Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 192 of 279
Found at i:63005871 original size:17 final size:19
Alignment explanation
Indices: 63005776--63005864 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
63005766 AATCTTCAAC
63005776 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
63005795 AATATGCAATCTTAAATAT
1 GATATGCAATCTTAGATAT
63005814 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
63005831 GAT-TGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
63005849 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
63005865 AGATATGATT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
17 15 0.24
18 16 0.25
19 32 0.51
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:63005890 original size:22 final size:22
Alignment explanation
Indices: 63005776--63005887 Score: 83
Period size: 19 Copynumber: 5.7 Consensus size: 22
63005766 AATCTTCAAC
63005776 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
63005795 AATATGCAATCTT--AA-ATAT
1 GATATGCAATCTTAGAAGATAT
63005814 GATA--CAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
63005831 GAT-TGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
63005849 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
63005871 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
63005888 GATTTAATTT
Statistics
Matches: 80, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.01
17 14 0.17
18 16 0.20
19 28 0.35
20 1 0.01
22 8 0.10
23 12 0.15
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:63006177 original size:18 final size:19
Alignment explanation
Indices: 63006154--63006189 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
63006144 TTTCCCTAAT
*
63006154 TTTTTTTATAT-ATTTTAA
1 TTTTTTTAAATAATTTTAA
63006172 TTTTTTTAAATAATTTTA
1 TTTTTTTAAATAATTTTA
63006190 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTTAAATAATTTTAA
Found at i:63014429 original size:89 final size:87
Alignment explanation
Indices: 63014300--63014460 Score: 207
Period size: 89 Copynumber: 1.8 Consensus size: 87
63014290 AGTCGACGGA
* *
63014300 GAGCAGATCGAAGACATAGTAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATG
1 GAGCAGATCGAAGACATAGCAGATCTAACCTTCAGATG-TTT-ACATCGAAGAAGATCCAAGATG
63014365 ATTTGGCATCCTTGCGTTTACAAT
64 ATTTGGCATCCTTGCGTTTACAAT
* ** * * * *
63014389 GAGCAGATCGAAGACATAGCAGATTTGGCTTTCATG-TGTTTACGTTGAAGAAGATCTAAGATGA
1 GAGCAGATCGAAGACATAGCAGATCTAACCTTCA-GATGTTTACATCGAAGAAGATCCAAGATGA
63014453 TTTGGCAT
65 TTTGGCAT
63014461 ATCTGTACTG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 27 0.44
88 3 0.05
89 31 0.50
90 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (87 bp):
GAGCAGATCGAAGACATAGCAGATCTAACCTTCAGATGTTTACATCGAAGAAGATCCAAGATGAT
TTGGCATCCTTGCGTTTACAAT
Found at i:63014565 original size:220 final size:220
Alignment explanation
Indices: 63014183--63014747 Score: 882
Period size: 220 Copynumber: 2.6 Consensus size: 220
63014173 CAGGCTAAAG
* * * * * **
63014183 CATAGCAGATTTGACCTTCAGGTGTTTACGCTGAA-ACAGATCCAAGATAATTTAACATCTCTGT
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGA-AGATCTAAGATGATTTGGCATCTCTGT
* * * * **
63014247 ATTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATAGTCGACGGAGAGCAGATCGAA
65 ACTGTTAGAGAACAAATTGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATAAAA
* *
63014312 GACATAGTAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCT
130 AACATAGCAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCT
*
63014377 TGCGTTTACAATGAGCAGATCGAAGA
195 TGCGTTTACAAGGAGCAGATCGAAGA
* * *
63014403 CATAGCAGATTTGGCTTTCATGTGTTTACGTTGAAGAAGATCTAAGATGATTTGGCATATCTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGAAGATCTAAGATGATTTGGCATCTCTGTA
*
63014468 CTGTTAGAGAACAAATTGAAGAAACATATTTGGCATCTCCATATTCGACGGAGAGCAGATAAAAA
66 CTGTTAGAGAACAAATTGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATAAAAA
* *
63014533 ACATAGCAGATCTAACCTTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGTATCCTT
131 ACATAGCAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
63014598 GCGTTTACAAGGAGCAGATCGAAGA
196 GCGTTTACAAGGAGCAGATCGAAGA
* *
63014623 CATAGCAGATTTTGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGAAGATCTAAGATGATTTGGCATCTCTGTA
63014688 CTGTTAGAGAACAAATCT-AAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGAT
66 CTGTTAGAGAACAAAT-TGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGAT
63014748 CGAAGACACA
Statistics
Matches: 316, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
220 314 0.99
221 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (220 bp):
CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGAAGATCTAAGATGATTTGGCATCTCTGTA
CTGTTAGAGAACAAATTGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATAAAAA
ACATAGCAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
GCGTTTACAAGGAGCAGATCGAAGA
Found at i:63014824 original size:78 final size:77
Alignment explanation
Indices: 63014714--63014978 Score: 377
Period size: 78 Copynumber: 3.4 Consensus size: 77
63014704 CTAAGAAACA
** * * *
63014714 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACACAGTAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAATAGAT-TGACCTTCATTGAA
63014779 GCAGATCCAAGAT
65 GCAGATCCAAGAT
* *
63014792 GATTTGGCATCTCTGTATTAGATGGGGAGCAGATCGAAGACACAACAGATTTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAATAGA-TTGACCTTCATTGAA
*
63014857 GTAGATCCAAGAT
65 GCAGATCCAAGAT
* * * * *
63014870 GATTTGGCATATCTTTATTAAACGGGGAGAAGATCGAAGACATAATAGATTAGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAATAGATT-GACCTTCATTGAA
63014935 GCAGATCCAAGAT
65 GCAGATCCAAGAT
*
63014948 TATTTGGCATCTCTGTATTAGACGGGGAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCA
63014979 AATCAGAGAT
Statistics
Matches: 164, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
77 2 0.01
78 161 0.98
79 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (77 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAATAGATTGACCTTCATTGAAG
CAGATCCAAGAT
Found at i:63015054 original size:44 final size:45
Alignment explanation
Indices: 63014949--63015123 Score: 262
Period size: 45 Copynumber: 3.9 Consensus size: 45
63014939 ATCCAAGATT
* *
63014949 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAGAGATAACAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACAG
* * *
63014994 ATTTGGCATCTCTGTATTTGACGGGGAGCAGATTAAAGA-AGCAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACAG
* *
63015038 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACAG
* *
63015083 ATATGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATA
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATA
63015124 GCATATATCG
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
44 39 0.33
45 78 0.67
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (45 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACAG
Found at i:63015100 original size:89 final size:90
Alignment explanation
Indices: 63014949--63015126 Score: 279
Period size: 89 Copynumber: 2.0 Consensus size: 90
63014939 ATCCAAGATT
* *
63014949 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAGAGATAACAGATTTGGCATCTCTGTATTTG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAGAGATAACAGATATGGCATCTCTGTATTAG
*
63015014 ACGGGGAGCAGATTAAAGA-AGCAG
66 ACGGGGAGCAGATCAAAGATAGCAG
* * *
63015038 ATTTGGCGTCTCTGTATTAGACGGGGAGCAGATC-GAAGATAACAGATATGGCGTCTCTGTATTA
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAG-AGATAACAGATATGGCATCTCTGTATTA
63015102 GACGGGGAGCAGATCAAAGATAGCA
65 GACGGGGAGCAGATCAAAGATAGCA
63015127 TATATCGCCT
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
88 1 0.01
89 76 0.94
90 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (90 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAGAGATAACAGATATGGCATCTCTGTATTAG
ACGGGGAGCAGATCAAAGATAGCAG
Found at i:63015491 original size:17 final size:19
Alignment explanation
Indices: 63015469--63015546 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
63015459 ATGGAAATAT
63015469 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGC
*
63015486 AATCTTAGATATGATATGC
1 AATCTTACATATGATATGC
*
63015505 AATCTTAGATATGATA--C
1 AATCTTACATATGATATGC
*
63015522 AATCTTAGATATGAT-TGC
1 AATCTTACATATGATATGC
63015540 AATCTTA
1 AATCTTA
63015547 AAAGATATGA
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
17 22 0.39
18 9 0.16
19 25 0.45
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (19 bp):
AATCTTACATATGATATGC
Found at i:63015501 original size:19 final size:19
Alignment explanation
Indices: 63015477--63015546 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
63015467 ATAATCTTCA
63015477 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
63015496 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
63015515 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
63015532 ATGAT-TGCAATCTTA
1 ATGATATGCAATCTTA
63015547 AAAGATATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.33
18 8 0.16
19 25 0.51
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:63015509 original size:36 final size:34
Alignment explanation
Indices: 63015469--63015547 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 34
63015459 ATGGAAATAT
63015469 AATCTTCAATGATATGCAATCTTAGATATGATATGC
1 AATCTT-AATGATATGCAATCTTAGATATGAT-TGC
*
63015505 AATCTTAGAT-ATGATACAATCTTAGATATGATTGC
1 AATCTTA-ATGAT-ATGCAATCTTAGATATGATTGC
63015540 AATCTTAA
1 AATCTTAA
63015548 AAGATATGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
34 1 0.03
35 13 0.32
36 26 0.65
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (34 bp):
AATCTTAATGATATGCAATCTTAGATATGATTGC
Found at i:63015859 original size:17 final size:18
Alignment explanation
Indices: 63015837--63015870 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
63015827 GTTTCCCTAT
*
63015837 TTTTTTATAT-ATTTTAA
1 TTTTTTAAATAATTTTAA
63015854 TTTTTTAAATAATTTTA
1 TTTTTTAAATAATTTTA
63015871 GTATCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTAAATAATTTTAA
Found at i:63017074 original size:16 final size:18
