Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 48 of 325
Found at i:12149096 original size:18 final size:18
Alignment explanation
Indices: 12149068--12149111 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
12149058 AAAAAATAAA
*
12149068 TTAAA-TTTTTATTATTT
1 TTAAATTTTTTATTAATT
12149085 TTAAATTTTTTATTAATT
1 TTAAATTTTTTATTAATT
*
12149103 TTAGATTTT
1 TTAAATTTT
12149112 AAAAAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTAAATTTTTTATTAATT
Found at i:12150120 original size:2 final size:2
Alignment explanation
Indices: 12150113--12150147 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
12150103 TCAACCAATT
12150113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12150148 ATCCCTCACT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12150519 original size:26 final size:25
Alignment explanation
Indices: 12150489--12150537 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
12150479 GGCACAACTA
12150489 TTTTTATTTTT-TAAATAAAATATTAC
1 TTTTTATTTTTAT-AA-AAAATATTAC
12150515 TTTTTATTTTTATAAAAAATATT
1 TTTTTATTTTTATAAAAAATATT
12150538 TAAATTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.36
26 13 0.59
27 1 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTTATTTTTATAAAAAATATTAC
Found at i:12150524 original size:25 final size:26
Alignment explanation
Indices: 12150489--12150537 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
12150479 GGCACAACTA
12150489 TTTTTATTTTTTA-AATAAAATATTAC
1 TTTTTATTTTTTATAA-AAAATATTAC
12150515 TTTTTA-TTTTTATAAAAAATATT
1 TTTTTATTTTTTATAAAAAATATT
12150538 TAAATTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTTATTTTTTATAAAAAATATTAC
Found at i:12157285 original size:9 final size:9
Alignment explanation
Indices: 12157243--12157334 Score: 58
Period size: 9 Copynumber: 9.8 Consensus size: 9
12157233 GTAAAAATCA
*
12157243 ATAAAAGTT
1 ATAAAAATT
*
12157252 ATAAAAATA
1 ATAAAAATT
* **
12157261 ATTAATTTT
1 ATAAAAATT
*
12157270 TTAAAAATT
1 ATAAAAATT
12157279 ATAAAAATT
1 ATAAAAATT
12157288 ATAAAAAATT
1 AT-AAAAATT
* *
12157298 ATAGAAATAA
1 ATAAAAAT-T
*
12157308 ATAGAAATAT
1 ATAAAAAT-T
*
12157318 AAAAAAATAT
1 ATAAAAAT-T
12157328 ATAAAAA
1 ATAAAAA
12157335 ATTTTATAAA
Statistics
Matches: 64, Mismatches: 17, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
9 32 0.50
10 32 0.50
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:12157294 original size:10 final size:10
Alignment explanation
Indices: 12157272--12157407 Score: 68
Period size: 10 Copynumber: 13.3 Consensus size: 10
12157262 TTAATTTTTT
12157272 AAAAATTAT-
1 AAAAATTATA
12157281 AAAAATTATA
1 AAAAATTATA
12157291 AAAAATTATA
1 AAAAATTATA
12157301 GAAATAA--AT-
1 -AAA-AATTATA
*
12157310 AGAAA-TATAA
1 AAAAATTAT-A
12157320 AAAAATATATA
1 AAAAAT-TATA
*
12157331 AAAAATTTTA
1 AAAAATTATA
* * *
12157341 TAAATTTGTA
1 AAAAATTATA
*
12157351 AGAAAAGTATA
1 A-AAAATTATA
12157362 AAAAATGTA-A
1 AAAAAT-TATA
**
12157372 AGAAAAAAATA
1 A-AAAATTATA
*
12157383 TAAAATTCATAA
1 AAAAATT-AT-A
12157395 AAAAATTATA
1 AAAAATTATA
12157405 AAA
1 AAA
12157408 TTTTATAACT
Statistics
Matches: 96, Mismatches: 17, Indels: 27
0.69 0.12 0.19
Matches are distributed among these distances:
7 2 0.02
8 4 0.04
9 9 0.09
10 41 0.43
11 28 0.29
12 12 0.12
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (10 bp):
AAAAATTATA
Found at i:12157295 original size:20 final size:20
Alignment explanation
Indices: 12157272--12157407 Score: 75
Period size: 21 Copynumber: 6.7 Consensus size: 20
12157262 TTAATTTTTT
12157272 AAAAATTATAAAAATTAT-A
1 AAAAATTATAAAAATTATAA
*
12157291 AAAAATTATAGAAA-TA-AA
1 AAAAATTATAAAAATTATAA
* *
12157309 TAGAAA-TATAAAAAAATATATA
1 -AAAAATTAT-AAAAATTATA-A
* * *
12157331 AAAAATTTTATAAATTTGTAA
1 AAAAATTATA-AAAATTATAA
* * *
12157352 GAAAAGTATAAAAAATGTAAAGA
1 AAAAATTAT-AAAAAT-TATA-A
*
12157375 AAAAAATAT-AAAATTCATAA
1 AAAAATTATAAAAATT-ATAA
12157395 AAAAATTATAAAA
1 AAAAATTATAAAA
12157408 TTTTATAACT
Statistics
Matches: 86, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
18 6 0.07
19 21 0.24
20 12 0.14
21 27 0.31
22 12 0.14
23 8 0.09
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAAATTATAAAAATTATAA
Found at i:12157382 original size:72 final size:71
Alignment explanation
Indices: 12157282--12157415 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 71
12157272 AAAAATTATA
* * * *
12157282 AAAATTATAAAAAATTATAGAAATAAATA-GAAA-T-ATAAAAAAATATATAAAAAATTTTATAA
1 AAAAGTATAAAAAATTAAAGAAAAAAATATAAAATTCATAAAAAAAT-TAT--AAAATTTTATAA
12157344 ATTTGTAAG
63 ATTTGTAAG
12157353 AAAAGTATAAAAAATGTAAAGAAAAAAATATAAAATTCATAAAAAAATTATAAAATTTTATAA
1 AAAAGTATAAAAAAT-TAAAGAAAAAAATATAAAATTCATAAAAAAATTATAAAATTTTATAA
12157416 CTTCTATTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
71 14 0.25
72 24 0.44
73 3 0.05
74 4 0.07
75 10 0.18
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (71 bp):
AAAAGTATAAAAAATTAAAGAAAAAAATATAAAATTCATAAAAAAATTATAAAATTTTATAAATT
TGTAAG
Found at i:12158721 original size:17 final size:17
Alignment explanation
Indices: 12158699--12158731 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12158689 GTAAAAACTA
12158699 AAAACTGAAAATAAAAC
1 AAAACTGAAAATAAAAC
12158716 AAAACTGAAAATAAAA
1 AAAACTGAAAATAAAA
12158732 AAGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.09, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAACTGAAAATAAAAC
Found at i:12159052 original size:2 final size:2
Alignment explanation
Indices: 12159047--12159072 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12159037 ATTCATTGTA
12159047 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
12159073 GGTTCTCAAC
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:12160687 original size:2 final size:2
Alignment explanation
Indices: 12160680--12160707 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12160670 AATACGTTTG
12160680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12160708 TTTTTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12167246 original size:19 final size:19
Alignment explanation
Indices: 12167224--12167285 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
12167214 ATGCGTCAAT
12167224 ATGCACTTCTTGTGCTAGG
1 ATGCACTTCTTGTGCTAGG
* *
12167243 ATGCAGTT-TGTATGCTAGG
1 ATGCACTTCT-TGTGCTAGG
* * *
12167262 ATACACTTCGTGTGCTAGT
1 ATGCACTTCTTGTGCTAGG
12167281 ATGCA
1 ATGCA
12167286 TTATGTGTGC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 1 0.03
19 32 0.97
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (19 bp):
ATGCACTTCTTGTGCTAGG
Found at i:12174290 original size:3 final size:3
Alignment explanation
Indices: 12174277--12174315 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
12174267 TTTATGCAAT
*
12174277 AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
12174316 GAAAATGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12175614 original size:17 final size:18
Alignment explanation
Indices: 12175594--12175628 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
12175584 ATGTAAGGTT
12175594 ATAAAAAATTT-TAAAAA
1 ATAAAAAATTTCTAAAAA
12175611 ATAAAAAATTTCTAAAAA
1 ATAAAAAATTTCTAAAAA
12175629 TACTTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAAAATTTCTAAAAA
Found at i:12182215 original size:19 final size:19
Alignment explanation
Indices: 12182191--12182230 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12182181 AAAAGAATAT
*
12182191 AATATTAAATTAAAAACAA
1 AATATTAAAATAAAAACAA
*
12182210 AATATTAAAATAAAAATAA
1 AATATTAAAATAAAAACAA
12182229 AA
1 AA
12182231 ATAAAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (19 bp):
AATATTAAAATAAAAACAA
Found at i:12188022 original size:30 final size:31
Alignment explanation
Indices: 12187985--12188054 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
12187975 GATACATAAT
* *
12187985 CTTTGATTTT-G-TGCAACTATACACATTAAA
1 CTTTGATTTTGGTTG-AAATATACACATAAAA
*
12188015 GTTTGATTTTGGTTGAAATATACACATAAAA
1 CTTTGATTTTGGTTGAAATATACACATAAAA
12188046 CTTTGATTT
1 CTTTGATTT
12188055 GATTCAATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.26
31 23 0.68
32 2 0.06
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (31 bp):
CTTTGATTTTGGTTGAAATATACACATAAAA
Found at i:12191002 original size:17 final size:16
Alignment explanation
Indices: 12190967--12191034 Score: 55
Period size: 18 Copynumber: 3.9 Consensus size: 16
12190957 CTAGGCTGGC
12190967 TTTTAATTTGTTTTCT
1 TTTTAATTTGTTTTCT
*
12190983 TTTTCAATTTCGTTTTTT
1 TTTT-AATTT-GTTTTCT
* *
12191001 TTATTATTTTGGTTCTTGT
1 TT-TTAATTT-GTT-TTCT
12191020 TTTTAATTATGTTTT
1 TTTTAATT-TGTTTT
12191035 TTTCTTCACT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
16 4 0.10
17 7 0.17
18 23 0.55
19 8 0.19
ACGTcount: A:0.13, C:0.06, G:0.09, T:0.72
Consensus pattern (16 bp):
TTTTAATTTGTTTTCT
Found at i:12208764 original size:62 final size:62
Alignment explanation
Indices: 12208698--12208824 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
12208688 TTGAATAAAG
*
12208698 AAAAAAGGACTTAAATGGTAATTAAACCATTTAAGGAGTTAGTAGACAATTTTGGGTAATTA
1 AAAAAACGACTTAAATGGTAATTAAACCATTTAAGGAGTTAGTAGACAATTTTGGGTAATTA
12208760 AAAAAACGACTTAAATGGTAATTAAACCATTTAAGGAGTTAGTAGACAATTTTGGGTAATTA
1 AAAAAACGACTTAAATGGTAATTAAACCATTTAAGGAGTTAGTAGACAATTTTGGGTAATTA
12208822 AAA
1 AAA
12208825 GCTTGAAAAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (62 bp):
AAAAAACGACTTAAATGGTAATTAAACCATTTAAGGAGTTAGTAGACAATTTTGGGTAATTA
Found at i:12209163 original size:19 final size:19
Alignment explanation
Indices: 12209139--12209176 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12209129 TTTTTATGTT
12209139 AAATTATGAATTTGAAATG
1 AAATTATGAATTTGAAATG
12209158 AAATTATGAATTTGAAATG
1 AAATTATGAATTTGAAATG
12209177 TTGGTTGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (19 bp):
AAATTATGAATTTGAAATG
Found at i:12217267 original size:89 final size:87
Alignment explanation
Indices: 12217149--12217324 Score: 298
Period size: 89 Copynumber: 2.0 Consensus size: 87
12217139 TGTTAGGAAT
* *
12217149 GAAAATATTTATGATTGATAAGCTTACTCATTTATGAGTTTGTGGTTACGTAGTTGATAAATTTT
1 GAAAATATTTATGATTGACAAGCTTACTCATTTATGAGTTGGTGGTTACGTAGTTGATAAATTTT
*
12217214 GAGGCATTGGTTTAGTTTTATA
66 GAGGCATTGGTATAGTTTTATA
12217236 GAAAATATTTATGATGTTGACAAGCTTACTCATTTATGAGTTGGTGGTTACGTAGTTGATAAATT
1 GAAAATATTTATGA--TTGACAAGCTTACTCATTTATGAGTTGGTGGTTACGTAGTTGATAAATT
*
12217301 TTGATGCATTGGTATAGTTTTATA
64 TTGAGGCATTGGTATAGTTTTATA
12217325 TTTATCATAT
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
87 14 0.17
89 69 0.83
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (87 bp):
GAAAATATTTATGATTGACAAGCTTACTCATTTATGAGTTGGTGGTTACGTAGTTGATAAATTTT
GAGGCATTGGTATAGTTTTATA
Found at i:12219573 original size:22 final size:22
Alignment explanation
Indices: 12219544--12219631 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 22
12219534 AACTTTGAGC
*
12219544 AATAGGCACCGTAGTGCAAATT
1 AATAGGCACCGAAGTGCAAATT
* * ** *
12219566 AATGGGCACCAAAGTGTGAATC
1 AATAGGCACCGAAGTGCAAATT
* *
12219588 AATAGGTACCGAAGTGCGAATT
1 AATAGGCACCGAAGTGCAAATT
* * *
12219610 AGTAGGCACCGTAGTGAAAATT
1 AATAGGCACCGAAGTGCAAATT
12219632 CCATACAAGC
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (22 bp):
AATAGGCACCGAAGTGCAAATT
Found at i:12222131 original size:4 final size:4
Alignment explanation
Indices: 12222122--12222147 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12222112 TGCTAGCAAC
12222122 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
12222148 GTTGAAGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:12224411 original size:15 final size:16
