Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g01505.N1
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, 937
Length: 1563
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Found at i:291 original size:105 final size:106
Alignment explanation
Indices: 182--410 Score: 266
Period size: 105 Copynumber: 2.2 Consensus size: 106
172 CAGCTCACAG
* * * *
182 ACTTATGTTCT-TAGCTGATGTTTAAAGGTTAGTTGCGTTAAGTTCACAACCTCCAAATTATTCG
1 ACTTATGTTCTCCAGCTGATATTTAAAGGTTAGTTGAGTTAAGCTCACAACCTCCAAATTATTCG
* * * * *
246 AGTTAATTTAGTTAAGCTTGTAACTCCAAAACAACTTGCAA
66 AGTTAACTGAGTTAAGCTGGCAACTCCAAAACAACTCGCAA
* ** * *
287 ACTTACGTT-TCCAGCTGATATTTAAAGGTTAGTTGAGTTAAGCTCGTAGCCTTCAAATTATTCG
1 ACTTATGTTCTCCAGCTGATATTTAAAGGTTAGTTGAGTTAAGCTCACAACCTCCAAATTATTCG
* ***
351 AGTTAGCTGAGTTAAGCTGGCAACTTTGAAACAACTCGCAA
66 AGTTAACTGAGTTAAGCTGGCAACTCCAAAACAACTCGCAA
*
392 ACTTATGTTC-CCAGTTGAT
1 ACTTATGTTCTCCAGCTGAT
411 TCTACTAAGG
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
104 1 0.01
105 101 0.99
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (106 bp):
ACTTATGTTCTCCAGCTGATATTTAAAGGTTAGTTGAGTTAAGCTCACAACCTCCAAATTATTCG
AGTTAACTGAGTTAAGCTGGCAACTCCAAAACAACTCGCAA
Found at i:649 original size:104 final size:106
Alignment explanation
Indices: 494--815 Score: 339
Period size: 104 Copynumber: 3.1 Consensus size: 106
484 CTAACCTATG
* * * * * * *
494 TTCCCAGTTGATGTTTAAGGGTTAGCTAAGTTAAGCTCGCAGTCTCCAGATTATTCGAGTTAGCT
1 TTCCCAGCTAATGTTTAAAGGTTAGTTGAGTTAAGCTCACAGCCTCCAGATTATTCGAGTTAG-T
* * *
559 T-AGTTAAGCTCGC-AACTTCGAAACAGTTCG-AGACTTGCA
65 TGAGTTAAGCTCGCAAACTTCGAAACAGCTCGTAGACCTACA
* * * *
598 TTCTCAGCTCATGTTTAAAGGTTAGTTGAGTTAAGCTCATAGCCTCTAGATTATTCGAGTTAGTT
1 TTCCCAGCTAATGTTTAAAGGTTAGTTGAGTTAAGCTCACAGCCTCCAGATTATTCGAGTTAGTT
* * *
663 GAGTTAAGCTCGCAAACTTTGAAAGAGCTCGTGGACCTACA
66 GAGTTAAGCTCGCAAACTTCGAAACAGCTCGTAGACCTACA
* * * * **
704 TTCCCAGCTAATGTTTAAAGGTTAGTTGAGTTAAAACTCACAACCTCCAAACTATTTAAGTTAGT
1 TTCCCAGCTAATGTTTAAAGGTTAGTTGAGTT-AAGCTCACAGCCTCCAGATTATTCGAGTTAGT
* * * *
769 TGAGTTAAGCTCGC-AA-TTCCGAAATAGCTCGCAGACTTATA
65 TGAGTTAAGCTCGCAAACTT-CGAAACAGCTCGTAGACCTACA
810 TTCCCA
1 TTCCCA
816 AGTCATTCTA
Statistics
Matches: 181, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
103 2 0.01
104 65 0.36
105 16 0.09
106 60 0.33
107 38 0.21
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (106 bp):
TTCCCAGCTAATGTTTAAAGGTTAGTTGAGTTAAGCTCACAGCCTCCAGATTATTCGAGTTAGTT
GAGTTAAGCTCGCAAACTTCGAAACAGCTCGTAGACCTACA
Found at i:1052 original size:68 final size:68
Alignment explanation
Indices: 943--1073 Score: 163
Period size: 68 Copynumber: 1.9 Consensus size: 68
933 AGGCTCGTTG
* *
943 ATTTAAGATCACAACCTCCAATTATTTGAGTTCGCCGATTTAAGAACGCAACTCCTAACAACTCG
1 ATTTAAGATCACAACCTCCAATTATTTAAGTTAGCCGATTTAAGAACGCAACTCCTAACAACTCG
1008 CTA
66 CTA
* * ** ** * * *
1011 ATTTAAGATTACAACTTCTGATTATTTAAGTTAGTTGATTTAAGATCGTAATTCCTAACAACT
1 ATTTAAGATCACAACCTCCAATTATTTAAGTTAGCCGATTTAAGAACGCAACTCCTAACAACT
1074 TGTTGACCTG
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 52 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (68 bp):
ATTTAAGATCACAACCTCCAATTATTTAAGTTAGCCGATTTAAGAACGCAACTCCTAACAACTCG
CTA
Done.