Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 182 of 189
Found at i:54100136 original size:19 final size:19
Alignment explanation
Indices: 54100081--54100138 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
54100071 TTTTTTAAAA
*
54100081 TTTTAAAATTTATTATTATT
1 TTTTAAAATTTTTTA-TATT
* *
54100101 TTAATT-TAATATTTTATATT
1 TT--TTAAAATTTTTTATATT
54100121 TTTTAAAATTTTTTATAT
1 TTTTAAAATTTTTTATAT
54100139 AGTCATCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
18 2 0.07
19 11 0.37
20 8 0.27
21 7 0.23
22 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAAAATTTTTTATATT
Found at i:54110443 original size:18 final size:18
Alignment explanation
Indices: 54110409--54110443 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54110399 CATGGTGGAA
*
54110409 TAAATTTTATATGTTTTC
1 TAAATTTTATATATTTTC
*
54110427 TAAATTTTATGTATTTT
1 TAAATTTTATATATTTT
54110444 TTATTTTTTG
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:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (18 bp):
TAAATTTTATATATTTTC
Found at i:54120669 original size:17 final size:18
Alignment explanation
Indices: 54120649--54120683 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54120639 TATGTTTCTA
54120649 AATAAATTT-TAAAATAC
1 AATAAATTTATAAAATAC
*
54120666 AATAATTTTATAAAATAC
1 AATAAATTTATAAAATAC
54120684 TCTAACATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATTTATAAAATAC
Found at i:54127968 original size:21 final size:20
Alignment explanation
Indices: 54127943--54127999 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
54127933 ATTAAAATAG
54127943 AAAAATTAT-AAATAATCATTA
1 AAAAATTATAAAATAAT-A-TA
*
54127964 AAAAATTCTAAAATAATAT-
1 AAAAATTATAAAATAATATA
*
54127983 AAAAATTACAAAA-AATA
1 AAAAATTATAAAATAATA
54128000 CACATTCAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.12
19 11 0.34
20 1 0.03
21 9 0.28
22 7 0.22
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATTATAAAATAATATA
Found at i:54127977 original size:22 final size:19
Alignment explanation
Indices: 54127943--54127987 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
54127933 ATTAAAATAG
54127943 AAAAATTATAAATAATCATTA
1 AAAAATTATAAATAAT-A-TA
*
54127964 AAAAATTCTAAAATAATATA
1 AAAAATTAT-AAATAATATA
54127984 AAAA
1 AAAA
54127988 TTACAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTATAAATAATATA
Found at i:54132148 original size:26 final size:27
Alignment explanation
Indices: 54132118--54132192 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 27
54132108 TCTTTGATCT
54132118 TATATTTTATAATTTTTATATACA-TA
1 TATATTTTATAATTTTTATATACATTA
* * * *
54132144 TATA-TATATGTATGTTTATATACATTTT
1 TATATTTTAT-AATTTTTATATACA-TTA
* *
54132172 TTTATTTTATAATTTATATAT
1 TATATTTTATAATTTTTATAT
54132193 GCCTATTTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
25 4 0.11
26 16 0.44
28 12 0.33
29 4 0.11
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (27 bp):
TATATTTTATAATTTTTATATACATTA
Found at i:54133649 original size:18 final size:17
Alignment explanation
Indices: 54133626--54133659 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54133616 TATTTCGATA
54133626 TTTTAATAAAATGTAATC
1 TTTTAA-AAAATGTAATC
*
54133644 TTTTAAACAATGTAAT
1 TTTTAAAAAATGTAAT
54133660 GTGATTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (17 bp):
TTTTAAAAAATGTAATC
Found at i:54133739 original size:11 final size:11
Alignment explanation
Indices: 54133721--54133753 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
54133711 TACACCAATG
54133721 AATAACAAACA
1 AATAACAAACA
*
54133732 ATTAACAAACA
1 AATAACAAACA
54133743 AAT-ACAAACA
1 AATAACAAACA
54133753 A
1 A
54133754 GCATAGCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12
Consensus pattern (11 bp):
AATAACAAACA
Found at i:54134421 original size:23 final size:23
Alignment explanation
Indices: 54134373--54134419 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
54134363 GCTAGAGGTT
*
54134373 TTTAGGTTAGTGGGTTAGGTTAAA
1 TTTAGGTT-TTGGGTTAGGTTAAA
*
54134397 TTTAGGTTTTGGGCTTGGGTTAA
1 TTTAGGTTTTGGG-TTAGGTTAA
54134420 TTGGGTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.19, C:0.02, G:0.34, T:0.45
Consensus pattern (23 bp):
TTTAGGTTTTGGGTTAGGTTAAA
Found at i:54146139 original size:22 final size:22
Alignment explanation
Indices: 54146114--54146162 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
54146104 TTAATTTTTT
54146114 AAATTATTTTAAAATCA-TAAAA
1 AAATTATTTTAAAAT-ATTAAAA
*
54146136 AAA-TATTTTTAAATATTAAAA
1 AAATTATTTTAAAATATTAAAA
54146157 AAATTA
1 AAATTA
54146163 AGTAAATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATTATTTTAAAATATTAAAA
Found at i:54150823 original size:18 final size:17
Alignment explanation
Indices: 54150796--54150840 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
54150786 ATATTTAGTT
*
54150796 ATTTATTTTTTTAATTTA
1 ATTTAATTTTTT-ATTTA
*
54150814 ATTTAATTTTTTATTTT
1 ATTTAATTTTTTATTTA
54150831 ATTT-ATTTTT
1 ATTTAATTTTT
54150841 CTACATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
18 11 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTAATTTTTTATTTA
Found at i:54152679 original size:43 final size:43
Alignment explanation
Indices: 54152561--54152706 Score: 107
Period size: 43 Copynumber: 3.4 Consensus size: 43
54152551 GATTACTTTG
* * * *
54152561 GTTTATCCGATGATGCACTATGCATGCCAATATAATTGGCCT-G
1 GTTTATCCGATGATGCACTATGTATGCCAGTATAATT-GCTTCA
** * * *
54152604 GTTCGTCCAATGATGCACCT-CGTGTGCCAGTATAATTGCTTCA
1 GTTTATCCGATGATGCA-CTATGTATGCCAGTATAATTGCTTCA
* * * ** *
54152647 GTTTGTCCGATGATGCACTATGTTTGCTAGTATCTTTCCTTCA
1 GTTTATCCGATGATGCACTATGTATGCCAGTATAATTGCTTCA
* *
54152690 GTATACCCGATGATGCA
1 GTTTATCCGATGATGCA
54152707 TTGCAATTCC
Statistics
Matches: 80, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
42 5 0.06
43 73 0.91
44 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.35
Consensus pattern (43 bp):
GTTTATCCGATGATGCACTATGTATGCCAGTATAATTGCTTCA
Found at i:54161171 original size:4 final size:4
Alignment explanation
Indices: 54161164--54161190 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
54161154 GTAGGAAAGA
54161164 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
54161191 AAGATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:54162785 original size:132 final size:133
Alignment explanation
Indices: 54162546--54163064 Score: 563
Period size: 132 Copynumber: 3.9 Consensus size: 133
54162536 ACTTTATTTT
* * * * **
54162546 ATGAACAAATTTTATTTGAGTTAGCTT-ATCTC-ATATTGCAAC-TCTTAATAGCTCGCTGGTTT
1 ATGAACAAATTTTATTTGAGTTAG-TTGATCTCAAGATCGCAACTTC-AAACAGCTCGCTAATTT
** ** * * *
54162608 AAGATTGCAACTGATATTGTTAAGGTTCGTTAATTTAATATTGCAACCTAAGTTCATTCGGTTTA
64 AAGATCACAACTGATATTGTTAAGGTTCACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTA
54162673 AGATC
129 AGATC
* *
54162678 AAGAACAAATTTTATTTGAGTTAGTTGATC-CAAGATCGCAACTTCAAACAGCTTGCTAATTTAA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAGATCGCAACTTCAAACAGCTCGCTAATTTAA
*
54162742 GATCGCAACTGATATTGTTAAGGTTCACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAAG
66 GATCACAACTGATATTGTTAAGGTTCACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAAG
*
54162807 ACC
131 ATC
* * * *
54162810 ATGAACAAATTTTATTTGAGTTAGTTGATCTC-AGATCGCAACTCCGAACAACTCACTAATTTAA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAGATCGCAACTTCAAACAGCTCGCTAATTTAA
* * * * * *
54162874 TATCACAGCTGATGTTGTTAAGGTT-AGCTGATTTAATATCGCAACCTAAGTTCATTCAATTTAA
66 GATCACAACTGATATTGTTAAGGTTCA-CTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAA
*
54162938 GATT
130 GATC
* * * * *
54162942 GTGAGCAAATTTTATTTGAGTTAGTTGATCT-TAGATCGCAACTCTGAATA-A-CTCACTAATTT
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAGATCGCAACT-TCAA-ACAGCTCGCTAATTT
* * * * * *
54163004 AAGATCATAGCTAATATTGTTAAGGTTCGA-TGATTTAAGATCGTAACCTAAGCTCATTCGA
64 AAGATCACAACTGATATTGTTAAGGTTC-ACTGATTTAAGATTGCAACCTAAGTTCATTCGA
54163065 AATTTTATTT
Statistics
Matches: 334, Mismatches: 43, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
131 4 0.01
132 323 0.97
133 5 0.01
134 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (133 bp):
ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAGATCGCAACTTCAAACAGCTCGCTAATTTAA
GATCACAACTGATATTGTTAAGGTTCACTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAAG
ATC
Found at i:54163023 original size:264 final size:253
Alignment explanation
Indices: 54162546--54163212 Score: 744
Period size: 264 Copynumber: 2.6 Consensus size: 253
54162536 ACTTTATTTT
* * ** * *
54162546 ATGAACAAATTTTATTTGAGTTAGCTT-ATCTCATATTGCAACTCTTAATAGCTCGCTGGTTTAA
1 ATGAACAAATTTTATTTGAGTTAG-TTGATCTCAAATCGCAACTCCAAACAGCTCGCTGATTTAA
** * * *
54162610 GATTGCAACTGATATTGTTAAGGTTCGTTAATTTAATATTGCAACCTAAGTTCATTCGGTTTAAG
65 GATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAG
* **
54162675 ATCAAGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACTTCAAACAGCTTGCTAATTT
130 ATCATGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACTTCAAACAGCTCACTAATTT
* * *
54162740 AAGATCGCAACTGATATTGTTAAGGTTC-ACTGATTTAAGATTGCAACCTAAGTTCATTCGATTT
195 AAGATCACAACTAATATTGTTAAGGTTCGA-TGATTTAAGATCGCAACCTAAG--C--TC-A-TT
54162804 AAGACC
253 -----C
* * * * * *
54162810 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAGATCGCAACTCCGAACAACTCACTAATTTAAT
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAGCTCGCTGATTTAAG
* * * * *
54162875 ATCACAGCTGATGTTGTTAAGGTTAGCTGATTTAATATCGCAACCTAAGTTCATTCAATTTAAGA
66 ATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAGA
** * ** *
54162940 TTGTGAGCAAATTTTATTTGAGTTAGTTGATCTTAGATCGCAACTCTGAATA-A-CTCACTAATT
131 TCATGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACT-TCAA-ACAGCTCACTAATT
* * *
54163003 TAAGATCATAGCTAATATTGTTAAGGTTCGATGATTTAAGATCGTAACCTAAGCTCATTC
194 TAAGATCACAACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTC
54163063 --G---AAATTTTATTTGAGTTAGTTGATCTCAAATC-CTAACTCCAAACAGCTCGCTGATTTAA
1 ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGC-AACTCCAAACAGCTCGCTGATTTAA
* * *
54163122 GATCATAACTGATATTGTTAAGTTTCGCTGATTTAAGATTGCAACCTAAGTTCATTCGATTTAAG
65 GATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAG
*
54163187 ATCATGATCAAA-TTTATTTGAGTTAG
130 ATCATGAACAAATTTTATTTGAGTTAG
54163213 CTAATTTAAT
Statistics
Matches: 346, Mismatches: 52, Indels: 27
0.81 0.12 0.06
Matches are distributed among these distances:
247 15 0.04
248 116 0.34
251 1 0.00
253 1 0.00
258 2 0.01
259 1 0.00
260 2 0.01
262 1 0.00
263 2 0.01
264 199 0.58
265 5 0.01
266 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (253 bp):
ATGAACAAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAGCTCGCTGATTTAAG
ATCACAACTGATATTGTTAAGGTTCGCTGATTTAATATTGCAACCTAAGTTCATTCGATTTAAGA
TCATGAACAAATTTTATTTGAGTTAGTTGATCCAAGATCGCAACTTCAAACAGCTCACTAATTTA
AGATCACAACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTC
Found at i:54163154 original size:116 final size:116
Alignment explanation
Indices: 54162948--54163180 Score: 315
Period size: 116 Copynumber: 2.0 Consensus size: 116
54162938 GATTGTGAGC
* * ** *
54162948 AAATTTTATTTGAGTTAGTTGATCTTAGATCGCAACTCTGAATAACTCACTAATTTAAGATCATA
1 AAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAACTCACTAATTTAAGATCATA
* *
54163013 GCTAATATTGTTAAGGTTCGATGATTTAAGATCGTAACCTAAGCTCATTCG
66 ACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTCG
* * *
