Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 165 of 325
Found at i:52149365 original size:26 final size:26
Alignment explanation
Indices: 52149316--52149367 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
52149306 TACGTTACTG
**
52149316 TTACTGGCAGCTTTGCTGTGATATTA
1 TTACTGGCAGCTTTGCTGCAATATTA
52149342 TTACTGGCAGCTTTGCTGCAATATTA
1 TTACTGGCAGCTTTGCTGCAATATTA
52149368 GTGTGTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCAATATTA
Found at i:52155554 original size:19 final size:20
Alignment explanation
Indices: 52155530--52155567 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
52155520 GGTACCACCA
52155530 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
52155549 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
52155568 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:52155863 original size:46 final size:46
Alignment explanation
Indices: 52155796--52155963 Score: 169
Period size: 46 Copynumber: 3.6 Consensus size: 46
52155786 CGCCCCTAAG
* *
52155796 TGAACTCAGACTCAACTCAACGAGCTCGGGCATTCGTATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGTATCCATAAA
* * * * **
52155842 TGAACTCGGACTCAACTCAACGAGTT-TGG-ATGCCTAGTTACATCTCA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGTA--TCCAT-AAA
* * * * * *
52155889 CGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGTATCCATAAA
52155935 TGAACTCGGACTCAACTCAACGAGTTCGG
1 TGAACTCGGACTCAACTCAACGAGTTCGG
52155964 ATGCTCAACC
Statistics
Matches: 96, Mismatches: 21, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
44 5 0.05
45 2 0.02
46 55 0.57
47 30 0.31
48 1 0.01
49 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGTATCCATAAA
Found at i:52155908 original size:93 final size:93
Alignment explanation
Indices: 52155797--52155967 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
52155787 GCCCCTAAGT
* * *
52155797 GAACTCAGACTCAACTCAACGAGCTCGGGCATTCGTATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
*
52155862 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
52155890 GAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
52155955 CGAGTTCGGATGC
66 CGAGTTCGGATGC
52155968 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:52155983 original size:46 final size:45
Alignment explanation
Indices: 52155794--52155983 Score: 115
Period size: 46 Copynumber: 4.1 Consensus size: 45
52155784 CCCGCCCCTA
* * * * *
52155794 AGTGAACTCAGACTCAACTCAACGAGCTCGGGCATTCGT-ATCCAT-A
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GG-ATGC-TCAACCATCT
* *
52155840 AATGAACTCGGACTCAACTCAACGAGTTTGGATGC-CTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT
* * * * *
52155887 CA-CGAACTCGGACTCAACTCAACGAGTTCAGACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTC-G-GATGCT-CAACCATCT
52155933 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
52155979 AGTGA
1 AGTGA
52155984 CATGTCACTT
Statistics
Matches: 110, Mismatches: 18, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
44 12 0.11
45 5 0.05
46 59 0.54
47 28 0.25
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Found at i:52159627 original size:37 final size:37
Alignment explanation
Indices: 52159577--52159655 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
52159567 TTATTACGAA
* * *
52159577 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
52159614 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
52159651 GTCTT
1 GTCTT
52159656 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:52159861 original size:47 final size:47
Alignment explanation
Indices: 52159774--52160410 Score: 922
Period size: 47 Copynumber: 13.4 Consensus size: 47
52159764 CCTTTCGGGA
* * * * * * * * *
52159774 CTTATCACATTTATGCACTTTCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* * *
52159821 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
52159868 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
52159915 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
52159962 CTTAT-ACATATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
52160008 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
52160055 CTTAT-ACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
52160101 CTTATTACATATACATACACTTTCACATTCATCAC-TCGGCTATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
52160149 CTTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
52160196 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* *
52160243 CTTAT-ACATATATACATATACTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACA-CT--TTCACATTCATCACATCGGCTATTAGGC
*
52160292 CTTATCACATATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATAT--ATACACTTTCACATTCATCACATCGGCTATTAGGC
52160343 CTTATCACATATACATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCTATTAGGC
*
52160392 CTTATCACACATATACACT
1 CTTATCACATATATACACT
52160411 CTCTTGGCTG
Statistics
Matches: 549, Mismatches: 28, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
46 120 0.22
47 254 0.46
48 23 0.04
49 104 0.19
50 2 0.00
51 36 0.07
52 4 0.01
53 1 0.00
54 5 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:52160022 original size:93 final size:94
Alignment explanation
Indices: 52159774--52160410 Score: 922
Period size: 93 Copynumber: 6.7 Consensus size: 94
52159764 CCTTTCGGGA
* * * * * * * * * * *
52159774 CTTATCACATTTATGCACTTTCACATCCATTACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
52159839 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
52159868 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
52159933 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
52159962 CTTAT-ACATATATACACTTTCACATTCATCACGTCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
52160026 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
52160055 CTTAT-ACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATTACATATACATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATAT--ATAC
*
52160119 ACTTTCACATTCATCAC-TCGGCTATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
* * *
52160149 CTTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
*
52160214 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
52160243 CTTAT-ACATATATACATATACTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 CTTATCACATATATACA-CT--TTCACATTCATCACATCGGCTATTAGGCCTTATCAC--ATAT-
52160307 CATACACTTTCACATTCATCACATCGGCCATTAGGC
60 -ATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52160343 CTTATCACATATACATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATAC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATAC
52160408 ACT
64 ACT
52160411 CTCTTGGCTG
Statistics
Matches: 497, Mismatches: 32, Indels: 26
0.90 0.06 0.05
Matches are distributed among these distances:
93 169 0.34
94 125 0.25
95 70 0.14
96 41 0.08
98 6 0.01
100 74 0.15
101 6 0.01
102 1 0.00
103 5 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:52165058 original size:19 final size:20
Alignment explanation
Indices: 52165034--52165071 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
52165024 GGTACCACCA
52165034 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
52165053 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
52165072 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:52165467 original size:46 final size:46
Alignment explanation
Indices: 52165296--52165468 Score: 165
Period size: 46 Copynumber: 3.7 Consensus size: 46
52165286 AACCCGCCCC
* * * * *
52165296 TAAGTGAACTCAGACTCAACTCAACAAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * * *
52165342 TAAATGAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTTACATCTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATC-CA
* *
52165393 -CA---AACTTGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
*
52165435 TAAGTGAACTCGGACTCAACTTAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52165469 TGCTCAACCA
Statistics
Matches: 101, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 8 0.08
44 1 0.01
46 54 0.53
47 26 0.26
49 1 0.01
50 7 0.07
51 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:52167885 original size:20 final size:20
Alignment explanation
Indices: 52167860--52167907 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
52167850 AACTAACATG
52167860 GGCGTGGGCTACCATACACA
1 GGCGTGGGCTACCATACACA
52167880 GGCGTGGGCTACCATACACA
1 GGCGTGGGCTACCATACACA
52167900 GGCGTGGG
1 GGCGTGGG
52167908 AGAAGCGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.27, G:0.38, T:0.15
Consensus pattern (20 bp):
GGCGTGGGCTACCATACACA
Found at i:52168473 original size:52 final size:52
Alignment explanation
Indices: 52168395--52168498 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
52168385 TAGATATTCC
52168395 CGTAGCATTATTCTCATAGTCCTATTTTAATAAGTTAATATATTTTCTTTAG
1 CGTAGCATTATTCTCATAGTCCTATTTTAATAAGTTAATATATTTTCTTTAG
*
52168447 CGTAGCATTATTCTCATATTCCTATTTTAATAAGTTAATATATTTTCTTTAG
1 CGTAGCATTATTCTCATAGTCCTATTTTAATAAGTTAATATATTTTCTTTAG
52168499 TTATTTTAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (52 bp):
CGTAGCATTATTCTCATAGTCCTATTTTAATAAGTTAATATATTTTCTTTAG
Found at i:52182675 original size:30 final size:30
Alignment explanation
Indices: 52182641--52182701 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
52182631 TTCCCGAGCC
52182641 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
52182671 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
52182701 T
1 T
52182702 GAGTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:52189894 original size:49 final size:48
Alignment explanation
Indices: 52189822--52190015 Score: 192
Period size: 50 Copynumber: 3.9 Consensus size: 48
52189812 GCCGAAGCTA
* *
52189822 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAGCAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCA-CAG
* * *
52189871 TCTGGTACACGTAGTAGCCTGCACTTAGTACTGCACACGTGACCTCACCA-
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-C-CA-CAG
** * * * *
52189921 TCTAATACACGTAGTAGCCTGCACTTAGAACTACACACGTGATCACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCACAG
* * *
52189969 TTTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
52190016 TCACAATAGA
Statistics
Matches: 119, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
47 2 0.02
48 2 0.02
49 37 0.31
50 39 0.33
51 39 0.33
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (48 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCACAG
Found at i:52190016 original size:101 final size:99
Alignment explanation
Indices: 52189833--52190019 Score: 250
Period size: 101 Copynumber: 1.9 Consensus size: 99
52189823 CTGGTACGCA
* * * *
