Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 164 of 175
Found at i:49320927 original size:28 final size:28
Alignment explanation
Indices: 49320887--49320989 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 28
49320877 CAATACCCAT
*
49320887 TCCCATTTCCCATTCCACCGTGCCCTCC
1 TCCCATTTCCCATTCCACCGTCCCCTCC
* *
49320915 TCCCATTTCCCATTCCCATC-TCCCCTCT
1 TCCCATTTCCCATT-CCACCGTCCCCTCC
* * *
49320943 TCCATCGATTCCCCTCTTCCACCGTTCCCTCC
1 TCC--C-ATTTCCC-ATTCCACCGTCCCCTCC
49320975 TCCCA-TTCCCATTCC
1 TCCCATTTCCCATTCC
49320990 CATTCCCATT
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.07
28 27 0.46
29 5 0.08
30 2 0.03
31 10 0.17
32 11 0.19
ACGTcount: A:0.11, C:0.53, G:0.04, T:0.32
Consensus pattern (28 bp):
TCCCATTTCCCATTCCACCGTCCCCTCC
Found at i:49320983 original size:21 final size:21
Alignment explanation
Indices: 49320894--49320983 Score: 50
Period size: 21 Copynumber: 4.4 Consensus size: 21
49320884 CATTCCCATT
*
49320894 TCCCATTCCACCGTGCCCTCC
1 TCCCATTCCACCGTTCCCTCC
* *
49320915 TCCCATTTC-CCATTCCCAT-C
1 TCCCATTCCACCGTTCCC-TCC
* *
49320935 TCCCCTCTTCCATCGATT-CC-CC
1 T-CCC-ATTCCACCG-TTCCCTCC
49320957 T--C-TTCCACCGTTCCCTCC
1 TCCCATTCCACCGTTCCCTCC
49320975 TCCCATTCC
1 TCCCATTCC
49320984 CATTCCCATT
Statistics
Matches: 50, Mismatches: 8, Indels: 22
0.62 0.10 0.28
Matches are distributed among these distances:
16 2 0.04
17 9 0.18
18 3 0.06
19 1 0.02
20 9 0.18
21 16 0.32
22 5 0.10
23 3 0.06
24 2 0.04
ACGTcount: A:0.10, C:0.54, G:0.04, T:0.31
Consensus pattern (21 bp):
TCCCATTCCACCGTTCCCTCC
Found at i:49320986 original size:6 final size:6
Alignment explanation
Indices: 49320975--49320999 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
49320965 CGTTCCCTCC
49320975 TCCCAT TCCCAT TCCCAT TCCCAT T
1 TCCCAT TCCCAT TCCCAT TCCCAT T
49321000 ATCAACAATA
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:0.16, C:0.48, G:0.00, T:0.36
Consensus pattern (6 bp):
TCCCAT
Found at i:49329913 original size:86 final size:87
Alignment explanation
Indices: 49329753--49330081 Score: 347
Period size: 87 Copynumber: 3.9 Consensus size: 87
49329743 AGACTTGATG
* * * *
49329753 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGA--TC---CTTTAATCCGCTCCAC-GTAACTT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGACTTTAATCCGCTCCACTGTAACTT
49329812 CAGGGAGATAGGATAGTGTCTT
66 CAGGGAGATAGGATAGTGTCTT
* *
49329834 CGATCTGCTCCGCTGTAATCTCAGGG-GATAAGATCTCTTATTTTAATCCGCTCCACTGTAACTT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGACTTTAATCCGCTCCACTGTAACTT
49329898 CAGGGAGATAGGATAGTGTCTT
66 CAGGGAGATAGGATAGTGTCTT
* * * *
49329920 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGACTTTAATCCGCTCCACTGTAACTT
* *
49329985 CAGGGAGATAAGAT-CTGAAATTCTT
66 CAGGGAGATAGGATAGTG----TCTT
* * * * * * ** *
49330010 TGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA-C-CTGA-TGTGATCTTCTCTACTGTAACTT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGACTTTAATCCGCTCCACTGTAACTT
*
49330072 CAGAGAGATA
66 CAGGGAGATA
49330082 AGATCCTTTA
Statistics
Matches: 212, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
80 7 0.03
81 22 0.10
82 2 0.01
85 15 0.07
86 57 0.27
87 71 0.33
88 3 0.01
89 1 0.00
90 34 0.16
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (87 bp):
CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGACTTTAATCCGCTCCACTGTAACTT
CAGGGAGATAGGATAGTGTCTT
Found at i:49329980 original size:44 final size:42
Alignment explanation
Indices: 49329765--49330213 Score: 264
Period size: 44 Copynumber: 10.5 Consensus size: 42
49329755 ATCTACTCTG
* * * *
49329765 CTGTAACCTCAGAGAGATAAGATC-C-T-TTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTCTTCTTGATCTGCTCCA
* * * *
49329804 C-GTAA-CTTCAGGGAGATAGGATAGT-GTCTTCGATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGAT-CTCTTCTT-GATCTGCTCCA
* * *
49329846 CTGTAATCTCAGGG-GATAAGATCTCTTATTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTC-T-TCTTGATCTGCTCCA
* * * *
49329889 CTGTAA-CTTCAGGGAGATAGGATAGT-GTCTTCGATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGAT-CTCTTCTT-GATCTGCTCCA
* *
49329932 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTCT-TCTT-GATCTGCTCCA
* * * *
49329976 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCT---CTTC-TTGATCTGCTCCA
** * *
49330022 CTGTAATCTCAGGGAGATAAGA-C-CTGATGTGATCTTCTCTA
1 CTGTAATCTCAGGGAGATAAGATCTCTTCT-TGATCTGCTCCA
* * *
49330063 CTGTAA-CTTCAGAGAGATAAGATC-C-T-TTAATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCTCTTCTTGATCTGCTCCA
* * * *
49330102 TTGTAATCTCAAGGAGATAGGAT-TACTATCCTTGATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATCT-CT-T-CTTGATCTGCTCCA
* * *
49330146 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCT---CTTC-TTGATCTGCTCCA
49330192 CTGTAATCTCAGGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
49330214 CCTGTATAAT
Statistics
Matches: 314, Mismatches: 60, Indels: 65
0.72 0.14 0.15
Matches are distributed among these distances:
37 1 0.00
38 17 0.05
39 26 0.08
40 6 0.02
41 31 0.10
42 24 0.08
43 58 0.18
44 79 0.25
45 4 0.01
46 63 0.20
47 5 0.02
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (42 bp):
CTGTAATCTCAGGGAGATAAGATCTCTTCTTGATCTGCTCCA
Found at i:49343750 original size:15 final size:16
Alignment explanation
Indices: 49343724--49343787 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 16
49343714 TAGTGTTTAG
49343724 GTGGGTTATTGGGTTT
1 GTGGGTTATTGGGTTT
49343740 GTGGG-TATTGGGTTAGGCT
1 GTGGGTTATTGGGTT----T
49343759 AGTTGGGTTATTGGGTTT
1 -G-TGGGTTATTGGGTTT
49343777 GTGGG-TATTGG
1 GTGGGTTATTGG
49343788 ATTAGGCTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
15 15 0.37
16 9 0.22
17 1 0.02
18 1 0.02
19 1 0.02
20 1 0.02
21 4 0.10
22 9 0.22
ACGTcount: A:0.09, C:0.02, G:0.45, T:0.44
Consensus pattern (16 bp):
GTGGGTTATTGGGTTT
Found at i:49343773 original size:37 final size:37
Alignment explanation
Indices: 49343725--49343802 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
49343715 AGTGTTTAGG
*
49343725 TGGGTTATTGGGTTTGTGGGTATTGGGTTAGGCTAGT
1 TGGGTTATTGGGTTTGTGGGTATTGGATTAGGCTAGT
49343762 TGGGTTATTGGGTTTGTGGGTATTGGATTAGGCTAGT
1 TGGGTTATTGGGTTTGTGGGTATTGGATTAGGCTAGT
49343799 TGGG
1 TGGG
49343803 CCTGGGTAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.12, C:0.03, G:0.44, T:0.42
Consensus pattern (37 bp):
TGGGTTATTGGGTTTGTGGGTATTGGATTAGGCTAGT
Found at i:49370518 original size:17 final size:17
Alignment explanation
Indices: 49370493--49370535 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
49370483 GTCAAGCATT
*
49370493 AGCGGCGCATTCTGTTA
1 AGCGACGCATTCTGTTA
49370510 AGCGACGCATTCTGTTA
1 AGCGACGCATTCTGTTA
*
49370527 AGCGCCGCA
1 AGCGACGCA
49370536 AAAAGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (17 bp):
AGCGACGCATTCTGTTA
Found at i:49370773 original size:25 final size:25
Alignment explanation
Indices: 49370745--49370805 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
49370735 CGGTTTAAGG
* *
49370745 TTTATAGTTTATATATGTTTTATGA
1 TTTAGAGTTTATATATGTTCTATGA
*
49370770 TTTAGGGTTTATATATGTTCTATGA
1 TTTAGAGTTTATATATGTTCTATGA
* *
49370795 TTCAGGGTTTA
1 TTTAGAGTTTA
49370806 AGGAATATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (25 bp):
TTTAGAGTTTATATATGTTCTATGA
Found at i:49370901 original size:21 final size:21
Alignment explanation
Indices: 49370857--49370902 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
49370847 TAGTTGGGGT
* * *
49370857 TTAAGGTTTAAGTGTTTAGGG
1 TTAAGGGTTAAGGGTTTAGAG
*
49370878 TTAAGGGTTAAGGGTTTATAG
1 TTAAGGGTTAAGGGTTTAGAG
49370899 TTAA
1 TTAA
49370903 TGTTTTATGA
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:0.28, C:0.00, G:0.30, T:0.41
Consensus pattern (21 bp):
TTAAGGGTTAAGGGTTTAGAG
Found at i:49376353 original size:67 final size:67
Alignment explanation
Indices: 49376211--49376353 Score: 155
Period size: 67 Copynumber: 2.1 Consensus size: 67
49376201 AATATAACAT
* * * *
49376211 ATATTAATATGGACATATAACCTATATTCCAATTTTATTAATAATAAATTTTATAACTTATCAAA
1 ATATAAAT-TGGACATATAACCTATATTCCAAATTTATTAATAATAAATTTTATAAATTATAAAA
49376276 TAA
65 TAA
* * * * *
49376279 ATGTAAATTGGATATATAACCTATATTTCAAATTTATTAGTAA-ACAATTTT-TAAATTTTAAAA
1 ATATAAATTGGACATATAACCTATATTCCAAATTTATTAATAATA-AATTTTATAAATTAT-AAA
49376342 ATAA
64 ATAA
*
49376346 TTATAAAT
1 ATATAAAT
49376354 AAGAAGTATA
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
66 7 0.11
67 49 0.79
68 6 0.10
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (67 bp):
ATATAAATTGGACATATAACCTATATTCCAAATTTATTAATAATAAATTTTATAAATTATAAAAT
AA
Found at i:49377067 original size:98 final size:98
Alignment explanation
Indices: 49376893--49377087 Score: 318
Period size: 98 Copynumber: 2.0 Consensus size: 98
49376883 ATAATGAAAA
* * *
49376893 ACTTTAAAGGAACATTCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACAATT
* *
49376958 CCTTTAGAATCCCAAACTCGGAATATTTCCTTC
66 CCTTTAGAATCCCAAACTCGAAAAATTTCCTTC
* *
49376991 ACTTTAAAAGAACATCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACAATT
*
49377056 CCTTTATAATCCCAAACTCGAAAAATTTCCTT
66 CCTTTAGAATCCCAAACTCGAAAAATTTCCTT
49377088 TATGATTTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAAACACACCCAATACGTTAGGGCACAATT
CCTTTAGAATCCCAAACTCGAAAAATTTCCTTC
Found at i:49378884 original size:9 final size:9
Alignment explanation
Indices: 49378866--49379294 Score: 303
Period size: 9 Copynumber: 49.0 Consensus size: 9
49378856 CACATATAGA
*
49378866 AACTTGCAT
1 AACTTACAT
49378875 AACTTACAT
1 AACTTACAT
*
49378884 AAATTACAT
1 AACTTACAT
* *
49378893 AAATTAAAT
1 AACTTACAT
49378902 AACTTACAT
1 AACTTACAT
*
49378911 AACTTAAAT
1 AACTTACAT
49378920 AACTTACAT
