Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 159 of 207
Found at i:48930808 original size:32 final size:32
Alignment explanation
Indices: 48930767--48930831 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
48930757 TAATGCTTGA
48930767 TGAACTCTTTACATGGTAGTTTTTCTAGGCAT
1 TGAACTCTTTACATGGTAGTTTTTCTAGGCAT
48930799 TGAACTCTTTACATGGTAGTTTTTCTAGGCAT
1 TGAACTCTTTACATGGTAGTTTTTCTAGGCAT
48930831 T
1 T
48930832 CACTGAGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (32 bp):
TGAACTCTTTACATGGTAGTTTTTCTAGGCAT
Found at i:48934596 original size:17 final size:19
Alignment explanation
Indices: 48934570--48934604 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
48934560 AAAAAACATG
48934570 AAGCATTAAAA-TAGTTTC
1 AAGCATTAAAAGTAGTTTC
48934588 AAGCA-TAAAAGTAGTTT
1 AAGCATTAAAAGTAGTTT
48934605 GGCACGTCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (19 bp):
AAGCATTAAAAGTAGTTTC
Found at i:48951254 original size:23 final size:23
Alignment explanation
Indices: 48951224--48951269 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
48951214 CCTGACAGAC
48951224 CAACAACACAGATTAAAAAATAT
1 CAACAACACAGATTAAAAAATAT
48951247 CAACAACACAGATTAAAAAATAT
1 CAACAACACAGATTAAAAAATAT
48951270 ATTTTCTCTT
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:0.61, C:0.17, G:0.04, T:0.17
Consensus pattern (23 bp):
CAACAACACAGATTAAAAAATAT
Found at i:48952456 original size:24 final size:24
Alignment explanation
Indices: 48952420--48952469 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
48952410 AATGGAAAAT
*
48952420 AAAGAAAAAAAAA-AAGAAAAGTTA
1 AAAGAAAAAAAAAGAA-AAAAATTA
* *
48952444 AAAGAATATAAAAGAAAAAAATTA
1 AAAGAAAAAAAAAGAAAAAAATTA
48952468 AA
1 AA
48952470 TTACTCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (24 bp):
AAAGAAAAAAAAAGAAAAAAATTA
Found at i:48953260 original size:14 final size:14
Alignment explanation
Indices: 48953241--48953267 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48953231 AAGAATAGTT
48953241 TAATATTTTTATTA
1 TAATATTTTTATTA
48953255 TAATATTTTTATT
1 TAATATTTTTATT
48953268 GTTAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TAATATTTTTATTA
Found at i:48956844 original size:22 final size:22
Alignment explanation
Indices: 48956815--48956871 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
48956805 AATATATGTT
*
48956815 ATAA-TTTTTTTATTTTTAAAA
1 ATAATTTTTTTTATTTTAAAAA
*
48956836 ATAGTTTTTTTTATTTTAAAAA
1 ATAATTTTTTTTATTTTAAAAA
*
48956858 ATAATTGTTTTTAT
1 ATAATTTTTTTTAT
48956872 GGCATCCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
ATAATTTTTTTTATTTTAAAAA
Found at i:48961905 original size:18 final size:18
Alignment explanation
Indices: 48961872--48961919 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
48961862 ATTCACCCAA
*
48961872 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
* *
48961891 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
48961909 ACCCAACCCAA
1 ACCCAACCCAA
48961920 TCATAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.42, C:0.46, G:0.02, T:0.10
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:48961912 original size:13 final size:13
Alignment explanation
Indices: 48961896--48961920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48961886 CAAGTATCCA
48961896 ACCCAACCCAATT
1 ACCCAACCCAATT
48961909 ACCCAACCCAAT
1 ACCCAACCCAAT
48961921 CATAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:48962010 original size:6 final size:6
Alignment explanation
Indices: 48961961--48962009 Score: 71
Period size: 6 Copynumber: 8.0 Consensus size: 6
48961951 AAATAAAATT
* *
48961961 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAGT CTAAAA ATAAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAA-A CTAAAA CTAAAA
48962010 AACATATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
6 34 0.87
7 5 0.13
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.18
Consensus pattern (6 bp):
CTAAAA
Found at i:48962030 original size:9 final size:9
Alignment explanation
Indices: 48962016--48962074 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
48962006 AAAAAACATA
48962016 TAATTCAGG
1 TAATTCAGG
48962025 TAATTCAGG
1 TAATTCAGG
48962034 TAATTC-GG
1 TAATTCAGG
* *
48962042 TTAGTTCAGT
1 -TAATTCAGG
*
48962052 TAATTCAGT
1 TAATTCAGG
*
48962061 TAATTCAGT
1 TAATTCAGG
48962070 TAATT
1 TAATT
48962075 TTTAACCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
8 2 0.04
9 42 0.93
10 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (9 bp):
TAATTCAGG
Found at i:48962039 original size:18 final size:18
Alignment explanation
Indices: 48962016--48962074 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
48962006 AAAAAACATA
*
48962016 TAATTCAGGTAATTCAGG
1 TAATTCAGGTAATTCAGT
*
48962034 TAATTC-GGTTAGTTCAGT
1 TAATTCAGG-TAATTCAGT
*
48962052 TAATTCAGTTAATTCAGT
1 TAATTCAGGTAATTCAGT
48962070 TAATT
1 TAATT
48962075 TTTAACCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 2 0.06
18 32 0.91
19 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (18 bp):
TAATTCAGGTAATTCAGT
Found at i:48962057 original size:27 final size:27
Alignment explanation
Indices: 48962019--48962071 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
48962009 AAACATATAA
*
48962019 TTCAGGTAATTCAGGTAATTCGGTTAG
1 TTCAGGTAATTCAGGTAATTCAGTTAG
* *
48962046 TTCAGTTAATTCAGTTAATTCAGTTA
1 TTCAGGTAATTCAGGTAATTCAGTTA
48962072 ATTTTTAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (27 bp):
TTCAGGTAATTCAGGTAATTCAGTTAG
Found at i:48962775 original size:30 final size:30
Alignment explanation
Indices: 48962580--48962775 Score: 198
Period size: 30 Copynumber: 6.6 Consensus size: 30
48962570 GTAAGTAGGT
* *
48962580 GCCTTTGTGGCTA-CTTAAAGTTCTGTGGAC
1 GCCTTTGTGGCTATC-TAATGTTATGTGGAC
* * * *
48962610 GCCCTTGTGGCTATCTAA-GTCAAGTGGAA
1 GCCTTTGTGGCTATCTAATGTTATGTGGAC
* * *
48962639 GCCTTTGTGGCTATCTGATGTTGTGTGGAT
1 GCCTTTGTGGCTATCTAATGTTATGTGGAC
* * ** *
48962669 GCCTTTGTGGCTATTTGATGTTACATGGAT
1 GCCTTTGTGGCTATCTAATGTTATGTGGAC
* * * *
48962699 GCCTTCGTGACTATTTGATGTTATGTGGAC
1 GCCTTTGTGGCTATCTAATGTTATGTGGAC
48962729 GCCTTTGTGGCTATCTAATGTTATGTGGAC
1 GCCTTTGTGGCTATCTAATGTTATGTGGAC
*
48962759 GCCTTTGTAGCTATCTA
1 GCCTTTGTGGCTATCTA
48962776 TCTATTATGC
Statistics
Matches: 139, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
29 23 0.17
30 115 0.83
31 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (30 bp):
GCCTTTGTGGCTATCTAATGTTATGTGGAC
Found at i:48964731 original size:9 final size:9
Alignment explanation
Indices: 48964717--48964745 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
48964707 TGGATACGAA
48964717 TTTAAAGGT
1 TTTAAAGGT
48964726 TTTAAAGGT
1 TTTAAAGGT
48964735 TTTAAAGGT
1 TTTAAAGGT
48964744 TT
1 TT
48964746 CAAGTGAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (9 bp):
TTTAAAGGT
Found at i:48978189 original size:83 final size:84
Alignment explanation
Indices: 48977993--48978303 Score: 232
Period size: 83 Copynumber: 3.7 Consensus size: 84
48977983 TCCACAAGGT
* * * * * *
48977993 CTTCATTTAACTGAGATAGCCACAAAGACATCTTTTTAACAGAGATAGCCAT-AAAGACTT-CGT
1 CTTCCTTTAACAGAGATAGCCACAAAGGCTTC-CTTTAACAGAGATAGCCATAAAAG-CTTACCT
* * * *
48978056 TATAACAGAGGTCA-TCAC-AAAGG
64 T-T-ACAAAGAT-AGCCACGAAA-A
* * *
48978079 CTTCCTTATAACAGAGATCA-CCACAAAGGCTTCCTTATAACAGAGAT-TCCA-ACAAAGTTTTC
1 CTTCCTT-TAACAGAGAT-AGCCACAAAGGCTTCCTT-TAACAGAGATAGCCATA-AAAGCTTAC
**
48978141 CTTTACAGGGATAGCCAC-AAAGGA
62 CTTTACAAAGATAGCCACGAAA--A
* * * * *
48978165 -TT-TTTTAACAGAGATAGCCACAAAGGCTTCCTTTAATAGTGATAGCCATAAAGGCTTACTTTT
1 CTTCCTTTAACAGAGATAGCCACAAAGGCTTCCTTTAACAGAGATAGCCATAAAAGCTTACCTTT
48978228 ACAAAGATAGCCACGAAAA
66 ACAAAGATAGCCACGAAAA
* *
48978247 CTTCCTTTAACAGAGATAGCCACAAAGGCTTCCTTT--CAGAGATAGCCACAAAGGCTT
1 CTTCCTTTAACAGAGATAGCCACAAAGGCTTCCTTTAACAGAGATAGCCATAAAAGCTT
48978304 CCATTTAGAG
Statistics
Matches: 185, Mismatches: 26, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
82 28 0.15
83 52 0.28
84 38 0.21
85 14 0.08
86 15 0.08
87 37 0.20
88 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (84 bp):
CTTCCTTTAACAGAGATAGCCACAAAGGCTTCCTTTAACAGAGATAGCCATAAAAGCTTACCTTT
ACAAAGATAGCCACGAAAA
Found at i:48978208 original size:28 final size:28
Alignment explanation
Indices: 48977960--48978329 Score: 305
Period size: 29 Copynumber: 13.2 Consensus size: 28
48977950 TCTCGCCAGG
* * **
48977960 AAGGCATCCTTTTAACAAAGATTTCCAC-
1 AAGGCTTCC-TTTAACAGAGATAGCCACA
* *
48977988 AAGGTCTTCATTTAACTGAGATAGCCACA
1 AAGG-CTTCCTTTAACAGAGATAGCCACA
* * * *
48978017 AAGACATCTTTTTAACAGAGATAGCCATA
1 AAGGCTTC-CTTTAACAGAGATAGCCACA
* * * *
48978046 AAGACTTCGTTATAACAGAGGTCA-TCACA
1 AAGGCTTCCTT-TAACAGAGAT-AGCCACA
48978075 AAGGCTTCCTTATAACAGAGATCA-CCACA
1 AAGGCTTCCTT-TAACAGAGAT-AGCCACA
*
48978104 AAGGCTTCCTTATAACAGAGAT-TCCAACA
1 AAGGCTTCCTT-TAACAGAGATAGCC-ACA
** *
48978133 AAGTTTTCCTTT-ACAGGGATAGCCACA
1 AAGGCTTCCTTTAACAGAGATAGCCACA
* *
48978160 AAGGATT-TTTTAACAGAGATAGCCACA
1 AAGGCTTCCTTTAACAGAGATAGCCACA
* * *
48978187 AAGGCTTCCTTTAATAGTGATAGCCATA
1 AAGGCTTCCTTTAACAGAGATAGCCACA
* * *
48978215 AAGGCTTACTTTTACAAAGATAGCCACGA
1 AAGGCTTCCTTTAACAGAGATAGCCAC-A
*
48978244 AA-ACTTCCTTTAACAGAGATAGCCACA
1 AAGGCTTCCTTTAACAGAGATAGCCACA
48978271 AAGGCTTCCTTT--CAGAGATAGCCACA
1 AAGGCTTCCTTTAACAGAGATAGCCACA
48978297 AAGGCTTCCATTT---AGAGATAGCCACA
1 AAGGCTTCC-TTTAACAGAGATAGCCACA
*
48978323 AACGCTT
1 AAGGCTT
48978330 GCTTAGATTG
Statistics
Matches: 284, Mismatches: 45, Indels: 28
0.80 0.13 0.08
Matches are distributed among these distances:
26 45 0.16
27 41 0.14
28 93 0.33
29 104 0.37
30 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (28 bp):
AAGGCTTCCTTTAACAGAGATAGCCACA
Found at i:48978293 original size:26 final size:27
Alignment explanation
Indices: 48977898--48978329 Score: 254
Period size: 28 Copynumber: 15.5 Consensus size: 27
48977888 TTCAAATTTT
* *
48977898 GCCACAAAGGCGTTCCTTTCCAAAGATA
1 GCCACAAAGGC-TTCCTTTACAGAGATA
* * * * *
48977926 GCCACAGAGGTTTTCCTTT-TAGAGTCTC
1 GCCACAAAGG-CTTCCTTTACAGAG-ATA
** * * *
48977954 GCCAGGAAGGCATCCTTTTAACAAAGATT
1 GCCACAAAGGCTTCC-TTT-ACAGAGATA
* * *
48977983 TCCAC-AAGGTCTTCATTTAACTGAGATA
1 GCCACAAAGG-CTTCCTTT-ACAGAGATA
* * *
48978011 GCCACAAAGACATCTTTTTAACAGAGATA
1 GCCACAAAGGCTTC-CTTT-ACAGAGATA
* * * *
48978040 GCCATAAAGACTTCGTTATAACAGAGGTCA
1 GCCACAAAGGCTTCCTT-T-ACAGAGAT-A
*
48978070 -TCACAAAGGCTTCCTTATAACAGAGATCA
1 GCCACAAAGGCTTCCTT-T-ACAGAGAT-A
48978099 -CCACAAAGGCTTCCTTATAACAGAGAT-
1 GCCACAAAGGCTTCCTT-T-ACAGAGATA
* ** *
48978126 TCCAACAAAGTTTTCCTTTACAGGGATA
1 GCC-ACAAAGGCTTCCTTTACAGAGATA
* *
48978154 GCCACAAAGGATT-TTTTAACAGAGATA
1 GCCACAAAGGCTTCCTTT-ACAGAGATA
* *
48978181 GCCACAAAGGCTTCCTTTAATAGTGATA
1 GCCACAAAGGCTTCCTTT-ACAGAGATA
* * *
48978209 GCCATAAAGGCTTACTTTTACAAAGATA
1 GCCACAAAGGCTT-CCTTTACAGAGATA
*
48978237 GCCACGAAA-ACTTCCTTTAACAGAGATA
1 GCCAC-AAAGGCTTCCTTT-ACAGAGATA
48978265 GCCACAAAGGCTTCCTTT-CAGAGATA
1 GCCACAAAGGCTTCCTTTACAGAGATA
