Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167938.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_20, whole genome shotgun sequence
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: 19866354
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 74000 characters in sequence are not A, C, G, or T
File 86 of 100
Found at i:17290928 original size:13 final size:13
Alignment explanation
Indices: 17290910--17290934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17290900 AAAGTAAAAA
17290910 AATTTTAAAATAT
1 AATTTTAAAATAT
17290923 AATTTTAAAATA
1 AATTTTAAAATA
17290935 AAAAAAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTTAAAATAT
Found at i:17290941 original size:22 final size:22
Alignment explanation
Indices: 17290916--17290972 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
17290906 AAAAAATTTT
17290916 AAAATATAATTTTAAA-ATAAAA
1 AAAATATAATTTTAAATAT-AAA
* *
17290938 AAAATAAAAGTTTTAAATATTAA
1 AAAATATAA-TTTTAAATATAAA
*
17290961 AAAACATAATTT
1 AAAATATAATTT
17290973 GGAAACATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 11 0.38
23 16 0.55
24 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATAATTTTAAATATAAA
Found at i:17290951 original size:23 final size:24
Alignment explanation
Indices: 17290916--17290969 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
17290906 AAAAAATTTT
*
17290916 AAAATATAATTTTAAA-A-TAAAA
1 AAAATAAAATTTTAAATATTAAAA
17290938 AAAATAAAAGTTTTAAATATTAAAA
1 AAAATAAAA-TTTTAAATATTAAAA
*
17290963 AACATAA
1 AAAATAA
17290970 TTTGGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 8 0.30
23 7 0.26
24 1 0.04
25 11 0.41
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAATAAAATTTTAAATATTAAAA
Found at i:17299649 original size:21 final size:19
Alignment explanation
Indices: 17299613--17299650 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
17299603 AATTATAAAC
17299613 TACATTTTCAAATTTTTTT
1 TACATTTTCAAATTTTTTT
17299632 TACATATTATC-AATTTTTT
1 TACAT-TT-TCAAATTTTTT
17299651 CATTGAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 10 0.59
21 2 0.12
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (19 bp):
TACATTTTCAAATTTTTTT
Found at i:17314187 original size:3 final size:3
Alignment explanation
Indices: 17314179--17314214 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
17314169 ATATATCTTC
17314179 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17314215 AAATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17314223 original size:3 final size:3
Alignment explanation
Indices: 17314217--17314306 Score: 153
Period size: 3 Copynumber: 30.0 Consensus size: 3
17314207 AATAATAAAA
17314217 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
17314265 ATT ATT ATT ATT ATT ATC ATT ATC ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17314307 TTTACTTGCT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:17319393 original size:23 final size:23
Alignment explanation
Indices: 17319350--17319393 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
17319340 TCCATCTTGA
*
17319350 AATTAGCAATAAAGTTATAAATG
1 AATTAGCAATAAAGTAATAAATG
*
17319373 AATTAGCACTAAA-TAACTAAA
1 AATTAGCAATAAAGTAA-TAAA
17319394 AAAGGATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (23 bp):
AATTAGCAATAAAGTAATAAATG
Found at i:17323271 original size:32 final size:32
Alignment explanation
Indices: 17323235--17323298 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
17323225 TATTTCTAAG
* *
17323235 GAAAATTAATACTTTCCACTTTTCCTCAAAAA
1 GAAAATTAATACTTTCAAATTTTCCTCAAAAA
*
17323267 GAAAATTAATACTTTCAAATTTTTCTCAAAAA
1 GAAAATTAATACTTTCAAATTTTCCTCAAAAA
17323299 TATTTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (32 bp):
GAAAATTAATACTTTCAAATTTTCCTCAAAAA
Found at i:17323341 original size:91 final size:91
Alignment explanation
Indices: 17323176--17323356 Score: 265
Period size: 91 Copynumber: 2.0 Consensus size: 91
17323166 TTATACAAGA
* * * *
17323176 AAAATTGATACTTTCAACTTTTTCTCAAAAATGCCTTTTTTGAAATTTTTATTTCTAAGGAAAAT
1 AAAATTAATACTTTCAAATTTTTCTCAAAAAT-CATTTTTTGAAATTTTTATTTCTAAGAAAAAT
*
17323241 TAATACTTTCCACTTTTCCTCAAAAAG
65 TAATACTTTCAACTTTTCCTCAAAAAG
*
17323268 AAAATTAATACTTTCAAATTTTTCTCAAAAAT-ATTTGTTTGAAATTTTTATTTTTAAGAAAAAT
1 AAAATTAATACTTTCAAATTTTTCTCAAAAATCATTT-TTTGAAATTTTTATTTCTAAGAAAAAT
* *
17323332 TGATACTTTCAACTTTTCCTTAAAA
65 TAATACTTTCAACTTTTCCTCAAAA
17323357 TTTTTTTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 3 0.04
91 47 0.59
92 30 0.38
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (91 bp):
AAAATTAATACTTTCAAATTTTTCTCAAAAATCATTTTTTGAAATTTTTATTTCTAAGAAAAATT
AATACTTTCAACTTTTCCTCAAAAAG
Found at i:17323384 original size:60 final size:60
Alignment explanation
Indices: 17323268--17323441 Score: 215
Period size: 60 Copynumber: 2.9 Consensus size: 60
17323258 CCTCAAAAAG
* * * * * * * *
17323268 AAAATTAATACTTTCAAATTTTTCTCAAAA-ATATTTGTTTGAAATTTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTTAAAATTTTTTTTTTTGAAATTTTTATCTTTAAGA
*
17323327 AAAATTGATACTTTCAACTTTTCCTTAAAATTTTTTTTTTTGAAATTTTTATCTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTTAAAATTTTTTTTTTTGAAATTTTTATCTTTAAGA
* *
17323387 AAAATTGATACTTTCATCTTTTCCTTAAAGTATTTTTTTTGTTTAAAATTTTTAT
1 AAAATTGATACTTTCAACTTTTCCTTAAA--ATTTTTTTT-TTTGAAATTTTTAT
17323442 TTGTATTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
59 26 0.26
60 52 0.52
62 9 0.09
63 13 0.13
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.53
Consensus pattern (60 bp):
AAAATTGATACTTTCAACTTTTCCTTAAAATTTTTTTTTTTGAAATTTTTATCTTTAAGA
Found at i:17324436 original size:110 final size:110
Alignment explanation
Indices: 17324306--17324513 Score: 287
Period size: 109 Copynumber: 1.9 Consensus size: 110
17324296 TGTAAATATA
* * *
17324306 TCTAATTATTACACCATTTGGGCCAAATTAAAAATATTTTTTCTTTTTG-AATTTCTAAATTTTT
1 TCTAAATATTACACCATTTGGGCCAAATTAAAAATA-TTTTT-TTTTCGAAATTTCTAAAATTTT
*
17324370 CATCATTTGGGTC-TATTT-AAAAATTTTTTATTTCTTTTTTTTTATT
64 CACCATTTGGG-CATATTTAAAAAATTTTTTATTTCTTTTTTTTTATT
* * * *
17324416 TCTAAATATTTCACCATTTGGGTCAATTTAGAAATATTTTTTTTTCGAAATTTCTAAAATTTTCA
1 TCTAAATATTACACCATTTGGGCCAAATTAAAAATATTTTTTTTTCGAAATTTCTAAAATTTTCA
17324481 CCATTTGGGCATATTTAGAAAAATTTTTTATTT
66 CCATTTGGGCATATTTA-AAAAATTTTTTATTT
17324514 TTAAAGAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
108 6 0.07
109 34 0.40
110 31 0.36
111 15 0.17
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (110 bp):
TCTAAATATTACACCATTTGGGCCAAATTAAAAATATTTTTTTTTCGAAATTTCTAAAATTTTCA
CCATTTGGGCATATTTAAAAAATTTTTTATTTCTTTTTTTTTATT
Found at i:17325023 original size:25 final size:25
Alignment explanation
Indices: 17324980--17325028 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
17324970 TTTTCACCTA
17324980 GAAATTTTATAGAAATTTATCATTT
1 GAAATTTTATAGAAATTTATCATTT
*
17325005 GAAATTTCTATA-AATTTTATCATT
1 GAAATTT-TATAGAAATTTATCATT
17325029 AAATAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (25 bp):
GAAATTTTATAGAAATTTATCATTT
Found at i:17325137 original size:22 final size:21
Alignment explanation
Indices: 17325111--17325153 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
17325101 TAAAAATGAA
*
17325111 AAAAAAAACATAAAAAATAAATT
1 AAAAAAACCA-AAAAAA-AAATT
17325134 AAAAAAACCAAAAAAAAAAT
1 AAAAAAACCAAAAAAAAAAT
17325154 ACTACTCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAAAAACCAAAAAAAAAATT
Found at i:17326028 original size:22 final size:22
Alignment explanation
Indices: 17326002--17326054 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
17325992 CTTTCTTTTC
* *
17326002 TTTTTAAATTTTATTTATTATT
1 TTTTTAAATTTTAATCATTATT
*
17326024 TTTTTTAATTTTAATCATTATT
1 TTTTTAAATTTTAATCATTATT
*
17326046 TCTTTAAAT
1 TTTTTAAAT
17326055 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTAAATTTTAATCATTATT
Found at i:17326304 original size:15 final size:14
Alignment explanation
Indices: 17326280--17326324 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
17326270 TTCCAACACA
*
17326280 TTCATCTTTTCCTTT
1 TTCAT-TTTTTCTTT
17326295 TTCATTTTTTCTTT
1 TTCATTTTTTCTTT
17326309 TT-ATTTTTTTCTTT
1 TTCA-TTTTTTCTTT
17326323 TT
1 TT
17326325 TTTTGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 1 0.04
14 22 0.79
15 5 0.18
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCATTTTTTCTTT
Found at i:17326483 original size:42 final size:42
Alignment explanation
Indices: 17326347--17326725 Score: 374
Period size: 42 Copynumber: 8.9 Consensus size: 42
17326337 TAAACAAAGT
* * * *
17326347 TCCTCTAAATAGAGGC-TCAACGACTTTGAAAAA-ATAAATGC
1 TCCTCTAAACAGAGGCAACCACAACTTTGAAAAATA-AAATGC
* * *
17326388 TCCTCTAAATAAAGGC-ACCAC-ACTTTTTGAAAAATAAAAATGT
1 TCCTCTAAACAGAGGCAACCACAAC--TTTGAAAAAT-AAAATGC
* * *
17326431 TCCTCTAAACAGA-GCCACCACAACTTTAAAAAAATAAATTGC
1 TCCTCTAAACAGAGGCAACCACAACTTT-GAAAAATAAAATGC
*
17326473 TCCTTTAAACAGAGGC-ACCACAACTTTAGAAAAAATAAAATGC
1 TCCTCTAAACAGAGGCAACCACAACTTT-G-AAAAATAAAATGC
* * * * *
17326516 TCTTCTAAACAGAGGCAACCATAACTTTGGAAAATAAATTAC
1 TCCTCTAAACAGAGGCAACCACAACTTTGAAAAATAAAATGC
* * * *
17326558 TGCTCTAAACAGAGACAACCATAACTTTGGAAAATAAAATGC
1 TCCTCTAAACAGAGGCAACCACAACTTTGAAAAATAAAATGC
* * * *
17326600 TTCTCTAAACAGAGGTAACCATAACTTTAGGAAAAACTAAAATAC
1 TCCTCTAAACAGAGGCAACCACAACTTT--GAAAAA-TAAAATGC
* * *
17326645 TCCTCTAAACAAAGGCAACCACAACTTTGAAAAATAAATTAC
1 TCCTCTAAACAGAGGCAACCACAACTTTGAAAAATAAAATGC
*
17326687 TCCTCTAAATAGAGGCAACCACAACTTTGAAAAATAAAA
1 TCCTCTAAACAGAGGCAACCACAACTTTGAAAAATAAAA
17326726 GGCTTTTATG
Statistics
Matches: 289, Mismatches: 36, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.01
