Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g01862.F18
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: 3478
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Found at i:546 original size:127 final size:127
Alignment explanation
Indices: 393--813 Score: 743
Period size: 127 Copynumber: 3.3 Consensus size: 127
383 GGTGGAAGTT
393 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
* * *
458 TTTCTAGTTCAATTGAAACAGTCCTATTTTATGTGTTTGACTGCAGGAAACAAAGATTTCTA
66 TTTCTAGTTCAATTAAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
* * *
520 AGAGAGAAACGCTGATTTTGTGTTTGTTGAATTATATTTGTTGAGATTTAGATTGGGACTTCAAA
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
*
585 TTTCTAGTTCAATTTAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
66 TTTCTAGTTCAATTAAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
* *
647 AGAGAGAAACACTGATTTTGTGTTTGTTGAATTATATTTGGTGAGATTTAGATTGGGACTTCAAA
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
* *
712 TTTCTAGTTCAGTTAAAACAGTCTTATTTTATTTGTTTGAATGCAGGAAACAAAGATTTCTA
66 TTTCTAGTTCAATTAAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
774 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAG
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAG
814 ATGACTCCTA
Statistics
Matches: 281, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 281 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (127 bp):
AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
TTTCTAGTTCAATTAAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
Found at i:1495 original size:369 final size:366
Alignment explanation
Indices: 812--1645 Score: 1352
Period size: 369 Copynumber: 2.3 Consensus size: 366
802 GAATTATATT
* *
812 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGTTGTAAAGAGGCTGGGGATTCATGCCTT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
* * *
877 CCCTTTCCCAAAATTGGTTCTCAACAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGAT
66 CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGAT
* * *
942 TTTAGTTTACAGGAGGAAGAAACGGTGGGGCTGCAGCAGCAGTGCTAGTGCTGTTGTTGCCAACT
131 TTCAGTTTACAGGAGGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAGTGCTGTTGTTGCCAACT
* * * *
1007 TTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGTGTGGATTGTTTTTCTGTTCTTAGTTCTAAT
196 TTTATGCACAGGAGCTGGTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAAT
*
1072 GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCGAGTTGAACATGAAACTGCAACAAA
261 GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAA
1137 GACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGC-
326 GACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTT-GCA
*
1178 AGATGATTCCTAAATGTGATGGTACTTCAC-AAGCTGGATGTAAAGAGGCTGAGGATTCATGCCT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAG-TGGATGTAAAGAGGCTGAGGATTCATGCCT
* * * *
1242 TCCCTTACCCAAAACTGGTTCTCAGCAGCCATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGA
65 TCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGA
*
1307 TTTCAGTTTACAGTAGGGGGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAGCT-CTGTTGTTGC
130 TTTCAGTTTAC---AGGAGGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAG-TGCTGTTGTTGC
* *
1371 CAACTTTTATGCACGGGAGCAT-GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGT
191 CAACTTTTATGCACAGGAGC-TGGTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGT
* * *
1435 TCTGATGCACTTTCGGAGGCAGTTATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
255 TCTAATGCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
*
1500 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGCA
320 AACAAAGACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGCA
1547 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
1612 CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTG
66 CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTG
1646 AGCTGGTTAA
Statistics
Matches: 433, Mismatches: 27, Indels: 13
0.92 0.06 0.03
Matches are distributed among these distances:
365 3 0.01
366 125 0.29
368 2 0.00
369 298 0.69
370 5 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (366 bp):
AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGAT
TTCAGTTTACAGGAGGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAGTGCTGTTGTTGCCAACT
TTTATGCACAGGAGCTGGTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAAT
GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAA
GACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGCA
Found at i:1850 original size:258 final size:258
Alignment explanation
Indices: 1393--1903 Score: 869
Period size: 258 Copynumber: 2.0 Consensus size: 258
1383 ACGGGAGCAT
* * *
1393 GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCGGAGGCAGT
1 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
1458 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
66 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
* * * *
1523 GGATGTCTGGTAATGAAACTTGCAAGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGT
131 GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
*
1588 AAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
196 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
*
1651 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCGCTTTCAGAGGCAGT
1 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
*
1716 TATGGAGCGAAAGGGAGTTTCTCAAGTTGATCATGAAACTGCAACAAAGATTTCTTTATGTGATT
66 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
* ** *
1781 GGATATCTGATAATGAAACTTTCCGGATGACTCCTAAATGTGATAGTACTTCACAACCTGGATGT
131 GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
* * *
1846 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCGAAACTGGTTCTCAGCGGTTATCTG
196 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTG
1904 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.