Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 106 of 150
Found at i:33095135 original size:19 final size:18
Alignment explanation
Indices: 33095111--33095173 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 18
33095101 GACTTTGATT
33095111 TTTTTTGTTTTTCTTTTGA
1 TTTTTTGTTTTT-TTTTGA
33095130 TTTTTTGATTTTTTTTTGA
1 TTTTTTG-TTTTTTTTTGA
*
33095149 TTTTTT-TGATTTTTTTGA
1 TTTTTTGT-TTTTTTTTGA
33095167 TTTTTTG
1 TTTTTTG
33095174 AATTAATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
17 1 0.03
18 15 0.38
19 19 0.47
20 5 0.12
ACGTcount: A:0.08, C:0.02, G:0.11, T:0.79
Consensus pattern (18 bp):
TTTTTTGTTTTTTTTTGA
Found at i:33095136 original size:29 final size:29
Alignment explanation
Indices: 33095104--33095172 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
33095094 TATTTTTGAC
*
33095104 TTTGA-TTTTTTTTGTTTTTCTTTTGA-TTT
1 TTTGATTTTTTTTTG-ATTT-TTTTGATTTT
33095133 TTTGATTTTTTTTTGATTTTTTTGATTTT
1 TTTGATTTTTTTTTGATTTTTTTGATTTT
33095162 TTTGATTTTTT
1 TTTGATTTTTT
33095173 GAATTAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 6 0.16
29 22 0.59
30 9 0.24
ACGTcount: A:0.09, C:0.01, G:0.10, T:0.80
Consensus pattern (29 bp):
TTTGATTTTTTTTTGATTTTTTTGATTTT
Found at i:33095144 original size:9 final size:9
Alignment explanation
Indices: 33095104--33095172 Score: 77
Period size: 9 Copynumber: 7.2 Consensus size: 9
33095094 TATTTTTGAC
33095104 TTTGATTTTT
1 TTTGA-TTTT
*
33095114 TTTGTTTTTCT
1 TTTG-ATTT-T
33095125 TTTGA-TTT
1 TTTGATTTT
33095133 TTTGATTTTTT
1 TTTGA--TTTT
33095144 TTTGATTTT
1 TTTGATTTT
33095153 TTTGATTTT
1 TTTGATTTT
33095162 TTTGATTTT
1 TTTGATTTT
33095171 TT
1 TT
33095173 GAATTAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.12
9 26 0.50
10 7 0.13
11 13 0.25
ACGTcount: A:0.09, C:0.01, G:0.10, T:0.80
Consensus pattern (9 bp):
TTTGATTTT
Found at i:33095145 original size:18 final size:18
Alignment explanation
Indices: 33095111--33095192 Score: 87
Period size: 18 Copynumber: 4.4 Consensus size: 18
33095101 GACTTTGATT
*
33095111 TTTTTTGTTTTTCTTTTGA
1 TTTTTTGATTTT-TTTTGA
33095130 TTTTTTGATTTTTTTTTGA
1 TTTTTTGA-TTTTTTTTGA
33095149 TTTTTTTGA-TTTTTTTGA
1 -TTTTTTGATTTTTTTTGA
**
33095167 TTTTTTGAATTAATTTT-A
1 TTTTTTG-ATTTTTTTTGA
33095185 TTTTTTGA
1 TTTTTTGA
33095193 GTCTGAACTC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
17 8 0.14
18 18 0.32
19 18 0.32
20 12 0.21
ACGTcount: A:0.13, C:0.01, G:0.10, T:0.76
Consensus pattern (18 bp):
TTTTTTGATTTTTTTTGA
Found at i:33098788 original size:108 final size:108
Alignment explanation
Indices: 33098651--33098859 Score: 364
Period size: 108 Copynumber: 1.9 Consensus size: 108
33098641 AATTTGGCTA
* * * *
33098651 AACGTGAAATCGAAACCCAGTACCATAGGGCACGTTCCTTGAATTTCCAAACGCAAAATATTGTC
1 AACGAGAAATCGAAACCCAATACCATAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
33098716 TTATTTTGAAAATTTTTGAAAAGGATATTAACTCATTTGGTCG
66 TTATTTTGAAAATTTTTGAAAAGGATATTAACTCATTTGGTCG
*
33098759 AACGAGAAATCGAAACCCAATACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
1 AACGAGAAATCGAAACCCAATACCATAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
*
33098824 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCAT
66 TTATTTTGAAAATTTTTGAAAAGGATATTAACTCAT
33098860 NNNNNNNNNN
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 95 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (108 bp):
AACGAGAAATCGAAACCCAATACCATAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
TTATTTTGAAAATTTTTGAAAAGGATATTAACTCATTTGGTCG
Found at i:33100931 original size:17 final size:18
Alignment explanation
Indices: 33100894--33100932 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
33100884 AATCAGAAAT
* *
33100894 AAATAAAAAAAACTTGCG
1 AAATAAAAAAAACTAGAG
33100912 AAATAAAAAAAA-TAGAG
1 AAATAAAAAAAACTAGAG
33100929 AAAT
1 AAAT
33100933 CAAGTGGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (18 bp):
AAATAAAAAAAACTAGAG
Found at i:33103194 original size:19 final size:19
Alignment explanation
Indices: 33103170--33103216 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
33103160 CGACGTCTTT
*
33103170 TTTGCATT-CATTTCATTCA
1 TTTGCATTACATTACA-TCA
33103189 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
33103208 TATGCATTA
1 TTTGCATTA
33103217 AAGTCCACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:33103386 original size:24 final size:24
Alignment explanation
Indices: 33103359--33103406 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
33103349 TAAAAAACTT
* *
33103359 CAAAGGGAGATGCAAGACCAGCTA
1 CAAAGGCAAATGCAAGACCAGCTA
* *
33103383 CAAATGCAAATGCAAGAGCAGCTA
1 CAAAGGCAAATGCAAGACCAGCTA
33103407 GCTAAGATTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (24 bp):
CAAAGGCAAATGCAAGACCAGCTA
Found at i:33110415 original size:52 final size:54
Alignment explanation
Indices: 33110336--33110471 Score: 213
Period size: 52 Copynumber: 2.6 Consensus size: 54
33110326 ACTTCACCAG
*
33110336 AAGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCT-AAAAAAAATG-
1 AAGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCTAAAAAAAAAAGA
* * *
33110388 GAGAGACCAAGGTGAAAACCCGTAAAGGGCGCTTTGAATTCTAAAAAAAAAAGA
1 AAGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCTAAAAAAAAAAGA
*
33110442 AAGAGGCCAAGGTGAAAACCCGCAAAGGGC
1 AAGAGACCAAGGTGAAAACCCGCAAAGGGC
33110472 CCCTTGAGAC
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
52 39 0.52
53 9 0.12
54 27 0.36
ACGTcount: A:0.44, C:0.18, G:0.26, T:0.12
Consensus pattern (54 bp):
AAGAGACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAATCCTAAAAAAAAAAGA
Found at i:33111774 original size:45 final size:45
Alignment explanation
Indices: 33111632--33111798 Score: 146
Period size: 44 Copynumber: 3.8 Consensus size: 45
33111622 TCTTATTTCT
* * * **
33111632 CTGAAGTTGCAGTGGAGCAGATTAAAG-TCA-CTAATCTTATCCCC
1 CTGAAGTTGCAGTGGAGCAGACTGAAGAT-AGCGAGCCTTATCCCC
* * * * *
33111676 TTGAAGTTGCAGTGGGGCAGA-TCGAAGTTA-CCAGCCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGACT-GAAGATAGCGAGCCTTATCCCC
*
33111720 CTGAAGTTGCAATGGAGCAGACTGAAGATAGCGAGTCC-TATCCCC
1 CTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAG-CCTTATCCCC
** *
33111765 CTGAAGTTGCAGCAGAGCAGACTGAAGACAGCGA
1 CTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGA
33111799 ATCTTATTTC
Statistics
Matches: 101, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
43 1 0.01
44 57 0.56
45 41 0.41
46 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (45 bp):
CTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAGCCTTATCCCC
Found at i:33113557 original size:21 final size:22
Alignment explanation
Indices: 33113520--33113562 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
33113510 GTGATTTTTA
33113520 TGTTTAATTTTGC-TTTTATTT
1 TGTTTAATTTTGCTTTTTATTT
*
33113541 TGTTTTATTTT-CTTTTTTATTT
1 TGTTTAATTTTGC-TTTTTATTT
33113563 GTGAACTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 10 0.53
22 8 0.42
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.77
Consensus pattern (22 bp):
TGTTTAATTTTGCTTTTTATTT
Found at i:33113620 original size:18 final size:18
Alignment explanation
Indices: 33113587--33113625 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
33113577 TGTTATTATA
33113587 ATTATTATTACTATTTTT
1 ATTATTATTACTATTTTT
*
33113605 ATTATTATTAGTATTTTT
1 ATTATTATTACTATTTTT
33113623 ATT
1 ATT
33113626 TTGTTGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTATTATTACTATTTTT
Found at i:33115298 original size:17 final size:17
Alignment explanation
Indices: 33115278--33115310 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
33115268 CAAATCACAG
33115278 ATCTCACCAAAACATAA
1 ATCTCACCAAAACATAA
33115295 ATCTCACCAAAACATA
1 ATCTCACCAAAACATA
33115311 GATTTTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (17 bp):
ATCTCACCAAAACATAA
Found at i:33117146 original size:44 final size:44
Alignment explanation
Indices: 33117097--33117181 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
33117087 GGTTTTTTTC
*
33117097 TCCCACTTAAACTTTGATTAATGTAGATTATTTTAATATTAGTT
1 TCCCACTTAAACTCTGATTAATGTAGATTATTTTAATATTAGTT
* *
33117141 TCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATATTA
1 TCCCACTTAAACTCTGATTAATGTAGATTATTTTAATATTA
33117182 TTTGACCTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (44 bp):
TCCCACTTAAACTCTGATTAATGTAGATTATTTTAATATTAGTT
Found at i:33125281 original size:17 final size:17
Alignment explanation
Indices: 33125259--33125292 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
33125249 GACATCTTTA
33125259 ATTTTTCATGCTAAAAT
1 ATTTTTCATGCTAAAAT
*
33125276 ATTTTTCATGTTAAAAT
1 ATTTTTCATGCTAAAAT
33125293 GCTTGTAGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTTTCATGCTAAAAT
Found at i:33125708 original size:17 final size:17
Alignment explanation
Indices: 33125688--33126003 Score: 210
Period size: 17 Copynumber: 17.9 Consensus size: 17
33125678 TTTTTAAATG
33125688 AAATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
*
33125705 AAATTTTAGAAACAC-A
1 AAATTTTTGAAACACGA
** *
33125721 ATTTTTTTTTAAACACGA
1 A-AATTTTTGAAACACGA
33125739 AAATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
* * *
33125756 GAATTTTTTCAAAACACAA
1 -AAATTTTT-GAAACACGA
*
33125775 AAATTTTTTAAAACACGA
1 AAA-TTTTTGAAACACGA
* *
33125793 AAATTTGTGAAACACTA
1 AAATTTTTGAAACACGA
* * * *
33125810 GAGTTGTTGAAAACACGG
1 AAATTTTTG-AAACACGA
*
33125828 AAATTTGTGAAA-AC-A
1 AAATTTTTGAAACACGA
*
33125843 CAAATTTTTGAAACACGG
1 -AAATTTTTGAAACACGA
*
33125861 AAATTTTTAGAAAACACAA
1 AAATTTTT-G-AAACACGA
* *
33125880 AAATTTTTGGATCAACG-
1 AAATTTTTGAAAC-ACGA
*
33125897 AAATTTTTGAAAACACAA
1 AAATTTTTG-AAACACGA
*
33125915 AAATTTTCT-AAACACCA
1 AAATTTT-TGAAACACGA
*
33125932 GAATTTTTGAAAACACGA
1 AAATTTTTG-AAACACGA
**
33125950 GGATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
** *
33125967 ATTTTTTTTTGAAAATACGA
1 A--AATTTTTG-AAACACGA
33125987 AAATTTTTGAAAACACG
1 AAATTTTTG-AAACACG
33126004 GAATTTTTTT
Statistics
Matches: 231, Mismatches: 48, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
16 16 0.07
17 100 0.43
18 74 0.32
19 33 0.14
20 8 0.03
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (17 bp):
AAATTTTTGAAACACGA
Found at i:33125735 original size:34 final size:36
Alignment explanation
Indices: 33125691--33126052 Score: 155
Period size: 35 Copynumber: 10.2 Consensus size: 36
33125681 TTAAATGAAA
* *
33125691 TTTTTGAAACACGAAAATTTTAGAAACAC-A-ATTT
1 TTTTTAAAACACGAAAATTTTAGAAACACGAGAATT
* *
33125725 TTTTTTAAACACGAAAATTTTTGAAACACGAGAATT
1 TTTTTAAAACACGAAAATTTTAGAAACACGAGAATT
* * *
33125761 TTTTCAAAACACAAAAATTTTTTA-AAACACGA-AA-A
1 TTTTTAAAACACGAAAA--TTTTAGAAACACGAGAATT
* * * * * *
33125796 TTTGTGAAACACTAGAGTTGTT-GAAAACACG-GAAAT
1 TTTTTAAAACACGAAAATT-TTAG-AAACACGAGAATT
* * *
33125832 TTGTGAAAACAC--AAATTTTTGAAACACG-GAAATT
1 TTTTTAAAACACGAAAATTTTAGAAACACGAG-AATT
** * * * *
33125866 TTTAGAAAACACAAAAATTTTTGGATCAACGA-AA-T