1 AACTTACAT
*
49378929 AA--TATAT
1 AACTTACAT
*
49378936 AACCTT-CCT
1 AA-CTTACAT
49378945 AACTTACAT
1 AACTTACAT
* *
49378954 TATTTACAT
1 AACTTACAT
49378963 AA--TACAT
1 AACTTACAT
49378970 AACTTAGTACAT
1 AAC-T--TACAT
49378982 AACTTACAT
1 AACTTACAT
* *
49378991 AATTTTTTCTAAAT
1 AA----CT-TACAT
49379005 AACTTACAT
1 AACTTACAT
* *
49379014 AAATTAAAT
1 AACTTACAT
*
49379023 AACTTGCAT
1 AACTTACAT
49379032 AACTTACAT
1 AACTTACAT
*
49379041 AACTTAAAT
1 AACTTACAT
49379050 AACTTACAT
1 AACTTACAT
49379059 AA--TACAT
1 AACTTACAT
* *
49379066 AGCCTT-CCT
1 A-ACTTACAT
49379075 AACTTACAT
1 AACTTACAT
* *
49379084 TATTTACAT
1 AACTTACAT
49379093 AA--TACAT
1 AACTTACAT
* *
49379100 AGCCTACAT
1 AACTTACAT
49379109 AACTTACAT
1 AACTTACAT
49379118 AACTTACAT
1 AACTTACAT
* *
49379127 AAATTAAAT
1 AACTTACAT
49379136 AACTTACAT
1 AACTTACAT
49379145 AACTTACAT
1 AACTTACAT
49379154 AACTTACAT
1 AACTTACAT
49379163 AA--TACAT
1 AACTTACAT
*
49379170 AACCTT-CCT
1 AA-CTTACAT
49379179 AACTTACAT
1 AACTTACAT
* *
49379188 TA--TACAC
1 AACTTACAT
49379195 AACTTACAT
1 AACTTACAT
49379204 AA-TTA-AT
1 AACTTACAT
** *
49379211 -GTTATACAC
1 AACT-TACAT
49379220 AACTTACAT
1 AACTTACAT
49379229 AA--TACAT
1 AACTTACAT
*
49379236 TACTTACAT
1 AACTTACAT
49379245 AACTTACAT
1 AACTTACAT
*
49379254 TACTTACAT
1 AACTTACAT
49379263 AA--TACAT
1 AACTTACAT
49379270 AA--TACAT
1 AACTTACAT
49379277 AACTTACAT
1 AACTTACAT
49379286 AACTTACAT
1 AACTTACAT
49379295 TTCTTGTTGA
Statistics
Matches: 331, Mismatches: 55, Indels: 68
0.73 0.12 0.15
Matches are distributed among these distances:
7 60 0.18
8 14 0.04
9 236 0.71
10 5 0.02
11 1 0.00
12 8 0.02
13 1 0.00
14 6 0.02
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:49379078 original size:34 final size:34
Alignment explanation
Indices: 49379003--49379294 Score: 201
Period size: 34 Copynumber: 8.6 Consensus size: 34
49378993 TTTTTTCTAA
* * * *
49379003 ATAACTTACATAAATTAAATAACTTGCATA-ACTTAC
1 ATAACTTACATAACTTACATAA--TACATAGCCTT-C
*
49379039 ATAACTTAAATAACTTACATAATACATAGCCTTC
1 ATAACTTACATAACTTACATAATACATAGCCTTC
* * * *
49379073 CTAACTTACATTATTTACATAATACATAGCCTAC
1 ATAACTTACATAACTTACATAATACATAGCCTTC
* *
49379107 ATAACTTACATAACTTACATAAATTAAATA-ACTTAC
1 ATAACTTACATAACTTACAT-AA-TACATAGCCTT-C
*
49379143 ATAACTTACATAACTTACATAATACATAACCTTC
1 ATAACTTACATAACTTACATAATACATAGCCTTC
* * * * *
49379177 CTAACTTACATTA--TACACAACTTACATA--ATTA
1 ATAACTTACATAACTTACATAA--TACATAGCCTTC
** *
49379209 AT-GTTATACACAACTTACATAATACATTA--CTTAC
1 ATAACT-TACATAACTTACATAATACA-TAGCCTT-C
* * *
49379243 ATAACTTACATTACTTACATAATACATA--ATAC
1 ATAACTTACATAACTTACATAATACATAGCCTTC
49379275 ATAACTTACATAACTTACAT
1 ATAACTTACATAACTTACAT
49379295 TTCTTGTTGA
Statistics
Matches: 205, Mismatches: 38, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
31 1 0.00
32 38 0.19
33 7 0.03
34 101 0.49
35 13 0.06
36 45 0.22
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.34
Consensus pattern (34 bp):
ATAACTTACATAACTTACATAATACATAGCCTTC
Found at i:49379203 original size:104 final size:101
Alignment explanation
Indices: 49379002--49379271 Score: 323
Period size: 104 Copynumber: 2.7 Consensus size: 101
49378992 ATTTTTTCTA
* * * * *
49379002 AATAACTTACATAAATTAAATAACTTGCATAACTTACATAACTTAAATAACTTACATAATACATA
1 AATAACTTACATAACTTACATAAATTACATAACTTACATAACTTACATAACTTACATAATACATA
* * *
49379067 GCCTTCCTAACTTACATTATTTACATAATACATAGCCT
66 ACCTTCCTAACTTACATTA-TTACACAATACATA-ACT
*
49379105 ACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTACATAACTTACATAATACAT
1 A-ATAACTTACATAACTTACATAAATTACATAACTTACATAACTTACATAACTTACATAATACAT
*
49379170 AACCTTCCTAACTTACATTA-TACACAACTTACATAATT
65 AACCTTCCTAACTTACATTATTACACAA--TACATAACT
** * * *
49379208 AAT-GTTATACACAACTTACAT-AA-TACATTACTTACATAACTTACATTACTTACATAATACAT
1 AATAACT-TACATAACTTACATAAATTACATAACTTACATAACTTACATAACTTACATAATACAT
49379270 AA
65 AA
49379272 TACATAACTT
Statistics
Matches: 147, Mismatches: 16, Indels: 11
0.84 0.09 0.06
Matches are distributed among these distances:
100 38 0.26
101 3 0.02
102 21 0.14
103 3 0.02
104 82 0.56
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.34
Consensus pattern (101 bp):
AATAACTTACATAACTTACATAAATTACATAACTTACATAACTTACATAACTTACATAATACATA
ACCTTCCTAACTTACATTATTACACAATACATAACT
Found at i:49379268 original size:25 final size:25
Alignment explanation
Indices: 49379215--49379294 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
49379205 ATTAATGTTA
* * *
49379215 TACACAACTTACA-TAATACATTAC
1 TACATAACTTACATTATTACATAAC
49379239 TTACATAACTTACATTACTTACATAA-
1 -TACATAACTTACATTA-TTACATAAC
*
49379265 TACATAA--TACATAACTTACATAAC
1 TACATAACTTACATTA-TTACATAAC
49379289 TTACAT
1 -TACAT
49379295 TTCTTGTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
23 15 0.32
25 24 0.51
26 2 0.04
27 6 0.13
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (25 bp):
TACATAACTTACATTATTACATAAC
Found at i:49379962 original size:25 final size:25
Alignment explanation
Indices: 49379940--49379994 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
49379930 AAGGTTTATA
*
49379940 GTTTATATATGTTTTATGATTTAAG
1 GTTTATATATGTTCTATGATTTAAG
* *
49379965 GTTTATATATGTTCTATGATTCAGG
1 GTTTATATATGTTCTATGATTTAAG
49379990 GTTTA
1 GTTTA
49379995 AGGAATATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.53
Consensus pattern (25 bp):
GTTTATATATGTTCTATGATTTAAG
Found at i:49380067 original size:15 final size:15
Alignment explanation
Indices: 49380041--49380094 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
49380031 TGTAATAGTT
* *
49380041 GGGTTTAAGGTTTAA
1 GGGTTTAGGGTTAAA
*
49380056 GTGTTTAGGGTTAAA
1 GGGTTTAGGGTTAAA
* *
49380071 GGGTTAAGGGTT-AG
1 GGGTTTAGGGTTAAA
49380085 GGGTTTAGGG
1 GGGTTTAGGG
49380095 GTTTATAGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 10 0.31
15 22 0.69
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (15 bp):
GGGTTTAGGGTTAAA
Found at i:49380089 original size:22 final size:22
Alignment explanation
Indices: 49380041--49380086 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
49380031 TGTAATAGTT
* * *
49380041 GGGTTTAAGGTTTAAGTGTTTA
1 GGGTTAAAGGGTTAAGTGGTTA
49380063 GGGTTAAAGGGTTAAG-GGTTA
1 GGGTTAAAGGGTTAAGTGGTTA
49380084 GGG
1 GGG
49380087 GTTTAGGGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (22 bp):
GGGTTAAAGGGTTAAGTGGTTA
Found at i:49380161 original size:35 final size:36
Alignment explanation
Indices: 49380086--49380155 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
49380076 AAGGGTTAGG
* * *
49380086 GGTTTAGGGGTTTATAGTTAATGTTTTATGATTAAA
1 GGTTTAGGGGTATATAGTTAAGGGTTTATGATTAAA
*
49380122 GGTTTAGGGG-ATATGGTTAAGGGTTTATGTATTA
1 GGTTTAGGGGTATATAGTTAAGGGTTTATG-ATTA
49380156 TGGTTTGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 15 0.52
36 14 0.48
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (36 bp):
GGTTTAGGGGTATATAGTTAAGGGTTTATGATTAAA
Found at i:49380324 original size:15 final size:15
Alignment explanation
Indices: 49380304--49380348 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
49380294 ATACGTTATT
**
49380304 GTTTAAGGTTTGTGG
1 GTTTAAGGTTTAAGG
49380319 GTTTAAGGTTTAAGG
1 GTTTAAGGTTTAAGG
*
49380334 GTTTAGGGTTTAAGG
1 GTTTAAGGTTTAAGG
49380349 TCTAAGGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (15 bp):
GTTTAAGGTTTAAGG
Found at i:49380330 original size:22 final size:21
Alignment explanation
Indices: 49380304--49380355 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
49380294 ATACGTTATT
*
49380304 GTTTAAGGTTTGTGGGTTTAAG
1 GTTTAAGGTTT-AGGGTTTAAG
49380326 GTTTAAGGGTTTAGGGTTTAAG
1 GTTTAA-GGTTTAGGGTTTAAG
*
49380348 GTCTAAGG
1 GTTTAAGG
49380356 AATAGAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 20 0.74
23 5 0.19
ACGTcount: A:0.21, C:0.02, G:0.37, T:0.40
Consensus pattern (21 bp):
GTTTAAGGTTTAGGGTTTAAG
Found at i:49403288 original size:42 final size:42
Alignment explanation
Indices: 49403203--49403350 Score: 228
Period size: 42 Copynumber: 3.6 Consensus size: 42
49403193 TAAACACCAC
*
49403203 TAAAGGTCATGTTCTTTAGCGGCGCTT--AAAAAAACGCCGT
1 TAAAGATCATGTTCTTTAGCGGCGCTTCAAAAAAAACGCCGT
* *
49403243 TAAAGATCATATTCTTTAGCGGTGCTTCAAAAAAAACGCCGT
1 TAAAGATCATGTTCTTTAGCGGCGCTTCAAAAAAAACGCCGT
* *
49403285 TAAAGATCATGTTCTTTAGTGGCGCTTCAAAAAAAACGCCGC
1 TAAAGATCATGTTCTTTAGCGGCGCTTCAAAAAAAACGCCGT
*
49403327 TAAAGGTCATGTTCTTTAGCGGCG
1 TAAAGATCATGTTCTTTAGCGGCG
49403351 TTTGTTGTAA
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 24 0.25
42 73 0.75
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (42 bp):
TAAAGATCATGTTCTTTAGCGGCGCTTCAAAAAAAACGCCGT
Found at i:49403757 original size:66 final size:67
Alignment explanation
Indices: 49403687--49403823 Score: 204
Period size: 68 Copynumber: 2.0 Consensus size: 67
49403677 TTCTACTCTG
* *
49403687 CTCTGCTTCTCTCGATGC-CGCATCTGTTTTAAGTTGTAGCTGCAGTTCTTCATATTTCTTTTGA
1 CTCTGCTTCTCTCGATGCGCGCATCTGCTTTAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGA
49403751 AC
66 AC
* * * *
49403753 CTCTGTTTCTCTCGCTGCGTCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTG
1 CTCTGCTTCTCTCGATGCG-CGCATCTGCTTTAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTG
49403818 AAC
65 AAC
49403821 CTC
1 CTC
49403824 AACTGTGGTC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 16 0.25
68 47 0.75
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.43
Consensus pattern (67 bp):
CTCTGCTTCTCTCGATGCGCGCATCTGCTTTAAGTTGTAGCTGCAGTTCTTCATATTTCCTTTGA
AC
Found at i:49405415 original size:48 final size:48
Alignment explanation
Indices: 49405350--49405460 Score: 213
Period size: 48 Copynumber: 2.3 Consensus size: 48
49405340 TGCAATACAC
