Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g02290.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: 3744
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Found at i:354 original size:39 final size:39
Alignment explanation
Indices: 303--379 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
293 GCTACAGCAG
303 AAAATGGCTAGCAAAAAGGAAGACCCGTCTAAAGCACAA
1 AAAATGGCTAGCAAAAAGGAAGACCCGTCTAAAGCACAA
* *
342 AAAATGGCTAGCAAAAAGGAAGAGCCGTCTCAAGCACA
1 AAAATGGCTAGCAAAAAGGAAGACCCGTCTAAAGCACA
380 CCAGAAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (39 bp):
AAAATGGCTAGCAAAAAGGAAGACCCGTCTAAAGCACAA
Found at i:1718 original size:9 final size:9
Alignment explanation
Indices: 1706--1739 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1696 ATGATGAGTC
1706 TGATGAAGA
1 TGATGAAGA
1715 TGATGAAGA
1 TGATGAAGA
*
1724 TTATGAAGA
1 TGATGAAGA
*
1733 CGATGAA
1 TGATGAA
1740 TGTGATGACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.29, T:0.24
Consensus pattern (9 bp):
TGATGAAGA
Found at i:2818 original size:87 final size:87
Alignment explanation
Indices: 2668--2998 Score: 484
Period size: 87 Copynumber: 3.8 Consensus size: 87
2658 AGAAGCAAGA
* * ** *
2668 AGGAAATGAAAGTGGACAAAGCGGAAGGTGAGAAAGGGAAGAAGCAAGAATCATCTATGGCAAAT
1 AGGAAACGAATGTGGACAAAGCGGAATCTGAGAAAGGGAAGAAGCAAGAATCATCTACGGCAAAT
*
2733 AAACACAAGAATCTGGTTCAGC
66 AAACAAAAGAATCTGGTTCAGC
* * *
2755 AGGAAATGGATGTGGACAAAGCGGAATCTGAGAAAGGGAAGAAGCAAGAATCATCTACAGCAAAT
1 AGGAAACGAATGTGGACAAAGCGGAATCTGAGAAAGGGAAGAAGCAAGAATCATCTACGGCAAAT
* *
2820 AAACATAAGAATCCGGTTCAGC
66 AAACAAAAGAATCTGGTTCAGC
* * *
2842 AGGAAACGAATGTGGACAAAGCTGAATCCGAGAAAGGGAAGAAGCAAGAATCAT-TCACGGAAAA
1 AGGAAACGAATGTGGACAAAGCGGAATCTGAGAAAGGGAAGAAGCAAGAATCATCT-ACGGCAAA
*
2906 TAAACAAAAGAATCTGCTTCAGC
65 TAAACAAAAGAATCTGGTTCAGC
** *
2929 AGGAAACGAATGTGGACAAAGTAGAACCTGAGAAAGGGAAGAAGCAAGAATCATCTACGGCAAAT
1 AGGAAACGAATGTGGACAAAGCGGAATCTGAGAAAGGGAAGAAGCAAGAATCATCTACGGCAAAT
2994 AAACA
66 AAACA
2999 TTCACCTCAA
Statistics
Matches: 220, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
86 1 0.00
87 218 0.99
88 1 0.00
ACGTcount: A:0.46, C:0.15, G:0.26, T:0.14
Consensus pattern (87 bp):
AGGAAACGAATGTGGACAAAGCGGAATCTGAGAAAGGGAAGAAGCAAGAATCATCTACGGCAAAT
AAACAAAAGAATCTGGTTCAGC
Done.