Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 69 of 206
Found at i:19560576 original size:14 final size:14
Alignment explanation
Indices: 19560536--19560578 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
19560526 AAACCAATTC
*
19560536 AATAA-TTTAAAAC
1 AATAATTTTAAAAA
19560549 AATAATTATTAAAAA
1 AATAATT-TTAAAAA
*
19560564 AATACTTTTAAAAA
1 AATAATTTTAAAAA
19560578 A
1 A
19560579 CTTTAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 5 0.19
14 9 0.35
15 12 0.46
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATTTTAAAAA
Found at i:19563898 original size:10 final size:10
Alignment explanation
Indices: 19563883--19563918 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
19563873 GAGATAAAGA
19563883 AGAAAGAGAG
1 AGAAAGAGAG
19563893 AGAAAGAGAG
1 AGAAAGAGAG
*
19563903 AGAGAGAGAG
1 AGAAAGAGAG
19563913 ATGAAA
1 A-GAAA
19563919 TCAATATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 20 0.87
11 3 0.13
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.03
Consensus pattern (10 bp):
AGAAAGAGAG
Found at i:19571036 original size:56 final size:50
Alignment explanation
Indices: 19570959--19571253 Score: 261
Period size: 50 Copynumber: 5.8 Consensus size: 50
19570949 ATTTGGGTAA
* *
19570959 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACA-C--CGAG---ATG
* * * * *
19571015 AGAGGTCTCATGTAAGGCCATGTCTGAGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
* * * *
19571065 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
* * * *
19571115 AGAGGTCCC-TCGTAAGACCATGTCTGGGACATGACGTTGGCACCAAGATG
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
* * * * *
19571165 AGAGGTCCC-TCGTAAGACCATGTCTGGGACATGACATGGGCACCTATATG
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
** ** * * *
19571215 AGAACTCTTATGTAATACCATATCTGGGATATGGCATTG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTG
19571254 GCAGTACAAG
Statistics
Matches: 212, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.00
50 170 0.80
51 1 0.00
53 3 0.01
55 1 0.00
56 36 0.17
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACACCGAGATG
Found at i:19571146 original size:100 final size:100
Alignment explanation
Indices: 19570959--19571240 Score: 316
Period size: 100 Copynumber: 2.8 Consensus size: 100
19570949 ATTTGGGTAA
* * * *
19570959 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCATTGAGATTATGAGAGGTCTC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCA---AG---ATGAGAGGTCTC
* * *
19571024 ATGTAAGGCCATGTCTGAGACATGGCGTTGGCACCGAGATG
60 ATGTAAGACCATGTCTGAGACATGACGTTGGCACCAAGATG
* *
19571065 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACGTTGGCACCAAGATGAGAGGTC-CCTCGTA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATGAGAGGTCTCAT-GTA
*
19571129 AGACCATGTCTGGGACATGACGTTGGCACCAAGATG
65 AGACCATGTCTGAGACATGACGTTGGCACCAAGATG
* * * ** *
19571165 AGAGGTCCC-TCGTAAGACCATGTCTGGGACATGACATGGGCACCTATATGAGAACTCTTATGTA
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGACATTGGCACCAAGATGAGAGGTCTCATGTA
* *
19571229 ATACCATATCTG
65 AGACCATGTCTG
19571241 GGATATGGCA
Statistics
Matches: 153, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
99 3 0.02
100 107 0.70
101 1 0.01
103 2 0.01
106 40 0.26
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (100 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATGAGAGGTCTCATGTAA
GACCATGTCTGAGACATGACGTTGGCACCAAGATG
Found at i:19571235 original size:50 final size:50
Alignment explanation
Indices: 19571012--19571217 Score: 299
Period size: 50 Copynumber: 4.1 Consensus size: 50
19571002 CATTGAGATT
* * * * *
19571012 ATGAGAGGTCTCAT-GTAAGGCCATGTCTGAGACATGGCGTTGGCACCGAG
1 ATGAGAGGTC-CCTCGTAAGACCATGTCTGGGACATGACGTTGGCACCAAG
19571062 ATGAGAGGTCCCAT-GTAAGACCATGTCTGGGACATGACGTTGGCACCAAG
1 ATGAGAGGTCCC-TCGTAAGACCATGTCTGGGACATGACGTTGGCACCAAG
19571112 ATGAGAGGTCCCTCGTAAGACCATGTCTGGGACATGACGTTGGCACCAAG
1 ATGAGAGGTCCCTCGTAAGACCATGTCTGGGACATGACGTTGGCACCAAG
* * * *
19571162 ATGAGAGGTCCCTCGTAAGACCATGTCTGGGACATGACATGGGCACCTAT
1 ATGAGAGGTCCCTCGTAAGACCATGTCTGGGACATGACGTTGGCACCAAG
19571212 ATGAGA
1 ATGAGA
19571218 ACTCTTATGT
Statistics
Matches: 145, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
49 2 0.01
50 143 0.99
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCTCGTAAGACCATGTCTGGGACATGACGTTGGCACCAAG
Found at i:19575016 original size:11 final size:11
Alignment explanation
Indices: 19575000--19575026 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
19574990 AGATAAATGT
19575000 TATTTAATTAA
1 TATTTAATTAA
19575011 TATTTAATTAA
1 TATTTAATTAA
19575022 TATTT
1 TATTT
19575027 TTAGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTAATTAA
Found at i:19579254 original size:21 final size:21
Alignment explanation
Indices: 19579212--19579290 Score: 112
Period size: 19 Copynumber: 3.9 Consensus size: 21
19579202 TACAAAATCA
*
19579212 CATATTCTAAGATT--ACATAT
1 CATA-TCTAAGATTGCATATAT
19579232 CATATCTAAGATTGCATATAT
1 CATATCTAAGATTGCATATAT
19579253 CATATCTAAGATTGC--ATAT
1 CATATCTAAGATTGCATATAT
19579272 CATATCTAAGATTGCATAT
1 CATATCTAAGATTGCATAT
19579291 CCTCGAAGAT
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
19 28 0.52
20 4 0.07
21 22 0.41
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (21 bp):
CATATCTAAGATTGCATATAT
Found at i:19579265 original size:40 final size:41
Alignment explanation
Indices: 19579212--19579290 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 41
19579202 TACAAAATCA
19579212 CATATTCTAAGATTACATATCATATCTAAGATTGCATATAT
1 CATATTCTAAGATTACATATCATATCTAAGATTGCATATAT
*
19579253 CATA-TCTAAGATTGCATATCATATCTAAGATTGCATAT
1 CATATTCTAAGATTACATATCATATCTAAGATTGCATAT
19579291 CCTCGAAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 33 0.89
41 4 0.11
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (41 bp):
CATATTCTAAGATTACATATCATATCTAAGATTGCATATAT
Found at i:19579301 original size:17 final size:18
Alignment explanation
Indices: 19579220--19579301 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 18
19579210 CACATATTCT
* *
19579220 AAGATTACATATCATATCT
1 AAGATTGCATATCA-ATCG
*
19579239 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCA-ATCG
*
19579260 AAGATTGCATATCATATCT
1 AAGATTGCATATCA-ATCG
*
19579279 AAGATTGCATATC-CTCG
1 AAGATTGCATATCAATCG
19579296 AAGATT
1 AAGATT
19579302 ATGTTTCCAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.14
19 31 0.53
21 19 0.33
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (18 bp):
AAGATTGCATATCAATCG
Found at i:19579797 original size:44 final size:44
Alignment explanation
Indices: 19579673--19579826 Score: 149
Period size: 44 Copynumber: 3.6 Consensus size: 44
19579663 TATTTAGTCT
* * * *
19579673 GCTCCACTGCAACTTCAGAGAGATAAGA-CTAGATGC-GT--TCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTA-AGGCTTTAATCC
* * *
19579714 GCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTAAGGCTTTAATCC
* * * *
19579757 GCTTCACTGCAACTTCAGGGAGATAGGAT-TATCGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTA-AGGCTTTAATCC
19579801 GCTCCACTGCAACTTCAGGGAGATAA
1 GCTCCACTGCAACTTCAGGGAGATAA
19579827 AATTTGCCAT
Statistics
Matches: 94, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
40 25 0.27
41 7 0.07
43 7 0.07
44 55 0.59
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTAAGGCTTTAATCC
Found at i:19580119 original size:44 final size:43
Alignment explanation
Indices: 19580058--19580697 Score: 551
Period size: 44 Copynumber: 14.6 Consensus size: 43
19580048 CTGTCGGTGC
* * *
19580058 AGGAAGGCCAGATCTGCTATCTTCGATCTACTTCACACCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CACCAATAT
* * * *
19580102 ATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCAACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-C-ACCAATAT
* * *
19580147 GGGAAGACAAGATATG-TATCTTCGATCCACTTCCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCC-ACCAATAT
* * * *
19580190 AGGAAGACAGGA-CTTGCTATTTTCGACCTACTTCACACCAATAC
1 AGGAAGACAAGATC-TGCTATCTTCGATCTACTTC-CACCAATAT
* * * *
19580234 ATGAAGACAAGATCTGCTTTCTTCGATCTACTT-CGCCACTAGT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCCACCAATA-T
**
19580277 ATGGAAAGACAAGATCTGC-ATCTTCGATCCCCTTCCTACCAATAT
1 A-GG-AAGACAAGATCTGCTATCTTCGATCTACTTCC-ACCAATAT
* * * * * *
19580322 AGGAAGACAGGACCTACTATCTTTGATCTACTT-TATGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCCA--CCAATAT
* * *
19580366 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTT--CCACCAATAT
* *
19580411 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-C-ACCAATAT
* * * *
19580455 AGGAAGACAGGATCTACTATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CACCAATAT
* * *
19580499 ATGAAGACAAGATCTGC-ATCTTCGATCCACTTCTTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CACCAATAT
* * * *
19580542 AGGAAGACATGACCTGCTATCTTCGATCTACTTCACGCCAATAA
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-CACCAATAT
* * * * * *
19580586 ATGAAGACAATATCTGCTTTCTTCGATCTAC-TCCGCCACTAAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCCACCAAT-AT
*
19580629 ATGAGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATAT
1 A-G-GAAGACAAGATCTGCTATCTTCGATCTACTTCC-ACCAATAT
* *
19580674 AGGAAGACAGGACCTGCTATCTTC
1 AGGAAGACAAGATCTGCTATCTTC
19580698 ACTGATCTGC
Statistics
Matches: 472, Mismatches: 98, Indels: 52
0.76 0.16 0.08
Matches are distributed among these distances:
42 14 0.03
43 85 0.18
44 270 0.57
45 93 0.20
46 9 0.02
47 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCCACCAATAT
Found at i:19580300 original size:132 final size:132
Alignment explanation
Indices: 19580074--19580697 Score: 735
Period size: 132 Copynumber: 4.7 Consensus size: 132
19580064 GCCAGATCTG
* *
19580074 CTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCA
1 CTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
* *
19580139 ACCAGTATGGGAAGACAAGATATGTATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACT
66 ACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACT
*
19580204 TG
131 TA
* *
19580206 CTATTTTCGACCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 CTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
* * * *
19580271 ACTAGTATGGAAAGACAAGATCTGCATCTTCGATCCCCTTCCTACCAATATAGGAAGACAGGACC
66 ACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACT
19580336 TA
131 TA
* * **
19580338 CTATCTTTGATCTACTTTATGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
1 CTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
19580403 ACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGA-
66 ACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGAC
19580467 TCTA
130 T-TA
* * * **
19580471 CTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC-ATCTTCGATCCACTTC-TT
1 CTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
* * * * * * * * **
19580534 ACCAATATAGGAAGACATGACCTGCTATCTTCGATCTACTTCAC-GCCAATAAATGAAGACAATA
66 ACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGA
*
19580598 -TCTG
129 CT-TA
* * * * *
19580602 CTTTCTTCGATCTAC-TC-CGCCACTAACATGAGAAGACAAGATCTGC-ATCTTCGATCCACTTC
