Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g04035.P1
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: 6556
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Found at i:178 original size:75 final size:75
Alignment explanation
Indices: 55--207 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
45 TGGTATTCAC
55 AGATAGAAAGAGAGAGGTAAGTTCAAGAGTAACTTCCACTTCGCAAAAGAAACAGCGCAGAAGAT
1 AGATAGAAAGAGAGAGGTAAGTTCAAGAGTAACTTCCACTTCGCAAAAGAAACAGCGCAGAAGAT
120 AGTTCAGTGA
66 AGTTCAGTGA
130 AGATAGAAAGAGAGAGGTAAGTTCAAGAGTAACTTCCACTTCGCAAAAGAAACAGCGCAGAAGAT
1 AGATAGAAAGAGAGAGGTAAGTTCAAGAGTAACTTCCACTTCGCAAAAGAAACAGCGCAGAAGAT
195 AGTTCAGTGA
66 AGTTCAGTGA
205 AGA
1 AGA
208 CTATCAACAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.43, C:0.14, G:0.25, T:0.17
Consensus pattern (75 bp):
AGATAGAAAGAGAGAGGTAAGTTCAAGAGTAACTTCCACTTCGCAAAAGAAACAGCGCAGAAGAT
AGTTCAGTGA
Found at i:3180 original size:201 final size:201
Alignment explanation
Indices: 2828--3234 Score: 636
Period size: 201 Copynumber: 2.0 Consensus size: 201
2818 GAAATTACTA
* * * * *
2828 AGAATGGCTCTCGTCTTTGTTGCTATCCGAAATTGAGAATTCTTAAGATAGACGATTGCAGAAGT
1 AGAATGACTCTCGTCTCTGTTGCTACCCCAAATTGAAAATTCTTAAGATAGACGATTGCAGAAGT
* * *
2893 TTAAAATATGTTTGTTCAAGCACTTCGACTCAAGGGCTTCAATCATTGGAATCTGTCAAAATAAG
66 TTAAAATATGTTTGTGCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAAG
* *
2958 TAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAATGGGCAAGGTGTTGTGG
131 TAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTGG
3023 TTCCTC
196 TTCCTC
* * * *
3029 AGAATGACTCTCGTCTCTGTTGCTGCCCCAAATTGAAAATTCTTGAGATAGGA-TATTGCAGTAG
1 AGAATGACTCTCGTCTCTGTTGCTACCCCAAATTGAAAATTCTTAAGATA-GACGATTGCAGAAG
*
3093 TTTAAAATATGTTTGTGCAAACACTTTGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAA
65 TTTAAAATATGTTTGTGCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATAA
**
3158 GTGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTG
130 GTAATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGTG
*
3223 GTTTCTC
195 GTTCCTC
3230 AGAAT
1 AGAAT
3235 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:3340 original size:166 final size:166
Alignment explanation
Indices: 3066--3398 Score: 553
Period size: 166 Copynumber: 2.0 Consensus size: 166
3056 CCAAATTGAA
* * *
3066 AATTCTTGAGATAGGATATTGCAGTAGTTTAAAATATGTTTGTGCAAACACTTTGACTCAAGGGC
1 AATTCTTGAGATAGGAAATTGCAGTAGTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGC
*
3131 TTCAATCATTAGAATCTGTCAAAATAAGTGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAA
66 TTCAATCATTAGAATCTGTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAA
*
3196 CAAAATGAGAAAGAGCAAGGTGTTGTGGTTTCTCAG
131 CAAAATGAGAAAGAGCAAGGTGTTGTGGTTCCTCAG
*
3232 AATTCTTGAGATA-GACAATTGCAG-AGGTTTAAAATATGTTTGTCCAAGCACTTCGACTCAAGG
1 AATTCTTGAGATAGGA-AATTGCAGTA-GTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGG
*
3295 GCTTCAATCATTGGAATCTGTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGG
64 GCTTCAATCATTAGAATCTGTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGG
* *
3360 AACAAAATGAGAATGGGCAAGGTGTTGTGGTTCCTCAG
129 AACAAAATGAGAAAGAGCAAGGTGTTGTGGTTCCTCAG
3398 A
1 A
3399 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.