Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold433
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1285081
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 132229 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:4649 original size:11 final size:11
Alignment explanation
Indices: 4642--4666 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4632 ACTAGAGTGG
4642 ACCCAGAGTAA
1 ACCCAGAGTAA
4653 ACCCAGAGTAA
1 ACCCAGAGTAA
4664 ACC
1 ACC
4667 AAAAGTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.32, G:0.16, T:0.08
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:4863 original size:11 final size:11
Alignment explanation
Indices: 4847--4885 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4837 AGCAATTTCC
4847 AAGTAAACCCA
1 AAGTAAACCCA
*
4858 AAGTAAACCCC
1 AAGTAAACCCA
* *
4869 GAGTAAAACCA
1 AAGTAAACCCA
4880 AAGTAA
1 AAGTAA
4886 CCCCGAGTGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.23, G:0.13, T:0.10
Consensus pattern (11 bp):
AAGTAAACCCA
Found at i:4889 original size:21 final size:22
Alignment explanation
Indices: 4848--4893 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
4838 GCAATTTCCA
*
4848 AGTAAACCCAAAGTAAACCCCG
1 AGTAAAACCAAAGTAAACCCCG
4870 AGTAAAACCAAAGT-AACCCCG
1 AGTAAAACCAAAGTAAACCCCG
4891 AGT
1 AGT
4894 GGACCCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.46, C:0.28, G:0.15, T:0.11
Consensus pattern (22 bp):
AGTAAAACCAAAGTAAACCCCG
Found at i:4901 original size:21 final size:22
Alignment explanation
Indices: 4848--4902 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
4838 GCAATTTCCA
4848 AGTAAACCCAAAGTAAACCCCG
1 AGTAAACCCAAAGTAAACCCCG
*
4870 AGTAAAACCAAAGT-AACCCCG
1 AGTAAACCCAAAGTAAACCCCG
**
4891 AGTGGACCCAAA
1 AGTAAACCCAAA
4903 TTTTCAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.45, C:0.29, G:0.16, T:0.09
Consensus pattern (22 bp):
AGTAAACCCAAAGTAAACCCCG
Found at i:5313 original size:14 final size:14
Alignment explanation
Indices: 5294--5326 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5284 TAAATCTTAA
*
5294 AGCCAGTTACTATT
1 AGCCAGTTACTAGT
5308 AGCCAGTTACTAGT
1 AGCCAGTTACTAGT
5322 AGCCA
1 AGCCA
5327 ATTCTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (14 bp):
AGCCAGTTACTAGT
Found at i:6298 original size:21 final size:21
Alignment explanation
Indices: 6272--6351 Score: 108
Period size: 21 Copynumber: 3.8 Consensus size: 21
6262 TTCTCTTAAT
6272 TATGTTGACATGCAAGATAAA
1 TATGTTGACATGCAAGATAAA
6293 TATGTTGACATGCAAGAT-AA
1 TATGTTGACATGCAAGATAAA
** * *
6313 TAATGTCAACATGCAACATAAC
1 T-ATGTTGACATGCAAGATAAA
6335 TATGTTGACATGCAAGA
1 TATGTTGACATGCAAGA
6352 AAACTGCAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.06
21 45 0.90
22 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (21 bp):
TATGTTGACATGCAAGATAAA
Found at i:6454 original size:21 final size:21
Alignment explanation
Indices: 6430--6599 Score: 173
Period size: 21 Copynumber: 8.1 Consensus size: 21
6420 ATACGCTACC
*
6430 TATTGATGTCAACATGCAACT
1 TATTTATGTCAACATGCAACT
*
6451 TATTTATGTTAACATGCAACT
1 TATTTATGTCAACATGCAACT
* * *
6472 TCTTTATGTCGACATGGAAC-
1 TATTTATGTCAACATGCAACT
*
6492 TATTTATGTCAACATGCAATT
1 TATTTATGTCAACATGCAACT
* * *
6513 TAGTTATGTTAACATGCAAGAT
1 TATTTATGTCAACATGCAA-CT
* ** *
6535 TA-ATATGTTGACATGCAACA
1 TATTTATGTCAACATGCAACT
6555 TATTTATGTCAACATGCAACT
1 TATTTATGTCAACATGCAACT
* **
6576 TAGTTATGTTGACATGCAACT
1 TATTTATGTCAACATGCAACT
6597 TAT
1 TAT
6600 AAGTTGCATG
Statistics
Matches: 121, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
20 18 0.15
21 100 0.83
22 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (21 bp):
TATTTATGTCAACATGCAACT
Found at i:6487 original size:42 final size:42
Alignment explanation
Indices: 6430--6599 Score: 191
Period size: 42 Copynumber: 4.1 Consensus size: 42
6420 ATACGCTACC
*
6430 TATTGATGTCAACATGCAACTTATTTATGTTAACATGCAACT
1 TATTTATGTCAACATGCAACTTATTTATGTTAACATGCAACT
* * * * *
6472 TCTTTATGTCGACATGGAAC-TATTTATGTCAACATGCAATT
1 TATTTATGTCAACATGCAACTTATTTATGTTAACATGCAACT
* * * * * *
6513 TAGTTATGTTAACATGCAAGATTA-ATATGTTGACATGCAACA
1 TATTTATGTCAACATGCAA-CTTATTTATGTTAACATGCAACT
* *
6555 TATTTATGTCAACATGCAACTTAGTTATGTTGACATGCAACT
1 TATTTATGTCAACATGCAACTTATTTATGTTAACATGCAACT
6597 TAT
1 TAT
6600 AAGTTGCATG
Statistics
Matches: 103, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
41 36 0.35
42 65 0.63
43 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (42 bp):
TATTTATGTCAACATGCAACTTATTTATGTTAACATGCAACT
Found at i:6505 original size:62 final size:61
Alignment explanation
Indices: 6429--6598 Score: 232
Period size: 62 Copynumber: 2.7 Consensus size: 61
6419 GATACGCTAC
* * ** *
6429 CTATTGATGTCAACATGCAACTTATTTATGTTAACATGCAACTTCTTTATGTCGACATGGAA
1 CTATTTATGTCAACATGCAACTTAGTTATGTTAACATGCAACTT-AATATGTCGACATGCAA
* * *
6491 CTATTTATGTCAACATGCAATTTAGTTATGTTAACATGCAAGATTAATATGTTGACATGCAA
1 CTATTTATGTCAACATGCAACTTAGTTATGTTAACATGCAA-CTTAATATGTCGACATGCAA
*
6553 CATATTTATGTCAACATGCAACTTAGTTATGTTGACATGCAACTTA
1 C-TATTTATGTCAACATGCAACTTAGTTATGTTAACATGCAACTTA
6599 TAAGTTGCAT
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
62 55 0.58
63 40 0.42
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (61 bp):
CTATTTATGTCAACATGCAACTTAGTTATGTTAACATGCAACTTAATATGTCGACATGCAA
Found at i:6680 original size:42 final size:42
Alignment explanation
Indices: 6599--6785 Score: 119
Period size: 42 Copynumber: 4.5 Consensus size: 42
6589 ATGCAACTTA
* *
6599 TAAGTTGCATGTCAACATATTTATCTCGCATGTAAACATAAC
1 TAAGTTGCATGTCAACATATTCATCTAGCATGTAAACATAAC
* ** ** *
6641 TAAGTTGTATGTTGACATATTCATCTAGCATGTCGACATAAA
1 TAAGTTGCATGTCAACATATTCATCTAGCATGTAAACATAAC
* ** * * * * ** *
6683 TAACTTGCATACCGACATAGATAAGT-T-TCATGTTGACATAAA
1 TAAGTTGCATGTCAACATA-TTCA-TCTAGCATGTAAACATAAC
* * * *
6725 TAAGTTGCATGTCAGCATATTTATCTTGCATGTTAACATAGA-
1 TAAGTTGCATGTCAACATATTCATCTAGCATGTAAACATA-AC
*
6767 TAAGTTGCATGTCGACATA
1 TAAGTTGCATGTCAACATA
6786 GAAAGATAGC
Statistics
Matches: 112, Mismatches: 28, Indels: 10
0.75 0.19 0.07
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 103 0.92
43 4 0.04
44 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (42 bp):
TAAGTTGCATGTCAACATATTCATCTAGCATGTAAACATAAC
Found at i:6786 original size:21 final size:21
Alignment explanation
Indices: 6668--6787 Score: 107
Period size: 21 Copynumber: 5.7 Consensus size: 21
6658 TATTCATCTA
* *
6668 GCATGTCGACATAAATAACTT
1 GCATGTCGACATAGATAAGTT
**
6689 GCATACCGACATAGATAAGTT
1 GCATGTCGACATAGATAAGTT
* * *
6710 TCATGTTGACATAAATAAGTT
1 GCATGTCGACATAGATAAGTT
** **
6731 GCATGTC-AGCATATTTATCTT
1 GCATGTCGA-CATAGATAAGTT
**
6752 GCATGTTAACATAGATAAGTT
1 GCATGTCGACATAGATAAGTT
6773 GCATGTCGACATAGA
1 GCATGTCGACATAGA
6788 AAGATAGCAA
Statistics
Matches: 75, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 1 0.01
21 73 0.97
22 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (21 bp):
GCATGTCGACATAGATAAGTT
Found at i:6934 original size:42 final size:42
Alignment explanation
Indices: 6865--6944 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
6855 GATTGCAATT
* *
6865 TCTTGCATGTCAACATAGTTATGTTGCATGTTGACATAACTA
1 TCTTGCATGTCAACATAGTTATCTTGCATGTCGACATAACTA
*
6907 TCTTGCATGTCAACATATTTATCTTGCATGTCGACATA
1 TCTTGCATGTCAACATAGTTATCTTGCATGTCGACATA
6945 TTTGATAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (42 bp):
TCTTGCATGTCAACATAGTTATCTTGCATGTCGACATAACTA