Alignment explanation
Indices: 63017048--63017080 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
63017038 TAGAACTGGG
63017048 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
63017065 TTGA-AAAATTAATTTA
1 TTGAGAAAATTAATTTA
63017081 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:63018276 original size:29 final size:29
Alignment explanation
Indices: 63018236--63018293 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
63018226 GAATCTTGAG
63018236 TTTTGAACTGCAGTAAGTGAGAATTAGGT
1 TTTTGAACTGCAGTAAGTGAGAATTAGGT
63018265 TTTTGAACTGCAGTAAGTGAGAATTAGGT
1 TTTTGAACTGCAGTAAGTGAGAATTAGGT
63018294 GAGTCTCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (29 bp):
TTTTGAACTGCAGTAAGTGAGAATTAGGT
Found at i:63019948 original size:32 final size:27
Alignment explanation
Indices: 63019884--63019950 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 27
63019874 CAAATTATGC
*
63019884 ATAATAATAGATATATATAAAATAATA
1 ATAATAATAGATATATATAAAAGAATA
63019911 A-AATAATAGAATATATATTATAAAGAATAA
1 ATAATAATAG-ATATATA-TA-AAAGAAT-A
63019941 AGTAATAATA
1 A-TAATAATA
63019951 TAGATTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
26 8 0.24
27 8 0.24
28 2 0.06
29 6 0.18
30 2 0.06
32 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (27 bp):
ATAATAATAGATATATATAAAAGAATA
Found at i:63019950 original size:27 final size:27
Alignment explanation
Indices: 63019884--63019961 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 27
63019874 CAAATTATGC
* *
63019884 ATAATAATAGATATATATAAAATAATAAA
1 ATAATAATATATAT-TAT-AAAGAATAAA
63019913 ATAATAGAATATATATTATAAAGAATAAA
1 ATAAT--AATATATATTATAAAGAATAAA
* *
63019942 GTAATAATATAGATTATAAA
1 ATAATAATATATATTATAAA
63019962 ATGAAGTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
27 14 0.33
29 18 0.42
30 3 0.07
31 8 0.19
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (27 bp):
ATAATAATATATATTATAAAGAATAAA
Found at i:63020056 original size:29 final size:30
Alignment explanation
Indices: 63020024--63020106 Score: 71
Period size: 34 Copynumber: 2.6 Consensus size: 30
63020014 TTTCAAAATT
*
63020024 ATATATAATAATATATAA-TAAAATATGAAA
1 ATATATAATAATATATAATTAAAACAT-AAA
*
63020054 TATCCTATTATATAATATATATATTAAAACATAAA
1 -AT-ATA-TA-ATAATATATA-ATTAAAACATAAA
63020089 ATAATATAAT-ATATATAA
1 AT-ATATAATAATATATAA
63020107 CATTTAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
30 1 0.02
31 9 0.21
32 4 0.09
33 4 0.09
34 14 0.33
35 4 0.09
36 7 0.16
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (30 bp):
ATATATAATAATATATAATTAAAACATAAA
Found at i:63020097 original size:5 final size:5
Alignment explanation
Indices: 63020026--63020162 Score: 59
Period size: 5 Copynumber: 27.0 Consensus size: 5
63020016 TCAAAATTAT
* * * *
63020026 ATATA ATA-A TATATA ATAAA ATATGAA ATATC CTATT ATATA ATAT-
1 ATATA ATATA -ATATA ATATA ATAT--A ATATA ATATA ATATA ATATA
* * * * * *
63020072 ATATA TTAAA ACATA AAATA ATATA ATAT- ATATAA CATTTA ATAAA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA
* * *
63020123 AAATA ATAT- ATGTTA ATATA ATATAA AAATA ATAT- ATATA
1 ATATA ATATA AT-ATA ATATA ATAT-A ATATA ATATA ATATA
63020163 CTTGGAAATG
Statistics
Matches: 96, Mismatches: 24, Indels: 24
0.67 0.17 0.17
Matches are distributed among these distances:
4 15 0.16
5 65 0.68
6 8 0.08
7 8 0.08
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:63020102 original size:36 final size:36
Alignment explanation
Indices: 63020024--63020162 Score: 114
Period size: 36 Copynumber: 4.0 Consensus size: 36
63020014 TTTCAAAATT
* *
63020024 ATATATAATAATATATAATAAAATATGAAATATCCTA
1 ATATATAATAATATATAATAAAATATAAAATAT-ATA
* * *
63020061 TTATATAAT-ATATATATTAAAACATAAAATAATATA
1 ATATATAATAATATATAATAAAATATAAAAT-ATATA
* *
63020097 ATATAT-ATAACATTTAATAAAATATAAAATA-AT-
1 ATATATAATAATATATAATAAAATATAAAATATATA
* *
63020130 ATATGT--TAATATA-ATATAAAA-ATAATATATATA
1 ATATATAATAATATATA-ATAAAATATAAAATATATA
63020163 CTTGGAAATG
Statistics
Matches: 83, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
31 8 0.10
32 13 0.16
33 5 0.06
34 2 0.02
35 3 0.04
36 42 0.51
37 10 0.12
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (36 bp):
ATATATAATAATATATAATAAAATATAAAATATATA
Found at i:63020145 original size:25 final size:26
Alignment explanation
Indices: 63020110--63020159 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
63020100 TATATAACAT
63020110 TTAATAAAATAT-AAAATAATATATG
1 TTAATAAAATATAAAAATAATATATG
*
63020135 TTAATATAATATAAAAATAATATAT
1 TTAATAAAATATAAAAATAATATAT
63020160 ATACTTGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
TTAATAAAATATAAAAATAATATATG
Found at i:63020272 original size:15 final size:16
Alignment explanation
Indices: 63020252--63020281 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63020242 TAAAAATATA
63020252 TAAAAA-GATTAAAAT
1 TAAAAATGATTAAAAT
63020267 TAAAAATGATTAAAA
1 TAAAAATGATTAAAA
63020282 CTTTGGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (16 bp):
TAAAAATGATTAAAAT
Found at i:63026209 original size:23 final size:22
Alignment explanation
Indices: 63026140--63026214 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 22
63026130 CTGAGCTGAT
* *
63026140 GCTGAAAGGGTAAGCTCTATTGA
1 GCTGAAA-GGTAAGCTCCAATGA
* *
63026163 GCTGAATA-GTAAACT-CATACGA
1 GCTGAA-AGGTAAGCTCCA-ATGA
63026185 GCTGAAACGGTAAGCTCCAATGA
1 GCTGAAA-GGTAAGCTCCAATGA
63026208 GCTGAAA
1 GCTGAAA
63026215 ATAGTATATC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
21 2 0.05
22 14 0.34
23 22 0.54
24 3 0.07
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.21
Consensus pattern (22 bp):
GCTGAAAGGTAAGCTCCAATGA
Found at i:63028423 original size:130 final size:130
Alignment explanation
Indices: 63028059--63028425 Score: 407
Period size: 130 Copynumber: 2.8 Consensus size: 130
63028049 AGAGCCGAGT
* * * * * *
63028059 GAAATTTTGAAGGGATATTTGATTGTTTTAAAC-AATCGAGAAATTGCTACCCAACACGTTAGGG
1 GAAATTTTGAAGGGATATTCGATTATTTTGAGCAAAT-GCGAAATTGCAACCCAACACGTTAGGG
* ** * * * * * * *
63028123 CACGATCCCACGAATTGCCAAATACCAGATATCGCCTTCGTTTTAGGGATTTTAAAAGACACGAG
65 CACGATTCTGCGAATTGCCGAACATCAAATATCGTCTTCGTTTAAGGGATTTTAAAAGACACGAA
63028188 C
130 C
* * *
63028189 GAAATTTTAAAGTGATATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGC
1 GAAATTTTGAAGGGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGC
* * * * ***
63028254 ACGATT-TCGAGAATTG-CGAAACATCAAATCTCATATTCGTTTAAGGGATTTTAAAAGATGTGA
66 ACGATTCT-GCGAATTGCCG-AACATCAAATATCGTCTTCGTTTAAGGGATTTTAAAAGACACGA
*
63028317 AT
129 AC
* * *
63028319 GGAATTTTGAAGGGAAATTCGATTATTTTGAGCAAATGCGAAATTACAACCCAACACGTTAGGGC
1 GAAATTTTGAAGGGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGC
*
63028384 ACGATTCTGCGAATTGCCGAACATCAAATTTCGTCTTCGTTT
66 ACGATTCTGCGAATTGCCGAACATCAAATATCGTCTTCGTTT
63028426 TGAAGAATTT
Statistics
Matches: 195, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
129 1 0.01
130 188 0.96
131 6 0.03
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (130 bp):
GAAATTTTGAAGGGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGC
ACGATTCTGCGAATTGCCGAACATCAAATATCGTCTTCGTTTAAGGGATTTTAAAAGACACGAAC
Found at i:63029449 original size:23 final size:23
Alignment explanation
Indices: 63029419--63029464 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
63029409 ATATAAACAT
63029419 GTATAAAAATAATTTAAACTTTA
1 GTATAAAAATAATTTAAACTTTA
63029442 GTATAAAAATAATTTAAACTTTA
1 GTATAAAAATAATTTAAACTTTA
63029465 CGTAGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
GTATAAAAATAATTTAAACTTTA
Found at i:63031675 original size:132 final size:132
Alignment explanation
Indices: 63031351--63031869 Score: 583
Period size: 132 Copynumber: 3.9 Consensus size: 132
63031341 CAATCGTCAG
** * * * * *
63031351 CCTACTCCACTACAACTTTAGGGAGCTAGGACGATAG-TCTAAATCTACTTCACTGCAACATCAG
1 CCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCT-TAAATCTGCCTCACTGCAACTTCAG
* * * * * * * *
63031415 GAAGCCTAGATTCACCGTCTTTGATCTGTTCCACTGCAA-TCCCAGGGAAACAAAATCTATATTT
65 GAAGCCAAGATTCACCGTCTTCGATCTGCTCCACTGCAACT-TCAGAGAAACAAGATCTAAAATT
*
63031479 CTCAG
129 -TCAA
* * * * ** *
63031484 CCTACTCCAATACAAATTTAGGGAGCTAGGTTAGTGACTTAAATCTGGTTCACTGCAACTTTAGG
1 CCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCCTCACTGCAACTTCAGG
* * * * *
63031549 AAGCCAAGATTCATCATCTTCGATCTGCTCTACTGTAACTTCAGGGAAACAAGATCTAAAATTTC
66 AAGCCAAGATTCACCGTCTTCGATCTGCTCCACTGCAACTTCAGAGAAACAAGATCTAAAATTTC
63031614 AA
131 AA
* *
63031616 CCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGTTTTAATCTGCCTCACTGCAACTTCAGG
1 CCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCCTCACTGCAACTTCAGG
* ** * * *
63031681 AAGCCAAGATCCGTCGTCTTCAATCTGCTCCATTGCAACTTCAGATAAACAAGATCTAAAATTTC
66 AAGCCAAGATTCACCGTCTTCGATCTGCTCCACTGCAACTTCAGAGAAACAAGATCTAAAATTTC
63031746 AA
131 AA
* *
63031748 CCTACTCCATTACAACTTTAGGGAGCTAGGTTGGTGGCTTTAATCTGCCTCACTGCAACTTCAGG
1 CCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCCTCACTGCAACTTCAGG
* ** * * * * *
63031813 AAGCCTAGATTTGCCGTCTTTGATATGCTTCACTGTAACTTCAAAGAAACAAGATCT
66 AAGCCAAGATTCACCGTCTTCGATCTGCTCCACTGCAACTTCAGAGAAACAAGATCT
63031870 GTAGGATCAG
Statistics
Matches: 328, Mismatches: 56, Indels: 5
0.84 0.14 0.01
Matches are distributed among these distances:
132 225 0.69
133 101 0.31
134 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (132 bp):
CCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTTAAATCTGCCTCACTGCAACTTCAGG
AAGCCAAGATTCACCGTCTTCGATCTGCTCCACTGCAACTTCAGAGAAACAAGATCTAAAATTTC
AA
Found at i:63040507 original size:22 final size:22
Alignment explanation
Indices: 63040481--63040525 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
63040471 GCTCTTAATT
*
63040481 CCCATCGCTTTTTTCTGCTTTC
1 CCCATCGCTTATTTCTGCTTTC
63040503 CCCATCGCTTATTTCTGCTTTC
1 CCCATCGCTTATTTCTGCTTTC
63040525 C
1 C
63040526 GACAGACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.07, C:0.38, G:0.09, T:0.47
Consensus pattern (22 bp):
CCCATCGCTTATTTCTGCTTTC
Found at i:63043618 original size:131 final size:129