52189833 TAGTAGCCTGCACTTAGTACTACACATGCGACCAGCAGTCTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGAACTACACACGCGACCAGCAGTCGGGTACACATAGTAGCCTGCACTTA
* *
52189898 GTACTGCACACGTGACCTCACCATCTAATACACG
66 GTACTACACACGCGACCTCACCATCTAATACACG
* * *
52189932 TAGTAGCCTGCACTTAGAACTACACACGTGATCA-CAGTTTTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGAACTACACACGCGACCAGCAG---TCGGGTACACATAGTAGCCTGCAC
*
52189996 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACACGCGACCTCAC
52190020 AATAGATCAT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
98 3 0.04
99 30 0.40
101 42 0.56
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGAACTACACACGCGACCAGCAGTCGGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTCACCATCTAATACACG
Found at i:52190348 original size:14 final size:16
Alignment explanation
Indices: 52190316--52190354 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
52190306 ATTTACATAA
*
52190316 CATATATCACATATTT
1 CATATATCACATATGT
52190332 CATATATCAC-T-TGT
1 CATATATCACATATGT
52190346 CATATATCA
1 CATATATCA
52190355 TCATTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 1 0.05
16 10 0.45
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
CATATATCACATATGT
Found at i:52192198 original size:15 final size:15
Alignment explanation
Indices: 52192142--52192206 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
52192132 TAAAGATAAC
*
52192142 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
52192156 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
52192171 GAA-AAACCCAGAATA
1 -AAGAAATCCAGAATA
52192186 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
52192201 AAGAAA
1 AAGAAA
52192207 CCCAAGATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 11 0.26
15 29 0.67
16 3 0.07
ACGTcount: A:0.63, C:0.14, G:0.14, T:0.09
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:52192208 original size:30 final size:31
Alignment explanation
Indices: 52192142--52192210 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
52192132 TAAAGATAAC
*
52192142 AAGAAAACC-GAATAAAGAAATCCAAGATAG
1 AAGAAACCCAGAATAAAGAAATCCAAGATAG
52192172 AA-AAACCCAGAATAAAGAAATCC-AGAATA-
1 AAGAAACCCAGAATAAAGAAATCCAAG-ATAG
52192201 AAGAAACCCA
1 AAGAAACCCA
52192211 AGATACGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.61, C:0.17, G:0.13, T:0.09
Consensus pattern (31 bp):
AAGAAACCCAGAATAAAGAAATCCAAGATAG
Found at i:52195332 original size:51 final size:49
Alignment explanation
Indices: 52195201--52195341 Score: 167
Period size: 51 Copynumber: 2.8 Consensus size: 49
52195191 GAAGCTATCT
* *
52195201 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCG
* * * * *
52195250 AGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCG
* *
52195301 GGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACC
52195342 TCACAATAGA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
48 4 0.05
49 35 0.47
51 36 0.48
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.25
Consensus pattern (49 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCG
Found at i:52195662 original size:14 final size:16
Alignment explanation
Indices: 52195630--52195668 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
52195620 ATTTACATAA
*
52195630 CATATATCACATATTT
1 CATATATCACATATGT
52195646 CATATATCAC-T-TGT
1 CATATATCACATATGT
52195660 CATATATCA
1 CATATATCA
52195669 TCATTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 1 0.05
16 10 0.45
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
CATATATCACATATGT
Found at i:52197267 original size:41 final size:40
Alignment explanation
Indices: 52197222--52197298 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 40
52197212 TGTGTGAAAC
* * *
52197222 GTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTT
1 GTGTAAGACCATATCTGGGACAATGGAATCG-ATATGATTT
*
52197263 GTGTAAGACCCTATCTGGGACAATGGAATCGATATG
1 GTGTAAGACCATATCTGGGACAATGGAATCGATATG
52197299 TGATAGCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 5 0.16
41 27 0.84
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (40 bp):
GTGTAAGACCATATCTGGGACAATGGAATCGATATGATTT
Found at i:52198944 original size:16 final size:16
Alignment explanation
Indices: 52198923--52198955 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52198913 AAATATTCGA
52198923 ATGGTATGAATATGAT
1 ATGGTATGAATATGAT
52198939 ATGGTATGAATATGAT
1 ATGGTATGAATATGAT
52198955 A
1 A
52198956 GTAAATAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (16 bp):
ATGGTATGAATATGAT
Found at i:52199481 original size:32 final size:32
Alignment explanation
Indices: 52199419--52199482 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
52199409 CACAAAGAAA
* ***
52199419 GAAGAAAATAAATGAACACTCTAGTTGTGTTT
1 GAAGAAAATAAATGAACACTCCACCCGTGTTT
52199451 GAAGAAAATAAATGAACACTCCACCCGTGTTT
1 GAAGAAAATAAATGAACACTCCACCCGTGTTT
52199483 CACTACGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.27
Consensus pattern (32 bp):
GAAGAAAATAAATGAACACTCCACCCGTGTTT
Found at i:52202417 original size:16 final size:16
Alignment explanation
Indices: 52202396--52202427 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52202386 TTGGTAAATC
52202396 CTGAAATACCGAAAAG
1 CTGAAATACCGAAAAG
52202412 CTGAAATACCGAAAAG
1 CTGAAATACCGAAAAG
52202428 TCAAAATTTT
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:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
CTGAAATACCGAAAAG
Found at i:52202697 original size:29 final size:29
Alignment explanation
Indices: 52202653--52202730 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
52202643 ACTATGTATT
52202653 TGATTTGGGCCTAATGGGCCATACGAATG
1 TGATTTGGGCCTAATGGGCCATACGAATG
* *
52202682 TGATTTGGGCCCAATGGGCCATATGAATG
1 TGATTTGGGCCTAATGGGCCATACGAATG
*
52202711 AGA-TTGGGCCTAATGGGCCA
1 TGATTTGGGCCTAATGGGCCA
52202731 ATGGGCCATA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 16 0.36
29 29 0.64
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (29 bp):
TGATTTGGGCCTAATGGGCCATACGAATG
Found at i:52203821 original size:17 final size:18
Alignment explanation
Indices: 52203788--52203821 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52203778 TTTAAGGAAG
52203788 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
52203806 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
52203822 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:52213215 original size:38 final size:38
Alignment explanation
Indices: 52213165--52213324 Score: 198
Period size: 38 Copynumber: 4.2 Consensus size: 38
52213155 CAGACTATAA
52213165 GCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTCAT
1 GCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCAT
*
52213203 GCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCGT
1 GCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCAT
* *
52213241 GCTGGTATTATATCCGGGTTAAATCCCGCAGGCCT-AGT
1 GCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCA-T
* * * * *
52213279 GCTGGTATTATATCTGAGTTTAAAGTCCCGTAGGCTTCGT
1 GCTGGTAATATATCCG-GGTTAAA-TCCCGCAGGCTTCAT
52213319 GCTGGT
1 GCTGGT
52213325 GTTATGTTTG
Statistics
Matches: 108, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
38 83 0.77
39 8 0.07
40 17 0.16
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (38 bp):
GCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCAT
Found at i:52213263 original size:76 final size:78
Alignment explanation
Indices: 52213165--52213329 Score: 237
Period size: 76 Copynumber: 2.1 Consensus size: 78
52213155 CAGACTATAA
* *
52213165 GCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCA-TGCTGGTAATATATCCG-GGTTAAA-T
1 GCTGGTATTATATCCGGGTTAAATCCCGCAGGCCT-AGTGCTGGTAATATATCCGAGGTTAAAGT
52213227 CCCGCAGGCTTCGT
65 CCCGCAGGCTTCGT
* * *
52213241 GCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTATATCTGAGTTTAAAGTC
1 GCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTAATATATCCGAGGTTAAAGTC
*
52213306 CCGTAGGCTTCGT
66 CCGCAGGCTTCGT
*
52213319 GCTGGTGTTAT
1 GCTGGTATTAT
52213330 GTTTGGGTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
75 1 0.01
76 48 0.61
77 6 0.08
78 24 0.30
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (78 bp):
GCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTAATATATCCGAGGTTAAAGTC
CCGCAGGCTTCGT
Found at i:52214360 original size:33 final size:33
Alignment explanation
Indices: 52214318--52214382 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
52214308 ATGGGTTGTA
52214318 GGGCCCATAACAGGCAAAATTGGCAACTTGATC
1 GGGCCCATAACAGGCAAAATTGGCAACTTGATC
* *
52214351 GGGCCCATAATAGGTAAAATTGGCAACTTGAT
1 GGGCCCATAACAGGCAAAATTGGCAACTTGAT
52214383 ACTAAGTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (33 bp):
GGGCCCATAACAGGCAAAATTGGCAACTTGATC
Found at i:52214498 original size:28 final size:29
Alignment explanation
Indices: 52214416--52214504 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 29
52214406 AAAGCATGAC
* *
52214416 TATGTATGCGATTTGGGCCTAATGGGCCA
1 TATGAATGAGATTTGGGCCTAATGGGCCA
* * * *
52214445 TACGAATGTGATTTGGGCCCAATGGGTCA
1 TATGAATGAGATTTGGGCCTAATGGGCCA
*
52214474 TATGAATGAGA-TTGGGCCTAGTGGGCCA
1 TATGAATGAGATTTGGGCCTAATGGGCCA
52214502 TAT
1 TAT
52214505 ACATGTATGT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 17 0.34
29 33 0.66
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (29 bp):
TATGAATGAGATTTGGGCCTAATGGGCCA
Found at i:52215198 original size:17 final size:18
Alignment explanation
Indices: 52215165--52215198 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52215155 TTTAAGGAAG
52215165 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
52215183 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
52215199 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:52216670 original size:47 final size:46
Alignment explanation
Indices: 52216584--52216683 Score: 114
Period size: 47 Copynumber: 2.2 Consensus size: 46
52216574 TATCTTAATC
* *
52216584 TAAGACACATTAAAAAGCTATACTTATTATAACATATTAATTAAACT
1 TAAGGCACATTAAAAAGCTATACTTAATATAACATATTAA-TAAACT
* * *
52216631 TAAGGCACATTAAAATGCTGTAC-TAAT-TAACATGCATTAATAGACT
1 TAAGGCACATTAAAAAGCTATACTTAATATAACAT--ATTAATAAACT
52216677 TAAGGCA
1 TAAGGCA
52216684 TATTTAAGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
45 6 0.13
46 15 0.33
47 25 0.54
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (46 bp):
TAAGGCACATTAAAAAGCTATACTTAATATAACATATTAATAAACT
Found at i:52218472 original size:12 final size:11
Alignment explanation
Indices: 52218449--52218489 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
52218439 ACGGTATTGT
*
52218449 AATTTGAAAAA
1 AATTTCAAAAA
52218460 AATTTCAAAAA
