Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 161 of 343
Found at i:53260815 original size:22 final size:22
Alignment explanation
Indices: 53260787--53260830 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
53260777 GCTTAGTAAG
53260787 CTCGTATGAAAGAAATAAACTA
1 CTCGTATGAAAGAAATAAACTA
53260809 CTCGTATGAAAGAAATAAACTA
1 CTCGTATGAAAGAAATAAACTA
53260831 ACCTTACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.23
Consensus pattern (22 bp):
CTCGTATGAAAGAAATAAACTA
Found at i:53261968 original size:27 final size:26
Alignment explanation
Indices: 53261908--53262032 Score: 93
Period size: 27 Copynumber: 4.9 Consensus size: 26
53261898 ACAGACATCA
* * *
53261908 CATAGGGGTAAAACAGTCATCTTAC-
1 CATAAGGGCAAAACAGTCATTTTACT
*
53261933 CATAAAAGGGCAAAATAGTCATTTTACT
1 CAT--AAGGGCAAAACAGTCATTTTACT
*
53261961 ACATAAGGGTAAAACAGTCA--TT--T
1 -CATAAGGGCAAAACAGTCATTTTACT
* * *
53261984 --TAAGGGTAAAATAGTTATTTTACCT
1 CATAAGGGCAAAACAGTCATTTTA-CT
53262009 CATAAGGGCAAAACAGTCATTTTA
1 CATAAGGGCAAAACAGTCATTTTA
53262033 TTAACTTAGG
Statistics
Matches: 78, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
20 15 0.19
22 2 0.03
23 1 0.01
25 6 0.08
27 51 0.65
29 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (26 bp):
CATAAGGGCAAAACAGTCATTTTACT
Found at i:53261989 original size:20 final size:20
Alignment explanation
Indices: 53261964--53262005 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
53261954 TTTTACTACA
53261964 TAAGGGTAAAACAGTCATTT
1 TAAGGGTAAAACAGTCATTT
* *
53261984 TAAGGGTAAAATAGTTATTT
1 TAAGGGTAAAACAGTCATTT
53262004 TA
1 TA
53262006 CCTCATAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (20 bp):
TAAGGGTAAAACAGTCATTT
Found at i:53262013 original size:47 final size:47
Alignment explanation
Indices: 53261938--53262032 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
53261928 CTTACCATAA
*
53261938 AAGGGCAAAATAGTCATTTTACTACATAAGGGTAAAACAGTCATTTT
1 AAGGGCAAAATAGTCATTTTACTACATAAGGGCAAAACAGTCATTTT
* *
53261985 AAGGGTAAAATAGTTATTTTACCT-CATAAGGGCAAAACAGTCATTTT
1 AAGGGCAAAATAGTCATTTTA-CTACATAAGGGCAAAACAGTCATTTT
53262032 A
1 A
53262033 TTAACTTAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 42 0.95
48 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.31
Consensus pattern (47 bp):
AAGGGCAAAATAGTCATTTTACTACATAAGGGCAAAACAGTCATTTT
Found at i:53263473 original size:12 final size:12
Alignment explanation
Indices: 53263456--53263480 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53263446 TCGCCTAAAA
53263456 CCCTCCTCAAAT
1 CCCTCCTCAAAT
53263468 CCCTCCTCAAAT
1 CCCTCCTCAAAT
53263480 C
1 C
53263481 TCTCAACTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.52, G:0.00, T:0.24
Consensus pattern (12 bp):
CCCTCCTCAAAT
Found at i:53274774 original size:46 final size:46
Alignment explanation
Indices: 53274724--53274896 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
53274714 TGGTTGAGCA
*
53274724 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACG
* * * * *
53274770 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTAACT-AG-GCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-TGAGAACG
*
53274817 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACG
* * * *
53274863 GCTGAGCTTGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
53274897 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
44 1 0.01
45 3 0.03
46 63 0.61
47 32 0.31
48 4 0.04
49 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACG
Found at i:53274880 original size:93 final size:93
Alignment explanation
Indices: 53274721--53274891 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
53274711 GGATGGTTGA
* *
53274721 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACGGCCGAACTCGTTGAGT
53274786 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * * *
53274814 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGGCTGAGCTTGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACGGCCGAACTCGTTGAGT
53274879 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
53274892 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACGGCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:53275798 original size:21 final size:21
Alignment explanation
Indices: 53275760--53275805 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
53275750 CTGTTCTGAC
* *
53275760 TTTAAAAATTCATAATAAATT
1 TTTAAAAAATAATAATAAATT
* *
53275781 TTTAAAAAATAATTATAAGTT
1 TTTAAAAAATAATAATAAATT
53275802 TTTA
1 TTTA
53275806 TTTATATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTAAAAAATAATAATAAATT
Found at i:53277446 original size:28 final size:28
Alignment explanation
Indices: 53277371--53277435 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
53277361 GGCATAATTG
* *
53277371 TCATTTTACCATA-AAGGGGTATTACGG
1 TCATTTTACCCTACAAGGGGTATTACGA
53277398 TCATTTTACCCTACAAGGGGTATTACGA
1 TCATTTTACCCTACAAGGGGTATTACGA
53277426 TCATTTTACC
1 TCATTTTACC
53277436 TATTTTGGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 12 0.34
28 23 0.66
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (28 bp):
TCATTTTACCCTACAAGGGGTATTACGA
Found at i:53282912 original size:56 final size:56
Alignment explanation
Indices: 53282821--53282928 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 56
53282811 TCTTACATGT
* **
53282821 AATCACATATTGATGCCACTGTCCTAGACAGGGTCTTACTCGCACACATATAGCAG
1 AATCACATATTGATGCCAATGTAATAGACAGGGTCTTACTCGCACACATATAGCAG
53282877 AATCACATATTGATGCCAATGTAATA-A-ATGCGGTCTTACTCGCACACATATA
1 AATCACATATTGATGCCAATGTAATAGACA-G-GGTCTTACTCGCACACATATA
53282929 TCGATGCCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
54 1 0.02
55 2 0.04
56 44 0.94
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (56 bp):
AATCACATATTGATGCCAATGTAATAGACAGGGTCTTACTCGCACACATATAGCAG
Found at i:53285123 original size:27 final size:27
Alignment explanation
Indices: 53285069--53285125 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
53285059 CATCTCATAA
* *
53285069 GGGCATATCAGTCATTTTACCATGTAG
1 GGGCATATCAGTCATTTCACAATGTAG
*
53285096 GGGCATTTCAGTCATTTCATCAAT-TAG
1 GGGCATATCAGTCATTTCA-CAATGTAG
53285123 GGG
1 GGG
53285126 GTCTAGATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (27 bp):
GGGCATATCAGTCATTTCACAATGTAG
Found at i:53286192 original size:16 final size:16
Alignment explanation
Indices: 53286171--53286212 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
53286161 GTGAAGAAAA
53286171 AGGAAAGAATTGAGAG
1 AGGAAAGAATTGAGAG
53286187 AGGAAAGAATTGAGAG
1 AGGAAAGAATTGAGAG
53286203 AGGAAAGAAT
1 AGGAAAGAAT
53286213 AAGCAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.36, T:0.12
Consensus pattern (16 bp):
AGGAAAGAATTGAGAG
Found at i:53289487 original size:46 final size:46
Alignment explanation
Indices: 53289328--53289487 Score: 141
Period size: 46 Copynumber: 3.5 Consensus size: 46
53289318 GCGAACTAAA
* * * * *
53289328 ACTCAACTCAACAAGCTCGGGCGTTCACATCTATAAGTGAACTCAG
1 ACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGG
* * *
53289374 ACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATCTCA-CA---AACTTGG
1 ACTCAACTCAACGAGCTCGGA---C-A-TTCACATC-CATAAGTGAACTCGG
*
53289421 ACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGG
1 ACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGG
*
53289467 ACTCAACTCAACGAGTTCGGA
1 ACTCAACTCAACGAGCTCGGA
53289488 TGCCCAAATA
Statistics
Matches: 90, Mismatches: 13, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
42 4 0.04
43 6 0.07
44 1 0.01
46 44 0.49
47 25 0.28
49 1 0.01
50 6 0.07
51 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (46 bp):
ACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGG
Found at i:53304923 original size:23 final size:21
Alignment explanation
Indices: 53304890--53304935 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
53304880 TCATGCTTAT
*
53304890 AATCATATCAAAATCATGCCA
1 AATCATATCAAAATCATACCA
*
53304911 AATCATAATTCAAAGTCATACCA
1 AATCAT-A-TCAAAATCATACCA
53304934 AA
1 AA
53304936 ACGTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (21 bp):
AATCATATCAAAATCATACCA
Found at i:53312531 original size:64 final size:64
Alignment explanation
Indices: 53312450--53312632 Score: 174
Period size: 67 Copynumber: 2.8 Consensus size: 64
53312440 AGACATTATG
* *
53312450 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * * *
53312514 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGTCAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
53312579 AA
63 AA
** * * *
53312581 ACTG--GCTAGGTCATATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAG
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAG
53312633 TCGAACTATA
Statistics
Matches: 94, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
62 1 0.01
63 17 0.18
64 21 0.22
65 8 0.09
66 15 0.16
67 30 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:53316138 original size:23 final size:21
Alignment explanation
Indices: 53316105--53316150 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
53316095 TCATGCTTAT
53316105 AATCATATCAAAATCATGCCA
1 AATCATATCAAAATCATGCCA
*
53316126 AATCATAATTCAAAGTCATGCCA
1 AATCAT-A-TCAAAATCATGCCA
53316149 AA
1 AA
53316151 ACTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 1 0.05
23 15 0.68
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.24
Consensus pattern (21 bp):
AATCATATCAAAATCATGCCA
Found at i:53317845 original size:19 final size:19
Alignment explanation
Indices: 53317821--53317860 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
53317811 TGTAAAGAAA
*
53317821 TATATATGTGACTATGGTT
1 TATATATGTGACTATAGTT
53317840 TATATATGTGACTATAGTT
1 TATATATGTGACTATAGTT
53317859 TA
1 TA
53317861 AGTACAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.47
Consensus pattern (19 bp):
TATATATGTGACTATAGTT
Found at i:53317953 original size:40 final size:41
Alignment explanation
Indices: 53317887--53317997 Score: 104
Period size: 40 Copynumber: 2.8 Consensus size: 41
53317877 GACTATGTTT
** * *
53317887 GGCACTAAGTGTGC-ATTTCAAAATAGCTTCAGCTATAAAT-A
1 GGCACTAAGTGTGCGATACCGAGATAGCTTCAGCTAT--ATGA
* ** *
53317928 -GCACTAAGTGTGGGA-ATTGAGATAGCTTCGGCTATATGA
1 GGCACTAAGTGTGCGATACCGAGATAGCTTCAGCTATATGA
53317967 GGCACTAAGTGTGCGATACCGAGATAGCTTC
1 GGCACTAAGTGTGCGATACCGAGATAGCTTC
53317998 GGTTTATTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
38 2 0.04
39 1 0.02
40 41 0.72
41 13 0.23
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (41 bp):
