Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_859 ID=scaffold_859-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: 3758
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.24
Warning! 726 characters in sequence are not A, C, G, or T
Found at i:2939 original size:19 final size:18
Alignment explanation
Indices: 2912--3005 Score: 73
Period size: 19 Copynumber: 5.2 Consensus size: 18
2902 CAGTGGAGGC
2912 AAAAACAAAAAAACAAAA
1 AAAAACAAAAAAACAAAA
*
2930 AAAAAGCAAAAAAGCAAAA
1 AAAAA-CAAAAAAACAAAA
* ** *
2949 AAAATAAAAAAAAAGGAAG
1 AAAA-ACAAAAAAACAAAA
* * *
2968 CAAAA-AAAAAGAGAAAA
1 AAAAACAAAAAAACAAAA
* *
2985 CAAAAGAAAAAAACAAAA
1 AAAAACAAAAAAACAAAA
3003 AAA
1 AAA
3006 TAAAAAATAA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
17 14 0.23
18 18 0.30
19 27 0.45
20 1 0.02
ACGTcount: A:0.83, C:0.07, G:0.09, T:0.01
Consensus pattern (18 bp):
AAAAACAAAAAAACAAAA
Found at i:2969 original size:32 final size:33
Alignment explanation
Indices: 2910--2974 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
2900 TTCAGTGGAG
2910 GCAAAAACAAAAAAACAAAAAAAAAGCAAAAAA
1 GCAAAAACAAAAAAACAAAAAAAAAGCAAAAAA
**
2943 GCAAAAA-AAATAAAA-AAAAAGGAAGCAAAAAA
1 GCAAAAACAAA-AAAACAAAAAAAAAGCAAAAAA
2975 AAAGAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.80, C:0.09, G:0.09, T:0.02
Consensus pattern (33 bp):
GCAAAAACAAAAAAACAAAAAAAAAGCAAAAAA
Found at i:2974 original size:17 final size:17
Alignment explanation
Indices: 2913--3012 Score: 71
Period size: 17 Copynumber: 5.8 Consensus size: 17
2903 AGTGGAGGCA
*
2913 AAAACAAAAAAACAAAAA
1 AAAACAAAAAAA-AAAAG
**
2931 AAAAGCAAAAAAGCAAA-
1 AAAA-CAAAAAAAAAAAG
*
2948 AAAA-ATAAAAAAAAAG
1 AAAACAAAAAAAAAAAG
* * *
2964 GAAGCAAAAAAAAAGAG
1 AAAACAAAAAAAAAAAG
*
2981 AAAACAAAAGAAAAAAAC
1 AAAACAAAA-AAAAAAAG
2999 AAAA-AAATAAAAAA
1 AAAACAAA-AAAAAA
3013 TAAAAAATAA
Statistics
Matches: 64, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
15 8 0.12
16 2 0.03
17 29 0.45
18 18 0.28
19 7 0.11
ACGTcount: A:0.83, C:0.07, G:0.08, T:0.02
Consensus pattern (17 bp):
AAAACAAAAAAAAAAAG
Found at i:3011 original size:35 final size:33
Alignment explanation
Indices: 2912--3033 Score: 95
Period size: 35 Copynumber: 3.4 Consensus size: 33
2902 CAGTGGAGGC
*
2912 AAAAACAAAAAAACAAAAAAAAAGCAAAAAAGCAAA
1 AAAAAGAAAAAAACAAAAAAAAA--AAAAAAG-AAA
* *
2948 AAAAATAAAAAAA-AAGGAAGCAAAAAAAAAGAGAAA
1 AAAAAGAAAAAAACAA--AA--AAAAAAAAAAAGAAA
2984 ACAAAAGAAAAAAACAAAAAAATAAAAAATAA-AAA
1 A-AAAAGAAAAAAACAAAAAAA-AAAAAA-AAGAAA
*
3019 ATAAGAGAAAAAAAC
1 A-AAAAGAAAAAAAC
3034 CTCTACCGGG
Statistics
Matches: 72, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
34 3 0.04
35 24 0.33
36 19 0.26
37 19 0.26
38 2 0.03
39 5 0.07
ACGTcount: A:0.82, C:0.07, G:0.08, T:0.03
Consensus pattern (33 bp):
AAAAAGAAAAAAACAAAAAAAAAAAAAAAGAAA
Found at i:3031 original size:14 final size:13
Alignment explanation
Indices: 2912--3032 Score: 66
Period size: 14 Copynumber: 8.8 Consensus size: 13
2902 CAGTGGAGGC
*
2912 AAAAACAAAAAAAC
1 AAAAA-AAAAAAAT
2926 AAAAAAAAAGCAAA-
1 AAAAAAAAA--AAAT
*
2940 AAAGCAAAAAAAAT
1 AAA-AAAAAAAAAT
* *
2954 AAAAAAAAAGGAAG
1 AAAAAAAAA-AAAT
* * *
2968 CAAAAAAAAAGAG
1 AAAAAAAAAAAAT
*
2981 AAAACAAAAGAAA-
1 AAAA-AAAAAAAAT
*
2994 AAAACAAAAAAAT
1 AAAAAAAAAAAAT
3007 AAAAAATAAAAAAT
1 AAAAAA-AAAAAAT
*
3021 AAGAGAAAAAAA
1 AA-AAAAAAAAA
3033 CCTCTACCGG
Statistics
Matches: 84, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
12 6 0.07
13 26 0.31
14 41 0.49
15 11 0.13
ACGTcount: A:0.83, C:0.06, G:0.08, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:3032 original size:1 final size:1
Alignment explanation
Indices: 2912--3019 Score: 54
Period size: 1 Copynumber: 108.0 Consensus size: 1
2902 CAGTGGAGGC
* * ** ** * ** **
2912 AAAAACAAAAAAACAAAAAAAAAGCAAAAAAGCAAAAAAAATAAAAAAAAAGGAAGCAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
2977 AGAGAAAACAAAAGAAAAAAACAAAAAAATAAAAAATAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3020 TAAGAGAAAA
Statistics
Matches: 76, Mismatches: 31, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.83, C:0.06, G:0.07, T:0.03
Consensus pattern (1 bp):
A
Done.