Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 66 of 208
Found at i:24435678 original size:37 final size:37
Alignment explanation
Indices: 24435634--24435742 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
24435624 GATAGCTTTA
24435634 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
24435671 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
24435708 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
24435743 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:24473084 original size:41 final size:41
Alignment explanation
Indices: 24472988--24473085 Score: 99
Period size: 41 Copynumber: 2.4 Consensus size: 41
24472978 CTAACATTTA
* *
24472988 ATATATCAAGTTTTATACTTGAAAAGTATTTCTAATGTTTG
1 ATATGTCAAATTTTATACTTGAAAAGTATTTCTAATGTTTG
* * * * *
24473029 ATATGTCAAGTTTTATAGTTGGAAAGTGTTTTTAACT-TTTG
1 ATATGTCAAATTTTATACTTGAAAAGTATTTCTAA-TGTTTG
* *
24473070 GTATGTTAAATTTTAT
1 ATATGTCAAATTTTAT
24473086 TTACTTTTCC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 47 0.98
42 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (41 bp):
ATATGTCAAATTTTATACTTGAAAAGTATTTCTAATGTTTG
Found at i:24474159 original size:20 final size:20
Alignment explanation
Indices: 24474136--24474203 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
24474126 ATTTTTTAAC
*
24474136 ACTTTTAATAGAATTT-TATA
1 ACTTTTAA-ACAATTTCTATA
24474156 ACTTTTTAAACAATTTCTATA
1 AC-TTTTAAACAATTTCTATA
* * * *
24474177 AATTTTATATATTTTTCTATA
1 ACTTTTAAACA-ATTTCTATA
24474198 ACTTTT
1 ACTTTT
24474204 GTTTATAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.54
Consensus pattern (20 bp):
ACTTTTAAACAATTTCTATA
Found at i:24474324 original size:10 final size:9
Alignment explanation
Indices: 24474305--24474369 Score: 67
Period size: 9 Copynumber: 7.0 Consensus size: 9
24474295 TGTTAATATC
24474305 TTATAATTT
1 TTATAATTT
24474314 TTATAATTT
1 TTATAATTT
24474323 TTATAATTT
1 TTATAATTT
*
24474332 TCTATTATTT
1 T-TATAATTT
* *
24474342 TCAAAATTT
1 TTATAATTT
*
24474351 TATATCATTT
1 T-TATAATTT
*
24474361 TAATAATTT
1 TTATAATTT
24474370 ATAGATTTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
9 31 0.69
10 14 0.31
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (9 bp):
TTATAATTT
Found at i:24474328 original size:18 final size:19
Alignment explanation
Indices: 24474305--24474369 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
24474295 TGTTAATATC
24474305 TTATAATTTT-TATAATTT
1 TTATAATTTTATATAATTT
* *
24474323 TTATAATTTTCTATTATTT
1 TTATAATTTTATATAATTT
* * *
24474342 TCAAAATTTTATATCATTT
1 TTATAATTTTATATAATTT
*
24474361 TAATAATTT
1 TTATAATTT
24474370 ATAGATTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
18 10 0.26
19 29 0.74
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATAATTTTATATAATTT
Found at i:24479133 original size:46 final size:46
Alignment explanation
Indices: 24479062--24479408 Score: 599
Period size: 46 Copynumber: 7.6 Consensus size: 46
24479052 TACGTATGAT
* * *
24479062 CACTTATCA-TTTGTC-CCTGATCAGATAAGTGTAGTTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
24479106 CACTTATCACTTAGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
24479152 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
24479198 CACTTATCATTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
24479244 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
24479290 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCCAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
24479336 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
24479382 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
24479409 AGTACTCAAA
Statistics
Matches: 288, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
44 9 0.03
45 5 0.02
46 274 0.95
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:24483275 original size:18 final size:20
Alignment explanation
Indices: 24483233--24483275 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
24483223 GTTAGAAGGG
24483233 AGAAAATGAAATAAAAAGTA
1 AGAAAATGAAATAAAAAGTA
24483253 A-AAAA-GAAATAAAAAG-A
1 AGAAAATGAAATAAAAAGTA
24483270 AGAAAA
1 AGAAAA
24483276 ATTAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.09
18 15 0.68
19 4 0.18
20 1 0.05
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
AGAAAATGAAATAAAAAGTA
Found at i:24483282 original size:15 final size:14
Alignment explanation
Indices: 24483245--24483303 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
24483235 AAAATGAAAT
*
24483245 AAAAAGTAAAAAAG
1 AAAAATTAAAAAAG
*
24483259 AAATAA--AAAGAAG
1 AAA-AATTAAAAAAG
24483272 AAAAATTAAAAAA-
1 AAAAATTAAAAAAG
24483285 ATATAAATTAAAAAAG
1 A-A-AAATTAAAAAAG
24483301 AAA
1 AAA
24483304 TGATATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
12 2 0.05
13 10 0.27
14 10 0.27
15 14 0.38
16 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (14 bp):
AAAAATTAAAAAAG
Found at i:24483283 original size:16 final size:15
Alignment explanation
Indices: 24483262--24483303 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
24483252 AAAAAAGAAA
24483262 TAAAAAGAAGAAAAAT
1 TAAAAA-AAGAAAAAT
* *
24483278 TAAAAAAATATAAAT
1 TAAAAAAAGAAAAAT
24483293 T-AAAAAAGAAA
1 TAAAAAAAGAAA
24483304 TGATATTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 8 0.36
15 8 0.36
16 6 0.27
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
TAAAAAAAGAAAAAT
Found at i:24485284 original size:10 final size:10
Alignment explanation
Indices: 24485269--24485294 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
24485259 CTTACTGATC
24485269 TGTTAGTATT
1 TGTTAGTATT
24485279 TGTTAGTATT
1 TGTTAGTATT
24485289 TGTTAG
1 TGTTAG
24485295 CAATTAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (10 bp):
TGTTAGTATT
Found at i:24486708 original size:56 final size:50
Alignment explanation
Indices: 24486612--24486809 Score: 218
Period size: 50 Copynumber: 3.8 Consensus size: 50
24486602 ATTTGGGTAA
* * *
24486612 AGAGATCCCATGTAATACCATGTCTGGGACATGGCATTGGCATCTTTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
24486668 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
24486718 AGAGGTTCCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGG-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
24486768 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
24486810 GTACAAAAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
49 4 0.03
50 74 0.60
51 4 0.03
53 3 0.02
55 1 0.01
56 38 0.31
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:24486808 original size:100 final size:103
Alignment explanation
Indices: 24486623--24486809 Score: 245
Period size: 100 Copynumber: 1.8 Consensus size: 103
24486613 GAGATCCCAT
* * **
24486623 GTAATACCATGTCTGGGACATGGCATTGGCATCTTTGAGATTATGAGAGGTCCCATATAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATGGGCATC--T-AGATTATGAGAACTCCCATATAAGACCA
* *
24486688 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTTCCCC
63 TATCTGGGACATGGCATTGGCACCGAGATGAGAGGTTCCCC
* *
24486729 GTAAGACCATGTCTGGGACATGGCATGGGCA-C-CGA-TATGAGAACTCCCATGTAAGACCATAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCTAGATTATGAGAACTCCCATATAAGACCATAT
*
24486791 CTGGGATATGGCATTGGCA
66 CTGGGACATGGCATTGGCA
24486810 GTACAAAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 40 0.56
101 2 0.03
105 1 0.01
106 29 0.40
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (103 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCATCTAGATTATGAGAACTCCCATATAAGACCATAT
CTGGGACATGGCATTGGCACCGAGATGAGAGGTTCCCC
Found at i:24488722 original size:35 final size:36
Alignment explanation
Indices: 24488645--24488725 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
24488635 ATTTATAACA
*
24488645 TATATATAATCAAATTTCTGTTAATGTATATTTTTT
1 TATAAATAATCAAATTTCTGTTAATGTATATTTTTT
*
24488681 TATAAATAATCAAATTTCTTTTAATGTATA-TTTTT
1 TATAAATAATCAAATTTCTGTTAATGTATATTTTTT
24488716 TATAAATAAT
1 TATAAATAAT
24488726 ATGTTAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 15 0.35
36 28 0.65
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (36 bp):
TATAAATAATCAAATTTCTGTTAATGTATATTTTTT
Found at i:24492008 original size:14 final size:15
Alignment explanation
Indices: 24491989--24492026 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
24491979 ATTCAAAAAT
24491989 AAATTATTTT-TCAA
1 AAATTATTTTCTCAA
*
24492003 AAATTATTTTCTGAA
1 AAATTATTTTCTCAA
24492018 AAA-TATTTT
1 AAATTATTTT
24492027 AACAAACAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (15 bp):
AAATTATTTTCTCAA
Found at i:24500498 original size:126 final size:126
Alignment explanation
Indices: 24500273--24500518 Score: 483
Period size: 126 Copynumber: 2.0 Consensus size: 126
24500263 CCTGTTAAAG
24500273 CTTCTGTTAGTAGTCATAAGAAGTTGGGATCTGCTGGTCTTGCATTGCACTATGCCAATATCATT
1 CTTCTGTTAGTAGTCATAAGAAGTTGGGATCTGCTGGTCTTGCATTGCACTATGCCAATATCATT
24500338 ACTCAAATTGATACCCTTGTAAGTTTAAGATTTTCTGCCTAATAATGGCTTTTCTTTACCT
66 ACTCAAATTGATACCCTTGTAAGTTTAAGATTTTCTGCCTAATAATGGCTTTTCTTTACCT
*
24500399 CTTCTGTTAGTAGTTATAAGAAGTTGGGATCTGCTGGTCTTGCATTGCACTATGCCAATATCATT
1 CTTCTGTTAGTAGTCATAAGAAGTTGGGATCTGCTGGTCTTGCATTGCACTATGCCAATATCATT
24500464 ACTCAAATTGATACCCTTGTAAGTTTAAGATTTTCTGCCTAATAATGGCTTTTCT
66 ACTCAAATTGATACCCTTGTAAGTTTAAGATTTTCTGCCTAATAATGGCTTTTCT
24500519 AAGCAGTCAT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 119 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (126 bp):
