Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_130 ID=scaffold_130-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: 11826
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.30
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:77 original size:5 final size:5
Alignment explanation
Indices: 67--100 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
57 TATATTTCTT
*
67 TTTTA TTTTA TTTTA TTTTA TTTTTC TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTT
101 CGTTTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:80 original size:11 final size:11
Alignment explanation
Indices: 66--100 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
56 ATATATTTCT
66 TTTTTATTTTA
1 TTTTTATTTTA
77 -TTTTATTTTA
1 TTTTTATTTTA
*
87 TTTTTCTTTTA
1 TTTTTATTTTA
98 TTT
1 TTT
101 CGTTTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:106 original size:21 final size:21
Alignment explanation
Indices: 66--107 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
56 ATATATTTCT
*
66 TTTTTATTTTATTTTATTTTA
1 TTTTTATTTTATTTCATTTTA
* *
87 TTTTTCTTTTATTTCGTTTTA
1 TTTTTATTTTATTTCATTTTA
108 AATAACAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTATTTTATTTCATTTTA
Found at i:962 original size:13 final size:12
Alignment explanation
Indices: 936--978 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 12
926 CTTCACACGC
936 ATATATTT-TTT
1 ATATATTTATTT
947 ATATAGTTTATTT
1 ATATA-TTTATTT
960 ATATATTATATTT
1 ATATATT-TATTT
973 ATATAT
1 ATATAT
979 ATTTTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 19 0.66
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
ATATATTTATTT
Found at i:4779 original size:20 final size:20
Alignment explanation
Indices: 4746--4785 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4736 TTCATCTCAT
*
4746 GCATCGCATCATATGCATTA
1 GCATCACATCATATGCATTA
*
4766 GCATCACATTATATGCATTA
1 GCATCACATCATATGCATTA
4786 TAGACCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (20 bp):
GCATCACATCATATGCATTA
Found at i:6838 original size:9 final size:9
Alignment explanation
Indices: 6824--6860 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
6814 TATAGTTTGA
6824 TATTCGAAT
1 TATTCGAAT
6833 TATTCGAAT
1 TATTCGAAT
*
6842 TATTCGAGT
1 TATTCGAAT
6851 TATTCGAAT
1 TATTCGAAT
6860 T
1 T
6861 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6930 original size:9 final size:9
Alignment explanation
Indices: 6913--6943 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6903 TCGAGTTGAT
6913 TCGAATAAC
1 TCGAATAAC
*
6922 TCGATTAAC
1 TCGAATAAC
6931 TCGAATAAC
1 TCGAATAAC
6940 TCGA
1 TCGA
6944 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:7970 original size:20 final size:19
Alignment explanation
Indices: 7928--7968 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
7918 GCAAATGTTC
7928 TTTCATTCTTTATGATTTT
1 TTTCATTCTTTATGATTTT
7947 TTTCATTCTTT-TGGATTTT
1 TTTCATTCTTTAT-GATTTT
7966 TTT
1 TTT
7969 TCTGCCAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (19 bp):
TTTCATTCTTTATGATTTT
Found at i:8913 original size:7 final size:7
Alignment explanation
Indices: 8901--8942 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
8891 AAATGACGAG
8901 ATGAAAA
1 ATGAAAA
8908 ATGAAAA
1 ATGAAAA
8915 ATG-AAA
1 ATGAAAA
8921 ATGAAAA
1 ATGAAAA
* *
8928 CTAAAAA
1 ATGAAAA
8935 ATGGAAAA
1 AT-GAAAA
8943 GTAAAATGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 6 0.21
7 19 0.66
8 4 0.14
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.14
Consensus pattern (7 bp):
ATGAAAA
Found at i:8918 original size:14 final size:14
Alignment explanation
Indices: 8901--8942 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
8891 AAATGACGAG
8901 ATGAAAAATGAAAA
1 ATGAAAAATGAAAA
8915 ATG-AAAATGAAAA
1 ATGAAAAATGAAAA
* *
8928 CTAAAAAATGGAAAA
1 ATGAAAAAT-GAAAA
8943 GTAAAATGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 11 0.46
14 8 0.33
15 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.14
Consensus pattern (14 bp):
ATGAAAAATGAAAA
Found at i:8934 original size:20 final size:20
Alignment explanation
Indices: 8887--8942 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
8877 CTTTGAGTCG
*
8887 TAAAAAATGACGAGATGAAAAA
1 TAAAAAATGA--AAATGAAAAA
* *
8909 TGAAAAATGAAAATGAAAAC
1 TAAAAAATGAAAATGAAAAA
8929 TAAAAAATGGAAAA
1 TAAAAAAT-GAAAA
8943 GTAAAATGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.52
21 5 0.17
22 9 0.31
ACGTcount: A:0.66, C:0.04, G:0.16, T:0.14
Consensus pattern (20 bp):
TAAAAAATGAAAATGAAAAA
Found at i:9086 original size:42 final size:42
Alignment explanation
Indices: 9025--9125 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
9015 GAAAAGGGCG
* *
9025 GCTCAAATATTGATTAGAATGGGGCATGAGATTATCGAAGTA
1 GCTCAAATATTGATCAGAATGCGGCATGAGATTATCGAAGTA
* *
9067 GCTCAAATATTGATCAGAATGCGGCATGAGATTATTGGAGTA
