Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2531.1
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: 231018
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 7437 characters in sequence are not A, C, G, or T
Found at i:6095 original size:4 final size:4
Alignment explanation
Indices: 6086--6114 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
6076 AGCAAACGTG
6086 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
6115 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:10003 original size:11 final size:11
Alignment explanation
Indices: 9989--10029 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
9979 TATTTTCTCT
9989 CTATTTTGCTA
1 CTATTTTGCTA
10000 CTATTTTGCTA
1 CTATTTTGCTA
* *
10011 TTATGTTGCTA
1 CTATTTTGCTA
10022 CTATTTTG
1 CTATTTTG
10030 TTGTTATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:10078 original size:11 final size:11
Alignment explanation
Indices: 10058--10087 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
10048 TGTATAAAAC
10058 TTATTTTTTTA
1 TTATTTTTTTA
10069 TTAATTTTTTTA
1 TT-ATTTTTTTA
10081 TTATTTT
1 TTATTTT
10088 AAAGACATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTTTTA
Found at i:10106 original size:30 final size:30
Alignment explanation
Indices: 10070--10130 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
10060 ATTTTTTTAT
*
10070 TAATTTTTTTATTATTTTAAAGACATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
* *
10100 TAATTTTGTTATTATTTTAGAGGCATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
10130 T
1 T
10131 TGTTAAGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGACATTTGC
Found at i:10282 original size:12 final size:12
Alignment explanation
Indices: 10252--10284 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
10242 TACATATTTT
10252 AAAATT-ATATA
1 AAAATTAATATA
10263 AAAA-TAATATA
1 AAAATTAATATA
10274 AAAATTAATAT
1 AAAATTAATAT
10285 GGGCAGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:12249 original size:17 final size:19
Alignment explanation
Indices: 12223--12275 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
12213 TTTTACTTTT
12223 ATAATTTTT-TAAATTATTA
1 ATAATTTTTAT-AATTATTA
*
12242 ATAATTTTTAGTTATTATTA
1 ATAATTTTTA-TAATTATTA
12262 ATAA-TTTTATAATT
1 ATAATTTTTATAATT
12276 TCTAATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 4 0.13
19 14 0.47
20 11 0.37
21 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATAATTTTTATAATTATTA
Found at i:12892 original size:57 final size:58
Alignment explanation
Indices: 12781--12913 Score: 196
Period size: 57 Copynumber: 2.3 Consensus size: 58
12771 AAATTATATT
* * * *
12781 AATAGCCACTCAACTATTAGTAGATTTTTTTTTGTCATCCAACTATGAAAAGTTATAA
1 AATAGTCACTCAACTATTAGTAGATTTTTTTTGGTCACCCAACTATAAAAAGTTATAA
* *
12839 AATGGTCACTCAACTATTAGTA-ATTTTTTTTGGTCACCCAACTCTAAAAAGTTATAA
1 AATAGTCACTCAACTATTAGTAGATTTTTTTTGGTCACCCAACTATAAAAAGTTATAA
*
12896 AATAGTCACCCAACTATT
1 AATAGTCACTCAACTATT
12914 CAATTTTATC
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
57 47 0.70
58 20 0.30
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (58 bp):
AATAGTCACTCAACTATTAGTAGATTTTTTTTGGTCACCCAACTATAAAAAGTTATAA
Found at i:13945 original size:19 final size:18
Alignment explanation
Indices: 13919--13956 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13909 AAAAAAATAT
**
13919 TTTTAAAAAACCTTAAAA
1 TTTTAAAAAAAATTAAAA
13937 TTTTAAAAAAAATTAAAA
1 TTTTAAAAAAAATTAAAA
13955 TT
1 TT
13957 ATTTTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTTAAAAAAAATTAAAA
Found at i:20548 original size:50 final size:50
Alignment explanation
Indices: 20473--20654 Score: 240
Period size: 55 Copynumber: 3.5 Consensus size: 50
20463 CCATGGCAAC
20473 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGAAAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGAAAAGTGA
*
20523 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTTATCTGATCAAGGGAAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCT--AC--A-CTTATCTGATCAAGGAAAAGTGA
* *
20578 AAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAATGACAAA-TGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTGA
* * *
20628 CAAGTGAAAAGTGGTAACTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
20655 CTGATCAGTG
Statistics
Matches: 117, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
50 41 0.35
51 26 0.22
52 2 0.02
53 1 0.01
54 1 0.01
55 46 0.39
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGAAAAGTGA
Found at i:20668 original size:31 final size:31
Alignment explanation
Indices: 20630--20901 Score: 476
Period size: 31 Copynumber: 8.8 Consensus size: 31
20620 ACAAATGACA
* *
20630 AGTGAAAAGTGGTAACTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
20661 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
20692 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
20723 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
20754 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
20785 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
20816 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
20847 AGTGAAAAGTGGTAG-TACCGGCTACCTGATT
1 AGTGAAAAGTGGTAGCT-CCGGCTACCTGATC
* *
20878 A-TGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
20902 AAGTGACAAG
Statistics
Matches: 234, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
30 20 0.09
31 214 0.91
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:21037 original size:46 final size:47
Alignment explanation
Indices: 20924--21042 Score: 150
Period size: 47 Copynumber: 2.6 Consensus size: 47
20914 ATTTTCGTAC
* * * *
20924 AAGACCATATCTGGGATATGTCATCGGTGTGATATATGCTACTGTAT
1 AAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACTGTAT
* * *
20971 AAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATTC-GTGT
1 AAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACTGTAT
* *
21017 AAGACCATAGCTGGGCTATGGCATCA
1 AAGACCATATCTGGGATATGGCATCA
21043 TTATGTGAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
46 27 0.43
47 36 0.57
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (47 bp):
AAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACTGTAT
Found at i:24964 original size:24 final size:25
Alignment explanation
Indices: 24936--24987 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
24926 ATAAGTTTTG
24936 TATAATT-TATGAATA-TTAATATTA
1 TATAATTATAT-AATATTTAATATTA
*
24960 TATAATTATATAATATTTAATTTTA
1 TATAATTATATAATATTTAATATTA
24985 TAT
1 TAT
24988 TTTAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TATAATTATATAATATTTAATATTA
Found at i:24985 original size:25 final size:24
Alignment explanation
Indices: 24931--24987 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
24921 AAATGATAAG
*
24931 TTTTGTATAATTTATGAATATTAA
1 TTTTATATAATTTATGAATATTAA
*
24955 TATTATATAATTATAT-AATATTTAA
1 TTTTATATAATT-TATGAATA-TTAA
24980 TTTTATAT
1 TTTTATAT
24988 TTTAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTTATATAATTTATGAATATTAA
Found at i:28444 original size:53 final size:53
Alignment explanation
Indices: 28381--28483 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 53
28371 AGAATACTTC
* *
28381 GGGGTGGTAGATATGAGAATACTTAATTTCAATAGGAAGCTCGGTTGGATATT
1 GGGGTGGTAGATATGAGAATACTTAATTCCAATAGGAAGCTCGGCTGGATATT
*
28434 GGGGTGGTAGATATGAGAATACTTAGTTCCAATAGGAAGCTCGGCTGGAT
1 GGGGTGGTAGATATGAGAATACTTAATTCCAATAGGAAGCTCGGCTGGAT
28484 TAGGCATAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.29
Consensus pattern (53 bp):
GGGGTGGTAGATATGAGAATACTTAATTCCAATAGGAAGCTCGGCTGGATATT
Found at i:38774 original size:50 final size:51
Alignment explanation
Indices: 38697--38825 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
38687 GACCATAGCA
* *
38697 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
*
38748 A-AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
38798 ACAAGTGAAAAGTGGTAGTTTCGGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
38826 CTGATCAGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 47 0.67
51 23 0.33
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:38839 original size:31 final size:31
Alignment explanation
Indices: 38801--38949 Score: 192
Period size: 31 Copynumber: 4.8 Consensus size: 31
38791 ACAAATGACA
*
38801 AGTGAAAAGTGGTAGTTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
38832 AGTGAAAAGTGGTAGCTTCTGCTACCTGATT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
38863 AGTGAAAAATGGTAGCTCCGACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
38894 AGTGAAAAATGGTAGC-TCTAGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTC-GGCTACCTGATC
*
38925 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
38950 AAGTGACAAG
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
30 1 0.01
31 98 0.97
32 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:39053 original size:47 final size:46
Alignment explanation
Indices: 38967--39089 Score: 131
Period size: 47 Copynumber: 2.7 Consensus size: 46
38957 AAGTGATTTC
* *
38967 CGTATAAGACCATATCTGGGATATGGCATCGGTATGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTATGATATATGATA
* * * *
39013 CTGTATAAGACCATATCTGGGATATGGTATCATTGA-GATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGT-ATGATATATGATA
* * * *
39060 CGTGTAAGACCATAGCTGGGCTATGACATC
1 CGTATAAGACCATATCTGGGATATGGCATC
39090 GATAAATGAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
46 25 0.39
47 38 0.59
48 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTATGATATATGATA
Found at i:39126 original size:42 final size:43
Alignment explanation
Indices: 39061--39143 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 43
39051 TATGTGATTC
** *
39061 GTGTAAGACCATAGCTGGGCTATGACATCGA-TAAATGAAGAT
1 GTGTAAGACCATAGCTGAACTATGACATCGAGTAAACGAAGAT
* *
39103 GTGTAAGACCATTGTTGAACTATGACATCGAGTAAACGAAG
1 GTGTAAGACCATAGCTGAACTATGACATCGAGTAAACGAAG
39144 TACTCAATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 27 0.77
43 8 0.23
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.24
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGAACTATGACATCGAGTAAACGAAGAT
Found at i:41888 original size:29 final size:26
Alignment explanation
Indices: 41810--41889 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 26
41800 TAAATGAAAT
41810 AGTTTAAAATAAATAATATATAAAAG
1 AGTTTAAAATAAATAATATATAAAAG
* *
41836 AGTTTAAAATAAATAACATGTAAAAG
1 AGTTTAAAATAAATAATATATAAAAG
* *
41862 AGAAATTTGAAATAAATAATGTATAAAA
1 AG---TTTAAAATAAATAATATATAAAA
41890 ACCGTTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 26 0.58
29 19 0.42
ACGTcount: A:0.60, C:0.01, G:0.10, T:0.29
Consensus pattern (26 bp):
AGTTTAAAATAAATAATATATAAAAG
Found at i:41975 original size:25 final size:24
Alignment explanation
Indices: 41947--42041 Score: 68
Period size: 25 Copynumber: 3.8 Consensus size: 24
41937 AAAATAAATA
41947 ATATATAAAAGTTTAAAATAATAAG
1 ATATATAAAA-TTTAAAATAATAAG
41972 ATATATAGATAATTTCAAAATAAGTAAG
1 ATATATA-A-AATTT-AAAATAA-TAAG
* * * *
42000 GTA-A-AATAGTTTGAAATAAATAAT
1 ATATATAA-AATTTAAAAT-AATAAG
*
42024 ATATGTAAAATTTAAAAT
1 ATATATAAAATTTAAAAT
42042 GAATGATAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
24 9 0.16
25 23 0.42
26 7 0.13
27 10 0.18
28 6 0.11
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.34
Consensus pattern (24 bp):
ATATATAAAATTTAAAATAATAAG
Found at i:42257 original size:17 final size:18
Alignment explanation
Indices: 42235--42271 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
42225 GATTAGGGAT
42235 TAAATTGGAA-CAAAAAC
1 TAAATTGGAAGCAAAAAC
*
42252 TAAATTTGAAGCAAAAAC
1 TAAATTGGAAGCAAAAAC
42270 TA
1 TA
42272 CAACAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.22
Consensus pattern (18 bp):
TAAATTGGAAGCAAAAAC