Alignment explanation
Indices: 12224383--12224420 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
12224373 AAGGACAAAA
12224383 AGAAATTCCTTTACTT
1 AGAAATTCCTTTACTT
*
12224399 AGAATTTCC-TTACTT
1 AGAAATTCCTTTACTT
12224414 AGAAATT
1 AGAAATT
12224421 AAAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (16 bp):
AGAAATTCCTTTACTT
Found at i:12224668 original size:5 final size:5
Alignment explanation
Indices: 12224658--12224691 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
12224648 AAGACAAAGG
*
12224658 AGACT AGACT AGACT AGACT AGACC AGACT AGAC
1 AGACT AGACT AGACT AGACT AGACT AGACT AGAC
12224692 CAGATTAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.15
Consensus pattern (5 bp):
AGACT
Found at i:12224692 original size:10 final size:10
Alignment explanation
Indices: 12224658--12224695 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
12224648 AAGACAAAGG
*
12224658 AGACTAGACT
1 AGACCAGACT
*
12224668 AGACTAGACT
1 AGACCAGACT
12224678 AGACCAGACT
1 AGACCAGACT
12224688 AGACCAGA
1 AGACCAGA
12224696 TTAATGTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.13
Consensus pattern (10 bp):
AGACCAGACT
Found at i:12230398 original size:16 final size:16
Alignment explanation
Indices: 12230359--12230404 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
12230349 TTTAAGAAAT
* *
12230359 TAAGTAGTGAATTT-T
1 TAAGTATTGAATTTAA
12230374 TAA-TATTGAATTTAA
1 TAAGTATTGAATTTAA
12230389 TAAGTATTGAATTTAA
1 TAAGTATTGAATTTAA
12230405 ATTATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (16 bp):
TAAGTATTGAATTTAA
Found at i:12248630 original size:30 final size:30
Alignment explanation
Indices: 12248591--12248648 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
12248581 TAATGCCAAG
*
12248591 CACATAGGAGTGTGTCCAGGCCGTGTAAGC
1 CACACAGGAGTGTGTCCAGGCCGTGTAAGC
*
12248621 CACACAGGAGTGTGTCTAGGCCGTGTAA
1 CACACAGGAGTGTGTCCAGGCCGTGTAA
12248649 CTCACTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (30 bp):
CACACAGGAGTGTGTCCAGGCCGTGTAAGC
Found at i:12250866 original size:93 final size:93
Alignment explanation
Indices: 12250759--12250931 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
12250749 CGCCCATAAG
*
12250759 CGAACTCGAACTCAACTCAACGAGGTCGGGCGTTCCCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGGTCGGACGTTCCCATCCATAAGTGAACTCGGACTCAACTCA
12250824 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* * * *
12250852 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTTGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGGTCGGACGTTCCCATCCATAAGTGAACTCGGACTCAACTCA
12250917 ACGAGCTCGGATGCC
66 ACGAGCTCGGATGCC
12250932 CAAATATCCG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (93 bp):
CGAACTCGAACTCAACTCAACGAGGTCGGACGTTCCCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:12250927 original size:46 final size:46
Alignment explanation
Indices: 12250752--12250927 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
12250742 TGTAACCCGC
* * * *
12250752 CCATAAGCGAACTCGAACTCAACTCAACGAGGTCGGGCGTTCCCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACAT
*
12250798 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCACAT
* * *
12250848 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACAT
* *
12250891 CCATAAGTGAACTTGGACTCAACTCAACGAGCTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
12250928 TGCCCAAATA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 2 0.02
46 60 0.56
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACAT
Found at i:12259326 original size:3 final size:3
Alignment explanation
Indices: 12259318--12259345 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12259308 ACATTACTAT
12259318 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12259346 ATATAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12259549 original size:3 final size:3
Alignment explanation
Indices: 12259541--12259596 Score: 53
Period size: 3 Copynumber: 18.0 Consensus size: 3
12259531 AATAGGGGTG
*
12259541 ATA ATA ATA ATA ATA ATA ATA ATA CA-A ACA ATA ATA CAT- ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA ATA -ATA
12259587 TATA ATA ATA
1 -ATA ATA ATA
12259597 GTAGTCAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
2 3 0.06
3 34 0.72
4 10 0.21
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12259556 original size:12 final size:13
Alignment explanation
Indices: 12259541--12259596 Score: 59
Period size: 12 Copynumber: 4.7 Consensus size: 13
12259531 AATAGGGGTG
12259541 ATAATAATAATA-
1 ATAATAATAATAC
12259553 ATAATAATAATAC
1 ATAATAATAATAC
*
12259566 A-AACAATAATAC
1 ATAATAATAATAC
*
12259578 AT-AT-AT-ATAT
1 ATAATAATAATAC
12259588 ATAATAATA
1 ATAATAATA
12259597 GTAGTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
10 5 0.14
11 4 0.11
12 26 0.72
13 1 0.03
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATAATAC
Found at i:12259684 original size:3 final size:3
Alignment explanation
Indices: 12259671--12259753 Score: 59
Period size: 3 Copynumber: 27.3 Consensus size: 3
12259661 GAGGGTATAT
12259671 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
12259715 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
12259754 AAAAATAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
2 9 0.14
3 45 0.69
4 9 0.14
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:12259695 original size:12 final size:12
Alignment explanation
Indices: 12259671--12259754 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 12
12259661 GAGGGTATAT
12259671 ATAATAT-AATA
1 ATAATATAAATA
12259682 ATAATATAAATA
1 ATAATATAAATA
12259694 ATAATATATACATGA
1 ATAATATA-A-AT-A
12259709 GA-AATA-ATAATA
1 -ATAATATA-AATA
12259721 ATAATATAAATA
1 ATAATATAAATA
* *
12259733 ATAGTAAAAATA
1 ATAATATAAATA
*
12259745 ATAAAATAAA
1 ATAATATAAA
12259755 AAAATAAAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
11 8 0.13
12 38 0.62
13 4 0.07
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:12259715 original size:21 final size:18
Alignment explanation
Indices: 12259676--12259735 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
12259666 TATATATAAT
*
12259676 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
12259694 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AGAAATA
*
12259715 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
12259733 ATA
1 ATA
12259736 GTAAAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 15 0.41
19 5 0.14
20 5 0.14
21 12 0.32
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAATAATAATAGAAATA
Found at i:12260333 original size:30 final size:30
Alignment explanation
Indices: 12260259--12260340 Score: 139
Period size: 30 Copynumber: 2.7 Consensus size: 30
12260249 ATTTGATGGT
12260259 GTAGGTGCAAGT-GGAGGACAAGGTGGTGGA
1 GTAGGTGCAAGTGGGAGG-CAAGGTGGTGGA
12260289 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
1 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
*
12260319 GTAGGTGCAAGTGGGAAGCAAG
1 GTAGGTGCAAGTGGGAGGCAAG
12260341 ATGACTAGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 45 0.90
31 5 0.10
ACGTcount: A:0.27, C:0.07, G:0.50, T:0.16
Consensus pattern (30 bp):
GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
Found at i:12265503 original size:28 final size:27
Alignment explanation
Indices: 12265440--12265509 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
12265430 ATAGTGAGTC
*
12265440 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
12265467 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
12265495 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12265510 GTACAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:12273439 original size:28 final size:27
Alignment explanation
Indices: 12273376--12273445 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
12273366 ATAGTGAGTC
12273376 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
12273403 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
12273431 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
12273446 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:12296670 original size:46 final size:46
Alignment explanation
Indices: 12296546--12296671 Score: 130
Period size: 46 Copynumber: 2.7 Consensus size: 46
12296536 CAGGGCTTAA
*
12296546 TATTCATGTATTC-TCGAGTCCGTAACATATGCAGAAGCTCGGAACC
1 TATTCATGTATTCTTC-AGTCCGCAACATATGCAGAAGCTCGGAACC
** * * ** *
12296592 TAAACCTGTATTCTTAAGTCTACAACTTATGCATG-AGCTCGGAACC
1 TATTCATGTATTCTTCAGTCCGCAACATATGCA-GAAGCTCGGAACC
* *
12296638 TATTCTTGTATTCTTCAGTCCGCAACACATGCAG
1 TATTCATGTATTCTTCAGTCCGCAACATATGCAG
12296672 TAACCCAGAA
Statistics
Matches: 62, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
45 1 0.02
46 59 0.95
47 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (46 bp):
TATTCATGTATTCTTCAGTCCGCAACATATGCAGAAGCTCGGAACC
Found at i:12297342 original size:20 final size:21
Alignment explanation
Indices: 12297304--12297342 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12297294 GGAAACTTTA
*
12297304 AAAAACTTCAATAGTTTAGCT
1 AAAAACTTCAATAGGTTAGCT
*
12297325 AAAAACTTC-ATGGGTTAG
1 AAAAACTTCAATAGGTTAG
12297343 AAAAATTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
AAAAACTTCAATAGGTTAGCT
Found at i:12300514 original size:82 final size:82
Alignment explanation
Indices: 12300298--12300569 Score: 246
Period size: 82 Copynumber: 3.3 Consensus size: 82
12300288 AATAATATTA
* * ** * *
12300298 TGAATTGTACATACGTGCCTCTGTTTGTACTTCGGTACCTTTGAATTACACATACGAGCCCTTGT
1 TGAATTGCACATACGTGCCCCTGTTAATACTTTGGTACCTTTGAATTACACATACGTGCCCTTGT
* * **
12300363 TTATACTTCGGTAATCT
66 TTGTACTTCAGTACCCT
* * * ** ** * *
12300380 TGAATTGCACGTACGTGCTCCTATTTCTACTTTAATAGCC-CT-AATTTGCACATACGTGCCCTT
1 TGAATTGCACATACGTGCCCCTGTTAATACTTTGGTA-CCTTTGAA-TTACACATACGTGCCCTT
* * *
12300443 TTTTGTTCTTCAATACCCT
64 GTTTGTACTTCAGTACCCT
* *
12300462 TGAATTACACATACGTGCCCCTGTTAATACTTTGGTACCTTTGAATTACACATACATGCCAC-TG
1 TGAATTGCACATACGTGCCCCTGTTAATACTTTGGTACCTTTGAATTACACATACGTGCC-CTTG
12300526 TTTGTACTTCAGTACTCC-
65 TTTGTACTTCAGTAC-CCT
* *
12300544 TGAATTGCACATACGTACTCCTGTTA
1 TGAATTGCACATACGTGCCCCTGTTA
12300570 GACTTCAGAA
Statistics
Matches: 148, Mismatches: 36, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
81 4 0.03
82 137 0.93
83 7 0.05
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (82 bp):
TGAATTGCACATACGTGCCCCTGTTAATACTTTGGTACCTTTGAATTACACATACGTGCCCTTGT
TTGTACTTCAGTACCCT
Found at i:12300534 original size:123 final size:123
Alignment explanation
Indices: 12300298--12300559 Score: 282
Period size: 123 Copynumber: 2.1 Consensus size: 123
12300288 AATAATATTA
* ** * *
12300298 TGAATTGTACATACGTGCCTCTGTTTGTACTTCGGTACCTTTGAATTACACATACGAGCCCTTGT
1 TGAATTGCACATACGTGCCTCTGTTTGTACTTCAATACCCTTGAATTACACATACGAGCCCCTGT
* * * * *
12300363 TTATACTTCGGTAATCTTGAATTGCACGTACGTGCTCCTATTTCTACTTTAATAGC-CC
66 TAATACTTCGGTAATCTTGAATTACACATACATGCTCCTATTTCTACTTCAATA-CTCC
* * *
12300421 T-AATTTGCACATACGTGCC-CTTTTTTGTTCTTCAATACCCTTGAATTACACATACGTGCCCCT
1 TGAA-TTGCACATACGTGCCTC-TGTTTGTACTTCAATACCCTTGAATTACACATACGAGCCCCT
* * * * *
12300484 GTTAATACTTTGGT-ACCTTTGAATTACACATACATGC-CACTGTTTGTACTTCAGTACTCC
64 GTTAATACTTCGGTAATC-TTGAATTACACATACATGCTC-CTATTTCTACTTCAATACTCC
12300544 TGAATTGCACATACGT
1 TGAATTGCACATACGT
12300560 ACTCCTGTTA
Statistics
Matches: 115, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
122 7 0.06
123 106 0.92
124 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (123 bp):
TGAATTGCACATACGTGCCTCTGTTTGTACTTCAATACCCTTGAATTACACATACGAGCCCCTGT