1 CTATCTTCGATCTACTTCACACCAAT-ACAT--GAAGACAAGATCTGCTTTCTTCGATCTACTTC
* * * * *
19580664 -CTACCAATATAGGAAGACAGGACCTGCTATCTTC
63 GCCACCAGTATGGGAAGACAAGATCTGC-ATCTTC
19580698 ACTGATCTGC
Statistics
Matches: 442, Mismatches: 44, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
129 6 0.01
130 6 0.01
131 53 0.12
132 311 0.70
133 66 0.15
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (132 bp):
CTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCC
ACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACT
TA
Found at i:19581938 original size:23 final size:23
Alignment explanation
Indices: 19581911--19581954 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
19581901 CTCCATTTTT
*
19581911 CTTTTCTTTTTCT-TTTTTTATCA
1 CTTTTATTTTT-TATTTTTTATCA
19581934 CTTTTATTTTTTATTTTTTAT
1 CTTTTATTTTTTATTTTTTAT
19581955 TTTGATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (23 bp):
CTTTTATTTTTTATTTTTTATCA
Found at i:19586631 original size:23 final size:25
Alignment explanation
Indices: 19586586--19586647 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
19586576 AAATTGAAAT
*
19586586 AAAAATAAATAAAAAGGTAAATTA-A
1 AAAAATAAA-AAAAAGCTAAATTACA
*
19586611 AAAAATAAAAAAAA-CTTAATTACA
1 AAAAATAAAAAAAAGCTAAATTACA
*
19586635 AAAACATTAAAAA
1 AAAA-ATAAAAAA
19586648 GCGAAGGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 6 0.19
24 10 0.31
25 16 0.50
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (25 bp):
AAAAATAAAAAAAAGCTAAATTACA
Found at i:19586977 original size:19 final size:19
Alignment explanation
Indices: 19586940--19587018 Score: 113
Period size: 19 Copynumber: 4.0 Consensus size: 19
19586930 TACAAAATCA
*
19586940 CATATTCTAAGATTACATAT
1 CATA-TCTAAGATTGCATAT
*
19586960 CATATCTAATATTGCATATAT
1 CATATCTAAGATTGC--ATAT
19586981 CATATCTAAGATTGCATAT
1 CATATCTAAGATTGCATAT
19587000 CATATCTAAGATTGCATAT
1 CATATCTAAGATTGCATAT
19587019 TCTCGAAGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
19 32 0.59
20 4 0.07
21 18 0.33
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (19 bp):
CATATCTAAGATTGCATAT
Found at i:19586989 original size:40 final size:41
Alignment explanation
Indices: 19586940--19587018 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 41
19586930 TACAAAATCA
*
19586940 CATATTCTAAGATTACATATCATATCTAATATTGCATATAT
1 CATATTCTAAGATTACATATCATATCTAAGATTGCATATAT
*
19586981 CATA-TCTAAGATTGCATATCATATCTAAGATTGCATAT
1 CATATTCTAAGATTACATATCATATCTAAGATTGCATAT
19587019 TCTCGAAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (41 bp):
CATATTCTAAGATTACATATCATATCTAAGATTGCATATAT
Found at i:19587029 original size:17 final size:18
Alignment explanation
Indices: 19586948--19587029 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 18
19586938 CACATATTCT
* *
19586948 AAGATTACATATCATATCT
1 AAGATTGCATAT-ATATCG
* *
19586967 AATATTGCATATATCATATCT
1 AAGATTGC--ATAT-ATATCG
*
19586988 AAGATTGCATATCATATCT
1 AAGATTGCATAT-ATATCG
*
19587007 AAGATTGCATAT-TCTCG
1 AAGATTGCATATATATCG
19587024 AAGATT
1 AAGATT
19587030 ATGTTTCCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
17 9 0.16
19 29 0.52
21 18 0.32
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (18 bp):
AAGATTGCATATATATCG
Found at i:19587874 original size:13 final size:13
Alignment explanation
Indices: 19587856--19587882 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19587846 CCAATTTTTC
19587856 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
19587869 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
19587882 C
1 C
19587883 CTTCTCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:19589777 original size:20 final size:19
Alignment explanation
Indices: 19589752--19589808 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
19589742 TTGGTACGAT
19589752 AATTTTTATATTTTTTTAC
1 AATTTTTATATTTTTTTAC
*
19589771 GAA-TTTTATATTTCTTTAC
1 -AATTTTTATATTTTTTTAC
*
19589790 -ATTTTTATAATTTTCTTAC
1 AATTTTTAT-ATTTTTTTAC
19589809 TACTTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.03
18 6 0.19
19 23 0.72
20 2 0.06
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (19 bp):
AATTTTTATATTTTTTTAC
Found at i:19589896 original size:10 final size:10
Alignment explanation
Indices: 19589852--19589898 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
19589842 ATACTATATA
*
19589852 TTTTATATTT
1 TTTTCTATTT
19589862 TTTTACTATTT
1 TTTT-CTATTT
* *
19589873 TTATC-AATT
1 TTTTCTATTT
19589882 TTTTCTATTT
1 TTTTCTATTT
19589892 TTTTCTA
1 TTTTCTA
19589899 AGTTTTAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 7 0.23
10 15 0.50
11 8 0.27
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTCTATTT
Found at i:19590645 original size:86 final size:86
Alignment explanation
Indices: 19590474--19590729 Score: 372
Period size: 86 Copynumber: 3.0 Consensus size: 86
19590464 TTTTTTGAAA
* * ** * * * *
19590474 AAAAAGTTTGAG-GACCTTTTTGATACATTTTGGCAGTTCAAATACACAATTAAGAG-AAAAAAT
1 AAAAAGTTTGAGAG-CTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAAT
*
19590537 AGGGGCTTAATTGCTTTCTTTG
65 AGGGGCTTAATTGCTTTTTTTG
*
19590559 AAAAAGTTTGTGAGCTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAATA
1 AAAAAGTTTGAGAGCTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAATA
19590624 GGGGCTTAATTGCTTTTTTTG
66 GGGGCTTAATTGCTTTTTTTG
*
19590645 AAAAAGTTTGAGAGCTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTAAAAAAAATA
1 AAAAAGTTTGAGAGCTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAATA
* *
19590710 GGGGCTTAAATGTTTTTTTT
66 GGGGCTTAATTGCTTTTTTT
19590730 AAGGGTTTGA
Statistics
Matches: 155, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
85 45 0.29
86 110 0.71
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (86 bp):
AAAAAGTTTGAGAGCTTTTTTGATATATTTTGAAAGTTTAAATACCCAATTGAGTGAAAAAAATA
GGGGCTTAATTGCTTTTTTTG
Found at i:19591905 original size:20 final size:20
Alignment explanation
Indices: 19591880--19591933 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
19591870 AAATTAAGTT
*
19591880 AAAATGATTTTAACCTAGCC
1 AAAATGATTTTAACCAAGCC
* **
19591900 AAAATGATTTCAACCAAGTT
1 AAAATGATTTTAACCAAGCC
*
19591920 AAAATAATTTTAAC
1 AAAATGATTTTAAC
19591934 ACATCAAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAATGATTTTAACCAAGCC
Found at i:19591951 original size:40 final size:40
Alignment explanation
Indices: 19591875--19591958 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
19591865 TTTTAAAATT
* *
19591875 AAGTTAAAATGATTTTAACCTAGCCAAAATGATTTCAACC
1 AAGTTAAAATAATTTTAACCTAGCCAAAATGATTTCAAAC
* *
19591915 AAGTTAAAATAATTTTAACAC-A-TCAAAGTGATTTTCAAAC
1 AAGTTAAAATAATTTTAAC-CTAGCCAAAATGA-TTTCAAAC
19591955 AAGT
1 AAGT
19591959 CAGAATTGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 7 0.18
40 30 0.79
41 1 0.03
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (40 bp):
AAGTTAAAATAATTTTAACCTAGCCAAAATGATTTCAAAC
Found at i:19592142 original size:21 final size:20
Alignment explanation
Indices: 19592104--19592142 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
19592094 TTTTTGAAGT
*
19592104 ATCGATATTTTCTGAAAATA
1 ATCGATACTTTCTGAAAATA
*
19592124 ATCGATACCTTTCTTAAAA
1 ATCGATA-CTTTCTGAAAA
19592143 ACGATACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (20 bp):
ATCGATACTTTCTGAAAATA
Found at i:19594916 original size:39 final size:38
Alignment explanation
Indices: 19594859--19594932 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 38
19594849 ATTCCCCGAT
19594859 TATTAATAACATAATTATTTAATTTAATTATTATTTTTAC
1 TATTAATAACATAATTATTT-ATTTAATTA-TATTTTTAC
* *
19594899 TATTATTAAC-TAATTATTTATTTTATTATATTTT
1 TATTAATAACATAATTATTTATTTAATTATATTTT
19594933 AATTCCTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 6 0.19
38 8 0.25
39 9 0.28
40 9 0.28
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.59
Consensus pattern (38 bp):
TATTAATAACATAATTATTTATTTAATTATATTTTTAC
Found at i:19599608 original size:18 final size:18
Alignment explanation
Indices: 19599573--19599611 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
19599563 CTTGAGAAAC
* **
19599573 TTTATATCCTTCTGGGAT
1 TTTAAATCCTTCAAGGAT
19599591 TTTAAATCCTTCAAGGAT
1 TTTAAATCCTTCAAGGAT
19599609 TTT
1 TTT
19599612 CATATAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (18 bp):
TTTAAATCCTTCAAGGAT
Found at i:19609396 original size:11 final size:11
Alignment explanation
Indices: 19609379--19609408 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
19609369 ATAATGCTTA
19609379 AGATAATCTAC
1 AGATAATCTAC
*
19609390 GGATAATCTAC
1 AGATAATCTAC
19609401 AGATAATC
1 AGATAATC
19609409 ATGCAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (11 bp):
AGATAATCTAC
Found at i:19613108 original size:71 final size:71
Alignment explanation
Indices: 19612987--19613135 Score: 244
Period size: 71 Copynumber: 2.1 Consensus size: 71
19612977 GGATACTACA
* * *
19612987 ACATATAAGCTTTCTATAGGTTAAGGGGTGTCTGTATCATCTCAGCATATCAAATCAATAATGTG
1 ACATGTAAGCTTTCTACAGGTTAAGGGGTGTCTCTATCATCTCAGCATATCAAATCAATAATGTG
19613052 GTCTCG
66 GTCTCG
* * *
19613058 ACATGTAAGCTTTTTACAGGTTAAGGGGTGTCTCTATCATCTTAGCATATCAAATCTATAATGTG
1 ACATGTAAGCTTTCTACAGGTTAAGGGGTGTCTCTATCATCTCAGCATATCAAATCAATAATGTG
19613123 GTCTCG
66 GTCTCG
19613129 ACATGTA
1 ACATGTA
19613136 TAACTGAAGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (71 bp):
ACATGTAAGCTTTCTACAGGTTAAGGGGTGTCTCTATCATCTCAGCATATCAAATCAATAATGTG
GTCTCG
Found at i:19614816 original size:116 final size:116
Alignment explanation
Indices: 19614612--19614844 Score: 412
Period size: 116 Copynumber: 2.0 Consensus size: 116
19614602 TATGTCCGAC
*
19614612 CAATAGAAAGAGGTCGAGTGATAGATGTGTCATAGGAGGAAGAAGAACTTGGCCATGGCTAAAAA
1 CAATAGAAAGAGGTCGAGTGATAGATGTGTCATAGGAGGAAGAAGAACTCGGCCATGGCTAAAAA
19614677 ATCATCAGAATATAAGCTGAGAGTGACACCAAAGCCTGCAATAGTAAAATG
66 ATCATCAGAATATAAGCTGAGAGTGACACCAAAGCCTGCAATAGTAAAATG
* * *
19614728 CAATAGAAAGAGGTCGAGTGATAGATGTGTCGTAGGAGGAGGAAGAACTCGGTCATGGCTAAAAA
1 CAATAGAAAGAGGTCGAGTGATAGATGTGTCATAGGAGGAAGAAGAACTCGGCCATGGCTAAAAA
* *
19614793 ATCATTAGAATATAGGCTGAGAGTGACACCAAAGCCTGCAATAGTAAAATG
66 ATCATCAGAATATAAGCTGAGAGTGACACCAAAGCCTGCAATAGTAAAATG
19614844 C
1 C
19614845 CGAGTGATAG
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 111 1.00
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (116 bp):
CAATAGAAAGAGGTCGAGTGATAGATGTGTCATAGGAGGAAGAAGAACTCGGCCATGGCTAAAAA
ATCATCAGAATATAAGCTGAGAGTGACACCAAAGCCTGCAATAGTAAAATG
Found at i:19615386 original size:23 final size:24
Alignment explanation
Indices: 19615356--19615415 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 24
19615346 ACAATAGTAG
* *
19615356 TAATAATAACAATAAAA-ATAACA
1 TAATAATAAAAATAAAATAAAACA
* *
19615379 TAATAATAATACTAAAATAAAACA
1 TAATAATAAAAATAAAATAAAACA
19615403 -AATAATAAAAATA
1 TAATAATAAAAATA
19615416 CTAAAAAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 26 0.84
24 5 0.16
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (24 bp):
TAATAATAAAAATAAAATAAAACA
Found at i:19615420 original size:9 final size:9