49405350 ATAAAATAGTTGAAAACTTAATAACTAATTACAACAATAACAACACAT
1 ATAAAATAGTTGAAAACTTAATAACTAATTACAACAATAACAACACAT
*
49405398 ATAAAATAGTTGAAAACTTAATAACTAATTACAACAATAACAGCACAT
1 ATAAAATAGTTGAAAACTTAATAACTAATTACAACAATAACAACACAT
49405446 ATAAAATAGTTGAAA
1 ATAAAATAGTTGAAA
49405461 TATATAATAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.25
Consensus pattern (48 bp):
ATAAAATAGTTGAAAACTTAATAACTAATTACAACAATAACAACACAT
Found at i:49409110 original size:9 final size:9
Alignment explanation
Indices: 49409096--49409578 Score: 313
Period size: 9 Copynumber: 55.4 Consensus size: 9
49409086 ACTATAAATG
49409096 AGTTATGTA
1 AGTTATGTA
49409105 AGTTATGTA
1 AGTTATGTA
*
49409114 AGTTGTGT-
1 AGTTATGTA
*
49409122 A-TTATGTG
1 AGTTATGTA
49409130 AGTTATGT-
1 AGTTATGTA
*
49409138 AGATTGTGT-
1 AG-TTATGTA
49409147 A-TTATGTA
1 AGTTATGTA
49409155 AGTTATGTA
1 AGTTATGTA
49409164 AGTTATGT-
1 AGTTATGTA
*
49409172 A-TTTTGT-
1 AGTTATGTA
49409179 A-TTATGTA
1 AGTTATGTA
*
49409187 AGTAATGTA
1 AGTTATGTA
49409196 AGTTATGTA
1 AGTTATGTA
*
49409205 AGTAATGT-
1 AGTTATGTA
49409213 A-TTATGTA
1 AGTTATGTA
*
49409221 AGTTGTGTA
1 AGTTATGTA
*
49409230 TA-ATAT-TA
1 -AGTTATGTA
49409238 A-TTATGTA
1 AGTTATGTA
*
49409246 AGTTGTGT-
1 AGTTATGTA
*
49409254 A-TAATGTA
1 AGTTATGTA
*
49409262 AGTTA-GGA
1 AGTTATGTA
49409270 AGGTTATGT-
1 A-GTTATGTA
49409279 A-TTATGTA
1 AGTTATGTA
*
49409287 AATTATGTA
1 AGTTATGTA
49409296 AGTTATGTA
1 AGTTATGTA
*
49409305 AGTTATTTA
1 AGTTATGTA
*
49409314 ATTTATGTA
1 AGTTATGTA
49409323 AGTTATGTA
1 AGTTATGTA
*
49409332 AGTTATTTA
1 AGTTATGTA
* *
49409341 GGCTATGT-
1 AGTTATGTA
49409349 A-TTATGTA
1 AGTTATGTA
* *
49409357 AATAATGTA
1 AGTTATGTA
*
49409366 AGTTA-GGA
1 AGTTATGTA
*
49409374 AGGCTATGT-
1 A-GTTATGTA
49409383 A-TTATGTA
1 AGTTATGTA
*
49409391 AGTTATTTA
1 AGTTATGTA
49409400 AGTTATGTA
1 AGTTATGTA
*
49409409 AGTTAAGTA
1 AGTTATGTA
*
49409418 AGTTATTTA
1 AGTTATGTA
*
49409427 ATTTATGTA
1 AGTTATGTA
*
49409436 AGTTATTTAGAAAA
1 AGTTA--T-G--TA
*
49409450 AATTATGTA
1 AGTTATGTA
49409459 AGTTATGTACTA
1 AGTTATG---TA
49409471 AGTTATGT-
1 AGTTATGTA
*
49409479 A-TTGTGTA
1 AGTTATGTA
* *
49409487 AATAATGTA
1 AGTTATGTA
*
49409496 AGTTA-GGA
1 AGTTATGTA
*
49409504 AGGTTATAT-
1 A-GTTATGTA
49409513 A-TTATGTA
1 AGTTATGTA
*
49409521 AGTTATTTA
1 AGTTATGTA
49409530 AGTTATGTA
1 AGTTATGTA
*
49409539 AGTTATTTA
1 AGTTATGTA
*
49409548 ATTTATGTA
1 AGTTATGTA
*
49409557 ATTTATGTA
1 AGTTATGTA
*
49409566 AGTTATGCA
1 AGTTATGTA
49409575 AGTT
1 AGTT
49409579 TCTATATGTG
Statistics
Matches: 370, Mismatches: 66, Indels: 76
0.72 0.13 0.15
Matches are distributed among these distances:
7 60 0.16
8 31 0.08
9 258 0.70
10 3 0.01
11 2 0.01
12 11 0.03
14 5 0.01
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.46
Consensus pattern (9 bp):
AGTTATGTA
Found at i:49409135 original size:34 final size:34
Alignment explanation
Indices: 49409097--49409633 Score: 346
Period size: 34 Copynumber: 15.8 Consensus size: 34
49409087 CTATAAATGA
* *
49409097 GTTATGTAAGTTATGTAAGTTGTGT-A-TTATGTGA
1 GTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAA
*
49409131 GTTATGT-AGATTGTGTATTATGTAAGTTATGTAA
1 GTTATGTAAG-TTATGTATTATGTAAGTTATGTAA
* *
49409165 GTTATGT-A-TTTTGTATTATGTAAGTAATGTAA
1 GTTATGTAAGTTATGTATTATGTAAGTTATGTAA
* *
49409197 GTTATGTAAGTAATGTATTATGTAAGTTGTGTATA
1 GTTATGTAAGTTATGTATTATGTAAGTTATGTA-A
* * *
49409232 -ATAT-TAA-TTATGTAAGTTGTGT-A-TAATGTAA
1 GTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAA
* *
49409263 GTTA-GGAAGGTTATGTATTATGTAAATTATGTAA
1 GTTATGTAA-GTTATGTATTATGTAAGTTATGTAA
*
49409297 GTTATGTAAGTTATTTAATTTATGTAAGTTATGTAA
1 GTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAA
* * * * *
49409333 GTTATTTAGGCTATGTATTATGTAAATAATGTAA
1 GTTATGTAAGTTATGTATTATGTAAGTTATGTAA
* * *
49409367 GTTA-GGAAGGCTATGTATTATGTAAGTTATTTAA
1 GTTATGTAA-GTTATGTATTATGTAAGTTATGTAA
*
49409401 GTTATGTAAG---T-TA--A-GTAAGTTATTTAA
1 GTTATGTAAGTTATGTATTATGTAAGTTATGTAA
* * * ** *
49409428 TTTATGTAAGTTATTTA-GA-AAAAATTATGTAA
1 GTTATGTAAGTTATGTATTATGTAAGTTATGTAA
* * *
49409460 GTTATGTACTAAGTTATGTATTGTGTAAATAATGTAA
1 GTTATG---TAAGTTATGTATTATGTAAGTTATGTAA
* * *
49409497 GTTA-GGAAGGTTATATATTATGTAAGTTATTTAA
1 GTTATGTAA-GTTATGTATTATGTAAGTTATGTAA
* *
49409531 GTTATGTAAGTTATTTAATTTATGTAATTTATGTAA
1 GTTATGTAAGTTATGT-A-TTATGTAAGTTATGTAA
* * * *
49409567 GTTATGCAAGTT-TCTATATGTGTAAGTTATATATTGTAT
1 GTTATGTAAGTTATGTAT-TATGTAAG---T-TA-TGTAA
*
49409606 GTTATTTAAGTTATGTATTATGTAAGTT
1 GTTATGTAAGTTATGTATTATGTAAGTT
49409634 TATATATAAG
Statistics
Matches: 398, Mismatches: 65, Indels: 79
0.73 0.12 0.15
Matches are distributed among these distances:
27 22 0.06
28 1 0.00
30 3 0.01
31 4 0.01
32 68 0.17
33 16 0.04
34 160 0.40
35 26 0.07
36 56 0.14
37 15 0.04
38 2 0.01
39 21 0.05
40 4 0.01
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.46
Consensus pattern (34 bp):
GTTATGTAAGTTATGTATTATGTAAGTTATGTAA
Found at i:49409553 original size:27 final size:27
Alignment explanation
Indices: 49409096--49409578 Score: 313
Period size: 25 Copynumber: 18.5 Consensus size: 27
49409086 ACTATAAATG
*
49409096 AGTTATGTAAGTTATGTAAGTTGTGT-
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
49409122 A-TTATGTGAGTTATGT-AGATTGTGT-
1 AGTTATGTAAGTTATGTAAG-TTATGTA
49409147 A-TTATGTAAGTTATGTAAGTTATGT-
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
49409172 A-TTTTGT-A-TTATGTAAGTAATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
*
49409196 AGTTATGTAAGTAATGT-A-TTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
49409221 AGTTGTGTATA-ATAT-TAA-TTATGTA
1 AGTTATGTA-AGTTATGTAAGTTATGTA
* * *
49409246 AGTTGTGT-A-TAATGTAAGTTA-GGA
1 AGTTATGTAAGTTATGTAAGTTATGTA
*
49409270 AGGTTATGT-A-TTATGTAAATTATGTA
1 A-GTTATGTAAGTTATGTAAGTTATGTA
* *
49409296 AGTTATGTAAGTTATTTAATTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* * *
49409323 AGTTATGTAAGTTATTTAGGCTATGT-
1 AGTTATGTAAGTTATGTAAGTTATGTA
* * *
49409349 A-TTATGTAAATAATGTAAGTTA-GGA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
49409374 AGGCTATGT-A-TTATGTAAGTTATTTA
1 A-GTTATGTAAGTTATGTAAGTTATGTA
* *
49409400 AGTTATGTAAGTTAAGTAAGTTATTTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* * *
49409427 ATTTATGTAAGTTATTTAGAAAAAATTATGTA
1 AGTTATGTAAGTTA--T-G--TAAGTTATGTA
*
49409459 AGTTATGTACTAAGTTATGT-A-TTGTGTA
1 AGTTATG---TAAGTTATGTAAGTTATGTA
* * * *
49409487 AATAATGTAAGTTA-GGAAGGTTATAT-
1 AGTTATGTAAGTTATGTAA-GTTATGTA
*
49409513 A-TTATGTAAGTTATTTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* * *
49409539 AGTTATTTAATTTATGTAATTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
*
49409566 AGTTATGCAAGTT
1 AGTTATGTAAGTT
49409579 TCTATATGTG
Statistics
Matches: 364, Mismatches: 59, Indels: 67
0.74 0.12 0.14
Matches are distributed among these distances:
23 17 0.05
24 13 0.04
25 169 0.46
26 19 0.05
27 110 0.30
28 11 0.03
29 1 0.00
30 1 0.00
32 15 0.04
33 1 0.00
35 7 0.02
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.46
Consensus pattern (27 bp):
AGTTATGTAAGTTATGTAAGTTATGTA
Found at i:49409591 original size:70 final size:64
Alignment explanation
Indices: 49409491--49409633 Score: 153
Period size: 70 Copynumber: 2.1 Consensus size: 64
49409481 TGTGTAAATA
* * *
49409491 ATGTAAGTTAGGAAGGTTATATATTATGTAAGTTATTTAAGTTATGTAAGTTATTTAATTTATGT
1 ATGTAAGTTAGCAAGGTTATATATTATGTAAGTTATAT-A--T-TGTAAGTTATTTAAGTTATGT
49409556 AATTT
62 -A-TT
* * * *
49409561 ATGTAAGTTATGCAAGTTTCTATA-TGTGTAAGTTATATATTGTATGTTATTTAAGTTATGTATT
1 ATGTAAGTTA-GCAAGGTTATATATTATGTAAGTTATATATTGTAAGTTATTTAAGTTATGTATT
49409625 ATGTAAGTT
1 ATGTAAGTT
49409634 TATATATAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
64 11 0.17
65 1 0.02
66 19 0.29
67 1 0.02
69 1 0.02
70 22 0.34
71 10 0.15
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.49
Consensus pattern (64 bp):
ATGTAAGTTAGCAAGGTTATATATTATGTAAGTTATATATTGTAAGTTATTTAAGTTATGTATT
Found at i:49411500 original size:98 final size:98
Alignment explanation
Indices: 49411358--49411552 Score: 309
Period size: 98 Copynumber: 2.0 Consensus size: 98
49411348 AAAAATCATA
* * * *
49411358 AAGGAAATTTTTCGAGTTTGGGATTATAAATGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGGGATTATAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
* *
49411423 AAATCTTGGATAAGCGGATGTTCTTTTAAAGTG
66 AAATCTTGGATAAGCGAATGTTCCTTTAAAGTG
* *
49411456 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGTTTTCTT
1 AAGGAAATATTCCGAGTTTGGGATTATAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
*
49411521 AAATCTTGGATAAGTGAATGTTCCTTTAAAGT
66 AAATCTTGGATAAGCGAATGTTCCTTTAAAGT
49411553 TTTTCATTAT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGGGATTATAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGCGAATGTTCCTTTAAAGTG
Found at i:49415699 original size:24 final size:24
Alignment explanation
Indices: 49415631--49415709 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
49415621 TAAAAATCAT
*
49415631 AATA-AATAATAAAGTAACATATATA
1 AATATAATAAT-AAGAAACATA-ATA
*
49415656 CATATAGATAA-ATAGAAACATAATCA
1 AATATA-ATAATA-AGAAACATAAT-A
49415682 AATATAATAATAAG-AACAATAATA
1 AATATAATAATAAGAAAC-ATAATA
49415706 AATA
1 AATA
49415710 GTGACAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
24 8 0.18
25 17 0.38
26 16 0.36
27 4 0.09
ACGTcount: A:0.63, C:0.06, G:0.05, T:0.25
Consensus pattern (24 bp):
AATATAATAATAAGAAACATAATA
Found at i:49415705 original size:15 final size:15
Alignment explanation
Indices: 49415685--49415740 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
49415675 ATAATCAAAT
49415685 ATAATAATAAGAACA
1 ATAATAATAAGAACA
*
49415700 ATAATAA-ATAGTGACA
1 ATAATAATA-AG-AACA
