Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 130 of 310
Found at i:41940186 original size:47 final size:46
Alignment explanation
Indices: 41940120--41940467 Score: 216
Period size: 47 Copynumber: 7.5 Consensus size: 46
41940110 GACGAGGGCT
* * * *
41940120 AGTGTAAGACGTGTTTGGGACATACGTCAGCCACATTATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGATAGCC
* * * * *
41940166 AGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGA-GATGAGT-GCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGC-CACATTATGA-TAGCC
*
41940214 AGTGTAAGACATGTCTGGGGCATGCATCAGCCACATTATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGATAGCC
* * * *
41940260 AGTGTAAGACCATGTCTGGGAC--G-AT--GCGAGATGA-G-T-GCT
1 AGTGTAAGA-CATGTCTGGGACATGCATCAGCCACATTATGATAGCC
* * *
41940299 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGATAGCC
** * * * * * *
41940346 AGCATAAGACGTGTCTGGGACATGCATCAG-CACGTATACACGAGATCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC--AT-TATGATAGCC
* * * *
41940394 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGATGGA-GATAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCAC-AT-TATGATAGCC
*
41940443 AGCGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
41940468 GCAGCAGCAA
Statistics
Matches: 232, Mismatches: 49, Indels: 40
0.72 0.15 0.12
Matches are distributed among these distances:
38 12 0.05
39 11 0.05
40 2 0.01
41 3 0.01
42 6 0.03
43 2 0.01
44 6 0.03
45 5 0.02
46 34 0.15
47 66 0.28
48 33 0.14
49 41 0.18
50 9 0.04
51 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGATAGCC
Found at i:41940244 original size:94 final size:95
Alignment explanation
Indices: 41940076--41940470 Score: 406
Period size: 94 Copynumber: 4.3 Consensus size: 95
41940066 AGAGCTAGTA
** * * * *
41940076 TAAGACCATGTCTGGGACATGGCATCGGTATTGAGACGAGGGCTAGTGTAAGACGTGTTTGGGAC
1 TAAGACCATGTCTGGGACATGGCATCGGCGTAGAGACGAGTGCTAGTGTAAGACATGTCTGGGAC
* * * *
41940141 ATACGTCAGCCAC-ATTATGATAGCCAGTG
66 ATGCATCAGCCACGATGATGATAGCCAGCG
* *
41940170 TAAGACCATGTCTGGGACATGGCATCGGCGTAGAGATGAGTGCTAGTGTAAGACATGTCTGGGGC
1 TAAGACCATGTCTGGGACATGGCATCGGCGTAGAGACGAGTGCTAGTGTAAGACATGTCTGGGAC
* *
41940235 ATGCATCAGCCAC-ATTATGATAGCCAGTG
66 ATGCATCAGCCACGATGATGATAGCCAGCG
*
41940264 TAAGACCATGTCTGGGAC---G-AT--GC---GAGATGAGTGCTAGTGTAAGACATGTCTGGGAC
1 TAAGACCATGTCTGGGACATGGCATCGGCGTAGAGACGAGTGCTAGTGTAAGACATGTCTGGGAC
* * *
41940320 ATGCATCGGCCTCGATGATGATAGCCAGCA
66 ATGCATCAGCCACGATGATGATAGCCAGCG
* * * * *
41940350 TAAGA-CGTGTCTGGGACAT-GCATCAGCACGTATACACGAGAT-CTAGTGTAAGACCATGTTTG
1 TAAGACCATGTCTGGGACATGGCATC-G-GCGTAGAGACGAG-TGCTAGTGTAAGA-CATGTCTG
* *
41940412 GGACATGGCATCGGCCTCGATGGA-GATAGCCAGCG
62 GGACAT-GCATCAGCCACGAT-GATGATAGCCAGCG
41940447 TAAGACCATGTCTGGGACATGGCA
1 TAAGACCATGTCTGGGACATGGCA
41940471 GCAGCAACTT
Statistics
Matches: 260, Mismatches: 24, Indels: 29
0.83 0.08 0.09
Matches are distributed among these distances:
85 54 0.21
86 18 0.07
87 1 0.00
88 4 0.02
90 2 0.01
91 1 0.00
92 1 0.00
94 102 0.39
95 16 0.06
96 14 0.05
97 29 0.11
98 15 0.06
99 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (95 bp):
TAAGACCATGTCTGGGACATGGCATCGGCGTAGAGACGAGTGCTAGTGTAAGACATGTCTGGGAC
ATGCATCAGCCACGATGATGATAGCCAGCG
Found at i:41940361 original size:85 final size:87
Alignment explanation
Indices: 41940201--41940467 Score: 294
Period size: 85 Copynumber: 3.0 Consensus size: 87
41940191 GCATCGGCGT
* * * * *
41940201 AGAGATGAGTGCTAGTGTAAGACATGTCTGGGGCATGCATCAGCCAC-ATTATGATAGCCAGTGT
1 AGAGATGAGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATGATGATAGCCAGCGT
41940265 AAGACCATGTCTGGGACGATG-C
66 AAGACCATGTCTGGGAC-ATGAC
*
41940287 -GAGATGAGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATGATGATAGCCAGCAT
1 AGAGATGAGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATGATGATAGCCAGCGT
*
41940351 AAGA-CGTGTCTGGGACATGCATC
66 AAGACCATGTCTGGGACATG-A-C
*
41940374 AGCACGTATACACGAGAT-CTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGATGGA-G
1 AG-A-G-AT----GAG-TGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAT-GATG
41940437 ATAGCCAGCGTAAGACCATGTCTGGGACATG
55 ATAGCCAGCGTAAGACCATGTCTGGGACATG
41940468 GCAGCAGCAA
Statistics
Matches: 154, Mismatches: 10, Indels: 22
0.83 0.05 0.12
Matches are distributed among these distances:
84 3 0.02
85 54 0.35
86 18 0.12
87 1 0.01
88 1 0.01
89 1 0.01
90 1 0.01
91 2 0.01
95 14 0.09
96 14 0.09
97 29 0.19
98 16 0.10
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (87 bp):
AGAGATGAGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATGATGATAGCCAGCGT
AAGACCATGTCTGGGACATGAC
Found at i:41940432 original size:97 final size:97
Alignment explanation
Indices: 41940297--41940476 Score: 276
Period size: 97 Copynumber: 1.9 Consensus size: 97
41940287 GAGATGAGTG
*
41940297 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAT-GATGATAGCCAGCATAAGA-CGTGT
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATGGA-GATAGCCAGCATAAGACCATGT
*
41940360 CTGGGACAT-GCATCAGCACGTATACACGAGAT
65 CTGGGACATGGCAGCAGCACGTATACACGAGAT
* *
41940392 CTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGATGGAGATAGCCAGCGTAAGACCATG
1 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGATGGAGATAGCCAGCATAAGACCATG
41940457 TCTGGGACATGGCAGCAGCA
64 TCTGGGACATGGCAGCAGCA
41940477 ACTTAACCCA
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
95 11 0.14
96 13 0.17
97 29 0.38
98 15 0.20
99 8 0.11
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (97 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATGGAGATAGCCAGCATAAGACCATGTC
TGGGACATGGCAGCAGCACGTATACACGAGAT
Found at i:41940470 original size:49 final size:47
Alignment explanation
Indices: 41940302--41940467 Score: 165
Period size: 49 Copynumber: 3.4 Consensus size: 47
41940292 GAGTGCTAGT
*
41940302 GTAAGACATGTCTGGGACATGCATCGGCCTCGATGATGATAGCCAGC
1 GTAAGACATGTCTGGGACATGCATCGGCCTCGATGACGATAGCCAGC
* * * * * * * * *
41940349 ATAAGACGTGTCTGGGACATGCATCAG-CACGTATACACGAGATCTAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCTCG-AT-GACGATAGCCAGC
*
41940397 GTAAGACCATGTTTGGGACATGGCATCGGCCTCGATGGA-GATAGCCAGC
1 GTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAT-GACGATAGCCAGC
41940446 GTAAGACCATGTCTGGGACATG
1 GTAAGA-CATGTCTGGGACATG
41940468 GCAGCAGCAA
Statistics
Matches: 92, Mismatches: 22, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
46 3 0.03
47 26 0.28
48 13 0.14
49 38 0.41
50 9 0.10
51 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (47 bp):
GTAAGACATGTCTGGGACATGCATCGGCCTCGATGACGATAGCCAGC
Found at i:41941333 original size:55 final size:54
Alignment explanation
Indices: 41941218--41941334 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 54
41941208 CTTAAACTTT
* * *
41941218 TAAA-TCAGTATTGTCCACGGTTAGGCCACACGGGCATGTGCCATAGCCATGTC
1 TAAAGTCAGTATTGCCCACGGGTAGGCCACACGGGCATGTGCCATAGCCATGCC
* * * * *
41941271 TATAAGTCATTATTGCCCACGGGTAGGCCACACGGGCGTGTGTCATGGCCGTGCCC
1 TA-AAGTCAGTATTGCCCACGGGTAGGCCACACGGGCATGTGCCATAGCCATG-CC
41941327 TAAAGTCA
1 TAAAGTCA
41941335 CTATCGCACA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.04
54 2 0.04
55 46 0.87
56 3 0.06
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.24
Consensus pattern (54 bp):
TAAAGTCAGTATTGCCCACGGGTAGGCCACACGGGCATGTGCCATAGCCATGCC
Found at i:41942038 original size:12 final size:12
Alignment explanation
Indices: 41942021--41942045 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41942011 GTAGTCATAA
41942021 TACTATATAGTT
1 TACTATATAGTT
41942033 TACTATATAGTT
1 TACTATATAGTT
41942045 T
1 T
41942046 CATTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TACTATATAGTT
Found at i:41944931 original size:16 final size:16
Alignment explanation
Indices: 41944910--41944941 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41944900 GGATACTCAC
41944910 ATACAACAGGTACTGA
1 ATACAACAGGTACTGA
41944926 ATACAACAGGTACTGA
1 ATACAACAGGTACTGA
41944942 TTCAATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (16 bp):
ATACAACAGGTACTGA
Found at i:41946898 original size:92 final size:92
Alignment explanation
Indices: 41946740--41946922 Score: 289
Period size: 92 Copynumber: 2.0 Consensus size: 92
41946730 TCATGCATAT
41946740 TTATAAAATAACGTCATCACATACCCAAAACCAGGTTTGTTAACCATACCAATGGCTAACTCTAC
1 TTATAAAATAACGTCATCACATACCCAAAACCAGGTTTGTTAACCATACCAATGGCTAACTCTAC
41946805 ATTCATTTCACA-GAATCATTTACTTTA
66 ATTCATTTCACATGAA-CATTTACTTTA
* * * *
41946832 TTATAAGATAACGTCATCACATATCTAAAACCAGGTTTGTTAACCAT-CCTAATGGCTAACTTTA
1 TTATAAAATAACGTCATCACATACCCAAAACCAGGTTTGTTAACCATACC-AATGGCTAACTCTA
*
41946896 CATTCATTTCACATTAACATTTACTTT
65 CATTCATTTCACATGAACATTTACTTT
41946923 GTTAGCTTAT
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
91 2 0.02
92 80 0.95
93 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (92 bp):
TTATAAAATAACGTCATCACATACCCAAAACCAGGTTTGTTAACCATACCAATGGCTAACTCTAC
ATTCATTTCACATGAACATTTACTTTA
Found at i:41961827 original size:25 final size:25
Alignment explanation
Indices: 41961792--41961865 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
41961782 TCACAGTTCG
41961792 TGAGAGCTTACCAATTCTCAACTCA
1 TGAGAGCTTACCAATTCTCAACTCA
* *
41961817 T-ATGAGTTTACCGATT-TACAACTCA
1 TGA-GAGCTTACCAATTCT-CAACTCA
* *
41961842 TGAGAGCATACCAATTCACAACTC
1 TGAGAGCTTACCAATTCTCAACTC
41961866 GTGTAAGCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
24 2 0.05
25 36 0.92
26 1 0.03
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (25 bp):
TGAGAGCTTACCAATTCTCAACTCA
Found at i:41964689 original size:27 final size:25
Alignment explanation
Indices: 41964637--41964687 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
41964627 AATTCAAGTG
41964637 TGTGAAAAATAATGACCCAATGCTC
1 TGTGAAAAATAATGACCCAATGCTC
41964662 TGTGAAAAATAATGACCCAATGCTC
1 TGTGAAAAATAATGACCCAATGCTC
41964687 T
1 T
41964688 CTTTATATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (25 bp):
TGTGAAAAATAATGACCCAATGCTC
Found at i:41966842 original size:40 final size:40
Alignment explanation
Indices: 41966787--41966889 Score: 154
Period size: 40 Copynumber: 2.6 Consensus size: 40
41966777 GATTCGGATA
41966787 TATATATGGCACTTAGTGTGCGATTC-GAGATAGCTTCGGC
1 TATATATGGCACTTAGTGTGCGATTCGGA-ATAGCTTCGGC
* * * *
41966827 TATATGTGGCCCTTAGTGTGCAATTCGGAATAGCTTGGGC
1 TATATATGGCACTTAGTGTGCGATTCGGAATAGCTTCGGC
41966867 TATATATGGCACTTAGTGTGCGA
1 TATATATGGCACTTAGTGTGCGA
41966890 GGCCATGATA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 53 0.96
41 2 0.04
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCGATTCGGAATAGCTTCGGC
Found at i:41966952 original size:41 final size:41
Alignment explanation
Indices: 41966855--41966954 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 41
41966845 TGCAATTCGG
* * * * *
41966855 AATAGCTTGGGCTATATATGGCACTTAGTGTGCGAGGCCAT
1 AATAGCTTAGGCTATGTAAGGCACTTAGTGTGCAAGACCAT
* * * * **
41966896 GATAACTTCGACTATGTAAGGCACTTAGTGTGCAAGATTAT
1 AATAGCTTAGGCTATGTAAGGCACTTAGTGTGCAAGACCAT
41966937 AATAGCTTAGGCTATGTA
1 AATAGCTTAGGCTATGTA
41966955 TTAGCACTTA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (41 bp):
AATAGCTTAGGCTATGTAAGGCACTTAGTGTGCAAGACCAT
Found at i:41972503 original size:6 final size:6
Alignment explanation
Indices: 41972494--41972567 Score: 78
Period size: 6 Copynumber: 12.2 Consensus size: 6
41972484 TCACAGAACT
* * *
41972494 AGAATC AGAATC AGAATC AGAATC AAAATC AAAATC AGTATC AGGTAA-C
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC A-G-AATC
* *
41972543 AGAATC AAAATC AGAATC AGTATC A
1 AGAATC AGAATC AGAATC AGAATC A
41972568 AGTAACAGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
5 2 0.03
6 52 0.90
7 3 0.05
8 1 0.02
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:41972549 original size:31 final size:31
Alignment explanation
Indices: 41972494--41972623 Score: 174
Period size: 32 Copynumber: 4.2 Consensus size: 31
41972484 TCACAGAACT
*
41972494 AGAATCAGAATCA-G-AATCAGAATCAAAATC
1 AGAATCAGTATCAGGTAA-CAGAATCAAAATC
*
41972524 AAAATCAGTATCAGGTAACAGAATCAAAATC
