Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold39
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: 4724573
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 178835 characters in sequence are not A, C, G, or T
File 2 of 27
Found at i:154915 original size:30 final size:31
Alignment explanation
Indices: 154881--155125 Score: 102
Period size: 35 Copynumber: 7.5 Consensus size: 31
154871 TCCATGACTT
154881 AGTGGCA-TTTTTCTTCCAAGTCCACAACTC
1 AGTGGCACTTTTTCTTCCAAGTCCACAACTC
* * * ** *
154911 AGTGGCAATTCTTC-TCCAAGTCTATGACTT
1 AGTGGCACTTTTTCTTCCAAGTCCACAACTC
* *
154941 AGTGGCATCCTTTTTCTTCTAGGTCCACAACTC
1 AGTGGCA--CTTTTTCTTCCAAGTCCACAACTC
* ** *
154974 CGTGGCACCTTTTTCTTTTAAAGCCCACAACTC
1 AGTGGCA-CTTTTTC-TTCCAAGTCCACAACTC
* **
155007 CGTGGCACCCTTTTTCCTTTTAAAGTCCACAACTCC
1 AGTGGCA--CTTTTT-C-TTCCAAGTCCACAACT-C
** *
155043 A-TGGCACCCTTTTTCCTTTTAAAGCCCACAACTTC
1 AGTGGCA--CTTTTT-C-TTCCAAGTCCACAAC-TC
* **
155078 -GTGGCACCTCTTTTTTTTTTAAGTCCACAACTC
1 AGTGGCA---CTTTTTCTTCCAAGTCCACAACTC
*
155111 AATGGCACCTTTTTC
1 AGTGGCA-CTTTTTC
155126 CCCTTTTAAG
Statistics
Matches: 175, Mismatches: 28, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
30 26 0.15
31 5 0.03
32 19 0.11
33 38 0.22
34 25 0.14
35 53 0.30
36 9 0.05
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.36
Consensus pattern (31 bp):
AGTGGCACTTTTTCTTCCAAGTCCACAACTC
Found at i:155037 original size:35 final size:33
Alignment explanation
Indices: 154942--156066 Score: 719
Period size: 34 Copynumber: 34.8 Consensus size: 33
154932 CTATGACTTA
* *
154942 GTGGCATCCTTTTT-CTTCTAGGTCCACAACTCC
1 GTGGCA-CCTTTTTCCTTTTAAGTCCACAACTCC
*
154975 GTGGCACCTTTTT-CTTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCCTTTT-AAGTCCACAACTCC
155008 GTGGCACCCTTTTTCCTTTTAAAGTCCACAACTCC
1 GTGGCA-CCTTTTTCCTTTT-AAGTCCACAACTCC
* * *
155043 ATGGCACCCTTTTTCCTTTTAAAGCCCACAACTTC
1 GTGGCA-CCTTTTTCCTTTT-AAGTCCACAACTCC
** *
155078 GTGGCACCTCTTTTTTTTTTAAGTCCACAACTCA
1 GTGGCACCT-TTTTCCTTTTAAGTCCACAACTCC
*
155112 ATGGCACCTTTTTCCCCTTTTAAGTCCACAACTCC
1 GTGGCACCTTTTT--CCTTTTAAGTCCACAACTCC
* * *
155147 TTAGCACCTTTTT-CTTTTCAAAG-CCTATAACTCC
1 GTGGCACCTTTTTCCTTTT--AAGTCC-ACAACTCC
* * * *
155181 GTGACACCTTTTTCTTTTTAAAGCCCACAACTCT
1 GTGGCACCTTTTTCCTTTT-AAGTCCACAACTCC
155215 GTGGCA-C-----CCTTTTAAGTCCACAACTCC
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
* * * **
155242 GTGGTACCTTTTT-CTTTCCAAAAG-CCTATAACTTT
1 GTGGCACCTTTTTCCTTT---TAAGTCC-ACAACTCC
* * *
155277 GTGACACATTTTTTCCTTTTAAGTCCATAACTCC
1 GTGGCAC-CTTTTTCCTTTTAAGTCCACAACTCC
* * *
155311 ATGGCACCTTTTT-CTTTTCAAAGCCCATAACTCC
1 GTGGCACCTTTTTCCTTTT--AAGTCCACAACTCC
*
155345 GTGGCA-CTCTTTTCCTTTTAAAGTCCATAACTCC
1 GTGGCACCT-TTTTCCTTTT-AAGTCCACAACTCC
*
155379 GTGACACCCTTTTTCCTTTTAAGTCCACAACTCC
1 GTGGCA-CCTTTTTCCTTTTAAGTCCACAACTCC
* * * * *
155413 GTGGCA-ATTTTTTCTTTTCCAAGCCCATAACTTC
1 GTGGCACCTTTTTCCTTTT--AAGTCCACAACTCC
* *
155447 GTGGCACCTTTTT-CTTTTCAAAG-CCATAACTTC
1 GTGGCACCTTTTTCCTTTT--AAGTCCACAACTCC
* *
155480 ATGGCA-CTCTTTTCTTTTTAAGTCCACAACTCC
1 GTGGCACCT-TTTTCCTTTTAAGTCCACAACTCC
**
155513 GTGGCA-C-----CCTTTTAAGTTTACAACTCC
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
* * * * *
155540 ATGGCA-CTTTTTTCTTTTCAAAGCCCATAACTCT
1 GTGGCACCTTTTTCCTTTT--AAGTCCACAACTCC
*
155574 GTGGCA-C-----CCTTTTAAGTCCACAACTCA
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
155601 GTGGCACCTTTTTTCCCTTTTAAGTCCACAACTCC
1 GTGGCACC-TTTTT-CCTTTTAAGTCCACAACTCC
* *
155636 GTGGCACCTTTTT-CTTTTCAAAGCCCACAACTTC
1 GTGGCACCTTTTTCCTTTT--AAGTCCACAACTCC
* *
155670 GTGGCACCTTTTTCTTTTTAAAG--C-CAACTCG
1 GTGGCACCTTTTTCCTTTT-AAGTCCACAACTCC
* *
155701 GTGGCA------TCTTTTTAAGTCCATAACTCC
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
* * *
155728 ATGGAACCTTTTT-CTTTCCAAAAGTCCACAACTCC
1 GTGGCACCTTTTTCCTTT---TAAGTCCACAACTCC
* *
155763 GTGGCACCTTTTTTCCCTTTAAGTCCATAACTCC
1 GTGGCACC-TTTTTCCTTTTAAGTCCACAACTCC
* **
155797 ATGGCACCTTTTT-CTTTTCCAA-TCCCACAACTTT
1 GTGGCACCTTTTTCCTTTT--AAGT-CCACAACTCC
*
155831 GTGGCACC-TTTTCCTTTTAAGTCCACAATTCC
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
*
155863 GTGGCA-C-----CCTTTTAAGTTCACAACTCC
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
** * *
155890 GTGATACC-TTTTCCTTTTAAGTCCATAACTCT
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
*
155922 GTGGCA-C-----CCTTTTAAGTCCACAACTTC
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
* *
155949 GTGGCA-CATTTTCCTTTTAAGTCCACAACTCT
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
* *
155981 ATGGCA------GCCTTTTAAGTCCACAACTCC
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
* * *
156008 ATGGCACC-TTTTCCTTTCAAGTCCACAACTTC
1 GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
*
156040 GTGGCACC-TTTCCCTTTTAAGTCCACA
1 GTGGCACCTTTTTCCTTTTAAGTCCACA
156067 TAAGTCGGTG
Statistics
Matches: 877, Mismatches: 127, Indels: 177
0.74 0.11 0.15
Matches are distributed among these distances:
24 3 0.00
25 7 0.01
26 1 0.00
27 137 0.16
28 8 0.01
29 5 0.01
31 13 0.01
32 159 0.18
33 83 0.09
34 259 0.30
35 183 0.21
36 12 0.01
37 7 0.01
ACGTcount: A:0.22, C:0.31, G:0.11, T:0.36
Consensus pattern (33 bp):
GTGGCACCTTTTTCCTTTTAAGTCCACAACTCC
Found at i:155237 original size:27 final size:28
Alignment explanation
Indices: 155196--155254 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
155186 ACCTTTTTCT
*
155196 TTTTAAAGCCCACAACTCTGTGGCACCC
1 TTTTAAAGCCCACAACTCCGTGGCACCC
* * *
155224 TTTT-AAGTCCACAACTCCGTGGTACCT
1 TTTTAAAGCCCACAACTCCGTGGCACCC
155251 TTTT
1 TTTT
155255 CTTTCCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.34
Consensus pattern (28 bp):
TTTTAAAGCCCACAACTCCGTGGCACCC
Found at i:155535 original size:27 final size:27
Alignment explanation
Indices: 155495--155613 Score: 78
Period size: 27 Copynumber: 4.1 Consensus size: 27
155485 ACTCTTTTCT
*
155495 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCATGGCACCC
** *
155522 TTTTAAGTTTACAACTCCATGGCACTTTTTTC
1 TTTTAAGTCCACAACTCCATGGCAC-----CC
* * **
155554 TTTTCAAAGCCCATAACTCTGTGGCACCC
1 TTTT--AAGTCCACAACTCCATGGCACCC
*
155583 TTTTAAGTCCACAACT-CAGTGGCACCT
1 TTTTAAGTCCACAACTCCA-TGGCACCC
155610 TTTT
1 TTTT
155614 TCCCTTTTAA
Statistics
Matches: 68, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
27 43 0.63
29 5 0.07
32 5 0.07
34 15 0.22
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCATGGCACCC
Found at i:155581 original size:61 final size:61
Alignment explanation
Indices: 155393--155842 Score: 254
Period size: 69 Copynumber: 7.1 Consensus size: 61
155383 CACCCTTTTT
* * *
155393 CCTTTTAAGTCCACAACTCCGTGGCAATTTTTTCTTTTCCAAGCCCATAACT-TCGTGGCAC
1 CCTTTTAAGTCCACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCT-GTGGCAC
* * * * * * *
155454 CTTTTTCTTTTCAAAG-CCATAACTTCATGGCACTCTTTTCTTTT-TAAGTCCACAACTCCGTGG
1 C-----CTTTT--AAGTCCACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCTGTGG
155517 CAC
59 CAC
**
155520 CCTTTTAAGTTTACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCTGTGGCAC
* * *
155581 CCTTTTAAGTCCACAACT-CAGTGGCACCTTTTTTCCCTTTT--AAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCA-TGGCA-CTTTTTT--CTTTTCAAAGCCCATAACTCTGTGGCAC
* * * * * *
155643 CTTTTTCTTTTCAAAGCCCACAACTTCGTGGCACCTTTTTCTTTTTAAAG-CC--AACTCGGTGG
1 C-----CTTTT--AAGTCCACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCTGTGG
*
155705 CAT
59 CAC
* * * * * * * *
155708 CTTTTTAAGTCCATAACTCCATGGAACCTTTTTCTTTCCAAAAGTCCACAACTCCGTGGCACC
1 CCTTTTAAGTCCACAACTCCATGGCACTTTTTTCTTTTC-AAAGCCCATAACTCTGTGGCA-C
* * * * * * *
155771 TTTTTTCCCTTTAAGTCCATAACTCCATGGCACCTTTTTCTTTTCCAATCCCACAACTTTGTGGC
1 ------CCTTTTAAGTCCACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCTGTGGC
155836 A-
60 AC
155837 CCTTTT
1 CCTTTT
155843 CCTTTTAAGT
Statistics
Matches: 306, Mismatches: 48, Indels: 71
0.72 0.11 0.17
Matches are distributed among these distances:
58 26 0.08
59 7 0.02
60 36 0.12
61 45 0.15
62 37 0.12
64 5 0.02
65 12 0.04
66 28 0.09
67 30 0.10
68 28 0.09
69 51 0.17
70 1 0.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (61 bp):
CCTTTTAAGTCCACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCTGTGGCAC
Found at i:155737 original size:127 final size:127
Alignment explanation
Indices: 155339--155842 Score: 342
Period size: 127 Copynumber: 3.9 Consensus size: 127
155329 CAAAGCCCAT
* * * * * * * * *
155339 AACTCCGTGGCACTCTTTTCCTTTTAAAGTCCATAACTCCGTGACACCCTTTTTCCTTTTAAGTC
1 AACTCAGTGGAAC-CTTTTTCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTTCCCTTTAAGCC
* ** *
155404 CACAACTCCGTGGCAATTTTTTCTTTTCCAAGCCCATAACTTC-GTGGCACCTTTTTCTTTTCAA
65 CACAACTCCATGGCACCTTTTTCTTTTCAAAGCCCA-AAC-TCGGTGGCACC-----CTTTT--A
*
155468 AG-CCAT
121 AGTCCAC
* ** * *
155474 AACTTCA-TGGCA-CTCTTTTCTTTTTAAGTCCACAACTCCGTGGCA-C------CCTTTTAAGT
1 AAC-TCAGTGGAACCT-TTTTCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTTCCCTTTAAGC
** * *
155530 TTACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCTGTGGCACCCTTTTAAGTCCAC
64 CCACAACTCCATGGCACCTTTTTCTTTTCAAAGCCCA-AACTCGGTGGCACCCTTTTAAGTCCAC
* * *
155595 AACTCAGTGGCACCTTTTTTCCCTTT-TAAGTCCACAACTCCGTGGCACC-TTTTT-CTTTTCAA
1 AACTCAGTGGAACC-TTTTT--CTTTCAAAGTCCACAACTCCGTGGCACCTTTTTTCCCTTT--A
* * * * *
155657 AGCCCACAACTTCGTGGCACCTTTTTCTTTTTAAAG-CC-AACTCGGTGGCATCTTTTTAAGTCC
61 AGCCCACAACTCCATGGCACCTTTTTCTTTTCAAAGCCCAAACTCGGTGGCACCCTTTTAAGTCC
*
155720 AT
126 AC
155722 AACTCCA-TGGAACCTTTTTCTTTCCAAAAGTCCACAACTCCGTGGCACCTTTTTTCCCTTTAAG
1 AACT-CAGTGGAACCTTTTTCTTT-C-AAAGTCCACAACTCCGTGGCACCTTTTTTCCCTTTAAG
* * * * **
155786 TCCATAACTCCATGGCACCTTTTTCTTTTCCAATCCCACAACTTTGTGGCA-CCTTTT
63 CCCACAACTCCATGGCACCTTTTTCTTTTCAAAGCCCA-AACTCGGTGGCACCCTTTT
155843 CCTTTTAAGT
Statistics
Matches: 308, Mismatches: 35, Indels: 58
0.77 0.09 0.14
Matches are distributed among these distances:
120 6 0.02
121 11 0.04
122 10 0.03
123 22 0.07
124 9 0.03
126 7 0.02
127 139 0.45
128 14 0.05
129 11 0.04
130 40 0.13
133 3 0.01
134 26 0.08
135 8 0.03
136 2 0.01
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (127 bp):
AACTCAGTGGAACCTTTTTCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTTCCCTTTAAGCCC
ACAACTCCATGGCACCTTTTTCTTTTCAAAGCCCAAACTCGGTGGCACCCTTTTAAGTCCAC
Found at i:155761 original size:223 final size:216
Alignment explanation
Indices: 155291--155875 Score: 565
Period size: 223 Copynumber: 2.6 Consensus size: 216
155281 CACATTTTTT
* * *
155291 CCTTTTAAGTCCATAACTCCATGGCACCTTTTTCTTTTCAAAGCCCATAACTCCGTGGCACTCTT
1 CCTTTAAAGTCCACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCCGTGGCA--C--
* * * * **
155356 TTCCTTTTAAAGTCCATAACTCCGTGACACCCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAAT
62 --CCTTTTCAAGTCCACAACTCAGTGGCA-CCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* *
155421 TTTTTCTTTTCCAAGCCCATAACTTCGTGGCACCTTTTTCTTTTCAAAGCCATAACTTCATGGCA
124 TTTTTCTTTTCAAAGCCCACAACTTCGTGGCACCTTTTTCTTTTCAAAGCCA-AACTTCATGGCA
* *
155486 CTCTTTTCTTTTTAAGTCCACAACTCCGTGGCAC
188 -----TTCTTTTTAAGTCCACAACTCCATGGAAC
* ** *
155520 CCTTTTAAGTTTACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCTGTGGCACCCTT
1 CCTTTAAAGTCCACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCCGTGGCACCCTT
155585 TT-AAGTCCACAACTCAGTGGCACCTTTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
66 TTCAAGTCCACAACTCAGTGGCACC-TTTTT-CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
155649 CTTTTCAAAGCCCACAACTTCGTGGCACCTTTTTCTTTTTAAAGCC-AAC-TCGGTGGCA-TCTT