Alignment explanation
Indices: 19615312--19615422 Score: 55
Period size: 9 Copynumber: 12.2 Consensus size: 9
19615302 CTACAGTGAT
19615312 AATAATAAA
1 AATAATAAA
* *
19615321 TATAATACA
1 AATAATAAA
*
19615330 AAGAATAAA
1 AATAATAAA
* * *
19615339 GACAATAAC
1 AATAATAAA
* **
19615348 AATAGTAGT
1 AATAATAAA
*
19615357 AATAATAAC
1 AATAATAAA
*
19615366 AATAAAAATA
1 AATAATAA-A
*
19615376 ACATAATAAT
1 A-ATAATAAA
*
19615386 AATACT-AA
1 AATAATAAA
19615394 AATAA-AACA
1 AATAATAA-A
19615403 AATAATAAA
1 AATAATAAA
*
19615412 AATACTAAA
1 AATAATAAA
19615421 AA
1 AA
19615423 GGAAAGGGAG
Statistics
Matches: 73, Mismatches: 24, Indels: 10
0.68 0.22 0.09
Matches are distributed among these distances:
8 6 0.08
9 57 0.78
10 4 0.05
11 6 0.08
ACGTcount: A:0.68, C:0.07, G:0.04, T:0.22
Consensus pattern (9 bp):
AATAATAAA
Found at i:19615835 original size:22 final size:22
Alignment explanation
Indices: 19615810--19615852 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19615800 TATCCAAACA
19615810 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
19615832 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
19615853 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:19617038 original size:6 final size:6
Alignment explanation
Indices: 19617022--19617058 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
19617012 TTAAATTAAT
19617022 AAAAT- AAAATA AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
19617059 TGTACTAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:19618690 original size:40 final size:40
Alignment explanation
Indices: 19618625--19618719 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
19618615 ACTATGTTTA
* * **
19618625 GCACTTAGTGTGCGATTCGAGATAGCTTCGGCTATTTATG
1 GCACTTAGTGTGCGATTCGAAATAGCTTCAGCTATAAATG
* *
19618665 GCACTTAGTGTGCTATTGGAAATAGCTTCAGCTATAAATG
1 GCACTTAGTGTGCGATTCGAAATAGCTTCAGCTATAAATG
19618705 GCACTTAGTGTGCGA
1 GCACTTAGTGTGCGA
19618720 GACTGAGATA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
GCACTTAGTGTGCGATTCGAAATAGCTTCAGCTATAAATG
Found at i:19621342 original size:20 final size:20
Alignment explanation
Indices: 19621317--19621354 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19621307 GACTGTACAA
*
19621317 ATTAAATTAAAAACAAAACT
1 ATTAAAATAAAAACAAAACT
*
19621337 ATTAAAATAAAAATAAAA
1 ATTAAAATAAAAACAAAA
19621355 ATAGCTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
ATTAAAATAAAAACAAAACT
Found at i:19624119 original size:17 final size:16
Alignment explanation
Indices: 19624097--19624136 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
19624087 TCTATTATTT
*
19624097 TATATACATATTGTACA
1 TATATACATATT-TAAA
19624114 TATATACATATTTAAA
1 TATATACATATTTAAA
19624130 TATATAC
1 TATATAC
19624137 GAATGCGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (16 bp):
TATATACATATTTAAA
Found at i:19626479 original size:26 final size:27
Alignment explanation
Indices: 19626450--19626501 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
19626440 ACTAAATTTC
19626450 CAAAAA-AGGGCC-ATTTTAAAAAAATA
1 CAAAAATA-GGCCAATTTTAAAAAAATA
*
19626476 CAAAAATAGGCCAATTTTTAAAAAAT
1 CAAAAATAGGCCAATTTTAAAAAAAT
19626502 TTATTAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.23
Consensus pattern (27 bp):
CAAAAATAGGCCAATTTTAAAAAAATA
Found at i:19627667 original size:16 final size:15
Alignment explanation
Indices: 19627631--19627659 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19627621 GAGTATAGTA
19627631 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
19627646 AAATATTTAAAAAA
1 AAATATTTAAAAAA
19627660 AGAGATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:19628550 original size:23 final size:23
Alignment explanation
Indices: 19628499--19628550 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
19628489 AAGTTAACAA
*
19628499 AATGTAAAAAAAATAGAAATTAT
1 AATGTAAAAAAAATAGAAAATAT
** * *
19628522 TTTGTAAAAAAATTATAAAATAT
1 AATGTAAAAAAAATAGAAAATAT
19628545 AATGTA
1 AATGTA
19628551 GCATTTAATC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.33
Consensus pattern (23 bp):
AATGTAAAAAAAATAGAAAATAT
Found at i:19628853 original size:29 final size:28
Alignment explanation
Indices: 19628789--19628854 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
19628779 TATAAAGGCG
*
19628789 CATTTTTTTTAAATTTTTAAAAAATTAG
1 CATTTTTTTTAAATTTTTAAAAAATTAA
*
19628817 C-TTATTTTTGTAAATCTTTTTAAAAA-TAA
1 CATT-TTTTT-TAAAT-TTTTAAAAAATTAA
19628846 CATTTTTTT
1 CATTTTTTT
19628855 AGAAATTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 2 0.06
28 6 0.19
29 13 0.41
30 11 0.34
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (28 bp):
CATTTTTTTTAAATTTTTAAAAAATTAA
Found at i:19635273 original size:107 final size:107
Alignment explanation
Indices: 19635084--19635301 Score: 382
Period size: 107 Copynumber: 2.0 Consensus size: 107
19635074 AATCTGGATG
*
19635084 TGAACAAACCATAGCATACATGAGAGATCCCATTGCACTAGAGTATGGAACATGTGACATGTACT
1 TGAACAAACCATAGCATACATGAGAGATCCCACTGCACTAGAGTATGGAACATGTGACATGTACT
* * *
19635149 CAATCTTATCATCTGATTGTGGAGACAAAGCCGATGAAAGTT
66 CAATCTCATCATCTGATTATGAAGACAAAGCCGATGAAAGTT
*
19635191 TGAACAAACCATAGCATACATGAGAGATCCCACTGCACTAGATTATGGAACATGTGACATGTACT
1 TGAACAAACCATAGCATACATGAGAGATCCCACTGCACTAGAGTATGGAACATGTGACATGTACT
*
19635256 CAATCTCATCATTTGATTATGAAGACAAAGCCGATGAAAGTT
66 CAATCTCATCATCTGATTATGAAGACAAAGCCGATGAAAGTT
19635298 TGAA
1 TGAA
19635302 ATGGACTGCT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (107 bp):
TGAACAAACCATAGCATACATGAGAGATCCCACTGCACTAGAGTATGGAACATGTGACATGTACT
CAATCTCATCATCTGATTATGAAGACAAAGCCGATGAAAGTT
Found at i:19643339 original size:3 final size:3
Alignment explanation
Indices: 19643333--19643410 Score: 54
Period size: 3 Copynumber: 26.3 Consensus size: 3
19643323 GTTGTTGTTG
* * *
19643333 TTA TTA TTA TTA TTA TTA TTA TTA -CA CTA TTT TTA TTA TT- TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* * * *
19643377 TTA TAA TATA TT- TTA CTA TTA TTG TTA GTA TTA T
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
19643411 AGATAACTAT
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
2 5 0.09
3 48 0.84
4 4 0.07
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:19643736 original size:2 final size:2
Alignment explanation
Indices: 19643729--19643768 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
19643719 ACCTAGACTC
* *
19643729 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19643769 TTTATATTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:19648057 original size:18 final size:17
Alignment explanation
Indices: 19648035--19648073 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
19648025 GAAAATGATG
19648035 GAAAAAT-AAAAGAAAA
1 GAAAAATGAAAAGAAAA
19648051 TGAAAAATGAAAAGAAAA
1 -GAAAAATGAAAAGAAAA
19648069 GAAAA
1 GAAAA
19648074 GAAAAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (17 bp):
GAAAAATGAAAAGAAAA
Found at i:19648063 original size:23 final size:22
Alignment explanation
Indices: 19648037--19648084 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
19648027 AAATGATGGA
* *
19648037 AAAATAAAAGAAAATGAAAAATG
1 AAAAGAAAAGAAAA-GAAAAAGG
19648060 AAAAGAAAAGAAAAGAAAAAGG
1 AAAAGAAAAGAAAAGAAAAAGG
19648082 AAA
1 AAA
19648085 GGCCAAGGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (22 bp):
AAAAGAAAAGAAAAGAAAAAGG
Found at i:19650384 original size:45 final size:45
Alignment explanation
Indices: 19650326--19650608 Score: 341
Period size: 45 Copynumber: 6.3 Consensus size: 45
19650316 GTAGCAGTGG
* * * *
19650326 AGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTAGCAGTGA
1 AGTAGATTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGA
** * *
19650371 AGTAGATCAAAGATAACAGATCTTGTCTTTCTATATTGGCAGCGA
1 AGTAGATTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
19650416 AGTAGATTGAAGATAGCAGATCTTATCTTCCTGTATTGGCACCGA
1 AGTAGATTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGA
** * * *
19650461 AGTAGACCGAAGATAAAAGATATTTTCTTCCTGTATTGGCAGCGA
1 AGTAGATTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGA
*
19650506 AGTAGATTGAAGATAACAGATCTTGTCTTCCTGTATTGGCGGCGA
1 AGTAGATTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGA
* * ** * *
19650551 AGTAGATTAAAGATAGCAGATCTTACCTTCCTATACTGGCAGCGA
1 AGTAGATTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGA
* *
19650596 AGCAGATCGAAGA
1 AGTAGATTGAAGA
19650609 CACTAGCCTT
Statistics
Matches: 200, Mismatches: 38, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 200 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (45 bp):
AGTAGATTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGA
Found at i:19650568 original size:135 final size:135
Alignment explanation
Indices: 19650351--19650608 Score: 390
Period size: 135 Copynumber: 1.9 Consensus size: 135
19650341 GCAGATCTTG
* *
19650351 TCTTCCTGTATTAGCAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTTCTATATTGGCAGCGA
1 TCTTCCTGTATTAGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGCGA
* * * * *
19650416 AGTAGATTGAAGATAGCAGATCTTATCTTCCTGTATTGGCACCGAAGTAGACCGAAGATAAAAGA
66 AGTAGATTAAAGATAGCAGATCTTACCTTCCTATACTGGCACCGAAGCAGACCGAAGATAAAAGA
19650481 TATTT
131 TATTT
* ** * *
19650486 TCTTCCTGTATTGGCAGCGAAGTAGATTGAAGATAACAGATCTTGTCTTCCTGTATTGGCGGCGA
1 TCTTCCTGTATTAGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGCGA
* *
19650551 AGTAGATTAAAGATAGCAGATCTTACCTTCCTATACTGGCAGCGAAGCAGATCGAAGA
66 AGTAGATTAAAGATAGCAGATCTTACCTTCCTATACTGGCACCGAAGCAGACCGAAGA
19650609 CACTAGCCTT
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
135 109 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (135 bp):
TCTTCCTGTATTAGCAGCGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATATTGGCAGCGA
AGTAGATTAAAGATAGCAGATCTTACCTTCCTATACTGGCACCGAAGCAGACCGAAGATAAAAGA
TATTT
Found at i:19650637 original size:44 final size:44
Alignment explanation
Indices: 19650589--19650732 Score: 139
Period size: 44 Copynumber: 3.2 Consensus size: 44
19650579 TCCTATACTG
*
19650589 GCAGCGAAGCAGATCGAAGACACTAGCCTTACCTCCCTGAGTTT
1 GCAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGAGTTT
* * * * * * * * *
19650633 GCAGCGGAGCCGA-CTAAAGATAGTAGATCTTGCCTTCCTGTA-CTG
1 GCAGCGAAGCAGATC-GAAGACACTAG-CCTTGCCTCCCTG-AGTTT
*
19650678 GCAGCGAAGCAGATCGAAAACACTAGCCTTGCCTCCCTGAGTTT
1 GCAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGAGTTT
*
19650722 GCAGCGGAGCA
1 GCAGCGAAGCA
19650733 AACTAAAGAT
Statistics
Matches: 74, Mismatches: 21, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
43 2 0.03
44 41 0.55
45 29 0.39
46 2 0.03
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (44 bp):
GCAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGAGTTT
Found at i:19650797 original size:89 final size:89
Alignment explanation
Indices: 19650558--19650804 Score: 343
Period size: 89 Copynumber: 2.8 Consensus size: 89
19650548 CGAAGTAGAT
* * * *
19650558 TAAAGATAGCAGATCTTACCTTCCTATACTGGCAGCGAAGCAGATCGAAGACACTAGCCTTACCT
1 TAAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCAAAGACACTAGCCTTGCCT
