Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 177 of 292
Found at i:52764792 original size:40 final size:40
Alignment explanation
Indices: 52764686--52764869 Score: 147
Period size: 40 Copynumber: 4.6 Consensus size: 40
52764676 TGCTGGAAAT
* * * * * **
52764686 TATAACCGGGTTAAGACCCGAAGGCAATGGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
*
52764726 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * *
52764766 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATC-G
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * * * * *
52764804 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTAC
1 T-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * *
52764845 CATATCCGGGCTATGTCCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGC
52764870 GTTTGAACGA
Statistics
Matches: 115, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.01
39 29 0.25
40 85 0.74
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
Found at i:52767804 original size:34 final size:34
Alignment explanation
Indices: 52767741--52767852 Score: 109
Period size: 34 Copynumber: 3.3 Consensus size: 34
52767731 AGTGCTATAT
* * *
52767741 GACATGCTTAT-ACAGATCAATACGGTAGCAAGG
1 GACATGCTTATAACAAATCAATACGATAGCAAGA
* * * *
52767774 GGCATGCTTATAACATATCAATACTATAGCAATA
1 GACATGCTTATAACAAATCAATACGATAGCAAGA
* * ** *
52767808 GACATGCTTATATCAAATCAATATGGCAGCAAAA
1 GACATGCTTATAACAAATCAATACGATAGCAAGA
52767842 GACATGCTTAT
1 GACATGCTTAT
52767853 CATGTATTTG
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
33 10 0.16
34 54 0.84
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (34 bp):
GACATGCTTATAACAAATCAATACGATAGCAAGA
Found at i:52769028 original size:2 final size:2
Alignment explanation
Indices: 52769021--52769056 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
52769011 ACTCAATCGG
*
52769021 AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52769057 TGGGACGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52777448 original size:46 final size:46
Alignment explanation
Indices: 52777395--52777557 Score: 153
Period size: 47 Copynumber: 3.5 Consensus size: 46
52777385 TGTGTGATCT
*
52777395 AGTGTAAGA-CATGTCTGGGACATGCATCGGCCACATTATGGGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGG-CACATTATGGGTGCC
*
52777441 AGTGTAAGACCATGTCTGGGACATTGCATCGG--CATTGA-GACGAGTGCT
1 AGTGTAAGACCATGTCTGGGACA-TGCATCGGCACATT-ATG--G-GTGCC
* * *
52777489 AGTGTAAGA-CATGTTTGGGACATGCATCGGCTACGA-GAT--GTGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGC-AC-ATTATGGGTGCC
52777533 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
52777558 GCATTAGCAT
Statistics
Matches: 98, Mismatches: 7, Indels: 25
0.75 0.05 0.19
Matches are distributed among these distances:
44 12 0.12
45 19 0.19
46 18 0.18
47 26 0.27
48 21 0.21
49 1 0.01
50 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCACATTATGGGTGCC
Found at i:52777584 original size:94 final size:93
Alignment explanation
Indices: 52777393--52777607 Score: 263
Period size: 94 Copynumber: 2.3 Consensus size: 93
52777383 CTTGTGTGAT
*
52777393 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGGGAGCCAGTGTAAGACCATGTCT
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGAT-GGAGCCAGTGTAAGACCATGTCT
* * * * *
52777458 GGGACATTGCATCGGCATTGAGACGAGTG
65 GGGACATGGCATCAGCATGGACACGAGAG
* * * *
52777487 CTAGTGTAAGACATGTTTGGGACATGCATCGGCTACGA-GAT-GTGTCAGTGTAAGACCATGTCT
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATGGAGCCAGTGTAAGACCATGTCT
* *
52777550 GGGACATGGCATTAGCATGGACATGTGAGAG
65 GGGACATGGCATCAGCATGGACA--CGAGAG
52777581 CTAGTGTAAGACCATGTCTGGGACATG
1 CTAGTGTAAGA-CATGTCTGGGACATG
52777608 TCGTTGGCCT
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
92 38 0.37
94 51 0.49
95 15 0.14
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (93 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGGAGCCAGTGTAAGACCATGTCTG
GGACATGGCATCAGCATGGACACGAGAG
Found at i:52777664 original size:49 final size:49
Alignment explanation
Indices: 52777440--52777666 Score: 159
Period size: 49 Copynumber: 4.7 Consensus size: 49
52777430 TTATGGGAGC
* * * * * * *
52777440 CAGTGTAAGACCATGTCTGGGACATTGCATCGGCATTG-AGACGAGTGCT
1 CAGTGTAAGACCATGTCTGGGACATGGCATTGGCA-TGCACATGTGAGAT
* * * *
52777489 -AGTGTAAGA-CATGTTTGGGACAT-GCATCGGC-TACGAGATGT--G-T
1 CAGTGTAAGACCATGTCTGGGACATGGCATTGGCATGC-ACATGTGAGAT
* * *
52777532 CAGTGTAAGACCATGTCTGGGACATGGCATTAGCATGGACATGTGAGAG
1 CAGTGTAAGACCATGTCTGGGACATGGCATTGGCATGCACATGTGAGAT
* * * * *
52777581 CTAGTGTAAGACCATGTCTGGGACATGTCGTTGGCCT-CA-ATTTCGATATT
1 C-AGTGTAAGACCATGTCTGGGACATGGCATTGGCATGCACATGT-GAGA-T
*
52777631 CAGTGTAAGACCATGTTTGGGACATGGCATTGGCAT
1 CAGTGTAAGACCATGTCTGGGACATGGCATTGGCAT
52777667 TATACGCTAT
Statistics
Matches: 143, Mismatches: 23, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
43 1 0.01
44 11 0.08
45 13 0.09
46 23 0.16
47 14 0.10
48 13 0.09
49 36 0.25
50 32 0.22
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (49 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATTGGCATGCACATGTGAGAT
Found at i:52779844 original size:23 final size:23
Alignment explanation
Indices: 52779793--52779844 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
52779783 ACTTGCTTGT
* *
52779793 CCACTAAGAGAGTCTATTGTTTC
1 CCACCAAGAGAGTCTATTGTTGC
*
52779816 CTACCAAGAGAGTCTATTGTTGC
1 CCACCAAGAGAGTCTATTGTTGC
52779839 CCACCA
1 CCACCA
52779845 CTCGCTACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (23 bp):
CCACCAAGAGAGTCTATTGTTGC
Found at i:52781311 original size:25 final size:25
Alignment explanation
Indices: 52781283--52781345 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
52781273 TAGGATCATC
52781283 ATGACATTTCATTATCAAAATCAAA
1 ATGACATTTCATTATCAAAATCAAA
** *
52781308 ATGACATGGCATTTTCAAAATCAAA
1 ATGACATTTCATTATCAAAATCAAA
52781333 ATGAC-TTATCATT
1 ATGACATT-TCATT
52781346 TTTAGGATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 1 0.03
25 31 0.97
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (25 bp):
ATGACATTTCATTATCAAAATCAAA
Found at i:52785607 original size:46 final size:46
Alignment explanation
Indices: 52785540--52785746 Score: 308
Period size: 46 Copynumber: 4.5 Consensus size: 46
52785530 TGGCAACCTG
*
52785540 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* *
52785586 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
*
52785632 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* ** *
52785678 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAA
* *
52785724 TGAGTAAGACCATAGTTGAAAGA
1 TGTGTAAGACCATGGTTGAAAGA
52785747 CACTACGGCA
Statistics
Matches: 149, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.01
46 148 0.99
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
Found at i:52785735 original size:138 final size:130
Alignment explanation
Indices: 52785491--52785746 Score: 361
Period size: 138 Copynumber: 1.9 Consensus size: 130
52785481 AGTGTGCTCT
*
52785491 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGAGTAAGACCATGGT
* * * *
52785556 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATAGTTGAAAGATACCATGGCAAC
* *
52785621 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG---TG---AG--TAAG
52785686 ACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
58 ACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAGTAAGACCATAGTTGAAAGA
52785747 CACTACGGCA
Statistics
Matches: 110, Mismatches: 7, Indels: 10
0.87 0.06 0.08
Matches are distributed among these distances:
130 47 0.43
133 2 0.02
136 1 0.01
137 1 0.01
138 59 0.54
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.22
Consensus pattern (130 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGAGTAAGACCATGGT
TGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATAGTTGAAAGATACCATGGCAAC
Found at i:52787610 original size:40 final size:40
Alignment explanation
Indices: 52787550--52787773 Score: 281
Period size: 40 Copynumber: 5.5 Consensus size: 40
52787540 TATTCGGATG
*
52787550 ATATCCGGGCTAAGTGCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
52787590 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
52787633 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
52787673 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
52787713 ATATCCGGGCTAAGACCCGAAGGCATTTGTTCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
52787753 ATATCC-GGCTCAA-TCCCGAAG
1 ATATCCGGGCT-AAGTCCCGAAG
52787774 ATACTTGGGT
Statistics
Matches: 163, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
39 11 0.07
40 114 0.70
41 1 0.01
43 37 0.23
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:52787693 original size:83 final size:80
Alignment explanation
Indices: 52787554--52787773 Score: 277
Period size: 83 Copynumber: 2.7 Consensus size: 80
52787544 CGGATGATAT
* * **
52787554 CCGGGCTAAGTGCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
52787619 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
*