1 AGAATCAGTATCAGGTAACAGAATCAAAATC
* *
41972555 AGAATCAGTATCAAGTAACAGAATAAAAAATC
1 AGAATCAGTATCAGGTAACAGAAT-CAAAATC
*
41972587 AGAATTAGTATCAGGTAACAGAATCAAAAATC
1 AGAATCAGTATCAGGTAACAGAATC-AAAATC
41972619 AGAAT
1 AGAAT
41972624 GTGAATGCAA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
30 11 0.12
31 36 0.41
32 41 0.47
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.19
Consensus pattern (31 bp):
AGAATCAGTATCAGGTAACAGAATCAAAATC
Found at i:41985348 original size:27 final size:27
Alignment explanation
Indices: 41985318--41985710 Score: 525
Period size: 27 Copynumber: 14.6 Consensus size: 27
41985308 GGGGCAAAAT
* * * *
41985318 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
41985345 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41985372 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41985399 AGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41985426 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
41985453 GGTATTTCTACCCTACAAGGGTATATA
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41985480 GATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** *
41985507 AATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** *
41985534 AATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
41985561 GGTAATTCTATTCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41985588 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
41985615 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41985642 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** *
41985669 AATAATTCTACCCTACAGGGATATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41985696 GGTAATTTTACCCTA
1 GGTAATTCTACCCTA
41985711 TTCTACCCTA
Statistics
Matches: 324, Mismatches: 42, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 324 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:41985377 original size:54 final size:54
Alignment explanation
Indices: 41985318--41985955 Score: 808
Period size: 54 Copynumber: 11.6 Consensus size: 54
41985308 GGGGCAAAAT
* * * *
41985318 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* * * *
41985372 AGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* * * * *
41985426 AGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATATA
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* * ** *
41985480 GATAATTCTACCCTATAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
** * **
41985534 AATAATTCTACCCTATAGGGGTATTTCGGTAATTCTATTCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
*
41985588 GATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* ** *
41985642 GGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGATATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* *
41985696 GGTAATTTTACCCTATTCTACCCTACAGGGGTATTTCGGTAATTTTACCCTACAGAGGTATTTC
1 GG------TA----ATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* * * *
41985760 GGTAATTCTACCCTATACGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* * *
41985814 GGTAATTCTACCCTATATGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* * * *
41985868 GATAATTCTACCCTACAGGGGTATTTCGATAATTCTATCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
*
41985922 GGTAATTCTACCCGACAGGGGTATTTCGGTAATT
1 GGTAATTCTACCCTACAGGGGTATTTCGGTAATT
41985956 TTGTAAAGCG
Statistics
Matches: 513, Mismatches: 61, Indels: 20
0.86 0.10 0.03
Matches are distributed among these distances:
54 463 0.90
58 2 0.00
60 2 0.00
64 46 0.09
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (54 bp):
GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
Found at i:41985462 original size:81 final size:81
Alignment explanation
Indices: 41985318--41985955 Score: 810
Period size: 81 Copynumber: 7.8 Consensus size: 81
41985308 GGGGCAAAAT
* * * * * *
41985318 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
*
41985383 CCTACAAGGGTATTTC
66 CCTACAGGGGTATTTC
* * *
41985399 AGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
* * *
41985464 CCTACAAGGGTATATA
66 CCTACAGGGGTATTTC
* * * * **
41985480 GATAATTCTACCCTATAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCAATAATTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
*
41985545 CCTATAGGGGTATTTC
66 CCTACAGGGGTATTTC
**
41985561 GGTAATTCTATTCTACAGGGGTATTTC-GATAATTCTACCCTACAGGGGTATTTCGGTAATTCTA
1 GGTAATTCTACCCTACAGGGGTATTTCAG-TAATTCTACCCTACAGGGGTATTTCGGTAATTCTA
41985625 CCCTACAGGGGTATTTC
65 CCCTACAGGGGTATTTC
* * *
41985642 GGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGATATTTCGGTAATTTTAC
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGG------TA-
41985707 CCTATTCTACCCTACAGGGGTATTTC
59 ---ATTCTACCCTACAGGGGTATTTC
* * * * * *
41985733 GGTAATTTTACCCTACAGAGGTATTTCGGTAATTCTACCCTATACGGGTATTTCGGTATTTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
*
41985798 CCTACAAGGGTATTTC
66 CCTACAGGGGTATTTC
* * *
41985814 GGTAATTCTACCCTATATGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
41985879 CCTACAGGGGTATTTC
66 CCTACAGGGGTATTTC
* * * * *
41985895 GATAATTCTATCCTACAGGGGTATTCCGGTAATTCTACCCGACAGGGGTATTTCGGTAATT
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATT
41985956 TTGTAAAGCG
Statistics
Matches: 479, Mismatches: 66, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
81 404 0.84
85 2 0.00
87 2 0.00
91 71 0.15
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (81 bp):
GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTAC
CCTACAGGGGTATTTC
Found at i:41985723 original size:37 final size:37
Alignment explanation
Indices: 41985673--41985747 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
41985663 TATTTCAATA
41985673 ATTCTACCCTACAGGGATATTTCGGTAATTTTACCCT
1 ATTCTACCCTACAGGGATATTTCGGTAATTTTACCCT
*
41985710 ATTCTACCCTACAGGGGTATTTCGGTAATTTTACCCT
1 ATTCTACCCTACAGGGATATTTCGGTAATTTTACCCT
41985747 A
1 A
41985748 CAGAGGTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (37 bp):
ATTCTACCCTACAGGGATATTTCGGTAATTTTACCCT
Found at i:41985744 original size:27 final size:27
Alignment explanation
Indices: 41985710--41985955 Score: 366
Period size: 27 Copynumber: 9.1 Consensus size: 27
41985700 ATTTTACCCT
41985710 ATTCTACCCTACAGGGGTATTTCGGTA
1 ATTCTACCCTACAGGGGTATTTCGGTA
* *
41985737 ATTTTACCCTACAGAGGTATTTCGGTA
1 ATTCTACCCTACAGGGGTATTTCGGTA
* *
41985764 ATTCTACCCTATACGGGTATTTCGGTA
1 ATTCTACCCTACAGGGGTATTTCGGTA
* *
41985791 TTTCTACCCTACAAGGGTATTTCGGTA
1 ATTCTACCCTACAGGGGTATTTCGGTA
* * *
41985818 ATTCTACCCTATATGGGTATTTCAGTA
1 ATTCTACCCTACAGGGGTATTTCGGTA
*
41985845 ATTCTACCCTACAGGGGTATTTCGATA
1 ATTCTACCCTACAGGGGTATTTCGGTA
*
41985872 ATTCTACCCTACAGGGGTATTTCGATA
1 ATTCTACCCTACAGGGGTATTTCGGTA
* *
41985899 ATTCTATCCTACAGGGGTATTCCGGTA
1 ATTCTACCCTACAGGGGTATTTCGGTA
*
41985926 ATTCTACCCGACAGGGGTATTTCGGTA
1 ATTCTACCCTACAGGGGTATTTCGGTA
41985953 ATT
1 ATT
41985956 TTGTAAAGCG
Statistics
Matches: 196, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 196 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (27 bp):
ATTCTACCCTACAGGGGTATTTCGGTA
Found at i:41986081 original size:27 final size:27
Alignment explanation
Indices: 41986005--41986124 Score: 100
Period size: 27 Copynumber: 4.4 Consensus size: 27
41985995 GGTACGTTGG
* * *
41986005 TAATTTTACAAGTCGAGGGTATTTCAA
1 TAATTTTACAAATCGAGGATATTTTAA
* *
41986032 TAATTTTACAAGTCGAGGGTATTTTAA
1 TAATTTTACAAATCGAGGATATTTTAA
* **
41986059 TAATTTCACAAATC-AGGAATATTTTGG
1 TAATTTTACAAATCGAGG-ATATTTTAA
* * * *
41986086 TAATTTTACAAA-CTAGGGGTTTTTTGA
1 TAATTTTACAAATCGA-GGATATTTTAA
41986113 TAATTTTACAAA
1 TAATTTTACAAA
41986125 CCAGGGGTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
26 4 0.05
27 74 0.93
28 2 0.03
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (27 bp):
TAATTTTACAAATCGAGGATATTTTAA
Found at i:41992059 original size:76 final size:76
Alignment explanation
Indices: 41991933--41992079 Score: 267
Period size: 76 Copynumber: 1.9 Consensus size: 76
41991923 CAGTACACTT
*
41991933 TAGTAGGCAGAATCGCGTAGCAAGGAGATAGTACACTTTAGAAATTCATCGGGTGTACAAGATAG
1 TAGTAGGCAGAATCACGTAGCAAGGAGATAGTACACTTTAGAAATTCATCGGGTGTACAAGATAG
41991998 CTCATCACCAA
66 CTCATCACCAA
**
41992009 TAGTAGGCAGAATCACGTAGCAAGGAGATAGTACACTTTAGGCATTCATCGGGTGTACAAGATAG
1 TAGTAGGCAGAATCACGTAGCAAGGAGATAGTACACTTTAGAAATTCATCGGGTGTACAAGATAG
41992074 CTCATC
66 CTCATC
41992080 GAGTACCCGG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (76 bp):
TAGTAGGCAGAATCACGTAGCAAGGAGATAGTACACTTTAGAAATTCATCGGGTGTACAAGATAG
CTCATCACCAA
Found at i:41994992 original size:40 final size:40
Alignment explanation
Indices: 41994013--41994959 Score: 1776
Period size: 40 Copynumber: 23.7 Consensus size: 40
41994003 GCTCCTCGTT
* * *
41994013 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAAT-TCACA
1 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGT-ATCTCGCA
** *
41994053 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTATCTCGCA
41994093 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994133 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994173 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994213 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994253 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994293 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994333 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994373 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994413 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994453 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994493 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994533 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994573 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994613 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994653 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994693 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994733 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994773 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994813 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994853 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994893 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
41994933 CAAATGCCTTCGGATCTTAGTCCGGAT
1 CAAATGCCTTCGGATCTTAGTCCGGAT
41994960 ATGGTCACTT
Statistics
Matches: 897, Mismatches: 7, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
39 4 0.00
40 891 0.99
41 2 0.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (40 bp):
CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
Found at i:41996625 original size:43 final size:43
Alignment explanation
Indices: 41996523--41996625 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 43
41996513 GGTGTAATTT
* * ** *
41996523 CATGTAATACCATGTCTGGGACATTGGCATCGATATGAGATTA
1 CATGTAAGACCATATCTGGGACAGAGGCATCGATATGAGATAA
* * * *
41996566 CGTGTAAGACCCTATCTGGGACAGAGGCATCGGTATGTGATAA
1 CATGTAAGACCATATCTGGGACAGAGGCATCGATATGAGATAA
*
41996609 CATGTAAGACTATATCT
1 CATGTAAGACCATATCT
41996626 AGGATATGGC
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (43 bp):
CATGTAAGACCATATCTGGGACAGAGGCATCGATATGAGATAA
Found at i:42016085 original size:18 final size:18
Alignment explanation
Indices: 42016042--42016086 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
42016032 AGCCCATTAC
* *
42016042 AGTAACAATAAATAGTGT
1 AGTAACAGTAAATAATGT
*
42016060 AGTAACAGTAATTAATGT
1 AGTAACAGTAAATAATGT
42016078 AGTAACAGT
1 AGTAACAGT
42016087 TTAAACAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.29
Consensus pattern (18 bp):
AGTAACAGTAAATAATGT
Found at i:42016446 original size:27 final size:27
Alignment explanation
Indices: 42016428--42016502 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
42016418 GGAAAAATAT
* *
42016428 TCATCTTACTATATAAGGGCAAAACAA
1 TCATCTTACCACATAAGGGCAAAACAA
* *
42016455 TCATTTTACCACATAAGGGCAAAACAG
1 TCATCTTACCACATAAGGGCAAAACAA
* *
42016482 TTATTTTACCACATAAGGGCA
1 TCATCTTACCACATAAGGGCA
