Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g02625.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: 3667
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Found at i:1869 original size:205 final size:205
Alignment explanation
Indices: 1539--1916 Score: 580
Period size: 205 Copynumber: 1.8 Consensus size: 205
1529 CCCAAGTGTC
* * * ** *
1539 AGAGTTGGTTACCATTCTAAAGCATTACTCTTCTATCTGAATGTGACTTTTCATAGCTGCTTGGC
1 AGAGTTAGTTACCATTCCAAAGCATTACTCATCTATCTGAACATGACTCTTCATAGCTGCTTGGC
* * * *
1604 TACCAAGATTCTTCCAAACTCGCATGTTATGATTTTACTTCGATTATGATATCTTTTCATTGTGG
66 TACCAAGATGCTTCCAAACTCACATGTTATGATTTTACTTCGATTATGATATCCTTTCATTGTGA
1669 GTGGATTTGTAGTCAGGGTAGTTGGATTTATGAAACATTGTTAATTCAAGTTTCTTAGTTCGAGG
131 GTGGATTTGTAGTCAGGGTAGTTGGATTTATGAAACATTGTTAATTCAAGTTTCTTAGTTCGAGG
1734 TCTGGGTGAA
196 TCTGGGTGAA
* * * *
1744 AGAGTTAGTTATCATTCCAAAGCTTTACTCATCTATTTGAACATGACTCTTCATTGCTGCTTGG-
1 AGAGTTAGTTACCATTCCAAAGCATTACTCATCTATCTGAACATGACTCTTCATAGCTGCTTGGC
* *
1808 TAATCAAGATGC-TCACAAACTCACATGTTATGATTTTACTTTGATTATGATATCCTTTCATTGT
66 T-ACCAAGATGCTTC-CAAACTCACATGTTATGATTTTACTTCGATTATGATATCCTTTCATTGT
1872 GAGTGGATTTGTAGTCAGGGTAGTTGGATTTATGAAACATTGTTA
129 GAGTGGATTTGTAGTCAGGGTAGTTGGATTTATGAAACATTGTTA
1917 GTTATCATTC
Statistics
Matches: 155, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
204 3 0.02
205 152 0.98
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (205 bp):
AGAGTTAGTTACCATTCCAAAGCATTACTCATCTATCTGAACATGACTCTTCATAGCTGCTTGGC
TACCAAGATGCTTCCAAACTCACATGTTATGATTTTACTTCGATTATGATATCCTTTCATTGTGA
GTGGATTTGTAGTCAGGGTAGTTGGATTTATGAAACATTGTTAATTCAAGTTTCTTAGTTCGAGG
TCTGGGTGAA
Found at i:2021 original size:166 final size:166
Alignment explanation
Indices: 1747--2082 Score: 636
Period size: 166 Copynumber: 2.0 Consensus size: 166
1737 GGGTGAAAGA
*
1747 GTTAGTTATCATTCCAAAGCTTTACTCATCTATTTGAACATGACTCTTCATTGCTGCTTGGTAAT
1 GTTAGTTATCATTCCAAAGCTTTACTCATCTATCTGAACATGACTCTTCATTGCTGCTTGGTAAT
1812 CAAGATGCTCACAAACTCACATGTTATGATTTTACTTTGATTATGATATCCTTTCATTGTGAGTG
66 CAAGATGCTCACAAACTCACATGTTATGATTTTACTTTGATTATGATATCCTTTCATTGTGAGTG
1877 GATTTGTAGTCAGGGTAGTTGGATTTATGAAACATT
131 GATTTGTAGTCAGGGTAGTTGGATTTATGAAACATT
* *
1913 GTTAGTTATCATTCTAAAGCTTTACTCATCTATCTGAACATGACTTTTCATTGCTGCTTGGTAAT
1 GTTAGTTATCATTCCAAAGCTTTACTCATCTATCTGAACATGACTCTTCATTGCTGCTTGGTAAT
*
1978 CAAGATGCTCACAAACTCACATGTTATGATTTTTCTTTGATTATGATATCCTTTCATTGTGAGTG
66 CAAGATGCTCACAAACTCACATGTTATGATTTTACTTTGATTATGATATCCTTTCATTGTGAGTG
2043 GATTTGTAGTCAGGGTAGTTGGATTTATGAAACATT
131 GATTTGTAGTCAGGGTAGTTGGATTTATGAAACATT
2079 GTTA
1 GTTA
2083 ATTCAAGCTC
Statistics
Matches: 166, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
166 166 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (166 bp):
GTTAGTTATCATTCCAAAGCTTTACTCATCTATCTGAACATGACTCTTCATTGCTGCTTGGTAAT
CAAGATGCTCACAAACTCACATGTTATGATTTTACTTTGATTATGATATCCTTTCATTGTGAGTG
GATTTGTAGTCAGGGTAGTTGGATTTATGAAACATT
Done.