48978291 GCCACAAAGGCTTCCATTT--AGAGATA
1 GCCACAAAGGCTTCC-TTTACAGAGATA
*
48978317 GCCACAAACGCTT
1 GCCACAAAGGCTT
48978330 GCTTAGATTG
Statistics
Matches: 324, Mismatches: 60, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
26 45 0.14
27 51 0.16
28 112 0.35
29 112 0.35
30 4 0.01
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (27 bp):
GCCACAAAGGCTTCCTTTACAGAGATA
Found at i:48997248 original size:21 final size:20
Alignment explanation
Indices: 48997199--48997258 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
48997189 GGTGAACCGG
48997199 TTTTTA-TAAATTTTTAATA
1 TTTTTATTAAATTTTTAATA
48997218 TATTTT-TTAAATCTTTT-ATGA
1 T-TTTTATTAAAT-TTTTAAT-A
*
48997239 TTTTTATTAATTTATTTAAT
1 TTTTTATTAAATT-TTTAAT
48997259 TTAAAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
19 1 0.03
20 16 0.48
21 14 0.42
22 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTATTAAATTTTTAATA
Found at i:48997999 original size:18 final size:18
Alignment explanation
Indices: 48997976--48998016 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
48997966 TTACAAAATA
**
48997976 AAAATATATAACCTTTTT
1 AAAATATATAAAATTTTT
48997994 AAAATATATAAAATTTTT
1 AAAATATATAAAATTTTT
48998012 AAAAT
1 AAAAT
48998017 TTTCAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATATATAAAATTTTT
Found at i:49001138 original size:6 final size:6
Alignment explanation
Indices: 49001129--49001225 Score: 59
Period size: 6 Copynumber: 15.7 Consensus size: 6
49001119 TAATGAAATC
* ** * * **
49001129 GAAAAA GAAAAC GAAAAA GAAAAA GAAATT GTAAAA GAATAA GAAATC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
** * * *
49001177 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAA
49001226 TTAAGATTGA
Statistics
Matches: 64, Mismatches: 24, Indels: 6
0.68 0.26 0.06
Matches are distributed among these distances:
6 53 0.83
7 7 0.11
8 4 0.06
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (6 bp):
GAAAAA
Found at i:49001150 original size:18 final size:18
Alignment explanation
Indices: 49001129--49001225 Score: 68
Period size: 18 Copynumber: 5.2 Consensus size: 18
49001119 TAATGAAATC
49001129 GAAAAAGAAAACGAAAAA
1 GAAAAAGAAAACGAAAAA
** *
49001147 GAAAAAGAAATTGTAAAA
1 GAAAAAGAAAACGAAAAA
* *
49001165 GAATAAGAAATCGAAAAA
1 GAAAAAGAAAACGAAAAA
** * * *
49001183 GTGAGAGAAAAAGAAAAT
1 GAAAAAGAAAACGAAAAA
*
49001201 GAAGAAAAGAAAATTGAAAAA
1 G-A-AAAAGAAAA-CGAAAAA
49001222 GAAA
1 GAAA
49001226 TTAAGATTGA
Statistics
Matches: 58, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
18 42 0.72
19 2 0.03
20 8 0.14
21 6 0.10
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
GAAAAAGAAAACGAAAAA
Found at i:49001256 original size:16 final size:18
Alignment explanation
Indices: 49001235--49001273 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
49001225 ATTAAGATTG
49001235 AGAAAAA-A-ATTGAAAA
1 AGAAAAAGATATTGAAAA
*
49001251 AGAAAAAGATGTTGAAAA
1 AGAAAAAGATATTGAAAA
49001269 AGAAA
1 AGAAA
49001274 CGAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (18 bp):
AGAAAAAGATATTGAAAA
Found at i:49003464 original size:20 final size:20
Alignment explanation
Indices: 49003428--49003486 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
49003418 TTTTAGCTTA
*
49003428 ATTCCAGCTCCAA-TCAGCTC
1 ATTCAAGCT-CAATTCAGCTC
*
49003448 ATTTAAGCTCAATTCAGCTC
1 ATTCAAGCTCAATTCAGCTC
* *
49003468 ATTCGAGCTCAATTTAGCT
1 ATTCAAGCTCAATTCAGCT
49003487 TTCTTCCAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (20 bp):
ATTCAAGCTCAATTCAGCTC
Found at i:49009255 original size:15 final size:14
Alignment explanation
Indices: 49009234--49009269 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
49009224 ATAATCCTTA
*
49009234 ATAATTATCTTAAT
1 ATAATTATCCTAAT
49009248 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
49009263 ATAATTA
1 ATAATTA
49009270 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:49014007 original size:29 final size:29
Alignment explanation
Indices: 49013974--49014045 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
49013964 CAATTCTAAT
* *
49013974 AATAAAAAAATAAATATAATACT-AATAA
1 AATAAATAAATAAATATAATAATAAATAA
49014002 CAAT-AATAAATAAAATATAATAATAAATAA
1 -AATAAATAAAT-AAATATAATAATAAATAA
49014032 AATAAATAAATAAA
1 AATAAATAAATAAA
49014046 AAGGAAGGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 6 0.16
29 20 0.53
30 12 0.32
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (29 bp):
AATAAATAAATAAATATAATAATAAATAA
Found at i:49014021 original size:20 final size:17
Alignment explanation
Indices: 49013970--49014045 Score: 72
Period size: 17 Copynumber: 4.6 Consensus size: 17
49013960 AACACAATTC
49013970 TAATAATAAA-AAAATA
1 TAATAATAAATAAAATA
*
49013986 -AAT-AT-AATACTAATAA
1 TAATAATAAATA-AAAT-A
*
49014002 CAATAATAAATAAAATA
1 TAATAATAAATAAAATA
49014019 TAATAATAAATAAAATA
1 TAATAATAAATAAAATA
49014036 -AATAAATAAA
1 TAAT-AATAAA
49014046 AAGGAAGGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
13 2 0.04
14 3 0.06
15 6 0.12
16 4 0.08
17 26 0.52
18 5 0.10
19 4 0.08
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
TAATAATAAATAAAATA
Found at i:49014037 original size:9 final size:9
Alignment explanation
Indices: 49013974--49014045 Score: 51
Period size: 9 Copynumber: 7.7 Consensus size: 9
49013964 CAATTCTAAT
49013974 AATAAA-AA
1 AATAAATAA
*
49013982 AATAAATAT
1 AATAAATAA
49013991 AATACTAATAA
1 AATA--AATAA
49014002 CAAT-AATAA
1 -AATAAATAA
*
49014011 ATAAAATATAA
1 A-ATAA-ATAA
49014022 TAATAAATAA
1 -AATAAATAA
49014032 AATAAAT-A
1 AATAAATAA
49014040 AATAAA
1 AATAAA
49014046 AAGGAAGGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
8 14 0.27
9 18 0.35
10 5 0.10
11 11 0.21
12 4 0.08
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (9 bp):
AATAAATAA
Found at i:49017854 original size:20 final size:20
Alignment explanation
Indices: 49017825--49017868 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
49017815 ATTAAAATGT
* *
49017825 AAAA-ATTAAATTAGAAACA
1 AAAATATTAAAATAAAAACA
*
49017844 AAAATATTAAAATAAAAATA
1 AAAATATTAAAATAAAAACA
49017864 AAAAT
1 AAAAT
49017869 GGCTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATATTAAAATAAAAACA
Found at i:49020090 original size:33 final size:33
Alignment explanation
Indices: 49020036--49020115 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
49020026 ACTTACCTCA
* *
49020036 TGTTTACTGTCTCAGGAGACTTTA-TCTGTTTCG
1 TGTTTACTGTCCCAGGAGAC-TTACTCTATTTCG
* *
49020069 TGTTTACTATCCCAGTG-GACTTACTCTATTTTG
1 TGTTTACTGTCCCAG-GAGACTTACTCTATTTCG
49020102 TGTTTACTGTCCCA
1 TGTTTACTGTCCCA
49020116 ACAGACTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 3 0.08
33 36 0.90
34 1 0.03
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.45
Consensus pattern (33 bp):
TGTTTACTGTCCCAGGAGACTTACTCTATTTCG
Found at i:49020123 original size:33 final size:33
Alignment explanation
Indices: 49020036--49020132 Score: 88
Period size: 33 Copynumber: 2.9 Consensus size: 33
49020026 ACTTACCTCA
* * *
49020036 TGTTTACTGTCTCAGGAGACTTTA-TCTGTTTCG
1 TGTTTACTGTCCCAGCAGAC-TTACTCTATTTCG
* ** *
49020069 TGTTTACTATCCCAGTGGACTTACTCTATTTTG
1 TGTTTACTGTCCCAGCAGACTTACTCTATTTCG
*
49020102 TGTTTACTGTCCCAACAGACTTCATCTCTAT
1 TGTTTACTGTCCCAGCAGACTT-A-CTCTAT
49020133 GGATGCCATG
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
32 3 0.06
33 41 0.80
34 1 0.02
35 6 0.12
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTTTACTGTCCCAGCAGACTTACTCTATTTCG
Found at i:49034629 original size:16 final size:16
Alignment explanation
Indices: 49034608--49034638 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49034598 GTTTCACTTT
49034608 GACTGCATAGCATTTA
1 GACTGCATAGCATTTA
*
49034624 GACTGCATGGCATTT
1 GACTGCATAGCATTT
49034639 CGTTATAGAA
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:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (16 bp):
GACTGCATAGCATTTA
Found at i:49038034 original size:13 final size:13
Alignment explanation
Indices: 49037996--49038026 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
49037986 AAGTGATGTG
49037996 GAAAATGAAAAGAT
1 GAAAATGAAAA-AT
49038010 GAAAATGAAAAAT
1 GAAAATGAAAAAT
49038023 GAAA
1 GAAA
49038027 TTGTAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (13 bp):
GAAAATGAAAAAT
Found at i:49039566 original size:132 final size:132
Alignment explanation
Indices: 49039386--49040684 Score: 1867
Period size: 132 Copynumber: 9.9 Consensus size: 132
49039376 TAGACAGCGA
* * *
49039386 AGCAGATCGAAGATGG-TGAATTTTACCTCCCT-ATGGTTACAGTAGAGTACATTGAAGCCAGTA
1 AGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGA-GGTTACAGTGGAGTACATTGAAGCCAGTA
* **
49039449 ATTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
64 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTA
49039514 GTGG
129 GTGG
* * * * *
49039518 AGCAGATCGAATG-TGGCAGATTTTACCTCCTTGTGGTTACAGTGGAGTACAATGAAGCCAGCAA
1 AGCAGATC-AAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* *
49039582 TTCTACTTCCCTGAGTAGCAGTGG---A-A-T--AGATTTCAGATCTTACCTCCCTAAGCAGTAG
65 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAG
49039640 TGG
130 TGG
* *
49039643 AGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
49039708 TCTA-TCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCTAAGCAGTAG
66 TCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAG
49039772 TGG
130 TGG
* * * *
49039775 AGCAGATCAAGGATGGCGGATTTTACCTCCTTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* **
49039840 TCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAGT
49039905 GG
131 GG
* * * *
49039907 GGCAGATCAAAGATGG-TGAATTTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 AGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
*
49039971 TTCTA-TCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTA
65 TTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTA
49040035 GTGG
129 GTGG
49040039 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
49040104 TCTA-TCTCCCAGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCACTAAGCAGTAG
66 TCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAG
49040168 TGG
130 TGG
* ** * *
49040171 AGCAGATCAAGGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * **
49040236 TCTACTTCCCTAGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAGT
49040301 GG
131 GG
* * * *
49040303 GGCAGATCAAAGATGG-TGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAA
1 AGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
49040367 TTCTA-TCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTA
65 TTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTA
49040431 GTGG
129 GTGG
* * * *
49040435 AGCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTGCATTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* **
49040500 TCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAGT
49040565 GG
131 GG
* * * *
49040567 GGCAGATCAAAGATGG-TGAATTTTACCTCCCTGTGGATACAGTGGAGTACATTGAAGCCAGTAA
1 AGCAGATCAAAGATGGCAG-ATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * *
49040631 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTGCAGATCTTATCTCC
65 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCC
49040685 TTGAAGTTGC
Statistics
Matches: 1051, Mismatches: 94, Indels: 44
0.88 0.08 0.04
Matches are distributed among these distances:
124 4 0.00
125 104 0.10
127 1 0.00
128 2 0.00
129 2 0.00
130 1 0.00
131 5 0.00
132 924 0.88
133 8 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (132 bp):
AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAGT
GG
Found at i:49039994 original size:43 final size:44
Alignment explanation
Indices: 49039946--49040530 Score: 167
Period size: 44 Copynumber: 13.3 Consensus size: 44
49039936 CCTGTGGTTA
* *
49039946 CAGTGGAGTACATTGAAGCCAGTA-ATTCTATCTCCCTAGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAGATTCTACCTCCCTAGGCAG
* * *
49039989 CAGTGGAATAGATTGAAG--ATTTCAGA-TCTTACCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAGCCA-GT-AGATTC-TACCTCCCTAGGCAG
* * ** *** * * *
49040033 TAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTA-
1 CAGTGGAGTAGATTGAAGCCAGTAGATTCTACCTCCCT-AGG-CAG
* *
49040078 CAGTGGAGTACATTGAAGCCAGTA-ATTCTATCTCCC-AGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAGATTCTACCTCCCTA-GGCAG
* * * *
49040121 CAGTGGAATAGATTGAAG--ATTTCAGA-TCTTACCTCACTAAGCAG
1 CAGTGGAGTAGATTGAAGCCA-GT-AGATTC-TACCTCCCTAGGCAG
* * * * * * **
49040165 TAGTGGAGCAGA-TCAAG-GATGGTGGATTTTACCTCCCTGAGGTTG
1 CAGTGGAGTAGATTGAAGCCA--GTAGATTCTACCTCCCT-AGGCAG
*
49040210 CAGTGGAGTAGATTGAAGCCAGTA-ATTCTACTTCCCTAGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAGATTCTACCTCCCTAGGCAG
* * * ** *
49040253 CAGTGGAATAGATTAAAG--ATTTCAGA-TCTTGTCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAGCCA-GT-AGATTC-TACCTCCCTAGGCAG
* * * ** *** * * *
49040297 TAGTGGGGCAGATCAAAGATGGT-GAATTTTACCTCCCTGTGGTTA-
1 CAGTGGAGTAGATTGAAGCCAGTAG-ATTCTACCTCCCT-AGG-CAG
* * * *
49040342 CAGTGGAGTACATTGAAGCTAGTA-ATTCTATCTCCCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAGATTCTACCTCCCTAGGCAG
* * *
49040385 CAGTGGAATAGATTGAAG--ATTTCAGA-TCTTACCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAGCCA-GT-AGATTC-TACCTCCCTAGGCAG
* * * * ** * **
49040429 TAGTGGAGCAGA-TCAAG-GATGGCGGATTTTACCTCCCTGAGGTTG
1 CAGTGGAGTAGATTGAAGCCA--GTAGATTCTACCTCCCT-AGGCAG
* * * *
49040474 CATTGGAGTACATTGAAGCCAGTA-ATTCTACTTCCCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAGATTCTACCTCCCTAGGCAG
*
49040517 CAGTGGAATAGATT
1 CAGTGGAGTAGATT
49040531 AAAGATTTCA
Statistics
Matches: 377, Mismatches: 121, Indels: 88
0.64 0.21 0.15
Matches are distributed among these distances:
41 4 0.01
42 7 0.02
43 107 0.28
44 180 0.48
45 67 0.18
46 10 0.03
47 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (44 bp):
CAGTGGAGTAGATTGAAGCCAGTAGATTCTACCTCCCTAGGCAG
Found at i:49040038 original size:44 final size:44
Alignment explanation
Indices: 49039609--49040441 Score: 208
Period size: 44 Copynumber: 18.9 Consensus size: 44
49039599 GCAGTGGAAT
* * **
49039609 AGATTTCAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAA
1 AGATGTCAGATCTTACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* * * *
49039653 AGATGACAGATTTTACCTCCCTGAG--GTTACAGTGGAGTACATTGA
1 AGATGTCAGATCTTACCTCCCTAAGCAG-T--AGTGGAGTAGATTGA
* * ** * * *
49039698 AGCTAGT-A-AT-TCTATCTCCCTGGGCAGCAATGGAATAGATTGA
1 AGAT-GTCAGATCT-TACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* * * *
49039741 AGATTTCAGATATTACCTCCCTAAGCAGTAGTGGAGCAGA-TCA
1 AGATGTCAGATCTTACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* * * * * ** * *
49039784 AGGATGGCGGATTTTACCTCCTTGAGGTTGCAGTGGAGTACATTGA
1 A-GATGTCAGATCTTACCTCCCT-AAGCAGTAGTGGAGTAGATTGA
* ** * * *
49039830 AGCCA-GT-A-AT-TCTACTTCCCTGGGCAGCAGTGGAATAGATTAA
1 AG--ATGTCAGATCT-TACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* ** * * **
49039873 AGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAA
1 AGATGTCAGATCTTACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* * * ** *
49039917 AGATGGTGA-ATTTTACCTTCCT--GTGGTTACAGTGGAGTACATTGA
1 AGAT-GTCAGATCTTACCTCCCTAAGCAG-T--AGTGGAGTAGATTGA
* * * *
49039962 AGCCA-GT-A-AT-TCTATCTCCCTAGGCAGCAGTGGAATAGATTGA
1 AG--ATGTCAGATCT-TACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* * **
49040005 AGATTTCAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAA
1 AGATGTCAGATCTTACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* * * *
49040049 AGATGGCAGATTTTACCTCCCTGAG--GTTACAGTGGAGTACATTGA
1 AGATGTCAGATCTTACCTCCCTAAGCAG-T--AGTGGAGTAGATTGA
* * * *
49040094 AGCCA-GT-A-AT-TCTATCTCCC-AGGGCAGCAGTGGAATAGATTGA
1 AG--ATGTCAGATCT-TACCTCCCTA-AGCAGTAGTGGAGTAGATTGA
* * * *
49040137 AGATTTCAGATCTTACCTCACTAAGCAGTAGTGGAGCAGA-TCA
1 AGATGTCAGATCTTACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* * * ** *
49040180 AGGATGGT-GGATTTTACCTCCCTGAGGTTGCAGTGGAGTAGATTGA
1 A-GAT-GTCAGATCTTACCTCCCT-AAGCAGTAGTGGAGTAGATTGA
* * * * *
49040226 AGCCA-GT-A-AT-TCTACTTCCCTAGGCAGCAGTGGAATAGATTAA
1 AG--ATGTCAGATCT-TACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* ** * * **
49040269 AGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAA
1 AGATGTCAGATCTTACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* * ** *
49040313 AGATGGTGA-ATTTTACCTCCCT--GTGGTTACAGTGGAGTACATTGA
1 AGAT-GTCAGATCTTACCTCCCTAAGCAG-T--AGTGGAGTAGATTGA
* * ** * *
49040358 AGCTAGT-A-AT-TCTATCTCCCTGGGCAGCAGTGGAATAGATTGA
1 AGAT-GTCAGATCT-TACCTCCCTAAGCAGTAGTGGAGTAGATTGA
* *
49040401 AGATTTCAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGAT
1 AGATGTCAGATCTTACCTCCCTAAGCAGTAGTGGAGTAGAT
49040442 CAAGGATGGC
Statistics
Matches: 557, Mismatches: 164, Indels: 136
0.65 0.19 0.16
Matches are distributed among these distances:
41 4 0.01
42 12 0.02
43 121 0.22
44 302 0.54
45 99 0.18
46 15 0.03
47 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
AGATGTCAGATCTTACCTCCCTAAGCAGTAGTGGAGTAGATTGA
Found at i:49040175 original size:396 final size:395
Alignment explanation
Indices: 49039386--49040684 Score: 2068
Period size: 396 Copynumber: 3.3 Consensus size: 395
49039376 TAGACAGCGA
*
49039386 AGCAGATCGAA-GATGGTGAATTTTACCTCCCT-ATGGTTACAGTAGAGTACATTGAAGCCAGTA
1 AGCAGATC-AAGGATGGTGAATTTTACCTCCCTGA-GGTTACAGTGGAGTACATTGAAGCCAGTA
*
49039449 ATTCTACTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
64 ATTCTACTTCCCTAGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
* * * *
49039514 GTGGAGCAGATCGAATG-TGG-CAGATTTTACC-TCCTTGTGGTTACAGTGGAGTACAATGAAGC
129 GTGGGGCAGATC-AAAGATGGTGA-ATTTTACCTTCC-TGTGGTTACAGTGGAGTACATTGAAGC
* *
49039576 CAGCAATTCTA-CTTCCCTGAGTAGCAGTGG---A-A-T--AGATTTCAGATCTTACCTCCCTAA
191 CAGTAATTCTATC-TCCCTG-GCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAA
*
49039633 GCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGA
254 GCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGA
* * *
49039698 AGCTAGTAATTCTATCTCCCTGGGCAGCAATGGAATAGATTGAAGATTTCAGATATTACCTCCCT
319 AGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCT
49039763 AAGCAGTAGTGG
384 AAGCAGTAGTGG
* * * *
49039775 AGCAGATCAAGGATGGCGGATTTTACCTCCTTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAGGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
49039840 TCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTAGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
49039905 GGGGCAGATCAAAGATGGTGAATTTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
131 GGGGCAGATCAAAGATGGTGAATTTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
49039970 ATTCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTA
196 ATTCTATCTCCCT-GGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTA
49040035 GTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAG
260 GTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAG
* *
49040100 TAATTCTATCTCCCAGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCACTAAGCAG
325 TAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAG
49040165 TAGTGG
390 TAGTGG
* * *
49040171 AGCAGATCAAGGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGCCAGTAAT
1 AGCAGATCAAGGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
49040236 TCTACTTCCCTAGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTAGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
* *
49040301 GGGGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTA
131 GGGGCAGATCAAAGATGGTGAATTTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
49040366 ATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTA
196 ATTCTATCTCCCT-GGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTA
* * * *
49040431 GTGGAGCAGATCAAGGATGGCGGATTTTACCTCCCTGAGGTTGCATTGGAGTACATTGAAGCCAG
260 GTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAG
* **
49040496 TAATTCTA-CTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCA
325 TAATTCTATC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCA
49040560 GTAGTGG
389 GTAGTGG
* * * *
49040567 GGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGATACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCAAGGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
49040632 TCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATTGCAGATCTTATCTCC
66 TCTACTTCCCTAGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCC
49040685 TTGAAGTTGC
Statistics
Matches: 850, Mismatches: 45, Indels: 23
0.93 0.05 0.03
Matches are distributed among these distances:
388 5 0.01
389 188 0.22
390 7 0.01
392 1 0.00
393 1 0.00
394 1 0.00
395 1 0.00
396 646 0.76
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (395 bp):
AGCAGATCAAGGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTAGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
GGGGCAGATCAAAGATGGTGAATTTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
ATTCTATCTCCCTGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGTAG
TGGAGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGT
AATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGCAGT
AGTGG
Found at i:49043926 original size:32 final size:32
Alignment explanation
Indices: 49043890--49043953 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
49043880 AAACTTTATC
49043890 AATCTATCAACTATCACCCAAATTGAATTCTT
1 AATCTATCAACTATCACCCAAATTGAATTCTT
49043922 AATCTATCAACTATCACCCAAATTGAATTCTT
1 AATCTATCAACTATCACCCAAATTGAATTCTT
49043954 CTTTCTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (32 bp):
AATCTATCAACTATCACCCAAATTGAATTCTT
Found at i:49048649 original size:41 final size:41
Alignment explanation
Indices: 49048585--49048697 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
49048575 CCTTTCGGGT
* * *
49048585 CTTTAGCGGCGTTTTTAAAAAAGCGTCGCTAATGCT-GGTGA
1 CTTTAGCGGCGTTTTT-GAAAAGCGCCGCTAATGCTGGGGGA
49048626 CTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTGGGGGA
1 CTTTAGCGGCGTTTTTGA-AAAGCGCCGCTAATGCTGGGGGA
*
49048668 -TTTAGCAGCG-TTTTGAAAAGGCGCCGCTAA
1 CTTTAGCGGCGTTTTTGAAAA-GCGCCGCTAA
49048698 AATATTTTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