**
19650623 CCCTGAGTTTGCAGCGGAGCCGAC
66 CCCTGAGTTTGCAGCGGAGCAAAC
*
19650647 TAAAGATAGTAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGAAA-ACACTAGCCTTGCC
1 TAAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATC-AAAGACACTAGCCTTGCC
19650711 TCCCTGAGTTTGCAGCGGAGCAAAC
65 TCCCTGAGTTTGCAGCGGAGCAAAC
* * * * * * * *
19650736 TAAAGATAGCAAATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCAAAGTCACAAGCCTTGTCT
1 TAAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCAAAGACACTAGCCTTGCCT
19650801 CCCT
66 CCCT
19650805 AAGCAGTAGT
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
88 3 0.02
89 135 0.96
90 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (89 bp):
TAAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCAAAGACACTAGCCTTGCCT
CCCTGAGTTTGCAGCGGAGCAAAC
Found at i:19651031 original size:132 final size:132
Alignment explanation
Indices: 19650796--19651224 Score: 637
Period size: 132 Copynumber: 3.2 Consensus size: 132
19650786 TCACAAGCCT
* * *
19650796 TGTCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGGCGAAA-CTTATCTTCCCAATGTAATAGG
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC-AAATCTTATCTTCCCAAGGTAGTAGG
* * *
19650860 GAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGCAGCGGAATAGGTTGACGATTGTAGA
65 GAAGCAAATTTAAGCCACCAATCCTATCTCCTTGAGCAGCAGCGGAATAGGTTGAAGATTGTAGA
*
19650925 TCT
130 TCC
* *
19650928 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCTCAAGGTAGTAAGG
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCCCAAGGTAGTAGGG
* * * *
19650993 AAGCAAATTTAAGCCACCAGTCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGAT
66 AAGCAAATTTAAGCCACCAATCCTATCTCCTTGAGCAGCAGCGGAATAGGTTGAAGATTGTAGAT
19651058 CC
131 CC
*** *
19651060 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAGCAAATCCTATCTTCCCAAGGTAGTAGGG
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCCCAAGGTAGTAGGG
* * * *
19651125 AAGCAAATTTAAGCCACCAATCCCT-TCTTCTTGAGCAGTAGCAGATTAGGTTGAAGATTGTAGA
66 AAGCAAATTTAAGCCACCAAT-CCTATCTCCTTGAGCAGCAGCGGAATAGGTTGAAGATTGTAGA
19651189 TCC
130 TCC
19651192 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
19651225 GCAGCTAATC
Statistics
Matches: 269, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
131 3 0.01
132 263 0.98
133 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (132 bp):
TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCCCAAGGTAGTAGGG
AAGCAAATTTAAGCCACCAATCCTATCTCCTTGAGCAGCAGCGGAATAGGTTGAAGATTGTAGAT
CC
Found at i:19651399 original size:44 final size:44
Alignment explanation
Indices: 19651336--19651500 Score: 118
Period size: 44 Copynumber: 3.7 Consensus size: 44
19651326 TATAACCAAC
* * * *
19651336 CTTATCTCTTTAAAGTTGCAGCGAAGCCGGTTGAAGATATCAA-T
1 CTTATCTCCTTGAAGTTGCAGCGAAGCAGATTGAAGATA-CAAGT
** ** *
19651380 CTTATCTCCTTGAAGTTGCAATGGGGCAGATTGAAGTTACAAGT
1 CTTATCTCCTTGAAGTTGCAGCGAAGCAGATTGAAGATACAAGT
* * * * * *
19651424 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAGGATGACGAA-T
1 CTTATCTCCTTGAAGTTGCAGCGAAGCAGATTGAAGAT-AC-AAGT
* * * *
19651469 CTTGTCTCCCTGAAGTTGCAGTGGAGCAGATT
1 CTTATCTCCTTGAAGTTGCAGCGAAGCAGATT
19651501 AAAGCCAATA
Statistics
Matches: 99, Mismatches: 19, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
43 3 0.03
44 62 0.63
45 32 0.32
46 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (44 bp):
CTTATCTCCTTGAAGTTGCAGCGAAGCAGATTGAAGATACAAGT
Found at i:19651486 original size:89 final size:89
Alignment explanation
Indices: 19651377--19651541 Score: 226
Period size: 89 Copynumber: 1.9 Consensus size: 89
19651367 TGAAGATATC
* * * ** *
19651377 AATCTTATCTCCTTGAAGTTGCAATGGGGCAGATTGAAGTTACA-AGTCTTA-TCTCCCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCA-ATAGTCCTACT-TCCCTGAAGT
19651440 TGCAGTGGAGTAGACTGAGGATGACG
64 TGCAGTGGAGTAGACTGAGGATGACG
* *
19651466 AATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAGTCCTACTTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCAATAGTCCTACTTCCCTGAAGTTG
19651531 CAGTGGAGTAG
66 CAGTGGAGTAG
19651542 GTTGAAGGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
88 1 0.02
89 64 0.97
90 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (89 bp):
AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGCCAATAGTCCTACTTCCCTGAAGTTG
CAGTGGAGTAGACTGAGGATGACG
Found at i:19651566 original size:89 final size:89
Alignment explanation
Indices: 19651377--19651581 Score: 218
Period size: 89 Copynumber: 2.3 Consensus size: 89
19651367 TGAAGATATC
* * * * ** *
19651377 AATCTTATCTCCTTGAAGTTGCAATGGGGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAGTCCTATCTCCCTGAAGTTG
*
19651442 CAGTGGAGTAGACTGAGGATGACG
66 CAGTGGAGTAGACTGAGGAAGACG
*
19651466 AATCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-ATAGTCCTA-CTTCCCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA-AGTCCTATC-TCCCTGAAGT
** *
19651529 TGCAGTGGAGTAGGTTGAAGGAAG-TG
64 TGCAGTGGAGTAGACTG-AGGAAGACG
* * * *
19651555 AGTCTTATCTCCCCGAAGCTACAGTGG
1 AATCTTATCTCCCTGAAGTTGCAGTGG
19651582 GTTAGGAAGA
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
88 2 0.02
89 89 0.93
90 5 0.05
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (89 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAGTCCTATCTCCCTGAAGTTG
CAGTGGAGTAGACTGAGGAAGACG
Found at i:19652795 original size:3 final size:3
Alignment explanation
Indices: 19652787--19652867 Score: 58
Period size: 3 Copynumber: 26.3 Consensus size: 3
19652777 GTCATGTTTG
* *
19652787 TTA TTA TTA TTA TTA TTA TTA TTA TTA CCCTA TTG TTA TTA TT- TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA --TTA TTA TTA TTA TTA TT-A
* * * *
19652834 TTA TAA TATA TT- TTA CTA TTA TTC TTA GTA TTA T
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
19652868 AGATTACTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
2 4 0.07
3 50 0.83
4 4 0.07
5 2 0.03
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:19654672 original size:22 final size:22
Alignment explanation
Indices: 19654630--19654670 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19654620 TGCCATTAGG
19654630 GTTCAAATGGAAAAAGGAAATT
1 GTTCAAATGGAAAAAGGAAATT
*
19654652 GTTC-AATTGAAAAAGGAAA
1 GTTCAAATGGAAAAAGGAAA
19654671 ATGAGTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (22 bp):
GTTCAAATGGAAAAAGGAAATT
Found at i:19656200 original size:18 final size:18
Alignment explanation
Indices: 19656177--19656213 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19656167 CATAACTGGA
19656177 CTCAACAATTGGCTTGGG
1 CTCAACAATTGGCTTGGG
19656195 CTCAACAATTGGCTTGGG
1 CTCAACAATTGGCTTGGG
19656213 C
1 C
19656214 AAAGGGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (18 bp):
CTCAACAATTGGCTTGGG
Found at i:19658180 original size:16 final size:16
Alignment explanation
Indices: 19658159--19658190 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19658149 TTACAACGTC
19658159 ATTTTTAGTTGCATTA
1 ATTTTTAGTTGCATTA
19658175 ATTTTTAGTTGCATTA
1 ATTTTTAGTTGCATTA
19658191 TTATTAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (16 bp):
ATTTTTAGTTGCATTA
Found at i:19659339 original size:32 final size:31
Alignment explanation
Indices: 19659273--19659339 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
19659263 TGTATAAAAT
*
19659273 ATTTCAAAAAATTAAATATAAAAATAAATAA
1 ATTTCAAAAAATTAAATATAAAAAGAAATAA
* *
19659304 ATTTTAAATAAATT-AATATAAAACAGAAATCA
1 ATTTCAAA-AAATTAAATATAAAA-AGAAATAA
19659336 ATTT
1 ATTT
19659340 AATTTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 16 0.52
32 15 0.48
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (31 bp):
ATTTCAAAAAATTAAATATAAAAAGAAATAA
Found at i:19662439 original size:27 final size:27
Alignment explanation
Indices: 19662364--19662439 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
19662354 GACTATCCCA
* * *
19662364 TGTTTACTATCCCAGCAGACTATCTCG
1 TGTTTACTGTCCTAGCAGACTACCTCG
*
19662391 TGTTTACTGT-CTCG-ACGAACTACCTCG
1 TGTTTACTGTCCTAGCA-G-ACTACCTCG
*
19662418 TGTTTACTGTCCTGGCAGACTA
1 TGTTTACTGTCCTAGCAGACTA
19662440 TATTGATTGC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
25 1 0.03
26 3 0.08
27 31 0.77
28 4 0.10
29 1 0.03
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (27 bp):
TGTTTACTGTCCTAGCAGACTACCTCG
Found at i:19663388 original size:21 final size:21
Alignment explanation
Indices: 19663362--19663402 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19663352 TTTAACCTAA
*
19663362 AATATGAATTGGATTGAATTG
1 AATATGAATTGGATTAAATTG
*
19663383 AATATGAATTGTATTAAATT
1 AATATGAATTGGATTAAATT
19663403 AATTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (21 bp):
AATATGAATTGGATTAAATTG
Found at i:19677594 original size:34 final size:34
Alignment explanation
Indices: 19677556--19677624 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
19677546 GAAAAAGTTT
19677556 GAAAATGATGTTAAAGTAGAGTTTATTATATAAG
1 GAAAATGATGTTAAAGTAGAGTTTATTATATAAG
*
19677590 GAAAATGATGTTAAAGTAGATTTTATTATATAAG
1 GAAAATGATGTTAAAGTAGAGTTTATTATATAAG
19677624 G
1 G
19677625 TTCCATGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.36
Consensus pattern (34 bp):
GAAAATGATGTTAAAGTAGAGTTTATTATATAAG
Found at i:19684606 original size:18 final size:18
Alignment explanation
Indices: 19684583--19684637 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
19684573 AATTTGGCAA
*
19684583 ATTAATATAGTTCGCCAT
1 ATTAATATAGTTCACCAT
* * *
19684601 ATTAATACAGATCACCAA
1 ATTAATATAGTTCACCAT
*
19684619 ATTAACATAGTTCACCAT
1 ATTAATATAGTTCACCAT
19684637 A
1 A
19684638 ATCATATAAG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (18 bp):
ATTAATATAGTTCACCAT
Found at i:19684652 original size:36 final size:36
Alignment explanation
Indices: 19684580--19684674 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 36
19684570 CATAATTTGG
* * *
19684580 CAAATTAATATAGTTCGCCATATTAATACAGATCAC
1 CAAATTAACATAGTTCACCATATCAATACAGATCAC
19684616 CAAATTAACATAGTTCACCATAATCATATA-AG-TCAC
1 CAAATTAACATAGTTCACCAT-ATCA-ATACAGATCAC
* * *
19684652 CAAGTTAACATGGTTCACAATAT
1 CAAATTAACATAGTTCACCATAT
19684675 AACACAATGC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
35 2 0.04
36 41 0.80
37 5 0.10
38 3 0.06
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.29
Consensus pattern (36 bp):
CAAATTAACATAGTTCACCATATCAATACAGATCAC
Found at i:19685028 original size:33 final size:31
Alignment explanation
Indices: 19684929--19685041 Score: 122
Period size: 33 Copynumber: 3.6 Consensus size: 31
19684919 CCCATATATG
* *
19684929 CATATATATTATATATA-ATCAAAACTCACA
1 CATATATATTATATATATAACAAAACCCACA
* **
19684959 CATATATATTTTATATATAACATAAA-CCATG
1 CATATATATTATATATATAACA-AAACCCACA
*
19684990 TATATATATTACATATATATAACAAAACCCACA
1 CATATATATT--ATATATATAACAAAACCCACA
*
19685023 CATATATATTGTATATATA
1 CATATATATTATATATATA
19685042 CGTATACCAT
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
30 16 0.24
31 22 0.33
32 6 0.09
33 23 0.34
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (31 bp):
CATATATATTATATATATAACAAAACCCACA
Found at i:19700672 original size:22 final size:22
