Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g00762.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: 4159
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:47 original size:26 final size:26
Alignment explanation
Indices: 11--63 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1 AAGGACATAC
11 GATGTTTTCCTTAGCTTCAGAGGCAA
1 GATGTTTTCCTTAGCTTCAGAGGCAA
37 GATGTTTTCCTTAGCTTCAGAGGCAA
1 GATGTTTTCCTTAGCTTCAGAGGCAA
63 G
1 G
64 GATACTCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (26 bp):
GATGTTTTCCTTAGCTTCAGAGGCAA
Found at i:2516 original size:189 final size:188
Alignment explanation
Indices: 2187--2779 Score: 634
Period size: 189 Copynumber: 3.0 Consensus size: 188
2177 GGCTTTGAAG
* * * * ** *
2187 GAATTACCATCCTCAATTGAAAATCTTATTAGTCTTGATTGCTTGAGCTTGAACTACTGTGAAAA
1 GAATTACCATTCTCAATTGACAATCTTATTGGTCTTGAGTATTTGAGCTTGAACAACTGTGAAAA
* * * * * *
2252 CCTTATTGGCCTTCCTGATAGCTTTTATAAATTGAAATCTCTTGAGACATTCTATCTTCATA-GT
66 CCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTTTAGACATTC-AACTT-AAAGGT
* * * *
2316 TGCTTGAGATTGGAGATTTTCCCAAAAGTCATGGACACCATGGAGGAACTATATAAACTT
129 TGCTCGAGATTGGAGATTTTCCCAGAAGTCATGGACACCATGGAGGAACTGTATGAACTT
* * *
2376 GAATTACCATTCTCAATTGACAATCTTATTGGTCTTGAGTATTTGAGCTTGCACGACTGTGAAAT
1 GAATTACCATTCTCAATTGACAATCTTATTGGTCTTGAGTATTTGAGCTTGAACAACTGTGAAAA
*
2441 CCTTGTTTGCCTTCCTGACAGCTTTTATAAATCGAAATCTCTTTAGACATTCGAACTTAAAGGTT
66 CCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTTTAGACATTC-AACTTAAAGGTT
2506 GCTCGAGATTGGAGATTTTCCCAGAAGTCATGGACACCATGGAGGAACTGTATGAACTT
130 GCTCGAGATTGGAGATTTTCCCAGAAGTCATGGACACCATGGAGGAACTGTATGAACTT
* * * * * *
2565 GATTTAAGCGGAACGGCTT-TGAAGGAATTACCATCCTCAATTGACAATCTTATTGGTCTTGTGT
1 GAATT-A-C----C--ATTCT----CAATT--GA----CAA-TC------TTATTGGTCTTGAGT
*
2629 ATTTGAGCTTGAACAATTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCT
41 ATTTGAGCTTGAACAACTGTGAAAACCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCT
*
2694 C-TTAGCACATTCAATCTTAAAGGTTGCTCGAGATTAGAGATTTTCCCAGAAGTCATGGACACCA
106 CTTTAG-ACATTCAA-CTTAAAGGTTGCTCGAGATTGGAGATTTTCCCAGAAGTCATGGACACCA
2758 TGGAGGAACTGTATGAACTT
169 TGGAGGAACTGTATGAACTT
2778 GA
1 GA
2780 TTTAAGCAGA
Statistics
Matches: 343, Mismatches: 33, Indels: 32
0.84 0.08 0.08
Matches are distributed among these distances:
188 2 0.01
189 169 0.49
190 1 0.00
191 1 0.00
195 1 0.00
196 1 0.00
197 2 0.01
200 4 0.01
202 1 0.00
206 3 0.01
207 1 0.00
212 6 0.02
213 151 0.44
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (188 bp):
GAATTACCATTCTCAATTGACAATCTTATTGGTCTTGAGTATTTGAGCTTGAACAACTGTGAAAA
CCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTTTAGACATTCAACTTAAAGGTTG
CTCGAGATTGGAGATTTTCCCAGAAGTCATGGACACCATGGAGGAACTGTATGAACTT
Found at i:2743 original size:213 final size:212
Alignment explanation
Indices: 2376--2909 Score: 944
Period size: 213 Copynumber: 2.5 Consensus size: 212
2366 ATATAAACTT
* * *
2376 GAATTACCATTCTCAATTGACAATCTTATTGGTCTTGAGTATTTGAGCTTGCACGACTGTGAAAT
1 GAATTACCATCCTCAATTGACAATCTTATTGGTCTTGAGTATTTGAGCTTGAACGACTGTGAAAA
*
2441 CCTTGTTTGCCTTCCTGACAGCTTTTATAAATCGAAATCTCTTTAGACATTCGAACTTAAAGGTT
66 CCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTC-TTAGACATTCGAACTTAAAGGTT
*
2506 GCTCGAGATTGGAGATTTTCCCAGAAGTCATGGACACCATGGAGGAACTGTATGAACTTGATTTA
130 GCTCGAGATTAGAGATTTTCCCAGAAGTCATGGACACCATGGAGGAACTGTATGAACTTGATTTA
*
2571 AGCGGAACGGCTTTGAAG
195 AGCAGAACGGCTTTGAAG
* * *
2589 GAATTACCATCCTCAATTGACAATCTTATTGGTCTTGTGTATTTGAGCTTGAACAATTGTGAAAA
1 GAATTACCATCCTCAATTGACAATCTTATTGGTCTTGAGTATTTGAGCTTGAACGACTGTGAAAA
2654 CCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTTAGCACATTC-AATCTTAAAGGT
66 CCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTTAG-ACATTCGAA-CTTAAAGGT
2718 TGCTCGAGATTAGAGATTTTCCCAGAAGTCATGGACACCATGGAGGAACTGTATGAACTTGATTT
129 TGCTCGAGATTAGAGATTTTCCCAGAAGTCATGGACACCATGGAGGAACTGTATGAACTTGATTT
2783 AAGCAGAACGGCTTTGAAG
194 AAGCAGAACGGCTTTGAAG
*
2802 GAATTACCATCCTCAATTGATAATCTTATTGGTCTTGAGTATTTGAGCTTGAACGACTGTGAAAA
1 GAATTACCATCCTCAATTGACAATCTTATTGGTCTTGAGTATTTGAGCTTGAACGACTGTGAAAA
2867 CCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTT
66 CCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTT
2910 TTGTGTCTTA
Statistics
Matches: 306, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
212 6 0.02
213 300 0.98
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (212 bp):
GAATTACCATCCTCAATTGACAATCTTATTGGTCTTGAGTATTTGAGCTTGAACGACTGTGAAAA
CCTTGTTTGCCTTCCTGACAGCTTTTATAAATTGAAATCTCTTAGACATTCGAACTTAAAGGTTG
CTCGAGATTAGAGATTTTCCCAGAAGTCATGGACACCATGGAGGAACTGTATGAACTTGATTTAA
GCAGAACGGCTTTGAAG
Done.