39 3 0.05
40 17 0.26
41 41 0.63
42 4 0.06
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTGGGGGA
Found at i:49049107 original size:15 final size:15
Alignment explanation
Indices: 49049087--49049120 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
49049077 TGGGATTTAA
*
49049087 GGTTTAAGGGTTATG
1 GGTTTAAGGGTTAGG
*
49049102 GGTTTATGGGTTAGG
1 GGTTTAAGGGTTAGG
49049117 GGTT
1 GGTT
49049121 AGACGTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:49049363 original size:15 final size:15
Alignment explanation
Indices: 49049343--49049406 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
49049333 GCTATTTAAA
49049343 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
49049358 GGTTTAGGGATTATG
1 GGTTTATGGATTATG
* * *
49049373 AGTTTAAGGTTTA-G
1 GGTTTATGGATTATG
49049387 GGTTTAT-GATTTAT-
1 GGTTTATGGA-TTATG
49049401 GGTTTA
1 GGTTTA
49049407 AGGGTTGGGG
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.03
14 15 0.38
15 24 0.60
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:49049406 original size:28 final size:28
Alignment explanation
Indices: 49049368--49049448 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
49049358 GGTTTAGGGA
*
49049368 TTATGAGTTTAAGGTTTAGGGTTTATGAT
1 TTATG-GTTTAAGGTTTAGGGTTTAAGAT
* * *
49049397 TTATGGTTTAAGGGTTGGGGTTCAAGAT
1 TTATGGTTTAAGGTTTAGGGTTTAAGAT
* *
49049425 TTAAGG-TTAGGGGTTTAGGGTTTA
1 TTATGGTTTA-AGGTTTAGGGTTTA
49049449 GTTTAATTAG
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
27 3 0.07
28 34 0.81
29 5 0.12
ACGTcount: A:0.22, C:0.01, G:0.33, T:0.43
Consensus pattern (28 bp):
TTATGGTTTAAGGTTTAGGGTTTAAGAT
Found at i:49049410 original size:22 final size:21
Alignment explanation
Indices: 49049343--49049412 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 21
49049333 GCTATTTAAA
49049343 GGTTTATGGA-TTATGGGTTTAG
1 GGTTTAT-GATTTAT-GGTTTAG
* *
49049365 GGATTATGAGTTTAAGGTTTAG
1 GGTTTATGA-TTTATGGTTTAG
49049387 GGTTTATGATTTATGGTTTAAG
1 GGTTTATGATTTATGGTTT-AG
49049409 GGTT
1 GGTT
49049413 GGGGTTCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 11 0.27
22 27 0.66
23 3 0.07
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (21 bp):
GGTTTATGATTTATGGTTTAG
Found at i:49049448 original size:21 final size:21
Alignment explanation
Indices: 49049374--49049448 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
49049364 GGGATTATGA
**
49049374 GTTTAAGGTTT-AGGGTTTATG
1 GTTTAAGGTTTAAGGG-TTGGG
* *
49049395 ATTTATGGTTTAAGGGTTGGG
1 GTTTAAGGTTTAAGGGTTGGG
* *
49049416 GTTCAAGATTTAA-GGTTAGGG
1 GTTTAAGGTTTAAGGGTT-GGG
*
49049437 GTTTAGGGTTTA
1 GTTTAAGGTTTA
49049449 GTTTAATTAG
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 4 0.10
21 33 0.80
22 4 0.10
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.43
Consensus pattern (21 bp):
GTTTAAGGTTTAAGGGTTGGG
Found at i:49051747 original size:193 final size:191
Alignment explanation
Indices: 49051445--49051800 Score: 459
Period size: 193 Copynumber: 1.9 Consensus size: 191
49051435 ATCTATAATG
* * * **
49051445 GGTTTAAGTCATGGTTTTCATTTGGAGCTTTGTGATTAAAACACTATTATTACTTGAATGGAAAT
1 GGTTCAAGTCATGGTTTTCATTTGGAACTTTGTGATTAAAACACAACAATTACTTGAATGGAAAT
* * * * * * * * *
49051510 GCATTTGCATTTGTGTATCCTGCAATGCTTTTTAATTGAACTTTGGGGTTGGAATTGTTATTAGG
66 GCACTTGCATTTGTATATCCTACAAAGCTTCTTAAGTCAACTTTGGAGTTGAAATTGTTATTAGG
*
49051575 AAGTAATTGATG-TTTTTATGTTGATGTTAATGAATACAATAGACTAAGTTGAATTTTTTATA
131 AAGTAATTGATGATTTTT-T-ATGATGTTAATGAATACAATAGACTAAGTTGAATTTTTTATA
*
49051637 GGTTCAAGTCATTGGTTTTCATTT-GAACTTTGTGATTACAACACAACAATTTACTTGAATGGAA
1 GGTTCAAGTCA-TGGTTTTCATTTGGAACTTTGTGATTAAAACACAACAA-TTACTTGAATGGAA
**
49051701 ATGCACTTGTGTTT-TCATATCCTACAAAGCTTCCTT-AGTCAACTTTGGAGTTGAAATTGTTAT
64 ATGCACTTGCATTTGT-ATATCCTACAAAGCTT-CTTAAGTCAACTTTGGAGTTGAAATTGTTAT
*
49051764 TAGGATGTAATTGATGATTTTTTATGATGTTAATGAA
127 TAGGAAGTAATTGATGATTTTTTATGATGTTAATGAA
49051801 CATAATAATA
Statistics
Matches: 140, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
192 44 0.31
193 89 0.64
194 7 0.05
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (191 bp):
GGTTCAAGTCATGGTTTTCATTTGGAACTTTGTGATTAAAACACAACAATTACTTGAATGGAAAT
GCACTTGCATTTGTATATCCTACAAAGCTTCTTAAGTCAACTTTGGAGTTGAAATTGTTATTAGG
AAGTAATTGATGATTTTTTATGATGTTAATGAATACAATAGACTAAGTTGAATTTTTTATA
Found at i:49052992 original size:87 final size:86
Alignment explanation
Indices: 49052819--49053067 Score: 286
Period size: 87 Copynumber: 2.9 Consensus size: 86
49052809 TTTTTGTTAA
* * * * * * *
49052819 CGCCGCTAAAGGA-CATGATCTTTAGCGACGTTTG-AGATAAAAGCGCCACTAAAGGTAATGATC
1 CGCCGCCAAA-GATCATGTTCTTTAGCGGCGTTTGTA-ATAAAAGCGCCGCTAAAGATCATGTTC
* *
49052882 TTTAGCGGCATTTGTGGGCAAAG
64 TTTAGCGGCATTTGTGAGAAAAG
*
49052905 CGCCGCCAAAGATCATGTTATTTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGATCATGTTCT
1 CGCCGCCAAAGATCATGTT-CTTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGATCATGTTCT
* * *
49052970 TTAGCTGCGTTTGTGATAAAAG
65 TTAGCGGCATTTGTGAGAAAAG
** * * * *
49052992 CGCCGTTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAATGATCATGTTCTA
1 CGCCGCCAAAGATCATGTTCTTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGATCATGTTCTT
49053057 TAGCGGCATTT
66 TAGCGGCATTT
49053068 TCCACATAAA
Statistics
Matches: 138, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
85 2 0.01
86 65 0.47
87 70 0.51
88 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (86 bp):
CGCCGCCAAAGATCATGTTCTTTAGCGGCGTTTGTAATAAAAGCGCCGCTAAAGATCATGTTCTT
TAGCGGCATTTGTGAGAAAAG
Found at i:49053051 original size:43 final size:43
Alignment explanation
Indices: 49052819--49053063 Score: 294
Period size: 43 Copynumber: 5.7 Consensus size: 43
49052809 TTTTTGTTAA
* * *
49052819 CGCCGCTAAAGGA-CATGATCTTTAGCGACGTTTGAGATAAAAG
1 CGCCGCTAAA-GATCATGTTCTTTAGCGGCGTTTGTGATAAAAG
* * * * * ***
49052862 CGCCACTAAAGGTAATGATCTTTAGCGGCATTTGTGGGCAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGATAAAAG
* * *
49052905 CGCCGCCAAAGATCATGTTATTTTAGCGGCGTTTGTAATAAAAG
1 CGCCGCTAAAGATCATGTT-CTTTAGCGGCGTTTGTGATAAAAG
*
49052949 CGCCGCTAAAGATCATGTTCTTTAGCTGCGTTTGTGATAAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGATAAAAG
* *
49052992 CGCCGTTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAG
1 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGATAAAAG
* *
49053035 CGCCGCTAATGATCATGTTCTATAGCGGC
1 CGCCGCTAAAGATCATGTTCTTTAGCGGC
49053064 ATTTTCCACA
Statistics
Matches: 169, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
42 1 0.01
43 132 0.78
44 36 0.21
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (43 bp):
CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGATAAAAG
Found at i:49053052 original size:130 final size:130
Alignment explanation
Indices: 49052819--49053053 Score: 330
Period size: 130 Copynumber: 1.8 Consensus size: 130
49052809 TTTTTGTTAA
49052819 CGCCGCTAAAGGACATGATCTTTAGCGACGTTTGAGATAAAAGCGCCACTAAAGGTAATGATCTT
1 CGCCGCTAAAGGACATGATCTTTAGCGACGTTTGAGATAAAAGCGCCACTAAAGGTAATGATCTT
* *
49052884 TAGCGGCATTTGTGGGCAAAGCGCCGCCAAAGATCATGTTATTTTAGCGGCGTTTGTAATAAAAG
66 TAGCGGCATTTGTGAGAAAAGCGCCGCCAAAGATCATGTTATTTTAGCGGCGTTTGTAATAAAAG
* * ** * *
49052949 CGCCGCTAAA-GATCATGTTCTTTAGCTG-CGTTTGTGATAAAAGCGCCGTTAAAGGTCATGTTC
1 CGCCGCTAAAGGA-CATGATCTTTAGC-GACGTTTGAGATAAAAGCGCCACTAAAGGTAATGATC
* * * *
49053012 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAATGATCATGTT
64 TTTAGCGGCATTTGTGAGAAAAGCGCCGCCAAAGATCATGTT
49053054 CTATAGCGGC
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
129 2 0.02
130 88 0.97
131 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (130 bp):
CGCCGCTAAAGGACATGATCTTTAGCGACGTTTGAGATAAAAGCGCCACTAAAGGTAATGATCTT
TAGCGGCATTTGTGAGAAAAGCGCCGCCAAAGATCATGTTATTTTAGCGGCGTTTGTAATAAAAG
Found at i:49063851 original size:30 final size:30
Alignment explanation
Indices: 49063815--49063872 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
49063805 GGAATTGAGA
*
49063815 AAAAGAAACAGAGAAAAGAAAACAAAAGGC
1 AAAAGAAACAAAGAAAAGAAAACAAAAGGC
* *
49063845 AAAAGAAAGAAAGAAAAGAAAAGAAAAG
1 AAAAGAAACAAAGAAAAGAAAACAAAAG
49063873 AAATAGAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (30 bp):
AAAAGAAACAAAGAAAAGAAAACAAAAGGC
Found at i:49063855 original size:4 final size:5
Alignment explanation
Indices: 49063826--49063880 Score: 60
Period size: 5 Copynumber: 10.8 Consensus size: 5
49063816 AAAGAAACAG
*
49063826 AGAAA AGAAA ACAAA AGGCAAA AG-AA AG-AA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA A-G-AAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
49063876 TAGAA
1 -AGAA
49063881 CGTAAGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
4 8 0.18
5 27 0.61
6 5 0.11
7 4 0.09
ACGTcount: A:0.75, C:0.04, G:0.20, T:0.02
Consensus pattern (5 bp):
AGAAA
Found at i:49068615 original size:27 final size:28
Alignment explanation
Indices: 49068562--49068621 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
49068552 AAAATAATTA
*
49068562 AAATTCAATATTTTAATAATTTAAGTAT
1 AAATTCAATATTTTAATAATTAAAGTAT
49068590 AAATT-AATTATTTT-ATAATTAAAGTAT
1 AAATTCAA-TATTTTAATAATTAAAGTAT
*
49068617 GAATT
1 AAATT
49068622 TCGACAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (28 bp):
AAATTCAATATTTTAATAATTAAAGTAT
Found at i:49069064 original size:21 final size:21
Alignment explanation
Indices: 49069040--49069095 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
49069030 ACAAGTCACA
49069040 TGGATGGTTTGGGCATGCATG
1 TGGATGGTTTGGGCATGCATG
*
49069061 TGGATGGTTTAGGCATGCATG
1 TGGATGGTTTGGGCATGCATG
*
49069082 TGGATGATTTGGGC
1 TGGATGGTTTGGGC
49069096 TCCTTTAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.16, C:0.09, G:0.41, T:0.34
Consensus pattern (21 bp):
TGGATGGTTTGGGCATGCATG
Found at i:49070271 original size:16 final size:18
Alignment explanation
Indices: 49070244--49070276 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
49070234 TAGAATTGGG
49070244 TTGAGAAAATTA-TTTAA
1 TTGAGAAAATTAGTTTAA
49070261 TTGAG-AAATTAGTTTA
1 TTGAGAAAATTAGTTTA
49070277 TTTAAATTAA
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:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAGTTTAA
Found at i:49076524 original size:15 final size:15
Alignment explanation
Indices: 49076486--49076524 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
49076476 TATTTGTTTC
*
49076486 TTTAATTTATTTTAG
1 TTTAATTTTTTTTAG
49076501 TTTAATTTTTTTTA-
1 TTTAATTTTTTTTAG
49076515 TTTAATTTTT
1 TTTAATTTTT
49076525 CACATAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTAATTTTTTTTAG
Found at i:49080486 original size:30 final size:32
Alignment explanation
Indices: 49080450--49080509 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 32
49080440 TCAAATACGA
49080450 AAAGAAAGGAAA-T-AAAAAA-AAAAGAAAGGG
1 AAAGAAA-GAAACTAAAAAAAGAAAAGAAAGGG
49080480 AAAGAAAGAAACTAGAAAAAAGAAAAGAAA
1 AAAGAAAGAAACTA-AAAAAAGAAAAGAAA
49080510 AGAAAAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 4 0.15
30 8 0.31
32 6 0.23