Alignment explanation
Indices: 19700644--19700687 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19700634 GGCGCCAATG
19700644 AATAAAATAATAATATT-TTTTT
1 AATAAAAT-ATAATATTATTTTT
*
19700666 AATAAAATATAATTTTATTTTT
1 AATAAAATATAATATTATTTTT
19700688 TAAATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATAAAATATAATATTATTTTT
Found at i:19700798 original size:27 final size:27
Alignment explanation
Indices: 19700768--19700834 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
19700758 CCTCTCAAGT
19700768 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
19700795 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
19700822 AGGCGCCAATGAA
1 AGGCGCCAATGAA
19700835 TATTGTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.33, T:0.12
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:19700929 original size:21 final size:21
Alignment explanation
Indices: 19700904--19700947 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19700894 TGGATTAGTA
19700904 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
19700925 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
19700946 TT
1 TT
19700948 GTAATTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:19700950 original size:29 final size:28
Alignment explanation
Indices: 19700913--19700999 Score: 133
Period size: 29 Copynumber: 3.1 Consensus size: 28
19700903 ATTTTGTATG
19700913 AATATTGTAATTTTTTGTATGAATATTGT
1 AATATTGTAA-TTTTTGTATGAATATTGT
*
19700942 AATTTTGTAATTTTTGTATTGAATATTGT
1 AATATTGTAATTTTTGTA-TGAATATTGT
19700971 AATATTGTAA--TTTGTATGAATATTGT
1 AATATTGTAATTTTTGTATGAATATTGT
19700997 AAT
1 AAT
19701000 GTCGGGATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
26 13 0.24
27 6 0.11
28 8 0.15
29 28 0.51
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (28 bp):
AATATTGTAATTTTTGTATGAATATTGT
Found at i:19701228 original size:16 final size:16
Alignment explanation
Indices: 19701185--19701228 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
19701175 AAAATCAAAT
*
19701185 AAAATTTAATTATATA
1 AAAATTAAATTATATA
* *
19701201 AAAGTTACATTATATA
1 AAAATTAAATTATATA
19701217 AAAATTAAATTA
1 AAAATTAAATTA
19701229 GTTAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTATATA
Found at i:19701544 original size:60 final size:60
Alignment explanation
Indices: 19701451--19701572 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
19701441 ATATTAAACT
* * * * *
19701451 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
*
19701511 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
19701571 AA
1 AA
19701573 TATTCATACA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 4 0.07
60 51 0.93
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:19701600 original size:8 final size:8
Alignment explanation
Indices: 19701587--19701790 Score: 72
Period size: 8 Copynumber: 23.4 Consensus size: 8
19701577 CATACAAAAA
19701587 ATTACAAT
1 ATTACAAT
19701595 ATTACAAT
1 ATTACAAT
* * *
19701603 ATATCCCGAC
1 AT-T-ACAAT
19701613 ATTACAAT
1 ATTACAAT
*
19701621 ATTCATACAAA
1 A-T--TACAAT
*
19701632 ATTACAAA
1 ATTACAAT
19701640 ATTACAAT
1 ATTACAAT
*
19701648 ATTCATACAAA
1 A-T--TACAAT
*
19701659 ATTATAAT
1 ATTACAAT
19701667 ATTACAAT
1 ATTACAAT
19701675 ATT-C-AT
1 ATTACAAT
* * *
19701681 A-CAAAAA
1 ATTACAAT
19701688 ATTACAAT
1 ATTACAAT
19701696 ATTACAAT
1 ATTACAAT
*
19701704 ATTCATACAAA
1 A-T--TACAAT
19701715 ATTACAAT
1 ATTACAAT
*
19701723 ATTCATACAAA
1 A-T--TACAAT
19701734 ATTACAAT
1 ATTACAAT
*
19701742 ATTCATACAAA
1 A-T--TACAAT
*
19701753 ATTATAAT
1 ATTACAAT
19701761 ATTACAAT
1 ATTACAAT
*
19701769 ATTCATACAAA
1 A-T--TACAAT
19701780 ATTACAAT
1 ATTACAAT
19701788 ATT
1 ATT
19701791 CATACAAAAT
Statistics
Matches: 145, Mismatches: 28, Indels: 46
0.66 0.13 0.21
Matches are distributed among these distances:
6 3 0.02
7 3 0.02
8 85 0.59
9 8 0.06
10 10 0.07
11 36 0.25
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.33
Consensus pattern (8 bp):
ATTACAAT
Found at i:19701629 original size:29 final size:29
Alignment explanation
Indices: 19701613--19701790 Score: 165
Period size: 27 Copynumber: 6.1 Consensus size: 29
19701603 ATATCCCGAC
*
19701613 ATTACAATATTCATAC-AAA-ATTACAAA
1 ATTACAATATTCATACAAAATATTACAAT
*
19701640 ATTACAATATTCATAC-AAA-ATTATAAT
1 ATTACAATATTCATACAAAATATTACAAT
*
19701667 ATTACAATATTCATACAAAAAATTACAAT
1 ATTACAATATTCATACAAAATATTACAAT
19701696 ATTACAATATTCATAC-AAA-ATTACAAT
1 ATTACAATATTCATACAAAATATTACAAT
* * *
19701723 ATTCATACAAAATTACAATATTCATACAAAATTATAAT
1 A-T--TACAATATT-C-ATA--CA-A-AATATTACAAT
19701761 ATTACAATATTCATAC-AAA-ATTACAAT
1 ATTACAATATTCATACAAAATATTACAAT
19701788 ATT
1 ATT
19701791 CATACAAAAT
Statistics
Matches: 131, Mismatches: 7, Indels: 26
0.80 0.04 0.16
Matches are distributed among these distances:
27 60 0.46
28 9 0.07
29 24 0.18
30 8 0.06
31 2 0.02
32 3 0.02
33 3 0.02
34 2 0.02
35 8 0.06
36 1 0.01
37 3 0.02
38 8 0.06
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (29 bp):
ATTACAATATTCATACAAAATATTACAAT
Found at i:19701637 original size:19 final size:19
Alignment explanation
Indices: 19701634--19701873 Score: 147
Period size: 19 Copynumber: 12.1 Consensus size: 19
19701624 CATACAAAAT
19701634 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
19701653 TACAAAATTATAATA-T--
1 TACAAAATTACAATATTCA
* **
19701669 TACAATATTCATACAA-A-AAA
1 TACAA-AAT--TACAATATTCA
*
19701689 TTACAATATTACAATATTCA
1 -TACAAAATTACAATATTCA
19701709 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
19701728 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
19701747 TACAAAATTATAATATTACAATATTCA
1 TAC------A-AA-ATTACAATATTCA
19701774 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
* *
19701793 TACAAAA-TACTA-ATCCAA
1 TACAAAATTACAATATTC-A
* *
19701811 AACTCTAAA-TACAAATTTAATT-A
1 TA--CAAAATTAC-AA--T-ATTCA
*
19701834 TAAAAAAATTACAATATTCA
1 T-ACAAAATTACAATATTCA
19701854 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
19701873 T
1 T
19701874 TGGCGCCTCC
Statistics
Matches: 175, Mismatches: 19, Indels: 54
0.71 0.08 0.22
Matches are distributed among these distances:
16 5 0.03
17 5 0.03
18 13 0.07
19 100 0.57
20 14 0.08
21 7 0.04
22 5 0.03
23 4 0.02
24 1 0.01
25 3 0.02
26 2 0.01
27 16 0.09
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:19701684 original size:46 final size:46
Alignment explanation
Indices: 19701634--19701800 Score: 250
Period size: 46 Copynumber: 3.6 Consensus size: 46
19701624 CATACAAAAT
19701634 TACAAAATTACAATATTCATACAAAATTATAATATTACAATATTCA
1 TACAAAATTACAATATTCATACAAAATTATAATATTACAATATTCA
* *
19701680 TACAAAAAATTACAATA-T--TACAATATTCATACAAAATTACAATATTCA
1 TAC--AAAATTACAATATTCATACAAAATT-AT--AATATTACAATATTCA
19701728 TACAAAATTACAATATTCATACAAAATTATAATATTACAATATTCA
1 TACAAAATTACAATATTCATACAAAATTATAATATTACAATATTCA
19701774 TACAAAATTACAATATTCATACAAAAT
1 TACAAAATTACAATATTCATACAAAAT
19701801 ACTAATCCAA
Statistics
Matches: 109, Mismatches: 4, Indels: 16
0.84 0.03 0.12
Matches are distributed among these distances:
45 8 0.07
46 59 0.54
47 2 0.02
48 32 0.29
49 8 0.07
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (46 bp):
TACAAAATTACAATATTCATACAAAATTATAATATTACAATATTCA
Found at i:19701740 original size:27 final size:27
Alignment explanation
Indices: 19701613--19701725 Score: 190
Period size: 27 Copynumber: 4.1 Consensus size: 27
19701603 ATATCCCGAC
*
19701613 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTACAAT
*
19701640 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
19701667 ATTACAATATTCATACAAAAAATTACAAT
1 ATTACAATATTCATAC--AAAATTACAAT
19701696 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
19701723 ATT
1 ATT
19701726 CATACAAAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
27 55 0.68
29 26 0.32
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:19701823 original size:46 final size:46
Alignment explanation
Indices: 19701634--19701825 Score: 124
Period size: 46 Copynumber: 4.1 Consensus size: 46
19701624 CATACAAAAT
** * **
19701634 TACAAAATTACAATATTCATACAAAATTATAATATTACAATATTCA
1 TACAAAATTACAATATTCATACAAAATTATAATACCAAAATATAAA
* * ** * **
19701680 TACAAAAAATTACAATA-T--TACAATATTCATACAAAATTACAATATTCA
1 TAC--AAAATTACAATATTCATACAAAATT-AT--AATACCAAAATATAAA
** * **
19701728 TACAAAATTACAATATTCATACAAAATTATAATATTACAATATTCA
1 TACAAAATTACAATATTCATACAAAATTATAATACCAAAATATAAA
*
19701774 TACAAAATTACAATATTCATACAAAA-TACTAAT-CCAAAACTCTAAA
1 TACAAAATTACAATATTCATACAAAATTA-TAATACCAAAA-TATAAA
19701820 TACAAA
1 TACAAA
19701826 TTTAATTATA
Statistics
Matches: 126, Mismatches: 10, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
45 13 0.10
46 71 0.56
47 2 0.02
48 32 0.25
49 8 0.06
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (46 bp):
TACAAAATTACAATATTCATACAAAATTATAATACCAAAATATAAA
Found at i:19701908 original size:27 final size:27
Alignment explanation
Indices: 19701870--19701939 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
19701860 ATTACAATAT
* *
19701870 TCATTGGCGCCTCCCTATG-AGGCACCA
1 TCATTGGCGCCTCCC-AGGTAGGCACAA
19701897 TCATTGGCGCCTCCCAGGTAGGCACAA
1 TCATTGGCGCCTCCCAGGTAGGCACAA
*
19701924 CCATTGGCGCCTCCCA
1 TCATTGGCGCCTCCCA
19701940 AATAGGCGCC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
26 2 0.05
27 37 0.95
ACGTcount: A:0.19, C:0.39, G:0.23, T:0.20
Consensus pattern (27 bp):
TCATTGGCGCCTCCCAGGTAGGCACAA
Found at i:19709642 original size:26 final size:26
Alignment explanation
Indices: 19709582--19709634 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
19709572 AAAAACTTCA
19709582 AAAATTAATAAAATATATTTAAAATT
1 AAAATTAATAAAATATATTTAAAATT
*
19709608 AAAATTAATAAAATATATTTAACATT
1 AAAATTAATAAAATATATTTAAAATT
19709634 A
1 A
19709635 TTAATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATTAATAAAATATATTTAAAATT
Found at i:19710409 original size:20 final size:21
Alignment explanation
Indices: 19710369--19710415 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
19710359 TTTGTAATAT
*
19710369 TTTTATTAATTTTTTAAATAAC
1 TTTTATTAA-TTTTAAAATAAC
*
19710391 TTTTATTAA-TTTAAAATAAT
1 TTTTATTAATTTTAAAATAAC
19710411 TTTTA
1 TTTTA
19710416 AATTTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
22 9 0.39
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATTAATTTTAAAATAAC
Found at i:19711067 original size:30 final size:29
Alignment explanation
Indices: 19711031--19711088 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
19711021 AAGTAGAAGA
19711031 AGTTGTGTTT-GGGATTTGAGAAAAAATTAG
1 AGTTGTGTTTAGGG-TTTGA-AAAAAATTAG
19711061 AGTTGTGTTTAGGGTTTGAAAAAAATTA
1 AGTTGTGTTTAGGGTTTGAAAAAAATTA
19711089 ATCTAGAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 9 0.33
30 15 0.56
31 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (29 bp):
AGTTGTGTTTAGGGTTTGAAAAAAATTAG
Found at i:19711432 original size:48 final size:49
Alignment explanation
Indices: 19711366--19711487 Score: 201
Period size: 48 Copynumber: 2.5 Consensus size: 49
19711356 GAAAGAATAT
* *