CTTCTGTTAGTAGTCATAAGAAGTTGGGATCTGCTGGTCTTGCATTGCACTATGCCAATATCATT
ACTCAAATTGATACCCTTGTAAGTTTAAGATTTTCTGCCTAATAATGGCTTTTCTTTACCT
Found at i:24500569 original size:126 final size:126
Alignment explanation
Indices: 24500313--24500569 Score: 304
Period size: 126 Copynumber: 2.0 Consensus size: 126
24500303 CTGCTGGTCT
24500313 TGCATTGCACTATGCCAATATCATTACTCAAATTGATACCCTTGTAAGTTTAAGATTTTCTGCCT
1 TGCATTGCACTATGCCAATATCATTACTCAAATTGATACCCTTGTAAGTTTAAGATTTTCTGCCT
* ** * ** * * *** **
24500378 AATAATGGCTTTTCTTTACCTCTTCTGTTAGTAGTTATAAGAAGTTGGGATCTGCTGGTCT
66 AATAATGGCTTTTCTTAACCTCTTCTGAGAGGACATATAAGAAGTAGAGATCTAAGGGTAG
24500439 TGCATTGCACTATGCCAATATCATTACTCAAATTGATACCCTTGTAAGTTTAAGATTTTCTGCCT
1 TGCATTGCACTATGCCAATATCATTACTCAAATTGATACCCTTGTAAGTTTAAGATTTTCTGCCT
* * * **
24500504 AATAATGGCTTTTC-TAAGCAGTCATTTTGAGAGGACATAT-TGTCGTAGAGAT-TAAGGGTAG
66 AATAATGGCTTTTCTTAA-C-CTC-TTCTGAGAGGACATATAAGAAGTAGAGATCTAAGGGTAG
24500565 TGCAT
1 TGCAT
24500570 CTTTTGTAGT
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
125 2 0.02
126 89 0.81
127 9 0.08
128 10 0.09
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (126 bp):
TGCATTGCACTATGCCAATATCATTACTCAAATTGATACCCTTGTAAGTTTAAGATTTTCTGCCT
AATAATGGCTTTTCTTAACCTCTTCTGAGAGGACATATAAGAAGTAGAGATCTAAGGGTAG
Found at i:24505733 original size:19 final size:22
Alignment explanation
Indices: 24505687--24505732 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
24505677 TCATCATGTA
*
24505687 AAAAATAATAAAAATATATTTT
1 AAAAATAATAAAAATATATTAT
24505709 AAAAAT-ATAAAAATA-ATTAT
1 AAAAATAATAAAAATATATTAT
24505729 AAAA
1 AAAA
24505733 TTGATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 9 0.39
22 6 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAATAATAAAAATATATTAT
Found at i:24506118 original size:31 final size:30
Alignment explanation
Indices: 24506059--24506122 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
24506049 CAGTTAGACT
** *
24506059 TGAATTTTAAAATTTAAAAAGTAGAGGGAC
1 TGAATTTTAAAATCCAAAAAGTACAGGGAC
*
24506089 TGAATTTTAAAAATCCAAAGAGTACAGGGAC
1 TGAATTTT-AAAATCCAAAAAGTACAGGGAC
24506120 TGA
1 TGA
24506123 TGGCAGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (30 bp):
TGAATTTTAAAATCCAAAAAGTACAGGGAC
Found at i:24509183 original size:29 final size:29
Alignment explanation
Indices: 24509150--24509228 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
24509140 TTTAAATCTG
*
24509150 AAAAGTAAAGGGATTAAATTCTTGAAAAT
1 AAAAGTAAAGGGACTAAATTCTTGAAAAT
* *
24509179 AAAAGTACAA-GAACTAAATTCTTTAAAAT
1 AAAAGTA-AAGGGACTAAATTCTTGAAAAT
*
24509208 AAAAGTATAGGGACTAAATTC
1 AAAAGTAAAGGGACTAAATTC
24509229 CAAATTTGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 1 0.02
29 40 0.93
30 2 0.05
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.27
Consensus pattern (29 bp):
AAAAGTAAAGGGACTAAATTCTTGAAAAT
Found at i:24509461 original size:16 final size:14
Alignment explanation
Indices: 24509412--24509462 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
24509402 GAAATATTAA
* *
24509412 ATAATATATTA-AA
1 ATAATAAATTATAT
24509425 ATAATAAATTATAT
1 ATAATAAATTATAT
24509439 -TAATAAATTATTAT
1 ATAATAAATTA-TAT
24509453 ATAATTAAAT
1 ATAA-TAAAT
24509463 ATGTATGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 20 0.62
14 4 0.12
15 3 0.09
16 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATAAATTATAT
Found at i:24509862 original size:34 final size:34
Alignment explanation
Indices: 24509822--24509892 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
24509812 TTATTTTTCC
*
24509822 TCTATTTTCCTTTTCCTTTTCCCTTTCACCTTCT
1 TCTATTTTCCTTTCCCTTTTCCCTTTCACCTTCT
*
24509856 TCTATTTTCCTTTCCCTTTTCCCTTTCACGTTCT
1 TCTATTTTCCTTTCCCTTTTCCCTTTCACCTTCT
24509890 TCT
1 TCT
24509893 CTTATGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.06, C:0.35, G:0.01, T:0.58
Consensus pattern (34 bp):
TCTATTTTCCTTTCCCTTTTCCCTTTCACCTTCT
Found at i:24512031 original size:14 final size:14
Alignment explanation
Indices: 24511995--24512035 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
24511985 CCCTAAAGTC
*
24511995 ACTCTAAAT-TTAA
1 ACTCTAAATCTTGA
24512008 ACTC-AAATCTTGA
1 ACTCTAAATCTTGA
24512021 ACTCTAAATCTTGA
1 ACTCTAAATCTTGA
24512035 A
1 A
24512036 TTATGAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 4 0.16
13 11 0.44
14 10 0.40
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (14 bp):
ACTCTAAATCTTGA
Found at i:24512071 original size:21 final size:22
Alignment explanation
Indices: 24512047--24512101 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
24512037 TATGAGATTC
24512047 GAGTTTATAATTTA-AAGTTTA
1 GAGTTTATAATTTACAAGTTTA
* * *
24512068 GAGTTTAAAATTCACAATTTTA
1 GAGTTTATAATTTACAAGTTTA
*
24512090 -AATTTATAATTT
1 GAGTTTATAATTT
24512102 GATATTCAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (22 bp):
GAGTTTATAATTTACAAGTTTA
Found at i:24513042 original size:31 final size:32
Alignment explanation
Indices: 24513007--24513071 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
24512997 GTTATCCTTT
* *
24513007 TAACAATAACTGAA-CTTTAAATTTTGAAAAA
1 TAACAATAACTAAATCTATAAATTTTGAAAAA
* * *
24513038 TAACATTAACTAAATCTATAACTTTTGCAAAA
1 TAACAATAACTAAATCTATAAATTTTGAAAAA
24513070 TA
1 TA
24513072 CAAAGAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (32 bp):
TAACAATAACTAAATCTATAAATTTTGAAAAA
Found at i:24518710 original size:12 final size:11
Alignment explanation
Indices: 24518682--24518713 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
24518672 ATATATTTTT
24518682 TATTTTTAAAA
1 TATTTTTAAAA
24518693 TATTTTTAAAA
1 TATTTTTAAAA
24518704 TACTTTTTAA
1 TA-TTTTTAA
24518714 TTTTCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:24520944 original size:797 final size:791
Alignment explanation
Indices: 24519262--24520849 Score: 2663
Period size: 797 Copynumber: 2.0 Consensus size: 791
24519252 TAAATTTTAA
* * * * * ** ** *
24519262 GAAATTAACTTAAATAAATTAAATTCTAAACTTTTCTAGGCTATTATTCTTCTAATTTTCAGTCC
1 GAAA-TAACTTAAATAAATTGAATACTAAACTTTTATAAGATATTATTCTGATAATGATCAATCC
**
24519327 AAAAACACCATTGAAGGTTCTCTAAGCTGGTTTTTCATATTTTTGCATCATACCAAAAGCTCATA
65 AAAAACACCATTGAA-GACCTCTAAGCTGGTTTTTCATATTTTTGCATCATACCAAAAGCTCATA
* *** *
24519392 GATCAACGAGAAAAAGGGAAATTAGTCGAGTAGTCTCTGAACTACTACCAATTTTACAATCCAAC
129 AATCAACGAGAAAAAAAAAAATTAGTCGAGTAGTCTCTAAACTACTACCAATTTTACAATCCAAC
*
24519457 CCAGATAAGTTCATATGGTTTAACTTTCATGATTATTTGTTAATTTAGGAATGATATAATATATT
194 CCAGATAAGTTCATATGGTTAAACTTTCATGATTATTTGTTAATTTAGGAATGATATAATATATT
*
24519522 TATTCATATTTTGTTGTTGAAATTAAGATTATTGTAAAAGTATAAAAATTGAATTGAATGTTTAA
259 TATTCATATTTTGTTGTTGAAATTAAGATTATTGTAAAAGTATAAAAATTGAATTGAATATTTAA
* *
24519587 AACGAGTAGAATGCAGGATTGAGTATGATTGTTCCGTGACAAAGAATGAATTGACGGATAAGACC
324 AACGAGTAGAATGCAGGATTGAGTATGATCGTTCCGTGACAAAGAATGAATTGACGGATAAAACC
24519652 ATGGTTGGACCATGGCAATGTTTAAATGTAAGACCAAAGCTAGGCTATGGCATTTTAATGAAAAG
389 ATGGTTGGACCATGGCAATGTTTAAATGTAAGACCAAAGCTAGGCTATGGCATTTTAATGAAAAG
* *
24519717 ACCATAATTGGGTTATGGCACCTTGAACGTAAGACCATGGTTGGACCATAGCAGTATAGATACAT
454 ACCATAATTGGGTTATGGCACCTTGAACGTAAGACCATGGTTGGACCATAGCAGTATAGATAAAC
*
24519782 GTATAAAACCATAGCTAGGTTATGGCATTCTGATGATAAGACCACAACTGGGTTGTGGCACTACA
519 GTATAAAACCATAGCTAGGCTATGGCATTCTGATGATAAGACCACAACTGGGTTGTGGCACTACA
* * *
24519847 AATGTAAGACCATGGCAGGGTCATGGCAATGCTTGTGTAAGACCATAGTTGGACTATGGCACAAA
584 AATGTAAGACCATGGCAGCGCCATGGCAATGCATGTGTAAGACCATAGTTGGACTATGGCACAAA
24519912 AGAACGATGTACTCATATCCGTATGCCGTTCTTCGATTCAGTAAGAAATGGTAAGAGACTTATGT
649 AGAACGATGTACTCATATCCGTATGCCGTTCTTCGATTCAGTAAGAAATGGTAAGAGACTTATGT
*
24519977 GATTGAATTGAAAGATTTATAGATTATTATTGATATTGATCTGAAGGAAGTGTGTTTATTGATTA
714 GATTGAATTGAAAGATTTATAGATTATTATTGATATTGATCTGAAGGAAGAGTGTTTATTGATTA
* *
24520042 TATTGTATTTTAT
779 TATTGTATTTCAG
* * * * ** ** *
24520055 GAAATTAACTTAAATAAATTGAATTCTAAACTTTTCTAGGCTATTATTCTTCTAATTTTCAGTCC
1 GAAA-TAACTTAAATAAATTGAATACTAAACTTTTATAAGATATTATTCTGATAATGATCAATCC
* *
24520120 AAAAACACCATTGAAGGTCCTCTAAGCTGGTTTTTCATATTTTTGCATCATACCAAGAGCTCATA
65 AAAAACACCATTGAA-GACCTCTAAGCTGGTTTTTCATATTTTTGCATCATACCAAAAGCTCATA
*
24520185 AATCAACGAAAAGAAAAGAAAAAAATTAGTTGAGTAGTCTCTAAACTACTACCAATTTTACAATC
129 AATCAACG---AGAAAA-AAAAAAATTAGTCGAGTAGTCTCTAAACTACTACCAATTTTACAATC
*
24520250 CAACCCATATAAGTTCATATGGTTAAACTTTCATGATTATTTGTTAATTTAGGAATGATATAATA
190 CAACCCAGATAAGTTCATATGGTTAAACTTTCATGATTATTTGTTAATTTAGGAATGATATAATA
24520315 TATTTATTCATATTTTGTTGTTGAAATTAAGATTATTGTAAAAGTATAAAAATTGAATTGAATAT
255 TATTTATTCATATTTTGTTGTTGAAATTAAGATTATTGTAAAAGTATAAAAATTGAATTGAATAT
**
24520380 TTAAAACGAGTAGAATGCAGGATTGAGTATGATCGTTCCGTGACAAAGAATGAATTGGTGGATAA
320 TTAAAACGAGTAGAATGCAGGATTGAGTATGATCGTTCCGTGACAAAGAATGAATTGACGGATAA
24520445 AACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCAAAGCTAGGCTATGGCATTTTAATGA
385 AACCATGGTTGGACCATGGCAATGTTTAAATGTAAGACCAAAGCTAGGCTATGGCATTTTAATGA
*
24520510 AAAGACCATAATTGGGTTATGGCATCTTGAACGTAAGACCATGGTTGGACCATAGCAGTATAGAT
450 AAAGACCATAATTGGGTTATGGCACCTTGAACGTAAGACCATGGTTGGACCATAGCAGTATAGAT
* *
24520575 AAACGTATAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCACAACTGGGTTGTGGCAC
515 AAACGTATAAAACCATAGCTAGGCTATGGCATTCTGATGATAAGACCACAACTGGGTTGTGGCAC
24520640 TACAAATGTAAGACCATGGCAGCGCCATGGCAATGCATGTGTAAGACCATAGTTGGACTATGGCA
580 TACAAATGTAAGACCATGGCAGCGCCATGGCAATGCATGTGTAAGACCATAGTTGGACTATGGCA
24520705 CAAAAAGAACGATGTACTCATATCCGTATGCCGTTCTTCGATTCAGTAAGAAATGGTAAGAGACT