54163064 AAATTTTATTTGAGTTAGTTGATCTCAAATC-CTAACTCCAAACAGCTCGCTGATTTAAGATCAT
1 AAATTTTATTTGAGTTAGTTGATCTCAAATCGC-AACTCCAAACAACTCACTAATTTAAGATCAT
* * * * *
54163128 AACTGATATTGTTAAGTTTCGCTGATTTAAGATTGCAACCTAAGTTCATTCG
65 AACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTCG
54163180 A
1 A
54163181 TTTAAGATCA
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
115 1 0.01
116 100 0.99
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (116 bp):
AAATTTTATTTGAGTTAGTTGATCTCAAATCGCAACTCCAAACAACTCACTAATTTAAGATCATA
ACTAATATTGTTAAGGTTCGATGATTTAAGATCGCAACCTAAGCTCATTCG
Found at i:54169675 original size:20 final size:21
Alignment explanation
Indices: 54169627--54169680 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
54169617 AACTTGTCGA
* * *
54169627 TTGTCTCGAGATAATGACCCC
1 TTGTCTCGAGACAAAGACCAC
54169648 TATGTCTCGAGACAAAG-CCAC
1 T-TGTCTCGAGACAAAGACCAC
54169669 TTGTCTCGAGAC
1 TTGTCTCGAGAC
54169681 CCTAAAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.38
21 5 0.17
22 13 0.45
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (21 bp):
TTGTCTCGAGACAAAGACCAC
Found at i:54171192 original size:26 final size:26
Alignment explanation
Indices: 54171163--54171214 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
54171153 GATTAAACTA
* *
54171163 AATAAATTACTTACCTTAAATTAACC
1 AATAAATTACTTACATAAAATTAACC
54171189 AATAAATTACTTACATAAAATTAACC
1 AATAAATTACTTACATAAAATTAACC
54171215 TAATGTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (26 bp):
AATAAATTACTTACATAAAATTAACC
Found at i:54172416 original size:46 final size:46
Alignment explanation
Indices: 54172341--54172581 Score: 392
Period size: 46 Copynumber: 5.2 Consensus size: 46
54172331 TACCCTGTTT
*
54172341 TGGACAGCATTTATATATCAAATTGGACAGCATTAATATGCTCAAAA
1 TGGACAGCA-TTATACATCAAATTGGACAGCATTAATATGCTCAAAA
* * *
54172388 TGGATAGCATTATACATCAAATTAGACAGCATCAATATGCTCAAAA
1 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
* *
54172434 TGGACAGCATTATACATCAAATTGGACAGCTTTAATATGCTCAAAT
1 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
* *
54172480 TGGACAGCATTATACATCAAATTGGATAGCATCAATATGCTCAAAA
1 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
*
54172526 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAT
1 TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
54172572 TGGACAGCAT
1 TGGACAGCAT
54172582 CATAACATAT
Statistics
Matches: 178, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 170 0.96
47 8 0.04
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (46 bp):
TGGACAGCATTATACATCAAATTGGACAGCATTAATATGCTCAAAA
Found at i:54172764 original size:16 final size:18
Alignment explanation
Indices: 54172729--54172766 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
54172719 TGGACATCTT
54172729 TATTATCACACAATTATA
1 TATTATCACACAATTATA
54172747 TATTATCACACAATTATA
1 TATTATCACACAATTATA
54172765 TA
1 TA
54172767 CTATATAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (18 bp):
TATTATCACACAATTATA
Found at i:54173342 original size:41 final size:40
Alignment explanation
Indices: 54173274--54173407 Score: 112
Period size: 41 Copynumber: 3.3 Consensus size: 40
54173264 AATGTTTCGT
* * * *
54173274 ACACTAATTGCCATTGCATAGCCGAAGCTATTATAATCTCAC
1 ACACTAAGTGCC-TTACATAACCGAAGCTATT-CAATCTCAC
* * *
54173316 ACACTAAGTGCCTTACATAACCGAAGCCATCTCAGTCTCGC
1 ACACTAAGTGCCTTACATAACCGAAGCTAT-TCAATCTCAC
* *
54173357 ACACTAAGTGCC--ACATATAGCCGAAGCTATTCCAA-ATCGC
1 ACACTAAGTGCCTTACATA-A-CCGAAGCTATT-CAATCTCAC
54173397 ACACTAAGTGC
1 ACACTAAGTGC
54173408 AATAAATAGC
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
39 5 0.06
40 17 0.22
41 44 0.56
42 12 0.15
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (40 bp):
ACACTAAGTGCCTTACATAACCGAAGCTATTCAATCTCAC
Found at i:54176668 original size:15 final size:15
Alignment explanation
Indices: 54176648--54176688 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54176638 AGCCTTTTTT
*
54176648 TTGTTTTTTTTTATC
1 TTGTTTTATTTTATC
54176663 TTGTTTTATTTTA--
1 TTGTTTTATTTTATC
54176676 TT-TTTTATTTTAT
1 TTGTTTTATTTTAT
54176689 TTTCGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
15 12 0.50
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.80
Consensus pattern (15 bp):
TTGTTTTATTTTATC
Found at i:54177561 original size:26 final size:24
Alignment explanation
Indices: 54177531--54177589 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
54177521 TACATCCTTG
54177531 ATATATAC-TTTATAATTTATATATAC
1 ATATATACATTT-TAA-TT-TATATAC
* *
54177557 ATATACACATTTTAATTTATGTAC
1 ATATATACATTTTAATTTATATAC
54177581 ATATATACA
1 ATATATACA
54177590 CATATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 14 0.48
25 2 0.07
26 10 0.34
27 3 0.10
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATATACATTTTAATTTATATAC
Found at i:54177590 original size:26 final size:26
Alignment explanation
Indices: 54177543--54177592 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
54177533 ATATACTTTA
*
54177543 TAATTTATATATACATATACACATTT
1 TAATTTATATACACATATACACATTT
* *
54177569 TAATTTATGTACATATATACACAT
1 TAATTTATATACACATATACACAT
54177593 ATTTTCATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATTTATATACACATATACACATTT
Found at i:54177694 original size:22 final size:23
Alignment explanation
Indices: 54177655--54177722 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 23
54177645 CTTAAAATCC
* * *
54177655 ATATTTTTCTTATGTATATATTT
1 ATATATTTCATATATATATATTT
*
54177678 -TATATTTCATATATATATTTTT
1 ATATATTTCATATATATATATTT
54177700 ATATATTCTACAATATATATATA
1 ATATATT-T-C-ATATATATATA
54177723 CATAATAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 18 0.50
23 6 0.17
24 1 0.03
25 1 0.03
26 10 0.28
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.57
Consensus pattern (23 bp):
ATATATTTCATATATATATATTT
Found at i:54182810 original size:20 final size:19
Alignment explanation
Indices: 54182771--54182831 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 19
54182761 AATAATGTTC
54182771 AAAAAATAAGAAGAAAAAGAAGG
1 AAAAAA-AA-AAG-AAAAGAA-G
54182794 AAAAAAAAAAGAAAAGAAG
1 AAAAAAAAAAGAAAAGAAG
54182813 AAAAAGAAAATA-AAAAGAA
1 AAAAA-AAAA-AGAAAAGAA
54182832 AAAGGAGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.17
20 18 0.50
21 4 0.11
22 2 0.06
23 6 0.17
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAGAAG
Found at i:54182821 original size:25 final size:26
Alignment explanation
Indices: 54182771--54182833 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
54182761 AATAATGTTC
*
54182771 AAAAAATAAGAAGAAAAAGAAGGAAAA
1 AAAAAAGAA-AAGAAAAAGAAGGAAAA
54182798 AAAAAAGAAAAGAAGAAA-AA-GAAAA
1 AAAAAAGAAAAGAA-AAAGAAGGAAAA
*
54182823 TAAAAAGAAAA
1 AAAAAAGAAAA
54182834 AGGAGAGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 15 0.45
26 7 0.21
27 11 0.33
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (26 bp):
AAAAAAGAAAAGAAAAAGAAGGAAAA
Found at i:54183292 original size:97 final size:97
Alignment explanation
Indices: 54183126--54183307 Score: 310
Period size: 97 Copynumber: 1.9 Consensus size: 97
54183116 GTATCTTAGC
* * *
54183126 AAAATTTTCTATCTTGATTAATTTATTCATTTCGAGCTGTGCTCTCAATAAAATTTCATCTTATC
1 AAAATTTGCTATCTTCATTAATTTATTCATTTCAAGCTGTGCTCTCAATAAAATTTCATCTTATC
54183191 CATTGTGATAATCTTTTTCATCTTATTCTAGA
66 CATTGTGATAATCTTTTTCATCTTATTCTAGA
* * *
54183223 AAAATTTGCTATCTTCATTAATTTATTCATTTCAAGCTTTGTTCTCAATAAAATTTCATCTTGTC
1 AAAATTTGCTATCTTCATTAATTTATTCATTTCAAGCTGTGCTCTCAATAAAATTTCATCTTATC
54183288 CATTGTGATAATCTTTTTCA
66 CATTGTGATAATCTTTTTCA
54183308 AGCATTTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 79 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (97 bp):
AAAATTTGCTATCTTCATTAATTTATTCATTTCAAGCTGTGCTCTCAATAAAATTTCATCTTATC
CATTGTGATAATCTTTTTCATCTTATTCTAGA
Found at i:54184199 original size:44 final size:44
Alignment explanation
Indices: 54184111--54184201 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 44
54184101 CAGATCAGCG
* * * *
54184111 AAGTCACAAACCTTGTCTCTCTGAAGTTGCAGTGGAGTAGGTTA
1 AAGTCACAAACCTTATCCCTCTGAAGTTGCAGTGGAGCAAGTTA
* ** *
54184155 AAGTCACTAACCTTATCCCTCTGAAGTTGTGGTGGGGCAAGTTA
1 AAGTCACAAACCTTATCCCTCTGAAGTTGCAGTGGAGCAAGTTA
54184199 AAG
1 AAG
54184202 ATATGAGTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (44 bp):
AAGTCACAAACCTTATCCCTCTGAAGTTGCAGTGGAGCAAGTTA
Found at i:54184897 original size:45 final size:46
Alignment explanation
Indices: 54184777--54184929 Score: 127
Period size: 45 Copynumber: 3.4 Consensus size: 46
54184767 ATGACAAGTT
* * * *
54184777 TTATCTCTCTGAAGTTGTAGTGGAGCAGATTG-ATCATATCAAACC
1 TTATCTCACTGAAGTTGCAGTGGAGCAGACTGAATCATAGCAAACC
* ** * * *
54184822 TTATCTCACTGAGGTTGCAGTAAAGTAGACTGAAT-ATAGCGAGCC
1 TTATCTCACTGAAGTTGCAGTGGAGCAGACTGAATCATAGCAAACC
* * * *
54184867 TTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAAC-TA-CTAATCC
1 TTATCTCACTGAAGTTGCAGTGGAGCAGACTGAATCATAGC-AAACC
*
54184912 -TATCTCCCTGAAGTTGCA
1 TTATCTCACTGAAGTTGCA
54184930 ACAGAGCGAA
Statistics
Matches: 85, Mismatches: 20, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
44 18 0.21
45 65 0.76
46 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (46 bp):
TTATCTCACTGAAGTTGCAGTGGAGCAGACTGAATCATAGCAAACC
Found at i:54185802 original size:19 final size:19
Alignment explanation
Indices: 54185779--54185822 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54185769 GGTTAAGCCT
*
54185779 TTTTTTTGTTTTTTATCTTA
1 TTTTTTT-TTATTTATCTTA
* *
54185799 TTTTTTTTTATTTTTTTTA
1 TTTTTTTTTATTTATCTTA
54185818 TTTTT
1 TTTTT
54185823 GATTTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.86
Consensus pattern (19 bp):
TTTTTTTTTATTTATCTTA
Found at i:54185807 original size:15 final size:13
Alignment explanation
Indices: 54185780--54185831 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 13
54185770 GTTAAGCCTT
54185780 TTTTTTGTTTTTTA
1 TTTTTT-TTTTTTA
54185794 TCTTATTTTTTTTTA
1 T-TT-TTTTTTTTTA
54185809 TTTTTTTTATTTTTGA
1 -TTTTTTT-TTTTT-A
54185825 TTTTTTT
1 TTTTTTT
54185832 ATACTAGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.15
15 23 0.70
16 5 0.15
ACGTcount: A:0.10, C:0.02, G:0.04, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTTTA
Found at i:54186570 original size:3 final size:3
Alignment explanation
Indices: 54186556--54186598 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
54186546 TTTTGCTATC
*
54186556 ATT ATC ATT ATT ATT ATT ATT ATT GA-T ATT ATT ATT ACTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT A-TT ATT
54186599 TATTTATACC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 1 0.03
3 30 0.86
4 4 0.11
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:54186698 original size:26 final size:24
Alignment explanation
Indices: 54186669--54186727 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
54186659 CACTTTTTTT
54186669 ATATATAC-TTTATAATTTATATATAC
1 ATATATACATTT-TAA-TT-TATATAC
* *
54186695 ATATACACATTTTAATTTATGTAC
1 ATATATACATTTTAATTTATATAC
54186719 ATATATACA
1 ATATATACA
54186728 CTTATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 14 0.48
25 2 0.07
26 10 0.34
27 3 0.10
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATATACATTTTAATTTATATAC
Found at i:54186728 original size:26 final size:26
Alignment explanation
Indices: 54186668--54186730 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
54186658 CCACTTTTTT
* *
54186668 TATATATACTTTATAATTTATATATA