1 TTTTTAAAACACGAAAATTTTAGAAAC-ACGAGAATT
* * ** *
33125901 TTTTGAAAACACAAAAATTTTCTAAACACCAGAA-T
1 TTTTTAAAACACGAAAATTTTAGAAACACGAGAATT
* ** * *
33125936 TTTTGAAAACACGAGGATTTTTGAAACACGA-ATTTT
1 TTTTTAAAACACGAAAATTTTAGAAACACGAGA-ATT
* *
33125972 TTTTTGAAAATACGAAAATTTTTGAAAACACG-GAATTTT
1 TTTTT-AAAACACGAAAATTTTAG-AAACACGAGAA--TT
* * *
33126011 TTTTTGAAAACATGAGAATTTT-GAAAGACGA-AATCT
1 TTTTT-AAAACACGAAAATTTTAGAAACACGAGAAT-T
33126047 TTTTTA
1 TTTTTA
33126053 TTTTTATTTT
Statistics
Matches: 255, Mismatches: 48, Indels: 49
0.72 0.14 0.14
Matches are distributed among these distances:
33 12 0.05
34 50 0.20
35 74 0.29
36 51 0.20
37 34 0.13
38 13 0.05
39 21 0.08
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (36 bp):
TTTTTAAAACACGAAAATTTTAGAAACACGAGAATT
Found at i:33125763 original size:35 final size:35
Alignment explanation
Indices: 33125691--33126012 Score: 207
Period size: 35 Copynumber: 9.1 Consensus size: 35
33125681 TTAAATGAAA
* * *
33125691 TTTTTGAAACACGAAAATTTTAGAAACAC-A-ATTT
1 TTTTTAAAACACGAAAATTTTTGAAACACGAGA-AT
*
33125725 TTTTTTAAACACGAAAATTTTTGAAACACGAGAAT
1 TTTTTAAAACACGAAAATTTTTGAAACACGAGAAT
* * *
33125760 TTTTTCAAAACACAAAAATTTTTTAAAACACGA-AAA
1 TTTTT-AAAACACGAAAA-TTTTTGAAACACGAGAAT
* * * * * *
33125796 TTTGTGAAACACTAGAGTTGTTGAAAACACG-GAAAT
1 TTTTTAAAACACGAAAATTTTTG-AAACACGAG-AAT
* *
33125832 TTGTGAAAACAC--AAATTTTTGAAACACG-GAAAT
1 TTTTTAAAACACGAAAATTTTTGAAACACGAG-AAT
* * * *
33125865 TTTTAGAAAACACAAAAATTTTTGGATCAACGA-AAT
1 TTTT-TAAAACACGAAAATTTTTGAAAC-ACGAGAAT
* * *
33125901 TTTTGAAAACACAAAAATTTTCT-AAACACCAGAAT
1 TTTTTAAAACACGAAAATTTT-TGAAACACGAGAAT
* ** *
33125936 TTTTGAAAACACGAGGATTTTTGAAACACGA-ATTTT
1 TTTTTAAAACACGAAAATTTTTGAAACACGAGA--AT
*
33125972 TTTTTGAAAATACGAAAATTTTTGAAAACACG-GAAT
1 TTTTT-AAAACACGAAAATTTTTG-AAACACGAGAAT
33126008 TTTTT
1 TTTTT
33126013 TTTGAAAACA
Statistics
Matches: 230, Mismatches: 38, Indels: 38
0.75 0.12 0.12
Matches are distributed among these distances:
33 15 0.07
34 50 0.22
35 69 0.30
36 57 0.25
37 31 0.13
38 8 0.03
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (35 bp):
TTTTTAAAACACGAAAATTTTTGAAACACGAGAAT
Found at i:33125838 original size:18 final size:18
Alignment explanation
Indices: 33125688--33126003 Score: 235
Period size: 18 Copynumber: 17.9 Consensus size: 18
33125678 TTTTTAAATG
33125688 AAATTTTTG-AAACACGA
1 AAATTTTTGAAAACACGA
*
33125705 AAATTTTAG-AAACAC-A
1 AAATTTTTGAAAACACGA
** **
33125721 ATTTTTTTTTAAACACGA
1 AAATTTTTGAAAACACGA
33125739 AAATTTTTG-AAACACGA
1 AAATTTTTGAAAACACGA
* * *
33125756 GAATTTTTTCAAAACACAA
1 -AAATTTTTGAAAACACGA
*
33125775 AAATTTTTTAAAACACGA
1 AAATTTTTGAAAACACGA
* *
33125793 AAATTTGTG-AAACACTA
1 AAATTTTTGAAAACACGA
* * * *
33125810 GAGTTGTTGAAAACACGG
1 AAATTTTTGAAAACACGA
*
33125828 AAATTTGTGAAAACAC--
1 AAATTTTTGAAAACACGA
*
33125844 AAATTTTTG-AAACACGG
1 AAATTTTTGAAAACACGA
*
33125861 AAATTTTTAGAAAACACAA
1 AAATTTTT-GAAAACACGA
* *
33125880 AAATTTTTG-GATCAACG-
1 AAATTTTTGAAAAC-ACGA
*
33125897 AAATTTTTGAAAACACAA
1 AAATTTTTGAAAACACGA
*
33125915 AAATTTTCT--AAACACCA
1 AAATTTT-TGAAAACACGA
*
33125932 GAATTTTTGAAAACACGA
1 AAATTTTTGAAAACACGA
**
33125950 GGATTTTTG-AAACACGA
1 AAATTTTTGAAAACACGA
** *
33125967 ATTTTTTTTTGAAAATACGA
1 A--AATTTTTGAAAACACGA
33125987 AAATTTTTGAAAACACG
1 AAATTTTTGAAAACACG
33126004 GAATTTTTTT
Statistics
Matches: 234, Mismatches: 47, Indels: 35
0.74 0.15 0.11
Matches are distributed among these distances:
15 6 0.03
16 15 0.06
17 82 0.35
18 95 0.41
19 28 0.12
20 8 0.03
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (18 bp):
AAATTTTTGAAAACACGA
Found at i:33126015 original size:22 final size:22
Alignment explanation
Indices: 33125953--33126032 Score: 77
Period size: 18 Copynumber: 4.0 Consensus size: 22
33125943 AACACGAGGA
33125953 TTTTTG-AAACAC--GAATTTT
1 TTTTTGAAAACACGAGAATTTT
* *
33125972 TTTTTGAAAATACGA-AA---A
1 TTTTTGAAAACACGAGAATTTT
33125990 TTTTTGAAAACACG-GAATTTT
1 TTTTTGAAAACACGAGAATTTT
*
33126011 TTTTTGAAAACATGAGAATTTT
1 TTTTTGAAAACACGAGAATTTT
33126033 GAAAGACGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
18 15 0.31
19 6 0.12
20 5 0.10
21 15 0.31
22 7 0.15
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (22 bp):
TTTTTGAAAACACGAGAATTTT
Found at i:33126031 original size:39 final size:38
Alignment explanation
Indices: 33125935--33126036 Score: 145
Period size: 39 Copynumber: 2.7 Consensus size: 38
33125925 AACACCAGAA
*
33125935 TTTTTGAAAACACGAGGATTTTTG-AAACACGAATTTT
1 TTTTTGAAAACACGAGAATTTTTGAAAACACGAATTTT
* *
33125972 TTTTTGAAAATACGAAAATTTTTGAAAACACGGAATTTT
1 TTTTTGAAAACACGAGAATTTTTGAAAACAC-GAATTTT
*
33126011 TTTTTGAAAACATGAGAA-TTTTGAAA
1 TTTTTGAAAACACGAGAATTTTTGAAA
33126037 GACGAAATCT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 21 0.37
38 14 0.25
39 22 0.39
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (38 bp):
TTTTTGAAAACACGAGAATTTTTGAAAACACGAATTTT
Found at i:33126050 original size:39 final size:36
Alignment explanation
Indices: 33125935--33126051 Score: 135
Period size: 37 Copynumber: 3.1 Consensus size: 36
33125925 AACACCAGAA
*
33125935 TTTTTGAAAACACGAGGATTTTTGAAACACGAATTTT
1 TTTTTGAAAACACGA-GAATTTTGAAACACGAATTTT
* *
33125972 TTTTTGAAAATACGAAAATTTTTGAAAACACGGAATTTT
1 TTTTTGAAAACACGAGAA-TTTTG-AAACAC-GAATTTT
* * * *
33126011 TTTTTGAAAACATGAGAATTTTGAAAGACGAAATCT
1 TTTTTGAAAACACGAGAATTTTGAAACACGAATTTT
33126047 TTTTT
1 TTTTT
33126052 ATTTTTATTT
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
36 11 0.16
37 24 0.35
38 11 0.16
39 22 0.32
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (36 bp):
TTTTTGAAAACACGAGAATTTTGAAACACGAATTTT
Found at i:33126302 original size:19 final size:19
Alignment explanation
Indices: 33126280--33126322 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
33126270 GACACAAAGA
* *
33126280 TTTTGGAACACAGGAATTT
1 TTTTGGAAAACACGAATTT
*
33126299 TTTTCGAAAACACGAATTT
1 TTTTGGAAAACACGAATTT
33126318 TTTTG
1 TTTTG
33126323 AATATTTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTTGGAAAACACGAATTT
Found at i:33126499 original size:14 final size:14
Alignment explanation
Indices: 33126480--33126506 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33126470 GAATTAAATT
33126480 AAAAATATAAAAAC
1 AAAAATATAAAAAC
33126494 AAAAATATAAAAA
1 AAAAATATAAAAA
33126507 TGCATAAAAT
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:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAATATAAAAAC
Found at i:33126660 original size:8 final size:8
Alignment explanation
Indices: 33126641--33126696 Score: 52
Period size: 8 Copynumber: 7.6 Consensus size: 8
33126631 TTAAACCTTT
33126641 TTTTTCTC
1 TTTTTCTC
33126649 -TTTTCTC
1 TTTTTCTC
33126656 TTTTT-TC
1 TTTTTCTC
33126663 TTTTT-TCC
1 TTTTTCT-C
33126671 TTTTT-TC
1 TTTTTCTC
*
33126678 --TTTCTT
1 TTTTTCTC
33126684 TTTTTCTC
1 TTTTTCTC
33126692 TTTTT
1 TTTTT
33126697 TTCTCTCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 3 0.07
6 1 0.02
7 16 0.39
8 21 0.51
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTCTC
Found at i:33126664 original size:14 final size:14
Alignment explanation
Indices: 33126638--33126724 Score: 74
Period size: 14 Copynumber: 6.4 Consensus size: 14
33126628 AAATTAAACC
33126638 TTTT-TTTTCTCTT
1 TTTTCTTTTCTCTT
* *
33126651 TTCTCTTTTTTCTT
1 TTTTCTTTTCTCTT
*
33126665 TTTTCCTTTTTTCTT
1 TTTT-CTTTTCTCTT
33126680 TCTTT-TTTTCTC-T
1 T-TTTCTTTTCTCTT
*
33126693 TTTT-TTCTCTCTT
1 TTTTCTTTTCTCTT
**
33126706 TTTTCTCCTCTCTT
1 TTTTCTTTTCTCTT
33126720 TTTTC
1 TTTTC
33126725 GGCCTGCCTC
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
12 9 0.14
13 10 0.16
14 30 0.48
15 11 0.17
16 3 0.05
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTTTTCTCTT
Found at i:33126667 original size:22 final size:21
Alignment explanation
Indices: 33126642--33126697 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
33126632 TAAACCTTTT
*
33126642 TTTTCTCTTTTCTCTTTTTTC
1 TTTTCTCTTTTTTCTTTTTTC
*
33126663 TTTTTTCCTTTTTTCTTTCTTT-
1 TTTTCT-CTTTTTTCTTT-TTTC
33126685 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
33126698 TCTCTCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 12 0.40
22 15 0.50
23 3 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTCTCTTTTTTCTTTTTTC
Found at i:33126685 original size:10 final size:10
Alignment explanation
Indices: 33126639--33126712 Score: 69
Period size: 10 Copynumber: 7.0 Consensus size: 10
33126629 AATTAAACCT
33126639 TTTTTTTCTC
1 TTTTTTTCTC
* *
33126649 TTTTCTCTTTTT
1 TTTT-T-TTCTC
33126661 TCTTTTTTC-C
1 T-TTTTTTCTC
*
33126671 TTTTTTCTTTC
1 TTTTTT-TCTC
33126682 TTTTTTTCTC
1 TTTTTTTCTC
33126692 TTTTTTTCTC
1 TTTTTTTCTC
33126702 TCTTTTTTCTC
1 T-TTTTTTCTC
33126713 CTCTCTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
9 5 0.10
10 20 0.38
11 19 0.37
12 5 0.10
13 3 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:33126874 original size:19 final size:20
Alignment explanation
Indices: 33126850--33126899 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
33126840 GCCTGTTGCA
33126850 TTTTTTTTCTGCTTTG--TT
1 TTTTTTTTCTGCTTTGCCTT
**
33126868 TTTTTTTTGGGGCTTTGCCTT
1 TTTTTTTT-CTGCTTTGCCTT
33126889 TTTTTTTTCTG
1 TTTTTTTTCTG
33126900 GCCTGGAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.32
19 6 0.24
20 1 0.04
21 10 0.40
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (20 bp):
TTTTTTTTCTGCTTTGCCTT
Found at i:33126984 original size:7 final size:7
Alignment explanation
Indices: 33126968--33127086 Score: 91
Period size: 7 Copynumber: 16.9 Consensus size: 7
33126958 TGAATTAATA
*
33126968 TTTTTAT
1 TTTTTCT
33126975 TTTTTC-
1 TTTTTCT
33126981 TTTTTCT
1 TTTTTCT
33126988 TTTTTCT
1 TTTTTCT
*
33126995 TTCTT-T
1 TTTTTCT
*
33127001 TTCTTCT
1 TTTTTCT
**
33127008 TCCTTCT
1 TTTTTCT
*
33127015 TCTTTCT
1 TTTTTCT
*
33127022 TCTTTCT
1 TTTTTCT
33127029 TTCTTTCT
1 TT-TTTCT
33127037 TTCTTTCT
1 TT-TTTCT
33127045 TTCTTTCT
1 TT-TTTCT
*
33127053 TTCTTCT
1 TTTTTCT
*
33127060 CTTTTC-
1 TTTTTCT
*
33127066 TTTCTCT
1 TTTTTCT
33127073 TTTTTCT
1 TTTTTCT
33127080 TTCTTTC
1 TT-TTTC
33127087 CCGATCAACC
Statistics
Matches: 96, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
6 16 0.17
7 53 0.55
8 27 0.28
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCT
Found at i:33126999 original size:4 final size:4
Alignment explanation
Indices: 33126983--33127086 Score: 117
Period size: 4 Copynumber: 26.0 Consensus size: 4
33126973 ATTTTTTCTT
* *
33126983 TTTC TTT- TTTC TTTC TTTT TCTTC -TTC CTTC -TTC TTTC -TTC TTTC
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC
*
33127028 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTCTC TTTTC TTTC TCTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTTC TTTC T-TTC TTTC
33127079 TTTC TTTC
1 TTTC TTTC
33127087 CCGATCAACC
Statistics
Matches: 88, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
3 12 0.14