129 CTTTTCAAAGCCCACAACTTCGTGGCACCTTTTTCTTTTCAAAGCCAAACTTC-ATGGCATTCTT
*
155711 TTTAAGTCCATAACTCCATGGAAC
193 TTTAAGTCCACAACTCCATGGAAC
* * * *
155735 CTTTTTCTTTCCAAAAGTCCACAACTCCGTGGCACCTTTTTTCCCTTT--AAGTCCATAACTCCA
1 C-----CTTT---AAAGTCCACAACTCCATGGCA-CTTTTTT-CTTTTCAAAGCCCATAACTCCG
** *
155798 TGGCACCTTTTTCTTTTCCAA-TCCCACAACTTTGTGGCACC-TTTTCCTTTTAAGTCCACAATT
56 TGGCACC-----CTTTT-CAAGT-CCACAACTCAGTGGCACCTTTTTCCTTTTAAGTCCACAACT
*
155861 CCGTGGCACCCTTTT
114 CCGTGGCACCTTTTT
155876 AAGTTCACAA
Statistics
Matches: 306, Mismatches: 29, Indels: 44
0.81 0.08 0.12
Matches are distributed among these distances:
215 26 0.08
220 6 0.02
221 10 0.03
222 22 0.07
223 116 0.38
224 7 0.02
225 4 0.01
227 32 0.10
228 9 0.03
229 56 0.18
230 18 0.06
ACGTcount: A:0.21, C:0.31, G:0.11, T:0.37
Consensus pattern (216 bp):
CCTTTAAAGTCCACAACTCCATGGCACTTTTTTCTTTTCAAAGCCCATAACTCCGTGGCACCCTT
TTCAAGTCCACAACTCAGTGGCACCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCT
TTTCAAAGCCCACAACTTCGTGGCACCTTTTTCTTTTCAAAGCCAAACTTCATGGCATTCTTTTT
AAGTCCACAACTCCATGGAAC
Found at i:155884 original size:27 final size:27
Alignment explanation
Indices: 155843--156047 Score: 158
Period size: 27 Copynumber: 7.0 Consensus size: 27
155833 GGCACCTTTT
*
155843 CCTTTTAAGTCCACAATTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
* **
155870 CCTTTTAAGTTCACAACTCCGTGATACC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
* *
155898 TTTTCCTTTTAAGTCCATAACTCTGTGGCAC
1 ----CCTTTTAAGTCCACAACTCCGTGGCAC
*
155929 CCTTTTAAGTCCACAACTTCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
** *
155956 ATTTTCCTTTTAAGTCCACAACTCTATGGCAG
1 -----CCTTTTAAGTCCACAACTCCGTGGCAC
*
155988 CCTTTTAAGTCCACAACTCCATGGCACC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
* *
156016 TTTTCCTTTCAAGTCCACAACTTCGTGGCAC
1 ----CCTTTTAAGTCCACAACTCCGTGGCAC
156047 C
1 C
156048 TTTCCCTTTT
Statistics
Matches: 142, Mismatches: 21, Indels: 30
0.74 0.11 0.16
Matches are distributed among these distances:
27 72 0.51
28 1 0.01
31 2 0.01
32 67 0.47
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.33
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:155899 original size:59 final size:59
Alignment explanation
Indices: 155749--156047 Score: 330
Period size: 59 Copynumber: 4.9 Consensus size: 59
155739 TTCTTTCCAA
* * *
155749 AAGTCCACAACTCCGTGGCACCTTTTTTCCCTTTAAGTCCATAACTCCATGGCACCTTTTTCTTT
1 AAGTCCACAACTCCGTGGCACC--TTTTCCTTTTAAGTCCACAACTCCGTGGCACC-----CTTT
155814 T
59 T
** *
155815 CCAA-TCCCACAACTTTGTGGCACCTTTTCCTTTTAAGTCCACAATTCCGTGGCACCCTTTT
1 --AAGT-CCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
* ** * *
155876 AAGTTCACAACTCCGTGATACCTTTTCCTTTTAAGTCCATAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
* * ** *
155935 AAGTCCACAACTTCGTGGCACATTTTCCTTTTAAGTCCACAACTCTATGGCAGCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
* * *
155994 AAGTCCACAACTCCATGGCACCTTTTCCTTTCAAGTCCACAACTTCGTGGCACC
1 AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
156048 TTTCCCTTTT
Statistics
Matches: 199, Mismatches: 30, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
59 146 0.73
60 1 0.01
61 5 0.03
66 28 0.14
67 1 0.01
68 18 0.09
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (59 bp):
AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
Found at i:156193 original size:52 final size:52
Alignment explanation
Indices: 156137--156314 Score: 252
Period size: 52 Copynumber: 3.4 Consensus size: 52
156127 AATGTCACTG
* *
156137 GCCTTTAATCAGCACATAGGCATCTTTTTTTTTCTTAAGCCCAATGTTGCTA
1 GCCTTGAATCAGCACATTGGCATCTTTTTTTTTCTTAAGCCCAATGTTGCTA
*
156189 GCCTTGAATTAGCACATTGGCATCTTTTTTTTTCTTAAGCCCAATGTTGCTA
1 GCCTTGAATCAGCACATTGGCATCTTTTTTTTTCTTAAGCCCAATGTTGCTA
* ** * *
156241 GCCTTGAATCAGCACATTGGCATC-TTTGTCATCTTTAAGTCCAATGTTGCTG
1 GCCTTGAATCAGCACATTGGCATCTTTTTTTTTC-TTAAGCCCAATGTTGCTA
156293 GCCTTGAATCCA-CACATTGGCA
1 GCCTTGAAT-CAGCACATTGGCA
156315 CCTCTAATTC
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
51 6 0.05
52 107 0.93
53 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (52 bp):
GCCTTGAATCAGCACATTGGCATCTTTTTTTTTCTTAAGCCCAATGTTGCTA
Found at i:156394 original size:52 final size:49
Alignment explanation
Indices: 156241--156615 Score: 174
Period size: 52 Copynumber: 7.5 Consensus size: 49
156231 AATGTTGCTA
* * **
156241 GCCTTGAATCAGCACATTGGCATCTTTGTCATCTTTAAGTCCAATGTTGCTG
1 GCCTTGAATCAGCATATTGGCA-C-TT-TCATCTTTAAGTCCAATATCACTG
* * * * * *
156293 GCCTTGAATCCA-CACATTGGCAC---C-TC--TAATTCTAATGTCGCTA
1 GCCTTGAAT-CAGCATATTGGCACTTTCATCTTTAAGTCCAATATCACTG
* *
156336 GTCTTGAATCAGCATATTGGCACATTTACCATCTTTAAGTCCAATGTCACTG
1 GCCTTGAATCAGCATATTGGCAC-TTT--CATCTTTAAGTCCAATATCACTG
* ** *
156388 GCCTTGAATCAGCACATTGGCACTTTCATCTTTAAGTCTGATATCATTG
1 GCCTTGAATCAGCATATTGGCACTTTCATCTTTAAGTCCAATATCACTG
* * * * * * *
156437 GCCTTGAATCAGCATAGTGGCATCTTTGACAT-TCCTGAGCCCAATGTCGCTA
1 GCCTTGAATCAGCATATTGGCA-CTTT--CATCT-TTAAGTCCAATATCACTG
* * * ** * *
156489 GCCTTGAATCAACACATTGGCATTCTTCTCATCTTCAAGTGTAATGT-AGTTG
1 GCCTTGAATCAGCATATTGGCA--CTT-TCATCTTTAAGTCCAATATCA-CTG
* * * * * * *
156541 GTCGTGAATCAGCACATTGACATTCTTTGTATCTTTAAGCCCAATATCGCTG
1 GCCTTGAATCAGCATATTGGCA--CTTT-CATCTTTAAGTCCAATATCACTG
* *
156593 GCCTTGAATTAGCATGTTGGCAC
1 GCCTTGAATCAGCATATTGGCAC
156616 CTTTTTCACT
Statistics
Matches: 245, Mismatches: 57, Indels: 44
0.71 0.16 0.13
Matches are distributed among these distances:
42 2 0.01
43 31 0.13
45 2 0.01
46 1 0.00
49 40 0.16
50 7 0.03
51 6 0.02
52 148 0.60
53 7 0.03
54 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (49 bp):
GCCTTGAATCAGCATATTGGCACTTTCATCTTTAAGTCCAATATCACTG
Found at i:156394 original size:95 final size:95
Alignment explanation
Indices: 156231--156410 Score: 265
Period size: 95 Copynumber: 1.9 Consensus size: 95
156221 TCTTAAGCCC
* ** **
156231 AATGTTGCTAGCCTTGAATCAGCACATTGGCATCTTTGTCATCTTTAAGTCCAATGTTGCTGGCC
1 AATGTCGCTAGCCTTGAATCAGCACATTGGCATCTTTACCATCTTTAAGTCCAATGTCACTGGCC
156296 TTGAATCCA-CACATTGGCACCTCTAATTCT
66 TTGAAT-CAGCACATTGGCACCTCTAATTCT
* *
156326 AATGTCGCTAGTCTTGAATCAGCATATTGGCA-CATTTACCATCTTTAAGTCCAATGTCACTGGC
1 AATGTCGCTAGCCTTGAATCAGCACATTGGCATC-TTTACCATCTTTAAGTCCAATGTCACTGGC
156390 CTTGAATCAGCACATTGGCAC
65 CTTGAATCAGCACATTGGCAC
156411 TTTCATCTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
94 3 0.04
95 73 0.96
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (95 bp):
AATGTCGCTAGCCTTGAATCAGCACATTGGCATCTTTACCATCTTTAAGTCCAATGTCACTGGCC
TTGAATCAGCACATTGGCACCTCTAATTCT
Found at i:156439 original size:49 final size:51
Alignment explanation
Indices: 156338--156450 Score: 158
Period size: 49 Copynumber: 2.2 Consensus size: 51
156328 TGTCGCTAGT
* *
156338 CTTGAATCAGCATATTGGCACATTTACCATCTTTAAGTCCAATGTCACTGGC
1 CTTGAATCAGCACATTGGCACATTTA-CATCTTTAAGTCCAATATCACTGGC
** *
156390 CTTGAATCAGCACATTGGCAC-TTT-CATCTTTAAGTCTGATATCATTGGC
1 CTTGAATCAGCACATTGGCACATTTACATCTTTAAGTCCAATATCACTGGC
156439 CTTGAATCAGCA
1 CTTGAATCAGCA
156451 TAGTGGCATC
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
49 33 0.59
51 3 0.05
52 20 0.36
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.34
Consensus pattern (51 bp):
CTTGAATCAGCACATTGGCACATTTACATCTTTAAGTCCAATATCACTGGC
Found at i:156585 original size:104 final size:99
Alignment explanation
Indices: 156245--156601 Score: 246
Period size: 101 Copynumber: 3.6 Consensus size: 99
156235 TTGCTAGCCT
* * * * *
156245 TGAATCAGCACATTGGCATCTTTGTCATCTTTAAGTCCAATGTTGCTGGCCTTGAATCCACACAT
1 TGAATCAGCACAGTGACATCTTTG--ATCTTTAAGCCCAATGTCGCTGGCCTTGAATCAACACAT
* * ** * * *
156310 TGGCAC---C-TC-T-AATTCTAATGTCGCTAGTCT
64 TGGCACTTTCATCTTCAAGTCTAATATCATTGGCCG
* * ** * * *
156340 TGAATCAGCATATTGGCACAT-TTACCATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCACA
1 TGAATCAGCACAGT-G-ACATCTT-TGATCTTTAAGCCCAATGTCGCTGGCCTTGAATCAACACA
* * *
156404 TTGGCACTTTCATCTTTAAGTCTGATATCATTGGCCT
63 TTGGCACTTTCATCTTCAAGTCTAATATCATTGGCCG
* * * *
156441 TGAATCAGCATAGTGGCATCTTTGA-CATTCCTGAGCCCAATGTCGCTAGCCTTGAATCAACACA
1 TGAATCAGCACAGTGACATCTTTGATC-TT--TAAGCCCAATGTCGCTGGCCTTGAATCAACACA
* * *
156505 TTGGCATTCTTCTCATCTTCAAGTGTAATGT-AGTTGGTCG
63 TTGGCA--CTT-TCATCTTCAAGTCTAATATCA-TTGGCCG
* *
156545 TGAATCAGCACATTGACATTCTTTGTATCTTTAAGCCCAATATCGCTGGCCTTGAAT
1 TGAATCAGCACAGTGACA-TCTTTG-ATCTTTAAGCCCAATGTCGCTGGCCTTGAAT
156602 TAGCATGTTG
Statistics
Matches: 206, Mismatches: 36, Indels: 31
0.75 0.13 0.11
Matches are distributed among these distances:
95 54 0.26
96 3 0.01
97 3 0.01
98 2 0.01
99 8 0.04
100 4 0.02
101 60 0.29
103 4 0.02
104 58 0.28
105 6 0.03
106 3 0.01
107 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (99 bp):
TGAATCAGCACAGTGACATCTTTGATCTTTAAGCCCAATGTCGCTGGCCTTGAATCAACACATTG
GCACTTTCATCTTCAAGTCTAATATCATTGGCCG
Found at i:156668 original size:61 final size:61
Alignment explanation
Indices: 156570--156697 Score: 184
Period size: 61 Copynumber: 2.1 Consensus size: 61
156560 ACATTCTTTG
* * * * * *
156570 TATCTTTAAGCCCAATATCGCTGGCCTTGAATTAGCATGTTGGCACCTTTTTCACTCTTCT
1 TATCTTTAAGCCCAATATCGCTAGCCCTGAATCAGCATATTGGCACCTTTATCACTCATCT
*
156631 TATCTTTAAGCCCAATATCGCTAGCCCTGAATCAGCATATTGGCATCTTTATCACTCATCT
1 TATCTTTAAGCCCAATATCGCTAGCCCTGAATCAGCATATTGGCACCTTTATCACTCATCT
*
156692 CATCTT
1 TATCTT
156698 CATCATCTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (61 bp):
TATCTTTAAGCCCAATATCGCTAGCCCTGAATCAGCATATTGGCACCTTTATCACTCATCT
Found at i:157581 original size:16 final size:16
Alignment explanation
Indices: 157560--157592 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
157550 TCCCAAAAAC
157560 ACTTCTTCATTTCAGA
1 ACTTCTTCATTTCAGA
157576 ACTTCTTCATTTCAGA
1 ACTTCTTCATTTCAGA
157592 A
1 A
157593 AACACAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.42
Consensus pattern (16 bp):
ACTTCTTCATTTCAGA
Found at i:161175 original size:21 final size:20
Alignment explanation
Indices: 161124--161177 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
161114 CATTTCAGAC
*
161124 ATGTATTGATGCATTCACTT
1 ATGTATTGATACATTCACTT
161144 ATGTATTGATACATTCACTAT
1 ATGTATTGATACATTCACT-T
* *
161165 TTGTATCGATACA
1 ATGTATTGATACA
161178 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATTGATACATTCACTT
Found at i:164027 original size:156 final size:154
Alignment explanation
Indices: 163837--164123 Score: 344
Period size: 156 Copynumber: 1.9 Consensus size: 154
163827 GACCCGGTGT
* **
163837 CGACCTAGGAGTTGATTCTAAAAAATTATAAAAATGCCCATAGGGGATACCTTCAACGTAAAACT
1 CGACCTAGGAGTTGATTCTAAAAAATTATAAAAATACCCATAAAGGATACCTTCAACGTAAAACT
* * * * *
163902 ACCAGATAGCTCT-TAAGAACTTAAAATGGATTTTAAAAGGGATGAACCTATCCTAAATACCCAC
66 ACCAGATACCCCTAAAAGAACTAAAAAT-GA-TCTAAAAGGGATGAACCTATCCTAAATACCCAC
163966 CTTCGGAATTAAAACGAACCTAGTGA
129 CTTCGGAATTAAAACGAACCTAGTGA
* * * * *
163992 CGACCTAGGAGTT-AGTTCTGAGAAAATTATGAAAATACTCTTAAAGGATACCTTCGACGTAAAA
1 CGACCTAGGAGTTGA-TTCT-AAAAAATTATAAAAATACCCATAAAGGATACCTTCAACGTAAAA
* * * * * * *
164056 GTACCTGATACCCCTAAAAGACCTAAAAATGATCTAGATGGGATGAATCTATCCTAAATGCCCAC
64 CTACCAGATACCCCTAAAAGAACTAAAAATGATCTAAAAGGGATGAACCTATCCTAAATACCCAC
164121 CTT
129 CTT
164124 TGGCATAAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
154 1 0.01
155 48 0.44
156 49 0.45
157 11 0.10
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (154 bp):
CGACCTAGGAGTTGATTCTAAAAAATTATAAAAATACCCATAAAGGATACCTTCAACGTAAAACT
ACCAGATACCCCTAAAAGAACTAAAAATGATCTAAAAGGGATGAACCTATCCTAAATACCCACCT