Alignment explanation
Indices: 63043470--63043811 Score: 325
Period size: 130 Copynumber: 2.6 Consensus size: 129
63043460 AATAAAGACC
* * * * * *
63043470 TAAAGGAATACTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAAGGCATGATTC
1 TAAAGGGATATTCGATTGTTTTGAACAAA-GAGAAATTACAACCCAACACGATAAGGCACGATCC
* *
63043535 C-CGAATTGTCAAACACCA-AGTATTGCCATCGTTTTAAAGGATTTTTAGAAGAGC-CGAG-TGA
65 CACGAATTGCCAAACACCAGA-TATTGCCATCGTTTT-AAGGA-TTTTAAAAGA-CACGAGCT-A
63043596 AATTT
125 AATTT
* * * * * * * *
63043601 TGAAGGGATATTTGATTGTTTTAAACAATAGAGAAATTGCTACCCAACATGTTAGGGCACGATCC
1 TAAAGGGATATTCGATTGTTTTGAACAA-AGAGAAATTACAACCCAACACGATAAGGCACGATCC
* * *
63043666 CACGAATTGCCAAATACCAGATATTGCCTTCGTTTTAGGGATTTTAAAAGACACGAGCTAAATTT
65 CACGAATTGCCAAACACCAGATATTGCCATCGTTTTAAGGATTTTAAAAGACACGAGCTAAATTT
* * * * *
63043731 TAAAGTGATATTCGATTATTTTGAGCAAATACGAAATTACAACCCAACACGAT-AGTGCACGATT
1 TAAAGGGATATTCGATTGTTTTGAACAAAGA-GAAATTACAACCCAACACGATAAG-GCACGATC
***
63043795 TTGCGAATTGCCAAACA
64 CCACGAATTGCCAAACA
63043812 TCAAATCTCA
Statistics
Matches: 168, Mismatches: 36, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
129 4 0.02
130 78 0.46
131 55 0.33
132 30 0.18
133 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (129 bp):
TAAAGGGATATTCGATTGTTTTGAACAAAGAGAAATTACAACCCAACACGATAAGGCACGATCCC
ACGAATTGCCAAACACCAGATATTGCCATCGTTTTAAGGATTTTAAAAGACACGAGCTAAATTT
Found at i:63043767 original size:130 final size:127
Alignment explanation
Indices: 63043509--63043941 Score: 390
Period size: 130 Copynumber: 3.3 Consensus size: 127
63043499 CGAGAAATCA
* * * * * * *
63043509 CAACCCAGCACGATAAGGCATGATTCC-CGAATTGTCAAACACCAAGTATTGCCATCGTTTTAAA
1 CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAA-TATTGCCTTCGTTTT-AG
* * * * * *
63043573 GGATTTTTAGAAGAGCCGAGTGAAATTTTGAAGGGATATTTGATTGTTTTAAAC-AATAGAGAAA
64 GGA-TTTTAAAAGA-CCGAGTGAAATTTTGAA-GGATATTCGATTATTTTGAGCAAATA-CGAAA
63043637 TTG
125 TTG
* * * * *
63043640 CTACCCAACATGTTAGGGCACGATCCCACGAATTGCCAAATACCAGATATTGCCTTCGTTTTAGG
1 CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCA-ATATTGCCTTCGTTTTAGG
*
63043705 GATTTTAAAAGACACGAGCT-AAATTTTAAAGTGATATTCGATTATTTTGAGCAAATACGAAATT
65 GATTTTAAAAGAC-CGAG-TGAAATTTTGAAG-GATATTCGATTATTTTGAGCAAATACGAAATT
*
63043769 A
127 G
* * ** * *
63043770 CAACCCAACACGATAGTGCACGATTTTGCGAATTGCCAAACATCAA-ATCT-CATCTTCGTTTAA
1 CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAATAT-TGC--CTTCGTTTTA
** * * * * *
63043833 GGGATTTTAAAAGATGTGAATGGAATTTCGAAGGAAAATTCGATTATTTTGAGCAAATGCGAAAT
63 GGGATTTTAAAAGA-CCGAGTGAAATTTTGAAGG-ATATTCGATTATTTTGAGCAAATACGAAAT
63043898 TG
126 TG
*
63043900 CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCGAACA
1 CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACA
63043942 TCAAATTTCG
Statistics
Matches: 246, Mismatches: 44, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
128 3 0.01
129 6 0.02
130 178 0.72
131 29 0.12
132 29 0.12
133 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (127 bp):
CAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAATATTGCCTTCGTTTTAGGG
ATTTTAAAAGACCGAGTGAAATTTTGAAGGATATTCGATTATTTTGAGCAAATACGAAATTG
Found at i:63045096 original size:2 final size:2
Alignment explanation
Indices: 63045091--63045115 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63045081 ATGTACACAC
63045091 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
63045116 AAAGAGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63047781 original size:16 final size:17
Alignment explanation
Indices: 63047760--63047818 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 17
63047750 ATATTTAGTC
63047760 ATATAATAAATTA-TTA
1 ATATAATAAATTATTTA
63047776 ATATAATAAATATAATTTA
1 ATATAATAAAT-T-ATTTA
63047795 TTATATTAATAAATTATTTA
1 --ATA-TAATAAATTATTTA
63047815 ATAT
1 ATAT
63047819 TTCAATTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 11 0.30
17 2 0.05
18 4 0.11
19 3 0.08
20 5 0.14
21 4 0.11
22 8 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATAAATTATTTA
Found at i:63047790 original size:22 final size:22
Alignment explanation
Indices: 63047765--63047808 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
63047755 TAGTCATATA
63047765 ATAAATTATTA-ATATAATAAAT
1 ATAAATTATTATAT-TAATAAAT
*
63047787 ATAATTTATTATATTAATAAAT
1 ATAAATTATTATATTAATAAAT
63047809 TATTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTATTATATTAATAAAT
Found at i:63047844 original size:13 final size:14
Alignment explanation
Indices: 63047828--63047869 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
63047818 TTTCAATTTT
63047828 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
63047841 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
63047856 ATTTTAAATAATAT
1 ATTTT-AATAATAT
63047870 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:63047854 original size:16 final size:16
Alignment explanation
Indices: 63047832--63047868 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
63047822 AATTTTATTT
63047832 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
63047849 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
63047864 TAATA
1 TAATA
63047869 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:63047921 original size:15 final size:15
Alignment explanation
Indices: 63047901--63047956 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
63047891 ATTCAATATT
63047901 AATATTTTAATAATA
1 AATATTTTAATAATA
*
63047916 AATATTTATTAAAATTATA
1 AATA-TT-TT--AATAATA
*
63047935 AATATATTAATAATA
1 AATATTTTAATAATA
63047950 AAT-TTTT
1 AATATTTT
63047957 TGTAATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
14 3 0.09
15 13 0.39
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:63050887 original size:19 final size:18
Alignment explanation
Indices: 63050863--63050898 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
63050853 TCTAGATTTT
63050863 ACACAAAAAAAATATTTAC
1 ACACAAAAAAAA-ATTTAC
63050882 ACACAAAAAAAAATTTA
1 ACACAAAAAAAAATTTA
63050899 GATTGAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (18 bp):
ACACAAAAAAAAATTTAC
Found at i:63053885 original size:21 final size:21
Alignment explanation
Indices: 63053857--63053905 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
63053847 TTTACTCCTC
*
63053857 TCTT-GTTCATTTTATAATTT
1 TCTTAGTTCATTTTACAATTT
63053877 TCTTAGTTCATTTTACAATTT
1 TCTTAGTTCATTTTACAATTT
*
63053898 TATTAGTT
1 TCTTAGTT
63053906 TATGAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.61
Consensus pattern (21 bp):
TCTTAGTTCATTTTACAATTT
Found at i:63054302 original size:16 final size:16
Alignment explanation
Indices: 63054283--63054315 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
63054273 AATTAATGTA
63054283 TTATATCATT-TATATT
1 TTATAT-ATTATATATT
63054299 TTATATATTATATATT
1 TTATATATTATATATT
63054315 T
1 T
63054316 GAATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATATATTATATATT
Found at i:63061210 original size:9 final size:9
Alignment explanation
Indices: 63061198--63061248 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
63061188 TAAAAAATAT
63061198 TTTTTATAA
1 TTTTTATAA
63061207 TTTTTATACA
1 TTTTTATA-A
63061217 TTTTTAATAA
1 TTTTT-ATAA
* *
63061227 TTTTAATGA
1 TTTTTATAA
63061236 -TTTTA-AA
1 TTTTTATAA
63061243 TTTTTA
1 TTTTTA
63061249 AAAAAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
7 1 0.03
8 9 0.26
9 11 0.31
10 11 0.31
11 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:63070837 original size:29 final size:32
Alignment explanation
Indices: 63070755--63070852 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 32
63070745 TAAGCCTGAC
* * *
63070755 TATATTATT-TTTTAATTTCTTTTAAAAA-TAT
1 TATA-TATTATTTTAATTTATATTAAAAATTTT
* *
63070786 T-TATATTATTTTAATTTAATATTTAATATTTT
1 TATATATTATTTTAATTT-ATATTAAAAATTTT
63070818 TATATATTATTTT-A-TT-TATTAAAAATTTT
1 TATATATTATTTTAATTTATATTAAAAATTTT
63070847 TATATA
1 TATATA
63070853 GTCATCTTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
29 21 0.38
30 11 0.20
31 9 0.16
32 4 0.07
33 11 0.20
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (32 bp):
TATATATTATTTTAATTTATATTAAAAATTTT
Found at i:63071333 original size:34 final size:34
Alignment explanation
Indices: 63071290--63071357 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
63071280 CCTAAATTAT
63071290 GCTAATATCTCTCTTCAAGGCTAAAAATAACTAA
1 GCTAATATCTCTCTTCAAGGCTAAAAATAACTAA
*
63071324 GCTAATATCTCTCTTCAAGGTTAAAAATAACTAA
1 GCTAATATCTCTCTTCAAGGCTAAAAATAACTAA
63071358 CTCTAGGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (34 bp):
GCTAATATCTCTCTTCAAGGCTAAAAATAACTAA
Found at i:63072937 original size:21 final size:21
Alignment explanation
Indices: 63072912--63072956 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
63072902 TTAATTATAA
* *
63072912 ATTCTAAATTCTCACTTTTTG
1 ATTCTAAATTCTCAATTCTTG
* *
63072933 ATTCTCAATTGTCAATTCTTG
1 ATTCTAAATTCTCAATTCTTG
63072954 ATT
1 ATT
63072957 TTTTATTCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (21 bp):
ATTCTAAATTCTCAATTCTTG
Found at i:63074816 original size:63 final size:63
Alignment explanation
Indices: 63074716--63074887 Score: 177
Period size: 63 Copynumber: 2.7 Consensus size: 63
63074706 ATTTTTTTGT
* * * ** *
63074716 CACAAACATCACAGCACACACACTTATTCCCCACATCATCACCTTCACAT-CC-GATTTATTTTA
1 CACAAACACCACAGCACACACAATCATTCCTTACATCAACACCTTCA-ATACCAG-TTTATTTTA
* * * * *
63074779 CACAACCACCACAGCACACACAATCATTCCTTGCATCAACACATTTAGTACCAGTTTATTTTA
1 CACAAACACCACAGCACACACAATCATTCCTTACATCAACACCTTCAATACCAGTTTATTTTA
* * * *
63074842 CACAAGCACCACAACACGCACAATCATTCCTTACATTAACACCTTC
1 CACAAACACCACAGCACACACAATCATTCCTTACATCAACACCTTC
63074888 TCTAAAGATA
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
62 1 0.01
63 87 0.98
64 1 0.01
ACGTcount: A:0.35, C:0.35, G:0.05, T:0.25
Consensus pattern (63 bp):
CACAAACACCACAGCACACACAATCATTCCTTACATCAACACCTTCAATACCAGTTTATTTTA
Found at i:63078665 original size:49 final size:49
Alignment explanation
Indices: 63078588--63078684 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
