Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g01862.M21
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: 4709
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Found at i:205 original size:56 final size:56
Alignment explanation
Indices: 137--265 Score: 240
Period size: 56 Copynumber: 2.3 Consensus size: 56
127 TTGCAATTCC
137 AGGAAACAAAGATTTCTAAGAGAGAAACACTGATTTTGTGTTTGTTGAATTATATT
1 AGGAAACAAAGATTTCTAAGAGAGAAACACTGATTTTGTGTTTGTTGAATTATATT
* *
193 TGGAAACAAAGATTTCTAAGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATT
1 AGGAAACAAAGATTTCTAAGAGAGAAACACTGATTTTGTGTTTGTTGAATTATATT
249 AGGAAACAAAGATTTCT
1 AGGAAACAAAGATTTCT
266 TTATGTGATT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 70 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (56 bp):
AGGAAACAAAGATTTCTAAGAGAGAAACACTGATTTTGTGTTTGTTGAATTATATT
Found at i:1015 original size:369 final size:366
Alignment explanation
Indices: 253--1133 Score: 1446
Period size: 369 Copynumber: 2.4 Consensus size: 366
243 TATATTAGGA
253 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG
1 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG
* * * *
318 ATGGTACTTCACAAAGTGGTTGTAAAGAGGCTGGGGATTCATGCCTTCCCTTTCCCAAAATTGGT
66 ATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGT
* *
383 TCTCAACAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTTAGTTTACAGGAGGAA
131 TCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTCAGTTTACAGGAGGAA
* * *
448 GAAACGGTGGGGCTGCAGCAGCAGTGCTAGTGCTGTTGTTGCCAACTTTTGTGCACAGGAGCTGG
196 GAAACGGTGGGGCAGCAGCAGCAGCGCTAGTGCTGTTGTTGCCAACTTTTATGCACAGGAGCTGG
* * *
513 TTAATTCAAAGAGAAGTGTGGATTGTTTTTCTGTTCTTAGTTCTAATGCACTTTCAGAGGCAGTT
261 TTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAATGCACTTTCAGAGGCAGTT
*
578 ATGGAGCAAAAGGGAGTTTCTCGAGTTGAACATGAAACTGC
326 ATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
* *
619 AACAAAGACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGATTCCTAAATGTG
1 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG
684 ATGGTACTTCAC-AAGCTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG
66 ATGGTACTTCACAAAG-TGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG
* * * * *
748 TTCTCAGCAGCCATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGATTTCAGTTTACAGTAGGG
130 TTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTCAGTTTAC---AGGA
*
813 GGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAGCT-CTGTTGTTGCCAACTTTTATGCACGGGA
192 GGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAG-TGCTGTTGTTGCCAACTTTTATGCACAGGA
* * *
877 GCAT-GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCGGAG
256 GC-TGGTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAATGCACTTTCAGAG
*
941 GCAGTTATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
320 GCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
988 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTT-GCAAGATGACTCCTAAATGT
1 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGC-AGATGACTCCTAAATGT
1052 GATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG
65 GATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG
1117 TTCTCAGCAGTCATCTG
130 TTCTCAGCAGTCATCTG
1134 AGCTGGTTAA
Statistics
Matches: 479, Mismatches: 28, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
365 3 0.01
366 171 0.36
368 2 0.00
369 298 0.62
370 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (366 bp):
AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG
ATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGT
TCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTCAGTTTACAGGAGGAA
GAAACGGTGGGGCAGCAGCAGCAGCGCTAGTGCTGTTGTTGCCAACTTTTATGCACAGGAGCTGG
TTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAATGCACTTTCAGAGGCAGTT
ATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
Found at i:1338 original size:258 final size:258
Alignment explanation
Indices: 881--1391 Score: 869
Period size: 258 Copynumber: 2.0 Consensus size: 258
871 ACGGGAGCAT
* * *
881 GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCGGAGGCAGT
1 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
946 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
66 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
* * * *
1011 GGATGTCTGGTAATGAAACTTGCAAGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGT
131 GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
*
1076 AAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
196 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
*
1139 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCGCTTTCAGAGGCAGT
1 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
*
1204 TATGGAGCGAAAGGGAGTTTCTCAAGTTGATCATGAAACTGCAACAAAGATTTCTTTATGTGATT
66 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
* ** *
1269 GGATATCTGATAATGAAACTTTCCGGATGACTCCTAAATGTGATAGTACTTCACAACCTGGATGT
131 GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
* * *
1334 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCGAAACTGGTTCTCAGCGGTTATCTG
196 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTG
1392 TGAGTGTGAT
Statistics
Matches: 236, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
258 236 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (258 bp):
GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
Done.