GGCACTAAGTGTGCGATACCGAGATAGCTTCAGCTATATGA
Found at i:53335924 original size:53 final size:53
Alignment explanation
Indices: 53335741--53335947 Score: 184
Period size: 53 Copynumber: 3.8 Consensus size: 53
53335731 ATTAGGTTTT
* * *
53335741 AAGGATACCAAGTAAGACCATGCCAAGGCATGG-AATTGGTAAGTT-TTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAA-TGGTAAGTTCATA-AA-GC
* * * * * * * *
53335795 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAAGC
* * * * * *
53335850 AAAGATCCCATGCAAGACCATGCCAAGGCATTGCAATGGTGAGTTCATAAAGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAAGC
* *
53335903 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
53335948 TAAAAAGGAA
Statistics
Matches: 116, Mismatches: 33, Indels: 9
0.73 0.21 0.06
Matches are distributed among these distances:
53 43 0.37
54 34 0.29
55 36 0.31
56 1 0.01
57 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAAGC
Found at i:53342368 original size:40 final size:39
Alignment explanation
Indices: 53342324--53342508 Score: 210
Period size: 40 Copynumber: 4.7 Consensus size: 39
53342314 GCCACTAGCT
*
53342324 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* *
53342364 CAAATGCCTCCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* *
53342403 CAAATGCCTTCGGGAGTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
** * * ** * *
53342443 TGAATGCCTTCGGGACTTTGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
53342483 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
53342509 TATCATCCGA
Statistics
Matches: 121, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 38 0.31
40 83 0.69
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:53349504 original size:40 final size:40
Alignment explanation
Indices: 53349437--53349642 Score: 249
Period size: 40 Copynumber: 5.2 Consensus size: 40
53349427 CCTTCGGAGT
** * *
53349437 TTAG-CCGGATATAGCCACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* *
53349476 TTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
*
53349516 TTAGCCCGG-TATAATAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* *
53349555 TTAGCCCGGATATAGTAGCTCGCACGAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* ** * *
53349595 TTAGCCCGAAT-TAGCCACTAGCTCAAATG-CTCTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCT-TCGGGAC
53349634 TTAGCCCGG
1 TTAGCCCGG
53349643 TTATCATCCG
Statistics
Matches: 146, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
38 2 0.01
39 68 0.47
40 76 0.52
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:53349558 original size:79 final size:79
Alignment explanation
Indices: 53349453--53349646 Score: 257
Period size: 79 Copynumber: 2.5 Consensus size: 79
53349443 GGATATAGCC
* *
53349453 ACTAGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTT
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
* *
53349518 AGCCCG-GTATAATA
66 AGCCCGAAT-TAACA
* * * *
53349532 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACGAATGCCTTCGGGACTT
1 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
* *
53349597 AGCCCGAATTAGCC
66 AGCCCGAATTAACA
*
53349611 ACTAGCTCAAATG-CTCTCGGGACTTAGCCCGGTTAT
1 ACTAGCACAAATGCCT-TCGGGACTTAGCCCGGTTAT
53349647 CATCCGAACA
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
78 2 0.02
79 97 0.97
80 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (79 bp):
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
AGCCCGAATTAACA
Found at i:53357746 original size:27 final size:27
Alignment explanation
Indices: 53357692--53357799 Score: 139
Period size: 27 Copynumber: 4.0 Consensus size: 27
53357682 AGCATGACTG
* *
53357692 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
53357718 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
* *
53357745 CCAGAACAGAT-ATATGGGGCCGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
53357772 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
53357799 C
1 C
53357800 AGGACGATTC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
26 15 0.21
27 54 0.76
28 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:53357782 original size:54 final size:53
Alignment explanation
Indices: 53357692--53357799 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 53
53357682 AGCATGACTG
* *
53357692 CCAGAACAGATAATGTGACAGAGTCACCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATGGGACAGAGCCACCAGAACAGATAATTGTGGCAGAGCCA
* * * *
53357745 CCAGAACAGATATATGGGGCCGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATA-ATGGGACAGAGCCACCAGAACAGATAATTGTGGCAGAGCCA
53357799 C
1 C
53357800 AGGACGATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 12 0.25
54 36 0.75
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (53 bp):
CCAGAACAGATAATGGGACAGAGCCACCAGAACAGATAATTGTGGCAGAGCCA
Found at i:53359246 original size:24 final size:24
Alignment explanation
Indices: 53359208--53359308 Score: 132
Period size: 24 Copynumber: 4.2 Consensus size: 24
53359198 CCAACACTGT
* *
53359208 TCTCCCTAATTAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
53359232 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
* * *
53359256 TATCCCTTATCAACTCCTAAGTCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
53359280 TATCCCTTATC-GACTCCTAAATCC
1 TCTCCCTTATCAG-CTCCTAAATCC
53359304 TCTCC
1 TCTCC
53359309 TGACAGACTT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.23, C:0.40, G:0.04, T:0.34
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:53365631 original size:27 final size:27
Alignment explanation
Indices: 53365578--53365660 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
53365568 GCATGGCTGG
* *
53365578 CAGAACAGATAA-TGTGACAAAGTCAC
1 CAGAACAGATAATTGTGGCAAAGCCAC
*
53365604 CAGAACAGATAATTGTGGCAGAGCCAC
1 CAGAACAGATAATTGTGGCAAAGCCAC
* *
53365631 CAGATCAGATAATTGTGGCATAGCCAC
1 CAGAACAGATAATTGTGGCAAAGCCAC
53365658 CAG
1 CAG
53365661 TGTGACAGCA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 12 0.24
27 39 0.76
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.17
Consensus pattern (27 bp):
CAGAACAGATAATTGTGGCAAAGCCAC
Found at i:53368064 original size:47 final size:47
Alignment explanation
Indices: 53368012--53368562 Score: 814
Period size: 47 Copynumber: 11.6 Consensus size: 47
53368002 GATAATTGTG
* *
53368012 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGGTGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
53368059 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
53368106 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
53368155 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCGATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
53368202 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * *
53368251 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
53368298 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
53368347 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCTATGTGATGA
1 ATGTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
53368396 ATGTGAAAGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
53368443 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * * * *
53368490 ATGTGAAAATGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
53368537 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTATATATATGTGATAAG
53368563 TCCCGAAGGG
Statistics
Matches: 463, Mismatches: 35, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
47 281 0.61
49 182 0.39
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:53368119 original size:96 final size:96
Alignment explanation
Indices: 53368012--53368562 Score: 898
Period size: 96 Copynumber: 5.8 Consensus size: 96
53368002 GATAATTGTG
*
53368012 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGGTGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
53368075 ATGTGATAAGGCCGAATGGCCGATGTGATGA
66 ATGTGATAAGGCCGAATGGCCGATGTGATGA
53368106 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
53368171 ATGTGATAAGGCCGAATGGCCGATGTGATGA
66 ATGTGATAAGGCCGAATGGCCGATGTGATGA
53368202 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
53368267 ATGTGATAAGGCCGAATGGCCAATGTGATGA
66 ATGTGATAAGGCCGAATGGCCGATGTGATGA
53368298 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
* *
53368363 ATATGTGATAAGGCCTAATGGCCTATGTGATGA
64 ATATGTGATAAGGCCGAATGGCCGATGTGATGA
*
53368396 ATGTGAAA--GTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* *
53368459 ATGTGATGAGGCCTAATGGCCGATGTGATGA
66 ATGTGATAAGGCCGAATGGCCGATGTGATGA
* * * * * * * * *
53368490 ATGTGAAAATG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
53368553 ATGTGATAAG
66 ATGTGATAAG
53368563 TCCCGAAGGG
Statistics
Matches: 434, Mismatches: 17, Indels: 12
0.94 0.04 0.03
Matches are distributed among these distances:
94 99 0.23
95 2 0.00
96 291 0.67
98 42 0.10
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (96 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCGAATGGCCGATGTGATGA
Found at i:53371542 original size:24 final size:24
Alignment explanation
Indices: 53371510--53371586 Score: 136
Period size: 24 Copynumber: 3.2 Consensus size: 24
53371500 CCAACATTGT
53371510 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
53371534 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
* *
53371558 TATCCCTTATCAACTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
53371582 TCTCC
1 TCTCC
53371587 TGACAGACTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.22, C:0.42, G:0.03, T:0.34
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:53372220 original size:29 final size:27
Alignment explanation
Indices: 53372120--53372238 Score: 141
Period size: 27 Copynumber: 4.4 Consensus size: 27
53372110 ATATATACAT
* * *
53372120 CACAT-AGGGCAAAGCATTCATCTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
53372146 CATATAAGGGCAGAATAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
53372173 CATATAAAGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
53372200 CACATAAGGGCAAAACACAGTCATTTTAC
1 CACATAAGGGC-AAA-ACAGTCATTTTAC
53372229 CACATAAGGG
1 CACATAAGGG
53372239 GTCCAAGCAC
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
26 4 0.05
27 49 0.62
28 3 0.04
29 23 0.29
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:53374509 original size:8 final size:8
Alignment explanation
Indices: 53374496--53374521 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
53374486 AAAGCTCCTA
53374496 ACCACTTT
1 ACCACTTT
53374504 ACCACTTT
1 ACCACTTT
53374512 ACCACTTT
