Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 154 of 211
Found at i:48532306 original size:10 final size:10
Alignment explanation
Indices: 48532243--48532325 Score: 64
Period size: 10 Copynumber: 8.3 Consensus size: 10
48532233 TTTTCTTCCC
*
48532243 CTTTCCTTTT
1 CTTTCTTTTT
48532253 CTTTC--TTT
1 CTTTCTTTTT
48532261 CTTT-TTCTTT
1 CTTTCTT-TTT
* *
48532271 CTTTCCTCTT
1 CTTTCTTTTT
*
48532281 CTTTCCTTTT
1 CTTTCTTTTT
*
48532291 CCTTCTTTTT
1 CTTTCTTTTT
48532301 CTTTCTTCATTT
1 CTTTCTT--TTT
*
48532313 CTTTCTTCTT
1 CTTTCTTTTT
48532323 CTT
1 CTT
48532326 CCCCTCTCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
8 7 0.12
10 42 0.70
11 1 0.02
12 10 0.17
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:48532404 original size:27 final size:27
Alignment explanation
Indices: 48532374--48532440 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
48532364 AATTTAAGGG
**
48532374 TGGTGCCACCAACAAGGACTCCTTGTT
1 TGGTGCCACCAACAACCACTCCTTGTT
* ** *
48532401 TGGTGCCGCCAACCCCCTCTCCTTGTT
1 TGGTGCCACCAACAACCACTCCTTGTT
48532428 TGGTGCCACCAAC
1 TGGTGCCACCAAC
48532441 CTGCTTCCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.16, C:0.37, G:0.21, T:0.25
Consensus pattern (27 bp):
TGGTGCCACCAACAACCACTCCTTGTT
Found at i:48532517 original size:18 final size:21
Alignment explanation
Indices: 48532478--48532526 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
48532468 AAATCGGTCC
48532478 AGTTTTTTTTTCCTGTTCTTTT
1 AGTTTTTTTTT-CTGTTCTTTT
48532500 A-TTTTTTTTT-TGTT-TTTT
1 AGTTTTTTTTTCTGTTCTTTT
48532518 AGTTTTTTT
1 AGTTTTTTT
48532527 GATATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.19
19 11 0.42
21 9 0.35
22 1 0.04
ACGTcount: A:0.06, C:0.06, G:0.08, T:0.80
Consensus pattern (21 bp):
AGTTTTTTTTTCTGTTCTTTT
Found at i:48539800 original size:32 final size:29
Alignment explanation
Indices: 48539764--48539843 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 29
48539754 CTCAAGAAAT
48539764 TATAAATAAATTAAAAATTAAATAAATTAATA
1 TATAAA-AAATTAAAAATTAAA-AAA-TAATA
*
48539796 TATAAAAAATTTTAAAATTTTAAAAAATAATA
1 TATAAAAAA--TTAAAA-ATTAAAAAATAATA
*
48539828 TATAAAAAATAAAAAA
1 TATAAAAAATTAAAAA
48539844 ACTATAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
30 5 0.12
31 3 0.07
32 20 0.48
33 9 0.21
34 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
TATAAAAAATTAAAAATTAAAAAATAATA
Found at i:48539801 original size:16 final size:15
Alignment explanation
Indices: 48539764--48539806 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
48539754 CTCAAGAAAT
48539764 TATAAATAAATTAAA
1 TATAAATAAATTAAA
*
48539779 AATTAAATAAATTAATA
1 TA-TAAATAAATTAA-A
48539796 TATAAA-AAATT
1 TATAAATAAATT
48539807 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.25
16 16 0.67
17 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TATAAATAAATTAAA
Found at i:48540293 original size:13 final size:14
Alignment explanation
Indices: 48540269--48540297 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
48540259 GTGTACATAT
48540269 TAAATAATAAAATA
1 TAAATAATAAAATA
48540283 TAAAT-ATAAAATA
1 TAAATAATAAAATA
48540296 TA
1 TA
48540298 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATAATAAAATA
Found at i:48541117 original size:32 final size:32
Alignment explanation
Indices: 48541057--48541119 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
48541047 ATTAATTTGT
* *
48541057 ATGAATTATCAAATTAAATTAATTAATTTATC
1 ATGAATTATCAAATTAAAGTAATCAATTTATC
* * *
48541089 ATGAGTTATTAAATTCAAGTAATCAATTTAT
1 ATGAATTATCAAATTAAAGTAATCAATTTAT
48541120 AAGTTTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (32 bp):
ATGAATTATCAAATTAAAGTAATCAATTTATC
Found at i:48548770 original size:21 final size:23
Alignment explanation
Indices: 48548746--48548789 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
48548736 AAATATTAAA
48548746 AATTAAATCAAAAT-TTT-TTTT
1 AATTAAATCAAAATATTTATTTT
*
48548767 AATTAACTCAAAATATTTATTTT
1 AATTAAATCAAAATATTTATTTT
48548790 CTCACATGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 3 0.15
23 4 0.20
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (23 bp):
AATTAAATCAAAATATTTATTTT
Found at i:48552867 original size:21 final size:21
Alignment explanation
Indices: 48552807--48552899 Score: 98
Period size: 22 Copynumber: 4.2 Consensus size: 21
48552797 ATGAATGTTG
48552807 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATA-TATTAT
48552831 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATAT-ATTAT
*
48552853 TTTAAGTTT-TCATATATTAT
1 TTTAAATTTATCATATATTAT
* *
48552873 TCTTCAAATTTATTATGTATTAT
1 T-TT-AAATTTATCATATATTAT
48552896 TTTA
1 TTTA
48552900 TACATTTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
20 6 0.10
21 10 0.16
22 24 0.39
23 10 0.16
24 11 0.18
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAAATTTATCATATATTAT
Found at i:48555106 original size:40 final size:41
Alignment explanation
Indices: 48554916--48555274 Score: 316
Period size: 41 Copynumber: 8.8 Consensus size: 41
48554906 TTTTTTAAAC
* *
48554916 CTTTAGCGGCGTTTTTGTGTAAGCGCCGCTAATGCTCCGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
* * ** * *
48554957 CTTTCGCGACGTTTTTGTGAAAGCGCCGCTAATGCCCCGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
* * * *
48554998 CTTTAGCGGTGATTTCGTCTAAGTGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
* *
48555039 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATTCTCGGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
* *
48555080 CTTTAGCGGCG-TTTTGTCTATGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
* *
48555120 CTTTAGCGGCGTTTTTATAC-AA-CGCCGCTAATTCTCGGAT
1 CTTTAGCGGCGTTTTTGT-CTAAGCGCCGCTAATGCTCGGAT
* * ** * * *
48555160 CTTTAGCAGCGTTTCTAACTGAGCGCCACTAATTCGCT-TG-T
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAA-T-GCTCGGAT
* * * ** *** *
48555201 CTTCAGCGGCGTTTGTATCTAAGCGCCATTAATG-TATTTAC
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCT-CGGAT
* *
48555242 CTTTAGCGGCGTTTTTGCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAT
48555275 AGTAACAAAA
Statistics
Matches: 261, Mismatches: 48, Indels: 18
0.80 0.15 0.06
Matches are distributed among these distances:
38 1 0.00
39 2 0.01
40 72 0.28
41 181 0.69
42 3 0.01
43 2 0.01
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.34
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
Found at i:48555203 original size:81 final size:81
Alignment explanation
Indices: 48555026--48555221 Score: 218
Period size: 81 Copynumber: 2.4 Consensus size: 81
48555016 CTAAGTGCCG
* * * * *
48555026 CTAATGCTCGGATCTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATTCTCGGATCTTTAGCGGCG
1 CTAATGCGCGGGTCTTTAGCGGCGTTTTTATCTATACGCCGCTAATTCTCGGATCTTTAGCAGCG
** *
48555091 TTTTGTCTATGCGCCG
66 TTTTAACTATGCGCCA
*
48555107 CTAATGCTCGGGTCTTTAGCGGCGTTTTTATAC-A-ACGCCGCTAATTCTCGGATCTTTAGCAGC
1 CTAATGCGCGGGTCTTTAGCGGCGTTTTTAT-CTATACGCCGCTAATTCTCGGATCTTTAGCAGC
48555170 GTTTCTAACTGA-GCGCCA
65 GTTT-TAACT-ATGCGCCA
* ** * *
48555188 CTAATTCGCTTGTCTTCAGCGGCGTTTGTATCTA
1 CTAATGCGCGGGTCTTTAGCGGCGTTTTTATCTA
48555222 AGCGCCATTA
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
80 32 0.33
81 64 0.65
82 2 0.02
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (81 bp):
CTAATGCGCGGGTCTTTAGCGGCGTTTTTATCTATACGCCGCTAATTCTCGGATCTTTAGCAGCG
TTTTAACTATGCGCCA
Found at i:48555773 original size:15 final size:15
Alignment explanation
Indices: 48555752--48555789 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
48555742 TTTAAGGTTA
48555752 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
48555767 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
48555782 ATTTAGGG
1 ATTTAGGG
48555790 TTAATTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:48556072 original size:14 final size:14
Alignment explanation
Indices: 48556053--48556079 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48556043 ATTTTTTTGA
48556053 TATATATATATGGC
1 TATATATATATGGC
48556067 TATATATATATGG
1 TATATATATATGG
48556080 TTAATTAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
TATATATATATGGC
Found at i:48557157 original size:28 final size:28
Alignment explanation
Indices: 48557118--48557172 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
48557108 AGGGGGATTT
* *
48557118 AGGGTTTAAGGGTTATGCTTTAGGGGTC
1 AGGGTTTAAGGGTAATGCGTTAGGGGTC
*
48557146 AGGGATTT-AGGGTAATGGGTTAGGGGT
1 AGGG-TTTAAGGGTAATGCGTTAGGGGT
48557173 TATGATTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.20, C:0.04, G:0.44, T:0.33
Consensus pattern (28 bp):
AGGGTTTAAGGGTAATGCGTTAGGGGTC
Found at i:48557394 original size:34 final size:36
Alignment explanation
Indices: 48557336--48557404 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 36
48557326 AATTTATTTA
* *
48557336 TTTATCAATAAAATTAAATCTTATAA-ATTTCAAAC
1 TTTATCAATAAAATTAAATATTATAATATTACAAAC
48557371 TTTATACAA-AAAA-TAAATATTATAATATTACAAA
1 TTTAT-CAATAAAATTAAATATTATAATATTACAAA
48557405 TTAAAAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 11 0.37
35 16 0.53
36 3 0.10
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (36 bp):
TTTATCAATAAAATTAAATATTATAATATTACAAAC
Found at i:48560240 original size:31 final size:30
Alignment explanation
Indices: 48560205--48561079 Score: 838
Period size: 31 Copynumber: 29.2 Consensus size: 30
48560195 AATATAAGAT
48560205 ATTACATAACTTACATTAATATTATACATAA
1 ATTACATAACTTA-ATTAATATTATACATAA
*
48560236 ATTACATAACTTAATTAATTAATATACATAA
1 ATTACATAACTTAATTAA-TATTATACATAA
* *
48560267 ATTACATAACATACATTAATATTATACAGAA
1 ATTACATAACTTA-ATTAATATTATACATAA
* * *
48560298 ATTACATAACTTAGTT-A-ATTA-ATAT-T
