Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold281
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: 622278
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 2 of 4
Found at i:137680 original size:62 final size:62
Alignment explanation
Indices: 137539--138276 Score: 505
Period size: 62 Copynumber: 11.1 Consensus size: 62
137529 CACTCTTTTT
*
137539 CCCTTTTCAAAGCCCACAACTCCGTGGCACC-----CTTTTAAAGCCCACAATTCCGTGGCA
1 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCA
** * *
137596 CTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTTCGTG
1 CCCTTTTCA-----AAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGTG
137661 GCA
60 GCA
* * *
137664 CCCTTTT-AAAGCCCACAATTCCGTGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCA
1 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC-T-TTTAAAGCCCACAACTCCGTGGCA
* * *
137726 CCCTTTT-AAAGCCCACAATTCCGTGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCA
1 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC-T-TTTAAAGCCCACAACTCCGTGGCA
* * *
137788 CCTTTTTCTGTTTAAAGCCCACAACTTCGTGGCACC-----CTTTTAAAGCCCACAATTCCGTGG
1 CCCTTTTC-----AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGG
137848 CA
61 CA
** *
137850 CTTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGT
1 C-CCTTTTCA-----AAGCCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCGT
137915 GGCA
59 GGCA
*
137919 CTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCG
1 --------CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCG
137984 TGGCA
58 TGGCA
* * * * * * *
137989 CTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGT
1 C-CCTTTT--C---AAAGCCCACAACTCCGTGGCACCTTT-T-TCTT-TTAAAG-CC-CACAACT
*
138054 CGGTGGCAA
55 CCGTGGC-A
* **
138063 CCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGG
1 -C--C--CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGG
138128 CA
61 CA
* * *
138130 CTCTTTTTTCCTTTTTAAAGCCCACAACACCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCC
1 --C------CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT-CTTTTAAAGCCCACAACTCC
138195 GTGGCA
57 GTGGCA
*
138201 CTCTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGT
1 --C-----CCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGT
138266 GGCA
59 GGCA
*
138270 CTCTTTT
1 CCCTTTT
138277 TCCCTTTTAA
Statistics
Matches: 562, Mismatches: 58, Indels: 117
0.76 0.08 0.16
Matches are distributed among these distances:
57 7 0.01
58 1 0.00
61 3 0.01
62 158 0.28
63 36 0.06
65 1 0.00
67 5 0.01
68 83 0.15
69 51 0.09
70 100 0.18
71 61 0.11
72 6 0.01
73 34 0.06
74 1 0.00
75 1 0.00
76 9 0.02
77 1 0.00
78 4 0.01
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (62 bp):
CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCA
Found at i:137977 original size:70 final size:69
Alignment explanation
Indices: 137726--138313 Score: 679
Period size: 70 Copynumber: 8.5 Consensus size: 69
137716 CTCCGTGGCA
* *
137726 CCCTTTTAAAGCCCACAATTCCGTGGCACTTTTTTCATCTTT-AAGTCCACAACTCCGTGGCAC-
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTC-T-TTTAAAGCCCACAACTCCGTGGCACT
137789 CTTTTT
64 CTTTTT
* * *
137795 --CTGTTTAAAGCCCACAACTTCGTGGCAC-----CCTTTTAAAGCCCACAATTCCGTGGCACT-
1 CCCT-TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
137852 TTTTT
65 TTTTT
* * * *
137857 TCATCTTT-AAGTCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACT
1 CCCT-TTTAAAGCCCACAACTCCGTGGCACTTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACT
137921 CTTTTT
64 CTTTTT
137927 CCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
137992 TTTTT
65 TTTTT
* ** * * *
137997 CCCTTTT-AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTGGC
1 CCCTTTTAAAGCCCACAACTCCGTGGCA-CTTT-TTTCTT-TTAAAG-CC-CACAACTCCGTGGC
*
138061 AAC-CTTCTT
61 -ACTCTTTTT
* * **
138070 --CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTC
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
138133 TTTTTT
65 -TTTTT
* * * *
138139 CCTTTTTAAAGCCCACAACACCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTC
1 CCCTTTTAAAGCCCACAACTCCGTGGCA-CTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
138204 TTTTT
65 TTTTT
138209 -CCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTC
138273 TTTTT
65 TTTTT
*
138278 CCCTTTT-AAGTCCACAACTCCGTGGCATCTTTTTTC
1 CCCTTTTAAAGCCCACAACTCCGTGGCA-CTTTTTTC
138314 CTTCCCAAAG
Statistics
Matches: 444, Mismatches: 45, Indels: 60
0.81 0.08 0.11
Matches are distributed among these distances:
61 3 0.01
62 25 0.06
63 20 0.05
64 4 0.01
67 4 0.01
68 75 0.17
69 90 0.20
70 106 0.24
71 74 0.17
72 5 0.01
73 36 0.08
74 2 0.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.34
Consensus pattern (69 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
TTTT
Found at i:138314 original size:35 final size:35
Alignment explanation
Indices: 137822--138314 Score: 532
Period size: 35 Copynumber: 14.1 Consensus size: 35
137812 CTTCGTGGCA
*
137822 CCCTTTTAAAGCCCACAATTCCGTGGCACTTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTT
* * * *
137857 TCATCTTT-AAGTCCACAACTCCGTGGCACCTTTTT
1 CCCT-TTTAAAGCCCACAACTCCGTGGCACTTTTTT
137892 --CTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCT-TTTAAAGCCCACAACTCCGTGGCACT-TTTTT
137927 CCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTT
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTT
137963 --CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACT-TTTTT
* *
137997 CCCTTTT-AAGTCCACAACTCCGTGGCA-TCTTTCT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACT-TTTTT
* * * * *
138031 CCCTTCCTAAAGCCCACACAAGTCGGTGGCAACCTTCTT
1 CCCTT-TTAAAG-CC-CACAACTCCGTGGC-ACTTTTTT
* *
138070 --CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTT
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTT
**
138104 --CTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCA--CTTTTTT
* * *
138139 CCTTTTTAAAGCCCACAACACCGTGGCACCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTT
*
138174 -CCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACT-TTTTT
138209 -CCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTT
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTT
138244 --CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACT-TTTTT
*
138278 CCCTTTT-AAGTCCACAACTCCGTGGCATCTTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCA-CTTTTTT
138313 CC
1 CC
138315 TTCCCAAAGC
Statistics
Matches: 396, Mismatches: 36, Indels: 52
0.82 0.07 0.11
Matches are distributed among these distances:
33 69 0.17
34 89 0.22
35 115 0.29
36 52 0.13
37 55 0.14
38 12 0.03
39 4 0.01
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (35 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTT
Found at i:138392 original size:33 final size:33
Alignment explanation
Indices: 138314--138410 Score: 162
Period size: 32 Copynumber: 3.0 Consensus size: 33
138304 ATCTTTTTTC
*
138314 CTTCCCAAAGCCCACACAAGTCGGTGGCAA-CT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCT
138346 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACC-T
138380 CTT-CTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACC
138411 CCTCTAAGCC
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
32 29 0.47
33 29 0.47
34 4 0.06
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.18
Consensus pattern (33 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCT
Found at i:138637 original size:49 final size:49
Alignment explanation
Indices: 138415--138950 Score: 715
Period size: 49 Copynumber: 10.8 Consensus size: 49
138405 GCAACCCCTC
* *
138415 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTT
* ** *
138467 TAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCCCCTC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* *
138519 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTT
* * *
138571 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
138620 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * *
138672 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
138721 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
138770 TAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGACACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
138819 TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
138868 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
138911 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
138951 ATTTTCCATC
Statistics
Matches: 437, Mismatches: 39, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
43 40 0.09
45 1 0.00
49 222 0.51
50 4 0.01
51 2 0.00
52 168 0.38
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:138950 original size:43 final size:43
Alignment explanation
Indices: 138767--138984 Score: 181
Period size: 49 Copynumber: 4.8 Consensus size: 43
138757 GCACCTTCAT
* * * *
138767 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGACACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* * *
138814 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
*
138863 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
138908 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
138951 ATTT---TCCATCTTTAAGCTGGCCTTGAATCAGCAC
1 CTTTAAGTCCA-ATAT-AGCTGGCCTTGAATCAGCAC
138985 GTTGACATCC
Statistics
Matches: 153, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
40 4 0.03
41 2 0.01
42 19 0.12
43 44 0.29
45 1 0.01
49 83 0.54
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:138982 original size:42 final size:41
Alignment explanation
Indices: 138872--138984 Score: 138
Period size: 43 Copynumber: 2.7 Consensus size: 41
138862 CATCTTTAAG
* *
138872 TCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAA
1 TCCAATATAGCTGGCCTTGAATCAGCACATTGGCACATTT-A
*
138914 GTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTT-
1 -TCCAATATAGCTGGCCTTGAATCAGCACATTGGCACATTTA
* *
138955 TCCATCTTTAAGCTGGCCTTGAATCAGCAC
1 TCCA-ATAT-AGCTGGCCTTGAATCAGCAC
138985 GTTGACATCC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
40 4 0.06
41 2 0.03
42 19 0.31
43 37 0.60
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (41 bp):
TCCAATATAGCTGGCCTTGAATCAGCACATTGGCACATTTA
Found at i:139141 original size:49 final size:49
Alignment explanation
Indices: 139066--139489 Score: 548
Period size: 49 Copynumber: 8.8 Consensus size: 49
139056 CTTTTCTCAT
*
139066 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
139115 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
*
139164 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
139213 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
139262 CTTCATCTTGAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
139310 ---C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
139354 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
139402 ---C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
139446 ATTTTCCATCTTTAAGTTCAATGTAGCCGGCCTTGAATCAGCAC
1 --CTT-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
139490 GTTGACATCC
Statistics
Matches: 326, Mismatches: 34, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
43 77 0.24
45 2 0.01
47 1 0.00
49 214 0.66
50 1 0.00
52 31 0.10
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:139232 original size:98 final size:98
Alignment explanation
Indices: 139063--139555 Score: 704
Period size: 98 Copynumber: 5.1 Consensus size: 98
139053 TCACTTTTCT
139063 CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAG
1 CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAG
139128 TCCAATATCGCTGGCCTTGAATCAGCATATTGG
66 TCCAATATCGCTGGCCTTGAATCAGCATATTGG
139161 CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAG
1 CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAG
139226 TCCAATATCGCTGGCCTTGAATCAGCATATTGG
66 TCCAATATCGCTGGCCTTGAATCAGCATATTGG
*
139259 CATCTTCATCTTGAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTTTAAG
1 CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAG
139318 TCCAATATCGCTGGCCTTGAATCAGCATATTGG
66 TCCAATATCGCTGGCCTTGAATCAGCATATTGG
*
139351 CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAG
1 CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAG
*
139410 TCCAATATAGCTGGCCTTGAATCAGCATATTGG
66 TCCAATATCGCTGGCCTTGAATCAGCATATTGG
* * * * * *
139443 CACATTTTCCATCTTTAAGTTCAATGTAGCCGGCCTTGAATCAGCACGTTGACATCCTTTTTCTC
1 --CATCTT-CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CC----T-TC
* * * *
139508 ATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGG
57 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
139550 CATCTT
1 CATCTT
139556 TATCACTTTT
Statistics
Matches: 365, Mismatches: 15, Indels: 23
0.91 0.04 0.06
Matches are distributed among these distances:
92 129 0.35
94 6 0.02
95 41 0.11
98 148 0.41
105 6 0.02
107 35 0.10
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (98 bp):
CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAG
TCCAATATCGCTGGCCTTGAATCAGCATATTGG
Found at i:139333 original size:43 final size:44
Alignment explanation
Indices: 139267--139445 Score: 236
Period size: 43 Copynumber: 4.0 Consensus size: 44
139257 GGCATCTTCA
* * * *
139267 TCTTGAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
*
139311 -CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C
* *
139358 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 -TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
139403 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
139446 ATTTTCCATC
Statistics
Matches: 119, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
43 78 0.66
45 1 0.01
47 1 0.01
49 39 0.33
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (44 bp):
TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:139339 original size:92 final size:92
Alignment explanation
Indices: 139219--139489 Score: 461
Period size: 92 Copynumber: 2.9 Consensus size: 92
139209 GCACCTTCAT
*
139219 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
*
139284 GCTGGCCTTGACTCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
139311 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
139376 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
139403 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAAT
*
139468 GTAGCCGGCCTTGAATCAGCAC
63 GTAGCTGGCCTTGAATCAGCAC
139490 GTTGACATCC
Statistics
Matches: 170, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
92 129 0.76
94 5 0.03
95 36 0.21
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:139692 original size:170 final size:164
Alignment explanation
Indices: 139403--139789 Score: 639
Period size: 170 Copynumber: 2.3 Consensus size: 164
139393 ACATTGGCAC
*
139403 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTTCAAT
139468 GTAGCCGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
63 GTAGCCGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
139533 ATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
128 ATGAATCAACATATTGGCATCTTTATCAC-TTT-T--TCAT
*
139574 CATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATG
1 C--TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATG
* *
139639 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCA
64 TAGCCGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCA
139704 TGAATCAACATATTGGCATCTTTATCACTTTTTCAT
129 TGAATCAACATATTGGCATCTTTATCACTTTTTCAT
* *
139740 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
139790 ATCTCTAAAA
Statistics
Matches: 208, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
164 47 0.23
166 5 0.02
168 1 0.00
169 3 0.01
170 108 0.52
171 6 0.03
173 38 0.18
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (164 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
GCCGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATG
AATCAACATATTGGCATCTTTATCACTTTTTCAT
Found at i:139742 original size:60 final size:61
Alignment explanation
Indices: 139671--139790 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 61
139661 TTGACATCCT
* * * *
139671 TTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCAC
1 TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCAC
* * * *
139732 TTTT-TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCA
1 TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCA
139791 TCTCTAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 47 0.92
61 4 0.08
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (61 bp):
TTTTCTCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCAC
Found at i:140626 original size:33 final size:33
Alignment explanation
Indices: 140589--140658 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
140579 TTCAACGATT
140589 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
140622 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
140655 TGTA
1 TGTA
140659 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:140627 original size:13 final size:13
Alignment explanation
Indices: 140609--140633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
140599 CATAAAATGT
140609 TGTATCGATACAA
1 TGTATCGATACAA
140622 TGTATCGATACA
1 TGTATCGATACA
140634 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:140717 original size:13 final size:13
Alignment explanation
Indices: 140699--140723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
140689 ATTACTCACA
140699 TGTATCGATACAT
1 TGTATCGATACAT
140712 TGTATCGATACA
1 TGTATCGATACA
140724 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:140788 original size:52 final size:52
Alignment explanation
Indices: 140732--140860 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
140722 CACTGATCTT
*
140732 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
140784 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
140836 TGTATCGATACATGCAAATAAATTT
1 TGTATCGATACATGCAGACAAATTT
140861 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:146351 original size:37 final size:37
Alignment explanation
Indices: 146301--146374 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
146291 AATAATCAAA
* *
146301 CTCCTTGATGGTATGACACAATTTTAATTAGTCTAGT
1 CTCCTTGATGGTATGACACAATTCTAAGTAGTCTAGT
*
146338 CTCCTTGATGGTATGACGCAATTCTAAGTAGTCTAGT
1 CTCCTTGATGGTATGACACAATTCTAAGTAGTCTAGT
146375 TTATATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.38
Consensus pattern (37 bp):
CTCCTTGATGGTATGACACAATTCTAAGTAGTCTAGT
Found at i:147853 original size:21 final size:21
Alignment explanation
Indices: 147809--147851 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
147799 TATATCATAG
**
147809 TTATTTATTAATAATGTATTT
1 TTATTTATTAATAATCAATTT
147830 TTATTTATT-ATAATCAATTT
1 TTATTTATTAATAATCAATTT
147850 TT
1 TT
147852 TAATTAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTATTTATTAATAATCAATTT
Found at i:147920 original size:21 final size:21
Alignment explanation
Indices: 147871--147922 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
147861 AATAATGATC
*
147871 ATTTAATTAATTTTAAAATTAT
1 ATTTAATT-ATTTTAAAATTAA
*
147893 CTTTAATTATTTT-AAATTAA
1 ATTTAATTATTTTAAAATTAA
147913 ATTCTAATTA
1 ATT-TAATTA
147923 GATGCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.31
21 11 0.42
22 7 0.27
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAATTATTTTAAAATTAA
Found at i:148080 original size:14 final size:15
Alignment explanation
Indices: 148040--148086 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
148030 ATTAATTATC
*
148040 ATTATTTTAAAAAAA
1 ATTAATTTAAAAAAA
148055 ATTAATTGTAAAAAAA
1 ATTAATT-TAAAAAAA
*
148071 ATTGA-TTAAAATAAA
1 ATTAATTTAAAA-AAA
148086 A
1 A
148087 AAAGAGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 12 0.43
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (15 bp):
ATTAATTTAAAAAAA
Found at i:150261 original size:3 final size:3
Alignment explanation
Indices: 150253--150280 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
150243 TGGGTGATTG
150253 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
150281 GTTGGGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:150846 original size:22 final size:21
Alignment explanation
Indices: 150818--150883 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
150808 ATTTTTAAAA
150818 ATAAAAA-CAATTCAAAAAATTT
1 ATAAAAATC-ATT-AAAAAATTT
150840 ATAAAAATCATTAAAAAATTT
1 ATAAAAATCATTAAAAAATTT
*
150861 TTAAAAAT--TT-AAAAATTT
1 ATAAAAATCATTAAAAAATTT
150879 A-AAAA
1 ATAAAA
150884 TTAAAATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.10
18 8 0.20
19 2 0.05
21 16 0.39
22 10 0.24
23 1 0.02
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAAAATCATTAAAAAATTT
Found at i:150873 original size:8 final size:8
Alignment explanation
Indices: 150860--150889 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
150850 TTAAAAAATT
150860 TTTAAAAA
1 TTTAAAAA
150868 TTTAAAAA
1 TTTAAAAA
150876 TTTAAAAA
1 TTTAAAAA
150884 -TTAAAA
1 TTTAAAA
150890 TAAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TTTAAAAA
Found at i:153348 original size:2 final size:2
Alignment explanation
Indices: 153332--153383 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
153322 AAACAGTCAG
*
153332 TA TA -A TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
153373 TA TA TA TA TA T
1 TA TA TA TA TA T
153384 CAAGTCTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:161329 original size:17 final size:18
Alignment explanation
Indices: 161304--161341 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
161294 GCCCAAAGTT
161304 AGAGAAGAAAGA-AGAAA
1 AGAGAAGAAAGAGAGAAA
* *
161321 AGAGTAGAAATAGAGAAA
1 AGAGAAGAAAGAGAGAAA
161339 AGA
1 AGA
161342 AAAGGGAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (18 bp):
AGAGAAGAAAGAGAGAAA
Found at i:167449 original size:29 final size:28
Alignment explanation
Indices: 167408--167486 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
167398 TTTTAGAGGT
* *
167408 ATTTAAGTTATTTTCTGTGATCTAGAAAC
1 ATTTTAGTCATTTTCT-TGATCTAGAAAC
* * *
167437 ATTTTTGTCA-TTTCTTGCATTCTAGCACC
1 ATTTTAGTCATTTTCTTG-A-TCTAGAAAC
167466 ATTTTAGTCATTTTCTATGAT
1 ATTTTAGTCATTTTCT-TGAT
167487 TTAAGAGTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
27 2 0.05
28 6 0.15
29 24 0.60
30 6 0.15
31 2 0.05
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.49
Consensus pattern (28 bp):
ATTTTAGTCATTTTCTTGATCTAGAAAC
Found at i:167613 original size:29 final size:28
Alignment explanation
Indices: 167573--167667 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 28
167563 TTTCATACTA
*
167573 TTTTAGGGTCATTTTAGTAATTTGACATC
1 TTTTAGAGTCATTTTAGTAATTTG-CATC
* *
167602 TTTTAGTGTCA-TTTATGTAAATT-CATGC
1 TTTTAGAGTCATTTTA-GTAATTTGCAT-C
* *
167630 ATTTTAGAGTCATTTTAATAATTTGTCATG
1 -TTTTAGAGTCATTTTAGTAATTTG-CATC
167660 TTTTAGAG
1 TTTTAGAG
167668 ATTTTATGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.06
28 5 0.09
29 39 0.72
30 4 0.07
31 3 0.06
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.49
Consensus pattern (28 bp):
TTTTAGAGTCATTTTAGTAATTTGCATC
Found at i:170988 original size:13 final size:13
Alignment explanation
Indices: 170970--170994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