TAATACTTCGGTAATCTTGAATTACACATACATGCTCCTATTTCTACTTCAATACTCC
Found at i:12300568 original size:41 final size:39
Alignment explanation
Indices: 12300298--12300577 Score: 177
Period size: 41 Copynumber: 6.9 Consensus size: 39
12300288 AATAATATTA
* * *
12300298 TGAATTGTACATACGTGCCTCTGTTTGTACTTCGGTACCTT
1 TGAATTGCACATACGTGCC-CTGTTTGTACTTCAGTACC-C
* * * * * *
12300339 TGAATTACACATACGAGCCCTTGTTTATACTTCGGTAATCT
1 TGAATTGCACATACGTGCCC-TGTTTGTACTTCAGT-ACCC
* * * * *
12300380 TGAATTGCACGTACGTGCTCCTATTTCTACTTTAATAGCCC
1 TGAATTGCACATACGTGC-CCTGTTTGTACTTCAGTA-CCC
* * *
12300421 T-AATTTGCACATACGTGCCCTTTTTTGTTCTTCAATACCC
1 TGAA-TTGCACATACGTGCCC-TGTTTGTACTTCAGTACCC
* ** ** *
12300461 TTGAATTACACATACGTGCCCCTGTTAATACTTTGGTACCTT
1 -TGAATTGCACATACGTG-CCCTGTTTGTACTTCAGTACC-C
* *
12300503 TGAATTACACATACATGCCACTGTTTGTACTTCAGTACTCC
1 TGAATTGCACATACGTGCC-CTGTTTGTACTTCAGTAC-CC
* *
12300544 TGAATTGCACATACGTACTCCTGTTAG-ACTTCAG
1 TGAATTGCACATACGTGC-CCTGTTTGTACTTCAG
12300578 AAATTTTGAA
Statistics
Matches: 187, Mismatches: 39, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
40 18 0.10
41 158 0.84
42 11 0.06
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (39 bp):
TGAATTGCACATACGTGCCCTGTTTGTACTTCAGTACCC
Found at i:12302089 original size:29 final size:30
Alignment explanation
Indices: 12302032--12302089 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
12302022 GGTGAATAGT
*
12302032 TTATAATTATATAAAATTTATAAATTAAAG
1 TTATAATTATATAAAATATATAAATTAAAG
*
12302062 TTATAA-TGTATAAAATATA-AAATATAAA
1 TTATAATTATATAAAATATATAAAT-TAAA
12302090 ATAATACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 15 0.60
30 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (30 bp):
TTATAATTATATAAAATATATAAATTAAAG
Found at i:12310939 original size:3 final size:3
Alignment explanation
Indices: 12310915--12311462 Score: 164
Period size: 3 Copynumber: 177.7 Consensus size: 3
12310905 AAGTACCTAT
*
12310915 TAA TAA TAT TATA TAA -ATA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
12310962 TAA TAA TAA TAA TAA TAA CAA CAA TAA TAG CAA TAA TAG TAA AAA TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * * * *
12311011 AAA GAA -AG T-A TAA CGTAA TAA TGAGG TAA GGAA -AA TAA -AA T-A
1 TAA TAA TAA TAA TAA --TAA TAA T-A-A TAA -TAA TAA TAA TAA TAA
* * **
12311053 TAA T-A TAT TAGA TATA TAA -ATA TAA TAG TAA -ATA TAA TAA TGT TAA
1 TAA TAA TAA TA-A TA-A TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
*
12311099 -AA -AA TACCA TACA TAA -AGA GT-A TATA TAA -ACA TAGA TAA TAA AAA
1 TAA TAA TA--A TA-A TAA TA-A -TAA TA-A TAA TA-A TA-A TAA TAA TAA
* * * *
12311144 T-A TACA CTAA TAT TTA TAAA TAA TAA TAG TAA -ATG TAA TAA TAA TAA
1 TAA TA-A -TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* * * * *
12311191 TAA TAA TAT TAA GT-A TAG T-A TAAA TAA TATG TACA TAA CAG TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TA-A TA-A TAA TAA TAA TAA
*
12311238 TAA TAA GTAA CAA TAA TAA TAA TAA TAA T-A TAGA -AA TTCAA TAA -AA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA -T-AA TAA TAA
* * *
12311284 GTAA -ACA TAA T-A TAA TGA TAT TAA -AA TAA -AA T-A TACA CTAA TAT
1 -TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A -TAA TAA
* *
12311328 TTA TAAA TAA TAA TAG TAA -ATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * *
12311374 TAA TAA TAA TAA TAA TAA TAT TAA GT-A TAG T-A TAAA TAA TATG TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TA-A TA-A
* *
12311421 TAA TAG TAA TAA TAA TAA GTAA CAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
12311463 TAGAATTTCA
Statistics
Matches: 405, Mismatches: 73, Indels: 134
0.66 0.12 0.22
Matches are distributed among these distances:
2 42 0.10
3 285 0.70
4 65 0.16
5 13 0.03
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:12311523 original size:16 final size:16
Alignment explanation
Indices: 12311488--12311520 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12311478 AACTAAACAT
*
12311488 AATATAATAATATTAA
1 AATAAAATAATATTAA
12311504 AATAAAATAAT-TTAA
1 AATAAAATAATATTAA
12311519 AA
1 AA
12311521 ATACTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATAATATTAA
Found at i:12313589 original size:52 final size:50
Alignment explanation
Indices: 12313507--12313612 Score: 149
Period size: 52 Copynumber: 2.1 Consensus size: 50
12313497 AAAGTAGAAA
* *
12313507 TTGAAAATACCTCAGCGTGCCCTGACGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAATACCTCAGCGCGCCCTGACGCTCAACTCACCTCTCGC-A-ATGAG
* * *
12313559 TTGAAATTACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATGAG
1 TTGAAAATACCTCAGCGCGCCCTGACGCTCAACTCACCTCTCGCAATGAG
12313609 TTGA
1 TTGA
12313613 TTTTTTGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
50 9 0.18
51 1 0.02
52 39 0.80
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (50 bp):
TTGAAAATACCTCAGCGCGCCCTGACGCTCAACTCACCTCTCGCAATGAG
Found at i:12313676 original size:72 final size:72
Alignment explanation
Indices: 12313559--12314765 Score: 780
Period size: 72 Copynumber: 15.9 Consensus size: 72
12313549 GCAATATGAG
* * * **
12313559 TTGAAATTACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGC-A-ATGAGTTGATTTTTTGAA
1 TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTGAA
12313622 AGACA-AAA
65 A-ACAGAAA
*
12313630 TTTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTG
1 -TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--TTTTTG
*
12313695 AAAACAAAAA
63 AAAACAGAAA
* * *
12313705 TTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AA
1 TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA
*
12313769 ACATAAA
66 ACAGAAA
* ** * * ** * * * * * *
12313776 TTAAGAAACAAAAAT-TGCCAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCATTATG
1 TT--GAAA-ATACCTCAG-C-GTGTCT-TGAG-G-CTC-A-ACTC-A-T---TTCTCGCAATATG
* *
12313840 AGTTGATTTTTTTTTTTAAAAATAGAAA
51 AGTTGA------TTTTTGAAAACAGAAA
* * * ** * *
12313868 TTGAAAATACCTCAGCATGTGAAC-CGAGGGTCAACTCACCTCTCTCAATAGGAGTTGATTTTTG
1 TTGAAAATACCTCAGC--GTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG
*
12313932 AAAACATAAA
63 AAAACAGAAA
* * * *
12313942 TTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATATGAGTTGAATTTTGAAA
1 TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA
12314007 ACAGAAA
66 ACAGAAA
* * ** *
12314014 TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTT
1 TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-------TT
12314079 TTTGAAAAACAGAAA
59 TTTG-AAAACAGAAA
* * * * * *
12314094 TTGAAAATACCTCATCATGTCTTGAGGCTCAACTCATTTCTCGAAATCTAAGTTGAATTTTGAAA
1 TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA
*
12314159 ACAAAAA
66 ACAGAAA
* * * *
12314166 TTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTTGCAATATGAGTTGAATTTTG-AA
1 TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA
*
12314230 ACATAAA
66 ACAGAAA
* ** * * ** * * * * * *
12314237 TTAAGAAACAAAAAT-TGCCAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCATTATG
1 TT--GAAA-ATACCTCAG-C-GTGTCT-TGAG-G--CTCA-ACTC-A-T---TTCTCGCAATATG
* *
12314301 AGTTAATTTTTTTTTTTGAAAGATAGAAA
51 AGTTGA------TTTTTGAAA-ACAGAAA
* * ** *
12314330 TTGAAAATACCTCAGCATGTGAAC-CGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTG
1 TTGAAAATACCTCAGC--GTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG
*
12314394 AAAACATAAA
63 AAAACAGAAA
* * * *
12314404 TTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATATGAGTTGAATTTTGAAA
1 TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA
*
12314469 ACAAAAA
66 ACAGAAA
* ** *
12314476 TT-AAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTT
1 TTGAAAA-TACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--------
12314540 TTTTTGAAAAACAGAAA
57 TTTTTG-AAAACAGAAA
* * * *
12314557 TTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCTCAATCTGAGTTGAATTTTGAAA
1 TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA
*
12314622 ACAAAAA
66 ACAGAAA
* ** * *
12314629 TTGAAATTACCTCAATGTGTCTTGAGGTTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAA
1 TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA
*
12314694 ATAGAAA
66 ACAGAAA
* * * *
12314701 -TAAAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGTAATATGAGTTGAATTTTGAA
1 TTGAAAA-TACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAA
12314765 A
65 A
12314766 GTAGAAATAA
Statistics
Matches: 888, Mismatches: 170, Indels: 154
0.73 0.14 0.13
Matches are distributed among these distances:
71 30 0.03
72 415 0.47
73 19 0.02
74 119 0.13
75 28 0.03
76 4 0.00
77 2 0.00
78 2 0.00
79 9 0.01
80 83 0.09
81 71 0.08
82 6 0.01
84 1 0.00
85 36 0.04
86 4 0.00
87 4 0.00
88 1 0.00
89 7 0.01
90 12 0.01
91 16 0.02
92 12 0.01
93 7 0.01
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (72 bp):
TTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA
ACAGAAA
Found at i:12314491 original size:462 final size:461
Alignment explanation
Indices: 12313562--12314693 Score: 1976
Period size: 463 Copynumber: 2.5 Consensus size: 461
12313552 ATATGAGTTG
* *
12313562 AAATTACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGC-A-ATGAGTTGA------TTTTTT
1 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTTTT
* *
12313619 GAAAGACA-AAATTTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
66 GAAAAACAGAAA-TTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATCTGAG
*
12313683 TTGATTTTTTTGAAAACAAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCG
130 TTGA--ATTTTGAAAACAAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCG
12313748 CAATATGAGTTGAATTTTGAAACATAAATTAAGAAACAAAAATTGCCAATACCTCAGCGTGCCCC
193 CAATATGAGTTGAATTTTGAAACATAAATTAAGAAACAAAAATTGCCAATACCTCAGCGTGCCCC
*
12313813 GAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTTTTAAAAATAGAAATTGAAAATAC
258 GAGGCTCAACTCACCTCTCGCATTATGAGTTAATTTTTTTTTTTAAAAATAGAAATTGAAAATAC
* *
12313878 CTCAGCATGTGAACCGAGGGTCAACTCACCTCTCTCAATAGGAGTTGATTTTTGAAAACATAAAT
323 CTCAGCATGTGAACCGAGGCTCAACTCACCTCTCACAATAGGAGTTGATTTTTGAAAACATAAAT
12313943 TGAAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATATGAGTTGAATTTTGAAAA
388 TGAAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATATGAGTTGAATTTTGAAAA
* *
12314008 CAGAAATTG
453 CAAAAATTA
12314017 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTTTT
1 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTTTT
* * *
12314082 GAAAAACAGAAATTGAAAATACCTCATCATGTCTTGAGGCTCAACTCATTTCTCGAAATCTAAGT
66 GAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATCTGAGT
*
12314147 TGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTTGCAA
131 TGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
*
12314212 TATGAGTTGAATTTTGAAACATAAATTAAGAAACAAAAATTGCCAATACCTCAGCGTGCCCTGAG
196 TATGAGTTGAATTTTGAAACATAAATTAAGAAACAAAAATTGCCAATACCTCAGCGTGCCCCGAG
*
12314277 GCTCAACTCACCTCTCGCATTATGAGTTAATTTTTTTTTTTGAAAGATAGAAATTGAAAATACCT
261 GCTCAACTCACCTCTCGCATTATGAGTTAATTTTTTTTTTT-AAAAATAGAAATTGAAAATACCT
*
12314342 CAGCATGTGAACCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAACATAAATTG
325 CAGCATGTGAACCGAGGCTCAACTCACCTCTCACAATAGGAGTTGATTTTTGAAAACATAAATTG
12314407 AAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATATGAGTTGAATTTTGAAAACA
390 AAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATATGAGTTGAATTTTGAAAACA
12314472 AAAATTA
455 AAAATTA
12314479 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTTTT
1 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGA-TTTTTTTTTTT
*
12314544 TGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCTCAATCTGAG
65 TGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATCTGAG
* *
12314609 TTGAATTTTGAAAACAAAAATTGAAATTACCTCAATGTGTCTTGAGGTTCAACTCATTTCTCGCA
130 TTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCA
12314674 ATATGAGTTGAATTTTGAAA
195 ATATGAGTTGAATTTTGAAA
12314694 ATAGAAATAA
Statistics
Matches: 642, Mismatches: 24, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
455 40 0.06
456 1 0.00
457 8 0.01
461 164 0.26
462 207 0.32
463 219 0.34
464 3 0.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (461 bp):
AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTTTT
GAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATCTGAGT
TGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAA
TATGAGTTGAATTTTGAAACATAAATTAAGAAACAAAAATTGCCAATACCTCAGCGTGCCCCGAG
GCTCAACTCACCTCTCGCATTATGAGTTAATTTTTTTTTTTAAAAATAGAAATTGAAAATACCTC
AGCATGTGAACCGAGGCTCAACTCACCTCTCACAATAGGAGTTGATTTTTGAAAACATAAATTGA
AAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATATGAGTTGAATTTTGAAAACAA
AAATTA
Found at i:12314633 original size:225 final size:223
Alignment explanation
Indices: 12314258--12314761 Score: 731
Period size: 225 Copynumber: 2.2 Consensus size: 223
12314248 AAATTGCCAA
* * * *
12314258 TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCATTATGAGTTAATTTTTTTTTTTGAAAG
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTGAATTTTTTTTTTTGAAAA
*
12314323 ATAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCACAATATGAGTTGA
66 ACAGAAATTGAAAATACCTCAGCATGT--ACCGAGGCTCAACTCACCTCTCACAATATGAGTTGA
* *
12314388 TTTTTGAAAACATAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATAT
129 ATTTTGAAAACAAAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATAT
*
12314453 GAGTTGAATTTTGAAAACAAAAATTAAAAT
194 GAGTTGAATTTTGAAAACAAAAATAAAAAT
*
12314483 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTTTTTGAA
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT-GA-ATTTTTTTTTTTGAA
* ** * *
12314548 AAACAGAAATTGAAAATACCTCAGCATGT-CTTGAGGCTCAACTCATTTCTCTCAATCTGAGTTG
64 AAACAGAAATTGAAAATACCTCAGCATGTAC-CGAGGCTCAACTCACCTCTCACAATATGAGTTG
* * *
12314612 AATTTTGAAAACAAAAATTGAAATTACCTCAATGTGTCTTGAGGTTCAACTCATTTCTCGCAATA
128 AATTTTGAAAACAAAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATA
* *
12314677 TGAGTTGAATTTTGAAAATAGAAATAAAAAT
193 TGAGTTGAATTTTGAAAACAAAAATAAAAAT
* * ** *
12314708 TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGTAATATGAGTTGAATTTT
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG-TGAATTTT
12314762 GAAAGTAGAA
Statistics
Matches: 250, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
224 5 0.02
225 202 0.81
226 2 0.01
227 41 0.16
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (223 bp):
TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTGAATTTTTTTTTTTGAAAA
ACAGAAATTGAAAATACCTCAGCATGTACCGAGGCTCAACTCACCTCTCACAATATGAGTTGAAT
TTTGAAAACAAAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCATTACTCGCAATATGA
GTTGAATTTTGAAAACAAAAATAAAAAT
Found at i:12327207 original size:3 final size:3
Alignment explanation
Indices: 12327118--12327198 Score: 103
Period size: 3 Copynumber: 26.7 Consensus size: 3
12327108 AAGTACCTAT
*
12327118 TAA TAA TAT TATA TAA -ATA TAA TAAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
12327164 TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12327199 GCAATAATAG
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 3 0.04
3 60 0.87
4 6 0.09
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12327377 original size:3 final size:3
Alignment explanation
Indices: 12327369--12327665 Score: 149
Period size: 3 Copynumber: 98.3 Consensus size: 3
12327359 AATATTTATA
* * * *
12327369 AAT AAT AAT AGT AA- AAT -GT AAT AAT AAT AAT AAT ATT AA- AGT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
12327413 AGT -AT AAAT AAT ATGT ACAT AAC AGT AAT AAT AAT AAGT AAC AAT AAT
1 AAT AAT -AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
12327461 AAT AAT AAT AAT AAT -AT AGA- AATT CAAT AA- AAGT AA- ACAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AA-T -AAT AAT AA-T AAT A-AT AAT
* * * *
12327504 -AT AAT GAT ATT AA- AAT AA- AAT -AT ACACT AAT ATT TAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT -AAT AAT
*
12327548 AAT AGT AA- ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
12327593 AAT ATT AAGT -AT AGT -AT AAAT AAT AAGT AACT AAC AGT AAT AAT AAT
1 AAT AAT AA-T AAT AAT AAT -AAT AAT AA-T AA-T AAT AAT AAT AAT AAT
*
12327640 AAGT AAC AAT AAT AAT AAT AAT AAT A
1 AA-T AAT AAT AAT AAT AAT AAT AAT A
12327666 TAAAATTAAA
Statistics
Matches: 222, Mismatches: 40, Indels: 64
0.68 0.12 0.20
Matches are distributed among these distances:
2 23 0.10
3 164 0.74
4 31 0.14
5 4 0.02
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12327422 original size:25 final size:25
Alignment explanation
Indices: 12327365--12327618 Score: 77
Period size: 25 Copynumber: 10.5 Consensus size: 25
12327355 CACTAATATT
*
12327365 TATAAATAATAATAGTAAAATGTAA
1 TATAAATAATAATAGTAAAATATAA
* * *
12327390 TA-ATAATAATAATATTAAAGTATAG
1 TATA-AATAATAATAGTAAAATATAA
*
12327415 TATAAATAAT-AT-GT-ACATA-ACA
1 TATAAATAATAATAGTAAAATATA-A
*
12327437 -GT-AATAATAATAAGTAACAATAATAA
1 TATAAATAATAAT-AGTAA-AAT-ATAA
12327463 TA-ATAATAATAATA-TAGAAAT-TCAA
1 TATA-AATAATAATAGTA-AAATAT-AA
* * *
12327488 TA-AAAGTAA-ACATAATATAATGATAT
1 TATAAA-TAATA-ATAGTAAAAT-ATAA
*
12327514 TA-AAATAA-AATA-TACACTAATAT-T
1 TATAAATAATAATAGTA-A--AATATAA
12327538 TATAAATAATAATAGT-AAATAT-A
1 TATAAATAATAATAGTAAAATATAA
* *
12327561 -AT-AATAATAATAATAATA-ATAA
1 TATAAATAATAATAGTAAAATATAA
* * *
12327583 TA-ATAATAATAATA-TTAAGTATAG
1 TATA-AATAATAATAGTAAAATATAA
12327607 TATAAATAATAA
1 TATAAATAATAA
12327619 GTAACTAACA
Statistics
Matches: 175, Mismatches: 21, Indels: 67
0.67 0.08 0.25
Matches are distributed among these distances:
20 6 0.03
21 17 0.10
22 8 0.05
23 13 0.07
24 37 0.21
25 57 0.33
26 23 0.13
27 5 0.03
28 9 0.05
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (25 bp):
TATAAATAATAATAGTAAAATATAA
Found at i:12334056 original size:1 final size:1
Alignment explanation
Indices: 12334052--12334082 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
12334042 CTCTTTTTCC
12334052 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12334083 GGTTTTCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12340387 original size:16 final size:16
Alignment explanation
Indices: 12340368--12340403 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12340358 AACCTAACCC
*
12340368 AAAAAAAAA-ACAAAG
1 AAAAAAAAAGAAAAAG
12340383 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
12340399 AAAAA
1 AAAAA
12340404 CCTACCCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:12340418 original size:16 final size:15
Alignment explanation
Indices: 12340399--12340433 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12340389 AAAGAAAAAG
*
12340399 AAAAACCTACCCCAA
1 AAAAACCTAACCCAA
12340414 AAAAACCTAACCCAA
1 AAAAACCTAACCCAA
12340429 AAAAA
1 AAAAA
12340434 AAAAAGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.31, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAACCTAACCCAA
Found at i:12340434 original size:16 final size:15
Alignment explanation
Indices: 12340399--12340434 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
12340389 AAAGAAAAAG
*
12340399 AAAAACCTACCCCAA
1 AAAAACCTACCCAAA
12340414 AAAAACCTAACCCAAA
1 AAAAACCT-ACCCAAA
12340430 AAAAA
1 AAAAA
12340435 AAAAGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.64, C:0.31, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAACCTACCCAAA
Found at i:12341264 original size:11 final size:11
Alignment explanation
Indices: 12341246--12341275 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12341236 GTGTATATTG
12341246 TATATATTATA
1 TATATATTATA
*
12341257 TTTATATTATA
1 TATATATTATA
12341268 TATATATT
1 TATATATT
12341276 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:12343529 original size:12 final size:12
Alignment explanation
Indices: 12343509--12343544 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12343499 ATTCATTTAA
12343509 CATTCATGCATT
1 CATTCATGCATT
*
12343521 CATTTATGCATT
1 CATTCATGCATT
*
12343533 CATTCATTCATT
1 CATTCATGCATT
12343545 GCATATTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:12346838 original size:21 final size:21
Alignment explanation
Indices: 12346800--12346842 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
12346790 AAGAGCATGT
*
12346800 ATTGTTCGAACAGGCTGAAGAA
1 ATTGTTCGAACAGACTG-AGAA
12346822 ATTGTTCG-ACAGACTGAGAA
1 ATTGTTCGAACAGACTGAGAA
12346842 A
1 A
12346843 GTTCCAGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGTTCGAACAGACTGAGAA
Found at i:12350572 original size:70 final size:69
Alignment explanation
Indices: 12350453--12351081 Score: 399
Period size: 72 Copynumber: 9.1 Consensus size: 69
12350443 TGATTAAGCC
*
12350453 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
12350517 TGAGGTA
63 TGAGGTA
* * ** * *
12350524 TTTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTG
1 TTTTCAATTTTTGT-TTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTG
12350589 AGGTA
65 AGGTA
* *
12350594 TTTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTCAATTTTTGTTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT
12350659 GA-GTA
64 GAGGTA
* * * ** * * *
12350664 TTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT---------TTTA
1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
12350720 ---A
66 GGTA
*** ** *
12350721 TTTTTGTTTTTCA----AAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
12350782 GGTA
66 GGTA
* * *
12350786 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAA-TTTT-TGTTTTAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
12350851 TGAGGTA
63 TGAGGTA
* * ** * * * * ** * *** * *
12350858 TTTTCAATTTCTGTTTTCAATTTACGT--TGTT-CAAGA-ATCAACTCATATTGCGAGAGGTAGG
1 TTTTCAATTTTTGTTTTAAATCAAC-TCATATTGCGAGAGGTGAGTTGAGCCT-CG-G-GGCACG
* ***
12350919 TTGA-ACC
62 CTGAGGTA
* *
12350926 TTTT-AATTTCTACT-TTTTCAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGCAC
1 TTTTCAATTT-T--TGTTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC
12350989 GCTGAGGTA
61 GCTGAGGTA
* * * **
12350998 TTTTCAATTTTTATGTTTTAATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
1 TTTTCAA-TTTT-TGTTTTAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GGCAC
12351063 GCTGAGGTA
61 GCTGAGGTA
12351072 TTTTCAATTT
1 TTTTCAATTT
12351082 CCGTTTTTCA
Statistics
Matches: 419, Mismatches: 96, Indels: 84
0.70 0.16 0.14
Matches are distributed among these distances:
53 31 0.07
57 9 0.02
59 2 0.00
62 2 0.00
65 5 0.01
66 9 0.02
67 10 0.02
68 39 0.09
69 16 0.04
70 86 0.21
71 65 0.16
72 103 0.25
73 15 0.04
74 27 0.06
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (69 bp):
TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA
GGTA
Found at i:12350647 original size:71 final size:69
Alignment explanation
Indices: 12350453--12350715 Score: 323
Period size: 70 Copynumber: 3.7 Consensus size: 69
12350443 TGATTAAGCC
* *
12350453 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
12350518 GAGGTAT
63 GAGGTAT
* * ** * *
12350525 TTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTG
1 TTTTAATTTTTGT-TTTAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGGGGCACGCTG
12350589 AGGTAT
64 AGGTAT
12350595 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
1 TTTTAATTTTTGTTTT--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
12350660 A-GTAT
64 AGGTAT
* * ** * *