1 ATTACATAACTTAATTAATATTATACATAA
48560324 A-TACATAACTTACATTAATATTATACATAA
1 ATTACATAACTTA-ATTAATATTATACATAA
* *
48560354 ATTACATAACTTAATTAGTTAATATACATAA
1 ATTACATAACTTAATTA-ATATTATACATAA
* * *
48560385 ATTACATAACATAATTAGTTAATATACATAA
1 ATTACATAACTTAATTA-ATATTATACATAA
* *
48560416 ATTACATAACTTAATTAGTTAATATACATAA
1 ATTACATAACTTAATTA-ATATTATACATAA
*
48560447 ATTACATAACTTAATTAGTTAATTATACATAA
1 ATTACATAACTTAATTA-AT-ATTATACATAA
* *
48560479 ATTACATAACATACATTAATATTATACAGAA
1 ATTACATAACTTA-ATTAATATTATACATAA
* * *
48560510 ATTACATAACTTAGTT-AT-TTA-ATAT-T
1 ATTACATAACTTAATTAATATTATACATAA
48560536 A-TACATAACTTACATTAATATTATACATAA
1 ATTACATAACTTA-ATTAATATTATACATAA
* * *
48560566 ATTACATAACTTAGTT-AT-TTA-ATAT-T
1 ATTACATAACTTAATTAATATTATACATAA
48560592 A-TACATAACTTACATTAATATTATACATAA
1 ATTACATAACTTA-ATTAATATTATACATAA
* *
48560622 ATTACATAACTTAATTAGTTAATATACATAA
1 ATTACATAACTTAATTA-ATATTATACATAA
* * *
48560653 ATTACATAACATAATTAGTTAATATACATAA
1 ATTACATAACTTAATTA-ATATTATACATAA
* * *
48560684 ATTACATAACTTAGTTATTTAATATACATAA
1 ATTACATAACTTAATTA-ATATTATACATAA
*
48560715 ATTACATAACTTAATTAGTTAATTATACATAA
1 ATTACATAACTTAATTA-AT-ATTATACATAA
* *
48560747 ATTACATAACATACATTAATATTATACAGAA
1 ATTACATAACTTA-ATTAATATTATACATAA
* * *
48560778 ATTACATAACTTAGTT-AT-TTA-ATAT-T
1 ATTACATAACTTAATTAATATTATACATAA
48560804 A-TACATAACTTACATTAATATTATACATAA
1 ATTACATAACTTA-ATTAATATTATACATAA
* * *
48560834 ATTACATAACTTAGTTATTTAATATACATAA
1 ATTACATAACTTAATTA-ATATTATACATAA
*
48560865 ATTACATAACTTAATTAGTTAATTATACATAA
1 ATTACATAACTTAATTA-AT-ATTATACATAA
* *
48560897 ATTACATAACATACATTAATATTATACAGAA
1 ATTACATAACTTA-ATTAATATTATACATAA
* * *
48560928 ATTACATAACTTAGTT-A-ATTA-ATAT-T
1 ATTACATAACTTAATTAATATTATACATAA
48560954 A-TACATAACTTACATTAATATTATACATAA
1 ATTACATAACTTA-ATTAATATTATACATAA
* * *
48560984 ATTACATAACTTAGTT-AT-TTA-ATAT-T
1 ATTACATAACTTAATTAATATTATACATAA
48561010 A-TACATAACTTACATTAATATTATACATAA
1 ATTACATAACTTA-ATTAATATTATACATAA
48561040 ATTACATAACTTAGTTATTTAATATTATACATAA
1 ATTACATAACTTA---A-TTAATATTATACATAA
*
48561074 CTTACA
1 ATTACA
48561080 ACTTACATAA
Statistics
Matches: 715, Mismatches: 79, Indels: 97
0.80 0.09 0.11
Matches are distributed among these distances:
25 66 0.09
26 18 0.03
27 24 0.03
28 40 0.06
29 28 0.04
30 34 0.05
31 397 0.56
32 74 0.10
33 13 0.02
34 21 0.03
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (30 bp):
ATTACATAACTTAATTAATATTATACATAA
Found at i:48560294 original size:22 final size:21
Alignment explanation
Indices: 48560207--48560294 Score: 53
Period size: 22 Copynumber: 4.2 Consensus size: 21
48560197 TATAAGATAT
*
48560207 TACATAACTTACATTAATATTA
1 TACATAACATACA-TAATATTA
48560229 TACATAA-ATTACATAACTTAATTA
1 TACATAACA-TACATAA--T-ATTA
* *
48560253 -A-TTAATATACATAA-A-T-
1 TACATAACATACATAATATTA
48560269 TACATAACATACATTAATATTA
1 TACATAACATACA-TAATATTA
48560291 TACA
1 TACA
48560295 GAAATTACAT
Statistics
Matches: 51, Mismatches: 4, Indels: 22
0.66 0.05 0.29
Matches are distributed among these distances:
17 2 0.04
18 9 0.18
19 3 0.06
20 1 0.02
21 4 0.08
22 25 0.49
23 3 0.06
24 4 0.08
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (21 bp):
TACATAACATACATAATATTA
Found at i:48560328 original size:25 final size:22
Alignment explanation
Indices: 48560300--48560353 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
48560290 ATACAGAAAT
48560300 TACATAACTTAGTTAATTAATATTA
1 TACATAACTTA---AATTAATATTA
*
48560325 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
48560347 TACATAA
1 TACATAA
48560354 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
25 11 0.39
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:48560343 original size:22 final size:22
Alignment explanation
Indices: 48560315--48560360 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
48560305 AACTTAGTTA
*
48560315 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
48560337 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
48560359 AT
1 AT
48560361 AACTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:48560556 original size:22 final size:22
Alignment explanation
Indices: 48560528--48560572 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
48560518 ACTTAGTTAT
*
48560528 TTAATATTATACATAACTTACA
1 TTAATATTATACATAAATTACA
48560550 TTAATATTATACATAAATTACA
1 TTAATATTATACATAAATTACA
48560572 T
1 T
48560573 AACTTAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATTATACATAAATTACA
Found at i:48560612 original size:22 final size:22
Alignment explanation
Indices: 48560584--48560628 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
48560574 ACTTAGTTAT
*
48560584 TTAATATTATACATAACTTACA
1 TTAATATTATACATAAATTACA
48560606 TTAATATTATACATAAATTACA
1 TTAATATTATACATAAATTACA
48560628 T
1 T
48560629 AACTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATTATACATAAATTACA
Found at i:48560688 original size:268 final size:267
Alignment explanation
Indices: 48560205--48561079 Score: 1287
Period size: 268 Copynumber: 3.3 Consensus size: 267
48560195 AATATAAGAT
* * * *
48560205 ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATTAATATACATAAATT
1 ATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTATTTAATAT---T--A-T
* * *
48560270 ACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTAATTAATATTATACATAACTT
60 ACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATTATACATAACTT
48560335 ACATTAATATTATACATAAATTACATAACTTAATTAGTTAATATACATAAATTACATAACATAAT
125 ACATTAATATTATACATAAATTACATAACTTAATTAGTTAATATACATAAATTACATAACATAAT
48560400 TAGTTAATATACATAAATTACATAACTTAATTAGTTAATATACATAAATTACATAACTTAATTAG
190 TAGTTAATATACATAAATTACATAACTTAATTA-TTAATATACATAAATTACATAACTTAATTAG
48560465 TTAATTATACATAA
254 TTAATTATACATAA
48560479 ATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTATTTAATATTATACATAA
1 ATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTATTTAATATTATACATAA
48560544 CTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATTATACATAACTTACATTA
66 CTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATTATACATAACTTACATTA
48560609 ATATTATACATAAATTACATAACTTAATTAGTTAATATACATAAATTACATAACATAATTAGTTA
131 ATATTATACATAAATTACATAACTTAATTAGTTAATATACATAAATTACATAACATAATTAGTTA
*
48560674 ATATACATAAATTACATAACTTAGTTATTTAATATACATAAATTACATAACTTAATTAGTTAATT
196 ATATACATAAATTACATAACTTAATTA-TTAATATACATAAATTACATAACTTAATTAGTTAATT
48560739 ATACATAA
260 ATACATAA
48560747 ATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTATTTAATATTATACATAA
1 ATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTATTTAATATTATACATAA
48560812 CTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATACATAAATTACATAACTT
66 CTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATAT---T--A-TACATAACTT
* * * * *
48560877 A-ATTAGTTAATTATACATAAATTACATAACATACATTA-ATATTATACAGAAATTACATAAC--
125 ACATTA-AT-ATTATACATAAATTACATAACTTA-ATTAGTTAATATACATAAATTACATAACAT
* * * *
48560938 --TTAGTTAAT-TA-AT-ATTATACATAACTTACATTAATATTATACATAAATTACATAACTTAG
187 AATTAGTTAATATACATAAAT-TACATAACTTA-ATTATTAATATACATAAATTACATAACTTAA
*
48560998 TTATTTAA-TAT---T--
250 TTAGTTAATTATACATAA
* *
48561010 A-TACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATTATACATAA
1 ATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTATTTAATATTATACATAA
48561074 CTTACA
66 CTTACA
48561080 ACTTACATAA
Statistics
Matches: 568, Mismatches: 22, Indels: 34
0.91 0.04 0.05
Matches are distributed among these distances:
262 67 0.12
263 1 0.00
265 1 0.00
268 322 0.57
269 45 0.08
270 5 0.01
271 11 0.02
273 5 0.01
274 64 0.11
275 43 0.08
276 4 0.01
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (267 bp):
ATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTATTTAATATTATACATAA
CTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATTATACATAACTTACATTA
ATATTATACATAAATTACATAACTTAATTAGTTAATATACATAAATTACATAACATAATTAGTTA
ATATACATAAATTACATAACTTAATTATTAATATACATAAATTACATAACTTAATTAGTTAATTA
TACATAA
Found at i:48560824 original size:22 final size:22
Alignment explanation
Indices: 48560796--48560840 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
48560786 ACTTAGTTAT
*
48560796 TTAATATTATACATAACTTACA
1 TTAATATTATACATAAATTACA
48560818 TTAATATTATACATAAATTACA
1 TTAATATTATACATAAATTACA
48560840 T
1 T
48560841 AACTTAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATTATACATAAATTACA
Found at i:48560958 original size:25 final size:22
Alignment explanation
Indices: 48560930--48560983 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
48560920 ATACAGAAAT
48560930 TACATAACTTAGTTAATTAATATTA
1 TACATAACTTA---AATTAATATTA
*
48560955 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
48560977 TACATAA
1 TACATAA
48560984 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
25 11 0.39
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:48560968 original size:56 final size:57
Alignment explanation
Indices: 48560354--48561079 Score: 622
Period size: 56 Copynumber: 12.3 Consensus size: 57
48560344 TTATACATAA
* * *
48560354 ATTACATAACTTA-ATTAGTTAATATACATAAATTACATAACATAATTAGTTAATATACATA-A
1 ATTACATAACTTACATTA-ATATTATACATAAATTACATAAC----TTAGTTAAT-TA-ATATT
* * * *
48560416 ATTACATAACTTA-ATTAGTTAATATACATAAATTACATAACTTAATTAGTTAATTATACATAA
1 ATTACATAACTTACATTA-ATATTATACATAAATTACATAAC----TTAGTTAATTA-ATAT-T
* * *
48560479 ATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTATTTAATATT
1 ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTAATTAATATT
*
48560536 A-TACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATT
1 ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTAATTAATATT
* *