170960 ATGTTGCACA
170970 GTATCGATACATT
1 GTATCGATACATT
170983 GTATCGATACAT
1 GTATCGATACAT
170995 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:171007 original size:20 final size:21
Alignment explanation
Indices: 170982--171034 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
170972 ATCGATACAT
**
170982 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
171002 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
171023 TGTATCGATACA
1 TGTATCGATACA
171035 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:175810 original size:328 final size:331
Alignment explanation
Indices: 175222--176244 Score: 1104
Period size: 328 Copynumber: 3.1 Consensus size: 331
175212 AAAACATTAG
** * * *
175222 ATGAATTTTAAAAATTTTAAATCAAGAAAAATTCC-CCCGAAAA-AATTTATGGAGTAGAAAACT
1 ATGAATTTTAAAAATTAAAAACCAAGAAAAA-TCCTCCTGAAAATAA-TTACGGAGTAGAAAACT
* * * * * ** * *
175285 C-AGTTTTTTAGAGAA-AGGA-AATTTCAGGAAAAAAATTCAAAA-TACATGGAAATGAATGAAT
64 CTA-TTTCTCA-AAAATAGGAGAATTTCAAGAAGAAAA-TCAAAATTTTATGAAAATGAATAAAT
* * *
175346 TTTTGAA-AA-TAAATTAATATAAAATAAATAATAATATTTGAAGAATTTTAAAAATTAAAACTA
126 TTTT-AAGAACTGATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAC-A
* *
175409 AT-AAAAAT-CTCCTCGAAAAAATTTACGGAGTAGAAAACTCTA-TATTTCAAAAAAAGAGAAAT
189 ATGAAAAATCCT-C-CGAAAAAATTTACGGAGTAGAAAA-TCTATTTTTTGAAAAAAAGAGAAAT
* *
175471 TTCAA-GAAAAAAATCAAACTTTTATGAAAATGAATGAATTTTTGAGATCTCATTTAATATGAAA
251 TTCAAGGAAAAAAATCAAAATTTTATGAAAATGAATGAATTTTTGAGATCTGATTTAATATGAAA
175535 TAAATAATAATATTTT
316 TAAATAATAATATTTT
* * * * * *
175551 ATGAATTTCAAAAATTAAAAGCCAAGAAAAATCCTCTTGAGAAA-ATTTACGTAGTAGAAAACTT
1 ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCTGA-AAATAATTACGGAGTAGAAAACTC
* * *
175615 TATTTCTCAAAAA-A-GAGGAATTTCAAGGA-AAAATCAAAATTTTATGAACATGAATGAA-TTT
65 TATTTCTCAAAAATAGGA-GAATTTCAAGAAGAAAATCAAAATTTTATGAAAATGAATAAATTTT
* * *
175676 TAAGAACTGATTTAATATGAAATAAATAATATTATTTGATGAATTTTAAAAATTAAAAACCATGA
129 TAAGAACTGATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATT-AAAACAATGA
175741 AAAATCCTCCG-AAAAATTTACGGAGTAGAAAATCTATTTTTTGAAAAAAAG-GAGAATTTCAAG
193 AAAATCCTCCGAAAAAATTTACGGAGTAGAAAATCTATTTTTTGAAAAAAAGAGA-AATTTCAAG
* * * *
175804 GAAAAAAATCAAAATTTTATGAAAATGATTGAATTTGTGGGAAT-TGATTTAATATAAAATAAAT
257 GAAAAAAATCAAAATTTTATGAAAATGAATGAATTTTTGAG-ATCTGATTTAATATGAAATAAAT
175868 AATAATATTTT
321 AATAATATTTT
* * * *
175879 AAGAATTTTAAAAATTAAAAACCAAAAAAAAATTCTCCTGAAAATAATTATGGAGTAGAAAACTC
1 ATGAATTTTAAAAATTAAAAACC-AAGAAAAATCCTCCTGAAAATAATTACGGAGTAGAAAACTC
* *
175944 TGTTTTTCAAAAATAGGAGAATTTCAAGAAGAAAATCAAAATTTTATGAAAATGAATAAATTTTT
65 TATTTCTCAAAAATAGGAGAATTTCAAGAAGAAAATCAAAATTTTATGAAAATGAATAAATTTTT
* * *
176009 TAGAACTGATTTAATATTAAATAAATGATAATATTTGATGAATTTTAAAAAATTTAAAACTAA-G
130 AAGAACTGATTTAATATAAAATAAATAATAATATTTGATGAATTTT-AAAAA-TTAAAAC-AATG
* *
176073 AAAAATCCTTCCGAAAAAATTTACGGAGTAGAAAA-CTTCGTTTTTTG-AAAACAGAGAAATTT-
192 AAAAATCC-TCCGAAAAAATTTACGGAGTAGAAAATC-T-ATTTTTTGAAAAAAAGAGAAATTTC
** * * ** * * * * * * *
176135 TGGGGAAAAATTCAAAAACTAATGAAAATAAAAGAATTTTTGAAAACTGATTTTATATGAATTAA
254 AAGGAAAAAAATCAAAATTTTATGAAAATGAATGAATTTTTGAGATCTGATTTAATATGAAATAA
*
176200 ATAATAATATTTG
319 ATAATAATATTTT
* *
176213 ATGAATTTTGAATATTAAAAACCAAGAAAAAT
1 ATGAATTTTAAAAATTAAAAACCAAGAAAAAT
176245 TCTTCCGAAA
Statistics
Matches: 586, Mismatches: 78, Indels: 56
0.81 0.11 0.08
Matches are distributed among these distances:
326 8 0.01
327 55 0.09
328 160 0.27
329 113 0.19
330 19 0.03
331 29 0.05
332 46 0.08
333 28 0.05
334 86 0.15
335 33 0.06
336 9 0.02
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (331 bp):
ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCTGAAAATAATTACGGAGTAGAAAACTCT
ATTTCTCAAAAATAGGAGAATTTCAAGAAGAAAATCAAAATTTTATGAAAATGAATAAATTTTTA
AGAACTGATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAACAATGAAAA
ATCCTCCGAAAAAATTTACGGAGTAGAAAATCTATTTTTTGAAAAAAAGAGAAATTTCAAGGAAA
AAAATCAAAATTTTATGAAAATGAATGAATTTTTGAGATCTGATTTAATATGAAATAAATAATAA
TATTTT
Found at i:176024 original size:167 final size:163
Alignment explanation
Indices: 175221--176256 Score: 1068
Period size: 167 Copynumber: 6.3 Consensus size: 163
175211 GAAAACATTA
** * * *
175221 GATGAATTTTAAAAATTTTAAATCAAGAAAAATTCCCCCGAAAAAATTTATGGAGTAGAAAACTC
1 GATGAATTTTAAAAATTAAAAACCAAGAAAAATT-CTCCGAAAAAA-TTACGGAGTAGAAAACTC
* * * * ** *
175286 AGTTTTTTAGAGAAAGGA-AATTTCAGGAAAAAAATTCAAAA-TACATGGAAATGAATGAATTTT
64 TGTTTTTCA-AAAAAGGAGAATTTCAAGAAAAAAA-TCAAAATTTTATGAAAATGAATGAATTTT
* * * *
175349 TGA-AAATAAATTAATATAAAATAAATAATAATATTT
127 TGAGAACTGATTTAATATGAAATAAATAATAATATTT
* * *
175385 GAAGAATTTTAAAAATT-AAAACTAATAAAAA-TCTCCTCGAAAAAATTTACGGAGTAGAAAACT
1 GATGAATTTTAAAAATTAAAAACCAAGAAAAATTCT-C-CGAAAAAA-TTACGGAGTAGAAAACT
* * * *
175448 CTATATTTCAAAAAAAGAGAAATTTCAAGAAAAAAATCAAACTTTTATGAAAATGAATGAATTTT
63 CTGTTTTTCAAAAAAGGAG-AATTTCAAGAAAAAAATCAAAATTTTATGAAAATGAATGAATTTT
* *
175513 TGAGATCTCATTTAATATGAAATAAATAATAATATTT
127 TGAGAACTGATTTAATATGAAATAAATAATAATATTT
* * * * * * * *
175550 TATGAATTTCAAAAATTAAAAGCCAAGAAAAATCCTCTTGAGAAAATTTACGTAGTAGAAAACTT
1 GATGAATTTTAAAAATTAAAAACCAAGAAAAATTCTC-CGA-AAAAATTACGGAGTAGAAAACTC
* * * *
175615 TATTTCTCAAAAAA-GAGGAATTTCAAG-GAAAAATCAAAATTTTATGAACATGAATGAA-TTTT
64 TGTTTTTCAAAAAAGGA-GAATTTCAAGAAAAAAATCAAAATTTTATGAAAATGAATGAATTTTT
* *
175677 AAGAACTGATTTAATATGAAATAAATAATATTATTT
128 GAGAACTGATTTAATATGAAATAAATAATAATATTT
* * *
175713 GATGAATTTTAAAAATTAAAAACCATGAAAAATCCTCCGAAAAATTTACGGAGTAGAAAA-TCTA
1 GATGAATTTTAAAAATTAAAAACCAAGAAAAATTCTCCGAAAAAATTACGGAGTAGAAAACTCT-
* * * *
175777 TTTTTTGAAAAAAAGGAGAATTTCAAGGAAAAAAATCAAAATTTTATGAAAATGATTGAATTTGT
65 GTTTTT-CAAAAAAGGAGAATTTCAA-GAAAAAAATCAAAATTTTATGAAAATGAATGAATTTTT
* * *
175842 GGGAATTGATTTAATATAAAATAAATAATAATATTT
128 GAGAACTGATTTAATATGAAATAAATAATAATATTT
* * * *
175878 TAAGAATTTTAAAAATTAAAAACCAAAAAAAAATTCTCCTGAAAATAATTATGGAGTAGAAAACT
1 GATGAATTTTAAAAATTAAAAACC-AAGAAAAATTCTCC-GAAAA-AATTACGGAGTAGAAAACT
* *
175943 CTGTTTTTCAAAAATAGGAGAATTTCAAGAAGAAAATCAAAATTTTATGAAAATGAATAAATTTT
63 CTGTTTTTCAAAAA-AGGAGAATTTCAAGAAAAAAATCAAAATTTTATGAAAATGAATGAATTTT
* * *
176008 TTAGAACTGATTTAATATTAAATAAATGATAATATTT
127 TGAGAACTGATTTAATATGAAATAAATAATAATATTT
* * *
176045 GATGAATTTTAAAAAATTTAAAACTAAGAAAAATCCTTCCGAAAAAATTTACGGAGTAGAAAACT
1 GATGAATTTT-AAAAATTAAAAACCAAGAAAAATTC-TCCGAAAAAA-TTACGGAGTAGAAAACT
* * *** * * ** * * *
176110 -TCGTTTTTTGAAAACA-GAGAAATTTTGGGGAAAAATTCAAAAACTAATGAAAATAAAAGAATT
63 CT-G-TTTTTCAAAAAAGGAG-AATTTCAAGAAAAAAATCAAAATTTTATGAAAATGAATGAATT
* * *
176173 TTTGAAAACTGATTTTATATGAATTAAATAATAATATTT
125 TTTGAGAACTGATTTAATATGAAATAAATAATAATATTT
* *
176212 GATGAATTTTGAATATTAAAAACCAAGAAAAATTCTTCCGAAAAA
1 GATGAATTTTAAAAATTAAAAACCAAGAAAAATTC-TCCGAAAAA
176257 TTTATAGAGT
Statistics
Matches: 733, Mismatches: 112, Indels: 52
0.82 0.12 0.06
Matches are distributed among these distances:
160 2 0.00
161 24 0.03
162 25 0.03
163 118 0.16
164 109 0.15
165 109 0.15
166 91 0.12
167 195 0.27
168 57 0.08
169 3 0.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (163 bp):
GATGAATTTTAAAAATTAAAAACCAAGAAAAATTCTCCGAAAAAATTACGGAGTAGAAAACTCTG
TTTTTCAAAAAAGGAGAATTTCAAGAAAAAAATCAAAATTTTATGAAAATGAATGAATTTTTGAG
AACTGATTTAATATGAAATAAATAATAATATTT
Found at i:177777 original size:41 final size:41
Alignment explanation
Indices: 177729--177910 Score: 145
Period size: 41 Copynumber: 4.4 Consensus size: 41
177719 GTTTACCAAG
* * *
177729 GACTGAGCCGACAGGTAAACAATGGATGAAGGTTGATCGGA
1 GACTAAGCTGACAGGTAAACAATGGATGAAAGTTGATCGGA
* * * * * * * *
177770 GATTGAGCTGATAGGTCACCATAATGG-T-AATGGGTTTATCGGG
1 GACTAAGCTGACAGGT-A-AACAATGGATGAA--AGTTGATCGGA
* * * *
177813 GACTAAGGTGACCGGTAAATAGTGGATGAAAGTTGATCGGA
1 GACTAAGCTGACAGGTAAACAATGGATGAAAGTTGATCGGA
*
177854 GACTAAGCTGACAGGTAAACAATGGATGAAAGTTGATCAGA
1 GACTAAGCTGACAGGTAAACAATGGATGAAAGTTGATCGGA
*
177895 AACCT-AGCTGACAGGT
1 GA-CTAAGCTGACAGGT
177911 CACCATAATG
Statistics
Matches: 111, Mismatches: 23, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
41 77 0.69
42 6 0.05
43 28 0.25
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (41 bp):
GACTAAGCTGACAGGTAAACAATGGATGAAAGTTGATCGGA
Found at i:177806 original size:84 final size:84
Alignment explanation
Indices: 177567--177869 Score: 231
Period size: 84 Copynumber: 3.6 Consensus size: 84
177557 CCTAGGATTG
* * * * *
177567 AGCCGACAGGTAAACAATGGATGGAGGTTGACCAAAGACTGAG-TAATAGGTCACCATAAGGGTA
1 AGCCGACAGGTAAACAATGGATGAAAGTTGACCAGAGACTGAGCTGATAGGTCACCATAAAGGTA
* * * *
177631 GTTGGTTTACTGGGGACTA
66 ATGGGTTTACCGAGGACTA
* * * *
177650 AGTCGATAGGTAAATAATGGATGAAAGTTGACCAGAAACT-AGGCTGATAAGGT--CC-TAAAGA
1 AGCCGACAGGTAAACAATGGATGAAAGTTGACCAGAGACTGA-GCTGAT-AGGTCACCATAAAG-
* * *
177711 G-AGAAGAGGTTTACCAAGGACTG
63 GTA-ATG-GGTTTACCGAGGACTA
* * * * *
177734 AGCCGACAGGTAAACAATGGATGAAGGTTGATCGGAGATTGAGCTGATAGGTCACCATAATGGTA
1 AGCCGACAGGTAAACAATGGATGAAAGTTGACCAGAGACTGAGCTGATAGGTCACCATAAAGGTA
* *
177799 ATGGGTTTATCGGGGACTA
66 ATGGGTTTACCGAGGACTA
** * * * * * * *
177818 AGGTGACCGGTAAATAGTGGATGAAAGTTGATCGGAGACTAAGCTGACAGGT
1 AGCCGACAGGTAAACAATGGATGAAAGTTGACCAGAGACTGAGCTGATAGGT
177870 AAACAATGGA
Statistics
Matches: 170, Mismatches: 39, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
82 6 0.04
83 41 0.24
84 108 0.64
85 10 0.06
86 5 0.03
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (84 bp):
AGCCGACAGGTAAACAATGGATGAAAGTTGACCAGAGACTGAGCTGATAGGTCACCATAAAGGTA
ATGGGTTTACCGAGGACTA
Found at i:177833 original size:168 final size:167
Alignment explanation
Indices: 177545--177848 Score: 423
Period size: 168 Copynumber: 1.8 Consensus size: 167
177535 TCACCAAGGA
* * * *
177545 AGAAAAGGTTTGCCTAGGATTGAGCCGACAGGTAAACAATGGATGGAGGTTGACCAAAGACTGAG
1 AGAAAAGGTTTACCAAGGACTGAGCCGACAGGTAAACAATGGATGAAGGTTGACCAAAGACTGAG
* * *
177610 TAATAGGTCACCATAAGGGTAGTTGGTTTACTGGGGACTAAGTCGATAGGTAAATAATGGATGAA
66 TAATAGGTCACCATAAGGGTAATGGGTTTACTGGGGACTAAGTCGACAGGTAAATAATGGATGAA
177675 AGTTGACCAGAAACTAGGCTGATAAGGTCCTAAAGAG
131 AGTTGACCAGAAACTAGGCTGATAAGGTCCTAAAGAG
* * ** *
177712 AGAAGAGGTTTACCAAGGACTGAGCCGACAGGTAAACAATGGATGAAGGTTGATCGGAGATTGAG
1 AGAAAAGGTTTACCAAGGACTGAGCCGACAGGTAAACAATGGATGAAGGTTGACCAAAGACTGAG
* * * *
177777 CTGATAGGTCACCATAATGGTAATGGGTTTA-TCGGGGACTAAGGT-GACCGGTAAATAGTGGAT
66 -TAATAGGTCACCATAAGGGTAATGGGTTTACT-GGGGACTAA-GTCGACAGGTAAATAATGGAT
177840 GAAAGTTGA
128 GAAAGTTGA
177849 TCGGAGACTA
Statistics
Matches: 118, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
167 57 0.48
168 59 0.50
169 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.22
Consensus pattern (167 bp):
AGAAAAGGTTTACCAAGGACTGAGCCGACAGGTAAACAATGGATGAAGGTTGACCAAAGACTGAG
TAATAGGTCACCATAAGGGTAATGGGTTTACTGGGGACTAAGTCGACAGGTAAATAATGGATGAA
AGTTGACCAGAAACTAGGCTGATAAGGTCCTAAAGAG
Found at i:177973 original size:125 final size:125
Alignment explanation
Indices: 177729--177994 Score: 279
Period size: 125 Copynumber: 2.1 Consensus size: 125
177719 GTTTACCAAG
* * * * * *
177729 GACTGAGCCGACAGGTAAACAATGGATGAAGGTTGATCGGAGATTGAGCTGATAGGTCACCATAA
1 GACTAAGCCGACAGGTAAACAATGGATGAAAGTTGATCAGAAACTGAGCTGACAGGTCACCATAA
* * *** ** *
177794 TGGTAATGGGTTTATCGGGGACTAAGGTGACCGGTAAATAGTGGATGAAAGTTGATCGGA
66 TGGTAATGAGTTTATCGAGGACTAAGCCAACAAGTAAAGAGTGGATGAAAGTTGATCGGA
*
177854 GACTAAGCTGACAGGTAAACAATGGATGAAAGTTGATCAGAAACCT-AGCTGACAGGTCACCATA
1 GACTAAGCCGACAGGTAAACAATGGATGAAAGTTGATCAGAAA-CTGAGCTGACAGGTCACCATA
* * * *
177918 ATGGTAAT-AGTTTATCGAGGATTGAGCCAACAAGTAAACGA-TGGAT-AAAGGGTTGATTGGG
