Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold663
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: 8030
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1724 original size:46 final size:44
Alignment explanation
Indices: 1649--1736 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 44
1639 AAGTATGAGG
* *
1649 TTTATAAAAGGGGGATAATTTGTTAAGGGAGACTAGTAAATTAT
1 TTTATAAAAGGGGGAAAATTTGTTAAGGGAGACTACTAAATTAT
* *
1693 TTTATTAAAGGGGAGAAAATTTTGTTAAGGGAGAGTACTAAATT
1 TTTATAAAAGGGG-GAAAA-TTTGTTAAGGGAGACTACTAAATT
1737 GATAATTTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 12 0.32
45 4 0.11
46 22 0.58
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (44 bp):
TTTATAAAAGGGGGAAAATTTGTTAAGGGAGACTACTAAATTAT
Found at i:3054 original size:13 final size:13
Alignment explanation
Indices: 3036--3060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3026 TTTTACAAAT
3036 TGTATCGATACAA
1 TGTATCGATACAA
3049 TGTATCGATACA
1 TGTATCGATACA
3061 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4080 original size:21 final size:20
Alignment explanation
Indices: 4054--4094 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
4044 TAACCCATGA
4054 TTCATGCATTTTGAGCTATGT
1 TTCATGCATTTTGAG-TATGT
*
4075 TTCATGCATTTTTAGTATGT
1 TTCATGCATTTTGAGTATGT
4095 CCAACACCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (20 bp):
TTCATGCATTTTGAGTATGT
Found at i:5450 original size:69 final size:69
Alignment explanation
Indices: 5370--5520 Score: 241
Period size: 69 Copynumber: 2.2 Consensus size: 69
5360 ATTCCGAGGG
* *
5370 GATACTCCAACCCTGTTTTTTAAGCTTGTCCA-GATCATTCTTATTTTTACCTAAACTATTATTG
1 GATACTCCAACCCTATTTTTGAAGCTTGT-CATGATCATTCTTATTTTTACCTAAACTATTATTG
5434 TCGGC
65 TCGGC
*
5439 GATACTCCAACCCTATTTTTGAAGCTTGTCATGATCATTTTTATTTTTACCTAAACTATTATTGT
1 GATACTCCAACCCTATTTTTGAAGCTTGTCATGATCATTCTTATTTTTACCTAAACTATTATTGT
*
5504 CGGG
66 CGGC
*
5508 GACACTCCAACCC
1 GATACTCCAACCC
5521 CATTATTCCG
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
68 2 0.03
69 74 0.97
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.40
Consensus pattern (69 bp):
GATACTCCAACCCTATTTTTGAAGCTTGTCATGATCATTCTTATTTTTACCTAAACTATTATTGT
CGGC
Found at i:5539 original size:96 final size:96
Alignment explanation
Indices: 5439--5642 Score: 291
Period size: 96 Copynumber: 2.1 Consensus size: 96
5429 TATTGTCGGC
* * *
5439 GATACTCCAACCCTATTTTTGAAGCTTGTCATGATCATTTTTATTTTTACCTAAACTATTATTGT
1 GATACTCCAACCCTATTTTTGAAGCTTGTCAAGATCATTCTTATTTTTACCAAAACTATTATTGT
* *
5504 CGGGGACACTCCAACCCCATTATTCCGAGGG
66 CGGGGACACTCCAACCCCATCATTCCGAAGG
* * * ** *
5535 GATACTCTAATCCTGTTTTTTTAGCTTGTCAAGATCATTCTTATTTTTACCAAAATTATTATTGT
1 GATACTCCAACCCTATTTTTGAAGCTTGTCAAGATCATTCTTATTTTTACCAAAACTATTATTGT
* *
5600 CGGGGACACTCCAACGCCATCCTTCCGAAGG
66 CGGGGACACTCCAACCCCATCATTCCGAAGG
5631 GATACTCCAACC
1 GATACTCCAACC
5643 TCGTTTTTTA
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (96 bp):
GATACTCCAACCCTATTTTTGAAGCTTGTCAAGATCATTCTTATTTTTACCAAAACTATTATTGT
CGGGGACACTCCAACCCCATCATTCCGAAGG
Found at i:6398 original size:13 final size:13
Alignment explanation
Indices: 6380--6405 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6370 CAATTTTTTG
6380 TGTATCGATACAT
1 TGTATCGATACAT
6393 TGTATCGATACAT
1 TGTATCGATACAT
6406 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7148 original size:21 final size:21
Alignment explanation
Indices: 7107--7150 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
7097 CTCCCCTTTA
* *
7107 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
7128 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
7149 TC
1 TC
7151 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Done.