48560592 A-TACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAGTTAATATACAT
1 ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTAATTAATAT---T
* * * *
48560651 AAATTACATAACATA-ATTAGTTAATATACATAAATTACATAACTTAGTTATTTAATATACAT
1 --ATTACATAACTTACATTA-ATATTATACATAAATTACATAACTTAGTTAATTAATAT---T
* * * * *
48560713 AAATTACATAACTTA-ATTAGTTAATTATACATAAATTACATAACATACATTAATATTATACAGA
1 --ATTACATAACTTACATTA-AT-ATTATACATAAATTACATAACTTA-GTT-A-ATTA-ATA-T
*
48560777 A
57 T
* * *
48560778 ATTACATAACTTAGTTATTTAATATTATACATAACTTACATTAA--TA-TT-A-TACATA-A
1 ATTACATAACTTA--CA-TTAATATTATACATAAATTACA-TAACTTAGTTAATTA-ATATT
* * * * *
48560834 ATTACATAACTTA-GTTATTTAATATACATAAATTACATAACTTAATTAGTTAATTATACATAA
1 ATTACATAACTTACATTA-ATATTATACATAAATTACATAAC----TTAGTTAATTA-ATAT-T
* *
48560897 ATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTAATTAATATT
1 ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTAATTAATATT
*
48560954 A-TACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATT
1 ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTAATTAATATT
*
48561010 A-TACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATT
1 ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTAATTAATATT
48561066 A-TACATAACTTACA
1 ATTACATAACTTACA
48561080 ACTTACATAA
Statistics
Matches: 583, Mismatches: 47, Indels: 74
0.83 0.07 0.11
Matches are distributed among these distances:
52 6 0.01
53 16 0.03
56 242 0.42
57 2 0.00
58 12 0.02
59 25 0.04
60 1 0.00
61 13 0.02
62 124 0.21
63 101 0.17
64 11 0.02
65 17 0.03
66 8 0.01
67 5 0.01
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.40
Consensus pattern (57 bp):
ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTAATTAATATT
Found at i:48560973 original size:22 final size:22
Alignment explanation
Indices: 48560945--48560990 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
48560935 AACTTAGTTA
*
48560945 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
48560967 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
48560989 AT
1 AT
48560991 AACTTAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:48561030 original size:22 final size:22
Alignment explanation
Indices: 48561002--48561046 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
48560992 ACTTAGTTAT
*
48561002 TTAATATTATACATAACTTACA
1 TTAATATTATACATAAATTACA
48561024 TTAATATTATACATAAATTACA
1 TTAATATTATACATAAATTACA
48561046 T
1 T
48561047 AACTTAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATTATACATAAATTACA
Found at i:48561088 original size:16 final size:16
Alignment explanation
Indices: 48561067--48561111 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
48561057 TTTAATATTA
48561067 TACATAACTTACAACT
1 TACATAACTTACAACT
48561083 TACATAACTTACAACT
1 TACATAACTTACAACT
48561099 TACATAACTTACA
1 TACATAACTTACA
48561112 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.31
Consensus pattern (16 bp):
TACATAACTTACAACT
Found at i:48561091 original size:9 final size:9
Alignment explanation
Indices: 48561067--48561185 Score: 80
Period size: 9 Copynumber: 14.3 Consensus size: 9
48561057 TTTAATATTA
48561067 TACATAACT
1 TACATAACT
48561076 TAC--AACT
1 TACATAACT
48561083 TACATAACT
1 TACATAACT
48561092 TAC--AACT
1 TACATAACT
48561099 TACATAACT
1 TACATAACT
**
48561108 TACATATTTT
1 TACATA-ACT
*
48561118 TA-ATTA-T
1 TACATAACT
* *
48561125 T-CGTAAAT
1 TACATAACT
48561133 TACATAACT
1 TACATAACT
*
48561142 TACATAATT
1 TACATAACT
*
48561151 TTCATAA--
1 TACATAACT
*
48561158 TAAATAACT
1 TACATAACT
48561167 TACATAA--
1 TACATAACT
48561174 TACATAACT
1 TACATAACT
48561183 TAC
1 TAC
48561186 GTAGCTTAAT
Statistics
Matches: 85, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
7 30 0.35
8 2 0.02
9 50 0.59
10 3 0.04
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:48561170 original size:34 final size:34
Alignment explanation
Indices: 48561095--48561180 Score: 95
Period size: 34 Copynumber: 2.6 Consensus size: 34
48561085 CATAACTTAC
* * ***
48561095 AACTTACATAACTTACATATTTTTAATTATTCGT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
* *
48561129 AAATTACATAACTTACATAATTTTCATAATAAAT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
48561163 AACTTACATAA--TACATAA
1 AACTTACATAACTTACATAA
48561181 CTTACGTAGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 7 0.16
34 37 0.84
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.40
Consensus pattern (34 bp):
AACTTACATAACTTACATAATTTTAATAATAAAT
Found at i:48561172 original size:16 final size:16
Alignment explanation
Indices: 48561153--48561185 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
48561143 ACATAATTTT
48561153 CATAATAAATAACTTA
1 CATAATAAATAACTTA
*
48561169 CATAATACATAACTTA
1 CATAATAAATAACTTA
48561185 C
1 C
48561186 GTAGCTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (16 bp):
CATAATAAATAACTTA
Found at i:48566705 original size:66 final size:65
Alignment explanation
Indices: 48566610--48566780 Score: 200
Period size: 66 Copynumber: 2.6 Consensus size: 65
48566600 GAGCAAATTA
* * * *
48566610 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAATAAAAG-TATGAAGAACTCCA
48566674 G
65 G
* * *
48566675 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAACTGAGGTTCAATGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAATAAAAGTATGAAGAACTCCA
48566740 G
65 G
* * * * *
48566741 CAGTAGCTTAAAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
48566781 CGGCAGCGAG
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
65 2 0.02
66 83 0.93
67 4 0.04
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAATAAAAGTATGAAGAACTCCAG
Found at i:48566775 original size:21 final size:21
Alignment explanation
Indices: 48566751--48566795 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
48566741 CAGTAGCTTA
*
48566751 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCGGCAGCAAGAG
*
48566772 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
48566793 AAG
1 AAG
48566796 TACAGGCTAC
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:0.38, C:0.18, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:48566802 original size:21 final size:21
Alignment explanation
Indices: 48566759--48566802 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
48566749 TAAAGCAGAT
*
48566759 GCGGCAGCAAGAGAAGCAGAG
1 GCGGCAGCAAGAGAAGCACAG
* *
48566780 GCGGCAGCGAGAGAAGTACAG
1 GCGGCAGCAAGAGAAGCACAG
48566801 GC
1 GC
48566803 TACAACGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.43, T:0.02
Consensus pattern (21 bp):
GCGGCAGCAAGAGAAGCACAG
Found at i:48566832 original size:21 final size:21
Alignment explanation
Indices: 48566771--48566842 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
48566761 GGCAGCAAGA
*** *
48566771 GAAGCAGAGGCGGCAGCGAGA
1 GAAGCAGAGGCTAAAGCGAGG
* *
48566792 GAAGTACAGGCTACAA-CGAGG
1 GAAGCAGAGGCTA-AAGCGAGG
48566813 GAAGCAGAGGCTAAAGCGAGG
1 GAAGCAGAGGCTAAAGCGAGG
48566834 GAAGCAGAG
1 GAAGCAGAG
48566843 CAGCGTCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.05
21 38 0.93
22 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.42, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGGCTAAAGCGAGG
Found at i:48567048 original size:19 final size:21
Alignment explanation
Indices: 48567007--48567046 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
48566997 AATACGAATT
*
48567007 TTATTTTATTTATTGATATTTA
1 TTATATTATTTATT-ATATTTA
48567029 TTATATTATTTATT-TATT
1 TTATATTATTTATTATATT
48567047 ATATAGAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
22 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTATATTATTTATTATATTTA
Found at i:48567232 original size:43 final size:43
Alignment explanation
Indices: 48567143--48567473 Score: 221
Period size: 43 Copynumber: 7.7 Consensus size: 43
48567133 TTTTACAAAT
* * * * **
48567143 CGCCACTAAAGATAAGGGTCTTTTTAGTGGTGTTTTTGGTCAAAG
1 CGCCGCTAAAGATAAGGGTC--TTTAGCGGCGTTTGTGGAAAAAG
*
48567188 CGCCGCTAAAGATAAGGGTCTTTAGCGGCATTTGTGGAAAAAG
1 CGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAG
* * * * * *
48567231 CGCCACTAAAGATCATGGTCTTTGGCGGTGTTTGT-GAGAAAG
1 CGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAG
* * * * **
48567273 CGCTGCTATAGATCAA-AGTCTATT-GCGGCGTTTGAGGGGAAAG
1 CGCCGCTAAAGAT-AAGGGTCT-TTAGCGGCGTTTGTGGAAAAAG
* **
48567316 CGCCGCTAAAGA-ATA-GGTCTTTAGTGGCGTTTAG-GGTCAAAG
1 CGCCGCTAAAGATA-AGGGTCTTTAGCGGCGTTT-GTGGAAAAAG
* * * *
48567358 CGCCGCTAAAGA-ATAGGTTTTTTAGTGGCGTTTGTGGTATAAA-
1 CGCCGCTAAAGATA-AGGGTCTTTAGCGGCGTTTGTGG-AAAAAG
* * * * **
48567401 CGCCGCTATAGATCAGGGTCTTTAGCGGCGCTTCTCCCAAAAA-
1 CGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGT-GGAAAAAG
*
48567444 CGCCGCTAAAGATCAGGGTCTTTAGCGGCG
1 CGCCGCTAAAGATAAGGGTCTTTAGCGGCG
48567474 CTTCCACTAA
Statistics
Matches: 232, Mismatches: 43, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
41 3 0.01
42 64 0.28
43 143 0.62
44 3 0.01
45 19 0.08
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (43 bp):
CGCCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAG
Found at i:48567474 original size:43 final size:42
Alignment explanation
Indices: 48567398--48567496 Score: 153
Period size: 43 Copynumber: 2.3 Consensus size: 42
48567388 TTTGTGGTAT
* *
48567398 AAACGCCGCTATAGATCAGGGTCTTTAGCGGCGCTTCTCCCAA
1 AAACGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTC-CACAA
*
48567441 AAACGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTCCACTA
1 AAACGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTCCACAA
*
48567483 AAGCGCCGCTAAAG
1 AAACGCCGCTAAAG
48567497 GTCTTACTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 16 0.31
43 36 0.69
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.20