1 GCTCAAATATTGATCAGAATGCGGCATGAGATTATCGAAGTA
*
9109 GCTCAAATACTGATCAG
1 GCTCAAATATTGATCAG
9126 CATAAGGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.28
Consensus pattern (42 bp):
GCTCAAATATTGATCAGAATGCGGCATGAGATTATCGAAGTA
Found at i:10446 original size:45 final size:45
Alignment explanation
Indices: 10348--10813 Score: 351
Period size: 45 Copynumber: 10.4 Consensus size: 45
10338 ACTAGTGGCG
** ** *
10348 AAGCAGATCTTGTCTTCATGTACTGG-CCTGAAGTAGATCAAAGGT
1 AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAA-GA
* * ** *
10393 AA-CAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAGA
1 AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGA
** * *
10437 AAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGGT
1 AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAA-GA
* ** *
10482 AA-CAGATCTTGTCTTCCCATACTGGTGGTGAAACAGATCGAAGA
1 AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGA
** **
10526 AAGCAGATCTTGTCTTCATGTACTGG-CATGAAGTAGATCAAAGA
1 AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGA
* * * **
10570 TAA-CAGATCTTGTTTTCTCATACTGGTGGCGAAACAGATCAAAGA
1 -AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGA
* ** * *
10615 AAGTAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAAGT
1 AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATC-AAAGA
* * *
10660 AA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGGAAA
1 AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATC-AA--AGA
* ** * *
10707 AAGTAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGA
1 AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGA
* * * * * *
10751 CAA-CAAATCTTGTCTCCCCACACTGGTGGTGGAGTAGATCGAAGA
1 -AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGA
*
10796 GAA-CAGACCTTGTCTTCA
1 -AAGCAGATCTTGTCTTCA
10814 TTGGCGTGAA
Statistics
Matches: 319, Mismatches: 87, Indels: 30
0.73 0.20 0.07
Matches are distributed among these distances:
44 136 0.43
45 149 0.47
46 2 0.01
47 14 0.04
48 18 0.06
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (45 bp):
AAGCAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGA
Found at i:10499 original size:89 final size:89
Alignment explanation
Indices: 10348--10832 Score: 692
Period size: 89 Copynumber: 5.5 Consensus size: 89
10338 ACTAGTGGCG
*
10348 AAGCAGATCTTGTCTTCATGTACTGGCCTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCAT
1 AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCAT
10413 ACTGGTGGCGAAACAGATCGAAGA
66 ACTGGTGGCGAAACAGATCGAAGA
10437 AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCAT
1 AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCAT
*
10502 ACTGGTGGTGAAACAGATCGAAGA
66 ACTGGTGGCGAAACAGATCGAAGA
* * * *
10526 AAGCAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACAGATCTTGTTTTCTCAT
1 AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCAT
*
10591 ACTGGTGGCGAAACAGATCAAAGA
66 ACTGGTGGCGAAACAGATCGAAGA
* *
10615 AAGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAGTAACAGATCTTGTCTTCCCAT
1 AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCAT
**
10680 ACTGGTGGCGAAGTAGATCGAAGGAAA
66 ACTGGTGGCGAAACAGATCGAA-G--A
* * ** * * *
10707 AAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGACAACAAATCTTGTCTCCCCAC
1 AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCAT
* * **
10772 ACTGGTGGTGGAGTAGATCGAAGA
66 ACTGGTGGCGAAACAGATCGAAGA
*
10796 GAA-CAGACCTTGTCTTCA--T--TGGCGTGAAGTAGATCAA
1 -AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAA
10833 GCGCAGCAGA
Statistics
Matches: 364, Mismatches: 28, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
85 18 0.05
87 1 0.00
89 262 0.72
90 3 0.01
91 1 0.00
92 79 0.22
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (89 bp):
AAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCAT
ACTGGTGGCGAAACAGATCGAAGA
Found at i:11763 original size:5 final size:5
Alignment explanation
Indices: 11753--11786 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
11743 TATATTTCTT
*
11753 TTTTA TTTTA TTTTA TTTTA TTTTTC TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTT
11787 CGTTTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:11766 original size:11 final size:11
Alignment explanation
Indices: 11752--11786 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
11742 ATATATTTCT
11752 TTTTTATTTTA
1 TTTTTATTTTA
11763 -TTTTATTTTA
1 TTTTTATTTTA
*
11773 TTTTTCTTTTA
1 TTTTTATTTTA
11784 TTT
1 TTT
11787 CGTTTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:11792 original size:21 final size:21
Alignment explanation
Indices: 11752--11793 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11742 ATATATTTCT
*
11752 TTTTTATTTTATTTTATTTTA
1 TTTTTATTTTATTTCATTTTA
* *
11773 TTTTTCTTTTATTTCGTTTTA
1 TTTTTATTTTATTTCATTTTA
11794 AATAACAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTATTTTATTTCATTTTA
Done.