12350665 TTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
12350716 TTTAATTTTT
Statistics
Matches: 166, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
68 31 0.19
69 4 0.02
70 74 0.45
71 41 0.25
72 16 0.10
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAG
GTAT
Found at i:12350760 original size:121 final size:124
Alignment explanation
Indices: 12350595--12350840 Score: 383
Period size: 121 Copynumber: 2.0 Consensus size: 124
12350585 GTTGAGGTAT
12350595 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
1 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
* *
12350660 A-GTATTTT-TA-GTTTATGTTTTAAATT-GACTCATATTGCGAGAGGTGAGTTAAGCC
66 AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
* *
12350715 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
* * * *
12350780 GAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCC
65 GAGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
12350840 T
1 T
12350841 CAGGTCACGC
Statistics
Matches: 113, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
120 12 0.11
121 52 0.46
122 7 0.06
123 1 0.01
124 13 0.12
125 28 0.25
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (124 bp):
TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:12351053 original size:212 final size:214
Alignment explanation
Indices: 12350687--12351143 Score: 696
Period size: 212 Copynumber: 2.1 Consensus size: 214
12350677 TTTTAAATTG
**
12350687 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCT
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTACTTTTTCAAAATCAACTCATATTGCT
* *
12350752 AGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCA
66 AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTATGTTTTAATTTCAACTCA
* *
12350817 TATTGCGAGAGGTGAGTTGAGCCTCAGGT-CACGCTGAGGTATTTTCAATTTCTG-TTTTCAATT
131 TATTGCGAGAGGCGAGTTGAGCCTCAGGTACACGCTGAGGTATTTTCAATTTCCGTTTTTCAATT
*
12350880 TAC-GT-TGTTC-AAGAATCA
196 T-CTGTCT-TTCAAAAAATCA
12350898 ACTCATATTGCGAGAGGT-AGGTTGAA-CCTTTTAATTTCTACTTTTTCAAAATCAACTCATATT
1 ACTCATATTGCGAGAGGTGA-GTT-AAGCCTTTTAATTT-TACTTTTTCAAAATCAACTCATATT
12350961 G-TGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTATGTTTTAATTTCAA
63 GCT-AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTATGTTTTAATTTCAA
*
12351025 CTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTCAATTTCCGTTTTT
127 CTCATATTGCGAGAGGCGAGTTGAGCCTCAGGT-ACACGCTGAGGTATTTTCAATTTCCGTTTTT
12351090 CAATTTCTGTCTTTCAAAAAAAATCA
191 CAATTTCTGTCTTTC--AAAAAATCA
*
12351116 ACTCATATTGCGAGAGGTGAGTTGAGCC
1 ACTCATATTGCGAGAGGTGAGTTAAGCC
12351144 CAGGACACGC
Statistics
Matches: 223, Mismatches: 9, Indels: 21
0.88 0.04 0.08
Matches are distributed among these distances:
210 1 0.00
211 33 0.15
212 116 0.52
214 25 0.11
215 15 0.07
216 1 0.00
217 1 0.00
218 30 0.13
219 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (214 bp):
ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTACTTTTTCAAAATCAACTCATATTGCT
AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTATGTTTTAATTTCAACTCA
TATTGCGAGAGGCGAGTTGAGCCTCAGGTACACGCTGAGGTATTTTCAATTTCCGTTTTTCAATT
TCTGTCTTTCAAAAAATCA
Found at i:12351091 original size:14 final size:14
Alignment explanation
Indices: 12351072--12351106 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12351062 CGCTGAGGTA
12351072 TTTTCAATTTCCGT
1 TTTTCAATTTCCGT
*
12351086 TTTTCAATTTCTGT
1 TTTTCAATTTCCGT
*
12351100 CTTTCAA
1 TTTTCAA
12351107 AAAAAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCCGT
Found at i:12351211 original size:73 final size:77
Alignment explanation
Indices: 12351087--12351778 Score: 316
Period size: 73 Copynumber: 8.8 Consensus size: 77
12351077 AATTTCCGTT
* *
12351087 TTTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-CAGG-AC
1 TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCAC
*
12351150 ACGCTGAGGTAA
66 ACGCCGAGGTAA
* *
12351162 TTTCAATTTCTGT-TGTC-AAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCA
1 TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-CA
*
12351225 CACGCCGAGGTAT
65 CACGCCGAGGTAA
* * * * * * *
12351238 TTTCAATTTCCGTTTTTCAATTTTTGCCTTTCAAAAA--AA-TCAACTCATAT-TGCGAGAGGTG
1 TTTCAATTTCTGTCTGTCAA-----------AAAAAATCAACTC-A-T-AT-TGCGAGA--GGCG
*
12351299 AGTTGAGCCTCAGG-ACACGCTGAGGTAA
49 AGTTGAGCCTCAGGCACACGCCGAGGTAA
* * * *
12351327 TTTCAATTTCTGT-TGTC-AAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCA
1 TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAG-GCA
*
12351390 CACGTCGAGGTATTTTCAA
65 CACGCCGAGG-----T-AA
* * ** *
12351409 TTTCCATTTTTCAATTTCTGCCTTTAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 TTT-CA-ATTTC--TGTCTG--TCAAAAAAA----ATCAACTCATATTGCGAGAGGCGAGTTGAG
* *
12351474 CCTC-GGGACACGCTGAGGTAA
56 CCTCAGGCACACGCCGAGGTAA
* * *** *
12351495 TTTCAATTTCTGT-TTTC---AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-AC
1 TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCAC
** *
12351555 ACGTTGAGGTAT
66 ACGCCGAGGTAA
* * * * * * *
12351567 TTTTAATTTCTGT-TTTC--AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCT-TGGCTC
1 TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCAC
* *
12351628 ATGCGCTGAGCT-A
66 A--CGCCGAGGTAA
* * * * *
12351641 TTTCCAATTTCTATCTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATC
1 TTT-CAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAG-GC
* * *
12351705 ACACACTGAGGTATTT
64 ACACGCCGAGGTA--A
* * * * * * *
12351721 TTTCAATTTATATTTTTC-AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTC
1 TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTC
12351779 GGGTTACATG
Statistics
Matches: 485, Mismatches: 73, Indels: 114
0.72 0.11 0.17
Matches are distributed among these distances:
72 60 0.12
73 70 0.14
74 27 0.06
75 29 0.06
76 50 0.10
77 46 0.09
78 4 0.01
79 56 0.12
80 3 0.01
81 2 0.00
82 7 0.01
83 2 0.00
84 8 0.02
85 2 0.00
86 9 0.02
87 6 0.01
88 4 0.01
89 34 0.07
90 7 0.01
91 17 0.04
92 9 0.02
93 1 0.00
94 32 0.07
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (77 bp):
TTTCAATTTCTGTCTGTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCAC
ACGCCGAGGTAA
Found at i:12351220 original size:165 final size:165
Alignment explanation
Indices: 12350945--12351721 Score: 924
Period size: 165 Copynumber: 4.8 Consensus size: 165
12350935 CTACTTTTTC
* * *
12350945 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT-T
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
*** ** *
12351009 -TATGT-TTTAATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCTGAGGTA
66 GT-TGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTA
*
12351072 TTTTCAATTTCCGTTTTTCAATTTCTGTCTTTCAAAA
130 TTTTCAATTTCCGTTTTTCAATTTCTGCCTTTC-AAA
12351109 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-CAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* * *
12351173 GTTGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTAT
66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTAT
*
12351238 TTTCAATTTCCGTTTTTCAATTTTTGCCTTTCAAA
131 TTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAA
12351273 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* *
12351338 GTTGTCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACG-TCGAGGTA
66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCT-GAGGTA
* *
12351402 TTTTCAATTTCCATTTTTCAATTTCTGCCTTTAAAAAAA
130 TTTTCAATTTCCGTTTTTCAATTTCTGCCTTT---CAAA
*
12351441 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* * * ** * *
12351506 GTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG--ACACGTTGAGG---
66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTAT
*
12351564 --T--A------TTTTT-AATTTCTG-TTTTC-AA
131 TTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAA
* * * * *
12351586 AAAATCAACTTATATTGCGAGAGGTGAGTTGACCCT-TGGCTCATGCGCTGAGCT-ATTTCCAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACA--CGCTGAGGTAATTT-CAAT
* * * * * *
12351649 TTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGA
62 TTCTGT-TGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGA
12351714 GGTATTTT
126 GGTATTTT
12351722 TTCAATTTAT
Statistics
Matches: 546, Mismatches: 44, Indels: 53
0.85 0.07 0.08
Matches are distributed among these distances:
144 2 0.00
145 38 0.07
146 4 0.01
147 17 0.03
148 4 0.01
149 3 0.01
150 43 0.08
151 5 0.01
152 9 0.02
157 2 0.00
159 1 0.00
163 25 0.05
164 85 0.16
165 201 0.37
166 35 0.06
168 72 0.13
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (165 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTAT
TTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAA
Found at i:12351541 original size:72 final size:73
Alignment explanation
Indices: 12351439--12351781 Score: 357
Period size: 72 Copynumber: 4.6 Consensus size: 73
12351429 CCTTTAAAAA
12351439 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTT
12351504 CTGTTTTC
66 CTGTTTTC
* ** ** * * *
12351512 -AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTT
12351576 CTGTTTTC
66 CTGTTTTC
* * * ** *
12351584 AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCT-ATTTCCAA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA--CGCTGAGGTAATTT-CAA
*
12351648 TTTCTATCTTTC
63 TTTCTGT-TTTC
* ** * *
12351660 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACGCTGAGGTA--ATTTC
* *
12351725 AATTTATATTTTTC
61 AATTTCT-GTTTTC
* *
12351739 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGG
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
12351782 TTACATGTCG
Statistics
Matches: 219, Mismatches: 39, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
72 64 0.29
73 34 0.16
74 3 0.01
75 15 0.07
76 4 0.02
77 42 0.19
78 2 0.01
79 51 0.23
80 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (73 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTT
CTGTTTTC
Found at i:12351769 original size:79 final size:76
Alignment explanation
Indices: 12351438--12352155 Score: 409
Period size: 77 Copynumber: 9.0 Consensus size: 76
12351428 GCCTTTAAAA
** *
12351438 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACGCTGAGGTAATTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
12351501 TTTCTGTTTTC
66 TTTCTGTTTTC
* ** * * *
12351512 --AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-A-GACACGTTGAGGTATTTTTAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
12351573 TTTCTGTTTTC
66 TTTCTGTTTTC
* * ** * ** * *
12351584 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTCCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
*
12351648 TTTCTATCTTTC
66 TTTCTGT-TTTC
* *
12351660 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTA--TTTTC
* *
12351725 AATTTATATTTTTC
64 AATTTCT-GTTTTC
* * * * * *
12351739 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCT-GAGGTATTTTCA
** *
12351803 AAATCTATTTTTC
65 ATTTCT-GTTTTC
* ** * **
12351816 AAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA
1 -AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGA
*
12351881 GCTATTTTCAATTTCTGTTTTTTTTTTC
55 GGTATTTTCAATTTCTG------TTTTC
* * * * * *
12351909 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA-ATTTCTGCGAGAGTTGAGTT
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--CTCAGA--TC-AC-A-CGCTGAGGT
*
12351973 GAGTCTTTTAATTTCTGTTTTTC
58 -A-T-TTTCAATTTCTG-TTTTC
* **
12351996 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCCAG-TCACA-TATCGAGGTATTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-CAGATCACACGCT-GAGGTATTTTC
**
12352057 AAAATCTGCTTTTC
64 AATTTCTG-TTTTC
** * *
12352071 AAGTTAAGTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAG
1 ------A----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAG
*
12352136 CTATTTTCAATTTCTGTTTT
56 GTATTTTCAATTTCTGTTTT
12352156 TAATGTCTGT
Statistics
Matches: 501, Mismatches: 86, Indels: 102
0.73 0.12 0.15
Matches are distributed among these distances:
72 64 0.13
73 32 0.06
75 34 0.07
76 5 0.01
77 65 0.13
78 7 0.01
79 63 0.13
80 2 0.00
81 2 0.00
82 6 0.01
83 30 0.06
84 29 0.06
85 7 0.01
86 7 0.01
87 63 0.13
88 58 0.12
89 7 0.01
90 1 0.00
91 1 0.00
92 13 0.03
93 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (76 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
TTTCTGTTTTC
Found at i:12351964 original size:30 final size:30
Alignment explanation
Indices: 12351928--12351989 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
12351918 CAACTCATAT
12351928 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
12351958 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
12351988 TG
1 TG
12351990 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:12352142 original size:254 final size:248
Alignment explanation
Indices: 12351578--12352156 Score: 726
Period size: 254 Copynumber: 2.3 Consensus size: 248
12351568 TTTAATTTCT
* * *
12351578 GTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATT
1 GTTTT-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
* *
12351643 TCCAATTTC-----TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGA
65 TTCAATTTCTGTTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGA
* *
12351703 TCACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTG
130 TCACACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTG
* ** * * * **
12351768 AGTTGAGCCTCGGGTTACATGTCGAGGTATTTTCAAAATCTATTTTTCAAATTCT
194 AGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAATTAA
* * *
12351823 GTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTT
1 GTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTT
* *
12351888 TCAATTTCTGTTTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA
66 TCAATTTCTGTTTTTTCTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCA
* * * * * * *
12351953 -ATTTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGC
128 GA--TC-AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGC
* *
12352015 GAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAA
186 GAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAATTAA
12352078 G-TTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTT
1 GTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTT
12352142 TCAATTTCTGTTTTT
66 TCAATTTCTGTTTTT
12352157 AATGTCTGTT
Statistics
Matches: 287, Mismatches: 32, Indels: 21
0.84 0.09 0.06
Matches are distributed among these distances:
244 61 0.21
245 5 0.02
249 13 0.05
250 30 0.10
251 1 0.00
252 3 0.01
253 2 0.01
254 76 0.26
255 73 0.25
256 5 0.02
257 13 0.05
258 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (248 bp):
GTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTT
TCAATTTCTGTTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
CACACACTGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGTGAG
TTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAATTAA
Found at i:12352821 original size:16 final size:16
Alignment explanation
Indices: 12352802--12352837 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12352792 AACCTAACCC
*
12352802 AAAAAAAAA-ACAAAG
1 AAAAAAAAAGAAAAAG
12352817 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
12352833 AAAAA
1 AAAAA
12352838 CTTACCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:12353697 original size:11 final size:11
Alignment explanation
Indices: 12353679--12353708 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12353669 GTGTATATTG
12353679 TATATATTATA
1 TATATATTATA
*
12353690 TTTATATTATA
1 TATATATTATA
12353701 TATATATT
1 TATATATT
12353709 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:12354206 original size:2 final size:2
Alignment explanation
Indices: 12354199--12354229 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12354189 GTATGTCATG
*
12354199 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12354230 GTATGTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12356743 original size:21 final size:20
Alignment explanation
Indices: 12356717--12356773 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
12356707 TAGATTTTTT
12356717 TATTTTTTGAATTTTTTTGAA
1 TATTTTTTG-ATTTTTTTGAA
** *
12356738 TATTTTATCCATTGTTTTGAA
1 TATTTT-TTGATTTTTTTGAA
*
12356759 T-TTTTTAGATTTTTT
1 TATTTTTTGATTTTTT
12356774 ATATATACGG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 7 0.24
20 4 0.14
21 17 0.59
22 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.09, T:0.67
Consensus pattern (20 bp):
TATTTTTTGATTTTTTTGAA
Found at i:12357565 original size:19 final size:18
Alignment explanation
Indices: 12357541--12357576 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12357531 TCATGAGCTA
*
12357541 AGGTTAAAGTTTCTCATTC
1 AGGTTAAACTTT-TCATTC
12357560 AGGTTAAACTTTTCATT
1 AGGTTAAACTTTTCATT
12357577 AATTTTATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (18 bp):
AGGTTAAACTTTTCATTC
Found at i:12360250 original size:21 final size:21
Alignment explanation
Indices: 12360224--12360264 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12360214 TTTTTTTCTG
*
12360224 TTGTTGTTTTGCTATTATTTA
1 TTGTTGTTTTACTATTATTTA
*
12360245 TTGTTGTTTTATTATTATTT
1 TTGTTGTTTTACTATTATTT
12360265 TGCTATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.02, G:0.12, T:0.71
Consensus pattern (21 bp):
TTGTTGTTTTACTATTATTTA
Found at i:12362799 original size:17 final size:17
Alignment explanation
Indices: 12362779--12362812 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12362769 TGGTTTAGGT
12362779 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
**
12362796 TTAAATTTTTTAATTAA
1 TTAAAAATTTTAATTAA
12362813 AAATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:12363348 original size:3 final size:3
Alignment explanation
Indices: 12363340--12363373 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12363330 ATCTGATTCA
12363340 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12363374 GCCTATTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12378109 original size:48 final size:47
Alignment explanation
Indices: 12378044--12378374 Score: 306
Period size: 48 Copynumber: 6.9 Consensus size: 47
12378034 GACATTTGGG
* * ** *
12378044 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGAAATCGAACA
1 TGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCG-GCA
* * * *
12378092 CGATATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAA
1 TGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-A
* *
12378140 TG-TAACGAGAGCTAGTGCAAGACCATGTCTGGGACATGGCATCGGCA
1 TGAT-ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
* * * *
12378187 TTGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGACATCAGTCA
1 -TGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GGCA
* * * * *
12378236 CGATATGAAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCA
1 TGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
* * * *
12378283 TTGAGACGAGAGCTAGTGTAAGACCATGTATGGGACATGGCATCTGTC-
1 -TGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GGCA
* * * * * *
12378331 TCGACATGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATC
1 T-GATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC
12378375 AACAATTCAC
Statistics
Matches: 230, Mismatches: 45, Indels: 16
0.79 0.15 0.05
Matches are distributed among these distances:
47 7 0.03
48 217 0.94
49 6 0.03
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (47 bp):
TGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
Found at i:12378306 original size:144 final size:145
Alignment explanation
Indices: 12378044--12378375 Score: 474
Period size: 144 Copynumber: 2.3 Consensus size: 145
12378034 GACATTTGGG
* * *
12378044 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGAAATC-GAACACGATATGAGAGCCAGT
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGACATCAGAACACGATATGAAAGCCAGT
*
12378108 GTAAGACCATGTTTGGAACATGGCATCGGCAATGTAACGAGAGCTAGTGCAAGACCATGTCTGGG
66 GTAAGACCATGTTTGGAACATGGCATCGGCAATGTAACGAGAGCTAGTGCAAGACCATGTATGGG
12378173 ACATGGCATC-GGCAT
131 ACATGGCATCTGGC-T
* *
12378188 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGACATCAG-TCACGATATGAAAGCCAGT
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGACATCAGAACACGATATGAAAGCCAGT
* *
12378252 GTAAGACCATGTTTGGAACATGGCATCGGCATTG-AGACGAGAGCTAGTGTAAGACCATGTATGG
66 GTAAGACCATGTTTGGAACATGGCATCGGCAATGTA-ACGAGAGCTAGTGCAAGACCATGTATGG
*
12378316 GACATGGCATCTGTCT
130 GACATGGCATCTGGCT
* * * * * * *
12378332 CGACATGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATCA
1 TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGACATCA
12378376 ACAATTCACC
Statistics
Matches: 169, Mismatches: 16, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
143 1 0.01
144 165 0.98
145 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (145 bp):
TGATATGTGAGCTAGTGTAAGACCATGTCTGGGACATGACATCAGAACACGATATGAAAGCCAGT
GTAAGACCATGTTTGGAACATGGCATCGGCAATGTAACGAGAGCTAGTGCAAGACCATGTATGGG
ACATGGCATCTGGCT
Found at i:12386098 original size:144 final size:144
Alignment explanation
Indices: 12385806--12386133 Score: 428
Period size: 144 Copynumber: 2.3 Consensus size: 144
12385796 TTTGGGTGAT
* * * *
12385806 ATGTGTGCTAGTGTAAAACCATGTCTGGGACATGGTATCAACCATGATATGAAAGCCAGTGTAAG
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACCACGATATGAAAGCCAGTGTAAG
* *
12385871 ACCATGTTTGGAACATGGCATCGGCAATATAATAAGAGCTAGTGCAAGACCATGTCTGGGACATG
66 ACCATGTTTGGAACATGGCATCGGCAATATAACAAGAGCTAGTGCAAGACCATGTATGGGACATG
* *
12385936 GCATCGGCATTGAT
131 GCATCGGCATCGAC
* * ***
12385950 ATGTGCGCTAGTGTAAGACCATGTCTGGGACATGACATCGGTCACGATATGAAAGCCAGTGTAAG
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACCACGATATGAAAGCCAGTGTAAG
* *
12386015 ACCATGTTTGGAACATGGCATCGGC-AT-TGAGACGAGAGCTAGTGTAAGACCATGTATGGGACA
66 ACCATGTTTGGAACATGGCATCGGCAATAT-A-ACAAGAGCTAGTGCAAGACCATGTATGGGACA
*
12386078 TGGCATCTGTC-TCGAC
129 TGGCATC-GGCATCGAC
* * * *
12386094 ATGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATCA
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCA
12386134 GCAATTCACC
Statistics
Matches: 159, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
142 1 0.01
143 3 0.02
144 153 0.96
145 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (144 bp):
ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACCACGATATGAAAGCCAGTGTAAG
ACCATGTTTGGAACATGGCATCGGCAATATAACAAGAGCTAGTGCAAGACCATGTATGGGACATG
GCATCGGCATCGAC
Found at i:12386109 original size:48 final size:48
Alignment explanation
Indices: 12385815--12386132 Score: 295
Period size: 48 Copynumber: 6.6 Consensus size: 48
12385805 TATGTGTGCT
* * ** *
12385815 AGTGTAAAACCATGTCTGGGACATGGTATCAACCAT-GATATGAAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GGCATCGATATGAGAGCC
* * * *
12385863 AGTGTAAGACCATGTTTGGAACATGGCATCGGCAAT--ATAATAAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ATCGAT-ATGAGAGCC
* * * * *
12385911 AGTGCAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGAGAGCC
* *
12385959 AGTGTAAGACCATGTCTGGGACATGACATCGGTCA-CGATATGAAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CATCGATATGAGAGCC
* * * * * *
12386007 AGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGAGAGCC
* * * *
12386055 AGTGTAAGACCATGTATGGGACATGGCATCTGTC-TCGACATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GGCATCGATATGAGAGCC