TCGGAATTAAAACGAACCTAGTGA
Found at i:165939 original size:20 final size:19
Alignment explanation
Indices: 165914--165951 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
165904 AATCCTACAA
*
165914 TTTTTCTTTTTTTATTTTCT
1 TTTTTCTTTCTTT-TTTTCT
165934 TTTTTCTTTCTTTTTTTC
1 TTTTTCTTTCTTTTTTTC
165952 CTCTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTCTTTCTTTTTTTCT
Found at i:165950 original size:12 final size:12
Alignment explanation
Indices: 165916--165965 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
165906 TCCTACAATT
*
165916 TTTCTTTTTTTA
1 TTTCTTTTTTTC
165928 TTT-TCTTTTTTC
1 TTTCT-TTTTTTC
165940 TTTCTTTTTTTCC
1 TTTCTTTTTTT-C
*
165953 TCTCTTTTTTTC
1 TTTCTTTTTTTC
165965 T
1 T
165966 CCAAGTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 1 0.03
12 20 0.61
13 12 0.36
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:165958 original size:24 final size:24
Alignment explanation
Indices: 165916--165962 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
165906 TCCTACAATT
* *
165916 TTTCTTTTTTTATTTTCTTTTTTC
1 TTTCTTTTTTTACTCTCTTTTTTC
*
165940 TTTCTTTTTTTCCTCTCTTTTTT
1 TTTCTTTTTTTACTCTCTTTTTT
165963 TCTCCAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTCTTTTTTTACTCTCTTTTTTC
Found at i:166111 original size:13 final size:13
Alignment explanation
Indices: 166095--166129 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
166085 TTTTTCCATT
*
166095 TTTTTTATTGTTA
1 TTTTTTATTGTCA
*
166108 TTTTTTCTTGTCA
1 TTTTTTATTGTCA
166121 TTTTTTATT
1 TTTTTTATT
166130 TGATGTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (13 bp):
TTTTTTATTGTCA
Found at i:166723 original size:166 final size:167
Alignment explanation
Indices: 166487--166843 Score: 413
Period size: 167 Copynumber: 2.1 Consensus size: 167
166477 ATTTTGTAAC
* * * * * *
166487 AATATTAGATGAATTTAAAAAATTTAAAATCGAGAAAAATCCTCCTGAAAATATTTGTGGGATAG
1 AATATTTGATGAATTTTAAAAATTAAAAAACAAAAAAAATCCTCCTGAAAATATTTGTGGGATAG
** * * * * * * * *
166552 AAAATTT-GGTTTTTGGAAA-AGATGGGCATTTCAAGAAAAAAATTCATAACT-TATGGAAATA-
66 AAAATTTCGCATTTTGAAAACAGA--AGAATTTCAAGAAAAAAATTAAAAAATGAAT-GAAAAAG
*
166613 AATTAATTTTTCAAAACTAATTTAATATGAATTAAATAAT
128 AATGAATTTTTCAAAACTAATTTAATATGAATTAAATAAT
166653 AAT-TTTGATGAATTTTAAAAATTAAAAAACAAAAAAAATCC-CCTCGAAAACTATTTGT-GGAG
1 AATATTTGATGAATTTTAAAAATTAAAAAACAAAAAAAATCCTCCT-GAAAA-TATTTGTGGGA-
*
166715 TAGAAAATTTCGCATTTTGAAAACAGAAGAATTTCAAGCAAAAAATTAAAAAATGAATGAAAAAG
63 TAGAAAATTTCGCATTTTGAAAACAGAAGAATTTCAAGAAAAAAATTAAAAAATGAATGAAAAAG
* * *
166780 AATGCATTTTTGAAAACTAATTTAATATGAATTAAATGAT
128 AATGAATTTTTCAAAACTAATTTAATATGAATTAAATAAT
*
166820 AATATTTGATGAATTTTAGAAATT
1 AATATTTGATGAATTTTAAAAATT
166844 TTAAATCGGT
Statistics
Matches: 161, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
164 3 0.02
165 40 0.25
166 46 0.29
167 50 0.31
168 22 0.14
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (167 bp):
AATATTTGATGAATTTTAAAAATTAAAAAACAAAAAAAATCCTCCTGAAAATATTTGTGGGATAG
AAAATTTCGCATTTTGAAAACAGAAGAATTTCAAGAAAAAAATTAAAAAATGAATGAAAAAGAAT
GAATTTTTCAAAACTAATTTAATATGAATTAAATAAT
Found at i:176644 original size:7 final size:7
Alignment explanation
Indices: 176634--176667 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
176624 AAAAAAATTA
176634 AAAAAAC
1 AAAAAAC
176641 -AAAAAC
1 AAAAAAC
176647 AAAAAAC
1 AAAAAAC
*
176654 AAAAAAA
1 AAAAAAC
176661 AAAAAAC
1 AAAAAAC
176668 GTAAAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:176665 original size:13 final size:13
Alignment explanation
Indices: 176633--176665 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
176623 AAAAAAAATT
176633 AAAAAAACAAAAA
1 AAAAAAACAAAAA
*
176646 CAAAAAACAAAAA
1 AAAAAAACAAAAA
176659 AAAAAAA
1 AAAAAAA
176666 ACGTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:177700 original size:13 final size:13
Alignment explanation
Indices: 177667--177700 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
177657 CATATTAGAC
*
177667 TTCACATCATGCT
1 TTCACATCATGCA
177680 TTCAACATCATGCA
1 TTC-ACATCATGCA
177694 TTCACAT
1 TTCACAT
177701 TACCATCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (13 bp):
TTCACATCATGCA
Found at i:178196 original size:30 final size:30
Alignment explanation
Indices: 178161--178295 Score: 112
Period size: 32 Copynumber: 4.4 Consensus size: 30
178151 CAACCCTCTC
*
178161 AAAGTCCACAACTTCGTGGCATCTCTTTTT
1 AAAGCCCACAACTTCGTGGCATCTCTTTTT
* * * * ** *
178191 AAAGTCCACCACTCCATAACATCTATTTTT
1 AAAGCCCACAACTTCGTGGCATCTCTTTTT
*
178221 AAAGCCCACGCAAGTTCGTGGCATCTCTTTTT
1 AAAGCCCA--CAACTTCGTGGCATCTCTTTTT
*
178253 AAAGCCCACGCAAGTT-GATGGCATCT-TTTTT
1 AAAGCCCA--CAACTTCG-TGGCATCTCTTTTT
178284 CAAAGCCCACAA
1 -AAAGCCCACAA
178296 GTCAATGGCA
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
30 34 0.39
31 6 0.07
32 47 0.54
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (30 bp):
AAAGCCCACAACTTCGTGGCATCTCTTTTT
Found at i:178252 original size:32 final size:32
Alignment explanation
Indices: 178173--178293 Score: 133
Period size: 32 Copynumber: 3.8 Consensus size: 32
178163 AGTCCACAAC
* *
178173 TTCGTGGCATCTCTTTTTAAAGTCCAC-C-AC
1 TTCGTGGCATCTCTTTTTAAAGCCCACGCAAG
* * ** *
178203 TCCATAACATCTATTTTTAAAGCCCACGCAAG
1 TTCGTGGCATCTCTTTTTAAAGCCCACGCAAG
178235 TTCGTGGCATCTCTTTTTAAAGCCCACGCAAG
1 TTCGTGGCATCTCTTTTTAAAGCCCACGCAAG
178267 TT-GATGGCATCT-TTTTTCAAAGCCCAC
1 TTCG-TGGCATCTCTTTTT-AAAGCCCAC
178294 AAGTCAATGG
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
30 21 0.28
31 7 0.09
32 47 0.63
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (32 bp):
TTCGTGGCATCTCTTTTTAAAGCCCACGCAAG
Found at i:178297 original size:62 final size:61
Alignment explanation
Indices: 178159--178297 Score: 156
Period size: 62 Copynumber: 2.2 Consensus size: 61
178149 GGCAACCCTC
* * *
178159 TCAAAGTCCACAACTTCGTGGCATCTCTTTTTAAAGTCCACCACTCCATAACATCTATTTT
1 TCAAAGCCCACAAGTTCGTGGCATCTCTTTTTAAAGCCCACCACTCCATAACATCTATTTT
* ** **
178220 T-AAAGCCCACGCAAGTTCGTGGCATCTCTTTTTAAAGCCCACGCAAGTTGATGGCATCT-TTTT
1 TCAAAGCCCA--CAAGTTCGTGGCATCTCTTTTTAAAGCCCAC-C-ACTCCATAACATCTATTTT
178283 TCAAAGCCCACAAGT
1 TCAAAGCCCACAAGT
178298 CAATGGCACC
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
60 7 0.11
61 1 0.02
62 34 0.52
63 6 0.09
64 17 0.26
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (61 bp):
TCAAAGCCCACAAGTTCGTGGCATCTCTTTTTAAAGCCCACCACTCCATAACATCTATTTT
Found at i:178382 original size:28 final size:29
Alignment explanation
Indices: 178280--178382 Score: 97
Period size: 28 Copynumber: 3.6 Consensus size: 29
178270 ATGGCATCTT
**
178280 TTTTCAAAGCCCACAAGTCAATGGCACCC
1 TTTTCAAAGCCCACAAGTCAATTACACCC
* * *
178309 TTTT-AAAGTCCACAAATCAGTGGTA-A-CC
1 TTTTCAAAGCCCACAAGTCAAT--TACACCC
*
178337 TTTTCAAAGCCCAAAAGTCAATTACACCC
1 TTTTCAAAGCCCACAAGTCAATTACACCC
*
178366 TTTT-AAAACCCACAAGT
1 TTTTCAAAGCCCACAAGT
178383 TGATGGCAGC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
27 2 0.03
28 32 0.55
29 24 0.41
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.25
Consensus pattern (29 bp):
TTTTCAAAGCCCACAAGTCAATTACACCC
Found at i:178567 original size:52 final size:52
Alignment explanation
Indices: 178491--178931 Score: 270
Period size: 52 Copynumber: 8.5 Consensus size: 52
178481 GTCTCTTTCG
* * * * * *
178491 AAGTCTAATATCGTTGGCCTTGAATCAACACATTGCCATTCTTCTCATCTTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAACATATTGGCATTCTTATCATCTTT
* * * ** * * *
178543 AGGTCCAACGTCGCTGGCCTTGAATTAATGTATTAACGC-CT-TTGTCATCTTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAACATATT--GGCATTCTTATCATCTTT
* * * * * *
178595 AAATCCAATATCACTGGCCTTGAATTAGCATATTGGCACTTC-TATCATTTTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAACATATTGGCA-TTCTTATCATCTTT
* * * * **
178647 AAG-CCTAATGTTGTTGACCTTGAATCAACATTTTGGCACCCTTATCATCTTT
1 AAGTCC-AATGTCGCTGGCCTTGAATCAACATATTGGCATTCTTATCATCTTT
** * * *
178699 AAGTTTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTT-TT-TCATCTTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAACATATTGGCA--TTCTTATCATCTTT
* * * ** * * *
178751 ATGTCCGATATCATTGGCCTTGAATTAGCATATTGGCACTTC-TATCATTTTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAACATATTGGCA-TTCTTATCATCTTT
* ** * *
178803 AAGCCCAACATCGCTAGCCTTGAATCAACATATTGGCATAT-TTATCATGTTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAACATATTGGCAT-TCTTATCATCTTT
* * * * *
178855 AAGTCCAATGTCGCTAGCCTTGAATCAACACATTAGCATTCTTCTCATCTTC
1 AAGTCCAATGTCGCTGGCCTTGAATCAACATATTGGCATTCTTATCATCTTT
* * *
178907 AAG-CCTAATGTTGCGGGCTTTGAAT
1 AAGTCC-AATGTCGCTGGCCTTGAAT
178932 TAGCTTATTG
Statistics
Matches: 292, Mismatches: 81, Indels: 32
0.72 0.20 0.08
Matches are distributed among these distances:
50 2 0.01
51 11 0.04
52 275 0.94
53 3 0.01
54 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (52 bp):
AAGTCCAATGTCGCTGGCCTTGAATCAACATATTGGCATTCTTATCATCTTT
Found at i:178779 original size:156 final size:156
Alignment explanation
Indices: 178507--178888 Score: 451
Period size: 156 Copynumber: 2.4 Consensus size: 156
178497 AATATCGTTG
* * ** * * * * * *
178507 GCCTTGAATCAACACATTGCCATTCTTCTCATCTTTAGGTCCAACGTCGCTGGCCTTGAATTAAT
1 GCCTTGAATCAACATATTGGCACACTTATCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAAC
** ** *
178572 GTATTAACGCCTTTGTCATCTTTAAATCCAATATCACTGGCCTTGAATTAGCATATTGGCACTTC
66 ACATTGGCACCTTTGTCATCTTTAAATCCAATATCACTGGCCTTGAATTAGCATATTGGCACTTC
* ** * *
178637 TATCATTTTTAAGCCTAATGTTG-TT
131 TATCATTTTTAAGCCCAACATCGCTA
* * ** *
178662 GACCTTGAATCAACATTTTGGCACCCTTATCATCTTTAAGTTTAATGTCGCTAGCCTTGAATCAG
1 G-CCTTGAATCAACATATTGGCACACTTATCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAA
* ** * *
178727 CACATTGGCACCTTTTTCATCTTTATGTCCGATATCATTGGCCTTGAATTAGCATATTGGCACTT
65 CACATTGGCACCTTTGTCATCTTTAAATCCAATATCACTGGCCTTGAATTAGCATATTGGCACTT
178792 CTATCATTTTTAAGCCCAACATCGCTA
130 CTATCATTTTTAAGCCCAACATCGCTA
* * *
178819 GCCTTGAATCAACATATTGGCATATTTATCATGTTTAAGTCCAATGTCGCTAGCCTTGAATCAAC
1 GCCTTGAATCAACATATTGGCACACTTATCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAAC
178884 ACATT
66 ACATT
178889 AGCATTCTTC
Statistics
Matches: 188, Mismatches: 37, Indels: 3
0.82 0.16 0.01
Matches are distributed among these distances:
155 1 0.01
156 185 0.98
157 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (156 bp):
GCCTTGAATCAACATATTGGCACACTTATCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAAC
ACATTGGCACCTTTGTCATCTTTAAATCCAATATCACTGGCCTTGAATTAGCATATTGGCACTTC
TATCATTTTTAAGCCCAACATCGCTA
Found at i:183708 original size:20 final size:20
Alignment explanation
Indices: 183679--183716 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
183669 AACCCTAAGT
*
183679 GAATTGTATCGATACATTAC
1 GAATTATATCGATACATTAC
183699 GAATTATATCGATACATT
1 GAATTATATCGATACATT
183717 GAGCCCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
GAATTATATCGATACATTAC
Found at i:192537 original size:13 final size:13
Alignment explanation
Indices: 192519--192549 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
192509 ACAATTCATC
192519 ATGTATCGATACA
1 ATGTATCGATACA
192532 ATGTATCGATACA
1 ATGTATCGATACA
*
192545 TTGTA
1 ATGTA
192550 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:192537 original size:33 final size:33
Alignment explanation
Indices: 192499--192563 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
192489 ATTACAAGTT
*
192499 ATGTATCGATACAATT-CATCATGTATCGATACA
1 ATGTATCGATAC-ATTGCACCATGTATCGATACA
*
