Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000580.1 Hibiscus syriacus cultivar Beakdansim tig00001132_pilon, whole genome shotgun sequence
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: 209095
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
File 2 of 2
Found at i:179228 original size:13 final size:13
Alignment explanation
Indices: 179210--179234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
179200 ATATAATATG
179210 TATTTTCAAAAAA
1 TATTTTCAAAAAA
179223 TATTTTCAAAAA
1 TATTTTCAAAAA
179235 CTATATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTTTCAAAAAA
Found at i:179771 original size:46 final size:46
Alignment explanation
Indices: 179704--179798 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
179694 AACTTAACTC
*
179704 GATAGGATCAATGTGGCAGATTCGAATGAAGATAATATGCTTCTCA
1 GATAGGATCAATGTAGCAGATTCGAATGAAGATAATATGCTTCTCA
*
179750 GATAGGATCAATGTATCAGATTCGAATGAAGATAATATGCTTCTCA
1 GATAGGATCAATGTAGCAGATTCGAATGAAGATAATATGCTTCTCA
179796 GAT
1 GAT
179799 CGGGTTAATC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (46 bp):
GATAGGATCAATGTAGCAGATTCGAATGAAGATAATATGCTTCTCA
Found at i:184461 original size:31 final size:31
Alignment explanation
Indices: 184425--184483 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
184415 AACTTAAAAG
* * *
184425 AGTTTTGCTATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
184456 AGTTTTACAATATTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
184484 CTATACAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:184533 original size:22 final size:22
Alignment explanation
Indices: 184508--184550 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
184498 TAATAAATTA
184508 TTTAAAATAAAACAATCCATAT
1 TTTAAAATAAAACAATCCATAT
* *
184530 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAAACAATCCATA
184551 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAAACAATCCATAT
Found at i:184567 original size:54 final size:54
Alignment explanation
Indices: 184498--184798 Score: 332
Period size: 54 Copynumber: 5.5 Consensus size: 54
184488 ACAACTAAAA
*
184498 TAATAAATTATTTAAAATAAAACAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
* *** * *
184552 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AAT-AAATCA-ATC
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATTCATA-C
184605 T-AT--A-T-TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAA-TCTATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATTC-ATAC
*
184664 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
*
184718 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
*
184772 AAATAAATTATTTAAAATAAATCAATC
1 TAATAAATTATTTAAAATAAATCAATC
184799 TATACTAATA
Statistics
Matches: 209, Mismatches: 17, Indels: 42
0.78 0.06 0.16
Matches are distributed among these distances:
48 16 0.08
49 2 0.01
50 1 0.00
52 3 0.01
53 7 0.03
54 131 0.63
55 8 0.04
56 2 0.01
57 5 0.02
58 7 0.03
59 5 0.02
60 3 0.01
62 1 0.00
63 2 0.01
64 16 0.08
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
Found at i:184649 original size:14 final size:14
Alignment explanation
Indices: 184632--184685 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
184622 CAATCCATAC
184632 AAATAAATTATTTA
1 AAATAAATTATTTA
*
184646 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
184663 CTAATAAATTATTTA
1 -AAATAAATTATTTA
184678 AAATAAAT
1 AAATAAAT
184686 CAATCTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:184754 original size:22 final size:22
Alignment explanation
Indices: 184728--184770 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
184718 TAATAAATTA
184728 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
184750 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
184771 CAAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:184779 original size:22 final size:22
Alignment explanation
Indices: 184730--184778 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
184720 ATAAATTATT
***
184730 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATAAAA
184752 TAAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATA-AAA
184775 TAAA
1 TAAA
184779 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATAAAA
Found at i:184789 original size:14 final size:14
Alignment explanation
Indices: 184772--184825 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
184762 CAATCCATAC
184772 AAATAAATTATTTA
1 AAATAAATTATTTA
*
184786 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
184803 CTAATAAATTATTTA
1 -AAATAAATTATTTA
184818 AAATAAAT
1 AAATAAAT
184826 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:184840 original size:22 final size:22
Alignment explanation
Indices: 184814--184858 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
184804 TAATAAATTA
184814 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
184836 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
184858 T
1 T