19711366 TTTATTTTTTTATGTAATTTATTTGTCCTATGTGTTTTAGGTTTATTAGA
1 TTTA-TTTTTTATGTAATTTATTTGTCATATGTATTTTAGGTTTATTAGA
*
19711416 TTTA-TTTTTATATAATTTATTTGTCATATGTATTTTAGGTTTATTAGA
1 TTTATTTTTTATGTAATTTATTTGTCATATGTATTTTAGGTTTATTAGA
19711464 TTTATTTTTTATGTAATTTATTTG
1 TTTATTTTTTATGTAATTTATTTG
19711488 GCATGTTTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
48 45 0.67
49 18 0.27
50 4 0.06
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.63
Consensus pattern (49 bp):
TTTATTTTTTATGTAATTTATTTGTCATATGTATTTTAGGTTTATTAGA
Found at i:19711590 original size:27 final size:27
Alignment explanation
Indices: 19711548--19711619 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
19711538 AAAAGATGAG
* *
19711548 ACCATTGAGATGGAATTTGTGAATGGA
1 ACCATTGAGTTGGAATTTGTGAATAGA
*
19711575 ACCATTGAGTTAGAATTTGTGAATAGA
1 ACCATTGAGTTGGAATTTGTGAATAGA
19711602 ACCATTGAGTTGGAATTT
1 ACCATTGAGTTGGAATTT
19711620 ATGAGATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (27 bp):
ACCATTGAGTTGGAATTTGTGAATAGA
Found at i:19713738 original size:18 final size:18
Alignment explanation
Indices: 19713717--19713760 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
19713707 ATACGAGCTA
*
19713717 GAGCCTGAGCTAGAGCCC
1 GAGCCTGAGCTAGAGACC
*
19713735 GAGCCCGAGCTAGAGACC
1 GAGCCTGAGCTAGAGACC
*
19713753 GACCCTGA
1 GAGCCTGA
19713761 AATCGAGCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.34, G:0.32, T:0.09
Consensus pattern (18 bp):
GAGCCTGAGCTAGAGACC
Found at i:19717219 original size:4 final size:4
Alignment explanation
Indices: 19717206--19717242 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
19717196 ATAAAAATAC
19717206 CTTT CTTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
19717243 TCCCTCTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:19717396 original size:27 final size:27
Alignment explanation
Indices: 19717327--19717398 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
19717317 AAAAATTAAT
*
19717327 ACTGGTGCCGCCTATCAAATAAGAGTC
1 ACTGGTGCCGCCTATCAGATAAGAGTC
*** * *
19717354 ACCAATGCCGCTTATCAGATAAGGGTC
1 ACTGGTGCCGCCTATCAGATAAGAGTC
*
19717381 ACTGGTGCTGCCTATCAG
1 ACTGGTGCCGCCTATCAG
19717399 GTAGGCACCA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (27 bp):
ACTGGTGCCGCCTATCAGATAAGAGTC
Found at i:19719456 original size:21 final size:21
Alignment explanation
Indices: 19719430--19719483 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
19719420 AGAGCTAATT
*
19719430 AAAACACTAACTCACGCAGTG
1 AAAACACTAACTCACGCAATG
*
19719451 AAAACACTAACTCATGCAATG
1 AAAACACTAACTCACGCAATG
19719472 AAAACACTAACT
1 AAAACACTAACT
19719484 TATTCGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.48, C:0.26, G:0.09, T:0.17
Consensus pattern (21 bp):
AAAACACTAACTCACGCAATG
Found at i:19720288 original size:78 final size:78
Alignment explanation
Indices: 19720198--19720343 Score: 292
Period size: 78 Copynumber: 1.9 Consensus size: 78
19720188 AAGATCATTG
19720198 CCAATAAATAACAAAGTGTACTATTCAATTTAATAAGACTACTTTAAAGAACAACCTACTCATAC
1 CCAATAAATAACAAAGTGTACTATTCAATTTAATAAGACTACTTTAAAGAACAACCTACTCATAC
19720263 AAAGTGTACTATT
66 AAAGTGTACTATT
19720276 CCAATAAATAACAAAGTGTACTATTCAATTTAATAAGACTACTTTAAAGAACAACCTACTCATAC
1 CCAATAAATAACAAAGTGTACTATTCAATTTAATAAGACTACTTTAAAGAACAACCTACTCATAC
19720341 AAA
66 AAA
19720344 ATTGGATCAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (78 bp):
CCAATAAATAACAAAGTGTACTATTCAATTTAATAAGACTACTTTAAAGAACAACCTACTCATAC
AAAGTGTACTATT
Found at i:19720966 original size:14 final size:15
Alignment explanation
Indices: 19720939--19720967 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19720929 ACAGTTAGAG
19720939 GGGAAGAGAGAAAGA
1 GGGAAGAGAGAAAGA
19720954 GGGAAGA-AGAAAGA
1 GGGAAGAGAGAAAGA
19720968 AAATGGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (15 bp):
GGGAAGAGAGAAAGA
Found at i:19730196 original size:169 final size:169
Alignment explanation
Indices: 19729917--19730255 Score: 552
Period size: 169 Copynumber: 2.0 Consensus size: 169
19729907 GGACCCCACC
*
19729917 AGGTGGAGTCATTAGGGGGATCGCGAGCCCAGTTCGCACATCCTTAGATGTCCACGAGCATAGGA
1 AGGTGGAGTCATTAGGGGGATCGCGAGCCCAGTTCGCACATCCCTAGATGTCCACGAGCATAGGA
*
19729982 TACGAGGTCAAACAAATAAACCGATGAGCACCTGGACCAGTGAACACGTGTTGAGTTTAGGGTAA
66 TACAAGGTCAAACAAATAAACCGATGAGCACCTGGACCAGTGAACACGTGTTGAGTTTAGGGTAA
* * *
19730047 CATACGTGTTGACATGCATGGAGCCTACCTAGAACGTCA
131 CATACATGTCGACATGCATAGAGCCTACCTAGAACGTCA
* * *
19730086 AGGTGGAGTCATTAGGGGGCTCGCGAGCCCAGTTCGCACATCCCTGGATGTCCACGAGCATAGGG
1 AGGTGGAGTCATTAGGGGGATCGCGAGCCCAGTTCGCACATCCCTAGATGTCCACGAGCATAGGA
* * * * *
19730151 TACAAGGTCAAACGAATGAACTGATGAGCACCTGGACTAGTGAACATGTGTTGAGTTTAGGGTAA
66 TACAAGGTCAAACAAATAAACCGATGAGCACCTGGACCAGTGAACACGTGTTGAGTTTAGGGTAA
*
19730216 CATACATGTCGACATGTATAGAGCCTACCTAGAACGTCA
131 CATACATGTCGACATGCATAGAGCCTACCTAGAACGTCA
19730255 A
1 A
19730256 TTCCATGAAC
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
169 156 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (169 bp):
AGGTGGAGTCATTAGGGGGATCGCGAGCCCAGTTCGCACATCCCTAGATGTCCACGAGCATAGGA
TACAAGGTCAAACAAATAAACCGATGAGCACCTGGACCAGTGAACACGTGTTGAGTTTAGGGTAA
CATACATGTCGACATGCATAGAGCCTACCTAGAACGTCA
Found at i:19735450 original size:25 final size:24
Alignment explanation
Indices: 19735422--19735469 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
19735412 TTTTCTACTA
19735422 AAAAAAAT-AGGTAAATTAGTTCTT
1 AAAAAAATGA-GTAAATTAGTTCTT
19735446 AAAAAAATGAGTAAATTAGTTCTT
1 AAAAAAATGAGTAAATTAGTTCTT
19735470 GTATGTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.33
Consensus pattern (24 bp):
AAAAAAATGAGTAAATTAGTTCTT
Found at i:19735815 original size:16 final size:16
Alignment explanation
Indices: 19735773--19735821 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
19735763 TTCGCTGTAT
*
19735773 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
19735789 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
19735805 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
19735821 T
1 T
19735822 AGCAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.39, C:0.04, G:0.35, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:19736028 original size:16 final size:16
Alignment explanation
Indices: 19735991--19736032 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
19735981 TTAATCATAT
*
19735991 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
19736007 TT-AAATATATTATAA
1 TTAAAATATATTATAA
19736022 TTAAAATATAT
1 TTAAAATATAT
19736033 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:19736039 original size:14 final size:15
Alignment explanation
Indices: 19736000--19736041 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
19735990 TTTAAACATA
*
19736000 ATTATTATTAAATAT
1 ATTATAATTAAATAT
19736015 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
19736029 A-TATAATTTAATA
1 ATTATAATTAAATA
19736042 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:19736524 original size:92 final size:90
Alignment explanation
Indices: 19736355--19736525 Score: 263
Period size: 92 Copynumber: 1.9 Consensus size: 90
19736345 NNNNNNNNNC
* *
19736355 ATATAATTTAATAATAATATATAATTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTA
1 ATATAATTTAATAATAATATATAATTCATAAAATTCTTAATAATAAATGTTCTTATATGAATTTA
* *
19736420 TACAATTTAAAATAATTAATATTAA
66 TACAAATCAAAATAATTAATATTAA
*
19736445 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAAAATGTTCTTATATGAATT
1 ATATAATTTAATAATAATATATAA-TTCATAAAATTCTTAATAAT-AAATGTTCTTATATGAATT
19736510 TACTA-AAATCAAAATA
64 TA-TACAAATCAAAATA
19736526 TAACTTGAGA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
90 23 0.32
91 19 0.26
92 29 0.40
93 2 0.03
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (90 bp):
ATATAATTTAATAATAATATATAATTCATAAAATTCTTAATAATAAATGTTCTTATATGAATTTA
TACAAATCAAAATAATTAATATTAA
Found at i:19740324 original size:13 final size:13
Alignment explanation
Indices: 19740306--19740330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19740296 ATCAAATTTG
19740306 TATGTACTCTTTA
1 TATGTACTCTTTA
19740319 TATGTACTCTTT
1 TATGTACTCTTT
19740331 CACTAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:19740857 original size:3 final size:3
Alignment explanation
Indices: 19740849--19740904 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
19740839 TAATTAGTGG
19740849 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19740897 TAT TAT TA
1 TAT TAT TA
19740905 GCTTCCCTAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:19741528 original size:5 final size:5
Alignment explanation
Indices: 19741512--19741591 Score: 124
Period size: 5 Copynumber: 16.0 Consensus size: 5
19741502 GTGAATGGAA
* * * *
19741512 AAACC CAACA AAACA AAACA AAACC AAACC AAACC AAACC AAACC AAACC
1 AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAACC
19741562 AAACC AAACC AAACC AAACC AAACC AAACC
1 AAACC AAACC AAACC AAACC AAACC AAACC
19741592 TAGCTTGCAA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 71 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:19743903 original size:3 final size:3
Alignment explanation
Indices: 19743895--19743955 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
19743885 CAAGGTATGT
19743895 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19743943 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
19743956 CTTTTTCCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19752818 original size:17 final size:17
Alignment explanation
Indices: 19752784--19752815 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19752774 ATTAATCAAA
19752784 TTAATTAAATTAATTTC
1 TTAATTAAATTAATTTC
19752801 TTAATTAAA-TAATTT
1 TTAATTAAATTAATTT
19752816 TCTCAATCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATTAAATTAATTTC
Found at i:19759113 original size:14 final size:16
Alignment explanation
Indices: 19759082--19759115 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
19759072 AAATAATATA
19759082 TAATATAATAATATTTT
1 TAATATAAT-ATATTTT
19759099 TAATATAAT-TATTTT
1 TAATATAATATATTTT
19759114 TA
1 TA
19759116 TATTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATATAATATATTTT
Found at i:19759123 original size:58 final size:56
Alignment explanation
Indices: 19758995--19759111 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 56
19758985 TTAGTAGGAT
* * * *
19758995 TATTATTAAA-ATAATTTAAT-AAAAAATAATAATGTAATCATATTTTAATATAAG
1 TATTATTAAATATAAATCAATAAAAAAATAATAATATAATAATATTTTAATATAAG
*
19759049 TATTATTAAATATAAATCAATAAAAATAATATATAATATAATAATATTTTTAATATAAT
1 TATTATTAAATATAAATCAATAAAAA-AATA-ATAATATAATAATA-TTTTAATATAAG
19759108 TATT
1 TATT
19759112 TTTATATTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 10 0.19
55 8 0.15
56 4 0.08
57 4 0.08
58 12 0.23
59 15 0.28
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (56 bp):
TATTATTAAATATAAATCAATAAAAAAATAATAATATAATAATATTTTAATATAAG
Found at i:19759150 original size:34 final size:31
Alignment explanation
Indices: 19759111--19759219 Score: 112
Period size: 34 Copynumber: 3.3 Consensus size: 31