41 18 0.06
42 158 0.55
43 62 0.21
44 18 0.06
45 31 0.11
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (42 bp):
TCCTCTAAACAGAGGCAACCACAACTTTGAAAAATAAAATGC
Found at i:17326661 original size:129 final size:126
Alignment explanation
Indices: 17326369--17326730 Score: 417
Period size: 129 Copynumber: 2.8 Consensus size: 126
17326359 AGGCTCAACG
* * * *
17326369 ACTTT-GAAAAAAT-AAATGCTCCTCTAAATAAAGGC-ACCAC-ACTTTTTGAAAAATAAAAATG
1 ACTTTAGAAAAAATAAAATACTCCTCTAAACAAAGGCAACCACAAC--TTTGAAAAAT-AAATTA
* * * * * * *
17326430 TTCCTCTAAACAGAGCCACCACAACTTTAAAAAAATAAATTGCTCCTTTAAACAGAGGCACCACA
63 CTCCTCTAAACAGAGCAACCACAACTTT-GAAAAATAAAATGCTTCTCTAAACAGAGGAACCACA
* * * * * *
17326495 ACTTTAGAAAAAATAAAATGCTCTTCTAAACAGAGGCAACCATAACTTTGGAAAATAAATTACTG
1 ACTTTAGAAAAAATAAAATACTCCTCTAAACAAAGGCAACCACAACTTTGAAAAATAAATTACTC
* * *
17326560 CTCTAAACAGAGACAACCATAACTTTGGAAAATAAAATGCTTCTCTAAACAGAGGTAACCATA
66 CTCTAAACAGAG-CAACCACAACTTTGAAAAATAAAATGCTTCTCTAAACAGAGG-AACCACA
*
17326623 ACTTTAGGAAAAACTAAAATACTCCTCTAAACAAAGGCAACCACAACTTTGAAAAATAAATTACT
1 ACTTTA-GAAAAAATAAAATACTCCTCTAAACAAAGGCAACCACAACTTTGAAAAATAAATTACT
* *
17326688 CCTCTAAATAGAGGCAACCACAACTTTGAAAAATAAAAGGCTT
65 CCTCTAAACAGA-GCAACCACAACTTTGAAAAATAAAATGCTT
17326731 TTATGATACA
Statistics
Matches: 199, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
126 5 0.03
127 49 0.25
128 50 0.25
129 92 0.46
130 3 0.02
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (126 bp):
ACTTTAGAAAAAATAAAATACTCCTCTAAACAAAGGCAACCACAACTTTGAAAAATAAATTACTC
CTCTAAACAGAGCAACCACAACTTTGAAAAATAAAATGCTTCTCTAAACAGAGGAACCACA
Found at i:17333787 original size:25 final size:24
Alignment explanation
Indices: 17333736--17333787 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
17333726 AATAAATAAT
*
17333736 AAATAAAATAAAATGCATGATTGA
1 AAATAAAATAAAATGCATGATAGA
*
17333760 AAATCAAATAAAAATGCATG-TAGCA
1 AAATAAAAT-AAAATGCATGATAG-A
17333785 AAA
1 AAA
17333788 ATGATGTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.21
Consensus pattern (24 bp):
AAATAAAATAAAATGCATGATAGA
Found at i:17335238 original size:14 final size:13
Alignment explanation
Indices: 17335208--17335240 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
17335198 ACAACTCATC
17335208 AAAAAAATAGAGG
1 AAAAAAATAGAGG
17335221 AAAAAAGATA-AGG
1 AAAAAA-ATAGAGG
17335234 AAAAAAA
1 AAAAAAA
17335241 AGTAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 15 0.79
14 3 0.16
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (13 bp):
AAAAAAATAGAGG
Found at i:17335247 original size:23 final size:24
Alignment explanation
Indices: 17335222--17335265 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
17335212 AAATAGAGGA
*
17335222 AAAAAG-ATAAGGAAAA-AAAAGT
1 AAAAAGAAAAAGGAAAACAAAAGT
17335244 AAAAAGAAAAAGGAAAACAAAA
1 AAAAAGAAAAAGGAAAACAAAA
17335266 TTATTGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (24 bp):
AAAAAGAAAAAGGAAAACAAAAGT
Found at i:17338473 original size:24 final size:24
Alignment explanation
Indices: 17338445--17338498 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
17338435 ATTAAAACCG
*
17338445 CAAACC-TGAAACCCCAAATTCCAT
1 CAAACCTTG-AACCCCAAATCCCAT
*
17338469 CAAACCTTGAACCCTAAATCCCAT
1 CAAACCTTGAACCCCAAATCCCAT
*
17338493 GAAACC
1 CAAACC
17338499 CTAGTTCCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.41, C:0.37, G:0.06, T:0.17
Consensus pattern (24 bp):
CAAACCTTGAACCCCAAATCCCAT
Found at i:17338548 original size:21 final size:21
Alignment explanation
Indices: 17338522--17338561 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
17338512 TCTAAAACCT
17338522 AACCCTAAACCTT-AAACCCAA
1 AACCCTAAA-CTTCAAACCCAA
17338543 AACCCTAAACTTCAAACCC
1 AACCCTAAACTTCAAACCC
17338562 TAAGTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.45, C:0.40, G:0.00, T:0.15
Consensus pattern (21 bp):
AACCCTAAACTTCAAACCCAA
Found at i:17339016 original size:17 final size:17
Alignment explanation
Indices: 17338994--17339026 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17338984 GAGAATGAAA
17338994 AAAGTG-TTTTGATATTT
1 AAAGTGCTTTT-ATATTT
17339011 AAAGTGCTTTTATATT
1 AAAGTGCTTTTATATT
17339027 GATCCAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (17 bp):
AAAGTGCTTTTATATTT
Found at i:17339811 original size:9 final size:9
Alignment explanation
Indices: 17339797--17339825 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
17339787 TTTCTTCCAC
17339797 TCTTTTTAT
1 TCTTTTTAT
17339806 TC-TTTTAT
1 TCTTTTTAT
17339814 TCTTTTTAT
1 TCTTTTTAT
17339823 TCT
1 TCT
17339826 CCTTTTAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (9 bp):
TCTTTTTAT
Found at i:17342297 original size:13 final size:14
Alignment explanation
Indices: 17342275--17342303 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17342265 GGAATCTTAT
17342275 TTTTTGTAATTTGA
1 TTTTTGTAATTTGA
17342289 TTTTT-TAATTTGA
1 TTTTTGTAATTTGA
17342302 TT
1 TT
17342304 GAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (14 bp):
TTTTTGTAATTTGA
Found at i:17347423 original size:26 final size:25
Alignment explanation
Indices: 17347362--17347424 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
17347352 ATAATGTTCT
*
17347362 ACTTATAATGAAAAATAATGAATTA
1 ACTTATAATGAAAAATAATGAACTA
* *
17347387 A-TTGATCATGAGAAATCAATGAACTA
1 ACTT-ATAATGAAAAAT-AATGAACTA
*
17347413 ACTTATGATGAA
1 ACTTATAATGAA
17347425 TCATTCCTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
24 2 0.07
25 11 0.37
26 15 0.50
27 2 0.07
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (25 bp):
ACTTATAATGAAAAATAATGAACTA
Found at i:17354365 original size:21 final size:17
Alignment explanation
Indices: 17354330--17354372 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 17
17354320 TCATTTTTTA
17354330 TTTTTTATTTTTTATCAT
1 TTTTTTATTTTTTAT-AT
17354348 TTTTTTATTATTACTTATAT
1 TTTTTTATT-TT--TTATAT
17354368 TTTTT
1 TTTTT
17354373 CCATGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 7 0.32
21 4 0.18
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTATTTTTTATAT
Found at i:17355793 original size:24 final size:23
Alignment explanation
Indices: 17355760--17355804 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
17355750 CCTTGTCCTC
17355760 TTTTTAACTTTCTCTATTTTTTCT
1 TTTTTAACTTTCT-TATTTTTTCT
* *
17355784 TTTTTGACTTTCTTGTTTTTT
1 TTTTTAACTTTCTTATTTTTT
17355805 AAATTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTTTAACTTTCTTATTTTTTCT
Found at i:17357690 original size:63 final size:63
Alignment explanation
Indices: 17357591--17357737 Score: 231
Period size: 63 Copynumber: 2.3 Consensus size: 63
17357581 TGTATTATGC
* * * *
17357591 TTGTTGATGAATTATTTTTATTGTTACGTATTTAGTCTTTGTGATTCTGGTTGTATATTGTGA
1 TTGTTGATGAACTACTTTTATTGTTACATATTTAGTCTTTGTGATTCTGGTTGTATACTGTGA
*
17357654 TTGTTGATGAACTACTTTTATTGTTACATATTTAGTCTTTGTGATTTTGGTTGTATACTGTGA
1 TTGTTGATGAACTACTTTTATTGTTACATATTTAGTCTTTGTGATTCTGGTTGTATACTGTGA
* *
17357717 TTATTGATAAACTACTTTTAT
1 TTGTTGATGAACTACTTTTAT
17357738 AGTAATTGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 77 1.00
ACGTcount: A:0.22, C:0.07, G:0.18, T:0.54
Consensus pattern (63 bp):
TTGTTGATGAACTACTTTTATTGTTACATATTTAGTCTTTGTGATTCTGGTTGTATACTGTGA
Found at i:17359730 original size:14 final size:15
Alignment explanation
Indices: 17359711--17359740 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17359701 ACAACATGCA
17359711 ATTATTT-AAATTTT
1 ATTATTTAAAATTTT
17359725 ATTATTTAAAATTTT
1 ATTATTTAAAATTTT
17359740 A
1 A
17359741 ATTTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATTTAAAATTTT
Found at i:17360520 original size:4 final size:4
Alignment explanation
Indices: 17360511--17360541 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
17360501 CCTGCCCAGG
17360511 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
17360542 GCAATTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:17364798 original size:30 final size:30
Alignment explanation
Indices: 17364762--17364822 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
17364752 ATGAATGATC
** *
17364762 TGCAATTCATAAAGTAGTTCCTCAAAGTTT
1 TGCAATTCATAAAGTAGCACCTCAAAATTT
*
17364792 TGCAATTCATAAATTAGCACCTCAAAATTT
1 TGCAATTCATAAAGTAGCACCTCAAAATTT
17364822 T
1 T
17364823 CATAATTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (30 bp):
TGCAATTCATAAAGTAGCACCTCAAAATTT
Found at i:17366954 original size:22 final size:22
Alignment explanation
Indices: 17366926--17366971 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
17366916 AGTACTAGTT
* *
17366926 AGGAAGGAAACCCATTGATAAA
1 AGGAAGGAAACCAAGTGATAAA
17366948 AGGAAGGAAACCAAGTGATAAA
1 AGGAAGGAAACCAAGTGATAAA
17366970 AG
1 AG
17366972 CATACCACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.52, C:0.11, G:0.26, T:0.11
Consensus pattern (22 bp):
AGGAAGGAAACCAAGTGATAAA
Found at i:17382094 original size:20 final size:20
Alignment explanation
Indices: 17382057--17382098 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17382047 CATATTTTGT
*
17382057 TTATAATTTTTGTTATTTTA
1 TTATAATTTTTGTAATTTTA
17382077 TTATAATTTTT-TAAATTTTA
1 TTATAATTTTTGT-AATTTTA
17382097 TT
1 TT
17382099 TTAAAGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTATAATTTTTGTAATTTTA
Found at i:17388393 original size:17 final size:18
Alignment explanation
Indices: 17388373--17388410 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
17388363 CATTTGATCA
17388373 CTTTTTTTTA-AAATTTT
1 CTTTTTTTTACAAATTTT
17388390 C-TTTTTTTACAAATTTT
1 CTTTTTTTTACAAATTTT
17388407 -TTTT
1 CTTTT