65 ATGGTAATGAGTTTATCGAGGACTAAGCCAACAAGTAAA-GAGTGGATGAAA--GTTGATCGGA
* *
177979 GACTAAGTCGATAGGT
1 GACTAAGCCGACAGGT
177995 CACCAAGGAA
Statistics
Matches: 115, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
123 3 0.03
124 26 0.23
125 85 0.74
126 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (125 bp):
GACTAAGCCGACAGGTAAACAATGGATGAAAGTTGATCAGAAACTGAGCTGACAGGTCACCATAA
TGGTAATGAGTTTATCGAGGACTAAGCCAACAAGTAAAGAGTGGATGAAAGTTGATCGGA
Found at i:186030 original size:159 final size:159
Alignment explanation
Indices: 185666--186049 Score: 424
Period size: 159 Copynumber: 2.4 Consensus size: 159
185656 GATGAAAGAT
* *
185666 TTGATATTTTGGAGATAAAA-TCGAGGTTGGAGTATCCCCTCAAAAAT-AGTGGGGTTAGAGTAT
1 TTGATATTTTGGAGATAAAACTAGA-GTTGGAGTATCCCCTCAAAAATAACT-GGGTTAGAGTAT
** * * *
185729 CCCTGATACGAAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCCCTTTAGAAAATA
64 CCCCAATACGAAAATATTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCCCCTCAGAAAATA
*
185794 ACAGGGTTGAAGTATCCACAAGAGTGAAAAA
129 ACAGGATTGAAGTATCCACAAGAGTGAAAAA
* * ** * * *
185825 TCGATATTTTGGAGACAAAACCGGGGTTAGAGTATCCCCTCAAAAATAACTGGGTTGGAGTATCC
1 TTGATATTTTGGAGATAAAACTAGAGTTGGAGTATCCCCTCAAAAATAACTGGGTTAGAGTATCC
** * *
185890 CCAATGGTGAAAA-ATTGATATTTT-AGAAAT-AAAACCGAGGTTGGAGTATCCCCTCA-AAAAT
66 CCAAT-ACGAAAATATTAATATTTTGA-AAATAAAAACAG-GGTTGGAGTATCCCCTCAGAAAAT
* * *
185951 AACAGGATTGGAGTATCCCCAATGA-TGACAAA
128 AACAGGATTGAAGTATCCACAA-GAGTGAAAAA
* * *
185983 TTGATATTTTGGAAATAAAACTAGAGTTGGAGTAACCCCTTCGAAAATAAC-GGGTTAGAGTATC
1 TTGATATTTTGGAGATAAAACTAGAGTTGGAGTATCCCC-TCAAAAATAACTGGGTTAGAGTATC
186047 CCC
65 CCC
186050 TCAAAAATAA
Statistics
Matches: 187, Mismatches: 31, Indels: 15
0.80 0.13 0.06
Matches are distributed among these distances:
158 83 0.44
159 96 0.51
160 8 0.04
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (159 bp):
TTGATATTTTGGAGATAAAACTAGAGTTGGAGTATCCCCTCAAAAATAACTGGGTTAGAGTATCC
CCAATACGAAAATATTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCCCCTCAGAAAATAAC
AGGATTGAAGTATCCACAAGAGTGAAAAA
Found at i:186044 original size:28 final size:29
Alignment explanation
Indices: 186012--186079 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
186002 ACTAGAGTTG
* *
186012 GAGTAACCCCTTCGAAAATAACG-GGTTA
1 GAGTATCCCCTTCAAAAATAACGTGGTTA
* *
186040 GAGTATCCCC-TCAAAAATAATGTGGTTG
1 GAGTATCCCCTTCAAAAATAACGTGGTTA
186068 GAGTATCCCCTT
1 GAGTATCCCCTT
186080 TTGATGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.29
28 23 0.68
29 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (29 bp):
GAGTATCCCCTTCAAAAATAACGTGGTTA
Found at i:186049 original size:79 final size:78
Alignment explanation
Indices: 185655--186049 Score: 368
Period size: 79 Copynumber: 5.0 Consensus size: 78
185645 GTACATCCCC
* * ***
185655 TGATGAAAGATTTGATATTTTGGAGATAAAATC-GAGGTTGGAGTATCCCCTCAAAAATAGTGGG
1 TGATGAAA-AATTGATATTTTGGAAATAAAA-CAGA-GTTGGAGTATCCCCTCAAAAATAACAGG
**
185719 GTTAGAGTATCCCTGA
63 GTTAGAGTATCCCCAA
* * * * * * *
185735 T-ACGAAAATTTTAATATTTTGAAAATAAAAACAGGGTTGGAGTATCCCTTTAGAAAATAACAGG
1 TGATGAAAA-ATTGATATTTTGGAAAT-AAAACAGAGTTGGAGTATCCCCTCA-AAAATAACAGG
*
185799 GTT-GAAGTATCCACAA
63 GTTAG-AGTATCCCCAA
* * * * * * *
185815 -GAGTGAAAAATCGATATTTTGGAGACAAAACCGGGGTTAGAGTATCCCCTCAAAAATAACTGGG
1 TGA-TGAAAAATTGATATTTTGGAAATAAAA-CAGAGTTGGAGTATCCCCTCAAAAATAACAGGG
*
185879 TTGGAGTATCCCCAA
64 TTAGAGTATCCCCAA
* * * *
185894 TGGTGAAAAATTGATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCAAAAATAACAGGAT
1 TGATGAAAAATTGATATTTTGGAAATAAAACAGA-GTTGGAGTATCCCCTCAAAAATAACAGGGT
*
185959 TGGAGTATCCCCAA
65 TAGAGTATCCCCAA
* * *
185973 TGATGACAAATTGATATTTTGGAAATAAAACTAGAGTTGGAGTAACCCCTTCGAAAATAAC-GGG
1 TGATGAAAAATTGATATTTTGGAAATAAAAC-AGAGTTGGAGTATCCCC-TCAAAAATAACAGGG
186037 TTAGAGTATCCCC
64 TTAGAGTATCCCC
186050 TCAAAAATAA
Statistics
Matches: 258, Mismatches: 44, Indels: 27
0.78 0.13 0.08
Matches are distributed among these distances:
78 3 0.01
79 182 0.71
80 68 0.26
81 5 0.02
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (78 bp):
TGATGAAAAATTGATATTTTGGAAATAAAACAGAGTTGGAGTATCCCCTCAAAAATAACAGGGTT
AGAGTATCCCCAA
Found at i:191883 original size:20 final size:20
Alignment explanation
Indices: 191854--191929 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
191844 AAAGTACCCA
191854 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * * *
191874 AATATATCGATATATGTATG
1 AATGTATCGATACATTTTTC
*
191894 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTTTTC
*
191914 AATGTATTGATACATT
1 AATGTATCGATACATT
191930 CTGTCTTTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:205842 original size:19 final size:17
Alignment explanation
Indices: 205805--205864 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 17
205795 CCTTTATACC
*
205805 AAAAACAAACAAACAAA
1 AAAAACAAAAAAACAAA
*
205822 AAAAACAGAAAAAACCAA
1 AAAAACA-AAAAAACAAA
205840 AAAAACAACAAAAAACAAA
1 AAAAAC-A-AAAAAACAAA
205859 AAAAAC
1 AAAAAC
205865 CAAGAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.19
18 14 0.38
19 16 0.43
ACGTcount: A:0.82, C:0.17, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAAAACAAA
Found at i:205863 original size:9 final size:9
Alignment explanation
Indices: 205805--205874 Score: 79
Period size: 9 Copynumber: 7.6 Consensus size: 9
205795 CCTTTATACC
205805 AAAAAC-AA
1 AAAAACAAA
*
205813 ACAAACAAA
1 AAAAACAAA
*
205822 AAAAACAGA
1 AAAAACAAA
*
205831 AAAAACCAA
1 AAAAACAAA
205840 AAAAACAACA
1 AAAAACAA-A
205850 AAAAACAAA
1 AAAAACAAA
205859 AAAAACCAAGA
1 AAAAA-CAA-A
205870 AAAAA
1 AAAAA
205875 ATAGCAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
8 5 0.10
9 29 0.56
10 12 0.23
11 6 0.12
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAACAAA
Found at i:205872 original size:19 final size:18
Alignment explanation
Indices: 205805--205873 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
205795 CCTTTATACC
*
205805 AAAAACAA-ACAAACAAA
1 AAAAACAAGAAAAACAAA
*
205822 AAAAAC-AGAAAAAACCAA
1 AAAAACAAG-AAAAACAAA
*
205840 AAAAACAACAAAAAACAAA
1 AAAAACAA-GAAAAACAAA
205859 AAAAACCAAGAAAAA
1 AAAAA-CAAGAAAAA
205874 AATAGCAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 1 0.02
17 6 0.14
18 13 0.31
19 19 0.45
20 3 0.07
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAACAAGAAAAACAAA
Found at i:207195 original size:28 final size:28
Alignment explanation
Indices: 207098--207789 Score: 838
Period size: 28 Copynumber: 24.5 Consensus size: 28
207088 CATTCATCTC
* *
207098 TTCAAAGCCTACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
207126 TTC-AA--CCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* *
207152 TTTAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
207180 CTCAAAGCCCACAAGTCAGTGGCATCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
207208 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
207237 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
207265 TTTAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
207293 TTTAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
207321 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
207349 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * *
207378 TTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
207406 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** *
207434 TTCAAAGCCCACGCAAGTCAGTTTCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCATCCT
* *
207464 TTCAAAGCCTACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * *
207493 TTCAAAGCCCACAAGTTAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
207521 TT-TAA--CCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
*
207547 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
207575 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
207603 TTCTAAGCCCACAAATCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
207631 TTCAAAGCCCACGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCATCCT
*
207661 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * * * *
207690 TTCAAAGCTCATAAGTTAATGGAATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
207718 TTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
207746 TTCAAAGCCGACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
*
207775 TTCAATGCCCACAAG
1 TTCAAAGCCCACAAG
207790 CTAGTGGTAA
Statistics
Matches: 571, Mismatches: 76, Indels: 33
0.84 0.11 0.05
Matches are distributed among these distances:
25 30 0.05
26 8 0.01
27 8 0.01
28 338 0.59
29 138 0.24
30 49 0.09
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:207244 original size:85 final size:84
Alignment explanation
Indices: 207098--207789 Score: 883
Period size: 85 Copynumber: 8.2 Consensus size: 84
207088 CATTCATCTC
* * * *
207098 TTCAAAGCCTACAAGTCAGTGGCACCCTTTC-AA--CCACAAGTCAGTGGCACTCTTTTTAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGC
*
207160 CCACAAGTTAGTGGCATCCT
65 CCACAAGTCAGTGGCATCCT
* * * *
207180 CTCAAAGCCCACAAGTCAGTGGCATCCCTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGC
207245 CCACAAGTCAGTGGCATCCT
65 CCACAAGTCAGTGGCATCCT
* *
207265 TTTAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
*
207330 CACAAGTCAGTGGCACCCT
66 CACAAGTCAGTGGCATCCT
* * *
207349 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCATAAGTTAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
*
207414 CCACAAGTTAGTGGCATCCT
65 CCACAAGTCAGTGGCATCCT
** * * *
207434 TTCAAAGCCCACGCAAGTCAGTTTCACCCTTTCAAAGCCTACAAGTCAGTGGCACTCTTTTCAAA
1 TTCAAAGCCCA--CAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAA
* * *
207499 GCCCACAAGTTAATGGCACCCT
63 GCCCACAAGTCAGTGGCATCCT
* * *
207521 TT-TAA--CCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
*
207583 CCACAAGTTAGTGGCATCCT
65 CCACAAGTCAGTGGCATCCT
* *
207603 TTCTAAGCCCACAAATCAGTGGCATCCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAG
*
207668 CCCACAAGTCAGTGGCACTCTT
64 CCCACAAGTCAGTGGCA-TCCT
* * * * * *
207690 TTCAAAGCTCATAAGTTAATGGAATCCTTTCAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* *
207755 GACAAGTCAGTGGCACTCTT
66 CACAAGTCAGTGGCA-TCCT
*
207775 TTCAATGCCCACAAG
1 TTCAAAGCCCACAAG
207790 CTAGTGGTAA
Statistics
Matches: 538, Mismatches: 58, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
82 67 0.12
83 31 0.06
84 69 0.13
85 229 0.43
86 66 0.12
87 76 0.14
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (84 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
CACAAGTCAGTGGCATCCT
Found at i:207796 original size:57 final size:57
Alignment explanation
Indices: 207098--207789 Score: 888
Period size: 57 Copynumber: 12.3 Consensus size: 57
207088 CATTCATCTC
* *
207098 TTCAAAGCCTACAAGTCAGTGGCACCCTTTC-AA--CCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * * *
207152 TTTAAAGCCCACAAGTTAGTGGCATCCTCTCAAAGCCCACAAGTCAGTGGCA-TCCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
207208 TTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
207265 TTTAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
*
207321 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
207378 TTCAAAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
** * *
207434 TTCAAAGCCCACGCAAGTCAGTTTCACCCTTTCAAAGCCTACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * * *
207493 TTCAAAGCCCACAAGTTAATGGCACCCTTT-TAA--CCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
*
207547 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
207603 TTCTAAGCCCACAAATCAGTGGCATCCTTTCAAAGCCCACGCAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCCT
* * * * * *