Found at i:6945 original size:21 final size:21
Alignment explanation
Indices: 6865--6947 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 21
6855 GATTGCAATT
*
6865 TCTTGCATGTCAACATAGTTA
1 TCTTGCATGTCAACATATTTA
* ** **
6886 TGTTGCATGTTGACATAACTA
1 TCTTGCATGTCAACATATTTA
6907 TCTTGCATGTCAACATATTTA
1 TCTTGCATGTCAACATATTTA
*
6928 TCTTGCATGTCGACATATTT
1 TCTTGCATGTCAACATATTT
6948 GATAGAAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (21 bp):
TCTTGCATGTCAACATATTTA
Found at i:7930 original size:37 final size:37
Alignment explanation
Indices: 7876--8068 Score: 282
Period size: 37 Copynumber: 5.2 Consensus size: 37
7866 GTAACTAGTA
* *
7876 ACTAGAAGCCAAGTTTCT-TTT-ATCTCGTAGCCAGTT
1 ACTAGTAGCCAACTTT-TATTTCATCTCGTAGCCAGTT
** * * * *
7912 ACTAGTAGTTAGCTTTTCTTACTTCTCGTAGCCAGTT
1 ACTAGTAGCCAACTTTTATTTCATCTCGTAGCCAGTT
7949 ACTAGTAGCCAACTTTTATTTCATCTCGTAGCCAGTT
1 ACTAGTAGCCAACTTTTATTTCATCTCGTAGCCAGTT
7986 ACTAGTAGCCAACTTTTATTTCATCTCGTAGCCAGTT
1 ACTAGTAGCCAACTTTTATTTCATCTCGTAGCCAGTT
8023 ACTAGTAGCCAACTTTTATTTCATCTCGTAGCCAGTT
1 ACTAGTAGCCAACTTTTATTTCATCTCGTAGCCAGTT
*
8060 ACCAGTAGC
1 ACTAGTAGC
8069 TAGATTTACC
Statistics
Matches: 141, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
35 1 0.01
36 13 0.09
37 127 0.90
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (37 bp):
ACTAGTAGCCAACTTTTATTTCATCTCGTAGCCAGTT
Found at i:12292 original size:24 final size:24
Alignment explanation
Indices: 12258--12386 Score: 107
Period size: 24 Copynumber: 5.3 Consensus size: 24
12248 CAAATGCAGT
* *
12258 CTCGATAAGAGAACAAAAAACGGC
1 CTCGTTAAGAGAACCAAAAACGGC
* * *
12282 CACGTTAAGAGGACCAAATACGGC
1 CTCGTTAAGAGAACCAAAAACGGC
* ** *
12306 CTCGTAAAGAGAACCAAATGCGGT
1 CTCGTTAAGAGAACCAAAAACGGC
*
12330 CTCGTTAAGAGAACCAAGAACGGC
1 CTCGTTAAGAGAACCAAAAACGGC
* * *
12354 TTCGTTATGAGGACCCAAACAA-GGC
1 CTCGTTAAGA-GAACCAAA-AACGGC
*
12379 CTCATTAA
1 CTCGTTAA
12387 TGAACATTGC
Statistics
Matches: 81, Mismatches: 22, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
24 65 0.80
25 14 0.17
26 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (24 bp):
CTCGTTAAGAGAACCAAAAACGGC
Found at i:13293 original size:65 final size:65
Alignment explanation
Indices: 13204--13672 Score: 421
Period size: 65 Copynumber: 7.5 Consensus size: 65
13194 GTTTATTTCT
*
13204 TAAATATTAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACATTGAAT
1 TAAATA-TAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAAT
13269 G
65 G
*
13270 TAAATAGAGAAAATTGAACGTCGCAGATTT-C----C--A-AT---GGGAAATATACACTGAATG
1 TAAATATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAATG
* * *
13324 TAAATACATGTATAGAAAATTGAATGTCGCAGATTTCCAGTGCAAACACAAGGGGAAATATACAC
1 T--A-A-A--TATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACAC
13389 TGAATGCTTATG
60 TG-A-----ATG
* * * * *
13401 TAAATAAAGAAAATTAAATGTCGCAGA--T-C--T-C---C--AAGGGGAAATGTACACTGCATG
1 TAAATATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAATG
* *
13455 TAAATATAGAAAATTGAACCTCGCAGATTTCCAATGCAAACATAAGGGGAAATATGCACTGAATG
1 TAAATATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAATG
* *
13520 TAAATATAGAAAATTGAACGTCGCA-AATT----T-----C-TAAGGGGAAATATACACTAAATG
1 TAAATATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAATG
* *
13574 T-AATAATAGAAAATTGAACGTCGCAGTTTTCCAATGCAAACATAAGGGGAACTATACACTGAAT
1 TAAAT-ATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAAT
13638 G
65 G
*
13639 TAAATTTAGAAAATTGAACGTCGCAGATTTCCAA
1 TAAATATAGAAAATTGAACGTCGCAGATTTCCAA
13673 GGGGAAATAT
Statistics
Matches: 330, Mismatches: 26, Indels: 95
0.73 0.06 0.21
Matches are distributed among these distances:
53 3 0.01
54 87 0.26
55 3 0.01
56 2 0.01
57 4 0.01
58 2 0.01
59 2 0.01
60 44 0.13
61 1 0.00
62 1 0.00
63 1 0.00
64 5 0.02
65 117 0.35
66 10 0.03
67 1 0.00
68 2 0.01
69 1 0.00
71 36 0.11
72 1 0.00
73 1 0.00
74 1 0.00
75 1 0.00
77 4 0.01
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.25
Consensus pattern (65 bp):
TAAATATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAATG
Found at i:13480 original size:54 final size:54
Alignment explanation
Indices: 13398--13719 Score: 277
Period size: 54 Copynumber: 5.6 Consensus size: 54
13388 CTGAATGCTT
* * * * *
13398 ATGTAAATAAAGAAAATTAAATGTCGCAGATCTCCAAGGGGAAATGTACACTGC
1 ATGTAAATATAGAAAATTGAACGTCGCAGATCTCCAAGGGGAAATATACACTGA
* *
13452 ATGTAAATATAGAAAATTGAACCTCGCAGATTTCCAATGCAAACATAAGGGGAAATATGCACTGA
1 ATGTAAATATAGAAAATTGAACGTCGCAGA--T-C--T-C---C--AAGGGGAAATATACACTGA
* * * *
13517 ATGTAAATATAGAAAATTGAACGTCGCAAATTTCTAAGGGGAAATATACACTAA
1 ATGTAAATATAGAAAATTGAACGTCGCAGATCTCCAAGGGGAAATATACACTGA
* *
13571 ATGT-AATAATAGAAAATTGAACGTCGCAGTTTTCCAATGCAAACATAAGGGGAACTATACACTG
1 ATGTAAAT-ATAGAAAATTGAACGTCGCAG--AT-C--T-C---C--AAGGGGAAATATACACTG
13635 A
54 A
* *
13636 ATGTAAATTTAGAAAATTGAACGTCGCAGATTTCCAAGGGGAAATATACACTGA
1 ATGTAAATATAGAAAATTGAACGTCGCAGATCTCCAAGGGGAAATATACACTGA
* *
13690 ATTTAAATATAGAAAATTAAACGTCGCAGA
1 ATGTAAATATAGAAAATTGAACGTCGCAGA
13720 GGACTATACA
Statistics
Matches: 218, Mismatches: 26, Indels: 48
0.75 0.09 0.16
Matches are distributed among these distances:
53 3 0.01
54 112 0.51
56 3 0.01
57 1 0.00
59 4 0.02
60 4 0.02
63 3 0.01
65 85 0.39
66 3 0.01
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (54 bp):
ATGTAAATATAGAAAATTGAACGTCGCAGATCTCCAAGGGGAAATATACACTGA
Found at i:13589 original size:119 final size:120
Alignment explanation
Indices: 13206--13719 Score: 703
Period size: 119 Copynumber: 4.2 Consensus size: 120
13196 TTATTTCTTA
*
13206 AATAT-TAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACATTGAATG
1 AATATATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAATG
* *
13270 TAAATAGAGAAAATTGAACGTCGCAGATTTCCAATGGGAAATATACACTGAATGT
66 TAAATATAGAAAATTGAACGTCGCAGATTTCCAAGGGGAAATATACACTGAATGT
* * *
13325 AAATACATGTATAGAAAATTGAATGTCGCAGATTTCCAGTGCAAACACAAGGGGAAATATACACT
1 -AAT--A--TATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACT
* * * * * *
13390 GAATGCTTATGTAAATAAAGAAAATTAAATGTCGCAGATCTCCAAGGGGAAATGTACACTGCATG
61 G-A-----ATGTAAATATAGAAAATTGAACGTCGCAGATTTCCAAGGGGAAATATACACTGAATG
13455 T
120 T
* *
13456 AA-ATATAGAAAATTGAACCTCGCAGATTTCCAATGCAAACATAAGGGGAAATATGCACTGAATG
1 AATATATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAATG
* * *
13520 TAAATATAGAAAATTGAACGTCGCAAATTTCTAAGGGGAAATATACACTAAATGT
66 TAAATATAGAAAATTGAACGTCGCAGATTTCCAAGGGGAAATATACACTGAATGT
* *
13575 AATA-ATAGAAAATTGAACGTCGCAGTTTTCCAATGCAAACATAAGGGGAACTATACACTGAATG
1 AATATATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAATG
* *
13639 TAAATTTAGAAAATTGAACGTCGCAGATTTCCAAGGGGAAATATACACTGAATTT
66 TAAATATAGAAAATTGAACGTCGCAGATTTCCAAGGGGAAATATACACTGAATGT
*
13694 AA-ATATAGAAAATTAAACGTCGCAGA
1 AATATATAGAAAATTGAACGTCGCAGA
13720 GGACTATACA
Statistics
Matches: 345, Mismatches: 36, Indels: 27
0.85 0.09 0.07
Matches are distributed among these distances:
118 1 0.00
119 179 0.52
120 4 0.01
122 1 0.00
124 2 0.01
125 103 0.30
126 1 0.00
127 1 0.00
130 2 0.01
131 51 0.15
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.25
Consensus pattern (120 bp):
AATATATAGAAAATTGAACGTCGCAGATTTCCAATGCAAACATAAGGGGAAATATACACTGAATG
TAAATATAGAAAATTGAACGTCGCAGATTTCCAAGGGGAAATATACACTGAATGT
Found at i:14389 original size:65 final size:65
Alignment explanation
Indices: 14308--14461 Score: 238
Period size: 65 Copynumber: 2.4 Consensus size: 65
14298 CTTTCCAAGA