42016503 TAGTCATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (27 bp):
TCATCTTACCACATAAGGGCAAAACAA
Found at i:42026156 original size:30 final size:30
Alignment explanation
Indices: 42026122--42026185 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
42026112 GAGGCAGGCA
*
42026122 TGTGTAGTACACAGCCTGACCACACGGGCG
1 TGTGTAGTACACAGCCTGACCACACGGACG
*
42026152 TGTGTAGTACACGGCCTGACCACACGGACG
1 TGTGTAGTACACAGCCTGACCACACGGACG
42026182 TGTG
1 TGTG
42026186 AGCCTTGTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (30 bp):
TGTGTAGTACACAGCCTGACCACACGGACG
Found at i:42051934 original size:40 final size:40
Alignment explanation
Indices: 42051864--42052068 Score: 317
Period size: 40 Copynumber: 5.2 Consensus size: 40
42051854 CGGATGATAA
* *
42051864 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
42051904 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
42051944 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
42051984 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
42052024 CGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCC
42052063 CGAAGG
1 CGAAGG
42052069 TACTTGGTTT
Statistics
Matches: 157, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 16 0.10
40 140 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:42053864 original size:93 final size:95
Alignment explanation
Indices: 42053645--42053900 Score: 366
Period size: 93 Copynumber: 2.8 Consensus size: 95
42053635 GTGAACTCGG
* * *
42053645 GGACTCAGCTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAACGAGCT
1 GGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
*
42053710 C-G--G-CGTTCACATCCATAAATGAACTC
66 CGGATGCCGTTCACATCCATAAACGAACTC
42053736 GGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 GGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
*
42053801 CGGATGCCTAGTT-ACAT-C-T-CACGAACTC
66 CGGATGCC--GTTCACATCCATAAACGAACTC
* * *
42053829 GGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 GGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
42053894 CGGATGC
66 CGGATGC
42053901 TCAACCATCC
Statistics
Matches: 151, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
91 63 0.42
92 1 0.01
93 76 0.50
94 2 0.01
95 2 0.01
96 4 0.03
97 3 0.02
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (95 bp):
GGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACGAGTT
CGGATGCCGTTCACATCCATAAACGAACTC
Found at i:42053897 original size:46 final size:46
Alignment explanation
Indices: 42053632--42053897 Score: 317
Period size: 46 Copynumber: 5.7 Consensus size: 46
42053622 AACCCGCCCC
* *
42053632 TAAGTGAACTCGGGGACTCAGCTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTC--GGACTCAACTCAACGAGCTCGGACGTTCGCATCCA
* *
42053680 TAAATGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCA
* *
42053725 TAAATGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCA
* *
42053771 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCATCCA
* * * *
42053819 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCA
*
42053864 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
42053898 TGCTCAACCA
Statistics
Matches: 194, Mismatches: 14, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 2 0.01
45 46 0.24
46 92 0.47
47 29 0.15
48 12 0.06
49 2 0.01
50 3 0.02
51 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCA
Found at i:42056819 original size:27 final size:27
Alignment explanation
Indices: 42056789--42056866 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 27
42056779 CAATTTGATG
*
42056789 AAATGATTGTTTTTCCCCTATGTGGTA
1 AAATGATTGTTTTGCCCCTATGTGGTA
* **** **
42056816 AAATGACTAAAATGCCCCTACATGGTA
1 AAATGATTGTTTTGCCCCTATGTGGTA
*
42056843 AATTGATTGTTTTGCCCCTATGTG
1 AAATGATTGTTTTGCCCCTATGTG
42056867 AGGTATTTAT
Statistics
Matches: 35, Mismatches: 16, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (27 bp):
AAATGATTGTTTTGCCCCTATGTGGTA
Found at i:42058106 original size:44 final size:44
Alignment explanation
Indices: 42057970--42058126 Score: 164
Period size: 43 Copynumber: 3.6 Consensus size: 44
42057960 AGCTTGTACA
* * * *
42057970 ATGCCAACGTCTCAGACGTGGTCTTACATGT-AATCA-AATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATAA-ATCG
* *
42058013 ATGCCACTGTCCCA-A-ATAGAGTCTTACACG-AAATCATATA-CG
1 ATGCCAATGTCCCAGACAT-G-GTCTTACACGTAAATCATAAATCG
*
42058055 ATGCCAATGTCTCAGACATGGTCTTACACGTAAATCATAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATAAATCG
* *
42058099 ATGCCAATGTCCCAGACGTGGTCGTACA
1 ATGCCAATGTCCCAGACATGGTCTTACA
42058127 TGATGACACA
Statistics
Matches: 94, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 26 0.28
43 37 0.39
44 30 0.32
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATAAATCG
Found at i:42060692 original size:20 final size:20
Alignment explanation
Indices: 42060640--42060712 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
42060630 GTCAGTATAT
* *
42060640 GGCACAAAGTCATGAGTAGC
1 GGCACAAAGCCATCAGTAGC
* * *
42060660 GGCTCGAATCCATCAGTAGC
1 GGCACAAAGCCATCAGTAGC
* *
42060680 GGCACAAAGCCATCAATAGT
1 GGCACAAAGCCATCAGTAGC
42060700 GGCACAAAGCCAT
1 GGCACAAAGCCAT
42060713 AAATATTGCA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (20 bp):
GGCACAAAGCCATCAGTAGC
Found at i:42060717 original size:20 final size:20
Alignment explanation
Indices: 42060680--42060717 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42060670 CATCAGTAGC
*
42060680 GGCACAAAGCCATCAATAGT
1 GGCACAAAGCCATAAATAGT
42060700 GGCACAAAGCCATAAATA
1 GGCACAAAGCCATAAATA
42060718 TTGCAGCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.13
Consensus pattern (20 bp):
GGCACAAAGCCATAAATAGT
Found at i:42067413 original size:21 final size:20
Alignment explanation
Indices: 42067374--42067414 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
42067364 ATACATGTGT
42067374 ATTTTGAAGTTTCTTGATAG
1 ATTTTGAAGTTTCTTGATAG
42067394 ATTTTGAGTAGTTT-TTGATAG
1 ATTTTGA--AGTTTCTTGATAG
42067415 TTAAAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.24, C:0.02, G:0.22, T:0.51
Consensus pattern (20 bp):
ATTTTGAAGTTTCTTGATAG
Found at i:42067415 original size:10 final size:10
Alignment explanation
Indices: 42067375--42067416 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
42067365 TACATGTGTA
42067375 TTTTGA-AGT
1 TTTTGATAGT
*
42067384 TTCTTGATAGA
1 TT-TTGATAGT
42067395 TTTTGAGTAGT
1 TTTTGA-TAGT
42067406 TTTTGATAGT
1 TTTTGATAGT
42067416 T
1 T
42067417 AAAAAAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 2 0.07
10 13 0.46
11 13 0.46
ACGTcount: A:0.21, C:0.02, G:0.21, T:0.55
Consensus pattern (10 bp):
TTTTGATAGT
Found at i:42069139 original size:13 final size:13
Alignment explanation
Indices: 42069121--42069145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42069111 CGTGTGTGAC
42069121 ACACGGCCTTGTT
1 ACACGGCCTTGTT
42069134 ACACGGCCTTGT
1 ACACGGCCTTGT
42069146 GTCCCCTAGT
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:0.16, C:0.32, G:0.24, T:0.28
Consensus pattern (13 bp):
ACACGGCCTTGTT
Found at i:42069318 original size:29 final size:29
Alignment explanation
Indices: 42069273--42069339 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
42069263 TACACGGCCT
*
42069273 GGCACACGGGCGTGTGTGGCCATTTTTAT
1 GGCACACGGGCGTGTGTGGCCATTTTTAG
* *
42069302 GGTACACGGGTGTGTGTGGCCATTTTTAG
1 GGCACACGGGCGTGTGTGGCCATTTTTAG
42069331 GGCACACGG
1 GGCACACGG
42069340 ACTAGGCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.28
Consensus pattern (29 bp):
GGCACACGGGCGTGTGTGGCCATTTTTAG
Found at i:42091431 original size:21 final size:21
Alignment explanation
Indices: 42091405--42091515 Score: 123
Period size: 21 Copynumber: 5.0 Consensus size: 21
42091395 AAAAGACACC
42091405 CCAATTTTGACCATTACCATT
1 CCAATTTTGACCATTACCATT
42091426 CCAATTTTGACCATTACCATT
1 CCAATTTTGACCATTACCATT
**
42091447 CCAATTTTGACCATTAAAATTAGCCT
1 CCAATTTTGACCATTACCA-T----T
*
42091473 GCCAATTTTGACCAGTACCATT
1 -CCAATTTTGACCATTACCATT
* *
42091495 CCAACTTTGACCAGTACCATT
1 CCAATTTTGACCATTACCATT
42091516 AGCTTGCCAA
Statistics
Matches: 78, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
21 58 0.74
22 2 0.03
26 2 0.03
27 16 0.21
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (21 bp):
CCAATTTTGACCATTACCATT
Found at i:42091497 original size:48 final size:48
Alignment explanation
Indices: 42091426--42091540 Score: 176
Period size: 48 Copynumber: 2.4 Consensus size: 48
42091416 CATTACCATT
* *
42091426 CCAATTTTGACCATTACCATTCCAATTTTGACCATTAAAATTAGCCTG
1 CCAATTTTGACCATTACCATTCCAACTTTGACCAGTAAAATTAGCCTG
* ** *
42091474 CCAATTTTGACCAGTACCATTCCAACTTTGACCAGTACCATTAGCTTG
1 CCAATTTTGACCATTACCATTCCAACTTTGACCAGTAAAATTAGCCTG
42091522 CCAATTTTGACCATTACCA
1 CCAATTTTGACCATTACCA
42091541 CCATTGCCAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (48 bp):
CCAATTTTGACCATTACCATTCCAACTTTGACCAGTAAAATTAGCCTG
Found at i:42091525 original size:27 final size:27
Alignment explanation
Indices: 42091447--42091540 Score: 92
Period size: 27 Copynumber: 3.7 Consensus size: 27
42091437 CATTACCATT
* ** *
42091447 CCAATTTTGACCATTAAAATTAGCCTG
1 CCAATTTTGACCAGTACCATTAGCTTG
42091474 CCAATTTTGACCAGTACC---A--TT-
1 CCAATTTTGACCAGTACCATTAGCTTG
*
42091495 CCAACTTTGACCAGTACCATTAGCTTG
1 CCAATTTTGACCAGTACCATTAGCTTG
*
42091522 CCAATTTTGACCATTACCA
1 CCAATTTTGACCAGTACCA
42091541 CCATTGCCAT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
21 17 0.31
22 1 0.02
24 2 0.04
26 2 0.04
27 32 0.59
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.32
Consensus pattern (27 bp):
CCAATTTTGACCAGTACCATTAGCTTG
Found at i:42099265 original size:40 final size:39
Alignment explanation
Indices: 42099234--42099443 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
42099224 GGACTAAGAT
* *
42099234 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
42099274 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
42099314 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
42099354 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
42099394 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
42099433 CCGAAGGCATT
1 CCGAAGGCATT
42099444 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:42099397 original size:120 final size:120
Alignment explanation
Indices: 42099181--42099443 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
42099171 TTGAATGCTG
* *
42099181 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
42099245 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
42099301 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
42099364 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
42099420 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42099444 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:42099463 original size:79 final size:80
Alignment explanation
Indices: 42099234--42099478 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
42099224 GGACTAAGAT
* * * * * * * ** *
42099234 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
42099297 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
42099314 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
42099379 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
42099394 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
42099458 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
42099472 CCGAAGG
1 CCGAAGG
42099479 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:42110167 original size:23 final size:22
Alignment explanation
Indices: 42110115--42110167 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42110105 TCCATGTCTT
*
42110115 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
42110137 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
42110160 TTTCTTTT
1 TTTCTTTT
42110168 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:42112182 original size:53 final size:54
Alignment explanation
Indices: 42112115--42112220 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 54
42112105 CCCTAGAAAT
42112115 TGGGGATTTTTGGGCTGATTCCTTAAGATAG-AAAAAGGCTGAAAACACAATAA