17388411 CATGTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTTTTTTACAAATTTT
Found at i:17388394 original size:16 final size:16
Alignment explanation
Indices: 17388374--17388410 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
17388364 ATTTGATCAC
17388374 TTTTTTTTA-AAATTT
1 TTTTTTTTACAAATTT
17388389 TCTTTTTTTACAAATTT
1 T-TTTTTTTACAAATTT
17388406 TTTTT
1 TTTTT
17388411 CATGTGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 12 0.60
17 7 0.35
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTTACAAATTT
Found at i:17390070 original size:2 final size:2
Alignment explanation
Indices: 17390063--17390103 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
17390053 AAACATTGTT
* *
17390063 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17390104 GTAGGGATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17390572 original size:22 final size:22
Alignment explanation
Indices: 17390547--17390594 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
17390537 ATGCTAAAGG
17390547 TAAAAGATTTACAAATGGAAAT
1 TAAAAGATTTACAAATGGAAAT
* * * *
17390569 TAAAATATTTATAATTTGAAAT
1 TAAAAGATTTACAAATGGAAAT
17390591 TAAA
1 TAAA
17390595 GGTTTCTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (22 bp):
TAAAAGATTTACAAATGGAAAT
Found at i:17391055 original size:37 final size:37
Alignment explanation
Indices: 17391005--17391076 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
17390995 AAATTCAATC
17391005 AAATAAAAAAAGTATGCTTGCTCTTTAATCATTACTT
1 AAATAAAAAAAGTATGCTTGCTCTTTAATCATTACTT
*
17391042 AAATAACAAAAGTATGCTTGCTCTTTAATCATTAC
1 AAATAAAAAAAGTATGCTTGCTCTTTAATCATTAC
17391077 CATCAAAGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.36
Consensus pattern (37 bp):
AAATAAAAAAAGTATGCTTGCTCTTTAATCATTACTT
Found at i:17415556 original size:47 final size:48
Alignment explanation
Indices: 17415502--17415598 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
17415492 TTTGCTATCT
* *
17415502 CACCATGTCT-TGATAAAATGCTTTGACACATACCTGCATCCGACAGC
1 CACCATGTCTCAGATAAAATGCTTTGACACATACCTGCATCCAACAGC
*
17415549 CACCATGTCTCAGATAAAATGTTTTGACACATACCTGCATCCAACAGC
1 CACCATGTCTCAGATAAAATGCTTTGACACATACCTGCATCCAACAGC
17415597 CA
1 CA
17415599 TGCTTGAGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 10 0.22
48 36 0.78
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.25
Consensus pattern (48 bp):
CACCATGTCTCAGATAAAATGCTTTGACACATACCTGCATCCAACAGC
Found at i:17418235 original size:2 final size:2
Alignment explanation
Indices: 17418228--17418252 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17418218 TGATACTTTA
17418228 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 A
17418253 AATGAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17421570 original size:13 final size:13
Alignment explanation
Indices: 17421554--17421585 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17421544 TTAATTATAC
*
17421554 CTTTTTAACCACA
1 CTTTTTAAACACA
17421567 CTTTTTAAACACA
1 CTTTTTAAACACA
17421580 CTTTTT
1 CTTTTT
17421586 TCAATCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (13 bp):
CTTTTTAAACACA
Found at i:17421572 original size:14 final size:14
Alignment explanation
Indices: 17421555--17421606 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
17421545 TAATTATACC
17421555 TTTTTAACCACAC-
1 TTTTTAACCACACT
*
17421568 TTTTTAAACACACT
1 TTTTTAACCACACT
*
17421582 TTTTTCAATCCAAACT
1 TTTTT-AA-CCACACT
17421598 TTTTATAAC
1 TTTT-TAAC
17421607 TGCAACAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 12 0.38
14 5 0.16
15 3 0.09
16 11 0.34
17 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTTTAACCACACT
Found at i:17424622 original size:19 final size:19
Alignment explanation
Indices: 17424585--17424622 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17424575 AGCAACAATG
**
17424585 TAGCCTATAGATATTTCTC
1 TAGCCTATAGATACATCTC
17424604 TAGCCTATAGATACATCTC
1 TAGCCTATAGATACATCTC
17424623 AAACAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (19 bp):
TAGCCTATAGATACATCTC
Found at i:17433430 original size:26 final size:26
Alignment explanation
Indices: 17433401--17433504 Score: 61
Period size: 30 Copynumber: 3.9 Consensus size: 26
17433391 ATCCGAAATT
*
17433401 AATAAAAATATTATTTTTTAAATATAA
1 AATAAAAATATTATTATTTAAATAT-A
*
17433428 ATATTTAAAAATATTATTATATAAATATA
1 A-A--TAAAAATATTATTATTTAAATATA
* * * *
17433457 TATATAAATA--ATTAATTAAAAATTA
1 AATAAAAATATTATTATTTAAATA-TA
* * *
17433482 ATTAAAAAT-TAATTTTTTAAATA
1 AATAAAAATATTATTATTTAAATA
17433505 ATATCGGGTC
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
24 9 0.16
25 8 0.14
26 16 0.28
27 1 0.02
28 2 0.03
29 1 0.02
30 21 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAAAAATATTATTATTTAAATATA
Found at i:17433439 original size:30 final size:30
Alignment explanation
Indices: 17433403--17433461 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
17433393 CCGAAATTAA
* *
17433403 TAAAAATATTATTTTTTAAATATAAATATT
1 TAAAAATATTATTATATAAATATAAATATT
*
17433433 TAAAAATATTATTATATAAATATATATAT
1 TAAAAATATTATTATATAAATATAAATAT
17433462 AAATAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAAAATATTATTATATAAATATAAATATT
Found at i:17433482 original size:11 final size:11
Alignment explanation
Indices: 17433461--17433495 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
17433451 AATATATATA
17433461 TAAATAATTAAT
1 TAAA-AATTAAT
17433473 TAAAAATTAAT
1 TAAAAATTAAT
17433484 TAAAAATTAAT
1 TAAAAATTAAT
17433495 T
1 T
17433496 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAAAATTAAT
Found at i:17438881 original size:34 final size:34
Alignment explanation
Indices: 17438838--17438949 Score: 98
Period size: 34 Copynumber: 3.2 Consensus size: 34
17438828 ATATCCTCTA
17438838 GTTAGAAGAGTTATTTAAAGTTTTATTGCCTTTG
1 GTTAGAAGAGTTATTTAAAGTTTTATTGCCTTTG
* * **
17438872 GTTAAAAGAGGTTCTTTTTAAAGTTTTATAACCTTTG
1 GTTAGAAGA-G-T-TATTTAAAGTTTTATTGCCTTTG
* * ** * **
17438909 ATTAGATGAGCAATTTAGAGTTTTATTGCCCCTG
1 GTTAGAAGAGTTATTTAAAGTTTTATTGCCTTTG
17438943 GTTAGAA
1 GTTAGAA
17438950 AAACTTTTCA
Statistics
Matches: 58, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
34 29 0.50
35 1 0.02
36 2 0.03
37 26 0.45
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (34 bp):
GTTAGAAGAGTTATTTAAAGTTTTATTGCCTTTG
Found at i:17440275 original size:6 final size:5
Alignment explanation
Indices: 17440227--17440274 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
17440217 GTTTTTCTTT
*
17440227 TTTTA TTTTA TTTTA TTGTCTAA TTTTAA TTTTA ATTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TT-T-T-A TTTT-A TTTTA TTTTA TTTTA TTTT
17440275 TGTTATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 25 0.66
6 8 0.21
7 2 0.05
8 3 0.08
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:17440859 original size:25 final size:25
Alignment explanation
Indices: 17440831--17440878 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
17440821 GATTTATTTA
*
17440831 AATAATAAA-AATGACAAAAATAATG
1 AATAATAAATAAT-AAAAAAATAATG
17440856 AATAATAAATAATAAAAAAATAA
1 AATAATAAATAATAAAAAAATAA
17440879 AACCAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (25 bp):
AATAATAAATAATAAAAAAATAATG
Found at i:17443746 original size:9 final size:9
Alignment explanation
Indices: 17443717--17443750 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
17443707 CCTAAAAATC
17443717 TATTTTATA
1 TATTTTATA
17443726 TATTATTAATA
1 TATT-TT-ATA
17443737 TATTTTATA
1 TATTTTATA
17443746 TATTT
1 TATTT
17443751 AAAAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 12 0.52
10 4 0.17
11 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TATTTTATA
Found at i:17443759 original size:18 final size:20
Alignment explanation
Indices: 17443718--17443767 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
17443708 CTAAAAATCT
* *
17443718 ATTTTATATATTATTAATAT
1 ATTTTATATATTATTAAAAA
17443738 ATTTTATATA-T-TTAAAAA
1 ATTTTATATATTATTAAAAA
17443756 A-TTTAT-TATTAT
1 ATTTTATATATTAT
17443768 AAATAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.08
17 6 0.23
18 7 0.27
19 1 0.04
20 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTATATATTATTAAAAA
Found at i:17444307 original size:249 final size:248
Alignment explanation
Indices: 17443596--17444336 Score: 850
Period size: 249 Copynumber: 3.0 Consensus size: 248
17443586 ATAAAAATAA
*
17443596 AATTCACAATTATAAATAACATTTTTTCAACCAAATA-TTTTTTCTTATTATA--T-T-TA-TGT
1 AATTCACAATTATAAATAACATTTTTTCAACCAAATATTTTTTTCTTATTATATGTATATATTCT
* * * *
17443655 TA--ATAATATTTTTTTCTTATTATAATTTTCAATTTTGTTTTTATATATTGCACCTAAAAATCT
66 TATTATAACATTTTTTTCTTATTATAATTTT-AAATTTATTTTTATATATTGCACC-AAAAATTT
*
17443718 ATTTTATATATTATTAATATATTTTATATATTTAAAAAATTTATTATTATAAATAATTATTTTAT
129 TTTTTATATATTATTAATATATTTTATAT-TTTAAAAAA-TTATTATTATAAATAATTATTTTAT
** * ** *
17443783 GTGAGTATTTGCTTATTATAAGTTACATG-T-TT-TTAT-AGGTATTGTAATATATAAAAACAA
192 GTGAGTATTTGCTTATTATAAGTTACATGTTCTTATTATAACAT-TTGT--T-T-T--TATTAT
* * * * *
17443843 AATTTATAATTATAAATAATATTATTTTTCAACCAAATATTTTTTTC-TATTATATGTTACATGT
1 AATTCACAATTATAAATAACA-T-TTTTTCAACCAAATATTTTTTTCTTATTATATG-TATATAT
* *
17443907 TCTTATTATGACATTTTTTTCTTATTATAATTTTAAATTTATTTTTATATATTGCACCTAAAA-T
63 TCTTATTATAACATTTTTTTCTTATTATAATTTTAAATTTATTTTTATATATTGCACCAAAAATT
* ** *
17443971 TTTTTTATATATTATTAATATATTTTA-A----GAAAAGCTATTATTATAAATAATTATTTTATA
128 TTTTTTATATATTATTAATATATTTTATATTTTAAAAAATTATTATTATAAATAATTATTTTATG
17444031 TGAGTATTTGCTTATTATATA-TTACATGTTCTTATTATAACATTTGTTTTTATTAT
193 TGAGTATTTGCTTATTATA-AGTTACATGTTCTTATTATAACATTTGTTTTTATTAT