1 ACCACTTT
53374520 AC
1 AC
53374522 TCATTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35
Consensus pattern (8 bp):
ACCACTTT
Found at i:53376904 original size:12 final size:12
Alignment explanation
Indices: 53376887--53376914 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53376877 CGATCCAAGC
53376887 TTTAAAGGAAAT
1 TTTAAAGGAAAT
53376899 TTTAAAGGAAAT
1 TTTAAAGGAAAT
53376911 TTTA
1 TTTA
53376915 CTTCCTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (12 bp):
TTTAAAGGAAAT
Found at i:53381861 original size:37 final size:37
Alignment explanation
Indices: 53381811--53381889 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
53381801 TTATTACGAA
* *
53381811 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
53381848 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
53381885 GTCTT
1 GTCTT
53381890 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:53382086 original size:47 final size:47
Alignment explanation
Indices: 53382008--53382402 Score: 655
Period size: 47 Copynumber: 8.4 Consensus size: 47
53381998 CCCTTCGGGA
* * * * * * *
53382008 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53382055 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53382102 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53382149 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53382196 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53382243 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53382290 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53382337 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53382384 CTTATCACATATATACACT
1 CTTATCACATATATACACT
53382403 GTCTTGGCTG
Statistics
Matches: 329, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 329 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53398362 original size:34 final size:34
Alignment explanation
Indices: 53398319--53398389 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
53398309 AGCATAACTT
53398319 AGTCACTTTCCTTCCTTACTAAACATACAACGTA
1 AGTCACTTTCCTTCCTTACTAAACATACAACGTA
53398353 AGTCACTTTCCTTCCTTACTAAACATACAACGTA
1 AGTCACTTTCCTTCCTTACTAAACATACAACGTA
53398387 AGT
1 AGT
53398390 AAAGCTCGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.32
Consensus pattern (34 bp):
AGTCACTTTCCTTCCTTACTAAACATACAACGTA
Found at i:53414081 original size:27 final size:27
Alignment explanation
Indices: 53414051--53414142 Score: 132
Period size: 27 Copynumber: 3.4 Consensus size: 27
53414041 TTTACCAAAG
* * * *
53414051 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCATTT
53414078 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
53414105 TACCCTC-AGTTTACAAAATTACCATTT
1 TACCCTCGA-TTTACAAAATTACCATTT
53414132 TACCCTCGATT
1 TACCCTCGATT
53414143 GTGAAATTAC
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.02
27 57 0.97
28 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCATTT
Found at i:53414295 original size:53 final size:54
Alignment explanation
Indices: 53414205--53414364 Score: 135
Period size: 53 Copynumber: 2.9 Consensus size: 54
53414195 TTGTAACTAG
* * *** *
53414205 TTTGTAAAATTACCGAAATACCACTGGCTTGTGAAATTACATAAAT-CCCTCAA
1 TTTGTAAAATTACCAAAATACCACTGACTTACAAAATTACAGAAATACCCTCAA
* * * *
53414258 TTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGAC
1 TTTGTAAAATTACCAAAATACCACTGACTTACAAAATTACAGAAATACCC-TCAA
* * * ** *
53414313 TTTCTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCT
1 TTTGT-AAAATTACCA-AAATACCACTGACTTACAAAATTACAGAAATACCCT
53414365 TGGTTTGTAG
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
53 38 0.44
54 3 0.03
55 8 0.09
56 38 0.44
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCACTGACTTACAAAATTACAGAAATACCCTCAA
Found at i:53414358 original size:27 final size:27
Alignment explanation
Indices: 53414263--53414370 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
53414253 CTCAATTTGT
** * *
53414263 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
53414290 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
*
53414317 TAAAAATTA-TAGAAATACCATTGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
53414346 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
53414371 GTAGATTTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
27 41 0.61
28 7 0.10
29 19 0.28
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:53415324 original size:25 final size:24
Alignment explanation
Indices: 53415286--53415355 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 24
53415276 AAGACGTGTT
*
53415286 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
53415310 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
53415335 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
53415356 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:53415368 original size:24 final size:24
Alignment explanation
Indices: 53415284--53415368 Score: 100
Period size: 25 Copynumber: 3.5 Consensus size: 24
53415274 GGAAGACGTG
*
53415284 TTAAAAGGGCTCTGCCCCAGTTTA
1 TTAAAAGGGCTTTGCCCCAGTTTA
**
53415308 CCGAAAAGGGCTTTGCCCCAGTTTA
1 -TTAAAAGGGCTTTGCCCCAGTTTA
*
53415333 TCAGAAAGGGCTTTGCCCCAG-TTA
1 TTA-AAAGGGCTTTGCCCCAGTTTA
53415357 TTAAAAGAGGCT
1 TTAAAAG-GGCT
53415369 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (24 bp):
TTAAAAGGGCTTTGCCCCAGTTTA
Found at i:53415611 original size:31 final size:31
Alignment explanation
Indices: 53415576--53415747 Score: 290
Period size: 31 Copynumber: 5.5 Consensus size: 31
53415566 CGTTTACAGT
53415576 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* * *
53415607 AAAGGCTTCAGCCCAGTGATATTATTTATTA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
53415638 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
53415669 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
**
53415700 AAAGGCTTCAACCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
53415731 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
53415748 AACCGTTAAA
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 129 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:53418508 original size:37 final size:37
Alignment explanation
Indices: 53418401--53418518 Score: 166
Period size: 37 Copynumber: 3.2 Consensus size: 37
53418391 CTCAGACAAA
* * * *
53418401 ATCTCCATACGGAGTTATCGGGTCTTACCCGGACA-AA
1 ATCTCCACACGTAGTCATCGGGTCTTACCCGGA-ATAT
*
53418438 ATCTCCACATGTAGTCATCGGGTCTTACCCGGAATAT
1 ATCTCCACACGTAGTCATCGGGTCTTACCCGGAATAT
53418475 ATCTCCACACGTAGTCATCGGGTCTTACCCGGAATAT
1 ATCTCCACACGTAGTCATCGGGTCTTACCCGGAATAT
*
53418512 ATTTCCA
1 ATCTCCA
53418519 AGTTTCATGT
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
36 1 0.01
37 72 0.99
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (37 bp):
ATCTCCACACGTAGTCATCGGGTCTTACCCGGAATAT
Found at i:53418784 original size:50 final size:48
Alignment explanation
Indices: 53418654--53418838 Score: 273
Period size: 48 Copynumber: 3.8 Consensus size: 48
53418644 GCACATCGCC
53418654 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
*
53418702 TACATAGTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
53418752 TATATATTTCACA-TTGACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACACTAG-CCATTCGGCTTTACCACATATACATATCTCA
* * *
53418800 TACATATTTCACATTAGCCATTCGGCCTTATCACATATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA
53418839 TGCATGTTCA
Statistics
Matches: 123, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
48 78 0.63
49 4 0.03
50 41 0.33
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:53418811 original size:98 final size:98
Alignment explanation
Indices: 53418657--53418838 Score: 294
Period size: 98 Copynumber: 1.9 Consensus size: 98
53418647 CATCGCCTAC
53418657 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATAGTTCACACTAGCCA
1 ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATAGTTCACACTAGCCA
*
53418722 TTCGGCTTTACCACATATACATATCTCATATAT
66 TTCGGCCTTACCACATATACATATCTCATATAT
* * * *
53418755 ATATTTCACA-TTGACCATTCGGCTTTACCACATATGCATATCTCATACATATTTCACATTAGCC
1 ATATTTCACACTAG-CCATTCGGCTTTACCACATATACATATCTCATACATAGTTCACACTAGCC
*
53418819 ATTCGGCCTTATCACATATA
65 ATTCGGCCTTACCACATATA
53418839 TGCATGTTCA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 2 0.03
98 75 0.97
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (98 bp):
ATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATAGTTCACACTAGCCA
TTCGGCCTTACCACATATACATATCTCATATAT
Found at i:53418945 original size:47 final size:47
Alignment explanation
Indices: 53418808--53418932 Score: 196
Period size: 47 Copynumber: 2.7 Consensus size: 47
53418798 CATACATATT
* *
53418808 TCACATTAGCCATTCGGCCTTATCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
53418855 TCACATTGGCCATTTGGCCTTATCACACATATGCGTGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
53418902 TCACATTGGCCATTCGGCCTTATCTCATATA
1 TCACATTGGCCATTCGGCCTTATCACATATA
53418933 CACACAATCA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:53424340 original size:34 final size:34
Alignment explanation
Indices: 53424294--53424386 Score: 105
Period size: 34 Copynumber: 2.7 Consensus size: 34
53424284 AAATACATTA
* * *
53424294 TGGGCCTAAGCCCATATCAATAATAGTAGCAGTC
1 TGGGCCTTAGCCCATATCAATAACAATAGCAGTC
* * *
53424328 TGGGCCTTAGCCCATTTCAGTAACAATAGCGGTC
1 TGGGCCTTAGCCCATATCAATAACAATAGCAGTC
* * *
53424362 TGGGCTTTAGCCCATTTCAGTAACA
1 TGGGCCTTAGCCCATATCAATAACA
53424387 TTAATCAGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (34 bp):
TGGGCCTTAGCCCATATCAATAACAATAGCAGTC
Found at i:53424402 original size:18 final size:17
Alignment explanation
Indices: 53424379--53424455 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 17
53424369 TAGCCCATTT
53424379 CAGTAACATTAATCAGTG
1 CAGTAACA-TAATCAGTG
*
53424397 CAGTAATAATAATCAGTG
1 CAGTAA-CATAATCAGTG
*
53424415 -ATGTAACCATGATC-GATG
1 CA-GTAA-CATAATCAG-TG
*
53424433 CAGTAACAGTAATTAGTG
1 CAGTAACA-TAATCAGTG
53424451 CAGTA
1 CAGTA
53424456 TGCAAGCAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
17 4 0.09
18 40 0.85
19 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (17 bp):
CAGTAACATAATCAGTG
Found at i:53424828 original size:27 final size:27
Alignment explanation
Indices: 53424783--53424926 Score: 182
Period size: 27 Copynumber: 5.3 Consensus size: 27
53424773 GAATAAATTT
* * * *
53424783 GTCATTTTACCTTACAGGGGTATTACA
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