1 TGGGGATTTTTGGGCTGATTCCTTAAGATAGAAAAAAGGCTGAAAACACAATAA
*
42112168 TGGGGATTTTTGGGCTGATTCCTTAAGATAGAAAAAAGGTTGAAAACACAATA
1 TGGGGATTTTTGGGCTGATTCCTTAAGATAGAAAAAAGGCTGAAAACACAATA
42112221 GGAACAGAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 31 0.61
54 20 0.39
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (54 bp):
TGGGGATTTTTGGGCTGATTCCTTAAGATAGAAAAAAGGCTGAAAACACAATAA
Found at i:42124934 original size:613 final size:612
Alignment explanation
Indices: 42123728--42124955 Score: 2332
Period size: 613 Copynumber: 2.0 Consensus size: 612
42123718 ACTCGCTCTC
42123728 ACACCTTGATCTCTATCTTTCTCGACCATCTCGGGACAACACGAATGAAATGGTCTAGCGACCCA
1 ACACCTTGATCTCTATCTTTCTCGACCATCTCGGGACAACACGAATGAAATGGTCTAGCGACCCA
*
42123793 CATTTGAAATAGCCCCTTTCATTTCCTTGGCACTCCCAAAATGTCGTCTACCACACTGCGAACAC
66 CATTTGAAATAGCCCCTTTCATTTCCTTGGCACTCACAAAATGTCGTCTACCACACTGCGAACAC
42123858 TCTGGTTTATTTGGTCGAGCACTACCAATGCTCGTGATAGAGGTGGTTTGAGCTTTAGACGCTAT
131 TCTGGTTTATTTGGTCGAGCACTACCAATGCTCGTGATAGAGGTGGTTTGAGCTTTAGACGCTAT
42123923 ATACTATTTATTCTTGTTTCTACTCGAGAATCCTACTGGCGCATTTGATTAAGTAGGAAACTCTC
196 ATACTATTTATTCTTGTTTCTACTCGAGAATCCTACTGGCGCATTTGATTAAGTAGGAAACTCTC
* *
42123988 TCGATCTCTTTGATAAATTCTGATGTGATTTCCCCATCTGTCTTTTCTTTGAGTCATGATACTCA
261 TCGATCTCTTGGATAAATTCTGATGTGATTTCCCCATCTGTCTTTTCTTTGAGTCACGATACTCA
* *
42124053 ATATCAGCTCTTCTCTTCTCTTTGGCCAACTCTTTGGCCTTACACGCTCTCTCAATGAGTACCAC
326 ATATCAGCTCTTCTCTTCTCTTTAGCCAACTCTTTGGCCTTACACGCTCTCTCAATGAGCACCAC
42124118 AAATTCTTTTAACTCTAGGATGCCAACCAACAATCGGATGTCTTCATTCAACCCATCTTCAAACC
391 AAATTCTTTTAACTCTAGGATGCCAACCAACAATCGGATGTCTTCATTCAACCCATCTTCAAACC
42124183 TCTTACACATGGTGGCTTCTGCAGATTCGCACTCCCGCGCATATTTGCTGAGCCTCACGAACTCA
456 TCTTACACATGGTGGCTTCTGCAGATTCGCACTCCCGCGCATATTTGCTGAGCCTCACGAACTCA
*
42124248 TGTTCATATTTTGTCATTGTCATGCGGCCTTGCTTCAGTTCAAGAAATTCTTTCCTCTTTTGATC
521 TGTTCATATTTTGTCATTGTCATACGGCCTTGCTTCAGTTCAAGAAATTCTTTCCTCTTTTGATC
42124313 TATGAACCTTTGACTAATGTACTTTTT
586 TATGAACCTTTGACTAATGTACTTTTT
42124340 ACACCTTGATCTCTATCTTTCTCGACCATCTCGGGACAACTACGAATGAAATGGTCTAGCGACCC
1 ACACCTTGATCTCTATCTTTCTCGACCATCTCGGGACAAC-ACGAATGAAATGGTCTAGCGACCC
* *
42124405 ACATTTGAAATAGCCCCTTTCATTTCCTTGGCACTCATAAATTGTCGTCTACCACACTGCGAACA
65 ACATTTGAAATAGCCCCTTTCATTTCCTTGGCACTCACAAAATGTCGTCTACCACACTGCGAACA
*
42124470 CTCTGGTTTATTTGGTCGAGCACTACCAATGCTCGTGATAGAGGTGGTTTGAGCTTTAGGCGCTA
130 CTCTGGTTTATTTGGTCGAGCACTACCAATGCTCGTGATAGAGGTGGTTTGAGCTTTAGACGCTA
*
42124535 TATACTATTTATTCTTGTTTCTACTCGAGAATCCTACTGGCGCATTTGATTAAGTAGTAAACTCT
195 TATACTATTTATTCTTGTTTCTACTCGAGAATCCTACTGGCGCATTTGATTAAGTAGGAAACTCT
42124600 CTCGATCTCTTGGATAAATTCTGATGTGATTTCCCCATCTGTCTTTTCTTTGAGTCACGATACTC
260 CTCGATCTCTTGGATAAATTCTGATGTGATTTCCCCATCTGTCTTTTCTTTGAGTCACGATACTC
42124665 AATATCAGCTCTTCTCTTCTCTTTAGCCAACTCTTTGGCCTTACACGCTCTCTCAATGAGCACCA
325 AATATCAGCTCTTCTCTTCTCTTTAGCCAACTCTTTGGCCTTACACGCTCTCTCAATGAGCACCA
42124730 CAAATTCTTTTAACTCTAGGATGCCAACCAACAATCGGATGTCTTCATTCAACCCATCTTCAAAC
390 CAAATTCTTTTAACTCTAGGATGCCAACCAACAATCGGATGTCTTCATTCAACCCATCTTCAAAC
*
42124795 CTCTTACACATGGTGGCTTTTGCAGATTCGCACTCCCGCGCATATTTGCTGAGCCTCACGAACTC
455 CTCTTACACATGGTGGCTTCTGCAGATTCGCACTCCCGCGCATATTTGCTGAGCCTCACGAACTC
42124860 ATGTTCATATTTTGTCATTGTCATACGGCCTTGCTTCAGTTCAAGAAATTCTTTCCTCTTTTGAT
520 ATGTTCATATTTTGTCATTGTCATACGGCCTTGCTTCAGTTCAAGAAATTCTTTCCTCTTTTGAT
42124925 C-ATTGAACCTTTGACTAATGTACTTTTT
585 CTA-TGAACCTTTGACTAATGTACTTTTT
42124953 ACA
1 ACA
42124956 GAACTCTTCT
Statistics
Matches: 603, Mismatches: 11, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
612 41 0.07
613 562 0.93
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (612 bp):
ACACCTTGATCTCTATCTTTCTCGACCATCTCGGGACAACACGAATGAAATGGTCTAGCGACCCA
CATTTGAAATAGCCCCTTTCATTTCCTTGGCACTCACAAAATGTCGTCTACCACACTGCGAACAC
TCTGGTTTATTTGGTCGAGCACTACCAATGCTCGTGATAGAGGTGGTTTGAGCTTTAGACGCTAT
ATACTATTTATTCTTGTTTCTACTCGAGAATCCTACTGGCGCATTTGATTAAGTAGGAAACTCTC
TCGATCTCTTGGATAAATTCTGATGTGATTTCCCCATCTGTCTTTTCTTTGAGTCACGATACTCA
ATATCAGCTCTTCTCTTCTCTTTAGCCAACTCTTTGGCCTTACACGCTCTCTCAATGAGCACCAC
AAATTCTTTTAACTCTAGGATGCCAACCAACAATCGGATGTCTTCATTCAACCCATCTTCAAACC
TCTTACACATGGTGGCTTCTGCAGATTCGCACTCCCGCGCATATTTGCTGAGCCTCACGAACTCA
TGTTCATATTTTGTCATTGTCATACGGCCTTGCTTCAGTTCAAGAAATTCTTTCCTCTTTTGATC
TATGAACCTTTGACTAATGTACTTTTT
Found at i:42134277 original size:53 final size:54
Alignment explanation
Indices: 42134196--42134345 Score: 194
Period size: 53 Copynumber: 2.8 Consensus size: 54
42134186 TTTCCTTTTT
* * *
42134196 AAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 AAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATA
* * * * * *
42134249 GAACTCACCATTGTCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTGTA
1 AAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATA
* *
42134303 AAACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATC
1 AAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGGTATC
42134346 ATTAAACCCT
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
53 44 0.55
54 36 0.45
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (54 bp):
AAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:42141005 original size:46 final size:46
Alignment explanation
Indices: 42140952--42141125 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
42140942 TATTTGGGCA
42140952 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
42140998 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTGGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT--G
* * *
42141043 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
42141091 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT
42141126 AGGCGGGTTA
Statistics
Matches: 108, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 7 0.06
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:42141101 original size:93 final size:93
Alignment explanation
Indices: 42140946--42141119 Score: 303
Period size: 93 Copynumber: 1.9 Consensus size: 93
42140936 CTGGGATATT
* * *
42140946 TGGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTG
1 TGGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTG
42141011 AGTTGAGTCCGAGTTCGTGAGATGTAAC
66 AGTTGAGTCCGAGTTCGTGAGATGTAAC
* *
42141039 TGGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTG
1 TGGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTG
42141104 AGTTGAGTCCGAGTTC
66 AGTTGAGTCCGAGTTC
42141120 ACTTATAGGC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
TGGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTG
AGTTGAGTCCGAGTTCGTGAGATGTAAC
Found at i:42153711 original size:27 final size:27
Alignment explanation
Indices: 42153670--42153723 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
42153660 TGTCATGTGA
*
42153670 AATTGAATGGCAAATTATTATCACATG
1 AATTGAATGGCAAATTACTATCACATG
** *
42153697 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATCACATG
42153724 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATCACATG
Found at i:42154098 original size:50 final size:50
Alignment explanation
Indices: 42153976--42154151 Score: 194
Period size: 50 Copynumber: 3.5 Consensus size: 50
42153966 TGAGGTCATG
* ** * * *
42153976 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAACTTCGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TTAGGTCACA
* * ** *
42154027 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACA
* * *
42154077 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACA
42154126 TGTGTAGTACTAAGTGTC-GGCTACTA
1 TGTGTAGTACTAAGTG-CAGGCTACTA
42154152 TGCATACCAG
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 29 0.28
50 44 0.42
51 32 0.30
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACA
Found at i:42159995 original size:50 final size:49
Alignment explanation
Indices: 42159825--42160056 Score: 277
Period size: 49 Copynumber: 4.7 Consensus size: 49
42159815 TCTATTGTGA
* *
42159825 GGTCACGTGTGTAGTACTAAGTGCAGGCTATTACGTGTACCGGATAATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * ** *
42159874 GGTCGCATGTGTAGTACTAAATGCAGGCTACTATGCATACCCGATAACTT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * **
42159924 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
42159974 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
42160024 GGTCGCATGTGTAGTACTAAGTGTC-GGCTACTA
1 GGTCACGTGTGTAGTACTAAGTG-CAGGCTACTA
42160057 TGCATACTAG
Statistics
Matches: 153, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
49 68 0.44
50 49 0.32
51 36 0.24
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:42160070 original size:99 final size:99
Alignment explanation
Indices: 42159827--42160070 Score: 239
Period size: 100 Copynumber: 2.4 Consensus size: 99
42159817 TATTGTGAGG
* * * * * ** * *
42159827 TCACGTGTGTAGTACTAAGTGCAGGCTATTACGTGTACCGGATAATT-GGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTAC-TGCATCAGATGGTTAGGTCACGTGTGTAGTAC
*
42159891 TAAATGCAGGCTACTATGCATACCCGATAACTTCGA
65 TAAATGCAGGCTACTATG-ATACCAGATAACTTCGA
* *
42159927 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTAC-TGCATCAGATGGTTAGGTCACGTGTGTAGTAC
* *
42159992 TAAGTGCAGGCTACTACATG-TACCAGATAA-TT-GG
65 TAAATGCAGGCTACT--ATGATACCAGATAACTTCGA
*
42160026 TCGCATGTGTAGTACTAAGTGTC-GGCTACTA-TGCATACTAGATGG
1 TCACATGTGTAGTACTAAGTG-CAGGCTACTACTGCAT-C-AGATGG
42160071 CCTTGTCTAC
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
97 4 0.03
98 1 0.01
99 34 0.27
100 45 0.36
101 38 0.30
103 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (99 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACTGCATCAGATGGTTAGGTCACGTGTGTAGTACT
AAATGCAGGCTACTATGATACCAGATAACTTCGA
Found at i:42164668 original size:17 final size:17
Alignment explanation
Indices: 42164646--42164678 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42164636 TTTAGCACTA
*
42164646 ATTATGAGAAAGTAAAG
1 ATTATGAGAAACTAAAG
42164663 ATTATGAGAAACTAAA
1 ATTATGAGAAACTAAA
42164679 CCACTCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (17 bp):
ATTATGAGAAACTAAAG
Found at i:42166809 original size:12 final size:12
Alignment explanation
Indices: 42166789--42166826 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
42166779 AAAAATTGTC
42166789 AAAATTGAATTA
1 AAAATTGAATTA
*
42166801 AAAACTGAA-TA
1 AAAATTGAATTA
42166812 AAATATTGAATTA
1 AAA-ATTGAATTA
42166825 AA
1 AA
42166827 TCTTAATGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 5 0.23
12 13 0.59
13 4 0.18
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (12 bp):
AAAATTGAATTA
Found at i:42169884 original size:11 final size:12
Alignment explanation
Indices: 42169868--42169896 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
42169858 TCTTCAAATG
42169868 AAAAAACTC-TA
1 AAAAAACTCATA
42169879 AAAAAACTCATA
1 AAAAAACTCATA
42169891 AAAAAA
1 AAAAAA
42169897 AAGGTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAAAACTCATA
Found at i:42170873 original size:25 final size:25
Alignment explanation
Indices: 42170813--42170873 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
42170803 ATTCTAAAAA
* * *
42170813 TATAAAAATCTAAAAAATTATATATTT
1 TATAAAAA--TAAAAAATTACAAAATT
* *
42170840 TAGAGAAATAAAAAATTACAAAATT
1 TATAAAAATAAAAAATTACAAAATT
42170865 TATAAAAAT
1 TATAAAAAT
42170874 TAATACATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
25 21 0.78
27 6 0.22
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (25 bp):
TATAAAAATAAAAAATTACAAAATT
Found at i:42174718 original size:40 final size:40
Alignment explanation
Indices: 42174648--42174783 Score: 206
Period size: 40 Copynumber: 3.4 Consensus size: 40
42174638 AAACCAAGTA
* *
42174648 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCTCAAATG
*
42174687 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCTCAAATG
42174727 CCTTCGGGACTTAGCCCGGATATAGTAACTCG-TACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCT-CAAATG
42174767 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
42174784 AGTTATCATC
Statistics
