Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g04035.F3
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: 5869
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Found at i:3104 original size:201 final size:201
Alignment explanation
Indices: 2752--3158 Score: 636
Period size: 201 Copynumber: 2.0 Consensus size: 201
2742 GAAATTACTA
* * * * *
2752 AGAATGGCTCTCGTCTTTGTTGCTATCCGAAATTGAGAATTCTTAAGATAGACGATTGCAGAAGT
1 AGAATGACTCTCGTCTCTGTTGCTACCCCAAATTGAAAATTCTTAAGATAGACGATTGCAGAAGT
* * *
2817 TTAAAATATGTTTGTTCAAGCACTTCGACTCAAGGGCTTCAATCATTGGAATCTGTCAAAATAAG
66 TTAAAATATGTTTGTGCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAAG
* *
2882 TAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAATGGGCAAGGTGTTGTGG
131 TAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTGG
2947 TTCCTC
196 TTCCTC
* * * *
2953 AGAATGACTCTCGTCTCTGTTGCTGCCCCAAATTGAAAATTCTTGAGATAGGA-TATTGCAGTAG
1 AGAATGACTCTCGTCTCTGTTGCTACCCCAAATTGAAAATTCTTAAGATA-GACGATTGCAGAAG
*
3017 TTTAAAATATGTTTGTGCAAACACTTTGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAA
65 TTTAAAATATGTTTGTGCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAA
**
3082 GTGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTG
130 GTAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTG
*
3147 GTTTCTC
195 GTTCCTC
3154 AGAAT
1 AGAAT
3159 TCTTGAGATA
Statistics
Matches: 187, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
201 185 0.99
202 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (201 bp):
AGAATGACTCTCGTCTCTGTTGCTACCCCAAATTGAAAATTCTTAAGATAGACGATTGCAGAAGT
TTAAAATATGTTTGTGCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAAG
TAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTGG
TTCCTC
Found at i:3264 original size:166 final size:166
Alignment explanation
Indices: 2990--3322 Score: 553
Period size: 166 Copynumber: 2.0 Consensus size: 166
2980 CCAAATTGAA
* * *
2990 AATTCTTGAGATAGGATATTGCAGTAGTTTAAAATATGTTTGTGCAAACACTTTGACTCAAGGGC
1 AATTCTTGAGATAGGAAATTGCAGTAGTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGC
*
3055 TTCAATCATTAGAATCTGTCAAAATAAGTGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAA
66 TTCAATCATTAGAATCTGTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAA
*
3120 CAAAATGAGAAAGAGCAAGGTGTTGTGGTTTCTCAG
131 CAAAATGAGAAAGAGCAAGGTGTTGTGGTTCCTCAG
*
3156 AATTCTTGAGATA-GACAATTGCAG-AGGTTTAAAATATGTTTGTCCAAGCACTTCGACTCAAGG
1 AATTCTTGAGATAGGA-AATTGCAGTA-GTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGG
*
3219 GCTTCAATCATTGGAATCTGTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGG
64 GCTTCAATCATTAGAATCTGTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGG
* *
3284 AACAAAATGAGAATGGGCAAGGTGTTGTGGTTCCTCAG
129 AACAAAATGAGAAAGAGCAAGGTGTTGTGGTTCCTCAG
3322 A
1 A
3323 TCCATTGCTG
Statistics
Matches: 156, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
165 3 0.02
166 153 0.98
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (166 bp):
AATTCTTGAGATAGGAAATTGCAGTAGTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGC
TTCAATCATTAGAATCTGTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAA
CAAAATGAGAAAGAGCAAGGTGTTGTGGTTCCTCAG
Done.