Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g01030.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: 3748
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Found at i:725 original size:141 final size:135
Alignment explanation
Indices: 541--950 Score: 538
Period size: 141 Copynumber: 3.0 Consensus size: 135
531 CAGAGGAACT
* * **
541 GCAGAATGTCCAC-TTCAAAGTTAAG-AGACCTCAAGAACTACGAACTAAAGAGCTTGAACCACA
1 GCAGAATGTCCACATT-GAAGTTAAGCA-ACCTCAAGAACTACGAACCAAAGAGCTCAAACCACA
* * *
604 GATGTCTTTTGCAGCAGAGCAGCATAAGAAATCTAAAATGGCAACAGAAAGTTCTCAAATGCCAC
64 GATGTCTTTTGCAACAGAACAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCAC
669 AACTAAC
129 AACTAAC
676 GCAGAATGTCCACATTGAAGTTAAGCAACCTCAACCTCAAGAACTACGAACCAAAGAGCTCAAAC
1 GCAGAATGTCCACATTGAAGTTAAG------CAACCTCAAGAACTACGAACCAAAGAGCTCAAAC
* ** * * * * *
741 CGCAGACATCTTTTGCAACAGAACCGCATAAGAAATCAAAAATGGAAATAGGAAGTTCTGAAATG
60 CACAGATGTCTTTTGCAACAGAACAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATG
*
806 CCACAACTAAT
125 CCACAACTAAC
* *
817 GCAGAATGTCCACATTGAAGTTAAGCAACCTGAAGATCTACGAACCAAAGAGCTCAAACCACAGA
1 GCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCAAACCACAGA
* *
882 TGTCTTTTGCAAAAGAACCA-CATAAGAAATCAAAAATGGCAACAGAAAGTTCTCACATGCCACA
66 TGTCTTTTGCAACAGAA-CAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCACA
946 ACTAA
130 ACTAA
951 TGCCAATGGA
Statistics
Matches: 238, Mismatches: 28, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
135 116 0.49
136 3 0.01
141 118 0.50
142 1 0.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (135 bp):
GCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCAAACCACAGA
TGTCTTTTGCAACAGAACAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCACAA
CTAAC
Found at i:918 original size:135 final size:135
Alignment explanation
Indices: 540--953 Score: 546
Period size: 135 Copynumber: 3.0 Consensus size: 135
530 TCAGAGGAAC
* * **
540 TGCAGAATGTCCAC-TTCAAAGTTAAG-AGACCTCAAGAACTACGAACTAAAGAGCTTGAACCAC
1 TGCAGAATGTCCACATT-GAAGTTAAGCA-ACCTCAAGAACTACGAACCAAAGAGCTCAAACCAC
* * *
603 AGATGTCTTTTGCAGCAG-AGCAGCATAAGAAATCTAAAATGGCAACAGAAAGTTCTCAAATGCC
64 AGATGTCTTTTGCAACAGAACCA-CATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCC
667 ACAACTAA
128 ACAACTAA
*
675 CGCAGAATGTCCACATTGAAGTTAAGCAACCTCAACCTCAAGAACTACGAACCAAAGAGCTCAAA
1 TGCAGAATGTCCACATTGAAGTTAAG------CAACCTCAAGAACTACGAACCAAAGAGCTCAAA
* ** * * * * *
740 CCGCAGACATCTTTTGCAACAGAACCGCATAAGAAATCAAAAATGGAAATAGGAAGTTCTGAAAT
60 CCACAGATGTCTTTTGCAACAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAAT
805 GCCACAACTAA
125 GCCACAACTAA
* *
816 TGCAGAATGTCCACATTGAAGTTAAGCAACCTGAAGATCTACGAACCAAAGAGCTCAAACCACAG
1 TGCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCAAACCACAG
* *
881 ATGTCTTTTGCAAAAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCACATGCCACA
66 ATGTCTTTTGCAACAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCACA
946 ACTAA
131 ACTAA
951 TGC
1 TGC
954 CAATGGATTC
Statistics
Matches: 241, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
135 121 0.50
136 2 0.01
141 115 0.48
142 3 0.01
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.19
Consensus pattern (135 bp):
TGCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCAAACCACAG
ATGTCTTTTGCAACAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCACA
ACTAA
Done.