Matches: 90, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
39 14 0.16
40 76 0.84
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCTCAAATG
Found at i:42180270 original size:402 final size:403
Alignment explanation
Indices: 42179507--42180313 Score: 1391
Period size: 402 Copynumber: 2.0 Consensus size: 403
42179497 TTTTGGGGGG
*
42179507 TATCATTTTCTTCAACCTATCTTTTGAAGCTTTTCAGCTTTGGCAGCTTAAGCCTCCTACAGGTG
1 TATCATTTTCTTCAACCTATCTTTTGAAGCTTTTCAGCTTTGGCAGCTTAAGCATCCTACAGGTG
* * * *
42179572 AATCTATGTGAAAGGGATACAATTAGCTCTTGGCAAAGATCCCTAAGTAGGATACAAGAGGGAAT
66 AATCGACGTGAAAGGGATACAATTAGCTCTTGGCAAAGATCCCTAAGTACGACACAAGAGGGAAT
42179637 TGAGAGATCAAGTCGAGATTTTCTAGGAATAGTACTTTCCACTTGTTTCTTTTATATTTCTTTTC
131 TGAGAGATCAAGTCGAGATTTTCTAGGAATAGTACTTTCCACTTGTTTCTTTTATATTTCTTTTC
*
42179702 TAAACGTTGGTGATTACTTTCTATTTCATGTTTGTACGAAAGTATACATGATTTTTGGGTTAAAT
196 TAAACGTTGGTCATTACTTTCTATTTCATGTTTGTACGAAAGTATACATGATTTTTGGGTTAAAT
*
42179767 GTTATTTTATTCAATCTTGTTTCTACTGTTTAATCTTTGGGTTTGAATGTTTTTAACATAGAAGT
261 GTTATTTTATTCAATCTTGTTTCTACTATTTAATCTTTGGGTTTGAATGTTTTTAACATAGAAGT
* * *
42179832 GTTATTGCGATCACTAACACTGGAAAGTGCAGCTATAGTTCAAGCTAACAAGCATGACAACAGAA
326 GCTATTGCAATCACTAACACTGGAAAGTACAGCTATAGTTCAAGCTAACAAGCATGACAACAGAA
42179897 GTTGCTAGAGGAT
391 GTTGCTAGAGGAT
** *
42179910 TATCATTTTCTTCAACCTATCTTTTGAAGCTTTTCAGCTTTGGTGGCTTAAGCATCTTACAGGTG
1 TATCATTTTCTTCAACCTATCTTTTGAAGCTTTTCAGCTTTGGCAGCTTAAGCATCCTACAGGTG
* * * * *
42179975 AATCGACGTGAAAGGGGTGCAATTATCTCTTGGCGAAGATCCCTGAGTACGACACAAGAGGGAAT
66 AATCGACGTGAAAGGGATACAATTAGCTCTTGGCAAAGATCCCTAAGTACGACACAAGAGGGAAT
42180040 TGAGAGATCAAGTCGAGATTTTCTAGGAATAGTACTTTCCACTTGTTT-TTTTATATTTCTTTTC
131 TGAGAGATCAAGTCGAGATTTTCTAGGAATAGTACTTTCCACTTGTTTCTTTTATATTTCTTTTC
*
42180104 TAAACGTTGGTCATTACTTTCTATTTCATGTTTGTATGAAAGTATACATGATTTTTGGGTTAAAT
196 TAAACGTTGGTCATTACTTTCTATTTCATGTTTGTACGAAAGTATACATGATTTTTGGGTTAAAT
* *
42180169 GTTATTTTATTCAATCTTGTTTCTACTATTTAATCTTTGGGTTTGAATGTTTTTAGCATGGAAGT
261 GTTATTTTATTCAATCTTGTTTCTACTATTTAATCTTTGGGTTTGAATGTTTTTAACATAGAAGT
* * *
42180234 GCTCTTGCAATCTCTAACACTGGAAAGTATAGCTATAGTTCAAGCTAACAAGCATGACAACAGAA
326 GCTATTGCAATCACTAACACTGGAAAGTACAGCTATAGTTCAAGCTAACAAGCATGACAACAGAA
42180299 GTTGCTAGAGGAT
391 GTTGCTAGAGGAT
42180312 TA
1 TA
42180314 GAGGAATTTA
Statistics
Matches: 380, Mismatches: 24, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
402 215 0.57
403 165 0.43
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (403 bp):
TATCATTTTCTTCAACCTATCTTTTGAAGCTTTTCAGCTTTGGCAGCTTAAGCATCCTACAGGTG
AATCGACGTGAAAGGGATACAATTAGCTCTTGGCAAAGATCCCTAAGTACGACACAAGAGGGAAT
TGAGAGATCAAGTCGAGATTTTCTAGGAATAGTACTTTCCACTTGTTTCTTTTATATTTCTTTTC
TAAACGTTGGTCATTACTTTCTATTTCATGTTTGTACGAAAGTATACATGATTTTTGGGTTAAAT
GTTATTTTATTCAATCTTGTTTCTACTATTTAATCTTTGGGTTTGAATGTTTTTAACATAGAAGT
GCTATTGCAATCACTAACACTGGAAAGTACAGCTATAGTTCAAGCTAACAAGCATGACAACAGAA
GTTGCTAGAGGAT
Found at i:42183521 original size:23 final size:24
Alignment explanation
Indices: 42183467--42183521 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
42183457 CAGCTCTTCG
* *
42183467 TGAACGTCCTGATATAAGCTCTTA
1 TGAACTTCCTGATATAAGCTCCTA
*
42183491 TGAGCTTCCTGATAT-AGCTCGCT-
1 TGAACTTCCTGATATAAGCTC-CTA
42183514 TGAACTTC
1 TGAACTTC
42183522 TTGTTATGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (24 bp):
TGAACTTCCTGATATAAGCTCCTA
Found at i:42189796 original size:23 final size:23
Alignment explanation
Indices: 42189766--42189825 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
42189756 GGTTATGCCT
*
42189766 CACACGCCCGTGTGAAGGCAAAG
1 CACACGCCCATGTGAAGGCAAAG
*
42189789 CACACGCCCATGTGATGGCAAAG
1 CACACGCCCATGTGAAGGCAAAG
42189812 CACACGCCCATGTG
1 CACACGCCCATGTG
42189826 CTTGGGGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.33, G:0.27, T:0.12
Consensus pattern (23 bp):
CACACGCCCATGTGAAGGCAAAG
Found at i:42202316 original size:48 final size:48
Alignment explanation
Indices: 42202194--42202661 Score: 418
Period size: 48 Copynumber: 9.6 Consensus size: 48
42202184 GTAAGATCCT
* * *
42202194 GATGCCATGTTCCGAACATGGTCTTACACTGGCTCTCATATATCG-GTGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGC-C-CACATATCGAG-GCC
* * * *
42202244 GATGCCATGTTCCAAACATAGTCTTACAGTAGCCCAGATGTCGAGGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATCGAGGCC
** * * * * * * *
42202292 GATGCTGTGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAATGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATCGAGGCC
* * * **
42202340 GATGCCATGTTCCAAATATGGTCTTACACTAGCTCTTATATATCGATTCC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGC-C-CACATATCGAGGCC
* ** *
42202390 GATGCCATGTTCCAAACATGGTCTTACGCTAGCCCACATGCCGAGGCT
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATCGAGGCC
* * * * * * *
42202438 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAACGCT
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATCGAGGCC
* * * *
42202486 GATGCCATGTTCGAAACATGGTCTTACATTGGCTCTCATATATCG-GTGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGC-C-CACATATCGAG-GCC
* * *
42202536 GATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATGTTGAGGCT
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATCGAGGCC
* * * * * *
42202584 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATCGAGGCC
* * *
42202632 GATTCCATGTTCCAAGCATGGTTTTACACT
1 GATGCCATGTTCCAAACATGGTCTTACACT
42202662 GGCTCGTATA
Statistics
Matches: 331, Mismatches: 80, Indels: 16
0.78 0.19 0.04
Matches are distributed among these distances:
48 220 0.66
49 5 0.02
50 106 0.32
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (48 bp):
GATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATATCGAGGCC
Found at i:42202458 original size:146 final size:146
Alignment explanation
Indices: 42202194--42202666 Score: 732
Period size: 146 Copynumber: 3.2 Consensus size: 146
42202184 GTAAGATCCT
*
42202194 GATGCCATGTTCCGAACATGGTCTTACACTGGCTCTCATATATCGGTGCCGATGCCATGTTCCAA
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATATCGGTGCCGATGCCATGTTCCAA
* * * **
42202259 ACATAGTCTTACAG-TAGCCCAGATGTCGAGGCCGATGCTGTGTCCCAGACATGGTCTTACACTA
66 ACATGGTCTTAC-GCTAGCCCACATGTCGAGGCTGATGCCATGTCCCAGACATGGTCTTACACTA
*
42202323 GCTCTCATCTCAATGCC
130 GCTCTCATATCAATGCC
* * * * *
42202340 GATGCCATGTTCCAAATATGGTCTTACACTAGCTCTTATATATCGATTCCGATGCCATGTTCCAA
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATATCGGTGCCGATGCCATGTTCCAA
*
42202405 ACATGGTCTTACGCTAGCCCACATGCCGAGGCTGATGCCATGTCCCAGACATGGTCTTACACTAG
66 ACATGGTCTTACGCTAGCCCACATGTCGAGGCTGATGCCATGTCCCAGACATGGTCTTACACTAG
* *
42202470 CTCTCATATCAACGCT
131 CTCTCATATCAATGCC
* *
42202486 GATGCCATGTTCGAAACATGGTCTTACATTGGCTCTCATATATCGGTGCCGATGCCATGTTCCAA
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATATCGGTGCCGATGCCATGTTCCAA
* *
42202551 ACATGGTCTTACACTAGCCCACATGTTGAGGCTGATGCCATGTCCCAGACATGGTCTTACACTAG
66 ACATGGTCTTACGCTAGCCCACATGTCGAGGCTGATGCCATGTCCCAGACATGGTCTTACACTAG
42202616 CTCTCATATCAATGCC
131 CTCTCATATCAATGCC
* * *
42202632 GATTCCATGTTCCAAGCATGGTTTTACACTGGCTC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTC
42202667 GTATAACCCT
Statistics
Matches: 294, Mismatches: 32, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
145 1 0.00
146 293 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (146 bp):
GATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATATCGGTGCCGATGCCATGTTCCAA
ACATGGTCTTACGCTAGCCCACATGTCGAGGCTGATGCCATGTCCCAGACATGGTCTTACACTAG
CTCTCATATCAATGCC
Found at i:42207245 original size:48 final size:48
Alignment explanation
Indices: 42207181--42207503 Score: 335
Period size: 48 Copynumber: 6.7 Consensus size: 48
42207171 GGTTATGTGT
* * *
42207181 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGA
* * * ** *
42207229 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-ACCTCAATATGC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGA
* * * *
42207276 GAGCAAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGA
* * * ** *
42207324 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-ACCTCAATATGC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGA
* * * * *
42207371 GAGCAAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGA
* * * ** *
42207419 GAGCCAATATAAGACCATGTCTGGGACATAGCATTAGCACCGATGTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCG-T-TATGA
*
42207469 CAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
42207504 AAAATTTTAC
Statistics
Matches: 219, Mismatches: 52, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
47 76 0.35
48 108 0.49
49 1 0.00
50 34 0.16
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGA
Found at i:42207311 original size:95 final size:95
Alignment explanation
Indices: 42207181--42207452 Score: 490
Period size: 95 Copynumber: 2.9 Consensus size: 95
42207171 GGTTATGTGT
*
42207181 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAGTGTAAGACCA
1 GAGCAAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAGTGTAAGACCA
42207246 TGTCTGGGACATGGCATCACCTCAATATGC
66 TGTCTGGGACATGGCATCACCTCAATATGC
42207276 GAGCAAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAGTGTAAGACCA
1 GAGCAAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAGTGTAAGACCA
42207341 TGTCTGGGACATGGCATCACCTCAATATGC
66 TGTCTGGGACATGGCATCACCTCAATATGC
* * * *
42207371 GAGCAAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGTGAGCCAATATAAGACCA
1 GAGCAAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAGTGTAAGACCA
*
42207436 TGTCTGGGACATAGCAT
66 TGTCTGGGACATGGCAT
42207453 TAGCACCGAT
Statistics
Matches: 171, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 171 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (95 bp):
GAGCAAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGTTATGAGAGCTAGTGTAAGACCA
TGTCTGGGACATGGCATCACCTCAATATGC
Found at i:42209995 original size:20 final size:21
Alignment explanation
Indices: 42209970--42210008 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42209960 TCCTTAAAAT
42209970 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
42209990 AGGGCAACACGCCCGTGTG
1 AGGGCAACACGCCCGTGTG
42210009 ACCAACTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.21, C:0.31, G:0.38, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:42211319 original size:46 final size:45
Alignment explanation
Indices: 42211233--42211405 Score: 165
Period size: 46 Copynumber: 3.7 Consensus size: 45
42211223 GCATATCCGT
* *
42211233 GCCGATGCTATCTCCCAGACATGATCTTACACT-GACACATCTCGTA-
1 GCCGATGCT-TGTCCCAGACATG-TCTTACACTGGATACATCTC-TAG
42211279 GCCGATGCTTGTCCCAGACATGTCTTACACTGGATTACATCT-TAAG
1 GCCGATGCTTGTCCCAGACATGTCTTACACTGGA-TACATCTCT-AG
* * * * *
42211325 GCCGATGGTTGTCCCAGACATGTCTTACACTAGCACT-CGTCTCAAT
1 GCCGATGCTTGTCCCAGACATGTCTTACACT-GGA-TACATCTCTAG
*
42211371 GCCGATGCCATGTCCCAGACATGGTCTTACACTGG
1 GCCGATG-CTTGTCCCAGACAT-GTCTTACACTGG
42211406 CTCACACCAA
Statistics
Matches: 108, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
44 10 0.09
45 15 0.14
46 57 0.53
47 16 0.15
48 10 0.09
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (45 bp):
GCCGATGCTTGTCCCAGACATGTCTTACACTGGATACATCTCTAG
Found at i:42214752 original size:16 final size:16
Alignment explanation
Indices: 42214731--42214808 Score: 55
Period size: 16 Copynumber: 5.4 Consensus size: 16
42214721 ATAAGGGACA
42214731 ATATGATTAGTTTTAG
1 ATATGATTAGTTTTAG
**
42214747 ATATGAACAG---TA-
1 ATATGATTAGTTTTAG
42214759 ATATGATTAGTTTTAG
1 ATATGATTAGTTTTAG
**
42214775 ATATGAACAG---TA-
1 ATATGATTAGTTTTAG
*
42214787 ATATGATTATTTTTAG
1 ATATGATTAGTTTTAG
42214803 ATATGA
1 ATATGA
42214809 ACAGTAAATG
Statistics
Matches: 45, Mismatches: 9, Indels: 16
0.64 0.13 0.23
Matches are distributed among these distances:
12 15 0.33
13 4 0.09
15 4 0.09
16 22 0.49
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (16 bp):
ATATGATTAGTTTTAG
Found at i:42214762 original size:28 final size:28
Alignment explanation
Indices: 42214730--42214819 Score: 164
