Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g02935.F1
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: 2722
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Found at i:170 original size:30 final size:30
Alignment explanation
Indices: 129--250 Score: 82
Period size: 30 Copynumber: 3.9 Consensus size: 30
119 CGCCACAACC
* * *
129 ACCATCACCAGTGATTGAACCAAAACCGCA
1 ACCACCACCAGTGACTGAACCAAAACCACA
**
159 ACCACCACCAGTTCCTGAACCAAAACCACA
1 ACCACCACCAGTGACTGAACCAAAACCACA
* * * *
189 ACTACCACTAAACTCGCCGTCTGAACCAAAACCACA
1 ACCACCAC----C-AG-TGACTGAACCAAAACCACA
* * *
225 GCCACCACTAGTGCCTGAACCAAAAC
1 ACCACCACCAGTGACTGAACCAAAAC
251 GGCAGCCACA
Statistics
Matches: 70, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
30 45 0.64
31 1 0.01
34 1 0.01
35 1 0.01
36 22 0.31
ACGTcount: A:0.39, C:0.39, G:0.11, T:0.12
Consensus pattern (30 bp):
ACCACCACCAGTGACTGAACCAAAACCACA
Found at i:299 original size:84 final size:84
Alignment explanation
Indices: 203--509 Score: 310
Period size: 84 Copynumber: 3.5 Consensus size: 84
193 CCACTAAACT
* * * * *
203 CGCCGTCTGAACCAAAACCACAGCCACCACTAGTGCCTGAACCAAAACGGCAGCCACAACCACCA
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAAACCGCAGCCACAACCACCA
* * *
268 CCGGTAGCTAAACCGGACC
66 ACAGTAGCTAAACCGAACC
* * *
287 CGCCCTCTGAACCAAAACCACAACCACCACCAATTCCTAAACCAAATCCGCAGCCACAACCACCA
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAAACCGCAGCCACAACCACCA
* *
352 ACAGTGGCTAAACCTAACC
66 ACAGTAGCTAAACCGAACC
* * * * *
371 CGCCCTCTGAACCAAAACCGCAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAAACCG----C--AGCCACAA
*
436 CCGCAACCATTAACAGT-GACTAAACCTAACC
60 -C-C-ACC---AACAGTAG-CTAAACCGAACC
*
467 CGCCCTCTGAACCAAAACCACAACCATCACCAGTGCCTAAACC
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACC
510 TAACCCTCCT
Statistics
Matches: 188, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
84 116 0.62
88 1 0.01
90 6 0.03
91 1 0.01
92 1 0.01
93 3 0.02
95 1 0.01
96 59 0.31
ACGTcount: A:0.36, C:0.42, G:0.12, T:0.11
Consensus pattern (84 bp):
CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAAACCGCAGCCACAACCACCA
ACAGTAGCTAAACCGAACC
Found at i:308 original size:48 final size:48
Alignment explanation
Indices: 256--543 Score: 278
Period size: 48 Copynumber: 6.2 Consensus size: 48
246 AAAACGGCAG
* **
256 CCACAACCACCACCGGTAG-CTAAACCGGACCCGCCCTCTGAACCAAAA
1 CCACAACCACCACCAGT-GCCTAAACCTAACCCGCCCTCTGAACCAAAA
* * * * *
304 CCACAACCACCACCAATTCCTAAACCAAATCCG----C--AGCC---A
1 CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
* *
343 ---CAACCACCAACAGTGGCTAAACCTAACCCGCCCTCTGAACCAAAA
1 CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
*
388 CCGCAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
1 CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
* ** * *
436 CCGCAACCATTAACAGTGACTAAACCTAACCCGCCCTCTGAACCAAAA
1 CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
* * * **
484 CCACAACCATCACCAGTGCCTAAACCTAACCCTCCTTCAAAACCAAAA
1 CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
*
532 CCGCAACCACCA
1 CCACAACCACCA
544 TCTGAGGAGC
Statistics
Matches: 197, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
36 24 0.12
39 1 0.01
40 1 0.01
42 6 0.03
44 1 0.01
45 1 0.01
48 163 0.83
ACGTcount: A:0.36, C:0.43, G:0.09, T:0.11
Consensus pattern (48 bp):
CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
Found at i:460 original size:96 final size:96
Alignment explanation
Indices: 351--540 Score: 317
Period size: 96 Copynumber: 2.0 Consensus size: 96
341 CACAACCACC
* *
351 AACAGTGGCTAAACCTAACCCGCCCTCTGAACCAAAACCGCAACCACCACCAGTGCCTAAACCTA
1 AACAGTGACTAAACCTAACCCGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCTA
**
416 ACCCGCCCTCTGAACCAAAACCGCAACCATT
66 ACCCGCCCTCAAAACCAAAACCGCAACCATT
*
447 AACAGTGACTAAACCTAACCCGCCCTCTGAACCAAAACCACAACCATCACCAGTGCCTAAACCTA
1 AACAGTGACTAAACCTAACCCGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCTA
* *
512 ACCCTCCTTCAAAACCAAAACCGCAACCA
66 ACCCGCCCTCAAAACCAAAACCGCAACCA
541 CCATCTGAGG
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.37, C:0.41, G:0.09, T:0.13
Consensus pattern (96 bp):
AACAGTGACTAAACCTAACCCGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCTA
ACCCGCCCTCAAAACCAAAACCGCAACCATT
Done.