33 8 0.31
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.03
Consensus pattern (32 bp):
AAAGAAAGAAACTAAAAAAAGAAAAGAAAGGG
Found at i:49080503 original size:18 final size:17
Alignment explanation
Indices: 49080448--49080517 Score: 56
Period size: 19 Copynumber: 4.0 Consensus size: 17
49080438 TATCAAATAC
* *
49080448 GAAAAGAAAGGAAATAA
1 GAAAAGAAAAGAAAAAA
49080465 -AAAA-AAAAGAAAGGGAAA
1 GAAAAGAAAAGAAA---AAA
49080483 G-AAAGAAACTAGAAAAAA
1 GAAAAGAAA--AGAAAAAA
49080501 GAAAAGAAAAGAAAAAA
1 GAAAAGAAAAGAAAAAA
49080518 CTAATGTGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
15 7 0.16
16 4 0.09
17 8 0.19
18 9 0.21
19 10 0.23
21 5 0.12
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (17 bp):
GAAAAGAAAAGAAAAAA
Found at i:49080511 original size:28 final size:27
Alignment explanation
Indices: 49080467--49080520 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
49080457 GGAAATAAAA
* *
49080467 AAAAAAGAAAGGGAAAGAAAGAAACTAG
1 AAAAAAGAAAAGAAAAGAAA-AAACTAG
49080495 AAAAAAGAAAAGAAAAGAAAAAACTA
1 AAAAAAGAAAAGAAAAGAAAAAACTA
49080521 ATGTGAGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.04
Consensus pattern (27 bp):
AAAAAAGAAAAGAAAAGAAAAAACTAG
Found at i:49081268 original size:71 final size:71
Alignment explanation
Indices: 49081152--49081289 Score: 276
Period size: 71 Copynumber: 1.9 Consensus size: 71
49081142 CCACAAATGA
49081152 ATAAATCCATAAATAGATTCAAGATCTATTCTTCTTGGGTCTAGTAGATGTATTGACATTCTAGT
1 ATAAATCCATAAATAGATTCAAGATCTATTCTTCTTGGGTCTAGTAGATGTATTGACATTCTAGT
49081217 CAATAC
66 CAATAC
49081223 ATAAATCCATAAATAGATTCAAGATCTATTCTTCTTGGGTCTAGTAGATGTATTGACATTCTAGT
1 ATAAATCCATAAATAGATTCAAGATCTATTCTTCTTGGGTCTAGTAGATGTATTGACATTCTAGT
49081288 CA
66 CA
49081290 GTCACATCCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (71 bp):
ATAAATCCATAAATAGATTCAAGATCTATTCTTCTTGGGTCTAGTAGATGTATTGACATTCTAGT
CAATAC
Found at i:49089723 original size:38 final size:38
Alignment explanation
Indices: 49089662--49089755 Score: 125
Period size: 38 Copynumber: 2.5 Consensus size: 38
49089652 GGTGTATTAG
* * * * *
49089662 TGAATCCCGTGTGGCGTATTCTATAATGGCATATTTGG
1 TGAAGCCCATGTGGCGTAGTCTATAATGGCATATTCGA
* *
49089700 TGAGGCCCATGTGGTGTAGTCTATAATGGCATATTCGA
1 TGAAGCCCATGTGGCGTAGTCTATAATGGCATATTCGA
49089738 TGAAGCCCATGTGGCGTA
1 TGAAGCCCATGTGGCGTA
49089756 TTCTGTGATA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (38 bp):
TGAAGCCCATGTGGCGTAGTCTATAATGGCATATTCGA
Found at i:49092878 original size:23 final size:23
Alignment explanation
Indices: 49092850--49093261 Score: 216
Period size: 23 Copynumber: 17.6 Consensus size: 23
49092840 TTCACACCAA
*
49092850 AATTTGGACAGCGTATATACAAC
1 AATTTGGACAGCATATATACAAC
*
49092873 AATTTGGGCAGCATATATACAAC
1 AATTTGGACAGCATATATACAAC
* * * *
49092896 AAAATT-GAGCAGCATTTTTACACCAA
1 -AATTTGGA-CAGCATATATACA--AC
*
49092922 AAATTGGACAGCATATATACAAC
1 AATTTGGACAGCATATATACAAC
* * * *
49092945 AAATTGGGCAGCATATATATACC
1 AATTTGGACAGCATATATACAAC
* * * * *
49092968 AAATT-GAGCAACATTTTTACATCAA
1 AATTTGGA-CAGCATATATACA--AC
49092993 AATTT-GACAGCATATATACAAC
1 AATTTGGACAGCATATATACAAC
*
49093015 AATTTAGG-CAGCATATATATAAC
1 AATTT-GGACAGCATATATACAAC
* * * * *
49093038 AAATT-GAGCAACATTTTTACATCAA
1 AATTTGGA-CAGCATATATACA--AC
49093063 AATTT-GACAGCATATATACAAC
1 AATTTGGACAGCATATATACAAC
* *
49093085 AATTTAGG-CAGCATATATATACC
1 AATTT-GGACAGCATATATACAAC
* * * * *
49093108 AAATT-GAGCAACATTTTTACATC
1 AATTTGGA-CAGCATATATACAAC
*
49093131 AAAATTGGACAGCATATATACAAC
1 -AATTTGGACAGCATATATACAAC
*
49093155 AATTTAGG-CAGCATATATATAAC
1 AATTT-GGACAGCATATATACAAC
* * * * *
49093178 AAATT-GAGCAACATTTTTACATC
1 AATTTGGA-CAGCATATATACAAC
* *
49093201 AAAATTGGACAGCATATATATAAC
1 -AATTTGGACAGCATATATACAAC
*
49093225 AATTTAGG-CAGCATAAATACAAC
1 AATTT-GGACAGCATATATACAAC
* *
49093248 AAATTGGGCAGCAT
1 AATTTGGACAGCAT
49093262 TTAAGCATCA
Statistics
Matches: 296, Mismatches: 66, Indels: 54
0.71 0.16 0.13
Matches are distributed among these distances:
21 3 0.01
22 15 0.05
23 170 0.57
24 72 0.24
25 33 0.11
26 3 0.01
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.28
Consensus pattern (23 bp):
AATTTGGACAGCATATATACAAC
Found at i:49093006 original size:47 final size:47
Alignment explanation
Indices: 49092847--49093152 Score: 180
Period size: 47 Copynumber: 6.5 Consensus size: 47
49092837 ATTTTCACAC
* * * * * *
49092847 CAAAATTTGGACAGCGTATATACAACAATTTGGGCAGCATATATACAA
1 CAAAATTT-GACAGCATATATACACCAAATTGAGCAACATATATACAT
* * * *
49092895 CAAAA-TTGAGCAGCATTTTTACACCAAAAATTG-GACAGCATATATACAA
1 CAAAATTTGA-CAGCATATATACACC--AAATTGAG-CAACATATATACAT
* * * * *
49092944 C-AAATTGGGCAGCATATATATACCAAATTGAGCAACATTTTTACAT
1 CAAAATTTGACAGCATATATACACCAAATTGAGCAACATATATACAT
* * * * *
49092990 CAAAATTTGACAGCATATATACAAC-AATTTAGGCAGCATATATATAA
1 CAAAATTTGACAGCATATATACACCAAATTGA-GCAACATATATACAT
* * * * *
49093037 C-AAA-TTGAGCAACATTTTTACATCAAAATTTGA-CAGCATATATACA-
1 CAAAATTTGA-CAGCATATATACA-CCAAA-TTGAGCAACATATATACAT
* * * * *
49093083 -ACAATTTAGGCAGCATATATATACCAAATTGAGCAACATTTTTACAT
1 CAAAATTT-GACAGCATATATACACCAAATTGAGCAACATATATACAT
*
49093130 CAAAATTGGACAGCATATATACA
1 CAAAATTTGACAGCATATATACA
49093153 ACAATTTAGG
Statistics
Matches: 195, Mismatches: 45, Indels: 37
0.70 0.16 0.13
Matches are distributed among these distances:
45 8 0.04
46 53 0.27
47 80 0.41
48 29 0.15
49 25 0.13
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (47 bp):
CAAAATTTGACAGCATATATACACCAAATTGAGCAACATATATACAT
Found at i:49093275 original size:70 final size:70
Alignment explanation
Indices: 49092836--49093263 Score: 667
Period size: 70 Copynumber: 6.1 Consensus size: 70
49092826 AACTAGACAG
* * * * *
49092836 CATTTTCACACCAAAATTTGGACAGCGTATATACAACAATTTGGGCAGCATATATACAACAAAAT
1 CATTTTTACATCAAAA-TTGGACAGCATATATACAACAATTTAGGCAGCATATATATAAC-AAAT
*
49092901 TGAGCAG
64 TGAGCAA
* * * *
49092908 CATTTTTACACCAAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAAATT
1 CATTTTTACATC-AAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATT
49092973 GAGCAA
65 GAGCAA
*
49092979 CATTTTTACATCAAAATTTGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
1 CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
49093044 AGCAA
66 AGCAA
* *
49093049 CATTTTTACATCAAAATTTGACAGCATATATACAACAATTTAGGCAGCATATATATACCAAATTG
1 CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
49093114 AGCAA
66 AGCAA
49093119 CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
1 CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
49093184 AGCAA
66 AGCAA
* * *
49093189 CATTTTTACATCAAAATTGGACAGCATATATATAACAATTTAGGCAGCATAAATACAACAAATTG
1 CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
* *
49093254 GGCAG
66 AGCAA
49093259 CATTT
1 CATTT
49093264 AAGCATCAAA
Statistics
Matches: 336, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
70 261 0.78
71 21 0.06
72 50 0.15
73 4 0.01
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (70 bp):
CATTTTTACATCAAAATTGGACAGCATATATACAACAATTTAGGCAGCATATATATAACAAATTG
AGCAA
Found at i:49094017 original size:28 final size:28
Alignment explanation
Indices: 49093986--49094054 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
49093976 AATAAGTTCT
* *
49093986 CACACTTAGTGCTTAATAATCAATCTCG
1 CACACTTAGTGCTTAACAATCAAACTCG
* *
49094014 CACACTTAGTGCTTTACAATTAAACTCG
1 CACACTTAGTGCTTAACAATCAAACTCG
*
49094042 CACACTGAGTGCT
1 CACACTTAGTGCT
49094055 AATCTCATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (28 bp):
CACACTTAGTGCTTAACAATCAAACTCG
Found at i:49094141 original size:14 final size:15
Alignment explanation
Indices: 49094110--49094148 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
49094100 AAGCCAACAA
49094110 TTCAATACATCTTAT
1 TTCAATACATCTTAT
*
49094125 TTCAATA-ATCTTTT
1 TTCAATACATCTTAT
*
49094139 TTCACTACAT
1 TTCAATACAT
49094149 GTATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.49
Consensus pattern (15 bp):
TTCAATACATCTTAT
Found at i:49095342 original size:30 final size:30
Alignment explanation
Indices: 49095299--49095365 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
49095289 ATTTCAGGGG
* *
49095299 TCACACACTCGTGTGGCCAAGCCGTGTGCC
1 TCACACGCCCGTGTGGCCAAGCCGTGTGCC
*
49095329 TCACACGCCCGTGTGGCCAAGTCGTGTGCC
1 TCACACGCCCGTGTGGCCAAGCCGTGTGCC
49095359 TCACACG
1 TCACACG
49095366 ATTGAGACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.16, C:0.37, G:0.27, T:0.19
Consensus pattern (30 bp):
TCACACGCCCGTGTGGCCAAGCCGTGTGCC
Found at i:49096370 original size:18 final size:18
Alignment explanation
Indices: 49096344--49096417 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
49096334 ATTTCATATT
*
49096344 TCATATCTCATCTCATAA
1 TCATTTCTCATCTCATAA
49096362 TCATTTCTCATATTTCTCATTTCAA
1 TCATTTCTC--A--TCTCA--T-AA
49096387 T-ATTTTCTCATCTCATAA
1 TCA-TTTCTCATCTCATAA
49096405 TCATTTCTCATCT
1 TCATTTCTCATCT
49096418 TTTCCATTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 18
0.71 0.02 0.28
Matches are distributed among these distances:
18 21 0.46
19 2 0.04
20 1 0.02
21 5 0.11
22 5 0.11
23 1 0.02
24 2 0.04
25 9 0.20
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (18 bp):
TCATTTCTCATCTCATAA
Found at i:49096402 original size:43 final size:43
Alignment explanation
Indices: 49096349--49096432 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
49096339 ATATTTCATA
49096349 TCTCATCTCATAATCATTTCTCATA-TTTCTCATTTCAATATTT
1 TCTCATCTCATAATCATTTCTCATATTTTC-CATTTCAATATTT
* *
49096392 TCTCATCTCATAATCATTTCTCATCTTTTCCATTTCGATAT
1 TCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
49096433 CAATCACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 34 0.89
44 4 0.11
ACGTcount: A:0.24, C:0.25, G:0.01, T:0.50
Consensus pattern (43 bp):
TCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATATTT
Found at i:49101441 original size:6 final size:6
Alignment explanation
Indices: 49101430--49101491 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
49101420 CGTCGATTAG
*
49101430 TTATTT TTA--T TTAGTT TTATGTT TTA--T TTATTT TTATTT TTA-TT
1 TTATTT TTATTT TTATTT TTAT-TT TTATTT TTATTT TTATTT TTATTT
*
49101474 TTATTT TTATTG TTATTT
1 TTATTT TTATTT TTATTT
49101492 GTTTTTCTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 8 0.17
5 5 0.11
6 29 0.62
7 5 0.11
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:49101456 original size:17 final size:16
Alignment explanation
Indices: 49101430--49101496 Score: 82
Period size: 17 Copynumber: 4.1 Consensus size: 16
49101420 CGTCGATTAG
49101430 TTATTTTTATTTAGTT
1 TTATTTTTATTTAGTT
*
49101446 TTATGTTTTATTTATTT
1 TTAT-TTTTATTTAGTT
*
49101463 TTATTTTTATTTTATTT
1 TTATTTTTA-TTTAGTT
*
49101480 TTATTGTTATTT-GTT
1 TTATTTTTATTTAGTT
49101495 TT
1 TT
49101497 TCTTTTTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
15 4 0.09
16 12 0.26
17 30 0.65
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (16 bp):
TTATTTTTATTTAGTT
Found at i:49101468 original size:27 final size:26
Alignment explanation