63078578 TACAATATTG
63078588 TATCAACATTTGTTATTAATGAAGTCAGGTTAATTTCAAATCACATGCA
1 TATCAACATTTGTTATTAATGAAGTCAGGTTAATTTCAAATCACATGCA
* *
63078637 TATCTACATTTGTTATTAATGAAGTCAGGTTAATTTCAAGTCACATGC
1 TATCAACATTTGTTATTAATGAAGTCAGGTTAATTTCAAATCACATGC
63078685 TTTCTATCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (49 bp):
TATCAACATTTGTTATTAATGAAGTCAGGTTAATTTCAAATCACATGCA
Found at i:63086569 original size:13 final size:13
Alignment explanation
Indices: 63086551--63086616 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
63086541 CTTAAACTAA
*
63086551 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
63086564 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* * **
63086577 ACTTCTCTAGTGC
1 ACTTTTCAAAAGC
* *
63086590 ACTTTTCTACAGC
1 ACTTTTCAAAAGC
*
63086603 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
63086616 A
1 A
63086617 TAAACTAGTC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:63091654 original size:21 final size:20
Alignment explanation
Indices: 63091600--63091656 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
63091590 ACCTTTCAAT
* *
63091600 GGTATTGCGATATCCTTTTT
1 GGTATTGTGATATCCTTTTA
* *
63091620 GGATATCGTAATATCCTCTTTA
1 GG-TATTGTGATATCCT-TTTA
63091642 GGTATTGTGATATCC
1 GGTATTGTGATATCC
63091657 ACCCTTCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.07
21 22 0.76
22 5 0.17
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (20 bp):
GGTATTGTGATATCCTTTTA
Found at i:63091697 original size:30 final size:30
Alignment explanation
Indices: 63091661--63091721 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
63091651 ATATCCACCC
*
63091661 TTCAAAGAGGA-CCTCAAGGTTCAACATTGA
1 TTCAAAGAGGACCCT-AAGGCTCAACATTGA
63091691 TTCAAAGAGGACCCTAAGGCTCAACATTGA
1 TTCAAAGAGGACCCTAAGGCTCAACATTGA
63091721 T
1 T
63091722 CGAGGTATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (30 bp):
TTCAAAGAGGACCCTAAGGCTCAACATTGA
Found at i:63094674 original size:15 final size:16
Alignment explanation
Indices: 63094654--63094686 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
63094644 TCACAATTAT
63094654 TTTATA-AAGTAAATA
1 TTTATAGAAGTAAATA
*
63094669 TTTATAGAAGTTAATA
1 TTTATAGAAGTAAATA
63094685 TT
1 TT
63094687 CTTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (16 bp):
TTTATAGAAGTAAATA
Found at i:63100833 original size:25 final size:26
Alignment explanation
Indices: 63100776--63100834 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
63100766 ATTAACAATG
63100776 TATATATGATAATAATAGTAATAATA
1 TATATATGATAATAATAGTAATAATA
* * *
63100802 CAAATATGA-AATAATAGTGAACATATA
1 TATATATGATAATAATAGT-AATA-ATA
63100829 TATATA
1 TATATA
63100835 AAACATATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 9 0.35
26 10 0.38
27 7 0.27
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.34
Consensus pattern (26 bp):
TATATATGATAATAATAGTAATAATA
Found at i:63101066 original size:27 final size:25
Alignment explanation
Indices: 63100995--63101128 Score: 117
Period size: 25 Copynumber: 5.1 Consensus size: 25
63100985 AAGTATATAC
* *
63100995 ATAGTATTAGAAATATGTACATAAT
1 ATAGTATTAAAAATATATACATAAT
** *
63101020 ATAGCGTTAAAAATACATACATAAT
1 ATAGTATTAAAAATATATACATAAT
63101045 ATAGTTATTAAAAAATATATACATAAGAT
1 ATAG-TATT-AAAAATATATACAT-A-AT
** *
63101074 AATATGTAAGAAAAAATATATAAATAAT
1 -ATA-GT-ATTAAAAATATATACATAAT
*
63101102 ATAGTATT-AAAATATTTACATAAT
1 ATAGTATTAAAAATATATACATAAT
63101126 ATA
1 ATA
63101129 TACATATTAG
Statistics
Matches: 87, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
24 17 0.20
25 25 0.29
26 4 0.05
27 16 0.18
28 3 0.03
29 3 0.03
30 17 0.20
31 2 0.02
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.34
Consensus pattern (25 bp):
ATAGTATTAAAAATATATACATAAT
Found at i:63101201 original size:21 final size:20
Alignment explanation
Indices: 63101175--63101224 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
63101165 CTACATAAAT
* *
63101175 ATATATATTAAAGATATATAC
1 ATATATAATAAA-ACATATAC
63101196 ATATATAATAAAACATATAC
1 ATATATAATAAAACATATAC
63101216 -TA-ATAATAA
1 ATATATAATAA
63101225 TAATAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 7 0.26
19 2 0.07
20 7 0.26
21 11 0.41
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATATAATAAAACATATAC
Found at i:63101238 original size:15 final size:15
Alignment explanation
Indices: 63101218--63101263 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
63101208 ACATATACTA
63101218 ATAATAATAAT-AAT
1 ATAATAATAATAAAT
*
63101232 ATAAATAATAGTAAAT
1 AT-AATAATAATAAAT
*
63101248 ATAATAATAGTAAAT
1 ATAATAATAATAAAT
63101263 A
1 A
63101264 ATATTAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.76
16 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:63101238 original size:18 final size:17
Alignment explanation
Indices: 63101216--63101290 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 17
63101206 AAACATATAC
*
63101216 TAATAATAATAATAATA
1 TAATAATAGTAATAATA
63101233 TAAATAATAGT-A-AATA
1 T-AATAATAGTAATAATA
63101249 TAATAATAGTAAATAATA
1 TAATAATAGT-AATAATA
* *
63101267 T--TAAAAGTAATTAATT
1 TAATAATAGTAA-TAATA
63101283 TAATAATA
1 TAATAATA
63101291 AAGAAATGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
15 11 0.23
16 16 0.34
17 3 0.06
18 17 0.36
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (17 bp):
TAATAATAGTAATAATA
Found at i:63101277 original size:25 final size:24
Alignment explanation
Indices: 63101224--63101271 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
63101214 ACTAATAATA
63101224 ATAATAATATAAATAATAGTAAAT
1 ATAATAATATAAATAATAGTAAAT
*
63101248 ATAATAATAGTAAATAATATTAAA
1 ATAATAATA-TAAATAATAGTAAA
63101272 AGTAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAATAATATAAATAATAGTAAAT
Found at i:63104255 original size:5 final size:5
Alignment explanation
Indices: 63104245--63104273 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
63104235 TCTATGTGTT
63104245 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
63104274 TCATAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:63120730 original size:17 final size:18
Alignment explanation
Indices: 63120698--63120731 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
63120688 AATTCAACTT
63120698 TAATTAAATTTCTTAAAA
1 TAATTAAATTTCTTAAAA
*
63120716 TAATT-AATTTTTTAAA
1 TAATTAAATTTCTTAAA
63120732 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTTCTTAAAA
Found at i:63121308 original size:27 final size:27
Alignment explanation
Indices: 63121285--63121355 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
63121275 GAGTATGGTT
* *
63121285 TTGAGTTTAATGTTTAAGCTTATGGGC
1 TTGAATTTAAGGTTTAAGCTTATGGGC
63121312 TTGAATTTAAGGTTTAAGCTTATGGGC
1 TTGAATTTAAGGTTTAAGCTTATGGGC
* *
63121339 TCGAATTTAGGGTTTAA
1 TTGAATTTAAGGTTTAA
63121356 AAGTTTAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (27 bp):
TTGAATTTAAGGTTTAAGCTTATGGGC
Found at i:63122064 original size:21 final size:20
Alignment explanation
Indices: 63122038--63122104 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
63122028 TATGGTTTAT
63122038 GATTTTATATTTTAGGGTTGA
1 GATTTTATA-TTTAGGGTTGA
* * *
63122059 GATTTTAGATTTAAGGTTTA
1 GATTTTATATTTAGGGTTGA
*
63122079 TGA-TTTATAGTTTATGGTTTGA
1 -GATTTTATA-TTTA-GGGTTGA
63122101 GATT
1 GATT
63122105 CATGGTTATA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
20 14 0.40
21 16 0.46
22 5 0.14
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.52
Consensus pattern (20 bp):
GATTTTATATTTAGGGTTGA
Found at i:63122179 original size:22 final size:21
Alignment explanation
Indices: 63122138--63122180 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
63122128 ATATTTATTA
*
63122138 ATTTTAGGGTTTATGGTTTAG
1 ATTTTAGGGTTTATGATTTAG
63122159 ATTTTAAGGGTTTAAT-ATTTAG
1 ATTTT-AGGGTTT-ATGATTTAG
63122181 TGTTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 12 0.63
23 2 0.11
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (21 bp):
ATTTTAGGGTTTATGATTTAG
Found at i:63123554 original size:16 final size:16
Alignment explanation
Indices: 63123533--63123563 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63123523 CTATGAATAC
*
63123533 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
63123549 AAAATACAAAAGACA
1 AAAATACAAAAGACA
63123564 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:63123836 original size:22 final size:22
Alignment explanation
Indices: 63123806--63123871 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 22
63123796 AGTATTTTAA
* *
63123806 TTTAGGGTTTATGATTATAGTG
1 TTTAAGGTTTATGATTATAGAG
*
63123828 TTTAAGG-TTAT-A-TATCTGAG
1 TTTAAGGTTTATGATTAT-AGAG
*
63123848 TTTAAGGTTTA-GATTATATAG
1 TTTAAGGTTTATGATTATAGAG
63123869 TTT
1 TTT
63123872 TTAGTTTAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
19 3 0.09
20 10 0.29
21 13 0.37
22 9 0.26
ACGTcount: A:0.27, C:0.02, G:0.21, T:0.50
Consensus pattern (22 bp):
TTTAAGGTTTATGATTATAGAG
Found at i:63124416 original size:7 final size:7
Alignment explanation
Indices: 63124406--63124439 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
63124396 TATGTGTTTG
63124406 GGTTTAA
1 GGTTTAA
63124413 GGTTTAA
1 GGTTTAA
* *
63124420 GATTTCA
1 GGTTTAA
63124427 GGTTTAA
1 GGTTTAA
63124434 GGTTTA
1 GGTTTA
63124440 GAGTTTTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.44
Consensus pattern (7 bp):
GGTTTAA
Found at i:63124704 original size:29 final size:29
Alignment explanation
Indices: 63124656--63124724 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
63124646 TTAGTTTATG
*
63124656 GTTTAAGGTTTAGGATTTATGA-TTA-TAA
1 GTTTAAGGTTTAGGACTTAT-ATTTATTAA
63124684 GTTTAAAGGTTTAGTG-CTTATATTTATTAA
1 GTTT-AAGGTTTAG-GACTTATATTTATTAA
63124714 GTTTAAGGTTT
1 GTTTAAGGTTT
63124725 GGGTTCAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 5 0.14
29 23 0.64
30 8 0.22
ACGTcount: A:0.29, C:0.01, G:0.20, T:0.49
Consensus pattern (29 bp):
GTTTAAGGTTTAGGACTTATATTTATTAA
Found at i:63124922 original size:27 final size:25
Alignment explanation