184859 AATAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:184840 original size:54 final size:54
Alignment explanation
Indices: 184782--185157 Score: 473
Period size: 54 Copynumber: 6.9 Consensus size: 54
184772 AAATAAATTA
184782 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
184836 TTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
184890 TTTAAAATAAATCAAT-TCATACTAATAAATTATTTAAAATAAATCAATCAATACA
1 TTTAAAATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCAATCCATA-T
** * * *
184945 ACTACAAT-AATAAATCAAT-C-AAT--A-T-TTTAAAATAAATCAATCCATACAAATAAATT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T
185001 ATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 -TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
185056 TTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAAT-CATAT
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
185109 TTTAAAGTAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATC
185158 TATACAACTA
Statistics
Matches: 278, Mismatches: 24, Indels: 40
0.81 0.07 0.12
Matches are distributed among these distances:
48 16 0.06
49 2 0.01
50 1 0.00
52 3 0.01
53 51 0.18
54 157 0.56
55 6 0.02
56 2 0.01
57 5 0.02
58 11 0.04
59 1 0.00
60 4 0.01
62 1 0.00
63 2 0.01
64 16 0.06
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:184862 original size:18 final size:20
Alignment explanation
Indices: 184812--184910 Score: 79
Period size: 22 Copynumber: 5.1 Consensus size: 20
184802 ACTAATAAAT
184812 TATTTAAAATAAATCAATCCA
1 TATTT-AAATAAATCAATCCA
184833 TATTTTAAAATAAATCAATCCA
1 TA-TTT-AAATAAATCAATCCA
184855 TA-TT-AATAAAT---T--A
1 TATTTAAATAAATCAATCCA
*
184868 T-TTAAAATAAATCAATCCA
1 TATTTAAATAAATCAATCCA
*
184887 TATTTTAAAATAAATCAATTCA
1 TA-TTT-AAATAAATCAATCCA
184909 TA
1 TA
184911 CTAATAAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
13 3 0.05
14 7 0.11
15 1 0.02
17 1 0.02
18 7 0.11
19 2 0.03
20 2 0.03
21 4 0.06
22 37 0.58
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (20 bp):
TATTTAAATAAATCAATCCA
Found at i:184865 original size:22 final size:22
Alignment explanation
Indices: 184812--184864 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
184802 ACTAATAAAT
184812 TATT-TAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
*
184833 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
184855 TATTAATAAA
1 TATT-ATAAA
184865 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCCA
Found at i:184919 original size:22 final size:22
Alignment explanation
Indices: 184870--184918 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
184860 ATAAATTATT
**
184870 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
184892 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
184915 TAAA
1 TAAA
184919 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:185006 original size:32 final size:32
Alignment explanation
Indices: 184970--185162 Score: 185
Period size: 32 Copynumber: 6.7 Consensus size: 32
184960 CAATCAATAT
*
184970 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
185002 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
185034 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
185056 TTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
185088 TTTAAAATAAATCAAT-CATA-T--T---TTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
185113 ---AAG-TAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
185141 TTTAAAATAAATCAATCTATAC
1 TTTAAAATAAATCAATCCATAC
185163 AACTACAATA
Statistics
Matches: 133, Mismatches: 7, Indels: 42
0.73 0.04 0.23
Matches are distributed among these distances:
21 9 0.07
22 21 0.16
23 3 0.02
24 1 0.01
25 4 0.03
26 2 0.02
28 7 0.05
30 2 0.02
31 7 0.05
32 77 0.58
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:185009 original size:14 final size:14
Alignment explanation
Indices: 184992--185045 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
184982 CAATCCATAC
184992 AAATAAATTATTTA
1 AAATAAATTATTTA
*
185006 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
185023 CTAATAAATTATTTA
1 -AAATAAATTATTTA
185038 AAATAAAT
1 AAATAAAT
185046 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:185060 original size:22 final size:22
Alignment explanation
Indices: 185034--185078 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
185024 TAATAAATTA
185034 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
185056 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
185078 T
1 T
185079 AATAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:185082 original size:18 final size:20
Alignment explanation
Indices: 185032--185125 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 20
185022 ACTAATAAAT
185032 TATTTAAAATAAATCAATCCA
1 TATTT-AAATAAATCAATCCA
185053 TATTTTAAAATAAATCAATCCA
1 TA-TTT-AAATAAATCAATCCA
185075 TA-TT-AATAAAT---T--A
1 TATTTAAATAAATCAATCCA
*
185088 T-TTAAAATAAATCAAT-CA
1 TATTTAAATAAATCAATCCA
185106 TATTTTAAAGTAAATCAATC