Period size: 28 Copynumber: 3.2 Consensus size: 28
42214720 TATAAGGGAC
42214730 AATATGATTAGTTTTAGATATGAACAGT
1 AATATGATTAGTTTTAGATATGAACAGT
42214758 AATATGATTAGTTTTAGATATGAACAGT
1 AATATGATTAGTTTTAGATATGAACAGT
*
42214786 AATATGATTATTTTTAGATATGAACAGT
1 AATATGATTAGTTTTAGATATGAACAGT
42214814 AA-ATGA
1 AATATGA
42214820 CATGAACTAC
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
27 4 0.07
28 57 0.93
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (28 bp):
AATATGATTAGTTTTAGATATGAACAGT
Found at i:42216630 original size:15 final size:14
Alignment explanation
Indices: 42216597--42216623 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42216587 AAAAATATAT
42216597 AAATTTTAAAAATA
1 AAATTTTAAAAATA
42216611 AAATTTTAAAAAT
1 AAATTTTAAAAAT
42216624 GATAATTGAA
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATTTTAAAAATA
Found at i:42216879 original size:26 final size:25
Alignment explanation
Indices: 42216849--42216900 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
42216839 GCATTCAAAT
42216849 ATTTAATATTATAAT-TTTCTT-TTTTA
1 ATTTAA-ATT-TAATGTTT-TTATTTTA
42216875 ATTTAAATTTAATGTTTTTATTTTA
1 ATTTAAATTTAATGTTTTTATTTTA
42216900 A
1 A
42216901 ATAAACTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 6 0.25
25 12 0.50
26 6 0.25
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
ATTTAAATTTAATGTTTTTATTTTA
Found at i:42217157 original size:7 final size:7
Alignment explanation
Indices: 42217145--42217172 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
42217135 ATTAACAAAA
42217145 AAAATAT
1 AAAATAT
42217152 AAAATAT
1 AAAATAT
42217159 AAAATAT
1 AAAATAT
42217166 AAAATAT
1 AAAATAT
42217173 GAGGAGTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATAT
Found at i:42218216 original size:16 final size:15
Alignment explanation
Indices: 42218195--42218224 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42218185 TTTTTCATCG
42218195 TTTTCTACCTCTTTCA
1 TTTTCTACCT-TTTCA
42218211 TTTTCTACCTTTTC
1 TTTTCTACCTTTTC
42218225 CATCTATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.10, C:0.30, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTCTACCTTTTCA
Found at i:42220456 original size:41 final size:41
Alignment explanation
Indices: 42220399--42220480 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
42220389 GACCCATCTT
42220399 CCCTACACTTAGCCCTAGTCTCTCCCTTTTCATTACTAAGA
1 CCCTACACTTAGCCCTAGTCTCTCCCTTTTCATTACTAAGA
42220440 CCCTACACTTAGCCCTAGTCTCTCCCTTTTCATTACTAAGA
1 CCCTACACTTAGCCCTAGTCTCTCCCTTTTCATTACTAAGA
42220481 TAGACAAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.37, G:0.07, T:0.34
Consensus pattern (41 bp):
CCCTACACTTAGCCCTAGTCTCTCCCTTTTCATTACTAAGA
Found at i:42221096 original size:39 final size:39
Alignment explanation
Indices: 42221029--42221120 Score: 112
Period size: 39 Copynumber: 2.4 Consensus size: 39
42221019 TCCCTACCTT
* ** * *
42221029 CACTATTTAATTCCTCATTGTAATTTGGTAACTCTGCCC
1 CACTATTTAGTTCCTCATTACAAGTTGGTAACTCAGCCC
* * *
42221068 TACTCTTTAGTTCCTCATTACAAGTTGGTATCTCAGCCC
1 CACTATTTAGTTCCTCATTACAAGTTGGTAACTCAGCCC
42221107 CACTATTTAGTTCC
1 CACTATTTAGTTCC
42221121 ATTTCCATAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (39 bp):
CACTATTTAGTTCCTCATTACAAGTTGGTAACTCAGCCC
Found at i:42225442 original size:28 final size:28
Alignment explanation
Indices: 42225402--42225457 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
42225392 AGAGAAGGAA
42225402 GAATTATGCCAAGGCCATGCCACTAAAC
1 GAATTATGCCAAGGCCATGCCACTAAAC
42225430 GAATTATGCCAAGGCCATGCCACTAAAC
1 GAATTATGCCAAGGCCATGCCACTAAAC
42225458 TAACAGGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.18
Consensus pattern (28 bp):
GAATTATGCCAAGGCCATGCCACTAAAC
Found at i:42231259 original size:19 final size:20
Alignment explanation
Indices: 42231235--42231272 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42231225 GGTACCACCA
42231235 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
42231254 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
42231273 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:42231567 original size:46 final size:46
Alignment explanation
Indices: 42231500--42231621 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
42231490 CGCCCCTAAG
* * *
42231500 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
* *
42231546 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
42231592 TGAACTCGGACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA
42231622 TGCTCAACCA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
Found at i:42231640 original size:46 final size:45
Alignment explanation
Indices: 42231498--42231640 Score: 137
Period size: 46 Copynumber: 3.1 Consensus size: 45
42231488 CCCGCCCCTA
* ** *
42231498 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T
* ** **
42231543 AAATGAACTCGGACTCAACTCAACGAGTTCGGACATT-TGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T
*
42231589 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTC-ACCATCCT
42231636 AGTGA
1 AGTGA
42231641 CATGTCACTT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
46 78 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCCT
Found at i:42242529 original size:25 final size:25
Alignment explanation
Indices: 42242471--42242532 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
42242461 TTTGCTTGAA
*
42242471 AATTTATATGATAGGAAAATCGTATG
1 AATTTAT-TGATAGGAAAATCGTATC
** **
42242497 AAAATATTGATAGGAAAATTTTATC
1 AATTTATTGATAGGAAAATCGTATC
42242522 AATTTATTGAT
1 AATTTATTGAT
42242533 TAGTTAGAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.39
Consensus pattern (25 bp):
AATTTATTGATAGGAAAATCGTATC
Found at i:42249264 original size:19 final size:20
Alignment explanation
Indices: 42249240--42249277 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42249230 GGTACCACCA
42249240 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
42249259 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
42249278 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:42249572 original size:46 final size:45
Alignment explanation
Indices: 42249505--42249668 Score: 170
Period size: 46 Copynumber: 3.6 Consensus size: 45
42249495 CGCCCCTAAG
* *
42249505 TGAACTCGGATTCAACTCAACGAGCTCAGGCATTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTC-GGCATTCGCATCCATAAA
* * **
42249551 TGAACTCGGACTCAACTCAACGAGTTCGG-ATGC-CTAGTTACATCTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--TCCAT-AAA
* * * *
42249598 CGAACTCGAACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCATCCATAAA
42249644 TGAACTCGGACTCAACTCAACGAGT
1 TGAACTCGGACTCAACTCAACGAGT
42249669 CCGGATCCTC
Statistics
Matches: 95, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 2 0.02
46 52 0.55
47 32 0.34
49 3 0.03
50 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCATAAA
Found at i:42249665 original size:93 final size:93
Alignment explanation
Indices: 42249506--42249674 Score: 268
Period size: 93 Copynumber: 1.8 Consensus size: 93
42249496 GCCCCTAAGT
* *
42249506 GAACTCGGATTCAACTCAACGAGCTCAGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
42249571 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTCCGGATGCCTAGTTACATCTCAC
* * *
42249599 GAACTCGAACTCAACTCAACGAGTTC-GGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGAACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAATGAACTCGGACTCAACTCA
42249663 ACGAGTCCGGAT
65 ACGAGTCCGGAT
42249675 CCTCAACCAT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTCCGGATGCCTAGTTACATCTCAC
Found at i:42249692 original size:46 final size:45
Alignment explanation
Indices: 42249500--42249685 Score: 114
Period size: 46 Copynumber: 4.0 Consensus size: 45
42249490 TAACCCGCCC
* * *
42249500 CTAAGTGAACTCGGATTCAACTCAACGAGCTCAGGCATTCGC-ATCCA-
1 CTAAGTGAACTCGGACTCAACTCAACGAG-TCCGG-A-TC-CTAACCAT
* *
42249547 -TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTCCGGAT-CCTA---ACCAT
* * * * * ***
42249594 CTCA-CGAACTCGAACTCAACTCAACGAGTTCGGA-CATTTGCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTCCGGATCCTAACCAT
42249637 CCATAAGTGAACTCGGACTCAACTCAACGAGTCCGGATCCTCAACCAT
1 -C-TAAGTGAACTCGGACTCAACTCAACGAGTCCGGATCCT-AACCAT
42249685 C
1 C
42249686 CTAGTGACAT
Statistics
Matches: 107, Mismatches: 19, Indels: 26
0.70 0.12 0.17
Matches are distributed among these distances:
43 5 0.05
44 4 0.04
45 7 0.07
46 55 0.51
47 31 0.29
48 5 0.05
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (45 bp):
CTAAGTGAACTCGGACTCAACTCAACGAGTCCGGATCCTAACCAT
Found at i:42250131 original size:30 final size:30
Alignment explanation
Indices: 42250097--42250156 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
42250087 ATTTAATACG
42250097 AACTTGAAG-AAAATTACACTTTTGCCCCTA
1 AACTT-AAGCAAAATTACACTTTTGCCCCTA
** *
42250127 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTAAGCAAAATTACACTTTTGCCCCTA
42250157 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (30 bp):
AACTTAAGCAAAATTACACTTTTGCCCCTA
Found at i:42254180 original size:61 final size:63
Alignment explanation
Indices: 42254105--42254256 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 63
42254095 CTATTCAGAA
* *
42254105 ATCAGAGT-TAACTGGGCCTTAGCCCATATTAATATTAATCTGGGCCATAGCCC-CTTAC-AGT
1 ATCAGAGTAT-ACTGGGCCTTAGCCCATATTAATATCAATCTGGGCCATAGCCCTATTACAAGT
* * * *
42254166 ATCAGAGTATACTGGG-CTTAGCCCATATCAGTGTCAATCTGGGCCGTAGCCCTATTACAAGT
1 ATCAGAGTATACTGGGCCTTAGCCCATATTAATATCAATCTGGGCCATAGCCCTATTACAAGT
* **
42254228 -TGAGA-TATGTTGGGCCTT-GCCCATATTAA
1 ATCAGAGTATACTGGGCCTTAGCCCATATTAA
42254257 CACAGTTGGG
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
60 47 0.62
61 25 0.33
62 4 0.05
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (63 bp):
ATCAGAGTATACTGGGCCTTAGCCCATATTAATATCAATCTGGGCCATAGCCCTATTACAAGT
Found at i:42254271 original size:20 final size:20
Alignment explanation
Indices: 42254246--42254291 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
42254236 GTTGGGCCTT
42254246 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
42254266 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
42254285 GCCCATA
1 GCCCATA
42254292 ACAAAATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:42258670 original size:40 final size:40
Alignment explanation
Indices: 42258622--42258850 Score: 395
Period size: 40 Copynumber: 5.7 Consensus size: 40
42258612 ACAAACACAT
* *
42258622 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42258662 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
** *
42258702 TTGCCTTCGGGTCACAGCCCGGATATATCAACTCGCATAG
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42258742 TTGCCTTCGGGTCTTAGCCCGGATACATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42258782 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42258822 TTGCCTTCGGGTCTTAGCCCGGATATATC
1 TTGCCTTCGGGTCTTAGCCCGGATATATC
42258851 CAATGCTCAT
Statistics
Matches: 177, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 177 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:42272615 original size:30 final size:29
Alignment explanation
Indices: 42272579--42272720 Score: 126
Period size: 30 Copynumber: 4.8 Consensus size: 29
42272569 TCCTCTTGAC
42272579 TTAGATAGCCACAGAGGCATCCATACATCA
1 TTAGATAGCCACA-AGGCATCCATACATCA
* *
42272609 TTAGATAGCCACAAGGGAATCCACACATCA
1 TTAGATAGCCACAA-GGCATCCATACATCA
* * *
42272639 TTAGATAGTCACAAAGGCATCC--ACTTGAA
1 TTAGATAGCCAC-AAGGCATCCATACAT-CA
* * **
42272668 TTATATAGCCACAGAAGTGTCCATACATCA
1 TTAGATAGCCACA-AGGCATCCATACATCA
*
42272698 TTAGATAGTCACAAGGGCATCCA
1 TTAGATAGCCACAA-GGCATCCA
42272721 GATTCATACA
Statistics
Matches: 87, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
28 4 0.05
29 18 0.21
30 60 0.69
31 5 0.06
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (29 bp):
TTAGATAGCCACAAGGCATCCATACATCA
Found at i:42272852 original size:32 final size:31
Alignment explanation
Indices: 42272800--42272913 Score: 121
Period size: 30 Copynumber: 3.7 Consensus size: 31