1 AATTTCAAAAA
52218471 AATTTCAAAAA
1 AATTTCAAAAA
*
52218482 AAATTCAA
1 AATTTCAA
52218490 TATCCATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (11 bp):
AATTTCAAAAA
Found at i:52224536 original size:27 final size:27
Alignment explanation
Indices: 52224505--52224682 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
52224495 TAAATTGTAC
*
52224505 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
52224532 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
52224558 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
52224586 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
52224613 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
52224641 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
52224668 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52224683 GACTAATATA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:52224566 original size:54 final size:55
Alignment explanation
Indices: 52224505--52224682 Score: 236
Period size: 54 Copynumber: 3.3 Consensus size: 55
52224495 TAAATTGTAC
* **
52224505 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* * * *
52224560 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
* *
52224613 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
*
52224668 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52224683 GACTAATATA
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT
Found at i:52232505 original size:39 final size:41
Alignment explanation
Indices: 52232404--52232587 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
52232394 TTGAATGATG
* *
52232404 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
52232444 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
52232484 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
52232523 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
52232562 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
52232588 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:52232540 original size:79 final size:80
Alignment explanation
Indices: 52232404--52232587 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
52232394 TTGAATGATG
*
52232404 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
52232468 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
52232483 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
52232545 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
52232562 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
52232588 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:52232610 original size:78 final size:79
Alignment explanation
Indices: 52232457--52232620 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
52232447 GGACTAAGAT
* **
52232457 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
52232522 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
52232536 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
52232598 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
52232614 CCGAAGG
1 CCGAAGG
52232621 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:52235675 original size:36 final size:35
Alignment explanation
Indices: 52235643--52235810 Score: 127
Period size: 40 Copynumber: 4.6 Consensus size: 35
52235633 GAGCTAATTT
52235643 CCGAAGCATT-TGCGAGATACTAATTCCGGCTAAGC
1 CCGAAGCATTGTGCGAG-TACTAATTCCGGCTAAGC
52235678 CCGAAGCATTGTGCGAGTACTAATTCCGG----GC
1 CCGAAGCATTGTGCGAGTACTAATTCCGGCTAAGC
*
52235709 TCCGAAGGCATTTGTGCGA-TAC-AA-TCCGGGTTAAGTC
1 -CCGAA-GCA-TTGTGCGAGTACTAATTCC-GGCTAAG-C
* *
52235746 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAA-GCA-TTGTGCGAG-TACTAATTCC-GGCTAAG-C
52235786 CCGAAGGCATTTGTGCGAGTTACTA
1 CCGAA-GCA-TTGTGCGAG-TACTA
52235811 TAACCGGGCT
Statistics
Matches: 119, Mismatches: 0, Indels: 23
0.84 0.00 0.16
Matches are distributed among these distances:
31 5 0.04
32 9 0.08
33 6 0.05
34 8 0.07
35 22 0.18
36 25 0.21
37 1 0.01
38 3 0.03
39 2 0.02
40 38 0.32
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (35 bp):
CCGAAGCATTGTGCGAGTACTAATTCCGGCTAAGC
Found at i:52235730 original size:68 final size:70
Alignment explanation
Indices: 52235642--52235778 Score: 176
Period size: 68 Copynumber: 2.0 Consensus size: 70
52235632 AGAGCTAATT
*
52235642 TCCGAAGCATTTGCGAGATACTAATTCC-GGCTAAG-CCCGAA-GCA-TTGTGCGAG-TACTAAT
1 TCCGAAGCATTTGCGAGATAC-AA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
52235702 TCCGGGC
64 TCCGGGC
* * *
52235709 TCCGAAGGCATTTGTGCGATACAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 TCCGAA-GCATTTGCGAGATACAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
52235774 CCGGG
65 CCGGG
52235779 TTAAGTCCCG
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
66 3 0.05
67 14 0.23
68 19 0.32
69 3 0.05
70 9 0.15
71 12 0.20
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (70 bp):
TCCGAAGCATTTGCGAGATACAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC
CGGGC
Found at i:52235786 original size:40 final size:40
Alignment explanation
Indices: 52235710--52235838 Score: 196
Period size: 40 Copynumber: 3.3 Consensus size: 40
52235700 ATTCCGGGCT
52235710 CCGAAGGCATTTGTGCGA--TAC--AATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
52235746 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
* *
52235786 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTC
52235826 CCGAAGGCATTTG
1 CCGAAGGCATTTG
52235839 AACGAGGAGC
Statistics
Matches: 86, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
36 18 0.21
38 3 0.03
40 63 0.73
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:52235856 original size:80 final size:75
Alignment explanation
Indices: 52235710--52235871 Score: 182
Period size: 80 Copynumber: 2.1 Consensus size: 75
52235700 ATTCCGGGCT
* * ** *
52235710 CCGAAGGCATTTGTGCGATACAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC
1 CCGAAGGCATTTGTGCGATACAAACCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATC
*
52235775 CGGGTTAAGTC
66 C-GGTTAAATC
*
52235786 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCT
1 CCGAAGGCATTTGTGCGA--TAC-A-AACCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CT
* *
52235850 ATATCCGGTTAAATT
61 AAATCCGGTTAAATC
52235865 CCGAAGG
1 CCGAAGG
52235872 TACGTGATTT
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
76 18 0.25
78 3 0.04
79 16 0.22
80 35 0.49
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (75 bp):
CCGAAGGCATTTGTGCGATACAAACCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATC
CGGTTAAATC
Found at i:52242381 original size:20 final size:20
Alignment explanation
Indices: 52242356--52242405 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
52242346 CTATTTGGCA
*
52242356 GGCCGTGTGCTCGACGAGAT
1 GGCCGTGGGCTCGACGAGAT
52242376 GGCCGTGGGCTCGACGAGAT
1 GGCCGTGGGCTCGACGAGAT
52242396 GGCCGTGGGC
1 GGCCGTGGGC
52242406 GCTTTCATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.26, G:0.46, T:0.16
Consensus pattern (20 bp):
GGCCGTGGGCTCGACGAGAT
Found at i:52244454 original size:18 final size:16
Alignment explanation
Indices: 52244415--52244459 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
52244405 ATGAAATTGG
52244415 GAAAAGAAAAA-AAAT
1 GAAAAGAAAAAGAAAT
52244430 G-AAAGAAAAAGAAATT
1 GAAAAGAAAAAGAAA-T
52244446 GAAAAAGAAAAAGA
1 G-AAAAGAAAAAGA
52244460 GAGTGAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
16 2 0.08
18 11 0.42
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.07
Consensus pattern (16 bp):
GAAAAGAAAAAGAAAT
Found at i:52249465 original size:28 final size:28
Alignment explanation
Indices: 52249399--52249468 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
52249389 ATATTTTCCT
*
52249399 TCGCACACTTAGTGCTCGATAATCAAAC
1 TCGCACACTTAGTGCTCGATAACCAAAC
*
52249427 TTGCACACTTAGTGCTC-ATTAACCAAAC
1 TCGCACACTTAGTGCTCGA-TAACCAAAC
**
52249455 TCGCATGCTTAGTG
1 TCGCACACTTAGTG
52249469 AAATTTTCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 1 0.03
28 35 0.97
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (28 bp):
TCGCACACTTAGTGCTCGATAACCAAAC
Found at i:52253906 original size:42 final size:43
Alignment explanation
Indices: 52253818--52253967 Score: 146
Period size: 42 Copynumber: 3.5 Consensus size: 43
52253808 CAATGCTGAC
* * *
52253818 GTCCCAGAC-GTGGTCTTACATGTAATTCAGTATCGATGCCTTT
1 GTCCCAGACAG-GGTCTTACACGTAAGTCAGTATCGATGCCTAT
*
52253861 GTCCTAGACAGGGTCTTACACG-AAGTCAGATAT-GATGCCTAT
1 GTCCCAGACAGGGTCTTACACGTAAGTCAG-TATCGATGCCTAT
* * * * *
52253903 GTCCCAGACAGGGTCTTACACATAAATCTCA-AATCGAGGCCTGT
1 GTCCCAGACAGGGTCTTACACGT-AA-GTCAGTATCGATGCCTAT
*
52253947 GTCCCAGACACGGTCTTACAC
1 GTCCCAGACAGGGTCTTACAC
52253968 AATATCTCAG
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
42 34 0.38
43 23 0.26
44 30 0.33
45 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (43 bp):
GTCCCAGACAGGGTCTTACACGTAAGTCAGTATCGATGCCTAT
Found at i:52260920 original size:18 final size:18
Alignment explanation
Indices: 52260897--52260943 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
52260887 GGACTTGCAT
52260897 ACTGTTTACTGTTACCGC
1 ACTGTTTACTGTTACCGC
**
52260915 ACTGTTTACTGTTATTGC
1 ACTGTTTACTGTTACCGC
*
52260933 ACTATTTACTG
1 ACTGTTTACTG
52260944 CTACTGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (18 bp):
ACTGTTTACTGTTACCGC
Found at i:52263771 original size:27 final size:27
Alignment explanation
Indices: 52263741--52263857 Score: 162
Period size: 27 Copynumber: 4.3 Consensus size: 27
52263731 GGGGTATTTT
52263741 AGTCATTTTACCATATAAGGGCAAAAC
1 AGTCATTTTACCATATAAGGGCAAAAC
* * *
52263768 AGTCATTTTATCATATAAAGGTAAAAC
1 AGTCATTTTACCATATAAGGGCAAAAC
* *
52263795 AATCATTTTACCAAATAAGGGCAAAAC
1 AGTCATTTTACCATATAAGGGCAAAAC
* * *
52263822 AGTCATGTTACCATATAAGAGCAAAAT
1 AGTCATTTTACCATATAAGGGCAAAAC
52263849 AGTCATTTT
1 AGTCATTTT
52263858 GATCAACTAG
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 76 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (27 bp):
AGTCATTTTACCATATAAGGGCAAAAC
Found at i:52277487 original size:79 final size:80
Alignment explanation
Indices: 52277294--52277496 Score: 322
Period size: 79 Copynumber: 2.5 Consensus size: 80
52277284 ATTCGGATTG
*
52277294 ATAACCGGGCTAAGTCCCGAAGGCATTTGTA-CGAGTTACTATATCCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG-AGCGAGTTACTATATACGGGCTAAGTCCCGAAGGC
*
52277358 ATTTGTGCGAGTTACT
65 AATTGTGCGAGTTACT
* *
52277374 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATA-ACGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATATACGGGCTAAGTCCCGAAGGCA
52277438 ATTGTGCGAGTTACT
66 ATTGTGCGAGTTACT
*