* * *
14308 GGAAATATACACTGAATGTAAATAAAGAAAATTGATCGTCGCAGTTTTTC-AATGCAAACATAAG
1 GGAAATTTACACTGAATGTAAATAAAGAAAATTGAACGTCGCAG-TTTTCAAATGAAAACATAAG
14372 G
65 G
* *
14373 GGAAATTTACACTGAATGTAAATATAGAAAATTGAACGTCGCAGTTTTCAAATTAAAACATAAGG
1 GGAAATTTACACTGAATGTAAATAAAGAAAATTGAACGTCGCAGTTTTCAAATGAAAACATAAGG
*
14438 GGAAATTTACACTAAATGTAAATA
1 GGAAATTTACACTGAATGTAAATA
14462 CTAGTATAGA
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
64 5 0.06
65 77 0.94
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (65 bp):
GGAAATTTACACTGAATGTAAATAAAGAAAATTGAACGTCGCAGTTTTCAAATGAAAACATAAGG
Found at i:15250 original size:8 final size:8
Alignment explanation
Indices: 15237--15284 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
15227 GTGTCCGCCA
15237 GTCTGTCC
1 GTCTGTCC
*
15245 GTCTGTCT
1 GTCTGTCC
15253 GTCTGTCC
1 GTCTGTCC
* *
15261 GTCCGTTC
1 GTCTGTCC
* *
15269 GTCCGTCT
1 GTCTGTCC
15277 GTCTGTCC
1 GTCTGTCC
15285 CATTTCAGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.00, C:0.35, G:0.25, T:0.40
Consensus pattern (8 bp):
GTCTGTCC
Found at i:15284 original size:12 final size:12
Alignment explanation
Indices: 15237--15284 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
15227 GTGTCCGCCA
* *
15237 GTCTGTCCGTCT
1 GTCTGTCTGTCC
15249 GTCTGTCTGTCC
1 GTCTGTCTGTCC
*
15261 GTCCGT-TCGTCC
1 GTCTGTCT-GTCC
15273 GTCTGTCTGTCC
1 GTCTGTCTGTCC
15285 CATTTCAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 1 0.03
12 28 0.93
13 1 0.03
ACGTcount: A:0.00, C:0.35, G:0.25, T:0.40
Consensus pattern (12 bp):
GTCTGTCTGTCC
Found at i:31012 original size:2 final size:2
Alignment explanation
Indices: 31005--31049 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
30995 AAAAGCGCAT
31005 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
31047 GA G
1 GA G
31050 TAATTTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33979 original size:21 final size:21
Alignment explanation
Indices: 33953--33994 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
33943 TCCAAAGGGG
33953 TGGATCACGGGGGTTGCAACC
1 TGGATCACGGGGGTTGCAACC
33974 TGGATCACGGGGGTTGCAACC
1 TGGATCACGGGGGTTGCAACC
33995 CCCTCTCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.38, T:0.19
Consensus pattern (21 bp):
TGGATCACGGGGGTTGCAACC
Found at i:40037 original size:15 final size:15
Alignment explanation
Indices: 40017--40045 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40007 TGTTTTTACA
40017 TTCAATGGATATCCT
1 TTCAATGGATATCCT
40032 TTCAATGGATATCC
1 TTCAATGGATATCC
40046 GTTAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (15 bp):
TTCAATGGATATCCT
Found at i:44662 original size:147 final size:145
Alignment explanation
Indices: 44407--44669 Score: 411
Period size: 147 Copynumber: 1.8 Consensus size: 145
44397 TCTCTTATGG
44407 AGAAACATTGGAAGTTCTTACTTCACACAAAGATTGCTTATGACCTAAGGTGTGTCATGACCTTG
1 AGAAACATTGGAAGTTCTTACTTCACACAAAGATTGCTTATGACCTAAGGTGTGTCATGACCTTG
* * *
44472 ACCCAAAGTCATTTGGGCAAAGTCAAGGTCATTGGCAAAAAAAATGATGCAAATTTGTGTCCGGT
66 ACCCAAAGTCATTTGGGCAAAGGCAAGGTCACTAGCAAAAAAAA--ATGCAAATTTGTGTCCGGT
44537 CCTCTTCATTCTTATAA
129 CCTCTTCATTCTTATAA
*
44554 AGAAACATTGGAAGTTCTTACTTCACACAGAGATTGCTTATGACCTAAGGGTGTGTCATGACCTT
1 AGAAACATTGGAAGTTCTTACTTCACACAAAGATTGCTTATGACCTAA-GGTGTGTCATGACCTT
* * * **
44619 GACTCAAGGTCATTTGGGCAAGGGCAAGGTCACTAGC-TGAAAAAATGCAAA
65 GACCCAAAGTCATTTGGGCAAAGGCAAGGTCACTAGCAAAAAAAAATGCAAA
44670 ATTGGAAGTT
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
145 7 0.07
147 52 0.49
148 47 0.44
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (145 bp):
AGAAACATTGGAAGTTCTTACTTCACACAAAGATTGCTTATGACCTAAGGTGTGTCATGACCTTG
ACCCAAAGTCATTTGGGCAAAGGCAAGGTCACTAGCAAAAAAAAATGCAAATTTGTGTCCGGTCC
TCTTCATTCTTATAA
Found at i:53123 original size:2 final size:2
Alignment explanation
Indices: 53116--53140 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53106 TGATCTACAG
53116 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
53141 AGCTCTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:60285 original size:2 final size:2
Alignment explanation
Indices: 60278--60316 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
60268 ATAATTCCAC
60278 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
60317 ATATGTCTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:67280 original size:12 final size:12
Alignment explanation
Indices: 67236--67285 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
67226 ATCAATCTTA
67236 TTTTTT-TTTAT
1 TTTTTTATTTAT
**
67247 TCATTTATTTAT
1 TTTTTTATTTAT
* *
67259 TTGTTCATTTAT
1 TTTTTTATTTAT
67271 TTTTTTATTT-T
1 TTTTTTATTTAT
67282 TTTT
1 TTTT
67286 ATGAATTGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:76988 original size:177 final size:180
Alignment explanation
Indices: 76691--77076 Score: 591
Period size: 177 Copynumber: 2.2 Consensus size: 180
76681 GTGAAATGGA
* * *
76691 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTTAAAAGCTGGTATTTTTTTCATAAA
1 GTACCCTATATGCAATATTTTGCCAAAAAATGACAAAGTTCAAAAGCTGGTATTTTTTTCAAAAA
** *
76756 TTATTGGAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATTTGCAAAAG
66 TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATCTGCAAAAG
* * *
76821 ATCAA-CT-TA-TCTTGAAAACTGCAGGAGGAGTTATCCATACAATGAGG
131 AACAACCTCCATTCTTGAAAACTGCAAGAGGAGTTATCCATACAATGAGG
76868 GTACCCT-TAATGCAATATTTTGCCAAAAAATGACAAAGTTCAAAAGCTGGTATTTTTTTCAAAA
1 GTACCCTAT-ATGCAATATTTTGCCAAAAAATGACAAAGTTCAAAAGCTGGTATTTTTTTCAAAA
* * * *
76932 ATTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTATAATTGATCTGCAAAG
65 ATTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATCTGCAAAA
* *
76997 GAACAACCTCCATTCTTGAAAACTGTAAGAGGAGTTATCCGTACAATGAGG
130 GAACAACCTCCATTCTTGAAAACTGCAAGAGGAGTTATCCATACAATGAGG
*
77048 GTACCCTATATGGAATATTTTGCCAAAAA
1 GTACCCTATATGCAATATTTTGCCAAAAA
77077 NNNNNNNNNN
Statistics
Matches: 188, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
176 1 0.01
177 122 0.65
178 2 0.01
179 1 0.01
180 61 0.32
181 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (180 bp):
GTACCCTATATGCAATATTTTGCCAAAAAATGACAAAGTTCAAAAGCTGGTATTTTTTTCAAAAA
TTATCAGAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATCTGCAAAAG
AACAACCTCCATTCTTGAAAACTGCAAGAGGAGTTATCCATACAATGAGG
Found at i:81542 original size:2 final size:2
Alignment explanation
Indices: 81535--81588 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
81525 CATCATTTCA
81535 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
81577 TC TC TC TC TC TC
1 TC TC TC TC TC TC
81589 CTTGTTTGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:95481 original size:22 final size:22
Alignment explanation
Indices: 95456--95501 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
95446 TAAAGTGAAG
95456 AACAACTTGTGATTAAAAAAAA
1 AACAACTTGTGATTAAAAAAAA
*
95478 AACAACTTGTGATTACAAAAAA
1 AACAACTTGTGATTAAAAAAAA
95500 AA
1 AA
95502 TAACGTTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.59, C:0.11, G:0.09, T:0.22
Consensus pattern (22 bp):
AACAACTTGTGATTAAAAAAAA
Found at i:99895 original size:15 final size:15
Alignment explanation
Indices: 99875--99904 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
99865 AGTGGGGACT
*
99875 CAGATATCCGGACGC
1 CAGATAACCGGACGC
99890 CAGATAACCGGACGC
1 CAGATAACCGGACGC
99905 TTCAGTTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.27, T:0.10
Consensus pattern (15 bp):