4 65 0.74
5 9 0.10
6 2 0.02
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:33127227 original size:20 final size:21
Alignment explanation
Indices: 33127201--33127253 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
33127191 TCTTCTTTGC
*
33127201 TCTTTTTTTCTT-CTT-TTTT
1 TCTTTTTTGCTTGCTTGTTTT
*
33127220 TCCTTTTTGCTTGCTTGTTTT
1 TCTTTTTTGCTTGCTTGTTTT
33127241 TCTTTTTT-CTTGC
1 TCTTTTTTGCTTGC
33127254 CTCTTGGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.34
20 8 0.28
21 11 0.38
ACGTcount: A:0.00, C:0.19, G:0.08, T:0.74
Consensus pattern (21 bp):
TCTTTTTTGCTTGCTTGTTTT
Found at i:33127589 original size:29 final size:29
Alignment explanation
Indices: 33127547--33127651 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 29
33127537 TAAAACTTCT
* * *
33127547 AGGGTTAAAGTGTAATTTTGGAAAATTTA
1 AGGGTCAAAATGTAATTTTAGAAAATTTA
* * *
33127576 AGGGTTAAAATGTAATTTCAAAAAAGTTT-
1 AGGGTCAAAATGTAATTTTAGAAAA-TTTA
*
33127605 AGGGTCAAAATATAATTTTAAGAAAATTTA
1 AGGGTCAAAATGTAATTTT-AGAAAATTTA
* *
33127635 GGGGTCAAAATGCAATT
1 AGGGTCAAAATGTAATT
33127652 GTGTAAAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
29 40 0.65
30 22 0.35
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (29 bp):
AGGGTCAAAATGTAATTTTAGAAAATTTA
Found at i:33127981 original size:78 final size:78
Alignment explanation
Indices: 33127834--33128653 Score: 1107
Period size: 78 Copynumber: 10.7 Consensus size: 78
33127824 GCGACCTAAA
* *
33127834 GCTCAACTCACCTCTCG-AGTTATGA--CGATTTTTTTG--AAACAG-AATTGAAAAATACCTCA
1 GCTCAACTCACCTCTCGCA-ATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCA
*
33127893 GTGTGTGACCCGAG
65 GCGTGTGACCCGAG
33127907 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
33127972 CGTGTGACCCGAG
66 CGTGTGACCCGAG
*
33127985 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTGAAAAATACCTCA
33128050 GCGTGTGACCCGAG
65 GCGTGTGACCCGAG
*
33128064 GCTCAACTCAACTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
33128129 CGTGTGACCCGAG
66 CGTGTGACCCGAG
33128142 GCTCAACTCACCTCTCGC------A----A-TTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
33128196 CGTGTGACCCGAG
66 CGTGTGACCCGAG
* *
33128209 ACTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
*
33128274 CGTGTGATCCGAG
66 CGTGTGACCCGAG
* *
33128287 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAATACCTCAG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
33128352 CGTGTGACCCGAG
66 CGTGTGACCCGAG
* * *
33128365 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTTAAAAGAAATACTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAA-TT-GAA-AAATACCT
* * *
33128430 CGGCATGTG-TCCGAG
63 CAGCGTGTGACCCGAG
* *
33128445 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAAAAATTAAAAAAAATACCTC
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATT--GAAAAATACCTC
* * *
33128508 GGAGTGCGACCCGAG
64 AGCGTGTGACCCGAG
* * * *
33128523 ACTCAACTCACCT-TACGCAATATGAGCTGA--TTTTTGAAAAATAGAAATT-TAAAATACCTCA
1 GCTCAACTCACCTCT-CGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCA
* ** *
33128584 GTGTACGACCCGGG
65 GCGTGTGACCCGAG
*
33128598 GCTCAACTCACCTCTCACAATATGAGTTGA--TTTTTGCAAAAACAGAAATTGAAAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAAACAGAAATTGAAAAA
33128654 ATAATTTTTG
Statistics
Matches: 678, Mismatches: 42, Indels: 50
0.88 0.05 0.06
Matches are distributed among these distances:
67 63 0.09
68 1 0.00
72 1 0.00
73 23 0.03
74 1 0.00
75 62 0.09
76 13 0.02
77 27 0.04
78 358 0.53
79 78 0.12
80 37 0.05
81 14 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (78 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
CGTGTGACCCGAG
Found at i:33128066 original size:157 final size:155
Alignment explanation
Indices: 33127834--33128653 Score: 1110
Period size: 145 Copynumber: 5.4 Consensus size: 155
33127824 GCGACCTAAA
*
33127834 GCTCAACTCACCTCTCG-AGTTATGA--CGATTTTTTTG--AAACAG-AATTGAAAAATACCTCA
1 GCTCAACTCACCTCTCGCA-TTATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAATACCTCA
*
33127893 GTGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATT
64 GCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATT
33127958 GAAAAATACCTCAGCGTGTGACCCGAG
129 GAAAAATACCTCAGCGTGTGACCCGAG
33127985 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCA
1 GCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTGAAAAACAGAAATTGAAAAATACCTCA
*
33128050 GCGTGTGACCCGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATT
64 GCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATT
33128115 GAAAAATACCTCAGCGTGTGACCCGAG
129 GAAAAATACCTCAGCGTGTGACCCGAG
33128142 GCTCAACTCACCTCTCGC------A----ATTTTTTGAAAAACAGAAATTGAAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAATACCTCAGC
* *
33128197 GTGTGACCCGAGACTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGA
66 GTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGA
*
33128262 AAAATACCTCAGCGTGTGATCCGAG
131 AAAATACCTCAGCGTGTGACCCGAG
*
33128287 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAATACCTCAG
1 GCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
*
33128352 CGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTT
65 CGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAA-TT
* * * * *
33128417 AAAAGAAATACTTCGGCATGTG-TCCGAG
129 -GAA-AAATACCTCAGCGTGTGACCCGAG
* * * *
33128445 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAAAAATTAAAAAAAATACCTCG
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATT--GAAAAATACCTCA
* * * * *
33128509 GAGTGCGACCCGAGACTCAACTCACCT-TACGCAATATGAGCTGA--TTTTTGAAAAATAGAAAT
64 GCGTGTGACCCGAGGCTCAACTCACCTCT-CGCAATATGAGTTGATTTTTTTGAAAAACAGAAAT
* * ** *
33128571 T-TAAAATACCTCAGTGTACGACCCGGG
128 TGAAAAATACCTCAGCGTGTGACCCGAG
* *
33128598 GCTCAACTCACCTCTCACAATATGAGTTGA-TTTTTGCAAAAACAGAAATTGAAAAA
1 GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTG-AAAAACAGAAATTGAAAAA
33128654 ATAATTTTTG
Statistics
Matches: 605, Mismatches: 38, Indels: 51
0.87 0.05 0.07
Matches are distributed among these distances:
145 139 0.23
147 1 0.00
151 25 0.04
152 17 0.03
153 42 0.07
154 20 0.03
155 3 0.00
156 130 0.21
157 128 0.21
158 86 0.14
159 14 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (155 bp):
GCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAATACCTCAGC
GTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGA
AAAATACCTCAGCGTGTGACCCGAG
Found at i:33128327 original size:223 final size:223
Alignment explanation
Indices: 33127938--33128618 Score: 917
Period size: 223 Copynumber: 3.0 Consensus size: 223
33127928 ATGAGTTGAT
33127938 TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGC
1 TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGC
*
33128003 ATTATGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTC
66 AATATGAGTTGA-TTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTC
* *
33128068 AACTCAACTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTG
130 AACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAATACCTCAGCGTG
33128133 TGACCCGAGGCTCAACTCACCTCTCGCAA
195 TGACCCGAGGCTCAACTCACCTCTCGCAA
* *
33128162 TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGACCCGAGACTCAACTCACCTATCGC
1 TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGC
*
33128227 AATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGATCCGAGGCTCA
66 AATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCA
*
33128292 ACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAATACCTCAGCGTGT
131 ACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAATACCTCAGCGTGT
33128357 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
196 GACCCGAGGCTCAACTCACCTCTCGC------A----A
* * * * * *
33128395 TTTTTTTGAAAAACAAAAATTTAAAAGAAATACTTCGGCATGTG-TCCGAGGCTCAACTCACCTC
1 -TTTTTTGAAAAACAGAAA-TT-GAA-AAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTC
* * * * *
33128459 TCGCAATATGAGTTGA--TTTTTGAAAAACAAAAATTAAAAAAAATACCTCGGAGTGCGACCCGA
62 TCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATT--GAAAAATACCTCAGCGTGTGACCCGA
* * *
33128522 GACTCAACTCACCT-TACGCAATATGAGCTGA--TTTTTGAAAAATAGAAATT-TAAAATACCTC
125 GGCTCAACTCACCTCT-CGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAATACCTC
* ** * *
33128583 AGTGTACGACCCGGGGCTCAACTCACCTCTCACAA
189 AGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAA
33128618 T
1 T
33128619 ATGAGTTGAT
Statistics
Matches: 410, Mismatches: 30, Indels: 36
0.86 0.06 0.08
Matches are distributed among these distances:
222 1 0.00
223 141 0.34
224 74 0.18
227 1 0.00
229 1 0.00
233 39 0.10
234 54 0.13
235 3 0.01
236 82 0.20
237 14 0.03
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (223 bp):
TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGC
AATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCA
ACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAGAAATTGAAAAATACCTCAGCGTGT
GACCCGAGGCTCAACTCACCTCTCGCAA
Found at i:33129511 original size:1 final size:1
Alignment explanation
Indices: 33129507--33129564 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
33129497 TTTTTCCTTC
* * * * * * *
33129507 TTTTTTCTTTTTCTTTTTTGTTTTTTTTTGTTTTTGTTTTTTTTGTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33129565 AGGCATAATA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:33129523 original size:23 final size:23
Alignment explanation
Indices: 33129497--33129547 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
33129487 TTCATCTTGA
33129497 TTTTTCCTTCTTTTTTCTTTTTC
1 TTTTTCCTTCTTTTTTCTTTTTC
** * * *
33129520 TTTTTTGTTTTTTTTTGTTTTTG
1 TTTTTCCTTCTTTTTTCTTTTTC
33129543 TTTTT
1 TTTTT
33129548 TTTGTTTTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (23 bp):
TTTTTCCTTCTTTTTTCTTTTTC
Found at i:33129524 original size:14 final size:13
Alignment explanation
Indices: 33129507--33129564 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
33129497 TTTTTCCTTC
* *
33129507 TTTTTTCTTTTTC
1 TTTTTTGTTTTTT
33129520 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
* *
33129533 TTTGTT-TTTGTT
1 TTTTTTGTTTTTT
33129545 TTTTTTGTTTTGTT
1 TTTTTTGTTTT-TT
33129559 TTTTTT
1 TTTTTT
33129565 AGGCATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.27
13 19 0.51
14 8 0.22
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:33129531 original size:30 final size:30
Alignment explanation
Indices: 33129504--33129563 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
33129494 TGATTTTTCC
33129504 TTCT-TTTTTCTTTTTCTT-TTTTGTTTTT
1 TTCTGTTTTTCTTTTTCTTGTTTTGTTTTT
* * *
33129532 TTTTGTTTTTGTTTTTTTTGTTTTGTTTTT
1 TTCTGTTTTTCTTTTTCTTGTTTTGTTTTT
33129562 TT
1 TT
33129564 TAGGCATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 3 0.11
29 12 0.44
30 12 0.44
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (30 bp):
TTCTGTTTTTCTTTTTCTTGTTTTGTTTTT
Found at i:33129533 original size:16 final size:15
Alignment explanation
Indices: 33129514--33129564 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