1 TATATACACTTTATAATTTATATACA
* *
54186694 CATATACACATTT-TAATTTATGTACA
1 TATATACAC-TTTATAATTTATATACA
54186720 TATATACACTT
1 TATATACACTT
54186731 ATTTTCATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.06
26 26 0.84
27 3 0.10
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.48
Consensus pattern (26 bp):
TATATACACTTTATAATTTATATACA
Found at i:54186832 original size:22 final size:23
Alignment explanation
Indices: 54186798--54186861 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
54186788 AATCCATATT
* *
54186798 TTTCTTATGTATATA-TTTTATA
1 TTTCATATATATATATTTTTATA
54186820 TTTCATATATATATATTTTTTATA
1 TTTCATATATATATA-TTTTTATA
54186844 TTCTACAATATATATATA
1 TT-T-C-ATATATATATA
54186862 CATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 13 0.37
24 9 0.26
25 1 0.03
26 1 0.03
27 11 0.31
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTCATATATATATATTTTTATA
Found at i:54190064 original size:131 final size:131
Alignment explanation
Indices: 54189904--54190418 Score: 735
Period size: 131 Copynumber: 4.0 Consensus size: 131
54189894 AAGACTCGTC
* * * *
54189904 GCTTAAATATGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACT
1 GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATT
* * * *
54189969 ACTTAGGGAGATAAGATCTGTAATCTTCAACCTGTCCCACTTCCGACCAGGGAGATAGGACTAGT
66 GCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGT
54190034 G
131 G
*
54190035 GCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATT
1 GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATT
* * * * *
54190100 GCTTAGGGAGATAAGATCTGTAGTCTCCAACCTATTCTACTGCTG-CTTA-GGA-A-A--A-TAG
66 GCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGAC-CAGGGAGATAGGACTAG
54190158 -G
130 TG
* * * *
54190159 ACTT--GTCTGTTTCCCTACTCCTGGGGAAGATGAGATTCACCATCTTCGATCTGCTCCACTATT
1 GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATT
* *
54190222 GCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACAAGGGAAATAGGACTAGT
66 GCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGT
54190287 G
131 G
* *
54190288 GCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATT
1 GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATT
* *
54190353 GCTTAGGGTGATAAGATCTGTAATCTTCAACCTATCCCACTACTGACCAGGGAGATAGGACTAGT
66 GCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGT
54190418 G
131 G
54190419 TCTTTGATCG
Statistics
Matches: 339, Mismatches: 34, Indels: 22
0.86 0.09 0.06
Matches are distributed among these distances:
122 97 0.29
123 4 0.01
124 5 0.01
125 4 0.01
126 1 0.00
127 1 0.00
128 4 0.01
129 5 0.01
130 4 0.01
131 214 0.63
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (131 bp):
GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATT
GCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGT
G
Found at i:54190368 original size:253 final size:253
Alignment explanation
Indices: 54189916--54190387 Score: 800
Period size: 253 Copynumber: 1.9 Consensus size: 253
54189906 TTAAATATGC
* *
54189916 TTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGAT
1 TTCCCTACTCCTGGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGAGAT
* * * *
54189981 AAGATCTGTAATCTTCAACCTGTCCCACTTCCGACCAGGGAGATAGGACTAGTGGCTTAAATCTG
66 AAGATCTGTAATCTTCAACCTATCCCACTGCCGACAAGGGAAATAGGACTAGTGGCTTAAATCTG
54190046 TTTCCCTACTCCTAGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGA
131 TTTCCCTACTCCTAGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGA
*
54190111 TAAGATCTGTAGTCTCCAACCTATTCTACTGCTGCTTAGGAAAATAGGACTTGTCTGT
196 TAAGATCTGTAATCTCCAACCTATTCTACTGCTGCTTAGGAAAATAGGACTTGTCTGT
* * *
54190169 TTCCCTACTCCTGGGGAAGATGAGATTCACCATCTTCGATCTGCTCCACTATTGCTTAGGGAGAT
1 TTCCCTACTCCTGGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGAGAT
*
54190234 AAGATCTGTAATCTTCAACCTATCCCACTGCTGACAAGGGAAATAGGACTAGTGGCTTAAATCTG
66 AAGATCTGTAATCTTCAACCTATCCCACTGCCGACAAGGGAAATAGGACTAGTGGCTTAAATCTG
* * * *
54190299 TTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGTGA
131 TTTCCCTACTCCTAGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGA
*
54190364 TAAGATCTGTAATCTTCAACCTAT
196 TAAGATCTGTAATCTCCAACCTAT
54190388 CCCACTACTG
Statistics
Matches: 203, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
253 203 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (253 bp):
TTCCCTACTCCTGGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGAGAT
AAGATCTGTAATCTTCAACCTATCCCACTGCCGACAAGGGAAATAGGACTAGTGGCTTAAATCTG
TTTCCCTACTCCTAGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGA
TAAGATCTGTAATCTCCAACCTATTCTACTGCTGCTTAGGAAAATAGGACTTGTCTGT
Found at i:54202620 original size:3 final size:3
Alignment explanation
Indices: 54202607--54202637 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
54202597 TGATTTAAAC
54202607 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54202638 ATATGAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:54203358 original size:16 final size:15
Alignment explanation
Indices: 54203325--54203357 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
54203315 TTCGAAGTAC
54203325 AAATTACAAGTAAAA
1 AAATTACAAGTAAAA
54203340 AAATTACAAGTAAAA
1 AAATTACAAGTAAAA
54203355 AAA
1 AAA
54203358 AACATAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATTACAAGTAAAA
Found at i:54205824 original size:31 final size:29
Alignment explanation
Indices: 54205789--54205858 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
54205779 ACTATCAACA
* *
54205789 TAGTCACTTTTATTTGACTCATGTTACATTT
1 TAGTCACTTATATTTGA--AATGTTACATTT
* *
54205820 TAGTCACTCATATTTGAAATGTTACGTTT
1 TAGTCACTTATATTTGAAATGTTACATTT
*
54205849 TGGTCACTTA
1 TAGTCACTTA
54205859 CGTTATCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 18 0.55
31 15 0.45
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATATTTGAAATGTTACATTT
Found at i:54213010 original size:45 final size:45
Alignment explanation
Indices: 54212946--54213032 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
54212936 AACAGATACT
* *
54212946 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATATC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATATC
*
54212991 CGGTGGAATCAGCATATAGCAACCACCTTACTAATCAATGAT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGAT
54213033 GTTCAGTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATATC
Found at i:54213139 original size:51 final size:51
Alignment explanation
Indices: 54213041--54213172 Score: 149
Period size: 51 Copynumber: 2.6 Consensus size: 51
54213031 ATGTTCAGTT
* * * *
54213041 CACATAGTAGCCTGCACATAGTACTACGCATGTGACCATTACCATCTGATA
1 CACATAATAGCCTGCACATAGTACTACACACGTGACCATAACCATCTGATA
* * * *
54213092 CACGTAATAGCCTGCACATAGTACTACACACGTGATCGA-AACTATCTGGTA
1 CACATAATAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCTGATA
* * *
54213143 CGCATAGTAGCCTACACATAGTACTACACA
1 CACATAATAGCCTGCACATAGTACTACACA
54213173 TGCGACCTGT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 66 0.97
52 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.23
Consensus pattern (51 bp):
CACATAATAGCCTGCACATAGTACTACACACGTGACCATAACCATCTGATA
Found at i:54214837 original size:48 final size:48
Alignment explanation
Indices: 54214763--54214907 Score: 166
Period size: 48 Copynumber: 3.0 Consensus size: 48
54214753 CAGATTTTTC
* * * * * *
54214763 GGTGGCCTACACACAGTCTGTACCACCTTTGTGTAATAACAGACTCTCT
1 GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATAATAACAGAATAT-T
* * **
54214812 -GTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGAATATT
1 GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATAATAACAGAATATT
**
54214859 GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATCTTAACAGAATATT
1 GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATAATAACAGAATATT
54214907 G
1 G
54214908 ATATGCATAG
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
47 1 0.01
48 82 0.99
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (48 bp):
GGTGGCCTGCACACAGTCTGTGCCACCCTTGTATAATAACAGAATATT
Found at i:54218809 original size:13 final size:13
Alignment explanation
Indices: 54218791--54218822 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54218781 TTTCCAGCAA
54218791 TTATGAATTTATT
1 TTATGAATTTATT
54218804 TTATGAATTTATT
1 TTATGAATTTATT
*
54218817 TGATGA
1 TTATGA
54218823 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:54219030 original size:50 final size:50
Alignment explanation
Indices: 54218917--54219158 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 50
54218907 ATTTGGGTAA
* * * *
54218917 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
54218973 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
54219023 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* *
54219073 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
** *
54219123 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATATAAGACCATGTCTGGGACATGGC
54219159 TTTGGCATGT
Statistics
Matches: 164, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 90 0.55
51 29 0.18
52 1 0.01
53 3 0.02
55 2 0.01
56 38 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:54219105 original size:100 final size:103
Alignment explanation
Indices: 54218917--54219166 Score: 373
Period size: 100 Copynumber: 2.4 Consensus size: 103
54218907 ATTTGGGTAA
54218917 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
*
54218982 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
54219023 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
54219085 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
54219123 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
54219167 GTTATTATCA
Statistics
Matches: 134, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 52 0.39
101 39 0.29
105 2 0.01
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:54222718 original size:57 final size:59
Alignment explanation
Indices: 54222605--54222719 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 59
54222595 ATTGACGTTA
*
54222605 AAAAGGATCTAGCCTGGACGGGTGATCCTATCTTGATATAGCCCTCCCGAAGAATATGTGTGG
1 AAAAGGATCTAGCCTGGACGGGTG---C-ATCTTGATATAACCCTCCCGAAGAATATGTGTGG
*
54222668 AAAA-GATCTAGCCTGGACGGGTG-ATCTTGATATAACCCTCCCGAATAATATG
1 AAAAGGATCTAGCCTGGACGGGTGCATCTTGATATAACCCTCCCGAAGAATATG
54222720 CGAAAAATAG
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
57 27 0.54
62 19 0.38
63 4 0.08
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (59 bp):
AAAAGGATCTAGCCTGGACGGGTGCATCTTGATATAACCCTCCCGAAGAATATGTGTGG
Found at i:54222743 original size:57 final size:57
Alignment explanation
Indices: 54222634--54222746 Score: 138
Period size: 57 Copynumber: 2.0 Consensus size: 57
54222624 GGGTGATCCT
* * ** * *
54222634 ATCTTGATATAGCCCTCCCGAAGAATATGTGTGGAAAAGATCTAGCCTGGACGGGTG
1 ATCTTGATATAACCCTCCCGAAGAATATGCGTAAAAAAGATCTAACCCGGACGGGTG
* *
54222691 ATCTTGATATAACCCTCCCGAATAATATGCG-AAAAATAGATTTAACCCGGACGGGT
1 ATCTTGATATAACCCTCCCGAAGAATATGCGTAAAAA-AGATCTAACCCGGACGGGT
54222747 AATCCGAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
56 3 0.06
57 44 0.94
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (57 bp):
ATCTTGATATAACCCTCCCGAAGAATATGCGTAAAAAAGATCTAACCCGGACGGGTG
Found at i:54222982 original size:67 final size:67
Alignment explanation
Indices: 54222874--54223004 Score: 244
Period size: 67 Copynumber: 2.0 Consensus size: 67
54222864 TTTATATTTC
54222874 AGGGGATTTAGCCTGGACTAGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
1 AGGGGATTTAGCCTGGACTAGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
54222939 GT
66 GT
* *
54222941 AGGGGATTTAGCCTGGACTGGTAATCCTGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 AGGGGATTTAGCCTGGACTAGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
54223005 GAATTGGAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.28
Consensus pattern (67 bp):
AGGGGATTTAGCCTGGACTAGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
GT
Found at i:54231615 original size:34 final size:35
Alignment explanation
Indices: 54231547--54231615 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
54231537 CTCATATGCA
*
54231547 TGTTGTCGGATATAGGTGTTGGATACTTAGGACAG
1 TGTTGTCGGATATAGGTGTTGGATACTTACGACAG
*
54231582 TGTTGTTGGATATAGGTGTT-GATACTTACGACAG
1 TGTTGTCGGATATAGGTGTTGGATACTTACGACAG
54231616 ATTTTTATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 13 0.41
35 19 0.59
ACGTcount: A:0.23, C:0.09, G:0.32, T:0.36
Consensus pattern (35 bp):
TGTTGTCGGATATAGGTGTTGGATACTTACGACAG
Found at i:54243923 original size:25 final size:25
Alignment explanation
Indices: 54243870--54243920 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
54243860 TAAAAATAGT
* *
54243870 ATATGTTTTAAATGATATTGAATGA
1 ATATGTTTTAAATGATATTAAAAGA
*
54243895 ATATGTTTTAAATTATTATTAAAAGA
1 ATATGTTTTAAATGA-TATTAAAAGA
54243921 TATCTTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (25 bp):
ATATGTTTTAAATGATATTAAAAGA
Found at i:54247959 original size:20 final size:21
Alignment explanation
Indices: 54247934--54247972 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
54247924 TGATAAGAGA
*
54247934 TTATTAATATTA-TAATTACT
1 TTATTAATAGTAGTAATTACT
54247954 TTATTAATAGTAGTAATTA
1 TTATTAATAGTAGTAATTA
54247973 AAACAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (21 bp):
TTATTAATAGTAGTAATTACT
Found at i:54253297 original size:10 final size:10
Alignment explanation
Indices: 54253282--54253310 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54253272 TAGGTAAATA
54253282 ATATATATAC
1 ATATATATAC
54253292 ATATATATAC
1 ATATATATAC
54253302 ATATATATA
1 ATATATATA
54253311 ACTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATAC
Found at i:54254945 original size:44 final size:44
Alignment explanation
Indices: 54254897--54255016 Score: 160
Period size: 40 Copynumber: 2.8 Consensus size: 44
54254887 ATCTTCGACT
* * *
54254897 TGCTCCACTATTGCTTAGGGAGATAAGATCTGGTTTCTTTCG-TC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTATGT-GATC
*
54254941 TGCTCCACTACTGCTTAGGGAGATAAGA-C---TTGATGTGATC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTATGTGATC
54254981 TGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTT
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTT
54255017 TCTTCACTCT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
39 1 0.02
40 34 0.52
41 1 0.02
43 1 0.02
44 29 0.44
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (44 bp):
TGCTCCACTACTGCTTAGGGAGATAAGATCTGGTTTATGTGATC
Found at i:54256093 original size:134 final size:134
Alignment explanation
Indices: 54255017--54256072 Score: 1864
Period size: 134 Copynumber: 7.9 Consensus size: 134
54255007 GATCTGGTTT
* * * * *
54255017 TCTTCACTCTATTCTACTGCCAAACACAGGGAGATAGAGTTATCGGCTTCAATGCACTCCACTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
54255082 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
66 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
54255147 GCAA
131 GCAA
* *
54255151 TCTTTAATTTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
* * *
54255216 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTTGCTGCCAAATACAGAAAGACAAGATCT
66 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
54255281 GCAA
131 GCAA
* * *
54255285 TCTTCAATCTATTCCACTGCCAAATACAGGAAGATAGAATTATCGGCTTCAATGTACTCCACTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
* *
54255350 AGTCAGGGAGGTAAAATCCGCCATCTTCGACCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
66 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
54255415 GCAA
131 GCAA
* *
54255419 TCTTCAATCTATTCCACTGCC-AA-CCAGGGAGATAGAGTTATTGGCTTCAATGTACTCCTCTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
* *
54255482 AGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTACGCTGCCAAATACAGGAAGGCAAGATCT
66 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
54255547 GCAA
131 GCAA
*
54255551 TCTTTAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
54255616 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
66 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
54255681 GCAA
131 GCAA
* *
54255685 TCTTCAATCTATCCCACTGCCAAATACAGGGAGATAAAGTTATCGGCTTCAATGTACTCCTCTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
*
54255750 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAAATCT
66 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
54255815 GCAA
131 GCAA
54255819 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
54255884 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
66 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
54255949 GCAA
131 GCAA
* *
54255953 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTAT
1 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
*
54256018 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATATAGGAA
66 AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAA
54256073 AGAAAGGTCT
Statistics
Matches: 876, Mismatches: 44, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
132 120 0.14
133 4 0.00
134 752 0.86
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (134 bp):
TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCTCTGT
AGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCT
GCAA
Found at i:54256187 original size:86 final size:86
Alignment explanation
Indices: 54256041--54256390 Score: 511
Period size: 86 Copynumber: 4.1 Consensus size: 86
54256031 AAATCTGCCA
* ** * * *
54256041 TCTTCGATCTGCTTCGCTGCCAAATATAGGAAAGAAAGGTCTGATATCTTCAACCAGCTCTACTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTA
54256106 CAAACGAGAGAGGCAAGGTTTG
65 CAAACGAGAGAGGCAAGGTTTG
* ** * *
54256128 TCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATCTTCAAACAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
*
54256193 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
*
54256214 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
*
54256279 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
* * *
54256300 TCTTCGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGATAACTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
* * *
54256365 GACCGAGAGAGGCAAGGTTTA
66 AAACGAGAGAGGCAAGGTTTG
54256386 TCTTC
1 TCTTC
54256391 AATTTTTACT
Statistics
Matches: 239, Mismatches: 24, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
86 220 0.92
87 19 0.08
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
AAACGAGAGAGGCAAGGTTTG
Found at i:54256250 original size:42 final size:42
Alignment explanation
Indices: 54256203--54256336 Score: 105
Period size: 42 Copynumber: 3.1 Consensus size: 42
54256193 AAACGAGAGT
*
54256203 GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
1 GGCAAGGTTTGTCTTCGATCTGCTTCACTGTCAATGCAGGAA
* * * * * * * *
54256245 GGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGAGT
1 GGCAAGGT-T--TGTCTTCGATCTGCTTC-ACTGTCAATGCAG-GA-A
54256289 GGCAAGGTTTGTCTTCGATCTGCTTCACTGTCAATGCAGGAA
1 GGCAAGGTTTGTCTTCGATCTGCTTCACTGTCAATGCAGGAA
54256331 GGCAAG
1 GGCAAG
54256337 ATCTGATAAC
Statistics
Matches: 65, Mismatches: 17, Indels: 20
0.64 0.17 0.20
Matches are distributed among these distances:
41 13 0.20
42 19 0.29
43 8 0.12
44 13 0.20
45 12 0.18
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (42 bp):
GGCAAGGTTTGTCTTCGATCTGCTTCACTGTCAATGCAGGAA
Found at i:54260522 original size:19 final size:20
Alignment explanation
Indices: 54260498--54260541 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
54260488 CGTGAAAGTC
* *
54260498 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
54260517 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
54260537 -AATGC
1 TAATGC
54260542 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:54262896 original size:10 final size:10
Alignment explanation
Indices: 54262881--54262909 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
54262871 TAGGTAAATA
54262881 ATATATATAC
1 ATATATATAC
54262891 ATATATATAC
1 ATATATATAC
54262901 ATATATATA
1 ATATATATA
54262910 ACTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATAC
Found at i:54266148 original size:19 final size:18
Alignment explanation
Indices: 54266106--54266149 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
54266096 TTACTAACAT
* *
54266106 TAATTATACAAATTAAAT
1 TAATTATAAAAATTAAAA
54266124 TAAATTATTAAAAATTAAAA
1 T-AATTA-TAAAAATTAAAA
54266144 TAATTA
1 TAATTA
54266150 AATGTGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 10 0.45
20 11 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATTATAAAAATTAAAA
Found at i:54266980 original size:2 final size:2
Alignment explanation
Indices: 54266973--54266998 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54266963 TTCCATCATA
54266973 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54266999 GATTTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54289688 original size:13 final size:14
Alignment explanation
Indices: 54289657--54289694 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
54289647 TAATAATGTT
54289657 AAGAAAGAGATACA
1 AAGAAAGAGATACA
54289671 AAGAATAGA-ATA-A
1 AAGAA-AGAGATACA
54289684 AAGAAAGAGAT
1 AAGAAAGAGAT
54289695 GCTCATGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 8 0.36
14 8 0.36
15 3 0.14
ACGTcount: A:0.66, C:0.03, G:0.21, T:0.11
Consensus pattern (14 bp):
AAGAAAGAGATACA
Found at i:54293647 original size:17 final size:18
Alignment explanation
Indices: 54293609--54293647 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
54293599 ATTAAATTAA
54293609 AATTATCTCAATTAAAAT
1 AATTATCTCAATTAAAAT
*
54293627 -ATTATTTCAA-TAAAAT
1 AATTATCTCAATTAAAAT
54293643 AATTA
1 AATTA
54293648 AATTTCACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTATCTCAATTAAAAT
Found at i:54300055 original size:29 final size:29
Alignment explanation
Indices: 54300022--54300115 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
54300012 ATAGTCCAAA
54300022 TACCACATTGGAA-ATTTTCAAAGTACAAG
1 TACCACATT-GAACATTTTCAAAGTACAAG
* *
54300051 TACCACATTGAACATTTTCAAAGTATAAA
1 TACCACATTGAACATTTTCAAAGTACAAG
* * *
54300080 TATCACATTGAACATTTTATAAAAATACAAG
1 TACCACATTGAACA-TTT-TCAAAGTACAAG
54300111 TACCA
1 TACCA
54300116 AATGTGATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
28 3 0.06
29 36 0.67
30 3 0.06
31 12 0.22
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.30
Consensus pattern (29 bp):
TACCACATTGAACATTTTCAAAGTACAAG
Found at i:54300525 original size:22 final size:22
Alignment explanation
Indices: 54300468--54300529 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
54300458 CCCAAAACCC
54300468 AACTAACCTAGCCCAATACCCTAA
1 AACT-ACCTAGCCCAATA-CCTAA
* *
54300492 ACCAACCTAGCCCAAT-CCTAA
1 AACTACCTAGCCCAATACCTAA
54300513 AACTACCTGAGCCCAAT
1 AACTACCT-AGCCCAAT
54300530 TTACAAACCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 11 0.33
22 8 0.24
23 12 0.36
24 2 0.06
ACGTcount: A:0.39, C:0.39, G:0.06, T:0.16