CAGATAACCGGACGC
Found at i:112864 original size:10 final size:10
Alignment explanation
Indices: 112851--112882 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
112841 CAAGAGAGAC
112851 AGAGAGAAAG
1 AGAGAGAAAG
*
112861 AGAGAGACAG
1 AGAGAGAAAG
112871 AGAGAGAAAG
1 AGAGAGAAAG
112881 AG
1 AG
112883 TGTGTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.56, C:0.03, G:0.41, T:0.00
Consensus pattern (10 bp):
AGAGAGAAAG
Found at i:112882 original size:18 final size:17
Alignment explanation
Indices: 112842--112882 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 17
112832 AAATCACAAC
112842 AAGAGAGACAGAGAGAA
1 AAGAGAGACAGAGAGAA
112859 AGAGAGAGACAGAGAGAGA
1 A-AGAGAGACAGAGAGA-A
112878 AAGAG
1 AAGAG
112883 TGTGTGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.05
18 19 0.86
19 2 0.09
ACGTcount: A:0.56, C:0.05, G:0.39, T:0.00
Consensus pattern (17 bp):
AAGAGAGACAGAGAGAA
Found at i:114694 original size:2 final size:2
Alignment explanation
Indices: 114689--114781 Score: 161
Period size: 2 Copynumber: 47.0 Consensus size: 2
114679 ACTTTTTCTA
* *
114689 AG AG AG AG AG AG AG AG AG -G GG AG AG AA AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
114730 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
114772 AG AG AG AG AG
1 AG AG AG AG AG
114782 TTTTAAGAGT
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
1 1 0.01
2 86 0.99
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:119423 original size:17 final size:18
Alignment explanation
Indices: 119398--119451 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
119388 TACAATACGT
119398 ATGATACAATATTATATA
1 ATGATACAATATTATATA
*
119416 AT-ATACAATATTGTATCA
1 ATGATACAATATTATAT-A
* *
119434 TTGTTACAATATTATATA
1 ATGATACAATATTATATA
119452 TTGCAATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 13 0.43
18 5 0.17
19 12 0.40
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (18 bp):
ATGATACAATATTATATA
Found at i:119848 original size:20 final size:20
Alignment explanation
Indices: 119819--119872 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
119809 TTAAATAAAT
* *
119819 AATACAATATCATATTATAC
1 AATACTATATCATAATATAC
*
119839 AATATTATATCATAATATAC
1 AATACTATATCATAATATAC
119859 AATACTATA-CATAA
1 AATACTATATCATAA
119873 CAATATCATG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (20 bp):
AATACTATATCATAATATAC
Found at i:119908 original size:28 final size:28
Alignment explanation
Indices: 119855--119908 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
119845 ATATCATAAT
*
119855 ATACAATACTATACATAACAATATCATG
1 ATACAATACTATACATAACAACATCATG
119883 ATACAATA-TCATATCATAA-AACATCA
1 ATACAATACT-ATA-CATAACAACATCA
119909 AAAAAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 1 0.04
28 17 0.74
29 5 0.22
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.28
Consensus pattern (28 bp):
ATACAATACTATACATAACAACATCATG
Found at i:120995 original size:167 final size:167
Alignment explanation
Indices: 120500--121198 Score: 714
Period size: 167 Copynumber: 4.1 Consensus size: 167
120490 CTTTACCTTA
* * * *
120500 TCCAGCATCTGAAACCTAT-GTCTCAGATTCAGCATTCAAGCCTGTCAGGTGCGTCAGTATCATA
1 TCCAGCATCTAAAACCCATAG-CTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATA
* *** * * * ***
120564 AGACACACCATCCATGCAAGTTTGGTGAAGTTAG-GAC-AAG-TAATACCAGTAACTAAGATATC
65 AGACACACCAACCATGCAAGTTTGGACCAG-TAGTTACTAAGAT-ATA--A-TCA-TCAGAGGGC
120626 ACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
124 ACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
* * *
120670 TCCAGCATCT-AAACCTATAGCTCAAATTCAGCATTCAAGCCTGTCTGGTGCATCAATATCATAA
1 TCCAGCATCTAAAACCCATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
** * *
120734 -ATGCACAATCTGTGCAAGTTTGATG-AAGTTTTGACCAGTAGTAACTAAGATATAATCATCAGA
66 GA--CAC-A-C----CAA---CCATGCAAGTTTGGACCAGTAGTTACTAAGATATAATCATCAGA
120797 GGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
120 GGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
*
120845 TCCAGCATCTAAAACCCATAGCTCAGATTCAGCATTCAAGCCTGTCTGATGCATCAGTATCATAA
1 TCCAGCATCTAAAACCCATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
*
120910 GACACACCAACCATGCAAGTTTGGACCAGTAGTTACTTAGATATAATCATCAGAGGGCACCTGCA
66 GACACACCAACCATGCAAGTTTGGACCAGTAGTTACTAAGATATAATCATCAGAGGGCACCTGCA
120975 ACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
131 ACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
* * * * * *
121012 TCCAGCATCCAAAACCCATAGCTCAGATTTAGCATTTAAACCTGTCTTGTGCATCGGTATCATAA
1 TCCAGCATCTAAAACCCATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
* * * ** *
121077 GACACACCATCCGTGCAAGTTTGGTGAAGTTTTGACCAGCAGTTACTTGGATAT--TGCTATCAA
66 GACACACCAACCATGCAAG-TT--T---G----GACCAGTAGTTACTAAGATATAAT-C-ATCAG
* * *
121140 AGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTCAACCTCC
119 AGGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
*
121189 CCCAGCATCT
1 TCCAGCATCT
121199 GAAATTTAGG
Statistics
Matches: 456, Mismatches: 43, Indels: 53
0.83 0.08 0.10
Matches are distributed among these distances:
166 3 0.01
167 158 0.35
168 3 0.01
169 51 0.11
170 15 0.03
171 1 0.00
172 1 0.00
173 2 0.00
174 1 0.00
175 63 0.14
176 55 0.12
177 82 0.18
178 11 0.02
179 9 0.02
180 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (167 bp):
TCCAGCATCTAAAACCCATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
GACACACCAACCATGCAAGTTTGGACCAGTAGTTACTAAGATATAATCATCAGAGGGCACCTGCA
ACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
Found at i:121196 original size:344 final size:343
Alignment explanation
Indices: 120501--121198 Score: 906
Period size: 344 Copynumber: 2.0 Consensus size: 343
120491 TTTACCTTAT
* * * *
120501 CCAGCATCTGAAACCTATGTCTCAGATTCAGCATTCAAGCCTGTCAGGTGCGTCAGTATCATAAG
1 CCAGCATCTAAAACCCATGTCTCAGATTCAGCATTCAAGCCTGTCAGATGCATCAGTATCATAAG
* ** * *
120566 ACACACCATCCATGCAAGTTTGGTGAAGTTAGGACAAGTAATACCAGTAACTAAGATATCACCTG
66 ACACACCAACCATGCAAGTTTGGACAAGTTAGGACAAGTAATA-CAGTAACTAAGAGAGCACCTG
* *
120631 CAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCCAGCATCTAAACCTATAGCTCAAA
130 CAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCCAGCATCAAAACCCATAGCTCAAA
* ** *
120696 TTCAGCATTCAAGCCTGTCTGGTGCATCAATATCATAAATGCACAATCTGTGCAAGTTTGATGAA
195 TTCAGCATTCAAACCTGTCTGGTGCATCAATATCATAAACACACAATCCGTGCAAGTTTGATGAA
* *
120761 GTTTTGACCAGTAGTAACTAAGATATAATCATCAGAGGGCACCTGCAACAAAAACTTTAACCAGC
260 GTTTTGACCAGCAGTAACTAAGATAT-ATCATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC
* * *
120826 TCTAAAAACCTTAACCTCCT
324 TCCAAAAACCTCAACCTCCC
*
120846 CCAGCATCTAAAACCCATAG-CTCAGATTCAGCATTCAAGCCTGTCTGATGCATCAGTATCATAA
1 CCAGCATCTAAAACCCAT-GTCTCAGATTCAGCATTCAAGCCTGTCAGATGCATCAGTATCATAA
* * * * * *
120910 GACACACCAACCATGCAAGTTTGGACCAG-TAGTTACTTAG-ATATA-A-TCA-TCAGAGGGCAC
65 GACACACCAACCATGCAAGTTTGGACAAGTTAG-GAC-AAGTA-ATACAGTAACTAAGAGAGCAC
120970 CTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCCAGCATCCAAAACCCATAGCT
127 CTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCCAGCAT-CAAAACCCATAGCT
* * * * ** *
121035 CAGATTTAGCATTTAAACCTGTCTTGTGCATCGGTATCATAAGACACACCATCCGTGCAAGTTTG
191 CAAATTCAGCATTCAAACCTGTCTGGTGCATCAATATCATAA-ACACACAATCCGTGCAAGTTTG
* * **
121100 GTGAAGTTTTGACCAGCAGTTACTTGGATAT-TGCTATCAAAGGGCACCTGCAACAAAAACTTTA
255 ATGAAGTTTTGACCAGCAGTAACTAAGATATAT-C-ATCAAAGGGCACCTGCAACAAAAACTTTA
*
121164 ACCTGCTCCAAAAACCTCAACCTCCC