* *
17444087 AATTCACAATCACAAATAACATTTGTTTCAACCAAATATTTTTTTCTTATTATATGTGATATATT
1 AATTCACAATTATAAATAACATTT-TTTCAACCAAATATTTTTTTCTTATTATATGT-ATATATT
* * * *
17444152 CTTATTATAACA-TTTTTTCTTATTATAATTTTGAA-CT-TTTTTATATAGTGCACCCAAAATTT
64 CTTATTATAACATTTTTTTCTTATTATAATTTTAAATTTATTTTTATATATTGCACCAAAAATTT
* *
17444214 TTTTTTTATATTATTAATATATTTTATATTTTTTAAAAAATTATTATTATAAATAATTATTCTAT
129 TTTTTATATATTATTAATATATTTTATA--TTTTAAAAAATTATTATTATAAATAATTATTTTAT
17444279 GTGAGTATTTGCTTATTATAAGTTACATGTTCTTATTATAACA--T-TTTTTATTAT
192 GTGAGTATTTGCTTATTATAAGTTACATGTTCTTATTATAACATTTGTTTTTATTAT
17444333 AATT
1 AATT
17444337 TTGAATTTTG
Statistics
Matches: 425, Mismatches: 41, Indels: 57
0.81 0.08 0.11
Matches are distributed among these distances:
241 20 0.05
242 30 0.07
243 46 0.11
244 43 0.10
246 15 0.04
247 70 0.16
248 9 0.02
249 91 0.21
250 15 0.04
251 2 0.00
252 1 0.00
253 1 0.00
254 27 0.06
255 8 0.02
256 22 0.05
257 25 0.06
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (248 bp):
AATTCACAATTATAAATAACATTTTTTCAACCAAATATTTTTTTCTTATTATATGTATATATTCT
TATTATAACATTTTTTTCTTATTATAATTTTAAATTTATTTTTATATATTGCACCAAAAATTTTT
TTTATATATTATTAATATATTTTATATTTTAAAAAATTATTATTATAAATAATTATTTTATGTGA
GTATTTGCTTATTATAAGTTACATGTTCTTATTATAACATTTGTTTTTATTAT
Found at i:17444478 original size:165 final size:158
Alignment explanation
Indices: 17444132--17444548 Score: 536
Period size: 165 Copynumber: 2.6 Consensus size: 158
17444122 ATATTTTTTT
* * * *
17444132 CTTATTATATGTGATATATTCTTATTATAACATTTTTTCTTATTATAATTTTGAA--CT-TTTTT
1 CTTATTATATGTTACATGTTCTTATTATAACA--TTTT-TTATTATAATTTTGAATTTTGTTTTT
* * * * * * **
17444194 ATATAGTGCACCCAAAATTTTTTTTTTATATTATTAATATATTTTATATTTTTTAAAAAATTATT
63 ATATATTACACCTAAAAATCTTTTTATATATTATTAATATATTTTATATTTTGAAAAAAATTATT
*
17444259 ATTATAAATAATTATTCTATGTGAGTATTTG
128 ATTATAAATAATTATTCTATATGAGTATTTG
*
17444290 CTTATTATAAGTTACATGTTCTTATTATAACATTTTTTATTATAATTTTGAATTTTGTTTTTATA
1 CTTATTATATGTTACATGTTCTTATTATAACATTTTTTATTATAATTTTGAATTTTGTTTTTATA
17444355 TATTACACCTAAAAATCATTTTTATATATTATTAATATATTTTATTGATTTTAAGAAAAAATTAT
66 TATTACACCTAAAAATC-TTTTTATATATTATTAATATATTTTA-T-ATTTT--GAAAAAA--AT
*
17444420 TATTATTATAAATAATTATTTTATATGAGTATTTG
124 TATTATTATAAATAATTATTCTATATGAGTATTTG
* * *
17444455 CTTATTATATGTTACATGTTCTTATTATAATATTTTTTATTATAATTATGAATTTTG-ATTTATA
1 CTTATTATATGTTACATGTTCTTATTATAACATTTTTTATTATAATTTTGAATTTTGTTTTTATA
*
17444519 TATTATACCTAAAAAATCTTTTTATATATT
66 TATTACACCT-AAAAATCTTTTTATATATT
17444549 TTTTAAAAAA
Statistics
Matches: 228, Mismatches: 20, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
155 16 0.07
156 4 0.02
157 1 0.00
158 48 0.21
159 25 0.11
160 1 0.00
161 5 0.02
163 5 0.02
164 27 0.12
165 96 0.42
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (158 bp):
CTTATTATATGTTACATGTTCTTATTATAACATTTTTTATTATAATTTTGAATTTTGTTTTTATA
TATTACACCTAAAAATCTTTTTATATATTATTAATATATTTTATATTTTGAAAAAAATTATTATT
ATAAATAATTATTCTATATGAGTATTTG
Found at i:17446671 original size:13 final size:13
Alignment explanation
Indices: 17446653--17446680 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17446643 GTGTGGTGTT
17446653 AGTTGTTGGGATG
1 AGTTGTTGGGATG
17446666 AGTTGTTGGGATG
1 AGTTGTTGGGATG
17446679 AG
1 AG
17446681 AAGGGAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.46, T:0.36
Consensus pattern (13 bp):
AGTTGTTGGGATG
Found at i:17448330 original size:22 final size:20
Alignment explanation
Indices: 17448283--17448342 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
17448273 GAATAAAAAT
*
17448283 AAAATAAGAAATAGAAAAACAA
1 AAAATAAG-AATA-AAATACAA
17448305 AAAATAAGAATAAAATACGAA
1 AAAATAAGAATAAAATAC-AA
*
17448326 CAAAATAA-AATTAAATA
1 -AAAATAAGAATAAAATA
17448343 ACTAGAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 5 0.15
21 14 0.41
22 15 0.44
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAATAAGAATAAAATACAA
Found at i:17448725 original size:22 final size:21
Alignment explanation
Indices: 17448681--17448733 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
17448671 ATCATATAAG
*
17448681 ATAA-ATAAGAAGTCTTTAGA
1 ATAATATAAGAAATCTTTAGA
*
17448701 ATAAAATATAAGAAAT-TTTATA
1 AT--AATATAAGAAATCTTTAGA
17448723 ATAATATAAGA
1 ATAATATAAGA
17448734 TAAAGTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 11 0.39
22 9 0.32
23 8 0.29
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (21 bp):
ATAATATAAGAAATCTTTAGA
Found at i:17450614 original size:30 final size:30
Alignment explanation
Indices: 17450578--17450686 Score: 132
Period size: 30 Copynumber: 3.6 Consensus size: 30
17450568 ATGAAGCTAA
* *
17450578 GACTCTTTAAGAGAGTTTTGGTGGAACTGG
1 GACTCTTTGAGAGAGTTTTGGTGGAACTAG
*
17450608 GACTCTTTGGGAGAGTTTTGGTGGAACTAG
1 GACTCTTTGAGAGAGTTTTGGTGGAACTAG
* *
17450638 GACTCTTTGAGAGAG-TTTGAATGGAATTA-
1 GACTCTTTGAGAGAGTTTTG-GTGGAACTAG
*
17450667 GACTCTTTGGGCAGAGTTTT
1 GACTCTTTGAG-AGAGTTTT
17450687 AGTTTGGTGT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
29 14 0.20
30 52 0.75
31 3 0.04
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (30 bp):
GACTCTTTGAGAGAGTTTTGGTGGAACTAG
Found at i:17451451 original size:134 final size:133
Alignment explanation
Indices: 17451211--17451471 Score: 351
Period size: 134 Copynumber: 2.0 Consensus size: 133
17451201 TTATCACCCA
* * ** * *
17451211 AATTATCTCACTATGGTATTTATTTCAGTTATTTATCCTTTAAAAAGTTAATTATCATTTGGTAA
1 AATTATCTCACTATGATATTTATTCCAGTTATTTATCCCCTAAAAAGTCAATTATCATTTGATAA
* * * * * **
17451276 TGTCATTTTGGGAGGATAGATTCAAAAAACGCAAAATTAATCATGAAATTCGACCAAAAACACGA
66 TATCATTTTAGGAGGATAAATCCAAAAAACACAAAATTAATCACAAAATTCGACCAAAAACACGA
17451341 TCG
131 TCG
* *
17451344 AATTATCTCATTATGATATTTATTCCAGTTATTTATCCCCTAGAAAGTCAATTTATCATTTGATA
1 AATTATCTCACTATGATATTTATTCCAGTTATTTATCCCCTAAAAAGTCAA-TTATCATTTGATA
* * *
17451409 ATATTATTTTAGGAGGATAAATCCAAAAAATACAAAATTAATCACAAAATTTGACCAAAAACA
65 ATATCATTTTAGGAGGATAAATCCAAAAAACACAAAATTAATCACAAAATTCGACCAAAAACA
17451472 AGATGGGCTG
Statistics
Matches: 109, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
133 44 0.40
134 65 0.60
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (133 bp):
AATTATCTCACTATGATATTTATTCCAGTTATTTATCCCCTAAAAAGTCAATTATCATTTGATAA
TATCATTTTAGGAGGATAAATCCAAAAAACACAAAATTAATCACAAAATTCGACCAAAAACACGA
TCG
Found at i:17457259 original size:437 final size:435
Alignment explanation
Indices: 17456421--17457293 Score: 1584
Period size: 437 Copynumber: 2.0 Consensus size: 435
17456411 CCCCGTTACT
17456421 AAATACATTTTAATTTCAAATTAAATTTTCTATTTCTATTAAATATACCACATTCCTCAACAATT
1 AAATACATTTTAATTTCAAATTAAATTTTCTATTTCTATTAAATATACCACATTCCTCAACAATT
*
17456486 GATTTTCCTTTCATACCCTCAACATTTTTTCTTCTTTCTATTTTGTTTCTCTTTACTCTCAAACC
66 GATTTTCCTTTCATACCCTCAACATTTTTTCTTCTTTCTATTTTGTTTCTCTTTAATCTCAAACC
17456551 AAATTAACCCTAAAATTATCAATTTTTTAATCTTCTATTGATTAAAAATAAGATTTGAAGATTTA
131 AAATTAACCCTAAAATTATCAATTTTTTAATCTTCTATTGATTAAAAATAAGATTTGAAGATTTA
* *
17456616 TTTCGTTTGATTTGATTTAAATGCATGCGAATATAGGCTAAGATTTACGAAATGGATTTTGCAAA
196 TTTCATTTGATTTGATTTAAATGCATGCGAATATAAGCTAAGATTTACGAAATGGATTTTGCAAA
*
17456681 ATTCAAACTTCTCGAAAATCTATTTTCGAGAAGTCTTTAAGGCTATCACAAATTCATTTTCGAGA
261 ATTCAAACTTCTCGAAAATCTATTTTCGAGAAATCTTTAAGGCTATCACAAATTCATTTTCGAGA
*
17456746 AACCTCATTTTCAAAAATACAACATAAATTTTAGAAATTTATTTTTGAGAATACATCATAATTTC
326 AACCTCATTTTCAAAAATACAACATAAATTTTAGAAATTTATTTTCGAGAATACATCATAATTTC
*
17456811 AAAATTAAATTTTCATAAATATAAAAAAATCAAATTCAATTAGAA
391 AAAAATAAATTTTCATAAATATAAAAAAATCAAATTCAATTAGAA
*
17456856 AAATACATTTTAATTTCAAACTTAAATTTTCTATTTCTATTAAATATACCACATTTCTCAACAAT
1 AAATACATTTTAATTTCAAA-TTAAATTTTCTATTTCTATTAAATATACCACATTCCTCAACAAT
* * * *
17456921 TGATTTTCCTTTCGTACCCTCAACATTTTTTCTTTTTTCTCTTTTTTTCTCTCTTTAATCTCAAA
65 TGATTTTCCTTTCATACCCTCAACATTTTTTCTTCTTTCTATTTTGTT-TCTCTTTAATCTCAAA
*
17456986 CCAAATTAACCCTAAAATTATCAATTTTTTAGTCTTCTATTGATTAAAAATAAGATTTGAAGATT
129 CCAAATTAACCCTAAAATTATCAATTTTTTAATCTTCTATTGATTAAAAATAAGATTTGAAGATT
* *
17457051 TATTTCATTTGATTTGATTTAAATGCATGCGAATATAAGTTAGGATTTACGAAATGGATTTTGCA
194 TATTTCATTTGATTTGATTTAAATGCATGCGAATATAAGCTAAGATTTACGAAATGGATTTTGCA
*
17457116 AAATTCAAACTTCTCGAAAATCTATTTTCGAGAAATCTTTAAGGGTATCACAAATTCATTTTCGA
259 AAATTCAAACTTCTCGAAAATCTATTTTCGAGAAATCTTTAAGGCTATCACAAATTCATTTTCGA
17457181 GAAACCTCATTTTCAAAAATACAACATAAATTTTAGAAATTTATTTTCGAGAATACATCATAATT
324 GAAACCTCATTTTCAAAAATACAACATAAATTTTAGAAATTTATTTTCGAGAATACATCATAATT
*
17457246 TCAAAAATAAATTTTCATAAATATAAAAAAATCAGATTCAATTAGAA
389 TCAAAAATAAATTTTCATAAATATAAAAAAATCAAATTCAATTAGAA
17457293 A
1 A
17457294 GGATGATGAA
Statistics
Matches: 420, Mismatches: 16, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
435 20 0.05
436 87 0.21
437 313 0.75
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (435 bp):
AAATACATTTTAATTTCAAATTAAATTTTCTATTTCTATTAAATATACCACATTCCTCAACAATT
GATTTTCCTTTCATACCCTCAACATTTTTTCTTCTTTCTATTTTGTTTCTCTTTAATCTCAAACC
AAATTAACCCTAAAATTATCAATTTTTTAATCTTCTATTGATTAAAAATAAGATTTGAAGATTTA
TTTCATTTGATTTGATTTAAATGCATGCGAATATAAGCTAAGATTTACGAAATGGATTTTGCAAA
ATTCAAACTTCTCGAAAATCTATTTTCGAGAAATCTTTAAGGCTATCACAAATTCATTTTCGAGA
AACCTCATTTTCAAAAATACAACATAAATTTTAGAAATTTATTTTCGAGAATACATCATAATTTC
AAAAATAAATTTTCATAAATATAAAAAAATCAAATTCAATTAGAA
Found at i:17461206 original size:26 final size:26
Alignment explanation
Indices: 17461170--17461222 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
17461160 AAGAAACAGA
17461170 ATCACATCAAGCAGCAGCATATCTAT
1 ATCACATCAAGCAGCAGCATATCTAT
17461196 ATCACATCAAGCAGCAGCATATCTAT
1 ATCACATCAAGCAGCAGCATATCTAT
17461222 A
1 A
