Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g00702.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: 2228
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Found at i:276 original size:20 final size:20
Alignment explanation
Indices: 235--276 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
225 TTCTACAAAA
* *
235 AAAGAAAGAATTAGTTATTT
1 AAAGAAAGAATTAATTACTT
*
255 AAAGAAGGAATTAATTACTT
1 AAAGAAAGAATTAATTACTT
275 AA
1 AA
277 TGATGAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.31
Consensus pattern (20 bp):
AAAGAAAGAATTAATTACTT
Found at i:1088 original size:87 final size:86
Alignment explanation
Indices: 924--1269 Score: 428
Period size: 87 Copynumber: 4.0 Consensus size: 86
914 CTGTTAATCT
* * *
924 GATTCCCATTTTTGAAATGATTTTCTTCATGGC--GTGCATAACTTGCATCATGTTTATAAATTT
1 GATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTG-ATAA-TTACATCATGTTTATAAATTT
* * *
987 ACAAATGAGGCCAAGCCCGAGAG
64 ACGAACGAGGCCAAGCCCGAAAG
* * *
1010 GAATATCCACTTTTGAAATGATTTTCTTCGTGGCATGTGATAATTACATCATGTTTATAAATTTT
1 G-ATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTGATAATTACATCATGTTTATAAATTTA
* * *
1075 TGAACAAGCCCAAGCCTC-AAACG
65 CGAACGAGGCCAAGCC-CGAAA-G
**
1098 GATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTTTTAATTACATCATGTTTATAAATTTAC
1 GATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTGATAATTACATCATGTTTATAAATTTAC
*
1163 GAACGGGGCCAAGCCCGAAAG
66 GAACGAGGCCAAGCCCGAAAG
* * *
1184 GTATTTCCATTTTTGAAATGATTTTCTTTGTGGCATGCGTTAATTACATCATGTTTATAAATTTA
1 G-ATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTGATAATTACATCATGTTTATAAATTTA
* * *
1249 CAAATGAGCCCAAGCCCGAAA
65 CGAACGAGGCCAAGCCCGAAA
1270 CACTGTTGCC
Statistics
Matches: 225, Mismatches: 28, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
86 4 0.02
87 211 0.94
88 7 0.03
89 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (86 bp):
GATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTGATAATTACATCATGTTTATAAATTTAC
GAACGAGGCCAAGCCCGAAAG
Found at i:1219 original size:174 final size:174
Alignment explanation
Indices: 924--1247 Score: 488
Period size: 174 Copynumber: 1.9 Consensus size: 174
914 CTGTTAATCT
* *
924 GATTCCCATTTTTGAAATGATTTTCTTCATGGCGTGCATAACTTGCATCATGTTTATAAATTTAC
1 GATTCCCATTTTTGAAATGATTTTCTTCATGGCATGCATAACTTACATCATGTTTATAAATTTAC
* * *
989 AAATGAGGCCAAGCCCGAGAGGAATATCCACTTTTGAAATGATTTTCTTCGTGGCATGTGATAAT
66 AAACGAGGCCAAGCCCGAAAGGAATATCCACTTTTGAAATGATTTTCTTCGTGGCATGCGATAAT
1054 TACATCATGTTTATAAATTTTTGAACAAGCCCAAGCCTCAAACG
131 TACATCATGTTTATAAATTTTTGAACAAGCCCAAGCCTCAAACG
* * **
1098 GATTTCCATTTTTGAAATGATTTTCTTCGTGGCATGTTTTAA-TTACATCATGTTTATAAATTTA
1 GATTCCCATTTTTGAAATGATTTTCTTCATGGCATG-CATAACTTACATCATGTTTATAAATTTA
* * * * * * *
1162 CGAACGGGGCCAAGCCCGAAAGGTATTTCCATTTTTGAAATGATTTTCTTTGTGGCATGCGTTAA
65 CAAACGAGGCCAAGCCCGAAAGGAATATCCACTTTTGAAATGATTTTCTTCGTGGCATGCGATAA
1227 TTACATCATGTTTATAAATTT
130 TTACATCATGTTTATAAATTT
1248 ACAAATGAGC
Statistics
Matches: 133, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
174 130 0.98
175 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (174 bp):
GATTCCCATTTTTGAAATGATTTTCTTCATGGCATGCATAACTTACATCATGTTTATAAATTTAC
AAACGAGGCCAAGCCCGAAAGGAATATCCACTTTTGAAATGATTTTCTTCGTGGCATGCGATAAT
TACATCATGTTTATAAATTTTTGAACAAGCCCAAGCCTCAAACG
Found at i:1865 original size:150 final size:149
Alignment explanation
Indices: 1568--1867 Score: 417
Period size: 150 Copynumber: 2.0 Consensus size: 149
1558 TGTATACTAC
*
1568 AGTTCAAAAATGAGATGACAAATTAGGTGATGTGGAAATAAGTGGCTGACAAGGGGCTGAAGCAT
1 AGTTCAAAAATGAGACGACAAATTAGGTGATGTGGAAATAAGTGGCTGACAAGGGGCTGAAGCAT
* *
1633 CTTTTGCATGTAACTGTCAAGGCCAACACCTGTTTGAAGCAGGAAGAGGAATCTGTGTCTCTTAA
66 CTTTTGCATGTAACTGTCAAGGCCAACACCTGTTTGAAGCAGGAAGAGGAATCTGTATCACTTAA
* *
1698 AAAGCTTCGATAACACCCA
131 AAAGCTTCCAAAACACCCA
* * * *
1717 AGTTCAAAAAATGATACGACAAATTAGGTGCTGTGGAAATAGGTGGCTGACAAGGGGCTGGAGCA
1 AGTTC-AAAAATGAGACGACAAATTAGGTGATGTGGAAATAAGTGGCTGACAAGGGGCTGAAGCA
* * * *
1782 TCTTTTGCATGTAACTGTTGAA-GCCAACACTTGTTTGAAGCACGG-AGAGGAATTTTTATCACT
65 TCTTTTGCATGTAACTG-TCAAGGCCAACACCTGTTTGAAGCA-GGAAGAGGAATCTGTATCACT
*
1845 TAGAAAG-TTCCAAAACCACCCA
128 TAAAAAGCTTCCAAAA-CACCCA
1867 A
1 A
1868 AGTTTTAATC
Statistics
Matches: 133, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
149 11 0.08
150 117 0.88
151 5 0.04
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (149 bp):
AGTTCAAAAATGAGACGACAAATTAGGTGATGTGGAAATAAGTGGCTGACAAGGGGCTGAAGCAT
CTTTTGCATGTAACTGTCAAGGCCAACACCTGTTTGAAGCAGGAAGAGGAATCTGTATCACTTAA
AAAGCTTCCAAAACACCCA
Done.