42272790 ATAATTTTTT
*
42272800 CACAAAGG-TT-TACATGTAACATAGAACAAC
1 CACAAAGGCTTCTACATATAACA-AGAACAAC
* *
42272830 CACAAAGGCTTCTACATATAACAAGTTA-TAC
1 CACAAAGGCTTCTACATATAACAAG-AACAAC
*
42272861 CAAAAAGGC-TC-ACATATAACACAGAACAAC
1 CACAAAGGCTTCTACATATAACA-AGAACAAC
*
42272891 CACAAAGGCTTCCACATATAACA
1 CACAAAGGCTTCTACATATAACA
42272914 CGTTCCGCCA
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
29 11 0.16
30 22 0.31
31 16 0.23
32 21 0.30
ACGTcount: A:0.46, C:0.25, G:0.11, T:0.18
Consensus pattern (31 bp):
CACAAAGGCTTCTACATATAACAAGAACAAC
Found at i:42272876 original size:29 final size:30
Alignment explanation
Indices: 42272827--42272940 Score: 90
Period size: 29 Copynumber: 3.8 Consensus size: 30
42272817 AACATAGAAC
*
42272827 AACCACAAAGGCTTCTACATATAACAAGTTA
1 AACCAAAAAGGCTTC-ACATATAACAAGTTA
* *
42272858 TACCAAAAAGGC-TCACATATAACACAG-AA
1 AACCAAAAAGGCTTCACATATAACA-AGTTA
* * *
42272887 CAACCACAAAGGCTTCCACATATAACACGTTC
1 -AACCAAAAAGGCTT-CACATATAACAAGTTA
** *
42272919 CGCCAAAAAGG-ATCACATATAA
1 AACCAAAAAGGCTTCACATATAA
42272941 TAGATTTAGT
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
29 20 0.30
30 15 0.23
31 20 0.30
32 11 0.17
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.18
Consensus pattern (30 bp):
AACCAAAAAGGCTTCACATATAACAAGTTA
Found at i:42272887 original size:61 final size:61
Alignment explanation
Indices: 42272811--42272940 Score: 188
Period size: 61 Copynumber: 2.1 Consensus size: 61
42272801 ACAAAGGTTT
* * * * *
42272811 ACATGTAACATAGAACAACCACAAAGGCTTCTACATATAACAAGTTATACCAAAAAGGCTC
1 ACATATAACACAGAACAACCACAAAGGCTTCCACATATAACAAGTTACACCAAAAAGGATC
* * *
42272872 ACATATAACACAGAACAACCACAAAGGCTTCCACATATAACACGTTCCGCCAAAAAGGATC
1 ACATATAACACAGAACAACCACAAAGGCTTCCACATATAACAAGTTACACCAAAAAGGATC
42272933 ACATATAA
1 ACATATAA
42272941 TAGATTTAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.46, C:0.25, G:0.11, T:0.18
Consensus pattern (61 bp):
ACATATAACACAGAACAACCACAAAGGCTTCCACATATAACAAGTTACACCAAAAAGGATC
Found at i:42272914 original size:32 final size:32
Alignment explanation
Indices: 42272811--42272914 Score: 117
Period size: 32 Copynumber: 3.3 Consensus size: 32
42272801 ACAAAGGTTT
* * *
42272811 ACATGTAACATAGAACAACCACAAAGGCTTCT
1 ACATATAACACAGAACAACCACAAAGGCTTCC
* * *
42272843 ACATATAACA-AGTTA-TACCAAAAAGGC-T-C
1 ACATATAACACAG-AACAACCACAAAGGCTTCC
42272872 ACATATAACACAGAACAACCACAAAGGCTTCC
1 ACATATAACACAGAACAACCACAAAGGCTTCC
42272904 ACATATAACAC
1 ACATATAACAC
42272915 GTTCCGCCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
29 11 0.19
30 13 0.22
31 13 0.22
32 22 0.37
ACGTcount: A:0.47, C:0.26, G:0.10, T:0.17
Consensus pattern (32 bp):
ACATATAACACAGAACAACCACAAAGGCTTCC
Found at i:42279841 original size:8 final size:8
Alignment explanation
Indices: 42279830--42279854 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42279820 CGGCAAATCT
42279830 CGAAATGC
1 CGAAATGC
42279838 CGAAATGC
1 CGAAATGC
42279846 CGAAATGC
1 CGAAATGC
42279854 C
1 C
42279855 AAAAAACTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.24, T:0.12
Consensus pattern (8 bp):
CGAAATGC
Found at i:42280271 original size:29 final size:29
Alignment explanation
Indices: 42280091--42280269 Score: 270
Period size: 29 Copynumber: 6.2 Consensus size: 29
42280081 ATGAAACCAT
* *
42280091 CCATATGAATGTGATTTGGGCCAAATGGG
1 CCATACGAATGTGATTTGGGCCTAATGGG
*
42280120 CCATACGGATGTGATTTGGGCCTAATGGG
1 CCATACGAATGTGATTTGGGCCTAATGGG
*
42280149 CCATACAAATGTGATTTGGGCCTAATGGG
1 CCATACGAATGTGATTTGGGCCTAATGGG
42280178 CCATACGAATGTGATTTGGGCCTAATGGG
1 CCATACGAATGTGATTTGGGCCTAATGGG
*
42280207 CCATA-GAAATGTGATTTGGGCCTAGTGGG
1 CCATACG-AATGTGATTTGGGCCTAATGGG
* * *
42280236 CCATATGAATGAGATTTGGGCCTAGTGGG
1 CCATACGAATGTGATTTGGGCCTAATGGG
42280265 CCATA
1 CCATA
42280270 TGCATGTATG
Statistics
Matches: 140, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
28 1 0.01
29 138 0.99
30 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.27
Consensus pattern (29 bp):
CCATACGAATGTGATTTGGGCCTAATGGG
Found at i:42292543 original size:32 final size:32
Alignment explanation
Indices: 42292498--42292562 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
42292488 TGTCAACTGT
42292498 AGTCCAACCGATCGTCTTTTTGAATTTTTTTA
1 AGTCCAACCGATCGTCTTTTTGAATTTTTTTA
*
42292530 AGTCCAACGGATCGTCTTTTTGAATTTTTTTA
1 AGTCCAACCGATCGTCTTTTTGAATTTTTTTA
42292562 A
1 A
42292563 AACTTCGATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (32 bp):
AGTCCAACCGATCGTCTTTTTGAATTTTTTTA
Found at i:42296078 original size:40 final size:40
Alignment explanation
Indices: 42296023--42296251 Score: 377
Period size: 40 Copynumber: 5.7 Consensus size: 40
42296013 ATGAGCATTG
42296023 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
42296063 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* *
42296103 GATGTATCCGGGCTAAGACCCGAAGGCAACTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* ** *
42296143 GATATATCCGAGCTGTGACCCGAAGGCAATTATGCGAGAT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
42296183 GATACATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* *
42296223 GATATGTCCGGGTTAAGACCCGAAGGCAA
1 GATATATCCGGGCTAAGACCCGAAGGCAA
42296252 ATGTGTTTGT
Statistics
Matches: 173, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 173 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (40 bp):
GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
Found at i:42306221 original size:40 final size:39
Alignment explanation
Indices: 42306137--42306321 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
42306127 TCGAATGATG
* * * *
42306137 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
42306177 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
42306217 TCCGGGCTAAGCCCGAAGGCATTGGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
42306256 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
42306297 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
42306322 AATGAGTAGC
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 33 0.27
40 79 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42306273 original size:79 final size:81
Alignment explanation
Indices: 42306137--42306319 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
42306127 TCGAATGATG
* *
42306137 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
42306201 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
42306216 TTCCGGGCTAAG-CCCGAAGGCATTGGTG-TGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
42306278 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
42306296 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42306320 TGAATGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 29 0.33
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:42306343 original size:79 final size:79
Alignment explanation
Indices: 42306190--42306354 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
42306180 GGACTAAGAT
* **
42306190 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAATGAGTTACTAA
*
42306255 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
42306269 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAATGAGTTA-C
* *
42306332 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
42306348 CCGAAGG
1 CCGAAGG
42306355 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAATGAGTTACTAA
ATCCGGGTTAAATC
Found at i:42309989 original size:159 final size:159
Alignment explanation
Indices: 42309700--42310017 Score: 591
Period size: 159 Copynumber: 2.0 Consensus size: 159
42309690 GGAGGTAGAG
42309700 TTTGGTATTGAACTTGTACCTGGAACTACGCCAATTTCGATAGCTCCGTATCGTATGGCACCAAC
1 TTTGGTATTGAACTTGTACCTGGAACTACGCCAATTTCGATAGCTCCGTATCGTATGGCACCAAC
* * * *
42309765 TGAGTTAAAATAATTGAAAGCTCAGTTGCAAGAGTTGATGGATAGAGGTTTCGCTCGACCAAGTT
66 CGAGTTAAAAGAATTGAAAGCTCAATTGCAAGAGTTGACGGATAGAGGTTTCGCTCGACCAAGTT
42309830 TCTCACCTTGGGGTGCACCAGTATTGTTT
131 TCTCACCTTGGGGTGCACCAGTATTGTTT
42309859 TTTGGTATTGAACTTGTACCTGGAACTACGCCAATTTCGATAGCTCCGTATCGTATGGCACCAAC
1 TTTGGTATTGAACTTGTACCTGGAACTACGCCAATTTCGATAGCTCCGTATCGTATGGCACCAAC
*
42309924 CGAGTTAAAGGAATTGAAAGCTCAATTGCAAGAGTTGACGGATAGAGGTTTCGCTCGACCAAGTT
66 CGAGTTAAAAGAATTGAAAGCTCAATTGCAAGAGTTGACGGATAGAGGTTTCGCTCGACCAAGTT
42309989 TCTCACCTTGGGGTGCACCAGTATTGTTT
131 TCTCACCTTGGGGTGCACCAGTATTGTTT
42310018 GTGAAAAAGA
Statistics
Matches: 154, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
159 154 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (159 bp):
TTTGGTATTGAACTTGTACCTGGAACTACGCCAATTTCGATAGCTCCGTATCGTATGGCACCAAC
CGAGTTAAAAGAATTGAAAGCTCAATTGCAAGAGTTGACGGATAGAGGTTTCGCTCGACCAAGTT
TCTCACCTTGGGGTGCACCAGTATTGTTT
Found at i:42326299 original size:24 final size:24
Alignment explanation
Indices: 42326257--42326305 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
42326247 AGATCGGCAT
**
42326257 AAGCCGAAATGCCGCAAAGCCGAA
1 AAGCCGAAATGCCAAAAAGCCGAA
* *
42326281 AAGCTGAAATGCCAAAAAGTCGAA
1 AAGCCGAAATGCCAAAAAGCCGAA
42326305 A
1 A
42326306 GTTTGGCTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.08
Consensus pattern (24 bp):
AAGCCGAAATGCCAAAAAGCCGAA
Found at i:42326558 original size:29 final size:28
Alignment explanation
Indices: 42326528--42326690 Score: 170
Period size: 29 Copynumber: 5.7 Consensus size: 28
42326518 ATAATGTGAT
**
42326528 TTGGGCCGGATGGGCCATATAAATGAGA
1 TTGGGCCTAATGGGCCATATAAATGAGA
* * *
42326556 TTTGGCCTAACGGGCCATATAAATGTGAA
1 TTGGGCCTAATGGGCCATATAAATGAG-A
*
42326585 TTGGGCCTAATGGGCTATATGAACATGA-A
1 TTGGGCCTAATGGGCCATAT-AA-ATGAGA
42326614 TTGGGCCTAATGGGCCATATGAACATGA-A
1 TTGGGCCTAATGGGCCATAT-AA-ATGAGA
*
42326643 TTGGGCC-AGATGGGCCATATAAATGAGG
1 TTGGGCCTA-ATGGGCCATATAAATGAGA
* *
42326671 TTGGGCCTAGTGAGCCATAT
1 TTGGGCCTAATGGGCCATAT
42326691 GTATGTATGT
Statistics
Matches: 116, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.03
28 41 0.35
29 66 0.57
30 2 0.02
31 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (28 bp):
TTGGGCCTAATGGGCCATATAAATGAGA
Found at i:42328459 original size:29 final size:29
Alignment explanation
Indices: 42328422--42328495 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
42328412 TGAATGTGAC
*
42328422 TGGGCCTAATAGGCCATATAAATGTAATT
1 TGGGCCTAATAGGCCATATAAAGGTAATT
* * *
42328451 TGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAATAGGCCATATAAAGGTAATT
*
42328480 TGGGCCTAACAGGCCA
1 TGGGCCTAATAGGCCA
42328496 ATGAATATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (29 bp):
TGGGCCTAATAGGCCATATAAAGGTAATT
Found at i:42331973 original size:27 final size:27
Alignment explanation
Indices: 42331939--42332116 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42331929 TAAATTGTAC
42331939 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42331966 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42331992 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42332020 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42332048 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42332075 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42332102 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42332117 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42332053 original size:82 final size:81
Alignment explanation
Indices: 42331940--42332095 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42331930 AAATTGTACA
* *
42331940 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42332004 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42332021 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42332086 TGCGAGTTGA
65 TGCGAATTGA
42332096 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42332107 original size:82 final size:81
Alignment explanation
Indices: 42331936--42332116 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42331926 AATTAAATTG
* *