Consensus pattern (22 bp):
AACTACCTAGCCCAATACCTAA
Found at i:54301762 original size:3 final size:3
Alignment explanation
Indices: 54301754--54301823 Score: 67
Period size: 3 Copynumber: 23.7 Consensus size: 3
54301744 ATTCCTTAGT
* *
54301754 TTA TTA TTA TTA -TA TCA TT- TT- TTA TGTA TTTA TCTA -CA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA T-TA TTA TTA TTA
54301798 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
54301824 GAACACATCA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
2 7 0.12
3 43 0.75
4 6 0.11
5 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:54313524 original size:15 final size:15
Alignment explanation
Indices: 54313506--54313541 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54313496 GGCATCTTAA
*
54313506 AAAAAAAGAAATAAC
1 AAAAAAAGAAAAAAC
*
54313521 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAC
54313536 AAAAAA
1 AAAAAA
54313542 GGGGGATCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.86, C:0.03, G:0.08, T:0.03
Consensus pattern (15 bp):
AAAAAAAGAAAAAAC
Found at i:54314558 original size:71 final size:70
Alignment explanation
Indices: 54314393--54314777 Score: 555
Period size: 69 Copynumber: 5.5 Consensus size: 70
54314383 CTTTCCAAGG
* ** * ** *
54314393 AAAATCAACTCATATTGTGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT-
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
54314456 T-TTTT
65 TGTTTT
*
54314461 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
54314526 TGTTTT
65 TGTTTT
*
54314532 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGTCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
54314597 TGTTTT
65 TGTTTT
**
54314603 -AAATTGACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
*
54314667 GATTTC
66 G-TTTT
54314673 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
54314738 GTTTT
66 GTTTT
** * *
54314743 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
54314778 TTTAATTTTT
Statistics
Matches: 291, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
69 147 0.51
70 9 0.03
71 135 0.46
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
GTTTT
Found at i:54314645 original size:140 final size:140
Alignment explanation
Indices: 54314393--54314777 Score: 605
Period size: 140 Copynumber: 2.8 Consensus size: 140
54314383 CTTTCCAAGG
* ** * * *
54314393 AAAATCAACTCATATTGTGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT-
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGGGGCACGTCGAGGTATTTTTAGTTTA
**
54314456 T-TTTTAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTT
65 TGTTTT--AAATTGACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTT
*
54314520 AGTTTATGTTTTC
128 AGTTTATGATTTC
54314533 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGTCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGTCGAGGTATTTTTAGTTTAT
*
54314598 GTTTTAAATTGACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGT
66 GTTTTAAATTGACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGT
54314663 TTATGATTTC
131 TTATGATTTC
*
54314673 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGTCGAGGTATTTTTAGTTTAT
* *
54314738 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
66 GTTTTAAATTGACTCATATTGCGAGAAGTGAGTTGAGCCT
54314778 TTTAATTTTT
Statistics
Matches: 229, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
140 222 0.97
141 3 0.01
142 4 0.02
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (140 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGTCGAGGTATTTTTAGTTTAT
GTTTTAAATTGACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAGT
TTATGATTTC
Found at i:54316096 original size:21 final size:19
Alignment explanation
Indices: 54316034--54316102 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
54316024 TAAATTAATG
* *
54316034 AATTAATTGTAGATAAACTT
1 AATTAATTTTAGTTAAA-TT
54316054 -ATTACATTTTAGTTAAATT
1 AATTA-ATTTTAGTTAAATT
*
54316073 AATTAATTTTATTTATATATT
1 AATTAATTTTAGTTA-A-ATT
54316094 AATTAATTT
1 AATTAATTT
54316103 AAAATAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 15 0.36
20 15 0.36
21 12 0.29
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (19 bp):
AATTAATTTTAGTTAAATT
Found at i:54318428 original size:15 final size:15
Alignment explanation
Indices: 54318403--54318437 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54318393 AACACTATTT
*
54318403 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
54318417 TAATTAATATTAAGA
1 TAATTAATATTAAGA
54318432 TAATTA
1 TAATTA
54318438 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:54322358 original size:13 final size:12
Alignment explanation
Indices: 54322340--54322415 Score: 62
Period size: 13 Copynumber: 5.8 Consensus size: 12
54322330 GGCAACCCAA
54322340 TTTTTATTCTTAT
1 TTTTTATT-TTAT
54322353 TTTTTATTTTCAT
1 TTTTTATTTT-AT
*
54322366 TATTTATTTATTATT
1 TTTTTA-TT-TTA-T
*
54322381 TTCTTTACTTTAT
1 TT-TTTATTTTAT
*
54322394 TTATTATTTTAT
1 TTTTTATTTTAT
54322406 TTTATTATTT
1 TTT-TTATTT
54322416 ATTACTTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
12 12 0.24
13 24 0.47
14 6 0.12
15 5 0.10
16 4 0.08
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:54322374 original size:20 final size:21
Alignment explanation
Indices: 54322349--54322419 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 21
54322339 ATTTTTATTC
*
54322349 TTATTTTTTATTTTCATTA-T
1 TTATTTATTATTTTCATTACT
*
54322369 TTATTTATTATTTTCTTTACT
1 TTATTTATTATTTTCATTACT
*
54322390 TTATTTATTATTTT-ATT-TT
1 TTATTTATTATTTTCATTACT
54322409 ATTATTTATTA
1 -TTATTTATTA
54322420 CTTATTACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 29 0.64
21 15 0.33
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATTTATTATTTTCATTACT
Found at i:54325540 original size:27 final size:27
Alignment explanation
Indices: 54325509--54325567 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
54325499 ACTAAGAATA
54325509 GCCTTTGTGGCGAACTCTGAAAGAAAT
1 GCCTTTGTGGCGAACTCTGAAAGAAAT
* * *
54325536 GCCTTTGTGGCGAATTCTGAATGGAAT
1 GCCTTTGTGGCGAACTCTGAAAGAAAT
54325563 GCCTT
1 GCCTT
54325568 GGTGATGTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (27 bp):
GCCTTTGTGGCGAACTCTGAAAGAAAT
Found at i:54329698 original size:30 final size:33
Alignment explanation
Indices: 54329617--54329702 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 33
54329607 TTTTATAACC
54329617 TATATATA-AT-TAT-TATTTTCATAATCTATA
1 TATATATACATATATCTATTTTCATAATCTATA
*
54329647 TATATATACATGTACACATCTATTTT-ATAA-CT-TA
1 TATATATACA--T--ATATCTATTTTCATAATCTATA
54329681 TATATATACATATATCTATTTT
1 TATATATACATATATCTATTTT
54329703 TTTTTCACAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
30 18 0.38
31 1 0.02
32 1 0.02
33 1 0.02
34 12 0.26
35 2 0.04
36 6 0.13
37 6 0.13
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.50
Consensus pattern (33 bp):
TATATATACATATATCTATTTTCATAATCTATA
Found at i:54335643 original size:44 final size:44
Alignment explanation
Indices: 54335547--54336391 Score: 362
Period size: 44 Copynumber: 19.5 Consensus size: 44
54335537 AAGATGGCGA
* ***
54335547 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATGATAG
* * * *
54335591 AACCTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAATGATAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
* * * *** *
54335635 ATCTTATCTCTCTGAAGTTGCAG-AGAGCATA-TCGCAT-CTAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
* * * *
54335676 -TCTTATCTTCCTAAAGTTGCAGTGGAGCAGACTGAGTAA-GCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA-AAATG-ATAG
* ** *
54335720 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGCAA
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAA-ATGATAG
* **
54335764 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACCAATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-TGATAG
* * * *
54335808 ATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAGTGATAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
* * *** *
54335852 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT-CTAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
* * *
54335893 -TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTCAAGAAAGCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATG-ATAG
* * * *
54335938 -TCTTATCCCCCTGAAATTGCAGTGGGGCAGACTGAATAA-GCA-A-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATG-ATAG
* * * ** * * *
54335981 ATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAGAACGATGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
* * * ** * * *
54336025 ATCTTATCTCTCTAAAGTTGTAGTAAAGCAGA-TCATATCA-A-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
* * * ***
54336066 ATCTTATCCCCCTGAAGTTACAGTGGAGCAGCTTAAAGCCAATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATGATAG
* * * *
54336110 ATCATATCTCCCTGAAGTTGCAATAGAGCAGATTAAAGTGATAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
* * * * *** *
54336154 ATCTTATCTCTCTGAAGTTACAG-AGATCAGA-TCGCAT-CTA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
* * *
54336194 ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATG-ATAG
* * *
54336240 -TCTTATCCCCCTGAAATTGCAGTGG-GCCAGACTGAATAA-GCA-A-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGA-TTAA-AATG-ATAG
* * * ** *
54336283 ATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAGAATGAT-G
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
* * * * *
54336326 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCATATCA-A-
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
*
54336368 ATCTTATCTCCCTGAAATTGCAGT
1 ATCTTATCTCCCTGAAGTTGCAGT
54336392 AGAGTAGAAA
Statistics
Matches: 590, Mismatches: 165, Indels: 95
0.69 0.19 0.11
Matches are distributed among these distances:
40 59 0.10
41 73 0.12
42 16 0.03
43 46 0.08
44 294 0.50
45 99 0.17
46 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATAG
Found at i:54335897 original size:173 final size:172
Alignment explanation
Indices: 54335548--54336355 Score: 464
Period size: 173 Copynumber: 4.7 Consensus size: 172
54335538 AGATGGCGAA
* * * * * *
54335548 TCTTAT-CTCCCTGAAGTTGTAGTGGAGCAGA-TTAA-AGCCAATAAACCTATCTCCCTAAAGTT
1 TCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTAAAGAGGC-A-AATCTTATCTCCCTGAAGTT
* * * * *
54335610 ACAGTGGAGCAGATTAAAATG-ATAGATCTTATCTCTCTGAAGTTGCAG-AGAGC--ATATCGCA
63 GCAGTGGAGCAAATTAAAA-GCATA-ATCCTATCTCTCTGAAGTTGCAGTGGAGCGGAT-TAG-A
* ** * * *
54335671 TC--TAG-TCTTATCT-TCCTAAAGTTGCAGTGGAGCAGACTGAGTAAGCAAG
124 ACGATAGATCTTATCTCT-CTAAAGTTGCAGTAAAGCAGA-TCA--CATCAAG
54335720 TCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTG
1 TCTTATCCTCCTGAAGTTGCAGTGGA-GCAGACTAAAGA-GGCAAATCTTATCTCCCTGAAGTTG
* *
54335784 CAGTGGAGCAAATTAAAACCAATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTA-AAGTG
64 CAGTGGAGCAAATTAAAAGC-ATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAGAA-CG
* * * *
54335848 ATAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCATCTAG
127 ATAGATCTTATCTCTCTAAAGTTGCAGTAAAGCAGATCACATCAAG
* * * * * *
54335893 TCTTAT-CTCCCTGAAGTTGCAATGGAGCAGACTCAAGAAAGCAAGTCTTATCCCCCTGAAATTG
1 TCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTAAAG-AGGCAAATCTTATCTCCCTGAAGTTG
* * * * * * *
54335957 CAGTGGGGCAGACTGAATAAGCA-AATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAGAACG
64 CAGTGGAGCA-AATTAA-AAGCATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAGAACG
* * * *
54336021 ATGGATCTTATCTCTCTAAAGTTGTAGTAAAGCAGATCATATCAAA
127 ATAGATCTTATCTCTCTAAAGTTGCAGTAAAGCAGATCACATCAAG
* * * * *
54336067 TCTTATCCCCCTGAAGTTACAGTGGAGCAG-CTTAA-AGCCAATAATCATATCTCCCTGAAGTTG
1 TCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAAGAGGC-A-AATCTTATCTCCCTGAAGTTG
* * * * * * * * * * *
54336130 CAATAGAGCAGATT-AAAGTGATAGATCTTATCTCTCTGAAGTTACAG-AGATCAGA-TCGCATC
64 CAGTGGAGCAAATTAAAAG-CATA-ATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAG-AAC
* ** * *
54336192 --TA-ATCTTATCTC-CTTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAG
126 GATAGATCTTATCTCTC-TAAAGTTGCAGTAAAGCAGA-TC---ACATCAAG
* * * * * * * *
54336240 TCTTATCCCCCTGAAATTGCAGTGG-GCCAGACTGAATAAGCAAATCCTATCTCCCTAAAGTTGT
1 TCTTATCCTCCTGAAGTTGCAGTGGAG-CAGACTAAAGAGGCAAATCTTATCTCCCTGAAGTTGC
*** * * *
54336304 AGTGGAGTGGATTAGAATG-ATGAATCTTATCTCTCTGAAGTTGCAGTAGAGC
65 AGTGGAGCAAATTA-AAAGCAT-AATCCTATCTCTCTGAAGTTGCAGTGGAGC
54336356 AGATCATATC
Statistics
Matches: 500, Mismatches: 95, Indels: 80
0.74 0.14 0.12
Matches are distributed among these distances:
168 1 0.00
169 26 0.05
170 6 0.01
171 8 0.02
172 36 0.07
173 311 0.62
174 67 0.13
175 13 0.03
176 12 0.02
177 19 0.04
178 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (172 bp):
TCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAAGAGGCAAATCTTATCTCCCTGAAGTTGCA
GTGGAGCAAATTAAAAGCATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAGAACGATAG
ATCTTATCTCTCTAAAGTTGCAGTAAAGCAGATCACATCAAG
Found at i:54335912 original size:217 final size:218
Alignment explanation
Indices: 54335523--54336008 Score: 733
Period size: 217 Copynumber: 2.2 Consensus size: 218
54335513 GATTAGCTGA
* * * *
54335523 AGTGGGGCAGATTGAAGATGGCGAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCA
1 AGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAACCA
54335588 ATAAACCTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAATGATAGATCTTATCTCTCTGAAGT
66 ATAAACCTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAATGATAGATCTTATCTCTCTGAAGT
* * * * *
54335653 TGCAGAGAGCATATCGCATCTAGTCTTATCTTCCTAAAGTTGCAGTGGAGCAGACT-GAGTAAGC
131 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAATGGAGCAGACTCAAGAAAGC
* *
54335717 AAGTCTTATCCTCCTGAAGTTGC
196 AAGTCTTATCCCCCTGAAATTGC
* * *
54335740 AGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACCA
1 AGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAACCA
* * * * * *
54335805 ATAATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAGTGATAGATCTTATCTCTCTGAAGT
66 ATAAACCTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAATGATAGATCTTATCTCTCTGAAGT
*
54335870 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTCAAGAAAGC
131 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAATGGAGCAGACTCAAGAAAGC
54335935 AAGTCTTATCCCCCTGAAATTGC
196 AAGTCTTATCCCCCTGAAATTGC
* * * *
54335958 AGTGGGGCAGACTGAATA-AGCAAATCCTATCTCCCTAAAGTTGTAGTGGAG
1 AGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAG
54336009 TGGATTAGAA
Statistics
Matches: 240, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
217 198 0.82
218 42 0.17
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (218 bp):
AGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAACCA
ATAAACCTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAATGATAGATCTTATCTCTCTGAAGT
TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAATGGAGCAGACTCAAGAAAGC
AAGTCTTATCCCCCTGAAATTGC
Found at i:54336110 original size:302 final size:302
Alignment explanation
Indices: 54335761--54336383 Score: 1057
Period size: 302 Copynumber: 2.1 Consensus size: 302
54335751 CTAAAGATGG
* * *
54335761 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAACCAATAATCCTATCTCTCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAAATTAAAACCAATAATCATATCTCCCTGAAGT
* * * *
54335826 TGCAGTGGAGCGGATTAAAGTGATAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
66 TGCAATAGAGCAGATTAAAGTGATAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
*
54335891 AGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTCAAGAAAGCAAGTCTTATCCCCCTGAAATT
131 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGACTCAAGAAAGCAAGTCTTATCCCCCTGAAATT
*
54335956 GCAGTGGGGCAGACTGAATAAGCAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAGAACG
196 GCAGTGGGCCAGACTGAATAAGCAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAGAACG
* *
54336021 ATGGATCTTATCTCTCTAAAGTTGTAGTAAAGCAGATCATAT
261 ATGAATCTTATCTCTCTAAAGTTGCAGTAAAGCAGATCATAT
* ** *
54336063 CAAATCTTATCCCCCTGAAGTTACAGTGGAGCAGCTTAAAGCCAATAATCATATCTCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAAATTAAAACCAATAATCATATCTCCCTGAAGT
*
54336128 TGCAATAGAGCAGATTAAAGTGATAGATCTTATCTCTCTGAAGTTACAGAGATCAGATCGCATCT
66 TGCAATAGAGCAGATTAAAGTGATAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
* *
54336193 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCCCCCTGAAATT
131 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGACTCAAGAAAGCAAGTCTTATCCCCCTGAAATT
*
54336258 GCAGTGGGCCAGACTGAATAAGCAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAGAATG
196 GCAGTGGGCCAGACTGAATAAGCAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAGAACG
* *
54336323 ATGAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAT
261 ATGAATCTTATCTCTCTAAAGTTGCAGTAAAGCAGATCATAT
54336365 CAAATCTTATCTCCCTGAA
1 CAAATCTTATCTCCCTGAA
54336384 ATTGCAGTAG
Statistics
Matches: 299, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
302 299 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (302 bp):
CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAAATTAAAACCAATAATCATATCTCCCTGAAGT
TGCAATAGAGCAGATTAAAGTGATAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCT
AATCTTATCTCCCTGAAGTTGCAATGGAGCAGACTCAAGAAAGCAAGTCTTATCCCCCTGAAATT
GCAGTGGGCCAGACTGAATAAGCAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAGAACG
ATGAATCTTATCTCTCTAAAGTTGCAGTAAAGCAGATCATAT
Found at i:54336118 original size:129 final size:128
Alignment explanation
Indices: 54335938--54336227 Score: 300
Period size: 129 Copynumber: 2.3 Consensus size: 128
54335928 AGAAAGCAAG
* * * *
54335938 TCTTATCCCCCTGAAATTGCAGTGGGGCAGACTGAATAAGCAAATCCTATCTCCCTAAAGTTGTA
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAATAAGCAAATCATATCTCCCTAAAGTTGCA
* * ** * ** *
54336003 GTGGAGTGGATTAGAA-CGATGGATCTTATCTCTCTAAAGTTGTAGTAAAGCAGATCATATCAAA
66 ATAGAGCAGATTA-AAGCGATAGATCTTATCTCTCTAAAGTTACAG-AAAGCAGATCACATCAAA
* * *
54336067 TCTTATCCCCCTGAAGTTACAGTGGAGCAG-CT-TA-AAGCCAATAATCATATCTCCCTGAAGTT
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAATAAG-C-A-AATCATATCTCCCTAAAGTT
* * * * * *
54336129 GCAATAGAGCAGATTAAAGTGATAGATCTTATCTCTCTGAAGTTACAGAGATCAGATCGCATCTA
63 GCAATAGAGCAGATTAAAGCGATAGATCTTATCTCTCTAAAGTTACAGAAAGCAGATCACATCAA
54336194 A
128 A
* *
54336195 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGACT
1 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACT
54336228 CAAGAAAGCA
Statistics
Matches: 132, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
126 3 0.02
127 2 0.02
128 45 0.34
129 82 0.62
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (128 bp):
TCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAATAAGCAAATCATATCTCCCTAAAGTTGCA
ATAGAGCAGATTAAAGCGATAGATCTTATCTCTCTAAAGTTACAGAAAGCAGATCACATCAAA
Found at i:54337077 original size:3 final size:3
Alignment explanation
Indices: 54337069--54337100 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
54337059 TAATTTACTC
54337069 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54337101 TTTACATACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54356747 original size:48 final size:48
Alignment explanation
Indices: 54356680--54356910 Score: 399
Period size: 48 Copynumber: 4.8 Consensus size: 48
54356670 TGCGGGAGTA
* * * *
54356680 GGGGGTTTATATGGGGGAGTAGGAGCCTTGGTTGGTGGTGCTGGTGCT
1 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
* *
54356728 GGGGGCTTAAATGGTGGAGTTGGAGCCTTGGTTGGTGGTGCAGGAGCT
1 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
54356776 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
1 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
54356824 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
1 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
*
54356872 GGGGGTTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGT
1 GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGT
54356911 TTATATGGTG
Statistics
Matches: 174, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 174 1.00
ACGTcount: A:0.13, C:0.09, G:0.48, T:0.29
Consensus pattern (48 bp):
GGGGGCTTATATGGTGGAGTAGGAGCCTTGGTTGGTGGTGCAGGAGCT
Found at i:54356790 original size:27 final size:27
Alignment explanation
Indices: 54356760--54356897 Score: 79
Period size: 27 Copynumber: 5.6 Consensus size: 27
54356750 GAGCCTTGGT
*
54356760 TGGTGGTGCAGGAGCTGGGGGCTTATA
1 TGGTGGAGCAGGAGCTGGGGGCTTATA
* *
54356787 TGGTGGAGTAGGAGC------CTTGGT-
1 TGGTGGAGCAGGAGCTGGGGGCTT-ATA
*
54356808 TGGTGGTGCAGGAGCTGGGGGCTTATA
1 TGGTGGAGCAGGAGCTGGGGGCTTATA
* *
54356835 TGGTGGAGTAGGAGC------CTTGGT-
1 TGGTGGAGCAGGAGCTGGGGGCTT-ATA
* *
54356856 TGGTGGTGCAGGAGCTGGGGGTTTATA
1 TGGTGGAGCAGGAGCTGGGGGCTTATA
*
54356883 TGGTGGAGTAGGAGC
1 TGGTGGAGCAGGAGC
54356898 CTTGGTTGGT
Statistics
Matches: 80, Mismatches: 15, Indels: 32
0.63 0.12 0.25
Matches are distributed among these distances:
21 32 0.40
22 2 0.03
26 2 0.03
27 44 0.55
ACGTcount: A:0.15, C:0.09, G:0.49, T:0.27
Consensus pattern (27 bp):
TGGTGGAGCAGGAGCTGGGGGCTTATA
Found at i:54356917 original size:33 final size:33
Alignment explanation
Indices: 54356872--54356951 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
54356862 TGCAGGAGCT
*
54356872 GGGGGTTTATATGGTGGAGTAGGAGCCTTGGTT
1 GGGGGTTTATATGGTGGAGTAGGAGCCTTGGTA
* * *
54356905 GGTGGTTTATATGGTGGAGTGGGGGCCTTGGTA
1 GGGGGTTTATATGGTGGAGTAGGAGCCTTGGTA
54356938 GGGGGTTTATATGG
1 GGGGGTTTATATGG
54356952 AGTGGGGCCC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.14, C:0.05, G:0.47, T:0.34
Consensus pattern (33 bp):
GGGGGTTTATATGGTGGAGTAGGAGCCTTGGTA
Found at i:54356955 original size:30 final size:31
Alignment explanation
Indices: 54356871--54356973 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 31
54356861 GTGCAGGAGC
* *
54356871 TGGGGGTTTATATGGTGGAGTAGGAGCCTTGGT
1 TGGGGGTTTATA--GTGGAGTGGGGGCCTTGGT
*
54356904 TGGTGGTTTATATGGTGGAGTGGGGGCCTTGGT
1 TGGGGGTTTATA--GTGGAGTGGGGGCCTTGGT
* * *
54356937 AGGGGGTTTATA-TGGAGTGGGGCCCTTAGT
1 TGGGGGTTTATAGTGGAGTGGGGGCCTTGGT
54356967 TGGGGGT
1 TGGGGGT
54356974 GCTGGAGTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
30 22 0.35
33 40 0.65
ACGTcount: A:0.13, C:0.07, G:0.48, T:0.33
Consensus pattern (31 bp):
TGGGGGTTTATAGTGGAGTGGGGGCCTTGGT
Found at i:54359146 original size:25 final size:25
Alignment explanation
Indices: 54359098--54359148 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
54359088 TGATCATTAA
* **
54359098 TATCAATAGGCAATATTTTTCTATC
1 TATCAATACGCAATATTTCACTATC
54359123 TATCAATACGCAATATTTCACTATC
1 TATCAATACGCAATATTTCACTATC
54359148 T
1 T
54359149 CAATTTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (25 bp):
TATCAATACGCAATATTTCACTATC
Found at i:54359621 original size:23 final size:23
Alignment explanation
Indices: 54359532--54359621 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 23
54359522 ACCTGATCAG