645 C-AAAAGAACGATGTACTCATATCCGTATGCCGTTCTTCGATTCAGTAAGAAATGGTAAGAGACT
24520770 TATGTGATTGAATTGAAAGATTTATAGATTATTATTGATATTGATCTGAAGGAAGAGTGTTTATT
709 TATGTGATTGAATTGAAAGATTTATAGATTATTATTGATATTGATCTGAAGGAAGAGTGTTTATT
24520835 GATTATATTGTATTT
774 GATTATATTGTATTT
24520850 GACAGGGAAA
Statistics
Matches: 764, Mismatches: 26, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
793 134 0.18
796 6 0.01
797 482 0.63
798 142 0.19
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (791 bp):
GAAATAACTTAAATAAATTGAATACTAAACTTTTATAAGATATTATTCTGATAATGATCAATCCA
AAAACACCATTGAAGACCTCTAAGCTGGTTTTTCATATTTTTGCATCATACCAAAAGCTCATAAA
TCAACGAGAAAAAAAAAAATTAGTCGAGTAGTCTCTAAACTACTACCAATTTTACAATCCAACCC
AGATAAGTTCATATGGTTAAACTTTCATGATTATTTGTTAATTTAGGAATGATATAATATATTTA
TTCATATTTTGTTGTTGAAATTAAGATTATTGTAAAAGTATAAAAATTGAATTGAATATTTAAAA
CGAGTAGAATGCAGGATTGAGTATGATCGTTCCGTGACAAAGAATGAATTGACGGATAAAACCAT
GGTTGGACCATGGCAATGTTTAAATGTAAGACCAAAGCTAGGCTATGGCATTTTAATGAAAAGAC
CATAATTGGGTTATGGCACCTTGAACGTAAGACCATGGTTGGACCATAGCAGTATAGATAAACGT
ATAAAACCATAGCTAGGCTATGGCATTCTGATGATAAGACCACAACTGGGTTGTGGCACTACAAA
TGTAAGACCATGGCAGCGCCATGGCAATGCATGTGTAAGACCATAGTTGGACTATGGCACAAAAG
AACGATGTACTCATATCCGTATGCCGTTCTTCGATTCAGTAAGAAATGGTAAGAGACTTATGTGA
TTGAATTGAAAGATTTATAGATTATTATTGATATTGATCTGAAGGAAGAGTGTTTATTGATTATA
TTGTATTTCAG
Found at i:24525861 original size:92 final size:91
Alignment explanation
Indices: 24525705--24526130 Score: 559
Period size: 92 Copynumber: 4.6 Consensus size: 91
24525695 TGCTCAAACC
* * * * *
24525705 AATTCAGCAATATATATCCATATACAAATCAAATTCGGCAAGGTATAACCATATACAAATCAAAT
1 AATTCGGCAATGTATATCTATATACAAATC-AATTC-GCAATGTATAAACATATACAAATCAAAT
24525770 TCGACAATGTATATCTATATACAAATC-
64 TCGACAATGTATATCTATATACAAATCA
*
24525797 AATTCGGCAATGTATATCCATATACAAATCAAATTCAGCAATGTATAAACATATACAAATCAAAT
1 AATTCGGCAATGTATATCTATATACAAATC-AATTC-GCAATGTATAAACATATACAAATCAAAT
24525862 TCGACAATGTATATCTATATACAAATCA
64 TCGACAATGTATATCTATATACAAATCA
** **
24525890 AATTCAACAATGTATATCTATATACAAATCAATTCGACAATGTATATCCATATACAAATCAAATT
1 AATTCGGCAATGTATATCTATATACAAATCAATTCG-CAATGTATAAACATATACAAATCAAATT
* * *
24525955 CGACAATGTATAACCATATAAAAATCA
65 CGACAATGTATATCTATATACAAATCA
* * * * *
24525982 AATTAGGCAATGTATATCTATATAAAAATCAATTCGACAATGTAT-ATCTATAAACAATTCAAAT
1 AATTCGGCAATGTATATCTATATACAAATCAATTCG-CAATGTATAAAC-ATATACAAATCAAAT
* * *
24526046 TCGGCAATGTATACCTATAAACAAATCA
64 TCGACAATGTATATCTATATACAAATCA
*
24526074 AATTCGGCAATGTATATCTTTATACAAATCAATTCGGCAATGTATAAAACATATACA
1 AATTCGGCAATGTATATCTATATACAAATCAATTC-GCAATGTAT-AAACATATACA
24526131 TTTAAATTCA
Statistics
Matches: 297, Mismatches: 31, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
91 2 0.01
92 259 0.87
93 34 0.11
94 2 0.01
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.30
Consensus pattern (91 bp):
AATTCGGCAATGTATATCTATATACAAATCAATTCGCAATGTATAAACATATACAAATCAAATTC
GACAATGTATATCTATATACAAATCA
Found at i:24526130 original size:31 final size:31
Alignment explanation
Indices: 24525705--24526119 Score: 543
Period size: 31 Copynumber: 13.5 Consensus size: 31
24525695 TGCTCAAACC
* * *
24525705 AATTCAGCAATATATATCCATATACAAATCA
1 AATTCGGCAATGTATATCTATATACAAATCA
* * *
24525736 AATTCGGCAAGGTATAACCATATACAAATCA
1 AATTCGGCAATGTATATCTATATACAAATCA
*
24525767 AATTCGACAATGTATATCTATATACAAATC-
1 AATTCGGCAATGTATATCTATATACAAATCA
*
24525797 AATTCGGCAATGTATATCCATATACAAATCA
1 AATTCGGCAATGTATATCTATATACAAATCA
* *
24525828 AATTCAGCAATGTATAAAC-ATATACAAATCA
1 AATTCGGCAATGTAT-ATCTATATACAAATCA
*
24525859 AATTCGACAATGTATATCTATATACAAATCA
1 AATTCGGCAATGTATATCTATATACAAATCA
**
24525890 AATTCAACAATGTATATCTATATACAAATC-
1 AATTCGGCAATGTATATCTATATACAAATCA
* *
24525920 AATTCGACAATGTATATCCATATACAAATCA
1 AATTCGGCAATGTATATCTATATACAAATCA
* * * *
24525951 AATTCGACAATGTATAACCATATAAAAATCA
1 AATTCGGCAATGTATATCTATATACAAATCA
* *
24525982 AATTAGGCAATGTATATCTATATAAAAATC-
1 AATTCGGCAATGTATATCTATATACAAATCA
* * *
24526012 AATTCGACAATGTATATCTATAAACAATTCA
1 AATTCGGCAATGTATATCTATATACAAATCA
* *
24526043 AATTCGGCAATGTATACCTATAAACAAATCA
1 AATTCGGCAATGTATATCTATATACAAATCA
*
24526074 AATTCGGCAATGTATATCTTTATACAAATC-
1 AATTCGGCAATGTATATCTATATACAAATCA
24526104 AATTCGGCAATGTATA
1 AATTCGGCAATGTATA
24526120 AAACATATAC
Statistics
Matches: 344, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
30 99 0.29
31 243 0.71
32 2 0.01
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (31 bp):
AATTCGGCAATGTATATCTATATACAAATCA
Found at i:24526139 original size:123 final size:123
Alignment explanation
Indices: 24525705--24526119 Score: 604
Period size: 123 Copynumber: 3.4 Consensus size: 123
24525695 TGCTCAAACC
* * * * *
24525705 AATTCAGCAATATATATCCATATACAAATCAAATTCGGCAAGGTATAACCATATACAAATCAAAT
1 AATTCAGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAAT
24525770 TCGACAATGTATATCTATATACAAATCAATTCGGCAATGTATATCCATATACAAATCA
66 TCGACAATGTATATCTATATACAAATCAATTCGGCAATGTATATCCATATACAAATCA
* *
24525828 AATTCAGCAATGTATAAACATATACAAATCAAATTCGACAATGTATATCTATATACAAATCAAAT
1 AATTCAGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAAT
* *
24525893 TCAACAATGTATATCTATATACAAATCAATTCGACAATGTATATCCATATACAAATCA
66 TCGACAATGTATATCTATATACAAATCAATTCGGCAATGTATATCCATATACAAATCA
* * *
24525951 AATTC-GACAATGTATAACCATATAAAAATCAAATTAGGCAATGTATATCTATATAAAAATC-AA
1 AATTCAG-CAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAA
* * *
24526014 TTCGACAATGTATATCTATAAACAATTCAAATTCGGCAATGTATA-CCTATAAACAAATCA
65 TTCGACAATGTATATCTATATACAAATC-AATTCGGCAATGTATATCC-ATATACAAATCA
* * **
24526074 AATTCGGCAATGTATATCTTTATACAAATC-AATTCGGCAATGTATA
1 AATTCAGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATA
24526120 AAACATATAC
Statistics
Matches: 264, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
122 45 0.17
123 218 0.83
124 1 0.00
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (123 bp):
AATTCAGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAAT
TCGACAATGTATATCTATATACAAATCAATTCGGCAATGTATATCCATATACAAATCA
Found at i:24531767 original size:29 final size:29
Alignment explanation
Indices: 24531725--24531818 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
24531715 AGATAAGCTT
*
24531725 ATTGGATCTCTATAGACTATCAAGGTCAA
1 ATTGGATCTCTATAGACTTTCAAGGTCAA
24531754 ATTGGATCTCTATAGACTTTCAAGGTCAA
1 ATTGGATCTCTATAGACTTTCAAGGTCAA
24531783 ATTGGATCTCTATAGACTTTCAAGGTCAA
1 ATTGGATCTCTATAGACTTTCAAGGTCAA
24531812 ATTGGAT
1 ATTGGAT
24531819 AAGTAAAGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (29 bp):
ATTGGATCTCTATAGACTTTCAAGGTCAA
Found at i:24534747 original size:29 final size:31
Alignment explanation
Indices: 24534696--24534757 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
24534686 TAGTAATGGT
*
24534696 AAAATTACACTTTGATCCCTTAAAAATGATA
1 AAAATTACACTTTAATCCCTTAAAAATGATA
* *
24534727 AAAATTA-A-TTTAATCCTTTAAAAATTATA
1 AAAATTACACTTTAATCCCTTAAAAATGATA
24534756 AA
1 AA
24534758 GATATAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.71
30 1 0.04
31 7 0.25
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.35
Consensus pattern (31 bp):
AAAATTACACTTTAATCCCTTAAAAATGATA
Found at i:24534966 original size:15 final size:15
Alignment explanation
Indices: 24534946--24534978 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
24534936 CATATTTTTA
24534946 TTATTTTAATAATAT
1 TTATTTTAATAATAT
*
24534961 TTATTTTAATAATTT
1 TTATTTTAATAATAT
24534976 TTA
1 TTA
24534979 AAGGATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTTTAATAATAT
Found at i:24535447 original size:20 final size:20
Alignment explanation
Indices: 24535402--24535447 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
24535392 CCTCAAACCG
*
24535402 TAAACTCAAACCCTAAACTT
1 TAAACTCAAACCCTAAACTC
* *
24535422 TGAACTCAAACCCTGAACTC
1 TAAACTCAAACCCTAAACTC
24535442 TAAACT
1 TAAACT
24535448 TAAAACTCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.30, G:0.04, T:0.24
Consensus pattern (20 bp):
TAAACTCAAACCCTAAACTC
Found at i:24537292 original size:68 final size:67
Alignment explanation
Indices: 24537220--24537360 Score: 164
Period size: 68 Copynumber: 2.1 Consensus size: 67
24537210 TGACTAGTGT
*
24537220 TACAAAATAATA-ATAAAACATCAAGTTTG-T-TTTACTAATCAAATGTTAGATTTTGTTACAAC
1 TACAAAATAATACA-AAAA-AT-AA-TTTGATATTTACTAATCAAATGTTAGATTTTATTACAAC
24537282 AATTAA
62 AATTAA
* **
24537288 TAC-AATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAA
1 TACAAAATAATACAAAAAATAATTTGAT--ATTTACTAATCAAATGTTAGATTTTATTACAACAA
24537352 TTAA
64 TTAA
24537356 TACAA
1 TACAA
24537361 TTAACAATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
64 4 0.06
65 3 0.05
66 2 0.03
67 9 0.14
68 44 0.70
69 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.38
Consensus pattern (67 bp):
TACAAAATAATACAAAAAATAATTTGATATTTACTAATCAAATGTTAGATTTTATTACAACAATT
AA
Found at i:24537294 original size:9 final size:9
Alignment explanation
Indices: 24537280--24537307 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
24537270 TTTTGTTACA
24537280 ACAATTAAT
1 ACAATTAAT
24537289 ACAATTAAT
1 ACAATTAAT
24537298 ACAATTAAT
1 ACAATTAAT
24537307 A
1 A
24537308 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:24537361 original size:68 final size:66
Alignment explanation
Indices: 24537250--24537391 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
24537240 TCAAGTTTGT
*
24537250 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
24537315 AAA