Indices: 63124870--63124990 Score: 80
Period size: 27 Copynumber: 4.5 Consensus size: 25
63124860 TAAGGTTATG
* *
63124870 TGATTTATGGTTACATGTTTGAGTTTA
1 TGATTTAT-GTT-TATGTTTGGGTTTA
*
63124897 TTATTTAGTGTTTATGTTTAGGGTTTA
1 TGATTTA-TGTTTATGTTT-GGGTTTA
* * *
63124924 GGGTTTATGGTTTATAGTTTGGGTTGA
1 TGATTTAT-GTTTAT-GTTTGGGTTTA
*
63124951 TGATTTATGATTCTAGGTTTAGGGTTTA
1 TGATTTATG-TT-TATGTTT-GGGTTTA
* *
63124979 TGGTTTAAGTTT
1 TGATTTATGTTT
63124991 TAGTGTTATG
Statistics
Matches: 74, Mismatches: 13, Indels: 15
0.73 0.13 0.15
Matches are distributed among these distances:
26 9 0.12
27 45 0.61
28 20 0.27
ACGTcount: A:0.19, C:0.02, G:0.26, T:0.53
Consensus pattern (25 bp):
TGATTTATGTTTATGTTTGGGTTTA
Found at i:63124929 original size:14 final size:14
Alignment explanation
Indices: 63124900--63124985 Score: 70
Period size: 14 Copynumber: 6.3 Consensus size: 14
63124890 GAGTTTATTA
*
63124900 TTTAGTGTTTAT-G
1 TTTAGGGTTTATGG
*
63124913 TTTAGGGTTTAGGG
1 TTTAGGGTTTATGG
* *
63124927 TTTATGGTTTATAG
1 TTTAGGGTTTATGG
* *
63124941 TTT-GGGTTGATGA
1 TTTAGGGTTTATGG
* *
63124954 TTTATGATTCTA-GG
1 TTTAGGGTT-TATGG
63124968 TTTAGGGTTTATGG
1 TTTAGGGTTTATGG
63124982 TTTA
1 TTTA
63124986 AGTTTTAGTG
Statistics
Matches: 54, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
13 21 0.39
14 32 0.59
15 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.29, T:0.52
Consensus pattern (14 bp):
TTTAGGGTTTATGG
Found at i:63124947 original size:20 final size:21
Alignment explanation
Indices: 63124892--63124985 Score: 63
Period size: 20 Copynumber: 4.6 Consensus size: 21
63124882 ACATGTTTGA
*
63124892 GTTTATTA-TTTAGTGTTTAT-
1 GTTTA-TAGTTTAGGGTTTATG
**
63124912 GTTTAGGGTTTAGGGTTTATG
1 GTTTATAGTTTAGGGTTTATG
*
63124933 GTTTATAGTTT-GGGTTGATG
1 GTTTATAGTTTAGGGTTTATG
* *
63124953 ATTTAT-GATTCTA-GGTTTAGG
1 GTTTATAG-TT-TAGGGTTTATG
*
63124974 GTTTATGGTTTA
1 GTTTATAGTTTA
63124986 AGTTTTAGTG
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.02
20 33 0.57
21 23 0.40
22 1 0.02
ACGTcount: A:0.18, C:0.01, G:0.28, T:0.53
Consensus pattern (21 bp):
GTTTATAGTTTAGGGTTTATG
Found at i:63125236 original size:20 final size:20
Alignment explanation
Indices: 63125213--63125366 Score: 61
Period size: 20 Copynumber: 7.6 Consensus size: 20
63125203 AATTGTAGTT
63125213 TTTATGGTTTATATTTAGGG
1 TTTATGGTTTATATTTAGGG
* * *
63125233 TTTATAGTTTATGGTTT-TGG
1 TTTATGGTTTAT-ATTTAGGG
*
63125253 TTT-TGGTATTATGTTTAGGG
1 TTTATGGT-TTATATTTAGGG
** * *
63125273 TTTAAAGTTTGTTATTTTA-GA
1 TTTATGGTTT-ATA-TTTAGGG
* *
63125294 TTTAGGGTTTA-AGTTTAGTG
1 TTTATGGTTTATA-TTTAGGG
* * *
63125314 TTTAT-ATTTATGGTTTATGG
1 TTTATGGTTTAT-ATTTAGGG
63125334 TTTAT-GTTTA-AGGTTTAGGG
1 TTTATGGTTTATA--TTTAGGG
63125354 TTTTATGGTTTAT
1 -TTTATGGTTTAT
63125367 GGTTTAAATT
Statistics
Matches: 96, Mismatches: 24, Indels: 25
0.66 0.17 0.17
Matches are distributed among these distances:
19 16 0.17
20 51 0.53
21 20 0.21
22 9 0.09
ACGTcount: A:0.19, C:0.00, G:0.24, T:0.56
Consensus pattern (20 bp):
TTTATGGTTTATATTTAGGG
Found at i:63125242 original size:7 final size:7
Alignment explanation
Indices: 63125213--63125372 Score: 86
Period size: 7 Copynumber: 23.6 Consensus size: 7
63125203 AATTGTAGTT
63125213 TTTATGG
1 TTTATGG
*
63125220 TTTAT-A
1 TTTATGG
*
63125226 TTTAGGG
1 TTTATGG
*
63125233 TTTATAG
1 TTTATGG
63125240 TTTATGG
1 TTTATGG
63125247 TTT-TGG
1 TTTATGG
63125253 TTT-TGG
1 TTTATGG
63125259 TATTAT-G
1 T-TTATGG
*
63125266 TTTAGGG
1 TTTATGG
**
63125273 TTTAAAG
1 TTTATGG
* **
63125280 TTTGTTA
1 TTTATGG
*
63125287 TTT-TAGA
1 TTTAT-GG
*
63125294 TTTAGGG
1 TTTATGG
*
63125301 TTTA-AG
1 TTTATGG
63125307 TTTA-GTG
1 TTTATG-G
*
63125314 TTTAT-A
1 TTTATGG
63125320 TTTATGG
1 TTTATGG
63125327 TTTATGG
1 TTTATGG
63125334 TTTAT-G
1 TTTATGG
*
63125340 TTTAAGG
1 TTTATGG
*
63125347 TTTAGGG
1 TTTATGG
63125354 TTTTATGG
1 -TTTATGG
63125362 TTTATGG
1 TTTATGG
63125369 TTTA
1 TTTA
63125373 AATTCAGAGT
Statistics
Matches: 119, Mismatches: 23, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
6 33 0.28
7 79 0.66
8 7 0.06
ACGTcount: A:0.19, C:0.00, G:0.24, T:0.56
Consensus pattern (7 bp):
TTTATGG
Found at i:63125342 original size:13 final size:13
Alignment explanation
Indices: 63125213--63125372 Score: 78
Period size: 13 Copynumber: 11.8 Consensus size: 13
63125203 AATTGTAGTT
*
63125213 TTTATGGTTTATA
1 TTTATGGTTTATG
*
63125226 TTTAGGGTTTATAG
1 TTTATGGTTTAT-G
63125240 TTTATGGTTT-TGG
1 TTTATGGTTTAT-G
63125253 TTT-TGGTATTATG
1 TTTATGGT-TTATG
* *
63125266 TTTAGGGTTTAAAG
1 TTTATGGTTT-ATG
* **
63125280 TTTGTTATTT-TAG
1 TTTATGGTTTAT-G
* *
63125293 ATTTAGGGTTTAAG
1 -TTTATGGTTTATG
*
63125307 TTTA-GTGTTTATA
1 TTTATG-GTTTATG
63125320 TTTATGGTTTATGG
1 TTTATGGTTTAT-G
*
63125334 TTTAT-GTTTAAGG
1 TTTATGGTTT-ATG
*
63125347 TTTAGGGTTTTATGG
1 TTTATGG-TTTAT-G
63125362 TTTATGGTTTA
1 TTTATGGTTTA
63125373 AATTCAGAGT
Statistics
Matches: 109, Mismatches: 23, Indels: 29
0.68 0.14 0.18
Matches are distributed among these distances:
12 5 0.05
13 53 0.49
14 41 0.38
15 10 0.09
ACGTcount: A:0.19, C:0.00, G:0.24, T:0.56
Consensus pattern (13 bp):
TTTATGGTTTATG
Found at i:63125384 original size:28 final size:28
Alignment explanation
Indices: 63125327--63125384 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
63125317 ATATTTATGG
* * *
63125327 TTTATGGTTTATGTTTAAGGTTTAGGGT
1 TTTATGGTTTATGTTTAAGATTCAGAGT
63125355 TTTATGGTTTATGGTTTAA-ATTCAGAGT
1 TTTATGGTTTAT-GTTTAAGATTCAGAGT
63125383 TT
1 TT
63125385 ATTATTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.21, C:0.02, G:0.24, T:0.53
Consensus pattern (28 bp):
TTTATGGTTTATGTTTAAGATTCAGAGT
Found at i:63125430 original size:20 final size:20
Alignment explanation
Indices: 63125306--63125431 Score: 71
Period size: 20 Copynumber: 6.2 Consensus size: 20
63125296 TAGGGTTTAA
63125306 GTTTAGTGTTTATA-TTTATG
1 GTTTA-TGTTTATAGTTTATG
*
63125326 GTTTATGGTTTAT-GTTTAAG
1 GTTTAT-GTTTATAGTTTATG
* *
63125346 GTTTAGGGTTTTATGGTTTATG
1 GTTTA-TG-TTTATAGTTTATG
** * * *
63125368 GTTTAAATTCAGAGTTTATT
1 GTTTATGTTTATAGTTTATG
* * *
63125388 ATTTCAT-TATAATA-TTTAGG
1 GTTT-ATGT-TTATAGTTTATG
63125408 GTTTATGTTTATAGTTTATG
1 GTTTATGTTTATAGTTTATG
63125428 GTTT
1 GTTT
63125432 TAATTTTGTT
Statistics
Matches: 79, Mismatches: 18, Indels: 18
0.69 0.16 0.16
Matches are distributed among these distances:
19 7 0.09
20 52 0.66
21 9 0.11
22 11 0.14
ACGTcount: A:0.22, C:0.02, G:0.21, T:0.56
Consensus pattern (20 bp):
GTTTATGTTTATAGTTTATG
Found at i:63125552 original size:21 final size:21
Alignment explanation
Indices: 63125522--63125565 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
63125512 AGGGTTTAAT
* *
63125522 TTTAGTGTTTATAATTTAGGG
1 TTTAGCGTTTATAATTTAAGG
*
63125543 TTTAGCGTTTATTATTTAAGG
1 TTTAGCGTTTATAATTTAAGG
63125564 TT
1 TT
63125566 ATGGTTTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.20, T:0.55
Consensus pattern (21 bp):
TTTAGCGTTTATAATTTAAGG
Found at i:63125760 original size:13 final size:14
Alignment explanation
Indices: 63125708--63125767 Score: 79
Period size: 14 Copynumber: 4.4 Consensus size: 14
63125698 AGGGTTTATA
*
63125708 GTTT-GAGTTTAAG
1 GTTTAGAGTTTAGG
*
63125721 GTTTATAGTTTAGG
1 GTTTAGAGTTTAGG
*
63125735 GTTTAGAGTTTAGT
1 GTTTAGAGTTTAGG
63125749 GTTT-GAGTTTAGG
1 GTTTAGAGTTTAGG
63125762 GTTTAG
1 GTTTAG
63125768 GATTTGTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
13 16 0.40
14 24 0.60
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (14 bp):
GTTTAGAGTTTAGG
Found at i:63125767 original size:20 final size:20
Alignment explanation
Indices: 63125695--63125766 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
63125685 ATGGCTTATA
63125695 TTTAGGGTTTATAGTTTGAG
1 TTTAGGGTTTATAGTTTGAG
* *
63125715 TTTAAGGTTTATAGTTTAGGG
1 TTTAGGGTTTATAGTTT-GAG
*
63125736 TTTAGAGTTTAGT-GTTTGAG
1 TTTAGGGTTTA-TAGTTTGAG
63125756 TTTAGGGTTTA
1 TTTAGGGTTTA
63125767 GGATTTGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 28 0.64
21 15 0.34
22 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (20 bp):
TTTAGGGTTTATAGTTTGAG
Found at i:63125768 original size:7 final size:7
Alignment explanation
Indices: 63125695--63125767 Score: 62
Period size: 7 Copynumber: 10.7 Consensus size: 7
63125685 ATGGCTTATA
*
63125695 TTTAGGG
1 TTTAGAG
*
63125702 TTTATAG
1 TTTAGAG
63125709 TTT-GAG
1 TTTAGAG
63125715 TTTA-AGG
1 TTTAGA-G
*
63125722 TTTATAG
1 TTTAGAG
*
63125729 TTTAGGG
1 TTTAGAG
63125736 TTTAGAG
1 TTTAGAG
*
63125743 TTTAGTG
1 TTTAGAG
63125750 TTT-GAG
1 TTTAGAG
*
63125756 TTTAGGG
1 TTTAGAG
63125763 TTTAG
1 TTTAG
63125768 GATTTGTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
6 11 0.21
7 41 0.77
8 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (7 bp):
TTTAGAG
Found at i:63125784 original size:27 final size:27
Alignment explanation
Indices: 63125726--63125785 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
63125716 TTAAGGTTTA
*
63125726 TAGTTTAGGGTTTAGAGTTTAGTGTTT
1 TAGTTTAGGGTTTAGAGTTTAGTATTT
*
63125753 GAGTTTAGGGTTTAG-GATTT-GTTATTT
1 TAGTTTAGGGTTTAGAG-TTTAG-TATTT
63125780 TAGTTT
1 TAGTTT
63125786 TAAGGTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.53
Consensus pattern (27 bp):
TAGTTTAGGGTTTAGAGTTTAGTATTT
Found at i:63125876 original size:20 final size:20
Alignment explanation
Indices: 63125826--63125896 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
63125816 AATTATAGTA
*
63125826 TTTAAGGTTTATA-TTTAGGG
1 TTTAAGGTTTATAGTTT-GAG
* *
63125846 TTTATA-ATTTATAGTTTGTG
1 TTTA-AGGTTTATAGTTTGAG
63125866 TTTAAGGTTTAGT-GTTTGAG
1 TTTAAGGTTTA-TAGTTTGAG
63125886 TTT-AGGTTTAT
1 TTTAAGGTTTAT
63125897 GGGTTATGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 1 0.02
19 8 0.19
20 29 0.67
21 5 0.12
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (20 bp):
TTTAAGGTTTATAGTTTGAG
Found at i:63125927 original size:7 final size:7
Alignment explanation
Indices: 63125885--63125931 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
63125875 TAGTGTTTGA
63125885 GTTTA-G
1 GTTTATG