52787637 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
52787702 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * *
52787717 CCGGGCTAAGACCCGAAGGCATTTGTTCGAGTTG-CTATATCC-GGCTCAA-TCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCT-AAGTCCCGAAG
52787774 ATACTTGGGT
Statistics
Matches: 125, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
79 14 0.11
80 46 0.37
81 2 0.02
83 63 0.50
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:52789913 original size:40 final size:41
Alignment explanation
Indices: 52789808--52789983 Score: 224
Period size: 40 Copynumber: 4.5 Consensus size: 41
52789798 CGGATGATAA
* *
52789808 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-CTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATCTATA-T
*
52789848 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTATC-ATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATCTATAT
* *
52789887 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTA-CTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATCTATAT
*
52789927 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATCTATAT
*
52789967 CC-GGCTAA-ACCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
52789984 TTCTTGGTTT
Statistics
Matches: 122, Mismatches: 9, Indels: 12
0.85 0.06 0.08
Matches are distributed among these distances:
38 8 0.07
39 41 0.34
40 73 0.60
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (41 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATCTATAT
Found at i:52789973 original size:79 final size:79
Alignment explanation
Indices: 52789808--52789983 Score: 236
Period size: 79 Copynumber: 2.2 Consensus size: 79
52789798 CGGATGATAA
*
52789808 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAATTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATACCGGGCTAAGCCCGAAGGCAATTGT
*
52789873 GCGAGTTATCATAT
66 GCGAGTTAGCATAT
* *
52789887 CCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTGACTAAT-ACCGGGCTAAG-CCCGAAGGCAAT
52789950 TGTGCGAG-TAGCTATAT
63 TGTGCGAGTTAGC-ATAT
*
52789967 CC-GGCTAA-ACCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
52789984 TTCTTGGTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
78 11 0.12
79 52 0.59
80 25 0.28
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATACCGGGCTAAGCCCGAAGGCAATTGT
GCGAGTTAGCATAT
Found at i:52798907 original size:40 final size:40
Alignment explanation
Indices: 52798852--52799075 Score: 306
Period size: 40 Copynumber: 5.5 Consensus size: 40
52798842 TATTCGGATG
52798852 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
52798892 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
52798935 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
52798975 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
52799015 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
52799055 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
52799076 ATACTTGGGT
Statistics
Matches: 165, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
39 13 0.08
40 114 0.69
41 1 0.01
43 37 0.22
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:52798995 original size:83 final size:80
Alignment explanation
Indices: 52798856--52799075 Score: 302
Period size: 83 Copynumber: 2.7 Consensus size: 80
52798846 CGGATGATAT
* **
52798856 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
52798921 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
*
52798939 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
52799004 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * *
52799019 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
52799076 ATACTTGGGT
Statistics
Matches: 127, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
79 16 0.13
80 45 0.35
81 2 0.02
83 64 0.50
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:52806801 original size:16 final size:16
Alignment explanation
Indices: 52806780--52806810 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52806770 TATACATATA
*
52806780 TTTTGAATTTTTTATT
1 TTTTGAATATTTTATT
52806796 TTTTGAATATTTTAT
1 TTTTGAATATTTTAT
52806811 AATTTTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTGAATATTTTATT
Found at i:52806821 original size:26 final size:25
Alignment explanation
Indices: 52806777--52806826 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
52806767 ATATATACAT
* *
52806777 ATATTTTGAATTTTTTATTTTTTGA
1 ATATTTTGAATTTTATATTATTTGA
*
52806802 ATATTTTATAATTTTATATTATTTG
1 ATATTTT-GAATTTTATATTATTTG
52806827 TTGACATAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (25 bp):
ATATTTTGAATTTTATATTATTTGA
Found at i:52808159 original size:19 final size:19
Alignment explanation
Indices: 52808147--52808275 Score: 70
Period size: 19 Copynumber: 6.6 Consensus size: 19
52808137 TTTTTTGAAT
52808147 TTTATAAGTTTTTATAATA
1 TTTATAAGTTTTTATAATA
*
52808166 TTTATAAGTTTATATAA-A
1 TTTATAAGTTTTTATAATA
* *
52808184 TTT-TAAATATATTT-TATATG
1 TTTATAAGT-T-TTTATA-ATA
* * *
52808204 TTTCATATG-TTTTATTATT
1 TTT-ATAAGTTTTTATAATA
* *
52808223 TTTATAA-TTTATTAGAACTT
1 TTTATAAGTTT-TTATAA-TA
*
52808243 TTTATAAGTTTTTATGATTTA
1 TTTATAAGTTTTTAT-A-ATA
52808264 TTTATAAGTTTT
1 TTTATAAGTTTT
52808276 AAAAGTTTAT
Statistics
Matches: 83, Mismatches: 14, Indels: 24
0.69 0.12 0.20
Matches are distributed among these distances:
17 4 0.05
18 12 0.14
19 31 0.37
20 17 0.20
21 17 0.20
22 2 0.02
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (19 bp):
TTTATAAGTTTTTATAATA
Found at i:52808161 original size:10 final size:10
Alignment explanation
Indices: 52808146--52808289 Score: 70
Period size: 9 Copynumber: 14.8 Consensus size: 10
52808136 ATTTTTTGAA
52808146 TTTTATAAGT
1 TTTTATAAGT
52808156 TTTTATAA-T
1 TTTTATAAGT
*
52808165 ATTTATAAGT
1 TTTTATAAGT
* *
52808175 TTATATAA-A
1 TTTTATAAGT
*
52808184 TTTTA-AATAT
1 TTTTATAA-GT
*
52808194 ATTTTATATG-
1 -TTTTATAAGT
* *
52808204 TTTCATATG-
1 TTTTATAAGT
*
52808213 TTTTATTA-T
1 TTTTATAAGT
52808222 TTTTATAA-T
1 TTTTATAAGT
* *
52808231 TTATTAGAACT
1 TT-TTATAAGT
52808242 TTTTATAAGT
1 TTTTATAAGT
* *
52808252 TTTTATGATT
1 TTTTATAAGT
52808262 TATTTATAAG-
1 T-TTTATAAGT
*
52808272 TTTTAAAAGT
1 TTTTATAAGT
*
52808282 TTATATAA
1 TTTTATAA
52808290 ATTCTATGAA
Statistics
Matches: 101, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
8 2 0.02
9 42 0.42
10 42 0.42
11 14 0.14
12 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (10 bp):
TTTTATAAGT
Found at i:52808276 original size:30 final size:30
Alignment explanation
Indices: 52808212--52808289 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
52808202 TGTTTCATAT
*
52808212 GTTTTATTA-TTTTTATAATTTATTAGAAC
1 GTTTTATAAGTTTTTATAATTTATTAGAAC
* * *
52808241 TTTTTATAAGTTTTTATGATTTATTTATAA-
1 GTTTTATAAGTTTTTATAATTTA-TTAGAAC
* *
52808271 GTTTTAAAAGTTTATATAA
1 GTTTTATAAGTTTTTATAA
52808290 ATTCTATGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 7 0.18
30 27 0.69
31 5 0.13
ACGTcount: A:0.33, C:0.01, G:0.08, T:0.58
Consensus pattern (30 bp):
GTTTTATAAGTTTTTATAATTTATTAGAAC
Found at i:52810706 original size:18 final size:18
Alignment explanation
Indices: 52810685--52810725 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
52810675 AATTAATTAT
52810685 AAATTAT-TAATTTATAAA
1 AAATTATATAA-TTATAAA
52810703 AAA-TATATAATTATAAA
1 AAATTATATAATTATAAA
52810720 ATAATT
1 A-AATT
52810726 TAAACATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 11 0.55
18 8 0.40
19 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTATATAATTATAAA
Found at i:52812477 original size:20 final size:19
Alignment explanation
Indices: 52812439--52812482 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
52812429 TATATTTAAT
*
52812439 AATATTTACTATAAATAAA
1 AATATTTACAATAAATAAA
*
52812458 AATATTCTACAATTAATAAA
1 AATATT-TACAATAAATAAA
*
52812478 TATAT
1 AATAT
52812483 ATTTGCTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATTTACAATAAATAAA
Found at i:52812648 original size:2 final size:2
Alignment explanation
Indices: 52812643--52812668 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52812633 TAGTCACGTG
52812643 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
52812669 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52827076 original size:40 final size:40
Alignment explanation
Indices: 52826968--52827077 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
52826958 ATTGAATGAT
* * * * *
52826968 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
* * *
52827008 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
52827048 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
52827078 AAATTGTGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
Found at i:52827092 original size:40 final size:39
Alignment explanation
Indices: 52826968--52827117 Score: 133
Period size: 40 Copynumber: 3.8 Consensus size: 39
52826958 ATTGAATGAT
* * * * * * *
52826968 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGA-CAC
*
52827008 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGAC-AC