19759101 ATATAATTAT
*
19759111 TTTTATATTAAATTATATTAAAATGTTTAAAATA
1 TTTTATTTTAAATTATATTAAAA--TTT-AAATA
*
19759145 TTTTATTTTAAATTATATTTTGAAA-TTAAATA
1 TTTTATTTTAAATTATA--TTAAAATTTAAATA
*
19759177 TTTTATTTTAAATCATATTAAAACATTTTAAATA
1 TTTTATTTTAAATTATATT-AAA-A-TTTAAATA
19759211 TTTTATTTT
1 TTTTATTTT
19759220 TATATTTTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
30 2 0.03
31 2 0.03
32 22 0.34
33 2 0.03
34 32 0.49
36 5 0.08
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
TTTTATTTTAAATTATATTAAAATTTAAATA
Found at i:19762666 original size:78 final size:78
Alignment explanation
Indices: 19762537--19762697 Score: 313
Period size: 78 Copynumber: 2.1 Consensus size: 78
19762527 AATTAGTTTT
*
19762537 TGTGTTATAGAGCTCGCGAGGCTTAATAGTGATAGCAAAAGAGAGTGTTTTGATTGTTTTACTAC
1 TGTGTTATAGAGCTCGCGAGGCTTAATAGTGATAGCAAAAGAGAGTGTTTTGATTGTGTTACTAC
19762602 TGTTAATAATACA
66 TGTTAATAATACA
19762615 TGTGTTATAGAGCTCGCGAGGCTTAATAGTGATAGCAAAAGAGAGTGTTTTGATTGTGTTACTAC
1 TGTGTTATAGAGCTCGCGAGGCTTAATAGTGATAGCAAAAGAGAGTGTTTTGATTGTGTTACTAC
19762680 TGTTAATAATACA
66 TGTTAATAATACA
19762693 TGTGT
1 TGTGT
19762698 ATTGTGTTTG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (78 bp):
TGTGTTATAGAGCTCGCGAGGCTTAATAGTGATAGCAAAAGAGAGTGTTTTGATTGTGTTACTAC
TGTTAATAATACA
Found at i:19764645 original size:20 final size:22
Alignment explanation
Indices: 19764617--19764665 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
19764607 TAAAATATAT
* *
19764617 ATATGAGTATGTATA-TTA-AA
1 ATATAAGTATATATACTTACAA
19764637 ATATAAGTATATATACTTACGAA
1 ATATAAGTATATATACTTAC-AA
19764660 ATATAA
1 ATATAA
19764666 AAATGTATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.54
21 3 0.12
23 8 0.33
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (22 bp):
ATATAAGTATATATACTTACAA
Found at i:19764882 original size:3 final size:3
Alignment explanation
Indices: 19764874--19764915 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
19764864 TAACTGAATA
19764874 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19764916 GTCAACTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19765724 original size:22 final size:23
Alignment explanation
Indices: 19765698--19765742 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
19765688 AGAATATATT
*
19765698 AAATAT-ATATTTTTTATTTTAA
1 AAATATAATAGTTTTTATTTTAA
19765720 AAATATAATAGTTTTTATTTTAA
1 AAATATAATAGTTTTTATTTTAA
19765743 GTTTGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AAATATAATAGTTTTTATTTTAA
Found at i:19767154 original size:9 final size:9
Alignment explanation
Indices: 19767140--19767165 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19767130 GTTTTTGTAA
19767140 ATTAATTTG
1 ATTAATTTG
19767149 ATTAATTTG
1 ATTAATTTG
19767158 ATTAATTT
1 ATTAATTT
19767166 TAGCTTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (9 bp):
ATTAATTTG
Found at i:19767321 original size:9 final size:9
Alignment explanation
Indices: 19767307--19767333 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
19767297 TTTGTTACAG
19767307 CAATTAATA
1 CAATTAATA
19767316 CAATTAATA
1 CAATTAATA
19767325 CAATTAATA
1 CAATTAATA
19767334 ATTTGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (9 bp):
CAATTAATA
Found at i:19767357 original size:68 final size:66
Alignment explanation
Indices: 19767276--19767417 Score: 239
Period size: 68 Copynumber: 2.1 Consensus size: 66
19767266 TCAAGTTTGT
* *
19767276 TTTACTAATCAAATGTTAGATTTTGTTACAGCAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAAT--AATTAATAATTTGAT
19767341 AAA
64 AAA
19767344 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTAATAATTTGATAA
*
19767409 T
66 A
19767410 TTTACTAA
1 TTTACTAA
19767418 CAATTAATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 25 0.35
68 46 0.65
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTAATAATTTGATAA
A
Found at i:19767427 original size:16 final size:16
Alignment explanation
Indices: 19767406--19767447 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
19767396 AATAATTTGA
*
19767406 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
19767422 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
19767438 TAGTTTTAAT
1 TAATTTTAAT
19767448 TTCATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:19767436 original size:59 final size:65
Alignment explanation
Indices: 19767276--19767439 Score: 205
Period size: 68 Copynumber: 2.5 Consensus size: 65
19767266 TCAAGTTTGT
* *
19767276 TTTACTAATCAAATGTTAGATTTTGTTACAGCAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATA-AATTAATAATTTGAT
19767341 AAA
63 AAA
19767344 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAAT-AATTAATAATTTGATA
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATAAATTAATAATTTGATA
*
19767408 AT
64 AA
*
19767410 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
19767440 GTTTTAATTT
Statistics
Matches: 91, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 25 0.27
68 45 0.49
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (65 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATAAATTAATAATTTGATAAA
Found at i:19768549 original size:44 final size:44
Alignment explanation
Indices: 19768499--19768835 Score: 137
Period size: 44 Copynumber: 7.7 Consensus size: 44
19768489 AGATTCACCG
19768499 TCTTTGATCTGCTCCACTACTGCTTAGGGATACAGAATCTACAA
1 TCTTTGATCTGCTCCACTACTGCTTAGGGATACAGAATCTACAA
* ** * *
19768543 TCTTTGACCTATTCCACTACTGCTTAGGG-TGATAGGA-CT--AA
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAT-ACAGAATCTACAA
* * * * * *
19768584 TGGTTTAAATCTGCTTCTAGACTA-T-CTTGGGAAGATA-AGATTC-ACCA
1 T-CTTT-GATCTGC-TC--CACTACTGCTTAGG--GATACAGAATCTACAA
* *
19768631 TCTTTGATCTGCTCCACTACTGCTTAGGG-TGACAAAATCTGCAA
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAT-ACAGAATCTACAA
* * * * * *
19768675 TCTTCGACCTACTCCACTACTGCTTAGGGAGATAGGA-CT--AA
1 TCTTTGATCTGCTCCACTACTGCTTAGGGATACAGAATCTACAA
** * * * * * *
19768716 TGGCTTAAATCTGCTTCTCCAATGTCTTAGGAAGATA-A-AATTTACCA
1 T--CTTTGATCTGCTCCACTACTG-CTTAGG--GATACAGAATCTACAA
*
19768763 TCTTTGATCTGCTCCACTACTGCTTAGGG-TGACAGAATCTGCAA
1 TCTTTGATCTGCTCCACTACTGCTTAGGGAT-ACAGAATCTACAA
* * ** *
19768807 TCTTCGACCTATTCCACCACTGCTTAGGG
1 TCTTTGATCTGCTCCACTACTGCTTAGGG
19768836 TGATAGGACT
Statistics
Matches: 208, Mismatches: 56, Indels: 58
0.65 0.17 0.18
Matches are distributed among these distances:
41 8 0.04
42 11 0.05
43 27 0.13
44 118 0.57
45 26 0.12
46 13 0.06
47 5 0.02
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (44 bp):
TCTTTGATCTGCTCCACTACTGCTTAGGGATACAGAATCTACAA
Found at i:19768610 original size:132 final size:132
Alignment explanation
Indices: 19768476--19769369 Score: 1403
Period size: 132 Copynumber: 6.8 Consensus size: 132
19768466 TTCCCTACTA
* * *
19768476 TCTTGGGAAGATAAGATTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAT-ACAGAATCTA
1 TCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG-TGACAGAATCTG
* * * **
19768540 CAATCTTTGACCTATTCCACTACTGCTTAGGGTGATAGGACTAATGGTTTAAATCTGCTTCTAGA
65 CAATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
*
19768605 CTA
130 CTG
* *
19768608 TCTTGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGTGACAAAATCTGC
1 TCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGC
* *
19768673 AATCTTCGACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCAA
66 AATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
19768738 TG
131 TG
* * * *
19768740 TCTTAGGAAGATAAAATTTACCATCTTTGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGC
1 TCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGC
* *
19768805 AATCTTCGACCTATTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
66 AATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
19768870 TG
131 TG
* *
19768872 TATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCATTACTGCTTAGGGTGACAGAATCTGC
1 TCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGC
* *
19768937 AATCTTCGACCTACTCCACTACTACTTACGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
66 AATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
19769002 TG
131 TG
* * * *
19769004 TATCGGGAAAATAAGATTCACCATCTTCGATCTGCTCTACTACTGCTTAGGGTGACAGAATCTGC
1 TCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGC
* * * *
19769069 AACCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCAA
66 AATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
19769134 TG
131 TG
** *
19769136 TCTTGGGAAGATAAGATTTTCCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTTC
1 TCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGC
* *
19769201 AATCTTCGACCTATTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
66 AATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
19769266 TG
131 TG
*
19769268 TATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGC
1 TCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGC
* ** *
19769333 AATCTTCAACCTACTCTGCTACTGCTTAGGGAGATAG
66 AATCTTCGACCTACTCCACTACTGCTTAGGGTGATAG
19769370 AATTGGTTTC
Statistics
Matches: 699, Mismatches: 62, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
131 1 0.00
132 698 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (132 bp):
TCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGC
AATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
TG
Found at i:19768944 original size:44 final size:44
Alignment explanation
Indices: 19768630--19769372 Score: 227
Period size: 44 Copynumber: 16.9 Consensus size: 44
19768620 AAGATTCACC
* *
19768630 ATCTTTGATCTGCTCCACTACTGCTTAGGGTGACAAAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * *
19768674 ATCTTCGACCTACTCCACTACTGCTTAGGGAGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * ** * * * * *
19768715 ATGGCTTAAATCTGCTTCTCCAATGTCTTAGGAAGATAAAATTTACC
1 AT--CTTCGATCTGCTCCACTACTG-CTTAGGGTGACAGAATCTGCA
*
19768762 ATCTTTGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* ** * * *
19768806 ATCTTCGACCTATTCCACCACTGCTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * * * * * *
19768847 ATGGCTTAAATCTGCTTCTCCACTG-TATTGGGAAGATAAGATTC-ACC
1 AT--CTTCGATCTGCTCCACTACTGCT-TAGGG-TGA-CAGAATCTGCA
*
19768894 ATCTTCGATCTGCTCCATTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * * *
19768938 ATCTTCGACCTACTCCACTACTACTTACGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * ** * * * *
19768979 ATGGCTTAAATCTGCTTCTCCACTG-TATCGGGAAAATAAGATTC-ACC
1 AT--CTTCGATCTGCTCCACTACTGCT-TAGGG-TGA-CAGAATCTGCA
*
19769026 ATCTTCGATCTGCTCTACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * *
19769070 ACCTTCGACCTGCTCCACTACTGCTTAGGGAGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * * * * * *
19769111 ATGGCTTAAATCTGCTTCTCCAATGTCTT-GGGAAGATA-AGATTTTCC
1 AT--CTTCGATCTGCTCCACTACTG-CTTAGGG-TGACAGA-ATCTGCA
*
19769158 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTTCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* ** * * *
19769202 ATCTTCGACCTATTCCACTACTACTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * * * * * *
19769243 ATGGCTTAAATCTGCTTCTCCACTG-TATTGGGAAGATAAGATTC-ACC