* * *
12386103 AATGTAAGACCATGTTTGGAACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
12386133 AGCAATTCAC
Statistics
Matches: 222, Mismatches: 41, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
47 7 0.03
48 209 0.94
49 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGAGAGCC
Found at i:12387378 original size:20 final size:21
Alignment explanation
Indices: 12387339--12387378 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12387329 GTTAAATAGG
12387339 CACATGAGCGTGTCGCCCTTC
1 CACATGAGCGTGTCGCCCTTC
*
12387360 CACATGGGCGTGT-GCCCTT
1 CACATGAGCGTGTCGCCCTT
12387379 GTCTCCTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (21 bp):
CACATGAGCGTGTCGCCCTTC
Found at i:12391000 original size:23 final size:23
Alignment explanation
Indices: 12390956--12391001 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12390946 TAACCTTTAA
* *
12390956 ATTTTTTTATTTAATTATATTTT
1 ATTTTATTATTTAATTACATTTT
12390979 ATTTTATTATTATAA-TACATTTT
1 ATTTTATTATT-TAATTACATTTT
12391002 TAATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTTATTATTTAATTACATTTT
Found at i:12391220 original size:2 final size:2
Alignment explanation
Indices: 12391213--12391239 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12391203 CTAATATTTC
12391213 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12391240 GGTTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12391446 original size:41 final size:41
Alignment explanation
Indices: 12391370--12391711 Score: 452
Period size: 41 Copynumber: 8.4 Consensus size: 41
12391360 TTTAATTGTA
* *
12391370 AAAAACGCCGCTAAAGA-TAGAGCATTAGCGACGCTTTTGG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
*
12391410 CAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
* * * ****
12391451 AAAAACGCCGCTAATGACCAGAGTATTAGCGGCTCTTACAA
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
* *
12391492 AAAAACGCCGCTAATGACCAGAGCATTAGCGGTGCTTTTGG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
* * * *
12391533 TAAAACGCCGCTAAAGACAAGAGCATTAGCGACGCTTATGG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
* * *
12391574 CAAAACGCCGCTAAAGACAAGAGCATTAGCGGCGCTTTTGT
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
* * * *
12391615 AGAAACGCCGCTAAAGACTAGAGCATTAGTGGCGCTTTTGT
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
* *
12391656 AAAAATGCCGCTAAAGACTAGAGCATTAGCGGCGCTTTTGG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
12391697 AAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
12391712 AGTCATATAA
Statistics
Matches: 264, Mismatches: 37, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
40 16 0.06
41 248 0.94
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGG
Found at i:12391884 original size:7 final size:7
Alignment explanation
Indices: 12391869--12391966 Score: 52
Period size: 7 Copynumber: 13.4 Consensus size: 7
12391859 TTAATTATCA
*
12391869 TTATAGT
1 TTATGGT
12391876 TTATGGT
1 TTATGGT
*
12391883 TTATGAT
1 TTATGGT
* *
12391890 TTAAGAT
1 TTATGGT
*
12391897 ATATGGT
1 TTATGGT
*
12391904 TTAGGGT
1 TTATGGT
*
12391911 TTAAGGT
1 TTATGGT
12391918 TTATGAGT
1 TTATG-GT
12391926 TAACTATGGT
1 T---TATGGT
* *
12391936 TTAAGAT
1 TTATGGT
*
12391943 ATATGGT
1 TTATGGT
*
12391950 TTAGGGT
1 TTATGGT
*
12391957 TTAAGGT
1 TTATGGT
12391964 TTA
1 TTA
12391967 GGAGTTAACT
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
7 59 0.86
8 3 0.04
10 3 0.04
11 4 0.06
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.47
Consensus pattern (7 bp):
TTATGGT
Found at i:12391901 original size:21 final size:21
Alignment explanation
Indices: 12391877--12391961 Score: 89
Period size: 21 Copynumber: 3.9 Consensus size: 21
12391867 CATTATAGTT
* *
12391877 TATGGTTTATGATTTAAGATA
1 TATGGTTTAGGGTTTAAGATA
* *
12391898 TATGGTTTAGGGTTTAAGGTT
1 TATGGTTTAGGGTTTAAGATA
*
12391919 TATGAGTTAACTATGGTTTAAGATA
1 TATG-GTT---TAGGGTTTAAGATA
12391944 TATGGTTTAGGGTTTAAG
1 TATGGTTTAGGGTTTAAG
12391962 GTTTAGGAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 31 0.60
22 3 0.06
24 3 0.06
25 15 0.29
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (21 bp):
TATGGTTTAGGGTTTAAGATA
Found at i:12391941 original size:46 final size:46
Alignment explanation
Indices: 12391884--12391977 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
12391874 GTTTATGGTT
*
12391884 TATGATTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAAC
1 TATGATTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
*
12391930 TATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
1 TATGATTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
12391976 TA
1 TA
12391978 GTATTTGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.43
Consensus pattern (46 bp):
TATGATTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAAC
Found at i:12392033 original size:7 final size:7
Alignment explanation
Indices: 12392004--12392125 Score: 77
Period size: 7 Copynumber: 17.1 Consensus size: 7
12391994 GATGAATTAT
12392004 GGGTTTA
1 GGGTTTA
*
12392011 GGGATTA
1 GGGTTTA
* *
12392018 TGATTTA
1 GGGTTTA
12392025 GGGTTTA
1 GGGTTTA
*
12392032 GGGGTTA
1 GGGTTTA
12392039 GGG-TTA
1 GGGTTTA
*
12392045 GAGTTTA
1 GGGTTTA
* *
12392052 AGGTGTAA
1 GGGT-TTA
*
12392060 GGGTTTG
1 GGGTTTA
*
12392067 GGGTTAA
1 GGGTTTA
12392074 GGGTTTA
1 GGGTTTA
*
12392081 GAGTTTA
1 GGGTTTA
*
12392088 GTGTTTA
1 GGGTTTA
*
12392095 TGGG-ATA
1 -GGGTTTA
*
12392102 GGAGTTAA
1 GG-GTTTA
12392110 GAGGTTTA
1 G-GGTTTA
12392118 GGGTTTA
1 GGGTTTA
12392125 G
1 G
12392126 ATTAATTAGT
Statistics
Matches: 85, Mismatches: 24, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
6 7 0.08
7 63 0.74
8 14 0.16
9 1 0.01
ACGTcount: A:0.22, C:0.00, G:0.40, T:0.38
Consensus pattern (7 bp):
GGGTTTA
Found at i:12393318 original size:46 final size:46
Alignment explanation
Indices: 12393262--12393351 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
12393252 TATTTATATT
*
12393262 ATTTTTAATTTA-ATAT-TTAATATCCTATATATGTAATTGTATTAAA
1 ATTTTTAATTTATATATATTAAAAT--TATATATGTAATTGTATTAAA
* *
12393308 ATTTTTAATTTATATTTATTAAAATTTTATATGTAATTGTATTA
1 ATTTTTAATTTATATATATTAAAATTATATATGTAATTGTATTA
12393352 GTATTTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
46 30 0.77
47 3 0.08
48 6 0.15
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (46 bp):
ATTTTTAATTTATATATATTAAAATTATATATGTAATTGTATTAAA
Found at i:12393358 original size:23 final size:23
Alignment explanation
Indices: 12393289--12393351 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
12393279 TAATATCCTA
12393289 TATATGTAATTGTATTAAAATTT
1 TATATGTAATTGTATTAAAATTT
*
12393312 T-TAATTTATATT-TATTAAAATTT
1 TAT-ATGTA-ATTGTATTAAAATTT
12393335 TATATGTAATTGTATTA
1 TATATGTAATTGTATTA
12393352 GTATTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 4 0.12
23 26 0.76
24 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (23 bp):
TATATGTAATTGTATTAAAATTT
Found at i:12397411 original size:12 final size:12
Alignment explanation
Indices: 12397394--12397426 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
12397384 TCTTGCATAT
12397394 ATGATTAATAAC
1 ATGATTAATAAC
12397406 ATGATTAATAAC
1 ATGATTAATAAC
12397418 ATGATTAAT
1 ATGATTAAT
12397427 GGTTCTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (12 bp):
ATGATTAATAAC
Found at i:12397913 original size:16 final size:16
Alignment explanation
Indices: 12397892--12397925 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12397882 AAAGTGTGCA
12397892 TTCTATTAT-TATTTTG
1 TTCTATT-TGTATTTTG
12397908 TTCTATTTGTATTTTG
1 TTCTATTTGTATTTTG
12397924 TT
1 TT
12397926 AGATTTCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.71
Consensus pattern (16 bp):
TTCTATTTGTATTTTG
Found at i:12400596 original size:11 final size:11
Alignment explanation
Indices: 12400577--12400606 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12400567 TTATATTTCT
*
12400577 TTTTTTTTCCC
1 TTTTCTTTCCC
12400588 TTTTCTTTCCC
1 TTTTCTTTCCC
12400599 TTTTCTTT
1 TTTTCTTT
12400607 ACATCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTCTTTCCC
Found at i:12401735 original size:19 final size:20
Alignment explanation
Indices: 12401711--12401755 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
12401701 GGGGGGAAAG
* *
12401711 TGGGAGAGAGTAAAAGT-TT
1 TGGGAGAAAGTAAAAATATT
12401730 TGGGAGAAAGTAAAAATATT
1 TGGGAGAAAGTAAAAATATT
12401750 TGGGAG
1 TGGGAG
12401756 TTTAGGGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (20 bp):
TGGGAGAAAGTAAAAATATT
Found at i:12406619 original size:48 final size:48
Alignment explanation
Indices: 12406563--12406830 Score: 257
Period size: 48 Copynumber: 5.7 Consensus size: 48
12406553 GTGATCCTAC
*
12406563 GTAAGACCATGTCTGGGACATGGCATTGGCATCGTTATGAGATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGAGATCCCAT
* * *
12406611 GTAAGACCATGTCTGGGACATGGCATTGGTATC-ATTATAAGATCCTAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCATCGA-TATGAGATCCCAT
* * ** *
12406659 GTATGACCATGTCTGGGACATGGCATTGGCATTGACGTGTGATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGAGATCCCAT
* * ***
12406707 GTAAGACCATATCTGGGATATGGCATTGGCATCGATATGAGA-CATTGT
1 GTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGAGATC-CCAT
* * *
12406755 GTAAGACCATAG-CTGGG-CTAT--CA---GCTTCGATTTGTGATCCCAT
1 GTAAGACCAT-GTCTGGGAC-ATGGCATTGGCATCGATATGAGATCCCAT
* * *
12406798 GTAAGTCCATATCTGGGATATGGCATTGGCATC
1 GTAAGACCATGTCTGGGACATGGCATTGGCATC
12406831 TTACTATGTT
Statistics
Matches: 173, Mismatches: 34, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
43 28 0.16
44 1 0.01
45 2 0.01
46 2 0.01
47 1 0.01
48 138 0.80
49 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (48 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGAGATCCCAT
Found at i:12406763 original size:96 final size:96
Alignment explanation
Indices: 12406555--12406830 Score: 302
Period size: 96 Copynumber: 2.9 Consensus size: 96
12406545 GGTTATGTGT
* * * *
12406555 GATCCTACGTAAGACCATGTCTGGGACATGGCATTGGCATCGTTATGAGATCCCATGTAAGACCA
1 GATCCTATGTAAGACCATGTCTGGGACATGGCATTGGCATTGATATGTGATCCCATGTAAGACCA
* * *
12406620 TGTCTGGGACATGGCATTGGTATCATTATAA
66 TATCTGGGATATGGCATTGGCATCATTATAA
* **
12406651 GATCCTATGTATGACCATGTCTGGGACATGGCATTGGCATTGACGTGTGATCCCATGTAAGACCA
1 GATCCTATGTAAGACCATGTCTGGGACATGGCATTGGCATTGATATGTGATCCCATGTAAGACCA
*
12406716 TATCTGGGATATGGCATTGGCATCGA-TATGA
66 TATCTGGGATATGGCATTGGCATC-ATTATAA
* * *
12406747 GA-CATTGTGTAAGACCATAG-CTGGG-CTAT--CA---GC-TTCGATTTGTGATCCCATGTAAG
1 GATC-CTATGTAAGACCAT-GTCTGGGAC-ATGGCATTGGCATT-GATATGTGATCCCATGTAAG
*
12406803 TCCATATCTGGGATATGGCATTGGCATC
62 ACCATATCTGGGATATGGCATTGGCATC
12406831 TTACTATGTT
Statistics
Matches: 158, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
90 2 0.01
91 47 0.30
94 2 0.01
95 2 0.01
96 103 0.65
97 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (96 bp):
GATCCTATGTAAGACCATGTCTGGGACATGGCATTGGCATTGATATGTGATCCCATGTAAGACCA
TATCTGGGATATGGCATTGGCATCATTATAA
Found at i:12410671 original size:26 final size:26
Alignment explanation
Indices: 12410635--12410718 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
12410625 TGATACAAAT
12410635 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
12410661 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
12410687 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
12410713 TGATAA
1 TGATAA
12410719 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:12412225 original size:26 final size:26
Alignment explanation
Indices: 12412196--12412248 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