192532 ATGTATCGATACATTGTACCATGTATCGATAC
1 ATGTATCGATACATTGCACCATGTATCGATAC
192564 CAACAGTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (33 bp):
ATGTATCGATACATTGCACCATGTATCGATACA
Found at i:192638 original size:19 final size:19
Alignment explanation
Indices: 192594--192666 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
192584 CTGCCAATCT
* **
192594 CATGTATCGATACAATTGTC
1 CATGTATCGAAACAATT-AA
*
192614 CATGTATCGAAATAATTAA
1 CATGTATCGAAACAATTAA
*
192633 CATGTATCGATACAATTAA
1 CATGTATCGAAACAATTAA
*
192652 CATGTATCGATACAA
1 CATGTATCGAAACAA
192667 AGCATAATGT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 32 0.68
20 15 0.32
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (19 bp):
CATGTATCGAAACAATTAA
Found at i:194695 original size:156 final size:157
Alignment explanation
Indices: 194398--195723 Score: 1379
Period size: 156 Copynumber: 8.5 Consensus size: 157
194388 ATCTATAGTC
* * * *
194398 CTTTTTAAGTCCTTTAGGGGTACTAAGATACTTTCAGGTCGAAGGTAT-CCCCTAGGGGCATTTT
1 CTTTTTAAGTCCTTTAGGGGTGCTAGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTTT
* * * * * **
194462 CGTAATATTTTTAGAATCAACTCCTAGGTCATTACTGAGTCTGCTTTTATGCTAAAGGTGGGCAT
66 GGTAAT-TTTTTAGAACCAACTCCTAGGTCATCACCGGGTCTGCTTTTATGCCGAAGGTGGGCAT
* *
194527 TTAGGATAGGTTCATCCCTTTTATAAGC
130 TTAGGATAGGTTCATCCCTTTTATGAGT
* *
194555 CTTTTTAAGTCCTTTAGGGGTACTTGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTTT
1 CTTTTTAAGTCCTTTAGGGGTGCTAGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTTT
* * *
194620 GGTAATTTTTTAGAA-CAACTCCTAAGTCATCACCGGGTTTGCTTTTATGTCGAAGGTGGGCATT
66 GGTAATTTTTTAGAACCAACTCCTAGGTCATCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATT
* * *
194684 TGGGATAGGTTCATCTCTTTTATGAGG
131 TAGGATAGGTTCATCCCTTTTATGAGT
* * * ****
194711 CTTTTTAAGTCTTTTAGAGTTG-TCAGGATACTTTTACGTCGAAGGTATACCCCTA-TAATATTT
1 CTTTTTAAGTCCTTTAGGGGTGCT-AGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTT
* * * **
194774 TGGTAATTTTTTAGAACCAACTCCTAGGTCATCACCGGGTCCGCTTTTATGCTGAAAGTGAACAT
65 TGGTAATTTTTTAGAACCAACTCCTAGGTCATCACCGGGTCTGCTTTTATGCCGAAGGTGGGCAT
194839 TTAGGATAGGTTCATCCCTTTTATGAGT
130 TTAGGATAGGTTCATCCCTTTTATGAGT
** * * * *
194867 CTTTTTAAGTCCTTTAAAGTTGCCAGGATACTTTTACGTCGAAGGAATACCCCTAGGGGCATTCT
1 CTTTTTAAGTCCTTTAGGGGTGCTAGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTTT
* * * * * * *
194932 GGTAA-TTTTTGGAACTAACTCTTAGGTCATCACCGGGTGTGCTTTTATGACAAAGGTAGGCATT
66 GGTAATTTTTTAGAACCAACTCCTAGGTCATCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATT
*
194996 TAGGATAGCTTCATCCCTTTTATGAGT
131 TAGGATAGGTTCATCCCTTTTATGAGT
* * * * **
195023 CTTTTTAAGTCCTTTAAGGTTGCCAGGATACTTTTACGTCGAAGATATACCTTTAGGGGCATTTT
1 CTTTTTAAGTCCTTTAGGGGTGCTAGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTTT
* * *
195088 GGTAATTTTTTAGAACCAACTCCTAGGTCGTCACCGGGTCCGCTTTTGTGCCGAAGGTGGGCATT
66 GGTAATTTTTTAGAACCAACTCCTAGGTCATCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATT
* * *
195153 TACGATAGGTTCATCCTTTTTCT-AGT
131 TAGGATAGGTTCATCCCTTTTATGAGT
* * ** * * *
195179 CTTTTTAAGTCCTTTAGGGTTGCCAAAATACTTTTATGTCGAAGATAT-CCCCGA-GGGCATTTT
1 CTTTTTAAGTCCTTTAGGGGTGCTAGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTTT
** ** * * * ** ** * *
195242 CATAATTTCCTAGAATCGAGTTGTAGGTTGTCACTGGGTCTGCTTTTATGTCGAAGGTGGGCATT
66 GGTAATTTTTTAGAACCAACTCCTAGGTCATCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATT
*
195307 TAGGATAGGTTCATCCCATCTT-T-AGT
131 TAGGATAGGTTCATCCC-TTTTATGAGT
* * * * **
195333 CTTTTTAAGTCCTTTAGGGTTGCTAGGATACTTTTATGTCGAACGTATACCCTTAAAGGCATTTT
1 CTTTTTAAGTCCTTTAGGGGTGCTAGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTTT
* ** * * *
195398 CGTAATTTCCTAGAACCAACTCCTAGGTCATCACCGGGTCCGCTTTTATGCCGAAGGGGGGCAAT
66 GGTAATTTTTTAGAACCAACTCCTAGGTCATCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATT
* *
195463 TGGGATAGGTTCATCCCTCTTATGAGT
131 TAGGATAGGTTCATCCCTTTTATGAGT
* ** * * * * *
195490 CTTTTTAAGTTCTTTAGGATTG-TCGGGATACTTTTATGTCAAAGGTATA-CCCTAAGGGTATTT
1 CTTTTTAAGTCCTTTAGGGGTGCT-AGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTT
* * * * ** **
195553 TGATAATTTTTTAAAACCAACTCCGAGGTCGTCACTAGGTCTGCTTTTATGCCGAAGGTGGGTTT
65 TGGTAATTTTTTAGAACCAACTCCTAGGTCATCACCGGGTCTGCTTTTATGCCGAAGGTGGGCAT
* *
195618 TTAAGATAGGTTCATTCCTTTTAT-AGT
130 TTAGGATAGGTTCATCCCTTTTATGAGT
* * * * * * * ** *
195645 CTTTTTTAAATCCTTTAGAGGT-ATCGGGTACTTCTATGTTAAAGGTAT-CCCCTAAGGGCATTT
1 C-TTTTTAAGTCCTTTAGGGGTGCTAGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTT
* *
195708 TCGT-ATTTTTTTGAAC
65 TGGTAATTTTTTAGAAC
195724 TAGCCCTTTA
Statistics
Matches: 989, Mismatches: 165, Indels: 33
0.83 0.14 0.03
Matches are distributed among these distances:
154 132 0.13
155 74 0.07
156 587 0.59
157 175 0.18
158 21 0.02
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (157 bp):
CTTTTTAAGTCCTTTAGGGGTGCTAGGATACTTTTACGTCGAAGGTATACCCCTAGGGGCATTTT
GGTAATTTTTTAGAACCAACTCCTAGGTCATCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATT
TAGGATAGGTTCATCCCTTTTATGAGT
Found at i:199948 original size:52 final size:52
Alignment explanation
Indices: 199855--199988 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 52
199845 GAGAAAGGTG
* * * * *
199855 CCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGAT-ATGAAAAATG
1 CCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGA-GAAAAATA
* * * * *
199907 TCAATGTGCTGATTCACGACCAACGACATTAGACTTGAAGATGAGAAGAATA
1 CCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGAGAAAAATA
*
199959 CCAATGTGCTGATTCAAGGCCAGCGACATT
1 CCAATGTGCTGATTCAAGGCCAACGACATT
199989 GGGCTTAGGA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
52 66 0.99
53 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (52 bp):
CCAATGTGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGAGAAAAATA
Found at i:200052 original size:104 final size:100
Alignment explanation
Indices: 199855--200098 Score: 222
Period size: 104 Copynumber: 2.4 Consensus size: 100
199845 GAGAAAGGTG
* * * *
199855 CCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATATGAAAAATGTCAATGTGCTGAT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT-AAGATATGAAAAATGTCAATATGCTGAT
* * * * *
199920 TCACGACCAACGACATTAGACTTGAAGATGA-GAAGAATA
65 TCAAGACCAACAACATCAAACTTAAAGATGATG--G--TA
* * * *
199959 CCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAGGA-ATGTTAAAGATGTTAATATGTTGA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAGATATG--AAAAATGTCAATATGCTGA
* * * *
200023 TTCAAGGCCAGCAATATCAAACTTAAAGATGATGGTG
64 TTCAAGACCAACAACATCAAACTTAAAGATGATGGTA
* * * *
200060 CCAACGTGCTGATTCAAAGCCAGCAACATTGGACTTAAG
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAG
200099 GATAAGAAGG
Statistics
Matches: 115, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
101 35 0.30
102 3 0.03
103 4 0.03
104 72 0.63
105 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (100 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAGATATGAAAAATGTCAATATGCTGATT
CAAGACCAACAACATCAAACTTAAAGATGATGGTA
Found at i:200174 original size:43 final size:43
Alignment explanation
Indices: 200113--200200 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
200103 AGAAGGATGA
* * * *
200113 TAAAGGTGCTAATATGCTGATTCATGGCCAGCGATATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACACTGGACT
* *
200156 TAAAGGTGCCAATGTGCTGATTGAAGGCCAGCGACACTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACACTGGACT
200199 TA
1 TA
200201 GAAAGAGATG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACACTGGACT
Found at i:201255 original size:40 final size:40
Alignment explanation
Indices: 201211--201412 Score: 206
Period size: 40 Copynumber: 5.2 Consensus size: 40
201201 TAGCTCCAGT
* * * * *
201211 AGCTCCCACAACAGCCTCTAGCAACTTAGTAACCACGAGC
1 AGCTCCCACAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
* * *
201251 AGCTCCCACAGCAACTTCCAGCAGCT---C--CCAC-AGT
1 AGCTCCCACAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
* *
201285 AG---CCATCAGCAACCTCCAGCAGCTTAGCAACCACGAGC
1 AGCTCCCA-CAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
* *
201323 AGCTCCCACAGTAGCTTCCAGCAGCTCAGCAACCACGAGC
1 AGCTCCCACAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
* *
201363 AGCTCCAACAGCAGCCTCTAGCAGCTCAGCAACCACGAGC
1 AGCTCCCACAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
201403 AGCTCCCACA
1 AGCTCCCACA
201413 ACAACTTCCA
Statistics
Matches: 134, Mismatches: 18, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
32 17 0.13
34 4 0.03
35 5 0.04
37 4 0.03
38 4 0.03
40 94 0.70
41 3 0.02
ACGTcount: A:0.30, C:0.41, G:0.17, T:0.12
Consensus pattern (40 bp):
AGCTCCCACAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
Found at i:201315 original size:18 final size:18
Alignment explanation
Indices: 201292--201326 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
201282 AGTAGCCATC
*
201292 AGCAACCTCCAGCAGCTT
1 AGCAACCACCAGCAGCTT
*
201310 AGCAACCACGAGCAGCT
1 AGCAACCACCAGCAGCT
201327 CCCACAGTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.37, G:0.20, T:0.11
Consensus pattern (18 bp):
AGCAACCACCAGCAGCTT
Found at i:201319 original size:72 final size:72
Alignment explanation
Indices: 201241--201480 Score: 211
Period size: 72 Copynumber: 3.2 Consensus size: 72
201231 GCAACTTAGT
201241 AACCACGAGCAGCTCCCACAGCAACTTCCAGCAGCTCCCACAGTAGCCATCAGCAACCTCCAGCA
1 AACCACGAGCAGCTCCCACAGCAACTTCCAGCAGCTCCCACAGTAGCCATCAGCAACCTCCAGCA
*
201306 GCTTAGC
66 GCTCAGC
* * * * *
201313 AACCACGAGCAGCTCCCACAGTAGCTTCCAGCAGCTCAGCAACCACGAGCAGCTCCAACAGC-AG
1 AACCACGAGCAGCTCCCACAGCAACTTCCAGCAGCT---C--CCAC-AGTAG--CCATCAGCAAC
*
201377 C-CTC--TAGCAGCTCAGC
58 CTC-CAGCAG---CTCAGC
* * * ** *
201393 AACCACGAGCAGCTCCCACAACAACTTCCAACAGCTCCCACAGCT-GCCATCAGTAATTTTCAGC
1 AACCACGAGCAGCTCCCACAGCAACTTCCAGCAGCTCCCACAG-TAGCCATCAGCAACCTCCAGC
201457 AGCTCAGC
65 AGCTCAGC
201465 AACCACGAGCAGCTCC
1 AACCACGAGCAGCTCC
201481 TGCAGCAATA
Statistics
Matches: 133, Mismatches: 18, Indels: 34
0.72 0.10 0.18
Matches are distributed among these distances:
72 62 0.47
73 2 0.02
74 3 0.02
75 7 0.05
77 7 0.05
78 5 0.04
79 3 0.02
80 44 0.33
ACGTcount: A:0.30, C:0.40, G:0.17, T:0.13
Consensus pattern (72 bp):
AACCACGAGCAGCTCCCACAGCAACTTCCAGCAGCTCCCACAGTAGCCATCAGCAACCTCCAGCA
GCTCAGC
Found at i:201365 original size:18 final size:18
Alignment explanation
Indices: 201342--201407 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 18
201332 AGTAGCTTCC
201342 AGCAGCTCAGCAACCACG
1 AGCAGCTCAGCAACCACG
* * *
201360 AGCAGCTCCAACAGCAGCCTCT
1 AGCAGCT----CAGCAACCACG
201382 AGCAGCTCAGCAACCACG
1 AGCAGCTCAGCAACCACG
201400 AGCAGCTC
1 AGCAGCTC
201408 CCACAACAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
18 23 0.61
22 15 0.39
ACGTcount: A:0.30, C:0.39, G:0.21, T:0.09
Consensus pattern (18 bp):
AGCAGCTCAGCAACCACG
Found at i:201374 original size:22 final size:21
Alignment explanation
Indices: 201310--201417 Score: 66
Period size: 22 Copynumber: 5.3 Consensus size: 21
201300 CCAGCAGCTT
201310 AGCAACCACGAGCAGCTCCCAC
1 AGCAACCACGAGCAGCT-CCAC
* * ** *
201332 AGTAGCTTCCAGCAGCT---C
1 AGCAACCACGAGCAGCTCCAC
201350 AGCAACCACGAGCAGCTCCAAC
1 AGCAACCACGAGCAGCTCC-AC
* * *
201372 AGCAGCCTCTAGCAGCT---C
1 AGCAACCACGAGCAGCTCCAC
201390 AGCAACCACGAGCAGCTCCCAC
1 AGCAACCACGAGCAGCT-CCAC
*
201412 AACAAC
1 AGCAAC
201418 TTCCAACAGC
Statistics
Matches: 61, Mismatches: 17, Indels: 16
0.65 0.18 0.17
Matches are distributed among these distances:
18 28 0.46