207661 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCTCATAAGTTAATGG-AATCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
207718 TTCAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCGACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
*
207775 TTCAATGCCCACAAG
1 TTCAAAGCCCACAAG
207790 CTAGTGGTAA
Statistics
Matches: 553, Mismatches: 67, Indels: 33
0.85 0.10 0.05
Matches are distributed among these distances:
54 73 0.13
55 4 0.01
56 178 0.32
57 200 0.36
58 72 0.13
59 26 0.05
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
Found at i:208774 original size:20 final size:20
Alignment explanation
Indices: 208749--208799 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
208739 TACTCAGATG
* *
208749 TATCGATACATTTTTCAATA
1 TATCGATACATGTATCAATA
* *
208769 TATCGATACATGTATGAATG
1 TATCGATACATGTATCAATA
208789 TATCGATACAT
1 TATCGATACAT
208800 CTAGTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
TATCGATACATGTATCAATA
Found at i:216253 original size:162 final size:162
Alignment explanation
Indices: 215978--216280 Score: 419
Period size: 162 Copynumber: 1.9 Consensus size: 162
215968 CAAAAATATT
** * *
215978 AATTTAATTTAATTTTGTTTATTTTTAAAAATACCATTTCGTGCCCTAATGAAGCTCAAAAGAAT
1 AATTTAATTTAATTTAATTTATTTTTAAAAATAACATTTCGTGCCCTAATGAAGCCCAAAAGAAT
* * * **
216043 ACGAAATGTTTTTTGAAATCTTTTATACCCTTACGGATGCCCATAGGAATATAAAAGATTAGAAA
66 ACGAAAAGGTTTTTGAAATCTTTTATACCCCTACAAATGCCCATAGGAATATAAAAGATTAGAAA
*
216108 AAATAGATATTAGAATGTATCTCGATAATACC
131 AAATAAATATTAGAATGTATCTCGATAATACC
* * * * *
216140 AATTTAATTTAATTTAATTTATTTTTGAAAGTAACATTTTGTGCTCTAATGGAAGCCCGAAAGAA
1 AATTTAATTTAATTTAATTTATTTTTAAAAATAACATTTCGTGCCCTAAT-GAAGCCCAAAAGAA
* * * *
216205 TAC-AAAAGGTTTTTGAAATCTTTTATACCCCTATAAATTCCTATAGGAATATAAAAGATTAGAC
65 TACGAAAAGGTTTTTGAAATCTTTTATACCCCTACAAATGCCCATAGGAATATAAAAGATTAGAA
216269 AAAATAAATATT
130 AAAATAAATATT
216281 GTTTAATTTA
Statistics
Matches: 121, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
162 106 0.88
163 15 0.12
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (162 bp):
AATTTAATTTAATTTAATTTATTTTTAAAAATAACATTTCGTGCCCTAATGAAGCCCAAAAGAAT
ACGAAAAGGTTTTTGAAATCTTTTATACCCCTACAAATGCCCATAGGAATATAAAAGATTAGAAA
AAATAAATATTAGAATGTATCTCGATAATACC
Found at i:217375 original size:11 final size:11
Alignment explanation
Indices: 217359--217393 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
217349 CTAGCCTAGC
217359 TTTTCTATTTT
1 TTTTCTATTTT
217370 TTTTCTATATTT
1 TTTTCTAT-TTT
*
217382 TCTTCTATTTT
1 TTTTCTATTTT
217393 T
1 T
217394 CCTTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTCTATTTT
Found at i:218215 original size:19 final size:17
Alignment explanation
Indices: 218179--218218 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
218169 AAAACTCCGT
*
218179 ATTTCAAAAAAAAGAAA
1 ATTTCAAAAAAAACAAA
218196 ATTTCAAGAAAAAATCAAA
1 ATTTCAA-AAAAAA-CAAA
218215 ATTT
1 ATTT
218219 TATGAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 6 0.30
19 7 0.35
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (17 bp):
ATTTCAAAAAAAACAAA
Found at i:218562 original size:167 final size:166
Alignment explanation
Indices: 218003--219138 Score: 1387
Period size: 167 Copynumber: 6.9 Consensus size: 166
217993 AAATTTATGG
* * * * * *
218003 AGTAGAAAACT-AAGTTTTTCG-AAAAGGA-AATTTCAA-GAAAAATTCAAAA-TTCATGGAAAT
1 AGTAGAAAACTCCATTTTTTCGAAAAAAGAGAATTTCAAGGAAAAAATCAAAATTTTATGAAAAT
* * * * *
218063 GAATGAATTTTTGAAAACTAAATTAATATGAAATAAACAATAATATTTGATGAATTTTAAAAATC
66 GAATGAATTTTTGAGAACTGATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATT
* *
218128 AAAAACCAAGAAAAATCC-CCTCAACAAAATTTACGA
131 AAAAACCAAGAAAAATCCTCCTGAA-AAAATTTACAA
* * * *
218164 AGTAGAAAACTCC-GTATTTCAAAAAAAAGAAAATTTCAA-GAAAAAATCAAAATTTTATGAAAA
1 AGTAGAAAACTCCATTTTTTC-GAAAAAAGAGAATTTCAAGGAAAAAATCAAAATTTTATGAAAA
* *
218227 TGAATGAATTTTTGAGAACTGATTTAATTTAAAATAAATAATAATATTTGATGAATTTTAAAAAT
65 TGAATGAATTTTTGAGAACTGATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAAT
* * *
218292 TAAAAATCAAGAAAAATCCTCCCGAAAAAATTTACGA
130 TAAAAACCAAGAAAAATCCTCCTGAAAAAATTTACAA
* * *
218329 AGTAGAAAACTTCATTTTTT-GAAAAAAGAGAAATTTCAAGGAAAAAAACAAACTTTTATGAAAA
1 AGTAGAAAACTCCATTTTTTCGAAAAAAGAG-AATTTCAAGGAAAAAATCAAAATTTTATGAAAA
* * * *
218393 TGAATGAAATTTTAAGAACTAATTTAATATGAAATAAATAATAATATTTTATGAATTTTAAAAAT
65 TGAATGAATTTTTGAGAACTGATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAAT
*
218458 TAAAAAACTAAGAAAAATCCTCCTGAAAAAATTTACAA
130 T-AAAAACCAAGAAAAATCCTCCTGAAAAAATTTACAA
* * * *
218496 AATAAAAAACTCCATTTTTTCGAAAAAAGAGAATTTCAAGGAAAAAATCAAACTTTTATAAAAAT
1 AGTAGAAAACTCCATTTTTTCGAAAAAAGAGAATTTCAAGGAAAAAATCAAAATTTTATGAAAAT
* * * * *
218561 GAATTAATTTTTGAGAACTGCTTTAATATAAAATAAATAATAATATTTGATAAACTTTAAAAATT
66 GAATGAATTTTTGAGAACTGATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATT
* ***
218626 AAAAACCAAGAAAAATCC-CTTGAAAAAATTTATGG
131 AAAAACCAAGAAAAATCCTCCTGAAAAAATTTACAA
* * *
218661 AGTAGAAAACTTCA-TTTTTCG--AAAA-ACAATTTCAAGAAAAAAATCAAAATTTTATGAAAAT
1 AGTAGAAAACTCCATTTTTTCGAAAAAAGAGAATTTCAAGGAAAAAATCAAAATTTTATGAAAAT
218722 GAATGAATTTTTGAGAACTGATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATT
66 GAATGAATTTTTGAGAACTGATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATT
* * **
218787 AAAAACCAACAAAAATCATCCCAAAAAAATTTACAA
131 AAAAACCAAGAAAAATCCTCCTGAAAAAATTTACAA
* * **
218823 AATAGAAAACTCTA-TTTTTCGAAAAAAGGAGAATTTTTAGGAAAAAATCAAAATTTTATGAAAA
1 AGTAGAAAACTCCATTTTTTCGAAAAAA-GAGAATTTCAAGGAAAAAATCAAAATTTTATGAAAA
*
218887 TGAATGAATTTTTGAGAATTGATTTAAGTATGAAATAAATAATAATATTTGATGAATTTTAAAAA
65 TGAATGAATTTTTGAGAACTGATTTAA-TATGAAATAAATAATAATATTTGATGAATTTTAAAAA
* *
218952 TTAAAAACCAAGAAAAATCCTCC-CAAAAATATTTACAG
129 TTAAAAACCAAGAAAAATCCTCCTGAAAAA-ATTTACAA
* * * ** *
218990 AGTAGAAAACT-C-TGTTTTTCAAAAATAAAAGAATTTTAAGGAAAAAATTCAAAAACTAATGAA
1 AGTAGAAAACTCCAT-TTTTTCGAAAA-AAGAGAATTTCAAGGAAAAAA-TCAAAATTTTATGAA
* * * *
219053 AATAAAAGAATTTTTGA-AATCTAATTT--TATGTAAATTAAATAATAATATTTTGATAAATTTT
63 AATGAATGAATTTTTGAGAA-CTGATTTAATATG-AAA-TAAATAATAATA-TTTGATGAATTTT
*
219115 AAAAATTAAAAACTAAGAAAAATC
124 AAAAATTAAAAACCAAGAAAAATC
219139 ATTTCAAAAA
Statistics
Matches: 850, Mismatches: 99, Indels: 45
0.86 0.10 0.05
Matches are distributed among these distances:
161 125 0.15
162 33 0.04
163 6 0.01
164 39 0.05
165 143 0.17
166 172 0.20
167 253 0.30
168 79 0.09
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.30
Consensus pattern (166 bp):
AGTAGAAAACTCCATTTTTTCGAAAAAAGAGAATTTCAAGGAAAAAATCAAAATTTTATGAAAAT
GAATGAATTTTTGAGAACTGATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATT
AAAAACCAAGAAAAATCCTCCTGAAAAAATTTACAA
Found at i:218967 original size:494 final size:492
Alignment explanation
Indices: 218016--219160 Score: 1511
Period size: 494 Copynumber: 2.3 Consensus size: 492
218006 AGAAAACTAA
* * * *
218016 GTTTTTCG-AAAAGGA-AATTTCAA-GAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAA
1 GTTTTTCGAAAAAAGAGAATTTCAAGGAAAAAATCAAAATTAATGAAAATGAATGAATTTTTG-A
* * * * *
218078 AACTAAATTAATATGAAATAAACAATAATATTTGATGAATTTTAAAAATCAAAAACCAAGAAAAA
65 AACTAATTTAATATAAAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACCAAGAAAAA
* * *
218143 TCCCCTCAACAAAATTTACGAAGTAGAAAACTCCGTATTTCAAAAAAAAGAAAATTTCAAGAAAA
130 TCCCTTCAA-AAAATTTACGGAGTAGAAAACTCCATATTTC--AAAAAAGAAAATTTCAAGAAAA
*
218208 AATCAAAATTTTATGAAAATGAATGAATTTTTGAGAACTGATTTAATTTAAAATAAATAATAATA
192 AATCAAAATTTTATGAAAATGAATGAATTTTTGAGAACTGATTTAATATAAAATAAATAATAATA
* * * * * *
218273 TTTGATGAATTTTAAAAATTAAAAATCAAGAAAAATCCTCCCGAAAAAATTTACGAAGTAGAAAA
257 TTTGATGAATTTTAAAAATTAAAAACCAACAAAAATCATCCCAAAAAAATTTACAAAATAGAAAA
* *
218338 CTTCATTTTTTGAAAAAAGAGAAATTTCAAGGAAAAAAACAAACTTTTATGAAAATGAATGAAAT
322 CTTCATTTTTCGAAAAAAGAGAAATTTCAAGGAAAAAAACAAAATTTTATGAAAATGAATGAAAT
* *
218403 TTTAAGAACTAATTTAATATGAAATAAATAATAATATTTTATGAATTTTAAAAATTAAAAAACTA
387 TTTAAGAACTAATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAAACCA
*
218468 AGAAAAATCCTCCTGAAAAA-ATTTACAAAATAAAAAACTCCAT
452 AGAAAAATCCTCC-CAAAAATATTTACAAAATAAAAAACT-C-T
* * * *
218511 -TTTTTCGAAAAAAGAGAATTTCAAGGAAAAAATCAAACTTTTATAAAAATGAATTAATTTTTGA
1 GTTTTTCGAAAAAAGAGAATTTCAAGGAAAAAATCAAA-ATTAATGAAAATGAATGAATTTTTGA
** *
218575 GAACTGCTTTAATATAAAATAAATAATAATATTTGATAAACTTTAAAAATTAAAAACCAAGAAAA
65 -AACTAATTTAATATAAAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACCAAGAAAA
* * * * * *
218640 ATCCCTTGAAAAAATTTATGGAGTAGAAAACTTCATTTTTC-GAAAA-ACAATTTCAAGAAAAAA
129 ATCCCTTCAAAAAATTTACGGAGTAGAAAACTCCATATTTCAAAAAAGAAAATTTCAAG-AAAAA
*
218703 ATCAAAATTTTATGAAAATGAATGAATTTTTGAGAACTGATTTAATATGAAATAAATAATAATAT
193 ATCAAAATTTTATGAAAATGAATGAATTTTTGAGAACTGATTTAATATAAAATAAATAATAATAT
218768 TTGATGAATTTTAAAAATTAAAAACCAACAAAAATCATCCCAAAAAAATTTACAAAATAGAAAAC
258 TTGATGAATTTTAAAAATTAAAAACCAACAAAAATCATCCCAAAAAAATTTACAAAATAGAAAAC
** * *
218833 -TCTATTTTTCGAAAAAAG-GAGAATTTTTAGGAAAAAATCAAAATTTTATGAAAATGAATGAAT
323 TTC-ATTTTTCGAAAAAAGAGA-AATTTCAAGGAAAAAAACAAAATTTTATGAAAATGAATGAAA
* * *
218896 TTTTGAGAATTGATTTAAGTATGAAATAAATAATAATATTTGATGAATTTTAAAAATT-AAAAAC
386 TTTTAAGAACTAATTTAA-TATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAAAC
* * *
218960 CAAGAAAAATCCTCCCAAAAATATTTACAGAGTAGAAAACTCT
450 CAAGAAAAATCCTCCCAAAAATATTTACAAAATAAAAAACTCT
* * * * * *
219003 GTTTTTCAAAAATAAAAGAATTTTAAGGAAAAAATTCAAAAACTAATGAAAATAAAAGAATTTTT
1 GTTTTTCGAAAA-AAGAGAATTTCAAGGAAAAAA-TC-AAAATTAATGAAAATGAATGAATTTTT
* * * *
219068 GAAATCTAATTTTATGTAAATTAAATAATAATATTTTGATAAATTTTAAAAATTAAAAACTAAGA
63 GAAA-CTAATTTAATATAAAATAAATAATAATA-TTTGATAAATTTTAAAAATTAAAAACCAAGA
**
219133 AAAATCATTTC-AAAAATTTACGGAGTAG
126 AAAATCCCTTCAAAAAATTTACGGAGTAG
219161 GGGAACTTCA
Statistics
Matches: 566, Mismatches: 68, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
492 1 0.00
493 30 0.05
494 261 0.46
495 104 0.18
496 48 0.08
497 38 0.07
498 84 0.15
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (492 bp):
GTTTTTCGAAAAAAGAGAATTTCAAGGAAAAAATCAAAATTAATGAAAATGAATGAATTTTTGAA
ACTAATTTAATATAAAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACCAAGAAAAAT
CCCTTCAAAAAATTTACGGAGTAGAAAACTCCATATTTCAAAAAAGAAAATTTCAAGAAAAAATC
AAAATTTTATGAAAATGAATGAATTTTTGAGAACTGATTTAATATAAAATAAATAATAATATTTG
ATGAATTTTAAAAATTAAAAACCAACAAAAATCATCCCAAAAAAATTTACAAAATAGAAAACTTC
ATTTTTCGAAAAAAGAGAAATTTCAAGGAAAAAAACAAAATTTTATGAAAATGAATGAAATTTTA
AGAACTAATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAAACCAAGAA
AAATCCTCCCAAAAATATTTACAAAATAAAAAACTCT
Found at i:221756 original size:20 final size:21
Alignment explanation
Indices: 221717--221758 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
221707 AATTAATATG
*
221717 ATTTTTAACTAAATATATTTT
1 ATTTTTAACAAAATATATTTT
*
221738 ATTTTTACCAAAATA-ATTTT
1 ATTTTTAACAAAATATATTTT
221758 A
1 A
221759 AAATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTTTAACAAAATATATTTT
Found at i:222069 original size:2 final size:2
Alignment explanation
Indices: 222062--222091 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
222052 TAACTGGTCA
222062 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
222092 TATTAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:223407 original size:2 final size:2
Alignment explanation
Indices: 223400--223428 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
223390 ATAGCTCTAG
223400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
223429 TTAAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:233105 original size:14 final size:14
Alignment explanation
