Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g03790.P11
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: 2263
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Found at i:745 original size:154 final size:155
Alignment explanation
Indices: 459--773 Score: 492
Period size: 154 Copynumber: 2.0 Consensus size: 155
449 CAAACACTGC
* *
459 TTATATTGGTCTTCTTAAATCTTGTGATGTGTCTTTTTTTTGATAGTTTATCGCCCTGTTATGTG
1 TTATATTCGTCTTCTTAAATCTTGTGA-GTGTCATTTTTTTGATAGTTTATCGCCCTGTTATGTG
* *
524 TTTTATTATTATTTTTTGCTGTTTGTTTCCCGCTGTAATATGTATTGAGGGACATTTTCTTGGAA
65 TTTTATTATTATTTTCTGCTGTTTGTTTCCCGCTGTAATATGTATTGAGGGACATTTTCTTGCAA
589 ATC-ATTGAGTCCTATTTATGAGATT
130 ATCTATTGAGTCCTATTTATGAGATT
*
614 TTATATTCGTCTTCTTAAATCTTGTGA-TGTCATTTTTTTGATAGTTTATC-TCCTGTTATGTGT
1 TTATATTCGTCTTCTTAAATCTTGTGAGTGTCATTTTTTTGATAGTTTATCGCCCTGTTATGTGT
* * * *
677 TTTATTTATTTATTTTCTGTTGTTTGTTTCCTGTTGTAATATGTATTGAGGGACATTTTTTTGCA
66 TTTA-TTA-TTATTTTCTGCTGTTTGTTTCCCGCTGTAATATGTATTGAGGGACATTTTCTTGCA
*
742 AATCTTTTGAGTCCTATTTATGAGATT
129 AATCTATTGAGTCCTATTTATGAGATT
769 TTATA
1 TTATA
774 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:1095 original size:40 final size:40
Alignment explanation
Indices: 1039--1173 Score: 193
Period size: 40 Copynumber: 3.3 Consensus size: 40
1029 CCCGTCAATT
*
1039 AAAAAAAAAGAAGAAAAAGTACTGGGTTAATTGCCTT-AA
1 AAAAAAAAAAAAGAAAAAGTACTGGGTTAATTGCCTTCAA
1078 AGAAAAAAAAAAAGAAAAAGTACTGGGCTT-ATTGCCTTCAA
1 A-AAAAAAAAAAAGAAAAAGTACTGGG-TTAATTGCCTTCAA
*
1119 AAAGAAGAAGGAAAAGAAAAAGTACTGGGTTAATTGCCTTCAA
1 AAA-AA-AA-AAAAAGAAAAAGTACTGGGTTAATTGCCTTCAA
1162 AAAAAAAAAAAA
1 AAAAAAAAAAAA
1174 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:1123 original size:43 final size:43
Alignment explanation
Indices: 1039--1174 Score: 192
Period size: 43 Copynumber: 3.2 Consensus size: 43
1029 CCCGTCAATT
1039 AAAAAAAAAGAAGAAAAAGTACTGGGTTAATTGCCTT---AAAG
1 AAAAAAAAA-AAGAAAAAGTACTGGGTTAATTGCCTTCAAAAAG
1080 AAAAAAAAAAAGAAAAAGTACTGGGCTT-ATTGCCTTCAAAAAG
1 AAAAAAAAAAAGAAAAAGTACTGGG-TTAATTGCCTTCAAAAAG
* **
1123 AAGAAGGAAAAGAAAAAGTACTGGGTTAATTGCCTTCAAAAA-
1 AAAAAAAAAAAGAAAAAGTACTGGGTTAATTGCCTTCAAAAAG
1165 AAAAAAAAAA
1 AAAAAAAAAA
1175 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.