64 AAA
24537318 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
24537383 T
66 A
24537384 TTTACTAA
1 TTTACTAA
24537392 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:24537401 original size:16 final size:16
Alignment explanation
Indices: 24537380--24537421 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
24537370 AATAATTTGA
*
24537380 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
24537396 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
24537412 TAGTTTTAAT
1 TAATTTTAAT
24537422 TTTATTAAAA
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:24537405 original size:22 final size:23
Alignment explanation
Indices: 24537395--24537456 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
24537385 TTACTAACAA
* * *
24537395 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
24537417 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
24537440 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
24537457 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:24537410 original size:59 final size:66
Alignment explanation
Indices: 24537250--24537413 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 66
24537240 TCAAGTTTGT
*
24537250 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
24537315 AAA
64 AAA
24537318 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
24537381 AAT
64 AAA
*
24537384 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
24537414 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 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 27 0.29
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:24553463 original size:14 final size:15
Alignment explanation
Indices: 24553444--24553472 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24553434 AAAGTACCTG
24553444 AAAAAC-AAAATAAA
1 AAAAACAAAAATAAA
24553458 AAAAACAAAAATAAA
1 AAAAACAAAAATAAA
24553473 TTCAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAAACAAAAATAAA
Found at i:24553776 original size:132 final size:132
Alignment explanation
Indices: 24553537--24553803 Score: 498
Period size: 132 Copynumber: 2.0 Consensus size: 132
24553527 AATATTAGTA
*
24553537 TAATATAACTTAAAATTTTGGTTCCTAGAAATGGCACTAAAAACTTGATGTGAGAGAATTCGTTA
1 TAATATAACTTAAAATTTTGGTTCCTAGAAATGGCACCAAAAACTTGATGTGAGAGAATTCGTTA
* *
24553602 TGCAAGTGCACATGTGGATCAAGTAATACAGTGATAAAAAGATGTTGTTTTCACGAAAACTAAAT
66 TGCAAGTGCACATGTGGATCAAGTAATACAGTGATAAAAAGATGTTGTTTTCACAAAAACCAAAT
24553667 TC
131 TC
24553669 TAATATAACTTAAAATTTTGGTTCCTAGAAATGGCACCAAAAACTTGATGTGAGAGAATTCGTTA
1 TAATATAACTTAAAATTTTGGTTCCTAGAAATGGCACCAAAAACTTGATGTGAGAGAATTCGTTA
*
24553734 TGCAAGTGCACATGTGGATCAAGTAATACAGTGATAAGAAGATGTTGTTTTCACAAAAACCAAAT
66 TGCAAGTGCACATGTGGATCAAGTAATACAGTGATAAAAAGATGTTGTTTTCACAAAAACCAAAT
24553799 TC
131 TC
24553801 TAA
1 TAA
24553804 GTTGCTAATT
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 131 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (132 bp):
TAATATAACTTAAAATTTTGGTTCCTAGAAATGGCACCAAAAACTTGATGTGAGAGAATTCGTTA
TGCAAGTGCACATGTGGATCAAGTAATACAGTGATAAAAAGATGTTGTTTTCACAAAAACCAAAT
TC
Found at i:24554924 original size:16 final size:15
Alignment explanation
Indices: 24554886--24554915 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
24554876 AAAAGTAAGA
24554886 AAAAAAACATAATTC
1 AAAAAAACATAATTC
24554901 AAATAAAACATAATT
1 AAA-AAAACATAATT
24554916 AATCAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 3 0.21
16 11 0.79
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAAACATAATTC
Found at i:24580831 original size:17 final size:17
Alignment explanation
Indices: 24580809--24580844 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
24580799 ATCAAATACC
*
24580809 AATATATTTTTCCTTAA
1 AATATATTTCTCCTTAA
*
24580826 AATATATTTCTCTTTAA
1 AATATATTTCTCCTTAA
24580843 AA
1 AA
24580845 AGTTAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATATTTCTCCTTAA
Found at i:24595939 original size:31 final size:31
Alignment explanation
Indices: 24595904--24595968 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
24595894 TTAACAACTC
24595904 AATAACTTAAATAAAAACTT-TCGAATAGTTT
1 AATAACTTAAATAAAAACTTGT-GAATAGTTT
* *
24595935 AATAACTTAAATGAAAACTTGTGAGTAGTTT
1 AATAACTTAAATAAAAACTTGTGAATAGTTT
24595966 AAT
1 AAT
24595969 GATCATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (31 bp):
AATAACTTAAATAAAAACTTGTGAATAGTTT
Found at i:24609464 original size:21 final size:22
Alignment explanation
Indices: 24609430--24609472 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
24609420 CGACATTTGA
*
24609430 TGAACATCTTTG-AACTTGAGTT
1 TGAACATCGTTGAAAC-TGAGTT
24609452 TGAAC-TCGTTGAAACTGAGTT
1 TGAACATCGTTGAAACTGAGTT
24609473 GGGTTTCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (22 bp):
TGAACATCGTTGAAACTGAGTT
Found at i:24611508 original size:22 final size:23
Alignment explanation
Indices: 24611456--24611508 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
24611446 CCAGAAACGA
*
24611456 AAGAAATAAGAAGGAAGGAAGCAG
1 AAGAAA-AAGAAGGAAGGAAGAAG
24611480 AAG-AAAAGAAGGAAGGAA-AAG
1 AAGAAAAAGAAGGAAGGAAGAAG
24611501 AAGAAAAA
1 AAGAAAAA
24611509 AAATAGGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 5 0.19
22 17 0.63
23 2 0.07
24 3 0.11
ACGTcount: A:0.66, C:0.02, G:0.30, T:0.02
Consensus pattern (23 bp):
AAGAAAAAGAAGGAAGGAAGAAG
Found at i:24614706 original size:16 final size:15
Alignment explanation
Indices: 24614675--24614716 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
24614665 ACAAAATCAA
*
24614675 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
24614690 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
24614706 ATAAAAATTAA
1 ATAAAAGTTAA
24614717 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:24614796 original size:38 final size:39
Alignment explanation
Indices: 24614753--24614835 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 39
24614743 AAAAAGTCAG
24614753 TTATAATTAAACTTTTAATAAAATGATTTTTAA-TTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
*
24614791 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
24614830 TTATAA
1 TTATAA
24614836 AATTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 32 0.74
39 11 0.26
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (39 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
Found at i:24614933 original size:60 final size:60
Alignment explanation
Indices: 24614869--24614990 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 60
24614859 ATACTAAACT
* * * * * *
24614869 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAACCCCAAATTACTAA-AAATTAAATTATAAAATAATTAC
* * *
24614929 AAACACAAAAATTTATAACATAACCCCAAATTACTAACAATTTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAACCCCAAATTACTAAAAATTAAATTATAAAATAATTAC
24614989 AA
1 AA
24614991 TATTCATACA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 8 0.15
60 44 0.85
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.30
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAACCCCAAATTACTAAAAATTAAATTATAAAATAATTAC
Found at i:24614990 original size:22 final size:21
Alignment explanation
Indices: 24614965--24615016 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
24614955 CAAATTACTA
*
24614965 ACAAT-TTAATTATAAAATAATT
1 ACAATATTAA-TACAAAA-AATT
*
24614987 ACAATATTCATACAAAAAATT
1 ACAATATTAATACAAAAAATT
24615008 ACAATATTA
1 ACAATATTA
24615017 CAATATATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 12 0.46
22 11 0.42
23 3 0.12
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.35
Consensus pattern (21 bp):
ACAATATTAATACAAAAAATT
Found at i:24615067 original size:27 final size:26
Alignment explanation
Indices: 24615031--24615232 Score: 221
Period size: 27 Copynumber: 8.0 Consensus size: 26
24615021 ATATCTCCAC
24615031 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
24615058 ATTACAATATTCATAC-AAA--AAAT
1 ATTACAATATTCATACAAAATTAAAT
*
24615081 -TTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
24615107 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
* *
24615129 ATTATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTA-AAT
24615156 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
* *
24615178 ATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
*
24615205 ATTACGATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
24615232 A
1 A
24615233 GTCATACAAA
Statistics
Matches: 151, Mismatches: 9, Indels: 30
0.79 0.05 0.16
Matches are distributed among these distances:
22 44 0.29
23 16 0.11
24 3 0.02
25 3 0.02
26 16 0.11
27 69 0.46
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATTAAAT
Found at i:24615108 original size:49 final size:49
Alignment explanation
Indices: 24614978--24615224 Score: 315
Period size: 49 Copynumber: 5.1 Consensus size: 49
24614968 ATTTAATTAT
* *
24614978 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATATC-T-C
1 AAAAAAATTGCAATATTCATAC--AAAATTACAATATTACAATAT-TCATAC
* * *
24615028 ---CACATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
24615074 AAAAAATTTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTACAATATTACAATATTCATAC
** *
24615123 AAAAAAATTATAATATTCATACAAAATTACAAAATTACAATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTACAATATTACAATATTCATAC
* * *
24615172 AAAAAAATTGCAATATTCATACAAAACTATAATATTACGATATTCATAC
1 AAAAAAATTGCAATATTCATACAAAATTACAATATTACAATATTCATAC
24615221 AAAA
1 AAAA
