Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g00487.P1
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: 10213
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Found at i:5788 original size:45 final size:45
Alignment explanation
Indices: 5724--5815 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
5714 TGTGAGCAAT
5724 AAGTTAGTCCAAAGATTAATTCATTGTTTGACATAGTTTATTGTC
1 AAGTTAGTCCAAAGATTAATTCATTGTTTGACATAGTTTATTGTC
5769 AAGTTAGTCCAAAGATTAATTCATTGTTTGACATAGTTTATTGTC
1 AAGTTAGTCCAAAGATTAATTCATTGTTTGACATAGTTTATTGTC
5814 AA
1 AA
5816 TGTTTGATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (45 bp):
AAGTTAGTCCAAAGATTAATTCATTGTTTGACATAGTTTATTGTC
Found at i:7316 original size:21 final size:21
Alignment explanation
Indices: 7292--7332 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
7282 TCTCTAGTCA
7292 TAAACCCTAAACTA-TAAACCG
1 TAAACCCTAAA-TATTAAACCG
7313 TAAACCCTAAATATTAAACC
1 TAAACCCTAAATATTAAACC
7333 TTGAATCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.49, C:0.27, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAACCCTAAATATTAAACCG
Found at i:7372 original size:29 final size:29
Alignment explanation
Indices: 7340--7412 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
7330 ACCTTGAATC
*
7340 CTAAGCCATAAAACCC-TAAATTATAGACA
1 CTAAACCATAAAACCCTTAAA-TATAGACA
* *
7369 CTAAACCCTTAAACCCTTAAATATAGATTC-
1 CTAAACCATAAAACCCTTAAATATAGA--CA
*
7399 CTAAATCATAAAAC
1 CTAAACCATAAAAC
7413 GGTAAACCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 19 0.54
30 15 0.43
31 1 0.03
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.25
Consensus pattern (29 bp):
CTAAACCATAAAACCCTTAAATATAGACA
Found at i:7462 original size:21 final size:21
Alignment explanation
Indices: 7437--7479 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
7427 ACTAGACCAG
*
7437 CTTAAATTATAAACCCTAAAT
1 CTTAAACTATAAACCCTAAAT
7458 CTTAAACTATAAACCCTAAAT
1 CTTAAACTATAAACCCTAAAT
7479 C
1 C
7480 CAAAACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (21 bp):
CTTAAACTATAAACCCTAAAT
Found at i:7485 original size:21 final size:21
Alignment explanation
Indices: 7444--7491 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
7434 CAGCTTAAAT
**
7444 TATAAACCCTAAATCTTAAAC
1 TATAAACCCTAAATCCAAAAC
7465 TATAAACCCTAAATCCAAAAC
1 TATAAACCCTAAATCCAAAAC
*
7486 CATAAA
1 TATAAA
7492 ACCTTAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (21 bp):
TATAAACCCTAAATCCAAAAC
Found at i:7931 original size:26 final size:26
Alignment explanation
Indices: 7895--8004 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
7885 TGATACAAAT
7895 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
7921 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
7947 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
7973 TGATAAT-GAGTTAGGTAAATGTTTCA
1 TGATAATAG-GTTAGGTAAATGTTCCA
7999 TGATAA
1 TGATAA
8005 GAATTTCATG
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 1 0.01
26 80 0.99
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:9489 original size:26 final size:27
Alignment explanation
Indices: 9423--9496 Score: 96
Period size: 26 Copynumber: 2.7 Consensus size: 27
9413 AAAAGTAGCT
* *
9423 AAATTACTATAATACCCCTATGTATGAA
1 AAATTACTATTATACCCCTAAG-ATGAA
*
9451 AAATTACTATTATACCCCTAAG-TGCA
1 AAATTACTATTATACCCCTAAGATGAA
*
9477 AAATTACTGTTATACCCCTA
1 AAATTACTATTATACCCCTA
9497 GGGTTAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 22 0.52
28 20 0.48
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (27 bp):
AAATTACTATTATACCCCTAAGATGAA
Found at i:9642 original size:27 final size:27
Alignment explanation
Indices: 9601--9653 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
9591 GAGGAAGCGT
9601 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTATGCCACAAATATCTGA
* * *
9628 TCTGGTGGCTCTGCCACGATTATCTG
1 TCTGGTGGCTATGCCACAAATATCTG
9654 TGTTTGGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (27 bp):
TCTGGTGGCTATGCCACAAATATCTGA
Done.