Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g03962.P1
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: 18958
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:1644 original size:283 final size:283
Alignment explanation
Indices: 1137--1709 Score: 1146
Period size: 283 Copynumber: 2.0 Consensus size: 283
1127 ACATTTTGAG
1137 GATATTACCATGAATAATGTCTCTTCCCCTATCCTAATTGATCAACAATATTGCCCATGGAATAA
1 GATATTACCATGAATAATGTCTCTTCCCCTATCCTAATTGATCAACAATATTGCCCATGGAATAA
1202 ATGCAAGAAAAATGTATAACATTCTTATCAAAATCCTAATTGAGTGACAATATTTAATCGATCAT
66 ATGCAAGAAAAATGTATAACATTCTTATCAAAATCCTAATTGAGTGACAATATTTAATCGATCAT
1267 TGAATCATTGTTGTGTTGATGCAGGAAGAATCCAAAGTTAAACTAAGCAACATTAGCTTCAAGAA
131 TGAATCATTGTTGTGTTGATGCAGGAAGAATCCAAAGTTAAACTAAGCAACATTAGCTTCAAGAA
1332 CATCCGTGGCACATCTGCGCTTCCAGAAGCTATCAAGTTTATTTGCAGCGGTTCTTCGCCATGTC
196 CATCCGTGGCACATCTGCGCTTCCAGAAGCTATCAAGTTTATTTGCAGCGGTTCTTCGCCATGTC
1397 AAAATGTGGAACTTGCAGACATT
261 AAAATGTGGAACTTGCAGACATT
1420 GATATTACCATGAATAATGTCTCTTCCCCTATCCTAATTGATCAACAATATTGCCCATGGAATAA
1 GATATTACCATGAATAATGTCTCTTCCCCTATCCTAATTGATCAACAATATTGCCCATGGAATAA
1485 ATGCAAGAAAAATGTATAACATTCTTATCAAAATCCTAATTGAGTGACAATATTTAATCGATCAT
66 ATGCAAGAAAAATGTATAACATTCTTATCAAAATCCTAATTGAGTGACAATATTTAATCGATCAT
1550 TGAATCATTGTTGTGTTGATGCAGGAAGAATCCAAAGTTAAACTAAGCAACATTAGCTTCAAGAA
131 TGAATCATTGTTGTGTTGATGCAGGAAGAATCCAAAGTTAAACTAAGCAACATTAGCTTCAAGAA
1615 CATCCGTGGCACATCTGCGCTTCCAGAAGCTATCAAGTTTATTTGCAGCGGTTCTTCGCCATGTC
196 CATCCGTGGCACATCTGCGCTTCCAGAAGCTATCAAGTTTATTTGCAGCGGTTCTTCGCCATGTC
1680 AAAATGTGGAACTTGCAGACATT
261 AAAATGTGGAACTTGCAGACATT
1703 GATATTA
1 GATATTA
1710 AGCACAACGG
Statistics
Matches: 290, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
283 290 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (283 bp):
GATATTACCATGAATAATGTCTCTTCCCCTATCCTAATTGATCAACAATATTGCCCATGGAATAA
ATGCAAGAAAAATGTATAACATTCTTATCAAAATCCTAATTGAGTGACAATATTTAATCGATCAT
TGAATCATTGTTGTGTTGATGCAGGAAGAATCCAAAGTTAAACTAAGCAACATTAGCTTCAAGAA
CATCCGTGGCACATCTGCGCTTCCAGAAGCTATCAAGTTTATTTGCAGCGGTTCTTCGCCATGTC
AAAATGTGGAACTTGCAGACATT
Found at i:4675 original size:32 final size:32
Alignment explanation
Indices: 4639--4818 Score: 243
Period size: 32 Copynumber: 5.6 Consensus size: 32
4629 TAAAAGGGTG
*
4639 ACACTTGAAAAGGAAACGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
4671 ACACTTGAAAAGGAAACGTACACTTTGTATGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* **
4703 ACACTTGAAAAGTATTTGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* * * *
4735 GCACTTGAAAAGAAAATGTACCCTTTGTGTGC
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
4767 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
1 ACACTTGAAAAGGAAATGTACACTTTGTGTGT
* *
4799 ACCATTTGAAAAGGGAATGT
1 A-CACTTGAAAAGGAAATGT
4819 GCACCTCGGG
Statistics
Matches: 129, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
32 113 0.88
33 16 0.12
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (32 bp):
ACACTTGAAAAGGAAATGTACACTTTGTGTGT
Found at i:13301 original size:32 final size:32
Alignment explanation
Indices: 13256--13385 Score: 161
Period size: 32 Copynumber: 4.0 Consensus size: 32
13246 CTGTACACTT
*
13256 GAAAAGGTACACTTTGTGTGTACACTTGAAAA
1 GAAAATGTACACTTTGTGTGTACACTTGAAAA
* ** *
13288 GTATTTGTACACTTTGTGTGTGCACTTGAAAA
1 GAAAATGTACACTTTGTGTGTACACTTGAAAA
* *
13320 GAAAATGTACCCTTTGTGTGCACACTTGAAAA
1 GAAAATGTACACTTTGTGTGTACACTTGAAAA
* * *
13352 GGAAATATACACTTTGTGTGTACCATTTGAAAA
1 GAAAATGTACACTTTGTGTGTA-CACTTGAAAA
13385 G
1 G
13386 GGAATGTGCA
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
32 71 0.88
33 10 0.12
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (32 bp):
GAAAATGTACACTTTGTGTGTACACTTGAAAA
Done.