Found at i:44526 original size:17 final size:18
Alignment explanation
Indices: 44493--44537 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
44483 AAAGTTAATT
44493 AATTCAAATTAATTTTTCC
1 AATT-AAATTAATTTTTCC
*
44512 AATTAAATT-ATTTTTTC
1 AATTAAATTAATTTTTCC
*
44529 AATCAAATT
1 AATTAAATT
44538 CTAATTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
18 5 0.21
19 4 0.17
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTAAATTAATTTTTCC
Found at i:50835 original size:30 final size:30
Alignment explanation
Indices: 50801--50858 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
50791 ATAAATTTAT
50801 TTAAAAATTACTAAGAATT-ATAAAAAAATG
1 TTAAAAATTACTAA-AATTAATAAAAAAATG
*
50831 TTAAAAATTATTAAAATTAATAAAAAAA
1 TTAAAAATTACTAAAATTAATAAAAAAA
50859 GTCTAGAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (30 bp):
TTAAAAATTACTAAAATTAATAAAAAAATG
Found at i:50844 original size:10 final size:10
Alignment explanation
Indices: 50801--50856 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
50791 ATAAATTTAT
50801 TTAAAAATTA
1 TTAAAAATTA
* *
50811 CTAAGAATTA
1 TTAAAAATTA
* * *
50821 TAAAAAAATG
1 TTAAAAATTA
50831 TTAAAAATTA
1 TTAAAAATTA
50841 TT-AAAATTA
1 TTAAAAATTA
*
50850 ATAAAAA
1 TTAAAAA
50857 AAGTCTAGAA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
9 8 0.24
10 26 0.76
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:56855 original size:5 final size:5
Alignment explanation
Indices: 56845--56869 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
56835 CCCCCCAAAA
56845 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
56870 GTATAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:69361 original size:17 final size:17
Alignment explanation
Indices: 69331--69378 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
69321 TTATAGCTTT
69331 AGAAAATTTGAATTAAG
1 AGAAAATTTGAATTAAG
* * *
69348 AGAAATTTTTAATTAAAA
1 AGAAAATTTGAATT-AAG
69366 AGAAAGATTTGAA
1 AGAAA-ATTTGAA
69379 CTCTCTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 12 0.50
18 7 0.29
19 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (17 bp):
AGAAAATTTGAATTAAG
Found at i:76487 original size:13 final size:13
Alignment explanation
Indices: 76469--76504 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
76459 GATAATTATC
76469 AAATCATACATAT
1 AAATCATACATAT
*
76482 AAATCATATATAT
1 AAATCATACATAT
76495 AAATTCATAC
1 AAA-TCATAC
76505 CAAACTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATCATACATAT
Found at i:77888 original size:5 final size:5
Alignment explanation
Indices: 77878--77904 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
77868 AATTTCTCAT
77878 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
77905 CTTTCTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:101670 original size:25 final size:25
Alignment explanation
Indices: 101640--101688 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
101630 CTAAATATTT
101640 ATTTTAATAT-AATATTTATATTTTA
1 ATTTTAATATGAATATTT-TATTTTA
* *
101665 ATTTTATTATGCATATTTTATTTT
1 ATTTTAATATGAATATTTTATTTT
101689 TTCATCAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
ATTTTAATATGAATATTTTATTTTA
Found at i:102082 original size:91 final size:91
Alignment explanation
Indices: 101913--102089 Score: 225
Period size: 91 Copynumber: 1.9 Consensus size: 91
101903 TTCAAATGAC
** * * *
101913 CTGCTTCATTGTTTATTATATGTTTTTTAAAATTAACATATGTGTTCTAAGTACATAACTTCTAC
1 CTGCTTCATCATTTATCATATGTTTTTTAAAATTAACATACGTGTTCTAAATACATAACTTCTAC
**
101978 ATACATATGCATGTGATGAAAAATAAT
66 ATACATACACATGTGAT-AAAAATAAT
*
102005 CTGCTTCATCATTTATCATATGTTATTTTAAAATTAA-A-ACGTG-TCTTAAATACATAATTTCT
1 CTGCTTCATCATTTATCATATGTT-TTTTAAAATTAACATACGTGTTC-TAAATACATAACTTCT
*
102067 ACGTACATACACATGTGATAAAA
64 ACATACATACACATGTGATAAAA
102090 TTTATAATAT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
90 6 0.08
91 34 0.46
92 22 0.30
93 12 0.16
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (91 bp):
CTGCTTCATCATTTATCATATGTTTTTTAAAATTAACATACGTGTTCTAAATACATAACTTCTAC
ATACATACACATGTGATAAAAATAAT
Found at i:118823 original size:16 final size:18
Alignment explanation
Indices: 118785--118826 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
118775 TTTCATGTTT
118785 GTATTTTTCGAAATTTAA
1 GTATTTTTCGAAATTTAA
118803 GTATTTTT-G-AATTTGAA
1 GTATTTTTCGAAATTT-AA
118820 -TATTTTT
1 GTATTTTT
118827 AGATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 12 0.52
17 3 0.13
18 8 0.35
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (18 bp):
GTATTTTTCGAAATTTAA
Found at i:128640 original size:3 final size:3
Alignment explanation
Indices: 128632--128676 Score: 54
Period size: 3 Copynumber: 13.7 Consensus size: 3
128622 TGGAATATCC
128632 AAT AAT AAT AAT AAAT AAT AAAT AAT AAAT AAT AAAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT -AAT AAT -AAT AAT -AAT AAT AAT AA
128677 AGTAATACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 26 0.68
4 12 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:128648 original size:7 final size:7
Alignment explanation
Indices: 128632--128673 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
128622 TGGAATATCC
128632 AATAAT-
1 AATAATA
128638 AATAATA
1 AATAATA
128645 AATAATA
1 AATAATA
128652 AATAATA
1 AATAATA
128659 AATAATA
1 AATAATA
128666 AATAATA
1 AATAATA
128673 A
1 A
128674 TAAAGTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAATA
Found at i:138306 original size:9 final size:9
Alignment explanation
Indices: 138286--138329 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
138276 TGAAAAAAGG
138286 GAAAAA-AA
1 GAAAAAGAA
138294 -AAAAAGAA
1 GAAAAAGAA
138302 GAAAAAGAA
1 GAAAAAGAA
*
138311 GAAGAAGAA
1 GAAAAAGAA
138320 GAAGAAAGAA
1 GAA-AAAGAA
138330 TGCGTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 5 0.16
8 2 0.06
9 19 0.61
10 5 0.16
