Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g03790.P8
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: 5156
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Found at i:1686 original size:11 final size:11
Alignment explanation
Indices: 1670--1694 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1660 TGCAGTTTCT
1670 TCCAATGAAAG
1 TCCAATGAAAG
1681 TCCAATGAAAG
1 TCCAATGAAAG
1692 TCC
1 TCC
1695 GTGAAGCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (11 bp):
TCCAATGAAAG
Found at i:3638 original size:154 final size:155
Alignment explanation
Indices: 3352--3666 Score: 492
Period size: 154 Copynumber: 2.0 Consensus size: 155
3342 CAAACACTGC
* *
3352 TTATATTGGTCTTCTTAAATCTTGTGATGTGTCTTTTTTTTGATAGTTTATCGCCCTGTTATGTG
1 TTATATTCGTCTTCTTAAATCTTGTGA-GTGTCATTTTTTTGATAGTTTATCGCCCTGTTATGTG
* *
3417 TTTTATTATTATTTTTTGCTGTTTGTTTCCCGCTGTAATATGTATTGAGGGACATTTTCTTGGAA
65 TTTTATTATTATTTTCTGCTGTTTGTTTCCCGCTGTAATATGTATTGAGGGACATTTTCTTGCAA
3482 ATC-ATTGAGTCCTATTTATGAGATT
130 ATCTATTGAGTCCTATTTATGAGATT
*
3507 TTATATTCGTCTTCTTAAATCTTGTGA-TGTCATTTTTTTGATAGTTTATC-TCCTGTTATGTGT
1 TTATATTCGTCTTCTTAAATCTTGTGAGTGTCATTTTTTTGATAGTTTATCGCCCTGTTATGTGT
* * * *
3570 TTTATTTATTTATTTTCTGTTGTTTGTTTCCTGTTGTAATATGTATTGAGGGACATTTTTTTGCA
66 TTTA-TTA-TTATTTTCTGCTGTTTGTTTCCCGCTGTAATATGTATTGAGGGACATTTTCTTGCA
*
3635 AATCTTTTGAGTCCTATTTATGAGATT
129 AATCTATTGAGTCCTATTTATGAGATT
3662 TTATA
1 TTATA
3667 GCGAAGATAT
Statistics
Matches: 147, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
152 16 0.11
153 25 0.17
154 54 0.37
155 52 0.35
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.54
Consensus pattern (155 bp):
TTATATTCGTCTTCTTAAATCTTGTGAGTGTCATTTTTTTGATAGTTTATCGCCCTGTTATGTGT
TTTATTATTATTTTCTGCTGTTTGTTTCCCGCTGTAATATGTATTGAGGGACATTTTCTTGCAAA
TCTATTGAGTCCTATTTATGAGATT
Found at i:3988 original size:40 final size:40
Alignment explanation
Indices: 3932--4066 Score: 193
Period size: 40 Copynumber: 3.3 Consensus size: 40
3922 CCCGTCAATT
*
3932 AAAAAAAAAGAAGAAAAAGTACTGGGTTAATTGCCTT-AA
1 AAAAAAAAAAAAGAAAAAGTACTGGGTTAATTGCCTTCAA
3971 AGAAAAAAAAAAAGAAAAAGTACTGGGCTT-ATTGCCTTCAA
1 A-AAAAAAAAAAAGAAAAAGTACTGGG-TTAATTGCCTTCAA
*
4012 AAAGAAGAAGGAAAAGAAAAAGTACTGGGTTAATTGCCTTCAA
1 AAA-AA-AA-AAAAAGAAAAAGTACTGGGTTAATTGCCTTCAA
4055 AAAAAAAAAAAA
1 AAAAAAAAAAAA
4067 AGAATAAGAA
Statistics
Matches: 86, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
39 1 0.01
40 38 0.44
41 9 0.10
42 6 0.07
43 32 0.37
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (40 bp):
AAAAAAAAAAAAGAAAAAGTACTGGGTTAATTGCCTTCAA
Found at i:4016 original size:43 final size:43
Alignment explanation
Indices: 3932--4067 Score: 192
Period size: 43 Copynumber: 3.2 Consensus size: 43
3922 CCCGTCAATT
3932 AAAAAAAAAGAAGAAAAAGTACTGGGTTAATTGCCTT---AAAG
1 AAAAAAAAA-AAGAAAAAGTACTGGGTTAATTGCCTTCAAAAAG
3973 AAAAAAAAAAAGAAAAAGTACTGGGCTT-ATTGCCTTCAAAAAG
1 AAAAAAAAAAAGAAAAAGTACTGGG-TTAATTGCCTTCAAAAAG
* **
4016 AAGAAGGAAAAGAAAAAGTACTGGGTTAATTGCCTTCAAAAA-
1 AAAAAAAAAAAGAAAAAGTACTGGGTTAATTGCCTTCAAAAAG
4058 AAAAAAAAAA
1 AAAAAAAAAA
4068 GAATAAGAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
40 24 0.29
41 11 0.13
42 9 0.11
43 40 0.48
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (43 bp):
AAAAAAAAAAAGAAAAAGTACTGGGTTAATTGCCTTCAAAAAG
Done.