Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00446.F3
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, 678
Length: 1131
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Found at i:232 original size:45 final size:44
Alignment explanation
Indices: 155--550 Score: 359
Period size: 45 Copynumber: 8.8 Consensus size: 44
145 CACCACCATA
* * * *
155 TGAACCTAAGCCACCAGTGTATGAACCACCAAAAAAGGAGAAGCC
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAA-GAGAAGCC
* * * *
200 TGAACCTAAGCCACCGGTTTATGCACCTCCAAAGAAAGAGAAGCC
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAA-AAAGAGAAGCC
* * * *
245 TGGACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCC
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAA-AAAGAGAAGCC
* * *
290 TGAGCCAAAGCCACCAGTTTAT-ACACCTCCAAAGAAAGAGGAGCC
1 TGAACCAAAACCACCAGTTTATGA-ACCTCCAAA-AAAGAGAAGCC
* * * * *
335 TAAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACC
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAA-AAAGAGAAGCC
* *
380 TGAGCCAAAACCACC-GATTTAT-ACACCTCCAAAGAAAGAGAAACC
1 TGAACCAAAACCACCAG-TTTATGA-ACCTCCAAA-AAAGAGAAGCC
* * * *
425 TGAACCCAAACCACCCGTATATGAACCTCCAAAGAAGGAGAAGCC
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAA-AAAGAGAAGCC
* * * * *
470 CGAGCCAAAGCCACCGGTTTAT-ACACCTCCAAAGAAAGAGAAACC
1 TGAACCAAAACCACCAGTTTATGA-ACCTCCAAA-AAAGAGAAGCC
* *
515 TGAACCCAAACCACCAGTGTATGAACCTCCAAAAAA
1 TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAA
551 ACCTCCAATG
Statistics
Matches: 292, Mismatches: 50, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
44 7 0.02
45 278 0.95
46 7 0.02
ACGTcount: A:0.41, C:0.29, G:0.17, T:0.13
Consensus pattern (44 bp):
TGAACCAAAACCACCAGTTTATGAACCTCCAAAAAAGAGAAGCC
Found at i:318 original size:90 final size:90
Alignment explanation
Indices: 155--748 Score: 643
Period size: 90 Copynumber: 6.3 Consensus size: 90
145 CACCACCATA
* * * * * *
155 TGAACCTAAGCCACCAGTGTATGAACCACCAAAAAAGGAGAAGCCTGAACCTAAGCCACCGGTTT
1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
* *
220 ATGCACCTCCAAAGAAAGAGAAGCC
66 ATACACCTCCAAAGAAAGAGAAACC
* *
245 TGGACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCAGTTT
1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
* *
310 ATACACCTCCAAAGAAAGAGGAGCC
66 ATACACCTCCAAAGAAAGAGAAACC
* * * * * *
335 TAAACCTAAACCACCAGTATATGAACCTCCAAAGAAGGAGAAACCTGAGCCAAAACCACCGATTT
1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
400 ATACACCTCCAAAGAAAGAGAAACC
66 ATACACCTCCAAAGAAAGAGAAACC
* * *
425 TGAACCCAAACCACCCGTATATGAACCTCCAAAGAAGGAGAAGCCCGAGCCAAAGCCACCGGTTT
1 TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
490 ATACACCTCCAAAGAAAGAGAAACC
66 ATACACCTCCAAAGAAAGAGAAACC
* * *
515 TGAACCCAAACCACCAGTGTATGAACCTCCAAAAAAACCTCCAATGTACGAA-CCTAAGCCACCA
1 TGAACCCAAACCACCAGTGTATGAACCTCC----AAA----GAA-GGA-GAAGCCTGAG---CCA
*
579 AAACCACCGGTTTATACACCTCCAAAGAAAGAGAAACC
53 AAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACC
* * *
617 TGAACCCAAACCACCAATGTATGAACCTCCAAAAAAGCCTCCAATGTATGAA-CCTAAGCCACCA