52277453 ATAACCGGGCTAAGTCCCGAAGGTATTTGAGCGAG-TAGCTATAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTA-CTATAT
52277497 CCGGTTAAAC
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
78 2 0.02
79 71 0.63
80 40 0.35
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTTACTATATACGGGCTAAGTCCCGAAGGCA
ATTGTGCGAGTTACT
Found at i:52277495 original size:40 final size:40
Alignment explanation
Indices: 52277294--52277488 Score: 329
Period size: 40 Copynumber: 4.9 Consensus size: 40
52277284 ATTCGGATTG
*
52277294 ATAACCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52277334 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52277374 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52277414 ATAA-CGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
52277453 ATAACCGGGCTAAGTCCCGAAGGTATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
52277489 AGCTATATCC
Statistics
Matches: 147, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
39 39 0.27
40 108 0.73
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:52285464 original size:85 final size:76
Alignment explanation
Indices: 52285293--52285489 Score: 238
Period size: 85 Copynumber: 2.5 Consensus size: 76
52285283 ATTCGGATTG
*
52285293 ATAACCGGGCTAAGTCCCG-AGGCATTTGTGCGAGTTACTATATCCGGGCAAGCCCGAAGGCATT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCAAGCCCGAAGGCATT
52285357 GTGGAGTTTACT
66 GTGGAG-TTACT
*
52285369 ATCACCGGGCTAAGTCCCGAAGG-ATAATTGTGGCGAGTTAACTATAACGCGGGCTAAGTCCCGA
1 ATAACCGGGCTAAGTCCCGAAGGCAT--TTGT-GCGAGTT-ACTATAAC-CGGGC-AAG-CCCG-
52285433 AAGGCAATTGTGCGAG-TACT
58 AAGGC-ATTGTG-GAGTTACT
*
52285453 ATAACGCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 ATAAC-CGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
52285490 AGCTATATCC
Statistics
Matches: 104, Mismatches: 4, Indels: 19
0.82 0.03 0.15
Matches are distributed among these distances:
76 20 0.19
77 3 0.03
78 4 0.04
79 7 0.07
80 7 0.07
81 5 0.05
82 3 0.03
83 10 0.10
84 16 0.15
85 24 0.23
86 5 0.05
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (76 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCAAGCCCGAAGGCATT
GTGGAGTTACT
Found at i:52285496 original size:41 final size:40
Alignment explanation
Indices: 52285293--52285489 Score: 237
Period size: 41 Copynumber: 4.9 Consensus size: 40
52285283 ATTCGGATTG
52285293 ATAACCGGGCTAAGTCCCG-AGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
52285332 ATATCCGGGC-AAG-CCCGAAGGCA-TTGTG-GAGTTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TTACT
*
52285369 ATCACCGGGCTAAGTCCCGAAGG-ATAATTGTGGCGAGTTAACT
1 ATAACCGGGCTAAGTCCCGAAGGCAT--TTGT-GCGAGTT-ACT
*
52285412 ATAACGCGGGCTAAGTCCCGAAAGGCAATTGTGCGAG-TACT
1 ATAAC-CGGGCTAAGTCCCG-AAGGCATTTGTGCGAGTTACT
*
52285453 ATAACGCGGGCTAAGTCCCGAAGGCATTTGAGCGAGT
1 ATAAC-CGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
52285490 AGCTATATCC
Statistics
Matches: 137, Mismatches: 7, Indels: 26
0.81 0.04 0.15
Matches are distributed among these distances:
36 3 0.02
37 22 0.16
38 12 0.09
39 17 0.12
40 14 0.10
41 27 0.20
42 4 0.03
43 15 0.11
44 18 0.13
45 4 0.03
46 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:52294662 original size:1 final size:1
Alignment explanation
Indices: 52294656--52294796 Score: 282
Period size: 1 Copynumber: 141.0 Consensus size: 1
52294646 GAGGAGCACA
52294656 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
52294721 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
52294786 CCCCCCCCCCC
1 CCCCCCCCCCC
52294797 TAGGCGTGGG
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 140 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:52298282 original size:24 final size:25
Alignment explanation
Indices: 52298226--52298289 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
52298216 AGGAAGTGCC
52298226 AAAGGGCTTTGCCCCAGTTTACCAA
1 AAAGGGCTTTGCCCCAGTTTACCAA
*
52298251 AAAGGGCTTTGCCCCAGTTTA-CGA
1 AAAGGGCTTTGCCCCAGTTTACCAA
52298275 AAAGGGCTTTGCCCC
1 AAAGGGCTTTGCCCC
52298290 TGTAACACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 17 0.45
25 21 0.55
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (25 bp):
AAAGGGCTTTGCCCCAGTTTACCAA
Found at i:52309316 original size:30 final size:31
Alignment explanation
Indices: 52309282--52309364 Score: 116
Period size: 30 Copynumber: 2.7 Consensus size: 31
52309272 CATTTACAGC
52309282 AAAGGCTTCGGCCTAGTGATATG-ATAATGA
1 AAAGGCTTCGGCCTAGTGATATGAATAATGA
* * *
52309312 AAAGGGTTCGGCCTAGTGACATGAATAATGC
1 AAAGGCTTCGGCCTAGTGATATGAATAATGA
*
52309343 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCTAGTGATATG
52309365 TTGAGATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 25 0.54
31 21 0.46
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCTAGTGATATGAATAATGA
Found at i:52315647 original size:10 final size:11
Alignment explanation
Indices: 52315632--52315700 Score: 67
Period size: 11 Copynumber: 6.7 Consensus size: 11
52315622 ATTTTGATAT
*
52315632 ACATGATTTG-
1 ACATGATATGC
52315642 ACATGATATGC
1 ACATGATATGC
52315653 ACATGATATG-
1 ACATGATATGC
* *
52315663 -TATGATATAC
1 ACATGATATGC
52315673 ACATGATATG-
1 ACATGATATGC
*
52315683 -TATGATATGC
1 ACATGATATGC
52315693 ACATGATA
1 ACATGATA
52315701 AATTCATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
9 15 0.32
10 9 0.19
11 23 0.49
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (11 bp):
ACATGATATGC
Found at i:52315669 original size:20 final size:20
Alignment explanation
Indices: 52315644--52315700 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
52315634 ATGATTTGAC
52315644 ATGATATGCACATGATATGT
1 ATGATATGCACATGATATGT
*
52315664 ATGATATACACATGATATGT
1 ATGATATGCACATGATATGT
52315684 ATGATATGCACATGATA
1 ATGATATGCACATGATA
52315701 AATTCATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (20 bp):
ATGATATGCACATGATATGT
Found at i:52315780 original size:25 final size:25
Alignment explanation
Indices: 52315748--52315817 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
52315738 GAGGAAGTGC
*
52315748 AAAAGGGCTTTGCCCTAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
52315773 AAAAGGGCTTTGCCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
52315798 AAAAGGGCTTTACCTCAGTT
1 AAAAGGGCTTTGCCCCAGTT
52315818 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:52316072 original size:30 final size:31
Alignment explanation
Indices: 52316037--52316118 Score: 123
Period size: 30 Copynumber: 2.7 Consensus size: 31
52316027 CGTTTACAGT
52316037 AAAGGCTTTGGCCCAGTGATATG-ATAATGA
1 AAAGGCTTTGGCCCAGTGATATGAATAATGA
* *
52316067 AAAGGCTTTGGCCCAGTGACATGAATAATGC
1 AAAGGCTTTGGCCCAGTGATATGAATAATGA
*
52316098 AAAGGCTTCGGCCCAGT-ATAT
1 AAAGGCTTTGGCCCAGTGATAT
52316119 ATTGAGATTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
30 25 0.53
31 22 0.47
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (31 bp):
AAAGGCTTTGGCCCAGTGATATGAATAATGA
Found at i:52318009 original size:30 final size:30
Alignment explanation
Indices: 52317951--52318011 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52317941 TTCCCGAGCC
*
52317951 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTATAAATATGCAAAAGTT
* * * *
52317981 TAGGGGCAAAATTATAATTTTGCCAAAGTT
1 TAGGGGCAAAAGTATAAATATGCAAAAGTT
52318011 T
1 T
52318012 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTATAAATATGCAAAAGTT
Found at i:52318787 original size:68 final size:64
Alignment explanation
Indices: 52318671--52318928 Score: 204
Period size: 68 Copynumber: 3.9 Consensus size: 64
52318661 TGGATGATAC
* * * * *
52318671 AGATAGTATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGT-GTACAAGAGAGCTAC
1 AGATA-TATGTAGCTAGGTCACATGGATGATACTGAGTGTACACCATGTAG-ACAAGAGAGCTAC
52318735 AAG
64 --G
* * *
52318738 ACATTATGATGTAGCTAGGTCACATGGGTGATACT-ATGTGTACACCATGTAGACAAGAGACCTA
1 AGA-TAT-ATGTAGCTAGGTCACATGGATGATACTGA-GTGTACACCATGTAGACAAGAGAGCTA
52318802 CG
63 CG
* * * * *
52318804 TGATATATGTAGCTAGGTCGCATGCATGGTTCCAGGTGAAG-G-ACACCATGTAGACAAGAGAGC
1 AGATATATGTAGCTAGGTCACATGGAT-GAT--A-CTG-AGTGTACACCATGTAGACAAGAGAGC
52318867 TACG
61 TACG
* * * *
52318871 AGATAAAT-TGGCTAGGTCACATGGGTGATACTGAGTGTTCACCATGT-GTACAAGAGAG
1 AGATATATGTAGCTAGGTCACATGGATGATACTGAGTGTACACCATGTAG-ACAAGAGAG
52318929 TCGAACAATA
Statistics
Matches: 153, Mismatches: 25, Indels: 30
0.74 0.12 0.14
Matches are distributed among these distances:
61 2 0.01
62 4 0.03
63 18 0.12
64 18 0.12
65 7 0.05
66 16 0.10
67 35 0.23
68 50 0.33
69 2 0.01
70 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (64 bp):
AGATATATGTAGCTAGGTCACATGGATGATACTGAGTGTACACCATGTAGACAAGAGAGCTACG
Found at i:52320662 original size:16 final size:17
Alignment explanation
Indices: 52320635--52320669 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
52320625 ATTCCCCTTT
52320635 CACCTATTCATTCAACA
1 CACCTATTCATTCAACA
*
52320652 CACCT-TTCATTCCACA
1 CACCTATTCATTCAACA
52320668 CA
1 CA
52320670 TCTCTCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (17 bp):
CACCTATTCATTCAACA
Found at i:52321915 original size:24 final size:24
Alignment explanation
Indices: 52321883--52321930 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
52321873 TTGTTGAAAG
52321883 CATACATGGCAAAAACTGACTCCT
1 CATACATGGCAAAAACTGACTCCT
52321907 CATACATGGCAAAAACTGACTCCT
1 CATACATGGCAAAAACTGACTCCT
52321931 TGATCCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (24 bp):
CATACATGGCAAAAACTGACTCCT
Found at i:52324401 original size:43 final size:42
Alignment explanation
Indices: 52324353--52324518 Score: 158
Period size: 43 Copynumber: 3.9 Consensus size: 42
52324343 TTATTGAGAA
* *
52324353 GTGATTACATGTAAGACCATGTTTGGAACATTGGCATTATATT
1 GTGATTACATGTAAGACCATGTCTGGGACATTGGCATTATA-T
* *
52324396 GTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCATTAAT
1 GTGATTACATGTAAGACCATGTCTGGGACATTGGCATTA-T-AT
* * * * *
52324440 -CGATTTCGTATAAGACTC-TGTCTGGGACAGTGGCATTGATAT
1 GTGATTACATGTAAGAC-CATGTCTGGGACATTGGCATT-ATAT
* * *
52324482 GTGATAACATGTAAGACCATATCTGGGATA-TGGCATT
1 GTGATTACATGTAAGACCATGTCTGGGACATTGGCATT
52324519 GTACAAGCTA
Statistics
Matches: 101, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
42 10 0.10
43 86 0.85
44 4 0.04
45 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (42 bp):
GTGATTACATGTAAGACCATGTCTGGGACATTGGCATTATAT
Found at i:52325052 original size:28 final size:28
Alignment explanation
Indices: 52325002--52325056 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 28
52324992 CAGGGATTTC
52325002 CACACAGCCTGACACACATCCGTGTCCCT
1 CACACAGCCTGACACACA-CCGTGTCCCT
52325031 CACACAGCCATGACACAC-CCGTGTCC
1 CACACAGCC-TGACACACACCGTGTCC