1 AT--CTTCGATCTGCTCCACTACTGCT-TAGGG-TGA-CAGAATCTGCA
19769290 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * ** * *
19769334 ATCTTCAACCTACTCTGCTACTGCTTAGGGAGATAGAAT
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
19769373 TGGTTTCTTC
Statistics
Matches: 486, Mismatches: 167, Indels: 92
0.65 0.22 0.12
Matches are distributed among these distances:
41 14 0.03
42 3 0.01
43 105 0.22
44 248 0.51
45 100 0.21
46 6 0.01
47 10 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
Found at i:19769611 original size:100 final size:99
Alignment explanation
Indices: 19769389--19770538 Score: 1334
Period size: 100 Copynumber: 11.5 Consensus size: 99
19769379 CTTCTGTCTG
* * ** * * * **
19769389 TTTAACTGCAATGTTGGGGAAGCAAGATTCGTCGTCGTAGCTTCAATCTATTCCACTACACAACC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
** * * * *
19769454 AAAGAAAATAAGATTCGCCGTCGTGGCTTCAATAT
66 -TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
* ** ** * * *
19769489 TTTAGTTTGCAATACCGGGGAAGTGAGATTTATCGTCGTAGCTTCAATCTGTTCCACTGCACCGC
1 TTTA-ATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * *
19769554 CTGGGAAGTAAGATTCACCGTTGTGGCTTCGATAT
65 CTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
* * * * * * *
19769589 TTTAATTTACAATATCGGGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTACATCGC
1 TTTAA-TTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * *
19769654 CT-GGAAGTAAGATTCACCGTTGTGGCCTCAATAT
65 CTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
* * * * * *
19769688 TTTAAATTGCAATGTCGAGGAACCAGGATTCACCGTTGTAGCTTCAATCTGTTTCGCTGCATCGC
1 TTT-AATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * * *
19769753 CT-GAAAGTAAGATTTGCTGTTGTGGCCTCAATCT
65 CTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
* * * * * *
19769787 TTTAAATTGCAATGTTGGGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCAC
1 TTT-AATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * * * *
19769852 CT-AGAAGTAAGATTCGTCATTGTGGTTTCAAGCTT
65 CTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATC-T
19769887 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
* *
19769952 TGGGAAGTAAGATTCACCGTTGTGGCTTCATTCTT
66 TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATC-T
* * ** *
19769987 TTTAATTGCAATGTTGGGGAAGCAATATTTGCCGTTATAGCTTCAATCTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
* * *
19770052 TGGGAAGTAAGATTTGCTGTTGTGTCTTCAATCTT
66 TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATC-T
** * * *
19770087 TTTAATTGCAATGTTAGGGAAGCGAGATTCACCATTGTAGCTTCAATTTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
*
19770152 TGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
66 TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
* * * * *
19770186 TTTAATTGCAATGTCAGGGAAGCGAGATTCACCATTGTAGCTTCAATCTGCTCCACTGCACTGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
19770251 TGGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCT
66 TGGG-AAGTAAGATTCGCCGTTGTGGCTTCAATCT
* ** * * * *
19770286 TTTAATTGCAATGTCGAGGAAGTGAGATTCGCCATTGTAGCTTCAATCTATTTCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
* * * *
19770351 TGAGAAGTAAGATTTGCCATTGTGGCTTTAATCT
66 TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
* **
19770385 TTTAATTGTAATGTCGGGGAAGCAAGATTGGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
*
19770450 TGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTT
66 TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATC-T
* *
19770485 TTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCC
19770539 GCTGTAACCA
Statistics
Matches: 913, Mismatches: 130, Indels: 14
0.86 0.12 0.01
Matches are distributed among these distances:
99 431 0.47
100 434 0.48
101 48 0.05
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (99 bp):
TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
Found at i:19770208 original size:199 final size:199
Alignment explanation
Indices: 19769389--19770538 Score: 1339
Period size: 199 Copynumber: 5.8 Consensus size: 199
19769379 CTTCTGTCTG
* * * * * * **
19769389 TTTAACTGCAATGTTGGGGAAGCAAGATTCGTCGTCGTAGCTTCAATCTATTCCACTACACAACC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
** * * * * * ** **
19769454 AAAGAAAATAAGATTCGCCGTCGTGGCTTCAAT-ATTTTAGTTTGCAAT-ACCGGGGAAGTGAGA
66 -TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTA-ATTGCAATGTTC-GGGAAGCAAGA
* * * * *
19769517 TTTATCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCACCGTTGTGGCT
128 TTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCT
* *
19769582 TCGATAT
193 TCAATCT
* * * * * *
19769589 TTTAATTTACAATATCGGGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTACATCGC
1 TTTAA-TTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * * * * *
19769654 CT-GGAAGTAAGATTCACCGTTGTGGCCTCAATATTTTAAATTGCAATG-TCGAGGAACCAGGAT
65 CTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTCG-GGAAGCAAGAT
* * * * * *
19769717 TCACCGTTGTAGCTTCAATCTGTTTCGCTGCATCGCCTGA-AAGTAAGATTTGCTGTTGTGGCCT
129 TCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTT
19769781 CAATCT
194 CAATCT
* * * * *
19769787 TTTAAATTGCAATGTTGGGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCAC
1 TTT-AATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * * * *
19769852 CT-AGAAGTAAGATTCGTCATTGTGGTTTCAAGCTTTTTAATTGCAATG-TCGGGGAAGCAAGAT
65 CTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTC-GGGAAGCAAGAT
* *
19769915 TCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCACCGTTGTGGCTT
129 TCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTT
*
19769980 CATTCTT
194 CAATC-T
* * * *
19769987 TTTAATTGCAATGTTGGGGAAGCAATATTTGCCGTTATAGCTTCAATCTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
* * * * *
19770052 TGGGAAGTAAGATTTGCTGTTGTGTCTTCAATCTTTTTAATTGCAATGTTAGGGAAGCGAGATTC
66 TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTCGGGAAGCAAGATTC
* *
19770117 ACCATTGTAGCTTCAATTTGTTCCACTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCA
131 ACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCA
19770182 ATCT
196 ATCT
* * * * * *
19770186 TTTAATTGCAATGTCAGGGAAGCGAGATTCACCATTGTAGCTTCAATCTGCTCCACTGCACTGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
**
19770251 TGGGAAAGTAAGATTCGCCGTTGTGGCTTCAATC-TTTTAATTGCAATG-TCGAGGAAGTGAGAT
66 TGGG-AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTCG-GGAAGCAAGAT
* * * * * *
19770314 TCGCCATTGTAGCTTCAATCTATTTCACTGCACCGCCTGAGAAGTAAGATTTGCCATTGTGGCTT
129 TCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTT
*
19770379 TAATCT
194 CAATCT
* *
19770385 TTTAATTGTAATGTCGGGGAAGCAAGATTGGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
*
19770450 TGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATG-TCGGGGAAGCAAGATT
66 TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTC-GGGAAGCAAGATT
* *
19770514 CGCTGTTGTAGCTTCAATCTGTTCC
130 CACCGTTGTAGCTTCAATCTGTTCC
19770539 GCTGTAACCA
Statistics
Matches: 813, Mismatches: 123, Indels: 29
0.84 0.13 0.03
Matches are distributed among these distances:
198 198 0.24
199 412 0.51
200 154 0.19
201 49 0.06
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (199 bp):
TTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
TGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTTCGGGAAGCAAGATTC
ACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGAGAAGTAAGATTCGCCGTTGTGGCTTCA
ATCT
Found at i:19770636 original size:88 final size:88
Alignment explanation
Indices: 19770544--19770872 Score: 532
Period size: 88 Copynumber: 3.7 Consensus size: 88
19770534 GTTCCGCTGT
* * * *
19770544 AACCAAGAGAGGCAAGGTTTGTGTCTTCGATCTGTTTCGTTGTCAAGGCAGGAAGGTAAGATTTG
1 AACCAAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAAGGCAGGAAGGCAAGATCTG
*
19770609 TTGTCTTCAACCAACTCCACTAC
66 TTGTCTTCAACCAGCTCCACTAC
*
19770632 AACCAAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTAAGGCAGGAAGGCAAGATCTG
1 AACCAAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAAGGCAGGAAGGCAAGATCTG
19770697 TTGTCTTCAACCAGCTCCACTAC
66 TTGTCTTCAACCAGCTCCACTAC
* * *
19770720 AACCGAGAGAGACAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTAAGGCAGGAAGGCAAGATCTG
1 AACCAAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAAGGCAGGAAGGCAAGATCTG
*
19770785 TTGTCTTCAACCAGCTCCACTAT
66 TTGTCTTCAACCAGCTCCACTAC
* * * *
19770808 AACCAAGAAATGTAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG
1 AACCAAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAAGGCAGGAAGGCAAGATCTG
19770873 CTATCTTTGA
Statistics
Matches: 225, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 225 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (88 bp):
AACCAAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAAGGCAGGAAGGCAAGATCTG
TTGTCTTCAACCAGCTCCACTAC
Found at i:19770691 original size:44 final size:43
Alignment explanation
Indices: 19770553--19770867 Score: 170
Period size: 44 Copynumber: 7.2 Consensus size: 43
19770543 TAACCAAGAG
* *
19770553 AGGCAAGGTTTGTGTCTTCGATCTGTTTCGTTGTCAAGGCAGGA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAA-GCAGGA
* * * * ** * * * * *
19770597 AGGTAAGATTTGTTGTCTTCAACCAACTCCACT-ACAACCAAGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTCGCTGTCAAGCAGGA
*
19770640 GAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTAAGGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAA-GCAGGA
* * * * * * * * *
19770685 AGGCAAGATCTGTTGTCTTCAACCAGCTCCACT-ACAA-CCGAGA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTCGCTGTCAAGCAG-GA
* *
19770728 GAGACAAGGTTTGTGTCTTCGATCTGCTTCGCTGTTAAGGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAA-GCAGGA
* * * * * * * * * *
19770773 AGGCAAGATCTGTTGTCTTCAACCAGCTCCACTAT-AACCAAGAA
1 AGGCAAGGTTTG-TGTCTTCGATCTGCTTCGCTGTCAAGC-AGGA
* *
19770817 ATGTAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAA-GCAGGA
19770861 AGGCAAG
1 AGGCAAG
19770868 ATCTGCTATC
Statistics
Matches: 186, Mismatches: 71, Indels: 28
0.65 0.25 0.10
Matches are distributed among these distances:
42 2 0.01
43 52 0.28
44 80 0.43
45 50 0.27
46 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (43 bp):
AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAAGCAGGA
Found at i:19776062 original size:5 final size:6
Alignment explanation
Indices: 19776046--19776070 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19776036 CCGATAATGA
19776046 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
19776071 AAAGAGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:19776418 original size:20 final size:22
Alignment explanation
Indices: 19776390--19776438 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
19776380 TAAAATATAT
* *
19776390 ATATGAGTATGTATA-TTA-AA
1 ATATAAGTATATATACTTACAA
19776410 ATATAAGTATATATACTTACGAA
1 ATATAAGTATATATACTTAC-AA
19776433 ATATAA
1 ATATAA
19776439 AAATGTATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.54
21 3 0.12
23 8 0.33
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (22 bp):
ATATAAGTATATATACTTACAA
Done.