33129504 TTCTTTTTTC
*
33129514 TTTTTCTTTTTTGTT
1 TTTTTTTTTTTTGTT
33129529 TTTTTTTGTTTTTG-T
1 TTTTTTT-TTTTTGTT
*
33129544 TTTTTTTGTTTTGTT
1 TTTTTTTTTTTTGTT
33129559 TTTTTT
1 TTTTTT
33129565 AGGCATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 5 0.16
15 21 0.66
16 6 0.19
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTTGTT
Found at i:33129564 original size:30 final size:29
Alignment explanation
Indices: 33129508--33129564 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
33129498 TTTTCCTTCT
33129508 TTTTTCTTTTTCTTTTTTGTTTTTTTTTG
1 TTTTTCTTTTTCTTTTTTGTTTTTTTTTG
* *
33129537 TTTTTGTTTTTTTTGTTTTGTTTTTTTT
1 TTTTTCTTTTTCTT-TTTTGTTTTTTTT
33129565 AGGCATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.88
Consensus pattern (29 bp):
TTTTTCTTTTTCTTTTTTGTTTTTTTTTG
Found at i:33136977 original size:17 final size:17
Alignment explanation
Indices: 33136957--33137281 Score: 190
Period size: 17 Copynumber: 18.5 Consensus size: 17
33136947 TTTTTAAATG
33136957 AAATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
* *
33136974 AAATTTTAGAAACATG-
1 AAATTTTTGAAACACGA
** *
33136990 ATTTTTTTTAAACACGA
1 AAATTTTTGAAACACGA
*
33137007 CAATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
* * *
33137024 GAATTTTTTCAAAACACAA
1 -AAATTTTT-GAAACACGA
*
33137043 AAATTTTTTAAAACACGA
1 AAA-TTTTTGAAACACGA
* *
33137061 AAATTTGTGAAACACTA
1 AAATTTTTGAAACACGA
* * ** * *
33137078 GAGTCGTTGAAAACATGG
1 AAATTTTTG-AAACACGA
* *
33137096 AAATTTGTGAAAACACAA
1 AAATTTTTG-AAACACGA
*
33137114 AAATTTTTGAAACACGG
1 AAATTTTTGAAACACGA
*
33137131 AAATTTTTAGAAAACACAA
1 AAATTTTT-G-AAACACGA
* *
33137150 AAATTTTTGGATCACCG-
1 AAATTTTTGAAACA-CGA
*
33137167 GAATTTTTGAAAACACGA
1 AAATTTTTG-AAACACGA
*
33137185 AAATTTTCT-AAACACTA
1 AAATTTT-TGAAACACGA
*
33137202 GAATTTTTGAAAACACGA
1 AAATTTTTG-AAACACGA
**
33137220 GGATTTTTGAAACACGA
1 AAATTTTTGAAACACGA
** *
33137237 ATTTTTTTTTGAAAATACGA
1 A--AATTTTTG-AAACACGA
33137257 AAATTTTTGAAAACAC-A
1 AAATTTTTG-AAACACGA
*
33137274 GAATTTTT
1 AAATTTTT
33137282 TTTGAAAACA
Statistics
Matches: 232, Mismatches: 60, Indels: 32
0.72 0.19 0.10
Matches are distributed among these distances:
16 12 0.05
17 98 0.42
18 81 0.35
19 33 0.14
20 8 0.03
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (17 bp):
AAATTTTTGAAACACGA
Found at i:33137014 original size:19 final size:19
Alignment explanation
Indices: 33136990--33137066 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
33136980 TAGAAACATG
* *
33136990 ATTTTTTTTAAACACGACA
1 ATTTTTTTAAAACACGAAA
* *
33137009 A--TTTTTGAAACACGAGA
1 ATTTTTTTAAAACACGAAA
*
33137026 ATTTTTTCAAAACAC-AAA
1 ATTTTTTTAAAACACGAAA
*
33137044 AATTTTTTAAAACACGAAA
1 ATTTTTTTAAAACACGAAA
33137063 ATTT
1 ATTT
33137067 GTGAAACACT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
17 15 0.32
18 15 0.32
19 17 0.36
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.36
Consensus pattern (19 bp):
ATTTTTTTAAAACACGAAA
Found at i:33137127 original size:35 final size:35
Alignment explanation
Indices: 33136956--33137318 Score: 233
Period size: 35 Copynumber: 10.3 Consensus size: 35
33136946 TTTTTTAAAT
* *
33136956 GAAATTTTTG-AAACACGAAAATTTTAGAAACA-T
1 GAAATTTTTGAAAACACGAAAATTTTTGAAACACG
* ** *
33136989 G-ATTTTTTTTAAACACGACAATTTTTGAAACACG
1 GAAATTTTTGAAAACACGAAAATTTTTGAAACACG
* * * *
33137023 AGAATTTTTTCAAAACACAAAAATTTTTTAAAACACG
1 -GAAATTTTTGAAAACACGAAAA-TTTTTGAAACACG
* * * * * ** *
33137060 AAAATTTGTG-AAACACTAGAGTCGTTGAAAACATG
1 GAAATTTTTGAAAACACGAAAATTTTTG-AAACACG
* *
33137095 GAAATTTGTGAAAACACAAAAATTTTTGAAACACG
1 GAAATTTTTGAAAACACGAAAATTTTTGAAACACG
* * *
33137130 GAAATTTTTAGAAAACACAAAAATTTTTGGATCACCG
1 GAAATTTTT-GAAAACACGAAAATTTTTGAAACA-CG
33137167 G-AATTTTTGAAAACACGAAAATTTTCT-AAACAC-
1 GAAATTTTTGAAAACACGAAAATTTT-TGAAACACG
* **
33137200 TAGAATTTTTGAAAACACGAGGATTTTTGAAACAC-
1 GA-AATTTTTGAAAACACGAAAATTTTTGAAACACG
* * *
33137235 GAATTTTTTTTTGAAAATACGAAAATTTTTGAAAACACA
1 GAA---ATTTTTGAAAACACGAAAATTTTTG-AAACACG
* * * *
33137274 GAATTTTTTTTGAAAACATGAGAA-TTTTGAAAGAC-
1 GAA--ATTTTTGAAAACACGAAAATTTTTGAAACACG
33137309 GAAATCTTTT
1 GAAAT-TTTT
33137319 TTATTTTTAT
Statistics
Matches: 264, Mismatches: 47, Indels: 37
0.76 0.14 0.11
Matches are distributed among these distances:
32 6 0.02
33 22 0.08
34 10 0.04
35 89 0.34
36 69 0.26
37 41 0.16
38 24 0.09
39 3 0.01
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (35 bp):
GAAATTTTTGAAAACACGAAAATTTTTGAAACACG
Found at i:33137256 original size:20 final size:19
Alignment explanation
Indices: 33137205--33137291 Score: 81
Period size: 20 Copynumber: 4.6 Consensus size: 19
33137195 AACACTAGAA
***
33137205 TTTTTGAAAACACG-AGGA
1 TTTTTGAAAACACGAATTT
33137223 TTTTTG-AAACACGAATTTT
1 TTTTTGAAAACACGAA-TTT
* **
33137242 TTTTTGAAAATACGAA-AA
1 TTTTTGAAAACACGAATTT
33137260 TTTTTGAAAACACAGAATTT
1 TTTTTGAAAACAC-GAATTT
33137280 TTTTTGAAAACA
1 TTTTTGAAAACA
33137292 TGAGAATTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
17 7 0.13
18 19 0.35
19 9 0.16
20 20 0.36
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTTTGAAAACACGAATTT
Found at i:33137301 original size:18 final size:18
Alignment explanation
Indices: 33136999--33137305 Score: 181
Period size: 18 Copynumber: 17.1 Consensus size: 18
33136989 GATTTTTTTT
*
33136999 AAACACGACAATTTTTG-
1 AAACACGAGAATTTTTGA
*
33137016 AAACACGAGAATTTTTTCA
1 AAACACGAGAA-TTTTTGA
* * *
33137035 AAACACAAAAATTTTTTA
1 AAACACGAGAATTTTTGA
* *
33137053 AAACACGAAAATTTGTG-
1 AAACACGAGAATTTTTGA
* * **
33137070 AAACACTAGAGTCGTTGA
1 AAACACGAGAATTTTTGA
* *
33137088 AAACATG-GAAATTTGTGA
1 AAACACGAG-AATTTTTGA
* *
33137106 AAACACAAAAATTTTTG-
1 AAACACGAGAATTTTTGA
33137123 AAACACG-GAAATTTTTAGA
1 AAACACGAG-AATTTTT-GA
* *
33137142 AAACACAAAAATTTTTG-
1 AAACACGAGAATTTTTGA
* *
33137159 GATCACCG-GAATTTTTGA
1 AAACA-CGAGAATTTTTGA
*
33137177 AAACACGAAAATTTTCT--
1 AAACACGAGAATTTT-TGA
*
33137194 AAACACTAGAATTTTTGA
1 AAACACGAGAATTTTTGA
*
33137212 AAACACGAGGATTTTTG-
1 AAACACGAGAATTTTTGA
*
33137229 AAACACGA-ATTTTTTTTTGA
1 AAACACGAGA---ATTTTTGA
* *
33137249 AAATACGAAAATTTTTGA
1 AAACACGAGAATTTTTGA
33137267 AAACAC-AGAATTTTTTTTGA
1 AAACACGAGAA---TTTTTGA
*
33137287 AAACATGAGAA-TTTTGA
1 AAACACGAGAATTTTTGA
33137304 AA
1 AA
33137306 GACGAAATCT
Statistics
Matches: 220, Mismatches: 46, Indels: 48
0.70 0.15 0.15
Matches are distributed among these distances:
16 1 0.00
17 80 0.36
18 86 0.39
19 29 0.13
20 19 0.09
21 5 0.02
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (18 bp):
AAACACGAGAATTTTTGA
Found at i:33137301 original size:20 final size:20
Alignment explanation
Indices: 33137223--33137301 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
33137213 AACACGAGGA
33137223 TTTTTG-AAACAC-GAATTTT
1 TTTTTGAAAACACAGAA-TTT
* **
33137242 TTTTTGAAAATAC-GAA-AA
1 TTTTTGAAAACACAGAATTT
33137260 TTTTTGAAAACACAGAATTT
1 TTTTTGAAAACACAGAATTT
*
33137280 TTTTTGAAAACATGAGAATTT
1 TTTTTGAAAACA-CAGAATTT
33137301 T
1 T
33137302 GAAAGACGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
18 12 0.24
19 9 0.18
20 20 0.41
21 8 0.16
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (20 bp):
TTTTTGAAAACACAGAATTT
Found at i:33137302 original size:37 final size:37
Alignment explanation
Indices: 33137170--33137305 Score: 138
Period size: 37 Copynumber: 3.7 Consensus size: 37
33137160 ATCACCGGAA
**
33137170 TTTTTGAAAACACGAAAATTTTCTAAACACTAGAA---
1 TTTTTGAAAACACGAAAATTTTGAAAACAC-AGAATTT
* *
33137205 TTTTTGAAAACACGAGGATTTTTG-AAACAC-GAATTTT
1 TTTTTGAAAACACGA-AAATTTTGAAAACACAGAA-TTT
*
33137242 TTTTTGAAAATACGAAAATTTTTGAAAACACAGAATTT
1 TTTTTGAAAACACGAAAA-TTTTGAAAACACAGAATTT
* *
33137280 TTTTTGAAAACATGAGAATTTTGAAA
1 TTTTTGAAAACACGAAAATTTTGAAA
33137306 GACGAAATCT
Statistics
Matches: 84, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
33 3 0.04
35 21 0.25
36 6 0.07
37 27 0.32
38 24 0.29
39 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (37 bp):
TTTTTGAAAACACGAAAATTTTGAAAACACAGAATTT
Found at i:33137319 original size:37 final size:35
Alignment explanation
Indices: 33137205--33137320 Score: 115
Period size: 37 Copynumber: 3.1 Consensus size: 35
33137195 AACACTAGAA
* *
33137205 TTTTTGAAAACACGAGGATTTTTGAAACACGAATTTT
1 TTTTTGAAAACACGA-GAATTTTGAAA-ACGAAATTT
* * *
33137242 TTTTTGAAAATACGAAAATTTTTGAAAACACAGAATTT
1 TTTTTGAAAACACGAGAA-TTTTGAAAAC-GA-AATTT
* *
33137280 TTTTTGAAAACATGAGAATTTTGAAAGACGAAATCT
1 TTTTTGAAAACACGAGAATTTTGAAA-ACGAAATTT
33137316 TTTTT
1 TTTTT
33137321 ATTTTTATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
36 12 0.18
37 32 0.49
38 21 0.32
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (35 bp):
TTTTTGAAAACACGAGAATTTTGAAAACGAAATTT
Found at i:33137518 original size:20 final size:18
Alignment explanation
Indices: 33137493--33137577 Score: 73
Period size: 18 Copynumber: 4.4 Consensus size: 18
33137483 CGTTGCCTTA
33137493 TTTTTGAAAACACGACTATT
1 TTTTTGAAAACACGA--ATT
33137513 TTTTTG-AAACACGAGAAAATT
1 TTTTTGAAAACAC--G--AATT
* **
33137534 TTTTTGAAGACACGAAGA
1 TTTTTGAAAACACGAATT
*
33137552 TTTTGGAAAACACGAATT
1 TTTTTGAAAACACGAATT
33137570 TTTTTGAA
1 TTTTTGAA
33137578 TATTTTCGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
18 23 0.44
19 6 0.12
20 7 0.13
21 10 0.19
22 5 0.10
23 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (18 bp):
TTTTTGAAAACACGAATT
Found at i:33137784 original size:17 final size:16
Alignment explanation
Indices: 33137730--33137785 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
33137720 ATTGGATTAA
*
33137730 ATTAAAA-ATATAAAT
1 ATTAAAATATAAAAAT
*
33137745 ACTAAAATATAAAAAT
1 ATTAAAATATAAAAAT
* *
33137761 GTATAAAATACTAATAAT
1 AT-TAAAATA-TAAAAAT
33137779 ATTAAAA
1 ATTAAAA
33137786 GGAAATAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 6 0.19
16 7 0.22
17 12 0.38
18 7 0.22
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (16 bp):
ATTAAAATATAAAAAT
Found at i:33137836 original size:437 final size:437
Alignment explanation
Indices: 33137362--33138238 Score: 1682
Period size: 437 Copynumber: 2.0 Consensus size: 437
33137352 GAAACCACGG
33137362 AAAGATTTTTTTTTTCACAAACTTTTCGATTTTTTTTATTAAGCACGTATCGTATTTAACACGAA
1 AAAGATTTTTTTTTTCACAAACTTTTCGATTTTTTTTATTAAGCACGTATCGTATTTAACACGAA
* *
33137427 CCGGTGATATTCACTCAACATAGTAATGAAATCAACAAATTAGTGTCAAATCGATTCGTTGCCTT
66 CCGGTGATATTCACTCAACATAGCAATGAAATCAACAAATTAGTGTCAAATCGATTCGTTACCTT
***
33137492 ATTTTTGAAAACACGACTATTTTTTTGAAACACGAGAAAATTTTTTTGAAGACACGAAGATTTTG
131 ATTTTTGAAAACACGACTATTTTTTTGAAACACGAGAAAAAAATTTTGAAGACACGAAGATTTTG
*
33137557 GAAAACACGAATTTTTTTGAATATTTTCGATTTTTAAAAGGGCGTATCGAGTTTAACGCAAACCG
196 GAAAACACGAATTTTTTTGAATATTTTCGATTTTTAAAAGGGCATATCGAGTTTAACGCAAACCG
33137622 GTGATATTCACCCAACATAGCGATGAAATCAACGATTTTATGTTAAATCGATTCGTTGCCTTATT
261 GTGATATTCACCCAACATAGCGATGAAATCAACGATTTTATGTTAAATCGATTCGTTGCCTTATT
*
33137687 TATTAAAATTATTTAAAATAAAATAAAATTAAAATTGGATTAAATTAAAAATATAAATACTAAAA
