Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g00993.P3
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: 11139
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Found at i:510 original size:25 final size:26
Alignment explanation
Indices: 482--533 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
472 TTTACAGTTT
482 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
507 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
533 T
1 T
534 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:4722 original size:26 final size:26
Alignment explanation
Indices: 4663--4797 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
4653 TGATACAAAT
4663 TGATAATAGGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
4688 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
4714 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
4740 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
4766 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
4792 TGATAA
1 TGATAA
4798 GAATTCATGT
Statistics
Matches: 107, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
25 23 0.21
26 84 0.79
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:6309 original size:25 final size:25
Alignment explanation
Indices: 6281--6331 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
6271 TTTACAGTTT
6281 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAG-GATAAATTGACCGAAA
* *
6306 TACCCCTAGGTTAAATTGACCTAAA
1 TACCCCTAGGATAAATTGACCGAAA
6331 T
1 T
6332 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (25 bp):
TACCCCTAGGATAAATTGACCGAAA
Found at i:8850 original size:43 final size:43
Alignment explanation
Indices: 8789--8950 Score: 270
Period size: 43 Copynumber: 3.8 Consensus size: 43
8779 ATGAAACTTG
* *
8789 GTGAAATAATATCGGGCTTCAAGCCTAGCAGGCTATAATGCCT
1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA
*
8832 GTGAAATAATATCGGGCTTCGAGCCGAGCAGGCTATAATGCCA
1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA
* *
8875 GTGAAATAATATCGGGCCTCGAGCCTAGCAGGCTATAATGCCG
1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA
*
8918 GTGAAATAATATTGGGCTTCGAGCCTAGCAGGC
1 GTGAAATAATATCGGGCTTCGAGCCTAGCAGGC
8951 GAAATGCAGG
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 111 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (43 bp):
GTGAAATAATATCGGGCTTCGAGCCTAGCAGGCTATAATGCCA
Found at i:9559 original size:16 final size:18
Alignment explanation
Indices: 9528--9560 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
9518 AACTCATCAC
9528 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
9546 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
9561 AATTCGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:9843 original size:16 final size:16
Alignment explanation
Indices: 9824--9873 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
9814 ATTGTTTTGC
9824 TTAAATGTTGTTTAAA
1 TTAAATGTTGTTTAAA
9840 TTAAA---TGTTT--A
1 TTAAATGTTGTTTAAA
9851 TT--ATGTTGTTTAAA
1 TTAAATGTTGTTTAAA
9865 TTAAATGTT
1 TTAAATGTT
9874 TATTATGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 14
0.66 0.00 0.34
Matches are distributed among these distances:
9 1 0.04
11 3 0.11
12 5 0.19
13 5 0.19
14 3 0.11
16 10 0.37
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (16 bp):
TTAAATGTTGTTTAAA
Found at i:9856 original size:25 final size:25
Alignment explanation
Indices: 9828--9886 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
9818 TTTTGCTTAA
9828 ATGTTGTTTAAATTAAATGTTTATT
1 ATGTTGTTTAAATTAAATGTTTATT
9853 ATGTTGTTTAAATTAAATGTTTATT
1 ATGTTGTTTAAATTAAATGTTTATT
9878 ATGTTGTTT
1 ATGTTGTTT
9887 TGATGTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.58
Consensus pattern (25 bp):
ATGTTGTTTAAATTAAATGTTTATT
Done.