Indices: 49101430--49101484 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 26
49101420 CGTCGATTAG
49101430 TTATTTTTA-TTTAGTTTTATGTTTTAT
1 TTATTTTTATTTTA-TTTTAT-TTTTAT
49101457 TTATTTTTATTTTTATTTTATTTTTAT
1 TTATTTTTA-TTTTATTTTATTTTTAT
49101484 T
1 T
49101485 GTTATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 16 0.62
28 6 0.23
29 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (26 bp):
TTATTTTTATTTTATTTTATTTTTAT
Found at i:49101472 original size:33 final size:33
Alignment explanation
Indices: 49101430--49101503 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
49101420 CGTCGATTAG
*
49101430 TTATTTTTA-TTTAGTTTTATGTTTTATTTATTT
1 TTATTTTTATTTTAGTTTTAT-TGTTATTTATTT
* *
49101463 TTATTTTTATTTTATTTTTATTGTTATTTGTTT
1 TTATTTTTATTTTAGTTTTATTGTTATTTATTT
*
49101496 TTCTTTTT
1 TTATTTTT
49101504 TGGATTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 26 0.72
34 10 0.28
ACGTcount: A:0.15, C:0.01, G:0.05, T:0.78
Consensus pattern (33 bp):
TTATTTTTATTTTAGTTTTATTGTTATTTATTT
Found at i:49101482 original size:23 final size:24
Alignment explanation
Indices: 49101430--49101491 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
49101420 CGTCGATTAG
*
49101430 TTATTTTTA--TTTAGTTTTATGT
1 TTATTTTTATTTTTATTTTTATGT
*
49101452 TT-TATTTATTTTTATTTTTAT-T
1 TTATTTTTATTTTTATTTTTATGT
*
49101474 TTATTTTTATTGTTATTT
1 TTATTTTTATTTTTATTT
49101492 GTTTTTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 5 0.15
22 5 0.15
23 23 0.70
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (24 bp):
TTATTTTTATTTTTATTTTTATGT
Found at i:49105148 original size:31 final size:31
Alignment explanation
Indices: 49105103--49105173 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
49105093 TAATAAAAAT
*
49105103 AAAATTATATTTTAAATCTTTCT-AAAATAATA
1 AAAATTATAATTT-AAT-TTTCTAAAAATAATA
* *
49105135 AAAATT-TAATTTAATTTTTTAAAAATTATA
1 AAAATTATAATTTAATTTTCTAAAAATAATA
49105165 AAAA-TATAA
1 AAAATTATAA
49105174 ACTAAAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 5 0.15
30 18 0.53
31 5 0.15
32 6 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
AAAATTATAATTTAATTTTCTAAAAATAATA
Found at i:49105646 original size:6 final size:6
Alignment explanation
Indices: 49105639--49105671 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
49105629 TGAGACATTG
*
49105639 GGATTG GGATTT GGATTT GGATTT GGATTT GGA
1 GGATTT GGATTT GGATTT GGATTT GGATTT GGA
49105672 AGAGACATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.42
Consensus pattern (6 bp):
GGATTT
Found at i:49115794 original size:19 final size:20
Alignment explanation
Indices: 49115756--49115791 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
49115746 TAGTTTACAG
49115756 ATTTATAAAGAGAAATAATC
1 ATTTATAAAGAGAAATAATC
49115776 ATTT-TAAAG-GAAATAA
1 ATTTATAAAGAGAAATAA
49115792 ATCCTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 5 0.31
20 4 0.25
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.31
Consensus pattern (20 bp):
ATTTATAAAGAGAAATAATC
Found at i:49128611 original size:33 final size:33
Alignment explanation
Indices: 49128476--49128614 Score: 127
Period size: 33 Copynumber: 4.2 Consensus size: 33
49128466 ATTTGATGGG
* * * *
49128476 GAGGATGATGTTGAATGGGTAGAAGCTGCTGGA
1 GAGGGTGATGTTGAAAGGGTAGAAGCTACTAGA
* * *
49128509 AAGGGTGATGTTG-AAGGTGTAGAAGCTACTGGG
1 GAGGGTGATGTTGAAAGG-GTAGAAGCTACTAGA
* * * ** *
49128542 GAAGGTGATGTTGAAGGGGTAAAAGCTTTTAAA
1 GAGGGTGATGTTGAAAGGGTAGAAGCTACTAGA
* *
49128575 GAGGGTGATGTTTAAAGGGTAGAAGCTAATAGA
1 GAGGGTGATGTTGAAAGGGTAGAAGCTACTAGA
49128608 GAGGGTG
1 GAGGGTG
49128615 TGACTACTGC
Statistics
Matches: 83, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
32 3 0.04
33 77 0.93
34 3 0.04
ACGTcount: A:0.31, C:0.04, G:0.40, T:0.24
Consensus pattern (33 bp):
GAGGGTGATGTTGAAAGGGTAGAAGCTACTAGA
Found at i:49137493 original size:21 final size:21
Alignment explanation
Indices: 49137432--49137495 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
49137422 TTCGGGTGGA
*
49137432 TCAGCT-TTTGTGAGCTTCTAT
1 TCAGCTCTTT-TGAGCTTCTGT
* *
49137453 TAAGCTCTTGTGAGCTTCTGT
1 TCAGCTCTTTTGAGCTTCTGT
49137474 TCAGCTCTTTTGAGCTTCTGT
1 TCAGCTCTTTTGAGCTTCTGT
49137495 T
1 T
49137496 AGCGTGTTCG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (21 bp):
TCAGCTCTTTTGAGCTTCTGT
Found at i:49150934 original size:23 final size:24
Alignment explanation
Indices: 49150890--49150934 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
49150880 ATCCACCATA
49150890 AAACCCTAATATGAAGTTAATTAC
1 AAACCCTAATATGAAGTTAATTAC
49150914 AAACCCTGAA-ATG-AGTTAATT
1 AAACCCT-AATATGAAGTTAATT
49150935 TTCCTGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 10 0.50
25 2 0.10
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (24 bp):
AAACCCTAATATGAAGTTAATTAC
Found at i:49160695 original size:91 final size:91
Alignment explanation
Indices: 49160559--49160740 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
49160549 TTTTGAGTTG
49160559 TGCAAGTGTAGGTACTCGTAATGCAAAAGAATGAGACAAATGGCGAGATCCCAATAGGAATGGGA
1 TGCAAGTGTAGGTACTCGTAATGCAAAAGAATGAGACAAATGGCGAGATCCCAATAGGAATGGGA
49160624 TTGATTGAAAGGACTATAATGGTCGT
66 TTGATTGAAAGGACTATAATGGTCGT
49160650 TGCAAGTGTAGGTACTCGTAATGCAAAAGAATGAGACAAATGGCGAGATCCCAATAGGAATGGGA
1 TGCAAGTGTAGGTACTCGTAATGCAAAAGAATGAGACAAATGGCGAGATCCCAATAGGAATGGGA
49160715 TTGATTGAAAGGACTATAATGGTCGT
66 TTGATTGAAAGGACTATAATGGTCGT
49160741 GAACAACAAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (91 bp):
TGCAAGTGTAGGTACTCGTAATGCAAAAGAATGAGACAAATGGCGAGATCCCAATAGGAATGGGA
TTGATTGAAAGGACTATAATGGTCGT
Found at i:49172609 original size:21 final size:22
Alignment explanation
Indices: 49172585--49172629 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
49172575 AAAAATTATC
* *
49172585 AAAATTTATTAAA-AATTAAAA
1 AAAAATTAATAAAGAATTAAAA
*
49172606 AAAAATTAATAAAGAATTTAAA
1 AAAAATTAATAAAGAATTAAAA
49172628 AA
1 AA
49172630 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATTAATAAAGAATTAAAA
Found at i:49172628 original size:18 final size:19
Alignment explanation
Indices: 49172606--49172646 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
49172596 AAAATTAAAA
49172606 AAAAATTAATAAAGAAT-TT
1 AAAAATTAATAAA-AATGTT
49172625 AAAAATT-ATAAAAATGTT
1 AAAAATTAATAAAAATGTT
49172643 AAAA
1 AAAA
49172647 TTATAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 11 0.52
19 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAAATTAATAAAAATGTT
Found at i:49172648 original size:17 final size:18
Alignment explanation
Indices: 49172606--49172652 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
49172596 AAAATTAAAA
49172606 AAAAATTAATAAAGAATTT
1 AAAAATT-ATAAAGAATTT
49172625 AAAAATTATAAA-AATGTT
1 AAAAATTATAAAGAAT-TT
49172643 -AAAATTATAA
1 AAAAATTATAA
49172653 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.48
18 7 0.26
19 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (18 bp):
AAAAATTATAAAGAATTT
Found at i:49173043 original size:17 final size:17
Alignment explanation
Indices: 49173021--49173060 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
49173011 TAATAAAAAT
49173021 ATAATTTTATTAT-TTTA
1 ATAATTTTA-TATCTTTA
49173038 ATAA-TTTATATCTTTA
1 ATAATTTTATATCTTTA
49173054 A-AATTTT
1 ATAATTTT
49173061 TAAAGAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.24
16 12 0.57
17 4 0.19
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATATCTTTA
Found at i:49176158 original size:263 final size:263
Alignment explanation
Indices: 49175672--49176145 Score: 700
Period size: 263 Copynumber: 1.8 Consensus size: 263
49175662 ATAATTATTC
* * *
49175672 TACTGTCTCTATAGAGCGACATGAAGAAAAAGGAATATTAGTTCTTCGGAACAAGGATCAAAAGA
1 TACTGGCTCTATAGAGCGACATGAAGAAAAAGGAATATTAGTTCTTCAGAAAAAGGATCAAAAGA
* * *
49175737 TAGCACAAAGAATGGAGTGTATTAGTATAAGGTGTATAAATGTGTTAGATGATGTGTGGAGAATT
66 TAGCACAAAGAAGGGAGTGTAATAGTATAAGGTGCATAAATGTGTTAGATGATGTGTGGAGAATT
* * * * *
49175802 GCATGATGTGTAAAAGGTATGTGACATGGTTATGAAAGTTGTTCTATAATGTGGCATACCAATAG
131 GCATGATGTGTAAAAAGCATGTGAAATGGGTATGAAAGTTGTTCTATAATGTGGCATACCAATAA
* *
49175867 AATAGTAGTGATGTGTGCCCGTCAAATGTTGGTATCTGATAGCAGATAGTGTCCACCAAGGGGTT
196 AATAGTAGTAATGTGTGCCCATCAAATGTTGGTATCTGATAGCAGATAGTGTCCACCAAGGGGTT
49175932 GTA
261 GTA
* * ** *
49175935 TACTGGCTTTATAGAGCGGCATGAAGAAAAAGGAATATTAGTTCTTCAGAAAAAGGATCGGAAGC
1 TACTGGCTCTATAGAGCGACATGAAGAAAAAGGAATATTAGTTCTTCAGAAAAAGGATCAAAAGA
* * *
49176000 TAGTACAAGGAAGGGAGTGTAATAGTATAAGGTGCATAGATGTGTTAGATGATGTGTGG-GAAAT
66 TAGCACAAAGAAGGGAGTGTAATAGTATAAGGTGCATAAATGTGTTAGATGATGTGTGGAG-AAT
* *
49176064 TTCATGATGTGTAAAAAGCATGTGAAATGGGTATGAAAGTTGGTT-TATAATGTGTCATACCAAT
130 TGCATGATGTGTAAAAAGCATGTGAAATGGGTATGAAAGTT-GTTCTATAATGTGGCATACCAAT
*
49176128 AAAATAGTCGTAATGTGT
194 AAAATAGTAGTAATGTGT
49176146 TTCTATCAAA
Statistics
Matches: 186, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
262 1 0.01
263 182 0.98
264 3 0.02
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (263 bp):
TACTGGCTCTATAGAGCGACATGAAGAAAAAGGAATATTAGTTCTTCAGAAAAAGGATCAAAAGA
TAGCACAAAGAAGGGAGTGTAATAGTATAAGGTGCATAAATGTGTTAGATGATGTGTGGAGAATT
GCATGATGTGTAAAAAGCATGTGAAATGGGTATGAAAGTTGTTCTATAATGTGGCATACCAATAA
AATAGTAGTAATGTGTGCCCATCAAATGTTGGTATCTGATAGCAGATAGTGTCCACCAAGGGGTT
GTA
Found at i:49190103 original size:3 final size:3
Alignment explanation
Indices: 49190095--49190125 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
49190085 AAAAAACCCT
*
49190095 AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
49190126 AAGCTAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:49201462 original size:41 final size:40
Alignment explanation
Indices: 49201359--49201477 Score: 127
Period size: 37 Copynumber: 3.0 Consensus size: 40
49201349 CCTCATCGGA
* * *
49201359 TAATTTGAAGTAATAAATTGACACCCAGTGTCTCATCGGC
1 TAATCTGAAGTAATAAATTGACACCCAGTGTCTCATAGAC
* * * * *
49201399 TAAACCGAAG---TAAATTGGCACCCAGTGCCTCATAGAAT
1 TAATCTGAAGTAATAAATTGACACCCAGTGTCTCATAG-AC
*
49201437 TAATCTGAAGTAATAAATTGACACCCAGTGTCTCATCGAC
1 TAATCTGAAGTAATAAATTGACACCCAGTGTCTCATAGAC
49201477 T
1 T
49201478 CAAAGTCGAA
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
37 22 0.36
38 8 0.13
40 9 0.15
41 22 0.36
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (40 bp):
TAATCTGAAGTAATAAATTGACACCCAGTGTCTCATAGAC
Found at i:49202030 original size:15 final size:16
Alignment explanation
Indices: 49202010--49202040 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
49202000 CTTAAGTCCC
49202010 TAAATTTC-AAATTTT
1 TAAATTTCAAAATTTT
49202025 TAAATTTCAAAATTTT
1 TAAATTTCAAAATTTT
49202041 CATAATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATTTCAAAATTTT
Found at i:49207995 original size:26 final size:27
Alignment explanation
Indices: 49207954--49208031 Score: 95
Period size: 28 Copynumber: 2.9 Consensus size: 27
49207944 TGCAGAGGTC
* * **
49207954 ACACGGCCAAGTCACATGCCCGTGCG-
1 ACACGGCTAAGACACACACCCGTGCGA
*
49207980 ACACGGCTAAGACACACACCCGTGTGA