* *
52827048 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATTGTGA-A-
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGC---TAGTGACAC
* *
52827088 ATCCGGGTTAAGTCCCGAAGGCCTTTGTGC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGC
52827118 GGGTTACCAT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 86 0.93
41 1 0.01
43 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGACAC
Found at i:52830450 original size:29 final size:29
Alignment explanation
Indices: 52830418--52830553 Score: 157
Period size: 29 Copynumber: 4.7 Consensus size: 29
52830408 ATACCCTTCG
** * *
52830418 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
52830447 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
52830476 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
52830505 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
52830534 AGCACGCACACTTAGTGCCA
1 AGCTCGCACACTTAGTGCCA
52830554 ATCTCGTCAC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 93 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.29
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:52830545 original size:58 final size:58
Alignment explanation
Indices: 52830393--52830552 Score: 176
Period size: 58 Copynumber: 2.8 Consensus size: 58
52830383 AATTTAAGCC
* *** * * ** * *
52830393 CGCACACACAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
* * * * *
52830451 TGCACACATAGTGTCATATTTTTCCAGCATGCACACTTAGTGCCTTATATTTCCAGCA
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
*
52830509 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCC
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCC
52830553 AATCTCGTCA
Statistics
Matches: 83, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 83 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.28
Consensus pattern (58 bp):
CGCACACATAGTGCCATATATTTCCAGCACGCACACTTAGTGCCGTATATTTCCAGCA
Found at i:52838864 original size:40 final size:40
Alignment explanation
Indices: 52838756--52838865 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
52838746 ATTGAATGAT
* * * * *
52838756 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
* * *
52838796 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
52838836 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
52838866 AAATTGTGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
Found at i:52838880 original size:40 final size:39
Alignment explanation
Indices: 52838756--52838905 Score: 133
Period size: 40 Copynumber: 3.8 Consensus size: 39
52838746 ATTGAATGAT
* * * * * * *
52838756 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGA-CAC
*
52838796 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGAC-AC
* *
52838836 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATTGTGA-A-
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGC---TAGTGACAC
* *
52838876 ATCCGGGTTAAGTCCCGAAGGCCTTTGTGC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGC
52838906 GGGTTACCAT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 86 0.93
41 1 0.01
43 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGACAC
Found at i:52841095 original size:14 final size:15
Alignment explanation
Indices: 52841076--52841105 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
52841066 CTTACTTTAG
52841076 TTACTTTAGT-ACTT
1 TTACTTTAGTCACTT
52841090 TTACTTTAGTCACTT
1 TTACTTTAGTCACTT
52841105 T
1 T
52841106 AGTAAAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (15 bp):
TTACTTTAGTCACTT
Found at i:52841097 original size:23 final size:23
Alignment explanation
Indices: 52841053--52841109 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
52841043 AGGAACTTTG
52841053 TACTTTAGTTACACTTACTTTAGT
1 TACTTTAG-TACACTTACTTTAGT
**
52841077 TACTTTAGTACTTTTACTTTAGT
1 TACTTTAGTACACTTACTTTAGT
*
52841100 CACTTTAGTA
1 TACTTTAGTA
52841110 AAACTGTTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.51
Consensus pattern (23 bp):
TACTTTAGTACACTTACTTTAGT
Found at i:52843907 original size:29 final size:29
Alignment explanation
Indices: 52843854--52843956 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 29
52843844 TGTATGGCAA
* * **
52843854 ACCGTGTAGGTCACACGGCCATGTGGTTG
1 ACCGTGTGGGTCACACGACTGTGTGGTTG
* *
52843883 ACCGTGTGGGTCACACGATTGTGTGGTAG
1 ACCGTGTGGGTCACACGACTGTGTGGTTG
* *
52843912 ACCGTGTGGGTTACATGACTGTGTGGTTG
1 ACCGTGTGGGTCACACGACTGTGTGGTTG
* *
52843941 GCCGTGTGGGCCACAC
1 ACCGTGTGGGTCACAC
52843957 AAGTATGTGG
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.16, C:0.21, G:0.37, T:0.26
Consensus pattern (29 bp):
ACCGTGTGGGTCACACGACTGTGTGGTTG
Found at i:52848325 original size:40 final size:40
Alignment explanation
Indices: 52848270--52848493 Score: 306
Period size: 40 Copynumber: 5.5 Consensus size: 40
52848260 TATTCGGATG
52848270 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
52848310 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
52848353 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
52848393 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
52848433 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
52848473 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
52848494 ATACTTGGGT
Statistics
Matches: 165, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
39 13 0.08
40 114 0.69
41 1 0.01
43 37 0.22
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:52848413 original size:83 final size:80
Alignment explanation
Indices: 52848274--52848493 Score: 302
Period size: 83 Copynumber: 2.7 Consensus size: 80
52848264 CGGATGATAT
* **
52848274 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
52848339 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
*
52848357 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
52848422 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * *
52848437 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
52848494 ATACTTGGGT
Statistics
Matches: 127, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
79 16 0.13
80 45 0.35
81 2 0.02
83 64 0.50
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:52856565 original size:40 final size:40
Alignment explanation
Indices: 52856510--52856733 Score: 306
Period size: 40 Copynumber: 5.5 Consensus size: 40
52856500 TATTCGGATG
52856510 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
52856550 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
52856593 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
52856633 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
52856673 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
52856713 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
52856734 ATACTTGGGT
Statistics
Matches: 165, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
39 13 0.08
40 114 0.69
41 1 0.01
43 37 0.22
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:52856653 original size:83 final size:80
Alignment explanation
Indices: 52856514--52856733 Score: 302
Period size: 83 Copynumber: 2.7 Consensus size: 80
52856504 CGGATGATAT
* **
52856514 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
52856579 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
*
52856597 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
52856662 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * *
52856677 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
52856734 ATACTTGGGT
Statistics
Matches: 127, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
79 16 0.13
80 45 0.35
81 2 0.02
83 64 0.50
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:52859872 original size:34 final size:34
Alignment explanation
Indices: 52859829--52859930 Score: 123
Period size: 34 Copynumber: 3.0 Consensus size: 34
52859819 ACAGTCAAAT
* *
52859829 GCAGTTTGGGCCTAAGCCCATTTCAATTTCAATA
1 GCAGTTTGGGCCTTAGCCCATTTCAGTTTCAATA
* * * *
52859863 GCAGTTTGGGTCTTAGCCCATTTTAGTTTTAGTA
1 GCAGTTTGGGCCTTAGCCCATTTCAGTTTCAATA
** *
52859897 GCAGTTCAGGCCTTAGCCCATTTCGGTTTCAATA
1 GCAGTTTGGGCCTTAGCCCATTTCAGTTTCAATA
52859931 TCAGATATGC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (34 bp):
GCAGTTTGGGCCTTAGCCCATTTCAGTTTCAATA
Found at i:52861184 original size:20 final size:20
Alignment explanation
Indices: 52861142--52861182 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
52861132 ACGTCAACTG
* *
52861142 ATTTTGGAAAAGAGAGGAAA
1 ATTTTGGAAAAGAAAAGAAA
52861162 ATTTTGGGAAAAGAAAAGAAA
1 ATTTT-GGAAAAGAAAAGAAA
52861183 TTAAATTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.20
Consensus pattern (20 bp):
ATTTTGGAAAAGAAAAGAAA
Found at i:52864260 original size:40 final size:40
Alignment explanation
Indices: 52864204--52864381 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
52864194 TGGATGATAA
*
52864204 CCGGGCTAAGTCCCGAAGGCATTTGTCCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
52864244 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
** *
52864284 CCAAGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