22 33 0.54
ACGTcount: A:0.31, C:0.41, G:0.19, T:0.09
Consensus pattern (21 bp):
AGCAACCACGAGCAGCTCCAC
Found at i:201421 original size:80 final size:75
Alignment explanation
Indices: 201211--201436 Score: 262
Period size: 80 Copynumber: 3.0 Consensus size: 75
201201 TAGCTCCAGT
* * * *
201211 AGCTCCCACAACAGCCTCTAGCAACTTAGTAACCACGAGCAGCTCCCACAGCAACTTCCAGCAGC
1 AGCTCCAACAGCAGCCTCTAGCAGCTTAGCAACCACGAGCAGCTCCCACAGCAACTTCCAGCAGC
*
201276 T-CCCACAGT
66 TCCCCACAGC
* * * * *
201285 AG--CCATCAGCAACCTCCAGCAGCTTAGCAACCACGAGCAGCTCCCACAGTAGCTTCCAGCAGC
1 AGCTCCAACAGCAGCCTCTAGCAGCTTAGCAACCACGAGCAGCTCCCACAGCAACTTCCAGCAGC
201348 TCAGCAACCACGAGC
66 TC--C--CCAC-AGC
* * *
201363 AGCTCCAACAGCAGCCTCTAGCAGCTCAGCAACCACGAGCAGCTCCCACAACAACTTCCAACAGC
1 AGCTCCAACAGCAGCCTCTAGCAGCTTAGCAACCACGAGCAGCTCCCACAGCAACTTCCAGCAGC
201428 T-CCCACAGC
66 TCCCCACAGC
201437 TGCCATCAGT
Statistics
Matches: 126, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
72 53 0.42
74 5 0.04
75 5 0.04
77 5 0.04
78 4 0.03
80 54 0.43
ACGTcount: A:0.30, C:0.41, G:0.16, T:0.12
Consensus pattern (75 bp):
AGCTCCAACAGCAGCCTCTAGCAGCTTAGCAACCACGAGCAGCTCCCACAGCAACTTCCAGCAGC
TCCCCACAGC
Found at i:201428 original size:40 final size:40
Alignment explanation
Indices: 201291--201429 Score: 188
Period size: 40 Copynumber: 3.5 Consensus size: 40
201281 CAGTAGCCAT
*
201291 CAGCAACCTCCAGCAGCTTAGCAACCACGAGCAGCTCCCA
1 CAGCAACCTCCAGCAGCTCAGCAACCACGAGCAGCTCCCA
* * * *
201331 CAGTAGCTTCCAGCAGCTCAGCAACCACGAGCAGCTCCAA
1 CAGCAACCTCCAGCAGCTCAGCAACCACGAGCAGCTCCCA
* *
201371 CAGCAGCCTCTAGCAGCTCAGCAACCACGAGCAGCTCCCA
1 CAGCAACCTCCAGCAGCTCAGCAACCACGAGCAGCTCCCA
* * *
201411 CAACAACTTCCAACAGCTC
1 CAGCAACCTCCAGCAGCTC
201430 CCACAGCTGC
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.30, C:0.41, G:0.17, T:0.12
Consensus pattern (40 bp):
CAGCAACCTCCAGCAGCTCAGCAACCACGAGCAGCTCCCA
Found at i:202036 original size:13 final size:13
Alignment explanation
Indices: 202018--202042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
202008 AAGCAATACG
202018 AGCAAAGGAGAGC
1 AGCAAAGGAGAGC
202031 AGCAAAGGAGAG
1 AGCAAAGGAGAG
202043 AAAAAGGGAA
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:0.48, C:0.12, G:0.40, T:0.00
Consensus pattern (13 bp):
AGCAAAGGAGAGC
Found at i:204351 original size:234 final size:234
Alignment explanation
Indices: 203916--204389 Score: 743
Period size: 234 Copynumber: 2.0 Consensus size: 234
203906 ATTGGTGGCA
* * * * *
203916 ACTCCAAGAATATAGTCATTTCGCATTGACCATTTAGGGTTAAATTGAGCGAGCGATTCATCTCG
1 ACTCCAAGAAAATAGTCATTTCGCAATGACCATTTAGGGATAAATCGAGCGAGCAATTCATCTCG
* * * *
203981 ATGACTCAAGTCCCTTAAAAATACAAAACATCATCTTTTAATATGGCCCACAAAATAGGAGTCAT
66 ATGACCCAAGTCCCTAAAAAATACAAAACACCATCTTTTAATATGGCCCACAAAATAGAAGTCAT
* * * *
204046 CAAAATAATAGAATTTCATTGTTTCATCAATCATATGATCCAGAGCCATTTTATGTTAGGCTTGG
131 CAAAATAATAGAATTTCATTGTTTCATCAATCATATGATCCAGAGCCATTTCAAGTCAGGCTTGA
* *
204111 TCAGGATTCGTATCCGGGCCACGTTGCGACAGCTTGACG
196 TCAGGATTCGTATCCGAGCCACGTTGCAACAGCTTGACG
* *
204150 ACTCTAAGAAAATAGTCATTTCGTAATGACCATTTAGGGATAAATCGAGCGAGCAATTCATCTCG
1 ACTCCAAGAAAATAGTCATTTCGCAATGACCATTTAGGGATAAATCGAGCGAGCAATTCATCTCG
*
204215 ATGACCCAAGTCCCTAAAAAATACAAAACACCATCTTTTAATATGGCCCACAAAATAGAAGTCGT
66 ATGACCCAAGTCCCTAAAAAATACAAAACACCATCTTTTAATATGGCCCACAAAATAGAAGTCAT
*
204280 CAAAATAATAGAATTTCATTGTTTCATCAATCATATGATCCAG-GACCATTTCAAGTCGGGCTTG
131 CAAAATAATAGAATTTCATTGTTTCATCAATCATATGATCCAGAG-CCATTTCAAGTCAGGCTTG
* *
204344 ATCAGGATTCGTATCCGAGCCATGTTGCAACAGCTTGGCG
195 ATCAGGATTCGTATCCGAGCCACGTTGCAACAGCTTGACG
204384 ACTCCA
1 ACTCCA
204390 CTAGGAAAGT
Statistics
Matches: 217, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
233 1 0.00
234 216 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (234 bp):
ACTCCAAGAAAATAGTCATTTCGCAATGACCATTTAGGGATAAATCGAGCGAGCAATTCATCTCG
ATGACCCAAGTCCCTAAAAAATACAAAACACCATCTTTTAATATGGCCCACAAAATAGAAGTCAT
CAAAATAATAGAATTTCATTGTTTCATCAATCATATGATCCAGAGCCATTTCAAGTCAGGCTTGA
TCAGGATTCGTATCCGAGCCACGTTGCAACAGCTTGACG
Found at i:209763 original size:13 final size:13
Alignment explanation
Indices: 209744--209782 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
209734 ACTATTTATG
209744 ATGTATCGATACA
1 ATGTATCGATACA
*
209757 CTGTATCGATACA
1 ATGTATCGATACA
209770 ATGTATCGATACA
1 ATGTATCGATACA
209783 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:209857 original size:23 final size:23
Alignment explanation
Indices: 209817--209862 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
209807 TAACGGTACA
* * *
209817 TGAATAGTGATACGTGAATAGTG
1 TGAACAGTGATACATGAACAGTG
*
209840 TGAACAGTGATATATGAACAGTG
1 TGAACAGTGATACATGAACAGTG
209863 ATGTATCAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAACAGTGATACATGAACAGTG
Found at i:209885 original size:21 final size:21
Alignment explanation
Indices: 209860--209900 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
209850 TATATGAACA
209860 GTGATGTATCAATACATGAAG
1 GTGATGTATCAATACATGAAG
*
209881 GTGATGTATCGATACATGAA
1 GTGATGTATCAATACATGAA
209901 CAGTTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
GTGATGTATCAATACATGAAG
Found at i:210014 original size:53 final size:53
Alignment explanation
Indices: 209950--210086 Score: 211
Period size: 53 Copynumber: 2.6 Consensus size: 53
209940 CTACTACCAA
* *
209950 TGTATCAATACATATTTTGTGTATCGATACAAATTTGGCTACTGCTAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
210003 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
210056 TGTATCGATACATATTTGTATGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
210087 TATGCAATCT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
53 64 0.84
54 12 0.16
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:210192 original size:21 final size:21
Alignment explanation
Indices: 210166--210206 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
210156 GTCAACCTTG
210166 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
210187 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
210207 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:211812 original size:13 final size:13
Alignment explanation
Indices: 211794--211818 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
211784 ACTGAAGCAA
211794 TGTATCGATACAT
1 TGTATCGATACAT
211807 TGTATCGATACA
1 TGTATCGATACA
211819 ATCTGAAAAA
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:213503 original size:84 final size:84
Alignment explanation
Indices: 213348--213512 Score: 192
Period size: 84 Copynumber: 2.0 Consensus size: 84
213338 CATTTTCCAC
* * * * *
213348 TTGCAACTCATTTCTTTTCTCCTCTAATTTATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
213413 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
213432 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
213494 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
213513 TTCTTTGAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 53 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.53
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:213925 original size:21 final size:21
Alignment explanation
Indices: 213901--213942 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
213891 ATCCATTTCT
* *
213901 TCATTTTCATCAACCTCTTGA
1 TCATCTTCATCAACATCTTGA
*
213922 TCATCTTCATCATCATCTTGA
1 TCATCTTCATCAACATCTTGA
213943 ATGGTTGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (21 bp):
TCATCTTCATCAACATCTTGA
Found at i:215665 original size:23 final size:23
Alignment explanation
Indices: 215625--215670 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
215615 TAACGGTACA
* * *
215625 TGAATAGTGATACGTGAATAGTG
1 TGAACAGTGATACATGAACAGTG
*
215648 TGAACAGTGATATATGAACAGTG
1 TGAACAGTGATACATGAACAGTG
215671 ATGTATCGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAACAGTGATACATGAACAGTG
Found at i:215686 original size:22 final size:22
Alignment explanation
Indices: 215656--215712 Score: 89
Period size: 21 Copynumber: 2.6 Consensus size: 22
215646 TGTGAACAGT
*
215656 GATATATGAACAGTGATGTATC
1 GATACATGAACAGTGATGTATC
*
215678 GATACATGAA-GGTGATGTATC
1 GATACATGAACAGTGATGTATC
215699 GATACATGAACAGT
1 GATACATGAACAGT
215713 ATGAATAGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28
Consensus pattern (22 bp):
GATACATGAACAGTGATGTATC
Found at i:215821 original size:53 final size:53
Alignment explanation
Indices: 215757--215893 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
215747 CTACTACCAA
215757 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACT
* *
215810 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACT
215863 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
215894 TATGCAATCT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACT
Found at i:216472 original size:16 final size:16
Alignment explanation
Indices: 216460--216495 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
216450 AAAATAATTA
216460 AAATAT-AATATAAAT
1 AAATATGAATATAAAT
216475 AAATATGAATAT--AT
1 AAATATGAATATAAAT
216489 AAATATG
1 AAATATG
216496 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 6 0.30
16 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AAATATGAATATAAAT
Found at i:216523 original size:18 final size:18
Alignment explanation
Indices: 216446--216533 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 18
216436 CATAATATAA
*
216446 ATAAAAAATAATTAAAAT
1 ATAAAAAATAATTAATAT
216464 ATAATATAAATAAATATGAATAT
1 ATAA-A-AAAT-AAT-T-AATAT
** **
216487 ATAAATATGTTAAAAAATAT
1 ATAAA-A-AATAATTAATAT
216507 ATAAAAAATAATTAATAT
1 ATAAAAAATAATTAATAT
216525 ATAAAAAAT
1 ATAAAAAAT
216534 TTATATAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
18 21 0.38
19 2 0.04
20 14 0.25
21 3 0.05
22 6 0.11
23 9 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAAAAAATAATTAATAT
Found at i:216530 original size:16 final size:16
Alignment explanation
Indices: 216429--216540 Score: 58
Period size: 16 Copynumber: 7.2 Consensus size: 16
216419 TGAGACAACG
216429 ATATAAACATAATATAA-
1 ATATAAA-ATAAT-TAAT
* *
216446 ATAAAAAATAATTAAA
1 ATATAAAATAATTAAT
* *
216462 ATATAATATAAATAA-
1 ATATAAAATAATTAAT
* *
216477 ATAT-GAATATATAAAT
1 ATATAAAATA-ATTAAT
*
216493 ATGTTAAAA-AA-T-AT
1 AT-ATAAAATAATTAAT
*
216507 ATAAAAAATAATTAAT
1 ATATAAAATAATTAAT
*
216523 ATATAAAA-AATTTAT
1 ATATAAAATAATTAAT
216538 ATA
1 ATA
216541 AATTTTTAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
13 4 0.06
14 9 0.12
15 20 0.28
16 29 0.40
17 8 0.11
18 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (16 bp):
ATATAAAATAATTAAT
Found at i:216727 original size:24 final size:24
Alignment explanation
Indices: 216675--216720 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
216665 TATAATATTT
*
216675 TAAATAATAAAAAATTATAAATAA
1 TAAATAATAAAAAATCATAAATAA
216699 TAAATAATAAAAAA-CATAAATA
1 TAAATAATAAAAAATCATAAATA
216721 TGTAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
TAAATAATAAAAAATCATAAATAA
Found at i:217573 original size:36 final size:36
Alignment explanation
Indices: 217515--217589 Score: 84
Period size: 39 Copynumber: 2.1 Consensus size: 36
217505 TGATATTATA
*
217515 ATAAATAATTTTTAATTGATTAAAATTTGT-AAGATGATT
1 ATAAATAATTATT-ATTGATT-AAATTT-TAAAGAT-ATT
217554 ATAAATAATTATT-TT-ATTAAATTTTAAAGATATT
1 ATAAATAATTATTATTGATTAAATTTTAAAGATATT
217588 AT
1 AT
217590 TTATTAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
34 6 0.18
35 11 0.32
36 3 0.09
37 2 0.06
39 12 0.35