24615225 TTACAATAGT
Statistics
Matches: 173, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
44 2 0.01
45 22 0.13
46 1 0.01
47 16 0.09
49 132 0.76
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (49 bp):
AAAAAAATTGCAATATTCATACAAAATTACAATATTACAATATTCATAC
Found at i:24615149 original size:98 final size:98
Alignment explanation
Indices: 24615031--24615243 Score: 351
Period size: 98 Copynumber: 2.2 Consensus size: 98
24615021 ATATCTCCAC
* *
24615031 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAATTTGCAATATTCATAC
1 ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATAC
*
24615096 AAAATTATAATATTACAATATTCATACAAAAAA
66 AAAACTATAATATTACAATATTCATACAAAAAA
*
24615129 ATTATAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATAC
1 ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATAC
*
24615194 AAAACTATAATATTACGATATTCATAC---AAA
66 AAAACTATAATATTACAATATTCATACAAAAAA
*
24615224 ATTACAATAGTCATACAAAA
1 ATTACAATATTCATACAAAA
24615244 AATACTAATC
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
95 21 0.19
98 87 0.81
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (98 bp):
ATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATTCATAC
AAAACTATAATATTACAATATTCATACAAAAAA
Found at i:24615334 original size:20 final size:20
Alignment explanation
Indices: 24614976--24615367 Score: 114
Period size: 22 Copynumber: 17.4 Consensus size: 20
24614966 CAATTTAATT
*
24614976 ATAAAATAATTACAATATTC
1 ATAAAAAAATTACAATATTC
24614996 ATACAAAAAATTACAATATTAC
1 ATA-AAAAAATTACAATATT-C
** *
24615018 AATATATCTCCACATTACAATATTC
1 -ATA-A---AAAAATTACAATATTC
24615043 ATACAAAATTACAATATTACAATATTC
1 AT---AAA--A-AA-ATTACAATATTC
*
24615070 ATACAAAAAATTTGCAATATTC
1 ATA-AAAAAA-TTACAATATTC
24615092 ATACAAAATTATAATATTACAATATTC
1 AT---AAA--A-AA-ATTACAATATTC
*
24615119 ATACAAAAAAATTATAATATTC
1 AT--AAAAAAATTACAATATTC
24615141 ATACAAAATTACAAAATTACAATATTC
1 AT----AA--A-AAAATTACAATATTC
*
24615168 ATACAAAAAAATTGCAATATTC
1 AT--AAAAAAATTACAATATTC
*
24615190 ATACAAAACTATAATATTACGATATTC
1 AT---AAA--A-AA-ATTACAATATTC
* *
24615217 AT-ACAAAATTACAATAGTC
1 ATAAAAAAATTACAATATTC
* *
24615236 ATACAAAAAA-TACTA-ATCC
1 ATA-AAAAAATTACAATATTC
24615255 A-AAACTATAAA-TACAAATTTAATT-
1 ATAAA--A-AAATTAC-AA--T-ATTC
*
24615279 ATAAAATAATTACAATATTC
1 ATAAAAAAATTACAATATTC
* *
24615299 AT-ACAACATTACAATATTC
1 ATAAAAAAATTACAATATTC
*
24615318 ATAAAAAAATTATAATATTC
1 ATAAAAAAATTACAATATTC
*
24615338 ATACAAAAAAGTTAAAATATTC
1 ATA-AAAAAA-TTACAATATTC
24615360 ATACAAAA
1 ATA-AAAA
24615368 TTCTAATCTA
Statistics
Matches: 286, Mismatches: 38, Indels: 94
0.68 0.09 0.22
Matches are distributed among these distances:
17 2 0.01
18 1 0.00
19 35 0.12
20 35 0.12
21 29 0.10
22 66 0.23
23 16 0.06
24 10 0.03
25 13 0.05
26 21 0.07
27 57 0.20
28 1 0.00
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (20 bp):
ATAAAAAAATTACAATATTC
Found at i:24615559 original size:14 final size:14
Alignment explanation
Indices: 24615537--24615573 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 14
24615527 TTCTTTCTTT
24615537 CTTCTTCTTCTTCTC
1 CTTC-TCTTCTTCTC
24615552 CTTCTCTTCTTCTC
1 CTTCTCTTCTTCTC
24615566 CTTTCTCT
1 C-TTCTCT
24615574 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
CTTCTCTTCTTCTC
Found at i:24615576 original size:14 final size:13
Alignment explanation
Indices: 24615535--24615576 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
24615525 TTTTCTTTCT
*
24615535 TTCTTCTTCT-TC
1 TTCTCCTTCTCTC
24615547 TTCTCCTTCTCTTC
1 TTCTCCTTCTC-TC
24615561 TTCTCCTTTCTCTC
1 TTCTCC-TTCTCTC
24615575 TT
1 TT
24615577 TTTTTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 9 0.35
14 12 0.46
15 5 0.19
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTCCTTCTCTC
Found at i:24628628 original size:21 final size:21
Alignment explanation
Indices: 24628604--24628649 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
24628594 TTTGTAAATA
24628604 AACAGTTTGAATAGTAATAGG
1 AACAGTTTGAATAGTAATAGG
24628625 AACAGTTTGAATAGTAATAGG
1 AACAGTTTGAATAGTAATAGG
24628646 AACA
1 AACA
24628650 ATTTATTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.26
Consensus pattern (21 bp):
AACAGTTTGAATAGTAATAGG
Found at i:24629868 original size:6 final size:6
Alignment explanation
Indices: 24629857--24629920 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
24629847 AATATTACTT
24629857 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
24629905 ATAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAA
24629921 TTAAAAATAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:24637564 original size:3 final size:3
Alignment explanation
Indices: 24637551--24637590 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
24637541 AGATTCCTTT
*
24637551 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24637591 ACTAAAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:24638917 original size:17 final size:17
Alignment explanation
Indices: 24638895--24638929 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
24638885 ATATTTAAGT
24638895 AATATTATGT-ATTTTTA
1 AATATTAT-TAATTTTTA
24638912 AATATTATTAATTTTTA
1 AATATTATTAATTTTTA
24638929 A
1 A
24638930 TAAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
AATATTATTAATTTTTA
Found at i:24642096 original size:46 final size:46
Alignment explanation
Indices: 24642024--24642163 Score: 235
Period size: 46 Copynumber: 3.0 Consensus size: 46
24642014 ACAATGCTAT
* *
24642024 AACTCAGTATGGTTTCCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
24642070 AACTCAGTATGGTTTTCTTCATTGAAACATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
24642116 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACCTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
24642162 AA
1 AA
24642164 TTTGCCATGG
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:24645771 original size:26 final size:25
Alignment explanation
Indices: 24645728--24645938 Score: 105
Period size: 25 Copynumber: 8.5 Consensus size: 25
24645718 ACACATCGAA
**
24645728 GCTCTTATGAGCGCCCCGATATATG
1 GCTCTTATGAGCTTCCCGATATATG
**
24645753 GCTCTTAGTGAGCTTCCCGAT-TAAAA
1 GCTCTTA-TGAGCTTCCCGATAT-ATG
* *
24645779 GCTCTTTGTGAGCTTCCCGTTA-ATG
1 GCTC-TTATGAGCTTCCCGATATATG
*
24645804 GCT-TTCTGGAGCTTCCCGATAT-TG
1 GCTCTTAT-GAGCTTCCCGATATATG
* *
24645828 GCTCGCTTA--AACTTCCCGAT-TTTG
1 GCT--CTTATGAGCTTCCCGATATATG
* **
24645852 GCTCTTATGAGCTTCCCGTTATACA
1 GCTCTTATGAGCTTCCCGATATATG
* ** * * *
24645877 ACTCGAATGAGCTTCCTGTTACATG
1 GCTCTTATGAGCTTCCCGATATATG
** *
24645902 GCTCACATGAGCTTCCC-ATTTATG
1 GCTCTTATGAGCTTCCCGATATATG
*
24645926 TGCTCGTATGAGC
1 -GCTCTTATGAGC
24645939 ATTCTGCATA
Statistics
Matches: 139, Mismatches: 33, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
22 4 0.03
23 4 0.03
24 45 0.32
25 54 0.39
26 28 0.20
27 4 0.03
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCCGATATATG
Found at i:24645866 original size:24 final size:24
Alignment explanation
Indices: 24645728--24645873 Score: 97
Period size: 24 Copynumber: 6.0 Consensus size: 24
24645718 ACACATCGAA
**
24645728 GCTCTTATGAGCGCCCCGATATATG
1 GCTCTTATGAGCTTCCCGAT-TATG
**
24645753 GCTCTTAGTGAGCTTCCCGATTAAAA
1 GCTCTTA-TGAGCTTCCCGATT-ATG
*
24645779 GCTCTTTGTGAGCTTCCCG-TTAATG
1 GCTC-TTATGAGCTTCCCGATT-ATG
*
24645804 GCT-TTCTGGAGCTTCCCGA-TATTG
1 GCTCTTAT-GAGCTTCCCGATTA-TG
* *
24645828 GCTCGCTTA--AACTTCCCGATTTTG
1 GCT--CTTATGAGCTTCCCGATTATG
24645852 GCTCTTATGAGCTTCCCG-TTAT
1 GCTCTTATGAGCTTCCCGATTAT
24645874 ACAACTCGAA
Statistics
Matches: 96, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
22 4 0.04
23 7 0.07
24 38 0.40
25 16 0.17
26 27 0.28
27 4 0.04
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (24 bp):
GCTCTTATGAGCTTCCCGATTATG
Found at i:24658472 original size:24 final size:24
Alignment explanation
Indices: 24658440--24658485 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24658430 CTAATTAAAT
* *
24658440 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAATTTATTG
*
24658464 TTTAAAAATATTTAAAATTTAT
1 TTTAAAAATAATTAAAATTTAT
24658486 ATTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTTATTG
Found at i:24658707 original size:16 final size:13
Alignment explanation
Indices: 24658697--24658724 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
24658687 GCACTTCTCA
24658697 TCCACAGCACTTT
1 TCCACAGCACTTT
24658710 TCCACAGCACTTT
1 TCCACAGCACTTT
24658723 TC
1 TC
24658725 AAAAGCAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.39, G:0.07, T:0.32
Consensus pattern (13 bp):
TCCACAGCACTTT
Found at i:24659718 original size:20 final size:20
Alignment explanation
Indices: 24659686--24659737 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
24659676 AAAAATTACA
*
24659686 AAAAATTTTAAAATAATTT-T
1 AAAAATTTCAAAAT-ATTTAT
24659706 CAAAAA-TTCAAAATATTTAT
1 -AAAAATTTCAAAATATTTAT
24659726 AAAAATTTCAAA
1 AAAAATTTCAAA
24659738 TTTTATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 9 0.32
20 14 0.50
21 5 0.18
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAATTTCAAAATATTTAT
Found at i:24659738 original size:19 final size:18
Alignment explanation
Indices: 24659707--24659744 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
24659697 AATAATTTTC
24659707 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAAT-TTTAT
24659726 AAAAATTTC-AAATTTTAT
1 AAAAA-TTCAAAATTTTAT
24659744 A
1 A