326 TATTAAAATTATTTAAAATAAAATAAAATTAAAATTGGATTAAATTAAAAATATAAATACAAAAA
*
33137752 TATAAAAATGTATAAAATACTAATAATATTAAAAGGAAATAACATAA
391 TATAAAAATGCATAAAATACTAATAATATTAAAAGGAAATAACATAA
33137799 AAAGATTTTTTTTTTCACAAACTTTTCGATTTTTTTTATTAAGCACGTATCGTATTTAACACGAA
1 AAAGATTTTTTTTTTCACAAACTTTTCGATTTTTTTTATTAAGCACGTATCGTATTTAACACGAA
33137864 CCGGTGATATTCACTCAACATAGCAATGAAATCAACAAATTAGTGTCAAATCGATTCGTTACCTT
66 CCGGTGATATTCACTCAACATAGCAATGAAATCAACAAATTAGTGTCAAATCGATTCGTTACCTT
33137929 ATTTTTGAAAACACGACTATTTTTTTGAAACACGAGAAAAAAATTTTGAAGACACGAAGATTTTG
131 ATTTTTGAAAACACGACTATTTTTTTGAAACACGAGAAAAAAATTTTGAAGACACGAAGATTTTG
33137994 GAAAACACGAATTTTTTTGAATATTTTCGATTTTTAAAAGGGCATATCGAGTTTAACGCAAACCG
196 GAAAACACGAATTTTTTTGAATATTTTCGATTTTTAAAAGGGCATATCGAGTTTAACGCAAACCG
33138059 GTGATATTCACCCAACATAGCGATGAAATCAACGATTTTATGTTAAATCGATTCGTTGCCTTATT
261 GTGATATTCACCCAACATAGCGATGAAATCAACGATTTTATGTTAAATCGATTCGTTGCCTTATT
33138124 TATTAAAATTATTTAAAATAAAATAAAATTAAAATTGGATTAAATTAAAAATATAAATACAAAAA
326 TATTAAAATTATTTAAAATAAAATAAAATTAAAATTGGATTAAATTAAAAATATAAATACAAAAA
33138189 TATAAAAATGCATAAAATACTAATAATATTAAAAGGAAATAACATAA
391 TATAAAAATGCATAAAATACTAATAATATTAAAAGGAAATAACATAA
33138236 AAA
1 AAA
33138239 TACGAGCATT
Statistics
Matches: 432, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
437 432 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (437 bp):
AAAGATTTTTTTTTTCACAAACTTTTCGATTTTTTTTATTAAGCACGTATCGTATTTAACACGAA
CCGGTGATATTCACTCAACATAGCAATGAAATCAACAAATTAGTGTCAAATCGATTCGTTACCTT
ATTTTTGAAAACACGACTATTTTTTTGAAACACGAGAAAAAAATTTTGAAGACACGAAGATTTTG
GAAAACACGAATTTTTTTGAATATTTTCGATTTTTAAAAGGGCATATCGAGTTTAACGCAAACCG
GTGATATTCACCCAACATAGCGATGAAATCAACGATTTTATGTTAAATCGATTCGTTGCCTTATT
TATTAAAATTATTTAAAATAAAATAAAATTAAAATTGGATTAAATTAAAAATATAAATACAAAAA
TATAAAAATGCATAAAATACTAATAATATTAAAAGGAAATAACATAA
Found at i:33137993 original size:17 final size:18
Alignment explanation
Indices: 33137971--33138004 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33137961 CGAGAAAAAA
*
33137971 ATTTT-GAAGACACGAAG
1 ATTTTGGAAAACACGAAG
33137988 ATTTTGGAAAACACGAA
1 ATTTTGGAAAACACGAA
33138005 TTTTTTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (18 bp):
ATTTTGGAAAACACGAAG
Found at i:33138344 original size:11 final size:11
Alignment explanation
Indices: 33138328--33138397 Score: 61
Period size: 11 Copynumber: 6.1 Consensus size: 11
33138318 CAAATTAAAC
33138328 CTTTTTTTTCT
1 CTTTTTTTTCT
33138339 CTTTTTTCTT-T
1 CTTTTTT-TTCT
*
33138350 TTTCCTTTTTTCT
1 CTT--TTTTTTCT
*
33138363 TTCTTTTTTTCT
1 CT-TTTTTTTCT
33138375 CTTTTTTTTCT
1 CTTTTTTTTCT
**
33138386 CACTTTTTTCT
1 CTTTTTTTTCT
33138397 C
1 C
33138398 CTCTCTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
11 29 0.58
12 13 0.26
13 7 0.14
14 1 0.02
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (11 bp):
CTTTTTTTTCT
Found at i:33138348 original size:7 final size:7
Alignment explanation
Indices: 33138332--33138381 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
33138322 TTAAACCTTT
33138332 TTTTTCTC
1 TTTTT-TC
33138340 TTTTTTC
1 TTTTTTC
33138347 TTTTTTCC
1 TTTTTT-C
33138355 TTTTTTC
1 TTTTTTC
33138362 TTTCTTT-
1 TTT-TTTC
*
33138369 TTTTCTC
1 TTTTTTC
33138376 TTTTTT
1 TTTTTT
33138382 TTCTCACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
6 2 0.05
7 20 0.54
8 15 0.41
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:33138351 original size:8 final size:8
Alignment explanation
Indices: 33138330--33138381 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 8
33138320 AATTAAACCT
33138330 TTTTTTTC
1 TTTTTTTC
33138338 TCTTTTTTC
1 T-TTTTTTC
*
33138347 TTTTTTCCTT
1 TTTTTT--TC
33138357 TTTTCTTTC
1 TTTT-TTTC
33138366 TTTTTTTC
1 TTTTTTTC
33138374 TCTTTTTT
1 T-TTTTTT
33138382 TTCTCACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 11 0.30
9 19 0.51
10 5 0.14
11 2 0.05
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:33138365 original size:19 final size:19
Alignment explanation
Indices: 33138340--33138385 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
33138330 TTTTTTTCTC
33138340 TTTTTTCTTTTTTCCT-TT
1 TTTTTTCTTTTTTCCTCTT
*
33138358 TTTCTTTCTTTTTTTCTCTT
1 TTT-TTTCTTTTTTCCTCTT
33138378 TTTTTTCT
1 TTTTTTCT
33138386 CACTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 17 0.68
20 5 0.20
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTCTTTTTTCCTCTT
Found at i:33138392 original size:22 final size:21
Alignment explanation
Indices: 33138346--33138397 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
33138336 TCTCTTTTTT
33138346 CTTTTTTC-CTTTTTTCTTTC
1 CTTTTTTCTCTTTTTTCTTTC
*
33138366 TTTTTTTCTCTTTTTT-TTCTC
1 CTTTTTTCTCTTTTTTCTT-TC
33138387 ACTTTTTTCTC
1 -CTTTTTTCTC
33138398 CTCTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.33
21 9 0.33
22 9 0.33
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (21 bp):
CTTTTTTCTCTTTTTTCTTTC
Found at i:33138392 original size:34 final size:35
Alignment explanation
Indices: 33138330--33138396 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
33138320 AATTAAACCT
*
33138330 TTTTTTTCTCTTTTTTCTTTTTTCCTTTTTTCTTTC
1 TTTTTTTCTC-TTTTTCTTTTCTCCTTTTTTCTTTC
33138366 TTTTTTTCTC-TTTT-TTTTCTCACTTTTTTCT
1 TTTTTTTCTCTTTTTCTTTTCTC-CTTTTTTCT
33138397 CCTCTCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 6 0.21
34 13 0.45
36 10 0.34
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (35 bp):
TTTTTTTCTCTTTTTCTTTTCTCCTTTTTTCTTTC
Found at i:33138555 original size:16 final size:17
Alignment explanation
Indices: 33138530--33138583 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
33138520 AAATGGCCTG
*
33138530 TTGCTTTTTTTTCTGCT
1 TTGCTTTTTTTTCGGCT
*
33138547 TTG-TTTTTTTTGGGCT
1 TTGCTTTTTTTTCGGCT
*
33138563 TTGCCTTTTTTTTCGGGT
1 TTG-CTTTTTTTTCGGCT
33138581 TTG
1 TTG
33138584 GAGCTGCTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 14 0.45
17 3 0.10
18 14 0.45
ACGTcount: A:0.00, C:0.13, G:0.20, T:0.67
Consensus pattern (17 bp):
TTGCTTTTTTTTCGGCT
Found at i:33138650 original size:1 final size:1
Alignment explanation
Indices: 33138644--33138709 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
33138634 ACTGAATTAA
* * * * * * * * *
33138644 TTTTTTTATTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTTCTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33138709 T
1 T
33138710 CTTCTTCCTT
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:33138662 original size:7 final size:7
Alignment explanation
Indices: 33138645--33138698 Score: 101
Period size: 7 Copynumber: 7.9 Consensus size: 7
33138635 CTGAATTAAT
33138645 TTTTTTA
1 TTTTTTA
33138652 -TTTTTA
1 TTTTTTA
33138658 TTTTTTA
1 TTTTTTA
33138665 TTTTTTA
1 TTTTTTA
33138672 TTTTTTA
1 TTTTTTA
33138679 TTTTTTA
1 TTTTTTA
33138686 TTTTTTA
1 TTTTTTA
33138693 TTTTTT
1 TTTTTT
33138699 TCTTTCTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.13
7 40 0.87
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:33138706 original size:4 final size:4
Alignment explanation
Indices: 33138697--33138792 Score: 101
Period size: 4 Copynumber: 24.0 Consensus size: 4
33138687 TTTTTATTTT
* *
33138697 TTTC TTTC TTTT TCTTC -TTC CTTC -TTC TTTC -TTC TTTC TTTC TTTC
1 TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
33138743 TTTC TTTC TTTC TTTC TTT- TTCTC TTTTC TTTC TCTTT TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TT-TC -TTTC TTTC T-TTC TTTC TTTC TTTC
33138793 CCGATCAACC
Statistics
Matches: 80, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
3 11 0.14
4 60 0.75
5 7 0.09
6 2 0.03
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:33138786 original size:7 final size:7
Alignment explanation
Indices: 33138652--33138792 Score: 90
Period size: 7 Copynumber: 19.9 Consensus size: 7
33138642 AATTTTTTTA
*
33138652 TTTTTAT
1 TTTTTCT
*
33138659 TTTTTAT
1 TTTTTCT
*
33138666 TTTTTAT
1 TTTTTCT
*
33138673 TTTTTAT
1 TTTTTCT
*
33138680 TTTTTAT
1 TTTTTCT
*
33138687 TTTTTATT
1 TTTTT-CT
33138695 TTTTTCT
1 TTTTTCT
*
33138702 TTCTT-T
1 TTTTTCT
*
33138708 TTCTTCT
1 TTTTTCT
**
33138715 TCCTTCT
1 TTTTTCT
*
33138722 TCTTTCT
1 TTTTTCT
*
33138729 TCTTTCT
1 TTTTTCT
33138736 TTCTTTCT
1 TT-TTTCT
33138744 TTCTTTCT
1 TT-TTTCT
33138752 TTCTTTC-
1 TT-TTTCT
33138759 TTTTTCT
1 TTTTTCT
*
33138766 CTTTTC-
1 TTTTTCT
*
33138772 TTTCTCT
1 TTTTTCT
33138779 TTTTTCT
1 TTTTTCT
33138786 TTCTTTC
1 TT-TTTC
33138793 CCGATCAACC
Statistics
Matches: 118, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
6 14 0.12
7 74 0.63
8 30 0.25
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:33138787 original size:34 final size:33
Alignment explanation
Indices: 33138698--33138792 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 33
33138688 TTTTATTTTT
**
33138698 TTCTTTCTTTTTC-TTC-TTCCTTC-TTCTTTC
1 TTCTTTCTTTTTCTTTCTTTTTTTCTTTCTTTC
*
33138728 TTCTTTC--TTTCTTTCTTTCTTTCTTTCTTTC
1 TTCTTTCTTTTTCTTTCTTTTTTTCTTTCTTTC
33138759 TT-TTTCTCTTTTCTTTCTCTTTTTTCTTTCTTTC
1 TTCTTTCT-TTTTCTTTCT-TTTTTTCTTTCTTTC
33138793 CCGATCAACC
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.07
29 3 0.05
30 17 0.30
31 9 0.16
33 9 0.16
34 14 0.25
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (33 bp):
TTCTTTCTTTTTCTTTCTTTTTTTCTTTCTTTC
Found at i:33138931 original size:8 final size:9
Alignment explanation
Indices: 33138894--33138952 Score: 50
Period size: 8 Copynumber: 6.3 Consensus size: 9
33138884 TTCCCCCATC
33138894 TTTCTTCTT
1 TTTCTTCTT
*
33138903 TGCTCTT-TT
1 T-TTCTTCTT
33138912 TTTCTTCTT
1 TTTCTTCTT
33138921 TTT-TTCTT
1 TTTCTTCTT
33138929 TTTGCTTGCTT
1 TTT-CTT-CTT
*
33138940 GTTTTTTCTT
1 -TTTCTTCTT
33138950 TTT
1 TTT
33138953 TCTTGCCTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
8 12 0.29
9 12 0.29
10 9 0.22
11 5 0.12
12 3 0.07
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (9 bp):
TTTCTTCTT
Found at i:33139206 original size:31 final size:29
Alignment explanation
Indices: 33139137--33139210 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
33139127 GGCTCAGGTT
* *
33139137 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* * *
33139166 ACGTTTTAGTCAGTTATGTTATCATATTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
33139197 ACATTTTAGTCACT
1 ACATTTTAGTCACT
33139211 GAGCCATTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 18 0.50
30 2 0.06
31 16 0.44
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:33139808 original size:29 final size:30
Alignment explanation
Indices: 33139769--33139837 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
33139759 ACGATAACGC
* *
33139769 AAGTGACTAAAACGTAACAT-TTCAAACAT
1 AAGTGACTAAAACGTAACATAGTCAAACAA
*
33139798 AAGTGACTAAAATGTAACATGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT-AGTCAAACAA
33139829 AAGTGACTA
1 AAGTGACTA
33139838 TTTTGGTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (30 bp):