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
GAAAAAGAA
Found at i:141504 original size:16 final size:16
Alignment explanation
Indices: 141483--141537 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
141473 GTTTGGTTCA
*
141483 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
141499 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
141515 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
141531 CTGTAAT
1 CTGTAAT
141538 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:152563 original size:17 final size:17
Alignment explanation
Indices: 152543--152576 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
152533 ATTTATTTAT
152543 TAAAATAA-TTTTATAAA
1 TAAAATAAGTTTT-TAAA
152560 TAAAATAAGTTTTTAAA
1 TAAAATAAGTTTTTAAA
152577 AAACCCACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAAATAAGTTTTTAAA
Found at i:154527 original size:29 final size:29
Alignment explanation
Indices: 154462--154550 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 29
154452 ATCTCAAAAC
*
154462 TATACATAAATTATGATTTAATGTATAATTT
1 TATACATAAATTTTGATTTAAT-T-TAATTT
* *
154493 TATACATAAATTTTAATTTTATTTAATTT
1 TATACATAAATTTTGATTTAATTTAATTT
* *
154522 TATACACGAAATTTTGATTTAATTAAATT
1 TATACA-TAAATTTTGATTTAATTTAATT
154551 AAGGAGAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 12 0.24
30 19 0.38
31 19 0.38
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (29 bp):
TATACATAAATTTTGATTTAATTTAATTT
Found at i:154597 original size:21 final size:21
Alignment explanation
Indices: 154554--154598 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
154544 TTAAATTAAG
* *
154554 GAGAAATGAAAAATGGAGGAA
1 GAGAAATGAAAAATGAAGAAA
154575 GAGAAAT-AAAAATTGAAGAAA
1 GAGAAATGAAAAA-TGAAGAAA
154596 GAG
1 GAG
154599 GAAGAAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (21 bp):
GAGAAATGAAAAATGAAGAAA
Found at i:166066 original size:21 final size:21
Alignment explanation
Indices: 166040--166095 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
166030 AACAGCGGTG
*
166040 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
166061 GCGGTGAGATTGGATATTGTA
1 GCGGTGAGATTAGATACTGTA
166082 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
166096 AACAGCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:169495 original size:12 final size:13
Alignment explanation
Indices: 169476--169501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
169466 GATTGAGTAC
169476 CAAAAAAATTAAG
1 CAAAAAAATTAAG
169489 CAAAAAAATTAAG
1 CAAAAAAATTAAG
169502 GGTTCATTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
CAAAAAAATTAAG
Found at i:169841 original size:12 final size:12
Alignment explanation
Indices: 169824--169855 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
169814 CTTGGAACCG
169824 CCGATTTTTTTA
1 CCGATTTTTTTA
169836 CCGATTTTTTTA
1 CCGATTTTTTTA
*
169848 CCAATTTT
1 CCGATTTT
169856 AGTGAGAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (12 bp):
CCGATTTTTTTA
Found at i:170133 original size:12 final size:12
Alignment explanation
Indices: 170116--170142 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
170106 GCAACCCAAG
170116 GGGAAGGGGAAA
1 GGGAAGGGGAAA
170128 GGGAAGGGGAAA
1 GGGAAGGGGAAA
170140 GGG
1 GGG
170143 GAGAAGAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (12 bp):
GGGAAGGGGAAA
Found at i:177989 original size:20 final size:18
Alignment explanation
Indices: 177955--177991 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
177945 GCAACTCATA
177955 ATTTCAACTATTTTACAC
1 ATTTCAACTATTTTACAC
177973 ATTTACAACTCATTTTACA
1 ATTT-CAACT-ATTTTACA
177992 ACTTAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTCAACTATTTTACAC
Found at i:180839 original size:46 final size:45
Alignment explanation
Indices: 180772--181024 Score: 180
Period size: 46 Copynumber: 5.5 Consensus size: 45
180762 TCCATCTGTG
* * *
180772 TGTCCCAAACAGGTCTTACACTGA-CACATGTAACCGTGCCGATGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATCT--CCGTGCCGATGCA
* *
180818 TGTCCCAGACATGTCTTACACT-AGCACATCT-CGTAGCCAACGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATCTCCGT-GCCGATGCA
* * *
180862 TGTCCCAGACATGTCTGACATTG-GCTAACATCT-CGAGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTGAGC--ACATCTCCG-TGCCGATGCA
* * *
180908 TGTCCCAGACATGTCTTACACTGGATCTCATACT--GTGGCTGATGCA
1 TGTCCCAGACATGTCTTACACT-GAGCACAT-CTCCGT-GCCGATGCA
* * * **
180954 TGTCCCAAACATGTCTTACACT-AGCCCTTGTCTCAATGCCGATGCCA
1 TGTCCCAGACATGTCTTACACTGAGCAC--ATCTCCGTGCCGATG-CA
*
181001 TGTCCCATACATGGTCTTACACTG
1 TGTCCCAGACAT-GTCTTACACTG
181025 GCATACAAAT
Statistics
Matches: 167, Mismatches: 23, Indels: 31
0.76 0.10 0.14
Matches are distributed among these distances:
43 3 0.02
44 32 0.19
45 3 0.02
46 101 0.60
47 17 0.10
48 11 0.07
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (45 bp):
TGTCCCAGACATGTCTTACACTGAGCACATCTCCGTGCCGATGCA
Found at i:183431 original size:46 final size:46
Alignment explanation
Indices: 183361--183510 Score: 164
Period size: 46 Copynumber: 3.3 Consensus size: 46
183351 NNNNNNNNNN
* * *
183361 ACATGTCTTACACTAGC--ACATCTCGTAGCCGACGCATGTCCCAG
1 ACATGTCTGACACTGGCTAACATCTCGTAGCCGATGCATGTCCCAG
*
183405 ACATGTCTGACATTGGCTAACATCTCG-AGGCCGATGCATGTCCCAG
1 ACATGTCTGACACTGGCTAACATCTCGTA-GCCGATGCATGTCCCAG
* ** * *
183451 ACATGTCTTACACTGGCTCTCATACT-GTGGCTGATGCATGTCCCAG
1 ACATGTCTGACACTGGCTAACAT-CTCGTAGCCGATGCATGTCCCAG
*
183497 ACATGTCTTACACT
1 ACATGTCTGACACT
183511 AGCCCTCGTC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
44 14 0.15
45 1 0.01
46 74 0.81
47 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (46 bp):
ACATGTCTGACACTGGCTAACATCTCGTAGCCGATGCATGTCCCAG
Found at i:183533 original size:46 final size:46
Alignment explanation
Indices: 183437--183558 Score: 131
Period size: 46 Copynumber: 2.6 Consensus size: 46
183427 TCTCGAGGCC