17461223 AATGAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (26 bp):
ATCACATCAAGCAGCAGCATATCTAT
Found at i:17466267 original size:8 final size:8
Alignment explanation
Indices: 17466250--17466284 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
17466240 TTTAATTTTT
17466250 TATTTATA
1 TATTTATA
17466258 TATAATTATA
1 TAT--TTATA
17466268 TATTTATA
1 TATTTATA
17466276 TATTTATA
1 TATTTATA
17466284 T
1 T
17466285 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTTATA
Found at i:17466304 original size:21 final size:21
Alignment explanation
Indices: 17466273--17466330 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 21
17466263 TTATATATTT
17466273 ATATATTTATATTTAAAAAATA
1 ATAT-TTTATATTTAAAAAATA
*
17466295 ATATTTTATATTTTAAATAATA
1 ATATTTTATA-TTTAAAAAATA
17466317 ATATTTTATTATTT
1 ATATTTTA-TATTT
17466331 TAGGTCAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 6 0.18
22 25 0.76
23 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTTTATATTTAAAAAATA
Found at i:17471666 original size:17 final size:18
Alignment explanation
Indices: 17471631--17471674 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
17471621 ATTCCTAAAA
17471631 TTTATTTATGAAAAATATT
1 TTTA-TTATGAAAAATATT
*
17471650 TTTATTATG-AAATTATT
1 TTTATTATGAAAAATATT
*
17471667 ATTATTAT
1 TTTATTAT
17471675 TATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 14 0.61
18 5 0.22
19 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTATTATGAAAAATATT
Found at i:17471667 original size:3 final size:3
Alignment explanation
Indices: 17471661--17471711 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
17471651 TTATTATGAA
17471661 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17471709 ATT
1 ATT
17471712 GTATAAATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17471890 original size:89 final size:89
Alignment explanation
Indices: 17471778--17471953 Score: 343
Period size: 89 Copynumber: 2.0 Consensus size: 89
17471768 ATTTCAAAAA
17471778 AATTGACTACTTACAAAATTCTTGAAGTTTCATTATAAGATATTTTGTTTATTTATTAAAACTAA
1 AATTGACTACTTACAAAATTCTTGAAGTTTCATTATAAGATATTTTGTTTATTTATTAAAACTAA
17471843 TTTTAGAATTATCTTGATTCTTAG
66 TTTTAGAATTATCTTGATTCTTAG
17471867 AATTGACTACTTACAAAATTCTTGAAGTTTCATTATAAGATATTTTGTTTATTTATTAAAACTAA
1 AATTGACTACTTACAAAATTCTTGAAGTTTCATTATAAGATATTTTGTTTATTTATTAAAACTAA
*
17471932 TTTTGGAATTATCTTGATTCTT
66 TTTTAGAATTATCTTGATTCTT
17471954 TGGTTAAATC
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (89 bp):
AATTGACTACTTACAAAATTCTTGAAGTTTCATTATAAGATATTTTGTTTATTTATTAAAACTAA
TTTTAGAATTATCTTGATTCTTAG
Found at i:17474484 original size:30 final size:31
Alignment explanation
Indices: 17474443--17474513 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
17474433 TCCTCTAACT
*
17474443 AAAGGCTATGAAACTTTG-ATTAAAAATTTG
1 AAAGGCAATGAAACTTTGAATTAAAAATTTG
*
17474473 AAAGGTAATGAAACTTTGAATTAAAAATTTG
1 AAAGGCAATGAAACTTTGAATTAAAAATTTG
17474504 AAAGGCAATG
1 AAAGGCAATG
17474514 GTATTTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 16 0.43
31 21 0.57
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (31 bp):
AAAGGCAATGAAACTTTGAATTAAAAATTTG
Found at i:17477248 original size:17 final size:17
Alignment explanation
Indices: 17477226--17477267 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
17477216 CAAAAGTCAC
*
17477226 AAGCACATAATCTTTTT
1 AAGCACATAATCTTCTT
17477243 AAGCACATAATCTTCTT
1 AAGCACATAATCTTCTT
17477260 AAGCACAT
1 AAGCACAT
17477268 TCTATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.33
Consensus pattern (17 bp):
AAGCACATAATCTTCTT
Found at i:17477883 original size:19 final size:21
Alignment explanation
Indices: 17477842--17477883 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
17477832 AAATATTTAA
*
17477842 TTAATTTTTATTGTGATTTTT
1 TTAATTTTTATTGTGATTATT
*
17477863 TTAA-TTTT-TTGTTATTATT
1 TTAATTTTTATTGTGATTATT
17477882 TT
1 TT
17477884 CTATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 11 0.58
20 4 0.21
21 4 0.21
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (21 bp):
TTAATTTTTATTGTGATTATT
Found at i:17479600 original size:3 final size:3
Alignment explanation
Indices: 17479587--17479619 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
17479577 TGAAGAAAAG
*
17479587 ATA AAA ATA ATA ATA ATA AT- ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17479620 AATGATCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:17479612 original size:14 final size:14
Alignment explanation
Indices: 17479593--17479619 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17479583 AAAGATAAAA
17479593 ATAATAATAATAAT
1 ATAATAATAATAAT
17479607 ATAATAATAATAA
1 ATAATAATAATAA
17479620 AATGATCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:17479760 original size:24 final size:26
Alignment explanation
Indices: 17479733--17479780 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
17479723 TTTTCGAACA
*
17479733 AAATAGGTGTCAA-CA-AAGAAATTT
1 AAATAGATGTCAACCATAAGAAATTT
*
17479757 AAATAGATGTGAACCATAAGAAAT
1 AAATAGATGTCAACCATAAGAAAT
17479781 ATTACTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 2 0.10
26 7 0.35
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (26 bp):
AAATAGATGTCAACCATAAGAAATTT
Found at i:17479890 original size:17 final size:17
Alignment explanation
Indices: 17479868--17479903 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
17479858 GTTCAACTGA
*
17479868 TTTTAAATTCAAAA-AT
1 TTTTTAATTCAAAATAT
17479884 TTTTTAATTCAAAATAT
1 TTTTTAATTCAAAATAT
17479901 TTT
1 TTT
17479904 AGATTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTAATTCAAAATAT
Found at i:17481835 original size:114 final size:110
Alignment explanation
Indices: 17481638--17481848 Score: 293
Period size: 114 Copynumber: 1.9 Consensus size: 110
17481628 TGATCCTCCA
*
17481638 ATCATTTGGTAGAATTAAAATTTATTTTATTTTTTCTAAAAATTCATTATGAAAATTTTCAATCG
1 ATCATTTGGTAGAATTAAAATTTATTTTATTTTTTCAAAAAATTCATTATGAAAATTTTCAATCG
***
17481703 TTTGATAGAATTTATAATTTATTTTTTTAAAAAAAAAAATCATTCT
66 TTTGATAGAAGGCATAATTT-TTTTTTTAAAAAAAAAAATCATTCT
17481749 ATCATTTGGTATG-ATTGAAAATTTATTTTATTTTTTTCAAAAAAAATT-ATTATG-AAATTCTT
1 ATCATTTGGTA-GAATT-AAAATTTATTTTA-TTTTTTC--AAAAAATTCATTATGAAAATT-TT
*
17481811 CAATCGTTTGGTAGAAGGCATAATTTTTTTTTTAAAAA
60 CAATCGTTTGATAGAAGGCATAATTTTTTTTTTAAAAA
17481849 TCCTCCAATC
Statistics
Matches: 89, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
111 14 0.16
112 14 0.16
113 24 0.27
114 30 0.34
115 7 0.08
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (110 bp):
ATCATTTGGTAGAATTAAAATTTATTTTATTTTTTCAAAAAATTCATTATGAAAATTTTCAATCG
TTTGATAGAAGGCATAATTTTTTTTTTAAAAAAAAAAATCATTCT
Found at i:17489287 original size:22 final size:22
Alignment explanation
Indices: 17489262--17489305 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17489252 TACCACATCA
*
17489262 TAGCCATATCTTTATGGCACAG
1 TAGCCATATCTCTATGGCACAG
*
17489284 TAGCCATATCTCTATGGTACAG
1 TAGCCATATCTCTATGGCACAG
17489306 CTTTATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (22 bp):
TAGCCATATCTCTATGGCACAG
Found at i:17491529 original size:14 final size:14
Alignment explanation
Indices: 17491510--17491539 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17491500 TATGAATGCA
*
17491510 ATGTATGAGATATG
1 ATGTATGAAATATG
17491524 ATGTATGAAATATG
1 ATGTATGAAATATG
17491538 AT
1 AT
17491540 ATTTGCCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (14 bp):
ATGTATGAAATATG
Found at i:17493917 original size:109 final size:108
Alignment explanation
Indices: 17493722--17493929 Score: 285
Period size: 109 Copynumber: 1.9 Consensus size: 108
17493712 AAAAATTTTA
* ** *
17493722 AATCCTCCAATCATGTAGTAGAATTAAAATTTTATTTTATTTTTTTCTTAAAATTCATTTTGAAA
1 AATCATCCAATCATGTAGTAGAATTAAAATTTTATTTTATTTTTTTCAAAAAATTCATTATGAAA
*
17493787 TTCTCCAATCGTTTGGTAGAATTCATAATTTTTTTTTTAAATG
66 TTCTCCAATCATTTGGTAGAATTCATAATTTTTTTTTTAAATG
* * *
17493830 AATCATCCAATCATTTGGTAGGATTGAAAA-TTTATTTTATTTTTTTCAAAAAAAATT-ATTATG
1 AATCATCCAATCATGTAGTAGAATT-AAAATTTTATTTTATTTTTTTC--AAAAAATTCATTATG
* *
17493893 AAATTCTTCAATTATTTGGTAGAATTCATAATTTTTT
63 AAATTCTCCAATCATTTGGTAGAATTCATAATTTTTT
17493930 AAAAAAAATC
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
108 38 0.44
109 43 0.49
110 6 0.07
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.48
Consensus pattern (108 bp):
AATCATCCAATCATGTAGTAGAATTAAAATTTTATTTTATTTTTTTCAAAAAATTCATTATGAAA
TTCTCCAATCATTTGGTAGAATTCATAATTTTTTTTTTAAATG
Found at i:17498255 original size:26 final size:26
Alignment explanation
Indices: 17498205--17498275 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
17498195 TTAATAAAAC
*
17498205 TATTAAAATAT-TAAAAATTATTTAT
1 TATTAAAATATATTAAAATTATTTAT
*
17498230 TATTAAAATATATTGAAATTATTTAT
1 TATTAAAATATATTAAAATTATTTAT
*
17498256 TATTAAAAT-TATTAATATTA
1 TATTAAAATATATTAAAATTA
17498276 AAAAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 20 0.49
26 21 0.51
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TATTAAAATATATTAAAATTATTTAT
Found at i:17498266 original size:9 final size:9
Alignment explanation
Indices: 17498194--17498275 Score: 57
Period size: 9 Copynumber: 9.4 Consensus size: 9
17498184 TTGTAATAAT
*
17498194 ATTAATAAA
1 ATTATTAAA
*
17498203 ACTATTAAA
1 ATTATTAAA
17498212 A-TATTAAAA
1 ATTATT-AAA
*
17498221 ATTATT--T
1 ATTATTAAA
17498228 ATTATTAAA
1 ATTATTAAA
*
17498237 ATATATTGAA
1 AT-TATTAAA
*
17498247 ATTATT--T
1 ATTATTAAA
17498254 ATTATTAAA
1 ATTATTAAA
*
17498263 ATTATTAAT
1 ATTATTAAA
17498272 ATTA
1 ATTA