* * *
49415716 AAAATAATAATAGCA
1 ATAATAATAAGAACA
49415731 ATAATAATAA
1 ATAATAATAA
49415741 AAATAATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
14 1 0.03
15 20 0.62
16 10 0.31
17 1 0.03
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.23
Consensus pattern (15 bp):
ATAATAATAAGAACA
Found at i:49415745 original size:12 final size:12
Alignment explanation
Indices: 49415675--49415747 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 12
49415665 AAATAGAAAC
*
49415675 ATAATCAAATATA
1 ATAAT-AAAAATA
* *
49415688 ATAATAAGAACA
1 ATAATAAAAATA
49415700 ATAAT--AAATA
1 ATAATAAAAATA
* * *
49415710 GTGACAAAAATA
1 ATAATAAAAATA
**
49415722 ATAATAGCAATA
1 ATAATAAAAATA
49415734 ATAATAAAAATA
1 ATAATAAAAATA
49415746 AT
1 AT
49415748 TAAATGGTTT
Statistics
Matches: 43, Mismatches: 15, Indels: 5
0.68 0.24 0.08
Matches are distributed among these distances:
10 5 0.12
12 33 0.77
13 5 0.12
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.25
Consensus pattern (12 bp):
ATAATAAAAATA
Found at i:49417590 original size:25 final size:25
Alignment explanation
Indices: 49417562--49417616 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
49417552 CCATATTCCT
* *
49417562 TAAACCCTGAATCATAGAACATATA
1 TAAACCCTAAATCATAAAACATATA
49417587 TAAACCCTAAATCATAAAACATATA
1 TAAACCCTAAATCATAAAACATATA
49417612 TAAAC
1 TAAAC
49417617 TATAAACCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.24
Consensus pattern (25 bp):
TAAACCCTAAATCATAAAACATATA
Found at i:49417629 original size:25 final size:25
Alignment explanation
Indices: 49417574--49417629 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
49417564 AACCCTGAAT
* * *
49417574 CATAGAACATATATAAACCCTAAAT
1 CATAAAACATATATAAACCATAAAC
*
49417599 CATAAAACATATATAAACTATAAAC
1 CATAAAACATATATAAACCATAAAC
*
49417624 CTTAAA
1 CATAAA
49417630 CCGCAACCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.25
Consensus pattern (25 bp):
CATAAAACATATATAAACCATAAAC
Found at i:49417857 original size:17 final size:17
Alignment explanation
Indices: 49417832--49417874 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
49417822 TAAATCTTTT
*
49417832 TGCGGCGCTTAACAGAA
1 TGCGCCGCTTAACAGAA
49417849 TGCGCCGCTTAACAGAA
1 TGCGCCGCTTAACAGAA
49417866 TGCGCCGCT
1 TGCGCCGCT
49417875 AATGCTTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (17 bp):
TGCGCCGCTTAACAGAA
Found at i:49422016 original size:23 final size:23
Alignment explanation
Indices: 49421990--49422034 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
49421980 TTTGGAGAGG
*
49421990 TTAAAACATAATTTTATCATTTA
1 TTAAAACATAATTTCATCATTTA
**
49422013 TTAAATTATAATTTCATCATTT
1 TTAAAACATAATTTCATCATTT
49422035 TAAAGGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAAACATAATTTCATCATTTA
Found at i:49434736 original size:30 final size:30
Alignment explanation
Indices: 49434702--49434761 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
49434692 TCTTTCATTC
* *
49434702 TTTGTTTATTATTGTCTGGTATGAACTTTA
1 TTTGTATATTATTGTCTGGTATAAACTTTA
49434732 TTTGTATATTATTGTCTGGTATAAACTTTA
1 TTTGTATATTATTGTCTGGTATAAACTTTA
49434762 GTCCAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.23, C:0.07, G:0.15, T:0.55
Consensus pattern (30 bp):
TTTGTATATTATTGTCTGGTATAAACTTTA
Found at i:49435103 original size:33 final size:33
Alignment explanation
Indices: 49435065--49435138 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
49435055 CAGTTTTTAT
**
49435065 AAAATATTTT-CAGAAAATTTGTCCAAACACCAA
1 AAAATATTTTACAG-AAATTCATCCAAACACCAA
* * *
49435098 AAAATATTTTACAGAGATTCATCCAAACACTAG
1 AAAATATTTTACAGAAATTCATCCAAACACCAA
49435131 AAAATATT
1 AAAATATT
49435139 AACTTTTCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 32 0.91
34 3 0.09
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (33 bp):
AAAATATTTTACAGAAATTCATCCAAACACCAA
Found at i:49438071 original size:30 final size:30
Alignment explanation
Indices: 49438035--49438100 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
49438025 CACGATGGTC
* *
49438035 GATAATTGGGTGGTGGAGGAACAGACGATG
1 GATAATTGGGTGGCGGAGGAACAGACGACG
*
49438065 GATAATTGGGTGGCGGGGGAACAGACGACG
1 GATAATTGGGTGGCGGAGGAACAGACGACG
49438095 GATAAT
1 GATAAT
49438101 CTTGAGCTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.42, T:0.18
Consensus pattern (30 bp):
GATAATTGGGTGGCGGAGGAACAGACGACG
Found at i:49438219 original size:108 final size:108
Alignment explanation
Indices: 49438074--49438285 Score: 361
Period size: 108 Copynumber: 2.0 Consensus size: 108
49438064 GGATAATTGG
* **
49438074 GTGGCGGGGGAACAGACGACGGATAATCTTGAGCTACATAGCCAGGTGCATAAGGTTGTTGGTAT
1 GTGGCGGGGGAACAGACGACGGATAATCTTGAACTACATAGCCAGGTGCATAAGCCTGTTGGTAT
49438139 GGTGGTGGATATCCATCAATAGGAGGATTTTGATGATAACCGA
66 GGTGGTGGATATCCATCAATAGGAGGATTTTGATGATAACCGA
* * *
49438182 GTGGTGGGGGAACAGATGGCGGATAATCTTGAACTACATAGCCAGGTGCATAAGCCTGTTGGTAT
1 GTGGCGGGGGAACAGACGACGGATAATCTTGAACTACATAGCCAGGTGCATAAGCCTGTTGGTAT
*
49438247 GGTGGTGGATATCCATCCATAGGAGGATTTTGATGATAA
66 GGTGGTGGATATCCATCAATAGGAGGATTTTGATGATAA
49438286 TCGGTCCGCA
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 97 1.00
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.26
Consensus pattern (108 bp):
GTGGCGGGGGAACAGACGACGGATAATCTTGAACTACATAGCCAGGTGCATAAGCCTGTTGGTAT
GGTGGTGGATATCCATCAATAGGAGGATTTTGATGATAACCGA
Found at i:49438934 original size:9 final size:9
Alignment explanation
Indices: 49438920--49438964 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
49438910 ATTTCATAAT
49438920 AATTTTTTA
1 AATTTTTTA
* *
49438929 AATTTTATG
1 AATTTTTTA
49438938 AATTTTTTA
1 AATTTTTTA
*
49438947 TATATTTTTA
1 AAT-TTTTTA
49438957 AATTTTTT
1 AATTTTTT
49438965 GATTTTTTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
AATTTTTTA
Found at i:49438943 original size:18 final size:19
Alignment explanation
Indices: 49438920--49438964 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
49438910 ATTTCATAAT
*
49438920 AATTTTTTA-A-ATTTTATG
1 AATTTTTTATATATTTT-TA
49438938 AATTTTTTATATATTTTTA
1 AATTTTTTATATATTTTTA
49438957 AATTTTTT
1 AATTTTTT
49438965 GATTTTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 9 0.38
19 10 0.42
20 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
AATTTTTTATATATTTTTA
Found at i:49439518 original size:23 final size:22
Alignment explanation
Indices: 49439487--49439532 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
49439477 CCCTCAAAAG
*
49439487 TTAAAAATTTTTAATTAAACCC
1 TTAAAAAATTTTAATTAAACCC
49439509 TTAAAAAATTTTAATTAAACCC
1 TTAAAAAATTTTAATTAAACCC
49439531 TT
1 TT
49439533 CCAAAACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAAAAATTTTAATTAAACCC
Found at i:49440654 original size:29 final size:29
Alignment explanation
Indices: 49440620--49440675 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
49440610 ATAAAGACCG
* *
49440620 GATCAAATTAGTCCCTCTATTATTAAATA
1 GATCAAATTAGTCCCTATACTATTAAATA
*
49440649 GATCAATTTAGTCCCTATACTATTAAA
1 GATCAAATTAGTCCCTATACTATTAAA
49440676 AAGAACCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (29 bp):
GATCAAATTAGTCCCTATACTATTAAATA
Found at i:49441218 original size:13 final size:13
Alignment explanation
Indices: 49441200--49441227 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49441190 AATTAAAATA
49441200 ATATGTATCTTTT
1 ATATGTATCTTTT
49441213 ATATGTATCTTTT
1 ATATGTATCTTTT
49441226 AT
1 AT
49441228 CCAAAACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (13 bp):
ATATGTATCTTTT
Found at i:49442602 original size:10 final size:11
Alignment explanation
Indices: 49442576--49442601 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
49442566 GGCTCAAAAG
49442576 AAAAATTCTTC
1 AAAAATTCTTC
49442587 AAAAATTCTTC
1 AAAAATTCTTC
49442598 AAAA
1 AAAA
49442602 TAGAGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAATTCTTC
Found at i:49444663 original size:47 final size:46
Alignment explanation
Indices: 49444569--49444663 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 46
49444559 TAGGTTCTGG
* **
49444569 TCATATTTAATTTTTTGATACAATACTTAAAACTACTCATAGTCCA
1 TCATATTTAATTTTTTGAGACAATACTTAAAACTACTCATAACCCA
* * * *
49444615 TCATATTTGATCTTTTTGAGACAATGCTTAGAACTATTCATAACCCA
1 TCATATTTAAT-TTTTTGAGACAATACTTAAAACTACTCATAACCCA
49444662 TC
1 TC
49444664 CTCAACCCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 10 0.24
47 31 0.76
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (46 bp):
TCATATTTAATTTTTTGAGACAATACTTAAAACTACTCATAACCCA
Found at i:49471488 original size:30 final size:30
Alignment explanation
Indices: 49471449--49471507 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
49471439 TCTTTCATTC
* *
49471449 TTGTTTATTATTGTCTGGTATGAACTTTAT
1 TTGTATATTATTGTCTGGTATAAACTTTAT
49471479 TTGTATATTATTGTCTGGTATAAACTTTA
1 TTGTATATTATTGTCTGGTATAAACTTTA
49471508 GTCCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (30 bp):
TTGTATATTATTGTCTGGTATAAACTTTAT
Found at i:49471843 original size:33 final size:33
Alignment explanation
Indices: 49471805--49471878 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
49471795 AACAGTTTTT
**
49471805 AAAATATTTT-CAGAAAATTTGTCCAAACACCAA
1 AAAATATTTTACAG-AAATTCATCCAAACACCAA
* * *
49471838 AAAATATTTTACAGAGATTCATCCAAACACTAG
1 AAAATATTTTACAGAAATTCATCCAAACACCAA
49471871 AAAATATT
1 AAAATATT
49471879 AACTTTTCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 32 0.91
34 3 0.09
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (33 bp):
AAAATATTTTACAGAAATTCATCCAAACACCAA
Found at i:49475097 original size:25 final size:27
Alignment explanation
Indices: 49475046--49475097 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 27