53424810 GTCATTTTACGCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTCG
* *
53424837 GTCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
*
53424864 ATCATTTTACCCTAT-GAGGGTATTTCG
1 GTCATTTTACCCTATAG-GGGTATTTCG
53424891 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTCG
*
53424918 ATCATTTTA
1 GTCATTTTA
53424927 TCACATAAGG
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 1 0.01
27 99 0.98
28 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTCG
Found at i:53424951 original size:27 final size:27
Alignment explanation
Indices: 53424918--53425099 Score: 265
Period size: 27 Copynumber: 6.7 Consensus size: 27
53424908 GGGTATTTCG
53424918 ATCATTTTATCACATAAGGGCAAAATC
1 ATCATTTTATCACATAAGGGCAAAATC
* *
53424945 ATTATTTTATCACATAAGGGAAAAATC
1 ATCATTTTATCACATAAGGGCAAAATC
* *
53424972 ATCATTTTATCACATGAGGGCAAAGTC
1 ATCATTTTATCACATAAGGGCAAAATC
* *
53424999 GTCATTTTATCACATAAGGGCAAAATT
1 ATCATTTTATCACATAAGGGCAAAATC
*
53425026 GTCATTTTATCACATAAGGGCAAAATC
1 ATCATTTTATCACATAAGGGCAAAATC
* *
53425053 ATCATTTTATCACATAATGGTAAAATC
1 ATCATTTTATCACATAAGGGCAAAATC
* *
53425080 GTCATTTTATCACATGAGGG
1 ATCATTTTATCACATAAGGG
53425100 TTCAGGTACG
Statistics
Matches: 138, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 138 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Consensus pattern (27 bp):
ATCATTTTATCACATAAGGGCAAAATC
Found at i:53432256 original size:18 final size:18
Alignment explanation
Indices: 53432233--53432269 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
53432223 TAGATATAGG
53432233 ATCCACTTACTCCTATAT
1 ATCCACTTACTCCTATAT
53432251 ATCCACTTACTCCTATAT
1 ATCCACTTACTCCTATAT
53432269 A
1 A
53432270 GCCTGTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (18 bp):
ATCCACTTACTCCTATAT
Found at i:53444172 original size:23 final size:23
Alignment explanation
Indices: 53444145--53444202 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
53444135 ACGTTTACCG
53444145 CTATTAGTAGCTTTACTGCATTA
1 CTATTAGTAGCTTTACTGCATTA
*
53444168 CTATTAGTAGCTTTACTGCGTTA
1 CTATTAGTAGCTTTACTGCATTA
*
53444191 CTATTAGCAGCT
1 CTATTAGTAGCT
53444203 ACGCTGCGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (23 bp):
CTATTAGTAGCTTTACTGCATTA
Found at i:53444209 original size:23 final size:23
Alignment explanation
Indices: 53444145--53444210 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 23
53444135 ACGTTTACCG
* ** *
53444145 CTATTAGTAGCTTTACTGCATTA
1 CTATTAGCAGCTACACTGCGTTA
* **
53444168 CTATTAGTAGCTTTACTGCGTTA
1 CTATTAGCAGCTACACTGCGTTA
*
53444191 CTATTAGCAGCTACGCTGCG
1 CTATTAGCAGCTACACTGCG
53444211 ATATTGGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (23 bp):
CTATTAGCAGCTACACTGCGTTA
Found at i:53446397 original size:22 final size:20
Alignment explanation
Indices: 53446358--53446411 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
53446348 TGGGGAAGTG
*
53446358 TGGGAGCAAATTTAGGGATAAA
1 TGGGAG-AAAATTAGGGAT-AA
*
53446380 TGGGAGAAAATTAGGGGATTA
1 TGGGAGAAAATTA-GGGATAA
*
53446401 TGGGGGAAAAT
1 TGGGAGAAAAT
53446412 ATCCAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.39, C:0.02, G:0.37, T:0.22
Consensus pattern (20 bp):
TGGGAGAAAATTAGGGATAA
Found at i:53466130 original size:50 final size:49
Alignment explanation
Indices: 53466007--53466182 Score: 185
Period size: 50 Copynumber: 3.5 Consensus size: 49
53465997 CTGGTACGCA
* * **
53466007 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
* *
53466056 TAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCA-TCTAATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACG
* *** * *
53466106 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAG---TCTAATACACG
53466157 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
53466183 TGCGACGTCA
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 29 0.27
50 40 0.37
51 35 0.33
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
Found at i:53468000 original size:53 final size:55
Alignment explanation
Indices: 53467943--53468075 Score: 146
Period size: 55 Copynumber: 2.5 Consensus size: 55
53467933 CTTACCTTTT
** * *
53467943 CCATGTCTTGACATAGTCGTATGTGGTATCC-TTGCCTTAT-G-AACTCACCAATG
1 CCATGTCTTGACATAGTCGTACATGGGA-CCTTTACCTTATAGTAACTCACCAATG
* * * *
53467996 CCATGTCTTGGCATGGTCTTACATGGGACCTTTACCTTATAGTAACTCATCAATG
1 CCATGTCTTGACATAGTCGTACATGGGACCTTTACCTTATAGTAACTCACCAATG
* *
53468051 CCATGTCTTGACATGGTCTTACATG
1 CCATGTCTTGACATAGTCGTACATG
53468076 ATTTCCTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
52 2 0.03
53 30 0.44
54 1 0.01
55 35 0.51
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (55 bp):
CCATGTCTTGACATAGTCGTACATGGGACCTTTACCTTATAGTAACTCACCAATG
Found at i:53468123 original size:54 final size:56
Alignment explanation
Indices: 53467984--53468137 Score: 215
Period size: 55 Copynumber: 2.8 Consensus size: 56
53467974 TTGCCTTATG
* ** *
53467984 AACTCACCAATGCCATGTCTTGGCATGGTCTTACATGGGA-CCTTTACCTTATAGT
1 AACTCATCAATGCCATGTCTTGGCATGGTCTTACATGATATCCTTTACATTATAGT
* *
53468039 AACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTT-CATTATAG-
1 AACTCATCAATGCCATGTCTTGGCATGGTCTTACATGATATCCTTTACATTATAGT
* *
53468093 AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 AACTCATCAATGCCATGTCTTGGCATGGTCTTACATGATATCCTT
53468138 ATCTTACCAA
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
54 41 0.47
55 42 0.48
56 5 0.06
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (56 bp):
AACTCATCAATGCCATGTCTTGGCATGGTCTTACATGATATCCTTTACATTATAGT
Found at i:53468171 original size:47 final size:47
Alignment explanation
Indices: 53468116--53468237 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
53468106 CATGCCTTGG
* *
53468116 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
53468163 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
**
53468210 TGTGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
53468238 ATGCCAATGC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:53470518 original size:56 final size:56
Alignment explanation
Indices: 53470432--53470551 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
53470422 ACAAGGGATG
53470432 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
53470488 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
53470544 ATGGGCAA
1 ATGGGCAA
53470552 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:53477303 original size:14 final size:15
Alignment explanation
Indices: 53477280--53477308 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53477270 TGATTAAAGA
53477280 TATTTCTTGAAAAAT
1 TATTTCTTGAAAAAT
53477295 TATTT-TTGAAAAAT
1 TATTTCTTGAAAAAT
53477309 GTTAGTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (15 bp):
TATTTCTTGAAAAAT
Found at i:53477872 original size:61 final size:58
Alignment explanation
Indices: 53477795--53477907 Score: 181
Period size: 61 Copynumber: 1.9 Consensus size: 58
53477785 CGATTATCTT
*
53477795 AATATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTCTATTAATTTAATTGATTG
1 AATATTAAATTAAATTTAATATTTATC-T-T-GATAAGTATTATATTAATTTAATTGATTG
*
53477856 AATATTAAATTTAATTTAATATTTATCTTGATAAGTATTATATTAATTTAAT
1 AATATTAAATTAAATTTAATATTTATCTTGATAAGTATTATATTAATTTAAT
53477908 ATTAAAGTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
58 22 0.44
59 1 0.02
60 1 0.02
61 26 0.52
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (58 bp):
AATATTAAATTAAATTTAATATTTATCTTGATAAGTATTATATTAATTTAATTGATTG
Found at i:53477921 original size:58 final size:61
Alignment explanation
Indices: 53477795--53477928 Score: 179
Period size: 58 Copynumber: 2.2 Consensus size: 61
53477785 CGATTATCTT
* * *
53477795 AATATTAAATTAAATTTAATATTTATCTTGTAGATAAGTATTCTATTAATTTAATTGATTG
1 AATATTAAATTTAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATTGATTA
53477856 AATATTAAATTTAATTTAATATTTATC-T-T-GATAAGTATTATATTAATTTAA-T-ATTA
1 AATATTAAATTTAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATTGATTA
*
53477912 AAGTGATTAAGTTTAAT
1 AA-T-ATTAAATTTAAT
53477929 CATAGTTGAA
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
56 5 0.07
57 2 0.03
58 32 0.48
59 1 0.01
60 1 0.01
61 26 0.39
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
AATATTAAATTTAATTTAATATTTATCTTGTAGATAAGTATTATATTAATTTAATTGATTA
Found at i:53479622 original size:20 final size:20
Alignment explanation
Indices: 53479510--53479626 Score: 83
Period size: 20 Copynumber: 5.9 Consensus size: 20
53479500 TTGTATGAGA
* *
53479510 TTGCACTTCGATGCCTCTGT
1 TTGCACTTTGGTGCCTCTGT
*
53479530 TTGCACTTTGGTGCCTCT-A
1 TTGCACTTTGGTGCCTCTGT
* * *
53479549 TTACACTTTGGTGTCTTTGT
1 TTGCACTTTGGTGCCTCTGT
* ** * **
53479569 TTGCAATTCAGTACCTCTAA
1 TTGCACTTTGGTGCCTCTGT
** *
53479589 TTGCACAATCGTGCCTCTGT
1 TTGCACTTTGGTGCCTCTGT
*
53479609 TTGCACTCTGGTGCCTCT
1 TTGCACTTTGGTGCCTCT
53479627 ATTAGCATCT
Statistics
Matches: 69, Mismatches: 27, Indels: 2
0.70 0.28 0.02
Matches are distributed among these distances:
19 15 0.22
20 54 0.78
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.41
Consensus pattern (20 bp):
TTGCACTTTGGTGCCTCTGT
Found at i:53479626 original size:40 final size:39
Alignment explanation
Indices: 53479521--53479627 Score: 99
Period size: 40 Copynumber: 2.7 Consensus size: 39
53479511 TGCACTTCGA
** *
53479521 TGCCTCTGTTTGCACTTTGGTGCCTCT-ATTACACTTTGG
1 TGCCTCTGTTTGCAC-TTGGTGCCTCTAATTACACAATCG
* * * * * *
53479560 TGTCTTTGTTTGCAATTCAGTACCTCTAATTGCACAATCG
1 TGCCTCTGTTTGCACTT-GGTGCCTCTAATTACACAATCG
53479600 TGCCTCTGTTTGCACTCTGGTGCCTCTA
1 TGCCTCTGTTTGCACT-TGGTGCCTCTA
53479628 TTAGCATCTA
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
38 2 0.04
39 19 0.37
40 29 0.57
41 1 0.02
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.41
Consensus pattern (39 bp):
TGCCTCTGTTTGCACTTGGTGCCTCTAATTACACAATCG
Found at i:53482128 original size:46 final size:46
Alignment explanation
Indices: 53482077--53482177 Score: 123
Period size: 46 Copynumber: 2.2 Consensus size: 46
53482067 TTCGACATGA
* *
53482077 ACTTACATGAATTATTCCTGTCTCCAATGCCATATATAT-ATTATGG
1 ACTTACATGAATCATTCCTGTCTCCAAAGCCATATATATGA-TATGG
* ** * *
53482123 GCTTACATGGCTCATTCCTGTCTCCAAAGCCGTATATTTGATATGG
1 ACTTACATGAATCATTCCTGTCTCCAAAGCCATATATATGATATGG
53482169 ACTTACATG
1 ACTTACATG
53482178 GCTCATTTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (46 bp):
ACTTACATGAATCATTCCTGTCTCCAAAGCCATATATATGATATGG
Found at i:53482178 original size:46 final size:46
Alignment explanation
Indices: 53482090--53482190 Score: 141