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (36 bp):
ATAAATAATTATTATTGATTAAATTTTAAAGATATT
Found at i:217796 original size:3 final size:3
Alignment explanation
Indices: 217779--217873 Score: 77
Period size: 3 Copynumber: 30.3 Consensus size: 3
217769 AGATAGATAG
* *
217779 ATA ATA AAA AAA ATA ATA ATA ATA A-A TATA GAT- ATAA ATAA ATA GATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA AT-A AT-A ATA -ATA
* **
217827 ATAA AGA ACC ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
217873 A
1 A
217874 AAAGGTGGGC
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.04
3 61 0.78
4 14 0.18
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:220336 original size:40 final size:40
Alignment explanation
Indices: 220292--220493 Score: 206
Period size: 40 Copynumber: 5.2 Consensus size: 40
220282 TAGCTCCAGT
* * * * *
220292 AGCTCCCACAACAGCCTCTAGCAACTTAGTAACCACGAGC
1 AGCTCCCACAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
* * *
220332 AGCTCCCACAGCAACTTCCAGCAGCT---C--CCAC-AGT
1 AGCTCCCACAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
* *
220366 AG---CCATCAGCAACCTCCAGCAGCTTAGCAACCACGAGC
1 AGCTCCCA-CAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
* *
220404 AGCTCCCACAGTAGCTTCCAGCAGCTCAGCAACCACGAGC
1 AGCTCCCACAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
* *
220444 AGCTCCAACAGCAGCCTCTAGCAGCTCAGCAACCACGAGC
1 AGCTCCCACAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
220484 AGCTCCCACA
1 AGCTCCCACA
220494 ACAACTTCCA
Statistics
Matches: 134, Mismatches: 18, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
32 17 0.13
34 4 0.03
35 5 0.04
37 4 0.03
38 4 0.03
40 94 0.70
41 3 0.02
ACGTcount: A:0.30, C:0.41, G:0.17, T:0.12
Consensus pattern (40 bp):
AGCTCCCACAGCAGCCTCCAGCAGCTCAGCAACCACGAGC
Found at i:220396 original size:18 final size:18
Alignment explanation
Indices: 220373--220407 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
220363 AGTAGCCATC
*
220373 AGCAACCTCCAGCAGCTT
1 AGCAACCACCAGCAGCTT
*
220391 AGCAACCACGAGCAGCT
1 AGCAACCACCAGCAGCT
220408 CCCACAGTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.37, G:0.20, T:0.11
Consensus pattern (18 bp):
AGCAACCACCAGCAGCTT
Found at i:220400 original size:72 final size:72
Alignment explanation
Indices: 220322--220561 Score: 211
Period size: 72 Copynumber: 3.2 Consensus size: 72
220312 GCAACTTAGT
220322 AACCACGAGCAGCTCCCACAGCAACTTCCAGCAGCTCCCACAGTAGCCATCAGCAACCTCCAGCA
1 AACCACGAGCAGCTCCCACAGCAACTTCCAGCAGCTCCCACAGTAGCCATCAGCAACCTCCAGCA
*
220387 GCTTAGC
66 GCTCAGC
* * * * *
220394 AACCACGAGCAGCTCCCACAGTAGCTTCCAGCAGCTCAGCAACCACGAGCAGCTCCAACAGC-AG
1 AACCACGAGCAGCTCCCACAGCAACTTCCAGCAGCT---C--CCAC-AGTAG--CCATCAGCAAC
*
220458 C-CTC--TAGCAGCTCAGC
58 CTC-CAGCAG---CTCAGC
* * * ** *
220474 AACCACGAGCAGCTCCCACAACAACTTCCAACAGCTCCCACAGCT-GCCATCAGTAATTTTCAGC
1 AACCACGAGCAGCTCCCACAGCAACTTCCAGCAGCTCCCACAG-TAGCCATCAGCAACCTCCAGC
220538 AGCTCAGC
65 AGCTCAGC
220546 AACCACGAGCAGCTCC
1 AACCACGAGCAGCTCC
220562 TGCAGCAATA
Statistics
Matches: 133, Mismatches: 18, Indels: 34
0.72 0.10 0.18
Matches are distributed among these distances:
72 62 0.47
73 2 0.02
74 3 0.02
75 7 0.05
77 7 0.05
78 5 0.04
79 3 0.02
80 44 0.33
ACGTcount: A:0.30, C:0.40, G:0.17, T:0.13
Consensus pattern (72 bp):
AACCACGAGCAGCTCCCACAGCAACTTCCAGCAGCTCCCACAGTAGCCATCAGCAACCTCCAGCA
GCTCAGC
Found at i:220446 original size:18 final size:18
Alignment explanation
Indices: 220423--220488 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 18
220413 AGTAGCTTCC
220423 AGCAGCTCAGCAACCACG
1 AGCAGCTCAGCAACCACG
* * *
220441 AGCAGCTCCAACAGCAGCCTCT
1 AGCAGCT----CAGCAACCACG
220463 AGCAGCTCAGCAACCACG
1 AGCAGCTCAGCAACCACG
220481 AGCAGCTC
1 AGCAGCTC
220489 CCACAACAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
18 23 0.61
22 15 0.39
ACGTcount: A:0.30, C:0.39, G:0.21, T:0.09
Consensus pattern (18 bp):
AGCAGCTCAGCAACCACG
Found at i:220455 original size:22 final size:21
Alignment explanation
Indices: 220391--220498 Score: 66
Period size: 22 Copynumber: 5.3 Consensus size: 21
220381 CCAGCAGCTT
220391 AGCAACCACGAGCAGCTCCCAC
1 AGCAACCACGAGCAGCT-CCAC
* * ** *
220413 AGTAGCTTCCAGCAGCT---C
1 AGCAACCACGAGCAGCTCCAC
220431 AGCAACCACGAGCAGCTCCAAC
1 AGCAACCACGAGCAGCTCC-AC
* * *
220453 AGCAGCCTCTAGCAGCT---C
1 AGCAACCACGAGCAGCTCCAC
220471 AGCAACCACGAGCAGCTCCCAC
1 AGCAACCACGAGCAGCT-CCAC
*
220493 AACAAC
1 AGCAAC
220499 TTCCAACAGC
Statistics
Matches: 61, Mismatches: 17, Indels: 16
0.65 0.18 0.17
Matches are distributed among these distances:
18 28 0.46
22 33 0.54
ACGTcount: A:0.31, C:0.41, G:0.19, T:0.09
Consensus pattern (21 bp):
AGCAACCACGAGCAGCTCCAC
Found at i:220502 original size:80 final size:75
Alignment explanation
Indices: 220292--220517 Score: 262
Period size: 80 Copynumber: 3.0 Consensus size: 75
220282 TAGCTCCAGT
* * * *
220292 AGCTCCCACAACAGCCTCTAGCAACTTAGTAACCACGAGCAGCTCCCACAGCAACTTCCAGCAGC
1 AGCTCCAACAGCAGCCTCTAGCAGCTTAGCAACCACGAGCAGCTCCCACAGCAACTTCCAGCAGC
*
220357 T-CCCACAGT
66 TCCCCACAGC
* * * * *
220366 AG--CCATCAGCAACCTCCAGCAGCTTAGCAACCACGAGCAGCTCCCACAGTAGCTTCCAGCAGC
1 AGCTCCAACAGCAGCCTCTAGCAGCTTAGCAACCACGAGCAGCTCCCACAGCAACTTCCAGCAGC
220429 TCAGCAACCACGAGC
66 TC--C--CCAC-AGC
* * *
220444 AGCTCCAACAGCAGCCTCTAGCAGCTCAGCAACCACGAGCAGCTCCCACAACAACTTCCAACAGC
1 AGCTCCAACAGCAGCCTCTAGCAGCTTAGCAACCACGAGCAGCTCCCACAGCAACTTCCAGCAGC
220509 T-CCCACAGC
66 TCCCCACAGC
220518 TGCCATCAGT
Statistics
Matches: 126, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
72 53 0.42
74 5 0.04
75 5 0.04
77 5 0.04
78 4 0.03
80 54 0.43
ACGTcount: A:0.30, C:0.41, G:0.16, T:0.12
Consensus pattern (75 bp):
AGCTCCAACAGCAGCCTCTAGCAGCTTAGCAACCACGAGCAGCTCCCACAGCAACTTCCAGCAGC
TCCCCACAGC
Found at i:220509 original size:40 final size:40
Alignment explanation
Indices: 220372--220510 Score: 188
Period size: 40 Copynumber: 3.5 Consensus size: 40
220362 CAGTAGCCAT
*
220372 CAGCAACCTCCAGCAGCTTAGCAACCACGAGCAGCTCCCA
1 CAGCAACCTCCAGCAGCTCAGCAACCACGAGCAGCTCCCA
* * * *
220412 CAGTAGCTTCCAGCAGCTCAGCAACCACGAGCAGCTCCAA
1 CAGCAACCTCCAGCAGCTCAGCAACCACGAGCAGCTCCCA
* *
220452 CAGCAGCCTCTAGCAGCTCAGCAACCACGAGCAGCTCCCA
1 CAGCAACCTCCAGCAGCTCAGCAACCACGAGCAGCTCCCA
* * *
220492 CAACAACTTCCAACAGCTC
1 CAGCAACCTCCAGCAGCTC
220511 CCACAGCTGC
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.30, C:0.41, G:0.17, T:0.12
Consensus pattern (40 bp):
CAGCAACCTCCAGCAGCTCAGCAACCACGAGCAGCTCCCA
Found at i:221118 original size:13 final size:13
Alignment explanation
Indices: 221100--221124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
221090 ATGCAATACG
221100 AGCAAAGGAGAGC
1 AGCAAAGGAGAGC
221113 AGCAAAGGAGAG
1 AGCAAAGGAGAG
221125 AAAAAGGGAA
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:0.48, C:0.12, G:0.40, T:0.00
Consensus pattern (13 bp):
AGCAAAGGAGAGC
Found at i:228848 original size:13 final size:13
Alignment explanation
Indices: 228829--228867 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
228819 ACTATTTATG
228829 ATGTATCGATACA
1 ATGTATCGATACA
*
228842 CTGTATCGATACA
1 ATGTATCGATACA
228855 ATGTATCGATACA
1 ATGTATCGATACA
228868 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:228942 original size:23 final size:23
Alignment explanation
Indices: 228902--228947 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
228892 TAACGGTACA
* *
228902 TGAATAGTGATACGTGAATAGTG
1 TGAATAGTGATACATGAACAGTG
*
228925 TGAATAGTGATATATGAACAGTG
1 TGAATAGTGATACATGAACAGTG
228948 ATGTATCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.30
Consensus pattern (23 bp):
TGAATAGTGATACATGAACAGTG
Found at i:228970 original size:21 final size:21
Alignment explanation
Indices: 228945--228985 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
228935 TATATGAACA
228945 GTGATGTATCAATACATGAAG
1 GTGATGTATCAATACATGAAG
*
228966 GTGATGTATCGATACATGAA
1 GTGATGTATCAATACATGAA
228986 CAGTTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
GTGATGTATCAATACATGAAG
Found at i:229099 original size:53 final size:53
Alignment explanation
Indices: 229035--229171 Score: 211
Period size: 53 Copynumber: 2.6 Consensus size: 53
229025 CTACTACCAA
* *
229035 TGTATCAATACATATTTTGTGTATCGATACAAATTTGGCTACTGCTAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
229088 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
229141 TGTATCGATACATATTTGTATGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
229172 TATGCAATCT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
53 64 0.84
54 12 0.16
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:229277 original size:21 final size:21
Alignment explanation
Indices: 229251--229291 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
229241 GTCAACCTTG
229251 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
229272 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
229292 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:230896 original size:13 final size:13
Alignment explanation
Indices: 230878--230902 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230868 ACTGAAGCAA
230878 TGTATCGATACAT
1 TGTATCGATACAT
230891 TGTATCGATACA
1 TGTATCGATACA
230903 ATCTGGAAAA
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:231532 original size:23 final size:24
Alignment explanation
Indices: 231487--231533 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
231477 CAAAGGATTG
*
231487 AACACAAATTCAATTAAGCATAAA
1 AACACAAATTCAATTAAGAATAAA
231511 AACACAAATT-AATTGAA-AATAAA
1 AACACAAATTCAATT-AAGAATAAA
231534 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.21
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAATAAA
Found at i:232587 original size:84 final size:84
Alignment explanation
Indices: 232432--232596 Score: 192
Period size: 84 Copynumber: 2.0 Consensus size: 84
232422 CATTTTCCAC
* * * * *
232432 TTGCAACTCATTTCTTTTCTCCTCTAATTTATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
232497 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
232516 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
232578 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
232597 TTCTTTGAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 53 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.53
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:233009 original size:21 final size:21
Alignment explanation
Indices: 232985--233026 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
232975 ATCCATTTCT
* *
232985 TCATTTTCATCAACCTCTTGA
1 TCATCTTCATCAACATCTTGA
*
233006 TCATCTTCATCATCATCTTGA
1 TCATCTTCATCAACATCTTGA
233027 ACGGTTGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (21 bp):
TCATCTTCATCAACATCTTGA
Found at i:234749 original size:23 final size:23
Alignment explanation
Indices: 234709--234808 Score: 70
Period size: 23 Copynumber: 4.5 Consensus size: 23
234699 TAACGGTACA
* *
234709 TGAATAGTGATACGTGAATAGTG
1 TGAATAGTGATACATGAACAGTG
*
234732 TGAATAGTGATATATGAACAGTG
1 TGAATAGTGATACATGAACAGTG
234755 ATG--TA-TCGATACATG-A-AG-G
1 -TGAATAGT-GATACATGAACAGTG
* *
234774 TGATGTA-TCGATACATGAACAGTA
1 TGA-ATAGT-GATACATGAACAGTG
234798 TGAATAGTGAT
1 TGAATAGTGAT
234809 GAACAGTGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
18 2 0.03
19 1 0.02
20 2 0.03
21 14 0.23
22 10 0.16
23 27 0.44
24 6 0.10
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (23 bp):
TGAATAGTGATACATGAACAGTG
Found at i:234770 original size:22 final size:22