49475036 TTTCTATAAT
49475046 TTTTTAAATTTTATGAATTTTTTATTA
1 TTTTTAAATTTTATGAATTTTTTATTA
49475073 TTTTT-AATTTT-TG-ATTTTTTGATTA
1 TTTTTAAATTTTATGAATTTTTT-ATTA
49475098 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 7 0.29
25 6 0.25
26 6 0.25
27 5 0.21
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (27 bp):
TTTTTAAATTTTATGAATTTTTTATTA
Found at i:49475604 original size:20 final size:20
Alignment explanation
Indices: 49475579--49475617 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
49475569 CCTCAAAGTT
49475579 AAAATTTTAATTAACCCTTA
1 AAAATTTTAATTAACCCTTA
49475599 AAAATTTTAATTAACCCTT
1 AAAATTTTAATTAACCCTT
49475618 CCAAAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTTTAATTAACCCTTA
Found at i:49476654 original size:28 final size:29
Alignment explanation
Indices: 49476621--49476675 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
49476611 ATAAAGACCG
* *
49476621 GATCAA-TTAGTCCCTCTATTATTAAATA
1 GATCAATTTAGTCCCTATACTATTAAATA
49476649 GATCAATTTAGTCCCTATACTATTAAA
1 GATCAATTTAGTCCCTATACTATTAAA
49476676 AAGAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.38
Consensus pattern (29 bp):
GATCAATTTAGTCCCTATACTATTAAATA
Found at i:49477197 original size:12 final size:12
Alignment explanation
Indices: 49477180--49477205 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49477170 TAAAAATAAA
49477180 ATATGTATCTTT
1 ATATGTATCTTT
49477192 ATATGTATCTTT
1 ATATGTATCTTT
49477204 AT
1 AT
49477206 CCAAAACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.58
Consensus pattern (12 bp):
ATATGTATCTTT
Found at i:49480578 original size:47 final size:47
Alignment explanation
Indices: 49480483--49480578 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 47
49480473 TAGGTTCTGG
* * **
49480483 TCATATTTAATTTTTTTGATACAATACTTAAAACTACTCATAGTCCA
1 TCATATTTAATCTTTTTGAGACAATACTTAAAACTACTCATAACCCA
* * * *
49480530 TCATATTTGATCTTTTTGAGACAATGCTTAGAACTATTCATAACCCA
1 TCATATTTAATCTTTTTGAGACAATACTTAAAACTACTCATAACCCA
49480577 TC
1 TC
49480579 CTCAACCCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (47 bp):
TCATATTTAATCTTTTTGAGACAATACTTAAAACTACTCATAACCCA
Found at i:49490806 original size:133 final size:133
Alignment explanation
Indices: 49490564--49490831 Score: 446
Period size: 133 Copynumber: 2.0 Consensus size: 133
49490554 CTGCATATCT
*
49490564 CAGCCTAAATATTTCAGGAATGGTAGTTCTGAATTCCCCAGAGTTTGAAAGTGATTGTAAATTAT
1 CAGCCTAAATATTTCAGGAATGGTAGTTATGAATTCCCCAGAGTTTGAAAGTGATTGTAAATTAT
*
49490629 TTGTGTTAATTGTTTTTCTTTTGGTTTGGATTTGCATACCGGGGCAAGAATGTCTCTTCTTTTAC
66 TTGTGTTAAATGTTTTTCTTTTGGTTTGGATTTGCATACCGGGGCAAGAATGTCTCTTCTTTTAC
49490694 GAG
131 GAG
* *
49490697 CAGCCTAAATATTTCAGGAATGGTAGTTATGGATTCCCCAGAGTTTGAACGTGATTGTAAATTAT
1 CAGCCTAAATATTTCAGGAATGGTAGTTATGAATTCCCCAGAGTTTGAAAGTGATTGTAAATTAT
* * * * * *
49490762 TTGTGTTAAATGTTTTTTTTTTGGTTTGGGTTTGCATGCTGGGGCAAGAGTGTCTCTTCTTTTAT
66 TTGTGTTAAATGTTTTTCTTTTGGTTTGGATTTGCATACCGGGGCAAGAATGTCTCTTCTTTTAC
49490827 GAG
131 GAG
49490830 CA
1 CA
49490832 CATTGTGCAT
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
133 125 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (133 bp):
CAGCCTAAATATTTCAGGAATGGTAGTTATGAATTCCCCAGAGTTTGAAAGTGATTGTAAATTAT
TTGTGTTAAATGTTTTTCTTTTGGTTTGGATTTGCATACCGGGGCAAGAATGTCTCTTCTTTTAC
GAG
Found at i:49503205 original size:21 final size:21
Alignment explanation
Indices: 49503181--49503227 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
49503171 CAAACTCAAA
49503181 CTCAAACC-CTAAATCCTAAAC
1 CTCAAACCTC-AAATCCTAAAC
*
49503202 CTCAAACTTCAAATCCTAAAC
1 CTCAAACCTCAAATCCTAAAC
49503223 C-CAAA
1 CTCAAA
49503228 GAGTTTAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (21 bp):
CTCAAACCTCAAATCCTAAAC
Found at i:49505762 original size:24 final size:22
Alignment explanation
Indices: 49505730--49505773 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
49505720 TATTTTATAT
*
49505730 TTTATATATCATTATATCAAATTA
1 TTTAAATATCATT-TA-CAAATTA
49505754 TTTAAATATCATTTACAAAT
1 TTTAAATATCATTTACAAAT
49505774 ATCTTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAATATCATTTACAAATTA
Found at i:49507835 original size:9 final size:10
Alignment explanation
Indices: 49507815--49507848 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
49507805 AAATGACTAC
49507815 AAAATTAGAA
1 AAAATTAGAA
*
49507825 AAAATTAAAA
1 AAAATTAGAA
*
49507835 AAAAGTAGAA
1 AAAATTAGAA
49507845 AAAA
1 AAAA
49507849 AATAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (10 bp):
AAAATTAGAA
Found at i:49507948 original size:14 final size:12
Alignment explanation
Indices: 49507920--49507956 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
49507910 ATATAAACTT
49507920 ATAAAAATTATA
1 ATAAAAATTATA
49507932 ATAAAAA-TATA
1 ATAAAAATTATA
*
49507943 AT-AATATTATA
1 ATAAAAATTATA
49507954 ATA
1 ATA
49507957 CTATAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 3 0.14
11 12 0.55
12 7 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAAAAATTATA
Found at i:49508008 original size:23 final size:22
Alignment explanation
Indices: 49507963--49508008 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
49507953 AATACTATAA
**
49507963 AAAATTAAAATATAATTCTAAT
1 AAAATTAAAATATAATTAAAAT
*
49507985 AAAATATAAAATATATTTAAAAT
1 AAAAT-TAAAATATAATTAAAAT
49508008 A
1 A
49508009 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATTAAAATATAATTAAAAT
Found at i:49508076 original size:10 final size:10
Alignment explanation
Indices: 49507908--49508094 Score: 61
Period size: 10 Copynumber: 18.8 Consensus size: 10
49507898 ATTTTTAAAT
* *
49507908 TTATATAAAC
1 TTATAAAAAA
49507918 TTAT-AAAAA
1 TTATAAAAAA
49507927 TTATAATAAAA
1 TTATAA-AAAA
* *
49507938 ATATAATAATA
1 TTATAA-AAAA
*
49507949 TTAT--AATA
1 TTATAAAAAA
*
49507957 CTATAAAAAA
1 TTATAAAAAA
49507967 TTA-AAATATAA
1 TTATAAA-A-AA
*
49507978 TTCTAATAAAA
1 TTATAA-AAAA
49507989 -TATAAAATATA
1 TTATAAAA-A-A
*
49508000 TT-TAAAATA
1 TTATAAAAAA
49508009 TT-T--AAAA
1 TTATAAAAAA
* *
49508016 TTTTATAAAA
1 TTATAAAAAA
*
49508026 TGTAT-TAAAA
1 T-TATAAAAAA
* *
49508036 TTCTAAATAA
1 TTATAAAAAA
*
49508046 TTCTTAAAAAA
1 TT-ATAAAAAA
** *
49508057 ACATAGAAAA
1 TTATAAAAAA
49508067 TTATAAAAAA
1 TTATAAAAAA
*
49508077 TTATTAAAAA
1 TTATAAAAAA
49508087 TTATAAAA
1 TTATAAAA
49508095 TTGATAAAGA
Statistics
Matches: 133, Mismatches: 27, Indels: 34
0.69 0.14 0.18
Matches are distributed among these distances:
7 5 0.04
8 8 0.06
9 18 0.14
10 61 0.46
11 36 0.27
12 4 0.03
13 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:49509016 original size:9 final size:9
Alignment explanation
Indices: 49508999--49509141 Score: 67
Period size: 9 Copynumber: 14.7 Consensus size: 9
49508989 TCTTATGATT
49508999 TTTTAATAA
1 TTTTAATAA
*
49509008 TTTTCATAA
1 TTTTAATAA
*
49509017 GTTTATATCAA
1 TTTTA-AT-AA
49509028 TTTTAAT-A
1 TTTTAATAA
49509036 TTTTAAATAA
1 TTTT-AATAA
*
49509046 TTTTTTATAA
1 -TTTTAATAA
*
49509056 GTTTTTAAGAA
1 --TTTTAATAA
*
49509067 TTTTAATACGT
1 TTTTAATA--A
*
49509078 TTTTATAAAA
1 TTTTA-ATAA
49509088 TTTTAAATAA
1 TTTT-AATAA
*
49509098 TTTAAAT-A
1 TTTTAATAA
49509106 TGTTTAATTAA
1 T-TTTAA-TAA
49509117 TTTT-ATAA
1 TTTTAATAA
*
49509125 TTTATTAAAAA
1 -TT-TTAATAA
49509136 TTTTAA
1 TTTTAA
49509142 ATATCATTTG
Statistics
Matches: 103, Mismatches: 15, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
8 10 0.10
9 35 0.34
10 27 0.26
11 29 0.28
12 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (9 bp):
TTTTAATAA
Found at i:49509039 original size:39 final size:39
Alignment explanation
Indices: 49508996--49509091 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 39
49508986 AGTTCTTATG
*
49508996 ATTTTTTAATAATTTTCATAAGTTTATATCAATTTTAAT
1 ATTTTTTAATAATTTTCATAAGTTTATAACAATTTTAAT
* * * *
49509035 A-TTTTAAATAATTTTTTATAAGTTTTTAAGAATTTTAAT
1 ATTTTTTAATAA-TTTTCATAAGTTTATAACAATTTTAAT
49509074 ACGTTTTTATAA-AATTTT
1 A--TTTTT-TAATAATTTT
49509092 AAATAATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
38 9 0.20
39 25 0.54
41 4 0.09
42 6 0.13
43 2 0.04
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.56
Consensus pattern (39 bp):
ATTTTTTAATAATTTTCATAAGTTTATAACAATTTTAAT
Found at i:49509070 original size:20 final size:20
Alignment explanation
Indices: 49508998--49509093 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
49508988 TTCTTATGAT
*
49508998 TTTTTAATAATTTTCATAAG
1 TTTTTAATAATTTTAATAAG
*
49509018 TTTAT-ATCAATTTTAAT-A-
1 TTTTTAAT-AATTTTAATAAG
* *
49509036 TTTTAAATAATTTTTTATAAG
1 TTTTTAATAA-TTTTAATAAG
* *
49509057 TTTTTAAGAATTTTAATACG
1 TTTTTAATAATTTTAATAAG
*
49509077 TTTTTATAAAATTTTAA
1 TTTTTA-ATAATTTTAA
49509094 ATAATTTAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
18 5 0.08
19 11 0.18
20 27 0.45
21 17 0.28
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTAATAATTTTAATAAG
Found at i:49509092 original size:30 final size:29
Alignment explanation
Indices: 49508999--49509094 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
49508989 TCTTATGATT
* * *
49508999 TTTTAATAATTTTCATAAGTTTATAT-CAA
1 TTTTAA-AATTTTAATAAGTTTTTATAAAA
* * **
49509028 TTTTAATATTTTAAATAATTTTTTATAAGT
1 TTTTAAAATTTT-AATAAGTTTTTATAAAA
*
49509058 TTTTAAGAATTTTAATACGTTTTTATAAAA
1 TTTTAA-AATTTTAATAAGTTTTTATAAAA
49509088 TTTTAAA
1 TTTTAAA
49509095 TAATTTAAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
28 5 0.10
29 17 0.33
30 25 0.48
31 5 0.10
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTTAAAATTTTAATAAGTTTTTATAAAA
Found at i:49509099 original size:10 final size:10
Alignment explanation
Indices: 49508998--49509144 Score: 62
Period size: 10 Copynumber: 14.9 Consensus size: 10