* * * *
183437 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATACTGTGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCCCTCATACTATGGCA
*
183483 GATGCATGTCCCAGACATGTCTTACACTAGCCCTCGT-CTCAAT-GCA
1 GATGCATGTCCCAGACATGTCTTACACTAGCCCTCATACT--ATGGCA
* *
183529 GATGCCATGTCTCATACATGGTCTTACACT
1 GATG-CATGTCCCAGACAT-GTCTTACACT
183559 GGCACACAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
45 2 0.03
46 40 0.62
47 13 0.20
48 10 0.15
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCCCTCATACTATGGCA
Found at i:186847 original size:279 final size:280
Alignment explanation
Indices: 186346--186903 Score: 1055
Period size: 279 Copynumber: 2.0 Consensus size: 280
186336 GTTCAAACGG
186346 GATTTTTCCCCGTCTATTAAGGCTTTGTCTTATCATATTTCTATTAATCACATACACATTAATAT
1 GATTTTTCCCCGTCTATTAAGGCTTTGTCTTATCATATTTCTATTAATCACATACACATTAATAT
* *
186411 CTGTACAATTCATGTAATGATAACATTTAAATACATGTATAGCATGGTATTGTTTACATACGAAC
66 CTCTACAATTCATGTAATGATAACAATTAAATACATGTATAGCATGGTATTGTTTACATACGAAC
186476 TTACCTCGATACCACAAAGGTGAAAAGGACATACTCGTCCATAAATCGATTTCTTTCCGTTCTAG
131 TTACCTCGATACCACAAAGGTGAAAAGGACATACTCGTCCATAAATCGATTTCTTTCCGTTCTAG
186541 GTCCAAGTCTCAATTTTCATCATCTATAACATCACATTTAGCCTACCAATCAGTCACAATATTCA
196 GTCCAAGTCTCAATTTTCATCATCTATAACATCACATTTAGCCTACCAATCAGTCACAATATTCA
186606 TATGGGTCTAAAAATCATAA
261 TATGGGTCTAAAAATCATAA
* *
186626 GATTTTTCCTCGTCTATTAAGGCTTTGTCTTATCATATTTCTATTAATCACATACA-TTTAATAT
1 GATTTTTCCCCGTCTATTAAGGCTTTGTCTTATCATATTTCTATTAATCACATACACATTAATAT
* *
186690 TTCTACAATTCATGTAATGATAACAATTAAATACTTGTATAGCATGGTATTGTTTACATACGAAC
66 CTCTACAATTCATGTAATGATAACAATTAAATACATGTATAGCATGGTATTGTTTACATACGAAC
186755 TTACCTCGATACCACAAAGGTGAAAAGGACATACTCGTCCATAAATCGATTTCTTTCCGTTCTAG
131 TTACCTCGATACCACAAAGGTGAAAAGGACATACTCGTCCATAAATCGATTTCTTTCCGTTCTAG
186820 GTCCAAGTCTCAATTTTCATCATCTATAACATCACATTTAGCCTACCAATCAGTCACAATATTCA
196 GTCCAAGTCTCAATTTTCATCATCTATAACATCACATTTAGCCTACCAATCAGTCACAATATTCA
186885 TATGGGTCTAAAAATCATA
261 TATGGGTCTAAAAATCATA
186904 TCTTTTCCAG
Statistics
Matches: 272, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
279 217 0.80
280 55 0.20
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (280 bp):
GATTTTTCCCCGTCTATTAAGGCTTTGTCTTATCATATTTCTATTAATCACATACACATTAATAT
CTCTACAATTCATGTAATGATAACAATTAAATACATGTATAGCATGGTATTGTTTACATACGAAC
TTACCTCGATACCACAAAGGTGAAAAGGACATACTCGTCCATAAATCGATTTCTTTCCGTTCTAG
GTCCAAGTCTCAATTTTCATCATCTATAACATCACATTTAGCCTACCAATCAGTCACAATATTCA
TATGGGTCTAAAAATCATAA
Found at i:188217 original size:11 final size:12
Alignment explanation
Indices: 188203--188239 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
188193 AGAAAAAAAA
188203 AAGAGAG-AGGG
1 AAGAGAGAAGGG
188214 AAGAGAGAAGGG
1 AAGAGAGAAGGG
188226 -AGAGAGAAGGG
1 AAGAGAGAAGGG
188237 AAG
1 AAG
188240 GGGAAAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
AAGAGAGAAGGG
Found at i:188369 original size:13 final size:13
Alignment explanation
Indices: 188322--188373 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
188312 CCGCGTAATT
* *
188322 TTTTTTTAATATT
1 TTTTTTTATTATA
*
188335 TTTTTTTGTATATA
1 TTTTTTTAT-TATA
*
188349 TATTTTTATTATA
1 TTTTTTTATTATA
188362 TTTTTTTATTAT
1 TTTTTTTATTAT
188374 GATGTATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 22 0.69
14 10 0.31
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTTTTATTATA
Found at i:188435 original size:17 final size:17
Alignment explanation
Indices: 188415--188453 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
188405 AAATAAAATA
*
188415 AAAATAA-AAATAAGAGT
1 AAAATAATAAAGAAGA-T
188432 AAAATAATAAAGAAGAT
1 AAAATAATAAAGAAGAT
188449 AAAAT
1 AAAAT
188454 CATCTTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAATAATAAAGAAGAT
Found at i:188760 original size:17 final size:16
Alignment explanation
Indices: 188738--188784 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
188728 AAGGGTTCTT
188738 GGTTTTTTTAGGGGTTA
1 GGTTTTTTT-GGGGTTA
*
188755 GGTTTTTTTTTGGGTTA
1 GG-TTTTTTTGGGGTTA
188772 GGTTTTTTTGGGG
1 GGTTTTTTTGGGG
188785 GGCTTAATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 10 0.37
17 10 0.37
18 7 0.26
ACGTcount: A:0.06, C:0.00, G:0.36, T:0.57
Consensus pattern (16 bp):
GGTTTTTTTGGGGTTA
Found at i:188762 original size:16 final size:17
Alignment explanation
Indices: 188738--188784 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
188728 AAGGGTTCTT
*
188738 GGTTTTTTTAGGGGTTA
1 GGTTTTTTTTGGGGTTA
*
188755 GGTTTTTTTTTGGGTTA
1 GGTTTTTTTTGGGGTTA
188772 GG-TTTTTTTGGGG
1 GGTTTTTTTTGGGG
188785 GGCTTAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.06, C:0.00, G:0.36, T:0.57
Consensus pattern (17 bp):
GGTTTTTTTTGGGGTTA
Found at i:189171 original size:11 final size:11
Alignment explanation
Indices: 189155--189184 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
189145 TTTTCTATTA
189155 TATTTTGTTTC
1 TATTTTGTTTC
189166 TATTTTGTTTC
1 TATTTTGTTTC
189177 TATTTTGT
1 TATTTTGT
189185 AAGTGAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (11 bp):
TATTTTGTTTC
Found at i:190759 original size:16 final size:16
Alignment explanation
Indices: 190738--190791 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
190728 ATTAATCAGC
190738 TAAAAATTATAAAAAT
1 TAAAAATTATAAAAAT
* *
190754 TAAAAAATCAT-AAACT
1 T-AAAAATTATAAAAAT
*
190770 T-AAAATTATAAAAAA
1 TAAAAATTATAAAAAT
190785 TAAAAAT
1 TAAAAAT
190792 AAAATATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 11 0.37
17 8 0.27
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAAAATTATAAAAAT
Found at i:191059 original size:18 final size:18
Alignment explanation
Indices: 191036--191073 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
191026 AAAGAATACC
191036 AAAAAATATAATTTATAA
1 AAAAAATATAATTTATAA
191054 AAAAAATATAATTTATAA
1 AAAAAATATAATTTATAA
191072 AA
1 AA