Alignment explanation
Indices: 234740--234796 Score: 89
Period size: 21 Copynumber: 2.6 Consensus size: 22
234730 TGTGAATAGT
*
234740 GATATATGAACAGTGATGTATC
1 GATACATGAACAGTGATGTATC
*
234762 GATACATGAA-GGTGATGTATC
1 GATACATGAACAGTGATGTATC
234783 GATACATGAACAGT
1 GATACATGAACAGT
234797 ATGAATAGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28
Consensus pattern (22 bp):
GATACATGAACAGTGATGTATC
Found at i:234906 original size:53 final size:53
Alignment explanation
Indices: 234841--234977 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
234831 CTACTACCAA
*
234841 TGTATCAATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
234894 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCT
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
234947 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
234978 TATGCAATCT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:235010 original size:20 final size:20
Alignment explanation
Indices: 234947--235017 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
234937 GCCAATGTCT
**
234947 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
234967 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
234987 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
235007 TGTATCGATAC
1 TGTATCGATAC
235018 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:235555 original size:16 final size:16
Alignment explanation
Indices: 235543--235578 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
235533 AAAATAATTA
235543 AAATAT-AATATAAAT
1 AAATATGAATATAAAT
235558 AAATATGAATAT--AT
1 AAATATGAATATAAAT
235572 AAATATG
1 AAATATG
235579 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 6 0.30
16 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AAATATGAATATAAAT
Found at i:235798 original size:23 final size:23
Alignment explanation
Indices: 235763--235807 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
235753 TATAATATTT
**
235763 TAAATAATAAAAATTATAAATAA
1 TAAATAATAAAAAACATAAATAA
235786 TAAATAATAAAAAACATAAATA
1 TAAATAATAAAAAACATAAATA
235808 TGTAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAATAATAAAAAACATAAATAA
Found at i:236631 original size:17 final size:19
Alignment explanation
Indices: 236605--236643 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
236595 TATAATAAAT
*
236605 AATTTTTAAT-TGATTA-A
1 AATTTGTAATATGATTATA
236622 AATTTGTAATATGATTATA
1 AATTTGTAATATGATTATA
236641 AAT
1 AAT
236644 AATTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (19 bp):
AATTTGTAATATGATTATA
Found at i:236882 original size:3 final size:3
Alignment explanation
Indices: 236865--236959 Score: 77
Period size: 3 Copynumber: 30.3 Consensus size: 3
236855 AGATAGATAG
* *
236865 ATA ATA AAA AAA ATA ATA ATA ATA A-A TATA GAT- ATAA ATAA ATA GATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA AT-A AT-A ATA -ATA
* **
236913 ATAA AGA ACC ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
236959 A
1 A
236960 AAAGGTGGGC
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.04
3 61 0.78
4 14 0.18
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:239931 original size:214 final size:214
Alignment explanation
Indices: 239562--239992 Score: 862
Period size: 214 Copynumber: 2.0 Consensus size: 214
239552 CAAGGCTGAT
239562 AATAGTAGTTACCAAGAAGAAGAAAACAAAGAAGGACCGACTGAGAGCCGACAACAGGAGGATTT
1 AATAGTAGTTACCAAGAAGAAGAAAACAAAGAAGGACCGACTGAGAGCCGACAACAGGAGGATTT
239627 GTCTAGAAAAGCCAAAGAGAAAAGCCCGGAGGCTTCAAAGACAACTGCAAATGTCATGAACATCA
66 GTCTAGAAAAGCCAAAGAGAAAAGCCCGGAGGCTTCAAAGACAACTGCAAATGTCATGAACATCA
239692 CCTTTCAGGGTTCATCAGAGGCTGACAAATCTGGTGAAGGACAGGTTTATAGTTCTACAAATATT
131 CCTTTCAGGGTTCATCAGAGGCTGACAAATCTGGTGAAGGACAGGTTTATAGTTCTACAAATATT
239757 GTAGTAATCTGAATAGCCA
196 GTAGTAATCTGAATAGCCA
239776 AATAGTAGTTACCAAGAAGAAGAAAACAAAGAAGGACCGACTGAGAGCCGACAACAGGAGGATTT
1 AATAGTAGTTACCAAGAAGAAGAAAACAAAGAAGGACCGACTGAGAGCCGACAACAGGAGGATTT
239841 GTCTAGAAAAGCCAAAGAGAAAAGCCCGGAGGCTTCAAAGACAACTGCAAATGTCATGAACATCA
66 GTCTAGAAAAGCCAAAGAGAAAAGCCCGGAGGCTTCAAAGACAACTGCAAATGTCATGAACATCA
239906 CCTTTCAGGGTTCATCAGAGGCTGACAAATCTGGTGAAGGACAGGTTTATAGTTCTACAAATATT
131 CCTTTCAGGGTTCATCAGAGGCTGACAAATCTGGTGAAGGACAGGTTTATAGTTCTACAAATATT
239971 GTAGTAATCTGAATAGCCA
196 GTAGTAATCTGAATAGCCA
239990 AAT
1 AAT
239993 GTTTCTTACA
Statistics
Matches: 217, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
214 217 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (214 bp):
AATAGTAGTTACCAAGAAGAAGAAAACAAAGAAGGACCGACTGAGAGCCGACAACAGGAGGATTT
GTCTAGAAAAGCCAAAGAGAAAAGCCCGGAGGCTTCAAAGACAACTGCAAATGTCATGAACATCA
CCTTTCAGGGTTCATCAGAGGCTGACAAATCTGGTGAAGGACAGGTTTATAGTTCTACAAATATT
GTAGTAATCTGAATAGCCA
Found at i:241147 original size:8 final size:8
Alignment explanation
Indices: 241136--241166 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
241126 ATTATTTTAA
241136 TAATTTTT
1 TAATTTTT
241144 TAATTTTAT
1 TAATTTT-T
241153 TAATTTTT
1 TAATTTTT
241161 TAATTT
1 TAATTT
241167 AAAATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TAATTTTT
Found at i:241167 original size:16 final size:17
Alignment explanation
Indices: 241129--241166 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
241119 GTGATTTATT
241129 ATTTTAATAATTTTTTA
1 ATTTTAATAATTTTTTA
*
241146 ATTTTATTAATTTTTTA
1 ATTTTAATAATTTTTTA
241163 ATTT
1 ATTT
241167 AAAATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTAATAATTTTTTA
Found at i:242500 original size:14 final size:13
Alignment explanation
Indices: 242481--242510 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
242471 CTGAATCTTC
242481 TTCTTCCTTTCTCT
1 TTCTTCCTTTC-CT
242495 TTCTTCCTTTCCT
1 TTCTTCCTTTCCT
242508 TTC
1 TTC
242511 CTTTCTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TTCTTCCTTTCCT
Found at i:246932 original size:20 final size:21
Alignment explanation
Indices: 246907--246961 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
246897 CATTTTAAAC
246907 ATGTATCGATACATTCACTT-
1 ATGTATCGATACATTCACTTG
* * *
246927 ATGTATCAATACTTTCTCTTG
1 ATGTATCGATACATTCACTTG
* *
246948 TTGTAGCGATACAT
1 ATGTATCGATACAT
246962 CTAGATAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATTCACTTG
Found at i:247788 original size:31 final size:31
Alignment explanation
Indices: 247723--247976 Score: 170
Period size: 31 Copynumber: 7.7 Consensus size: 31
247713 GAAAAAGACC
*
247723 CCACCAACTTGTGCGGGCTTTGAAAAGGGTTG
1 CCACCAACTTGTGTGGGCTTT-AAAAGGGTTG
* *
247755 CCACCAACTTGTGTGAGCTTTAAAAAGGTTG
1 CCACCAACTTGTGTGGGCTTTAAAAGGGTTG
* * *
247786 CCACCGACTTATGTGGGCTTTAGAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTAAAAGGGTTG
** *
247817 CCACTTAC--GTGTAGGCTTTAGAGAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTA-A-AAGGGTTG
** **
247848 CCACTGACTTGTGTGAACTTTAGAGAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTA-A-AAGGGTTG
* *
247881 CCACTGACTGCCACCGACTTGTTTGGGCTTTAGAAGGGTTG
1 -C-C--A---CCA---ACTTGTGTGGGCTTTAAAAGGGTTG
** *
247922 CCACTGACTTGTGTGGGCTTTAGAAAAGGATTG
1 CCACCAACTTGTGTGGGCTTT--AAAAGGGTTG
*
247955 CCACCAACTTGTGTAGGCTTTA
1 CCACCAACTTGTGTGGGCTTTA
247977 GAAGAGGACT
Statistics
Matches: 175, Mismatches: 31, Indels: 33
0.73 0.13 0.14
Matches are distributed among these distances:
29 10 0.06
31 71 0.41
32 19 0.11
33 46 0.26
34 2 0.01
35 1 0.01
37 2 0.01
39 1 0.01
40 2 0.01
41 8 0.05
43 13 0.07
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (31 bp):
CCACCAACTTGTGTGGGCTTTAAAAGGGTTG
Found at i:247912 original size:43 final size:41
Alignment explanation
Indices: 247846--247930 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
247836 AGAGAAGGGT
*
247846 TGCCACTGACTTGTGTGAACTTTAGAGAAGGGTTGCCACTGAC
1 TGCCACCGACTTGTGTGAACTTT--AGAAGGGTTGCCACTGAC
* **
247889 TGCCACCGACTTGTTTGGGCTTTAGAAGGGTTGCCACTGAC
1 TGCCACCGACTTGTGTGAACTTTAGAAGGGTTGCCACTGAC
247930 T
1 T
247931 TGTGTGGGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 19 0.50
43 19 0.50
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.29
Consensus pattern (41 bp):
TGCCACCGACTTGTGTGAACTTTAGAAGGGTTGCCACTGAC
Found at i:247965 original size:33 final size:33
Alignment explanation
Indices: 247889--247990 Score: 127
Period size: 33 Copynumber: 3.2 Consensus size: 33
247879 TGCCACTGAC
* *
247889 TGCCACCGACTTGTTTGGGCTTTAG--AAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAAAGGAT
*
247920 TGCCACTGACTTGTGTGGGCTTTAGAAAAGGAT
1 TGCCACCGACTTGTGTGGGCTTTAGAAAAGGAT
* * * *
247953 TGCCACCAACTTGTGTAGGCTTTAGAAGAGGAC
1 TGCCACCGACTTGTGTGGGCTTTAGAAAAGGAT
247986 TGCCA
1 TGCCA
247991 TAGAGTAGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 23 0.38
33 38 0.62
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (33 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAAAGGAT
Found at i:248065 original size:59 final size:58
Alignment explanation
Indices: 247998--248127 Score: 188
Period size: 59 Copynumber: 2.2 Consensus size: 58
247988 CCATAGAGTA
* * * *
247998 GTGGACTTTAAAAACGGGTGCTATGAAGCTGTGGATTTAAAAAAAGGTGCCACGTAGTT
1 GTGGACTTTAAAAACAGGTGCTATGAAGCTGTGAACTT-AAAAAAGGTGCCACATAGTT
* * *
248057 GTGGACTTTAAAAGCAGGTGCTATGAAGTTGTGAACTTAAAAAGGGTGCCACATAGTT
1 GTGGACTTTAAAAACAGGTGCTATGAAGCTGTGAACTTAAAAAAGGTGCCACATAGTT
248115 GTGGACTTTAAAA
1 GTGGACTTTAAAA
248128 GAGATACAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 31 0.48
59 33 0.52
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (58 bp):
GTGGACTTTAAAAACAGGTGCTATGAAGCTGTGAACTTAAAAAAGGTGCCACATAGTT
Found at i:248143 original size:29 final size:29
Alignment explanation
Indices: 248027--248376 Score: 231
Period size: 29 Copynumber: 11.8 Consensus size: 29
248017 GCTATGAAGC
* * *
248027 TGTGGA-TTTAAAAAAAGGTGCCACGTAGT
1 TGTGGACTTT-AAAAGAGATGCCACGGAGT
* * * *
248056 TGTGGACTTTAAAAGCAGGTGCTATGAAGT
1 TGTGGACTTTAAAAG-AGATGCCACGGAGT
* * * **
248086 TGTGAACTTAAAAAG-GGTGCCACATAGT
1 TGTGGACTTTAAAAGAGATGCCACGGAGT
* *
248114 TGTGGACTTTAAAAGAGATACAACGGAGT
1 TGTGGACTTTAAAAGAGATGCCACGGAGT
* *
248143 TGTGGACTTTGAAGAA-AAATGTGTCACGGAGT
1 TGTGGACTTT-AA-AAGAGA--TGCCACGGAGT
248175 TGTGGACTTTAAAAGAGATGCCACGGAGT
1 TGTGGACTTTAAAAGAGATGCCACGGAGT
* **
248204 TGTGAACTTTAAAAGAGATGCCATTGAGT
1 TGTGGACTTTAAAAGAGATGCCACGGAGT
* * * **
248233 TATGGACTTTGAAGAAAAGGTGCCACAAAGT
1 TGTGGACTTT-AA-AAGAGATGCCACGGAGT
* * *
248264 TGTGAACTTTAGAAGAGATGCCACAGAGT
1 TGTGGACTTTAAAAGAGATGCCACGGAGT
* * **
248293 TGTGGACTTTAAAAAAGGTGCCACTAAGT
1 TGTGGACTTTAAAAGAGATGCCACGGAGT
* * *
248322 CGTGGACTTCGAGAAA-AGATGCCACTGAGT
1 TGTGGACTT-TA-AAAGAGATGCCACGGAGT
** * *
248352 CATGGACTTTGAGAGCAGATGCCAC
1 TGTGGACTTTAAAAG-AGATGCCAC
248377 TAAGTCATGG
Statistics
Matches: 254, Mismatches: 53, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
28 24 0.09
29 117 0.46
30 66 0.26
31 29 0.11
32 18 0.07
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.25
Consensus pattern (29 bp):
TGTGGACTTTAAAAGAGATGCCACGGAGT
Found at i:248239 original size:119 final size:116
Alignment explanation
Indices: 248027--248242 Score: 274
Period size: 119 Copynumber: 1.8 Consensus size: 116
248017 GCTATGAAGC
* * * *
248027 TGTGGATTTAAAAAAAGGTGCCACGTAGTTGTGGACTTTAAAAGCAGGTGCTATGAAGTTGTGAA
1 TGTGGATTTAAAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGCAGATGCCACGAAGTTGTGAA
* *
248092 CTTAAAAAGGGTGCCACATAGTTGTGGACTTTAAAAGAGATACAACGGAGT
66 CTTAAAAAGGATGCCACATAGTTATGGACTTTAAAAGAGATACAACGGAGT
* * *
248143 TGTGGACTTTGAAGAAAAATGTGTCACGGAGTTGTGGACTTTAAAAG-AGATGCCACGGAGTTGT
