Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g01862.F15
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: 2986
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Found at i:1003 original size:369 final size:366
Alignment explanation
Indices: 320--1153 Score: 1352
Period size: 369 Copynumber: 2.3 Consensus size: 366
310 GAATTATATT
* *
320 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGTTGTAAAGAGGCTGGGGATTCATGCCTT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
* * *
385 CCCTTTCCCAAAATTGGTTCTCAACAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGAT
66 CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGAT
* * *
450 TTTAGTTTACAGGAGGAAGAAACGGTGGGGCTGCAGCAGCAGTGCTAGTGCTGTTGTTGCCAACT
131 TTCAGTTTACAGGAGGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAGTGCTGTTGTTGCCAACT
* * * *
515 TTTGTGCACAGGAGCTGGTTAATTCAAAGAGAAGTGTGGATTGTTTTTCTGTTCTTAGTTCTAAT
196 TTTATGCACAGGAGCTGGTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAAT
*
580 GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCGAGTTGAACATGAAACTGCAACAAA
261 GCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAA
645 GACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGC-
326 GACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTT-GCA
*
686 AGATGATTCCTAAATGTGATGGTACTTCAC-AAGCTGGATGTAAAGAGGCTGAGGATTCATGCCT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAG-TGGATGTAAAGAGGCTGAGGATTCATGCCT
* * * *
750 TCCCTTACCCAAAACTGGTTCTCAGCAGCCATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGA
65 TCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGA
*
815 TTTCAGTTTACAGTAGGGGGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAGCT-CTGTTGTTGC
130 TTTCAGTTTAC---AGGAGGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAG-TGCTGTTGTTGC
* *
879 CAACTTTTATGCACGGGAGCAT-GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGT
191 CAACTTTTATGCACAGGAGC-TGGTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGT
* * *
943 TCTGATGCACTTTCGGAGGCAGTTATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
255 TCTAATGCACTTTCAGAGGCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
*
1008 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGCA
320 AACAAAGACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGCA
1055 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
1 AGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTT
1120 CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTG
66 CCCTTACCCAAAACTGGTTCTCAGCAGTCATCTG
1154 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:1358 original size:258 final size:258
Alignment explanation
Indices: 901--1411 Score: 869
Period size: 258 Copynumber: 2.0 Consensus size: 258
891 ACGGGAGCAT
* * *
901 GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCGGAGGCAGT
1 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
966 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
66 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
* * * *
1031 GGATGTCTGGTAATGAAACTTGCAAGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGT
131 GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
*
1096 AAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
196 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
*
1159 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCGCTTTCAGAGGCAGT
1 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
*
1224 TATGGAGCGAAAGGGAGTTTCTCAAGTTGATCATGAAACTGCAACAAAGATTTCTTTATGTGATT
66 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
* ** *
1289 GGATATCTGATAATGAAACTTTCCGGATGACTCCTAAATGTGATAGTACTTCACAACCTGGATGT
131 GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
* * *
1354 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCGAAACTGGTTCTCAGCGGTTATCTG
196 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTG
1412 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.