Period size: 46 Copynumber: 2.2 Consensus size: 46
53482080 TACATGAATT
* *
53482090 ATTCCTGTCTCCAATGCCATATATATATTATGGGCTTACATGGCTC
1 ATTCCTGTCTCCAAAGCCATATATATATTATGGACTTACATGGCTC
* *
53482136 ATTCCTGTCTCCAAAGCCGTATATTTGA-TATGGACTTACATGGCTC
1 ATTCCTGTCTCCAAAGCCATATATAT-ATTATGGACTTACATGGCTC
*
53482182 ATTTCTGTC
1 ATTCCTGTC
53482191 CTTTCCTGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 48 0.98
47 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.38
Consensus pattern (46 bp):
ATTCCTGTCTCCAAAGCCATATATATATTATGGACTTACATGGCTC
Found at i:53488049 original size:20 final size:20
Alignment explanation
Indices: 53488015--53488131 Score: 92
Period size: 20 Copynumber: 5.9 Consensus size: 20
53488005 TTGTATGAGA
* *
53488015 TTGCACTTCGATGCCTCTGT
1 TTGCACTTTGGTGCCTCTGT
* *
53488035 TTGGACTTTGGTGCCTCT-A
1 TTGCACTTTGGTGCCTCTGT
* *
53488054 TTACACTTTGGTGTCTCTGT
1 TTGCACTTTGGTGCCTCTGT
* ** **
53488074 TTGCAATTCAGTGCCTCTAA
1 TTGCACTTTGGTGCCTCTGT
** *
53488094 TTGCACAATCGTGCCTCTGT
1 TTGCACTTTGGTGCCTCTGT
*
53488114 TTGCACTCTGGTGCCTCT
1 TTGCACTTTGGTGCCTCT
53488132 ATTAGCTTCT
Statistics
Matches: 71, Mismatches: 25, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
19 15 0.21
20 56 0.79
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCACTTTGGTGCCTCTGT
Found at i:53488128 original size:40 final size:39
Alignment explanation
Indices: 53488026--53488132 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 39
53488016 TGCACTTCGA
* ** *
53488026 TGCCTCTGTTTGGACTTTGGTGCCTCT-ATTACACTTTGG
1 TGCCTCTGTTTGCAC-TTGGTGCCTCTAATTACACAATCG
* * * *
53488065 TGTCTCTGTTTGCAATTCAGTGCCTCTAATTGCACAATCG
1 TGCCTCTGTTTGCACTT-GGTGCCTCTAATTACACAATCG
53488105 TGCCTCTGTTTGCACTCTGGTGCCTCTA
1 TGCCTCTGTTTGCACT-TGGTGCCTCTA
53488133 TTAGCTTCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.04
39 20 0.37
40 31 0.57
41 1 0.02
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.40
Consensus pattern (39 bp):
TGCCTCTGTTTGCACTTGGTGCCTCTAATTACACAATCG
Found at i:53489441 original size:37 final size:36
Alignment explanation
Indices: 53489381--53489451 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 36
53489371 AGCTCAGATG
53489381 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTTATCGGGTC-TACCCGGACA
*
53489418 AAATCTCCACACGTAGTCT-TCGGGTCTACCCGGA
1 AAATCTCCACACGAAGT-TATCGGGTCTACCCGGA
53489452 ATATATTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 8 0.25
37 23 0.72
38 1 0.03
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.23
Consensus pattern (36 bp):
AAATCTCCACACGAAGTTATCGGGTCTACCCGGACA
Found at i:53489651 original size:48 final size:48
Alignment explanation
Indices: 53489599--53489737 Score: 260
Period size: 48 Copynumber: 2.9 Consensus size: 48
53489589 CACATCTCCA
* *
53489599 ACATATTTCACACTAGCCCTTCGGCTTTACCACATATACATATCTCAT
1 ACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAT
53489647 ACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAT
1 ACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAT
53489695 ACATATTTCACATTAGCCATTCGGCTTTACCACATATACATAT
1 ACATATTTCACATTAGCCATTCGGCTTTACCACATATACATAT
53489738 ATTTATCTTG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 89 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (48 bp):
ACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAT
Found at i:53494044 original size:46 final size:46
Alignment explanation
Indices: 53493945--53494060 Score: 144
Period size: 46 Copynumber: 2.5 Consensus size: 46
53493935 TCTTCGACAT
** * * *
53493945 GGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATTAT
1 GGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATTAC
* *
53493991 GGGCTTACATGGCTCATTCCTGTCTCCAAAGCCATATATTTGA-TAC
1 GGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATAT-ATTAC
*
53494037 GGACTTACATGGCTCATTTCTGTC
1 GGACTTACATGGCTCATTCCTGTC
53494061 CTGTCCTGTC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 59 0.98
47 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (46 bp):
GGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATTAC
Found at i:53498631 original size:44 final size:44
Alignment explanation
Indices: 53498556--53498676 Score: 124
Period size: 44 Copynumber: 2.8 Consensus size: 44
53498546 TTCTCAAATC
* * *
53498556 ACCGGCATT-TCGCCTGTTAGGATCG-AGGCCCGATATCAGT-TC-
1 ACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAT-T-AGTATCT
*
53498598 ATCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGATTAGTATCT
1 ACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGATTAGTATCT
** * *
53498642 ACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGA
1 ACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGA
53498677 ATAATCAAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
42 11 0.17
43 16 0.24
44 39 0.59
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (44 bp):
ACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGATTAGTATCT
Found at i:53499044 original size:43 final size:43
Alignment explanation
Indices: 53498996--53499206 Score: 350
Period size: 43 Copynumber: 4.9 Consensus size: 43
53498986 ACATATCATT
* * *
53498996 TCACCGGCATTACGCCTGCTAGGCACGAAGGCCCGAATATACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
53499039 TCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
* *
53499082 TCACCGGCACGAAGCCTGCTAGGCATGAAGGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
53499125 TCACCGGCACTAAGCCTGCTAGGCACGAAAGCCCGAATACACA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
*
53499168 TCACCGGTACTAAGCCTGCTAGGCACGAAGGCCCGAATA
1 TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATA
53499207 TAATACCAGC
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 158 1.00
ACGTcount: A:0.30, C:0.33, G:0.24, T:0.13
Consensus pattern (43 bp):
TCACCGGCACTAAGCCTGCTAGGCACGAAGGCCCGAATACACA
Found at i:53505814 original size:12 final size:12
Alignment explanation
Indices: 53505797--53505827 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
53505787 TGTGCAATCC
53505797 CGTACAAGCGCT
1 CGTACAAGCGCT
*
53505809 CGTACAAGTGCT
1 CGTACAAGCGCT
53505821 CGTACAA
1 CGTACAA
53505828 ACCCTATTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (12 bp):
CGTACAAGCGCT
Found at i:53508622 original size:46 final size:45
Alignment explanation
Indices: 53508518--53508734 Score: 181
Period size: 46 Copynumber: 4.7 Consensus size: 45
53508508 GCATATCTGT
* * ***
53508518 GCCGATGCCATGTCCTAGACATGGTCTTACACTGAC-AAATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTCGTCTCG-AG
* *
53508564 GCTGATACATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CGTCTCGAG
* * * *
53508610 GCCGAAGCATGTCCCAGACATGTCTTACACTAGCAATT-GTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC--TTCGTCTCGAG
* * * *
53508656 GCCGATGCCATGTCCCAGACATGGTATTACACTGGCTCTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TCGT-CTCGAG
53508704 GCCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
53508735 AGCTCACACA
Statistics
Matches: 139, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
44 12 0.09
45 14 0.10
46 62 0.45
47 29 0.21
48 21 0.15
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTCGTCTCGAG
Found at i:53511071 original size:27 final size:27
Alignment explanation
Indices: 53511037--53511210 Score: 197
Period size: 27 Copynumber: 6.4 Consensus size: 27
53511027 TAAATTGTAC
53511037 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
53511064 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
53511090 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
53511118 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
53511146 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
53511173 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
53511200 AGCACTGAGTG
1 AGCACTAAGTG
53511211 AGCGGACTCA
Statistics
Matches: 125, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:53511151 original size:82 final size:81
Alignment explanation
Indices: 53511038--53511193 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
53511028 AAATTGTACA
* *
53511038 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
53511102 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
53511119 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
53511184 TGCGAGTTGA
65 TGCGAATTGA
53511194 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:53519213 original size:81 final size:80
Alignment explanation
Indices: 53519075--53519228 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 80
53519065 AAATTGTACA
53519075 GCACTAAGTTGGATTTGACTATGTTGCACTAAGTGTGCGAAAATGAATATGATGCACTAAGTGTG
1 GCACTAAGTTGGATTTGACTATG-TGCACTAAGTGTGCGAAAATGAATATGATGCACTAAGTGTG
53519140 CGAATTGACCATGCCG
65 CGAATTGACCATGCCG
** *
53519156 GCACTAAGTGTGCGAGTTTGACTATG-GCACTAAGTGTGCG-ATTTGATTATG-TAGCACTAAGT
1 GCACTAAGT-TG-GA-TTTGACTATGTGCACTAAGTGTGCGAAAATGAATATGAT-GCACTAAGT
*
53519218 GTGCGAGTTGA
62 GTGCGAATTGA
53519229 TTATATAGCA
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
80 1 0.02
81 36 0.55
82 16 0.25
83 2 0.03
84 10 0.15
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (80 bp):
GCACTAAGTTGGATTTGACTATGTGCACTAAGTGTGCGAAAATGAATATGATGCACTAAGTGTGC
GAATTGACCATGCCG
Found at i:53519220 original size:27 final size:27
Alignment explanation
Indices: 53519074--53519245 Score: 156
Period size: 27 Copynumber: 6.4 Consensus size: 27
53519064 TAAATTGTAC
53519074 AGCACTAAGT-TG-GATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
53519099 TGCACTAAGTGTGCGAAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTTGACTATGT
* * *
53519126 ATGCACTAAGTGTGCGAATTGACCATGCC
1 A-GCACTAAGTGTGCGATTTGACTATG-T
*
53519155 GGCACTAAGTGTGCGAGTTTGACTATG-
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
53519182 -GCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
53519208 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
53519235 AGCACTGAGTG
1 AGCACTAAGTG
53519246 AGCGGACTCA
Statistics
Matches: 123, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
25 18 0.15
26 17 0.14
27 43 0.35
28 37 0.30
29 8 0.07
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:53519224 original size:53 final size:54
Alignment explanation
Indices: 53519074--53519226 Score: 177
Period size: 53 Copynumber: 2.9 Consensus size: 54
53519064 TAAATTGTAC
* ***
53519074 AGCACTAAGT-TG-GATTTGACTATGTTGCACTAAGTGTGCGAAAATGAATATG
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTTGAATATG
* * ** *