63125891 GTTTATG
1 GTTTATG
*
63125898 GGTTATG
1 GTTTATG
*
63125905 GTTTATA
1 GTTTATG
63125912 GTTTATG
1 GTTTATG
*
63125919 GTTTGTG
1 GTTTATG
63125926 GTTTAT
1 GTTTAT
63125932 ATATAGGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (7 bp):
GTTTATG
Found at i:63126021 original size:13 final size:13
Alignment explanation
Indices: 63126000--63126034 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
63125990 TAGTTTAGGA
63126000 TATGATTAGGGTT
1 TATGATTAGGGTT
*
63126013 TATGCTTAGGGTT
1 TATGATTAGGGTT
63126026 TATGATTAG
1 TATGATTAG
63126035 TAATTTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.03, G:0.29, T:0.46
Consensus pattern (13 bp):
TATGATTAGGGTT
Found at i:63126061 original size:13 final size:13
Alignment explanation
Indices: 63125826--63126061 Score: 54
Period size: 13 Copynumber: 17.3 Consensus size: 13
63125816 AATTATAGTA
* *
63125826 TTTAAGGTTTATA
1 TTTAGGGTTTATG
*
63125839 TTTAGGGTTTATAA
1 TTTAGGGTTTAT-G
** *
63125853 TTTATAGTTTGTG
1 TTTAGGGTTTATG
*
63125866 TTTAAGGTTTAGTG
1 TTTAGGGTTTA-TG
* *
63125880 TTT-GAGTTTAGG
1 TTTAGGGTTTATG
63125892 TTTATGGG-TTATGG
1 TTTA-GGGTTTAT-G
**
63125906 TTTATAGTTTATGG
1 TTTAGGGTTTAT-G
*
63125920 TTT-GTGGTTTATA
1 TTTAG-GGTTTATG
* *
63125933 TATAGGTTTTAGTG
1 TTTAGGGTTTA-TG
*
63125947 TTT-TGGTTTGAT-
1 TTTAGGGTTT-ATG
*
63125959 TTTAGGGTTTAATA
1 TTTAGGGTTT-ATG
*
63125973 TTTAGTGTTTGATG
1 TTTAGGGTTT-ATG
*
63125987 TTATAGTTTAGG-ATATG
1 TT-TAG----GGTTTATG
*
63126004 ATTAGGGTTTATG
1 TTTAGGGTTTATG
*
63126017 CTTAGGGTTTATG
1 TTTAGGGTTTATG
* **
63126030 ATTAGTAATTTTACT-
1 TTTAG--GGTTTA-TG
63126045 TTTAGGGTTTATG
1 TTTAGGGTTTATG
63126058 TTTA
1 TTTA
63126062 TAGTTTAGTA
Statistics
Matches: 161, Mismatches: 40, Indels: 44
0.66 0.16 0.18
Matches are distributed among these distances:
12 10 0.06
13 75 0.47
14 55 0.34
15 11 0.07
16 4 0.02
17 4 0.02
18 1 0.01
19 1 0.01
ACGTcount: A:0.21, C:0.01, G:0.25, T:0.53
Consensus pattern (13 bp):
TTTAGGGTTTATG
Found at i:63126115 original size:21 final size:21
Alignment explanation
Indices: 63126085--63126124 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
63126075 GTGACCAGGG
*
63126085 TTTAGTATTTAAGG-TTTATTT
1 TTTAGGATTT-AGGATTTATTT
63126106 TTTAGGATTTAGGATTTAT
1 TTTAGGATTTAGGATTTAT
63126125 GATTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.57
Consensus pattern (21 bp):
TTTAGGATTTAGGATTTATTT
Found at i:63126346 original size:7 final size:7
Alignment explanation
Indices: 63126334--63126565 Score: 139
Period size: 7 Copynumber: 33.9 Consensus size: 7
63126324 TTATACTTAG
63126334 GGTTTAA
1 GGTTTAA
63126341 GGTTTATA
1 GGTTTA-A
*
63126349 -ATTTAA
1 GGTTTAA
*
63126355 TGTTT-A
1 GGTTTAA
63126361 GGTTTAA
1 GGTTTAA
63126368 GGTTTAA
1 GGTTTAA
63126375 GGTTTAA
1 GGTTTAA
63126382 GGTTTAA
1 GGTTTAA
63126389 GGTTTATA
1 GGTTTA-A
*
63126397 -ATTTATA
1 GGTTTA-A
63126404 --TTTAA
1 GGTTTAA
*
63126409 CGTTTAA
1 GGTTTAA
63126416 GGTTT-A
1 GGTTTAA
* *
63126422 TGTTTAG
1 GGTTTAA
*
63126429 GGTTTAG
1 GGTTTAA
*
63126436 GGTTTAT
1 GGTTTAA
*
63126443 GGTTTAT
1 GGTTTAA
63126450 GGTTT-A
1 GGTTTAA
*
63126456 TGTTTAA
1 GGTTTAA
*
63126463 GGTATAA
1 GGTTTAA
63126470 GGTTTATA
1 GGTTTA-A
63126478 -GTTTATA
1 GGTTTA-A
*
63126485 -GTTTAG
1 GGTTTAA
63126491 GGTTTATA
1 GGTTTA-A
*
63126499 -GTTTAG
1 GGTTTAA
*
63126505 GGTTTAT
1 GGTTTAA
*
63126512 GATTCT-A
1 GGTT-TAA
*
63126519 GTTTTAA
1 GGTTTAA
*
63126526 GGTTTAT
1 GGTTTAA
63126533 GGTTTAA
1 GGTTTAA
63126540 GGTTTATA
1 GGTTTA-A
63126548 --TTTAA
1 GGTTTAA
*
63126553 GGTTTAG
1 GGTTTAA
63126560 GGTTTA
1 GGTTTA
63126566 TGATTTAATT
Statistics
Matches: 183, Mismatches: 25, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
5 2 0.01
6 24 0.13
7 152 0.83
8 5 0.03
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.50
Consensus pattern (7 bp):
GGTTTAA
Found at i:63126421 original size:20 final size:20
Alignment explanation
Indices: 63126207--63126573 Score: 112
Period size: 20 Copynumber: 18.2 Consensus size: 20
63126197 GAGTTTAAAG
* *
63126207 TTTAGGGTTTAAAGTTTA-A
1 TTTAAGGTTTAAGGTTTATA
* *
63126226 TCATAAGGTTTAAGATTTATA
1 T-TTAAGGTTTAAGGTTTATA
* * *
63126247 TTTAGGGTTTAAGATTTGTTA
1 TTTAAGGTTTAAGGTTT-ATA
* *
63126268 TTCT-AGTTTTAAGGTTTTAAGA
1 TT-TAAGGTTTAAGG-TTT-ATA
*
63126290 TTTAAGGTTT-AGG-ATATAA
1 TTTAAGGTTTAAGGTTTAT-A
*
63126309 TTCTAATGG-TT-AGGGTTATA
1 TT-TAA-GGTTTAAGGTTTATA
* *
63126329 CTTAGGGTTTAAGGTTTATAA
1 TTTAAGGTTTAAGGTTTAT-A
*
63126350 TTTAATGTTT-AGG------
1 TTTAAGGTTTAAGGTTTATA
63126363 TTTAAGGTTTAAGGTTTA-A
1 TTTAAGGTTTAAGGTTTATA
*
63126382 GGTTTAAGGTTTATA-ATTTATA
1 --TTTAAGGTTTA-AGGTTTATA
* *
63126404 TTTAACGTTTAAGGTTTATG
1 TTTAAGGTTTAAGGTTTATA
* *
63126424 TTTAGGGTTT-AGGGTT-TA
1 TTTAAGGTTTAAGGTTTATA
* *
63126442 --T--GGTTTATGGTTTATG
1 TTTAAGGTTTAAGGTTTATA
*
63126458 TTTAAGGTATAAGGTTTATA
1 TTTAAGGTTTAAGGTTTATA
*
63126478 GTTTATA-GTTTAGGGTTTATA
1 -TTTA-AGGTTTAAGGTTTATA
* * *
63126499 GTTTAGGGTTTATGATTCTAGTTTTAA
1 -TTTAAGGTTTAAGGTT-TA----T-A
*
63126526 GGTTTATGGTTTAAGGTTTATA
1 --TTTAAGGTTTAAGGTTTATA
*
63126548 TTTAAGGTTTAGGGTTTATGA
1 TTTAAGGTTTAAGGTTTAT-A
63126569 TTTAA
1 TTTAA
63126574 TTGTAAGGTT
Statistics
Matches: 259, Mismatches: 48, Indels: 80
0.67 0.12 0.21
Matches are distributed among these distances:
13 9 0.03
14 8 0.03
15 4 0.02
16 2 0.01
18 5 0.02
19 15 0.06
20 99 0.38
21 80 0.31
22 18 0.07
23 1 0.00
26 1 0.00
27 3 0.01
28 14 0.05
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.49
Consensus pattern (20 bp):
TTTAAGGTTTAAGGTTTATA
Found at i:63126573 original size:34 final size:34
Alignment explanation
Indices: 63126363--63126573 Score: 134
Period size: 34 Copynumber: 6.1 Consensus size: 34
63126353 AATGTTTAGG
*
63126363 TTTAAGGTTTA-AGGTTTAAGGTTTAAGGTTTATAA
1 TTTAAGGTTTATA-GTTTAAGGTTT-AGGTTTATGA
* * *
63126398 TTTATA--TTTA-ACGTTTAAGGTTTATGTTTAGGG
1 TTTA-AGGTTTATA-GTTTAAGGTTTAGGTTTATGA
* * * * * *
63126431 TTTAGGGTTTATGGTTTATGGTTTATGTTTAAGG
1 TTTAAGGTTTATAGTTTAAGGTTTAGGTTTATGA
*
63126465 TATAAGGTTTATAGTTTATA-GTTTAGGGTTTAT-A
1 TTTAAGGTTTATAGTTTA-AGGTTTA-GGTTTATGA
* * *
63126499 GTTTAGGGTTTAT-GATTCT-AGTTTTAAGGTTTATGG
1 -TTTAAGGTTTATAG-TT-TAAGGTTT-AGGTTTATGA
63126535 TTTAAGGTTTATA-TTTAAGGTTTAGGGTTTATGA
1 TTTAAGGTTTATAGTTTAAGGTTTA-GGTTTATGA
63126569 TTTAA
1 TTTAA
63126574 TTGTAAGGTT
Statistics
Matches: 138, Mismatches: 23, Indels: 31
0.72 0.12 0.16
Matches are distributed among these distances:
33 12 0.09
34 81 0.59
35 42 0.30
36 3 0.02
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.50
Consensus pattern (34 bp):
TTTAAGGTTTATAGTTTAAGGTTTAGGTTTATGA
Found at i:63126590 original size:27 final size:26
Alignment explanation
Indices: 63126334--63126602 Score: 143
Period size: 27 Copynumber: 9.9 Consensus size: 26
63126324 TTATACTTAG
* * *
63126334 GGTTTAAGGTTTATAATTTAATGTTTA
1 GGTTTATGGTTTATGATTTAAT-TTAA
* * *
63126361 GGTTTAAGGTTTAAGGTTTAAGGTTTAA
1 GGTTTATGGTTTATGATTTAA--TTTAA
**
63126389 GGTTTATAATTTAT-ATTTAACGTTTAA
1 GGTTTATGGTTTATGATTTAA--TTTAA
* * * *
63126416 GGTTTAT-GTTTAGGGTTTAGGGTTTAT
1 GGTTTATGGTTTATGATTTA--ATTTAA
*
63126443 GGTTTATGGTTTATG-TTTAAGGTATAA
1 GGTTTATGGTTTATGATTTAA--TTTAA
* *
63126470 GGTTTATAGTTTAT-AGTTTAGGGTTTATA
1 GGTTTATGGTTTATGA-TTTA--ATTTA-A
* *
63126499 -GTTTAGGGTTTATGATTCTAGTTTTAA
1 GGTTTATGGTTTATGATT-TA-ATTTAA
* *
63126526 GGTTTATGGTTTAAGGTTTATATTTAA
1 GGTTTATGGTTTATGATTTA-ATTTAA
*
63126553 GGTTTAGGGTTTATGATTTAATTGTAA
1 GGTTTATGGTTTATGATTTAATT-TAA
* * *
63126580 GGTTTTTGGTTTGTGATTCAATT
1 GGTTTATGGTTTATGATTTAATT
63126603 AAATATCATT
Statistics
Matches: 188, Mismatches: 37, Indels: 34
0.73 0.14 0.13
Matches are distributed among these distances:
26 7 0.04
27 118 0.63
28 58 0.31
29 5 0.03
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.51
Consensus pattern (26 bp):
GGTTTATGGTTTATGATTTAATTTAA
Found at i:63127230 original size:3 final size:3
Alignment explanation
Indices: 63127222--63127280 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
63127212 TTCCATTTTC
* *
63127222 TCT TCT TCT TCT T-T TCT TCT TCT TCT CCA T-T TCT TC- TCT TCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
63127266 TTT TGT TCT TCT TCT
1 TCT TCT TCT TCT TCT
63127281 ATTGCCCAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 7 0.15
3 39 0.85
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:63127238 original size:11 final size:11
Alignment explanation
Indices: 63127219--63127278 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
63127209 TACTTCCATT
*
63127219 TTCTCTTCTTC
1 TTCTTTTCTTC
63127230 TTCTTTTCTTC
1 TTCTTTTCTTC
* *
63127241 TTCTTCTCCAT-
1 TTCTT-TTCTTC
*
63127252 TTCTTCTCTTC
1 TTCTTTTCTTC
* *
63127263 TTTTTTTGTTC
1 TTCTTTTCTTC
63127274 TTCTT
1 TTCTT
63127279 CTATTGCCCA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
10 2 0.05
11 32 0.86
12 3 0.08
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (11 bp):
TTCTTTTCTTC
Found at i:63127241 original size:14 final size:14
Alignment explanation
Indices: 63127222--63127278 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
63127212 TTCCATTTTC
63127222 TCTTCTTCTTCTTT
1 TCTTCTTCTTCTTT
63127236 TCTTCTTCTTCTCCATT
1 TCTTCTTCTTCT---TT
63127253 TCTTC-TCTTCTTT
1 TCTTCTTCTTCTTT
* *
63127266 TTTTGTTCTTCTT
1 TCTTCTTCTTCTT
63127279 CTATTGCCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 5 0.14
14 19 0.51
16 6 0.16
17 7 0.19
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (14 bp):
TCTTCTTCTTCTTT
Found at i:63130228 original size:15 final size:15
Alignment explanation
Indices: 63130199--63130244 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
63130189 GAAATGAATG
*
63130199 AAGTTTTGCTCAATTT
1 AAGTTTGGCT-AATTT
*
63130215 AAGTTTGGCTAATTC
1 AAGTTTGGCTAATTT
*
63130230 AAGTTTGGTTAATTT
1 AAGTTTGGCTAATTT
63130245 TGGTCCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (15 bp):
AAGTTTGGCTAATTT
Found at i:63142193 original size:64 final size:63
Alignment explanation
Indices: 63142091--63142209 Score: 202
Period size: 64 Copynumber: 1.9 Consensus size: 63
