Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00446.F2
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, 617
Length: 1029
ACGTcount: A:0.35, C:0.28, G:0.17, 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--646 Score: 599
Period size: 90 Copynumber: 5.3 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 AAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACC
53 AAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACC
* * * *
617 AGAACCCAAGCCACCAATGTATCAACCTCC
1 TGAACCCAAACCACCAGTGTATGAACCTCC
647 CAACAACCCA
Statistics
Matches: 351, Mismatches: 38, Indels: 14
0.87 0.09 0.03
Matches are distributed among these distances:
90 271 0.77
94 3 0.01
98 2 0.01
99 6 0.02
100 3 0.01
102 66 0.19
ACGTcount: A:0.41, C:0.30, G:0.16, T:0.13
Consensus pattern (90 bp):
TGAACCCAAACCACCAGTGTATGAACCTCCAAAGAAGGAGAAGCCTGAGCCAAAGCCACCGGTTT
ATACACCTCCAAAGAAAGAGAAACC
Found at i:596 original size:102 final size:101
Alignment explanation
Indices: 474--748 Score: 316
Period size: 102 Copynumber: 2.7 Consensus size: 101
464 GAAGCCCGAG
*
474 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAGAAACCTGAACCCAAACCACCAGTGTATGA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGA-AAACCAGAACCCAAACCACCAGTGTATGA
* * * *
539 ACCTCCAAAAAAACCTCCAATGTACGAACCTAAGCCA
65 ACCTCCAAAAAAACCACCAATATACGAACCAAAACCA
* * *
576 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAAAAACCAGAACCCAAGCCACCAATGTATCA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAG-AAAACCAGAACCCAAACCACCAGTGTATGA
* * * * *
641 ACCTCCCAACAACCCACCAATATATGAGCCAAAACCA
65 ACCTCCAAAAAAACCACCAATATACGAACCAAAACCA
* * * * * * * * *
678 CCTAAGCCACCAGTTTATGCACCACCAAAGGAAGAAAAGCCAAAACCTAAACCATCAGTTTATGA
1 CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAAAA-CCAGAACCCAAACCACCAGTGTATGA
*
743 GCCTCC
65 ACCTCC
749 GGCACATGAG
Statistics
Matches: 145, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
101 4 0.03
102 140 0.97
103 1 0.01
ACGTcount: A:0.41, C:0.33, G:0.12, T:0.14
Consensus pattern (101 bp):
CCAAAGCCACCGGTTTATACACCTCCAAAGAAAGAAAACCAGAACCCAAACCACCAGTGTATGAA
CCTCCAAAAAAACCACCAATATACGAACCAAAACCA
Done.