AAGTGACTAAAACGTAACATAGTCAAACAA
Found at i:33140097 original size:29 final size:29
Alignment explanation
Indices: 33140056--33140159 Score: 120
Period size: 28 Copynumber: 3.6 Consensus size: 29
33140046 AAAACTTCGA
* *
33140056 GGGTCAAAGTGTAATTTTGGAAAATTTAG
1 GGGTCAAAATGTAATTTTAGAAAATTTAG
* ** *
33140085 GGGTCAAAATGTAATTTCA-AAAAAATAA
1 GGGTCAAAATGTAATTTTAGAAAATTTAG
*
33140113 GGGTCAAAATATAATTTTAAGAAAATTTAG
1 GGGTCAAAATGTAATTTT-AGAAAATTTAG
*
33140143 GGGTTAAAATGTAATTT
1 GGGTCAAAATGTAATTT
33140160 CGTAAAAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
28 22 0.37
29 17 0.28
30 21 0.35
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAGAAAATTTAG
Found at i:33140117 original size:28 final size:28
Alignment explanation
Indices: 33140085--33140170 Score: 91
Period size: 30 Copynumber: 3.0 Consensus size: 28
33140075 GAAAATTTAG
33140085 GGGTCAAAATGTAATTTCAAAAAAATAA
1 GGGTCAAAATGTAATTTCAAAAAAATAA
* * * *
33140113 GGGTCAAAATATAATTTTAAGAAAATTTAG
1 GGGTCAAAATGTAATTTCAA-AAAA-ATAA
* *
33140143 GGGTTAAAATGTAATTTCGTAAAAAATA
1 GGGTCAAAATGTAATTTC-AAAAAAATA
33140171 CGAGATTTGA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 18 0.39
29 6 0.13
30 21 0.46
31 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (28 bp):
GGGTCAAAATGTAATTTCAAAAAAATAA
Found at i:33140154 original size:58 final size:58
Alignment explanation
Indices: 33140055--33140170 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
33140045 CAAAACTTCG
* * *
33140055 AGGGTCAAAGTGTAATTTTGGAAAATTTAGGGGTCAAAATGTAATTTC-AAAAAAATA
1 AGGGTCAAAATATAATTTTAGAAAATTTAGGGGTCAAAATGTAATTTCGAAAAAAATA
* *
33140112 AGGGTCAAAATATAATTTTAAGAAAATTTAGGGGTTAAAATGTAATTTCGTAAAAAATA
1 AGGGTCAAAATATAATTTT-AGAAAATTTAGGGGTCAAAATGTAATTTCGAAAAAAATA
33140171 CGAGATTTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
57 17 0.33
58 27 0.52
59 8 0.15
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (58 bp):
AGGGTCAAAATATAATTTTAGAAAATTTAGGGGTCAAAATGTAATTTCGAAAAAAATA
Found at i:33156139 original size:20 final size:21
Alignment explanation
Indices: 33156114--33156173 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
33156104 TTGTACGGGA
33156114 TTGCAC-TTTAGTGCCTCTGT
1 TTGCACATTTAGTGCCTCTGT
* *
33156134 TTGCACTTTTA-TGCCTCTGA
1 TTGCACATTTAGTGCCTCTGT
*
33156154 TTACACATTT-GTGCCTCTGT
1 TTGCACATTTAGTGCCTCTGT
33156174 CTGTACTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 30 0.88
21 4 0.12
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (21 bp):
TTGCACATTTAGTGCCTCTGT
Found at i:33159239 original size:14 final size:14
Alignment explanation
Indices: 33159216--33159250 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
33159206 TAGTAAGTTG
*
33159216 GAGTGGAGGAGAGA
1 GAGTGTAGGAGAGA
33159230 GAGTGTAGGAGAGA
1 GAGTGTAGGAGAGA
*
33159244 GAATGTA
1 GAGTGTA
33159251 AGTTAGTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.14
Consensus pattern (14 bp):
GAGTGTAGGAGAGA
Found at i:33169085 original size:2 final size:2
Alignment explanation
Indices: 33169078--33169115 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
33169068 GACATGTGCG
33169078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33169116 TCACTAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33169394 original size:23 final size:22
Alignment explanation
Indices: 33169367--33169409 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
33169357 ATTAAATTTT
33169367 TAAGATTACCAAATCATATCTTC
1 TAAGATT-CCAAATCATATCTTC
* *
33169390 TAAGATTGCATATCATATCT
1 TAAGATTCCAAATCATATCT
33169410 AAGATTACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (22 bp):
TAAGATTCCAAATCATATCTTC
Found at i:33171891 original size:25 final size:24
Alignment explanation
Indices: 33171834--33171891 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
33171824 ATCCCTTCAC
* *
33171834 TTCCTCTTCTCTTCCTCTTTACAT
1 TTCCTCTTCTCTCCCACTTTACAT
33171858 TT-CTGCTTCTACTCCCACTTCT-CAT
1 TTCCT-CTTCT-CTCCCACTT-TACAT
33171883 TTCCTCTTC
1 TTCCTCTTC
33171892 CCCTGTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 2 0.07
24 7 0.25
25 16 0.57
26 3 0.11
ACGTcount: A:0.09, C:0.40, G:0.02, T:0.50
Consensus pattern (24 bp):
TTCCTCTTCTCTCCCACTTTACAT
Found at i:33174425 original size:23 final size:23
Alignment explanation
Indices: 33174385--33174430 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
33174375 TTTAGATTAT
** *
33174385 TTATTTTAATTTTTAAATTTTAA
1 TTATTTTAATTTAAAAATGTTAA
*
33174408 TTATTTTGATTTAAAAATGTTAA
1 TTATTTTAATTTAAAAATGTTAA
33174431 AAATTCCCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (23 bp):
TTATTTTAATTTAAAAATGTTAA
Found at i:33177087 original size:2 final size:2
Alignment explanation
Indices: 33177080--33177111 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33177070 TAAAAATAAC
33177080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33177112 TTATCTTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33192361 original size:45 final size:45
Alignment explanation
Indices: 33192297--33192383 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
33192287 CAGATACTCG
* *
33192297 GTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCA
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
*
33192342 GTGGAATCAGCACATAGCAACCACCTTACTAATTAATGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
33192384 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
Found at i:33192505 original size:51 final size:50
Alignment explanation
Indices: 33192385--33192579 Score: 144
Period size: 51 Copynumber: 3.9 Consensus size: 50
33192375 TAATGATGTT
* * * * *
33192385 CGGTTCACATAGTAGCTTGCACATAGTACTATCA-ATGTGACCATTACCA-TC
1 CGGTACACATAATAGCCTGCACATAGTACTA-CACACGTGACCA--AACATTC
* * * * * *
33192436 CGATACACGTAGTGGCCTGCATATAGTACTACACACGTGATCGAAAC-TATC
1 CGGTACACATAATAGCCTGCACATAGTACTACACACGTGA-CCAAACAT-TC
* * * * * * *
33192487 CGGTACGCATAATAGCCTGTACATAGTACTACAAATGCGACCTATCATTC
1 CGGTACACATAATAGCCTGCACATAGTACTACACACGTGACCAAACATTC
* *
33192537 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
1 CGGTACACATAATAGCCTGCACATAGTACTACACACGTGACCA
33192580 TCACTTTCAC
Statistics
Matches: 109, Mismatches: 30, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
50 44 0.40
51 63 0.58
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
CGGTACACATAATAGCCTGCACATAGTACTACACACGTGACCAAACATTC
Found at i:33198335 original size:30 final size:30
Alignment explanation
Indices: 33198301--33198360 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
33198291 TATTTTATTA
33198301 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
33198331 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
33198361 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:33202888 original size:16 final size:19
Alignment explanation
Indices: 33202840--33202895 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
33202830 TTTAGTCATA
33202840 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT-AT
33202860 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTAATATAT
33202878 TAATAAATTATTTAATAT
1 TAATAAATTA-TTAATAT
33202896 TTCAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 8 0.26
19 1 0.03
20 6 0.19
21 4 0.13
22 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAATATAT
Found at i:33202930 original size:15 final size:13
Alignment explanation
Indices: 33202905--33202944 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
33202895 TTTCAATTTT
33202905 ATTTT-AATAATA
1 ATTTTAAATAATA
33202917 GATTTTAAAATAATA
1 -ATTTT-AAATAATA
33202932 ATTTTAAATAATA
1 ATTTTAAATAATA
33202945 TTCCTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 5 0.20
15 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
ATTTTAAATAATA
Found at i:33203914 original size:19 final size:19
Alignment explanation
Indices: 33203872--33203920 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
33203862 ATAATATTAT
*
33203872 TTTAATAATAAAATTTAACA
1 TTTAATAAT-AAATTTAAAA
*
33203892 -TTAATAATAATTTTAAAA
1 TTTAATAATAAATTTAAAA
33203910 TTTAAATAATA
1 TTT-AATAATA
33203921 TTCTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAATAATAAATTTAAAA
Found at i:33207122 original size:17 final size:17
Alignment explanation
Indices: 33207100--33207133 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
33207090 TCTCTTAAAT
33207100 AGATATAACTATTCAAG
1 AGATATAACTATTCAAG
33207117 AGATATAACTATTCAAG
1 AGATATAACTATTCAAG
33207134 TATTACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
AGATATAACTATTCAAG
Found at i:33208505 original size:19 final size:19
Alignment explanation
Indices: 33208495--33208549 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
33208485 TTGAAATTTA
33208495 AAAATTATTTTAATTTTTG
1 AAAATTATTTTAATTTTTG
33208514 AAAATTATTTTAATTTTTG
1 AAAATTATTTTAATTTTTG
*
33208533 AAAATTATTTTGATTTT
1 AAAATTATTTTAATTTT
33208550 CTTTTTGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
AAAATTATTTTAATTTTTG
Found at i:33208510 original size:37 final size:38
Alignment explanation
Indices: 33208469--33208549 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
33208459 CAAATTTTGG
33208469 AATTTTT-ATAAA-TATTTTGAA-ATTTAAAAATTATTTT
1 AATTTTTGA-AAATTATTTT-AATATTTAAAAATTATTTT
* *
33208506 AATTTTTGAAAATTATTTTAATTTTTGAAAATTATTTT
1 AATTTTTGAAAATTATTTTAATATTTAAAAATTATTTT
*
33208544 GATTTT
1 AATTTT
33208550 CTTTTTGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 12 0.32
38 26 0.68
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (38 bp):
AATTTTTGAAAATTATTTTAATATTTAAAAATTATTTT
Found at i:33212638 original size:28 final size:31
Alignment explanation
Indices: 33212587--33212651 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 31
33212577 AAGAAGAAGA
33212587 GAGAAAAAAATAGTGAAGAGGT-GGAGAGTGG
1 GAGAAAAAAATAGTGAAGAGGTGGGA-AGTGG
* *
33212618 GTGAAAAGAAT-GTG-AGA-GTGGGAAGTGG
1 GAGAAAAAAATAGTGAAGAGGTGGGAAGTGG
33212646 GAGAAA
1 GAGAAA
33212652 TAATTTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 12 0.40
29 6 0.20
30 3 0.10
31 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (31 bp):
GAGAAAAAAATAGTGAAGAGGTGGGAAGTGG
Found at i:33225030 original size:60 final size:60
Alignment explanation
Indices: 33224932--33225054 Score: 228
Period size: 60 Copynumber: 2.0 Consensus size: 60
33224922 CTATTGAGTC
*
33224932 TTCCATTATACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCTAGGCA
1 TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCTAGGCA
*
33224992 TTCCATTAAACAAGAATCTATTATCAAGAGTTCTATACCATTGCCTTTGGTAGCTAGGCA
1 TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCTAGGCA
33225052 TTC
1 TTC
33225055 TTTCCACTCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (60 bp):
TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCTAGGCA
Found at i:33227936 original size:18 final size:18
Alignment explanation
Indices: 33227878--33227937 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