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTCCACAA
Found at i:48568605 original size:18 final size:17
Alignment explanation
Indices: 48568582--48568615 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48568572 GCCCCATAGC
48568582 TAGATACAAACAGAATAT
1 TAGATA-AAACAGAATAT
*
48568600 TAGATATAACAGAATA
1 TAGATAAAACAGAATA
48568616 ACAGATACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (17 bp):
TAGATAAAACAGAATAT
Found at i:48574756 original size:67 final size:67
Alignment explanation
Indices: 48574643--48574777 Score: 225
Period size: 67 Copynumber: 2.0 Consensus size: 67
48574633 TATGAGTTTA
* * *
48574643 TATTACAGGGGATTTAGCCTGGATTGGTAATCCCGTTGTAAGAAATGAGGTTCGCGGTAGTGTGC
1 TATTACAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGC
48574708 TC
66 TC
* *
48574710 TATTGCAGGGGATTTAGCCTGGACTGGTGATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGC
1 TATTACAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGC
48574775 TC
66 TC
48574777 T
1 T
48574778 CTGAATTGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (67 bp):
TATTACAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGC
TC
Found at i:48575924 original size:3 final size:3
Alignment explanation
Indices: 48575918--48575945 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
48575908 GTTGTTGTTG
48575918 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
48575946 ATTGTGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:48577656 original size:16 final size:16
Alignment explanation
Indices: 48577632--48577668 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
48577622 CGGTTGTACT
48577632 AGGTCATTAGGGTTCA
1 AGGTCATTAGGGTTCA
*
48577648 AGGTTATTAGGGTTCA
1 AGGTCATTAGGGTTCA
48577664 AGGTC
1 AGGTC
48577669 CAGTTCAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.32
Consensus pattern (16 bp):
AGGTCATTAGGGTTCA
Found at i:48582821 original size:23 final size:23
Alignment explanation
Indices: 48582792--48582867 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
48582782 ATAAGTGCCA
*
48582792 CACTGATATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
48582815 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
48582838 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48582861 CACTGAT
1 CACTGAT
48582868 CAATAACACT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:48584702 original size:19 final size:20
Alignment explanation
Indices: 48584675--48584719 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
48584665 TAGAAAAAAT
*
48584675 TATAAATATATAT-AAGAAA
1 TATATATATATATAAAGAAA
48584694 TATATATATATATAAAAGAAA
1 TATATATATATAT-AAAGAAA
48584715 TATAT
1 TATAT
48584720 GTCTATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
21 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
TATATATATATATAAAGAAA
Found at i:48584717 original size:17 final size:17
Alignment explanation
Indices: 48584678--48584719 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
48584668 AAAAAATTAT
*
48584678 AAATATATATAAGAAAT
1 AAATATATATAAGAAAG
*
48584695 ATATATATATATA-AAAG
1 AAATATATATA-AGAAAG
48584712 AAATATAT
1 AAATATAT
48584720 GTCTATAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
AAATATATATAAGAAAG
Found at i:48584732 original size:21 final size:21
Alignment explanation
Indices: 48584671--48584719 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
48584661 AAAATAGAAA
* *
48584671 AAAT-TATAAATATATATAAG
1 AAATATATATATATATAAAAG
48584691 AAATATATATATATATAAAAG
1 AAATATATATATATATAAAAG
48584712 AAATATAT
1 AAATATAT
48584720 GTCTATAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
AAATATATATATATATAAAAG
Found at i:48586643 original size:43 final size:43
Alignment explanation
Indices: 48586541--48586705 Score: 206
Period size: 44 Copynumber: 3.8 Consensus size: 43
48586531 TCGTCGTTTT
* * *
48586541 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTATCTTC
* *
48586585 AATTTGCTCCACTGCAACTTCAGGGAGATAAGATTGTATTTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTATCTTC
* *
48586628 AACCTGCTCCACTGCAACTTCAAGGG-GATAAGGTTTGTCATCTTC
1 AATCTGCTCCACTGCAACTTC-AGGGAGATAA-GATTGT-ATCTTC
* *
48586673 AGTCTGTTCCACTGCAACTTCAGGGAGATAAGA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
48586706 CTTATTATGG
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
43 30 0.29
44 46 0.44
45 28 0.27
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (43 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTATCTTC
Found at i:48586673 original size:88 final size:87
Alignment explanation
Indices: 48586546--48586705 Score: 234
Period size: 88 Copynumber: 1.8 Consensus size: 87
48586536 GTTTTAATCC
*
48586546 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATTTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGA
48586611 GATAAGATTGTATTTTCAACCT
66 GATAAGATTGTATTTTCAACCT
* * * *
48586633 GCTCCACTGCAACTTCAAGGG-GATAAGG-TTTGTCATCTTCAGTCTGTTCCACTGCAACTTCAG
1 GCTCCACTGCAACTTC-AGGGAGAT-AGGATTAGT-AGCTTCAATCTGCTCCACTGCAACTTCAG
48586696 GGAGATAAGA
63 GGAGATAAGA
48586706 CTTATTATGG
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
87 23 0.35
88 42 0.65
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (87 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGA
GATAAGATTGTATTTTCAACCT
Found at i:48587038 original size:129 final size:126
Alignment explanation
Indices: 48586861--48587111 Score: 358
Period size: 129 Copynumber: 2.0 Consensus size: 126
48586851 AATAAAATCT
* * *
48586861 GATGCGATGTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCACTCCACTGCA
*
48586926 ACTTCAGGAAGATAGGATTGGTTTCTTCAATCTACTCCGCTGCAACTTTAGGGAGATAAGACTG
66 ACTTCAGGAAGATAGGATTGGTTT-TTCAAT-T-CTCCACTGCAACTTTAGGGAGATAAGACTG
* * ** *
48586990 GATGCGATCTGCTCTACTGTAACTTCAGATAGATAAGATCTGTGATTTTAATCCACTCCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCACTCCACTGCA
* ** *
48587055 ACTTCAGGGAGATAGGATTGGTTTTTTTATTCTCCATTGCAACTTTAGGGAGATAAG
66 ACTTCAGGAAGATAGGATTGGTTTTTCAATTCTCCACTGCAACTTTAGGGAGATAAG
48587112 GTTGGTGGCT
Statistics
Matches: 109, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
126 24 0.22
127 1 0.01
128 4 0.04
129 80 0.73
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (126 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATCATTTTAATCCACTCCACTGCA
ACTTCAGGAAGATAGGATTGGTTTTTCAATTCTCCACTGCAACTTTAGGGAGATAAGACTG
Found at i:48587061 original size:44 final size:43
Alignment explanation
Indices: 48586876--48587068 Score: 135
Period size: 44 Copynumber: 4.5 Consensus size: 43
48586866 GATGTGCTCT
* * *
48586876 ACTGCAACTTCAGAGAGATAAGATCCAT-CATTTTAATCCGCTTC
1 ACTGCAACTTCAGAGAGATAAGAT-C-TGGATTTTAATCCACTCC
* * *
48586920 ACTGCAACTTCAG-GAAGATAGGAT-TGGTTTCTTCAATCTACTCC
1 ACTGCAACTTCAGAG-AGATAAGATCTGGATT-TT-AATCCACTCC
* * * *** ** *
48586964 GCTGCAACTTTAGGGAGATAAGA-CTGGA-TGCGATCTGCTCT
1 ACTGCAACTTCAGAGAGATAAGATCTGGATTTTAATCCACTCC
* *
48587005 ACTGTAACTTCAGATAGATAAGATCTGTGATTTTAATCCACTCC
1 ACTGCAACTTCAGAGAGATAAGATCTG-GATTTTAATCCACTCC
*
48587049 ACTGCAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATA
48587069 GGATTGGTTT
Statistics
Matches: 111, Mismatches: 29, Indels: 18
0.70 0.18 0.11
Matches are distributed among these distances:
41 26 0.23
42 5 0.05
43 6 0.05
44 73 0.66
45 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
ACTGCAACTTCAGAGAGATAAGATCTGGATTTTAATCCACTCC
Found at i:48587083 original size:44 final size:44
Alignment explanation
Indices: 48586906--48587117 Score: 116
Period size: 44 Copynumber: 5.0 Consensus size: 44
48586896 AGATCCATCA
* * *
48586906 TTTTAATCCGCTTCACTGCAACTTCAGGAAGATAGGATTGGTTT
1 TTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTT
* * * * * * *
48586950 CTTCAATCTACTCCGCTGCAACTTTAGGGAGATAAGACTGG---
1 TTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTT
* *** ** * * ** * **
48586991 ATGCGATCTGCTCTACTGTAACTTCAGATAGATAAGATCT-GTGA
1 TTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGAT-TGGTTT
48587035 TTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTT
1 TTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTT
* * *
48587079 TTTT-AT--TCTCCATTGCAACTTTAGGGAGATAAGG-TTGGT
1 TTTTAATCCACTCCACTGCAACTTCAGGGAGAT-AGGATTGGT
48587118 GGCTTAAATC
Statistics
Matches: 125, Mismatches: 37, Indels: 15
0.71 0.21 0.08
Matches are distributed among these distances:
41 54 0.43
42 4 0.03
43 3 0.02
44 64 0.51
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (44 bp):
TTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTT
Found at i:48587197 original size:44 final size:44
Alignment explanation
Indices: 48587149--48587532 Score: 233
Period size: 44 Copynumber: 8.8 Consensus size: 44
48587139 TACCTTGGGA
* * *
48587149 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATCTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * *
48587193 AGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGG
1 AGATAAGATCTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
48587237 AGATAAG-GCTGGTGACTTAAATCTGCTTCC-CTACTACCTT-GGCA
1 AGATAAGATCTGCTGTCTTCAATCTGC-TCCACTACT-GCTTAGG-G
* * *
48587281 AGATAAGAT-TCACCGTCTTCAATCTGCTCCACTACTTCTTAGGG
1 AGATAAGATCT-GCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
** * * * *
48587325 AGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGG
1 AGATAAGATCTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
48587369 AGATAAG-GCTGGTGGCTTAAATCTGCTTCC-CTGCTACCTTAGGA
1 AGATAAGATCTGCTGTCTTCAATCTGC-TCCACTACT-GCTTAGGG
* * * *
48587413 AGATAAGATTTTCTATCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATCTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