24659745 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 9 0.50
20 3 0.17
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTCAAAATTTTAT
Found at i:24671360 original size:21 final size:21
Alignment explanation
Indices: 24671334--24671374 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
24671324 TGTGTGAATA
24671334 TGAGCTACAGGATATTCAACT
1 TGAGCTACAGGATATTCAACT
*
24671355 TGAGCTACAGGATGTTCAAC
1 TGAGCTACAGGATATTCAAC
24671375 ATTTATCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (21 bp):
TGAGCTACAGGATATTCAACT
Found at i:24675575 original size:18 final size:18
Alignment explanation
Indices: 24675548--24675582 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24675538 GCTGATGTTT
24675548 AGAAAAAAAAAAAAGAAA
1 AGAAAAAAAAAAAAGAAA
* *
24675566 AGAAATAAAACAAAGAA
1 AGAAAAAAAAAAAAGAA
24675583 GTTTCAAGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (18 bp):
AGAAAAAAAAAAAAGAAA
Found at i:24692488 original size:86 final size:86
Alignment explanation
Indices: 24692343--24692506 Score: 283
Period size: 86 Copynumber: 1.9 Consensus size: 86
24692333 ACAAGTATCT
* *
24692343 TAATCATTACTAAGTCAAAACAAAATCAGGGAAGTAAGAAATACATGAGGAGAAGCAAGGGGAGA
1 TAATCATTACTAAGTCAAAACAAAATCAGGGAAGTAAGAAATACATGAGGAGAAACAAGGCGAGA
*
24692408 AGCGCTGTAAATTAGGTCCTG
66 AACGCTGTAAATTAGGTCCTG
* *
24692429 TAATCATTTCTAAGTCAAAACAAAATCAGGGAAGTAAGAACTACATGAGGAGAAACAAGGCGAGA
1 TAATCATTACTAAGTCAAAACAAAATCAGGGAAGTAAGAAATACATGAGGAGAAACAAGGCGAGA
24692494 AACGCTGTAAATT
66 AACGCTGTAAATT
24692507 TGTTCGCTAA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (86 bp):
TAATCATTACTAAGTCAAAACAAAATCAGGGAAGTAAGAAATACATGAGGAGAAACAAGGCGAGA
AACGCTGTAAATTAGGTCCTG
Found at i:24707674 original size:29 final size:31
Alignment explanation
Indices: 24707641--24707702 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
24707631 AGTTTATATC
*
24707641 TTTATAATTTTTAAAGGATTAAA-T-TAATT
1 TTTATAATTTTTAAAGGATCAAAGTGTAATT
* *
24707670 TTTATCATTTTTAAGGGATCAAAGTGTAATT
1 TTTATAATTTTTAAAGGATCAAAGTGTAATT
24707701 TT
1 TT
24707703 ACCATTACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.71
30 1 0.04
31 7 0.25
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.50
Consensus pattern (31 bp):
TTTATAATTTTTAAAGGATCAAAGTGTAATT
Found at i:24708309 original size:15 final size:15
Alignment explanation
Indices: 24708291--24708323 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
24708281 TATTATCCTT
24708291 TAAAAATTATTAAAA
1 TAAAAATTATTAAAA
*
24708306 TAAATATTATTAAAA
1 TAAAAATTATTAAAA
24708321 TAA
1 TAA
24708324 TAAAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAAATTATTAAAA
Found at i:24711084 original size:23 final size:22
Alignment explanation
Indices: 24711058--24711114 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
24711048 TATTATGAGC
*
24711058 TATAAAAATTCAAAAAATGAATA
1 TATAAAAATT-AAAAAATGAAAA
* *
24711081 TATAAAAAATGAAAAATGAAAA
1 TATAAAAATTAAAAAATGAAAA
*
24711103 TAAAAAAATTAA
1 TATAAAAATTAA
24711115 GTTAAAATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (22 bp):
TATAAAAATTAAAAAATGAAAA
Found at i:24711480 original size:23 final size:23
Alignment explanation
Indices: 24711454--24711511 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
24711444 CTAAATTTGT
24711454 TATTTTTATTTTCAA-TTTATATA
1 TATTTTTATTTTCAAGTTTATA-A
*
24711477 TATTCTTT-TTTTGAAGTTTATAA
1 TATT-TTTATTTTCAAGTTTATAA
24711500 T-TTTTATATTTT
1 TATTTT-TATTTT
24711512 TTTAACAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 2 0.07
22 3 0.10
23 16 0.53
24 9 0.30
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (23 bp):
TATTTTTATTTTCAAGTTTATAA
Found at i:24713449 original size:21 final size:21
Alignment explanation
Indices: 24713416--24713456 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
24713406 CCGCAGCAAA
*
24713416 AATAACAGTAAAAATAACAAG
1 AATAACAGCAAAAATAACAAG
*
24713437 AATAGCAGCAAAAATAACAA
1 AATAACAGCAAAAATAACAA
24713457 CAAAATAGTA
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:0.66, C:0.12, G:0.10, T:0.12
Consensus pattern (21 bp):
AATAACAGCAAAAATAACAAG
Found at i:24716566 original size:7 final size:7
Alignment explanation
Indices: 24716554--24716588 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
24716544 AAAGTATTTT
*
24716554 AAAATTA
1 AAAAATA
*
24716561 AAAATTA
1 AAAAATA
24716568 AAAAATA
1 AAAAATA
24716575 AAAAATA
1 AAAAATA
24716582 AAAAATA
1 AAAAATA
24716589 TATATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAAAATA
Found at i:24719247 original size:18 final size:19
Alignment explanation
Indices: 24719220--24719269 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
24719210 GATAGCATAA
*
24719220 AAGAATGAAGGTAAAA-AG
1 AAGAAGGAAGGTAAAAGAG
*
24719238 AAGAAGGAAGAATAAAAGAG
1 AAGAAGGAAG-GTAAAAGAG
24719258 ACAG-AGGAAGGT
1 A-AGAAGGAAGGT
24719270 TGAAAAAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 9 0.35
19 6 0.23
20 9 0.35
21 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.32, T:0.08
Consensus pattern (19 bp):
AAGAAGGAAGGTAAAAGAG
Found at i:24723415 original size:13 final size:13
Alignment explanation
Indices: 24723397--24723421 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24723387 TATTGGTTTG
24723397 ATTAACTGATTTT
1 ATTAACTGATTTT
24723410 ATTAACTGATTT
1 ATTAACTGATTT
24723422 GACCAATTGA
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
ATTAACTGATTTT
Found at i:24723996 original size:20 final size:20
Alignment explanation
Indices: 24723971--24724011 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
24723961 TGGTCAGATA
24723971 TGTCATTCAACATATCTCAT
1 TGTCATTCAACATATCTCAT
24723991 TGTCATTCAACATATCTCAT
1 TGTCATTCAACATATCTCAT
24724011 T
1 T
24724012 CCCAATCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (20 bp):
TGTCATTCAACATATCTCAT
Found at i:24724986 original size:14 final size:14
Alignment explanation
Indices: 24724967--24724994 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24724957 ACTAAATTCT
24724967 TGAAAATTAAATTA
1 TGAAAATTAAATTA
24724981 TGAAAATTAAATTA
1 TGAAAATTAAATTA
24724995 CAAATATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
TGAAAATTAAATTA
Found at i:24732707 original size:20 final size:21
Alignment explanation
Indices: 24732666--24732708 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
24732656 TAAAAATGAT
*
24732666 ATTAAATGTTTAATTGATTTA
1 ATTAAATGTTTAAATGATTTA
24732687 ATTAAA-GTTTAAAT-ATATTA
1 ATTAAATGTTTAAATGAT-TTA
24732707 AT
1 AT
24732709 ATCCATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.60
21 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
ATTAAATGTTTAAATGATTTA
Found at i:24732813 original size:14 final size:14
Alignment explanation
Indices: 24732794--24732820 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24732784 AAATGGCTAT
24732794 TTTAAAAAAAATTC
1 TTTAAAAAAAATTC
24732808 TTTAAAAAAAATT
1 TTTAAAAAAAATT
24732821 AATTCACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTAAAAAAAATTC
Found at i:24734826 original size:79 final size:79
Alignment explanation
Indices: 24734724--24734881 Score: 271
Period size: 79 Copynumber: 2.0 Consensus size: 79
24734714 TATTCTATCA
* *
24734724 ATTTAATCTTAGTTCTAAATAATTCAATAAATTTAACCTTTCACATTTATAAATTCTATCAATTT
1 ATTTAATCCTAGTTCTAAATAATTCAATAAATTCAACCTTTCACATTTATAAATTCTATCAATTT
*
24734789 GATCATCAAACTTT
66 GACCATCAAACTTT
* *
24734803 ATTTGATCCTAGTTCTAAATAATTTAATAAATTCAACCTTTCACATTTATAAATTCTATCAATTT
1 ATTTAATCCTAGTTCTAAATAATTCAATAAATTCAACCTTTCACATTTATAAATTCTATCAATTT
24734868 GACCATCAAACTTT
66 GACCATCAAACTTT
24734882 CTAATCAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.43
Consensus pattern (79 bp):
ATTTAATCCTAGTTCTAAATAATTCAATAAATTCAACCTTTCACATTTATAAATTCTATCAATTT
GACCATCAAACTTT
Found at i:24735887 original size:13 final size:13
Alignment explanation
Indices: 24735837--24735891 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
24735827 AAACTTTTAG
24735837 AAATTATTTTTTTT
1 AAATTA-TTTTTTT
*
24735851 AAATT-TATTTGTT
1 AAATTAT-TTTTTT
* *
24735864 ATATAATTTTTTT
1 AAATTATTTTTTT
24735877 AAATTATTTTTTT
1 AAATTATTTTTTT
24735890 AA
1 AA
24735892 CTATCGACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
12 1 0.03
13 26 0.79
14 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
AAATTATTTTTTT
Found at i:24742175 original size:19 final size:19
Alignment explanation
Indices: 24742137--24742175 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
24742127 AAATAGTGAG
*
24742137 AATTTATTTTCTAAGTATA
1 AATTTATTTTCTAAGAATA
24742156 AATTCTATTTTCT-AGAATA
1 AATT-TATTTTCTAAGAATA
24742175 A
1 A
24742176 CAATTCTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:24743061 original size:9 final size:9
Alignment explanation
Indices: 24743047--24743086 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
24743037 GTAGGGATTC
*
24743047 AATTCGGGT
1 AATTCGGTT
24743056 AATTCGGTT
1 AATTCGGTT
24743065 AATTCGGTT
1 AATTCGGTT
24743074 AATTCGGTT
1 AATTCGGTT
24743083 AATT
1 AATT
24743087 TTTAACCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:24752031 original size:29 final size:30
Alignment explanation
Indices: 24751998--24752054 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
24751988 TAGTCTAATG
*
24751998 TGCAATGTT-ATATATGGATT-TTGATTTTA
1 TGCAAT-TTGATATATGAATTGTTGATTTTA
24752027 TGCAATTTGATATATGAATTGTTGATTT
1 TGCAATTTGATATATGAATTGTTGATTT
24752055 GATTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.28, C:0.04, G:0.18, T:0.51