53519126 ATGCACTAAGTGTGCGAATTGACCATGCCGGCACTAAGTGTGCGAGTTTGACTATG
1 A-GCACTAAGTGTGCGATTTGACTATG-TAGCACTAAGTGTGCGAGTTTGAATATG
*
53519182 -GCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTGTGCGAGTT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTT
53519227 GATTATATAG
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
52 1 0.01
53 27 0.32
54 24 0.29
55 10 0.12
56 22 0.26
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTTGAATATG
Found at i:53520398 original size:15 final size:15
Alignment explanation
Indices: 53520380--53520409 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53520370 GGTACTAGCA
53520380 TGAAAACACCTAAAG
1 TGAAAACACCTAAAG
*
53520395 TGAAAACAGCTAAAG
1 TGAAAACACCTAAAG
53520410 GGACTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.13
Consensus pattern (15 bp):
TGAAAACACCTAAAG
Found at i:53521089 original size:47 final size:49
Alignment explanation
Indices: 53520941--53521303 Score: 235
Period size: 49 Copynumber: 7.7 Consensus size: 49
53520931 TTTCTTGTGT
* * * *
53520941 GCCAGTGTAAGA-CATGTCTGGGAAAT-GTATCAGCCAC-ATTATGAGT-
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATGATGA-TA
* ** * * *
53520987 GCCAGTATAAGACCATGTCTGGGACATGGCATTGGGAC-AGA-GACGAGTA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCA-TCAGCCTCGATGATGA-TA
** * **
53521036 -TTAGTGTAAGA-AATGTCTGGGACAT-GCATCAGCCTCGACAATGATA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATGATGATA
* * * * *
53521082 GCCAGTGTAACA-CGTGTCTGGGACA-CGCATCAG-CTAAGA-GTTG-T-
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCT-CGATGATGATA
* * * ** * *
53521126 GCTAGTGTAAGA-CACG-CTGGGACAT-GCATCAGTACATATAT-ACGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAG--CCTCGATGATGATA
*
53521173 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GACCTCGATGATGATA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAG-CCTCGATGATGATA
* *
53521222 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATGATGATA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATGATGATA
* *
53521271 GCCTGTGTAAGACCATGTTTGGGACATGGCATC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATC
53521304 GACAATTTAT
Statistics
Matches: 249, Mismatches: 46, Indels: 41
0.74 0.14 0.12
Matches are distributed among these distances:
43 15 0.06
44 12 0.05
45 7 0.03
46 23 0.09
47 69 0.28
48 23 0.09
49 94 0.38
50 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (49 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATGATGATA
Found at i:53528103 original size:30 final size:30
Alignment explanation
Indices: 53528069--53528126 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53528059 TTTTTGAGCA
* *
53528069 TAGGGGTAAAATGGTTATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTCATTTTGCCAAAGTT
*
53528099 TAGGGGCAAAATGGTCATTTTTCCAAAG
1 TAGGGGCAAAATGGTCATTTTGCCAAAG
53528127 ATGTGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTGCCAAAGTT
Found at i:53528684 original size:49 final size:49
Alignment explanation
Indices: 53528484--53528745 Score: 176
Period size: 49 Copynumber: 5.5 Consensus size: 49
53528474 AAGACATGTA
* * * * *
53528484 TAAGACCATGTTTAGGACATGGCATC-GGCACAGA-GATGAGTGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCAGCCAC-GATGATGAGAGCTAGTG
* * * * * *
53528532 TAA-AACATGACTGGGACAT-GCATCGGCCTCGACGATGATAGCCT-GTG
1 TAAGACCATGTCTGGGACATGGCATCAGCCACGATGATGAGAG-CTAGTG
* * * * * * * *
53528579 TAAGA-CGTGTCTGAGACA-CGCATCAGCTAAGA-GTTGTG-G-TAGCG
1 TAAGACCATGTCTGGGACATGGCATCAGCCACGATGATGAGAGCTAGTG
53528623 TAAGA-CATGTCTGGGACAT-GCATCAG-CACGTAT-ATACGAGAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCAGCCACG-ATGAT--GAGAGCTAGTG
* *
53528671 TAAGACCATGTCTGGGACATGGCATCAGCCTCGATGATGATAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCAGCCACGATGATGAGAGCTAGTG
53528720 TAAGACCATG-CTTGGGACATGGCATC
1 TAAGACCATGTC-TGGGACATGGCATC
53528746 GGCAACTTAT
Statistics
Matches: 167, Mismatches: 29, Indels: 35
0.72 0.13 0.15
Matches are distributed among these distances:
43 3 0.02
44 27 0.16
45 1 0.01
46 12 0.07
47 47 0.28
48 15 0.09
49 48 0.29
50 9 0.05
51 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (49 bp):
TAAGACCATGTCTGGGACATGGCATCAGCCACGATGATGAGAGCTAGTG
Found at i:53530529 original size:22 final size:22
Alignment explanation
Indices: 53530498--53530548 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
53530488 CTCCACGTAG
*
53530498 GAATTTTTTTT-TAAATTCATA
1 GAATTTTTTTTAAAAATTCATA
53530519 GAATTTTTTTTAAAAATTCATA
1 GAATTTTTTTTAAAAATTCATA
53530541 GAATTTTT
1 GAATTTTT
53530549 GTGAGCCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (22 bp):
GAATTTTTTTTAAAAATTCATA
Found at i:53530774 original size:17 final size:17
Alignment explanation
Indices: 53530749--53530800 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
53530739 ACTCATCACC
53530749 TTATATATATATTATAA
1 TTATATATATATTATAA
* *
53530766 TTATTTATAATACT-TAA
1 TTATATAT-ATATTATAA
*
53530783 TTATGT-TATATTATAA
1 TTATATATATATTATAA
53530799 TT
1 TT
53530801 TGATAGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 4 0.14
16 6 0.21
17 15 0.52
18 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTATATATATATTATAA
Found at i:53532611 original size:24 final size:24
Alignment explanation
Indices: 53532577--53532671 Score: 154
Period size: 24 Copynumber: 4.0 Consensus size: 24
53532567 CTGTCAGGAC
*
53532577 AGGATTAAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
53532601 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
*
53532625 AGGATTTAGGAGTTGATAAGGGAG
1 AGGATTTAGGAGTTGATAAGGGAT
* *
53532649 AGGATTTAGGAGCTGATTAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
53532672 GAACAGTGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.34, C:0.01, G:0.39, T:0.26
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:53533647 original size:8 final size:8
Alignment explanation
Indices: 53533634--53533666 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
53533624 CTAGATCGGC
53533634 AAAAGCCG
1 AAAAGCCG
53533642 AAAAGCCG
1 AAAAGCCG
53533650 AAATA-CCG
1 AAA-AGCCG
53533658 AAAAGCCG
1 AAAAGCCG
53533666 A
1 A
53533667 CATTTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.04
8 21 0.91
9 1 0.04
ACGTcount: A:0.52, C:0.24, G:0.21, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:53534092 original size:27 final size:27
Alignment explanation
Indices: 53534052--53534162 Score: 154
Period size: 27 Copynumber: 4.1 Consensus size: 27
53534042 AGGAAGCGTC
* *
53534052 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGTT
*
53534079 CTGGTGGCTCTGCC-CCATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGTT
53534106 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGTT
* *
53534133 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGTT
53534159 CTGG
1 CTGG
53534163 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 17 0.22
27 56 0.74
28 3 0.04
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGTT
Found at i:53540483 original size:24 final size:24
Alignment explanation
Indices: 53540384--53540484 Score: 157
Period size: 24 Copynumber: 4.2 Consensus size: 24
53540374 AAGTCTGTCA
*
53540384 GGAGAGGATTTAGGAGTTAATAAG
1 GGAGAGGATTTAGGAGTTGATAAG
*
53540408 GGATAGGATTTAGGAGTTGATAAG
1 GGAGAGGATTTAGGAGTTGATAAG
*
53540432 GGATAGGATTTAGGAGTTGATAAG
1 GGAGAGGATTTAGGAGTTGATAAG
* *
53540456 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGTTGATAAG
53540480 GGAGA
1 GGAGA
53540485 ACAGTGTTGG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.34, C:0.01, G:0.40, T:0.26
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGTTGATAAG
Found at i:53541909 original size:27 final size:27
Alignment explanation
Indices: 53541869--53541979 Score: 154
Period size: 27 Copynumber: 4.1 Consensus size: 27
53541859 AGGAAGCGTC
* *
53541869 CTGGTGGCTATGCCACCATTATCTGAT
1 CTGGTGGCTCTGCCACCATTATCTGTT
53541896 CTGGTGGCTCTGCC-CCATATATCTGTT
1 CTGGTGGCTCTGCCACCAT-TATCTGTT
*
53541923 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCACCATTATCTGTT
* *
53541950 CTGGTGACTCTGTCA-CATTATCTGTT
1 CTGGTGGCTCTGCCACCATTATCTGTT
53541976 CTGG
1 CTGG
53541980 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 18 0.24
27 55 0.72
28 3 0.04
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACCATTATCTGTT
Found at i:53553575 original size:79 final size:80
Alignment explanation
Indices: 53553477--53553659 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
53553467 TACTCCTTCA
* *
53553477 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAGT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
53553540 ATTTAGTAAC-TCGCACC
64 ATATAGTAACTTAGCA-C
* **
53553557 AATGCCTTCGGG-CTTAGCCCGGAGTTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAGTTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
* *
53553621 ATGGTCACTTAGCAC
66 ATAGTAACTTAGCAC
*
53553636 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
53553660 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAGTTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:53553592 original size:39 final size:40
Alignment explanation
Indices: 53553475--53553659 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
53553465 GCTACTCCTT
*
53553475 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
53553515 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
53553555 CCAATGCCTTCGGG-CTTAGCCCGGAGTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
53553594 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
53553635 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
53553660 CATCATTCGA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 78 0.62
41 13 0.10
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:53556184 original size:31 final size:31
Alignment explanation
Indices: 53556146--53556209 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
53556136 CCTTTTCATA
* *
53556146 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACAATGGGCCAAAGCCT
**
53556177 TTTCATATTTCATATTAATGGGCCAAAGCCT
1 TTTCATATTTCATAACAATGGGCCAAAGCCT
53556208 TT
1 TT
53556210 ACTGTAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACAATGGGCCAAAGCCT
Found at i:53556482 original size:23 final size:23
Alignment explanation
Indices: 53556422--53556519 Score: 142
Period size: 23 Copynumber: 4.2 Consensus size: 23
53556412 GGCCTATCCT
* *
53556422 CTTTCAATAACTGGGGAAAAAGCC
1 CTTT-AATAACTGGGGCATAAGCC