52325057 TAGCCCGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 8 0.32
29 9 0.36
30 8 0.32
ACGTcount: A:0.25, C:0.45, G:0.15, T:0.15
Consensus pattern (28 bp):
CACACAGCCTGACACACACCGTGTCCCT
Found at i:52335628 original size:25 final size:25
Alignment explanation
Indices: 52335557--52335632 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 25
52335547 GGAACACATT
* *
52335557 TTCA-CAAAATTTTACCAGGGGCAAA
1 TTCATCAAAATTTTACTA-GGGTAAA
* *
52335582 ATCGTCAAAATTTTACTAAGGGTAAA
1 TTCATCAAAATTTTACT-AGGGTAAA
52335608 TTCATCAAAATTTTACTAGGGTAAA
1 TTCATCAAAATTTTACTAGGGTAAA
52335633 ATAGGGATGA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
25 10 0.23
26 32 0.74
27 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (25 bp):
TTCATCAAAATTTTACTAGGGTAAA
Found at i:52336763 original size:27 final size:27
Alignment explanation
Indices: 52336686--52336764 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
52336676 GACTATCTTC
* * *
52336686 TGTTTAATGTCCCATTAGACTATCCCG
1 TGTTTAACGTCCTATTAGACTATCCCA
* * * *
52336713 TGTTTAACGTCCTCTCAAAGTATCCCA
1 TGTTTAACGTCCTATTAGACTATCCCA
* *
52336740 TGTTTAACGTCCTGTTAGATTATCC
1 TGTTTAACGTCCTATTAGACTATCC
52336765 TTGATGTCAT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (27 bp):
TGTTTAACGTCCTATTAGACTATCCCA
Found at i:52339111 original size:17 final size:17
Alignment explanation
Indices: 52339089--52339124 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
52339079 GAATTAATGG
52339089 TAAGTTTTCTTATTAAC
1 TAAGTTTTCTTATTAAC
52339106 TAAGTTTTCTTATTAAC
1 TAAGTTTTCTTATTAAC
52339123 TA
1 TA
52339125 TACAAGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.53
Consensus pattern (17 bp):
TAAGTTTTCTTATTAAC
Found at i:52343437 original size:15 final size:15
Alignment explanation
Indices: 52343391--52343438 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
52343381 AAACCTACAA
*
52343391 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
52343406 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
52343420 AAACTTCATATCCAT
1 AAACTTCATATCCAT
52343435 AAAC
1 AAAC
52343439 CCACCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:52343674 original size:10 final size:10
Alignment explanation
Indices: 52343659--52343685 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
52343649 AAGTAAGTTT
52343659 AAAAAAAACG
1 AAAAAAAACG
52343669 AAAAAAAACG
1 AAAAAAAACG
52343679 AAAAAAA
1 AAAAAAA
52343686 TTTCAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAACG
Found at i:52355431 original size:48 final size:48
Alignment explanation
Indices: 52355358--52355599 Score: 439
Period size: 48 Copynumber: 5.0 Consensus size: 48
52355348 CAAGATAAAT
52355358 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
52355406 ATATGTATATGTGGTAAAGCTGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
52355454 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
52355502 ATATGTATATGTGGTAAAGCCGAATAGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * *
52355550 ATATGTATATGTGGTAAAGCCGAAGGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
52355598 AT
1 AT
52355600 GTGTGTATAT
Statistics
Matches: 187, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 187 1.00
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:52361565 original size:15 final size:15
Alignment explanation
Indices: 52361519--52361566 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
52361509 AAACCTACAA
*
52361519 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
52361534 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
52361548 AAACTTCATATCCAT
1 AAACTTCATATCCAT
52361563 AAAC
1 AAAC
52361567 CCACCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:52362738 original size:30 final size:30
Alignment explanation
Indices: 52362702--52362760 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
52362692 CATTCAAATA
52362702 CAATTACTTAGCATTTCATACTTAATCAAC
1 CAATTACTTAGCATTTCATACTTAATCAAC
52362732 CAATTACTTAGCATTTCATACTTAATCAA
1 CAATTACTTAGCATTTCATACTTAATCAA
52362761 TCATCATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (30 bp):
CAATTACTTAGCATTTCATACTTAATCAAC
Found at i:52369611 original size:42 final size:42
Alignment explanation
Indices: 52369530--52369626 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
52369520 TTGAGATTTA
* ** *
52369530 CGTGTAAGACCATGTCTAGGACATCGGTATCGTATCTGAATT
1 CGTGTAAGACCATATCTAGGACAAAGGCATCGTATCTGAATT
* *
52369572 CGTGTAATACCCTATCTAGGACAAAGGCATCG-ATACTGAATT
1 CGTGTAAGACCATATCTAGGACAAAGGCATCGTAT-CTGAATT
*
52369614 ACATGTAAGACCA
1 -CGTGTAAGACCA
52369627 CGTCTGAGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 2 0.05
42 33 0.75
43 9 0.20
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
CGTGTAAGACCATATCTAGGACAAAGGCATCGTATCTGAATT
Found at i:52371783 original size:27 final size:27
Alignment explanation
Indices: 52371726--52371814 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
52371716 TACCTCAGTT
* *
52371726 TGTAAAATTACCAAAATACCCCCAGT-T
1 TGTAAAATTACCAAAATA-CCCCTGTAG
* *
52371753 TGTAAAATTACCAAAACACCCTTGTAG
1 TGTAAAATTACCAAAATACCCCTGTAG
* *
52371780 TGTAAAATTATCGAAATACCCCTGTAG
1 TGTAAAATTACCAAAATACCCCTGTAG
*
52371807 GGTAAAAT
1 TGTAAAAT
52371815 GACTTTTTTG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.10
27 47 0.90
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.27
Consensus pattern (27 bp):
TGTAAAATTACCAAAATACCCCTGTAG
Found at i:52373055 original size:27 final size:27
Alignment explanation
Indices: 52373031--52373094 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
52373021 AGAAATTACC
*
52373031 GAAATACCCCCAGCTTGTAAAATTATT
1 GAAATACCCCCAGCTTATAAAATTATT
* *
52373058 GAAATACCCTCAGTTTATAAAATTATT
1 GAAATACCCCCAGCTTATAAAATTATT
52373085 GAAATACCCC
1 GAAATACCCC
52373095 TATAGGGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
GAAATACCCCCAGCTTATAAAATTATT
Found at i:52373673 original size:32 final size:32
Alignment explanation
Indices: 52373590--52373675 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
52373580 ATTTACCCAA
* * *
52373590 GGCTTTGTGCCAATTATATTACCGTCGCTGAT
1 GGCTTTGTGCCAATTATAATACAGTCACTGAT
* ** *
52373622 GGCTATGTGCCAAACATAATACAGTTACTGAT
1 GGCTTTGTGCCAATTATAATACAGTCACTGAT
*
52373654 GGCTTTGTGCCACTTATAATAC
1 GGCTTTGTGCCAATTATAATAC
52373676 CACTACTGAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (32 bp):
GGCTTTGTGCCAATTATAATACAGTCACTGAT
Found at i:52373683 original size:32 final size:32
Alignment explanation
Indices: 52373590--52373690 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 32
52373580 ATTTACCCAA
* * *
52373590 GGCTTTGTGCCAATTATATTACC-GTCGCTGAT
1 GGCTTTGTGCCAATTATAATACCACT-ACTGAT
* ** *
52373622 GGCTATGTGCCAAACATAATA-CAGTTACTGAT
1 GGCTTTGTGCCAATTATAATACCA-CTACTGAT
* *
52373654 GGCTTTGTGCCACTTATAATACCACTACTGAA
1 GGCTTTGTGCCAATTATAATACCACTACTGAT
52373686 GGCTT
1 GGCTT
52373691 AGAGCCGCAT
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
31 1 0.02
32 50 0.93
33 3 0.06
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (32 bp):
GGCTTTGTGCCAATTATAATACCACTACTGAT
Found at i:52380590 original size:39 final size:39
Alignment explanation
Indices: 52380546--52380817 Score: 418
Period size: 39 Copynumber: 7.0 Consensus size: 39
52380536 ATTATATTAT
* * *
52380546 CAGCACAAAGCCTGCGAGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
52380585 CAGCACGAAGCCTGTGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* * *
52380624 CAACACGAAGCCTGCGGGACTTTAGTCCGGACACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* * *
52380663 CAGCACGAAGCCTGCGGGACTTTGGCCCGGAGATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
52380702 CAGCACGAAGCCTGCAGGACTTTAGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
52380741 CAGTACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
52380780 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
52380818 TCAGTGTCTT
Statistics
Matches: 211, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 211 1.00
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:52384746 original size:40 final size:40
Alignment explanation
Indices: 52384656--52384840 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
52384646 TCGAATGATG
* * *
52384656 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
52384695 ATCCAGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
52384736 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
52384775 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
52384814 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
52384841 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
39 36 0.29
40 78 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:52384862 original size:79 final size:79
Alignment explanation
Indices: 52384709--52384863 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
52384699 AGACTAAGAT
* **
52384709 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
52384774 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
52384788 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
52384851 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
52384864 ATTCTGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 41 0.61
80 24 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:52392573 original size:36 final size:37
Alignment explanation
Indices: 52392526--52392601 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
52392516 TGAGTTACAT
*
52392526 TTGTTTGAATT-AGCTCAAGAGCTTAGAGGACCATAG
1 TTGTTTGAATTAAGCTCAAGAGCTTAGAGGACCACAG
52392562 TTGTTTGAATTAAGCTCAAGAGCTTAGAGGACCACAG
1 TTGTTTGAATTAAGCTCAAGAGCTTAGAGGACCACAG
52392599 TTG
1 TTG
52392602 GATAAGGGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 11 0.29
37 27 0.71
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (37 bp):
TTGTTTGAATTAAGCTCAAGAGCTTAGAGGACCACAG
Found at i:52392954 original size:39 final size:40
Alignment explanation
Indices: 52392860--52393042 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
52392850 TCGAATGATG
* * *
52392860 TCCGGGCTAAGTCCC-AAGGC--TTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
52392897 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
52392938 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
52392977 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
52393016 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
52393043 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
38 12 0.10
39 42 0.34
40 62 0.50
41 8 0.06
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:52393064 original size:79 final size:79
Alignment explanation