17498276 AAAAATAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
7 12 0.21
8 4 0.07
9 30 0.52
10 12 0.21
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (9 bp):
ATTATTAAA
Found at i:17498279 original size:16 final size:16
Alignment explanation
Indices: 17498239--17498361 Score: 61
Period size: 16 Copynumber: 7.4 Consensus size: 16
17498229 TTATTAAAAT
*
17498239 ATATTGAAATTATTTA
1 ATATTAAAATTATTTA
*
17498255 TTATTAAAATTA-TTA
1 ATATTAAAATTATTTA
* *
17498270 ATATTAAAAAATAATTA
1 ATATT-AAAATTATTTA
* *
17498287 TATTTTAATAATAATATTTC
1 -ATATTAA-AAT--TATTTA
*
17498307 ATATTTAATATTATGTTA
1 ATA-TTAAAATTAT-TTA
* *
17498325 ATATAAAAAATATTTA
1 ATATTAAAATTATTTA
* *
17498341 A-AATAAAATTTTTTA
1 ATATTAAAATTATTTA
*
17498356 TTATTA
1 ATATTA
17498362 TTTATATTTT
Statistics
Matches: 78, Mismatches: 20, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
15 17 0.22
16 23 0.29
17 15 0.19
18 11 0.14
19 4 0.05
20 8 0.10
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (16 bp):
ATATTAAAATTATTTA
Found at i:17498302 original size:20 final size:20
Alignment explanation
Indices: 17498279--17498316 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17498269 AATATTAAAA
17498279 AATAATT-ATATTTTAATAAT
1 AATAATTCATA-TTTAATAAT
*
17498299 AATATTTCATATTTAATA
1 AATAATTCATATTTAATA
17498317 TTATGTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AATAATTCATATTTAATAAT
Found at i:17498370 original size:19 final size:20
Alignment explanation
Indices: 17498348--17498388 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
17498338 TTAAAATAAA
*
17498348 ATTTTTTATTATTAT-TTAT
1 ATTTTTTATTAATATATTAT
17498367 ATTTTTTATTAATATATTAT
1 ATTTTTTATTAATATATTAT
17498387 AT
1 AT
17498389 GAATAGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTTTTATTAATATATTAT
Found at i:17498406 original size:20 final size:19
Alignment explanation
Indices: 17498383--17498425 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
17498373 TATTAATATA
17498383 TTATATGAATAGT-ATATTAT
1 TTATAT-AATA-TAATATTAT
17498403 TTAT-TAATATAATATTAT
1 TTATATAATATAATATTAT
17498421 TTATA
1 TTATA
17498426 AGTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 15 0.71
19 1 0.05
20 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATATAATATAATATTAT
Found at i:17498416 original size:23 final size:22
Alignment explanation
Indices: 17498381--17498424 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
17498371 TTTATTAATA
17498381 TATTATATGAATAGTATATTATT
1 TATTATATGAATAGTAT-TTATT
*
17498404 TATTAATAT-AATATTATTTAT
1 TATT-ATATGAATAGTATTTAT
17498425 AAGTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TATTATATGAATAGTATTTATT
Found at i:17502732 original size:24 final size:24
Alignment explanation
Indices: 17502689--17502734 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
17502679 TTTTTTTTTC
* *
17502689 CTTAATTCTAGGGATGCAAATACT
1 CTTAATTCTAGAGATACAAATACT
*
17502713 CTTAATTTTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
17502735 TAAATATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (24 bp):
CTTAATTCTAGAGATACAAATACT
Found at i:17506602 original size:25 final size:25
Alignment explanation
Indices: 17506563--17506611 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
17506553 TTTGATATCA
17506563 TGTAGAAAAACTAAGAAATAAAACTG
1 TGTAGAAAAACTAAG-AATAAAACTG
*
17506589 TGTAG-AAAACTAAGAGTAAAACT
1 TGTAGAAAAACTAAGAATAAAACT
17506612 AAATGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 9 0.41
26 5 0.23
ACGTcount: A:0.55, C:0.08, G:0.16, T:0.20
Consensus pattern (25 bp):
TGTAGAAAAACTAAGAATAAAACTG
Found at i:17514596 original size:15 final size:17
Alignment explanation
Indices: 17514568--17514604 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
17514558 TTTTTATGTA
17514568 ATAATATAATTATAAAT
1 ATAATATAATTATAAAT
*
17514585 ATAATAT-A-TATATAT
1 ATAATATAATTATAAAT
17514600 ATAAT
1 ATAAT
17514605 TATTGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 1 0.05
17 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATATAATTATAAAT
Found at i:17515638 original size:18 final size:18
Alignment explanation
Indices: 17515602--17515640 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
17515592 CAAGAAAATA
*
17515602 TTTAATTTTATTTAATTT
1 TTTAATTTTATTGAATTT
*
17515620 TTTAATTTT-TTGAAGTT
1 TTTAATTTTATTGAATTT
17515637 TTTA
1 TTTA
17515641 TATAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTAATTTTATTGAATTT
Found at i:17516193 original size:33 final size:34
Alignment explanation
Indices: 17516120--17516195 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 34
17516110 AAAAAATCTG
*
17516120 ATTTAAAAAATTTTTAAAAAACTAATTGTTAAAA
1 ATTTAAAAAATTTTTAAAAAACTAAATGTTAAAA
* * * *
17516154 AATTAAAATATTTTTAAAAAATTAAAT-TTAATA
1 ATTTAAAAAATTTTTAAAAAACTAAATGTTAAAA
*
17516187 TTTTAAAAA
1 ATTTAAAAA
17516196 TACGAAAATT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (34 bp):
ATTTAAAAAATTTTTAAAAAACTAAATGTTAAAA
Found at i:17516824 original size:26 final size:24
Alignment explanation
Indices: 17516785--17516867 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 24
17516775 CAATGATCAC
*
17516785 ATTAATATTTTAATAATAAAAAATCA
1 ATTAA-ATTATAATAATAAAAAAT-A
* *
17516811 ATTAAATTAGTAATTAA-ATTAAAATT
1 ATTAAATTA-TAA-TAATA-AAAAATA
*
17516837 ATTAAATTAAAATAATAAAAAA-A
1 ATTAAATTATAATAATAAAAAATA
17516860 ATTAAATT
1 ATTAAATT
17516868 TATATAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
23 8 0.17
24 7 0.15
25 6 0.13
26 18 0.38
27 8 0.17
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (24 bp):
ATTAAATTATAATAATAAAAAATA
Found at i:17516842 original size:14 final size:14
Alignment explanation
Indices: 17516823--17516849 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17516813 TAAATTAGTA
17516823 ATTAAATTAAAATT
1 ATTAAATTAAAATT
17516837 ATTAAATTAAAAT
1 ATTAAATTAAAAT
17516850 AATAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAATTAAAATT
Found at i:17517470 original size:63 final size:61
Alignment explanation
Indices: 17517389--17517600 Score: 175
Period size: 63 Copynumber: 3.4 Consensus size: 61
17517379 TAAAAAAAAA
* * *
17517389 ATTATTTAAAATACTTTTAGACCAAAAACGTTTTAAAT-ATTCTTTAATATTTTTTTAATAAGG
1 ATTATTTAAGATATTTTTA-A-TAAAAACGTTTTAAATAATTCTTTAATATTTTTTTAATAA-G
* **
17517452 ATTATTTAAGGTATTTTTAATAAAAAAATATCTTAAATAATACTCTTT-A-ATTTTTTT-ATGAA
1 ATTATTTAAGATATTTTTAATAAAAACGT-T-TTAAATAAT--TCTTTAATATTTTTTTAAT-AA
*
17517514 T
61 G
* * * * * *
17517515 ATTATTTAAGGTGTTTTTAATTAAAAACGTCTTATATAATT-TTTAAT-TTTTTTAAAGAAG
1 ATTATTTAAGATATTTTTAA-TAAAAACGTTTTAAATAATTCTTTAATATTTTTTTAATAAG
*
17517575 ATTATTTAAGATATTTTTTATAAAAA
1 ATTATTTAAGATATTTTTAATAAAAA
17517601 AAAACCTTAA
Statistics
Matches: 121, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
59 9 0.07
60 27 0.22
61 7 0.06
62 10 0.08
63 43 0.36
64 19 0.16
65 1 0.01
66 5 0.04
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (61 bp):
ATTATTTAAGATATTTTTAATAAAAACGTTTTAAATAATTCTTTAATATTTTTTTAATAAG
Found at i:17517486 original size:124 final size:123
Alignment explanation
Indices: 17517325--17517627 Score: 279
Period size: 124 Copynumber: 2.5 Consensus size: 123
17517315 CAAAATATTG
* **** **
17517325 AGGATTATTTAAGGTGTTTTTAATTGGTAAACGTCTTAAATAATCCCTTT-ATTTTAAAAAAAAA
1 AGGATTATTTAAGGTATTTTTAATAAAAAAAAATCTTAAATAATCCCTTTAATTTTAAAAAAAAA
* * *
17517389 ATTATTTAAAATACTTTTAGACCAAAAACGTTTTAAAT-ATTCTTTAATATTTTTTTAATA
66 ATTATTTAAAATACTTTTA-ACCAAAAACGTCTTAAATAATT-TTTAAT-TTTTTTAAAGA
* * *** **
17517449 AGGATTATTTAAGGTATTTTTAATAAAAAAATATCTTAAATAATACTCTTTAATTTTTTTATGAA
1 AGGATTATTTAAGGTATTTTTAATAAAAAAAAATCTTAAATAAT-CCCTTTAATTTTAAAAAAAA
* ** ** ** *
17517514 TATTATTTAAGGTGTTTTTAATTAAAAACGTCTTATATAATTTTTAATTTTTTTAAAGA
65 AATTATTTAAAATACTTTTAACCAAAAACGTCTTAAATAATTTTTAATTTTTTTAAAGA
* * * * *
17517573 A-GATTATTTAAGATATTTTTTATAAAAAAAAACCTTAAATAATACCTTTCATTTT
1 AGGATTATTTAAGGTATTTTTAATAAAAAAAAATCTTAAATAATCCCTTTAATTTT
17517628 TTTAAACCTT
Statistics
Matches: 145, Mismatches: 31, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
122 9 0.06
123 38 0.26
124 47 0.32
125 25 0.17
126 26 0.18
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (123 bp):
AGGATTATTTAAGGTATTTTTAATAAAAAAAAATCTTAAATAATCCCTTTAATTTTAAAAAAAAA
ATTATTTAAAATACTTTTAACCAAAAACGTCTTAAATAATTTTTAATTTTTTTAAAGA
Found at i:17517640 original size:60 final size:61
Alignment explanation
Indices: 17517452--17517687 Score: 191
Period size: 62 Copynumber: 3.8 Consensus size: 61
17517442 TTTAATAAGG
* *
17517452 ATTATTTAAGGTATTTTTAATAAAAAAATATCTTAAATAATACTCTTTAATTTTTTTATGAAT
1 ATTATTTAAGGTATTTTTAATAAAAAAAAATCTTAAATAATAC-CTTTAATTTTTTTA-GAAC
* * ** * * *
17517515 ATTATTTAAGGTGTTTTTAAT-TAAAAACGTCTTATATAAT--TTTTAATTTTTTTAAAGAAG
1 ATTATTTAAGGTATTTTTAATAAAAAAAAATCTTAAATAATACCTTTAATTTTTTT--AGAAC
* * * *
17517575 ATTATTTAAGATATTTTTTATAAAAAAAAACCTTAAATAATACCTTTCATTTTTTTA-AACC
1 ATTATTTAAGGTATTTTTAATAAAAAAAAATCTTAAATAATACCTTTAATTTTTTTAGAA-C
* *
17517636 TTATTATTTAAAGCGT-TTTTTACT--AAAAATATCTTAAATAAT-CTCTTTAATT
1 --ATTATTT-AAG-GTATTTTTAATAAAAAAAAATCTTAAATAATAC-CTTTAATT
17517688 ACTTATAAGA
Statistics
Matches: 138, Mismatches: 24, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
59 12 0.09
60 23 0.17
61 17 0.12
62 38 0.28
63 38 0.28
64 9 0.07
65 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.48
Consensus pattern (61 bp):
ATTATTTAAGGTATTTTTAATAAAAAAAAATCTTAAATAATACCTTTAATTTTTTTAGAAC
Found at i:17517641 original size:123 final size:124
Alignment explanation
Indices: 17517403--17517687 Score: 328
Period size: 123 Copynumber: 2.3 Consensus size: 124