53556446 CTTTTAATAACTGGGGCATAAGCC
1 C-TTTAATAACTGGGGCATAAGCC
*
53556470 CTTTAATAGCTGGGGCATAAGCC
1 CTTTAATAACTGGGGCATAAGCC
*
53556493 CTTTAATAACTGGGGCGTAAGCC
1 CTTTAATAACTGGGGCATAAGCC
53556516 CTTT
1 CTTT
53556520 TACACTTCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
23 46 0.68
24 19 0.28
25 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (23 bp):
CTTTAATAACTGGGGCATAAGCC
Found at i:53556595 original size:20 final size:20
Alignment explanation
Indices: 53556570--53556636 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
53556560 TTATGATTAC
53556570 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
53556590 ATCATGTGCATATCATACAC
1 ATCATGTGCATATCATACAT
*
53556610 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
53556630 ACCATGT
1 ATCATGT
53556637 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:53559607 original size:26 final size:26
Alignment explanation
Indices: 53559529--53559737 Score: 282
Period size: 26 Copynumber: 8.2 Consensus size: 26
53559519 GGCCTAGTCT
* *
53559529 CTTTT-AAT-AACTGGGGCA-AAACC
1 CTTTTCAATAAACTAGGGCATAAGCC
** *
53559552 CTTTTCGGTAAACTAGGGC-GAAGCC
1 CTTTTCAATAAACTAGGGCATAAGCC
*
53559577 CTTTTCAATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTAGGGCATAAGCC
** *
53559603 CTTTTCGGTAAACTAGGGTATAAGCC
1 CTTTTCAATAAACTAGGGCATAAGCC
53559629 CTTTTCAATAAACTAGGGCATAAGCC
1 CTTTTCAATAAACTAGGGCATAAGCC
*
53559655 CTTTTCAATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTAGGGCATAAGCC
*
53559681 CTTTTCAATAAACTGGGGCATAAGCC
1 CTTTTCAATAAACTAGGGCATAAGCC
*
53559707 CTTTTCAATAAACTAGGGTATAAGCC
1 CTTTTCAATAAACTAGGGCATAAGCC
53559733 CTTTT
1 CTTTT
53559738 GCACTTCCTC
Statistics
Matches: 164, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
23 5 0.03
24 1 0.01
25 28 0.17
26 130 0.79
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (26 bp):
CTTTTCAATAAACTAGGGCATAAGCC
Found at i:53559853 original size:20 final size:20
Alignment explanation
Indices: 53559787--53559837 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
53559777 TTATGAATAC
53559787 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
53559807 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
53559827 ATCATGTGCAT
1 ATCATGTGCAT
53559838 ATGATATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:53560624 original size:27 final size:27
Alignment explanation
Indices: 53560563--53560626 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
53560553 GGCGTATTCA
53560563 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATACAAGGGTATTACGG
* *
53560590 TCACTTTACCCTACAAGGGCT-TTACGG
1 TCATTTTACCATACAAGGG-TATTACGG
*
53560617 TCTTTTTACC
1 TCATTTTACC
53560627 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAAGGGTATTACGG
Found at i:53560673 original size:27 final size:27
Alignment explanation
Indices: 53560633--53561344 Score: 218
Period size: 27 Copynumber: 26.3 Consensus size: 27
53560623 TACCTATTAG
* * *
53560633 GGGTGTTTAGGTAAATTTACAAATCAA
1 GGGTATTTTGGTAATTTTACAAATCAA
** * *
53560660 GGGTATTTCT-GTAATTTTGTAAATTAG
1 GGGTATTT-TGGTAATTTTACAAATCAA
* **
53560687 GGGTATTTTGGTAATTTTATAAATTGA
1 GGGTATTTTGGTAATTTTACAAATCAA
** * *
53560714 GGGTATTTCAGTAATTTAACAAA-CTA
1 GGGTATTTTGGTAATTTTACAAATCAA
*
53560740 GTGGTATTTTGGTAATTTTACAAA-CTAG
1 G-GGTATTTTGGTAATTTTACAAATC-AA
* * ** *
53560768 GGGTGTTTTGGTAATTCTAC-CCTACAG
1 GGGTATTTTGGTAATTTTACAAAT-CAA
* * *
53560795 GGGTATTTTAGTAATTTCAC-AATCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
**** **
53560821 GGGTAAAACGGTAATTTTGTAAATCAA
1 GGGTATTTTGGTAATTTTACAAATCAA
***** * **
53560848 GGGTAAAACAGTAATTCTGTAAATCAA
1 GGGTATTTTGGTAATTTTACAAATCAA
***** * * *
53560875 GGGTAAAACAGTAATTCTATAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
* * * *
53560902 GGGTACTTAGGTAATTTTTACAAGTCGA
1 GGGTATTTTGGTAA-TTTTACAAATCAA
**** *
53560930 GGGTATTTCAAAAATTTTACAAATCAG
1 GGGTATTTTGGTAATTTTACAAATCAA
* *
53560957 GTGGTATTTTAGTAATTTTACAAA-CCA
1 G-GGTATTTTGGTAATTTTACAAATCAA
* * * *
53560984 GAGGCATTTTAGTAATTTTACAAACCAG
1 G-GGTATTTTGGTAATTTTACAAATCAA
*** *
53561012 GGGTATTTTGGTAATTTTATTGATCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
** *
53561039 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCAA
** ** * *
53561066 GGGTATTTCAGTAATTTTGTAAACCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
*** * ** *
53561093 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
*** ** *
53561120 GGGTAAGATGGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
*** * * *
53561147 GGGTAAAATGGTAATTCTATAAATCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
*** * **
53561174 GGGTAAAATGGTAATTCTATCTTA-C-A
1 GGGTATTTTGGTAATTTTA-CAAATCAA
** *
53561200 GGAGTATTTCAGTAATTTTACAAAATCGA
1 GG-GTATTTTGGTAATTTTAC-AAATCAA
** * **
53561229 GGGTATTTCAGTAATTTTGCAAATTGA
1 GGGTATTTTGGTAATTTTACAAATCAA
* *
53561256 GGGTATTTCGGTAATTTTGCAAATCAA
1 GGGTATTTTGGTAATTTTACAAATCAA
* * ***
53561283 GGATA-TTTGGTTAATTTTATAAATTGG
1 GGGTATTTTGG-TAATTTTACAAATCAA
* * *
53561310 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTACAAATCAA
53561337 GGGTATTT
1 GGGTATTT
53561345 CAATAATTTG
Statistics
Matches: 540, Mismatches: 128, Indels: 34
0.77 0.18 0.05
Matches are distributed among these distances:
26 24 0.04
27 447 0.83
28 66 0.12
29 3 0.01
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.37
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAA
Found at i:53566552 original size:40 final size:40
Alignment explanation
Indices: 53566492--53566626 Score: 252
Period size: 40 Copynumber: 3.4 Consensus size: 40
53566482 CGGATGTAAC
*
53566492 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
53566532 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
53566572 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
53566612 AACCCACACGAATGC
1 AACCCGCACGAATGC
53566627 TATGCACATA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 93 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:53570765 original size:42 final size:42
Alignment explanation
Indices: 53570699--53570850 Score: 148
Period size: 42 Copynumber: 3.6 Consensus size: 42
53570689 CCGAGGCTAT
* *
53570699 GTGTAAGACCATATCTGAGATATGGTATCATTATGAGATTTC
1 GTGTAAGACCATATCTGGGATATGGTATCATTATGAGATCTC
* * * *
53570741 GTGTATGACCATATCTGGGGTATGGCATCGA-TATGAAATCTC
1 GTGTAAGACCATATCTGGGATATGGTATC-ATTATGAGATCTC
* * * *
53570783 GTATAAGACCATAGCTGGGCTAT--TAGCATTGATACGAGATCTC
1 GTGTAAGACCATATCTGGGATATGGTATCATT-AT--GAGATCTC
*
53570826 ATGTAAGACCATATCTGGGATATGG
1 GTGTAAGACCATATCTGGGATATGG
53570851 CATTGGTGTA
Statistics
Matches: 86, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 2 0.02
42 53 0.62
43 27 0.31
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGTATCATTATGAGATCTC
Found at i:53574925 original size:18 final size:17
Alignment explanation
Indices: 53574904--53574958 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
53574894 ACAATTCTTT
53574904 TCTCTTCTTCTTTTCTCC
1 TCTCTTCTTCTTTTCT-C
*
53574922 TCTCTTCATCTATTT-TC
1 TCTCTTCTTCT-TTTCTC
*
53574939 TCTTCCTCTTCTTTTC-C
1 TC-TCTTCTTCTTTTCTC
53574956 TCT
1 TCT
53574959 ATAGCCGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 9 0.29
18 18 0.58
19 3 0.10
ACGTcount: A:0.04, C:0.36, G:0.00, T:0.60
Consensus pattern (17 bp):
TCTCTTCTTCTTTTCTC
Found at i:53576228 original size:27 final size:26
Alignment explanation
Indices: 53576185--53576292 Score: 69
Period size: 27 Copynumber: 4.0 Consensus size: 26
53576175 AAGCATTCTG
*
53576185 GTGGCTCTGCC-CTAAATATCTGATCT
1 GTGGCTCTACCAC-AAATATCTGATCT
*
53576211 AGTGGCTCTACCACAAATAT-TTATTTCT
1 -GTGGCTCTACCACAAATATCTGA--TCT
* * *
53576239 GTGGCCCTGCCACAATTATCTGTATCT
1 GTGGCTCTACCACAAATATCTG-ATCT
* * *
53576266 GGTGACTCTATCAC-AATATCTGTTCT
1 -GTGGCTCTACCACAAATATCTGATCT
53576292 G
1 G
53576293 GTAGCCATGC
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
25 1 0.02
26 5 0.08
27 42 0.67
28 14 0.22
29 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (26 bp):
GTGGCTCTACCACAAATATCTGATCT
Found at i:53577932 original size:39 final size:40
Alignment explanation
Indices: 53577888--53578022 Score: 184
Period size: 40 Copynumber: 3.4 Consensus size: 40
53577878 CCTTCGGAGT
** *
53577888 TTAG-CCGGATATAGCCACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGAC
* *
53577927 TTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGAC
* *
53577967 TTAGCCCGG-TATAATAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGAC
*
53578006 TTAGCCTGGATATAGTA
1 TTAGCCCGGATATAGTA
53578023 GCACTTAGCC
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 40 0.47
40 45 0.53
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGAC
Found at i:53577955 original size:40 final size:39
Alignment explanation
Indices: 53577911--53578022 Score: 179
Period size: 39 Copynumber: 2.8 Consensus size: 39
53577901 GCCACTAGCT
*
53577911 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
53577951 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
*
53577990 CAAATGCCTTCGGGACTTAGCCTGGATATAGTA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTA
53578023 GCACTTAGCC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 36 0.54
40 31 0.46
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:53585959 original size:39 final size:40
Alignment explanation
Indices: 53585915--53586120 Score: 215
Period size: 40 Copynumber: 5.2 Consensus size: 40
53585905 CCTTCGGAGT
* *
53585915 TTAG-CCGGATATAGCCACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGAC
* * *
53585954 TTAGCCCGGTTATAGTAACTTGCA-AAATGCCTTCGGGAC
1 TTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGAC
** *
53585993 TTAGCCCGG-TATAATAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGAC
* * * * *
53586032 ATAGCCCGGATATAGTAGCTCGCACGAATGCCTTCGGGAC
1 TTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGAC
* * *
53586072 TTAGCCC-GAAATTAGCCACTAGCTCAAATG-CTCTCGGGAC
1 TTAGCCCGGATA-TAGCAACTAGCACAAATGCCT-TCGGGAC
53586112 TTAGCCCGG
1 TTAGCCCGG
53586121 TTATCATTCG
Statistics
Matches: 142, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
38 12 0.08
39 56 0.39
40 73 0.51
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGAC
Found at i:53586065 original size:40 final size:39
Alignment explanation
Indices: 53585938--53586121 Score: 219
Period size: 40 Copynumber: 4.7 Consensus size: 39
53585928 GCCACTAGCT
*
53585938 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
