Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gohir.A02G008000.1.v1.1
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: 3883
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Found at i:2983 original size:210 final size:210
Alignment explanation
Indices: 2615--3160 Score: 957
Period size: 210 Copynumber: 2.6 Consensus size: 210
2605 TCTGGAAATT
2615 TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
1 TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
* *
2680 AGATATATCGATCTGCGAGGATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
66 AGATATATCAATCTGCGAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
* *
2745 AGCTTCACATTTCCTCGTGTCCAAAATTAAGCAAGATAGGAGATGGGTTGTCTACCTCCATTTAT
131 AGCTTCACATTTCCTCGTGTCCAAAATTAAGCAAGATAGCAGACGGGTTGTCTACCTCCATTTAT
2810 CTTGAAGAATTGAAG
196 CTTGAAGAATTGAAG
2825 TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
1 TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
2890 AGATATATCAATCTGCGAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
66 AGATATATCAATCTGCGAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
* * * *
2955 AGCTTCGCATTTCCTCGTGTCGAAAATTAAGCAAGATAGCAGACGGGTTGTTTACCTCCTTTTAT
131 AGCTTCACATTTCCTCGTGTCCAAAATTAAGCAAGATAGCAGACGGGTTGTCTACCTCCATTTAT
3020 CTTGAAGAATTGAAG
196 CTTGAAGAATTGAAG
* * * *
3035 TTAAGTGATTGTCCTAATTTAAGCTCCACTCCAGATTTGGAAAGATTTTCCTCTCTTCAAAATTT
1 TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
* **
3100 AGATATATCAATCTGCAAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGCCCATCTCTT
66 AGATATATCAATCTGCGAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTT
3161 GAAGTGCTTG
Statistics
Matches: 321, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
210 321 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (210 bp):
TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
AGATATATCAATCTGCGAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
AGCTTCACATTTCCTCGTGTCCAAAATTAAGCAAGATAGCAGACGGGTTGTCTACCTCCATTTAT
CTTGAAGAATTGAAG
Found at i:3244 original size:210 final size:207
Alignment explanation
Indices: 2615--3224 Score: 818
Period size: 210 Copynumber: 2.9 Consensus size: 207
2605 TCTGGAAATT
2615 TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
1 TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
* *
2680 AGATATATCGATCTGCGAGGATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
66 AGATATATCAATCTGCGAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
* * * * *
2745 AGCTTCACATTTCCTCGTGTCCAAAATTAAGCAAGATAGG-AGATGGGTTGTCTACCTCCATTTA
131 AGCTTGACATTTCCTCGTGT-GAAAATTAAGCAAGATAGGAAGAT-GATTGCCT-CCTTCA-TTA
2809 TCTTGAAGAATTGAAG
192 TCTTGAAGAATTGAAG
2825 TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
1 TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
2890 AGATATATCAATCTGCGAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
66 AGATATATCAATCTGCGAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
* * * *
2955 AGCTTCG-CATTTCCTCGTGTCGAAAATTAAGCAAGATAGCAGACGGGTTGTTTACCTCCTT--T
131 AGCTT-GACATTTCCTCGTGT-GAAAATTAAGCAAGATAG--GA--AGATGATTGCCTCCTTCAT
3017 TATCTTGAAGAATTGAAG
190 TATCTTGAAGAATTGAAG
* * * *
3035 TTAAGTGATTGTCCTAATTTAAGCTCCACTCCAGATTTGGAAAGATTTTCCTCTCTTCAAAATTT
1 TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
* ** * *
3100 AGATATATCAATCTGCAAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGCCCATCTCTTGAAG
66 AGATATATCAATCTGCGAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
* * * * * *
3165 TGCTTGACA-TTCGTGCATGTGAAAAATTAAGCCACATAGGAAG-TGAACTGCCTCCCTTCA
131 AGCTTGACATTTCCT-CGTGTG-AAAATTAAGCAAGATAGGAAGATG-ATTGCCT-CCTTCA
3225 CCATGCTCAG
Statistics
Matches: 359, Mismatches: 28, Indels: 27
0.87 0.07 0.07
Matches are distributed among these distances:
205 2 0.01
206 5 0.01
207 4 0.01
208 2 0.01
209 6 0.02
210 329 0.92
212 1 0.00
213 3 0.01
214 5 0.01
215 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (207 bp):
TTAAGTGATTGTCCTAATTTAAGCTCCATTCCAGATTTGGAAGGATTTTCCTCTCTTCGAATTTT
AGATATATCAATCTGCGAGAATCTGGAAATTGTTCCGATAGGAGGGCAGTGTTCATCTCTTAAAA
AGCTTGACATTTCCTCGTGTGAAAATTAAGCAAGATAGGAAGATGATTGCCTCCTTCATTATCTT
GAAGAATTGAAG
Done.