Indices: 52392911--52393065 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
52392901 GGACTAAGAT
* **
52392911 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
52392976 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
52392990 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
52393053 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
52393066 ATTCGAAGGT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 41 0.61
80 24 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:52398047 original size:39 final size:39
Alignment explanation
Indices: 52398003--52398312 Score: 469
Period size: 39 Copynumber: 8.0 Consensus size: 39
52397993 ATTATATTAT
* *
52398003 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
52398042 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
52398081 CAGCACGAAGCCTGC-GGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
***
52398119 CAGCACGAAGCCTGCGGGACTTTAGTTTGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* * * *
52398158 CAGCACGAAGCCTGTGGGACTTTGGCCCAGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
** * *
52398197 CAGCACGAAGCCTGCAAGACTTTAGCCTGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
52398236 CAGTACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
52398275 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
52398313 TCAGTGTCTT
Statistics
Matches: 244, Mismatches: 26, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
38 38 0.16
39 206 0.84
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:52401189 original size:27 final size:27
Alignment explanation
Indices: 52401152--52401319 Score: 185
Period size: 27 Copynumber: 6.3 Consensus size: 27
52401142 CCCAGTTTGT
*
52401152 AAATTACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
52401179 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
52401206 AAATAACTGAAA-ACCCCCATAGGTTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * **
52401232 AAATGATCGAAATACCTCTGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* **
52401259 AAATGATCGAAATACCCCTTTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * **
52401286 AGATAACCAAAATACCCCTGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
52401313 AAATGAC
1 AAATGAC
52401320 TATAATACCC
Statistics
Matches: 120, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
26 22 0.18
27 98 0.82
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:52401222 original size:53 final size:54
Alignment explanation
Indices: 52401159--52401316 Score: 194
Period size: 53 Copynumber: 2.9 Consensus size: 54
52401149 TGTAAATTAC
**
52401159 CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATAA-
1 CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTGTAGGGTAAAATAAT
* * * *
52401212 CTGAAA-ACCCCCATAGGTTAAAATGATCGAAATACCTCTGTAGGGTAAAATGAT
1 C-GAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTGTAGGGTAAAATAAT
** * * *
52401266 CGAAATACCCCTTTAGGGTAAGATAACCAAAATACCCCTGTAGGGTAAAAT
1 CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTGTAGGGTAAAAT
52401317 GACTATAATA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
53 46 0.52
54 42 0.48
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (54 bp):
CGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTGTAGGGTAAAATAAT
Found at i:52410903 original size:16 final size:17
Alignment explanation
Indices: 52410882--52410914 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
52410872 GAATGTTAAT
*
52410882 TGAATTTTA-AAAATAA
1 TGAATTATATAAAATAA
52410898 TGAATTATATAAAATAA
1 TGAATTATATAAAATAA
52410915 AAAGACTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
TGAATTATATAAAATAA
Found at i:52412808 original size:177 final size:177
Alignment explanation
Indices: 52412512--52413270 Score: 951
Period size: 177 Copynumber: 4.3 Consensus size: 177
52412502 TGCTAAATTG
* *
52412512 CCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGCTACC
1 CCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTCCACTGCTACC
* * * *
52412577 TCGGGAAGATAAGACTCTCCATCTTCAATCTACTCCACAACTTCGTAGGGAGATAAGATCTTCAA
66 TCGGGAAGATAAGACTCGCCATCTTCAATCTGCTCCACAACTGCTTAGGGAGATAAGATCTTCAA
*
52412642 TCTTCAGTCTGCTTCCTTTCTACCTTAGGAAGATAAGACTACAATCA
131 TCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGACTACAATCA
* * * * * *
52412689 CCAACCTGCTCTCTTGCTACCTCAGAAAGATAAGGTTGGTGGCTTAAATCTACTTCATTGTTGA-
1 CCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTCCACTGCT-AC
* * * * * * * * *
52412753 TTCATGG-AGATAAGATTCTCCGTCTTCGATCTTCTCCACTACTGCTTAGGGAGATAAGATTTTC
65 CTC-GGGAAGATAAGACTCGCCATCTTCAATCTGCTCCACAACTGCTTAGGGAGATAAGATCTTC
* **
52412817 AATCTTCATTCTGCTTCCTTGCTACCTTAGGAAGATAAGACTACAATTG
129 AATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGACTACAATCA
* * * * * *
52412866 CCAACCTCCTCTTTTGCTACCT--TAGAGATAAGGCTGGTGGCTAAAATTTGCTCCCCTGCTACC
1 CCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTCCACTGCTACC
* * **
52412929 TCGGGAATATAAGACTCGCCATCTTCGATCTGCTCCACAACTGCTTATAGAGATAAGATCTTCAA
66 TCGGGAAGATAAGACTCGCCATCTTCAATCTGCTCCACAACTGCTTAGGGAGATAAGATCTTCAA
* ** *
52412994 TCTTCAGTTTGCTTCCTTGCTAGTTTAGGAAGATAAGAATACAATCA
131 TCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGACTACAATCA
* *
52413041 CCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTTCTCCATTACTGAT
1 CCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTCC---ACTGCT
* * * *
52413106 ACAT--GG-AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAG-TCTT
63 ACCTCGGGAAGATAAGACTCGCCATCTTCAATCTGCTCCACAACTGCTTAGGGAGATAAGATCTT
* * * *
52413167 CAATCTTTA-TCTGCTTCCTTACTGCCTCAGGAAGATAAGACTACAATCA
128 CAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGACTACAATCA
* *
52413216 CCAACCCGCTCTCTTGCTACCTCAGAGAGATAAGGCTAGTGGCTTAAATCTGCTC
1 CCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTC
52413271 TACTATAACT
Statistics
Matches: 494, Mismatches: 79, Indels: 20
0.83 0.13 0.03
Matches are distributed among these distances:
174 3 0.01
175 225 0.46
176 12 0.02
177 242 0.49
178 5 0.01
180 7 0.01
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (177 bp):
CCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTGCTCCACTGCTACC
TCGGGAAGATAAGACTCGCCATCTTCAATCTGCTCCACAACTGCTTAGGGAGATAAGATCTTCAA
TCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGACTACAATCA
Found at i:52412967 original size:352 final size:351
Alignment explanation
Indices: 52412507--52413270 Score: 1145
Period size: 352 Copynumber: 2.2 Consensus size: 351
52412497 TTCCTTGCTA
*
52412507 AATTGCCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTG
1 AATTGCCAACCTCCTCTCTTGCTACCT-AGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTG
* * *
52412572 CTACCTCGGGAAGATAAGACTCTCCATCTTCAATCTACTCCACAACTTCGTAGGGAGATAAGATC
65 CTACCTCGGGAAGATAAGACTCGCCATCTTCAATCTACTCCACAACTGCGTAGAGAGATAAGATC
* *
52412637 TTCAATCTTCAGTCTGCTTCCTTTCTACCTTAGGAAGATAAGACTACAATCACCAACCTGCTCTC
130 TTCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGAATACAATCACCAACCTGCTCTC
* * ** *
52412702 TTGCTACCTCAGAAAGATAAGGTTGGTGGCTTAAATCTACTTCATTGTTGATTCATGGAGATAAG
195 TTGCTACCTCAGAAAGATAAGGCTGGTGGCTTAAATCTACTCCATTACTGATACATGGAGATAAG
* * * *
52412767 ATTCTCCGTCTTCGATCTTCTCCACTACTGCTTAGGGAGATAAGATTTTCAATCTTCATTCTGCT
260 ATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAG-TCTTCAATCTTCA-TCTGCT
* *
52412832 TCCTTGCTACCTTAGGAAGATAAGACTAC
323 TCCTTACTACCTCAGGAAGATAAGACTAC
* * *
52412861 AATTGCCAACCTCCTCTTTTGCTACCT-TAGAGATAAGGCTGGTGGCTAAAATTTGCTCCCCTGC
1 AATTGCCAACCTCCTCTCTTGCTACCTAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGC
* * * * *
52412925 TACCTCGGGAATATAAGACTCGCCATCTTCGATCTGCTCCACAACTGCTTATAGAGATAAGATCT
66 TACCTCGGGAAGATAAGACTCGCCATCTTCAATCTACTCCACAACTGCGTAGAGAGATAAGATCT
* **
52412990 TCAATCTTCAGTTTGCTTCCTTGCTAGTTTAGGAAGATAAGAATACAATCACCAACCTGCTCTCT
131 TCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGAATACAATCACCAACCTGCTCTCT
* *
52413055 TGCTACCTCAGAGAGATAAGGCTGGTGGCTTAAATCTTCTCCATTACTGATACATGGAGATAAGA
196 TGCTACCTCAGAAAGATAAGGCTGGTGGCTTAAATCTACTCCATTACTGATACATGGAGATAAGA
*
52413120 TTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGTCTTCAATCTTTATCTGCTTCC
261 TTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGTCTTCAATCTTCATCTGCTTCC
*
52413185 TTACTGCCTCAGGAAGATAAGACTAC
326 TTACTACCTCAGGAAGATAAGACTAC
** * *
52413211 AATCACCAACC-CGCTCTCTTGCTACCTCAGAGAGATAAGGCTAGTGGCTTAAATCTGCTC
1 AATTGCCAACCTC-CTCTCTTGCTACCT-AGAGAGATAAGGCTGGTGGCTAAAATCTGCTC
52413271 TACTATAACT
Statistics
Matches: 368, Mismatches: 39, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
349 1 0.00
350 54 0.15
351 11 0.03
352 277 0.75
354 25 0.07
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (351 bp):
AATTGCCAACCTCCTCTCTTGCTACCTAGAGAGATAAGGCTGGTGGCTAAAATCTGCTCCCCTGC
TACCTCGGGAAGATAAGACTCGCCATCTTCAATCTACTCCACAACTGCGTAGAGAGATAAGATCT
TCAATCTTCAGTCTGCTTCCTTGCTACCTTAGGAAGATAAGAATACAATCACCAACCTGCTCTCT
TGCTACCTCAGAAAGATAAGGCTGGTGGCTTAAATCTACTCCATTACTGATACATGGAGATAAGA
TTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGTCTTCAATCTTCATCTGCTTCC
TTACTACCTCAGGAAGATAAGACTAC
Found at i:52413477 original size:182 final size:182
Alignment explanation
Indices: 52413263--52413939 Score: 1018
Period size: 182 Copynumber: 3.7 Consensus size: 182
52413253 AGTGGCTTAA
** * * * *
52413263 ATCTGCTCTACTATAACTTCAGAGAGATAAGATCTATTTATTTATAACTTCAATTTGTTCTAATG
1 ATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTATTTATTTATAACTTCAATCTGTTCCACTG
* * *
52413328 CAACTTCAGGGAAATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAGAC
66 CAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
52413393 CTGTCACTTCAACCTGCTCCACTGCAACTTTAGGGAGATAAGGTTTGCTATG
131 CTGTCACTTCAACCTGCTCCACTGCAACTTTAGGGAGATAAGGTTTGCTATG
* * * * * *
52413445 ATCTACTCTACTGCAACTTCAGAGATATAAGATCTGTTTATTTATAGCTTCAATCTGTTCCATTG
1 ATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTATTTATTTATAACTTCAATCTGTTCCACTG
* * * *
52413510 TAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAGAC
66 CAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* *
52413575 CTGTCACTTCAACCTACTCCACTACAACTTTAGGGAGATAAGGTTTGCTATG
131 CTGTCACTTCAACCTGCTCCACTGCAACTTTAGGGAGATAAGGTTTGCTATG
* * * * *
52413627 ATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTATTTATTTATAGCTTCAATTTATTGCACTA
1 ATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTATTTATTTATAACTTCAATCTGTTCCACTG
* *
52413692 CAACTTCAGGGAAATAAGACTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGAC
66 CAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
52413757 CTGTCACTTCAACCTGCTCCACTGCAAC-TTAGGGAGATAAGGTTTGCTATG