1 ACACGGCTAAGACACACACCCGTGCGA
49208007 CACACGGCTAAGACACACACCCGTG
1 -ACACGGCTAAGACACACACCCGTG
49208032 TCTCTGCCTG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 21 0.47
28 24 0.53
ACGTcount: A:0.29, C:0.37, G:0.23, T:0.10
Consensus pattern (27 bp):
ACACGGCTAAGACACACACCCGTGCGA
Found at i:49208770 original size:14 final size:16
Alignment explanation
Indices: 49208740--49208771 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
49208730 CATTCAATTC
49208740 ATCACTTCATAAACAT
1 ATCACTTCATAAACAT
49208756 ATCA-TTCAT-AACAT
1 ATCACTTCATAAACAT
49208770 AT
1 AT
49208772 TCAATTCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (16 bp):
ATCACTTCATAAACAT
Found at i:49208796 original size:22 final size:21
Alignment explanation
Indices: 49208771--49208813 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
49208761 TCATAACATA
*
49208771 TTCAATTCTCATCACTTGCTAT
1 TTCAAGTCTCAT-ACTTGCTAT
49208793 TTCAAGTCTCATACTTGCTAT
1 TTCAAGTCTCATACTTGCTAT
49208814 CAAATAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.23, C:0.26, G:0.07, T:0.44
Consensus pattern (21 bp):
TTCAAGTCTCATACTTGCTAT
Found at i:49209073 original size:37 final size:38
Alignment explanation
Indices: 49208977--49209073 Score: 97
Period size: 40 Copynumber: 2.5 Consensus size: 38
49208967 AACACACCAG
* * **
49208977 ATTGGTACCCAGTACCTCATCGGATAATTCGAAGTAATAA
1 ATTGGCACCCAGTACCTCATCAGATAAACCGAAG--ATAA
* ** *
49209017 ATTGACACCCAGTGTCTCATCAGCTAAACCGAAG-TAA
1 ATTGGCACCCAGTACCTCATCAGATAAACCGAAGATAA
49209054 ATTGGCACCCAGTACCTCAT
1 ATTGGCACCCAGTACCTCAT
49209074 AGAATTAATC
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
37 20 0.43
40 26 0.57
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (38 bp):
ATTGGCACCCAGTACCTCATCAGATAAACCGAAGATAA
Found at i:49218100 original size:16 final size:16
Alignment explanation
Indices: 49218068--49218101 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49218058 GGTAGGCAAC
* *
49218068 TTTTTTTTTGTGGTTT
1 TTTTTTTTTGCGCTTT
49218084 TTTTTTTTTGCGCTTT
1 TTTTTTTTTGCGCTTT
49218100 TT
1 TT
49218102 GCTTCTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.15, T:0.79
Consensus pattern (16 bp):
TTTTTTTTTGCGCTTT
Found at i:49228350 original size:36 final size:36
Alignment explanation
Indices: 49228310--49228465 Score: 177
Period size: 36 Copynumber: 4.1 Consensus size: 36
49228300 AGTGGTAGCA
49228310 TGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
1 TGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
* *
49228346 TGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAG
1 TGCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG
*
49228388 CTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATGAG
1 ---T-GCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
* *
49228428 TGCTATACTTATCTGATCAAGTGACAAAGTGATAAG
1 TGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
49228464 TG
1 TG
49228466 TTAGCCTTAG
Statistics
Matches: 102, Mismatches: 8, Indels: 20
0.78 0.06 0.15
Matches are distributed among these distances:
36 65 0.64
37 2 0.02
40 2 0.02
42 2 0.02
45 1 0.01
46 30 0.29
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (36 bp):
TGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
Found at i:49228398 original size:46 final size:45
Alignment explanation
Indices: 49228347--49228599 Score: 323
Period size: 46 Copynumber: 5.8 Consensus size: 45
49228337 AGTGATAAGT
*
49228347 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTA
*
49228393 GCTACACTTATCTGATCAAGTGAAAAAGTG---A-T-G-AG--T-
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTA
* *
49228429 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTA
*
49228475 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTA
* *
49228521 GCTACTCTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTA
*
49228565 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
49228600 ATCATATGTA
Statistics
Matches: 184, Mismatches: 13, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
36 28 0.15
37 1 0.01
39 1 0.01
40 3 0.02
41 1 0.01
42 15 0.08
43 6 0.03
44 17 0.09
45 2 0.01
46 110 0.60
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (45 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTA
Found at i:49228420 original size:82 final size:81
Alignment explanation
Indices: 49228277--49228599 Score: 420
Period size: 82 Copynumber: 3.9 Consensus size: 81
49228267 TTTGAATACT
* *
49228277 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCAT-GCTACACTTATCTGATCAAGTGAAAAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
49228341 ATAAGTGCTACACTTA
66 ATAAGTGCTACACTTA
*
49228357 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
49228422 GATGAGTGCTATACTTA
65 GATAAGTGCTACACTTA
* *
49228439 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAAGTGAAAAAGT
49228504 GATAAGTGGTAGCCTTAGCTACTCTTA
65 GATAA---GT-G-C-TA-C-A--CTTA
* * *
49228531 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CAGCTACACTTATCTGATC-AG-GGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
49228593 ATAAGTG
66 ATAAGTG
49228600 ATCATATGTA
Statistics
Matches: 215, Mismatches: 15, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
80 30 0.14
81 1 0.00
82 108 0.50
83 1 0.00
84 1 0.00
85 4 0.02
86 1 0.00
87 1 0.00
88 12 0.06
89 2 0.01
90 19 0.09
91 1 0.00
92 34 0.16
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (81 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
ATAAGTGCTACACTTA
Found at i:49234178 original size:17 final size:17
Alignment explanation
Indices: 49234158--49234204 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
49234148 AAAAAATTAA
49234158 AAATCCTTTAAAAGTAT
1 AAATCCTTTAAAAGTAT
*
49234175 AAATCAATTTAAAAAGTAT
1 AAATC-CTTT-AAAAGTAT
*
49234194 -AATTCTTTAAA
1 AAATCCTTTAAA
49234205 CATATTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 3 0.12
17 8 0.32
18 6 0.24
19 8 0.32
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (17 bp):
AAATCCTTTAAAAGTAT
Found at i:49235937 original size:17 final size:18
Alignment explanation
Indices: 49235897--49235937 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
49235887 CTTTTTTCAG
49235897 TTTAGGAGGTTGAATAACAA
1 TTTAGGAGGTTGAAT-A-AA
49235917 TTTAGGAGGTTGAAT-AA
1 TTTAGGAGGTTGAATAAA
49235934 TTTA
1 TTTA
49235938 TAAAGGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
20 15 0.71
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (18 bp):
TTTAGGAGGTTGAATAAA
Found at i:49239238 original size:15 final size:15
Alignment explanation
Indices: 49239220--49239255 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
49239210 TGGCCCCGAA
49239220 ACCACTATTTTCAAC
1 ACCACTATTTTCAAC
49239235 ACCACTATTTTCAAC
1 ACCACTATTTTCAAC
49239250 ACCACT
1 ACCACT
49239256 TAAAAACGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (15 bp):
ACCACTATTTTCAAC
Found at i:49242583 original size:20 final size:20
Alignment explanation
Indices: 49242558--49242600 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
49242548 TTAAGCTAGT
*
49242558 TAAAGTCTGTTTTAGTATAA
1 TAAAGTCTGGTTTAGTATAA
49242578 TAAAGTCTGGTTTAGTATAA
1 TAAAGTCTGGTTTAGTATAA
49242598 TAA
1 TAA
49242601 CATTGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
TAAAGTCTGGTTTAGTATAA
Found at i:49245220 original size:24 final size:23
Alignment explanation
Indices: 49245168--49245222 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
49245158 AAATAAAAAA
* *
49245168 ATAAAAAAAATATATTTTCATTT
1 ATAAAAATAATATATGTTCATTT
*
49245191 AAAAAAATAA-ATATGTTCATATAT
1 ATAAAAATAATATATGTTCAT-T-T
49245215 ATAAAAAT
1 ATAAAAAT
49245223 TAGTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.35
23 9 0.35
24 8 0.31
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAAAAATAATATATGTTCATTT
Found at i:49245293 original size:21 final size:22
Alignment explanation
Indices: 49245275--49245316 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
49245265 AACAAATATA
*
49245275 TACATATAGATAAA-AAATAAT
1 TACATATAAATAAATAAATAAT
49245296 TACATATAAATAAATAAATAA
1 TACATATAAATAAATAAATAA
49245317 AAAATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TACATATAAATAAATAAATAAT
Found at i:49246917 original size:44 final size:43
Alignment explanation
Indices: 49246855--49246965 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 43
49246845 GATCTGCTCT
*
49246855 CTGCAACTTCA-GAGAGATAAGATC-CAAGGTTTTAATCCACTCCA
1 CTGCAACTTCAGGA-AGATAAGATCAC-A-GCTTTAATCCACTCCA
* * **
49246899 CTGCAACTTCAGGAAGATAGGATTATCAGCTTTAATCTGCTCCA
1 CTGCAACTTCAGGAAGATAAGATCA-CAGCTTTAATCCACTCCA
* *
49246943 CTGTAACTTCAGGGAGATAAGAT
1 CTGCAACTTCAGGAAGATAAGAT
49246966 TTGCCATCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
44 52 0.93
45 3 0.05
46 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (43 bp):
CTGCAACTTCAGGAAGATAAGATCACAGCTTTAATCCACTCCA
Found at i:49246996 original size:45 final size:45
Alignment explanation
Indices: 49246894--49247489 Score: 313
Period size: 44 Copynumber: 13.6 Consensus size: 45
49246884 TTTTAATCCA
* * * * *
49246894 CTCCACTGCAACTTCAGGAAGATAGGATTAT--CAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-TGCCATCTTCAGTCTG
*
49246938 CTCCACTGTAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
*
49246983 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCCCA-CTT-AGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGATTTG-CCATCTTCAGTCTG
* * *
49247027 CTCCACTGCAACTTCAGGGAGATAAGACTAG--A--TGC-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAG-TCTG
* * * *** * * *
49247068 CT-CTCTGCAACTTCAGAGAGATAAGATCTGAGGT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
* * * ** * *
49247111 CTCCACTGTAACTTCAGGGAGATAGGA-TTGTCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
*
49247155 CTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
* * **
49247200 C-CTCACTGTAACTTCA-GGAGGATAAGACTTGCTTTACTT-AGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGATTTGCCAT-CTTCAGTCTG
* * ** *
49247245 CTCCAGTGCAACTTCAGGGAGATAAGA----CTAAATGC-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAG-TCTG
** * * * * *
49247286 CT-CTTTACAACTTCAGAGAGATAAGA--T-CCAAGGT-TTTAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGCC-A--TCTTCAGTCTG
* * * *
49247329 CTCCACTGCAACTTCAGGAAGATAGGATTATCGGC-T-TT-AATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-T-GCCATCTTCAGTCTG
* *
49247373 CTCCATTCCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
* * **
49247418 C-CTCACTGCAACTTTA-GGAGGATAAGACTTGCTTTACTT-AGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGATTTGCCAT-CTTCAGTCTG
**
49247463 CTTTACTGCAACTTCAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
49247490 CTAGATGCGA
Statistics
Matches: 429, Mismatches: 81, Indels: 83
0.72 0.14 0.14
Matches are distributed among these distances:
40 47 0.11
41 16 0.04
42 3 0.01
43 18 0.04
44 170 0.40
45 157 0.37
46 16 0.04
47 1 0.00
49 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
Found at i:49247344 original size:218 final size:218