42331936 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42332001 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42332017 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42332081 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42332099 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42332117 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42345650 original size:47 final size:45
Alignment explanation
Indices: 42345579--42346371 Score: 742
Period size: 46 Copynumber: 17.6 Consensus size: 45
42345569 CCCTTCGGGA
* * *
42345579 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCAGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
* *
42345626 CCTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
* * *
42345672 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCATCA-GC
*
42345719 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-CA--
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCATCAGC
** *
42345762 CTT-TCAC--AT-T-CA---TCACA-TCGGCCATTAGGCCTTATCA-C
1 CTTATCACATATATACACTTTCACATTCATCAATT-GGCC--ATCAGC
* * *
42345800 ATATAT-ACACT-T-T-CACATTCATCA--CATGGCCATTCGGCC-T----
1 CT-TATCACA-TATATACACTTTCA-CATTCAT--CAATT-GGCCATCAGC
*
42345840 --TATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
*
42345884 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
*
42345930 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
*
42345976 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
*
42346022 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
*
42346068 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
*
42346114 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
*
42346160 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
*
42346206 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
*
42346252 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCA-TCAGC
* *
42346298 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCA-ATTGGCCATCA-GC
42346345 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
42346372 TATTCAAATA
Statistics
Matches: 684, Mismatches: 27, Indels: 70
0.88 0.03 0.09
Matches are distributed among these distances:
33 2 0.00
34 7 0.01
35 5 0.01
36 1 0.00
37 6 0.01
38 11 0.02
39 9 0.01
40 12 0.02
41 7 0.01
42 4 0.01
43 4 0.01
44 4 0.01
45 2 0.00
46 501 0.73
47 109 0.16
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (45 bp):
CTTATCACATATATACACTTTCACATTCATCAATTGGCCATCAGC
Found at i:42345681 original size:46 final size:47
Alignment explanation
Indices: 42345579--42345759 Score: 265
Period size: 47 Copynumber: 3.9 Consensus size: 47
42345569 CCCTTCGGGA
* * ** * * *
42345579 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
*
42345626 CCTATCACATATATACACTTTCACATTCATCACAT-GGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
* *
42345672 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
42345719 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA
42345760 CACTTTCACA
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
46 43 0.35
47 79 0.65
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGC
Found at i:42345738 original size:93 final size:94
Alignment explanation
Indices: 42345579--42345759 Score: 267
Period size: 93 Copynumber: 1.9 Consensus size: 94
42345569 CCCTTCGGGA
* ** *
42345579 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCAGCCCTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTCAGCCCTATCACATATATACAC
42345644 TTTCACATTCATCACAT-GGCCATTCGGC
66 TTTCACATTCATCACATCGGCCATTCGGC
* * * *
42345672 CTTATCACATATATACACTTTCACATTCATCACATCGGCTA-TTAGGCCTTATCACATATATACA
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTCA-GCCCTATCACATATATACA
42345736 CTTTCACATTCATCACATCGGCCA
65 CTTTCACATTCATCACATCGGCCA
42345760 CACTTTCACA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.91
94 5 0.06
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTCAGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTCGGC
Found at i:42345765 original size:26 final size:26
Alignment explanation
Indices: 42345733--42345785 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
42345723 TCACATATAT
42345733 ACACTTTCACATTCATCACATCGGCC
1 ACACTTTCACATTCATCACATCGGCC
42345759 ACACTTTCACATTCATCACATCGGCC
1 ACACTTTCACATTCATCACATCGGCC
42345785 A
1 A
42345786 TTAGGCCTTA
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:0.28, C:0.38, G:0.08, T:0.26
Consensus pattern (26 bp):
ACACTTTCACATTCATCACATCGGCC
Found at i:42345765 original size:73 final size:72
Alignment explanation
Indices: 42345686--42345831 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 72
42345676 TCACATATAT
*
42345686 ACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCA
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
42345751 CATCGGCC
66 CAT-GGCC
42345759 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
42345824 CATGGCC
66 CATGGCC
42345831 A
1 A
42345832 TTCGGCCTTA
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 5 0.07
73 67 0.93
ACGTcount: A:0.29, C:0.32, G:0.08, T:0.31
Consensus pattern (72 bp):
ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
CATGGCC
Found at i:42345848 original size:46 final size:46
Alignment explanation
Indices: 42345759--42346371 Score: 1190
Period size: 46 Copynumber: 13.3 Consensus size: 46
42345749 CACATCGGCC
*
42345759 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACAT-GGCCATTCGGCCTTATCACATATAT
42345806 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
42345852 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
42345898 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
42345944 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
42345990 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
42346036 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
42346082 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
42346128 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
42346174 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
42346220 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
42346266 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
*
42346312 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
1 ACACTTTCACATTCATCACAT-GGCCATTCGGCCTTATCACATATAT
42346359 ACACTTTCACATT
1 ACACTTTCACATT
42346372 TATTCAAATA
Statistics
Matches: 563, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
46 505 0.90
47 58 0.10
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (46 bp):
ACACTTTCACATTCATCACATGGCCATTCGGCCTTATCACATATAT
Found at i:42350745 original size:223 final size:223
Alignment explanation
Indices: 42350094--42350758 Score: 1239
Period size: 220 Copynumber: 3.0 Consensus size: 223
42350084 TGTTGTTAGC
*
42350094 CAAAATTGAG-ATTTGGTGAGAGTTTTAATAGCCAATTGAGTATAATAAGGTGGAGAGATTTTAG
1 CAAAATTGAGAATTTGGTGAGAGTTTTAATAGCCAGTTGAGTATAATAAGGTGGAGAGATTTTAG
*
42350158 GAGAGGGATAAGGGAAGGAAAAAGGGGAGTTTGAGGTTTAGTGGAGTTGTACCGAATTTGGGGAG
66 GAGAGGGATAAGGGAAGGAAAAAGGGGAGTTTGAGGTTTAGTGGAGTTGTGCCGAATTTGGGGAG
*
42350223 TTGTGGATAGGGACTTTCGGCTGAGTGACTTTTCCCTAAGACTTTCGGTTTTGGCTACTCTTTTG
131 TTGTGGATAGGGACTTTCGGCTGAGTGACTTTTCCCTAAGACTTTCAGTTTTGGCTACTCTTTTG
*
42350288 GGGTTCTTTTCTCTATATTTTCTCTCAG
196 GGGTTCTTTTCTCTATATTTTCTCTCGG
42350316 CAAAATTGAGAATTTGGTGAGAGTTTTAATAGCCAGTTGAGTATAATAAGGTGGAGAGATTTTAG
1 CAAAATTGAGAATTTGGTGAGAGTTTTAATAGCCAGTTGAGTATAATAAGGTGGAGAGATTTTAG
42350381 GAGAGGGATAAGGG-A--AAAAAGGGGAGTTTGAGGTTTAGTGGAGTTGTGCCGAATTTGGGGAG
66 GAGAGGGATAAGGGAAGGAAAAAGGGGAGTTTGAGGTTTAGTGGAGTTGTGCCGAATTTGGGGAG
* *
42350443 TTATGGATAGGGACTTTCGGCTCAGTGACTTTTCCCTAAGACTTTCAGTTTTGGCTACTCTTTTG
131 TTGTGGATAGGGACTTTCGGCTGAGTGACTTTTCCCTAAGACTTTCAGTTTTGGCTACTCTTTTG
42350508 GGGTTCTTTTCTCTATATTTTCTCTCGG
196 GGGTTCTTTTCTCTATATTTTCTCTCGG
*
42350536 CAAAATTGAGAATTTAGTGAGAGTTTTAATAGCCAGTTGAGTATAATAAGGTGGAGAGATTTTAG
1 CAAAATTGAGAATTTGGTGAGAGTTTTAATAGCCAGTTGAGTATAATAAGGTGGAGAGATTTTAG
42350601 GAGAGGGATAAGGGAAGGAAAAAGGGGAGTTTGAGGTTTAGTGGAGTTGTGCCGAATTTGGGGAG
66 GAGAGGGATAAGGGAAGGAAAAAGGGGAGTTTGAGGTTTAGTGGAGTTGTGCCGAATTTGGGGAG
42350666 TTGTGGATAGGGACTTTCGGCTGAGTGACTTTTCCCTAAGACTTTCAGTTTTGGCTACTCTTTTG
131 TTGTGGATAGGGACTTTCGGCTGAGTGACTTTTCCCTAAGACTTTCAGTTTTGGCTACTCTTTTG
42350731 GGGTTCTTTTCTCTATATTTTCTCTCGG
196 GGGTTCTTTTCTCTATATTTTCTCTCGG
42350759 GTTTGTACAA
Statistics
Matches: 430, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
220 213 0.50
221 1 0.00
222 11 0.03
223 205 0.48
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.35
Consensus pattern (223 bp):
CAAAATTGAGAATTTGGTGAGAGTTTTAATAGCCAGTTGAGTATAATAAGGTGGAGAGATTTTAG
GAGAGGGATAAGGGAAGGAAAAAGGGGAGTTTGAGGTTTAGTGGAGTTGTGCCGAATTTGGGGAG
TTGTGGATAGGGACTTTCGGCTGAGTGACTTTTCCCTAAGACTTTCAGTTTTGGCTACTCTTTTG
GGGTTCTTTTCTCTATATTTTCTCTCGG
Found at i:42353252 original size:26 final size:28
Alignment explanation
Indices: 42353220--42353292 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 28
42353210 TCGATCATTG
**
42353220 AGCACTAAGTGTGCACGTTGG-TTTT-A
1 AGCACTAAGTGTGCAAATTGGATTTTCA
* *
42353246 AGTACTAAGTGTGCAAATTGGATTTTCG
1 AGCACTAAGTGTGCAAATTGGATTTTCA
42353274 AGCACTAAGTGTGCGAAAT
1 AGCACTAAGTGTGC-AAAT
42353293 CGGTTATTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 18 0.46
27 4 0.10
28 13 0.33
29 4 0.10
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCAAATTGGATTTTCA
Found at i:42353317 original size:28 final size:27
Alignment explanation
Indices: 42353190--42353317 Score: 116
Period size: 28 Copynumber: 4.7 Consensus size: 27
42353180 AATTTGATAC
* * *
42353190 TGAGCACTAAGTGTGTGAAATCGATCAT
1 TGAGCACTAAGTGTGCGAAATCGGT-TT
** *
42353218 TGAGCACTAAGTGTGC-ACGTTGGTTT
1 TGAGCACTAAGTGTGCGAAATCGGTTT
* * *
42353244 TAAGTACTAAGTGTGC-AAATTGGATTT
1 TGAGCACTAAGTGTGCGAAATCGG-TTT
42353271 TCGAGCACTAAGTGTGCGAAATCGGTTAT
1 T-GAGCACTAAGTGTGCGAAATCGGTT-T
*
42353300 TGAGCACTAAGTGCGCGA
1 TGAGCACTAAGTGTGCGA
42353318 GAAAATTTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
26 20 0.24
27 8 0.10
28 46 0.56
29 8 0.10
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
TGAGCACTAAGTGTGCGAAATCGGTTT
Found at i:42360078 original size:82 final size:82
Alignment explanation
Indices: 42359941--42360111 Score: 290
Period size: 82 Copynumber: 2.1 Consensus size: 82
42359931 TGCTAGATTT
* * *
42359941 TTTTAAAGTTGTAATAAGATTTCTATGTGATTTTGTGTATAAGGGACGAATTTGTAAAATTTTTG
1 TTTTAAAGTTGTAAGAAGATTTCTATGTGATTTTGTGTATAAAGGACGAAGTTGTAAAATTTTTG
*
42360006 AATAGAGAA-TGACTAGA
66 AATAGA-AAGGGACTAGA
42360023 TTTTAAAGTTGTAAGAAGATTTCTATGTGATTTTGTGTATAAAGGACGAAGTTGTAAAATTTTTG
1 TTTTAAAGTTGTAAGAAGATTTCTATGTGATTTTGTGTATAAAGGACGAAGTTGTAAAATTTTTG
42360088 AATAGAAAGGGACTAGA
66 AATAGAAAGGGACTAGA
42360105 TTTTAAA
1 TTTTAAA
42360112 TTAAATAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
81 2 0.02
82 82 0.98
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (82 bp):
TTTTAAAGTTGTAAGAAGATTTCTATGTGATTTTGTGTATAAAGGACGAAGTTGTAAAATTTTTG
AATAGAAAGGGACTAGA
Found at i:42360452 original size:57 final size:57
Alignment explanation
Indices: 42360378--42360486 Score: 200
Period size: 57 Copynumber: 1.9 Consensus size: 57
42360368 AATCGGATAG
42360378 TCGTGAAACGTAGTTCCCCGATATACGAAGTAAGTTTTTAAGCAATTAAGTCAATAA
1 TCGTGAAACGTAGTTCCCCGATATACGAAGTAAGTTTTTAAGCAATTAAGTCAATAA
* *
42360435 TCGTGAAACGTAGTTCCCCGATATACGAGGTAAGTTTTTAAGTAATTAAGTC
1 TCGTGAAACGTAGTTCCCCGATATACGAAGTAAGTTTTTAAGCAATTAAGTC
42360487 GAATTGGATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (57 bp):
TCGTGAAACGTAGTTCCCCGATATACGAAGTAAGTTTTTAAGCAATTAAGTCAATAA
Found at i:42360759 original size:26 final size:27
Alignment explanation
Indices: 42360685--42360759 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 27
42360675 TTTGATACAG
* *
42360685 AGCACTAAGTGTGCGAAATCGGTCATTG
1 AGCACTAAGTGTGC-AAATTGGTCATTA
** *
42360713 AGCACTAAGTGTGCACGTTGGT-TTTA
1 AGCACTAAGTGTGCAAATTGGTCATTA
*
42360739 AGCACTAAGTCTGCAAATTGG
1 AGCACTAAGTGTGCAAATTGG
42360760 ATTTCCGAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 20 0.51
27 5 0.13
28 14 0.36
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCAAATTGGTCATTA
Done.