63142081 TTTACTAATA
*
63142091 CTAAAACTGCAGTTAGTCTTCACAGCAACATACGTACGAAAAAGTGCCTGGCAACCCAACCTAT
1 CTAAAACTGCAGTTAGTCTTCACAGCAACATACATACG-AAAAGTGCCTGGCAACCCAACCTAT
* *
63142155 CTAAAAGTGCAGTTAGTCTTCACAGCAACATACATACGAAAAGTGTCTGGCAACC
1 CTAAAACTGCAGTTAGTCTTCACAGCAACATACATACGAAAAGTGCCTGGCAACC
63142210 ACCACCGATA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 16 0.31
64 36 0.69
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (63 bp):
CTAAAACTGCAGTTAGTCTTCACAGCAACATACATACGAAAAGTGCCTGGCAACCCAACCTAT
Found at i:63143291 original size:21 final size:21
Alignment explanation
Indices: 63143267--63143318 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
63143257 TATAGCATTT
63143267 AAATATATTATACCAATACTC
1 AAATATATTATACCAATACTC
*
63143288 AAATAAATTATACCAATACTC
1 AAATATATTATACCAATACTC
63143309 AAATAATATT
1 AAAT-ATATT
63143319 TTTAAAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATATTATACCAATACTC
Found at i:63148593 original size:52 final size:52
Alignment explanation
Indices: 63148531--63148739 Score: 411
Period size: 52 Copynumber: 4.0 Consensus size: 52
63148521 AACTGAAATC
63148531 CAACCTAAGCAATCCATGCAATAATTCCAAAATATCATAAAGGAAAAATTCT
1 CAACCTAAGCAATCCATGCAATAATTCCAAAATATCATAAAGGAAAAATTCT
63148583 CAACCTAAGCAATCCATGCAATAATTCCAAAATATCATAAAGGAAAAATTCT
1 CAACCTAAGCAATCCATGCAATAATTCCAAAATATCATAAAGGAAAAATTCT
63148635 CAACCTAAGCAATCCATGCAATAATTCCAAAATATCATAAAGGAAAAATTCT
1 CAACCTAAGCAATCCATGCAATAATTCCAAAATATCATAAAGGAAAAATTCT
63148687 CAACCTAAGCAATCCATGCAATAATTCCAAAATATCATAAAGG-AAAATTCT
1 CAACCTAAGCAATCCATGCAATAATTCCAAAATATCATAAAGGAAAAATTCT
63148738 CA
1 CA
63148740 CGCCACAGTC
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
51 10 0.06
52 147 0.94
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.23
Consensus pattern (52 bp):
CAACCTAAGCAATCCATGCAATAATTCCAAAATATCATAAAGGAAAAATTCT
Found at i:63150634 original size:15 final size:18
Alignment explanation
Indices: 63150604--63150641 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
63150594 TTTGTTTGTT
63150604 AAAAAGGAGATAAAAT-A
1 AAAAAGGAGATAAAATGA
63150621 AAAAAGGA-AT-AAATGA
1 AAAAAGGAGATAAAATGA
63150637 AAAAA
1 AAAAA
63150642 ATGAGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
17 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.11
Consensus pattern (18 bp):
AAAAAGGAGATAAAATGA
Found at i:63161390 original size:40 final size:40
Alignment explanation
Indices: 63161345--63161425 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
63161335 ATTATGCTTG
* * *
63161345 AAAAAAAGAAAATCAAGATGAAAACTCGAAAAGGGCATCTT
1 AAAAAAA-AGAATCAAGATGAAAACCCAAAAAGGGCATCTT
* *
63161386 AAAAAAAAGGATCAAGGTGAAAACCCAAAAAGGGCATCTT
1 AAAAAAAAGAATCAAGATGAAAACCCAAAAAGGGCATCTT
63161426 GATTAACACA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 28 0.80
41 7 0.20
ACGTcount: A:0.54, C:0.14, G:0.19, T:0.14
Consensus pattern (40 bp):
AAAAAAAAGAATCAAGATGAAAACCCAAAAAGGGCATCTT
Found at i:63162491 original size:90 final size:89
Alignment explanation
Indices: 63162260--63162587 Score: 462
Period size: 88 Copynumber: 3.7 Consensus size: 89
63162250 TCTGTTCGTC
* * **
63162260 AAAATTAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGACACGCTGAGGTATTTCCAATGTTG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATGTTG
*
63162325 GCTTTTCAATTTTTGCTTTTC-AA
66 GCTTTTCAATTTATGCTTTTCAAA
*
63162348 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTTAATGTTG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATGTTG
*
63162413 GCTTTTCAATTTCTGCTTTTCAAAA
66 GCTTTTCAATTTATGCTTTTC-AAA
* * * * **
63162438 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCATTAGGACACACTGAGGTATTTTAAAATCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTT-TAATGTT
* *
63162503 -GTTTTTCAATTTATGTTTTTCAAA
65 GGCTTTTCAATTTATGCTTTTCAAA
*
63162527 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTTA
63162588 GCTTCTGCTT
Statistics
Matches: 214, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
88 80 0.37
89 40 0.19
90 74 0.35
91 20 0.09
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (89 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATGTTG
GCTTTTCAATTTATGCTTTTCAAA
Found at i:63162737 original size:77 final size:77
Alignment explanation
Indices: 63162516--63162741 Score: 353
Period size: 79 Copynumber: 2.9 Consensus size: 77
63162506 TTTCAATTTA
63162516 TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
1 TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
63162581 ATTTTTAGCTTC
66 ATTTTTAGCTTC
* * * * *
63162593 TGCTTTTCAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCATCGGGTCACACACTAAG
1 TGTTTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAG
*
63162658 GTATTTTTAGTTTC
64 GTATTTTTAGCTTC
* * *
63162672 TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGGTGAGGT
1 TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
63162737 ATTTT
66 ATTTT
63162742 CAAAATCTAT
Statistics
Matches: 133, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
77 62 0.47
79 71 0.53
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (77 bp):
TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
ATTTTTAGCTTC
Found at i:63162755 original size:77 final size:77
Alignment explanation
Indices: 63162516--63162759 Score: 344
Period size: 77 Copynumber: 3.1 Consensus size: 77
63162506 TTTCAATTTA
63162516 TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
1 TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
*
63162581 ATTTTTAGCTTC
66 ATTTTTAGATTC
* * * * *
63162593 TGCTTTTCAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCATCGGGTCACACACTAAG
1 TGTTTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAG
*
63162658 GTATTTTTAGTTTC
64 GTATTTTTAGATTC
* * *
63162672 TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGGTGAGGT
1 TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
* * *
63162737 ATTTTCAAAATC
66 ATTTTTAGATTC
*
63162749 TATTTTTCAAA
1 TGTTTTTCAAA
63162760 TTAAGTTTCA
Statistics
Matches: 146, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
77 75 0.51
79 71 0.49
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (77 bp):
TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
ATTTTTAGATTC
Found at i:63164582 original size:3 final size:3
Alignment explanation
Indices: 63164576--63164697 Score: 61
Period size: 3 Copynumber: 40.0 Consensus size: 3
63164566 TCATTCCTAA
* * * *
63164576 TAT TAT TAA TAC TAT TAT T-T CTAT TAT TAT TAT TGT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* ** * * * *
63164621 TAT TCT GGT TAT TAA CA- TAT TAT TAT TTT TAAT GTAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT -TAT TAT TAT TAT
* *
63164667 TAGT TAT TAC TAT T-T CTAG TAT TAT TAT TAT
1 TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT
63164698 ATATAATATT
Statistics
Matches: 88, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
2 3 0.03
3 78 0.89
4 6 0.07
5 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:63165187 original size:30 final size:27
Alignment explanation
Indices: 63165134--63165189 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
63165124 ATTGTGTATA
*
63165134 TTCTTAATATTATATATTGTATATATT
1 TTCTTAATACTATATATTGTATATATT
63165161 TTCTTAATAACTATATTATATGTATATAT
1 TTCTTAAT-ACTATA-TAT-TGTATATAT
63165190 AGTACATGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 8 0.32
28 5 0.20
29 3 0.12
30 9 0.36
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (27 bp):
TTCTTAATACTATATATTGTATATATT
Found at i:63168702 original size:45 final size:45
Alignment explanation
Indices: 63168651--63168737 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
63168641 ATCAATGCCT
* * *
63168651 AAAATGAGTAAGACCATATCTAAAAGATGTTATGACATCATGATA
1 AAAATGAGTAAGACCATAGCTAAAAGACGCTATGACATCATGATA
* * *
63168696 AAAATGAGTAAGACTATAGCTGAAAGACGCTATGGCATCATG
1 AAAATGAGTAAGACCATAGCTAAAAGACGCTATGACATCATG
63168738 TGAAAACACG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.24
Consensus pattern (45 bp):
AAAATGAGTAAGACCATAGCTAAAAGACGCTATGACATCATGATA
Found at i:63183166 original size:6 final size:6
Alignment explanation
Indices: 63183157--63183239 Score: 123
Period size: 6 Copynumber: 13.8 Consensus size: 6
63183147 AGCATTAGCA
* *
63183157 TCAGCT TCAGCT TCAGCA TCAGCT TCAGCT TCAGCA TCAGCT TCAGCT
1 TCAGCT TCAGCT TCAGCT TCAGCT TCAGCT TCAGCT TCAGCT TCAGCT
*
63183205 TCAGAAT T-AGCT TCAGCT TCAGCT TCAGCT TCAGC
1 TCAG-CT TCAGCT TCAGCT TCAGCT TCAGCT TCAGC
63183240 ATTAGCATCA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
5 2 0.03
6 65 0.94
7 2 0.03
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.30
Consensus pattern (6 bp):
TCAGCT
Found at i:63183174 original size:18 final size:18
Alignment explanation
Indices: 63183153--63183249 Score: 151
Period size: 18 Copynumber: 5.4 Consensus size: 18
63183143 CATTAGCATT
63183153 AGCATCAGCTTCAGCTTC
1 AGCATCAGCTTCAGCTTC
63183171 AGCATCAGCTTCAGCTTC
1 AGCATCAGCTTCAGCTTC
63183189 AGCATCAGCTTCAGCTTC
1 AGCATCAGCTTCAGCTTC
* *
63183207 AGAATTAGCTTCAGCTTC
1 AGCATCAGCTTCAGCTTC
*
63183225 AGCTTCAGCTTCAGCATT-
1 AGCATCAGCTTCAGC-TTC
63183243 AGCATCA
1 AGCATCA
63183250 CCATCATCAT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
18 70 0.97
19 2 0.03
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (18 bp):
AGCATCAGCTTCAGCTTC
Found at i:63186131 original size:188 final size:190
Alignment explanation
Indices: 63185812--63186176 Score: 628
Period size: 188 Copynumber: 1.9 Consensus size: 190
63185802 ATTCTTCACG
* *
63185812 CACACACGCACACACGCAATCTTGTTTTGCTAAAACATTTTGATAAGCCAAATGTAAGCAGAACC
1 CACACACACACACACACAATCTTGTTTTGCTAAAACATTTTGATAAGCCAAATGTAAGCAGAACC
63185877 TTGAAATGTTTAGCACAAACTCACAGGGAAATACAAATGCAAATCTAATGAAACAAGTTGATCAA
66 TTGAAATGTTTAGCACAAACTCACAGGGAAATACAAATGCAAATCTAATGAAACAAGTTGATCAA
* *
63185942 ACCAGACGTTTTATAGAAAAAA-AA-AGGTCCCAAAGATCAAGTCCAGAGTCCAGACATA
131 ACCAAACGTTTTATAGAAAAAAGAACAGGTCCCAAAGATCAAATCCAGAGTCCAGACATA
* * *
63186000 CACACACACACACACACAATCTTGTTTTGCTAAACCATTTTGCTAAGCCAAATGTAAGTAGAACC