Consensus pattern (30 bp):
TGCAATTTGATATATGAATTGTTGATTTTA
Found at i:24755105 original size:166 final size:166
Alignment explanation
Indices: 24754908--24755240 Score: 621
Period size: 166 Copynumber: 2.0 Consensus size: 166
24754898 TGTGGTTATA
*
24754908 TTTTAAGTCGAAGATGATGCTTATTTGTTTAGTAGGTAGGTAGTTAACTAGATGAAAGCCTTCGC
1 TTTTAAGTCGAAGATGATGCTTATTTGTTTAGTAGGTAGGTAATTAACTAGATGAAAGCCTTCGC
24754973 TCTTTAAAGATATGAATAATCTAAGGGTTCTCATAGGTACTTACTGAAACCATGATGGGGCTTTG
66 TCTTTAAAGATATGAATAATCTAAGGGTTCTCATAGGTACTTACTGAAACCATGATGGGGCTTTG
*
24755038 ATTAGTGAAGTTATAATGTCTCTTAAGGAATATATG
131 ATTAGTGAAGTTATAATGTCTCTGAAGGAATATATG
* *
24755074 TTTTAAGTCGAAGATGATGCTTATTTGTTTAGTAGGTAGGTAATTAACTAGATGAAAGCCTTTGT
1 TTTTAAGTCGAAGATGATGCTTATTTGTTTAGTAGGTAGGTAATTAACTAGATGAAAGCCTTCGC
*
24755139 TCTTTAAAGATATGAATAATCTAAGGGTTCTCATAGGTACTTACTGAAATCATGATGGGGCTTTG
66 TCTTTAAAGATATGAATAATCTAAGGGTTCTCATAGGTACTTACTGAAACCATGATGGGGCTTTG
24755204 ATTAGTGAAGTTATAATGTCTCTGAAGGAATATATG
131 ATTAGTGAAGTTATAATGTCTCTGAAGGAATATATG
24755240 T
1 T
24755241 CTAACATCTT
Statistics
Matches: 162, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
166 162 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (166 bp):
TTTTAAGTCGAAGATGATGCTTATTTGTTTAGTAGGTAGGTAATTAACTAGATGAAAGCCTTCGC
TCTTTAAAGATATGAATAATCTAAGGGTTCTCATAGGTACTTACTGAAACCATGATGGGGCTTTG
ATTAGTGAAGTTATAATGTCTCTGAAGGAATATATG
Found at i:24755925 original size:2 final size:2
Alignment explanation
Indices: 24755920--24755956 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
24755910 CTTTTTTTTT
24755920 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
24755957 ACTATAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:24763165 original size:2 final size:2
Alignment explanation
Indices: 24763158--24763197 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
24763148 CCCTCCCCCT
24763158 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
24763198 AATGCAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:24775632 original size:30 final size:30
Alignment explanation
Indices: 24775596--24775684 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 30
24775586 AGAATAAGTT
* * *
24775596 GCTCACACAAGCTGACAGTATACCAAGGTC
1 GCTCACACAAGTTGACATTATAACAAGGTC
* ** *
24775626 GCTCACACAGGTTGACATTATAACAAAATT
1 GCTCACACAAGTTGACATTATAACAAGGTC
* *
24775656 GCTCACACAAGTTGATATTATATCAAGGT
1 GCTCACACAAGTTGACATTATAACAAGGT
24775685 TGACCGTCCT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (30 bp):
GCTCACACAAGTTGACATTATAACAAGGTC
Found at i:24781618 original size:178 final size:180
Alignment explanation
Indices: 24781238--24781646 Score: 374
Period size: 178 Copynumber: 2.3 Consensus size: 180
24781228 AGTTCAACTT
* * * * * * * * ** *
24781238 CAACATAACAACAATAATCATAATCAGTCAAAGAAATTCTGAACAAAGAAGCTAAACTGAAAGAC
1 CAACACAACAACAATCATCATAATTAATCATAGTAATTCAGAAGAAAGAAGCTAAACCAAAAAAC
* * * *
24781303 TAGTGGAAAGCAAGATTTAACCTATTACAACAC------GATCACAAGATTGTTTCCGGGACAAA
66 TAATGGAAAGCAAGATTCAACCTATTTCAACACATAGATGATCACAAGATTGTTT-CAGGACAAA
* * * * ** *
24781362 GTTCTGGAGTTTGAATTGTGTATAAATGAAGACCTATTTTTGTAAGTAGTC
130 GTTCAGCAGTTCGAATTGTGTATAAATCAAGACCTATTTACGTAAGCAGTC
* * *
24781413 CAACACAACAACTA-CTATCACAATTAATCCATAGTAATTCAGATGAAAGAAGCTAAACCAAAAA
1 CAACACAACAACAATC-ATCATAATTAAT-CATAGTAATTCAGAAGAAAGAAGCTAAACCAAAAA
* *
24781477 ACTAATTGAAAGCAAGATTCAAGCTATTTCAACACATAGATGATCACAA-ATTGTTTCAGGCACA
64 ACTAATGGAAAGCAAGATTCAACCTATTTCAACACATAGATGATCACAAGATTGTTTCAGG-ACA
* * * *
24781541 AAGTTCAGGAGTTCGAATTG-G-GT-AATCAAGACCTATATACGTAACCAGTC
128 AAGTTCAGCAGTTCGAATTGTGTATAAATCAAGACCTATTTACGTAAGCAGTC
* * *
24781591 AAACACAACAACAATCATCATAATTAATAACA-AATAATTAAGAAGAAAGAAGCTAA
1 CAACACAACAACAATCATCATAATTAAT--CATAGTAATTCAGAAGAAAGAAGCTAA
24781647 GCAACAACTC
Statistics
Matches: 187, Mismatches: 36, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
175 21 0.11
176 57 0.30
178 65 0.35
179 4 0.02
180 4 0.02
181 28 0.15
182 8 0.04
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.24
Consensus pattern (180 bp):
CAACACAACAACAATCATCATAATTAATCATAGTAATTCAGAAGAAAGAAGCTAAACCAAAAAAC
TAATGGAAAGCAAGATTCAACCTATTTCAACACATAGATGATCACAAGATTGTTTCAGGACAAAG
TTCAGCAGTTCGAATTGTGTATAAATCAAGACCTATTTACGTAAGCAGTC
Found at i:24783512 original size:24 final size:23
Alignment explanation
Indices: 24783484--24783530 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
24783474 ATTTTTAATA
24783484 ATCATAATTAAA-TTGTATATTTTT
1 ATCAT-ATTAAAGTTG-ATATTTTT
*
24783508 ATCATTTTAAAGTTGATATTTTT
1 ATCATATTAAAGTTGATATTTTT
24783531 TATAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (23 bp):
ATCATATTAAAGTTGATATTTTT
Found at i:24783531 original size:24 final size:24
Alignment explanation
Indices: 24783491--24783544 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
24783481 ATAATCATAA
*
24783491 TTAAATTGTATATTTTTATCA-TT
1 TTAAATTGTATATTTTTATAACTT
24783514 TTAAAGTTG-ATATTTTTTATAACTT
1 TTAAA-TTGTATA-TTTTTATAACTT
24783539 TTAAAT
1 TTAAAT
24783545 GGTTAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 8 0.30
24 12 0.44
25 7 0.26
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (24 bp):
TTAAATTGTATATTTTTATAACTT
Found at i:24783561 original size:30 final size:30
Alignment explanation
Indices: 24783525--24783589 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
24783515 TAAAGTTGAT
24783525 ATTTTTTATAACTTTTAAATGGTTAAA-T-TA
1 ATTTTTT-TAACTTTTAAA-GGTTAAAGTGTA
* *
24783555 ATTTTTTTTATTTTTAAAGGTTAAAGTGTA
1 ATTTTTTTAACTTTTAAAGGTTAAAGTGTA
24783585 ATTTT
1 ATTTT
24783590 ATAATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.23
29 10 0.32
30 14 0.45
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (30 bp):
ATTTTTTTAACTTTTAAAGGTTAAAGTGTA
Found at i:24785493 original size:26 final size:27
Alignment explanation
Indices: 24785457--24785519 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
24785447 ATAAAAAATA
24785457 ACCAAAATATTAT-AATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
*
24785483 ACTAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
24785510 ACCAAAATAT
1 ACCAAAATAT
24785520 ACTAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:24785617 original size:27 final size:27
Alignment explanation
Indices: 24785579--24785630 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
24785569 GGCTAATCAC
24785579 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
*
24785606 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGTGCCAAAG
24785631 GACTAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.23, G:0.33, T:0.13
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAG
Found at i:24786535 original size:30 final size:31
Alignment explanation
Indices: 24786496--24786555 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
24786486 GGAGGTGAGA
*
24786496 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
*
24786527 TGGG-AGGGAGTAAAAATTTTAGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
24786556 TAAAAGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:24786787 original size:9 final size:9
Alignment explanation
Indices: 24786769--24786805 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
24786759 TATAGTTTGA
24786769 TATTCGAAT
1 TATTCGAAT
*
24786778 TATTCAAAT
1 TATTCGAAT
*
24786787 TATTCGAGT
1 TATTCGAAT
24786796 TATTCGAAT
1 TATTCGAAT
24786805 T
1 T
24786806 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:24786850 original size:58 final size:59
Alignment explanation
Indices: 24786788--24786900 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 59
24786778 TATTCAAATT
24786788 ATTCGAGTT-ATTCGAAT-TCGAA-AACTCAACTCGATTCGAACTCGAAATTCGAAAAAAA
1 ATTCGAGTTGATTCGAATATCGAATAACTCAACTCG-TT-GAACTCGAAATTCGAAAAAAA
* *
24786846 ATTCGAGTTGATTCGAATAACTCGAATAACTCAATTCGTTTAACTCGAAATTCGA
1 ATTCGAGTTGATTCGAAT-A-TCGAATAACTCAACTCGTTGAACTCGAAATTCGA
24786901 TTTTTTTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
58 9 0.19
59 8 0.17
61 14 0.29
62 7 0.15
63 10 0.21
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (59 bp):
ATTCGAGTTGATTCGAATATCGAATAACTCAACTCGTTGAACTCGAAATTCGAAAAAAA
Found at i:24787660 original size:18 final size:18
Alignment explanation
Indices: 24787637--24787700 Score: 85
Period size: 18 Copynumber: 3.5 Consensus size: 18
24787627 TAAAATAGAG
24787637 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
* *
24787655 TTATTAAATTCA-AATAGAG
1 TTATTAAA-TGAGAATAG-T
24787674 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
24787692 TTATTAAAT
1 TTATTAAAT
24787701 TAAAATAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 24 0.62
19 15 0.38
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (18 bp):
TTATTAAATGAGAATAGT
Found at i:24787664 original size:37 final size:37
Alignment explanation
Indices: 24787621--24787716 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
24787611 TTTAATTTTT
24787621 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
*
24787658 TTAAATTCAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
24787695 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
24787717 CTTAATTAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.39
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:24787707 original size:18 final size:19
Alignment explanation
Indices: 24787621--24787716 Score: 115
Period size: 19 Copynumber: 5.2 Consensus size: 19