17517393 TTTAAAATAC
* * * * *
17517403 TTTTAGACCAAAAACGTTTTAAAT-ATTCTTTAATATTTTTTTAATAAGGATTATTTAAGGTATT
1 TTTTA-ACTAAAAACGTCTTAAATAATTCTTTAAT-TTTTTTAAAGAAGGATTATTTAAGATATT
* * * *
17517467 TTTAATAAAAAAATATCTTAAATAATACTCTTTAATTTTTTTATGAATATTATTTAAGGTGT
64 TTTAATAAAAAAAAACCTTAAATAATACTCTTTAATTTTTTTA-GAATATTATTTAAAGCGT
* *
17517529 TTTTAATTAAAAACGTCTTATATAATT-TTTAATTTTTTTAAAGAA-GATTATTTAAGATATTTT
1 TTTTAACTAAAAACGTCTTAAATAATTCTTTAATTTTTTTAAAGAAGGATTATTTAAGATATTTT
* *
17517592 TTATAAAAAAAAACCTTAAATAATAC-CTTTCATTTTTTTA-AACCTTATTATTTAAAGCGT
66 TAATAAAAAAAAACCTTAAATAATACTCTTTAATTTTTTTAGAA---TATTATTTAAAGCGT
* **
17517652 TTTTTACTAAAAATATCTTAAATAATCTCTTTAATT
1 TTTTAACTAAAAACGTCTTAAATAAT-TCTTTAATT
17517688 ACTTATAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
120 2 0.01
122 13 0.10
123 74 0.55
124 11 0.08
125 27 0.20
126 8 0.06
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (124 bp):
TTTTAACTAAAAACGTCTTAAATAATTCTTTAATTTTTTTAAAGAAGGATTATTTAAGATATTTT
TAATAAAAAAAAACCTTAAATAATACTCTTTAATTTTTTTAGAATATTATTTAAAGCGT
Found at i:17518008 original size:239 final size:240
Alignment explanation
Indices: 17517555--17517997 Score: 565
Period size: 239 Copynumber: 1.9 Consensus size: 240
17517545 CTTATATAAT
17517555 TTTTAATTTTTTTAAAGAAGATTATTTAAGATATTTTTTATAAAAAAAAACCTTAAATAATACCT
1 TTTTAATTTTTTTAAAGAAGATTATTTAAGATATTTTTTATAAAAAAAAACCTTAAATAATACCT
* * * *
17517620 TTCATTTTTTTAAACCTTATTATTTAAAGCGTTTTTTACTAAAAATATCTTAAATAATCTCTTTA
66 TTCAATTTTTTAAACCATATTATTTAAAGCATTTTTGACTAAAAATATCTTAAATAATCTCTTTA
* * * * * *
17517685 ATTACTTATAAGATTTAAGAGATAAAATATATAAAAACTGGAGTAGCTCAGTTGATTAGAGTATG
131 ATTACTTACAAGATTTAAGAGATAAAATATAAAAAAACTGAAGTAGCTCAGTTGATTAAAGCATA
* *
17517750 TGGTTATTAACCATAAAATTGTTAATTCAACCCTTTTTTTTGACC
196 CGGCTATTAACCATAAAATTGTTAATTCAACCCTTTTTTTTGACC
** * *
17517795 TTTTAA-TTTTTT-AAGGGGATTATTTTAAGGTA-TTTTTAGTAAAAAAACACCTTAAATAATAT
1 TTTTAATTTTTTTAAAGAAGATTA-TTTAAGATATTTTTTA-TAAAAAAAAACCTTAAATAATA-
** * * * * *
17517857 CC-TTCAATTTTTTGGATCATATTGTTTAAGGCATTTTTGATTAAAAATA-CTTTAAATAATCTT
63 CCTTTCAATTTTTTAAACCATATTATTTAAAGCATTTTTGACTAAAAATATC-TTAAATAATCTC
* * *
17517920 TTTCATTACTTACAAGATTTAAGAGATAAAATATAAAAAAATTGAAGTAGCTTAGTT-AGTTAAA
127 TTTAATTACTTACAAGATTTAAGAGATAAAATATAAAAAAACTGAAGTAGCTCAGTTGA-TTAAA
17517984 GCATACGGCTATTA
191 GCATACGGCTATTA
17517998 CTTATAAAAT
Statistics
Matches: 172, Mismatches: 26, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
238 16 0.09
239 148 0.86
240 8 0.05
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.42
Consensus pattern (240 bp):
TTTTAATTTTTTTAAAGAAGATTATTTAAGATATTTTTTATAAAAAAAAACCTTAAATAATACCT
TTCAATTTTTTAAACCATATTATTTAAAGCATTTTTGACTAAAAATATCTTAAATAATCTCTTTA
ATTACTTACAAGATTTAAGAGATAAAATATAAAAAAACTGAAGTAGCTCAGTTGATTAAAGCATA
CGGCTATTAACCATAAAATTGTTAATTCAACCCTTTTTTTTGACC
Found at i:17519016 original size:15 final size:16
Alignment explanation
Indices: 17518998--17519031 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
17518988 TAATTTTAAA
*
17518998 AATATAAAA-ATTTAT
1 AATATAAAATAATTAT
17519013 AATATAAAATAATTAT
1 AATATAAAATAATTAT
17519029 AAT
1 AAT
17519032 TTTTAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAAAATAATTAT
Found at i:17521979 original size:2 final size:2
Alignment explanation
Indices: 17521972--17522012 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
17521962 CAAGAGAAAC
*
17521972 AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17522013 GTCAATCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17523029 original size:3 final size:3
Alignment explanation
Indices: 17523021--17523053 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
17523011 CGATTAGTTT
*
17523021 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17523054 AGGCAATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:17523773 original size:25 final size:26
Alignment explanation
Indices: 17523745--17523802 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
17523735 TTTTTACTTG
*
17523745 TATATTTAAATAAATTTTTT-ATAAA
1 TATATATAAATAAATTTTTTAATAAA
* *
17523770 TATATATACATATATTTTTTAATAAA
1 TATATATAAATAAATTTTTTAATAAA
*
17523796 AATATAT
1 TATATAT
17523803 TATTTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 17 0.61
26 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TATATATAAATAAATTTTTTAATAAA
Found at i:17524804 original size:5 final size:5
Alignment explanation
Indices: 17524794--17524818 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
17524784 TTAAAATTAA
17524794 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
17524819 TTTGAGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:17526777 original size:2 final size:2
Alignment explanation
Indices: 17526770--17526794 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17526760 GATCTATAAG
17526770 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
17526795 ATTTTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:17532571 original size:60 final size:59
Alignment explanation
Indices: 17532472--17532830 Score: 413
Period size: 60 Copynumber: 6.0 Consensus size: 59
17532462 ATAAATAGAC
**
17532472 AAATTGATACTTTCAA-TTTTTTTC-AAAATATTTTTTTTGAAATTTTTATTTTCAAGAA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTGAAATTTTTATTTTCAAGAA
* * * * **
17532530 AAATTGATACTTTTAACTTTTCGTTAAAAATGTCTTTTTTGAAAACTTTATTTTCAAGAA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTGAAATTTTTATTTTCAAGAA
* * * * **
17532590 AAATTTATATTTTCAACTTTTCCTCAAAAATCTCTTTTTTTGAAATCTTTATTTTTGAGAA
1 AAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTTGAAATTTTTATTTTCAAGAA
* * * *
17532651 AAATTGATATTTTCAA-TTCTTCCTCAAAAATA-ATTTTTGAAAATTTTATTTTTAAGAA
1 AAATTGATACTTTCAACTT-TTCCTCAAAAATATTTTTTTGAAATTTTTATTTTCAAGAA
* * *
17532709 AAATTGATACTTTCAATTTTTCCTCAAAAATATTTCTTTTGGAAA-TTGTATTTTCAAGGA
1 AAATTGATACTTTCAACTTTTCCTCAAAAATATTT-TTTT-GAAATTTTTATTTTCAAGAA
*
17532769 CAATTGATACTTTCAACTTTTCCTCAAAAATAATTTTTTTGAAATTTTTATTTTCAAGAA
1 AAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTTGAAATTTTTATTTTCAAGAA
17532829 AA
1 AA
17532831 TCATTGAAAA
Statistics
Matches: 257, Mismatches: 32, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
58 65 0.25
59 14 0.05
60 119 0.46
61 57 0.22
62 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (59 bp):
AAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTTTATTTTCAAGAA
Found at i:17532785 original size:179 final size:178
Alignment explanation
Indices: 17532472--17532822 Score: 465
Period size: 179 Copynumber: 2.0 Consensus size: 178
17532462 ATAAATAGAC
** ** *
17532472 AAATTGATACTTTCAATTTTTTTCAAAATATTTTTTTTGAAATTTTTATTTTCAAGAAAAATTGA
1 AAATTGATACTTTCAATTTTCCTCAAAATATAATTTTTGAAAATTTTATTTTCAAGAAAAATTGA
* * * * * *
17532537 TACTTTTAACTTTTCGTTAAAAATGTCTTTTTTGAAAACTTTATTTTCAAGAAAAATTTATATTT
66 TACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAAACTTTATTTTCAAGAAAAATTGATACTT
**
17532602 TCAACTTTTCCTCAAAAATCTCTTTTTTTGAAATCTTTATTTTTGAGAA
131 TCAACTTTTCCTCAAAAAT-AATTTTTTTGAAATCTTTATTTTTGAGAA
* *
17532651 AAATTGATATTTTCAATTCTTCCTCAAAA-ATAATTTTTGAAAATTTTATTTTTAAGAAAAATTG
1 AAATTGATACTTTCAATT-TTCCTCAAAATATAATTTTTGAAAATTTTATTTTCAAGAAAAATTG
* * * *
17532715 ATACTTTCAATTTTTCCTCAAAAATAT-TTCTTTTGGAAA-TTGTATTTTCAAGGACAATTGATA
65 ATACTTTCAACTTTTCCTCAAAAATATCTT-TTTTGAAAACTT-TATTTTCAAGAAAAATTGATA
*
17532778 CTTTCAACTTTTCCTCAAAAATAATTTTTTTGAAATTTTTATTTT
128 CTTTCAACTTTTCCTCAAAAATAATTTTTTTGAAATCTTTATTTT
17532823 CAAGAAAATC
Statistics
Matches: 149, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
178 24 0.16
179 117 0.79
180 8 0.05
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (178 bp):
AAATTGATACTTTCAATTTTCCTCAAAATATAATTTTTGAAAATTTTATTTTCAAGAAAAATTGA
TACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAAACTTTATTTTCAAGAAAAATTGATACTT
TCAACTTTTCCTCAAAAATAATTTTTTTGAAATCTTTATTTTTGAGAA
Found at i:17532831 original size:119 final size:119
Alignment explanation
Indices: 17532472--17532830 Score: 451
Period size: 119 Copynumber: 3.0 Consensus size: 119
17532462 ATAAATAGAC
*
17532472 AAATTGATACTTTCAATTTTT-TTC-AAAATATTTTTTTTGAAATTTTTATTTTCAAGAAAAATT
1 AAATTGATACTTTCAATTTTTCCTCAAAAATATTTTTTTTGAAA-TTTTATTTTCAAGAAAAATT
* * * * *
17532535 GATACTTTTAACTTTTCGTTAAAAAT-GTCTTTTTTGAAAACTTTATTTTCAAGAA
65 GATACTTTCAACTTTTCCTCAAAAATAAT-TTTTTTGAAAATTTTATTTTCAAGAA
* * * * **
17532590 AAATTTATATTTTCAACTTTTCCTCAAAAATCTCTTTTTTTGAAATCTTTATTTTTGAGAAAAAT
1 AAATTGATACTTTCAATTTTTCCTCAAAAATAT-TTTTTTTGAAAT-TTTATTTTCAAGAAAAAT
* *
17532655 TGATATTTTCAA-TTCTTCCTCAAAAATAA--TTTTTGAAAATTTTATTTTTAAGAA
64 TGATACTTTCAACTT-TTCCTCAAAAATAATTTTTTTGAAAATTTTATTTTCAAGAA
* * * *
17532709 AAATTGATACTTTCAATTTTTCCTCAAAAATATTTCTTTTGGAAATTGTATTTTCAAGGACAATT
1 AAATTGATACTTTCAATTTTTCCTCAAAAATATTT-TTTTTGAAATTTTATTTTCAAGAAAAATT
*
17532774 GATACTTTCAACTTTTCCTCAAAAATAATTTTTTTGAAATTTTTATTTTCAAGAA
65 GATACTTTCAACTTTTCCTCAAAAATAATTTTTTTGAAAATTTTATTTTCAAGAA
17532829 AA
1 AA
17532831 TCATTGAAAA
Statistics
Matches: 204, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
118 58 0.28
119 65 0.32
120 34 0.17
121 47 0.23
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (119 bp):
AAATTGATACTTTCAATTTTTCCTCAAAAATATTTTTTTTGAAATTTTATTTTCAAGAAAAATTG
ATACTTTCAACTTTTCCTCAAAAATAATTTTTTTGAAAATTTTATTTTCAAGAA
Found at i:17534109 original size:86 final size:85
Alignment explanation
Indices: 17533922--17534251 Score: 297
Period size: 86 Copynumber: 3.8 Consensus size: 85
17533912 AAGTCTAAAA
* * * * * * ** *
17533922 TGGAATGA-CCAAAAAATGGATTTGACACAAGTCAAAAT-TCAAAATAAAATAACCCGGACTGAA
