Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g04035.C9
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: 6542
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--3232 Score: 632
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 AGA
1 AGA
3233 CAATTGCAGA
Statistics
Matches: 185, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
201 183 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:3366 original size:152 final size:152
Alignment explanation
Indices: 3083--3384 Score: 516
Period size: 152 Copynumber: 2.0 Consensus size: 152
3073 GAGATAGGAT
* *
3083 ATTGCAGTAGTTTAAAATATGTTTGTGCAAACACTTTGACTCAAGGGCTTCAATCATTAGAATCT
1 ATTGCAGTAGTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCT
*
3148 GTCAAAATAAGTGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCA
66 GTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCA
*
3213 AGGTGTTGTGGTTTCTCAGACA
131 AGGTGTTGTGGTTCCTCAGACA
* *
3235 ATTGCAG-AGGTTTAAAATATGTTTGTCCAAGCACTTCGACTCAAGGGCTTCAATCATTGGAATC
1 ATTGCAGTA-GTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATC
* *
3299 TGTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAATGGGC
65 TGTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGC
3364 AAGGTGTTGTGGTTCCTCAGA
130 AAGGTGTTGTGGTTCCTCAGA
3385 TCCATTGCTG
Statistics
Matches: 141, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
151 1 0.01
152 140 0.99
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (152 bp):
ATTGCAGTAGTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCT
GTCAAAATAAGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCA
AGGTGTTGTGGTTCCTCAGACA
Done.