24787611 TTTAATTTTT
24787621 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
24787640 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
*
24787658 TTAAATTCAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
24787677 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
24787695 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
24787714 TTA
1 TTA
24787717 CTTAATTAGA
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
18 29 0.48
19 32 0.52
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:24788065 original size:86 final size:86
Alignment explanation
Indices: 24787911--24788092 Score: 256
Period size: 86 Copynumber: 2.1 Consensus size: 86
24787901 TTTCTTTTTC
* * * * * *
24787911 TTTTTTTTTTAAGTTTGAGGGTCTTTTTGATTCATTTTGAAAGTTCAAGTATCCAATTGAGTGCA
1 TTTTTTTTTAAAGTTTGAAGGACTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCA
***
24787976 AAAAAAAAAGTGGGGGCTTAA
66 AAAAAAAAAGCAAGGGCTTAA
* *
24787997 TTTTTTTTTAAAGTTTGAAGGACTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGTGTGTA
1 TTTTTTTTTAAAGTTTGAAGGACTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCA
24788062 AAAAAAAAAGCAAGGGCTTAA
66 AAAAAAAAAGCAAGGGCTTAA
24788083 TTATTTTTTT
1 TT-TTTTTTT
24788093 TGAAGAAGTT
Statistics
Matches: 84, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 77 0.92
87 7 0.08
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (86 bp):
TTTTTTTTTAAAGTTTGAAGGACTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCA
AAAAAAAAAGCAAGGGCTTAA
Found at i:24789571 original size:21 final size:21
Alignment explanation
Indices: 24789531--24789571 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24789521 ATAAAATGAT
* *
24789531 TTTTCCTATAAAACCCCAAAA
1 TTTTCATATAAAAACCCAAAA
*
24789552 TTTTCATATAAAAACTCAAA
1 TTTTCATATAAAAACCCAAA
24789572 TAACAAAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (21 bp):
TTTTCATATAAAAACCCAAAA
Found at i:24793503 original size:5 final size:5
Alignment explanation
Indices: 24793488--24793522 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
24793478 TACTAATCAT
*
24793488 TCTTC TTTTC TCTTC TCTTC TCTTC TCTTC TCTTC
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC
24793523 AAGAATCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
TCTTC
Found at i:24797674 original size:14 final size:14
Alignment explanation
Indices: 24797655--24797704 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
24797645 ACAATGGCAT
24797655 ATAAATAATATAAA
1 ATAAATAATATAAA
**
24797669 ATAAATAA-ACGAA
1 ATAAATAATATAAA
*
24797682 ATGAATATATATAAA
1 ATAAATA-ATATAAA
24797697 A-AAATAAT
1 ATAAATAAT
24797705 CCATGACATG
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
13 11 0.39
14 13 0.46
15 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (14 bp):
ATAAATAATATAAA
Found at i:24798394 original size:22 final size:20
Alignment explanation
Indices: 24798369--24798408 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
24798359 GACAAATTTG
24798369 AAATTTAAAATAAATTAAAAGC
1 AAATTTAAAA-AAA-TAAAAGC
24798391 AAATTTAAAAAAATAAAA
1 AAATTTAAAAAAATAAAA
24798409 TAAACTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (20 bp):
AAATTTAAAAAAATAAAAGC
Found at i:24804167 original size:24 final size:23
Alignment explanation
Indices: 24804140--24804201 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
24804130 ACAAAAAATA
*
24804140 AAATATATTCTAAAAAGAAAAGGG
1 AAATATATTCTAAAAAGAAAA-AG
*
24804164 AAATCTAATT-TAAAAAGAAAAAG
1 AAATAT-ATTCTAAAAAGAAAAAG
* *
24804187 AAACATAATCTAAAA
1 AAATATATTCTAAAA
24804202 TATGGGAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 2 0.06
23 10 0.32
24 16 0.52
25 3 0.10
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.21
Consensus pattern (23 bp):
AAATATATTCTAAAAAGAAAAAG
Found at i:24804195 original size:23 final size:23
Alignment explanation
Indices: 24804133--24804201 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 23
24804123 TAAAGTAACA
*
24804133 AAAAATAAA-ATATATTCTAAAAAG
1 AAAAAGAAACATA-ATT-TAAAAAG
*
24804157 AAAAGGGAAATC-TAATTTAAAAAG
1 AAAA-AGAAA-CATAATTTAAAAAG
*
24804181 AAAAAGAAACATAATCTAAAA
1 AAAAAGAAACATAATTTAAAA
24804202 TATGGGAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
22 1 0.03
23 13 0.35
24 15 0.41
25 6 0.16
26 2 0.05
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAAAGAAACATAATTTAAAAAG
Found at i:24804397 original size:21 final size:21
Alignment explanation
Indices: 24804371--24804422 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
24804361 TTCAATAATT
24804371 GGCTTGGTGTTGTGA-TCTCGG
1 GGCTTGGTGTTGTGACT-TCGG
* *
24804392 GGCTTGGAGTTGTGACTTTGG
1 GGCTTGGTGTTGTGACTTCGG
24804413 GGCTTGGTGT
1 GGCTTGGTGT
24804423 CGCGACTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.06, C:0.12, G:0.44, T:0.38
Consensus pattern (21 bp):
GGCTTGGTGTTGTGACTTCGG
Found at i:24804429 original size:21 final size:21
Alignment explanation
Indices: 24804390--24804431 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24804380 TTGTGATCTC
* *
24804390 GGGGCTTGGAGTTGTGACTTT
1 GGGGCTTGGAGTCGCGACTTT
*
24804411 GGGGCTTGGTGTCGCGACTTT
1 GGGGCTTGGAGTCGCGACTTT
24804432 AACGACAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.14, G:0.43, T:0.36
Consensus pattern (21 bp):
GGGGCTTGGAGTCGCGACTTT
Found at i:24806275 original size:3 final size:3
Alignment explanation
Indices: 24806267--24806304 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
24806257 AACGGTACGG
* *
24806267 TGA TGA TGA TGA TCA TGA CGA TGA TGA TGA -GA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
24806305 GAAAAGTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.34, C:0.05, G:0.32, T:0.29
Consensus pattern (3 bp):
TGA
Found at i:24810237 original size:22 final size:22
Alignment explanation
Indices: 24810198--24810239 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
24810188 AGGATTGTAT
*
24810198 TTTTAAATAATTATTTTAAAGA
1 TTTTAAATAATTAGTTTAAAGA
24810220 TTTTAAATAATCT-GTTTAAA
1 TTTTAAATAAT-TAGTTTAAA
24810240 ACATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTTAAATAATTAGTTTAAAGA
Found at i:24810461 original size:14 final size:16
Alignment explanation
Indices: 24810442--24810474 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
24810432 AATATAATTT
24810442 TAAAAT-TTTAAA-GA
1 TAAAATATTTAAAGGA
24810456 TAAAATATTTAAAGGA
1 TAAAATATTTAAAGGA
24810472 TAA
1 TAA
24810475 TATTAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 6 0.35
16 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (16 bp):
TAAAATATTTAAAGGA
Found at i:24812481 original size:23 final size:23
Alignment explanation
Indices: 24812455--24812516 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
24812445 TTTTCTTGAG
24812455 TAAATTATATAATTTTAT-GATAA
1 TAAATTATATAATTTTATCGAT-A
* *
24812478 TAAA-AATGTAATTTTATCGATA
1 TAAATTATATAATTTTATCGATA
* *
24812500 TTAATT-TAAAATTTTAT
1 TAAATTATATAATTTTAT
24812517 AAAATATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (23 bp):
TAAATTATATAATTTTATCGATA
Found at i:24821654 original size:18 final size:16
Alignment explanation
Indices: 24821631--24821664 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
24821621 AATCAGGTTT
24821631 TCATTACTTAATTAAATA
1 TCATTA-TTAA-TAAATA
24821649 TCATTATTAATAAATA
1 TCATTATTAATAAATA
24821665 AAACTCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
TCATTATTAATAAATA
Found at i:24822489 original size:42 final size:43
Alignment explanation
Indices: 24822435--24822518 Score: 125
Period size: 42 Copynumber: 1.9 Consensus size: 43
24822425 GGCAGAACAA
* *
24822435 AGCAGAGGGCAGAGAGCAGT-GTAGCAGAGGGAACCAGCAAAG
1 AGCAGAGAGCAGAGAGCAGTAGCAGCAGAGGGAACCAGCAAAG
24822477 AGCAGAGAGCAGAGAGCAGTGAAGCAGCAGAGGGAACCAGCA
1 AGCAGAGAGCAGAGAGCAGT--AGCAGCAGAGGGAACCAGCA
24822519 TCGTGTGGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 19 0.51
45 18 0.49
ACGTcount: A:0.39, C:0.18, G:0.39, T:0.04
Consensus pattern (43 bp):
AGCAGAGAGCAGAGAGCAGTAGCAGCAGAGGGAACCAGCAAAG
Found at i:24822907 original size:52 final size:52
Alignment explanation
Indices: 24822769--24822927 Score: 221
Period size: 51 Copynumber: 3.1 Consensus size: 52
24822759 ACTTTAGCTC
* * * * * *
24822769 AAACTTCAACTTTTCTCAATTTTATTTTATTTTATTTGGTAAGCACTTTTTTT
1 AAACTTTAACTCTTCTCAATTTT-TTTGAGTTTATTTTGTAAGCACGTTTTTT
*
24822822 AAACTTTAGCTCTTCTCAA-TTTTTTGAGTTTATTTTGTAAGCACGTTTTTT
1 AAACTTTAACTCTTCTCAATTTTTTTGAGTTTATTTTGTAAGCACGTTTTTT
* *
24822873 AAACTTTAACTCTTCTCAATTTTTTTGAGCTTATTTTGCAAGCACGTTTTTT
1 AAACTTTAACTCTTCTCAATTTTTTTGAGTTTATTTTGTAAGCACGTTTTTT
24822925 AAA
1 AAA
24822928 TCCATGTGGT
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
51 43 0.45
52 36 0.38
53 16 0.17
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (52 bp):
AAACTTTAACTCTTCTCAATTTTTTTGAGTTTATTTTGTAAGCACGTTTTTT
Found at i:24823182 original size:34 final size:34
Alignment explanation
Indices: 24823129--24823195 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
24823119 GTGGTTCTTA
**
24823129 AACTTTAATTCCTCTCTAACTGTGTTAATTTCTG
1 AACTTTAATTCCTCTCTAACCATGTTAATTTCTG
*
24823163 AACTTTAGTT-CTCTCCTAACCATGTTAATTTCT
1 AACTTTAATTCCTCT-CTAACCATGTTAATTTCT
24823196 AAATGTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 4 0.14
34 25 0.86
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.46
Consensus pattern (34 bp):
AACTTTAATTCCTCTCTAACCATGTTAATTTCTG
Done.