54359532 TATACGACACAT-AAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
** *
54359554 -A-ACGACACACGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
*
54359575 AATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
*
54359598 TATACGACGCATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
54359621 T
1 T
54359622 CGACAAAACC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.14
21 10 0.17
22 1 0.02
23 39 0.67
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:54359731 original size:16 final size:16
Alignment explanation
Indices: 54359710--54359784 Score: 51
Period size: 16 Copynumber: 5.2 Consensus size: 16
54359700 AAGGTTTCCG
54359710 AATCACATTTCAATTC
1 AATCACATTTCAATTC
54359726 AATCAC-TTTC---TC
1 AATCACATTTCAATTC
54359738 -AT-AC-TTTCAATTC
1 AATCACATTTCAATTC
* *
54359751 AA--ATCATTCCAATTT
1 AATCA-CATTTCAATTC
*
54359766 AATCACAATTCAATTC
1 AATCACATTTCAATTC
54359782 AAT
1 AAT
54359785 ACAGTTTCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
10 6 0.13
11 2 0.04
12 2 0.04
13 3 0.07
14 2 0.04
15 13 0.28
16 17 0.37
17 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (16 bp):
AATCACATTTCAATTC
Found at i:54360276 original size:3 final size:3
Alignment explanation
Indices: 54360268--54360306 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
54360258 TAGCTACGAA
54360268 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
54360307 TGAATTTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54363679 original size:34 final size:34
Alignment explanation
Indices: 54363548--54363667 Score: 204
Period size: 34 Copynumber: 3.5 Consensus size: 34
54363538 TAAAAGTTAT
*
54363548 ATGATTTACATGGTTTATAAGTTACATAAAATAC
1 ATGATTTACATGGTTTATAAGTTACATGAAATAC
*
54363582 ATGATTTACATGGTTTATAAGTTATATGAAATAC
1 ATGATTTACATGGTTTATAAGTTACATGAAATAC
*
54363616 ATGATTTACATGGTTTATAAGCTACATGAAATAC
1 ATGATTTACATGGTTTATAAGTTACATGAAATAC
*
54363650 ATGATTTACATGGATTAT
1 ATGATTTACATGGTTTAT
54363668 TTGTTATATG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 81 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (34 bp):
ATGATTTACATGGTTTATAAGTTACATGAAATAC
Found at i:54375060 original size:4 final size:4
Alignment explanation
Indices: 54375051--54375114 Score: 53
Period size: 4 Copynumber: 15.5 Consensus size: 4
54375041 GCTGAAGGAG
54375051 AAGA AAGA AAGA GAAGA AAGA AA-A AAGA AAGAA AAGGA AAGGA GAAGA
1 AAGA AAGA AAGA -AAGA AAGA AAGA AAGA AAG-A AA-GA AA-GA -AAGA
*
54375099 AA-A AA-A AATA AAGA AA
1 AAGA AAGA AAGA AAGA AA
54375115 AGGAAAGGAG
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
3 9 0.17
4 26 0.49
5 15 0.28
6 3 0.06
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:54375098 original size:20 final size:19
Alignment explanation
Indices: 54375079--54375164 Score: 64
Period size: 20 Copynumber: 4.9 Consensus size: 19
54375069 AGAAAAAAGA
54375079 AAGAAAAGGAAAGGAGAAG
1 AAGAAAAGGAAAGGAGAAG
*
54375098 AA-AAAA--AAA-TA-AAG
1 AAGAAAAGGAAAGGAGAAG
*
54375112 ---AAAAGGAAAGGAGAATA
1 AAGAAAAGGAAAGGAGAA-G
*
54375129 AAGGAAAGGAAAGGAGAAG
1 AAGAAAAGGAAAGGAGAAG
*
54375148 AAGAAAAAG-AAGGAGAA
1 AAGAAAAGGAAAGGAGAA
54375165 AGAGGCGCAG
Statistics
Matches: 52, Mismatches: 7, Indels: 17
0.68 0.09 0.22
Matches are distributed among these distances:
12 4 0.08
14 6 0.12
15 2 0.04
16 5 0.10
18 12 0.23
19 9 0.17
20 14 0.27
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (19 bp):
AAGAAAAGGAAAGGAGAAG
Found at i:54375105 original size:30 final size:31
Alignment explanation
Indices: 54375057--54375131 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 31
54375047 GGAGAAGAAA
54375057 GAAA-GAGAAGAAAGAAAAAAGAAAGAAAAG
1 GAAAGGAGAAGAAAGAAAAAAGAAAGAAAAG
*
54375087 GAAAGGAGAAGAAA-AAAAAATAAAGAAAAG
1 GAAAGGAGAAGAAAGAAAAAAGAAAGAAAAG
*
54375117 GAAAGGAGAATAAAG
1 GAAAGGAGAAGAAAG
54375132 GAAAGGAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 32 0.78
31 9 0.22
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.03
Consensus pattern (31 bp):
GAAAGGAGAAGAAAGAAAAAAGAAAGAAAAG
Found at i:54375488 original size:15 final size:16
Alignment explanation
Indices: 54375456--54375489 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54375446 AAATAGCATT
*
54375456 AAAAATAAAATATTGA
1 AAAAATAAAATATCGA
54375472 AAAAATAAAATA-CGA
1 AAAAATAAAATATCGA
54375487 AAA
1 AAA
54375490 TAAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAAATAAAATATCGA
Found at i:54375723 original size:158 final size:158
Alignment explanation
Indices: 54375491--54376067 Score: 860
Period size: 158 Copynumber: 3.6 Consensus size: 158
54375481 ATACGAAAAT
* *
54375491 AAATAA-AAAA-ACAAAAATAGTATATTTATTGAAAGAAATAAAATTC-GAAAATAAGAAAAATA
1 AAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCGGAAAA-AAGAAAAATA
* *
54375553 CGAACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTAAAAAAAAAACACACTAAATTAATACA
65 CGAACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACA
* *
54375618 TTTCAAACATAATGTAGTAAGATAATATA
130 TTTCAAACATAATGTACTAAAATAATATA
* *
54375647 AAATAATAAAATACGAAAATAGTATATTTTTTTAAAGTAATAAAATTCAGGAAAAAAG-AAAATA
1 AAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTC-GGAAAAAAGAAAAATA
* *
54375711 CGAACAAAGGGCCAAAATAAGGTTATTTTTACTAAATTTATATAAAAAACACACTAAATTAATAA
65 CGAACAAAGGGCCAAAATAAGGGT-TTTTTACTAAATTTATATAAAAAACACACTAAATTAATAC
54375776 ATTTCAAACATAATGTACTAAAATAATATA
129 ATTTCAAACATAATGTACTAAAATAATATA
*
54375806 AAATAATAAAATACAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAGAAAAAAGAAAAATA
1 AAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCG-GAAAAAAGAAAAATA
* *
54375871 C-AA-AAAGGGCCAAAATAAGGGTTTTTTTACTAAATTTATTTAAAATACACACTAAATTAATAC
65 CGAACAAAGGGCCAAAATAAGGG-TTTTTTACTAAATTTATATAAAAAACACACTAAATTAATAC
54375934 ATTTCAAACATAATGTACTAAAATAATATA
129 ATTTCAAACATAATGTACTAAAATAATATA
* * *
54375964 AAATAATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAATCCGGGAAAAAATGAAAAAT
1 AAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTC-GGAAAAAA-GAAAAAT
* * * * *
54376029 ACGAATAAATGGTCAAAATAAGGGGTTTTTACTATATTT
64 ACGAACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTT
54376068 GTTTTGAAGT
Statistics
Matches: 385, Mismatches: 24, Indels: 20
0.90 0.06 0.05
Matches are distributed among these distances:
156 6 0.02
157 4 0.01
158 197 0.51
159 135 0.35
160 27 0.07
161 16 0.04
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (158 bp):
AAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATTCGGAAAAAAGAAAAATAC
GAACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACAT
TTCAAACATAATGTACTAAAATAATATA
Found at i:54378236 original size:40 final size:40
Alignment explanation
Indices: 54378173--54378271 Score: 171
Period size: 40 Copynumber: 2.4 Consensus size: 40
54378163 AAATTATTTC
*
54378173 AAATGAATTATACTTTTTCCAACTTAATTTGGAAACCATAT
1 AAAT-AATTATACTTTTTACAACTTAATTTGGAAACCATAT
54378214 AAATAATTATACTTTTTACAACTTAATTTGGAAACCATAT
1 AAATAATTATACTTTTTACAACTTAATTTGGAAACCATAT
54378254 AAATAATTATACATTTTT
1 AAATAATTATAC-TTTTT
54378272 TCATTATATT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
40 47 0.84
41 9 0.16
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (40 bp):
AAATAATTATACTTTTTACAACTTAATTTGGAAACCATAT
Found at i:54381700 original size:20 final size:20
Alignment explanation
Indices: 54381655--54381700 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
54381645 TTCTTCTCTT
*
54381655 TCTTTCTCCTTTCTCTTTTC
1 TCTTTCTCCTTTCTCTTTTA
*
54381675 TCTTTCTCTCTTTTTCTTTTA
1 TCTTTCTC-CTTTCTCTTTTA
54381696 T-TTTC
1 TCTTTC
54381701 CAGCACAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (20 bp):
TCTTTCTCCTTTCTCTTTTA
Found at i:54383136 original size:13 final size:13
Alignment explanation
Indices: 54383120--54383151 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54383110 ATTTTAGTTT
54383120 TTTATTTTTTAAA
1 TTTATTTTTTAAA
54383133 TTTATTTTTTAAA
1 TTTATTTTTTAAA
*
54383146 ATTATT
1 TTTATT
54383152 CTAAAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTTTTTAAA
Found at i:54385818 original size:28 final size:27
Alignment explanation
Indices: 54385785--54385868 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 27
54385775 TTAATGTTCG
54385785 GGGTTTAAGGTTTGAGATTTTAGATTTA
1 GGGTTTAAGGTTT-AGATTTTAGATTTA
** *
54385813 GGGTTTAATTTTTAAGATTTTATATTTA
1 GGGTTTAAGGTTT-AGATTTTAGATTTA
* *
54385841 GAGTTTAAGGTTTAGTATTTTAGGTTTA
1 GGGTTTAAGGTTTAG-ATTTTAGATTTA
54385869 AAATTCAAGG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
27 2 0.04
28 44 0.96
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (27 bp):
GGGTTTAAGGTTTAGATTTTAGATTTA
Found at i:54385859 original size:21 final size:20
Alignment explanation
Indices: 54385831--54385869 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54385821 TTTTTAAGAT
54385831 TTTATA-TTTAGAGTTTAAGG
1 TTTATATTTTAG-GTTTAAGG
54385851 TTTAGTATTTTAGGTTTAA
1 TTTA-TATTTTAGGTTTAA
54385870 AATTCAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (20 bp):
TTTATATTTTAGGTTTAAGG
Found at i:54386263 original size:49 final size:49
Alignment explanation
Indices: 54386196--54386292 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
54386186 TTATGCTATG
* * *
54386196 CATTTCTAAACTTGGTCTTCCACTGTCTATACTATTATCTA-TATTTATA
1 CATTGCTAAACTTAGTCTTCCACTGTCTACACTATTATC-ACTATTTATA
*
54386245 CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCACTATTTAT
1 CATTGCTAAACTTAGTCTTCCACTGTCTACACTATTATCACTATTTAT
54386293 CCTTTCTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 1 0.02
49 42 0.98
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (49 bp):
CATTGCTAAACTTAGTCTTCCACTGTCTACACTATTATCACTATTTATA
Found at i:54387629 original size:43 final size:43
Alignment explanation
Indices: 54387567--54387652 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
54387557 TCATATTTTA
* * *
54387567 TTTCTCGTCTCATAATCATTTCTCATATTTGCCTTTTCAATAT
1 TTTCTCATCTAATAATCATTTCTCATATTTGCCATTTCAATAT
* *
54387610 TTTCTCATCTAATATTCATTTCTCATCTTTGCCATTTCAATAT
1 TTTCTCATCTAATAATCATTTCTCATATTTGCCATTTCAATAT
54387653 CAATCACATA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.22, C:0.23, G:0.03, T:0.51
Consensus pattern (43 bp):
TTTCTCATCTAATAATCATTTCTCATATTTGCCATTTCAATAT
Found at i:54388849 original size:3 final size:3
Alignment explanation
Indices: 54388843--54388881 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
54388833 TGTTTTCATT
54388843 TTA TTA TCT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54388882 AAGTTACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54388856 original size:9 final size:8
Alignment explanation
Indices: 54388826--54388877 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 8
54388816 TTTCTATTTC
54388826 TTTATTAT
1 TTTATTAT
*
54388834 GTTT-TCAT
1 -TTTATTAT
54388842 TTTATTAT
1 TTTATTAT
54388850 CTTTATTAT
1 -TTTATTAT
54388859 TATTATTAT
1 T-TTATTAT
54388868 TATTATTAT
1 T-TTATTAT
54388877 T
1 T
54388878 ATTAAAGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
7 3 0.08
8 7 0.18
9 28 0.74
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (8 bp):
TTTATTAT
Found at i:54388856 original size:25 final size:24
Alignment explanation
Indices: 54388812--54388858 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
54388802 TTGTTTCATC
54388812 TTTCTTTCTATTTCTTTATTATGT
1 TTTCTTTCTATTTCTTTATTATGT
54388836 TTTCATTT-TATTATCTTTATTAT
1 TTTC-TTTCTATT-TCTTTATTAT