52864324 CCGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
52864364 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
52864382 TACTTGGCTT
Statistics
Matches: 122, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
39 15 0.12
40 107 0.88
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:52866226 original size:20 final size:20
Alignment explanation
Indices: 52866201--52866245 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
52866191 GTTGAGCGAA
*
52866201 CATCGCTCTATGGCTCAACG
1 CATCGCCCTATGGCTCAACG
52866221 CATCGCCCTATGGCTCAACG
1 CATCGCCCTATGGCTCAACG
52866241 CATCG
1 CATCG
52866246 GCCACCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.38, G:0.20, T:0.22
Consensus pattern (20 bp):
CATCGCCCTATGGCTCAACG
Found at i:52872184 original size:17 final size:19
Alignment explanation
Indices: 52872156--52872191 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
52872146 GGACAACCTG
52872156 TATGGACCCACAC-GCCCA
1 TATGGACCCACACGGCCCA
52872174 TATGG-CCCACACGGCCCA
1 TATGGACCCACACGGCCCA
52872192 AATTATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.25, C:0.44, G:0.19, T:0.11
Consensus pattern (19 bp):
TATGGACCCACACGGCCCA
Found at i:52873045 original size:23 final size:23
Alignment explanation
Indices: 52873015--52873061 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
52873005 TAAGTCAGAA
52873015 AAATTCCAAAATTTGCCAAAGCT
1 AAATTCCAAAATTTGCCAAAGCT
52873038 AAATTCCAAAATTTGCCAAAGCT
1 AAATTCCAAAATTTGCCAAAGCT
52873061 A
1 A
52873062 GGCTCGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.26
Consensus pattern (23 bp):
AAATTCCAAAATTTGCCAAAGCT
Found at i:52879038 original size:10 final size:11
Alignment explanation
Indices: 52879023--52879056 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
52879013 ATCATCCACA
52879023 CATATATAT-T
1 CATATATATAT
52879033 CATATATATAT
1 CATATATATAT
52879044 -ATATATATAT
1 CATATATATAT
52879054 CAT
1 CAT
52879057 TCTTTGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 19 0.86
11 3 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (11 bp):
CATATATATAT
Found at i:52880004 original size:21 final size:21
Alignment explanation
Indices: 52879957--52880004 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
52879947 CTTGCATATT
*
52879957 CTAATTTCATAAACTAATTTA
1 CTAAATTCATAAACTAATTTA
52879978 -TGAAATTCATAAACTAATTTA
1 CT-AAATTCATAAACTAATTTA
52879999 CTAAAT
1 CTAAAT
52880005 CAATGTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (21 bp):
CTAAATTCATAAACTAATTTA
Found at i:52889155 original size:39 final size:39
Alignment explanation
Indices: 52889129--52889222 Score: 136
Period size: 39 Copynumber: 2.4 Consensus size: 39
52889119 GGGACTTTAG
52889129 GCCCGGATAT-ATTCCAGCACGTAGCCTGCGGACCTCAA
1 GCCCGGATATGATTCCAGCACGTAGCCTGCGGACCTCAA
* * *
52889167 GTCCGGATATGTTTCCAGCACGTAGCCTACGGACCTCAA
1 GCCCGGATATGATTCCAGCACGTAGCCTGCGGACCTCAA
* *
52889206 GCTCGGATATGTTTCCA
1 GCCCGGATATGATTCCA
52889223 AATATCATGC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 9 0.18
39 41 0.82
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.23
Consensus pattern (39 bp):
GCCCGGATATGATTCCAGCACGTAGCCTGCGGACCTCAA
Found at i:52889892 original size:21 final size:21
Alignment explanation
Indices: 52889868--52889908 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
52889858 TGTATATTCT
*
52889868 AATTTCATTAACTAATTTACG
1 AATTTCATAAACTAATTTACG
52889889 AATTTCATAAACTAATTTAC
1 AATTTCATAAACTAATTTAC
52889909 TAAATCAATG
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:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (21 bp):
AATTTCATAAACTAATTTACG
Found at i:52899489 original size:14 final size:15
Alignment explanation
Indices: 52899472--52899504 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
52899462 GAATAAATTA
52899472 TATTATATTAT-TTT
1 TATTATATTATATTT
*
52899486 TATTTTATTATATTT
1 TATTATATTATATTT
52899501 TATT
1 TATT
52899505 TAAGATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTATATTATATTT
Found at i:52905818 original size:21 final size:21
Alignment explanation
Indices: 52905792--52905831 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
52905782 CATGACATAA
52905792 TTATATGGATAA-GTTGCTATG
1 TTATATGGA-AATGTTGCTATG
*
52905813 TTATATTGAAATGTTGCTA
1 TTATATGGAAATGTTGCTA
52905832 CACATGCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (21 bp):
TTATATGGAAATGTTGCTATG
Found at i:52907147 original size:21 final size:20
Alignment explanation
Indices: 52907123--52907161 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52907113 TGAATTGATT
52907123 AAATGTGTGATTAAATTAGTG
1 AAATGTGT-ATTAAATTAGTG
* *
52907144 AAATTTGTATTAATTTAG
1 AAATGTGTATTAAATTAG
52907162 ATCAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (20 bp):
AAATGTGTATTAAATTAGTG
Found at i:52910631 original size:24 final size:24
Alignment explanation
Indices: 52910581--52910635 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
52910571 TAGGAAGAAA
* **
52910581 ATGGTTGTTTGATATGTTTTTGAT
1 ATGGTTATTTGATATGTTTAAGAT
* *
52910605 ATGGTTATTTGGTATGTTTAAGGT
1 ATGGTTATTTGATATGTTTAAGAT
52910629 AT-GTTAT
1 ATGGTTAT
52910636 ATCAATGAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (24 bp):
ATGGTTATTTGATATGTTTAAGAT
Found at i:52912868 original size:16 final size:16
Alignment explanation
Indices: 52912847--52912879 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52912837 TTAGGGCACA
52912847 CACCCTTGTGGCCACC
1 CACCCTTGTGGCCACC
52912863 CACCCTTGTGGCCACC
1 CACCCTTGTGGCCACC
52912879 C
1 C
52912880 GTGTGGCTAG
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:0.12, C:0.52, G:0.18, T:0.18
Consensus pattern (16 bp):
CACCCTTGTGGCCACC
Found at i:52921730 original size:12 final size:13
Alignment explanation
Indices: 52921713--52921744 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52921703 ATAAAACATT
52921713 TCAAAAC-ATGCA
1 TCAAAACTATGCA
52921725 TCAAAACTATGCA
1 TCAAAACTATGCA
52921738 -CAAAACT
1 TCAAAACT
52921745 TAACATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (13 bp):
TCAAAACTATGCA
Found at i:52922365 original size:42 final size:42
Alignment explanation
Indices: 52922309--52922427 Score: 134
Period size: 44 Copynumber: 2.8 Consensus size: 42
52922299 GAAGCCTCTA
*
52922309 TCCCAGACAGGGTCTTACACGAAA-TCAGATACGATGCC-GATG
1 TCCCAGACACGGTCTTACACGAAATTCAGAT-CGATGCCAG-TG
* * * *
52922351 TTCTAGACATGGTCTTACACGTAAATTTCAAATCGATGCCAGTG
1 TCCCAGACACGGTCTTACACG-AAA-TTCAGATCGATGCCAGTG
52922395 TCCCAGACACGGTCTTACACGATAATTCAGATC
1 TCCCAGACACGGTCTTACACGA-AATTCAGATC
52922428 AATACCAACG
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
42 18 0.28
43 11 0.17
44 29 0.45
45 6 0.09
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
TCCCAGACACGGTCTTACACGAAATTCAGATCGATGCCAGTG
Found at i:52922403 original size:44 final size:42
Alignment explanation
Indices: 52922265--52922423 Score: 128
Period size: 44 Copynumber: 3.7 Consensus size: 42
52922255 TAATGCCGAC
* * * * *
52922265 GTCCCACACTTGGTCTTACATGT-AATTCAATATCGAAGCCTCT
1 GTCCCAGACATGGTCTTACACGTAAATTCAA-ATCGATGCC-GT
* * *
52922308 ATCCCAGACAGGGTCTTACACG-AAA-TCAGATACGATGCCGAT
1 GTCCCAGACATGGTCTTACACGTAAATTCAAAT-CGATGCCG-T
* *
52922350 GTTCTAGACATGGTCTTACACGTAAATTTCAAATCGATGCCAGT
1 GTCCCAGACATGGTCTTACACGTAAA-TTCAAATCGATGCC-GT
*
52922394 GTCCCAGACACGGTCTTACACG-ATAATTCA
1 GTCCCAGACATGGTCTTACACGTA-AATTCA
52922424 GATCAATACC
Statistics
Matches: 92, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
41 2 0.02
42 28 0.30
43 27 0.29
44 29 0.32
45 6 0.07
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGTAAATTCAAATCGATGCCGT
Found at i:52928887 original size:12 final size:13
Alignment explanation
Indices: 52928872--52928903 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52928862 ATAACACATT
52928872 TCAAAAC-ATGCA
1 TCAAAACTATGCA
52928884 TCAAAACTATGCA
1 TCAAAACTATGCA
52928897 -CAAAACT
1 TCAAAACT
52928904 TAACATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (13 bp):
TCAAAACTATGCA
Found at i:52929523 original size:42 final size:42
Alignment explanation
Indices: 52929465--52929585 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 42
52929455 TCGCAGCCTC
*
52929465 TGTCCCAGACAGGGTCTTACACGAAA-TCAGATACGATGCC-G
1 TGTCCCAGACACGGTCTTACACGAAATTCAGAT-CGATGCCAG
* * *
52929506 ATGTTCCAGACATGGTCTTACACGTAAATTTCAAATCGATGCCAG
1 -TGTCCCAGACACGGTCTTACACG-AAA-TTCAGATCGATGCCAG
52929551 TGTCCCAGACACGGTCTTACACGATAATTCAGATC
1 TGTCCCAGACACGGTCTTACACGA-AATTCAGATC
52929586 AATACCAACG
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
42 21 0.31
43 11 0.16
44 30 0.44
45 6 0.09
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (42 bp):
TGTCCCAGACACGGTCTTACACGAAATTCAGATCGATGCCAG
Found at i:52929559 original size:44 final size:42
Alignment explanation
Indices: 52929423--52929581 Score: 139
Period size: 44 Copynumber: 3.7 Consensus size: 42
52929413 CAATGCCGAC
** * *
52929423 GTCCCAGATGTGGTCTTACATGT-AATTCAATATCGCA-GCCTCT
