Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_286 ID=scaffold_286-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: 9663
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.30
Warning! 1012 characters in sequence are not A, C, G, or T
Found at i:165 original size:6 final size:6
Alignment explanation
Indices: 154--179 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
144 ACGAAATTAT
154 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
180 GTTCAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:1036 original size:43 final size:47
Alignment explanation
Indices: 942--1041 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 47
932 ATTGGACTGA
* * *
942 GTTTTATATATAGCTTGTACAACATTTAGTTGATTTAGAATTGCTTAG
1 GTTTTATATATAGCTTGTACAACAATTAGTTGATTTA-AACTGCTAAG
990 GTTTTATATATAGCTTGTACAACAATTA-TT-ATTCT-AACT-C-AAG
1 GTTTTATATATAGCTTGTACAACAATTAGTTGATT-TAAACTGCTAAG
1033 GTTTTATAT
1 GTTTTATAT
1042 CATGTGATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 11 0.23
44 1 0.02
45 3 0.06
46 3 0.06
47 3 0.06
48 27 0.56
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (47 bp):
GTTTTATATATAGCTTGTACAACAATTAGTTGATTTAAACTGCTAAG
Found at i:3865 original size:15 final size:15
Alignment explanation
Indices: 3830--3871 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3820 TTAAGAATTT
*
3830 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3844 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3858 TATTTAATAATAAT
1 TATTTAATTATAAT
3872 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:4114 original size:16 final size:16
Alignment explanation
Indices: 4093--4141 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
4083 TTGATTTGCT
4093 ATTATGCCTCTATTCC
1 ATTATGCCTCTATTCC
4109 ATTATGCCTCTATTCC
1 ATTATGCCTCTATTCC
**
4125 ATTACACCTCTATTCC
1 ATTATGCCTCTATTCC
4141 A
1 A
4142 ATACAGCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.22, C:0.33, G:0.04, T:0.41
Consensus pattern (16 bp):
ATTATGCCTCTATTCC
Found at i:4146 original size:16 final size:16
Alignment explanation
Indices: 4099--4146 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
4089 TGCTATTATG
**
4099 CCTCTATTCCATTATG
1 CCTCTATTCCATTACA
4115 CCTCTATTCCATTACA
1 CCTCTATTCCATTACA
*
4131 CCTCTATTCCAATACA
1 CCTCTATTCCATTACA
4147 GCGAACCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.25, C:0.35, G:0.02, T:0.38
Consensus pattern (16 bp):
CCTCTATTCCATTACA
Found at i:5214 original size:27 final size:27
Alignment explanation
Indices: 5158--5221 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
5148 TAGTTCGTCA
* * *
5158 GGACACTAAATAAGGGGTAGTCTATCG
1 GGACAGTAAATAAGGGATAGTCCATCG
* *
5185 GGACAGTAAATACGGGATAGTCCATTG
1 GGACAGTAAATAAGGGATAGTCCATCG
*
5212 GGATAGTAAA
1 GGACAGTAAA
5222 CATGAGCTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (27 bp):
GGACAGTAAATAAGGGATAGTCCATCG
Found at i:8667 original size:21 final size:21
Alignment explanation
Indices: 8630--8671 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8620 GATAAATGTT
8630 TATTTTTATTTACTAAATATA
1 TATTTTTATTTACTAAATATA
*
8651 TATTTTTAATTT-TTAAATATA
1 TATTTTT-ATTTACTAAATATA
8672 GAAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTTATTTACTAAATATA
Found at i:8707 original size:20 final size:20
Alignment explanation
Indices: 8672--8709 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8662 TTTAAATATA
**
8672 GAAAATAAAATTTATTTTTT
1 GAAAATAAAAAATATTTTTT
8692 GAAAATAAAAAATATTTT
1 GAAAATAAAAAATATTTT
8710 CAAAAACCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
GAAAATAAAAAATATTTTTT
Found at i:8785 original size:12 final size:13
Alignment explanation
Indices: 8750--8783 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
8740 AAAAATATTA
*
8750 ATATAATAATTTTT
1 ATATAA-AATCTTT
8764 ATATAAAATCTTT
1 ATATAAAATCTTT
8777 ATATAAA
1 ATATAAA
8784 TCAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATAAAATCTTT
Found at i:9487 original size:9 final size:9
Alignment explanation
Indices: 9470--9515 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
9460 TGAGTTTTCG
9470 AATTCGAAT
1 AATTCGAAT
*
9479 AACTCGAAT
1 AATTCGAAT
9488 AATTCGAAT
1 AATTCGAAT
9497 AATTCGAAT
1 AATTCGAAT
9506 AATTCGAAT
1 AATTCGAAT
9515 A
1 A
9516 TGAAACTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Done.