131 CTGTCACTTCAACCTGCTCCACTGCAACTTTAGGGAGATAAGGTTTGCTATG
* *
52413808 ATCTGCTCTACTGGAACTTCAAAGAGATAAGATCTGTTTATTTA-AAGCTTCAATCTGTTCCACT
1 ATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTATTTATTTATAA-CTTCAATCTGTTCCACT
* * * *
52413872 GCATCTTCAAGGAAATAAGATTCGTTATCTTCAGT-TGCTCCATTGCAACTTCAGGGAGATAAGA
65 GCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
52413936 CCTG
130 CCTG
52413940 ACTTCACAGA
Statistics
Matches: 448, Mismatches: 46, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
180 32 0.07
181 109 0.24
182 307 0.69
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (182 bp):
ATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTATTTATTTATAACTTCAATCTGTTCCACTG
CAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
CTGTCACTTCAACCTGCTCCACTGCAACTTTAGGGAGATAAGGTTTGCTATG
Found at i:52414104 original size:64 final size:64
Alignment explanation
Indices: 52414003--52414130 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 64
52413993 TCATGTATCT
*
52414003 ATGCTTATGCTAAATAATTAGAATGCTATGATTGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCTAAATAATTAGAATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
* *
52414067 ATGCTTATG-TCAAATAATTAGGATGTTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCT-AAATAATTAGAATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
52414131 TTACGAATGA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 1 0.02
64 59 0.98
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (64 bp):
ATGCTTATGCTAAATAATTAGAATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
Found at i:52415204 original size:31 final size:31
Alignment explanation
Indices: 52415159--52415237 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
52415149 TGACCTCTCA
*
52415159 TTTTTTTTCTTTTTTCAATTTTTGATTGATTC
1 TTTTTTTT-ATTTTTCAATTTTTGATTGATTC
** * *
52415191 TTTTTTTTATTTTTCTTTTTTTGATTGCTTT
1 TTTTTTTTATTTTTCAATTTTTGATTGATTC
52415222 TTTCCTTTTTATTTTT
1 TTT--TTTTTATTTTT
52415238 TTTATTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
31 21 0.52
32 8 0.20
33 11 0.28
ACGTcount: A:0.09, C:0.09, G:0.05, T:0.77
Consensus pattern (31 bp):
TTTTTTTTATTTTTCAATTTTTGATTGATTC
Found at i:52415206 original size:15 final size:15
Alignment explanation
Indices: 52415188--52415246 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
52415178 TTTTGATTGA
52415188 TTCTTTTTTTTATTT
1 TTCTTTTTTTTATTT
*
52415203 TTCTTTTTTTGA--T
1 TTCTTTTTTTTATTT
* **
52415216 TGC-TTTTTTCCTTT
1 TTCTTTTTTTTATTT
*
52415230 TTATTTTTTTTATTT
1 TTCTTTTTTTTATTT
52415245 TT
1 TT
52415247 TTAAGTTCTC
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
12 6 0.18
13 3 0.09
14 2 0.06
15 22 0.67
ACGTcount: A:0.07, C:0.08, G:0.03, T:0.81
Consensus pattern (15 bp):
TTCTTTTTTTTATTT
Found at i:52415842 original size:12 final size:11
Alignment explanation
Indices: 52415783--52415841 Score: 61
Period size: 12 Copynumber: 5.3 Consensus size: 11
52415773 TGTTTTGTTG
52415783 TTTTTATTCTT
1 TTTTTATTCTT
52415794 CTTTTTATTCTT
1 -TTTTTATTCTT
52415806 TTTTTATT-TT
1 TTTTTATTCTT
52415816 TTTTGTACTT-TT
1 TTTT-TA-TTCTT
52415828 TTATTT-TTCTT
1 TT-TTTATTCTT
52415839 TTT
1 TTT
52415842 AGATGCCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.21
11 14 0.33
12 18 0.42
13 2 0.05
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTATTCTT
Found at i:52420893 original size:24 final size:24
Alignment explanation
Indices: 52420866--52420912 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
52420856 TGACAATGTA
52420866 CATACAATAAAAAATAATTAAATT
1 CATACAATAAAAAATAATTAAATT
52420890 CATACAATAAAAAATAATTAAAT
1 CATACAATAAAAAATAATTAAAT
52420913 ATGTAAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.28
Consensus pattern (24 bp):
CATACAATAAAAAATAATTAAATT
Found at i:52429507 original size:50 final size:51
Alignment explanation
Indices: 52429430--52429558 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
52429420 GACCATGGCA
52429430 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAA-TG
* *
52429481 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAATG
* * *
52429531 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
52429559 TTGATCAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 44 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTAATCAAGGACAAATG
Found at i:52429572 original size:31 final size:31
Alignment explanation
Indices: 52429534--52429714 Score: 256
Period size: 31 Copynumber: 5.8 Consensus size: 31
52429524 ACAAATGACA
* *
52429534 AGTGAAAAGTGGTAGCTTCAGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
52429565 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
52429596 AGTGAAAAGTGGTAG-TTCCAGCTTCCTGATC
1 AGTGAAAAGTGGTAGCTT-CGGCTACCTGATC
*
52429627 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
52429658 AGTGAAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTG-AAAAGTGGTAGCTTCGGCTACCTGATC
*
52429690 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
52429715 AAGTGAAAGT
Statistics
Matches: 136, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
30 2 0.01
31 103 0.76
32 31 0.23
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:52429808 original size:47 final size:48
Alignment explanation
Indices: 52429738--52429863 Score: 161
Period size: 47 Copynumber: 2.7 Consensus size: 48
52429728 AAGTGATTTC
*
52429738 CGTATAAGACCATATCTGGGATATGGCATCGATGTGATATATGCT-ACT
1 CGTATAAGACCATATCTGGGATATGGCATCGATGTGAGATATG-TGACT
*
52429786 -GTATAAGACCATATCTGGGATATGGCATC-A-GTGAGATATGTGATT
1 CGTATAAGACCATATCTGGGATATGGCATCGATGTGAGATATGTGACT
* * * *
52429831 CGTGTAAGACCATAGCTAGGCTATGGCATCGAT
1 CGTATAAGACCATATCTGGGATATGGCATCGAT
52429864 ATATGAATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
44 1 0.01
45 11 0.16
46 26 0.38
47 30 0.44
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (48 bp):
CGTATAAGACCATATCTGGGATATGGCATCGATGTGAGATATGTGACT
Found at i:52429895 original size:42 final size:43
Alignment explanation
Indices: 52429832--52429946 Score: 153
Period size: 42 Copynumber: 2.7 Consensus size: 43
52429822 TATGTGATTC
* * *
52429832 GTGTAAGACCATAGCTAGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGAT
* *
52429874 GTGTAAAACCATAGTTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGAT
**
52429916 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGTTGGGCTATGGCATCGA
52429947 GAAAATGAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 61 0.97
43 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCATAGTTGGGCTATGGCATCGATTATATGAAGAT
Found at i:52434046 original size:28 final size:28
Alignment explanation
Indices: 52434014--52434097 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
52434004 AACTGTGATC
52434014 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
52434042 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
52434064 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
52434092 ACGTGT
1 ACGTGT
52434098 ACCAGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:52434132 original size:49 final size:49
Alignment explanation
Indices: 52433959--52434203 Score: 310
Period size: 49 Copynumber: 4.9 Consensus size: 49
52433949 TCTATTGTGA
* * * * *
52433959 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-T
* * * **
52434010 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
*
52434059 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
52434109 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTATACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
52434158 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
52434204 GCTTTGGCTA
Statistics
Matches: 170, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 87 0.51
50 46 0.27
51 37 0.22
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:52445609 original size:50 final size:48
Alignment explanation
Indices: 52445524--52445661 Score: 147
Period size: 49 Copynumber: 2.8 Consensus size: 48
52445514 TTGGGTCATT
* *
52445524 TGTGTGAGCTAGTGTAAGA-CATG-TCGGGGACATGGCAT-AGGCACGGATA
1 TGTGAGAGCTAGTGTAAGACCATGTTC-GGGACATGGCATCAGCCAC-G--A
* *
52445573 TGTGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGA
1 TGTGAGAGCTAGTGTAAGACCATGTTCGGGACATGGCATCAGCCACGA
* * *
52445621 TGATAATAGCAAGTGTAAGACCATGTTCGGGACATGGCATC
1 TG-TGAGAGCTAGTGTAAGACCATGTTCGGGACATGGCATC
52445662 GACAACTTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
48 3 0.04
49 52 0.68
50 17 0.22
51 5 0.06
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.24
Consensus pattern (48 bp):
TGTGAGAGCTAGTGTAAGACCATGTTCGGGACATGGCATCAGCCACGA
Found at i:52453614 original size:33 final size:33
Alignment explanation
Indices: 52453561--52453638 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 33
52453551 ACTTGTATAG
* *
52453561 ATATATAGACTTTTTGTGCATAAAAATATAAACT
1 ATATATACA-TTTGTGTGCATAAAAATATAAACT
52453595 ATATATACATTTGTGTGCATAAAAATATAAACT
1 ATATATACATTTGTGTGCATAAAAATATAAACT
*
52453628 ACATATACATT
1 ATATATACATT
52453639 CTTTTATACG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 33 0.80
34 8 0.20
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (33 bp):
ATATATACATTTGTGTGCATAAAAATATAAACT
Found at i:52454875 original size:18 final size:18
Alignment explanation
Indices: 52454852--52454894 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
52454842 TTAATCTTGA
52454852 ATGCTTATGGTTCAGGTC
1 ATGCTTATGGTTCAGGTC
52454870 ATGCTTATGGTTCAGGTC
1 ATGCTTATGGTTCAGGTC
*
52454888 AGGCTTA
1 ATGCTTA
52454895 AGTATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.37
Consensus pattern (18 bp):
ATGCTTATGGTTCAGGTC
Found at i:52460175 original size:29 final size:25
Alignment explanation
Indices: 52460146--52460195 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
52460136 TCATGAAAGA
52460146 AAGAAAGAAAACCAAGATTCAACAT
1 AAGAAAGAAAACCAAGATTCAACAT
52460171 AAGAAAGAAAACCAAGATTCAACAT
1 AAGAAAGAAAACCAAGATTCAACAT
52460196 TCAACCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.16, G:0.12, T:0.12
Consensus pattern (25 bp):
AAGAAAGAAAACCAAGATTCAACAT
Found at i:52460891 original size:29 final size:29
Alignment explanation
Indices: 52460850--52460914 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
52460840 CACGGCCAAG
52460850 ACACACGTCCGTGTTCTAGGCTGTGTGGC
1 ACACACGTCCGTGTTCTAGGCTGTGTGGC
52460879 ACACACGTCCGTGTTCTAGGCTGTGTGGC
1 ACACACGTCCGTGTTCTAGGCTGTGTGGC
52460908 ACACACG
1 ACACACG
52460915 GTTGAGACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (29 bp):
ACACACGTCCGTGTTCTAGGCTGTGTGGC
Found at i:52462653 original size:20 final size:20
Alignment explanation