1 TA-TTTAAA-TAAATCAATC
185126 TATACTAATA
Statistics
Matches: 60, Mismatches: 2, Indels: 21
0.72 0.02 0.25
Matches are distributed among these distances:
13 3 0.05
14 7 0.12
15 1 0.02
17 1 0.02
18 9 0.15
20 7 0.12
21 11 0.18
22 21 0.35
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (20 bp):
TATTTAAATAAATCAATCCA
Found at i:185085 original size:22 final size:22
Alignment explanation
Indices: 185032--185084 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
185022 ACTAATAAAT
185032 TATT-TAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
*
185053 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
185075 TATTAATAAA
1 TATT-ATAAA
185085 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCCA
Found at i:185241 original size:15 final size:15
Alignment explanation
Indices: 185212--185344 Score: 169
Period size: 15 Copynumber: 8.5 Consensus size: 15
185202 AATTCATACT
185212 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
185226 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
185241 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
185263 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
185278 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
185293 AATAAATTATTTTAT
1 AATAAATTATTTTAA
185308 AATAAATTATTTTAA
1 AATAAATTATTTTAA
185323 AATAAATTATTTTAA
1 AATAAATTATTTTAA
185338 AATAAAT
1 AATAAAT
185345 AACCTTATTA
Statistics
Matches: 107, Mismatches: 4, Indels: 15
0.85 0.03 0.12
Matches are distributed among these distances:
14 9 0.08
15 80 0.75
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
22 10 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:185289 original size:30 final size:30
Alignment explanation
Indices: 185255--185387 Score: 162
Period size: 30 Copynumber: 4.4 Consensus size: 30
185245 AATCAATCCA
185255 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
*
185285 TATTTTATAATAAATTATTTTATAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
*
185315 TATTTTAAAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
* ** *
185345 AACCTTAT--TAAATTATTTTTAATAAATAACTT
1 TATTTTATAATAAATTA-TTTT-A-AAATAA-AT
185377 TATTTTATAAT
1 TATTTTATAAT
185388 TATTCTTGAA
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
28 7 0.08
29 4 0.05
30 62 0.72
31 6 0.07
32 6 0.07
34 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
TATTTTATAATAAATTATTTTAAAATAAAT
Found at i:185319 original size:45 final size:45
Alignment explanation
Indices: 185255--185387 Score: 171
Period size: 45 Copynumber: 2.9 Consensus size: 45
185245 AATCAATCCA
185255 TATTTTATAATAAATTATTTTAAAATAAATTATTTTATAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAATTATTTTATAATAAAT
*
185300 TATTTTATAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAATTATTTTATAATAAAT
* ** *
185345 AACCTTAT--TAAATTATTTTTAATAAATAACTTTATTTTATAAT
1 TATTTTATAATAAATTA-TTTT-A-AAATAA-ATTATTTTATAAT
185388 TATTCTTGAA
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
43 7 0.09
44 4 0.05
45 50 0.64
46 6 0.08
47 11 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.50
Consensus pattern (45 bp):
TATTTTATAATAAATTATTTTAAAATAAATTATTTTATAATAAAT
Found at i:186914 original size:14 final size:14
Alignment explanation
Indices: 186879--186929 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
186869 TAAAAAATTA
186879 ATAATTTT-AATA-
1 ATAATTTTAAATAT
186891 ATAATTTTAAATAT
1 ATAATTTTAAATAT
*
186905 ATATTTTTAAATAT
1 ATAATTTTAAATAT
186919 -TAATTTATAAA
1 ATAATTT-TAAA
186930 CATTTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 8 0.24
13 9 0.26
14 17 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATAATTTTAAATAT
Found at i:187447 original size:31 final size:30
Alignment explanation
Indices: 187411--187481 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
187401 ATATAATTAA
*
187411 AAATTAAAATAATATGAAAGTTAAAGTCATT
1 AAATTAAAATAATATGAAAGTT-AAGTAATT
* *
187442 AAATTATGAATAATTTGAAAGTTAAGTAATT
1 AAATTA-AAATAATATGAAAGTTAAGTAATT
187473 AAATTAAAA
1 AAATTAAAA
187482 AATTAAACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.06
31 19 0.54
32 14 0.40
ACGTcount: A:0.55, C:0.01, G:0.10, T:0.34
Consensus pattern (30 bp):
AAATTAAAATAATATGAAAGTTAAGTAATT
Found at i:187455 original size:32 final size:31
Alignment explanation
Indices: 187418--187478 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
187408 TAAAAATTAA
*
187418 AATAATATGAAAGTTAAAGTCATTAAATTATG
1 AATAATATGAAAGTT-AAGTAATTAAATTATG
*
187450 AATAATTTGAAAGTTAAGTAATTAAATTA
1 AATAATATGAAAGTTAAGTAATTAAATTA
187479 AAAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (31 bp):
AATAATATGAAAGTTAAGTAATTAAATTATG
Found at i:202273 original size:2 final size:2
Alignment explanation
Indices: 202266--202293 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
202256 CTATGATCTT
202266 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
202294 AATGGCAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.