53585978 -AAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* *
53586016 CAAATGCCTTCGGGACATAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* ** ** * *
53586056 CGAATGCCTTCGGGACTTAGCCCGAAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
53586096 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
53586122 TATCATTCGA
Statistics
Matches: 123, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
38 12 0.10
39 50 0.41
40 61 0.50
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:53590656 original size:18 final size:17
Alignment explanation
Indices: 53590635--53590689 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
53590625 ACAATTCTTT
53590635 TCTCTTCTTCTTTTCTCC
1 TCTCTTCTTCTTTTCT-C
*
53590653 TCTCTTCATCTATTT-TC
1 TCTCTTCTTCT-TTTCTC
53590670 TCTTCTTCTTCTTTTC-C
1 TC-TCTTCTTCTTTTCTC
53590687 TCT
1 TCT
53590690 ATAGTCGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 1 0.03
17 9 0.28
18 19 0.59
19 3 0.09
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.62
Consensus pattern (17 bp):
TCTCTTCTTCTTTTCTC
Found at i:53591782 original size:27 final size:27
Alignment explanation
Indices: 53591752--53591809 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
53591742 TACTAAAATA
* *
53591752 CCCTAAGTATG-AAAATTACCATTATGC
1 CCCTAAG-ATGCAAAATGACCATTATAC
*
53591779 CCCT-AGGTGCAAAATGACCATTATAC
1 CCCTAAGATGCAAAATGACCATTATAC
53591805 CCCTA
1 CCCTA
53591810 GGGTTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 2 0.08
26 20 0.77
27 4 0.15
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (27 bp):
CCCTAAGATGCAAAATGACCATTATAC
Found at i:53591954 original size:28 final size:29
Alignment explanation
Indices: 53591912--53591976 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 29
53591902 GGAGGAAGCA
*
53591912 TTCTGGTGGCTCTGCCACAAATATCTG-T
1 TTCTGGTGGCCCTGCCACAAATATCTGTT
*
53591940 TTCTGGTGGCCCTGCCACAATTATCTGTT
1 TTCTGGTGGCCCTGCCACAAATATCTGTT
53591969 TTCTGGTG
1 TTCTGGTG
53591977 ACTCTATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 25 0.74
29 9 0.26
ACGTcount: A:0.14, C:0.25, G:0.23, T:0.38
Consensus pattern (29 bp):
TTCTGGTGGCCCTGCCACAAATATCTGTT
Found at i:53597806 original size:79 final size:81
Alignment explanation
Indices: 53597673--53597854 Score: 230
Period size: 79 Copynumber: 2.3 Consensus size: 81
53597663 AATGATGTCT
*
53597673 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGT
*
53597737 GCGAGATACTA-ATTCC
66 GCGAGATACTATA-ACC
* * * **
53597753 GGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTG
*
53597815 TGCGAGTTACTATAACC
65 TGCGAGATACTATAACC
*
53597832 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
53597855 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGT
GCGAGATACTATAACC
Found at i:53597868 original size:40 final size:40
Alignment explanation
Indices: 53597673--53597854 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
53597663 AATGATGTCT
* * * *
53597673 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACC
* * *
53597713 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-ACC
53597753 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
*
53597792 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
*
53597832 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
53597855 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
Found at i:53597876 original size:79 final size:79
Alignment explanation
Indices: 53597723--53597887 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
53597713 GGACTAAGAT
* **
53597723 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
53597788 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
53597802 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
53597865 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
53597881 CCGAAGG
1 CCGAAGG
53597888 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:53601381 original size:11 final size:11
Alignment explanation
Indices: 53601335--53601383 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
53601325 TTGTTCGATC
53601335 ATGATTCGACA
1 ATGATTCGACA
*
53601346 ACGATTCGACA
1 ATGATTCGACA
* *
53601357 GTAATTCGA-A
1 ATGATTCGACA
*
53601367 ATGATTCGACT
1 ATGATTCGACA
53601378 ATGATT
1 ATGATT
53601384 TGGTATTGGA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
10 8 0.27
11 22 0.73
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (11 bp):
ATGATTCGACA
Found at i:53608516 original size:27 final size:27
Alignment explanation
Indices: 53608467--53608673 Score: 256
Period size: 27 Copynumber: 7.7 Consensus size: 27
53608457 TTTGTTTACC
*
53608467 AAATTACC-AAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* ** * *
53608493 AAATTACTAAAATACCGTTTGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTA
53608520 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
53608547 AAATTACCAAAATGCCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
53608574 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * * *
53608601 AAATTATCAAAATACCACTGGTTTGTG
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
53608628 AAATTACCGAAATA-CCCTCAATTTGTA
1 AAATTACCAAAATACCCCT-AGTTTGTA
*
53608655 AAACTACCAAAATACCCCT
1 AAATTACCAAAATACCCCT
53608674 GATTTACAAA
Statistics
Matches: 154, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 10 0.06
27 140 0.91
28 4 0.03
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTTTGTA
Found at i:53608548 original size:54 final size:54
Alignment explanation
Indices: 53608458--53608688 Score: 243
Period size: 54 Copynumber: 4.3 Consensus size: 54
53608448 TAGAATACTT
** * * **
53608458 TTGTTTACCAAATTACC-AAATACCCCTGGTTTGTAAAATTACTAAAATACCGT
1 TTGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC
* *
53608511 TTGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATGCCCC
1 TTGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC
* * * *
53608565 TAGTTTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCAC
1 TTGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC
* * * * * *
53608619 TGGTTTGTGAAATTACCGAAATA-CCCTCAATTTGTAAAACTACCAAAATACC-C
1 TTGTTTATAAAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCAC
* *
53608672 CTGATTTACAAAATTAC
1 TTG-TTTATAAAATTAC
53608689 AGAAATATCC
Statistics
Matches: 150, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
53 21 0.14
54 129 0.86
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (54 bp):
TTGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCAC
Found at i:53608694 original size:27 final size:27
Alignment explanation
Indices: 53608628--53608755 Score: 87
Period size: 27 Copynumber: 4.7 Consensus size: 27
53608618 CTGGTTTGTG
* ** **
53608628 AAATTACCGAAATACCCTCAATTTGTA
1 AAATTACTGAAATACCCTTGATTTACA
* ** *
53608655 AAACTACCAAAATACCCCTGATTTACA
1 AAATTACTGAAATACCCTTGATTTACA
* *
53608682 AAATTACAGAAATATCCTTGACTTT-CTAA
1 AAATTACTGAAATACCCTTGA-TTTAC--A
* * *
53608711 AAATTATTGAAATACCATTGGTTTACA
1 AAATTACTGAAATACCCTTGATTTACA
*
53608738 AAATTACTGAAATGCCCT
1 AAATTACTGAAATACCCT
53608756 CAATTTGTAG
Statistics
Matches: 77, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
27 53 0.69
28 6 0.08
29 18 0.23
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATTACTGAAATACCCTTGATTTACA
Found at i:53608694 original size:54 final size:54
Alignment explanation
Indices: 53608487--53608773 Score: 190
Period size: 54 Copynumber: 5.3 Consensus size: 54
53608477 ATACCCCTGG
* ** *
53608487 TTTGTAAAATTACTAAAATACCGTTTG-TTTATAAAATTACCA-AAATACCC-CTAG
1 TTTGTAAAATTACCAAAATACC-ACTGATTTATAAAATTA-CAGAAATACCCTC-AA
* * * *
53608541 TTTGTAAAATTACCAAAATGCCCCT-AGTTTGTAAAATTATCA-AAATACCC-CTAG
1 TTTGTAAAATTACCAAAATACCACTGA-TTTATAAAATTA-CAGAAATACCCTC-AA
* * * * *
53608595 TTTGTAAAATTATCAAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAA
1 TTTGTAAAATTACCAAAATACCACTGATTTATAAAATTACAGAAATACCCTCAA
* * * * * *
53608649 TTTGTAAAACTACCAAAATACCCCTGATTTACAAAATTACAGAAATATCCTTGAC
1 TTTGTAAAATTACCAAAATACCACTGATTTATAAAATTACAGAAATA-CCCTCAA
* *** * * * * *
53608704 TTTCTAAAAATTATTGAAATACCATTGGTTTACAAAATTACTGAAATGCCCTCAA
1 TTTGT-AAAATTACCAAAATACCACTGATTTATAAAATTACAGAAATACCCTCAA
* *
53608759 TTTGTAGAATGACCA
1 TTTGTAAAATTACCA
53608774 TTTTACCCTC
Statistics
Matches: 183, Mismatches: 43, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
53 2 0.01
54 131 0.72
55 17 0.09
56 33 0.18
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.32
Consensus pattern (54 bp):
TTTGTAAAATTACCAAAATACCACTGATTTATAAAATTACAGAAATACCCTCAA
Found at i:53608793 original size:27 final size:27
Alignment explanation
Indices: 53608752--53608895 Score: 182
Period size: 27 Copynumber: 5.3 Consensus size: 27
53608742 TACTGAAATG
* * *
53608752 CCCTCAATTTGTAGAATGACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * *
53608779 CCCTCGATTTATAGAATTATCGTTTCA
1 CCCTCGATTTATAGAATTACCATTTTA
* * *
53608806 CCCTTGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
53608833 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
53608860 CCCTC-AGTTTATAAAATTACCATTTTA
1 CCCTCGA-TTTATAGAATTACCATTTTA
53608887 CCCTCGATT
1 CCCTCGATT
53608896 GTGAAATTAC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
26 1 0.01
27 97 0.98
28 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTTA
Found at i:53608797 original size:110 final size:110
Alignment explanation
Indices: 53608513--53608764 Score: 271
Period size: 108 Copynumber: 2.3 Consensus size: 110
53608503 AATACCGTTT
* * * * * **
53608513 GTTTATAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATGCCCCT-AGTTTGTAAA
1 GTTTACAAAATTACCGAAATACCCTC-AATTTGTAAAACTACCAAAATACCCCTGA-TTTACAAA
* * * *
53608576 ATTATCA-AAATACCCCT-AGTTTGT-AAAATTATCAAAATACCACTG
64 ATTA-CAGAAATATCCTTGACTTTCTAAAAATTATCAAAATACCACTG
***
53608621 GTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAACTACCAAAATACCCCTGATTTACAAAAT
1 GTTTACAAAATTACCGAAATACCCTCAATTTGTAAAACTACCAAAATACCCCTGATTTACAAAAT
** *
53608686 TACAGAAATATCCTTGACTTTCTAAAAATTATTGAAATACCATTG
66 TACAGAAATATCCTTGACTTTCTAAAAATTATCAAAATACCACTG
* *
53608731 GTTTACAAAATTACTGAAATGCCCTCAATTTGTA
1 GTTTACAAAATTACCGAAATACCCTCAATTTGTA
53608765 GAATGACCAT
Statistics
Matches: 119, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
107 2 0.02
108 63 0.53
109 7 0.06
110 47 0.39
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (110 bp):
GTTTACAAAATTACCGAAATACCCTCAATTTGTAAAACTACCAAAATACCCCTGATTTACAAAAT
TACAGAAATATCCTTGACTTTCTAAAAATTATCAAAATACCACTG
Done.