Indices: 233066--233113 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
233056 TTTATTTTTT
*
233066 ATATATAATTATATA
1 ATATATAAATAT-TA
*
233081 AT-TAAAAATATTA
1 ATATATAAATATTA
233094 ATATATAAATATTA
1 ATATATAAATATTA
233108 ATATAT
1 ATATAT
233114 TAATCTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 4 0.14
14 23 0.79
15 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATAAATATTA
Found at i:233124 original size:22 final size:20
Alignment explanation
Indices: 233088--233131 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
233078 ATAATTAAAA
233088 ATATTAATATATAAATATTAAT
1 ATATTAATATATAAA-A-TAAT
* *
233110 ATATTAATCTTTAAAATAAT
1 ATATTAATATATAAAATAAT
233130 AT
1 AT
233132 TAGAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 13 0.65
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTAATATATAAAATAAT
Found at i:233472 original size:15 final size:15
Alignment explanation
Indices: 233444--233486 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
233434 AAAATCTAAT
*
233444 AAATAATAATTAAAAA
1 AAAT-ATAAATAAAAA
233460 AAATATAAATAAAAA
1 AAATATAAATAAAAA
233475 AAAT-TAAA-AAAA
1 AAATATAAATAAAA
233487 GAGAACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.15
14 4 0.15
15 14 0.54
16 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATATAAATAAAAA
Found at i:233479 original size:25 final size:25
Alignment explanation
Indices: 233430--233486 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
233420 CGATTTTGGC
* *
233430 AAAAAAAATCTAATAAATAATAATT
1 AAAAAAAATATAATAAATAAAAATT
233455 AAAAAAAATATAAATAAA-AAAAATT
1 AAAAAAAATAT-AATAAATAAAAATT
233480 AAAAAAA
1 AAAAAAA
233487 GAGAACAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (25 bp):
AAAAAAAATATAATAAATAAAAATT
Found at i:238853 original size:88 final size:89
Alignment explanation
Indices: 238672--238858 Score: 263
Period size: 88 Copynumber: 2.1 Consensus size: 89
238662 GTAATCCTTG
* * * *
238672 CTCTGA-AGGGATATTCTAACCTTATTCTAACAAAAATTTAAATTTTTCTTCGTATAATTTTATC
1 CTCTGAGAGGGATATTCCAACCTCATTCTAACAAAAATTTAAATTTTCCTTCATATAATTTTATC
* *
238736 CTTAGGGAAACTCCATCCCCATTG
66 CTTAAGGAAACTCCATCCCCATTA
* * *
238760 TTCTGAGA-GGATATTCCAGCCTCATTCTAACAAAGATTTAAATTTTCCTTCATATAATTTTATC
1 CTCTGAGAGGGATATTCCAACCTCATTCTAACAAAAATTTAAATTTTCCTTCATATAATTTTATC
*
238824 CTTAAGGAAACTCTATCCCCATTA
66 CTTAAGGAAACTCCATCCCCATTA
238848 CTCTGAG-GGGA
1 CTCTGAGAGGGA
238859 GACTATAATC
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
88 85 0.99
89 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (89 bp):
CTCTGAGAGGGATATTCCAACCTCATTCTAACAAAAATTTAAATTTTCCTTCATATAATTTTATC
CTTAAGGAAACTCCATCCCCATTA
Found at i:244213 original size:189 final size:189
Alignment explanation
Indices: 243973--244346 Score: 667
Period size: 189 Copynumber: 2.0 Consensus size: 189
243963 CCATACCTAG
*
243973 AGTAATCACCAATAAAGATAATGAAGTATGAATATCCATTTCTAGCCATTGTGTTCATTAGTCCA
1 AGTAATCACCAATAAAGATAATGAAGTATGAATATCCATTTCTAACCATTGTGTTCATTAGTCCA
* * *
244038 TATGCATCATATATATCATGCCTAATAAAACGCTTCACCTTTTCCAATAAAGGAGTCTTAGTCAT
66 TATGCATCATATATATCATGCCTAATAAAACCCTTCACATTTTCCAATAAAAGAGTCTTAGTCAT
* *
244103 TTTACCAAAGAGACAACATTCGCATGTCCCATATGATTCATCATCAAATTGTTTGAAAT
131 TTTAACAAAGAGACAACATTCGCATGTCCCATATGATTCATCATCAAATGGTTTGAAAT
244162 AGTAATCACCAATAAAGATAATGAAGTATGAATATCCATTTCTAACCATTGTGTTCATTAGTCCA
1 AGTAATCACCAATAAAGATAATGAAGTATGAATATCCATTTCTAACCATTGTGTTCATTAGTCCA
* *
244227 TGTGCATCATATATATCATGCCTAATAAAACCCTTCACATTTTCCAATAAAAGAGTCTTAGTCCT
66 TATGCATCATATATATCATGCCTAATAAAACCCTTCACATTTTCCAATAAAAGAGTCTTAGTCAT
*
244292 TTTAACAAAGAGACAACATTCGCATGTCCCATATGATTCATCATTAAATGGTTTG
131 TTTAACAAAGAGACAACATTCGCATGTCCCATATGATTCATCATCAAATGGTTTG
244347 TGTAACTTGG
Statistics
Matches: 176, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
189 176 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (189 bp):
AGTAATCACCAATAAAGATAATGAAGTATGAATATCCATTTCTAACCATTGTGTTCATTAGTCCA
TATGCATCATATATATCATGCCTAATAAAACCCTTCACATTTTCCAATAAAAGAGTCTTAGTCAT
TTTAACAAAGAGACAACATTCGCATGTCCCATATGATTCATCATCAAATGGTTTGAAAT
Found at i:249943 original size:20 final size:20
Alignment explanation
Indices: 249918--249959 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
249908 ATATCAATAC
249918 AATGTATTGATACT-ATGAAT
1 AATGTATTGATA-TAATGAAT
249938 AATGTATTGATATAATGAAT
1 AATGTATTGATATAATGAAT
249958 AA
1 AA
249960 AAACTAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (20 bp):
AATGTATTGATATAATGAAT
Found at i:254296 original size:13 final size:13
Alignment explanation
Indices: 254278--254314 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
254268 GCCACCATAG
254278 CTTTTTTCTTTTA
1 CTTTTTTCTTTTA
*
254291 CTTTTTTTTTTTA
1 CTTTTTTCTTTTA
254304 -TTTTTTCTTTT
1 CTTTTTTCTTTT
254315 TCTACATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (13 bp):
CTTTTTTCTTTTA
Found at i:265614 original size:20 final size:21
Alignment explanation
Indices: 265589--265628 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
265579 GTTGGACACA
265589 ATGTATCGATACAAT-TATTT
1 ATGTATCGATACAATGTATTT
265609 ATGTATCGATACAATGTATT
1 ATGTATCGATACAATGTATT
265629 GATACATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACAATGTATTT
Found at i:265623 original size:33 final size:33
Alignment explanation
Indices: 265586--265654 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
265576 GCCGTTGGAC
*
265586 ACAATGTATCGATACAATTAT-TTATGTATCGAT
1 ACAATGTATCGATAC-ATTATCCTATGTATCGAT
* *
265619 ACAATGTATTGATACATTGTCCTATGTATCGAT
1 ACAATGTATCGATACATTATCCTATGTATCGAT
265652 ACA
1 ACA
265655 TTTCACTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 4 0.12
33 28 0.88
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (33 bp):
ACAATGTATCGATACATTATCCTATGTATCGAT
Found at i:265709 original size:20 final size:20
Alignment explanation
Indices: 265684--265737 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
265674 TGCCAGTTTC
265684 ATGTATCGATACAATTG-GAT
1 ATGTATCGATACAATTGAG-T
265704 ATGTATCGATACAA-TGAGT
1 ATGTATCGATACAATTGAGT
*
265723 ATATATCGATACAAT
1 ATGTATCGATACAAT
265738 GTATCGATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTGAGT
Found at i:266481 original size:10 final size:10
Alignment explanation
Indices: 266456--266511 Score: 67
Period size: 11 Copynumber: 5.3 Consensus size: 10
266446 GTCTTAGAGT
266456 TTTTATTTAGA
1 TTTTATTTA-A
266467 TTTTATTTAA
1 TTTTATTTAA
*
266477 TTTTAAATTAA
1 TTTT-ATTTAA
*
266488 TTTTATTTAT
1 TTTTATTTAA
266498 TTTTATTTATA
1 TTTTATTTA-A
266509 TTT
1 TTT
266512 AAATTACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 18 0.46
11 21 0.54
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:266505 original size:31 final size:32
Alignment explanation
Indices: 266456--266517 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
266446 GTCTTAGAGT
266456 TTTTATTTAGATTTTATTTA-ATTTTAAATTAA
1 TTTTATTTAGATTTTATTTATA-TTTAAATTAA
*
266488 TTTTATTTA-TTTTTATTTATATTTAAATTA
1 TTTTATTTAGATTTTATTTATATTTAAATTA
266518 CTTAGATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (32 bp):
TTTTATTTAGATTTTATTTATATTTAAATTAA
Found at i:266511 original size:21 final size:21
Alignment explanation
Indices: 266455--266511 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
266445 AGTCTTAGAG
266455 TTTTTATTTAGATTTTATTTAA
1 TTTTTATTTA-ATTTTATTTAA
* *
266477 TTTTAAATTAATTTTATTT-A
1 TTTTTATTTAATTTTATTTAA
266497 TTTTTATTTATATTT
1 TTTTTATTTA-ATTT
266512 AAATTACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 9 0.30
21 13 0.43
22 8 0.27
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTATTTAATTTTATTTAA
Found at i:271377 original size:59 final size:58
Alignment explanation
Indices: 271237--271435 Score: 156
Period size: 59 Copynumber: 3.4 Consensus size: 58
271227 AAATGGTCTT
* * * * * *
271237 AAATGCATAGAAAATGC-AAAATGATTCCTAGAT-TATATAAAATAACCAAAAGAGCCTTA
1 AAATGCA-AGAAAATTCTAAAATGATTTCTA-ATATACATGAAATAACTAAAAGA-CCCTA
* * * *
271296 AAATGCATGAAAATTGTAAAATGA-TTCTTCATATGCATGAAATAAACTAAAAGACCCTA
1 AAATGCAAGAAAATTCTAAAATGATTTC-TAATATACATGAAAT-AACTAAAAGACCCTA
* * *
271355 AAATGCAAGAAAATTACT-AAATGGTTTCTAATATACATGGAATAACTAAATGACCC-A
1 AAATGCAAGAAAATT-CTAAAATGATTTCTAATATACATGAAATAACTAAAAGACCCTA
* * * *
271412 AAATGTATGGAAATGCTAAAATGA
1 AAATGCAAGAAAATTCTAAAATGA
271436 CCTAAATTAT
Statistics
Matches: 111, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
56 2 0.02
57 17 0.15
58 22 0.20
59 57 0.51
60 13 0.12
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (58 bp):
AAATGCAAGAAAATTCTAAAATGATTTCTAATATACATGAAATAACTAAAAGACCCTA
Found at i:271511 original size:58 final size:59
Alignment explanation
Indices: 271395--271572 Score: 163
Period size: 58 Copynumber: 3.1 Consensus size: 59
271385 ATATACATGG
* * * * *
271395 AATAA-CTAAAT-GACCCAAAATGTATGG-AAATGCTAAAA-TG-ACCTAAATTATATAA
1 AATAACCTAAATATACCTAAAATGTATGGAAAATGC-AAAACGGTCCCTAGATTATATAA
* ** * *
271450 AATAACCTAAAT-TGTCCTAAAATGTAT-GAACTTGCAAAACGGTCTCTAGATTATATGA
1 AATAACCTAAATAT-ACCTAAAATGTATGGAAAATGCAAAACGGTCCCTAGATTATATAA
* * * *
271508 AATAACTTACATATACCTAAAATGTATGGAAAATGTAAAATGGTCCCTAGATTATATAA
1 AATAACCTAAATATACCTAAAATGTATGGAAAATGCAAAACGGTCCCTAGATTATATAA
271567 AATAAC
1 AATAAC
271573 TTGAATAGCT
Statistics
Matches: 97, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
55 5 0.05
56 11 0.11
57 16 0.16
58 33 0.34
59 32 0.33
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (59 bp):
AATAACCTAAATATACCTAAAATGTATGGAAAATGCAAAACGGTCCCTAGATTATATAA
Found at i:271571 original size:59 final size:59
Alignment explanation
Indices: 271395--271574 Score: 185
Period size: 59 Copynumber: 3.1 Consensus size: 59
271385 ATATACATGG
* * *
271395 AATAAC-TAAA-TGACCCAAAATGTATGG-AAATGCTAAAAT-G-ACCTAAATTATATAA
1 AATAACTTAAATTGACCTAAAATGTATGGAAAATG-TAAAATGGTCCCTAGATTATATAA
* * ** * * * *
271450 AATAACCTAAATTGTCCTAAAATGTAT-GAACTTGCAAAACGGTCTCTAGATTATATGA
1 AATAACTTAAATTGACCTAAAATGTATGGAAAATGTAAAATGGTCCCTAGATTATATAA
*
271508 AATAACTTACATAT-ACCTAAAATGTATGGAAAATGTAAAATGGTCCCTAGATTATATAA
1 AATAACTTAAAT-TGACCTAAAATGTATGGAAAATGTAAAATGGTCCCTAGATTATATAA
271567 AATAACTT
1 AATAACTT
271575 GAATAGCTAT
Statistics
Matches: 99, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
55 6 0.06
56 9 0.09
57 17 0.17
58 33 0.33
59 34 0.34
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (59 bp):
AATAACTTAAATTGACCTAAAATGTATGGAAAATGTAAAATGGTCCCTAGATTATATAA
Found at i:271681 original size:29 final size:30
Alignment explanation
Indices: 271649--271728 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
271639 TAAAATAAAA
*
271649 AAAAAATTCTAAAATGATCC-T-AAATTATG
1 AAAAAATTCTAAAATGA-CCTTAAAATGATG
*
271678 AAAAATAATCT-AAATGACCTTAAAATGATG
1 AAAAA-ATTCTAAAATGACCTTAAAATGATG
* *
271708 -AAAATTTCTAAAATAACCTTA
1 AAAAAATTCTAAAATGACCTTA
271729 GATTCTGTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
28 5 0.12
29 26 0.62
30 11 0.26
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (30 bp):
AAAAAATTCTAAAATGACCTTAAAATGATG
Found at i:272617 original size:24 final size:23
Alignment explanation
Indices: 272590--272642 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
272580 TCAAACAATA
*
272590 CTTTCTCTTCTTTTTCATTTTTTT
1 CTTTCTCTTATTTTTC-TTTTTTT
*
272614 CTTTTTTCTTATTTTTCTTTTTTT
1 C-TTTCTCTTATTTTTCTTTTTTT
272638 CTTTC
1 CTTTC
272643 AAGGTTGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 3 0.12
24 9 0.36
25 13 0.52
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (23 bp):
CTTTCTCTTATTTTTCTTTTTTT
Found at i:272618 original size:8 final size:8