191074 TCATAACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAAATATAATTTATAA
Found at i:196141 original size:18 final size:20
Alignment explanation
Indices: 196099--196135 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
196089 ATATTTTATG
*
196099 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
196118 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
196136 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:201113 original size:20 final size:18
Alignment explanation
Indices: 201088--201124 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
201078 ATTGCTAAGT
201088 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
201108 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
201125 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:201237 original size:29 final size:29
Alignment explanation
Indices: 201204--201259 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
201194 TTTACGAGCA
*
201204 TTGGGG-CAAAAGTGCAAATATGTAAAAGT
1 TTGGGGTCAAAA-TGAAAATATGTAAAAGT
*
201233 TTGGGGTCAAAATGAAAATTTGTAAAA
1 TTGGGGTCAAAATGAAAATATGTAAAA
201260 ATATGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.27
Consensus pattern (29 bp):
TTGGGGTCAAAATGAAAATATGTAAAAGT
Found at i:204652 original size:40 final size:40
Alignment explanation
Indices: 204520--204652 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
204510 GAATATAATT
** * * *
204520 TGGATAGGATTCGTTCCTGATTCACTATAATACCTCAAAG
1 TGGATAGGATTTATTCCTGATTCACTATAGTAACTTAAAG
* * * * *
204560 TAGATAGGATTTGTTCCTGATTCATTATGGTAATTTAAAG
1 TGGATAGGATTTATTCCTGATTCACTATAGTAACTTAAAG
* * *
204600 TGAATAGGATTTATTCCTGATTCACTACAGTAACTTAAGG
1 TGGATAGGATTTATTCCTGATTCACTATAGTAACTTAAAG
204640 TGGATAGGATTTA
1 TGGATAGGATTTA
204653 ACCTGAAAAG
Statistics
Matches: 76, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.37
Consensus pattern (40 bp):
TGGATAGGATTTATTCCTGATTCACTATAGTAACTTAAAG
Found at i:206076 original size:25 final size:25
Alignment explanation
Indices: 206048--206098 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
206038 ATAAATAAAG
206048 TTCATTTCACAATACTTCATTATTA
1 TTCATTTCACAATACTTCATTATTA
206073 TTCATTTCACAATACTTCATTATTA
1 TTCATTTCACAATACTTCATTATTA
206098 T
1 T
206099 GTCTTTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (25 bp):
TTCATTTCACAATACTTCATTATTA
Found at i:215915 original size:14 final size:15
Alignment explanation
Indices: 215896--215928 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
215886 CAATTTAATC
215896 ATAATT-TTAAAATA
1 ATAATTCTTAAAATA
*
215910 ATAATTCTTAAAATT
1 ATAATTCTTAAAATA
215925 ATAA
1 ATAA
215929 ATATTCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATTCTTAAAATA
Found at i:218425 original size:18 final size:18
Alignment explanation
Indices: 218404--218452 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
218394 TTATTATAAC
218404 TATTTATATATATCATCT
1 TATTTATATATATCATCT
*
218422 TATTATATATTTAT-ATCT
1 TATT-TATATATATCATCT
218440 TA-TTATATATATC
1 TATTTATATATATC
218453 TATATATCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 1 0.04
18 10 0.37
19 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATATATATCATCT
Found at i:218425 original size:33 final size:35
Alignment explanation
Indices: 218388--218452 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
218378 ATTTGTCCTA
218388 TTATTAT-TA-TTATAAC-TATTTATATATATCATC
1 TTATTATATATTTATAACTTA-TTATATATATCATC
*
218421 TTATTATATATTTATATCTTATTATATATATC
1 TTATTATATATTTATAACTTATTATATATATC
218453 TATATATCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 2 0.07
35 17 0.61
36 2 0.07
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (35 bp):
TTATTATATATTTATAACTTATTATATATATCATC
Found at i:222058 original size:9 final size:9
Alignment explanation
Indices: 222044--222128 Score: 104
Period size: 9 Copynumber: 9.3 Consensus size: 9
222034 TCAGGCTCAA
222044 AAAAAAATC
1 AAAAAAATC
222053 -AAAAAATC
1 AAAAAAATC
222061 AAAAAAATC
1 AAAAAAATC
222070 AAAAAAATC
1 AAAAAAATC
*
222079 AAAAACAATGAA
1 AAAAA-AAT--C
222091 AAAAAAATC
1 AAAAAAATC
222100 AAAAAAAATC
1 -AAAAAAATC
222110 --AAAAATC
1 AAAAAAATC
222117 AAAAAAATC
1 AAAAAAATC
222126 AAA
1 AAA
222129 GTCAAAATAG
Statistics
Matches: 67, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
7 7 0.10
8 8 0.12
9 32 0.48
10 12 0.18
11 3 0.04
12 5 0.07
ACGTcount: A:0.78, C:0.11, G:0.01, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:222123 original size:10 final size:10
Alignment explanation
Indices: 222043--222114 Score: 89
Period size: 10 Copynumber: 7.5 Consensus size: 10
222033 TTCAGGCTCA
222043 AAAAAAAATC
1 AAAAAAAATC
222053 --AAAAAATC
1 AAAAAAAATC
222061 -AAAAAAATC
1 AAAAAAAATC
222070 -AAAAAAATC
1 AAAAAAAATC
* *
222079 AAAAACAATGA
1 AAAAAAAAT-C
222090 AAAAAAAATC
1 AAAAAAAATC
222100 AAAAAAAATC
1 AAAAAAAATC
222110 AAAAA
1 AAAAA
222115 TCAAAAAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
8 8 0.15
9 17 0.31
10 22 0.40
11 8 0.15
ACGTcount: A:0.79, C:0.10, G:0.01, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:222123 original size:30 final size:29
Alignment explanation
Indices: 222061--222123 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 29
222051 TCAAAAAATC
222061 AAAAAAATCAAAAAAATCAAAAACAATGAA
1 AAAAAAATCAAAAAAATCAAAAACAA-GAA
222091 AAAAAAATCAAAAAAAATCAAAAATCAA-AA
1 AAAAAAATC-AAAAAAATCAAAAA-CAAGAA
222121 AAA
1 AAA
222124 TCAAAGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 14 0.45
31 14 0.45
32 3 0.10
ACGTcount: A:0.79, C:0.10, G:0.02, T:0.10
Consensus pattern (29 bp):
AAAAAAATCAAAAAAATCAAAAACAAGAA
Found at i:222150 original size:6 final size:6
Alignment explanation
Indices: 222141--222175 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
222131 CAAAATAGGA
*
222141 AAAAAG AAAAAG AAAAA- AAGAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