1 GTCCCAGACATGGTCTTACACGTAAATTCAA-ATCG-ATGCC-GT
* *
52929466 GTCCCAGACAGGGTCTTACACG-AAA-TCAGATACGATGCCGAT
1 GTCCCAGACATGGTCTTACACGTAAATTCAAAT-CGATGCCG-T
*
52929508 GTTCCAGACATGGTCTTACACGTAAATTTCAAATCGATGCCAGT
1 GTCCCAGACATGGTCTTACACGTAAA-TTCAAATCGATGCC-GT
*
52929552 GTCCCAGACACGGTCTTACACG-ATAATTCA
1 GTCCCAGACATGGTCTTACACGTA-AATTCA
52929582 GATCAATACC
Statistics
Matches: 96, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
41 3 0.03
42 29 0.30
43 28 0.29
44 30 0.31
45 6 0.06
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGTAAATTCAAATCGATGCCGT
Found at i:52931789 original size:13 final size:13
Alignment explanation
Indices: 52931771--52931796 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52931761 GCTCGGCAGG
52931771 GACACGCCCGTGT
1 GACACGCCCGTGT
52931784 GACACGCCCGTGT
1 GACACGCCCGTGT
52931797 TCAATTACTT
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:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:52933320 original size:2 final size:2
Alignment explanation
Indices: 52933313--52933341 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52933303 ATTCCATGTT
52933313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52933342 CATAGTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52933962 original size:42 final size:46
Alignment explanation
Indices: 52933899--52934109 Score: 170
Period size: 49 Copynumber: 4.6 Consensus size: 46
52933889 CTTCGTTTTC
** *
52933899 TCGATGCCATAGTTCAACTATGGTCTTACAC-AT-C-T-TCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACAATACATATCACAT-A
52933942 T-GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC--AAT-ACATATCACATA
* *
52933990 TCGATGCCATAGCCCAGCTATGGTCTTACACGAATAACATATCTCA-C
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-AAT-ACATATCACATA
* * * * *
52934037 T-GATGCCATATCCCAGATATGGTCTTATACAGTAGCATAT-ATCACA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACAATA-CATATCA-CATA
* *
52934083 -CTGATGCCATATCCCAGATATGGTCTT
1 TC-GATGCCATAGCCCAGCTATGGTCTT
52934110 GTACGAAAAT
Statistics
Matches: 142, Mismatches: 13, Indels: 22
0.80 0.07 0.12
Matches are distributed among these distances:
42 26 0.18
43 1 0.01
44 1 0.01
45 11 0.08
46 26 0.18
47 27 0.19
48 15 0.11
49 35 0.25
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (46 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACAATACATATCACATA
Found at i:52934000 original size:49 final size:47
Alignment explanation
Indices: 52933940--52934109 Score: 200
Period size: 47 Copynumber: 3.6 Consensus size: 47
52933930 ATCTTCACAT
*
52933940 AATGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCAC
1 AATGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCAC
* * *
52933987 ATATCGATGCCATAGCCCAGCTATGGTCTTACACG-AATAACATATCTC
1 A-AT-GATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCAC
* * * * *
52934035 ACTGATGCCATATCCCAGATATGGTCTTATACAGT-AGCATATATCAC
1 AATGATGCCATAGCCCAGATATGGTCTTACAC-GTAATCACATATCAC
* *
52934082 ACTGATGCCATATCCCAGATATGGTCTT
1 AATGATGCCATAGCCCAGATATGGTCTT
52934110 GTACGAAAAT
Statistics
Matches: 109, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
46 26 0.24
47 39 0.36
48 14 0.13
49 30 0.28
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (47 bp):
AATGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCAC
Found at i:52934167 original size:31 final size:31
Alignment explanation
Indices: 52934132--52934280 Score: 201
Period size: 31 Copynumber: 4.8 Consensus size: 31
52934122 CTTGTCACTT
*
52934132 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
52934163 GTAGCCGGTA-CTACCACTTTTCACTGATCTG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
* * *
52934194 GTAGCTGGAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
52934225 GTAGCCGGAGCTACCACTTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
52934256 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
52934281 TGTCATTTGT
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
30 2 0.02
31 99 0.96
32 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:52934217 original size:62 final size:62
Alignment explanation
Indices: 52934132--52934280 Score: 228
Period size: 62 Copynumber: 2.4 Consensus size: 62
52934122 CTTGTCACTT
* * * *
52934132 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCCGGTA-CTACCACTTTTCACTGATCTG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAAGTAGCCGG-AGCTACCACTTTTCACTGATCAG
* *
52934194 GTAGCTGGAGCTACCACTTTTCACTGATCAAGTAGCCGGAGCTACCACTTTTCATTGATCAG
1 GTAGCTGAAGCTACCACTTTTCACTGATCAAGTAGCCGGAGCTACCACTTTTCACTGATCAG
52934256 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCTGAAGCTACCACTTTTCACT
52934281 TGTCATTTGT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
61 1 0.01
62 78 0.99
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (62 bp):
GTAGCTGAAGCTACCACTTTTCACTGATCAAGTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:52934362 original size:50 final size:51
Alignment explanation
Indices: 52934256--52934380 Score: 191
Period size: 50 Copynumber: 2.5 Consensus size: 51
52934246 CATTGATCAG
* * *
52934256 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
52934307 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
52934357 GTAGCCGAAGCTATCACTTATCAC
1 GTAGCCGAAGCTATCACTTATCAC
52934381 CTGTTGCCAT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
50 43 0.62
51 26 0.38
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:52951210 original size:18 final size:19
Alignment explanation
Indices: 52951170--52951210 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52951160 GGCAGCTTAT
*
52951170 AAAATTTTTAACAGATTAT
1 AAAATTTTTAACAGATTAC
*
52951189 AAAATTTTTAATAGATT-C
1 AAAATTTTTAACAGATTAC
52951207 AAAA
1 AAAA
52951211 ACAAAGGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAATTTTTAACAGATTAC
Found at i:52951211 original size:19 final size:19
Alignment explanation
Indices: 52951166--52951205 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
52951156 CAATGGCAGC
52951166 TTATAAAATTTTTAACAGA
1 TTATAAAATTTTTAACAGA
*
52951185 TTATAAAATTTTTAATAGA
1 TTATAAAATTTTTAACAGA
52951204 TT
1 TT
52951206 CAAAAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (19 bp):
TTATAAAATTTTTAACAGA
Found at i:52957964 original size:48 final size:48
Alignment explanation
Indices: 52957912--52958088 Score: 221
Period size: 48 Copynumber: 3.7 Consensus size: 48
52957902 CTCGCACACT
* *
52957912 AAGTGCCAATATCATGGCCCGCAGCCAACTCAATATATCTCACACCCG
1 AAGTGCCAATATCATGGCCCGAAGCCAAATCAATATATCTCACACCCG
* * *
52957960 AAGTGCTAATATCATGGCCTGAAGCCAAATGAATATATCTCACACCCG
1 AAGTGCCAATATCATGGCCCGAAGCCAAATCAATATATCTCACACCCG
* * * * **
52958008 AAGTGCTAATATCATGGCCCGAAGCCAAGTCAATGA-AGCTCGCACCTT
1 AAGTGCCAATATCATGGCCCGAAGCCAAATCAAT-ATATCTCACACCCG
* *
52958056 AAGTGCCAATATTATGGCCTGAAGCCAAATCAA
1 AAGTGCCAATATCATGGCCCGAAGCCAAATCAA
52958089 AGTATCCCCT
Statistics
Matches: 112, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
48 111 0.99
49 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.21
Consensus pattern (48 bp):
AAGTGCCAATATCATGGCCCGAAGCCAAATCAATATATCTCACACCCG
Found at i:52957970 original size:24 final size:24
Alignment explanation
Indices: 52957943--52958019 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
52957933 CAGCCAACTC
52957943 AATATATCTCACACCCGAAGTGCT
1 AATATATCTCACACCCGAAGTGCT
* * *
52957967 AATATCATGGCCTGA-AGCC-AAATG--
1 AATAT-AT---CTCACACCCGAAGTGCT
52957991 AATATATCTCACACCCGAAGTGCT
1 AATATATCTCACACCCGAAGTGCT
52958015 AATAT
1 AATAT
52958020 CATGGCCCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 16
0.64 0.10 0.26
Matches are distributed among these distances:
20 3 0.08
21 3 0.08
22 4 0.10
23 2 0.05
24 15 0.38
25 2 0.05
26 4 0.10
27 3 0.08
28 3 0.08
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (24 bp):
AATATATCTCACACCCGAAGTGCT
Found at i:52958076 original size:96 final size:96
Alignment explanation
Indices: 52957912--52958085 Score: 251
Period size: 96 Copynumber: 1.8 Consensus size: 96
52957902 CTCGCACACT
* * *
52957912 AAGTGCCAATATCATGGCCCGCAGCCAACTCAATATATCTCACACCCGAAGTGCTAATATCATGG
1 AAGTGCCAATATCATGGCCCGAAGCCAACTCAATATAGCTCACACCCGAAGTGCCAATATCATGG
52957977 CCTGAAGCCAAATGAATATATCTCACACCCG
66 CCTGAAGCCAAATGAATATATCTCACACCCG
* * * ** *
52958008 AAGTGCTAATATCATGGCCCGAAGCCAAGTCAATGA-AGCTCGCACCTTAAGTGCCAATATTATG
1 AAGTGCCAATATCATGGCCCGAAGCCAACTCAAT-ATAGCTCACACCCGAAGTGCCAATATCATG
52958072 GCCTGAAGCCAAAT
65 GCCTGAAGCCAAAT
52958086 CAAAGTATCC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
96 67 0.99
97 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (96 bp):
AAGTGCCAATATCATGGCCCGAAGCCAACTCAATATAGCTCACACCCGAAGTGCCAATATCATGG
CCTGAAGCCAAATGAATATATCTCACACCCG
Found at i:52964918 original size:13 final size:13
Alignment explanation
Indices: 52964900--52964927 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52964890 ATAGATCAGT
52964900 AAGCTCATATGAA
1 AAGCTCATATGAA
52964913 AAGCTCATATGAA