49508988 TTCTTATGAT
*
49508998 TTTTTAATAA
1 TTTTAAATAA
*
49509008 TTTT-CATAA
1 TTTTAAATAA
* *
49509017 GTTTATATCAA
1 TTTTAAAT-AA
49509028 TTTT-AAT-A
1 TTTTAAATAA
49509036 TTTTAAATAA
1 TTTTAAATAA
**
49509046 TTTTTTATAA
1 TTTTAAATAA
* *
49509056 GTTTTTAAGAA
1 -TTTTAAATAA
*
49509067 TTTT-AATACGT
1 TTTTAAATA--A
49509078 TTTTATAA-AA
1 TTTTA-AATAA
49509088 TTTTAAATAA
1 TTTTAAATAA
49509098 -TTTAAAT-A
1 TTTTAAATAA
*
49509106 TGTTTAATTAA
1 T-TTTAAATAA
49509117 TTTT--ATAA
1 TTTTAAATAA
49509125 TTTATTAAA-AA
1 -TT-TTAAATAA
49509136 TTTTAAATA
1 TTTTAAATA
49509145 TCATTTGTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 36
0.68 0.09 0.23
Matches are distributed among these distances:
8 9 0.09
9 29 0.28
10 42 0.40
11 21 0.20
12 2 0.02
13 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:49518376 original size:16 final size:16
Alignment explanation
Indices: 49518339--49518378 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
49518329 TTAATAAAAT
* *
49518339 TAAAAGTAATTGTTAT
1 TAAAATTAATTGTTAG
49518355 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
49518371 TAAAATTA
1 TAAAATTA
49518379 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:49518457 original size:59 final size:59
Alignment explanation
Indices: 49518389--49518528 Score: 262
Period size: 59 Copynumber: 2.4 Consensus size: 59
49518379 TCAAATTATT
* *
49518389 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTATAATAAAATCTAACATTTGATTAGTAAATTTATCA
49518448 AATTATTAATTGTATTAATTGTTATAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTATAATAAAATCTAACATTTGATTAGTAAATTTATCA
49518507 AATTATTAATTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
49518529 ATTAATTGTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 79 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTATAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:49518522 original size:9 final size:9
Alignment explanation
Indices: 49518510--49518537 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
49518500 TTTATCAAAT
49518510 TATTAATTG
1 TATTAATTG
49518519 TATTAATTG
1 TATTAATTG
49518528 TATTAATTG
1 TATTAATTG
49518537 T
1 T
49518538 TATAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:49518655 original size:22 final size:20
Alignment explanation
Indices: 49518630--49518679 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 20
49518620 AAGTAAATAA
49518630 ATTTAAAATAAAAAACTATTAT
1 ATTTAAAATAAAAAA-TA-TAT
49518652 ATTTTAAAAATAAAAAATATAT
1 A-TTT-AAAATAAAAAATATAT
49518674 ATTTAA
1 ATTTAA
49518680 TATTTTTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.08
21 3 0.12
22 5 0.19
23 5 0.19
24 11 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTAAAATAAAAAATATAT
Found at i:49518664 original size:24 final size:22
Alignment explanation
Indices: 49518634--49518677 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
49518624 AAATAAATTT
49518634 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAA-TA-TATATTTTA
49518658 AAAATAAAAAATATATATTT
1 AAAATAAAAAATATATATTT
49518678 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATAAAAAATATATATTTTA
Found at i:49519052 original size:65 final size:66
Alignment explanation
Indices: 49518930--49519055 Score: 175
Period size: 65 Copynumber: 1.9 Consensus size: 66
49518920 TCAATTTTAT
* * *
49518930 CTTTTTTGGTCACCCAACTATTTTAGATTTTTTGAAGTCTTCATTTTGGTGACCAAAAAAGGTAA
1 CTTTTTTGCTCACCCAACTATCTTAGATTTTTGGAAGTCTTCATTTTGGTGACCAAAAAAGGTAA
49518995 A
66 A
* * *
49518996 CTTTTTTTCTCACCCAACTATCTTGGA-TTTTGGATGT-TTCCATTTTGGTGACCAAAAAAG
1 CTTTTTTGCTCACCCAACTATCTTAGATTTTTGGAAGTCTT-CATTTTGGTGACCAAAAAAG
49519056 ACAAAATTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 2 0.04
65 28 0.53
66 23 0.43
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (66 bp):
CTTTTTTGCTCACCCAACTATCTTAGATTTTTGGAAGTCTTCATTTTGGTGACCAAAAAAGGTAA
A
Found at i:49525497 original size:8 final size:8
Alignment explanation
Indices: 49525484--49525513 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
49525474 CTCATTTATT
*
49525484 TATATATA
1 TATATATG
49525492 TATATATG
1 TATATATG
49525500 TATATATG
1 TATATATG
49525508 TATATA
1 TATATA
49525514 AGATATTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (8 bp):
TATATATG
Found at i:49527392 original size:16 final size:18
Alignment explanation
Indices: 49527353--49527386 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49527343 TAAGATTATA
49527353 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
49527370 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
49527387 AATTTAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:49527969 original size:43 final size:42
Alignment explanation
Indices: 49527889--49527969 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 42
49527879 ATAAATATAT
*
49527889 ATATTTTTCTTTTTGCTTTTTTAATTTTAAAATTATTTAAAA
1 ATATTTTTATTTTTGCTTTTTTAATTTTAAAATTATTTAAAA
* *
49527931 ATATTTTTATTTTTGTTTTTTTTTATTTTTAAAA-TATTT
1 ATATTTTTATTTTTG--CTTTTTTAATTTTAAAATTATTT
49527970 TTTTGTGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 14 0.41
43 5 0.15
44 15 0.44
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (42 bp):
ATATTTTTATTTTTGCTTTTTTAATTTTAAAATTATTTAAAA
Found at i:49527984 original size:22 final size:21
Alignment explanation
Indices: 49527946--49527986 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49527936 TTTATTTTTG
*
49527946 TTTTTTTTTATTTTTAAAATA
1 TTTTTTTGTATTTTTAAAATA
*
49527967 TTTTTTTGTGTTTATTAAAA
1 TTTTTTTGTATTT-TTAAAA
49527987 ATCGGGCCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTTTTGTATTTTTAAAATA
Found at i:49547979 original size:20 final size:19
Alignment explanation
Indices: 49547949--49548005 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
49547939 AAATTACAAA
*
49547949 AAAAATT-AAAATAATTTTT
1 AAAAATTCAAAAT-ATTTAT
49547968 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
49547987 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
49548005 A
1 A
49548006 TTGATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
18 7 0.20
19 23 0.66
20 5 0.14
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:49548025 original size:26 final size:24
Alignment explanation
Indices: 49547979--49548031 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
49547969 AAAATTCAAA
* * *
49547979 ATATTTATAAAAATTCCAAAATTT
1 ATATTGATAAAAATTCAAAAATAT
49548003 ATATTGATAAAAAATTCAAAAAATAT
1 ATATTGAT-AAAAATTC-AAAAATAT
49548029 ATA
1 ATA
49548032 AATAAGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 8 0.33
26 9 0.38
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATTGATAAAAATTCAAAAATAT
Found at i:49548029 original size:24 final size:22
Alignment explanation
Indices: 49547967--49548030 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 22
49547957 AAATAATTTT
49547967 TAAAAATTC--AAAATAT-TTA
1 TAAAAATTCAAAAAATATATTA
**
49547986 TAAAAATTCCAAAATTTATATTGA
1 TAAAAATT-CAAAAAATATATT-A
49548010 TAAAAAATTCAAAAAATATAT
1 T-AAAAATTCAAAAAATATAT
49548031 AAATAAGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 8 0.23
20 1 0.03
22 5 0.14
23 2 0.06
24 12 0.34
25 7 0.20
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (22 bp):
TAAAAATTCAAAAAATATATTA
Found at i:49548069 original size:16 final size:17
Alignment explanation
Indices: 49548030--49548063 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49548020 AAAAAATATA
49548030 TAAATAAGTTAAAAAAT
1 TAAATAAGTTAAAAAAT
49548047 TAAATAAGTTAAAAAAT
1 TAAATAAGTTAAAAAAT
49548064 ATATAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAAATAAGTTAAAAAAT
Found at i:49549062 original size:9 final size:9
Alignment explanation
Indices: 49549048--49549132 Score: 93
Period size: 9 Copynumber: 9.4 Consensus size: 9
49549038 GTAGTGATTC
49549048 AATTCGGTT
1 AATTCGGTT
*
49549057 AATTCGGGT
1 AATTCGGTT
*
49549066 AATTCGATT
1 AATTCGGTT
*
49549075 AATTCGGGT
1 AATTCGGTT
49549084 AA-TCAGGTT
1 AATTC-GGTT
49549093 AATTCGGTT
1 AATTCGGTT
49549102 AATTCGAG-T
1 AATTCG-GTT
*
49549111 AATTCGGGT
1 AATTCGGTT
*
49549120 AAGTCGGTT
1 AATTCGGTT
49549129 AATT
1 AATT
49549133 TTTAACCAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
8 3 0.05
9 57 0.90
10 3 0.05
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.38
Consensus pattern (9 bp):
AATTCGGTT
Found at i:49549071 original size:18 final size:18
Alignment explanation
Indices: 49549048--49549132 Score: 111
Period size: 18 Copynumber: 4.7 Consensus size: 18
49549038 GTAGTGATTC
49549048 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
49549066 AATTCGATTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
49549084 AA-TCAGGTTAATTCGGTT
1 AATTC-GGTTAATTCGGGT
49549102 AATTCGAG-TAATTCGGGT
1 AATTCG-GTTAATTCGGGT
*
49549120 AAGTCGGTTAATT
1 AATTCGGTTAATT
49549133 TTTAACCAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.05
18 52 0.90
19 3 0.05
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.38
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:49549093 original size:36 final size:36
Alignment explanation
Indices: 49549051--49549132 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
49549041 GTGATTCAAT
*
49549051 TCGGTTAATTCGGGTAATTCGATTAATTCGGGTAA-
1 TCGGTTAATTCGGGTAATTCGAGTAATTCGGGTAAG
*
49549086 TCAGGTTAATTCGGTTAATTCGAGTAATTCGGGTAAG
1 TC-GGTTAATTCGGGTAATTCGAGTAATTCGGGTAAG
49549123 TCGGTTAATT
1 TCGGTTAATT
49549133 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
35 2 0.05
36 39 0.91
37 2 0.05
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.38
Consensus pattern (36 bp):
TCGGTTAATTCGGGTAATTCGAGTAATTCGGGTAAG
