Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_89 ID=scaffold_89-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: 14837
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Found at i:454 original size:98 final size:98
Alignment explanation
Indices: 328--606 Score: 486
Period size: 98 Copynumber: 2.8 Consensus size: 98
318 TCCGAGTTTG
* * *
328 CGAGTTTGGGATTTTGGAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTCAAATCTTGGATA
1 CGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATA
* *
393 GGTGGATGTTCTTTTAAAGTAAAGGAAATATTT
66 AGTGGATGTTCTTTTAAAGTAAAGGAAATATTC
* *
426 CGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTCCTTAAATCTTTGATA
1 CGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATA
491 AGTGGATGTTCTTTTAAAGTAAAGGAAATATTC
66 AGTGGATGTTCTTTTAAAGTAAAGGAAATATTC
*
524 CGAGTTTGGGATTTTAGTGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATA
1 CGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATA
589 AGTGGATGTTCTTTTAAA
66 AGTGGATGTTCTTTTAAA
607 ATTTTATTGC
Statistics
Matches: 171, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 171 1.00
ACGTcount: A:0.25, C:0.10, G:0.26, T:0.38
Consensus pattern (98 bp):
CGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATA
AGTGGATGTTCTTTTAAAGTAAAGGAAATATTC
Found at i:4758 original size:11 final size:11
Alignment explanation
Indices: 4742--4767 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4732 TTATTATTTA
4742 TTTTAAAATAC
1 TTTTAAAATAC
4753 TTTTAAAATAC
1 TTTTAAAATAC
4764 TTTT
1 TTTT
4768 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:4778 original size:11 final size:11
Alignment explanation
Indices: 4764--4822 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
4754 TTTAAAATAC
4764 TTTTTTTAAAA
1 TTTTTTTAAAA
4775 -TTTTTT-AAA
1 TTTTTTTAAAA
4784 ---TTTTAAAA
1 TTTTTTTAAAA
4792 TTTTTTTAAAA
1 TTTTTTTAAAA
4803 TACTTTTTT--AA
1 T--TTTTTTAAAA
4814 TTTTTTTAA
1 TTTTTTTAA
4823 TTTTAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
7 4 0.10
8 3 0.08
9 9 0.22
10 6 0.15
11 12 0.30
13 6 0.15
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTTTTAAAA
Found at i:4789 original size:17 final size:17
Alignment explanation
Indices: 4767--4840 Score: 67
Period size: 17 Copynumber: 4.0 Consensus size: 17
4757 AAAATACTTT
4767 TTTTAAAATTTTTTAAA
1 TTTTAAAATTTTTTAAA
4784 TTTTAAAATTTTTTTAAAATA
1 TTTTAAAA-TTTTTT--AA-A
** *
4805 CTTTTTTAATTTTTTTAA
1 -TTTTAAAATTTTTTAAA
4823 TTTTAAAATATTTTTAAA
1 TTTTAAAAT-TTTTTAAA
4841 ATACTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
17 15 0.33
18 14 0.31
19 1 0.02
20 2 0.04
21 7 0.16
22 6 0.13
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATTTTTTAAA
Found at i:4791 original size:31 final size:31
Alignment explanation
Indices: 4753--4818 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
4743 TTTAAAATAC
*
4753 TTTTAAAATACTTTTTTTAAA-A-TTTTTTAAA
1 TTTTAAAAT--TTTTTTAAAATACTTTTTTAAA
*
4784 TTTTAAAATTTTTTTAAAATACTTTTTTAAT
1 TTTTAAAATTTTTTTAAAATACTTTTTTAAA
4815 TTTT
1 TTTT
4819 TTAATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 9 0.29
30 1 0.03
31 21 0.68
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTAAAATTTTTTTAAAATACTTTTTTAAA
Found at i:4827 original size:39 final size:40
Alignment explanation
Indices: 4741--4858 Score: 184
Period size: 39 Copynumber: 2.9 Consensus size: 40
4731 TTTATTATTT
*
4741 ATTTTAAAATACTTTTAAAATACTTTTTTTAAAATTTTTTAA
1 ATTTTAAAATATTTTTAAAATACTTTTTTT--AATTTTTTAA
* *
4783 ATTTTAAAATTTTTTTAAAATAC-TTTTTTAATTTTTTTA
1 ATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTAA
4822 ATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTT
1 ATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTT
4859 GTTTTAATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
39 31 0.44
40 13 0.18
41 6 0.08
42 21 0.30
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (40 bp):
ATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTAA
Found at i:12684 original size:89 final size:90
Alignment explanation
Indices: 12578--12763 Score: 329
Period size: 89 Copynumber: 2.1 Consensus size: 90
12568 CATCTAGTCT
12578 TATCTCCCTGAAGTTGCAGTGGAGCAGAATAAGTAAGCAAGTCTTATCCTCCC-GAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAATAAGTAAGCAAGTCTTATCCTCCCTGAAGTTGCAGT
12642 GAGGCAGACTGAAGATGGCAAATCG