1 AAGCTCATATGAA
52964926 AA
1 AA
52964928 TAAGAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (13 bp):
AAGCTCATATGAA
Found at i:52965236 original size:48 final size:48
Alignment explanation
Indices: 52965183--52965311 Score: 154
Period size: 48 Copynumber: 2.7 Consensus size: 48
52965173 CTCGCACACT
* * * *
52965183 AAGTGCCAATATCATGGCTCAAAGCCAACTCAAT-ATATCTCA-CACCTA
1 AAGTGCCAATATCATGGCTCGAAGCCAAATCAATGA-AGCT-AGCACCCA
* * * *
52965231 AAGTGCTAATATCTTGGCCCGAAGCCAAATCAATGAAGCTAGCACCCG
1 AAGTGCCAATATCATGGCTCGAAGCCAAATCAATGAAGCTAGCACCCA
52965279 AAGTGCCAATATCATGGCTCGAAGCCAAATCAA
1 AAGTGCCAATATCATGGCTCGAAGCCAAATCAA
52965312 AGTATCCCCT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
47 1 0.01
48 66 0.97
49 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (48 bp):
AAGTGCCAATATCATGGCTCGAAGCCAAATCAATGAAGCTAGCACCCA
Found at i:52965839 original size:29 final size:27
Alignment explanation
Indices: 52965791--52965852 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
52965781 TTTTCATTTA
*
52965791 TTTCACATTTTAACCACTAAATTTACACT
1 TTTCACAATTTAACCACT-AATTTACA-T
* * *
52965820 TTTCACAATTTAGCCCCTAATTTGCAT
1 TTTCACAATTTAACCACTAATTTACAT
52965847 TTTCAC
1 TTTCAC
52965853 TAAAAATCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.24
28 7 0.24
29 15 0.52
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.42
Consensus pattern (27 bp):
TTTCACAATTTAACCACTAATTTACAT
Found at i:52969932 original size:29 final size:29
Alignment explanation
Indices: 52969890--52969949 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
52969880 GTAACTTGAA
52969890 TTGTATTTTTAAATACTTGAAATATGTGG
1 TTGTATTTTTAAATACTTGAAATATGTGG
52969919 TTGTATTTTTAAATACTTGAAATATGTGG
1 TTGTATTTTTAAATACTTGAAATATGTGG
52969948 TT
1 TT
52969950 ATGTGATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (29 bp):
TTGTATTTTTAAATACTTGAAATATGTGG
Found at i:52970365 original size:46 final size:46
Alignment explanation
Indices: 52970310--52970811 Score: 704
Period size: 46 Copynumber: 11.0 Consensus size: 46
52970300 GCTTTCTGAA
*
52970310 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
52970356 ATAAAATGTGTAATACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
52970402 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
52970448 ATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGTAACAAGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
52970494 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
52970540 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
52970586 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
52970632 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * ** ** * *
52970677 CGGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
**** * *
52970723 ATGAAATAAACAAGACCATGGTTGAAAGA-ACCATGGCAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
52970768 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
52970812 TCAAAGATAA
Statistics
Matches: 411, Mismatches: 42, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
44 1 0.00
45 72 0.18
46 338 0.82
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:52972867 original size:16 final size:17
Alignment explanation
Indices: 52972848--52972879 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
52972838 AAAACCAAAT
52972848 AAAAATAAAA-GAAAAC
1 AAAAATAAAAGGAAAAC
52972864 AAAAATAAAAGGAAAA
1 AAAAATAAAAGGAAAA
52972880 TAATGTCCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.81, C:0.03, G:0.09, T:0.06
Consensus pattern (17 bp):
AAAAATAAAAGGAAAAC
Found at i:52978100 original size:60 final size:61
Alignment explanation
Indices: 52977982--52978100 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 61
52977972 CTATTCAGAA
* * *
52977982 ATCAGAGTTAACTGGGCCTTAGCCCATATCAATATTAATTTGGGCCATAGCCCCTTACACT
1 ATCAGAGTTAACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACACT
* * * *
52978043 ATCAGAG-TATACTGGGCC-TAGCCCATATCAGTGTCAATCTGGGCCGTAGCCTATTACA
1 ATCAGAGTTA-ACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACA
52978101 AGTCGAGATA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 35 0.70
61 15 0.30
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (61 bp):
ATCAGAGTTAACTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACACT
Found at i:52983198 original size:16 final size:16
Alignment explanation
Indices: 52983177--52983207 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52983167 TTTAAAATGT
*
52983177 TAATTTGGTAATTAGG
1 TAATTTGGAAATTAGG
52983193 TAATTTGGAAATTAG
1 TAATTTGGAAATTAG
52983208 AAATGAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (16 bp):
TAATTTGGAAATTAGG
Found at i:52988513 original size:12 final size:12
Alignment explanation
Indices: 52988480--52988505 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52988470 TGCAACAGAA
52988480 AAACCATTTTTT
1 AAACCATTTTTT
52988492 AAACCATTTTTT
1 AAACCATTTTTT
52988504 AA
1 AA
52988506 GTCATTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (12 bp):
AAACCATTTTTT
Found at i:52993164 original size:55 final size:56
Alignment explanation
Indices: 52993099--52993213 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
52993089 AGCATGGCTG
* *
52993099 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
52993155 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
52993210 CCAG
1 CCAG
52993214 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.56
56 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:52993176 original size:27 final size:27
Alignment explanation
Indices: 52993124--52993213 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
52993114 GTGACAGAGT
52993124 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
52993153 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
52993180 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
52993208 CACCAG
1 CACCAG
52993214 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:52993616 original size:8 final size:8
Alignment explanation
Indices: 52993600--52993631 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
52993590 CCCAAAATAC
52993600 CGGCTTTT
1 CGGCTTTT
*
52993608 CGGCATTT
1 CGGCTTTT
52993616 CGGCTTTT
1 CGGCTTTT
52993624 CGGCTTTT
1 CGGCTTTT
52993632 GCCGATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.25, T:0.47
Consensus pattern (8 bp):
CGGCTTTT
Found at i:53001027 original size:28 final size:27
Alignment explanation
Indices: 53000940--53001029 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
53000930 GTGACAGAGT
*
53000940 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
* * *
53000969 CACCAGAACAGAT-ATATCTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
53000996 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
53001024 CACCAG
1 CACCAG
53001030 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:53001440 original size:16 final size:15
Alignment explanation
Indices: 53001419--53001448 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
53001409 AAAATACCGA
53001419 CTTTTCGGCATTTTGG
1 CTTTTCGGC-TTTTGG
53001435 CTTTTCGGCTTTTG
1 CTTTTCGGCTTTTG
53001449 CCGATCTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.03, C:0.20, G:0.23, T:0.53
Consensus pattern (15 bp):
CTTTTCGGCTTTTGG
Found at i:53001843 original size:25 final size:25
Alignment explanation
Indices: 53001815--53001864 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
53001805 AAATATGTAA
53001815 GAAGACTAAGTTTTGGAGAAGACTT
1 GAAGACTAAGTTTTGGAGAAGACTT
53001840 GAAGACTAAGTTTTGGAGAAGACTT
1 GAAGACTAAGTTTTGGAGAAGACTT
53001865 ACCACTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (25 bp):
GAAGACTAAGTTTTGGAGAAGACTT
Found at i:53008150 original size:23 final size:23
Alignment explanation
Indices: 53008123--53008174 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 23
53008113 TGCAAGAAAG
53008123 AAAAAAAATTCATATTATAAACTT
1 AAAAAAAA-TCATATTATAAACTT
53008147 AAAAAAAATCATATTATAAACTT
1 AAAAAAAATCATATTATAAACTT
53008170 AAAAA
1 AAAAA
53008175 TAGGTCGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAAAAATCATATTATAAACTT
Found at i:53008538 original size:18 final size:20
Alignment explanation
Indices: 53008502--53008543 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
53008492 ACTCTTAACC
53008502 TTTTAAAAAGAATCAAATT-
1 TTTTAAAAAGAATCAAATTA
* *
53008521 TTTTAAAAA-ATTCGAATTA
1 TTTTAAAAAGAATCAAATTA
53008540 TTTT
1 TTTT
53008544 TTAATAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTAAAAAGAATCAAATTA
Found at i:53010878 original size:40 final size:40
Alignment explanation
Indices: 53010834--53010972 Score: 260
Period size: 40 Copynumber: 3.5 Consensus size: 40
53010824 TGCTTGAATA
* *
53010834 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
53010874 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
53010914 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
53010954 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