Found at i:49558492 original size:177 final size:177
Alignment explanation
Indices: 49558239--49558628 Score: 629
Period size: 177 Copynumber: 2.2 Consensus size: 177
49558229 TGTATGTAGA
*
49558239 GTTGGTGAAACATACAGCGGAAA-GCCAGAGAAAGCTCCAGCAGATAGGGAAGGCAAACCACAGC
1 GTTGGTGAAACATACAAC-GAAAGGCCAGAGAAAGCTCCAGCAGATAGGGAAGGCAAACCACAGC
* * *
49558303 ACCATAAGAACCGATCCATCACTCTCGGGTCAGTTAAAGAATTCAATTTCGACAATATTAATGGA
65 ACCATAAGAACCGATCCATCACTCTCGGCTCACTTAAAGAATTCAATTTCGACAATATTAATGCA
* *
49558368 GAGATAGAAGAAAATGCTACTAAGTCAGTGGAAACTTATGAAGGTCGT
130 GAGATAGAAGAAAATGCTACCAAGTCAGTGGAAACTCATGAAGGTCGT
* *
49558416 GTTGGTGAAACATGCAACGAAAGGCCAGAGCAAGCTCCAGCAGATAGGGAAGGCAAACCACAGCA
1 GTTGGTGAAACATACAACGAAAGGCCAGAGAAAGCTCCAGCAGATAGGGAAGGCAAACCACAGCA
* * *
49558481 CCATAAGAACCGATCCATCACTCTTGGCTCACTTAAAGAATTCAATTTCGACAATGTTAATGCCG
66 CCATAAGAACCGATCCATCACTCTCGGCTCACTTAAAGAATTCAATTTCGACAATATTAATGCAG
* *
49558546 AGATAGAAGAAAATGCTACCAAGTCGGTGGAAACTCATGAATGTCGT
131 AGATAGAAGAAAATGCTACCAAGTCAGTGGAAACTCATGAAGGTCGT
* *
49558593 GTTGGTGAAACATACAATGAAAGACCAGAGAAAGCT
1 GTTGGTGAAACATACAACGAAAGGCCAGAGAAAGCT
49558629 GAAGTATCTC
Statistics
Matches: 195, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 4 0.02
177 191 0.98
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (177 bp):
GTTGGTGAAACATACAACGAAAGGCCAGAGAAAGCTCCAGCAGATAGGGAAGGCAAACCACAGCA
CCATAAGAACCGATCCATCACTCTCGGCTCACTTAAAGAATTCAATTTCGACAATATTAATGCAG
AGATAGAAGAAAATGCTACCAAGTCAGTGGAAACTCATGAAGGTCGT
Found at i:49560985 original size:23 final size:23
Alignment explanation
Indices: 49560945--49560993 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
49560935 TAAGAACTAG
* *
49560945 TTTAGTATTGCTTCTAAGAAACA
1 TTTAGCATTACTTCTAAGAAACA
*
49560968 TTTAGCATTACTTTTAAGAAACA
1 TTTAGCATTACTTCTAAGAAACA
49560991 TTT
1 TTT
49560994 TTAAGACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (23 bp):
TTTAGCATTACTTCTAAGAAACA
Found at i:49561013 original size:18 final size:18
Alignment explanation
Indices: 49560990--49561028 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
49560980 TTTAAGAAAC
*
49560990 ATTTTTAAGACAAAAAGT
1 ATTTTTAAGACAAAAAAT
* *
49561008 ATTTTTGAGATAAAAAAT
1 ATTTTTAAGACAAAAAAT
49561026 ATT
1 ATT
49561029 GTCAAACAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (18 bp):
ATTTTTAAGACAAAAAAT
Found at i:49561785 original size:18 final size:19
Alignment explanation
Indices: 49561756--49561791 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
49561746 TTAATAACAT
49561756 TAAAAAATTATTTTAAAAA
1 TAAAAAATTATTTTAAAAA
49561775 TAAAAAA-TATTTTAAAA
1 TAAAAAATTATTTTAAAA
49561792 GTATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAAATTATTTTAAAAA
Found at i:49562225 original size:30 final size:32
Alignment explanation
Indices: 49562189--49562258 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
49562179 ATTCATCAAA
*
49562189 ACAAAAAAC-AG-ATCTTGTAATAAAATGGTG
1 ACAAAAAACTAGAATCTTGTAATAAAATGATG
*
49562219 ACAAAAAACTCGAATCTTGTAATAAAATGATG
1 ACAAAAAACTAGAATCTTGTAATAAAATGATG
49562251 ACAAAAAA
1 ACAAAAAA
49562259 GTGAAGAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 9 0.25
31 1 0.03
32 26 0.72
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.21
Consensus pattern (32 bp):
ACAAAAAACTAGAATCTTGTAATAAAATGATG
Found at i:49568374 original size:16 final size:16
Alignment explanation
Indices: 49568344--49568378 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
49568334 ATTTTTATTA
49568344 TTTTTAAATTAAAAAT
1 TTTTTAAATTAAAAAT
49568360 TTTTATAAATT-AAAAT
1 TTTT-TAAATTAAAAAT
49568376 TTT
1 TTT
49568379 ACTATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTTAAATTAAAAAT
Found at i:49571912 original size:96 final size:96
Alignment explanation
Indices: 49571745--49571935 Score: 337
Period size: 96 Copynumber: 2.0 Consensus size: 96
49571735 ATCAATTGCA
49571745 TGTCTTGTATAATGTTGGAAAGTTCAAAAACAGTGTAAGGTCGTATCATAAGGATAAGGTTTCAC
1 TGTCTTGTATAATGTTGGAAAGTTCAAAAACAGTGTAAGGTCGTATCATAAGGATAAGGTTTCAC
*
49571810 AGAAGTATCCTGTCATCTGCAATTAATAGGG
66 AAAAGTATCCTGTCATCTGCAATTAATAGGG
* * *
49571841 TGTCTTGTATAATGTTGGAAAGTTTAAAAAGAGTTTAAGGTCGTATCATAAGGATAAGGTTTCAC
1 TGTCTTGTATAATGTTGGAAAGTTCAAAAACAGTGTAAGGTCGTATCATAAGGATAAGGTTTCAC
*
49571906 AAAAGTATCCTGTTATCTGCAATTAATAGG
66 AAAAGTATCCTGTCATCTGCAATTAATAGG
49571936 AAACTTCATA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 90 1.00
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (96 bp):
TGTCTTGTATAATGTTGGAAAGTTCAAAAACAGTGTAAGGTCGTATCATAAGGATAAGGTTTCAC
AAAAGTATCCTGTCATCTGCAATTAATAGGG
Found at i:49576348 original size:19 final size:19
Alignment explanation
Indices: 49576324--49576360 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49576314 AGTTTTGGGG
49576324 TTAGGAAAAGATGTGAATC
1 TTAGGAAAAGATGTGAATC
* *
49576343 TTAGGAGAGGATGTGAAT
1 TTAGGAAAAGATGTGAAT
49576361 GGGAATGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.32, T:0.27
Consensus pattern (19 bp):
TTAGGAAAAGATGTGAATC
Found at i:49576625 original size:48 final size:50
Alignment explanation
Indices: 49576537--49576639 Score: 147
Period size: 48 Copynumber: 2.1 Consensus size: 50
49576527 GTTTCTTCAT
49576537 CATCAAACTTAAAAAGCAACCACCAGCTTTTATGTTGTAACGTGGCAATCG
1 CATCAAACTTAAAAAGCAACCACCAGC-TTTATGTTGTAACGTGGCAATCG
* * * *
49576588 CATCAACCTT-AAATGCGACCACCAGC-TTATGTTGTAACGTGGCAATTG
1 CATCAAACTTAAAAAGCAACCACCAGCTTTATGTTGTAACGTGGCAATCG
49576636 CATC
1 CATC
49576640 TTCTTTAGCG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
48 25 0.52
50 14 0.29
51 9 0.19
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (50 bp):
CATCAAACTTAAAAAGCAACCACCAGCTTTATGTTGTAACGTGGCAATCG
Found at i:49576828 original size:12 final size:12
Alignment explanation
Indices: 49576806--49576840 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
49576796 ATTGGTATCA
49576806 AATTG-ATTAAT
1 AATTGAATTAAT
49576817 AATTGAATTAAT
1 AATTGAATTAAT
*
49576829 AGTTGAATTAAT
1 AATTGAATTAAT
49576841 TTTCATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (12 bp):
AATTGAATTAAT
Found at i:49579697 original size:19 final size:19
Alignment explanation
Indices: 49579673--49579709 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49579663 GAAGATTCAT
49579673 TCGAAAAAAAAATATAAAC
1 TCGAAAAAAAAATATAAAC
* *
49579692 TCGAAAAATAAGTATAAA
1 TCGAAAAAAAAATATAAA
49579710 AAATTAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (19 bp):
TCGAAAAAAAAATATAAAC
Found at i:49591449 original size:19 final size:17
Alignment explanation
Indices: 49591403--49591450 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
49591393 TTCAATTAAA
49591403 ATTTATTA-AAAATATT
1 ATTTATTACAAAATATT
49591419 ATTTTATATACAAAATAAATT
1 A-TTTAT-TACAAAAT--ATT
49591440 ATTTATTACAA
1 ATTTATTACAA
49591451 GGTTGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 2 0.07
19 10 0.37
20 5 0.19
21 4 0.15
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTATTACAAAATATT
Found at i:49598309 original size:18 final size:18
Alignment explanation
Indices: 49598286--49598362 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 18
49598276 ATGTTGTTTC
49598286 AATTTTTTATTTTTAATT
1 AATTTTTTATTTTTAATT
* *
49598304 AATTTTTTA--ATTAATA
1 AATTTTTTATTTTTAATT
* * *
49598320 AATATATTATTTCT-A--
1 AATTTTTTATTTTTAATT
49598335 AATTTTTTATTTTTAATT
1 AATTTTTTATTTTTAATT
*
49598353 CATCTTTTTA
1 AAT-TTTTTA
49598363 ATTAATAACT
Statistics
Matches: 43, Mismatches: 10, Indels: 11
0.67 0.16 0.17
Matches are distributed among these distances:
15 11 0.26
16 13 0.30
17 1 0.02
18 12 0.28
19 6 0.14
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
AATTTTTTATTTTTAATT
Found at i:49598511 original size:22 final size:20
Alignment explanation
Indices: 49598478--49598525 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
49598468 ACTCCTTCAT
* *
49598478 TTATATAAATAAATTAATAA
1 TTATATAAATAAAATAAAAA
49598498 TTATATAATTATAAAATAAAAA
1 TTATATAA--ATAAAATAAAAA
49598520 -TATATA
1 TTATATA
49598526 TTCTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 6 0.25
22 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTATATAAATAAAATAAAAA
Found at i:49599942 original size:63 final size:63
Alignment explanation
Indices: 49599843--49599971 Score: 258
Period size: 63 Copynumber: 2.0 Consensus size: 63
49599833 CACAAAGATG
49599843 AACCTACCGCCATCTGAATTCACAAGTGTTTATCCGGCTTGGCGAAGTACATTAACATATTTC
1 AACCTACCGCCATCTGAATTCACAAGTGTTTATCCGGCTTGGCGAAGTACATTAACATATTTC
49599906 AACCTACCGCCATCTGAATTCACAAGTGTTTATCCGGCTTGGCGAAGTACATTAACATATTTC
1 AACCTACCGCCATCTGAATTCACAAGTGTTTATCCGGCTTGGCGAAGTACATTAACATATTTC
49599969 AAC
1 AAC
49599972 GCATCTCGGC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (63 bp):
AACCTACCGCCATCTGAATTCACAAGTGTTTATCCGGCTTGGCGAAGTACATTAACATATTTC
Found at i:49607716 original size:8 final size:8
Alignment explanation
Indices: 49607703--49607728 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
49607693 TCCAAAAAGC
49607703 TTCCAAAT
1 TTCCAAAT
49607711 TTCCAAAT
1 TTCCAAAT
49607719 TTCCAAAT
1 TTCCAAAT
49607727 TT
1 TT
49607729 AATAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (8 bp):
TTCCAAAT
Found at i:49611768 original size:37 final size:37
Alignment explanation
Indices: 49611727--49611871 Score: 200
Period size: 37 Copynumber: 3.9 Consensus size: 37
49611717 TTACTTTTAT
* *
49611727 ATTTAATAACTCTATCTTAATTTAATAAAATATTTTT
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTTTC
* * * *
49611764 ATTTAATAACTTTATTTTAATTAAATAAATTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTTTC
* *
49611801 ATTTAATAAATTTATTTTAATTTAATAAAATATTTTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTTTC
* *
49611838 ATTTAATATCTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAAATATT
49611872 AAATTAAAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 94 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAAATATTTTC
Found at i:49611769 original size:18 final size:18
Alignment explanation
Indices: 49611721--49611871 Score: 140
Period size: 19 Copynumber: 8.1 Consensus size: 18
49611711 TACAACTTAC
*
49611721 TTTTATATTTAATAACTCTA
1 TTTTA-ATTTAATAAAT-TA
* *
49611741 TCTTAATTTAATAAAATA
1 TTTTAATTTAATAAATTA
* *
49611759 TTTTTATTTAATAACTTTA
1 TTTTAATTTAATAA-ATTA
*
49611778 TTTTAATTAAATAAATTA
1 TTTTAATTTAATAAATTA
* *
49611796 TTCTCATTTAATAAATTTA
1 TTTTAATTTAATAAA-TTA
*
49611815 TTTTAATTTAATAAAATA
1 TTTTAATTTAATAAATTA
* **
49611833 TTTTCATTTAATATCTCTA
1 TTTTAATTTAATAAAT-TA
*
49611852 TTTTAATTTAATAAACTA
1 TTTTAATTTAATAAATTA
49611870 TT
1 TT
49611872 AAATTAAAAT
Statistics
Matches: 104, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
18 47 0.45
19 53 0.51
20 4 0.04
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAATTTAATAAATTA
Found at i:49611883 original size:74 final size:72
Alignment explanation
Indices: 49611742--49611895 Score: 193
Period size: 74 Copynumber: 2.1 Consensus size: 72
49611732 ATAACTCTAT
* * * ** *
49611742 CTTAATTTAATAAAATATTTTTATTTAATAACTTTATTTTAATTAAATAAATTATTCTCATTTAA
1 CTTAATTTAATAAAATATTTTCATTTAATAACTCTATTTTAATTAAATAAACTATTCAAATTAAA
49611807 TAAATTTA
66 T-AATTTA
* * *
49611815 TTTTAATTTAATAAAATATTTTCATTTAATATCTCTATTTTAATTTAATAAACTATT-AAATTAA
1 -CTTAATTTAATAAAATATTTTCATTTAATAACTCTATTTTAATTAAATAAACTATTCAAATT-A
49611879 AATAATTTA
64 AATAATTTA
49611888 CTTAATTT
1 CTTAATTT
49611896 TTTTAAATTA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
72 7 0.10
73 9 0.13
74 53 0.77
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (72 bp):
CTTAATTTAATAAAATATTTTCATTTAATAACTCTATTTTAATTAAATAAACTATTCAAATTAAA
TAATTTA
Found at i:49617951 original size:9 final size:9
Alignment explanation
Indices: 49617931--49617966 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
49617921 CTTAAAAAAT
49617931 AAAATTAAA
1 AAAATTAAA
49617940 AAAATTAAAA
1 AAAATT-AAA
*
49617950 AAAATTTAA
1 AAAATTAAA
49617959 AAAATTAA
1 AAAATTAA
49617967 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAATTAAA
Found at i:49617952 original size:10 final size:10
Alignment explanation
Indices: 49617926--49617966 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
49617916 AAAATCTTAA
49617926 AAAATAAAATT
1 AAAA-AAAATT
49617937 -AAAAAAATT
1 AAAAAAAATT
49617946 AAAAAAAATT
1 AAAAAAAATT
*
49617956 -TAAAAAATT
1 AAAAAAAATT
49617965 AA
1 AA
49617967 TTATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 14 0.54
10 12 0.46
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:49617955 original size:19 final size:20
Alignment explanation
Indices: 49617926--49617966 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
49617916 AAAATCTTAA
49617926 AAAATAAAATTAAAAAAATT
1 AAAATAAAATTAAAAAAATT
*
49617946 AAAA-AAAATTTAAAAAATT
1 AAAATAAAATTAAAAAAATT
49617965 AA
1 AA
49617967 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATAAAATTAAAAAAATT
Found at i:49620355 original size:3 final size:3
Alignment explanation
Indices: 49620347--49620376 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
49620337 TTTTAGTACA
49620347 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49620377 GTAACAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:49620720 original size:14 final size:14
Alignment explanation
Indices: 49620701--49620731 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
49620691 CTTCTTTTTA
49620701 TTATTCAAAAATGC
1 TTATTCAAAAATGC
49620715 TTATTCAAAAATGC
1 TTATTCAAAAATGC
49620729 TTA
1 TTA
49620732 GTTTTAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (14 bp):
TTATTCAAAAATGC
Found at i:49630887 original size:21 final size:21
Alignment explanation
Indices: 49630861--49630901 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
49630851 ATCTGCTCAA
* *
49630861 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
49630882 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
49630902 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:49635213 original size:14 final size:15
Alignment explanation
Indices: 49635189--49635221 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
49635179 ACATCTTTTG
49635189 ATAATTGCTTCATCC
1 ATAATTGCTTCATCC
49635204 ATAA-TGCTTCATCC
1 ATAATTGCTTCATCC
49635218 ATAA
1 ATAA
49635222 ATTTGAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (15 bp):
ATAATTGCTTCATCC
Found at i:49640562 original size:17 final size:18
Alignment explanation
Indices: 49640515--49640554 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
49640505 AATGTTTCTT
* *
49640515 AAAAGTGCTTTTGGGACA
1 AAAAGTACTTTTAGGACA
49640533 AAAAGTACTTTTAGGACA
1 AAAAGTACTTTTAGGACA
49640551 AAAA
1 AAAA
49640555 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (18 bp):
AAAAGTACTTTTAGGACA
Found at i:49641569 original size:2 final size:2
Alignment explanation
Indices: 49641564--49641607 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
49641554 AAAGAATGGT
49641564 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
49641606 TC
1 TC
49641608 ACAACACTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:49645678 original size:37 final size:37
Alignment explanation
Indices: 49645636--49645710 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
49645626 AGAATAATTC
*
49645636 TATAATAGCTAAATTGACCAAAAGTGTATACGTGAGG
1 TATAATAGCCAAATTGACCAAAAGTGTATACGTGAGG
**
49645673 TATAATAGCCAAATTGACTGAAAGTGTATACGTGAGG
1 TATAATAGCCAAATTGACCAAAAGTGTATACGTGAGG
49645710 T
1 T
49645711 CCACTAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28
Consensus pattern (37 bp):
TATAATAGCCAAATTGACCAAAAGTGTATACGTGAGG
Found at i:49660586 original size:5 final size:5
Alignment explanation
Indices: 49660576--49660601 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
49660566 ATAAAAAGCA
49660576 TGCCT TGCCT TGCCT TGCCT TGCCT T
1 TGCCT TGCCT TGCCT TGCCT TGCCT T
49660602 TGCCCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.19, T:0.42
Consensus pattern (5 bp):
TGCCT
Found at i:49660987 original size:35 final size:35
Alignment explanation
Indices: 49660948--49661048 Score: 103
Period size: 35 Copynumber: 3.1 Consensus size: 35
49660938 TTTAATTTTC
49660948 TATTATATCGATCAAAATTATGTATAATTGATATA
1 TATTATATCGATCAAAATTATGTATAATTGATATA
* * * *
49660983 TATTAAATTGAT----A-TATAT-TAATT--T-TC
1 TATTATATCGATCAAAATTATGTATAATTGATATA
49661009 TATTATATCGATCAAAATTATGTATAATTGATATA
1 TATTATATCGATCAAAATTATGTATAATTGATATA
49661044 TATTA
1 TATTA
49661049 AATTGCTTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 18
0.65 0.11 0.24
Matches are distributed among these distances:
26 11 0.22
27 1 0.02
29 5 0.10
30 5 0.10
31 5 0.10
32 5 0.10
34 1 0.02
35 16 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (35 bp):
TATTATATCGATCAAAATTATGTATAATTGATATA
Found at i:49660990 original size:61 final size:63
Alignment explanation
Indices: 49660920--49661051 Score: 213
Period size: 61 Copynumber: 2.2 Consensus size: 63
49660910 GCTTAACAAA
49660920 ATATA-TAAATATTGGA-A-AT-TTAATTTTCTATTATATCGATCAAAATTATGTATAATTGAT
1 ATATATTAAATATT-GATATATATTAATTTTCTATTATATCGATCAAAATTATGTATAATTGAT
49660980 ATATATT-AA-ATTGATATATATTAATTTTCTATTATATCGATCAAAATTATGTATAATTGAT
1 ATATATTAAATATTGATATATATTAATTTTCTATTATATCGATCAAAATTATGTATAATTGAT
49661041 ATATATTAAAT
1 ATATATTAAAT
49661052 TGCTTTGTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
58 2 0.03
59 4 0.06
60 9 0.14
61 49 0.74
62 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (63 bp):
ATATATTAAATATTGATATATATTAATTTTCTATTATATCGATCAAAATTATGTATAATTGAT
Found at i:49660993 original size:15 final size:15
Alignment explanation
Indices: 49660973--49661003 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
49660963 AATTATGTAT
49660973 AATTGATATATATTA
1 AATTGATATATATTA
49660988 AATTGATATATATTA
1 AATTGATATATATTA
49661003 A
1 A
49661004 TTTTCTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
AATTGATATATATTA
Found at i:49661052 original size:61 final size:61
Alignment explanation
Indices: 49660939--49661053 Score: 230
Period size: 61 Copynumber: 1.9 Consensus size: 61
49660929 TATTGGAAAT
49660939 TTAATTTTCTATTATATCGATCAAAATTATGTATAATTGATATATATTAAATTGATATATA
1 TTAATTTTCTATTATATCGATCAAAATTATGTATAATTGATATATATTAAATTGATATATA
49661000 TTAATTTTCTATTATATCGATCAAAATTATGTATAATTGATATATATTAAATTG
1 TTAATTTTCTATTATATCGATCAAAATTATGTATAATTGATATATATTAAATTG
49661054 CTTTGTTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (61 bp):
TTAATTTTCTATTATATCGATCAAAATTATGTATAATTGATATATATTAAATTGATATATA
Found at i:49665750 original size:19 final size:20
Alignment explanation
Indices: 49665715--49665759 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
49665705 ACTATTATTC
*
49665715 TACATTTTTTCCCTTTT-TT
1 TACATTTTTTCCATTTTGTT
*
49665734 TACATTTTTTTCATTTTGTT
1 TACATTTTTTCCATTTTGTT
49665754 T-CATTT
1 TACATTT
49665760 AAAATAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.13, C:0.16, G:0.02, T:0.69
Consensus pattern (20 bp):
TACATTTTTTCCATTTTGTT
Found at i:49668165 original size:20 final size:19
Alignment explanation
Indices: 49668140--49668178 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
49668130 CCAATTTTTT
49668140 TGAAAATTTTAATTATACCC
1 TGAAAATTTTAATTA-ACCC
49668160 TGAAAATTTTAATTAACCC
1 TGAAAATTTTAATTAACCC
49668179 CCTCCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (19 bp):
TGAAAATTTTAATTAACCC
Done.