222176 GAGAGGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:222164 original size:17 final size:16
Alignment explanation
Indices: 222140--222174 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
222130 TCAAAATAGG
222140 AAAAAAGAAAAAGAAA
1 AAAAAAGAAAAAGAAA
222156 AAAAGAAGAAAAAGAAA
1 AAAA-AAGAAAAAGAAA
222173 AA
1 AA
222175 GGAGAGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAGAAA
Found at i:222995 original size:16 final size:18
Alignment explanation
Indices: 222973--223019 Score: 80
Period size: 16 Copynumber: 2.7 Consensus size: 18
222963 GAGTCAAGAA
222973 AAAAATGAAAAAAAA-TG
1 AAAAATGAAAAAAAATTG
222990 -AAAATGAAAAAAAATTG
1 AAAAATGAAAAAAAATTG
223007 AAAAATGAAAAAA
1 AAAAATGAAAAAA
223020 TAAAAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.50
17 2 0.07
18 12 0.43
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.13
Consensus pattern (18 bp):
AAAAATGAAAAAAAATTG
Found at i:223001 original size:18 final size:18
Alignment explanation
Indices: 222973--223019 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
222963 GAGTCAAGAA
222973 AAAAATG-AAAAAAAATG
1 AAAAATGAAAAAAAAATG
*
222990 -AAAATGAAAAAAAATTG
1 AAAAATGAAAAAAAAATG
223007 AAAAATGAAAAAA
1 AAAAATGAAAAAA
223020 TAAAAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.22
17 9 0.33
18 12 0.44
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.13
Consensus pattern (18 bp):
AAAAATGAAAAAAAAATG
Found at i:223020 original size:16 final size:17
Alignment explanation
Indices: 222973--223019 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
222963 GAGTCAAGAA
*
222973 AAAAATGAAAAAAAATG
1 AAAAATGAAAAAAATTG
222990 -AAAATGAAAAAAAATTG
1 AAAAATG-AAAAAAATTG
223007 AAAAATGAAAAAA
1 AAAAATGAAAAAA
223020 TAAAAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 6 0.22
17 15 0.56
18 6 0.22
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.13
Consensus pattern (17 bp):
AAAAATGAAAAAAATTG
Found at i:223033 original size:16 final size:16
Alignment explanation
Indices: 222981--223033 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
222971 AAAAAAATGA
* *
222981 AAAAAAATGAAAATGA
1 AAAAAAATGAAAAAGT
222997 AAAAAAATTGAAAAA-T
1 AAAAAAA-TGAAAAAGT
* *
223013 GAAAAAATAAAAAAGT
1 AAAAAAATGAAAAAGT
223029 AAAAA
1 AAAAA
223034 TAGAGAGGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 6 0.20
16 18 0.60
17 6 0.20
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.13
Consensus pattern (16 bp):
AAAAAAATGAAAAAGT
Found at i:223146 original size:21 final size:21
Alignment explanation
Indices: 223120--223164 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
223110 TCAAATATTA
223120 ATCAGAATGGGGCATGAAGTG
1 ATCAGAATGGGGCATGAAGTG
* *
223141 ATCAGATTGGGGCATGCAGTG
1 ATCAGAATGGGGCATGAAGTG
223162 ATC
1 ATC
223165 TTGCTATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.22
Consensus pattern (21 bp):
ATCAGAATGGGGCATGAAGTG
Found at i:225142 original size:45 final size:44
Alignment explanation
Indices: 224222--225230 Score: 308
Period size: 44 Copynumber: 22.9 Consensus size: 44
224212 AAGTTGCAGA
224222 TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAA-
1 TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-AAAG
* ** * * * *
224266 CCTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAACAG
1 TCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACAAAAG
* * *
224309 ATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGCCACCAAA-
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAG--ACAAAAG
* ** * * *
224355 CCTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAAAAG
1 TCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACAAAAG
* *
224398 ATATTGCCTTCCTGCATTGATAGCGAAGCAGGTCGAAGACACAAA-
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-AAAG
* ** * * *
224443 CCTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAAAAG
1 TCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACAAAAG
*
224486 ATCTTTCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAA-
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-AAAG
* ** * * * *
224531 CCTTGCC-TCTCTCGGTTGTGATA--G-AGCTGGTTGAAGACAACAG
1 TCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACAAAAG
**
224574 ATCTTGCCTTCCTATATTGACAGCGAAGCAGGTCGAAGACACAAA-
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-AAAG
* ** * * * *
224619 CCTTGCC-TCTCTCGGTTGTGATA--G-AGCTGGTTGAAGACAACAG
1 TCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACAAAAG
**
224662 ATCTTGCCTTCCTATATTGACAGCGAAGCAGGTCGAAGACACAAA-
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-AAAG
* ** * * * *
224707 CCTTGCC-TCTCTCGGTTGTGATA--G-AGCTGGTTGAAGACAACAG
1 TCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACAAAAG
**
224750 ATCTTGCCTTCCTATATTGACAGCGAAGCAGGTCGAAGACACAAA-
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-AAAG
* ** * * * *
224795 CCTTGCC-TCTCTCGGTTGTGATA--G-AGCTGGTTGAAGACAACAG
1 TCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACAAAAG
**
224838 ATCTTGCCTTCCTATATTGACAGCGAAGCAGGTCGAAGACACAAA-
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-AAAG
* ** * * ** *
224883 CCTTGCC-TCTCTCGGTTATGA-TG-G-AGCTGGTTAAAGACAACAG
1 TCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACAAAAG
*
224926 ATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAA-
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-AAAG
* * ** * * * * *
224971 CCTTGCCTCTCTTGGTTATGA-TG-G-AGCTGGTTGAAGAGAATAG
1 TCTTGCCT-TCCTGCAT-TGACAGCGAAGCAGGTCGAAGACAAAAG
*
225014 ATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAAGACACAAA-
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-AAAG
* ** * * *
225059 CCTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAAAAG
1 TCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGACAAAAG
*
225102 TTCTTACCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAA-