66 GAGGCAGACTGAAGATGGCAAATCG
*
12667 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAATAAGTAAGCAAGTCTTATCCTCCCTGAAGTTGCAGT
* * *
12732 GGGGCAGACTGAAGATGGCAAGTCT
66 GAGGCAGACTGAAGATGGCAAATCG
12757 TATCTCC
1 TATCTCC
12764 AGTGGAGCAG
Statistics
Matches: 92, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 52 0.57
90 40 0.43
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (90 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGAATAAGTAAGCAAGTCTTATCCTCCCTGAAGTTGCAGT
GAGGCAGACTGAAGATGGCAAATCG
Found at i:12686 original size:45 final size:44
Alignment explanation
Indices: 12573--13156 Score: 352
Period size: 44 Copynumber: 13.6 Consensus size: 44
12563 TATCACATCT
*
12573 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAATAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
*
12617 AGTCTTATCCTCCC-GAAGTTGCAGT-GAGGCAGACTGAAG-ATGGCA
1 AGTCTTAT-CTCCCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCA
* *
12662 AATCGTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* *
12706 AGTCTTATCCTCCCTGAAGTTGCAGTGGGGCAGACTGAAG-ATGGCA
1 AGTCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTA-AGCA
* **
12752 AGTCTTATCT--C--------CAGTGGAGCAGATTAAAG-CCGACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAG-CA
* * * ** * * *
12787 A-TCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAA--AATCTC
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-A
** * * * * *
12829 AGATCTTATCTTTCTGAAGTTGCAG-AGAGCAGA-T-TG-CATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
12870 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* *
12914 AGTCTTATC-CTCCTGAAGTGGCAGT-GAGGCAGACTGAAG-ATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCA
* * *
12959 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-CA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCA
* * * * * * *
13004 A-TCCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAA--AATCTC
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-A
* * * * * *
13046 AGATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T-CGT-ATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* * *
13087 AGTCTTATTTTCCTGAAGTTGCAGTGGAGCAGACTAAGGAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
*
13131 AATCTTATCTCCCTGAAGTTGCAGTG
1 AGTCTTATCTCCCTGAAGTTGCAGTG
13157 AAGTAGATTG
Statistics
Matches: 422, Mismatches: 71, Indels: 94
0.72 0.12 0.16
Matches are distributed among these distances:
34 8 0.02
35 18 0.04
36 1 0.00
40 40 0.09
41 20 0.05
42 12 0.03
43 24 0.06
44 175 0.41
45 104 0.25
46 19 0.05
47 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
Found at i:13041 original size:217 final size:208
Alignment explanation
Indices: 12667--13157 Score: 743
Period size: 217 Copynumber: 2.3 Consensus size: 208
12657 TGGCAAATCG
12667 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCCTGAAGTTGCAGT
* * *
12732 GGGGCAGACTGAAGATGGCAAGTCTTATCTCCAGTGGAGCAGATTAAAGCCGACAATCCTATCTC
66 GAGGCAGACTGAAGATGGCAAATCTTATCTCCAGTGGAGCAGATTAAAGCCAACAATCCTATCTC
* * * * *
12797 CCTAAAGTTGTAGTGGAGTGGATTAAAATCTCAGATCTTATCTTTCTGAAGTTGCAGAGAGCAGA
131 CCTAAAGTTGCAGTAGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGA
*
12862 TTGCATCTAGTCT
196 TCGCATCTAGTCT
*
12875 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCT-CCTGAAGTGGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCCTGAAGTTGCAGT
12939 GAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAACA
66 GAGGCAGACTGAAGATGGCAAATCTTATCT--C--------CAGTGGAGCAGATTAAAGCCAACA
13004 ATCCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTAC
121 ATCCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTAC
*
13069 AGAGAGCAGATCGTATCTAGTCT
186 AGAGAGCAGATCGCATCTAGTCT
* * * *
13092 TATTTTCCTGAAGTTGCAGTGGAGCAGACTAAGGAAGCAAATCTTAT-CTCCCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCCTGAAGTTGCAGT
13156 GA
66 GA
13158 AGTAGATTGA
Statistics
Matches: 256, Mismatches: 16, Indels: 13
0.90 0.06 0.05
Matches are distributed among these distances:
207 41 0.16
208 50 0.20
209 1 0.00
216 2 0.01
217 162 0.63
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (208 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCCTGAAGTTGCAGT
GAGGCAGACTGAAGATGGCAAATCTTATCTCCAGTGGAGCAGATTAAAGCCAACAATCCTATCTC
CCTAAAGTTGCAGTAGAGCGGATTAAAATCTCAGATCTTATCTCTCTGAAGTTACAGAGAGCAGA
TCGCATCTAGTCT
Done.