Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g04035.C7
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: 6633
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
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 GGTTTAAAAT
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:3348 original size:142 final size:142
Alignment explanation
Indices: 3092--3374 Score: 494
Period size: 142 Copynumber: 2.0 Consensus size: 142
3082 TATTGCAGTA
* *
3092 GTTTAAAATATGTTTGTGCAAACACTTTGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATA
1 GTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATA
*
3157 AGTGGTTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGT
66 AGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGT
*
3222 GGTTTCTCAGAG
131 GGTTCCTCAGAG
* *
3234 GTTTAAAATATGTTTGTCCAAGCACTTCGACTCAAGGGCTTCAATCATTGGAATCTGTCAAAATA
1 GTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATA
* *
3299 AGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAATGGGCAAGGTGTTGT
66 AGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGT
3364 GGTTCCTCAGA
131 GGTTCCTCAGA
3375 TCCATTGCTG
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 133 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (142 bp):
GTTTAAAATATGTTTGTCCAAACACTTCGACTCAAGGGCTTCAATCATTAGAATCTGTCAAAATA
AGTGATTGTCCTCAACTTATGCAAATCTTCAAGATGGAACAAAATGAGAAAGAGCAAGGTGTTGT
GGTTCCTCAGAG
Done.