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-AAAG
* ** * * *
225147 CCTTGCC-TCTCT-CGATTGTGATG-G-AGCTGGTTGAAGACAACAG
1 TCTTGCCTTC-CTGC-ATTGACA-GCGAAGCAGGTCGAAGACAAAAG
225190 ATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
1 -TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA
225231 CAAACCTTGC
Statistics
Matches: 684, Mismatches: 173, Indels: 215
0.64 0.16 0.20
Matches are distributed among these distances:
42 61 0.09
43 171 0.25
44 202 0.30
45 189 0.28
46 54 0.08
47 7 0.01
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (44 bp):
TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACAAAAG
Found at i:225492 original size:88 final size:88
Alignment explanation
Indices: 224218--225483 Score: 1944
Period size: 88 Copynumber: 14.4 Consensus size: 88
224208 AATGAAGTTG
224218 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
224283 GTGATGGAGCTGGTTGAAGACAA
66 GTGATGGAGCTGGTTGAAGACAA
* * *
224306 CAGATCTTGCCTTCCTACATTGACAGCGAAGCAGATCGAAGCCACCAAACCTTGCCTCTCTCGGT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACA-CAAACCTTGCCTCTCTCGGT
224371 TGTGATGGAGCTGGTTGAAGACAA
65 TGTGATGGAGCTGGTTGAAGACAA
* * *
224395 AAGATATTGCCTTCCTGCATTGATAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
224460 GTGATGGAGCTGGTTGAAGACAA
66 GTGATGGAGCTGGTTGAAGACAA
* *
224483 AAGATCTTTCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
*
224548 GTGATAGAGCTGGTTGAAGACAA
66 GTGATGGAGCTGGTTGAAGACAA
**
224571 CAGATCTTGCCTTCCTATATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
*
224636 GTGATAGAGCTGGTTGAAGACAA
66 GTGATGGAGCTGGTTGAAGACAA
**
224659 CAGATCTTGCCTTCCTATATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
*
224724 GTGATAGAGCTGGTTGAAGACAA
66 GTGATGGAGCTGGTTGAAGACAA
**
224747 CAGATCTTGCCTTCCTATATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
*
224812 GTGATAGAGCTGGTTGAAGACAA
66 GTGATGGAGCTGGTTGAAGACAA
**
224835 CAGATCTTGCCTTCCTATATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
* *
224900 ATGATGGAGCTGGTTAAAGACAA
66 GTGATGGAGCTGGTTGAAGACAA
* *
224923 CAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTTGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
* *
224988 ATGATGGAGCTGGTTGAAGAGAA
66 GTGATGGAGCTGGTTGAAGACAA
* *
225011 TAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
225076 GTGATGGAGCTGGTTGAAGACAA
66 GTGATGGAGCTGGTTGAAGACAA
* * * *
225099 AAGTTCTTACCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
225164 GTGATGGAGCTGGTTGAAGACAA
66 GTGATGGAGCTGGTTGAAGACAA
225187 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
* *
225252 ATGATGGAGCTGGTTGAAGATAA
66 GTGATGGAGCTGGTTGAAGACAA
* * * * *
225275 CAGATCTTGTCTTCCTGCATTGACAGTGAAGCAGATCGAAGACACAAACCTTGCCTCCCTTGGTT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
* * ** * * *
225340 GT-AGGGGAGCAGGTAAAAAATAG
66 GTGA-TGGAGCTGGTTGAAGACAA
* * ** * * *
225363 CAGATCTTGCCTTCCTACATTGATAGCGAAGCAAATCGAAGACACAAGCCTTGCCTCCCTCGATT
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
* * *
225428 GT-AGTCGAGCAGG-TGAAAGATAA
66 GTGA-TGGAGCTGGTTG-AAGACAA
* * *
225451 CAAATCTTGCCTTCCTGTATTGACAGCGGAGCA
1 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCA
225484 AACTGAAGAT
Statistics
Matches: 1101, Mismatches: 74, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
87 1 0.00
88 1018 0.92
89 82 0.07
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTT
GTGATGGAGCTGGTTGAAGACAA
Found at i:225777 original size:132 final size:133
Alignment explanation
Indices: 225521--225777 Score: 358
Period size: 132 Copynumber: 1.9 Consensus size: 133
225511 TAAGCAGTAA
* * *
225521 TGGAATAGGTTGAAGATTTCAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAGTAATGGC
1 TGGAATAGATTGAAGATTTCAGATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAATAATGGC
** * * *
225586 AGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAATCCAGTAATTTTATCTCCCTGGTGGG
66 AGATTTTACCTCCCTAAGATTACAATGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTGGG
225651 CAG
131 CAG
* *
225654 TGGAATAGATTGAAGATTAT-AGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAT-ATGG
1 TGGAATAGATTGAAGATT-TCAGATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAATAATGG
* * *
225717 C-GAATTTTACCTCCTTAAGGTTACAATGGAGTACTTTGAAGCCAGTAATTCTATCTCCCTG
65 CAG-ATTTTACCTCCCTAAGATTACAATGGAGTACATTGAAGCCAGTAATTCTATCTCCCTG
225778 ACGTTGCGGA
Statistics
Matches: 109, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
131 1 0.01
132 55 0.50
133 52 0.48
134 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (133 bp):
TGGAATAGATTGAAGATTTCAGATCATATCTCCCTAAGCAGTAGTGGAGCAGATCGAATAATGGC
AGATTTTACCTCCCTAAGATTACAATGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTGGG
CAG
Found at i:228004 original size:110 final size:110
Alignment explanation
Indices: 227877--228079 Score: 354
Period size: 110 Copynumber: 1.8 Consensus size: 110
227867 GAATATTTCC
227877 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
*
227942 CTCGTTCGACCAAATAG-CTAAATATCCTTTTAAAAAACTTTTCAA
66 CTCGTTCAACCAAATAGTC-AAATATCCTTTTAAAAAACTTTTCAA
*
227987 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
228052 CTCGTTTAACCAAATTGTCAAATATCCT
66 CTCGTTCAACCAAATAGTCAAATATCCT
228080 ATTGAATTTA
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
110 87 0.99
111 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (110 bp):
AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
CTCGTTCAACCAAATAGTCAAATATCCTTTTAAAAAACTTTTCAA
Found at i:229496 original size:19 final size:20
Alignment explanation
Indices: 229456--229499 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
229446 GTCTCTTTAG
* *
229456 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
229475 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
229494 GCATTA
1 GCATTA
229500 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Done.