1 TGAACCCAAACCACCAGTGTATGAACCTCC---AAAG-----AA-GGA-GAAGCCTGAG---CCA
*
681 AAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACC
53 AAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACC
* * * *
719 AGAACCCAAGCCACCAATGTATCAACCTCC
1 TGAACCCAAACCACCAGTGTATGAACCTCC
749 CAACAACCCA
Statistics
Matches: 444, Mismatches: 42, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
90 271 0.61
94 3 0.01
98 2 0.00
99 6 0.01
100 3 0.01
101 6 0.01
102 153 0.34
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.13
Consensus pattern (90 bp):
TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
ATACACCTCCAAAGAAAGAGAAACC
Found at i:583 original size:57 final size:56
Alignment explanation
Indices: 522--706 Score: 146
Period size: 57 Copynumber: 3.5 Consensus size: 56
512 ACCTGAACCC
522 AAACCACCAGTGTATGA-ACCTCCAAAAAAACCTCCAATGTACGAACCTAAGCCACCA
1 AAACCACCAGTGTAT-ACACCTCCAAAAAAACCTCCAATGTA-GAACCTAAGCCACCA
* * * *
579 AAACCACCGGTTTATACACCTCCAAAGAAA-----GA-G-A-AACCTGAA--C-CC-
1 AAACCACCAGTGTATACACCTCCAAAAAAACCTCCAATGTAGAACCT-AAGCCACCA
* *
624 AAACCACCAATGTATGA-ACCTCCAAAAAAGCCTCCAATGTATGAACCTAAGCCACCA
1 AAACCACCAGTGTAT-ACACCTCCAAAAAAACCTCCAATGTA-GAACCTAAGCCACCA
* * *
681 AAGCCACCGGTTTATACACCTCCAAA
1 AAACCACCAGTGTATACACCTCCAAA
707 GAAAGAAAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 34
0.67 0.10 0.23
Matches are distributed among these distances:
45 23 0.24
46 3 0.03
47 1 0.01
48 5 0.05
49 2 0.02
50 2 0.02
51 2 0.02
52 2 0.02
53 2 0.02
54 5 0.05
55 1 0.01
56 4 0.04
57 45 0.46
ACGTcount: A:0.41, C:0.32, G:0.11, T:0.15
Consensus pattern (56 bp):
AAACCACCAGTGTATACACCTCCAAAAAAACCTCCAATGTAGAACCTAAGCCACCA
Found at i:850 original size:102 final size:102
Alignment explanation
Indices: 474--833 Score: 488
Period size: 102 Copynumber: 3.5 Consensus size: 102
464 GAAGCCCGAG
* *
474 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCAGAACCCAAACCACCAATGTATGA
*
539 ACCTCCAAAAAAACCTCCAATGTACGAACCTAAGCCA
66 ACCTCCAAAAAAACCTCCAATGTATGAACCTAAGCCA
* *
576 CCAAAACCACCGGTTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAATGTATGA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCAGAACCCAAACCACCAATGTATGA
*
641 ACCTCCAAAAAAGCCTCCAATGTATGAACCTAAGCCA
66 ACCTCCAAAAAAACCTCCAATGTATGAACCTAAGCCA
* * *
678 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACCAGAACCCAAGCCACCAATGTATCA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCAGAACCCAAACCACCAATGTATGA
* * * * * * * *
743 ACCTCCCAACAACCCACCAATATATGAGCCAAAACCA
66 ACCTCCAAAAAAACCTCCAATGTATGAACCTAAGCCA
* * * * * * *
780 CCTAAGCCACCAGTTTATGCACCACCAAAGGAAGA-AAAGCCAAAACCTAAACCA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAA-CCAGAACCCAAACCA
834 TCAGTTTATG
Statistics
Matches: 232, Mismatches: 25, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
101 3 0.01
102 229 0.99
ACGTcount: A:0.42, C:0.33, G:0.12, T:0.13
Consensus pattern (102 bp):
CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCAGAACCCAAACCACCAATGTATGA
ACCTCCAAAAAAACCTCCAATGTATGAACCTAAGCCA
Done.