318 ACCAGCTCCAAAAACCTCAACCTCCC
121190 CCAGCATCT
1 CCAGCATCT
121199 GAAATTTAGG
Statistics
Matches: 306, Mismatches: 39, Indels: 17
0.85 0.11 0.05
Matches are distributed among these distances:
342 58 0.19
343 50 0.16
344 107 0.35
345 85 0.28
346 6 0.02
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.25
Consensus pattern (343 bp):
CCAGCATCTAAAACCCATGTCTCAGATTCAGCATTCAAGCCTGTCAGATGCATCAGTATCATAAG
ACACACCAACCATGCAAGTTTGGACAAGTTAGGACAAGTAATACAGTAACTAAGAGAGCACCTGC
AACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCCAGCATCAAAACCCATAGCTCAAAT
TCAGCATTCAAACCTGTCTGGTGCATCAATATCATAAACACACAATCCGTGCAAGTTTGATGAAG
TTTTGACCAGCAGTAACTAAGATATATCATCAAAGGGCACCTGCAACAAAAACTTTAACCAGCTC
CAAAAACCTCAACCTCCC
Found at i:126424 original size:20 final size:21
Alignment explanation
Indices: 126399--126487 Score: 128
Period size: 21 Copynumber: 4.3 Consensus size: 21
126389 TTAACATATA
* *
126399 TTCAAAT-ATTTGTACCAATC
1 TTCAAATCAATTGTACCTATC
126419 TTCAAAT-AATTGTACCTATC
1 TTCAAATCAATTGTACCTATC
*
126439 TTCAATTCAATTGTACCTATC
1 TTCAAATCAATTGTACCTATC
*
126460 TTCAATTCAATTGTACCTATC
1 TTCAAATCAATTGTACCTATC
126481 TTCAAAT
1 TTCAAAT
126488 TGAATTAGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
20 24 0.38
21 40 0.62
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (21 bp):
TTCAAATCAATTGTACCTATC
Found at i:126452 original size:21 final size:21
Alignment explanation
Indices: 126408--126485 Score: 131
Period size: 21 Copynumber: 3.8 Consensus size: 21
126398 ATTCAAATAT
* *
126408 TTGTACCAATCTTCAAAT-AA
1 TTGTACCTATCTTCAATTCAA
126428 TTGTACCTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
126449 TTGTACCTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
126470 TTGTACCTATCTTCAA
1 TTGTACCTATCTTCAA
126486 ATTGAATTAG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
20 16 0.29
21 39 0.71
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (21 bp):
TTGTACCTATCTTCAATTCAA
Found at i:126620 original size:21 final size:21
Alignment explanation
Indices: 126534--126627 Score: 116
Period size: 21 Copynumber: 4.2 Consensus size: 21
126524 TTTAATTCAT
* *
126534 TTGAAGATATGTACAATTGAT
1 TTGAAGATAGGTACAATTGAA
126555 TTGAAGATAGGTACAAATGCAATGAA
1 TTGAAGATAGGTAC-AAT----TGAA
126581 TTGAAGATAGGTACAATTGAA
1 TTGAAGATAGGTACAATTGAA
*
126602 TTAAAGATAGGTACAATTGAA
1 TTGAAGATAGGTACAATTGAA
126623 TTGAA
1 TTGAA
126628 CCTATCTTCA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
21 41 0.64
22 3 0.05
25 3 0.05
26 17 0.27
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (21 bp):
TTGAAGATAGGTACAATTGAA
Found at i:127566 original size:21 final size:21
Alignment explanation
Indices: 127534--127602 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
127524 TAGATATGTC
*
127534 TGAATTGAACCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
* *
127555 TCAATTGTACCTATCTTTAAA
1 TGAATTGTACCTATCTTCAAA
*
127576 TGAATTTTACCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
127597 TGAATT
1 TGAATT
127603 AGAGATAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
TGAATTGTACCTATCTTCAAA
Found at i:127630 original size:42 final size:42
Alignment explanation
Indices: 127584--127719 Score: 129
Period size: 42 Copynumber: 3.3 Consensus size: 42
127574 AATGAATTTT
127584 ACCTATCTTCAAATGAATTAGAGATAGGTATAATTCAATTGA
1 ACCTATCTTCAAATGAATTAGAGATAGGTATAATTCAATTGA
* * * *
127626 ACCTATCTTTAATTGAATT-GAAGATAGGTATAATTCATTTGT
1 ACCTATCTTCAAATGAATTAG-AGATAGGTATAATTCAATTGA
** * * *
127668 ACCTA-GGT-ATAATTATTTAGAGATAGGTATAATT--ATTTA
1 ACCTATCTTCA-AATGAATTAGAGATAGGTATAATTCAATTGA
127707 CACCTATCTTCAA
1 -ACCTATCTTCAA
127720 TTCAATTGTA
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
39 2 0.03
40 6 0.08
41 23 0.31
42 43 0.58
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (42 bp):
ACCTATCTTCAAATGAATTAGAGATAGGTATAATTCAATTGA
Found at i:127659 original size:21 final size:21
Alignment explanation
Indices: 127605--127701 Score: 72
Period size: 21 Copynumber: 4.7 Consensus size: 21
127595 AATGAATTAG
127605 AGATAGGTATAATTCAATTGA
1 AGATAGGTATAATTCAATTGA
** ** * *
127626 ACCTATCTTTAATTGAATTGA
1 AGATAGGTATAATTCAATTGA
* *
127647 AGATAGGTATAATTCATTTGT
1 AGATAGGTATAATTCAATTGA
** *
127668 ACCTAGGTATAATT--ATTTA
1 AGATAGGTATAATTCAATTGA
127687 GAGATAGGTATAATT
1 -AGATAGGTATAATT
127702 ATTTACACCT
Statistics
Matches: 54, Mismatches: 21, Indels: 3
0.69 0.27 0.04
Matches are distributed among these distances:
19 2 0.04
20 12 0.22
21 40 0.74
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.39
Consensus pattern (21 bp):
AGATAGGTATAATTCAATTGA
Found at i:127694 original size:20 final size:21
Alignment explanation
Indices: 127647--127706 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
127637 ATTGAATTGA
127647 AGATAGGTATAATTCATTT-GT
1 AGATAGGTATAATT-ATTTAGT
**
127668 ACCTAGGTATAATTATTTAG-
1 AGATAGGTATAATTATTTAGT
127688 AGATAGGTATAATTATTTA
1 AGATAGGTATAATTATTTA
127707 CACCTATCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 21 0.62
21 13 0.38
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.42
Consensus pattern (21 bp):
AGATAGGTATAATTATTTAGT
Found at i:127732 original size:21 final size:21
Alignment explanation
Indices: 127708--127782 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
127698 AATTATTTAC
127708 ACCTATCTTCAATTCAATTGT
1 ACCTATCTTCAATTCAATTGT
*
127729 ACCTATCTTTAATTCAATTGT
1 ACCTATCTTCAATTCAATTGT
* * *
127750 ATCTATCTTTAATTTAATTGT
1 ACCTATCTTCAATTCAATTGT
127771 ACCTATCTTCAA
1 ACCTATCTTCAA
127783 ATGATTTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (21 bp):
ACCTATCTTCAATTCAATTGT
Found at i:127848 original size:20 final size:20
Alignment explanation
Indices: 127780--127852 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
127770 TACCTATCTT
127780 CAAATGATTTGAAGATAGGTA
1 CAAAT-ATTTGAAGATAGGTA
* *
127801 CAATTAATTGAAGATAGGTA
1 CAAATATTTGAAGATAGGTA
*
127821 CAATTATTTGAAGATAGGTA
1 CAAATATTTGAAGATAGGTA
127841 CAAATATTTGAA
1 CAAATATTTGAA
127853 TATATGTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
20 44 0.92
21 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (20 bp):
CAAATATTTGAAGATAGGTA
Found at i:131212 original size:4 final size:4
Alignment explanation
Indices: 131203--131245 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
131193 GTTTCACCCT
* *
131203 GTCC GTCC GTCC GTCT GTCC GTCC GTCC GTCC GTCT GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
131246 TCTCCGTCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.44, G:0.26, T:0.30
Consensus pattern (4 bp):
GTCC
Found at i:131246 original size:8 final size:8
Alignment explanation
Indices: 131201--131265 Score: 67
Period size: 8 Copynumber: 7.6 Consensus size: 8
131191 TGGTTTCACC
131201 CTGTCCGT
1 CTGTCCGT
*
131209 CCGTCCGT
1 CTGTCCGT
131217 CTGTCCGT
1 CTGTCCGT
131225 CCGTCCGTCCGT
1 -C-T--GTCCGT
131237 CTGTCCGT
1 CTGTCCGT
*
131245 CTCTCCGT
1 CTGTCCGT
*
131253 CTCTCCGT
1 CTGTCCGT
131261 CTGTC
1 CTGTC
131266 TGTATACGCA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
8 39 0.80
9 1 0.02
10 2 0.04
11 1 0.02
12 6 0.12
ACGTcount: A:0.00, C:0.45, G:0.22, T:0.34
Consensus pattern (8 bp):
CTGTCCGT
Found at i:131251 original size:16 final size:17
Alignment explanation
Indices: 131201--131262 Score: 74
Period size: 16 Copynumber: 3.6 Consensus size: 17
131191 TGGTTTCACC
131201 CTGTCCGTC-CGTCCGT
1 CTGTCCGTCTCGTCCGT
