Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g00523.F6
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: 1924
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Found at i:1796 original size:9 final size:9
Alignment explanation
Indices: 1784--1893 Score: 60
Period size: 9 Copynumber: 11.4 Consensus size: 9
1774 ATTTTAAATA
1784 TTTTTATAT
1 TTTTTATAT
1793 TTTTGTA-ATT
1 TTTT-TATA-T
*
1803 TTTTTACGAT
1 TTTTTA-TAT
*
1813 TTTTATATTT
1 TTTT-TATAT
1823 TTTTTATAT
1 TTTTTATAT
**
1832 TTTCTTGCACT
1 TTT-TTATA-T
*
1843 TTTCTATAT
1 TTTTTATAT
*
1852 TTTTTACAT
1 TTTTTATAT
*
1861 TTGTTATGAT
1 TTTTTAT-AT
* *
1871 TTTCTATAA
1 TTTTTATAT
1880 TTTTTATGAT
1 TTTTTAT-AT
1890 TTTT
1 TTTT
1894 AACAATTTTA
Statistics
Matches: 75, Mismatches: 17, Indels: 17
0.69 0.16 0.16
Matches are distributed among these distances:
9 34 0.45
10 34 0.45
11 7 0.09
ACGTcount: A:0.20, C:0.06, G:0.05, T:0.68
Consensus pattern (9 bp):
TTTTTATAT
Found at i:1808 original size:19 final size:19
Alignment explanation
Indices: 1775--1834 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 19
1765 ATATATAAAA
*
1775 TTTTA-AATATTTTTATAT
1 TTTTATAATTTTTTTATAT
* *
1793 TTTTGTAATTTTTTTACGAT
1 TTTTATAATTTTTTTA-TAT
*
1813 TTTTATATTTTTTTTATAT
1 TTTTATAATTTTTTTATAT
1832 TTT
1 TTT
1835 CTTGCACTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 4 0.12
19 14 0.41
20 16 0.47
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTATAATTTTTTTATAT
Found at i:1845 original size:20 final size:19
Alignment explanation
Indices: 1822--1884 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
1812 TTTTTATATT
*
1822 TTTTTTATATTTTCTTGCA
1 TTTTTTATATTTTCTTACA
*
1841 CTTTTCTATATTTT-TTACA
1 -TTTTTTATATTTTCTTACA
*
1860 TTTGTTATGATTTTCTATA-A
1 TTTTTTAT-ATTTTCT-TACA
1880 TTTTT
1 TTTTT
1885 ATGATTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 6 0.17
19 9 0.26
20 18 0.51
21 2 0.06
ACGTcount: A:0.19, C:0.10, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTTATATTTTCTTACA
Found at i:1857 original size:29 final size:27
Alignment explanation
Indices: 1783--1894 Score: 86
Period size: 28 Copynumber: 3.9 Consensus size: 27
1773 AATTTTAAAT
* *
1783 ATTTT-TATATTTTTGTAATTTTTTTACG
1 ATTTTCTATATTTTT-T-ATATTTTTATG
1811 ATTTT-TATATTTTTTTTATATTTTCT-TG
1 ATTTTCTATA--TTTTTTATATTTT-TATG
*
1839 CACTTTTCTATATTTTTTACATTTGTTATG
1 -A-TTTTCTATATTTTTTATATTT-TTATG
*
1869 ATTTTCTATAATTTTTATGATTTTTA
1 ATTTTCTATATTTTTTAT-ATTTTTA
1895 ACAATTTTAA
Statistics
Matches: 70, Mismatches: 5, Indels: 18
0.75 0.05 0.19
Matches are distributed among these distances:
28 34 0.49
29 20 0.29
30 12 0.17
31 4 0.06
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.67
Consensus pattern (27 bp):
ATTTTCTATATTTTTTATATTTTTATG
Found at i:1900 original size:19 final size:18
Alignment explanation
Indices: 1852--1902 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
1842 TTTTCTATAT
1852 TTTTTAC-ATTTGTTATGA
1 TTTTTACAATTT-TTATGA
*
1870 TTTTCTATAATTTTTATGA
1 TTTT-TACAATTTTTATGA
1889 TTTTTAACAATTTT
1 TTTTT-ACAATTTT
1903 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 5 0.18
19 19 0.68
20 4 0.14
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTTTACAATTTTTATGA
Done.