Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1048
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: 13748
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2626 original size:20 final size:20
Alignment explanation
Indices: 2601--2639 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2591 TATTATCTAA
2601 TTATATTAGAATATTCATTT
1 TTATATTAGAATATTCATTT
2621 TTATATTAGAATATTCATT
1 TTATATTAGAATATTCATT
2640 CTATTGATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
TTATATTAGAATATTCATTT
Found at i:2683 original size:5 final size:5
Alignment explanation
Indices: 2668--2777 Score: 58
Period size: 5 Copynumber: 23.2 Consensus size: 5
2658 TAGTCTATTC
* * * *
2668 TATAT TCTAT TATAT TA-A- TATAT TCTAT TCTAT TA-AT TCTAT T-TAAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT
* * * *
2715 TCTAT TATAT TA-A- TATAT TCTAT TCTAT TA-AT TCTAT TATAT ATATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT
2763 TA-A- TATAT ATATAT T
1 TATAT TATAT -TATAT T
2778 CTCTAATTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
3 6 0.07
4 13 0.16
5 53 0.64
6 11 0.13
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:2708 original size:14 final size:14
Alignment explanation
Indices: 2689--2752 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
2679 ATATTAATAT
2689 ATTCTATTCTATTA
1 ATTCTATTCTATTA
2703 ATTCTA---T-TTA
1 ATTCTATTCTATTA
*
2713 ATTCTATTATATTAATA
1 ATTCTATTCTA-T--TA
2730 TATTCTATTCTATTA
1 -ATTCTATTCTATTA
2745 ATTCTATT
1 ATTCTATT
2753 ATATATATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 16
0.71 0.02 0.28
Matches are distributed among these distances:
10 9 0.22
11 1 0.02
13 1 0.02
14 14 0.34
15 3 0.07
17 3 0.07
18 10 0.24
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTCTATTCTATTA
Found at i:2725 original size:42 final size:44
Alignment explanation
Indices: 2661--2779 Score: 174
Period size: 42 Copynumber: 2.8 Consensus size: 44
2651 TTCTAATTAG
2661 TCTATTCTATATTCTATTATATTAATATATTCTATTCTATTAAT
1 TCTATTCTATATTCTATTATATTAATATATTCTATTCTATTAAT
2705 TCTATT-TA-ATTCTATTATATTAATATATTCTATTCTATTAAT
1 TCTATTCTATATTCTATTATATTAATATATTCTATTCTATTAAT
* *
2747 TCTATTATATA-TATATTA-ATATATATATATTCT
1 TCTATTCTATATTCTATTATAT-TA-ATATATTCT
2780 CTAATTTAAC
Statistics
Matches: 70, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
42 42 0.60
43 12 0.17
44 16 0.23
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (44 bp):
TCTATTCTATATTCTATTATATTAATATATTCTATTCTATTAAT
Found at i:2749 original size:32 final size:31
Alignment explanation
Indices: 2703--2763 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 31
2693 TATTCTATTA
2703 ATTCTATTTAATTCTATTATATTAATATATTCT
1 ATTCTATTTAATTCTATTATA-T-ATATATTCT
2736 ATTCTA-TTAATTCTATTATATATATATT
1 ATTCTATTTAATTCTATTATATATATATT
2764 AATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 7 0.25
31 1 0.04
32 14 0.50
33 6 0.21
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTCTATTTAATTCTATTATATATATATTCT
Found at i:7390 original size:14 final size:14
Alignment explanation
Indices: 7354--7403 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
7344 ACTCGCTTAG
7354 ATATACTTAGTATTTA
1 ATATACTTAGTA--TA
7370 TATATACTTAGTATA
1 -ATATACTTAGTATA
* *
7385 ATATACTAATTATA
1 ATATACTTAGTATA
7399 ATATA
1 ATATA
7404 ATCATTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 17 0.55
15 2 0.06
17 12 0.39
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (14 bp):
ATATACTTAGTATA
Found at i:12011 original size:11 final size:11
Alignment explanation
Indices: 11995--12031 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
11985 GGATAAATAT
11995 AATAAGTATAA
1 AATAAGTATAA
12006 AATAAGTAT-A
1 AATAAGTATAA
12016 AATAAGTATAA
1 AATAAGTATAA
*
12027 TATAA
1 AATAA
12032 TAAGGAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (11 bp):
AATAAGTATAA
Found at i:12019 original size:21 final size:21
Alignment explanation
Indices: 11967--12031 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
11957 AGATTTACTT
*
11967 ATATAGAATAAGTAATAAGGATAA
1 ATATA-AATAAGT-ATAA-AATAA
11991 ATAT-AATAAGTATAAAATAA
1 ATATAAATAAGTATAAAATAA
* *
12011 GTATAAATAAGTATAATATAA
1 ATATAAATAAGTATAAAATAA
12032 TAAGGAATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.19
21 19 0.51
22 7 0.19
24 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (21 bp):
ATATAAATAAGTATAAAATAA
Done.