131217 CTGTCCGTCCGTCCGTCCGT
1 CTGTCCGT-C-T-CGTCCGT
131237 CTGTCCGTCTC-TCCGT
1 CTGTCCGTCTCGTCCGT
*
131253 CTCTCCGTCT
1 CTGTCCGTCT
131263 GTCTGTATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 22 0.54
17 2 0.05
18 1 0.02
19 1 0.02
20 15 0.37
ACGTcount: A:0.00, C:0.45, G:0.21, T:0.34
Consensus pattern (17 bp):
CTGTCCGTCTCGTCCGT
Found at i:138282 original size:4 final size:4
Alignment explanation
Indices: 138275--138324 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
138265 CTGTCTATCT
* * * * *
138275 GTCC GTCC GTCT GTCT GTCC GTCC GTCT GTCC GTCT GTCT GTCC GTCC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
138323 GT
1 GT
138325 AACAAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36
Consensus pattern (4 bp):
GTCC
Found at i:138287 original size:12 final size:12
Alignment explanation
Indices: 138279--138324 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
138269 CTATCTGTCC
*
138279 GTCCGTCTGTCT
1 GTCCGTCCGTCT
138291 GTCCGTCCGTCT
1 GTCCGTCCGTCT
*
138303 GTCCGTCTGTCT
1 GTCCGTCCGTCT
138315 GTCCGTCCGT
1 GTCCGTCCGT
138325 AACAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (12 bp):
GTCCGTCCGTCT
Found at i:138318 original size:24 final size:24
Alignment explanation
Indices: 138279--138324 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
138269 CTATCTGTCC
138279 GTCCGTCTGTCTGTCCGTCCGTCT
1 GTCCGTCTGTCTGTCCGTCCGTCT
138303 GTCCGTCTGTCTGTCCGTCCGT
1 GTCCGTCTGTCTGTCCGTCCGT
138325 AACAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (24 bp):
GTCCGTCTGTCTGTCCGTCCGTCT
Found at i:138324 original size:16 final size:16
Alignment explanation
Indices: 138267--138305 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
138257 TTGTGTGTCT
*
138267 GTCTATCTGTCCGTCC
1 GTCTGTCTGTCCGTCC
138283 GTCTGTCTGTCCGTCC
1 GTCTGTCTGTCCGTCC
138299 GTCTGTC
1 GTCTGTC
138306 CGTCTGTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.03, C:0.36, G:0.23, T:0.38
Consensus pattern (16 bp):
GTCTGTCTGTCCGTCC
Found at i:138730 original size:166 final size:166
Alignment explanation
Indices: 138348--139132 Score: 997
Period size: 158 Copynumber: 4.8 Consensus size: 166
138338 GTCGCATTTA
* * * *
138348 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
* * * * *
138413 CGTGGGATATTTTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
66 TGTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGTTAAATGACGACTTTGTTTA-ATT
* * *
138478 TTAACTAAAATATTCAAACAAATTTTCT-TCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTT-TGTCAAAGATT
** *
138515 TCTCAGCAGTTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTTGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
*
138580 TGTGGGATATATTTTTGTACCAATCAGATGTCAACTTCCTGTTAAATGACGACTTTGTTTAATTT
66 TGTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGTTAAATGACGACTTTGTTTAATTT
* *
138645 TAGCAAAAATTTTCAAACAAATTTTTGTCAAAGAAT
131 TAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATT
* * * * **
138681 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAAGCATGCTTTAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
* * *
138746 CGTGGG----A----TGTACCAATTGGATGTCAACTTCCTGTGT-AATGA-GTACTTTGTTTATT
66 TGTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGT-TAAATGACG-ACTTTGTTTAAT
*
138801 TTTAGCCAAAATTTTCAAACAAATTTCTGTCAAAGATT
129 TTTAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATT
* * * * * *
138839 TCTCAGTAACTTTTTATTGCAGATGCTTGAAATTTTAACACACTATTTGTTTTGGTATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
*
138904 TGTGGGATATATTTTTGTACCAATCAGATGTCAACTTCCTGTTAAATGA-GTACTTTGTTT-ATT
66 TGTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGTTAAATGACG-ACTTTGTTTAATT
* **
138967 TTAGCCAAAATTTTCAAACCAA-TTTCCTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATT
* *
139003 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
* * * * * * *
139068 TGTGAGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTT-ATTT
66 TGTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGTTAAATGACGACTTTGTTTAATTT
139132 T
131 T
139133 GCATATTCAC
Statistics
Matches: 539, Mismatches: 66, Indels: 29
0.85 0.10 0.05
Matches are distributed among these distances:
157 1 0.00
158 135 0.25
159 1 0.00
162 2 0.00
164 125 0.23
165 26 0.05
166 135 0.25
167 114 0.21
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT
TGTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGTTAAATGACGACTTTGTTTAATTT
TAGCCAAAATTTTCAAACAAATTTTTGTCAAAGATT
Found at i:138946 original size:324 final size:324
Alignment explanation
Indices: 138348--139132 Score: 1037
Period size: 324 Copynumber: 2.4 Consensus size: 324
138338 GTCGCATTTA
*
138348 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTAA-GCATGCCATAT
138413 CGTGGGATATTTTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
65 CGTGGGA-A-----TTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* * *
138478 TTAACTAAAATATTCAAACAAATTTTCTTCAAAGATTTCTCAGCAGTTATTTATCGCAGATGCTT
124 TTAACCAAAATATTCAAACAAATTTTCTTCAAAGATTTCTCAGAACTTATTTATCGCAGATGCTT
*
138543 GAAATTTTTACACACTATTTGTTTTGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGA
189 GAAATTTTAACACACTATTTGTTTTGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGA
**
138608 TGTCAACTTCCTGTTAAATGACG-ACTTTGTTTAATTTTAGCAAAAATTTTCAAACAAATTTTTG
254 TGTCAACTTCCTGTTAAATGA-GTACTTTGTTT-ATTTTAGCAAAAATTTTCAAACAAA-TTTCC
138672 TCAAAGAAT
316 TCAAAGAAT
**
138681 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAAGCATGCTTTAT
1 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGT-TAAGCATGCCATAT
* * * *
138746 CGTGGG-A-TGTACCAATTGGATGTCAACTTCCTGTGT-AATGA-GTACTTTGTTTA-TTTTTAG
65 CGTGGGAATTGTACCAATCGGACGTCAACTTCCTGT-TAAATGACG-ACTTTGCTTATTTTTTAA
* *
138806 CCAAAATTTTCAAACAAA-TTTCTGTCAAAGATTTCTCAGTAACTT-TTTATTGCAGATGCTTGA
128 CCAAAATATTCAAACAAATTTTCT-TCAAAGATTTCTCAG-AACTTATTTATCGCAGATGCTTGA
*
138869 AATTTTAACACACTATTTGTTTTGGTATGCCATATTGTGGGATATATTTTTGTACCAATCAGATG
191 AATTTTAACACACTATTTGTTTTGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGATG
* *
138934 TCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCCAAAATTTTCAAACCAATTTCCTCAAA
256 TCAACTTCCTGTTAAATGAGTACTTTGTTTATTTTAGCAAAAATTTTCAAACAAATTTCCTCAAA
*
138999 GATT
321 GAAT
* * * * *
139003 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTG-TTAAGCATGCCATAT
* * * * * * *
139068 TGTGAGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
65 CGTG-G-GA-A--T-TGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
139133 GCATATTCAC
Statistics
Matches: 400, Mismatches: 34, Indels: 38
0.85 0.07 0.08
Matches are distributed among these distances:
322 70 0.17
323 31 0.08
324 146 0.37
325 42 0.10
326 2 0.00
329 1 0.00
330 36 0.09
331 5 0.01
333 64 0.16
334 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (324 bp):
TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTTAAGCATGCCATATC
GTGGGAATTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTTTTAACCA
AAATATTCAAACAAATTTTCTTCAAAGATTTCTCAGAACTTATTTATCGCAGATGCTTGAAATTT
TAACACACTATTTGTTTTGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGATGTCAAC
TTCCTGTTAAATGAGTACTTTGTTTATTTTAGCAAAAATTTTCAAACAAATTTCCTCAAAGAAT
Found at i:158806 original size:2 final size:2
Alignment explanation
Indices: 158799--158834 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
158789 TCAAAAATAT
158799 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
