Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_166 ID=scaffold_166-JGI_221_v2.0
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: 10246
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:4504 original size:20 final size:20
Alignment explanation
Indices: 4479--4519 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4469 GATCGTTCCT
4479 TAGTACAGCTAGTACTAAAA
1 TAGTACAGCTAGTACTAAAA
4499 TAGTACAGCTAGTACTAAAA
1 TAGTACAGCTAGTACTAAAA
4519 T
1 T
4520 CGAAGTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
TAGTACAGCTAGTACTAAAA
Found at i:7744 original size:13 final size:13
Alignment explanation
Indices: 7726--7797 Score: 66
Period size: 13 Copynumber: 5.7 Consensus size: 13
7716 TTATTTTTGT
7726 TTTATTATTATTA
1 TTTATTATTATTA
7739 TTTATTATT-TTA
1 TTTATTATTATTA
7751 TTTACTTTATTTATTA
1 TTTA--TTA-TTATTA
7767 CTTTATT-TTA-T-
1 -TTTATTATTATTA
7778 TTTATTA-T-TTA
1 TTTATTATTATTA
7789 TTTATTATT
1 TTTATTATT
7798 TGGATATTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 19
0.72 0.00 0.28
Matches are distributed among these distances:
10 8 0.16
11 7 0.14
12 9 0.18
13 12 0.24
14 3 0.06
15 4 0.08
16 3 0.06
17 4 0.08
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:7751 original size:21 final size:22
Alignment explanation
Indices: 7716--7798 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 22
7706 AACCCAATTT
*
7716 TTATTT-TTGTTTTA-TTATTA
1 TTATTTATTATTTTATTTATTA
*
7736 TTATTTATTATTTTATTTACT-
1 TTATTTATTATTTTATTTATTA
*
7757 TTATTTATTACTTTATTTTATTTTA
1 TTATTTATTATTTTA-TTTA--TTA
*
7782 TTATTTATT-TATTATTT
1 TTATTTATTATTTTATTT
7799 GGATATTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.12
21 21 0.41
22 8 0.16
23 3 0.06
24 4 0.08
25 9 0.18
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.73
Consensus pattern (22 bp):
TTATTTATTATTTTATTTATTA
Found at i:7754 original size:4 final size:4
Alignment explanation
Indices: 7736--7798 Score: 53
Period size: 4 Copynumber: 15.5 Consensus size: 4
7726 TTTATTATTA
7736 TTAT TTA- TTATT TTAT TTACT TTAT TTA- TTACT TTATT TTAT TT-T
1 TTAT TTAT TTA-T TTAT TTA-T TTAT TTAT TTA-T TTA-T TTAT TTAT
7781 ATTAT TTAT TTA- TTAT TT
1 -TTAT TTAT TTAT TTAT TT
7799 GGATATTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
3 10 0.20
4 25 0.50
5 15 0.30
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:7986 original size:22 final size:22
Alignment explanation
Indices: 7961--8003 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
7951 CCAAACTACT
* *
7961 TTATTCCTGCAGCCAACCACCC
1 TTATCCCTGCACCCAACCACCC
*
7983 TTATCCCTGCACCCAAGCACC
1 TTATCCCTGCACCCAACCACC
8004 ACCCCTCAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.47, G:0.09, T:0.21
Consensus pattern (22 bp):
TTATCCCTGCACCCAACCACCC
Found at i:9131 original size:101 final size:101
Alignment explanation
Indices: 8942--9135 Score: 273
Period size: 101 Copynumber: 1.9 Consensus size: 101
8932 AAGAACATGT
* * * *
8942 TGGGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCGATGTG
1 TGGGCTGAGTAACCGGGATGAGGTGCTTGGCTATCATCTCTCTTCGCATCAAAAGGTTCGATATG
* *
9007 TTCTTAAGAAAAAAATATAATAAATTAGGAGTCTAC
66 TCCTAAAGAAAAAAATATAATAAATTAGGAGTCTAC
*
9043 TGGGCTGAGTAACCGGGATGGGGTGCTTGGCTATCATCTCTCTTCGCATCAAAAGGTTCAGTATA
1 TGGGCTGAGTAACCGGGATGAGGTGCTTGGCTATCATCTCTCTTCGCATCAAAAGGTTC-G-ATA
9108 T-TCCTAAAGCATAAAAAATATAAATAAA
64 TGTCCTAAAG-A-AAAAAATAT-AATAAA
9136 AAAAATCAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
101 55 0.68
102 7 0.09
103 4 0.05
104 9 0.11
105 6 0.07
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (101 bp):
TGGGCTGAGTAACCGGGATGAGGTGCTTGGCTATCATCTCTCTTCGCATCAAAAGGTTCGATATG
TCCTAAAGAAAAAAATATAATAAATTAGGAGTCTAC
Done.