Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024511.1 Corchorus olitorius cultivar O-4 contig24544, 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: 13806
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:450 original size:11 final size:10
Alignment explanation
Indices: 429--455 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
419 TCAATCTTTC
429 AAAAGAAAAA
1 AAAAGAAAAA
439 AAAAGAAAAA
1 AAAAGAAAAA
449 AAAAGAA
1 AAAAGAA
456 GAGGACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:8051 original size:31 final size:32
Alignment explanation
Indices: 8003--8092 Score: 130
Period size: 31 Copynumber: 2.9 Consensus size: 32
7993 TTAGGGACTA
* *
8003 ATTTGAGCCGATTTTGCAATGTT-TGGATTTG
1 ATTTTAGCCGATTTTGCAATGTTATGGAATTG
*
8034 ATTTTAGCCAATTTTGCAATGTTAT-GAATTG
1 ATTTTAGCCGATTTTGCAATGTTATGGAATTG
*
8065 ATTTTAGTCGATTTTGCAATGTTATGGA
1 ATTTTAGCCGATTTTGCAATGTTATGGA
8093 CTTAATGAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.46
Consensus pattern (32 bp):
ATTTTAGCCGATTTTGCAATGTTATGGAATTG
Found at i:9216 original size:23 final size:22
Alignment explanation
Indices: 9190--9242 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
9180 GATGAAATCG
9190 CGGAGACTTCAGAGAAAA-AAGCA
1 CGGAG-CTT-AGAGAAAATAAGCA
*
9213 CGGAGCTTTGAGAAAATAAGCA
1 CGGAGCTTAGAGAAAATAAGCA
9235 CGGAGCTT
1 CGGAGCTT
9243 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 7 0.25
22 16 0.57
23 5 0.18
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.15
Consensus pattern (22 bp):
CGGAGCTTAGAGAAAATAAGCA
Found at i:9226 original size:21 final size:22
Alignment explanation
Indices: 9201--9242 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9191 GGAGACTTCA
9201 GAGAAAA-AAGCACGGAGCTTT
1 GAGAAAATAAGCACGGAGCTTT
9222 GAGAAAATAAGCACGGAGCTT
1 GAGAAAATAAGCACGGAGCTT
9243 GATTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (22 bp):
GAGAAAATAAGCACGGAGCTTT
Found at i:11064 original size:20 final size:21
Alignment explanation
Indices: 11041--11086 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
11031 ATTAATTAAT
11041 ATTTTAAAATAT-TTTTCATA
1 ATTTTAAAATATATTTTCATA
**
11061 ATTTT-TTATATATTTTCATA
1 ATTTTAAAATATATTTTCATA
11081 ATTTTA
1 ATTTTA
11087 TTTTAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTAAAATATATTTTCATA
Found at i:11650 original size:16 final size:16
Alignment explanation
Indices: 11623--11657 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
11613 GAAAAAATTT
*
11623 GAACTCGAAAATATCC
1 GAACTCGAAAATACCC
11639 GAACTCGAAAATACCC
1 GAACTCGAAAATACCC
11655 GAA
1 GAA
11658 TTCAATACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.26, G:0.14, T:0.14
Consensus pattern (16 bp):
GAACTCGAAAATACCC
Found at i:11944 original size:13 final size:13
Alignment explanation
Indices: 11926--11954 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11916 GATAGCCAAT
11926 AGAACTATAGAAG
1 AGAACTATAGAAG
11939 AGAACTATAGAAG
1 AGAACTATAGAAG
11952 AGA
1 AGA
11955 CCAAGCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.24, T:0.14
Consensus pattern (13 bp):
AGAACTATAGAAG
Done.