** * ** * * *
48587457 AGATAAGATCTGCAATCTTCAACCTATTCTACTGCTGCTCAGGG
1 AGATAAGATCTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * *
48587501 AGATAGGA-CTGGTGGCTTCGATCTGCTTCACT
1 AGATAAGATCTGCTGTCTTCAATCTGCTCCACT
48587533 GCCAGTACAG
Statistics
Matches: 249, Mismatches: 79, Indels: 25
0.71 0.22 0.07
Matches are distributed among these distances:
43 47 0.19
44 168 0.67
45 34 0.14
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (44 bp):
AGATAAGATCTGCTGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:48587250 original size:132 final size:132
Alignment explanation
Indices: 48587101--48587529 Score: 671
Period size: 132 Copynumber: 3.2 Consensus size: 132
48587091 TTGCAACTTT
* * *
48587101 AGGGAGATAAGGTTGGTGGCTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTTGCCGTC
1 AGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTTACCGTC
* *
48587166 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTGC
66 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGC
48587231 TC
131 TC
* * *
48587233 AGGGAGATAAGGCTGGTGACTTAAATCTGCTTCCCTACTACCTTGGCAAGATAAGATTCACCGTC
1 AGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTTACCGTC
* *
48587298 TTCAATCTGCTCCACTACTTCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGC
66 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGC
48587363 TC
131 TC
* * * **
48587365 AGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTGCTACCTTAGGAAGATAAGATTTTCTATC
1 AGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTTACCGTC
* *
48587430 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTATTCTACTGCTGC
66 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGC
48587495 TC
131 TC
**
48587497 AGGGAGAT-AGGACTGGTGGCTTCGATCTGCTTC
1 AGGGAGATAAGG-CTGGTGGCTTAAATCTGCTTC
48587530 ACTGCCAGTA
Statistics
Matches: 272, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
131 3 0.01
132 269 0.99
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (132 bp):
AGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTTACCGTC
TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGC
TC
Found at i:48587555 original size:88 final size:88
Alignment explanation
Indices: 48587461--48587645 Score: 244
Period size: 88 Copynumber: 2.1 Consensus size: 88
48587451 TTAGGGAGAT
* * *
48587461 AAGATCTGCAATCTTCAACCTATTCTACTGCTGCTCAGGGAGATAGGACTGGTGGCTTCGATCTG
1 AAGATCTGCAATCTTCAACCTATTCCACTGCTGCTCAAGGAGATAGGACTGGTGGCTTCGATCTA
* *
48587526 CTTCACTGCCAGTACAGGAAGAC
66 CTTCACTGCCAGTACAAGAAGAA
* * * * * *
48587549 AAGATCTACAATCTTCGACCTATTCCGCTGTTGTTCAAGGAGATAGGACTGGTGGCTTTGATCTA
1 AAGATCTGCAATCTTCAACCTATTCCACTGCTGCTCAAGGAGATAGGACTGGTGGCTTCGATCTA
* *
48587614 CTTCGCTGCCGGTACAAGAAGAA
66 CTTCACTGCCAGTACAAGAAGAA
*
48587637 AATATCTGC
1 AAGATCTGC
48587646 TATATTTAGT
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (88 bp):
AAGATCTGCAATCTTCAACCTATTCCACTGCTGCTCAAGGAGATAGGACTGGTGGCTTCGATCTA
CTTCACTGCCAGTACAAGAAGAA
Found at i:48589070 original size:1 final size:1
Alignment explanation
Indices: 48589064--48589124 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
48589054 CCCGATAGGG
* * * * * * *
48589064 TTTTTTTTGTTTTTTATTTTCTTGTTTTTTTTGTTTTTTTTGTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
48589125 GCCTCCACTA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.89
Consensus pattern (1 bp):
T
Found at i:48589077 original size:9 final size:9
Alignment explanation
Indices: 48589063--48589125 Score: 69
Period size: 9 Copynumber: 7.1 Consensus size: 9
48589053 CCCCGATAGG
48589063 GTTTTTTTT
1 GTTTTTTTT
48589072 G--TTTTTT
1 GTTTTTTTT
* *
48589079 -ATTTTCTT
1 GTTTTTTTT
48589087 GTTTTTTTT
1 GTTTTTTTT
48589096 GTTTTTTTT
1 GTTTTTTTT
48589105 GTTTTTTTTTT
1 G--TTTTTTTT
48589116 GTTTTTTTT
1 GTTTTTTTT
48589125 G
1 G
48589126 CCTCCACTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
7 6 0.13
8 5 0.11
9 26 0.57
11 9 0.20
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (9 bp):
GTTTTTTTT
Found at i:48589105 original size:33 final size:31
Alignment explanation
Indices: 48589063--48589124 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 31
48589053 CCCCGATAGG
48589063 GTTTTTTTTGTTTTTTATTTTCTTGTTTTTTTT
1 GTTTTTTTTGTTTTTT-TTTTCTT-TTTTTTTT
*
48589096 GTTTTTTTTGTTTTTTTTTTGTTTTTTTT
1 GTTTTTTTTGTTTTTTTTTTCTTTTTTTT
48589125 GCCTCCACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 6 0.21
32 6 0.21
33 16 0.57
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (31 bp):
GTTTTTTTTGTTTTTTTTTTCTTTTTTTTTT
Found at i:48599117 original size:23 final size:23
Alignment explanation
Indices: 48599091--48599163 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
48599081 ATTGGAAATG
48599091 ACATGTGTAACATTTAAATACAT
1 ACATGTGTAACATTTAAATACAT
* * * * * *
48599114 ACATTTATAATAATT-ATTACTT
1 ACATGTGTAACATTTAAATACAT
*
48599136 AACATGTGTAACATTTAAATGCAT
1 -ACATGTGTAACATTTAAATACAT
48599160 ACAT
1 ACAT
48599164 TTATAATAAT
Statistics
Matches: 35, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
22 5 0.14
23 26 0.74
24 4 0.11
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (23 bp):
ACATGTGTAACATTTAAATACAT
Found at i:48599161 original size:46 final size:46
Alignment explanation
Indices: 48599091--48599182 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
48599081 ATTGGAAATG
48599091 ACATGTGTAACATTTAAATACATACATTTATAATAATTATTACTTA
1 ACATGTGTAACATTTAAATACATACATTTATAATAATTATTACTTA
*
48599137 ACATGTGTAACATTTAAATGCATACATTTATAATAATTATTACTTA
1 ACATGTGTAACATTTAAATACATACATTTATAATAATTATTACTTA
48599183 CTTATTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.41
Consensus pattern (46 bp):
ACATGTGTAACATTTAAATACATACATTTATAATAATTATTACTTA
Found at i:48599292 original size:13 final size:12
Alignment explanation
Indices: 48599245--48599310 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 12
48599235 TAAAATAAAT
48599245 AAAAGAAGAAGAA
1 AAAAG-AGAAGAA
*
48599258 CAAAGTAGAACG-A
1 AAAAG-AGAA-GAA
*
48599271 AATAGAGAAGAA
1 AAAAGAGAAGAA
48599283 AAACAGAGAAAGAA
1 AAA-AGAG-AAGAA
48599297 AAAAGAGAA-AA
1 AAAAGAGAAGAA
48599308 AAA
1 AAA
48599311 TTAGGGTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 6 0.14
12 9 0.20
13 20 0.45
14 9 0.20
ACGTcount: A:0.71, C:0.05, G:0.21, T:0.03
Consensus pattern (12 bp):
AAAAGAGAAGAA
Found at i:48599292 original size:25 final size:26
Alignment explanation
Indices: 48599245--48599310 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
48599235 TAAAATAAAT
* *
48599245 AAAAGAAGAAGAACAAAGTAGAACG-A
1 AAAAG-AGAAGAAAAAAGTAGAAAGAA
*
48599271 AATAGAGAAGAAAAACAG-AGAAAGAA
1 AAAAGAGAAGAAAAA-AGTAGAAAGAA
48599297 AAAAGAGAA-AAAAA
1 AAAAGAGAAGAAAAA
48599311 TTAGGGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.71, C:0.05, G:0.21, T:0.03
Consensus pattern (26 bp):
AAAAGAGAAGAAAAAAGTAGAAAGAA
Found at i:48607312 original size:17 final size:17
Alignment explanation
Indices: 48607258--48607319 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 17
48607248 TAAAGGGTGA
48607258 GAAGTAAAAGTTTAGGG
1 GAAGTAAAAGTTTAGGG
* * *
48607275 AAAAAATAAAAAGTTTTGGG
1 --GAAGT-AAAAGTTTAGGG
48607295 GAA-TAAAAGTTTGAGGG
1 GAAGTAAAAGTTT-AGGG
48607312 GAAGTAAA
1 GAAGTAAA
48607320 TAGGGGGAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 8 0.23
17 7 0.20
18 6 0.17
19 3 0.09
20 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (17 bp):
GAAGTAAAAGTTTAGGG
Found at i:48607683 original size:9 final size:9
Alignment explanation
Indices: 48607669--48607705 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
48607659 TATAGTTTGA
48607669 TATTCGAAT
1 TATTCGAAT
48607678 TATTCGAAT
1 TATTCGAAT
*
48607687 TATTCGAGT
1 TATTCGAAT
*
48607696 TATTCAAAT
1 TATTCGAAT
48607705 T
1 T
48607706 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:48608785 original size:50 final size:50
Alignment explanation
Indices: 48608617--48608786 Score: 160
Period size: 50 Copynumber: 3.4 Consensus size: 50
48608607 TAACTCGTAA
* ** * *
48608617 CTTTAATCTGTTTAACTGTGATGTCAAGGAAGCAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTCAACTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAG
* * * * **** * *
48608667 CTTCAATCTATTCCACTACACCACCCGGAAAGTAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTCAACTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAG
* * * *
48608717 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTGG
1 CTTTAATCTGTTCAACTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAG
*
48608767 CTTTAATCTGTTCCACTGCA
1 CTTTAATCTGTTCAACTGCA
48608787 TCGCCTGGGG
Statistics
Matches: 89, Mismatches: 31, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (50 bp):
CTTTAATCTGTTCAACTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAG
Found at i:48609038 original size:45 final size:44
Alignment explanation
Indices: 48608910--48609065 Score: 138
Period size: 44 Copynumber: 3.5 Consensus size: 44
48608900 GATCCACTCT
* * * * * *
48608910 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCT
1 ACTGCAACCTCAGAGAGATAAGATTTATCACTTCAATCTGCTCC
* * * *
48608954 ACTACAACTTCA-AGGAGATAGGA-TTATCGGCTTCAATCTGCTCC
1 ACTGCAACCTCAGA-GAGATAAGATTTATC-ACTTCAATCTGCTCC
* *
48608998 ACTGCAACCTCAGAGAGATAAGATTTATCATCTTCGATCTGCCCC
1 ACTGCAACCTCAGAGAGATAAGATTTATCA-CTTCAATCTGCTCC
*
48609043 ACTGCAACCTTAG-GAGGATAAGA
1 ACTGCAACCTCAGAGA-GATAAGA
48609066 CCTGCTATTT
Statistics
Matches: 91, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
43 4 0.04
44 50 0.55
45 37 0.41
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (44 bp):
ACTGCAACCTCAGAGAGATAAGATTTATCACTTCAATCTGCTCC
Found at i:48609217 original size:132 final size:129