53010973 TTATCATCCA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 97 1.00
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:53019157 original size:2 final size:2
Alignment explanation
Indices: 53019150--53019180 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53019140 ATACTTGTTC
53019150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53019181 CAATCACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53019287 original size:15 final size:15
Alignment explanation
Indices: 53019267--53019309 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
53019257 GAAGCCCAGA
53019267 ATAAAGAAATCCATG
1 ATAAAGAAATCCATG
53019282 ATAAAGAAATCCATG
1 ATAAAGAAATCCATG
* *
53019297 ATTAGGAAATCCA
1 ATAAAGAAATCCA
53019310 AATTACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (15 bp):
ATAAAGAAATCCATG
Found at i:53032242 original size:23 final size:23
Alignment explanation
Indices: 53032211--53032260 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
53032201 ACACCACTAA
* *
53032211 GCACTAAAGTACTTTAATAATAG
1 GCACCAAAGTACTTTAACAATAG
* *
53032234 GCACCAAAGTGCTTTAACAGTAG
1 GCACCAAAGTACTTTAACAATAG
53032257 GCAC
1 GCAC
53032261 TAAACTGCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (23 bp):
GCACCAAAGTACTTTAACAATAG
Found at i:53032306 original size:44 final size:44
Alignment explanation
Indices: 53032251--53032336 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
53032241 AGTGCTTTAA
*
53032251 CAGTAGGCACTAAACTGC-AAGATAGTAAGCACCGAAGTGCAATG
1 CAGTAGGCACTAAACTGCAAAGA-AGTAAGCACCAAAGTGCAATG
* * * *
53032295 CAGTAGTCACTATACTGCAAAGAAGTAGGCACTAAAGTGCAA
1 CAGTAGGCACTAAACTGCAAAGAAGTAAGCACCAAAGTGCAA
53032337 ATCAATAGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 32 0.89
45 4 0.11
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (44 bp):
CAGTAGGCACTAAACTGCAAAGAAGTAAGCACCAAAGTGCAATG
Found at i:53032335 original size:22 final size:22
Alignment explanation
Indices: 53032252--53032371 Score: 82
Period size: 22 Copynumber: 5.5 Consensus size: 22
53032242 GTGCTTTAAC
*
53032252 AGTAGGCACTAAACTGC-AAGA
1 AGTAGGCACTAAAGTGCAAAGA
* ** * *
53032273 TAGTAAGCACCGAAGTGCAATGC
1 -AGTAGGCACTAAAGTGCAAAGA
* * *
53032296 AGTAGTCACTATACTGCAAAGA
1 AGTAGGCACTAAAGTGCAAAGA
*
53032318 AGTAGGCACTAAAGTGCAAATCA
1 AGTAGGCACTAAAGTGCAAA-GA
* * * *
53032341 A-TAGGGACCATAGTGCAAAGT
1 AGTAGGCACTAAAGTGCAAAGA
53032362 AGTAGGCACT
1 AGTAGGCACT
53032372 GTAGTGAAGA
Statistics
Matches: 70, Mismatches: 25, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
21 1 0.01
22 65 0.93
23 4 0.06
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (22 bp):
AGTAGGCACTAAAGTGCAAAGA
Found at i:53032387 original size:44 final size:44
Alignment explanation
Indices: 53032310--53032403 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
53032300 GTCACTATAC
* *
53032310 TGCAAAGAAGTAGGCACTAAAGTGCAAATCAATAGGGACC-ATA
1 TGCAAAGAAGTAGGCACTAAAGTGCAAAACAATAGGCACCAATA
* **
53032353 GTGCAAAGTAGTAGGCACTGTAGTG-AAGAACAATAGGCACCAATA
1 -TGCAAAGAAGTAGGCACTAAAGTGCAA-AACAATAGGCACCAATA
53032398 TGCAAA
1 TGCAAA
53032404 ACAGTTAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
43 2 0.05
44 38 0.88
45 3 0.07
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.17
Consensus pattern (44 bp):
TGCAAAGAAGTAGGCACTAAAGTGCAAAACAATAGGCACCAATA
Found at i:53034012 original size:27 final size:27
Alignment explanation
Indices: 53033964--53034016 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
53033954 CATTCTACCA
* *
53033964 TACAGGGGTATTACGGTCATTTTACAC
1 TACAAGGGTATTACGGTAATTTTACAC
**
53033991 TACAAGGGTATTTTGGTAATTTTACA
1 TACAAGGGTATTACGGTAATTTTACA
53034017 AACAGGAGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (27 bp):
TACAAGGGTATTACGGTAATTTTACAC
Found at i:53034391 original size:10 final size:9
Alignment explanation
Indices: 53034358--53034391 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
53034348 GTTTACAGAT
53034358 GGGCCCAT-
1 GGGCCCATC
53034366 GGGCCCATC
1 GGGCCCATC
53034375 GGGCCCATC
1 GGGCCCATC
53034384 GAGGCCCA
1 G-GGCCCA
53034392 GAATAGTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 10 0.42
10 6 0.25
ACGTcount: A:0.15, C:0.41, G:0.35, T:0.09
Consensus pattern (9 bp):
GGGCCCATC
Found at i:53037348 original size:27 final size:27
Alignment explanation
Indices: 53037300--53037352 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
53037290 TATTCTACCA
* * *
53037300 TATAAGGGTTTTACGGTCATTTTACAC
1 TATAAGGGTATTACGATAATTTTACAC
*
53037327 TATAAGGGTATTCCGATAATTTTACA
1 TATAAGGGTATTACGATAATTTTACA
53037353 AATCAGGGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (27 bp):
TATAAGGGTATTACGATAATTTTACAC
Found at i:53044578 original size:17 final size:18
Alignment explanation
Indices: 53044536--53044584 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
53044526 AGTTGAAAAG
53044536 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
53044555 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
53044572 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
53044585 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:53045473 original size:40 final size:40
Alignment explanation
Indices: 53045407--53045573 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
53045397 AAATTGAATG
* * *
53045407 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
53045446 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
53045486 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
53045526 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
53045566 ATATCCGG
1 ATATCCGG
53045574 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:53052569 original size:17 final size:18
Alignment explanation
Indices: 53052527--53052575 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
53052517 AGTTGAAAAG
53052527 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
53052546 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
53052563 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
53052576 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:53053461 original size:40 final size:40
Alignment explanation
Indices: 53053395--53053561 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
53053385 AAATTGAATG
* * *
53053395 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
53053434 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
53053474 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
53053514 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
53053554 ATATCCGG
1 ATATCCGG
53053562 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:53060940 original size:46 final size:47
Alignment explanation
Indices: 53060888--53061059 Score: 169
Period size: 46 Copynumber: 3.7 Consensus size: 47
53060878 TCTGGGCATC
*
53060888 CGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATAGATGCGAATG-TA
1 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATGCTA
* * * * *
53060934 CGAGCTCATTGAGTTGAGTCCGAGTT--CGT-GAGATG-TAACTAGGCATC
1 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAA-T--GC-TA
* *
53060981 CGAGCTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCTA
1 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATG-CTA
*
53061029 --AGCTCGTTGAGTTGAGTCCGAGTTCGCTTAT
1 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT
53061060 GGGTAGGTTA
Statistics
Matches: 101, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
42 2 0.02
43 6 0.06
44 2 0.02
45 1 0.01
46 53 0.52
47 25 0.25
48 2 0.02
49 3 0.03
50 5 0.05
51 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (47 bp):
CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATGCTA
Found at i:53061041 original size:93 final size:92
Alignment explanation
Indices: 53060882--53061054 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 92
53060872 AGGATATCTG
* *
53060882 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATAGATGCGAATGTACGAGCTCATTGAG
1 GGCATCCGAGCTCGTTAAGTTGAGTCCGAGTTCACTTATAGATGCGAATGTAC-AGCTCATTGAG
53060947 TTGAGTCCGAGTTCGTGAGATGTAACTA
65 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
53060975 GGCATCCGAGCTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCTA-AGCTCGTTGA
1 GGCATCCGAGCTCGTTAAGTTGAGTCCGAGTTCACTTATAGATGCGAATG--TACAGCTCATTGA
53061039 GTTGAGTCCGAGTTCG
64 GTTGAGTCCGAGTTCG
53061055 CTTATGGGTA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
93 72 0.97
95 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (92 bp):
GGCATCCGAGCTCGTTAAGTTGAGTCCGAGTTCACTTATAGATGCGAATGTACAGCTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:53063781 original size:28 final size:28
Alignment explanation
Indices: 53063749--53063805 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
53063739 CTGAATGAGA
* *
53063749 TATCAAATTAGATATTAATGAGTCTATT
1 TATCAAATTAGAGATTAATAAGTCTATT
*
53063777 TATCAAATTAGAGCTTAATAAGTCTATT
1 TATCAAATTAGAGATTAATAAGTCTATT
53063805 T
1 T
53063806 TCATATAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (28 bp):
TATCAAATTAGAGATTAATAAGTCTATT
