Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1831
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: 12354
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:4055 original size:14 final size:13
Alignment explanation
Indices: 4008--4057 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
3998 CCGTTACAAG
4008 CAATGTATCGATA
1 CAATGTATCGATA
4021 CAAT-T-TC-AT-
1 CAATGTATCGATA
4030 C-ATGTATCGATA
1 CAATGTATCGATA
4042 CAATGTACTCGATA
1 CAATGTA-TCGATA
4056 CA
1 CA
4058 TTGTCCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 4 0.13
12 2 0.06
13 9 0.29
14 8 0.26
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:4068 original size:34 final size:34
Alignment explanation
Indices: 4008--4078 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
3998 CCGTTACAAG
*
4008 CAATGTATCGATACAATTTCATCATGTATCGATA
1 CAATGTATCGATACAATTTCACCATGTATCGATA
4042 CAATGTACTCGATAC-ATTGTC-CCATGTATCGATA
1 CAATGTA-TCGATACAATT-TCACCATGTATCGATA
4076 CAA
1 CAA
4079 ACAGTGGTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
34 25 0.74
35 9 0.26
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (34 bp):
CAATGTATCGATACAATTTCACCATGTATCGATA
Found at i:8684 original size:22 final size:22
Alignment explanation
Indices: 8659--8700 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
8649 TTTTTAAAGA
*
8659 TTTGATAAAGGAGGAGAAATGT
1 TTTGATAAAGGAGGAAAAATGT
*
8681 TTTGATAAAGGTGGAAAAAT
1 TTTGATAAAGGAGGAAAAAT
8701 ATGTTTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (22 bp):
TTTGATAAAGGAGGAAAAATGT
Found at i:9346 original size:19 final size:20
Alignment explanation
Indices: 9274--9345 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
9264 CTCACCCATA
9274 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
9294 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
*
9314 TGTATCGATACATGT-T-CAT
1 TGTATCGATACAT-TATGCTT
9333 TGTATCGATACAT
1 TGTATCGATACAT
9346 GAAATTGGCA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
19 15 0.30
20 34 0.68
21 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:9412 original size:13 final size:13
Alignment explanation
Indices: 9391--9421 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9381 CGATACATGG
*
9391 TACAATGTATCGA
1 TACATTGTATCGA
9404 TACATTGTATCGA
1 TACATTGTATCGA
9417 TACAT
1 TACAT
9422 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:9433 original size:33 final size:33
Alignment explanation
Indices: 9375--9443 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
9365 CTACCACTGT
* *
9375 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGATACAATGTATCAATACA
*
9408 TTGTATCGATACATGATGA-ATTGTATCAATACA
1 TTGTATCGATACATGAT-ACAATGTATCAATACA
9441 TTG
1 TTG
9444 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATGTATCAATACA
Done.