Indices: 52462624--52462668 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
52462614 AGCATATGTA
* *
52462624 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
52462644 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
52462664 TTCAT
1 TTCAT
52462669 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:52466817 original size:31 final size:30
Alignment explanation
Indices: 52466772--52466854 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 30
52466762 TCAGTCTCCA
*
52466772 CATATACTGAGCCGAAGCCTTTTCATAAAT
1 CATATACTGGGCCGAAGCCTTTTCATAAAT
52466802 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
*
52466833 CATATAACT-GGCTGAAGCCTTT
1 CATAT-ACTGGGCCGAAGCCTTT
52466855 ACTGTAAGCG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 17 0.35
31 32 0.65
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (30 bp):
CATATACTGGGCCGAAGCCTTTTCATAAAT
Found at i:52467150 original size:26 final size:26
Alignment explanation
Indices: 52467083--52467195 Score: 165
Period size: 26 Copynumber: 4.4 Consensus size: 26
52467073 AACTTGTGCA
**
52467083 AAGCCCTTTTCGGTAAACTGGGGCA-
1 AAGCCCTTTTCAATAAACTGGGGCAT
*
52467108 AATCCCTTTTCAATAAACTGGGGCAT
1 AAGCCCTTTTCAATAAACTGGGGCAT
* **
52467134 AAGCCCTTTCCGGTAAACTGGGGCAT
1 AAGCCCTTTTCAATAAACTGGGGCAT
52467160 AAGCCCTTTTCAATAAACTGGGGCAT
1 AAGCCCTTTTCAATAAACTGGGGCAT
52467186 AAGCCCTTTT
1 AAGCCCTTTT
52467196 GCACTTCCTC
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 22 0.29
26 55 0.71
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (26 bp):
AAGCCCTTTTCAATAAACTGGGGCAT
Found at i:52467186 original size:52 final size:51
Alignment explanation
Indices: 52467083--52467194 Score: 197
Period size: 52 Copynumber: 2.2 Consensus size: 51
52467073 AACTTGTGCA
* *
52467083 AAGCCCTTTTCGGTAAACTGGGGCAAATCCCTTTTCAATAAACTGGGGCAT
1 AAGCCCTTTCCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCAT
52467134 AAGCCCTTTCCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCAT
1 AAGCCCTTTCCGGTAAACTGGGGCA-AAGCCCTTTTCAATAAACTGGGGCAT
52467186 AAGCCCTTT
1 AAGCCCTTT
52467195 TGCACTTCCT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 24 0.41
52 34 0.59
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (51 bp):
AAGCCCTTTCCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCAT
Found at i:52467270 original size:20 final size:20
Alignment explanation
Indices: 52467245--52467311 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
52467235 TTATGAATAC
52467245 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
52467265 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
52467285 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
52467305 ATCATGT
1 ATCATGT
52467312 ATATCATATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:52468049 original size:27 final size:27
Alignment explanation
Indices: 52468019--52468083 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
52468009 GGGCATATTC
52468019 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
52468046 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
52468073 GTCTTTTTACC
1 GTCATTTTACC
52468084 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:52468144 original size:27 final size:27
Alignment explanation
Indices: 52468114--52468500 Score: 215
Period size: 27 Copynumber: 14.3 Consensus size: 27
52468104 TTTCATCTTA
* * *
52468114 CAAGGGTGTTTTGGTAAATCTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* **
52468141 CAAGGGTATTTTTGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
52468168 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** * *
52468195 TGAGGGTATTTTGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
52468222 CAATGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * * **
52468248 CTAGGGGTGTTTTGGTAATTCTACCCTAT
1 C-AAGGGTATTTTGGTAATTTTA-CAAAT
* **
52468277 -AGGGGTATTTCAGTAA-TTT-CATAAT
1 CAAGGGTATTTTGGTAATTTTACA-AAT
* * **** *
52468302 CGAGAGTAAAACGGTAATTTTATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*** * * **
52468329 CAAGGGTAAAATAGTAATTCTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *** * * *
52468356 CGAGGGTAAAATAGTAATTCTATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
52468383 CGAGGGTACTTTGGTAATTTTTACAAGT
1 CAAGGGTATTTTGGTAA-TTTTACAAAT
**
52468411 CAAGGGTATTTCAGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
52468438 CAGGGGGTATTTTAGTAATTTTACAAAC
1 CA-AGGGTATTTTGGTAATTTTACAAAT
* * **
52468466 CAGGGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
52468493 CGAGGGTA
1 CAAGGGTA
52468501 AAACAGTAAT
Statistics
Matches: 284, Mismatches: 67, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
24 1 0.00
25 2 0.01
26 12 0.04
27 222 0.78
28 47 0.17
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:52468373 original size:54 final size:54
Alignment explanation
Indices: 52468299--52468578 Score: 201
Period size: 54 Copynumber: 5.2 Consensus size: 54
52468289 GTAATTTCAT
* ** *
52468299 AATCGAGAGTAAAACGGTAATTTTATAAATCAAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTGTA
* *** * *
52468353 AATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTACTTTGGTAATT-TTTA
1 AATCGAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTGTA
* ** * * ***
52468406 CAAGTCAAGGGT-ATTTCAGTAATTTTACAAATCAGGGGGTATTTTAGTAATT-T-TA
1 -AA-TCGAGGGTAAAAT-AGTAATTTTATAAATC-GAGGGTAAAATAGTAATTCTGTA
* * *** * * *
52468461 CAAACCAGGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTATA
1 -AATCGA-GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTGTA
* * * *
52468517 AATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAGAACAGTAATTCTGTA
1 AATCGAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTGTA
52468571 AATC-AGGG
1 AATCGAGGG
52468579 GTACTTTGGT
Statistics
Matches: 180, Mismatches: 38, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
53 7 0.04
54 103 0.57
55 49 0.27
56 21 0.12
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (54 bp):
AATCGAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTGTA
Found at i:52468438 original size:55 final size:54
Alignment explanation
Indices: 52468368--52468500 Score: 158
Period size: 55 Copynumber: 2.4 Consensus size: 54
52468358 AGGGTAAAAT
* * **
52468368 AGTAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACAAGTCAAGGGTATTTC
1 AGTAATTTTATAAATCGAGGGTACTTTAGTAA-TTTTACAAACCAAGGGTATTTC
* * * * *
52468423 AGTAATTTTACAAATCAGGGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTT
1 AGTAATTTTATAAATC-GAGGGTACTTTAGTAATTTTACAAACCAAGGGTATTTC
*
52468478 AGTAATTTTGTAAATCGAGGGTA
1 AGTAATTTTATAAATCGAGGGTA
52468501 AAACAGTAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
54 6 0.09
55 46 0.71
56 13 0.20
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (54 bp):
AGTAATTTTATAAATCGAGGGTACTTTAGTAATTTTACAAACCAAGGGTATTTC
Found at i:52468528 original size:191 final size:189
Alignment explanation
Indices: 52468181--52468593 Score: 501
Period size: 191 Copynumber: 2.2 Consensus size: 189
52468171 GGGTATTTTG
* * * * * **
52468181 GTAATTTTACAAATTGAGGGTATTTTGGTAA-TTTCACAAACCAATGGTATTTTGGTAATTTTAC
1 GTAATTCTATAAATCGAGGGTACTTTGGTAATTTTCACAAACCAAGGGTATTTCAGTAATTTTAC
* * ** *
52468245 AAACTAGGGGTGTTTTGGTAATTCTACCCTATAGGGGTATTTCAGTAATTTCATAATCGAGAGTA
66 AAACTAGGGGTATTTTAGTAATTCTACCAAACAGGGGTATTTCAGTAATTTCATAATCGAGAGTA
* * * *
52468310 AAACGGTAATTTTATAAATCAAGGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAATA
131 AAACAGTAATTCTATAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
* **
52468369 GTAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACAAGTCAAGGGTATTTCAGTAATTTTAC
1 GTAATTCTATAAATCGAGGGTACTTTGGTAATTTTCACAAACCAAGGGTATTTCAGTAATTTTAC
* * **
52468434 AAA-TCAGGGGGTATTTTAGTAATTTTA-CAAACCAGGGGTATTTTAGTAATTTTGTAAATCGAG
66 AAACT-A-GGGGTATTTTAGTAATTCTACCAAA-CAGGGGTATTTCAGTAATTTCAT-AATCGAG
* * * *
52468497 GGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAGAACA
127 AGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
*
52468560 GTAATTCTGTAAATC-AGGGGTACTTTGGTAATTT
1 GTAATTCTATAAATCGA-GGGTACTTTGGTAATTT
52468594 GGTAAACTAA
Statistics
Matches: 191, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
188 28 0.15
189 33 0.17
190 37 0.19
191 93 0.49
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (189 bp):
GTAATTCTATAAATCGAGGGTACTTTGGTAATTTTCACAAACCAAGGGTATTTCAGTAATTTTAC
AAACTAGGGGTATTTTAGTAATTCTACCAAACAGGGGTATTTCAGTAATTTCATAATCGAGAGTA
AAACAGTAATTCTATAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
Found at i:52468581 original size:27 final size:27
Alignment explanation
Indices: 52468287--52468578 Score: 171
Period size: 27 Copynumber: 10.8 Consensus size: 27
52468277 AGGGGTATTT
*
52468287 CAGTAATT-TCAT-AATCGAGAGTAAAA
1 CAGTAATTCT-ATAAATCGAGGGTAAAA
* * *
52468313 CGGTAATTTTATAAATCAAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
* *
52468340 TAGTAATTCTGTAAATCGAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
* ***
52468367 TAGTAATTCTATAAATCGAGGGTACTT
1 CAGTAATTCTATAAATCGAGGGTAAAA
** * * ***
52468394 TGGTAATT-TTTACAAGTCAAGGGTATTT
1 CAGTAATTCTATA-AA-TCGAGGGTAAAA
* * * ***
52468422 CAGTAATTTTACAAATCAGGGGGTATTT
1 CAGTAATTCTATAAATC-GAGGGTAAAA
* * * * ***
52468450 TAGTAATTTTACAAA-CCAGGGGTATTT
1 CAGTAATTCTATAAATCGA-GGGTAAAA
* * *
52468477 TAGTAATTTTGTAAATCGAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
52468504 CAGTAATTCTATAAATCGAGGGTAAAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
** *
52468531 TGGTAATTCTATAAATCGAGGGTAGAA
1 CAGTAATTCTATAAATCGAGGGTAAAA
*
52468558 CAGTAATTCTGTAAATC-AGGG
1 CAGTAATTCTATAAATCGAGGG
52468579 GTACTTTGGT
Statistics
Matches: 218, Mismatches: 40, Indels: 16
0.80 0.15 0.06
Matches are distributed among these distances:
26 16 0.07
27 158 0.72
28 42 0.19
29 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (27 bp):
CAGTAATTCTATAAATCGAGGGTAAAA
Found at i:52473899 original size:20 final size:20
Alignment explanation
Indices: 52473876--52473913 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52473866 TGTATTCATA
* *
52473876 AAATTTTAGAATTTTTCACC
1 AAATTTTACAACTTTTCACC
52473896 AAATTTTACAACTTTTCA
1 AAATTTTACAACTTTTCA
52473914 TTTTAGTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.45
Consensus pattern (20 bp):
AAATTTTACAACTTTTCACC
Found at i:52474896 original size:9 final size:9
Alignment explanation
Indices: 52474882--52474906 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52474872 TAAATTCGAT
52474882 TTTAGTTAA
1 TTTAGTTAA
52474891 TTTAGTTAA
1 TTTAGTTAA
52474900 TTTAGTT
1 TTTAGTT
52474907 TGAGTCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (9 bp):
TTTAGTTAA
Done.