Alignment explanation
Indices: 272595--272641 Score: 60
Period size: 9 Copynumber: 5.6 Consensus size: 8
272585 CAATACTTTC
272595 TCTTCTTTT
1 TCTT-TTTT
272604 TCATTTTTT
1 TC-TTTTTT
272613 TC-TTTTT
1 TCTTTTTT
272620 TCTTATTTT
1 TCTT-TTTT
272629 TCTTTTTT
1 TCTTTTTT
272637 TCTTT
1 TCTTT
272642 CAAGGTTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.20
8 10 0.29
9 16 0.46
10 2 0.06
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (8 bp):
TCTTTTTT
Found at i:272621 original size:16 final size:16
Alignment explanation
Indices: 272600--272636 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
272590 CTTTCTCTTC
272600 TTTTTCATT-TTTTTCT
1 TTTTTC-TTATTTTTCT
272616 TTTTTCTTATTTTTCT
1 TTTTTCTTATTTTTCT
272632 TTTTT
1 TTTTT
272637 TCTTTCAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTTATTTTTCT
Found at i:272629 original size:25 final size:24
Alignment explanation
Indices: 272595--272641 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
272585 CAATACTTTC
*
272595 TCTTCTTTTTCATTTTTTTCTTTTT
1 TCTTATTTTTC-TTTTTTTCTTTTT
272620 TCTTATTTTTCTTTTTTTCTTT
1 TCTTATTTTTCTTTTTTTCTTT
272642 CAAGGTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (24 bp):
TCTTATTTTTCTTTTTTTCTTTTT
Found at i:273575 original size:58 final size:58
Alignment explanation
Indices: 273485--273604 Score: 231
Period size: 58 Copynumber: 2.1 Consensus size: 58
273475 AAATTCATTA
*
273485 AAGTCCTATTGTTTGTTATTTAGTTAAAAATTCTAAGAAGATTGATAAAACATTCTAT
1 AAGTCCTATTGTTTGTTATTTAATTAAAAATTCTAAGAAGATTGATAAAACATTCTAT
273543 AAGTCCTATTGTTTGTTATTTAATTAAAAATTCTAAGAAGATTGATAAAACATTCTAT
1 AAGTCCTATTGTTTGTTATTTAATTAAAAATTCTAAGAAGATTGATAAAACATTCTAT
273601 AAGT
1 AAGT
273605 AAAACTTTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (58 bp):
AAGTCCTATTGTTTGTTATTTAATTAAAAATTCTAAGAAGATTGATAAAACATTCTAT
Found at i:273671 original size:22 final size:22
Alignment explanation
Indices: 273630--273671 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
273620 TCTTAAAAAG
*
273630 TTAAAATAAAAATCCTATTAGT
1 TTAAAATAAAAATCCAATTAGT
* *
273652 TTAAAATAAAAGTTCAATTA
1 TTAAAATAAAAATCCAATTA
273672 AACATTCTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
TTAAAATAAAAATCCAATTAGT
Found at i:273801 original size:25 final size:25
Alignment explanation
Indices: 273747--273801 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
273737 TTTCCAACCA
* * *
273747 ATTTTGATTAATTTTGACTTTTTTG
1 ATTTTGATCAATTTTCACATTTTTG
*
273772 GTTTTGATCAATTTATCACATTTTT-
1 ATTTTGATCAATTT-TCACATTTTTG
273797 ATTTT
1 ATTTT
273802 CCCAATTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.62
Consensus pattern (25 bp):
ATTTTGATCAATTTTCACATTTTTG
Found at i:275523 original size:16 final size:16
Alignment explanation
Indices: 275502--275535 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
275492 CACTAACAAT
*
275502 TTTTATCCAGGTGTGA
1 TTTTATCCAAGTGTGA
275518 TTTTATCCAAGTGTGA
1 TTTTATCCAAGTGTGA
275534 TT
1 TT
275536 AATAACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (16 bp):
TTTTATCCAAGTGTGA
Found at i:276102 original size:7 final size:8
Alignment explanation
Indices: 276079--276118 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
276069 TAAAATAAAT
276079 AACAATTA
1 AACAATTA
276087 AACAATTA
1 AACAATTA
276095 AA-AATTA
1 AACAATTA
*
276102 AACAAATA
1 AACAATTA
*
276110 AGCAATTA
1 AACAATTA
276118 A
1 A
276119 TAATTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.65, C:0.10, G:0.03, T:0.23
Consensus pattern (8 bp):
AACAATTA
Found at i:276106 original size:23 final size:23
Alignment explanation
Indices: 276079--276123 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
276069 TAAAATAAAT
*
276079 AACAATTAAACAATTAAAAATTA
1 AACAAATAAACAATTAAAAATTA
* *
276102 AACAAATAAGCAATTAATAATT
1 AACAAATAAACAATTAAAAATT
276124 TATATGCTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (23 bp):
AACAAATAAACAATTAAAAATTA
Found at i:278456 original size:16 final size:16
Alignment explanation
Indices: 278435--278466 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
278425 CTTAGTTTTT
278435 TTGGAAACCTTGGTAA
1 TTGGAAACCTTGGTAA
278451 TTGGAAACCTTGGTAA
1 TTGGAAACCTTGGTAA
278467 AAACTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
TTGGAAACCTTGGTAA
Found at i:278832 original size:9 final size:9
Alignment explanation
Indices: 278818--278864 Score: 50
Period size: 8 Copynumber: 5.8 Consensus size: 9
278808 TTTTTTATTT
278818 TATTTTTTA
1 TATTTTTTA
278827 TA-TTTTTA
1 TATTTTTTA
278835 TA-TTTTTA
1 TATTTTTTA
*
278843 -ATTTTTAA
1 TATTTTTTA
278851 T-TTTTTTA
1 TATTTTTTA
278859 -ATTTTT
1 TATTTTT
278865 CAAAATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 1 0.03
8 30 0.91
9 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TATTTTTTA
Found at i:278834 original size:8 final size:8
Alignment explanation
Indices: 278807--278855 Score: 63
Period size: 7 Copynumber: 6.8 Consensus size: 8
278797 CAATCTCTCA
278807 ATTTTT-T
1 ATTTTTAT
278814 A-TTTTAT
1 ATTTTTAT
278821 -TTTTTAT
1 ATTTTTAT
278828 ATTTTTAT
1 ATTTTTAT
278836 ATTTTTA-
1 ATTTTTAT
278843 ATTTTTA-
1 ATTTTTAT
278850 ATTTTT
1 ATTTTT
278856 TTAATTTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 4 0.10
7 21 0.54
8 14 0.36
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
ATTTTTAT
Found at i:278835 original size:15 final size:14
Alignment explanation
Indices: 278807--278864 Score: 66
Period size: 16 Copynumber: 4.0 Consensus size: 14
278797 CAATCTCTCA
278807 ATTTTTT-A-TTTT
1 ATTTTTTAATTTTT
278819 ATTTTTTATATTTTT
1 ATTTTTTA-ATTTTT
278834 ATATTTTTAATTTTT
1 AT-TTTTTAATTTTT
278849 AATTTTTTTAATTTTT
1 -A-TTTTTTAATTTTT
278865 CAAAATTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.17
14 1 0.03
15 12 0.30
16 19 0.47
17 1 0.03
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
ATTTTTTAATTTTT
Found at i:278864 original size:8 final size:7
Alignment explanation
Indices: 278807--278856 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 7
278797 CAATCTCTCA
278807 ATTTTTT
1 ATTTTTT
278814 A--TTTT
1 ATTTTTT
278819 ATTTTTT
1 ATTTTTT
278826 ATATTTTT
1 AT-TTTTT
278834 ATATTTTT
1 AT-TTTTT
*
278842 AATTTTTA
1 -ATTTTTT
278850 ATTTTTT
1 ATTTTTT
278857 TAATTTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 5 0.14
7 13 0.35
8 17 0.46
9 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
ATTTTTT
Found at i:278957 original size:11 final size:11
Alignment explanation
Indices: 278941--279009 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 11
278931 TAAGAAGAAA
278941 AAAATAAAAAT
1 AAAATAAAAAT
*
278952 AAAATAGGAAAT
1 AAAATA-AAAAT
278964 AAGAAATAAGAAAT
1 -A-AAATAA-AAAT
278978 -AAATGAAAAAT
1 AAAAT-AAAAAT
*
278989 ATGAAATAAATAT
1 A--AAATAAAAAT
279002 AAAATAAA
1 AAAATAAA
279010 TAGTAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
11 21 0.45
12 6 0.13
13 7 0.15
14 13 0.28
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:278970 original size:25 final size:26
Alignment explanation
Indices: 278942--279007 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
278932 AAGAAGAAAA
*
278942 AAATAAAAATAAAATAG-GAAATAAG
1 AAATAAAAATAAAATAGAAAAATAAG
*
278967 AAATAAGAAAT-AAAT-GAAAAATATG
1 AAATAA-AAATAAAATAGAAAAATAAG
*
278992 AAATAAATATAAAATA
1 AAATAAAAATAAAATA
279008 AATAGTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 4 0.12
25 26 0.76
26 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (26 bp):
AAATAAAAATAAAATAGAAAAATAAG
Found at i:278981 original size:18 final size:17
Alignment explanation
Indices: 278935--279008 Score: 69
Period size: 18 Copynumber: 4.1 Consensus size: 17
278925 ATGGACTAAG
*
278935 AAGAAAAAAATAAAAAT
1 AAGAAATAAATAAAAAT
*
278952 AA-AATAGGAAATAAGAAAT
1 AAGAA-A-TAAATAA-AAAT
278971 AAGAAATAAATGAAAAAT
1 AAGAAATAAAT-AAAAAT
*
278989 ATGAAATAAATATAAAAT
1 AAGAAATAAATA-AAAAT
279007 AA
1 AA
279009 ATAGTAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.04
17 4 0.09
18 30 0.64
19 9 0.19
20 2 0.04
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
AAGAAATAAATAAAAAT
Found at i:282384 original size:12 final size:12
Alignment explanation
Indices: 282364--282397 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
282354 CATCTCATAT
*
282364 TTGACCTTTTTAG
1 TTGA-CTTTTAAG
282377 TTGACTTTTAAG
1 TTGACTTTTAAG
282389 TTGACTTTT
1 TTGACTTTT
282398 GGCCTTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.18, C:0.12, G:0.15, T:0.56
Consensus pattern (12 bp):
TTGACTTTTAAG
Found at i:283391 original size:17 final size:16
Alignment explanation
Indices: 283371--283404 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
283361 ATGTAACATG
283371 TGCATGAATGTCATGAA
1 TGCATGAATGT-ATGAA
*
283388 TGCATGCATGTATGAA
1 TGCATGAATGTATGAA
283404 T
1 T
283405 ATAATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (16 bp):
TGCATGAATGTATGAA
Found at i:284899 original size:28 final size:26
Alignment explanation
Indices: 284832--284899 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 26
284822 ATTTAATCCT
* *
284832 AAAATATATATTAATATTAAATACTA
1 AAAATAAATATTAATATTAAAAACTA
* *
284858 AAAATAATACTATTATTATTAAAAATTA
1 AAAATAA-A-TATTAATATTAAAAACTA
284886 ATTAAATAAATATT
1 A--AAATAAATATT
284900 TTAAAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 6 0.18
27 1 0.03
28 20 0.59
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAATAAATATTAATATTAAAAACTA
Found at i:285064 original size:26 final size:26
Alignment explanation
Indices: 285030--285094 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
285020 TTAATATTAA
* *
285030 AATAGTAAAATTTTA-ATATAAT-TTGT
1 AATACTAAAATATTATAT-TAATGTT-T
285056 AATACTAAAATATTATATTAATGTTT
1 AATACTAAAATATTATATTAATGTTT
285082 AATACTTAAAATA
1 AATAC-TAAAATA
285095 ATACTATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 23 0.68
27 11 0.32
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (26 bp):
AATACTAAAATATTATATTAATGTTT
Found at i:285370 original size:15 final size:16
Alignment explanation
Indices: 285352--285382 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
285342 AATAATATAG
285352 TTTTATT-AAATAATA
1 TTTTATTAAAATAATA
285367 TTTTATTAAAATAATA
1 TTTTATTAAAATAATA
285383 AATTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTATTAAAATAATA
Found at i:285393 original size:18 final size:18
Alignment explanation
Indices: 285334--285393 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
285324 AATGTTACAA
* *
285334 TTTATTATAATAATATAGT
1 TTTATTAAAATAATA-AAT
285353 TTTATT-AAATAAT--AT
1 TTTATTAAAATAATAAAT
285368 TTTATTAAAATAATAAAT
1 TTTATTAAAATAATAAAT
*
285386 TATATTAA
1 TTTATTAA
285394 TTATATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 7 0.20
16 7 0.20
18 15 0.43
19 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTTATTAAAATAATAAAT
Found at i:285420 original size:19 final size:18
Alignment explanation
Indices: 285387--285443 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
285377 ATAATAAATT
*
285387 ATATTAATTATATTAATAA
1 ATATT-ATTACATTAATAA
*
285406 GTTATTATTACATTAATAA
1 -ATATTATTACATTAATAA
* *
285425 ATAATATTACATTATTAA
1 ATATTATTACATTAATAA
285443 A
1 A
285444 ATATATGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 16 0.50
19 12 0.38
20 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
ATATTATTACATTAATAA
Found at i:285500 original size:3 final size:3
Alignment explanation
Indices: 285494--285532 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
285484 TATATTATTA
285494 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
