Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_244 ID=scaffold_244-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: 9681
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.31
Warning! 651 characters in sequence are not A, C, G, or T
Found at i:3949 original size:20 final size:20
Alignment explanation
Indices: 3920--3977 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
3910 TTAAACTATG
* *
3920 TACCACTCCATTTACTTTCT
1 TACCATTCCATTTACTTACT
3940 TACCATTCCATTTACTTACT
1 TACCATTCCATTTACTTACT
* *
3960 TTCCATTTCATTTACTTA
1 TACCATTCCATTTACTTA
3978 GCATAAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.48
Consensus pattern (20 bp):
TACCATTCCATTTACTTACT
Found at i:6308 original size:11 final size:11
Alignment explanation
Indices: 6279--6308 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6269 AAGTATTTGG
6279 AAAAAAATTCA
1 AAAAAAATTCA
*
6290 AAACAAATTCA
1 AAAAAAATTCA
6301 AAAAAAAT
1 AAAAAAAT
6309 CATGAACTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:6797 original size:19 final size:18
Alignment explanation
Indices: 6763--6819 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
6753 TGCTTGAATA
*
6763 AATT-ACTCAACTTAGTT
1 AATTAACTCATCTTAGTT
*
6780 AATTAAGTTCATCTTAGTT
1 AATTAA-CTCATCTTAGTT
6799 AA-TAACTCATCTTAGCTT
1 AATTAACTCATCTTAG-TT
6817 AAT
1 AAT
6820 AAATGAGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 13 0.39
18 8 0.24
19 12 0.36
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (18 bp):
AATTAACTCATCTTAGTT
Found at i:6820 original size:18 final size:17
Alignment explanation
Indices: 6767--6821 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
6757 TGAATAAATT
*
6767 ACTCAACTTAGTTAATTA
1 ACTCATCTTAGTTAA-TA
*
6785 AGTTCATCTTAGTTAATA
1 A-CTCATCTTAGTTAATA
6803 ACTCATCTTAGCTTAATA
1 ACTCATCTTAG-TTAATA
6821 A
1 A
6822 ATGAGTTGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 9 0.28
18 11 0.34
19 12 0.38
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.40
Consensus pattern (17 bp):
ACTCATCTTAGTTAATA
Found at i:9035 original size:22 final size:22
Alignment explanation
Indices: 8994--9035 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
8984 TGTAGTTTCA
8994 AAAAAAAATTCGAAAAAAAATC
1 AAAAAAAATTCGAAAAAAAATC
*
9016 AAAAAATATT-GAAAAGAAAA
1 AAAAAAAATTCGAAAA-AAAA
9036 AAAATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.74, C:0.05, G:0.07, T:0.14
Consensus pattern (22 bp):
AAAAAAAATTCGAAAAAAAATC
Found at i:9037 original size:16 final size:15
Alignment explanation
Indices: 9016--9050 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
9006 AAAAAAAATC
*
9016 AAAAAATATTGAAAA
1 AAAAAAAATTGAAAA
9031 GAAAAAAAATTGAAAA
1 -AAAAAAAATTGAAAA
9047 AAAA
1 AAAA
9051 TTGCATACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (15 bp):
AAAAAAAATTGAAAA
Done.