Alignment explanation
Indices: 49246801--49247630 Score: 1266
Period size: 218 Copynumber: 3.8 Consensus size: 218
49246791 TCAACTTGAT
** * * *
49246801 TTAGTCTGCTCCTGGTGTAACTTCAGGAAGATAAGACTAAATACGATCTGCTCTCTGCAACTTCA
1 TTAGTCTGCTCC-ACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCA
*
49246866 GAGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCAGCTT
65 GAGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTT
*
49246931 TAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACT
130 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACT
**
49246996 TCAGGAGGATAAGACTTGC-CCAC
195 TCAGGAGGATAAGACTTGCTTTAC
*
49247019 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAG
** * * * *
49247084 AGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTGTCGGCTTT
66 AGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTT
* *
49247149 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACTT
131 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
49247214 CAGGAGGATAAGACTTGCTTTAC
196 CAGGAGGATAAGACTTGCTTTAC
* * *
49247237 TTAGTCTGCTCCAGTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTTTACAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAG
*
49247302 AGAGATAAGATCCAAGGTTTTAATCTACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTT
66 AGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTT
* *
49247367 AATCTGCTCCATTCCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
131 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
*
49247432 TAGGAGGATAAGACTTGCTTTAC
196 CAGGAGGATAAGACTTGCTTTAC
** * * *
49247455 TTAGTCTGCTTTACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGTAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAG
* ** ** * * *
49247520 AGAGATAAGATCTAAGGTTTTAATCCGTTTTACTGCAACTTCAGGGAGATATGATTGTCGGCTTT
66 AGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTT
* * * *
49247585 AATCTGCTCCTCTGTAATTTCAGAGAGATAAGATTTGCCATCTTCA
131 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCA
49247631 CTGATATGCT
Statistics
Matches: 554, Mismatches: 57, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
217 185 0.33
218 369 0.67
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (218 bp):
TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAAATGCGATCTGCTCTCTGCAACTTCAG
AGAGATAAGATCCAAGGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTT
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
CAGGAGGATAAGACTTGCTTTAC
Found at i:49259622 original size:22 final size:22
Alignment explanation
Indices: 49259594--49259636 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
49259584 AATAAAAAAA
*
49259594 TAAAAAAA-AATATATTTTCATT
1 TAAAAAAATAA-ATATGTTCATT
49259616 TAAAAAAATAAATATGTTCAT
1 TAAAAAAATAAATATGTTCAT
49259637 ATATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAAAAAATAAATATGTTCATT
Found at i:49259719 original size:21 final size:22
Alignment explanation
Indices: 49259701--49259742 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
49259691 AACAAATATA
*
49259701 TACATATAGATAAA-AAATAAT
1 TACATATAAATAAATAAATAAT
49259722 TACATATAAATAAATAAATAA
1 TACATATAAATAAATAAATAA
49259743 AATATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TACATATAAATAAATAAATAAT
Found at i:49261340 original size:44 final size:43
Alignment explanation
Indices: 49261278--49261388 Score: 109
Period size: 44 Copynumber: 2.5 Consensus size: 43
49261268 GATCTGCTCT
*
49261278 CTGCAACTTCA-GAGAGATAAGATC-CAAGGTTTTAATCCACTCCA
1 CTGCAACTTCAGGA-AGATAAGATCAC-A-GCTTTAATCCACTCCA
* * * **
49261322 CTGCAAATTCAGGAAGATAGGATTATCAGCTTTAATCTGCTCCA
1 CTGCAACTTCAGGAAGATAAGATCA-CAGCTTTAATCCACTCCA
*
49261366 CTGCAACTTCAGGGAGATAAGAT
1 CTGCAACTTCAGGAAGATAAGAT
49261389 TTGCCATCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
44 51 0.93
45 3 0.05
46 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (43 bp):
CTGCAACTTCAGGAAGATAAGATCACAGCTTTAATCCACTCCA
Found at i:49262319 original size:20 final size:20
Alignment explanation
Indices: 49262294--49262336 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
49262284 TTAAGCTAGT
*
49262294 TAAAGTCTGTTTTAGTATAA
1 TAAAGTCTGGTTTAGTATAA
49262314 TAAAGTCTGGTTTAGTATAA
1 TAAAGTCTGGTTTAGTATAA
49262334 TAA
1 TAA
49262337 CATTGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
TAAAGTCTGGTTTAGTATAA
Found at i:49265033 original size:21 final size:22
Alignment explanation
Indices: 49265015--49265056 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
49265005 AACAAATATA
*
49265015 TACATATAGATAAA-AAATAAT
1 TACATATAAATAAATAAATAAT
49265036 TACATATAAATAAATAAATAA
1 TACATATAAATAAATAAATAA
49265057 AATAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TACATATAAATAAATAAATAAT
Found at i:49268575 original size:31 final size:31
Alignment explanation
Indices: 49268537--49268598 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
49268527 ATGGCTATTG
* **
49268537 AACTATTCGAAAGCTTTCATTGAAATCATTA
1 AACTATTCAAAAAATTTCATTGAAATCATTA
* *
49268568 AACTATTCAAAAAATTTTATTGAAGTCATTA
1 AACTATTCAAAAAATTTCATTGAAATCATTA
49268599 GACTGTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (31 bp):
AACTATTCAAAAAATTTCATTGAAATCATTA
Found at i:49272664 original size:23 final size:23
Alignment explanation
Indices: 49272636--49272729 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
49272626 ATGTGTGTAT
* *
49272636 CTTTTCATATTCAAGCCTCTTAA
1 CTTTTCATATTCAAGTCTCTTCA
*
49272659 CTTTTCATCTTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
* * *
49272682 CTATTCATATTCAAGTTTTTTCA
1 CTTTTCATATTCAAGTCTCTTCA
49272705 CTTTTCATATTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
49272728 CT
1 CT
49272730 CTTCTAACTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (23 bp):
CTTTTCATATTCAAGTCTCTTCA
Found at i:49277168 original size:23 final size:23
Alignment explanation
Indices: 49277140--49277233 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
49277130 ATGTGTGTAT
* *
49277140 CTTTTCATATTCAAGCCTCTTAA
1 CTTTTCATATTCAAGTCTCTTCA
*
49277163 CTTTTCATCTTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
* * *
49277186 CTATTCATATTCAAGTTTTTTCA
1 CTTTTCATATTCAAGTCTCTTCA
49277209 CTTTTCATATTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
49277232 CT
1 CT
49277234 CTTCTAACTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (23 bp):
CTTTTCATATTCAAGTCTCTTCA
Found at i:49281608 original size:16 final size:15
Alignment explanation
Indices: 49281561--49281609 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
49281551 TTTTAAGATT
*
49281561 TTTAAAATGTTAATA
1 TTTAAAATGTTATTA
* *
49281576 TTTTAAATTTTATTTA
1 TTTAAAATGTTA-TTA
49281592 TTTAAAATGTTAGTTA
1 TTTAAAATGTTA-TTA
49281608 TT
1 TT
49281610 GTAATTGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTAAAATGTTATTA
Found at i:49281677 original size:16 final size:17
Alignment explanation
Indices: 49281639--49281685 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
49281629 TTAAAATTTT
49281639 ATAA-ATTATAAAATAAG
1 ATAATATTA-AAAATAAG
*
49281656 AAAATATTAAAAATAA-
1 ATAATATTAAAAATAAG
*
49281672 ATAATATAAAAAAT
1 ATAATATTAAAAAT
49281686 TTAAAATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.46
17 10 0.38
18 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (17 bp):
ATAATATTAAAAATAAG
Found at i:49286146 original size:5 final size:5
Alignment explanation
Indices: 49286125--49286208 Score: 55
Period size: 5 Copynumber: 16.8 Consensus size: 5
49286115 ATACGAAGCG
* * * *
49286125 TATCT TATCG TATCA TAGCA TATCA TATCA TATCA TATCGA -ATCA TAGCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATC-A TATCA TATCA
* * * * *
49286175 TTTCA TAATGA -ATCA AACCA TAGCA TATCA TATC
1 TATCA T-ATCA TATCA TATCA TATCA TATCA TATC
49286209 GAATCACAAC
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
4 4 0.07
5 54 0.89
6 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (5 bp):
TATCA
Found at i:49286158 original size:25 final size:24
Alignment explanation
Indices: 49286143--49286232 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 24
49286133 CGTATCATAG
* *
49286143 CATATCATATCATATC-ATATCGAAT
1 CATAGCATATCATATCGA-ATC-AAA
*
49286168 CATAGCATTTCATAAT-GAATCAAA
1 CATAGCATATCAT-ATCGAATCAAA
49286192 CCATAGCATATCATATCGAATCACAA
1 -CATAGCATATCATATCGAATCA-AA
49286218 CAT-GACATATCATAT
1 CATAG-CATATCATAT
49286233 TACGTCCTAC
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
24 5 0.09
25 45 0.82
26 5 0.09
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (24 bp):
CATAGCATATCATATCGAATCAAA
Found at i:49297502 original size:20 final size:20
Alignment explanation
Indices: 49297477--49297516 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
49297467 TCACTTTTGC
49297477 CTTGAATAAACCCGTTTGGA
1 CTTGAATAAACCCGTTTGGA
*
49297497 CTTGAATGAACCCGTTTGGA
1 CTTGAATAAACCCGTTTGGA
49297517 ATAGGGCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (20 bp):
CTTGAATAAACCCGTTTGGA
Found at i:49302529 original size:21 final size:22
Alignment explanation
Indices: 49302493--49302577 Score: 120
Period size: 21 Copynumber: 4.0 Consensus size: 22
49302483 CCAAGAACAA
*
49302493 AGCAAAAAAGAGGGGAGAAACC
1 AGCAAAAATGAGGGGAGAAACC
* *
49302515 AGCAAAAACGA-GGGAGAAACT
1 AGCAAAAATGAGGGGAGAAACC
*
49302536 AGCAAGAATGA-GGGAGAAACC
1 AGCAAAAATGAGGGGAGAAACC
49302557 AGCAAAAATGAGGGGAGAAAC
1 AGCAAAAATGAGGGGAGAAAC
49302578 GGCTGTTTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 37 0.66
22 19 0.34
ACGTcount: A:0.52, C:0.13, G:0.32, T:0.04
Consensus pattern (22 bp):
AGCAAAAATGAGGGGAGAAACC
Found at i:49305605 original size:23 final size:23
Alignment explanation
Indices: 49305572--49305624 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
49305562 TGTGTTTTTT
49305572 TATTTGTATTTGTATTTGTATTTG
1 TATTT-TATTTGTATTTGTATTTG
* *
49305596 TATTTTATTTGTATTTTTATTTT
1 TATTTTATTTGTATTTGTATTTG
49305619 TATTTT
1 TATTTT
49305625 TTTTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (23 bp):
TATTTTATTTGTATTTGTATTTG
Found at i:49305625 original size:6 final size:6
Alignment explanation
Indices: 49305572--49305623 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
49305562 TGTGTTTTTT
* *
49305572 TATTTG TATTTG TATTTG TATTTG TATTT- TATTTG TATTTT TATTTT
1 TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG TATTTG
49305619 TATTT
1 TATTT
49305624 TTTTTCTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (6 bp):
TATTTG
Found at i:49305626 original size:7 final size:6
Alignment explanation
Indices: 49305568--49305625 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
49305558 CTAATGTGTT
* * * * *
49305568 TTTTTA TTTGTA TTTGTA TTTGTA TTTGTA -TTTTA TTTGTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
49305615 TTTTTA TTTTT
1 TTTTTA TTTTT
49305626 TTTCTTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
5 4 0.09
6 43 0.91
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.76
Consensus pattern (6 bp):
TTTTTA
Done.