Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g02935.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, 612
Length: 1020
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Found at i:214 original size:24 final size:24
Alignment explanation
Indices: 158--214 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
148 CCAAAACCGC
* *
158 AACCACCACCAGTTCCTAAACCAA
1 AACCACAACCAGTGCCTAAACCAA
** *
182 AACGGCAACCAGTGCCTGAACCAA
1 AACCACAACCAGTGCCTAAACCAA
206 AACCACAAC
1 AACCACAAC
215 TACCACTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.39, G:0.11, T:0.09
Consensus pattern (24 bp):
AACCACAACCAGTGCCTAAACCAA
Found at i:267 original size:30 final size:31
Alignment explanation
Indices: 192--283 Score: 87
Period size: 36 Copynumber: 2.8 Consensus size: 31
182 AACGGCAACC
* *
192 AGTGCCTGAACCAAAACCACAACTACCACTAA
1 AGTGCCTGAACCAAAACCACAGCCACCACT-A
*
224 ACTCGCCGTCTGAACCAAAACCACAGCCACCACT-
1 AGT-G-C--CTGAACCAAAACCACAGCCACCACTA
**
258 AGTGCCTGAACCAAAACGGCAGCCAC
1 AGTGCCTGAACCAAAACCACAGCCAC
284 AACCACCACC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
30 19 0.38
32 3 0.06
33 2 0.04
34 3 0.06
36 23 0.46
ACGTcount: A:0.37, C:0.38, G:0.14, T:0.11
Consensus pattern (31 bp):
AGTGCCTGAACCAAAACCACAGCCACCACTA
Found at i:332 original size:48 final size:48
Alignment explanation
Indices: 280--567 Score: 278
Period size: 48 Copynumber: 6.2 Consensus size: 48
270 AAAACGGCAG
* **
280 CCACAACCACCACCGGTAG-CTAAACCGGACCCGCCCTCTGAACCAAAA
1 CCACAACCACCACCAGT-GCCTAAACCTAACCCGCCCTCTGAACCAAAA
* * * * *
328 CCACAACCACCACCAATTCCTAAACCAAATCCG----C--AGCC---A
1 CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
* *
367 ---CAACCACCAACAGTGGCTAAACCTAACCCGCCCTCTGAACCAAAA
1 CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
*
412 CCGCAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
1 CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
* ** * *
460 CCGCAACCATTAACAGTGACTAAACCTAACCCGCCCTCTGAACCAAAA
1 CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
* * * **
508 CCACAACCATCACCAGTGCCTAAACCTAACCCTCCTTCAAAACCAAAA
1 CCACAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
*
556 CCGCAACCACCA
1 CCACAACCACCA
568 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:354 original size:84 final size:84
Alignment explanation
Indices: 227--533 Score: 310
Period size: 84 Copynumber: 3.5 Consensus size: 84
217 CCACTAAACT
* * * * *
227 CGCCGTCTGAACCAAAACCACAGCCACCACTAGTGCCTGAACCAAAACGGCAGCCACAACCACCA
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAAACCGCAGCCACAACCACCA
* * *
292 CCGGTAGCTAAACCGGACC
66 ACAGTAGCTAAACCGAACC
* * *
311 CGCCCTCTGAACCAAAACCACAACCACCACCAATTCCTAAACCAAATCCGCAGCCACAACCACCA
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAAACCGCAGCCACAACCACCA
* *
376 ACAGTGGCTAAACCTAACC
66 ACAGTAGCTAAACCGAACC
* * * * *
395 CGCCCTCTGAACCAAAACCGCAACCACCACCAGTGCCTAAACCTAACCCGCCCTCTGAACCAAAA
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCAAAACCG----C--AGCCACAA
*
460 CCGCAACCATTAACAGT-GACTAAACCTAACC
60 -C-C-ACC---AACAGTAG-CTAAACCGAACC
*
491 CGCCCTCTGAACCAAAACCACAACCATCACCAGTGCCTAAACC
1 CGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACC
534 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:484 original size:96 final size:96
Alignment explanation
Indices: 375--564 Score: 317
Period size: 96 Copynumber: 2.0 Consensus size: 96
365 CACAACCACC
* *
375 AACAGTGGCTAAACCTAACCCGCCCTCTGAACCAAAACCGCAACCACCACCAGTGCCTAAACCTA
1 AACAGTGACTAAACCTAACCCGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCTA
**
440 ACCCGCCCTCTGAACCAAAACCGCAACCATT
66 ACCCGCCCTCAAAACCAAAACCGCAACCATT
*
471 AACAGTGACTAAACCTAACCCGCCCTCTGAACCAAAACCACAACCATCACCAGTGCCTAAACCTA
1 AACAGTGACTAAACCTAACCCGCCCTCTGAACCAAAACCACAACCACCACCAGTGCCTAAACCTA
* *
536 ACCCTCCTTCAAAACCAAAACCGCAACCA
66 ACCCGCCCTCAAAACCAAAACCGCAACCA
565 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.