Alignment explanation
Indices: 48609075--48609474 Score: 586
Period size: 132 Copynumber: 3.0 Consensus size: 129
48609065 ACCTGCTATT
* * * *
48609075 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGTGGCATAAATCTGCTTCTCACTATC
1 TTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTTCGGTGGCTTAAAT-TGCTTC-CACTATC
* *
48609140 TTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCTACTATTGTTTAGGGAGATAAGATCTACAA
64 TTGGAAAGATAAGATTTG-CGTCTTTGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAA
48609205 TC
128 TC
*
48609207 TTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTTCGGTGGCTTAAATTAGCTTCCCTCTATC
1 TTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTTCGGTGGCTTAAATT-GCTT-CCACTATC
*
48609272 TTGGAAAGATAAGATTTGCTGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
64 TTGGAAAGATAAGATTTGC-GTCTTTGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAA
48609337 TC
128 TC
48609339 TTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTTCGGTGGCTTAAATTTGCTTCCTACTATC
1 TTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTTCGGTGGCTTAAA-TTGCTTCC-ACTATC
* * * * *
48609404 TTAGAAAGATAAGATTTACCGTCTTCT-ATTTGCTCCACTACTGTTTAGGGAGATAAGATCTGCT
64 TTGGAAAGATAAGATTT-GCGTCTT-TGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACA
48609468 ATC
127 ATC
48609471 TTCA
1 TTCA
48609475 CTGATCTGTT
Statistics
Matches: 246, Mismatches: 15, Indels: 14
0.89 0.05 0.05
Matches are distributed among these distances:
131 4 0.02
132 237 0.96
133 5 0.02
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (129 bp):
TTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTTCGGTGGCTTAAATTGCTTCCACTATCTT
GGAAAGATAAGATTTGCGTCTTTGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATC
Found at i:48612398 original size:8 final size:8
Alignment explanation
Indices: 48612385--48612418 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
48612375 GGAATAATTG
48612385 AACAAATA
1 AACAAATA
*
48612393 AACAAACA
1 AACAAATA
48612401 AACAAATA
1 AACAAATA
48612409 AACAAATA
1 AACAAATA
48612417 AA
1 AA
48612419 TCGACCACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (8 bp):
AACAAATA
Found at i:48612419 original size:12 final size:12
Alignment explanation
Indices: 48612355--48612419 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
48612345 ACCACATTTT
48612355 AATAAACAAATA
1 AATAAACAAATA
**
48612367 AATGAAATGGAATA
1 AAT-AAA-CAAATA
* *
48612381 ATTGAACAAATA
1 AATAAACAAATA
* *
48612393 AACAAACAAACA
1 AATAAACAAATA
48612405 AATAAACAAATA
1 AATAAACAAATA
48612417 AAT
1 AAT
48612420 CGACCACACC
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
12 28 0.72
13 5 0.13
14 6 0.15
ACGTcount: A:0.68, C:0.09, G:0.06, T:0.17
Consensus pattern (12 bp):
AATAAACAAATA
Found at i:48612628 original size:13 final size:13
Alignment explanation
Indices: 48612610--48612639 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
48612600 TAACATAGTT
*
48612610 TAAAATGAATAAA
1 TAAAATAAATAAA
48612623 TAAAATAAATAAA
1 TAAAATAAATAAA
48612636 TAAA
1 TAAA
48612640 CACAAAACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
TAAAATAAATAAA
Found at i:48613877 original size:21 final size:19
Alignment explanation
Indices: 48613829--48613883 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
48613819 TACAAAAATC
* *
48613829 TTTTTTGTTCTCTTCTCTG
1 TTTTTTCTTCTGTTCTCTG
48613848 TTGTTTTCTTCTGTTCTCTTG
1 TT-TTTTCTTCTGTTCTC-TG
*
48613869 TCTTTTTCTTTTGTT
1 T-TTTTTCTTCTGTT
48613884 GTTTTCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 13 0.43
21 14 0.47
22 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.11, T:0.71
Consensus pattern (19 bp):
TTTTTTCTTCTGTTCTCTG
Found at i:48615284 original size:26 final size:26
Alignment explanation
Indices: 48615248--48615299 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
48615238 TCACATTTCT
48615248 CCGTCAGTTGAGAGATGAACCGAGCA
1 CCGTCAGTTGAGAGATGAACCGAGCA
48615274 CCGTCAGTTGAGAGATGAACCGAGCA
1 CCGTCAGTTGAGAGATGAACCGAGCA
48615300 ATGTCATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (26 bp):
CCGTCAGTTGAGAGATGAACCGAGCA
Found at i:48615305 original size:26 final size:26
Alignment explanation
Indices: 48615249--48615305 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
48615239 CACATTTCTC
*
48615249 CGTCAGTTGAGAGATGAACCGAGCAC
1 CGTCAGTTGAGAGATGAACCGAGCAA
48615275 CGTCAGTTGAGAGATGAACCGAGCAA
1 CGTCAGTTGAGAGATGAACCGAGCAA
*
48615301 TGTCA
1 CGTCA
48615306 TTCAACCGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.30, T:0.18
Consensus pattern (26 bp):
CGTCAGTTGAGAGATGAACCGAGCAA
Found at i:48622627 original size:20 final size:21
Alignment explanation
Indices: 48622592--48622636 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
48622582 TCTTTTTGCA
*
48622592 TTTGCTCCAGTTTCTTTAATC
1 TTTGATCCAGTTTCTTTAATC
*
48622613 TTTGATCCA-TTTCTTTAGTC
1 TTTGATCCAGTTTCTTTAATC
48622633 TTTG
1 TTTG
48622637 CTTAGATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.56
Consensus pattern (21 bp):
TTTGATCCAGTTTCTTTAATC
Found at i:48624845 original size:15 final size:15
Alignment explanation
Indices: 48624825--48624854 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48624815 ACGAAGCGGT
*
48624825 AATAATAATAGTAAA
1 AATAATAATAATAAA
48624840 AATAATAATAATAAA
1 AATAATAATAATAAA
48624855 CAATCAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:48626691 original size:17 final size:18
Alignment explanation
Indices: 48626659--48626692 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48626649 AATTTATTTT
48626659 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
48626677 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
48626693 AGCTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:48627391 original size:30 final size:34
Alignment explanation
Indices: 48627335--48627396 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
48627325 TCATAATATA
*
48627335 ATAATATTAATAATAATATTTAAATAA-AAAACC
1 ATAATAATAATAATAATATTTAAATAACAAAACC
48627368 ATAATAATAATAATAA-A-TT-AATAACAAAA
1 ATAATAATAATAATAATATTTAAATAACAAAA
48627397 TCTCAAGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 5 0.19
31 6 0.22
32 1 0.04
33 15 0.56
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.31
Consensus pattern (34 bp):
ATAATAATAATAATAATATTTAAATAACAAAACC
Found at i:48634104 original size:17 final size:18
Alignment explanation
Indices: 48634072--48634105 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48634062 AATTTCTTTT
48634072 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
48634090 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
48634106 AGCTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:48634797 original size:13 final size:13
Alignment explanation
Indices: 48634781--48634823 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
48634771 ATAGAAAACC
48634781 ATAATAATAATTA
1 ATAATAATAATTA
*
48634794 ATAATTATAATT-
1 ATAATAATAATTA
48634806 ATAATAATAAATTA
1 ATAATAAT-AATTA
48634820 ATAA
1 ATAA
48634824 CAAAATCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.27
13 15 0.58
14 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATAATAATTA
Found at i:48635229 original size:17 final size:18
Alignment explanation
Indices: 48635201--48635244 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
48635191 ATAATTGTTT
48635201 TAAAAGTAAAAC-AGAAAG
1 TAAAA-TAAAACTAGAAAG
48635219 TAAAATAAAACTAGAAAG
1 TAAAATAAAACTAGAAAG
48635237 --AAATAAAA
1 TAAAATAAAA
48635245 GTAAACCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 11 0.44
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (18 bp):
TAAAATAAAACTAGAAAG
Found at i:48635317 original size:19 final size:19
Alignment explanation
Indices: 48635293--48635333 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
48635283 AAAACTAATA
48635293 TTTTTAAAAAATTCATTTT
1 TTTTTAAAAAATTCATTTT
* *
48635312 TTTTTACAATATTCATTTT
1 TTTTTAAAAAATTCATTTT
48635331 TTT
1 TTT
48635334 CCTTAAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTAAAAAATTCATTTT
Found at i:48635855 original size:14 final size:14
Alignment explanation
Indices: 48635836--48635875 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
48635826 CGGCCCAGCC
48635836 ATATTAATTTTTTT
1 ATATTAATTTTTTT
48635850 ATATT-ATTATTTTT
1 ATATTAATT-TTTTT
48635864 ATA-TAATTTTTT
1 ATATTAATTTTTT
48635876 AAAAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATATTAATTTTTTT
Found at i:48636140 original size:14 final size:14
Alignment explanation
Indices: 48636107--48636152 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
48636097 AGAAATCAAC
*
48636107 AAAAAAATAATAAA
1 AAAAAAATAAAAAA
*
48636121 TAAAAAATAAAAAA
1 AAAAAAATAAAAAA
*
48636135 AAAAAAGTAAAAAGA
1 AAAAAAATAAAAA-A
48636150 AAA
1 AAA
48636153 CAGGTCGGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAAA
Found at i:48636148 original size:7 final size:7
Alignment explanation
Indices: 48636108--48636147 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
48636098 GAAATCAACA
48636108 AAAAAAT
1 AAAAAAT
*
48636115 AATAAAT
1 AAAAAAT
48636122 AAAAAAT
1 AAAAAAT
48636129 AAAAAA-
1 AAAAAAT
48636135 AAAAAAGT
1 AAAAAA-T
48636143 AAAAA
1 AAAAA
48636148 GAAAACAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 6 0.21
7 18 0.62
8 5 0.17
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:48638596 original size:30 final size:30
Alignment explanation
Indices: 48638556--48638630 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 30
48638546 TTCTCTAATC
* *
48638556 TTTATAATTTTTAAACGATTAAATTAAAAT
1 TTTATTATTTTTAAACGATTAAAGTAAAAT
* * *