Found at i:53066934 original size:31 final size:30
Alignment explanation
Indices: 53066877--53066935 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
53066867 GTAAATACTC
* * * *
53066877 AAAATTTGAGGGATTAAAGTGTAAATATAA
1 AAAAGTTGAAGGACTAAAGTGCAAATATAA
53066907 AAAAGTTGAAGGACTAATAGTGCAAATAT
1 AAAAGTTGAAGGACTAA-AGTGCAAATAT
53066936 TTTAAGGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.27
Consensus pattern (30 bp):
AAAAGTTGAAGGACTAAAGTGCAAATATAA
Found at i:53070390 original size:26 final size:26
Alignment explanation
Indices: 53070361--53070424 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
53070351 ATGGAAGAAG
* *
53070361 TACTG-TATTGGTGACTATGTCACATT
1 TACTGTTATTGGTGACT-TGCCACACT
* *
53070387 TACTGTTACTGGTGGCTTGCCACACT
1 TACTGTTATTGGTGACTTGCCACACT
53070413 TACTGTTATTGG
1 TACTGTTATTGG
53070425 CAACTGTGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 23 0.72
27 9 0.28
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (26 bp):
TACTGTTATTGGTGACTTGCCACACT
Found at i:53086168 original size:24 final size:24
Alignment explanation
Indices: 53086139--53086186 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
53086129 ACTCGCAACT
53086139 AATAGTAGCCTGATCTCAAATCTA
1 AATAGTAGCCTGATCTCAAATCTA
53086163 AATAGTAGCCTGATCTCAAATCTA
1 AATAGTAGCCTGATCTCAAATCTA
53086187 TCTTCGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (24 bp):
AATAGTAGCCTGATCTCAAATCTA
Found at i:53092503 original size:43 final size:43
Alignment explanation
Indices: 53092455--53092540 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
53092445 AAATCATACA
**
53092455 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAGTCACATATCG
1 ATGCCAACGTCCCAGACAG-GGTCTTACATGTAAACACATATCG
** * *
53092498 ATGCCATTGTCCTAGACAGGGTCTTACTTGTAAACACATATCG
1 ATGCCAACGTCCCAGACAGGGTCTTACATGTAAACACATATCG
53092541 GAATCACATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACATGTAAACACATATCG
Found at i:53093271 original size:6 final size:6
Alignment explanation
Indices: 53093250--53093365 Score: 58
Period size: 6 Copynumber: 18.8 Consensus size: 6
53093240 TACCAGAACT
* * *
53093250 AGAATC AAAATG AGAATC AGAATC AGAATC AG-GTGAC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * * * * * *
53093299 AGATTC ATAACC AGAATT AG-GTGAC AGAATC AAAATC AGTATC AGGTAA-C
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC A-G-AATC
*
53093349 AGAATA AGAATC AGAAT
1 AGAATC AGAATC AGAAT
53093366 GTGAATACAA
Statistics
Matches: 79, Mismatches: 22, Indels: 18
0.66 0.18 0.15
Matches are distributed among these distances:
5 4 0.05
6 64 0.81
7 8 0.10
8 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:53093291 original size:19 final size:19
Alignment explanation
Indices: 53093267--53093337 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
53093257 AAATGAGAAT
53093267 CAGAATCAGAATCAGGTGA
1 CAGAATCAGAATCAGGTGA
* *
53093286 CAGAATCAGAATCAGAT-T
1 CAGAATCAGAATCAGGTGA
* * *
53093304 CATAACCAGAATTAGGTGA
1 CAGAATCAGAATCAGGTGA
*
53093323 CAGAATCAAAATCAG
1 CAGAATCAGAATCAG
53093338 TATCAGGTAA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
18 13 0.32
19 27 0.68
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (19 bp):
CAGAATCAGAATCAGGTGA
Found at i:53093314 original size:37 final size:37
Alignment explanation
Indices: 53093250--53093343 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
53093240 TACCAGAACT
* *
53093250 AGAATCAAAATGAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAAAATCAGAATCAGAACCAGAATCAGGTGAC
* * * *
53093287 AGAATCAGAATCAGATTCATAACCAGAATTAGGTGAC
1 AGAATCAAAATCAGAATCAGAACCAGAATCAGGTGAC
*
53093324 AGAATCAAAATCAGTATCAG
1 AGAATCAAAATCAGAATCAG
53093344 GTAACAGAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (37 bp):
AGAATCAAAATCAGAATCAGAACCAGAATCAGGTGAC
Found at i:53093526 original size:27 final size:26
Alignment explanation
Indices: 53093485--53093590 Score: 140
Period size: 27 Copynumber: 4.0 Consensus size: 26
53093475 CATGGCTACT
* *
53093485 AGAACAGATATTGTGACAGAGTCACC
1 AGAACAGATATTGTGGCAGAGCCACC
*
53093511 AGATACAGATATTGTGGCAAAGCCACC
1 AGA-ACAGATATTGTGGCAGAGCCACC
53093538 AGAACAGATATTTGTGGCAGAGCCACC
1 AGAACAGATA-TTGTGGCAGAGCCACC
* *
53093565 AGAAACAGATAATGTGGCAAAGCCAC
1 AG-AACAGATATTGTGGCAGAGCCAC
53093591 TTAACAGAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 10 0.14
27 53 0.75
28 8 0.11
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.17
Consensus pattern (26 bp):
AGAACAGATATTGTGGCAGAGCCACC
Found at i:53093567 original size:54 final size:53
Alignment explanation
Indices: 53093485--53093590 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 53
53093475 CATGGCTACT
* * *
53093485 AGAACAGATATTGTGACAGAGTCACCAGATACAGATATTGTGGCAAAGCCACC
1 AGAACAGATATTGTGACAGAGCCACCAGAAACAGATAATGTGGCAAAGCCACC
*
53093538 AGAACAGATATTTGTGGCAGAGCCACCAGAAACAGATAATGTGGCAAAGCCAC
1 AGAACAGATA-TTGTGACAGAGCCACCAGAAACAGATAATGTGGCAAAGCCAC
53093591 TTAACAGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
53 10 0.21
54 38 0.79
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.17
Consensus pattern (53 bp):
AGAACAGATATTGTGACAGAGCCACCAGAAACAGATAATGTGGCAAAGCCACC
Found at i:53093616 original size:54 final size:54
Alignment explanation
Indices: 53093485--53093608 Score: 128
Period size: 54 Copynumber: 2.4 Consensus size: 54
53093475 CATGGCTACT
* * * * * *
53093485 AGAACAGATAT-TGTGACAGAGTCACCAGATACAGATATTGTGGCAAAGCCACC
1 AGAACAGATATACGTGGCAAAGCCACCAGAAACAGATAATGTGGCAAAGCCACC
** *
53093538 AGAACAGATATTTGTGGCAGAGCCACCAGAAACAGATAATGTGGCAAAGCCA-C
1 AGAACAGATATACGTGGCAAAGCCACCAGAAACAGATAATGTGGCAAAGCCACC
**
53093591 TTAACAGA-ATACGTGGCA
1 AGAACAGATATACGTGGCA
53093609 CAAAGCCATC
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
52 8 0.13
53 18 0.29
54 36 0.58
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (54 bp):
AGAACAGATATACGTGGCAAAGCCACCAGAAACAGATAATGTGGCAAAGCCACC
Found at i:53093777 original size:22 final size:22
Alignment explanation
Indices: 53093749--53093813 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
53093739 GCAAATACGT
*
53093749 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
53093771 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
* *
53093793 TTGGCGCAAAACCATAATCAG
1 TTGGCACAAAGCCATAATCAG
53093814 AATAATTGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:53094232 original size:27 final size:27
Alignment explanation
Indices: 53094202--53094282 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
53094192 GGGCAAAATG
*
53094202 GTAATTTTACCCCACAAGGGTATCTT-A
1 GTAATTCTACCCCACAAGGGTAT-TTCA
* *
53094229 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCCACAAGGGTATTTCA
* * *
53094256 GTAATTCTACCCTATAGGGGTATTTCA
1 GTAATTCTACCCCACAAGGGTATTTCA
53094283 ATAACTTTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 2 0.04
27 47 0.96
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCCACAAGGGTATTTCA
Found at i:53096103 original size:17 final size:18
Alignment explanation
Indices: 53096081--53096115 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53096071 AATGAATATG
*
53096081 ATAAGTTT-TTAATTAAT
1 ATAAGTTTATTAACTAAT
53096098 ATAAGTTTATTAACTAAT
1 ATAAGTTTATTAACTAAT
53096116 TTACATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (18 bp):
ATAAGTTTATTAACTAAT
Found at i:53096371 original size:17 final size:17
Alignment explanation
Indices: 53096349--53096383 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
53096339 ACAAACATCA
53096349 ATTCACACAAAATAAAC
1 ATTCACACAAAATAAAC
53096366 ATTCACACAAAATAAAC
1 ATTCACACAAAATAAAC
53096383 A
1 A
53096384 CAGTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.23, G:0.00, T:0.17
Consensus pattern (17 bp):
ATTCACACAAAATAAAC
Found at i:53102503 original size:40 final size:40
Alignment explanation
Indices: 53102445--53102520 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 40
53102435 ATGCATACTA
*
53102445 TATCTGAGATGGGATAAGGCCCTAATTTGTACCTGAAACTG
1 TATCTGAGATGGGATAAGG-CCTAAATTGTACCTGAAACTG
* *
53102486 TATCTGA-ATGGGCTAAGGCCTAAATTGTATCTGAA
1 TATCTGAGATGGGATAAGGCCTAAATTGTACCTGAA
53102521 TGTGTACTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 15 0.47
40 10 0.31
41 7 0.22
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (40 bp):
TATCTGAGATGGGATAAGGCCTAAATTGTACCTGAAACTG
Found at i:53113797 original size:9 final size:9
Alignment explanation
Indices: 53113756--53113827 Score: 58
Period size: 9 Copynumber: 8.0 Consensus size: 9
53113746 ATTTTAATCC
53113756 TTTTATATA
1 TTTTATATA
* *
53113765 -TATATACA
1 TTTTATATA
53113773 TTTTATATA
1 TTTTATATA
*
53113782 TAATTTATTTA
1 T--TTTATATA
*
53113793 TTTTAAATA
1 TTTTATATA
53113802 TTTTATATA
1 TTTTATATA
* *
53113811 TATTATTTA
1 TTTTATATA
53113820 TTTT-TATA
1 TTTTATATA
53113828 AATATTATTT
Statistics
Matches: 48, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
8 9 0.19
9 31 0.65
11 8 0.17
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTATATA
Done.