Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga04g01219.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: 3387
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Found at i:751 original size:46 final size:46
Alignment explanation
Indices: 684--775 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
674 AAGTAAAGGC
684 TTTAATAAATTTATGGTTGTGGCATGTCCTAGGTTTCATATTCCTT
1 TTTAATAAATTTATGGTTGTGGCATGTCCTAGGTTTCATATTCCTT
730 TTTAATAAATTTATGGTTGTGGCATGTCCTAGGTTTCATATTCCTT
1 TTTAATAAATTTATGGTTGTGGCATGTCCTAGGTTTCATATTCCTT
776 CACGAACTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (46 bp):
TTTAATAAATTTATGGTTGTGGCATGTCCTAGGTTTCATATTCCTT
Found at i:2712 original size:17 final size:17
Alignment explanation
Indices: 2692--2755 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
2682 ATTTCAAGAC
2692 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
2709 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
2728 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
2746 TTATGTAATG
1 TTATGTAATG
2756 ATTCAAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
17 19 0.53
18 4 0.11
19 4 0.11
20 9 0.25
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.50
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:2728 original size:37 final size:37
Alignment explanation
Indices: 2687--2762 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
2677 TGTTAATTTC
*
2687 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAATGATTCA
2724 AAGACTTATGTAATGTTTTTAATTATGTAATGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAATGATTCA
2761 AA
1 AA
2763 TTTGGGTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAATGATTCA
Found at i:2764 original size:17 final size:17
Alignment explanation
Indices: 2692--2764 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
2682 ATTTCAAGAC
* **
2692 TTATGTAATGTTTTTAA
1 TTATGTAATGATTCAAA
*
2709 TTATGTAGTGATTCAAAGA
1 TTATGTAATGATTC-AA-A
* **
2728 CTTATGTAATGTTTTTAA
1 -TTATGTAATGATTCAAA
2746 TTATGTAATGATTCAAA
1 TTATGTAATGATTCAAA
2763 TT
1 TT
2765 TGGGTGATTT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
17 27 0.64
18 2 0.05
19 2 0.05
20 11 0.26
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (17 bp):
TTATGTAATGATTCAAA
Found at i:2790 original size:9 final size:9
Alignment explanation
Indices: 2778--2836 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
2768 GTGATTTGGG
2778 TAATTCGGT
1 TAATTCGGT
**
2787 TAATTCGAA
1 TAATTCGGT
*
2796 TAATTCGGG
1 TAATTCGGT
*
2805 TAATTCGGG
1 TAATTCGGT
2814 TAATTCGGT
1 TAATTCGGT
2823 TAATTCGGT
1 TAATTCGGT
2832 TAATT
1 TAATT
2837 TTTAACCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (9 bp):
TAATTCGGT
Done.