1 CACACACACACACACACAATCTTGTTTTGCTAAAACATTTTGATAAGCCAAATGTAAGCAGAACC
63186065 TTGAAATGTTTAGCACAAACTCACAGGGAAATACAAATGCAAATCTAATGAAACAAGCTT-ATCA
66 TTGAAATGTTTAGCACAAACTCACAGGGAAATACAAATGCAAATCTAATGAAACAAG-TTGATCA
*
63186129 AACCAAAGGTTTTATAGAAAAAAGAACAGGTCCCAAAGATCAAATCCA
130 AACCAAACGTTTTATAGAAAAAAGAACAGGTCCCAAAGATCAAATCCA
63186177 CCAAAAAAAG
Statistics
Matches: 166, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
188 142 0.86
189 4 0.02
190 20 0.12
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (190 bp):
CACACACACACACACACAATCTTGTTTTGCTAAAACATTTTGATAAGCCAAATGTAAGCAGAACC
TTGAAATGTTTAGCACAAACTCACAGGGAAATACAAATGCAAATCTAATGAAACAAGTTGATCAA
ACCAAACGTTTTATAGAAAAAAGAACAGGTCCCAAAGATCAAATCCAGAGTCCAGACATA
Found at i:63187304 original size:14 final size:15
Alignment explanation
Indices: 63187285--63187313 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
63187275 TGATACAATT
63187285 AGAAAATTCA-AGAG
1 AGAAAATTCACAGAG
63187299 AGAAAATTCACAGAG
1 AGAAAATTCACAGAG
63187314 TAAAAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.10, G:0.21, T:0.14
Consensus pattern (15 bp):
AGAAAATTCACAGAG
Found at i:63192141 original size:9 final size:9
Alignment explanation
Indices: 63192127--63192201 Score: 96
Period size: 9 Copynumber: 8.3 Consensus size: 9
63192117 ATAAGTATAA
63192127 AATTAACCG
1 AATTAACCG
*
63192136 AATTAATCG
1 AATTAACCG
63192145 AATTAACCG
1 AATTAACCG
* *
63192154 AATTACCCA
1 AATTAACCG
* *
63192163 AATTACCCA
1 AATTAACCG
63192172 AATTAACCG
1 AATTAACCG
63192181 AATTAACCG
1 AATTAACCG
*
63192190 AATTAATCG
1 AATTAACCG
63192199 AAT
1 AAT
63192202 AAATTTATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:63192229 original size:5 final size:6
Alignment explanation
Indices: 63192214--63192254 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
63192204 ATTTATATGT
*
63192214 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
63192255 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:63194599 original size:26 final size:26
Alignment explanation
Indices: 63194560--63194618 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
63194550 CTATAACGCA
* *
63194560 ATCTCACCTTGCAACACCACCTTGCG
1 ATCTCACCTCGCAACACCACATTGCG
**
63194586 ATCTCACCTCGCAACACTGCATTGCG
1 ATCTCACCTCGCAACACCACATTGCG
63194612 ATCTCAC
1 ATCTCAC
63194619 GTTGCAGTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.24, C:0.41, G:0.12, T:0.24
Consensus pattern (26 bp):
ATCTCACCTCGCAACACCACATTGCG
Found at i:63199024 original size:17 final size:17
Alignment explanation
Indices: 63199002--63199043 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
63198992 TTGACAGGGT
*
63199002 AAAGAGAAAATAGAGGA
1 AAAGAGAAAATAGAGAA
*
63199019 AAAGAGAAAATCGAGAA
1 AAAGAGAAAATAGAGAA
63199036 AAAG-GAAA
1 AAAGAGAAA
63199044 TACTGAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.67, C:0.02, G:0.26, T:0.05
Consensus pattern (17 bp):
AAAGAGAAAATAGAGAA
Found at i:63202440 original size:22 final size:22
Alignment explanation
Indices: 63202415--63202456 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
63202405 TCAAAACTAT
*
63202415 TACCCATGTCGCGAA-ACCAATA
1 TACCAATGTCGC-AACACCAATA
63202437 TACCAATGTCGCAACACCAA
1 TACCAATGTCGCAACACCAA
63202457 AGACAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.38, C:0.33, G:0.12, T:0.17
Consensus pattern (22 bp):
TACCAATGTCGCAACACCAATA
Found at i:63203734 original size:20 final size:21
Alignment explanation
Indices: 63203697--63203735 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
63203687 TGCGAAAGGC
* *
63203697 ATATTTTATTATTGTAACTAA
1 ATATTTAATAATTGTAACTAA
63203718 ATATTTAATAATT-TAACT
1 ATATTTAATAATTGTAACT
63203736 GAGATGATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (21 bp):
ATATTTAATAATTGTAACTAA
Found at i:63212257 original size:20 final size:19
Alignment explanation
Indices: 63212234--63212283 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
63212224 AATATCCAAT
63212234 GATTTACCAATATTTCTAAG
1 GATTTACCAATATTTCT-AG
*
63212254 GATTTAACAATATTTCTAG
1 GATTTACCAATATTTCTAG
63212273 GACTTTACCAA
1 GA-TTTACCAA
63212284 AATATTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
GATTTACCAATATTTCTAG
Found at i:63212500 original size:25 final size:25
Alignment explanation
Indices: 63212472--63212522 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
63212462 TGTACCAAAG
63212472 TAAGTGTTGGCTTTCCCTGGTTTCA
1 TAAGTGTTGGCTTTCCCTGGTTTCA
63212497 TAAGTGTTGGCTTTCCCTGGTTTCA
1 TAAGTGTTGGCTTTCCCTGGTTTCA
63212522 T
1 T
63212523 TTCTTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.45
Consensus pattern (25 bp):
TAAGTGTTGGCTTTCCCTGGTTTCA
Found at i:63218170 original size:22 final size:22
Alignment explanation
Indices: 63218130--63218172 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
63218120 TAAATTATTA
*
63218130 ATATAATTTTATAATTGAGTTT
1 ATATAATTTTATAAATGAGTTT
63218152 ATATATATTTT-TAAATGAGTT
1 ATATA-ATTTTATAAATGAGTT
63218173 AGTGGTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
ATATAATTTTATAAATGAGTTT
Found at i:63218369 original size:6 final size:6
Alignment explanation
Indices: 63218358--63218382 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
63218348 CTATGTTTTT
63218358 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
63218383 AACAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:63218370 original size:23 final size:24
Alignment explanation
Indices: 63218326--63218370 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
63218316 GTAAAGTTTG
* * *
63218326 ATGTTTTTATTTTGAATTTAAACT
1 ATGTTTTTATTATAAATATAAACT
63218350 ATGTTTTTA-TATAAATATAAA
1 ATGTTTTTATTATAAATATAAA
63218371 TATAAATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (24 bp):
ATGTTTTTATTATAAATATAAACT
Found at i:63226035 original size:34 final size:34
Alignment explanation
Indices: 63225992--63226061 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
63225982 GAACTAAGCC
*
63225992 TTAGACTTAGTGTTGTCGAAGGTGCACTGTGCTG
1 TTAGACTTAGTGCTGTCGAAGGTGCACTGTGCTG
63226026 TTAGACTTAGTGCTGTCGAAGGTGCACTGTGCTG
1 TTAGACTTAGTGCTGTCGAAGGTGCACTGTGCTG
63226060 TT
1 TT
63226062 TTGGCTAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.17, C:0.16, G:0.31, T:0.36
Consensus pattern (34 bp):
TTAGACTTAGTGCTGTCGAAGGTGCACTGTGCTG
Found at i:63230753 original size:20 final size:21
Alignment explanation
Indices: 63230728--63230788 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
63230718 TGTTGTGTGT
63230728 AATTACACAAAATATTATC-C-
1 AATTACACAAAATATTA-CACG
*
63230748 AATTACACAAATTATTACAACG
1 AATTACACAAAATATTAC-ACG
*
63230770 AATTACACAAAACATTACA
1 AATTACACAAAATATTACA
63230789 AATTATTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 1 0.03
20 16 0.46
21 2 0.06
22 16 0.46
ACGTcount: A:0.52, C:0.20, G:0.02, T:0.26
Consensus pattern (21 bp):
AATTACACAAAATATTACACG
Found at i:63230776 original size:22 final size:21
Alignment explanation
Indices: 63230728--63230789 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
63230718 TGTTGTGTGT
63230728 AATTACACAAAATATTATC--C
1 AATTACACAAAATATTA-CAAC
*
63230748 AATTACACAAATTATTACAAC
1 AATTACACAAAATATTACAAC
*
63230769 GAATTACACAAAACATTACAA
1 -AATTACACAAAATATTACAA
63230790 ATTATTACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.03
20 16 0.44
21 1 0.03
22 18 0.50
ACGTcount: A:0.53, C:0.19, G:0.02, T:0.26
Consensus pattern (21 bp):
AATTACACAAAATATTACAAC
Found at i:63233895 original size:3 final size:3
Alignment explanation
Indices: 63233889--63233914 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
63233879 CAACAATGGC
63233889 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
63233915 GCATTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:63234816 original size:36 final size:36
Alignment explanation
Indices: 63234740--63234980 Score: 140
Period size: 36 Copynumber: 6.1 Consensus size: 36
63234730 TGGTAAAATT
* * * * * *
63234740 AACAATAAAATAAGAGTTATATAATATCCAAACAAT
1 AACAACAAAATAATAGTAATATAATAACAAAACAAC
63234776 AACAACAAAATAATAGTAATATAATAACAAAATAGCAAC
1 AACAACAAAATAATAGTAATATAATAAC-AAA-A-CAAC
* * * * *
63234815 AAACAATAACAATAAAATAAGAGTTATATAATATCCAAACAAT
1 -AAC---AAC---AAAATAATAGTAATATAATAACAAAACAAC
63234858 AACAACAAAATAATAGTAATATAATAACAAAATAGCAAC
1 AACAACAAAATAATAGTAATATAATAAC-AAA-A-CAAC
* * * * *
63234897 AAACAATAACAATAAAATAAGAGTTATATAATATCCAAACAAT
1 -AAC---AAC---AAAATAATAGTAATATAATAACAAAACAAC
* *
63234940 AACAACAAAATAATAGTAATATAATAACAAAATAGC
1 AACAACAAAATAATAGTAATATAATAACAAAACAAC
63234976 AACAA
1 AACAA
63234981 ACAATAACAA
Statistics
Matches: 157, Mismatches: 28, Indels: 40
0.70 0.12 0.18
Matches are distributed among these distances:
36 71 0.45
37 4 0.03
38 2 0.01
39 12 0.08
40 6 0.04
42 6 0.04
43 12 0.08
44 2 0.01
45 4 0.03
46 38 0.24
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.21
Consensus pattern (36 bp):
AACAACAAAATAATAGTAATATAATAACAAAACAAC
Found at i:63234828 original size:82 final size:82
Alignment explanation
Indices: 63234739--63234990 Score: 504
Period size: 82 Copynumber: 3.1 Consensus size: 82
63234729 GTGGTAAAAT
63234739 TAACAATAAAATAAGAGTTATATAATATCCAAACAATAACAACAAAATAATAGTAATATAATAAC
1 TAACAATAAAATAAGAGTTATATAATATCCAAACAATAACAACAAAATAATAGTAATATAATAAC
63234804 AAAATAGCAACAAACAA
66 AAAATAGCAACAAACAA
63234821 TAACAATAAAATAAGAGTTATATAATATCCAAACAATAACAACAAAATAATAGTAATATAATAAC
1 TAACAATAAAATAAGAGTTATATAATATCCAAACAATAACAACAAAATAATAGTAATATAATAAC
63234886 AAAATAGCAACAAACAA
66 AAAATAGCAACAAACAA
63234903 TAACAATAAAATAAGAGTTATATAATATCCAAACAATAACAACAAAATAATAGTAATATAATAAC
1 TAACAATAAAATAAGAGTTATATAATATCCAAACAATAACAACAAAATAATAGTAATATAATAAC
63234968 AAAATAGCAACAAACAA
66 AAAATAGCAACAAACAA
63234985 TAACAA
1 TAACAA
63234991 AACAATAGTA
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 170 1.00
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.21
Consensus pattern (82 bp):
TAACAATAAAATAAGAGTTATATAATATCCAAACAATAACAACAAAATAATAGTAATATAATAAC
AAAATAGCAACAAACAA
Done.