158835 TTCATAGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:182934 original size:15 final size:15
Alignment explanation
Indices: 182905--182954 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
182895 AACTACAGGT
*
182905 AACTCTCGATGGCTCG
1 AACT-TCGATCGCTCG
182921 AACTTCGATCGCTCG
1 AACTTCGATCGCTCG
*
182936 AAGTTCTTGATCGCTCG
1 AACTTC--GATCGCTCG
182953 AA
1 AA
182955 GTGAGTCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 15 0.50
16 4 0.13
17 11 0.37
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (15 bp):
AACTTCGATCGCTCG
Found at i:183023 original size:16 final size:16
Alignment explanation
Indices: 183002--183051 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
182992 AAGCAAATTT
*
183002 ACTCTTGATTTCTCGA
1 ACTCTTGATCTCTCGA
183018 ACTCTTGATCTCTCGAA
1 ACTCTTGATCTCTCG-A
* *
183035 ACCCTTGATCCCTCGA
1 ACTCTTGATCTCTCGA
183051 A
1 A
183052 GTCAAACTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (16 bp):
ACTCTTGATCTCTCGA
Found at i:183043 original size:17 final size:17
Alignment explanation
Indices: 183005--183051 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
182995 CAAATTTACT
* *
183005 CTTGATTTCTCG-AACT
1 CTTGATCTCTCGAAACC
183021 CTTGATCTCTCGAAACC
1 CTTGATCTCTCGAAACC
*
183038 CTTGATCCCTCGAA
1 CTTGATCTCTCGAA
183052 GTCAAACTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (17 bp):
CTTGATCTCTCGAAACC
Found at i:183786 original size:16 final size:16
Alignment explanation
Indices: 183753--183788 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
183743 CGGAAAATTC
*
183753 CGAACTCTTGAAATCT
1 CGAACTCTTGAAACCT
*
183769 CGAACTCTTGATACCT
1 CGAACTCTTGAAACCT
183785 CGAA
1 CGAA
183789 GTTTTTCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (16 bp):
CGAACTCTTGAAACCT
Found at i:188438 original size:16 final size:16
Alignment explanation
Indices: 188417--188448 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
188407 CACGAATGCT
188417 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
188433 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
188449 ATTTATAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.25, T:0.06
Consensus pattern (16 bp):
GGAGAAAACGTACCCA
Found at i:188494 original size:31 final size:31
Alignment explanation
Indices: 188456--188517 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
188446 CCAATTTATA
*
188456 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCAAGAGAAAACGTACCC
188487 GGGTACGTTTTCTCCAAGAGAAAACGTACCC
1 GGGTACGTTTTCTCCAAGAGAAAACGTACCC
188518 TATGGAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (31 bp):
GGGTACGTTTTCTCCAAGAGAAAACGTACCC
Found at i:189439 original size:31 final size:31
Alignment explanation
Indices: 189401--189462 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
189391 GATTTTCATA
189401 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
*
189432 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
189463 TGGAGATTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (31 bp):
GGGTACGTTTTCTCCAGGAGAAAACGTACCC
Found at i:189489 original size:16 final size:16
Alignment explanation
Indices: 189470--189503 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
189460 CCCTGGAGAT
189470 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
189486 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
189502 TG
1 TG
189504 ATACCAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.24, G:0.26, T:0.44
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:191670 original size:3 final size:3
Alignment explanation
Indices: 191662--191706 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
191652 AATCTGAAAC
191662 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
191707 CGTTCCAGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:201772 original size:8 final size:8
Alignment explanation
Indices: 201758--201803 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
201748 CCCCCCCCAA
201758 AAAAAAAC
1 AAAAAAAC
201766 AACAAAAAAC
1 -A-AAAAAAC
201776 AAAAAAAC
1 AAAAAAAC
*
201784 AAAACAAC
1 AAAAAAAC
201792 AAAAAAAC
1 AAAAAAAC
201800 AAAA
1 AAAA
201804 GCAAAACAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
8 25 0.74
9 2 0.06
10 7 0.21
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:201782 original size:23 final size:24
Alignment explanation
Indices: 201756--201803 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
201746 CCCCCCCCCC
201756 AAAAAAAAACAAC-AAAAAACAAA
1 AAAAAAAAACAACAAAAAAACAAA
*
201779 AAAACAAAACAACAAAAAAACAAA
1 AAAAAAAAACAACAAAAAAACAAA
201803 A
1 A
201804 GCAAAACAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (24 bp):
AAAAAAAAACAACAAAAAAACAAA
Found at i:201792 original size:16 final size:16
Alignment explanation
Indices: 201760--201821 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
201750 CCCCCCAAAA
201760 AAAAACAACAAAA-AAC
1 AAAAA-AACAAAACAAC
201776 AAAAAAACAAAACAAC
1 AAAAAAACAAAACAAC
201792 AAAAAAACAAAAGCAA-
1 AAAAAAACAAAA-CAAC
* *
201808 AACAAGACAAAACA
1 AAAAAAACAAAACA
201822 GAGTCAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
15 9 0.21
16 30 0.71
17 3 0.07
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAACAAC
Found at i:201809 original size:11 final size:10
Alignment explanation
Indices: 201755--201821 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 10
201745 CCCCCCCCCC
*
201755 CAAAAAAAAA
1 CAAAACAAAA
201765 CAACAA-AAAA
1 CAA-AACAAAA
201775 C-AAA-AAAA
1 CAAAACAAAA
201783 CAAAACAACAA
1 CAAAACAA-AA
*
201794 AAAAACAAAA
1 CAAAACAAAA
*
201804 GCAAAACAAGA
1 -CAAAACAAAA
201815 CAAAACA
1 CAAAACA
201822 GAGTCAAACT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
8 7 0.14
9 4 0.08
10 19 0.39
11 19 0.39
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (10 bp):
CAAAACAAAA
Found at i:201819 original size:22 final size:22
Alignment explanation
Indices: 201755--201812 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
201745 CCCCCCCCCC
201755 CAAAAA-AAAACAACAAAAAACA
1 CAAAAACAAAACAACAAAAAA-A
*
201777 AAAAAACAAAACAACAAAAAAA
1 CAAAAACAAAACAACAAAAAAA
*
201799 CAAAAGCAAAACAA
1 CAAAAACAAAACAA
201813 GACAAAACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (22 bp):
CAAAAACAAAACAACAAAAAAA
Found at i:206904 original size:2 final size:2
Alignment explanation
Indices: 206897--206934 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
206887 TTTGAAGAGG
206897 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
206935 CACTTTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:208526 original size:2 final size:2
Alignment explanation
Indices: 208519--208559 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
208509 CTGTACTTTA
208519 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
208560 AAAATACCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:216306 original size:18 final size:19
Alignment explanation
Indices: 216267--216314 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
216257 TGATCACAAT
*
216267 TTGTCCGTTGTCTGTCGTCG
1 TTGT-CGTTGTCTGTCGGCG
216287 TTGTCGTTGTC-GTCGGCG
1 TTGTCGTTGTCTGTCGGCG
*
216305 TTGGCGTTGT
1 TTGTCGTTGT
216315 AAACTTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 15 0.58
19 7 0.27
20 4 0.15
ACGTcount: A:0.00, C:0.21, G:0.35, T:0.44
Consensus pattern (19 bp):
TTGTCGTTGTCTGTCGGCG
Found at i:224753 original size:2 final size:2
Alignment explanation
