Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00159.F3
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: 2452
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Found at i:362 original size:152 final size:152
Alignment explanation
Indices: 65--355 Score: 582
Period size: 152 Copynumber: 1.9 Consensus size: 152
55 CATTTTCGAT
65 GCGCTATTTTTGCTTTAGATTTTAAGTTCTCTGTTTTGAGAGACCATAAACTAAAGCGATCATGG
1 GCGCTATTTTTGCTTTAGATTTTAAGTTCTCTGTTTTGAGAGACCATAAACTAAAGCGATCATGG
130 AATCCGGGTTTATGGAAACATAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCA
66 AATCCGGGTTTATGGAAACATAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCA
195 GATTCTAGGTAAAAATTCCGAC
131 GATTCTAGGTAAAAATTCCGAC
217 GCGCTATTTTTGCTTTAGATTTTAAGTTCTCTGTTTTGAGAGACCATAAACTAAAGCGATCATGG
1 GCGCTATTTTTGCTTTAGATTTTAAGTTCTCTGTTTTGAGAGACCATAAACTAAAGCGATCATGG
282 AATCCGGGTTTATGGAAACATAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCA
66 AATCCGGGTTTATGGAAACATAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCA
347 GATTCTAGG
131 GATTCTAGG
356 AGAAAATGTC
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 139 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (152 bp):
GCGCTATTTTTGCTTTAGATTTTAAGTTCTCTGTTTTGAGAGACCATAAACTAAAGCGATCATGG
AATCCGGGTTTATGGAAACATAGGGAACCACTCAGTCGATTCGATCAAGAAAGTGGCAAAAACCA
GATTCTAGGTAAAAATTCCGAC
Found at i:1020 original size:225 final size:225
Alignment explanation
Indices: 629--1080 Score: 708
Period size: 225 Copynumber: 2.0 Consensus size: 225
619 CAGTCCTCGG
* * * * *
629 TTAAGCCAGTTCTATATCCTCCTAGTCTGCTGCCATCATTTGAAACATCATTTACGGCCCAGAAA
1 TTAAGCCAGTTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACAGCCCAAAAA
* *
694 CCATCTCCATCACCTAAAGGATTGACACCACCTAAACCAACCACACCGTCTCTGAAACCCTCTTC
66 CCATCTCCATCACCTAAAGGACTGACACCACCTAAACCAACCACACCGTCTCCGAAACCCTCTTC
*
759 ATCGTCTTTTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
131 ATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
*
824 AAACACTCAATCCAGAGGATACATTACCGA
196 AAACACTCAATCCAAAGGATACATTACCGA
* ** *
854 TTAAGCC-GATTCTATATCCTCCTAGTCCGCTTCCATCATTTAAAATGTCATTCACAGCCGAAAA
1 TTAAGCCAG-TTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACAGCCCAAAA
* *
918 ACCATCTCCATCACCTAAAGGACTGACACCACCTAAATCAACCACACCGTCTCCGAAACGCTCTT
65 ACCATCTCCATCACCTAAAGGACTGACACCACCTAAACCAACCACACCGTCTCCGAAACCCTCTT
*
983 CATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCGGAACTAGGGAAAGGAAAGTAC
130 CATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTAC
* * **
1048 AAAACAGTCGATCCAAAGGATATGTTACCGA
195 AAAACACTCAATCCAAAGGATACATTACCGA
1079 TT
1 TT
1081 TACATGATTC
Statistics
Matches: 206, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
224 1 0.00
225 205 1.00
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (225 bp):
TTAAGCCAGTTCTATATCCTCCTAGTCCGCTGCCATCATTTAAAACATCATTCACAGCCCAAAAA
CCATCTCCATCACCTAAAGGACTGACACCACCTAAACCAACCACACCGTCTCCGAAACCCTCTTC
ATCGTCTTCTAAGCCAAGTCCATCCCTTAAGCCAACTCTATCAGAACTAGGGAAAGGAAAGTACA
AAACACTCAATCCAAAGGATACATTACCGA
Done.