285533 TGACTCGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:286904 original size:11 final size:11
Alignment explanation
Indices: 286885--286936 Score: 56
Period size: 10 Copynumber: 5.0 Consensus size: 11
286875 AAATATGATT
*
286885 ATATGAATAAA
1 ATATAAATAAA
286896 ATATAAAT-AA
1 ATATAAATAAA
*
286906 A-ATAATTAAA
1 ATATAAATAAA
*
286916 ATAT-AATATA
1 ATATAAATAAA
286926 ATATAAATAAA
1 ATATAAATAAA
286937 TATTTTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 5 0.15
10 14 0.42
11 14 0.42
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
ATATAAATAAA
Found at i:286976 original size:31 final size:33
Alignment explanation
Indices: 286894--286998 Score: 102
Period size: 29 Copynumber: 3.4 Consensus size: 33
286884 TATATGAATA
* *
286894 AAATAT-AAATA-AAATA-ATTAAAATATA-AT
1 AAATATAAAATATTAATATATTAAAATTTATAT
*
286923 ATAATAT-AAATA--AATAT-TTTAAATTT-TAT
1 A-AATATAAAATATTAATATATTAAAATTTATAT
*
286952 AAATATAAATTATTAATATATTAAAATTTATAT
1 AAATATAAAATATTAATATATTAAAATTTATAT
286985 AAATATAAAATATT
1 AAATATAAAATATT
286999 TTAAATATAA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
28 5 0.08
29 19 0.30
30 10 0.16
31 5 0.08
32 8 0.13
33 16 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
AAATATAAAATATTAATATATTAAAATTTATAT
Found at i:286990 original size:18 final size:17
Alignment explanation
Indices: 286943--287025 Score: 65
Period size: 16 Copynumber: 5.1 Consensus size: 17
286933 TAAATATTTT
286943 AAATTT-TATAAATAT-
1 AAATTTATATAAATATA
286958 AAA-TTAT-TAATATATTA
1 AAATTTATATAA-ATA-TA
286975 AAATTTATATAAATATA
1 AAATTTATATAAATATA
286992 AAATATT-T-TAAATAT-
1 AAAT-TTATATAAATATA
*
287007 AATTATTATAT-AATATA
1 AAAT-TTATATAAATATA
287024 AA
1 AA
287026 TATACCAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
14 5 0.09
15 13 0.23
16 14 0.25
17 13 0.23
18 9 0.16
19 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:286996 original size:27 final size:30
Alignment explanation
Indices: 286896--287029 Score: 79
Period size: 31 Copynumber: 4.5 Consensus size: 30
286886 TATGAATAAA
* *
286896 ATATAA-ATAAA-ATAATTAAAATATAATATA
1 ATATAATATAAATAT-ATT-AAATATATTATT
* * *
286926 ATAT-AAATAAATATTTTAAAT-T-TTATAA
1 ATATAATATAAATATATTAAATATATTAT-T
*
286954 ATATAAATTATTAATATATTAAA-AT-TTA-T
1 ATAT-AA-TATAAATATATTAAATATATTATT
*
286983 ATA-AATATAAAATATTTTAAATATAATTATT
1 ATATAATAT-AAATATATTAAATAT-ATTATT
287014 ATATAATATAAATATA
1 ATATAATATAAATATA
287030 CCAATTATAA
Statistics
Matches: 82, Mismatches: 9, Indels: 25
0.71 0.08 0.22
Matches are distributed among these distances:
26 3 0.04
27 15 0.18
28 8 0.10
29 8 0.10
30 15 0.18
31 28 0.34
32 5 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATAATATAAATATATTAAATATATTATT
Found at i:287028 original size:58 final size:61
Alignment explanation
Indices: 286885--287029 Score: 151
Period size: 58 Copynumber: 2.4 Consensus size: 61
286875 AAATATGATT
286885 ATATGAATAAA-ATATAA-ATAAA-ATAATTAAAATATAATATAATATAAATAAATATTTTAA
1 ATAT-AATAAATATATAATATAAATAT-ATTAAAATATAATATAATATAAATAAATATTTTAA
* * * * *
286945 ATTTTATAAATATA-AATTATTAATATATTAAAAT-TTATATAA-ATATA-AAATATTTTAA
1 ATATAATAAATATATAA-TATAAATATATTAAAATATAATATAATATAAATAAATATTTTAA
* *
287003 ATATAATTATTATATAATATAAATATA
1 ATATAATAAATATATAATATAAATATA
287030 CCAATTATAA
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
58 30 0.43
59 13 0.19
60 13 0.19
61 12 0.17
62 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (61 bp):
ATATAATAAATATATAATATAAATATATTAAAATATAATATAATATAAATAAATATTTTAA
Found at i:287029 original size:22 final size:24
Alignment explanation
Indices: 286919--287027 Score: 50
Period size: 22 Copynumber: 4.7 Consensus size: 24
286909 AATTAAAATA
*
286919 TAATATAATATAAAT-AAATATTT
1 TAATATAATATAAATAAAATATAT
**
286942 TAA-ATTTTATAAATATAAAT-TAT
1 TAATATAATATAAATA-AAATATAT
* * * *
286965 TAATATATTA-AAATTTATATAAAT
1 TAATATAATATAAA-TAAAATATAT
* * * *
286989 ATAAAATATTTTAAATATAAT-TAT
1 -TAATATAATATAAATAAAATATAT
287013 T-ATATAATATAAATA
1 TAATATAATATAAATA
287028 TACCAATTAT
Statistics
Matches: 63, Mismatches: 16, Indels: 15
0.67 0.17 0.16
Matches are distributed among these distances:
22 20 0.32
23 15 0.24
24 14 0.22
25 11 0.17
26 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATATAATATAAATAAAATATAT
Found at i:288021 original size:2 final size:2
Alignment explanation
Indices: 288014--288043 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
288004 GTTTACTCTC
288014 AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
288044 ATTATGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:289946 original size:31 final size:32
Alignment explanation
Indices: 289884--289947 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
289874 GATAAATATA
*
289884 AAAAATTTAATACATTTATTATATTTATATTT
1 AAAAATTTAATACATTTAATATATTTATATTT
* * *
289916 AAAATTTTAATATATTTAATA-ATTTTTATTT
1 AAAAATTTAATACATTTAATATATTTATATTT
289947 A
1 A
289948 TATTTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
AAAAATTTAATACATTTAATATATTTATATTT
Found at i:292790 original size:2 final size:2
Alignment explanation
Indices: 292780--292813 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
292770 TTCGATGGTG
292780 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
292814 ATTTGGTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:297022 original size:22 final size:21
Alignment explanation
Indices: 296984--297025 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
296974 TTAATTTTTT
296984 TTTAAAAATATTTTTTATATA
1 TTTAAAAATATTTTTTATATA
297005 TTTAAAAA-ATTATATTTATAT
1 TTTAAAAATATT-T-TTTATAT
297026 TTATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 9 0.47
22 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAAAAATATTTTTTATATA
Found at i:297297 original size:18 final size:19
Alignment explanation
Indices: 297267--297304 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
297257 TAAATATACA
297267 ATATAATATTTTTTAAAAT
1 ATATAATATTTTTTAAAAT
297286 ATATAA-ATTTTTTAAAAT
1 ATATAATATTTTTTAAAAT
297304 A
1 A
297305 AATTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATAATATTTTTTAAAAT
Found at i:297328 original size:13 final size:15
Alignment explanation
Indices: 297310--297341 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
297300 AAATAAATTA
297310 ATATATA-TA-ATAT
1 ATATATATTACATAT
297323 ATATATATTACATAT
1 ATATATATTACATAT
297338 ATAT
1 ATAT
297342 CTTTATCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATTACATAT
Found at i:301126 original size:22 final size:23
Alignment explanation
Indices: 301088--301135 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
301078 ATTTAAAATA
*
301088 TATGAAAAAAACGTAAATATATC
1 TATGAAAAAAACGTAAACATATC
*
301111 TATGTAAAAAAC-TAAACATATC
1 TATGAAAAAAACGTAAACATATC
301133 TAT
1 TAT
301136 ATTTAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.29
Consensus pattern (23 bp):
TATGAAAAAAACGTAAACATATC
Found at i:301578 original size:17 final size:17
Alignment explanation
Indices: 301552--301611 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 17
301542 ATTTGTTAAC
*
301552 AATAATTTAAATTTACA
1 AATAAATTAAATTTACA
*
301569 AATAAATT-AAGTT-CA
1 AATAAATTAAATTTACA
301584 AATAAA--AAATTTA-A
1 AATAAATTAAATTTACA
301598 AA-AAATTATAATTT
1 AATAAATTA-AATTT
301612 TATATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
13 3 0.09
14 7 0.20
15 9 0.26
16 9 0.26
17 7 0.20
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (17 bp):
AATAAATTAAATTTACA
Found at i:301676 original size:9 final size:9
Alignment explanation
Indices: 301628--301706 Score: 51
Period size: 9 Copynumber: 8.7 Consensus size: 9
301618 AAATTTGATC
301628 ATTTAA-AT
1 ATTTAATAT
301636 ATTT-ATATT
1 ATTTAATA-T
*
301645 ATTT-TTAT
1 ATTTAATAT
301653 ATTATAATAAT
1 ATT-TAAT-AT
301664 ATTTAATAT
1 ATTTAATAT
301673 ATTT-ATATT
1 ATTTAATA-T
301682 ATTTTAA-AT
1 A-TTTAATAT
*
301691 ATTTTATTAT
1 A-TTTAATAT
301701 ATTTAA
1 ATTTAA
301707 ATTATTTTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
7 1 0.02
8 12 0.21
9 27 0.47
10 12 0.21
11 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTTAATAT
Found at i:301703 original size:37 final size:36
Alignment explanation
Indices: 301628--301713 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 36
301618 AAATTTGATC
*
301628 ATTTAAATATTTATATTATTTTTATATTATAATAAT
1 ATTTAAATATTTATATTATTTTAATATTATAATAAT
* *
301664 ATTTAATATATTTATATTATTTTAAATATT-TTATTAT
1 ATTTAA-ATATTTATATTATTTT-AATATTATAATAAT
301701 ATTTAAATTATTT
1 ATTTAAA-TATTT
301714 TTCTTATATT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
36 7 0.16
37 32 0.73
38 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (36 bp):
ATTTAAATATTTATATTATTTTAATATTATAATAAT
Found at i:301712 original size:28 final size:28
Alignment explanation
Indices: 301629--301714 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 28
301619 AATTTGATCA
*
301629 TTTAAATATTTATATTATTTTTATATTAT
1 TTTAAATATTT-TATTATATTTATATTAT
** *
301658 AAT-AATA-TTTAATATATTTATATTAT
1 TTTAAATATTTTATTATATTTATATTAT
*
301684 TTTAAATATTTTATTATATTTAAATTAT
1 TTTAAATATTTTATTATATTTATATTAT
301712 TTT
1 TTT
301715 TCTTATATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
26 16 0.34
27 6 0.13
28 24 0.51
29 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTAAATATTTTATTATATTTATATTAT
Found at i:301720 original size:20 final size:20
Alignment explanation
Indices: 301662--301725 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
301652 TATTATAATA
*
301662 ATATTT-AATATATTTATATT
1 ATATTTAAAT-TATTTTTATT
301682 AT-TTTAAA-TA-TTTTATT
1 ATATTTAAATTATTTTTATT
*
301699 ATATTTAAATTATTTTTCTT
1 ATATTTAAATTATTTTTATT
301719 ATATTTA
1 ATATTTA
301726 TATCTTTCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 8 0.21
18 8 0.21
19 5 0.13
20 17 0.45
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTTAAATTATTTTTATT
Found at i:302270 original size:16 final size:17
Alignment explanation
Indices: 302248--302297 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
302238 TATTCATATA
302248 AAATTTAATATATTAAT
1 AAATTTAATATATTAAT
*
302265 AATTTATATGATATATTAAT
1 AAATT-TA--ATATATTAAT
302285 AAATTT-ATATATT
1 AAATTTAATATATT
302298 TATGTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 7 0.25
17 4 0.14
18 2 0.07
19 1 0.04
20 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AAATTTAATATATTAAT
Found at i:302278 original size:20 final size:21
Alignment explanation
Indices: 302255--302294 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
302245 ATAAAATTTA
302255 ATATATTAAT-AATTTATATG
1 ATATATTAATAAATTTATATG
302275 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
302295 ATTTATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
ATATATTAATAAATTTATATG
Found at i:304268 original size:20 final size:20
Alignment explanation
Indices: 304243--304382 Score: 85
Period size: 20 Copynumber: 6.9 Consensus size: 20
304233 GTTAGAAGTA
304243 ATGTATCGATACAAT-T-CAT
1 ATGTATCGATACAATGTAC-T
304262 CATGTATCGATACAATGTACT
1 -ATGTATCGATACAATGTACT
**
304283 ATGTATCGATACAAATAGTGGT
1 ATGTATCGATAC-AAT-GTACT
* * * *
304305 AGTGTAGCTACTACCA-GT-TT
1 A-TGTATCGA-TACAATGTACT
*
304325 CATATATCGATACAATTGT-CT
1 -ATGTATCGATACAA-TGTACT
*
304346 ATGTATCGATACAATGAAC-
1 ATGTATCGATACAATGTACT
*
304365 ATGTATTGATACAATGTA
1 ATGTATCGATACAATGTA
304383 TCGATACAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
19 22 0.23
20 47 0.49
21 11 0.12
22 5 0.05
23 7 0.07
24 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATGTACT
Done.