Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_88 ID=scaffold_88-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: 18563
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.30
Warning! 3680 characters in sequence are not A, C, G, or T
Found at i:4802 original size:21 final size:21
Alignment explanation
Indices: 4776--4818 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4766 GTGAGATTCT
*
4776 AACTTTTTATTGATTAAACTA
1 AACTTTTTATTCATTAAACTA
4797 AACTTTTTATTCATTAAACTA
1 AACTTTTTATTCATTAAACTA
4818 A
1 A
4819 GTGAGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (21 bp):
AACTTTTTATTCATTAAACTA
Found at i:5682 original size:11 final size:10
Alignment explanation
Indices: 5670--5719 Score: 59
Period size: 9 Copynumber: 4.9 Consensus size: 10
5660 ATGATGTGTA
5670 AATATAATAT
1 AATATAATAT
5680 AAATATAATAT
1 -AATATAATAT
5691 AAT-TAATAT
1 AATATAATAT
5700 AAT-TAATATCT
1 AATATAATA--T
5711 AATATAATA
1 AATATAATA
5720 AGAGATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
9 14 0.39
10 3 0.08
11 14 0.39
12 5 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATAATAT
Found at i:5691 original size:16 final size:15
Alignment explanation
Indices: 5670--5719 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
5660 ATGATGTGTA
5670 AATATAATATAAATAT
1 AATATAATAT-AATAT
5686 AATATAAT-TAATAT
1 AATATAATATAATAT
5700 AAT-TAATATCTAATAT
1 AATATAATA--TAATAT
5716 AATA
1 AATA
5720 AGAGATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.13
14 8 0.27
15 1 0.03
16 17 0.57
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATAATATAATAT
Found at i:5698 original size:25 final size:25
Alignment explanation
Indices: 5670--5718 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5660 ATGATGTGTA
5670 AATATAATATAA-ATATAATATAATT
1 AATATAAT-TAATATATAATATAATT
*
5695 AATATAATTAATATCTAATATAAT
1 AATATAATTAATATATAATATAAT
5719 AAGAGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATAATTAATATATAATATAATT
Found at i:5706 original size:4 final size:5
Alignment explanation
Indices: 5670--5719 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
5660 ATGATGTGTA
5670 AATAT AATAT AAATAT AATAT AAT-T AATAT AAT-T AATATCT AATAT
1 AATAT AATAT -AATAT AATAT AATAT AATAT AATAT AATA--T AATAT
5716 AATA
1 AATA
5720 AGAGATAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
4 8 0.20
5 22 0.55
6 5 0.12
7 5 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:5890 original size:2 final size:2
Alignment explanation
Indices: 5879--5916 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
5869 GTTAGGGATT
* *
5879 TA TA -A TA TA TA TA TA TA TA TA TA TA TA AA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5917 TATCATATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:10604 original size:10 final size:10
Alignment explanation
Indices: 10589--10621 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
10579 ATTTGCCAAA
10589 ACACAAACAC
1 ACACAAACAC
10599 ACACAAACAC
1 ACACAAACAC
10609 ACACAAACAC
1 ACACAAACAC
10619 ACA
1 ACA
10622 AACACATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.61, C:0.39, G:0.00, T:0.00
Consensus pattern (10 bp):
ACACAAACAC
Found at i:12657 original size:17 final size:17
Alignment explanation
Indices: 12635--12674 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
12625 AAATATACGA
*
12635 GTATCAGAAAGTTATGG
1 GTATCAGAAAGATATGG
12652 GTATCAGAAAGATATGG
1 GTATCAGAAAGATATGG
12669 GTATCA
1 GTATCA
12675 AAATCTAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (17 bp):
GTATCAGAAAGATATGG
Done.