Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g00035.F1
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: 3739
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Found at i:3089 original size:132 final size:131
Alignment explanation
Indices: 2938--3200 Score: 370
Period size: 132 Copynumber: 2.0 Consensus size: 131
2928 TTTTTGTGTA
2938 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATA-GCCATAGATGAG
1 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATAGGCCATAGATGAG
3002 CTAGATACAAATTGTAACATAGTGTTT-CTGATTCAGC-TGTAACCATGGATGTAACATAAATGC
66 CTAGATACAAATTGTAACATAG-GTTTGCTGA-TC--CTTGTAACCATGGATGTAACATAAATGC
3065 TCCCC
127 TCCCC
* * * *
3070 AGCACTTGTTCATGCTTGTATATACTTGTAATCGATATGTTAGTTTGTAATAGGGGCATAGATGA
1 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATA-GGCCATAGATGA
* * * * * *
3135 GCTTGATGCGAATTGTAACATAGGTTTGCTGATCCTTGTAACCGTTGATGTAACATACATGCTCC
65 GCTAGATACAAATTGTAACATAGGTTTGCTGATCCTTGTAACCATGGATGTAACATAAATGCTCC
3200 C
130 C
3201 TTTTTCTGTA
Statistics
Matches: 117, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
131 1 0.01
132 76 0.65
133 6 0.05
134 34 0.29
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (131 bp):
AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATAGGCCATAGATGAG
CTAGATACAAATTGTAACATAGGTTTGCTGATCCTTGTAACCATGGATGTAACATAAATGCTCCC
C
Found at i:3597 original size:135 final size:133
Alignment explanation
Indices: 3403--3644 Score: 396
Period size: 135 Copynumber: 1.8 Consensus size: 133
3393 TCGAAGTAAT
* * *
3403 ATACATGCTCTCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATATTTGTAATATATATG
1 ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG
*
3468 TTAGCATAGTAGTCATAGATGAGCTATATGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAA
66 TTAGC--A-TAGTCATAGATAAGCTATATGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAA
3533 CCATTG
128 CCATTG
*
3539 ATACATGCGCCCCAGTTTCTGTGTAAGCAC-TGTTCATGCTTTGTATATACTTGTAATATGTATG
1 ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG
*
3603 TTAGCATAGTCATTGATAAGCTATATGCAAATTGTAACATAG
66 TTAGCATAGTCATAGATAAGCTATATGCAAATTGTAACATAG
3645 GATTGCCGAT
Statistics
Matches: 100, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
132 34 0.34
133 1 0.01
135 37 0.37
136 28 0.28
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (133 bp):
ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG
TTAGCATAGTCATAGATAAGCTATATGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAACCA
TTG
Done.