33227868 ACAAGTTATT
* *
33227878 AAAATTATTAAAATTTTA
1 AAAATTATAAAAATTTAA
** *
33227896 AAAATATATAATTATTTAT
1 AAAAT-TATAAAAATTTAA
*
33227915 AAAATTATAAAAATATAA
1 AAAATTATAAAAATTTAA
33227933 AAAAT
1 AAAAT
33227938 GATTTTTTAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 19 0.59
19 13 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTATAAAAATTTAA
Found at i:33233460 original size:133 final size:132
Alignment explanation
Indices: 33233261--33233677 Score: 416
Period size: 133 Copynumber: 3.1 Consensus size: 132
33233251 GCGCTTCCCC
* * * * * * *
33233261 AAAAACGCCGCAAAA-AATTGGAATATAGCGGCATTTTCTGAGAAACGCCAGTAACA-ATAACGA
1 AAAAACG-CGGAAAAGAA-TGGCATATAGCGGCGTTTTC-GGGAAACGCCGGTAA-AGATATCTA
* *
33233324 ATTTGAGGAAAAAATCTGAGCAAAACAGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCG
62 ATTTGAGGAAAAATTTTGAGCAAAAC-GTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCG
33233389 CATTTTA
126 CATTTTA
33233396 AAAAACGTCGGAAAAGAAT-GCAT-TAGCGGCGTTTTCAGGGAAACGCCGGTAAAGATATCTAAT
1 AAAAACG-CGGAAAAGAATGGCATATAGCGGCGTTTTC-GGGAAACGCCGGTAAAGATATCTAAT
* * * *
33233459 TTGAGGAAAAATTTTG-GACAAAACGCTACTGTTTTATTGCTTCATTTTATTTCCTTAGTGGCGC
64 TTGAGGAAAAATTTTGAG-CAAAACG-TACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGC
*
33233523 ATTGTA
127 ATTTTA
* * * * * * * *
33233529 AAAAGCGCCGCAAATATTGGGATATAGTGGCGTTATT-GGAGAAACGCCGGTAAAGAAATCTAAT
1 AAAAACGCGGAAAAGAATGGCATATAGCGGCGTT-TTCGG-GAAACGCCGGTAAAGATATCTAAT
* *
33233593 TTGAGGAAAAATTTTGAGCAAAACGGTACCGTTTTGTTGTTTCCTTTT-TATGCTTTAGTGGCGA
64 TTGAGGAAAAATTTTGAGCAAAAC-GTACCGTTTTGTTGTTTCATTTTAT-TTCTTTAGTGGCG-
* *
33233657 AATGTTA
126 CATTTTA
33233664 AAAAACGCCGGAAA
1 AAAAACG-CGGAAA
33233678 CGGTTCGGAT
Statistics
Matches: 233, Mismatches: 36, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
132 10 0.04
133 103 0.44
134 86 0.37
135 28 0.12
136 6 0.03
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.30
Consensus pattern (132 bp):
AAAAACGCGGAAAAGAATGGCATATAGCGGCGTTTTCGGGAAACGCCGGTAAAGATATCTAATTT
GAGGAAAAATTTTGAGCAAAACGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATTT
TA
Found at i:33233651 original size:134 final size:131
Alignment explanation
Indices: 33233323--33233673 Score: 411
Period size: 134 Copynumber: 2.6 Consensus size: 131
33233313 AACAATAACG
* * *
33233323 AATTTGAGGAAAAAATCTGAGCAAAACAGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGC
1 AATTTGAGGAAAAATTTTGAGCAAAACGGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGC
* * *
33233388 GCATTTTAAAAAACGTCGGAAAAGAATGCATTAGCGGCGTTTTCAGGGAAACGCCGGTAAAGATA
66 GCATTGTAAAAAACG-CCGAAAAGAATGCATTAGCGGCGTTTT-AGGGAAACGCCGGTAAAGAAA
33233453 TCT
129 TCT
* * * * *
33233456 AATTTGAGGAAAAATTTTG-GACAAAACGCTACTGTTTTATTGCTTCATTTTATTTCCTTAGTGG
1 AATTTGAGGAAAAATTTTGAG-CAAAACGGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGG
* * * * * *
33233520 CGCATTGTAAAAAGCGCCGCAAATATTGGGATATAGTGGCGTTATT-GGAGAAACGCCGGTAAAG
65 CGCATTGTAAAAAACGCCGAAAAGAAT-GCAT-TAGCGGCGTT-TTAGG-GAAACGCCGGTAAAG
33233584 AAATCT
126 AAATCT
* *
33233590 AATTTGAGGAAAAATTTTGAGCAAAACGGTACCGTTTTGTTGTTTCCTTTT-TATGCTTTAGTGG
1 AATTTGAGGAAAAATTTTGAGCAAAACGGTACCGTTTTGTTGTTTCATTTTAT-TTCTTTAGTGG
* *
33233654 CGAAATGTTAAAAAACGCCG
65 CGCATTG-TAAAAAACGCCG
33233674 GAAACGGTTC
Statistics
Matches: 183, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
132 8 0.04
133 74 0.40
134 87 0.48
135 14 0.08
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (131 bp):
AATTTGAGGAAAAATTTTGAGCAAAACGGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGC
GCATTGTAAAAAACGCCGAAAAGAATGCATTAGCGGCGTTTTAGGGAAACGCCGGTAAAGAAATC
T
Found at i:33234061 original size:21 final size:20
Alignment explanation
Indices: 33234022--33234074 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
33234012 TTTGTGATTT
*
33234022 GGGCTTAGAGTTTAGGTTTA
1 GGGCTTAGAGTTGAGGTTTA
*
33234042 GGGCTTGGAGATTGAGGTTTA
1 GGGCTTAGAG-TTGAGGTTTA
* *
33234063 AGGTTTAGAGTT
1 GGGCTTAGAGTT
33234075 TGCATTTCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.21, C:0.04, G:0.38, T:0.38
Consensus pattern (20 bp):
GGGCTTAGAGTTGAGGTTTA
Found at i:33238530 original size:17 final size:17
Alignment explanation
Indices: 33238510--33238559 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
33238500 TTAATATCTA
33238510 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
33238527 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
33238541 -ATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
33238557 TAT
1 TAT
33238560 TTGTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.38
14 2 0.07
16 2 0.07
17 14 0.48
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:33238546 original size:13 final size:13
Alignment explanation
Indices: 33238528--33238555 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33238518 TTCTAAATTT
33238528 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
33238541 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
33238554 AT
1 AT
33238556 TTATTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
ATAAGTTTTCTAA
Found at i:33238586 original size:15 final size:15
Alignment explanation
Indices: 33238551--33238589 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
33238541 ATAAGTTTTC
*
33238551 TAAATTTATTTGTAT
1 TAAATTTATTAGTAT
33238566 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
33238582 TAAATTTA
1 TAAATTTA
33238590 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:33238632 original size:62 final size:62
Alignment explanation
Indices: 33238532--33238651 Score: 143
Period size: 62 Copynumber: 1.9 Consensus size: 62
33238522 AAATTTATAA
* *** * * *
33238532 GTTTTCTAAATAAGTTTTCTAAATTTATTTGTATTAAAATTTAT-TAGTATTAAATTTACTTC
1 GTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATATATGT-GTATTAAATTTACTTC
* *
33238594 GTTTTCTAAATAAGTGTTCTAAATTTGGGAGAAATAAAATATATGTGTATTAAGTTTA
1 GTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATATATGTGTATTAAATTTA
33238652 TAAGTTTTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
62 47 0.98
63 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (62 bp):
GTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATATATGTGTATTAAATTTACTTC
Found at i:33238836 original size:21 final size:21
Alignment explanation
Indices: 33238811--33238886 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
33238801 TATAATACAT
*
33238811 AACTTGTATATAAGCTTGCAG
1 AACTTATATATAAGCTTGCAG
* *
33238832 AACTTATATTTAAGCTTGCAT
1 AACTTATATATAAGCTTGCAG
* * * *
33238853 AACTTACATAATAA-TTTACAT
1 AACTTATAT-ATAAGCTTGCAG
33238874 AACTTATATATAA
1 AACTTATATATAA
33238887 TAGCATAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 4 0.09
21 39 0.85
22 3 0.07
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (21 bp):
AACTTATATATAAGCTTGCAG
Found at i:33238843 original size:116 final size:116
Alignment explanation
Indices: 33238716--33238953 Score: 406
Period size: 116 Copynumber: 2.1 Consensus size: 116
33238706 TATAATACAT
*
33238716 AACTTATATTTAAACTTGCATAACTTACATAATAATTTATAGAACTTATATATAATAACA-ACAT
1 AACTTATATTTAAACTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA-AT
33238780 AAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTGCAG
65 AAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTGCAG
* * *
33238832 AACTTATATTTAAGCTTGCATAACTTACATAATAATTTACATAACTTATATATAATAGCATAATA
1 AACTTATATTTAAACTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATAATA
* *
33238897 AATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTGTAT
66 AATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTGCAG
33238948 AACTTA
1 AACTTA
33238954 CATAAATTAA
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
116 114 0.99
117 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (116 bp):
AACTTATATTTAAACTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATAATA
AATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTGCAG
Found at i:33238976 original size:9 final size:9
Alignment explanation
Indices: 33238946--33239148 Score: 253
Period size: 9 Copynumber: 22.4 Consensus size: 9
33238936 ATAAGCTTGT
33238946 ATAACTTAC
1 ATAACTTAC
* *
33238955 ATAAATTAA
1 ATAACTTAC
33238964 ATAACTTAC
1 ATAACTTAC
*
33238973 ATAACCTAC
1 ATAACTTAC
*
33238982 ATAACCTAC
1 ATAACTTAC
* *
33238991 ATAAATTAA
1 ATAACTTAC
33239000 ATAACTTAC
1 ATAACTTAC
33239009 ATAACTTAC
1 ATAACTTAC
*
33239018 ATAACTTAA
1 ATAACTTAC
*
33239027 ATAGCTTAC
1 ATAACTTAC
33239036 ATAACTTAC
1 ATAACTTAC
*
33239045 ATAAACTTGC
1 AT-AACTTAC
* *
33239055 ATAAATTAA
1 ATAACTTAC
33239064 ATAACTTAC
1 ATAACTTAC
33239073 ATAACTTAC
1 ATAACTTAC
*
33239082 ATAACCTAC
1 ATAACTTAC
* *
33239091 ATAAATTAA
1 ATAACTTAC
33239100 ATAACTTAC
1 ATAACTTAC
33239109 ATAACTTAC
1 ATAACTTAC
* *
33239118 ATAAATTAA
1 ATAACTTAC
33239127 ATAACTTAC
1 ATAACTTAC
33239136 ATAACTTAC
1 ATAACTTAC
33239145 ATAA
1 ATAA
33239149 ATTCCGTGGA
Statistics
Matches: 163, Mismatches: 30, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
9 155 0.95
10 8 0.05
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:33238982 original size:27 final size:27
Alignment explanation
Indices: 33238946--33239174 Score: 251
Period size: 27 Copynumber: 8.4 Consensus size: 27
33238936 ATAAGCTTGT
*
33238946 ATAACTTACATAAATTAAATAACTTAC
1 ATAACTTACATAAATTACATAACTTAC
* ** * *
33238973 ATAACCTACATAACCTACATAAATTAA
1 ATAACTTACATAAATTACATAACTTAC
* *
33239000 ATAACTTACATAACTTACATAACTTAA
1 ATAACTTACATAAATTACATAACTTAC
* * *
33239027 ATAGCTTACATAACTTACATAAACTTGC
1 ATAACTTACATAAATTACAT-AACTTAC
* * *
33239055 ATAAATTAAATAACTTACATAACTTAC
1 ATAACTTACATAAATTACATAACTTAC
* *
33239082 ATAACCTACATAAATTAAATAACTTAC
1 ATAACTTACATAAATTACATAACTTAC
*
33239109 ATAACTTACATAAATTAAATAACTTAC
1 ATAACTTACATAAATTACATAACTTAC
* * *
33239136 ATAACTTACATAAATTCCGTGGACTTAC
1 ATAACTTACATAAATTACAT-AACTTAC
*
33239164 ATAACCTACAT
1 ATAACTTACAT
33239175 NNNNNNNNNN
Statistics
Matches: 173, Mismatches: 27, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
27 135 0.78
28 38 0.22
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (27 bp):
ATAACTTACATAAATTACATAACTTAC
Found at i:33239317 original size:9 final size:9
Alignment explanation
Indices: 33239289--33239444 Score: 97
Period size: 9 Copynumber: 18.7 Consensus size: 9
33239279 NNNNNNNNNN
*
33239289 ACATAAATT
1 ACATAACTT
* *
33239298 AAATTACTT
1 ACATAACTT
33239307 ACATAACTT
1 ACATAACTT
*
33239316 ACATTA--T
1 ACATAACTT
33239323 ACATAACCTT
1 ACATAA-CTT
*
33239333 -CTTAACTT
1 ACATAACTT
*
33239341 ACATTA--T
1 ACATAACTT
* *
33239348 ACACAACTC
1 ACATAACTT
33239357 ACATAA-TT
1 ACATAACTT
*
33239365 A-AT-ATTAT
1 ACATAACT-T
*
33239373 ACACAACTT
1 ACATAACTT
33239382 ACATAA--T
1 ACATAACTT
*
33239389 ACATTACTT
1 ACATAACTT
33239398 ACATAACTT
1 ACATAACTT
33239407 ACATAA--T
1 ACATAACTT
33239414 ACATAA--T
1 ACATAACTT
33239421 ACATAACTT
1 ACATAACTT
33239430 ACATAACTT
1 ACATAACTT
