Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g02265.F1
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: 2266
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Found at i:897 original size:69 final size:69
Alignment explanation
Indices: 791--952 Score: 234
Period size: 69 Copynumber: 2.3 Consensus size: 69
781 TTGAATAATT
* *
791 TACTAAAGAGAGGACCTTTTCACCCAATTTTTATTAGATGGTTGAGTCATTTGATGACAGAGCTT
1 TACTAAAGAGAGGACC-TTTCACCCAATTGTTATTAGATGGTTGAGTCATTTGATGAAAGAGCTT
*
856 GACTC
65 AACTC
* *
861 TATTAAAGAGAGGACCTTTCACCCAATTGTTGTTAGATGGTTGAGTCATTTGATGAAAGAGCTTA
1 TACTAAAGAGAGGACCTTTCACCCAATTGTTATTAGATGGTTGAGTCATTTGATGAAAGAGCTTA
*
926 ACTT
66 ACTC
* * *
930 TACTATAGATAGGATCTTTCACC
1 TACTAAAGAGAGGACCTTTCACC
953 TGATGTACCC
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
69 67 0.82
70 15 0.18
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (69 bp):
TACTAAAGAGAGGACCTTTCACCCAATTGTTATTAGATGGTTGAGTCATTTGATGAAAGAGCTTA
ACTC
Found at i:1496 original size:342 final size:333
Alignment explanation
Indices: 864--1499 Score: 796
Period size: 342 Copynumber: 1.9 Consensus size: 333
854 TTGACTCTAT
* *
864 TAAAGAGAGGACCTTTCACCCAATTGTTGTTAGATGGTTGAGTCATTTGATGAAAGAGCTTAACT
1 TAAAGAGAGGACCTTTCACCCAATTGCTGTTAGATGGTTGAGCCATTTGATGAAAGAGCTTAACT
* * * * * *
929 TTACTATAGATAGGATCTTTCACCTGATGTACCCCTTGGCTTGTGAACTCGGGCTTTTGGTAGAG
66 TTACTAAAGAGAGGACCTTTCACCTGATGTACCCCTTGGCCTATGAACTCGGGCTGTTGGTAGAG
*
994 TCGAGGTTAGCTCAAGTTGTAACATGCTCATGTGAACTCTTCAATTTGCACATGTTTCTGTCTGC
131 TCGAGGTTAGCTCAAGTTGTAACATGCTCATGTGAACTCTTCAATTTGCACATGTTTCTATCTGC
**
1059 TCAGGCACTCCGAGTCATTCTCACTCTATGAACCTGCTAAGGCTTTCGGTAGAGTAGAGAGACAA
196 TCAGGCACTCCGAGTCATTCTCACTCTATGAACCTGCTAAGGCTTTCGCCAGAGTAGAGAGACAA
***
1124 AACCCCGGCAAGGGATAATACCAAACTTGTTGAGGGTCTAACCCATGGGAATCGAGGAAGTTGAA
261 AACCCAAACAAGGGATAATACCAAACTTGTTGAGGGTCTAACCCATGGGAATCGAGGAAGTTGAA
1189 TAATTTAC
326 TAATTTAC
*
1197 TAAAGAGAGGACCTTTTCACCCAATTGCTGTTAGATGGTTGAGCCATTTGATGAAAGAGCTTAAT
1 TAAAGAGAGGACC-TTTCACCCAATTGCTGTTAGATGGTTGAGCCATTTGATGAAAGAGCTTAAC
* * *
1262 TTTACTAAAGAGAGGACCTTTTATCCAATTGGTTGATGTA-CCTTTCGGCCTATGAACTCGGTCT
65 TTTACTAAAGAGAGGACCTTTCA-CC-------TGATGTACCCCTT-GGCCTATGAACTCGGGCT
* * * * ***
1326 GTTGGTGGAGTCGAGGTTAGCTCAATTTGTATCATGCTCCTAG-GAACTCTTCAATTTGTGTATG
121 GTTGGTAGAGTCGAGGTTAGCTCAAGTTGTAACATGCTCAT-GTGAACTCTTCAATTTGCACATG
* * * * * * *
1390 TTTTTATCTGTTCAGGCACTCCGAGT-GTCTGTCACTTTGTGAACCT-CTTAATG-TTCTCGCCA
185 TTTCTATCTGCTCAGGCACTCCGAGTCAT-TCTCACTCTATGAACCTGC-TAAGGCTT-TCGCCA
* **
1452 GAGTAGAGAGACAAAACCCAAACAAGGGATAATATCGGACTTGTTGAG
247 GAGTAGAGAGACAAAACCCAAACAAGGGATAATACCAAACTTGTTGAG
1500 CCTTGACAAA
Statistics
Matches: 254, Mismatches: 35, Indels: 19
0.82 0.11 0.06
Matches are distributed among these distances:
333 13 0.05
334 67 0.26
335 2 0.01
341 8 0.03
342 163 0.64
343 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (333 bp):
TAAAGAGAGGACCTTTCACCCAATTGCTGTTAGATGGTTGAGCCATTTGATGAAAGAGCTTAACT
TTACTAAAGAGAGGACCTTTCACCTGATGTACCCCTTGGCCTATGAACTCGGGCTGTTGGTAGAG
TCGAGGTTAGCTCAAGTTGTAACATGCTCATGTGAACTCTTCAATTTGCACATGTTTCTATCTGC
TCAGGCACTCCGAGTCATTCTCACTCTATGAACCTGCTAAGGCTTTCGCCAGAGTAGAGAGACAA
AACCCAAACAAGGGATAATACCAAACTTGTTGAGGGTCTAACCCATGGGAATCGAGGAAGTTGAA
TAATTTAC
Done.