Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga07g00320.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: 2198
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Found at i:855 original size:259 final size:259
Alignment explanation
Indices: 396--1155 Score: 1360
Period size: 259 Copynumber: 3.0 Consensus size: 259
386 TTGTTCAAGC
396 CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCG
1 CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCG
461 AGTCTCGCGACTGTTACCTCAATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
66 AGTCTCGCGACTGTTACCTCAATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
526 CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCAT
131 CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCAT
591 TGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
196 TGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
655 CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCG
1 CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCG
* *
720 AGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
66 AGTCTCGCGACTGTTACCTCAATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
785 CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCAT
131 CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCAT
850 TGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAA----------GC---------
196 TGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
895 CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCG
1 CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCG
960 AGTCTCGCGACTGTTACCTCAATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
66 AGTCTCGCGACTGTTACCTCAATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
*
1025 CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAAAACCTTGCGTCAT
131 CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCAT
1090 TGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
196 TGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
1154 CC
1 CC
1156 CAAAGGGTTC
Statistics
Matches: 477, Mismatches: 5, Indels: 38
0.92 0.01 0.07
Matches are distributed among these distances:
240 235 0.49
249 2 0.00
250 2 0.00
259 238 0.50
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (259 bp):
CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCG
AGTCTCGCGACTGTTACCTCAATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCAT
TGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
Found at i:1083 original size:240 final size:240
Alignment explanation
Indices: 156--1134 Score: 1726
Period size: 240 Copynumber: 4.0 Consensus size: 240
146 TAAACCAAAT
*
156 CCCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCAGCGGAGGCGATGGCGGAGCCACCGGAGTC
1 CCCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTC
221 GAGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGA
66 GAGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGA
286 GCAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGA-CCCTTAAGAGAACCTTGCGTCA
131 GCAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCA
350 TTGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAG
196 TTGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAG
395 CCCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTC
1 CCCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTC
* *
460 GAGTCTCGCGACTGTTACCTCAATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGA
66 GAGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGA
525 GCAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCA
131 GCAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCA
590 TTGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGG
196 TTGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAA----------G
645 CAAGAAGTTTCCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCC
1 C---------CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCC
710 ACCGGAGTCGAGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGA
57 ACCGGAGTCGAGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGA
775 CCCGAATGAGCAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAAC
122 CCCGAATGAGCAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAAC
840 CTTGCGTCATTGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAG
187 CTTGCGTCATTGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAG
894 CCCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTC
1 CCCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTC
* *
959 GAGTCTCGCGACTGTTACCTCAATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGA
66 GAGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGA
*
1024 GCAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAAAACCTTGCGTCA
131 GCAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCA
1089 TTGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAG
196 TTGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAG
1134 C
1 C
1135 TTTGTTGGGC
Statistics
Matches: 712, Mismatches: 8, Indels: 39
0.94 0.01 0.05
Matches are distributed among these distances:
239 169 0.24
240 303 0.43
249 2 0.00
250 2 0.00
259 236 0.33
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (240 bp):
CCCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTC
GAGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGA
GCAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCA
TTGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAG
Found at i:1094 original size:499 final size:498
Alignment explanation
Indices: 157--1155 Score: 1971
Period size: 499 Copynumber: 2.0 Consensus size: 498
147 AAACCAAATC
157 CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCAGCGGAGGCGATGGCGGAGCCACCGGAGTCG
1 CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCAGCGGAGGCGATGGCGGAGCCACCGGAGTCG
222 AGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
66 AGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
287 CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCTTAAGAGAACCTTGCGTCATT
131 CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCTTAAGAGAACCTTGCGTCATT
352 GATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCCCTAATTCACCCGCTTTCTCC
196 GATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCCCTAATTCACCCGCTTTCTCC
417 TTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCGAGTCTCGCGACTGTTACCTCA
261 TTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCGAGTCTCGCGACTGTTACCTCA
482 ATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAGCAAAGGTTCGGTAAGTGACTC
326 ATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAGCAAAGGTTCGGTAAGTGACTC
*
547 AATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCATTGATAAACTAGGCAATATTTT
391 AATTGCGCTTTATCCAATGACCCCTTAAGAAAACCTTGCGTCATTGATAAACTAGGCAATATTTT
612 TAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
456 TAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
*
655 CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCG
1 CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCAGCGGAGGCGATGGCGGAGCCACCGGAGTCG
720 AGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
66 AGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
785 CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCCTTAAGAGAACCTTGCGTCAT
131 CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGA-CCCTTAAGAGAACCTTGCGTCAT
850 TGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCCCTAATTCACCCGCTTTCTC
195 TGATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCCCTAATTCACCCGCTTTCTC
915 CTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCGAGTCTCGCGACTGTTACCTC
260 CTTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCGAGTCTCGCGACTGTTACCTC
980 AATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAGCAAAGGTTCGGTAAGTGACT
325 AATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAGCAAAGGTTCGGTAAGTGACT
1045 CAATTGCGCTTTATCCAATGACCCCTTAAGAAAACCTTGCGTCATTGATAAACTAGGCAATATTT
390 CAATTGCGCTTTATCCAATGACCCCTTAAGAAAACCTTGCGTCATTGATAAACTAGGCAATATTT
1110 TTAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
455 TTAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
1154 CC
1 CC
1156 CAAAGGGTTC
Statistics
Matches: 498, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
498 170 0.34
499 328 0.66
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (498 bp):
CCTAATTCACCCGCTTTCTCCTTTCCCGCTCCTCAGCGGAGGCGATGGCGGAGCCACCGGAGTCG
AGTCTCGCGACTGTTACCTCAAGATCTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAG
CAAAGGTTCGGTAAGTGACTCAATTGCGCTTTATCCAATGACCCTTAAGAGAACCTTGCGTCATT
GATAAACTAGGCAATATTTTTAACAAGGAAGCTCTTGTTCAAGCCCTAATTCACCCGCTTTCTCC
TTTCCCGCTCCTCGGCGGAGGCGATGGCGGAGCCACCGGAGTCGAGTCTCGCGACTGTTACCTCA
ATATGTACGCTGTTAAAAAGCCCGACAAAGTCGACCCGAATGAGCAAAGGTTCGGTAAGTGACTC
AATTGCGCTTTATCCAATGACCCCTTAAGAAAACCTTGCGTCATTGATAAACTAGGCAATATTTT
TAACAAGGAAGCTCTTGTTCAAGCTTTGTTGGGCAAGAAGTTT
Done.