48638586 TTTATTATTTTTTAAAGGGTTAAAGTACAAT
1 TTTATTA-TTTTTAAACGATTAAAGTAAAAT
*
48638617 TTTATTATTATTAA
1 TTTATTATTTTTAA
48638631 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 12 0.32
31 26 0.68
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.51
Consensus pattern (30 bp):
TTTATTATTTTTAAACGATTAAAGTAAAAT
Found at i:48638601 original size:31 final size:31
Alignment explanation
Indices: 48638563--48638625 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
48638553 ATCTTTATAA
*
48638563 TTTTTAAACGATTAAATTAAAATTTTATTAT
1 TTTTTAAACGATTAAAGTAAAATTTTATTAT
* * *
48638594 TTTTTAAAGGGTTAAAGTACAATTTTATTAT
1 TTTTTAAACGATTAAAGTAAAATTTTATTAT
48638625 T
1 T
48638626 ATTAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (31 bp):
TTTTTAAACGATTAAAGTAAAATTTTATTAT
Found at i:48643140 original size:20 final size:19
Alignment explanation
Indices: 48643090--48643143 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 19
48643080 TTAAAATTAG
48643090 TAAAA-TATGATTATATATA
1 TAAAACTAT-ATTATATATA
*
48643109 T-ACAC-ATA-TATATATA
1 TAAAACTATATTATATATA
48643125 CTAAAACTATATTATATAT
1 -TAAAACTATATTATATAT
48643144 TCACATATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 8 0.29
17 2 0.07
18 7 0.25
19 4 0.14
20 7 0.25
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAAACTATATTATATATA
Found at i:48646154 original size:24 final size:24
Alignment explanation
Indices: 48646110--48646155 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
48646100 TCATGTGAAA
* *
48646110 ATATACTCATTTATCTTTAATTTC
1 ATATACTCATTCAGCTTTAATTTC
48646134 ATAT-CTCATTCAGCTTCTAATT
1 ATATACTCATTCAGCTT-TAATT
48646156 CAATTTCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.28, C:0.20, G:0.02, T:0.50
Consensus pattern (24 bp):
ATATACTCATTCAGCTTTAATTTC
Found at i:48646755 original size:46 final size:46
Alignment explanation
Indices: 48646688--48646906 Score: 359
Period size: 46 Copynumber: 4.8 Consensus size: 46
48646678 ACAATGCTAT
48646688 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
48646734 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
48646780 AACTCAGTATGGTTTTCGTT-ATTGAAATACCATACCTACTTCTCAC
1 AACTCAGTATGGTTTTC-TTCACTGAAATACCATACCTACTTTTCAC
* *
48646826 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * *
48646872 AACACAATATGGTTTTCTTTACTGAAATACCATAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATAC
48646907 TTACGTTCCA
Statistics
Matches: 164, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
45 2 0.01
46 160 0.98
47 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:48651359 original size:23 final size:24
Alignment explanation
Indices: 48651299--48651359 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
48651289 GTTCGGAAAC
48651299 ATTTA-TTTTA-ATATTTTTAGTAA
1 ATTTATTTTTATATATTTTTA-TAA
* *
48651322 ATTTGATGTAT-TATATTTTT-TAA
1 ATTT-ATTTTTATATATTTTTATAA
48651345 ATTTATTTTTATATA
1 ATTTATTTTTATATA
48651360 AAAATAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
22 4 0.13
23 15 0.50
24 1 0.03
25 10 0.33
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (24 bp):
ATTTATTTTTATATATTTTTATAA
Found at i:48659881 original size:33 final size:33
Alignment explanation
Indices: 48659790--48659907 Score: 134
Period size: 33 Copynumber: 3.6 Consensus size: 33
48659780 GTGAAGTTGT
* *
48659790 TTTTTGGTCAATTATACATACACCAACAATGT-T
1 TTTTAGGTCAATTATACATACACCAACAA-GTAA
* * *
48659823 TTTTAGGGT-AAATA-AAATTAAACCAACAAGTAA
1 TTTTA-GGTCAATTATACA-TACACCAACAAGTAA
*
48659856 TTTTAGGTCAATTATACATACACCAACAATTAA
1 TTTTAGGTCAATTATACATACACCAACAAGTAA
48659889 TTTTAGGTCAATTATACAT
1 TTTTAGGTCAATTATACAT
48659908 GCTTTATAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
32 7 0.10
33 59 0.83
34 5 0.07
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (33 bp):
TTTTAGGTCAATTATACATACACCAACAAGTAA
Found at i:48663001 original size:26 final size:27
Alignment explanation
Indices: 48662961--48663042 Score: 87
Period size: 26 Copynumber: 3.0 Consensus size: 27
48662951 TAAGAACATT
*
48662961 TTATGAAATTATATTTAATAATAATTA
1 TTATTAAATTATATTTAATAATAATTA
* *
48662988 TT-TTAAATTGTATTTAATCATATATT-
1 TTATTAAATTATATTTAATAATA-ATTA
* *
48663014 TTAATTAAAATATATTTAATATTAATTA
1 TT-ATTAAATTATATTTAATAATAATTA
48663042 T
1 T
48663043 AGTATCATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 19 0.43
27 8 0.18
28 17 0.39
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (27 bp):
TTATTAAATTATATTTAATAATAATTA
Found at i:48663107 original size:37 final size:38
Alignment explanation
Indices: 48663049--48663232 Score: 101
Period size: 37 Copynumber: 4.8 Consensus size: 38
48663039 TTATAGTATC
* * *
48663049 ATATATTATG-ATTTGAGTAAATTATATAAGAATATGA
1 ATATATTAAGAATTTTATTAAATTATATAAGAATATGA
** *
48663086 AT-TATTAAGAATTTTATTAAATTATATATTTTAAT-TAAA
1 ATATATTAAGAATTTTATTAAATTATATA--AGAATAT-GA
* * * * * * *
48663125 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT-C
1 ATATA-TTAAGAAT--TT-TATTAAATTATA--TAAGAATATGA
* * *
48663168 ATATATTATG-ATTTGAGTAAATTATATAAGAATATGA
1 ATATATTAAGAATTTTATTAAATTATATAAGAATATGA
48663205 AT-TATTAAGAATTTTATTAAATTATATA
1 ATATATTAAGAATTTTATTAAATTATATA
48663233 TTTTAATTAA
Statistics
Matches: 106, Mismatches: 27, Indels: 28
0.66 0.17 0.17
Matches are distributed among these distances:
36 18 0.17
37 36 0.34
38 9 0.08
39 8 0.08
40 2 0.02
41 9 0.08
42 3 0.03
43 7 0.07
44 12 0.11
45 1 0.01
46 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.47
Consensus pattern (38 bp):
ATATATTAAGAATTTTATTAAATTATATAAGAATATGA
Found at i:48663124 original size:18 final size:17
Alignment explanation
Indices: 48663096--48663130 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48663086 ATTATTAAGA
*
48663096 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48663113 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48663131 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48663243 original size:18 final size:17
Alignment explanation
Indices: 48663215--48663249 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48663205 ATTATTAAGA
*
48663215 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48663232 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48663250 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48663482 original size:18 final size:17
Alignment explanation
Indices: 48663454--48663488 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48663444 ATTATTAAGA
*
48663454 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48663471 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48663489 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48663556 original size:120 final size:120
Alignment explanation
Indices: 48663043--48663982 Score: 1778
Period size: 120 Copynumber: 7.9 Consensus size: 120
48663033 TATTAATTAT
*
48663043 AGTATCATATATTATGATTTGAGTAAATT-ATATAAGAATATGAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
48663107 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
66 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
*
48663162 AGTATCATATATTATGATTTGAGTAAATT-ATATAAGAATATGAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
48663226 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
66 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
*
48663281 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATGAATTATTAAGAATTTTATT-AA
1 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
48663345 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
66 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
48663400 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
48663465 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
66 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
* *
48663520 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAAAATTAATTATTAAAAATTTTATTAAA
1 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
48663585 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
66 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
*
48663640 AGTGTCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
*
48663705 TTATATATTTTAATTAAAATATATTTAATGATAATTATGTTAATTTATATTTTAC
66 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
*
48663760 AGTGTCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
48663825 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
66 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
48663880 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
1 AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
*
48663945 TTATATATTTTAATTAAAATATATTTAATAAAAATTAT
66 TTATATATTTTAATTAAAATATATTTAATAATAATTAT
48663983 ATTTAAATAT
Statistics
Matches: 809, Mismatches: 10, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
119 266 0.33
120 543 0.67
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
AGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAA
TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTAC
Found at i:48663602 original size:18 final size:17
Alignment explanation
Indices: 48663574--48663608 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48663564 ATTATTAAAA
*
48663574 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48663591 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48663609 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48663722 original size:18 final size:17
Alignment explanation
Indices: 48663694--48663728 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48663684 ATTATTAAGA
*
48663694 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48663711 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48663729 TTAATGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48663842 original size:18 final size:17
