Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g01806.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, 444
Length: 741
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.23
Found at i:274 original size:18 final size:17
Alignment explanation
Indices: 237--345 Score: 87
Period size: 18 Copynumber: 6.2 Consensus size: 17
227 CCAGAGAAGA
*
237 AAGAGGAACCAAAGAAAG
1 AAGATGAACCAAA-AAAG
*
255 AAGGTGAAGCCAAAAAAG
1 AAGATGAA-CCAAAAAAG
*
273 AAGATGAACAAAAGAAAG
1 AAGATGAACCAAA-AAAG
* * *
291 AAGGTGAACCCAAGAAGG
1 AAGATGAA-CCAAAAAAG
*
309 AAGATGAA-CAAAAGA-
1 AAGATGAACCAAAAAAG
*
324 AAGATGAAGCCAAAAAGG
1 AAGATGAA-CCAAAAAAG
342 AAGA
1 AAGA
346 AGGTAAGAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
15 8 0.11
16 4 0.06
17 9 0.13
18 42 0.59
19 8 0.11
ACGTcount: A:0.59, C:0.10, G:0.27, T:0.05
Consensus pattern (17 bp):
AAGATGAACCAAAAAAG
Found at i:288 original size:36 final size:36
Alignment explanation
Indices: 237--345 Score: 152
Period size: 36 Copynumber: 3.1 Consensus size: 36
227 CCAGAGAAGA
* * *
237 AAGAGGAACCAAAGAAAGAAGGTGAAGCCAAAAAAG
1 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
* *
273 AAGATGAACAAAAGAAAGAAGGTGAACCCAAGAAGG
1 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
309 AAGATGAACAAAAGAAAG-A--TGAAGCCAAAAAGG
1 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
342 AAGA
1 AAGA
346 AGGTAAGAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
33 16 0.24
35 1 0.02
36 49 0.74
ACGTcount: A:0.59, C:0.10, G:0.27, T:0.05
Consensus pattern (36 bp):
AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
Found at i:291 original size:15 final size:15
Alignment explanation
Indices: 268--331 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 15
258 GTGAAGCCAA
268 AAAAG-AAGATGAAC
1 AAAAGAAAGATGAAC
282 AAAAGAAAGAAGGTGAACCC
1 AAAAGAAAG-A--TGAA--C
*
302 AAGAAGGAAGATGAAC
1 AA-AAGAAAGATGAAC
318 AAAAGAAAGATGAA
1 AAAAGAAAGATGAA
332 GCCAAAAAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
14 5 0.12
15 14 0.34
16 4 0.10
18 8 0.20
20 4 0.10
21 6 0.15
ACGTcount: A:0.61, C:0.08, G:0.25, T:0.06
Consensus pattern (15 bp):
AAAAGAAAGATGAAC
Found at i:361 original size:33 final size:32
Alignment explanation
Indices: 248--375 Score: 87
Period size: 33 Copynumber: 3.8 Consensus size: 32
238 AGAGGAACCA
* * *
248 AAGAAAGAAGGTGAAGCCAAAAAAGAAGATGAACAA
1 AAGAAAGAAGATGAAGCC-AAAAAG--GAAGAAC-G
* * * *
284 AAGAAAGAAGGTGAACCCAAGAAGGAAG-ATG
1 AAGAAAGAAGATGAAGCCAAAAAGGAAGAACG
* *
315 AACAAAAGAAAGATGAAGCCAAAAAGGAAGAAGG
1 AA-GAAAG-AAGATGAAGCCAAAAAGGAAGAACG
*
349 TAAGAAAGAAGATGAAACCAAGAAAGG
1 -AAGAAAGAAGATGAAGCCAA-AAAGG
376 TGGTGAGAAG
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
31 2 0.03
32 5 0.07
33 33 0.44
34 11 0.15
35 7 0.09
36 17 0.23
ACGTcount: A:0.59, C:0.09, G:0.27, T:0.05
Consensus pattern (32 bp):
AAGAAAGAAGATGAAGCCAAAAAGGAAGAACG
Found at i:373 original size:18 final size:18
Alignment explanation
Indices: 243--374 Score: 73
Period size: 18 Copynumber: 7.6 Consensus size: 18
233 AAGAAAGAGG
*
243 AACCAAAGAAAGAAGGTGA
1 AACC-AAGAAAGAAGATGA
* *
262 AGCCAAAAAAGAAGATG-
1 AACCAAGAAAGAAGATGA
* *
279 AACAAAAGAAAGAAGGTGA
1 AAC-CAAGAAAGAAGATGA
* *
298 ACCCAAGAAGGAAGATG-
1 AACCAAGAAAGAAGATGA
315 AA-C-A-AAAGAAAGATGA
1 AACCAAGAAAG-AAGATGA
* *
331 AGCCAA-AAAG--GAAGA
1 AACCAAGAAAGAAGATGA
***
346 AGGTAAGAAAGAAGATGA
1 AACCAAGAAAGAAGATGA
364 AACCAAGAAAG
1 AACCAAGAAAG
375 GTGGTGAGAA
Statistics
Matches: 83, Mismatches: 21, Indels: 19
0.67 0.17 0.15
Matches are distributed among these distances:
14 3 0.04
15 15 0.18
16 6 0.07
17 4 0.05
18 50 0.60
19 5 0.06
ACGTcount: A:0.59, C:0.10, G:0.26, T:0.05
Consensus pattern (18 bp):
AACCAAGAAAGAAGATGA
Done.