Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g00523.F7
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: 1832
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Found at i:1704 original size:9 final size:9
Alignment explanation
Indices: 1692--1801 Score: 60
Period size: 9 Copynumber: 11.4 Consensus size: 9
1682 ATTTTAAATA
1692 TTTTTATAT
1 TTTTTATAT
1701 TTTTGTA-ATT
1 TTTT-TATA-T
*
1711 TTTTTACGAT
1 TTTTTA-TAT
*
1721 TTTTATATTT
1 TTTT-TATAT
1731 TTTTTATAT
1 TTTTTATAT
**
1740 TTTCTTGCACT
1 TTT-TTATA-T
*
1751 TTTCTATAT
1 TTTTTATAT
*
1760 TTTTTACAT
1 TTTTTATAT
*
1769 TTGTTATGAT
1 TTTTTAT-AT
* *
1779 TTTCTATAA
1 TTTTTATAT
1788 TTTTTATGAT
1 TTTTTAT-AT
1798 TTTT
1 TTTT
1802 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:1716 original size:19 final size:19
Alignment explanation
Indices: 1683--1742 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 19
1673 ATATATAAAA
*
1683 TTTTA-AATATTTTTATAT
1 TTTTATAATTTTTTTATAT
* *
1701 TTTTGTAATTTTTTTACGAT
1 TTTTATAATTTTTTTA-TAT
*
1721 TTTTATATTTTTTTTATAT
1 TTTTATAATTTTTTTATAT
1740 TTT
1 TTT
1743 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:1753 original size:20 final size:19
Alignment explanation
Indices: 1730--1792 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
1720 TTTTTATATT
*
1730 TTTTTTATATTTTCTTGCA
1 TTTTTTATATTTTCTTACA
*
1749 CTTTTCTATATTTT-TTACA
1 -TTTTTTATATTTTCTTACA
*
1768 TTTGTTATGATTTTCTATA-A
1 TTTTTTAT-ATTTTCT-TACA
1788 TTTTT
1 TTTTT
1793 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:1765 original size:29 final size:27
Alignment explanation
Indices: 1691--1802 Score: 86
Period size: 28 Copynumber: 3.9 Consensus size: 27
1681 AATTTTAAAT
* *
1691 ATTTT-TATATTTTTGTAATTTTTTTACG
1 ATTTTCTATATTTTT-T-ATATTTTTATG
1719 ATTTT-TATATTTTTTTTATATTTTCT-TG
1 ATTTTCTATA--TTTTTTATATTTT-TATG
*
1747 CACTTTTCTATATTTTTTACATTTGTTATG
1 -A-TTTTCTATATTTTTTATATTT-TTATG
*
1777 ATTTTCTATAATTTTTATGATTTTTA
1 ATTTTCTATATTTTTTAT-ATTTTTA
1803 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:1808 original size:19 final size:18
Alignment explanation
Indices: 1760--1810 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
1750 TTTTCTATAT
1760 TTTTTAC-ATTTGTTATGA
1 TTTTTACAATTT-TTATGA
*
1778 TTTTCTATAATTTTTATGA
1 TTTT-TACAATTTTTATGA
1797 TTTTTAACAATTTT
1 TTTTT-ACAATTTT
1811 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.