33239439 ACATAA
1 ACATAA
33239445 TACATAAAAA
Statistics
Matches: 113, Mismatches: 20, Indels: 28
0.70 0.12 0.17
Matches are distributed among these distances:
6 1 0.01
7 34 0.30
8 7 0.06
9 68 0.60
10 3 0.03
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (9 bp):
ACATAACTT
Found at i:33239402 original size:41 final size:40
Alignment explanation
Indices: 33239336--33239451 Score: 114
Period size: 41 Copynumber: 2.9 Consensus size: 40
33239326 TAACCTTCTT
* * *
33239336 AACTTACATTATACACAACTCACATAATTA-ATATTATACAC
1 AACTTACATAATACATAACTTACATAATTACATA--ATACAC
* *
33239377 AACTTACATAATACATTACTTACATAACTTACATAATACAT
1 AACTTACATAATACATAACTTACATAA-TTACATAATACAC
33239418 AA--TACATAACTTACATAACTTACATAA-TACATAA
1 AACTTACATAA--TACATAACTTACATAATTACATAA
33239452 AAATATATCA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
39 14 0.22
41 45 0.69
42 3 0.05
43 3 0.05
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (40 bp):
AACTTACATAATACATAACTTACATAATTACATAATACAC
Found at i:33239417 original size:32 final size:32
Alignment explanation
Indices: 33239289--33239451 Score: 136
Period size: 32 Copynumber: 5.0 Consensus size: 32
33239279 NNNNNNNNNN
* * * *
33239289 ACATAAATTAAATTACTTACATAACTTACATTAT
1 ACATAACTTACATAACTTACATAA--TACATAAT
* * *
33239323 ACATAACCTT-CTTAACTTACATTATACACAACT
1 ACATAA-CTTACATAACTTACATAATACATAA-T
* *
33239356 CACATAA-TTA-AT-ATTATACACAACTTACATAAT
1 -ACATAACTTACATAACT-TACATAA--TACATAAT
*
33239389 ACATTACTTACATAACTTACATAATACATAAT
1 ACATAACTTACATAACTTACATAATACATAAT
33239421 ACATAACTTACATAACTTACATAATACATAA
1 ACATAACTTACATAACTTACATAATACATAA
33239452 AAATATATCA
Statistics
Matches: 103, Mismatches: 16, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
31 2 0.02
32 56 0.54
33 5 0.05
34 36 0.35
35 4 0.04
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.34
Consensus pattern (32 bp):
ACATAACTTACATAACTTACATAATACATAAT
Found at i:33239441 original size:25 final size:24
Alignment explanation
Indices: 33239303--33239451 Score: 135
Period size: 25 Copynumber: 6.0 Consensus size: 24
33239293 AAATTAAATT
*
33239303 ACTTACATAACTTACATTATACATA
1 ACTTACATAA-TTACATAATACATA
* * *
33239328 ACCTT-CTTAACTTACATTATACACA
1 A-CTTACATAA-TTACATAATACATA
* *
33239353 ACTCACATAATTA-ATATTATACACA
1 ACTTACATAATTACATA--ATACATA
*
33239378 ACTTACATAA-TACATTACTTACATA
1 ACTTACATAATTACA-TA-ATACATA
33239403 ACTTACATAA-TACATAATACATA
1 ACTTACATAATTACATAATACATA
33239426 ACTTACATAACTTACATAATACATA
1 ACTTACATAA-TTACATAATACATA
33239451 A
1 A
33239452 AAATATATCA
Statistics
Matches: 106, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
23 18 0.17
24 9 0.08
25 74 0.70
26 5 0.05
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.34
Consensus pattern (24 bp):
ACTTACATAATTACATAATACATA
Found at i:33239451 original size:16 final size:16
Alignment explanation
Indices: 33239371--33239435 Score: 80
Period size: 16 Copynumber: 4.1 Consensus size: 16
33239361 AATTAATATT
*
33239371 ATACACAACTTACATA
1 ATACATAACTTACATA
*
33239387 ATACATTACTTACATA
1 ATACATAACTTACATA
33239403 ACTTACATAA--TACATA
1 A--TACATAACTTACATA
33239419 ATACATAACTTACATA
1 ATACATAACTTACATA
33239435 A
1 A
33239436 CTTACATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.17
16 29 0.69
18 6 0.14
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (16 bp):
ATACATAACTTACATA
Found at i:33242648 original size:21 final size:21
Alignment explanation
Indices: 33242624--33242672 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
33242614 CTACAACTTA
*
33242624 AAGCAGACACAGCAGCGAGGG
1 AAGCAGACACAGCAGCGAGAG
** *
33242645 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGACACAGCAGCGAGAG
33242666 AAGCAGA
1 AAGCAGA
33242673 GGTTCAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.39, T:0.02
Consensus pattern (21 bp):
AAGCAGACACAGCAGCGAGAG
Found at i:33242673 original size:21 final size:21
Alignment explanation
Indices: 33242635--33242674 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
33242625 AGCAGACACA
*
33242635 GCAGCGAGGGAAGCAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
33242656 GCAGCGAGAGAAGCAGAGG
1 GCAGCGAGAGAAGCAGAGG
33242675 TTCAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.47, T:0.03
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCT
Found at i:33243125 original size:42 final size:42
Alignment explanation
Indices: 33243056--33243214 Score: 194
Period size: 42 Copynumber: 3.8 Consensus size: 42
33243046 CTTTTTGTAC
*
33243056 AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-AT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAT
* *
33243097 AAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTATAT
1 -AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAT
* * * * * *
33243140 AAAAACGCCGCTAAAGACCATGTTCTTCAGTGGCGTTTTTCT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAT
* * *
33243182 CAAAGCGCCGCTAAAGAACATGATCTTTAGCGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGG
33243215 TGTTTTTGGT
Statistics
Matches: 100, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
42 98 0.98
43 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAT
Found at i:33243767 original size:2 final size:2
Alignment explanation
Indices: 33243762--33243812 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
33243752 TTTATGATAC
* *
33243762 TA TA TA TA CA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33243804 TA TA TA TA T
1 TA TA TA TA T
33243813 TAGGGATGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33249455 original size:14 final size:14
Alignment explanation
Indices: 33249438--33249467 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33249428 AAATAAAACT
*
33249438 AAGAAAATAGTATA
1 AAGAAAACAGTATA
33249452 AAGAAAACAGTATA
1 AAGAAAACAGTATA
33249466 AA
1 AA
33249468 AGCTCTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.17
Consensus pattern (14 bp):
AAGAAAACAGTATA
Found at i:33254591 original size:246 final size:246
Alignment explanation
Indices: 33254157--33254652 Score: 983
Period size: 246 Copynumber: 2.0 Consensus size: 246
33254147 TGATAAACTA
33254157 ACAACTCCGTTAGATTTAGAATTGCCACAAAAGATGAATCAACCAGTTCTAGTAAAGAATCCTCC
1 ACAACTCCGTTAGATTTAGAATTGCCACAAAAGATGAATCAACCAGTTCTAGTAAAGAATCCTCC
33254222 ACCACCCTACCCTCAAAGGATTCAAAAGCAGAAACAAGAAGTTTGGTTCAAGAAATTCTTAGATG
66 ACCACCCTACCCTCAAAGGATTCAAAAGCAGAAACAAGAAGTTTGGTTCAAGAAATTCTTAGATG
33254287 TACTTAAGTAACTACATATCAACATCCCGTTGGTAGAAGCACTTGAGCAGATGCCAAACTACGTC
131 TACTTAAGTAACTACATATCAACATCCCGTTGGTAGAAGCACTTGAGCAGATGCCAAACTACGTC
*
33254352 AAATTCATGTCCAAAAAATGGGGACTTGGAGAATTAGAGACGGTAGCCCTG
196 AAATTCATGTCCAAAAAATAGGGACTTGGAGAATTAGAGACGGTAGCCCTG
33254403 ACAACTCCGTTAGATTTAGAATTGCCACAAAAGATGAATCAACCAGTTCTAGTAAAGAATCCTCC
1 ACAACTCCGTTAGATTTAGAATTGCCACAAAAGATGAATCAACCAGTTCTAGTAAAGAATCCTCC
33254468 ACCACCCTACCCTCAAAGGATTCAAAAGCAGAAACAAGAAGTTTGGTTCAAGAAATTCTTAGATG
66 ACCACCCTACCCTCAAAGGATTCAAAAGCAGAAACAAGAAGTTTGGTTCAAGAAATTCTTAGATG
33254533 TACTTAAGTAACTACATATCAACATCCCGTTGGTAGAAGCACTTGAGCAGATGCCAAACTACGTC
131 TACTTAAGTAACTACATATCAACATCCCGTTGGTAGAAGCACTTGAGCAGATGCCAAACTACGTC
33254598 AAATTCATGTCCAAAAAATAGGGACTTGGAGAATTAGAGACGGTAGCCCTG
196 AAATTCATGTCCAAAAAATAGGGACTTGGAGAATTAGAGACGGTAGCCCTG
33254649 ACAA
1 ACAA
33254653 AGGAATGCAG
Statistics
Matches: 249, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 249 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (246 bp):
ACAACTCCGTTAGATTTAGAATTGCCACAAAAGATGAATCAACCAGTTCTAGTAAAGAATCCTCC
ACCACCCTACCCTCAAAGGATTCAAAAGCAGAAACAAGAAGTTTGGTTCAAGAAATTCTTAGATG
TACTTAAGTAACTACATATCAACATCCCGTTGGTAGAAGCACTTGAGCAGATGCCAAACTACGTC
AAATTCATGTCCAAAAAATAGGGACTTGGAGAATTAGAGACGGTAGCCCTG
Found at i:33256614 original size:9 final size:9
Alignment explanation
Indices: 33256596--33256637 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
33256586 TTTGGTTAAA
33256596 AATTACCCG
1 AATTACCCG
*
33256605 AATTAACCG
1 AATTACCCG
33256614 AAAATTACCCG
1 --AATTACCCG
33256625 AATTACCCG
1 AATTACCCG
33256634 AATT
1 AATT
33256638 GACACTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 21 0.72
11 8 0.28
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:33256619 original size:20 final size:20
Alignment explanation
Indices: 33256594--33256635 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
33256584 TTTTTGGTTA
33256594 AAAATTACCCGAATTAACCG
1 AAAATTACCCGAATTAACCG
*
33256614 AAAATTACCCGAATTACCCG
1 AAAATTACCCGAATTAACCG
33256634 AA
1 AA
33256636 TTGACACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.19
Consensus pattern (20 bp):
AAAATTACCCGAATTAACCG
Found at i:33257420 original size:16 final size:16
Alignment explanation
Indices: 33257397--33257436 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
33257387 GCCTAAGAAA
* *
33257397 AAATTGGGTTGGGTTT
1 AAATTGGGCTGAGTTT
*
33257413 ATATTGGGCTGAGTTT
1 AAATTGGGCTGAGTTT
33257429 AAATTGGG
1 AAATTGGG
33257437 AGGGAGTAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.03, G:0.35, T:0.40
Consensus pattern (16 bp):
AAATTGGGCTGAGTTT
Found at i:33262933 original size:12 final size:12
Alignment explanation
Indices: 33262916--33262946 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
33262906 GACCACACAC
33262916 CCGTGTGTCAGG
1 CCGTGTGTCAGG
33262928 CCGTGTGTCAGG
1 CCGTGTGTCAGG
*
33262940 ACGTGTG
1 CCGTGTG
33262947 CTAGGCCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.42, T:0.26
Consensus pattern (12 bp):
CCGTGTGTCAGG
Found at i:33267040 original size:2 final size:2
Alignment explanation
Indices: 33267033--33267064 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
33267023 ATGCTAATGC
*
33267033 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33267065 GTATTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33267236 original size:2 final size:2
Alignment explanation
Indices: 33267225--33267258 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
33267215 TGGTGTATGA
33267225 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33267259 AAATAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33267273 original size:7 final size:7
Alignment explanation
Indices: 33267252--33267359 Score: 62
Period size: 7 Copynumber: 15.0 Consensus size: 7
33267242 ATATATATAT
33267252 ATATATAA
1 ATATA-AA
33267260 A-ATAAA
1 ATATAAA
33267266 ATATAAA
1 ATATAAA
33267273 ATATAAA
1 ATATAAA
* *
33267280 AGA-ATA
1 ATATAAA
33267286 ATATATAA
1 ATATA-AA
*
33267294 ATATATAT
1 ATATA-AA
33267302 ATATACAA
1 ATATA-AA
33267310 ACGTATAAA
1 A--TATAAA
*
33267319 ATGTAAA
1 ATATAAA
*
33267326 ATGTAAA
1 ATATAAA
*
33267333 A-AAAAA
1 ATATAAA
33267339 AT-TAATA
1 ATATAA-A
*
33267346 GTATAAA
1 ATATAAA
33267353 ATATAAA
1 ATATAAA
33267360 TAGATATACG
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
6 13 0.16
7 40 0.51
8 19 0.24
9 3 0.04
10 4 0.05
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (7 bp):
ATATAAA
Done.