Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g02563.P1
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: 2485
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Found at i:687 original size:2 final size:2
Alignment explanation
Indices: 680--706 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
670 AAGGTTTGGC
680 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
707 ACTTGGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1299 original size:267 final size:267
Alignment explanation
Indices: 824--1891 Score: 1845
Period size: 267 Copynumber: 4.0 Consensus size: 267
814 TTCTGCATAT
* * *
824 AGGATCTTTTGTCACCGCGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCTGCCA
1 AGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCTGCCA
889 GATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAATATGAA
66 GATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAATATGAA
* * *
954 GCTGTCATATGAGAACATCTCTCCTGTCCAAGGGCATGCAGATTTTCATAACATCCTTGCAAACT
131 GCTGTCACATGAGAACACCTCTCCTGTCCAAGGGCATGCAGATTTTCAGAACATCCTTGCAAACT
*
1019 CTCTAACTGAAGCTGACCATTATATAGAAAGTAAACCAGAGAGGCTCGAGCTAAAAGACATCACA
196 CTCTAACTGAAGCTGACCATAATATAGAAAGTAAACCAGAGAGGCTCGAGCTAAAAGACATCACA
1084 AATATAG
261 AATATAG
* * * *
1091 AGGATCTTTCGTCGCTTTGGTTCTTTGATGTGGAAAAAAATGATTTGGAAAACCATCATCTGCCA
1 AGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCTGCCA
*
1156 GATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCGAATCAAGAGAATATGAA
66 GATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAATATGAA
*
1221 GCTGTCACATGAGAACACCTCTCCTGTCCAAGGGCATGCAGATTTTCAGAACATCCTTGCAAATT
131 GCTGTCACATGAGAACACCTCTCCTGTCCAAGGGCATGCAGATTTTCAGAACATCCTTGCAAACT
*
1286 CTCTAACTGAAGCTGACCATAATATAGAACGTAAACCAGAGAGGCTCGAGCTAAAAGACATCACA
196 CTCTAACTGAAGCTGACCATAATATAGAAAGTAAACCAGAGAGGCTCGAGCTAAAAGACATCACA
1351 AATATAG
261 AATATAG
*
1358 AGGATCTTTCGTCACTGTGGTTTTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCTGCCA
1 AGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCTGCCA
*
1423 GATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCTAGAGCAAATCAAGAGAATATGAA
66 GATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAATATGAA
*
1488 GCTGTCATATGAGAACACCTCTCCTGTCCAAGGGCATGCAGATTTTCAGAACATCCTTGCAAACT
131 GCTGTCACATGAGAACACCTCTCCTGTCCAAGGGCATGCAGATTTTCAGAACATCCTTGCAAACT
* *
1553 CTCTAACTGAAGCTGACCATAATGTAGAAAGTAAATCAGAGAGGCTCGAGCTAAAAGACATCACA
196 CTCTAACTGAAGCTGACCATAATATAGAAAGTAAACCAGAGAGGCTCGAGCTAAAAGACATCACA
1618 AATATAG
261 AATATAG
1625 AGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCTGCCA
1 AGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCTGCCA
1690 GATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAATATGAA
66 GATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAATATGAA
* * * * *
1755 GCTGTCACATGAGAACACCTCTCTTGTCCAAAGGCATGCATATTTTGAGAACATCCTTTCAAACT
131 GCTGTCACATGAGAACACCTCTCCTGTCCAAGGGCATGCAGATTTTCAGAACATCCTTGCAAACT
* * * * *
1820 CTCTAGCCGAAGCTGACCAT-A-A-AGAAAGTAACCCAGAGAGGCTCGGGCTAAGAGACATCACA
196 CTCTAACTGAAGCTGACCATAATATAGAAAGTAAACCAGAGAGGCTCGAGCTAAAAGACATCACA
*
1882 AATATGG
261 AATATAG
1889 AGG
1 AGG
1892 TAACGGTGCA
Statistics
Matches: 759, Mismatches: 42, Indels: 3
0.94 0.05 0.00
Matches are distributed among these distances:
264 45 0.06
266 1 0.00
267 713 0.94
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (267 bp):
AGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCTGCCA
GATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAATATGAA
GCTGTCACATGAGAACACCTCTCCTGTCCAAGGGCATGCAGATTTTCAGAACATCCTTGCAAACT
CTCTAACTGAAGCTGACCATAATATAGAAAGTAAACCAGAGAGGCTCGAGCTAAAAGACATCACA
AATATAG
Done.