1 TGGACTGAGCCAAAGAA-GGATTTGACATAAGTCAAAATCT-GAAACAAAATGACCTAGATTGAA
* *
17533985 CTGTAA-TCTAAAATAAATAACT
64 TTG-AAGTCTAAAATGAATAACT
* ** * * * *
17534007 TGGATTGAGCTGAAGAAAGATTTGACATAAGTCAAAATCTGAAGACAAAACGATCTAAATTGAAT
1 TGGACTGAGCCAAAGAAGGATTTGACATAAGTCAAAATCTGAA-ACAAAATGACCTAGATTGAAT
* *
17534072 TGAAGTTTGAAATGAATAACT
65 TGAAGTCTAAAATGAATAACT
* ** * *
17534093 TGGACTGAGCCAAAGAAGGATTTGACATAAGTCGAAATCCAAAAACCAAATGACCTGGATTGAAT
1 TGGACTGAGCCAAAGAAGGATTTGACATAAGTCAAAAT-CTGAAACAAAATGACCTAGATTGAAT
17534158 TGAAGTCTAAAATGAATAACT
65 TGAAGTCTAAAATGAATAACT
* * * * * *
17534179 TAGACTAAGCCAAAGAAGGATCTGGCATAGGTCAAAATCTAGAAACAAGATGACCTAGATTGAAT
1 TGGACTGAGCCAAAGAAGGATTTGACATAAGTCAAAATCT-GAAACAAAATGACCTAGATTGAAT
*
17534244 CGAAGTCT
65 TGAAGTCT
17534252 GTCTTTACAG
Statistics
Matches: 194, Mismatches: 45, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
85 31 0.16
86 160 0.82
87 3 0.02
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (85 bp):
TGGACTGAGCCAAAGAAGGATTTGACATAAGTCAAAATCTGAAACAAAATGACCTAGATTGAATT
GAAGTCTAAAATGAATAACT
Found at i:17534443 original size:18 final size:17
Alignment explanation
Indices: 17534405--17534443 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
17534395 AAAGATTTGC
* *
17534405 AATTCAAACATTCGCAG
1 AATTCAAAAATTCACAG
17534422 AATTCAAAAATTCACAAG
1 AATTCAAAAATTCAC-AG
17534440 AATT
1 AATT
17534444 TCGATTCGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.26
Consensus pattern (17 bp):
AATTCAAAAATTCACAG
Found at i:17534468 original size:33 final size:35
Alignment explanation
Indices: 17534414--17534490 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 35
17534404 CAATTCAAAC
*
17534414 ATTCGC-AGAATTCAAAAATTCACAAGAATTTC-G
1 ATTCGCAAGAATTCAAAAATTCACAAAAATTTCAG
* *
17534447 ATTCGCAAGAATT-GAAGATTCACAAAAATTTCAG
1 ATTCGCAAGAATTCAAAAATTCACAAAAATTTCAG
*
17534481 ATTCGTAAGA
1 ATTCGCAAGA
17534491 TTTTCAGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (35 bp):
ATTCGCAAGAATTCAAAAATTCACAAAAATTTCAG
Found at i:17534482 original size:17 final size:17
Alignment explanation
Indices: 17534431--17534500 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 17
17534421 GAATTCAAAA
17534431 ATTCACAAGAATTTC-G
1 ATTCACAAGAATTTCAG
* **
17534447 ATTCGCAAGAATTGAAG
1 ATTCACAAGAATTTCAG
*
17534464 ATTCACAAAAATTTCAG
1 ATTCACAAGAATTTCAG
** *
17534481 ATTCGTAAGATTTTCAG
1 ATTCACAAGAATTTCAG
17534498 ATT
1 ATT
17534501 TGCAAGAATC
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
16 12 0.29
17 30 0.71
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (17 bp):
ATTCACAAGAATTTCAG
Found at i:17534517 original size:34 final size:34
Alignment explanation
Indices: 17534479--17534704 Score: 154
Period size: 34 Copynumber: 6.6 Consensus size: 34
17534469 CAAAAATTTC
*
17534479 AGATTCGTAAGATTTTCAGATTTGCAAGAATCAA
1 AGATTCGTAAGATTTTCAGATTTGCAAGAATTAA
* ** * **
17534513 AGATTTGTAAGACATTCAGATTTACAAGAATTGG
1 AGATTCGTAAGATTTTCAGATTTGCAAGAATTAA
** * * *
17534547 AGATTCGTAAGA-CATCTAGATTCT-TAAAAATTAG
1 AGATTCGTAAGATTTTC-AGATT-TGCAAGAATTAA
** ** * *
17534581 AGATTCACAAGGCTTTCAGATTTGCAGGAATTGA
1 AGATTCGTAAGATTTTCAGATTTGCAAGAATTAA
* **
17534615 AGATTCGTAAGACTTTT-AGATTCGCAAGAATTGG
1 AGATTCGTAAGA-TTTTCAGATTTGCAAGAATTAA
* * *
17534649 AGATTCGTAAGATTTTTAAATTTGTAAG-ATATAA
1 AGATTCGTAAGATTTTCAGATTTGCAAGAAT-TAA
* *
17534683 AGATTCGTGAGATTTTTAGATT
1 AGATTCGTAAGATTTTCAGATT
17534705 GTAGATCCAT
Statistics
Matches: 148, Mismatches: 37, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
33 9 0.06
34 133 0.90
35 6 0.04
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (34 bp):
AGATTCGTAAGATTTTCAGATTTGCAAGAATTAA
Found at i:17534533 original size:17 final size:16
Alignment explanation
Indices: 17534476--17534558 Score: 51
Period size: 17 Copynumber: 4.9 Consensus size: 16
17534466 TCACAAAAAT
* *
17534476 TTCAGATTCGTAAGATT
1 TTCAGATTTGTAAGA-A
*
17534493 TTCAGATTTGCAAGAA
1 TTCAGATTTGTAAGAA
17534509 -TCAAAGATTTGTAAGACA
1 TTC--AGATTTGTAAGA-A
**
17534527 TTCAGATTTACAAGAA
1 TTCAGATTTGTAAGAA
* *
17534543 TTGGAGATTCGTAAGA
1 TT-CAGATTTGTAAGA
17534559 CATCTAGATT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
15 2 0.04
16 3 0.06
17 43 0.84
18 1 0.02
19 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (16 bp):
TTCAGATTTGTAAGAA
Found at i:17534635 original size:17 final size:17
Alignment explanation
Indices: 17534615--17534704 Score: 81
Period size: 17 Copynumber: 5.3 Consensus size: 17
17534605 CAGGAATTGA
*
17534615 AGATTCGTAAGACTTTT
1 AGATTCGTAAGATTTTT
* * **
17534632 AGATTCGCAAGAATTGG
1 AGATTCGTAAGATTTTT
17534649 AGATTCGTAAGATTTTT
1 AGATTCGTAAGATTTTT
* * * **
17534666 AAATTTGTAAGATATAA
1 AGATTCGTAAGATTTTT
*
17534683 AGATTCGTGAGATTTTT
1 AGATTCGTAAGATTTTT
17534700 AGATT
1 AGATT
17534705 GTAGATCCAT
Statistics
Matches: 54, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (17 bp):
AGATTCGTAAGATTTTT
Found at i:17534672 original size:68 final size:68
Alignment explanation
Indices: 17534479--17534704 Score: 204
Period size: 68 Copynumber: 3.3 Consensus size: 68
17534469 CAAAAATTTC
* * * * * *
17534479 AGATTCGTAAGA-TTTTCAGATTTGCAAGAATCAAAGATTTGTAAGACATTCAGATTTACAAGAA
1 AGATTCGTAAGACTTTT-AGATTCGCAAGAATTAGAGATTCGTAAGACTTTCAGATTTGCAAGAA
*
17534543 TTGG
65 TTGA
* * ** * ** * *
17534547 AGATTCGTAAGACATCTAGATTCTTAAAAATTAGAGATTCACAAGGCTTTCAGATTTGCAGGAAT
1 AGATTCGTAAGACTTTTAGATTCGCAAGAATTAGAGATTCGTAAGACTTTCAGATTTGCAAGAAT
17534612 TGA
66 TGA
* * * * *
17534615 AGATTCGTAAGACTTTTAGATTCGCAAGAATTGGAGATTCGTAAGATTTTTAAATTTGTAAG-AT
1 AGATTCGTAAGACTTTTAGATTCGCAAGAATTAGAGATTCGTAAGACTTTCAGATTTGCAAGAAT
*
17534679 ATAA
66 -TGA
* *
17534683 AGATTCGTGAGATTTTTAGATT
1 AGATTCGTAAGACTTTTAGATT
17534705 GTAGATCCAT
Statistics
Matches: 123, Mismatches: 33, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
67 2 0.02
68 119 0.97
69 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (68 bp):
AGATTCGTAAGACTTTTAGATTCGCAAGAATTAGAGATTCGTAAGACTTTCAGATTTGCAAGAAT
TGA
Found at i:17535941 original size:14 final size:14
Alignment explanation
Indices: 17535924--17535977 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
17535914 TTTTCTCCAT
*
17535924 TTTCATCTTTCATC
1 TTTCATTTTTCATC
17535938 TTTCATTTTTCA-C
1 TTTCATTTTTCATC
17535951 TTTTCATTTTTCTTATTC
1 -TTTCATTTTTC--A-TC
17535969 TTTCATTTT
1 TTTCATTTT
17535978 CTCTTTTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
13 1 0.03
14 22 0.65
16 1 0.03
17 9 0.26
18 1 0.03
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTCATTTTTCATC
Found at i:17535949 original size:21 final size:22
Alignment explanation
Indices: 17535923--17535983 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 22
17535913 TTTTTCTCCA
17535923 TTTTCATCTTTCATCTTTC-AT
1 TTTTCATCTTTCATCTTTCTAT
*
17535944 TTTTCA-CTTTTCATTTTTCTTAT
1 TTTTCATC-TTTCATCTTTC-TAT
17535967 TCTTTCAT-TTTC-TCTTT
1 T-TTTCATCTTTCATCTTT
17535984 TTTCCTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 1 0.03
21 16 0.48
22 4 0.12
23 7 0.21
24 5 0.15
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTCATCTTTCATCTTTCTAT
Found at i:17535992 original size:38 final size:37
Alignment explanation
Indices: 17535929--17536000 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
17535919 TCCATTTTCA
17535929 TCTTTCATCTTTCATTTTTCACTTTTCATTTTTCTTAT
1 TCTTTCATCTTTCATTTTTCACTTTT-ATTTTTCTTAT
* * *
17535967 TCTTTCATTTTCTCTTTTTTC-CTTTTTTTTTTCT
1 TCTTTCATCTT-TCATTTTTCACTTTTATTTTTCT
17536001 CTTTTTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 7 0.23
38 15 0.50
39 8 0.27
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (37 bp):
TCTTTCATCTTTCATTTTTCACTTTTATTTTTCTTAT
Found at i:17536004 original size:13 final size:13
Alignment explanation
Indices: 17535981--17536013 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17535971 TCATTTTCTC
17535981 TTTTTTC-CTTTT
1 TTTTTTCTCTTTT
17535993 TTTTTTCTCTTTT
1 TTTTTTCTCTTTT
*
17536006 TTGTTTCT
1 TTTTTTCT
17536014 TTTATTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTTTTCTCTTTT
Found at i:17536021 original size:21 final size:21
Alignment explanation
Indices: 17535976--17536021 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17535966 TTCTTTCATT
*
17535976 TTCTCTTTTTTCCTTTTTTTT
1 TTCTCTTTTTTCCTTTTTTTA
*
17535997 TTCTCTTTTTT-GTTTCTTTTA
1 TTCTCTTTTTTCCTTT-TTTTA
17536018 TTCT
1 TTCT
17536022 TTCACCCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (21 bp):
TTCTCTTTTTTCCTTTTTTTA
Found at i:17536400 original size:10 final size:10
Alignment explanation
Indices: 17536385--17536426 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
17536375 GCATTCATTT
17536385 TTTTGTTTTA
1 TTTTGTTTTA
*
17536395 TTTTGTTTTG
1 TTTTGTTTTA
17536405 TTTTGTTTT-
1 TTTTGTTTTA
*
17536414 TTTT-TTTCA
1 TTTTGTTTTA
17536423 TTTT
1 TTTT
17536427 TATTTCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 3 0.10
9 8 0.28
10 18 0.62
ACGTcount: A:0.05, C:0.02, G:0.10, T:0.83
Consensus pattern (10 bp):
TTTTGTTTTA
Found at i:17536405 original size:15 final size:14
Alignment explanation
Indices: 17536382--17536427 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
17536372 CTGGCATTCA
17536382 TTTTTTTGTTTTAT
1 TTTTTTTGTTTTAT
*
17536396 TTTGTTTTGTTTTGT
1 TTT-TTTTGTTTTAT
*
17536411 TTTTTTT-TTTCAT
1 TTTTTTTGTTTTAT
17536424 TTTT
1 TTTT
17536428 ATTTCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 8 0.29
14 7 0.25
15 13 0.46
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.85
Consensus pattern (14 bp):
TTTTTTTGTTTTAT
Done.