12 final size:12
Alignment explanation
Indices: 15801--15827 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15791 GCATTTAAGA
15801 TAGTTGTCATTT
1 TAGTTGTCATTT
15813 TAGTTGTCATTT
1 TAGTTGTCATTT
15825 TAG
1 TAG
15828 GCATAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.56
Consensus pattern (12 bp):
TAGTTGTCATTT
Found at i:22716 original size:6 final size:6
Alignment explanation
Indices: 22695--22741 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
22685 CGTACTTTTT
*
22695 GATATA G-TATA AATATA GATATA GATATA GATATA GATATA GATATA
1 GATATA GATATA GATATA GATATA GATATA GATATA GATATA GATATA
22742 AAAATATACA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (6 bp):
GATATA
Done.