1 TGTGGA-TTT-AA-AAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGCAGATGCCACGAAGTTGT
* *
248207 GAACTTTAAAAGAGATGCCA-TTGAGTTATGGACTTT
63 GAACTTAAAAAG-GATGCCACAT-AGTTATGGACTTT
248243 GAAGAAAAGG
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
116 6 0.07
117 3 0.04
118 27 0.32
119 48 0.57
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (116 bp):
TGTGGATTTAAAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGCAGATGCCACGAAGTTGTGAA
CTTAAAAAGGATGCCACATAGTTATGGACTTTAAAAGAGATACAACGGAGT
Found at i:248302 original size:89 final size:89
Alignment explanation
Indices: 248027--248346 Score: 310
Period size: 89 Copynumber: 3.6 Consensus size: 89
248017 GCTATGAAGC
* * * * **
248027 TGTGGA-TTTAAAAAAAGGTGCCAC-GTAGTTGTGGACTTT-AA-AAGCAGGTGCTATGAAGTTG
1 TGTGGACTTT-AAAAGAGATGCCACTG-AGTTGTGGACTTTGAAGAA-AAGGTGCCACAAAGTTG
* * *
248088 TGAACTTAAAAAG-GGTGCCACATAGT
63 TGAACTTTAAAAGAGATGCCACAGAGT
* * * * * **
248114 TGTGGACTTTAAAAGAGATACAACGGAGTTGTGGACTTTGAAGAAAAATGTGTCACGGAGTTGTG
1 TGTGGACTTTAAAAGAGATGCCACTGAGTTGTGGACTTTGAAG-AAAAGGTGCCACAAAGTTGTG
* *
248179 GACTTTAAAAGAGATGCCACGGAGT
65 AACTTTAAAAGAGATGCCACAGAGT
* * *
248204 TGTGAACTTTAAAAGAGATGCCATTGAGTTATGGACTTTGAAGAAAAGGTGCCACAAAGTTGTGA
1 TGTGGACTTTAAAAGAGATGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACAAAGTTGTGA
*
248269 ACTTTAGAAGAGATGCCACAGAGT
66 ACTTTAAAAGAGATGCCACAGAGT
* * * * * *
248293 TGTGGACTTTAAAAAAGGTGCCACTAAGTCGTGGACTTCG-AGAAAAGATGCCAC
1 TGTGGACTTTAAAAGAGATGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCAC
248347 TGAGTCATGG
Statistics
Matches: 190, Mismatches: 37, Indels: 11
0.80 0.16 0.05
Matches are distributed among these distances:
87 29 0.15
88 19 0.10
89 93 0.49
90 49 0.26
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.26
Consensus pattern (89 bp):
TGTGGACTTTAAAAGAGATGCCACTGAGTTGTGGACTTTGAAGAAAAGGTGCCACAAAGTTGTGA
ACTTTAAAAGAGATGCCACAGAGT
Found at i:248345 original size:30 final size:30
Alignment explanation
Indices: 248176--248492 Score: 252
Period size: 30 Copynumber: 10.5 Consensus size: 30
248166 TCACGGAGTT
** *
248176 GTGGACTTT-A-AAAGAGATGCCACGGAGTT
1 GTGGACTTTGAGAAA-AGATGCCACTAAGTC
* * * *
248205 GTGAACTTT-A-AAAGAGATGCCATTGAGTT
1 GTGGACTTTGAGAAA-AGATGCCACTAAGTC
* * * *
248234 ATGGACTTTGAAGAAAAGGTGCCACAAAGTT
1 GTGGACTTTG-AGAAAAGATGCCACTAAGTC
* * *
248265 GTGAACTTT-AGAAGAGATGCCAC-AGAGTT
1 GTGGACTTTGAGAAAAGATGCCACTA-AGTC
* *
248294 GTGGACTTT-AAAAAAGGTGCCACTAAGTC
1 GTGGACTTTGAGAAAAGATGCCACTAAGTC
* *
248323 GTGGACTTCGAGAAAAGATGCCACTGAGTC
1 GTGGACTTTGAGAAAAGATGCCACTAAGTC
* **
248353 ATGGACTTTGAGAGCAGATGCCACTAAGTC
1 GTGGACTTTGAGAAAAGATGCCACTAAGTC
* *
248383 ATGGACTTTGAGAAAAGATGCCACTTAGTC
1 GTGGACTTTGAGAAAAGATGCCACTAAGTC
* * *
248413 GTGTACTATAAGCAGATAAAAAAATGCCACTAAGTC
1 GTGGACT-T-TG-AG---AAAAGATGCCACTAAGTC
248449 GTGGACTTTGAGAAAAGATGCCACTAAGTC
1 GTGGACTTTGAGAAAAGATGCCACTAAGTC
*
248479 ATGGACTTTGAGAA
1 GTGGACTTTGAGAA
248493 GGAACTATGA
Statistics
Matches: 237, Mismatches: 39, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.00
29 79 0.33
30 105 0.44
31 20 0.08
32 4 0.02
33 4 0.02
34 1 0.00
35 1 0.00
36 22 0.09
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (30 bp):
GTGGACTTTGAGAAAAGATGCCACTAAGTC
Found at i:248372 original size:89 final size:88
Alignment explanation
Indices: 248103--248415 Score: 236
Period size: 89 Copynumber: 3.5 Consensus size: 88
248093 TTAAAAAGGG
* * * * ** * * *
248103 TGCCACATAGTTGTGGACTTTAAAAGAGATACAACGGAGTTGTGGACTTTGAAGAAAA-ATGTGT
1 TGCCACAGAGTTGTGGACTTTAAAAAAGATGCCACTAAGTCGTGGACTTCGAAGAAAAGA--TGC
** ** *
248167 CACGGAGTTGTGGACTTTAAAAGAGA
64 CACAAAGTCATGGACTTT-AGAGAGA
* * * * * ** * *
248193 TGCCACGGAGTTGTGAACTTTAAAAGAGATGCCATTGAGTTATGGACTTTGAAGAAAAGGTGCCA
1 TGCCACAGAGTTGTGGACTTTAAAAAAGATGCCACTAAGTCGTGGACTTCGAAGAAAAGATGCCA
** *
248258 CAAAGTTGTGAACTTTAGAAGAGA
66 CAAAGTCATGGACTTTAG-AGAGA
*
248282 TGCCACAGAGTTGTGGACTTTAAAAAAGGTGCCACTAAGTCGTGGACTTCG-AGAAAAGATGCCA
1 TGCCACAGAGTTGTGGACTTTAAAAAAGATGCCACTAAGTCGTGGACTTCGAAGAAAAGATGCCA
**
248346 CTGAGTCATGGACTTTGAGAGCAGA
66 CAAAGTCATGGACTTT-AGAG-AGA
** * *
248371 TGCCACTA-AGTCATGGACTTTGAGAAAAGATGCCACTTAGTCGTG
1 TGCCAC-AGAGTTGTGGACTTT-AAAAAAGATGCCACTAAGTCGTG
248416 TACTATAAGC
Statistics
Matches: 183, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
88 26 0.14
89 86 0.47
90 71 0.39
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (88 bp):
TGCCACAGAGTTGTGGACTTTAAAAAAGATGCCACTAAGTCGTGGACTTCGAAGAAAAGATGCCA
CAAAGTCATGGACTTTAGAGAGA
Found at i:249501 original size:33 final size:33
Alignment explanation
Indices: 249449--249536 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 33
249439 TAACAAGAAG
* *
249449 GGTGATATGGTTTGATTTATTTCTGACAAAAAA
1 GGTGATATGATTTGGTTTATTTCTGACAAAAAA
* * **
249482 GGTGATACGATTTGGTTTATTTCTGATAGGAAA
1 GGTGATATGATTTGGTTTATTTCTGACAAAAAA
* *
249515 GGTGATATGACTTGGTTCATTT
1 GGTGATATGATTTGGTTTATTT
249537 TCAACAAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (33 bp):
GGTGATATGATTTGGTTTATTTCTGACAAAAAA
Found at i:249806 original size:18 final size:18
Alignment explanation
Indices: 249783--249845 Score: 90
Period size: 18 Copynumber: 3.3 Consensus size: 18
249773 TTGTTTTTTT
249783 ATGAAGACAATTGATTGA
1 ATGAAGACAATTGATTGA
249801 ATGAAGACAATTGATTGA
1 ATGAAGACAATTGATTGA
*
249819 ATAAAGTTGACAATTGATTGA
1 ATGAA---GACAATTGATTGA
249840 ATGAAG
1 ATGAAG
249846 TTGACAGTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
18 23 0.57
21 17 0.43
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (18 bp):
ATGAAGACAATTGATTGA
Found at i:249832 original size:21 final size:21
Alignment explanation
Indices: 249788--249851 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
249778 TTTTTATGAA
249788 GACAATTGATTGAATGAA---
1 GACAATTGATTGAATGAAGTT
*
249806 GACAATTGATTGAATAAAGTT
1 GACAATTGATTGAATGAAGTT
249827 GACAATTGATTGAATGAAGTT
1 GACAATTGATTGAATGAAGTT
249848 GACA
1 GACA
249852 GTGCAAATGC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.41
21 24 0.59
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (21 bp):
GACAATTGATTGAATGAAGTT
Found at i:250722 original size:40 final size:40
Alignment explanation
Indices: 250649--250728 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
250639 GCATTCTAGA
* *
250649 AAGAAATTGTATCGATATATTTTTTAAAGTATCGATACAT
1 AAGAAATTGTATCGATATATTTCTCAAAGTATCGATACAT
*
250689 AAGAAATTGTATCGATATATTTCTCATTA-TATCGATACAT
1 AAGAAATTGTATCGATATATTTCTCA-AAGTATCGATACAT
250729 TCTGGGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 35 0.97
41 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (40 bp):
AAGAAATTGTATCGATATATTTCTCAAAGTATCGATACAT
Found at i:251755 original size:13 final size:13
Alignment explanation
Indices: 251737--251761 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
251727 TAATTCATCA
251737 TGTATCGATACAT
1 TGTATCGATACAT
251750 TGTATCGATACA
1 TGTATCGATACA
251762 ATGTGCCATG
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:251759 original size:33 final size:33
Alignment explanation
Indices: 251717--251814 Score: 112
Period size: 33 Copynumber: 3.0 Consensus size: 33
251707 TTTGAAGCAA
*
251717 TGTATCGATATAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATATCA-CATGTATCGATACAT
* *
251750 TGTATCGATACAATGTGC-CATGTTTCGATACAT
1 TGTATCGATACAATAT-CACATGTATCGATACAT
*
251783 TGTATCGATACAATAT-ACCAAGTATCGATACA
1 TGTATCGATACAATATCA-CATGTATCGATACA
251815 AACAGTGGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
33 54 0.96
34 1 0.02
35 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATATCACATGTATCGATACAT
Found at i:252570 original size:30 final size:30
Alignment explanation
Indices: 252482--252571 Score: 128
Period size: 31 Copynumber: 3.0 Consensus size: 30
252472 ATGAAGGCTC
*
252482 TCGTTTAAAA-AATTTCTCCCCCTTGATAA
1 TCGTTTAAAAGATTTTCTCCCCCTTGATAA
* * *
252511 TCGCTTAAAAGATTTTTTTCCCCCCTGATAA
1 TCGTTTAAAAGA-TTTTCTCCCCCTTGATAA
252542 TCGTTTAAAAGATTTTCTCCCCCTTGATAA
1 TCGTTTAAAAGATTTTCTCCCCCTTGATAA
252572 AAATTTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 9 0.17
30 17 0.33
31 26 0.50
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (30 bp):
TCGTTTAAAAGATTTTCTCCCCCTTGATAA
Found at i:256206 original size:13 final size:13
Alignment explanation
Indices: 256188--256212 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
256178 CAAAGATCAG
256188 TGTATCGATACAA
1 TGTATCGATACAA
256201 TGTATCGATACA
1 TGTATCGATACA
256213 TTTGAGTAAT
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:257976 original size:13 final size:13
Alignment explanation
Indices: 257958--257982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
257948 TAGTAACCCA
257958 TGTATCGATACAG
1 TGTATCGATACAG
257971 TGTATCGATACA
1 TGTATCGATACA
257983 AAGAATATTG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:264204 original size:19 final size:20
Alignment explanation
Indices: 264161--264215 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
264151 CTGCCAGTTT
* *
264161 CATGTATCGATACAATTGTA
1 CATGTATCGATACAAATGAA
264181 CATGTATCGATA-AAATGAA
1 CATGTATCGATACAAATGAA
264200 CATGTATCGATACAAA
1 CATGTATCGATACAAA
264216 GCATAATGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAAATGAA
Found at i:264225 original size:39 final size:34
Alignment explanation
Indices: 264199--264264 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
264189 GATAAAATGA
264199 ACATGTATCGATACAAAGCATAATGTATC--AAT
1 ACATGTATCGATACAAAGCATAATGTATCGAAAT
264231 ACAATGTATCGATACAAAGCATAATGTATCGAAA
1 AC-ATGTATCGATACAAAGCATAATGTATCGAAA
264265 CATCTGGGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 2 0.06
33 27 0.87
35 2 0.06
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (34 bp):
ACATGTATCGATACAAAGCATAATGTATCGAAAT
Found at i:264226 original size:20 final size:20
Alignment explanation
Indices: 264201--264262 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
264191 TAAAATGAAC
264201 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGCATA
*
264221 ATGTATC---A-ATA-C--A
1 ATGTATCGATACAAAGCATA
264234 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGCATA
264254 ATGTATCGA
1 ATGTATCGA
264263 AACATCTGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
13 8 0.24
15 1 0.03
16 3 0.09
17 3 0.09
18 1 0.03
20 17 0.52
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACAAAGCATA
Found at i:267334 original size:34 final size:35
Alignment explanation
Indices: 267296--267362 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
267286 CCTTACAACA
267296 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
267330 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
267363 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:267859 original size:13 final size:13
Alignment explanation
Indices: 267841--267866 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
267831 CTATTTATGA
267841 TGTATCGATACAC
1 TGTATCGATACAC
267854 TGTATCGATACAC
1 TGTATCGATACAC
267867 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:267951 original size:10 final size:10
Alignment explanation
Indices: 267927--267965 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
267917 TAGTGATACG
267927 TGAACAGTG-
1 TGAACAGTGA
267936 TGAACAGTGA
1 TGAACAGTGA
267946 TGAACAGTGA
1 TGAACAGTGA
*
267956 TGAATAGTGA
1 TGAACAGTGA
267966 AAATGAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (10 bp):
TGAACAGTGA
Done.