12412186 TTTACAGTTT
12412196 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
12412222 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
12412248 T
1 T
12412249 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:12415175 original size:26 final size:26
Alignment explanation
Indices: 12415123--12415177 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
12415113 GGGACAGTTT
12415123 TACCCCTAGGAGATAAATTACCGAAA
1 TACCCCTAGGAGATAAATTACCGAAA
* *
12415149 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGAGATAAATT-ACCGAAA
12415175 TAC
1 TAC
12415178 ATGTTTGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24
Consensus pattern (26 bp):
TACCCCTAGGAGATAAATTACCGAAA
Found at i:12422785 original size:29 final size:29
Alignment explanation
Indices: 12422753--12422854 Score: 159
Period size: 29 Copynumber: 3.5 Consensus size: 29
12422743 CTTCGAGCTC
* *
12422753 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACTCAGTGCCATATATTTCCAGCAT
*
12422782 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTCAGTGCCATATATTTCCAGCAT
*
12422811 GCACACTCAGTGCCATATATTTCCAGCAC
1 GCACACTCAGTGCCATATATTTCCAGCAT
*
12422840 GCACACTTAGTGCCA
1 GCACACTCAGTGCCA
12422855 ATCTCGTCAC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.25
Consensus pattern (29 bp):
GCACACTCAGTGCCATATATTTCCAGCAT
Found at i:12422786 original size:58 final size:58
Alignment explanation
Indices: 12422723--12422854 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
12422713 AATTTAAGCC
* * * *
12422723 CGCACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCCATATATTTCCAGCA
* * * *
12422781 TGCACACTTAGTGCCATATATTTCCAGCATGCACACTCAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCA
12422839 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
12422855 ATCTCGTCAC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 63 0.98
59 1 0.02
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (58 bp):
CGCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCA
Found at i:12429608 original size:29 final size:29
Alignment explanation
Indices: 12429449--12429608 Score: 144
Period size: 29 Copynumber: 5.6 Consensus size: 29
12429439 TACTCGATTT
** * *
12429449 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* *** * *
12429478 CGCACACATAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
** *
12429507 CGCACACCCAGTGCCGTATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
12429536 TGCACACTTAGTGCC-TATATTTCCAGAA
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
12429564 TGCACACTCAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
12429593 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
12429609 ATCTCGTCAC
Statistics
Matches: 106, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
28 28 0.26
29 78 0.74
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:12432308 original size:24 final size:24
Alignment explanation
Indices: 12432281--12432443 Score: 308
Period size: 24 Copynumber: 6.8 Consensus size: 24
12432271 CTTATTATGT
**
12432281 TCGCACACATAGTGCCATAGCGAA
1 TCGCACACATAGTGCCATAGTAAA
12432305 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
12432329 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
12432353 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
12432377 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
12432401 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
12432425 TCGCACACATAGTGCCATA
1 TCGCACACATAGTGCCATA
12432444 TATTTCCAGC
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
24 137 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:12440240 original size:24 final size:24
Alignment explanation
Indices: 12440213--12440351 Score: 260
Period size: 24 Copynumber: 5.8 Consensus size: 24
12440203 CTTATTATGT
**
12440213 TCGCACACATAGTGCCATAGCGAA
1 TCGCACACATAGTGCCATAGTAAA
12440237 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
12440261 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
12440285 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
12440309 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
12440333 TCGCACACATAGTGCCATA
1 TCGCACACATAGTGCCATA
12440352 TATTTCCAGC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 113 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:12453574 original size:30 final size:30
Alignment explanation
Indices: 12453529--12453588 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
12453519 ATTTAATACG
*
12453529 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
12453559 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
12453589 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:12459702 original size:2 final size:2
Alignment explanation
Indices: 12459695--12459741 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
12459685 AAATAACAGG
12459695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12459737 AT AT A
1 AT AT A
12459742 AACGTATCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12461449 original size:17 final size:17
Alignment explanation
Indices: 12461429--12461462 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12461419 ATAAGAGAAT
12461429 GATGGAAATAAATACAA
1 GATGGAAATAAATACAA
12461446 GATGGAAATAAATACAA
1 GATGGAAATAAATACAA
12461463 AATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
GATGGAAATAAATACAA
Found at i:12463082 original size:34 final size:34
Alignment explanation
Indices: 12463044--12463121 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
12463034 AGCTATTCAC
*
12463044 ATTCAATTTCAAAAACCTTTCTCATTAAACATAT
1 ATTCAATATCAAAAACCTTTCTCATTAAACATAT
** *
12463078 ATTCAATATCTTAAACCTTTCTCATTGAACATAT
1 ATTCAATATCAAAAACCTTTCTCATTAAACATAT
*
12463112 ATTCATTATC
1 ATTCAATATC
12463122 TTAATCAGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.37, C:0.21, G:0.01, T:0.41
Consensus pattern (34 bp):
ATTCAATATCAAAAACCTTTCTCATTAAACATAT
Found at i:12463122 original size:34 final size:34
Alignment explanation
Indices: 12463056--12463125 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
12463046 TCAATTTCAA
12463056 AAACCTTTCTCATTAAACATATATTCAATATCTT
1 AAACCTTTCTCATTAAACATATATTCAATATCTT
* *
12463090 AAACCTTTCTCATTGAACATATATTCATTATCTT
1 AAACCTTTCTCATTAAACATATATTCAATATCTT
12463124 AA
1 AA
12463126 TCAGGTTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.37, C:0.20, G:0.01, T:0.41
Consensus pattern (34 bp):
AAACCTTTCTCATTAAACATATATTCAATATCTT
Found at i:12463413 original size:43 final size:42
Alignment explanation
Indices: 12463280--12463434 Score: 127
Period size: 43 Copynumber: 3.6 Consensus size: 42
12463270 AAGCTCACAC
* * * * *
12463280 AATGCC-ATATCCCAGATATGGTCTTACATGTTAT-CACATAT
1 AATGCCAATGTCCCAGACATGGTCTTATACGTAATCCA-ATAT
* * * * * * *
12463321 CGATGCCACTGTCCCAGACAAGGTCTTATACGAAAACGATTA-
1 -AATGCCAATGTCCCAGACATGGTCTTATACGTAATCCAATAT
12463363 ACGATGCCAATGTCCCAGACATGGTCTTATACGTAATCTCAATAT
1 A--ATGCCAATGTCCCAGACATGGTCTTATACGTAATC-CAATAT
*
12463408 AATGCCAATGTCCTAGACATGGTCTTA
1 AATGCCAATGTCCCAGACATGGTCTTA
12463435 CGTGTAATCA
Statistics
Matches: 87, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
42 5 0.06
43 77 0.89
44 4 0.05
45 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (42 bp):
AATGCCAATGTCCCAGACATGGTCTTATACGTAATCCAATAT
Found at i:12471180 original size:46 final size:44
Alignment explanation
Indices: 12471122--12471236 Score: 144
Period size: 46 Copynumber: 2.5 Consensus size: 44
12471112 AGAGATAGTA
* *
12471122 TAAGAC-TGTCTGGGACATGTATCAGCCT-CGAGATGTAAGCCAGTG
1 TAAGACATGTCTGGGACATGCATCAG-CTACGAGATGT--GCCAATG
*
12471167 TAAGACATGTCTGGGACATGCATCAGCTATGAGATGTGCCAATG
1 TAAGACATGTCTGGGACATGCATCAGCTACGAGATGTGCCAATG
12471211 TAAGACTATGTCTGGGACATGGCATC
1 TAAGAC-ATGTCTGGGACAT-GCATC
12471237 GGCATGGATA
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
44 12 0.19
45 21 0.33
46 30 0.48
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (44 bp):
TAAGACATGTCTGGGACATGCATCAGCTACGAGATGTGCCAATG
Found at i:12482055 original size:30 final size:30
Alignment explanation
Indices: 12482021--12482124 Score: 208
Period size: 30 Copynumber: 3.5 Consensus size: 30
12482011 TCTATGGGGT
12482021 AAAATGGTCATTTTGTGAAAGTCTAAGGGC
1 AAAATGGTCATTTTGTGAAAGTCTAAGGGC
12482051 AAAATGGTCATTTTGTGAAAGTCTAAGGGC
1 AAAATGGTCATTTTGTGAAAGTCTAAGGGC
12482081 AAAATGGTCATTTTGTGAAAGTCTAAGGGC
1 AAAATGGTCATTTTGTGAAAGTCTAAGGGC
12482111 AAAATGGTCATTTT
1 AAAATGGTCATTTT
12482125 TCCCAATTAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 74 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.32
Consensus pattern (30 bp):
AAAATGGTCATTTTGTGAAAGTCTAAGGGC
Found at i:12482530 original size:47 final size:46
Alignment explanation
Indices: 12482464--12482589 Score: 150
Period size: 47 Copynumber: 2.7 Consensus size: 46
12482454 TTTGTGTTCT
*
12482464 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATT-ATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCC-CATTGACGAGAGCC
* *
12482510 AGTGTAAGACCATGTTTGGGACATGGCATCAG--CATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCCATT--GACGAGAGCC
*
12482558 AGTGTAAAACATGTCTGGGACATGCATCAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCC
12482590 TCGAGACATA
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
45 4 0.06
46 16 0.24
47 26 0.38
48 22 0.32
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCCATTGACGAGAGCC
Found at i:12482556 original size:48 final size:47
Alignment explanation
Indices: 12482464--12482613 Score: 157
Period size: 46 Copynumber: 3.2 Consensus size: 47
12482454 TTTGTGTTCT
* *
12482464 AGTGTAAGA-CATGTCTGGGACATGCATCAGCCA-C-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCAG-CATCGA-GACGAGAGCC
* * *
12482510 AGTGTAAGACCATGTTTGGGACATGGCATCAGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCAGCATCGAGACGAGAGCC
* * *
12482558 AGTGTAA-AACATGTCTGGGACATGCATCAGCCTCGAGAC-ATAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCAGCATCGAGACGA-GAGCC
12482604 AGTGTAAGAC
1 AGTGTAAGAC
12482614 ATGCATCGGC
Statistics
Matches: 86, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
45 1 0.01
46 33 0.38
47 30 0.35
48 21 0.24
49 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCAGCATCGAGACGAGAGCC
Found at i:12484115 original size:17 final size:18
Alignment explanation
Indices: 12484093--12484126 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12484083 TAAATGAGTT
12484093 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
12484110 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
12484127 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:12486722 original size:28 final size:29
Alignment explanation
Indices: 12486686--12486740 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
12486676 CACGGGCTGA
* *
12486686 GACACGGGCGTGT-CGAGGCCGTGTGAGG
1 GACAAGGGCGTGTGCCAGGCCGTGTGAGG
12486714 GACAAGGGCGTGTGCCAGGCCGTGTGA
1 GACAAGGGCGTGTGCCAGGCCGTGTGA
12486741 AAACCCCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.16, C:0.22, G:0.47, T:0.15
Consensus pattern (29 bp):
GACAAGGGCGTGTGCCAGGCCGTGTGAGG
Found at i:12486882 original size:21 final size:20
Alignment explanation
Indices: 12486858--12486897 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
12486848 TGTTCAAGTT
12486858 TCCACACGGGCGTGTTGCCCC
1 TCCACACGGGCGTG-TGCCCC
*
12486879 TCCACATGGGCGTGTGCCC
1 TCCACACGGGCGTGTGCCC
12486898 TGTTTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.10, C:0.40, G:0.30, T:0.20
Consensus pattern (20 bp):
TCCACACGGGCGTGTGCCCC
Done.