54388859 TATTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTCTTTCTATTTCTTTATTATGT
Found at i:54402356 original size:33 final size:33
Alignment explanation
Indices: 54402313--54402416 Score: 90
Period size: 33 Copynumber: 3.1 Consensus size: 33
54402303 TATTTAATGG
* *
54402313 TTATATTTAAATATTTAAAATATATTTTATATA
1 TTATAATTAAATATTTAAAATATATTTAATATA
54402346 TTATAATTAAAT-TTTATAAATA-A-TTAATAT-
1 TTATAATTAAATATTTA-AAATATATTTAATATA
* *
54402376 TTACTACTTAAAAATATTTAAAATTTATATTTCATATA
1 TTA-TAATT--AAATATTTAAAA--TATATTTAATATA
54402414 TTA
1 TTA
54402417 AAATATTACC
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
30 3 0.05
31 10 0.18
32 5 0.09
33 23 0.40
34 4 0.07
35 2 0.04
36 1 0.02
37 6 0.11
38 3 0.05
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (33 bp):
TTATAATTAAATATTTAAAATATATTTAATATA
Found at i:54403913 original size:29 final size:29
Alignment explanation
Indices: 54403881--54403936 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
54403871 AAAGACCCTT
54403881 TTTTTTCAA-AATTTACCGAAATGGGCCGG
1 TTTTTT-AATAATTTACCGAAATGGGCCGG
* *
54403910 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAATAATTTACCGAAATGGGCC
54403937 ATTTTCCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCGG
Found at i:54405771 original size:3 final size:3
Alignment explanation
Indices: 54405763--54405789 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54405753 CCATTGATGC
54405763 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
54405790 GTTATTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:54415080 original size:103 final size:103
Alignment explanation
Indices: 54414952--54415301 Score: 488
Period size: 103 Copynumber: 3.4 Consensus size: 103
54414942 TTGCATATAA
** * *
54414952 AGGGGTTGCTGTGTGCTGATTCCCCTATTCATTGGTGGTTGTTAAGTGCTGATTCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCTATCCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
54415017 TAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
66 TAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
*
54415055 AGGGGTTGCTAAGTGCTGATTCCCCTA-CCTATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
1 AGGGGTTGCTAAGTGCTGATTCCCCTATCC-ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
54415119 TTAAATGTGAAAGGAGGTTGCTAAGTGCTGATTCCCCCG
65 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
* * * * * * * *
54415158 AGTGGTTGCTAAGCGCTGATTCCCCAACCCATTTTGTGGTTACTAAGTGCTGATTCCACCGCATC
1 AGGGGTTGCTAAGTGCTGATTCCCCTATCCA-TTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
* *
54415223 TGAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCCA
65 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
** * *
54415261 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTG
1 AGGGGTTGCTAAGTGCTGATTCCCCTATCCATTGGTGGTTG
54415302 TTAACTGCGG
Statistics
Matches: 218, Mismatches: 26, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
102 9 0.04
103 171 0.78
104 38 0.17
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCTATCCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
TAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:54415100 original size:33 final size:28
Alignment explanation
Indices: 54415029--54415110 Score: 103
Period size: 27 Copynumber: 2.8 Consensus size: 28
54415019 AATGTGAAAG
54415029 GGGGTTGCTAAGTGCTGATT-CCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCCCGA
*
54415056 GGGGTTGCTAAGTGCTGATTCCCCTACCTA
1 GGGGTTGCTAAGTGCTGATTCCCC--CCGA
54415086 TTGGTGGTTGCTAAGTGCTGATTCC
1 --GG-GGTTGCTAAGTGCTGATTCC
54415111 ACCATATTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
27 20 0.42
28 3 0.06
30 3 0.06
32 2 0.04
33 20 0.42
ACGTcount: A:0.15, C:0.23, G:0.30, T:0.32
Consensus pattern (28 bp):
GGGGTTGCTAAGTGCTGATTCCCCCCGA
Found at i:54422385 original size:103 final size:103
Alignment explanation
Indices: 54422257--54422460 Score: 347
Period size: 103 Copynumber: 2.0 Consensus size: 103
54422247 TTGCATATAA
** *
54422257 AGGGGTTGCTGTGTGCTGATTCCCCTA-TTCATTGGTGGTTGCTAAGTGCTGATTCCAACGTATT
1 AGGGGTTGCTAAGTGCTGATTCCCCTACCT-ATTGGTGGTTGCTAAGTGCTGATTCCAACGTATT
*
54422321 TTAAATGTGAAAGGGGGTTGCTAAGTGTTGATTCCCCCG
65 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
*
54422360 AGGGGTTGCTAAGTGCTGATTCCCCTACCTATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCTACCTATTGGTGGTTGCTAAGTGCTGATTCCAACGTATTT
54422425 TAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCC
54422461 GACCCATTTT
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 94 0.99
104 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCTACCTATTGGTGGTTGCTAAGTGCTGATTCCAACGTATTT
TAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:54422457 original size:43 final size:41
Alignment explanation
Indices: 54422396--54422534 Score: 130
Period size: 42 Copynumber: 3.5 Consensus size: 41
54422386 ACCTATTGGT
*
54422396 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTA-TTCAAATGTG-AAGGG
** ** *
54422439 GGTTGCTAAGTGCTGATTCC-CCG-A--CCCAT-T--TTGT
1 GGTTGCTAAGTGCTGATTCCACCGTATTCAAATGTGAAGGG
*
54422473 GGTTGCTAAGTGCTGATTCCACCGTATCTGAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-TCAAATGTGAAGGG
*
54422515 GGTTGCTAAGTACTGATTCC
1 GGTTGCTAAGTGCTGATTCC
54422535 CCCAAGGGGT
Statistics
Matches: 75, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
34 21 0.28
35 3 0.04
36 1 0.01
37 1 0.01
38 2 0.03
39 2 0.03
40 1 0.01
41 1 0.01
42 23 0.31
43 20 0.27
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATTCAAATGTGAAGGG
Found at i:54422514 original size:76 final size:76
Alignment explanation
Indices: 54422361--54422536 Score: 282
Period size: 76 Copynumber: 2.3 Consensus size: 76
54422351 ATTCCCCCGA
* * * *
54422361 GGGGTTGCTAAGTGCTGATTCCCCTACCTATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGACCCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTG
54422426 AAATGTGAAAG
66 AAATGTGAAAG
*
54422437 GGGGTTGCTAAGTGCTGATTCCCCGACCCATTTTGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 GGGGTTGCTAAGTGCTGATTCCCCGACCCA-TTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
54422502 GAAATGTG-AAG
65 GAAATGTGAAAG
*
54422513 GGGGTTGCTAAGTACTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
54422537 CAAGGGGTTG
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
76 54 0.58
77 39 0.42
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (76 bp):
GGGGTTGCTAAGTGCTGATTCCCCGACCCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTG
AAATGTGAAAG
Found at i:54427737 original size:103 final size:103
Alignment explanation
Indices: 54427577--54427914 Score: 516
Period size: 103 Copynumber: 3.3 Consensus size: 103
54427567 CCGCAGTAAA
** **
54427577 CAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACTTAGCAACC
1 CAACCACCAATGGGTCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACC
* * *
54427642 CCC-TTCACATTTCAGATGCGGTGGAATCAGCACTTAG
66 CCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAG
* *
54427679 CAACCACCAAATGGGTCGGAGAATCAGCACTTAGCAACCCCTTGGGGGAATCAACACTTAGCAAC
1 CAACCACC-AATGGGTCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAAC
*
54427744 CCCCTTTCACATTTAAAATACGTTGGAATCAGCACTTAG
65 CCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAG
* *
54427783 CAACCACCAATAGGTAGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACC
1 CAACCACCAATGGGTCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACC
*
54427848 CCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAA
66 CCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAG
** *
54427886 CAACCACCAATGAATAGGGGAATCAGCAC
1 CAACCACCAATGGGTCGGGGAATCAGCAC
54427915 ACAGAACCCC
Statistics
Matches: 215, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
102 8 0.04
103 169 0.79
104 38 0.18
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (103 bp):
CAACCACCAATGGGTCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACC
CCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAG
Found at i:54427810 original size:33 final size:27
Alignment explanation
Indices: 54427768--54427849 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 27
54427758 AAAATACGTT
54427768 GGAATCAGCACTTAGCAACCACCAATAGGTAGG
1 GGAATCAGCACTTAGCAACC-CC--T---TAGG
*
54427801 GGAATCAGCACTTAGCAACCCCTTGGG
1 GGAATCAGCACTTAGCAACCCCTTAGG
54427828 GGAATCAGCACTTAGCAACCCC
1 GGAATCAGCACTTAGCAACCCC
54427850 CTTTCACATT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
27 25 0.52
30 1 0.02
32 2 0.04
33 20 0.42
ACGTcount: A:0.32, C:0.29, G:0.23, T:0.16
Consensus pattern (27 bp):
GGAATCAGCACTTAGCAACCCCTTAGG
Found at i:54429210 original size:13 final size:13
Alignment explanation
Indices: 54429189--54429219 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54429179 TAAAGTGAAA
*
54429189 TTTACTTTTATTT
1 TTTATTTTTATTT
54429202 TTTATTTTTATTT
1 TTTATTTTTATTT
54429215 TTTAT
1 TTTAT
54429220 CGTGGGCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTTTATTT
Found at i:54430799 original size:26 final size:26
Alignment explanation
Indices: 54430764--54430815 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
54430754 AAATGAAAAG
*
54430764 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
54430790 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
54430816 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:54430822 original size:102 final size:104
Alignment explanation
Indices: 54430583--54430951 Score: 575
Period size: 104 Copynumber: 3.6 Consensus size: 104
54430573 TGTATATAAA
** * * *
54430583 AGGGGTTGCTGTGTGCTAATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTATCT
**
54430647 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
54430687 AGGGGTTGCTAAGTGCTGATT-CCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
54430751 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATT-CCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * *
54430789 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGATGCTAAGTGCGATATTCATCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
54430854 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
54430893 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCG
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCG
54430952 ATAACGGTTA
Statistics
Matches: 245, Mismatches: 15, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
102 68 0.28
103 59 0.24
104 117 0.48
105 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:54437968 original size:103 final size:104
Alignment explanation
Indices: 54437697--54438006 Score: 507
Period size: 104 Copynumber: 3.0 Consensus size: 104
54437687 TGTATATAAA
** * * *
54437697 AGGGGTTGCTGTGTGTTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTATCT
**
54437761 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
54437801 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
54437866 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
54437905 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGATGCTAAGTGCGATATTCACCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
54437970 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCC
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCC
54438007 GATTCAGTGG
Statistics
Matches: 195, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
103 43 0.22
104 110 0.56
105 41 0.21
106 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Done.