Alignment explanation
Indices: 48663814--48663848 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48663804 ATTATTAAGA
*
48663814 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48663831 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48663849 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48663962 original size:18 final size:18
Alignment explanation
Indices: 48663934--48663984 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
48663924 ATTATTAAGA
48663934 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
48663951 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
*
48663967 A-TTTAATAAAAATTATAT
1 ATTTTAAT-TAAATTATAT
48663985 TTAAATATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 6 0.21
16 8 0.28
17 5 0.17
18 10 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:48663968 original size:16 final size:16
Alignment explanation
Indices: 48663934--48663986 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 16
48663924 ATTATTAAGA
48663934 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
48663951 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
48663967 A-TTTAATAAAAATTAT
1 ATTTTAATTAAAA-TAT
48663983 ATTT
1 ATTT
48663987 AAATATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.31
16 9 0.28
17 7 0.22
18 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:48663987 original size:16 final size:15
Alignment explanation
Indices: 48663947--48663988 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
48663937 TTATTAAATT
*
48663947 ATATATTTTAATTAAA
1 ATATA-TTTAATAAAA
48663963 ATATATTTAATAAAA
1 ATATATTTAATAAAA
48663978 ATTATATTTAA
1 A-TATATTTAA
48663989 ATATGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATTTAATAAAA
Found at i:48664231 original size:16 final size:16
Alignment explanation
Indices: 48664210--48664245 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
48664200 GATTAGCTAT
48664210 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
48664226 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
48664242 TACA
1 TACA
48664246 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:48664414 original size:9 final size:9
Alignment explanation
Indices: 48664400--48664484 Score: 98
Period size: 9 Copynumber: 9.4 Consensus size: 9
48664390 TTTGGTTAAA
48664400 AATTAACCG
1 AATTAACCG
*
48664409 AATTAACAG
1 AATTAACCG
*
48664418 AATTACCCG
1 AATTAACCG
48664427 AATTAACCG
1 AATTAACCG
*
48664436 AATTACCCG
1 AATTAACCG
* *
48664445 AATTAATCA
1 AATTAACCG
*
48664454 AATTACCCG
1 AATTAACCG
**
48664463 AATTAATTG
1 AATTAACCG
48664472 AATTAACCG
1 AATTAACCG
48664481 AATT
1 AATT
48664485 GAATCACTAC
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 60 1.00
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:48664427 original size:18 final size:18
Alignment explanation
Indices: 48664400--48664484 Score: 109
Period size: 18 Copynumber: 4.7 Consensus size: 18
48664390 TTTGGTTAAA
*
48664400 AATTAACCGAATTAACAG
1 AATTACCCGAATTAACAG
*
48664418 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACAG
48664436 AATTACCCGAATTAATCA-
1 AATTACCCGAATTAA-CAG
**
48664454 AATTACCCGAATTAATTG
1 AATTACCCGAATTAACAG
*
48664472 AATTAACCGAATT
1 AATTACCCGAATT
48664485 GAATCACTAC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
18 58 0.98
19 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (18 bp):
AATTACCCGAATTAACAG
Found at i:48670234 original size:22 final size:21
Alignment explanation
Indices: 48670193--48670235 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
48670183 GCTACTTTGC
*
48670193 ATTTTTAATTATTATTTGAAA
1 ATTTTTAATTATTATCTGAAA
48670214 ATTTTT-ATTATAATATCTGAAA
1 ATTTTTAATTAT--TATCTGAAA
48670236 TAATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTTTTAATTATTATCTGAAA
Found at i:48671779 original size:2 final size:2
Alignment explanation
Indices: 48671772--48671811 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
48671762 TAGCACAGGA
48671772 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
48671812 TGTGTGTGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48672643 original size:2 final size:2
Alignment explanation
Indices: 48672636--48672671 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
48672626 TTCTTGCACC
48672636 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
48672672 TTTTCTGCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:48677993 original size:20 final size:20
Alignment explanation
Indices: 48677968--48678005 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48677958 AAAAATAAGT
48677968 TTTCAAA-ATATTTTGAATTA
1 TTTCAAATAT-TTTTGAATTA
48677988 TTTCAAATATTTTTGAAT
1 TTTCAAATATTTTTGAAT
48678006 AAACCTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTCAAATATTTTTGAATTA
Found at i:48678298 original size:39 final size:38
Alignment explanation
Indices: 48678254--48678329 Score: 134
Period size: 39 Copynumber: 2.0 Consensus size: 38
48678244 ATTGATAGCT
48678254 TGCCCCAAAGTATCAATACCATAGCTTGGTGTCTATACA
1 TGCCCCAAAGTATCAATACCATAGC-TGGTGTCTATACA
*
48678293 TGCCCCAAAGTATCAATACCATATCTGGTGTCTATAC
1 TGCCCCAAAGTATCAATACCATAGCTGGTGTCTATAC
48678330 CATATTGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 12 0.33
39 24 0.67
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (38 bp):
TGCCCCAAAGTATCAATACCATAGCTGGTGTCTATACA
Found at i:48681592 original size:18 final size:18
Alignment explanation
Indices: 48681565--48681599 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
48681555 ATTTTTTTTT
48681565 TTTACATTATAT-TATTA
1 TTTACATTATATATATTA
48681582 TTTATCATTATATATATT
1 TTTA-CATTATATATATT
48681600 TGTTGTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTACATTATATATATTA
Found at i:48687561 original size:10 final size:10
Alignment explanation
Indices: 48687531--48687580 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
48687521 TTGTCTACCG
*
48687531 TTTTGATAAT
1 TTTTAATAAT
*
48687541 ATTTTAGTAAT
1 -TTTTAATAAT
48687552 TTTTAATAAT
1 TTTTAATAAT
48687562 TTTTAA-AACT
1 TTTTAATAA-T
48687572 TTTTAATAA
1 TTTTAATAA
48687581 AAATTACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 22 0.65
11 10 0.29
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:48701650 original size:14 final size:15
Alignment explanation
Indices: 48701630--48701666 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
48701620 TATTATTGAA
48701630 AAATATTTCAAT-AT
1 AAATATTTCAATAAT
*
48701644 TAATATTTCAATAAT
1 AAATATTTCAATAAT
48701659 AAATATTT
1 AAATATTT
48701667 ATTACAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATTTCAATAAT
Found at i:48702093 original size:27 final size:26
Alignment explanation
Indices: 48702056--48702106 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
48702046 TACAGTAACT
48702056 TATGACATATTTAAATCTAGTATAAAAA
1 TATGACATATTTAAAT-TA-TATAAAAA
*
48702084 TATGA-ATATTTTAATTATATAAA
1 TATGACATATTTAAATTATATAAA
48702107 TATGAGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 2 0.09
27 9 0.41
28 5 0.23
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (26 bp):
TATGACATATTTAAATTATATAAAAA
Found at i:48711825 original size:27 final size:27
Alignment explanation
Indices: 48711787--48711843 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
48711777 ACACAAAAAG
48711787 ATTACGTAGAAGATCAAGAATCTAAGT
1 ATTACGTAGAAGATCAAGAATCTAAGT
48711814 ATTACGTAGAAGATCAAGAATCTAAGT
1 ATTACGTAGAAGATCAAGAATCTAAGT
48711841 ATT
1 ATT
48711844 CTTAGGTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.28
Consensus pattern (27 bp):
ATTACGTAGAAGATCAAGAATCTAAGT
Found at i:48713516 original size:13 final size:13
Alignment explanation
Indices: 48713498--48713522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48713488 CACTCTCCTC
48713498 ACCTTTCTGTCTT
1 ACCTTTCTGTCTT
48713511 ACCTTTCTGTCT
1 ACCTTTCTGTCT
48713523 CCACCGATTC
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:0.08, C:0.32, G:0.08, T:0.52
Consensus pattern (13 bp):
ACCTTTCTGTCTT
Found at i:48714377 original size:13 final size:13
Alignment explanation
Indices: 48714359--48714385 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48714349 TGTTGTTCAA
48714359 GGATATTACCATT
1 GGATATTACCATT
48714372 GGATATTACCATT
1 GGATATTACCATT
48714385 G
1 G
48714386 CTTAAAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (13 bp):
GGATATTACCATT
Found at i:48716793 original size:15 final size:15
Alignment explanation
Indices: 48716758--48716799 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48716748 TTAAGAATTT
*
48716758 TATTAAATTAT-ATA
1 TATTTAATTATAATA
48716772 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
48716786 TATTTAATAATAAT
1 TATTTAATTATAAT
48716800 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:48720611 original size:22 final size:22
Alignment explanation
Indices: 48720571--48720612 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
48720561 GGGGACGCGT
*
48720571 CAGGAAATTGCGCTGACGTCGC
1 CAGGAAATTGCGCTCACGTCGC
48720593 CAGGAAATTGCG-TCCACGTC
1 CAGGAAATTGCGCT-CACGTC
48720613 AGCAAAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.19
Consensus pattern (22 bp):
CAGGAAATTGCGCTCACGTCGC
Found at i:48721942 original size:7 final size:7
Alignment explanation
Indices: 48721930--48721954 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48721920 AGTCGATTGA
48721930 TATTTAG
1 TATTTAG
48721937 TATTTAG
1 TATTTAG
48721944 TATTTAG
1 TATTTAG
48721951 TATT
1 TATT
48721955 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Done.