Indices: 224746--224781 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
224736 GTGGTATAAT
224746 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
224782 CAGACAGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:224786 original size:4 final size:4
Alignment explanation
Indices: 224779--224819 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
224769 AGAGAGAGAG
224779 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC A
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC A
224820 AAGAGAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.24, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:225695 original size:19 final size:20
Alignment explanation
Indices: 225671--225716 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
225661 GGGTTTTAGA
225671 GCCTTTT-TCACGTAATTAC
1 GCCTTTTCTCACGTAATTAC
**
225690 GCCTTTTCTCGTGTAATTAC
1 GCCTTTTCTCACGTAATTAC
*
225710 GACTTTT
1 GCCTTTT
225717 ATTTTATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.46
Consensus pattern (20 bp):
GCCTTTTCTCACGTAATTAC
Found at i:233607 original size:13 final size:13
Alignment explanation
Indices: 233589--233613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
233579 GGCTGAAGCT
233589 AGCAGCCACTAAC
1 AGCAGCCACTAAC
233602 AGCAGCCACTAA
1 AGCAGCCACTAA
233614 GACCGTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.36, G:0.16, T:0.08
Consensus pattern (13 bp):
AGCAGCCACTAAC
Found at i:234854 original size:326 final size:326
Alignment explanation
Indices: 234261--235259 Score: 1962
Period size: 326 Copynumber: 3.1 Consensus size: 326
234251 AAGGGTCGGT
*
234261 TTAGCTCACGCGAACTTTGTCCTATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
1 TTAGCTCACGCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
234326 TTATCTCTTTTATCTTTGAAGTGTGCATTAAACGGATACCAGGGCAGTGTAGGGGACCTATGGAG
66 TTATCTCTTTTATCTTTGAAGTGTGCATTAAACGGATACCAGGGCAGTGTAGGGGACCTATGGAG
* *
234391 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGGGGTACCACCAAGTGGCTCCCAGGGGTTCTGG
131 CTATTATTTCCCGGTCTCAAATTGGGGCTGTAGGGGTACCACCAAGTGGCTCCCAGGGGTTCTGA
234456 CTCATTTCAGGGGTCTATATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAAGATTAGG
196 CTCATTTCAGGGGTCTATATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAAGATTAGG
234521 TAGAGGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGTACCTATGACCCCTGCAAGGGTTCA
261 TAGAGGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGTACCTATGACCCCTGCAAGGGTTCA
234586 G
326 G
234587 TTAGCTCACGCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
1 TTAGCTCACGCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
*
234652 TTATCTCTTTTATCTATGAAGTGTGCATTAAACGGATACCAGGGCAGTGTAGGGGACCTATGGAG
66 TTATCTCTTTTATCTTTGAAGTGTGCATTAAACGGATACCAGGGCAGTGTAGGGGACCTATGGAG
234717 CTATTATTTCCCGGTCTCAAATTGGGGCTGTAGGGGTACCACCAAGTGGCTCCCAGGGGTTCTGA
131 CTATTATTTCCCGGTCTCAAATTGGGGCTGTAGGGGTACCACCAAGTGGCTCCCAGGGGTTCTGA
234782 CTCATTTCAGGGGTCTATATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAAGATTAGG
196 CTCATTTCAGGGGTCTATATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAAGATTAGG
234847 TAGAGGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGTACCTATGACCCCTGCAAGGGTTCA
261 TAGAGGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGTACCTATGACCCCTGCAAGGGTTCA
234912 G
326 G
234913 TTAGCTCACGCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
1 TTAGCTCACGCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
234978 TTATCTCTTTTATCTTTGAAGTGTGCATTAAACGGATACCAGGGCAGTGTAGGGGACCTATGGAG
66 TTATCTCTTTTATCTTTGAAGTGTGCATTAAACGGATACCAGGGCAGTGTAGGGGACCTATGGAG
235043 CTATTATTTCCCGGTCTCAAATTGGGGCTGTAGGGGTACCACCAAGTGGCTCCCAGGGGTTCTGA
131 CTATTATTTCCCGGTCTCAAATTGGGGCTGTAGGGGTACCACCAAGTGGCTCCCAGGGGTTCTGA
235108 CTCATTTCAGGGGTCTATATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAAGATTAGG
196 CTCATTTCAGGGGTCTATATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAAGATTAGG
235173 TAGAGGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGTACCTATGACCCCTGCAAGGGTTCA
261 TAGAGGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGTACCTATGACCCCTGCAAGGGTTCA
235238 G
326 G
235239 TTAGCTCACGCGAACTTTGTC
1 TTAGCTCACGCGAACTTTGTC
235260 NNNNNNNNNN
Statistics
Matches: 668, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
326 668 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (326 bp):
TTAGCTCACGCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
TTATCTCTTTTATCTTTGAAGTGTGCATTAAACGGATACCAGGGCAGTGTAGGGGACCTATGGAG
CTATTATTTCCCGGTCTCAAATTGGGGCTGTAGGGGTACCACCAAGTGGCTCCCAGGGGTTCTGA
CTCATTTCAGGGGTCTATATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAAGATTAGG
TAGAGGACCTCAAGAGGTATTCATAATAAGCATTAGAGGGTACCTATGACCCCTGCAAGGGTTCA
G
Found at i:240668 original size:312 final size:312
Alignment explanation
Indices: 240103--240840 Score: 1244
Period size: 312 Copynumber: 2.4 Consensus size: 312
240093 NNNNNNNNNN
240103 CCCTGTTATTCGTTTGATGCACACTTCAAAGATAAGGAAGATAATGGACCACTTTTAACCCCTAT
1 CCCTGTTATTCGTTTGATGCACACTTCAAAGATAAGGAAGATAATGGACCACTTTTAACCCCTAT
240168 ATCATTGTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACCGAACCCTTGTAGGGGTCAT
66 ATCATTGTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACCGAACCCTTGTAGGGGTCAT
240233 AGGTGCCCTCTATCGCTTATAAGACCCTCTACCTAATCCTAGTGTTATCAAGTTCTTGTGGTCAA
131 AGGTGCCCTCTATCGCTTATAAGACCCTCTACCTAATCCTAGTGTTATCAAGTTCTTGTGGTCAA
240298 TCTCAAGTGAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCCACTTGGTGGTACCCCT
196 TCTCAAGTGAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCCACTTGGTGGTACCCCT
* * *
240363 ACAGCCCAAATCTGAGACCGGGAAATAATAGCCCCATATGCCCCCTACACTA
261 ACAGCCCAAATCTGAGACCGGGAAAAAATAGCCCCATAGGCCCCATACACTA
240415 CCCTGTTATTCGTTTGATGCACACTTCAAAGATAAGGAAGATAATGGACCACTTTTAACCCCTAT
1 CCCTGTTATTCGTTTGATGCACACTTCAAAGATAAGGAAGATAATGGACCACTTTTAACCCCTAT
240480 ATCATTGTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACCGAACCCTTGTAGGGGTCAT
66 ATCATTGTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACCGAACCCTTGTAGGGGTCAT
240545 AGGTGCCCTCTATCGCTTATAAGACCCTCTACCTAATCCTAGTGTTATCAAGTTCTTGTGGTCAA
131 AGGTGCCCTCTATCGCTTATAAGACCCTCTACCTAATCCTAGTGTTATCAAGTTCTTGTGGTCAA
240610 TCTCAAGTGAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCCACTTGGTGGTACCCCT
196 TCTCAAGTGAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCCACTTGGTGGTACCCCT
* * * *
240675 ACAGCCCAAATTTGAGACTGGGAAAAAATAGCCCCATAGGTCCCATACACTG
261 ACAGCCCAAATCTGAGACCGGGAAAAAATAGCCCCATAGGCCCCATACACTA
* * * * * * * *** * *
240727 CCCTGGTATCCGTTTAATGCACACTTTAAAGATAA-AAGAGATAATGGCCCGCCGCTCACCCATA
1 CCCTGTTATTCGTTTGATGCACACTTCAAAGATAAGGA-AGATAATGGACCACTTTTAACCCCTA
* * * *
240791 TAGCAGTGTGAAATGCTTAAATATGACAAAGTTTGGGTGAGCTAAACCGA
65 TATCATTGTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCT-AACCGA
240841 CCTTTTTCAT
Statistics
Matches: 401, Mismatches: 23, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
311 1 0.00
312 394 0.98
313 6 0.01
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (312 bp):
CCCTGTTATTCGTTTGATGCACACTTCAAAGATAAGGAAGATAATGGACCACTTTTAACCCCTAT
ATCATTGTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACCGAACCCTTGTAGGGGTCAT
AGGTGCCCTCTATCGCTTATAAGACCCTCTACCTAATCCTAGTGTTATCAAGTTCTTGTGGTCAA
TCTCAAGTGAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCCACTTGGTGGTACCCCT
ACAGCCCAAATCTGAGACCGGGAAAAAATAGCCCCATAGGCCCCATACACTA
Found at i:241360 original size:13 final size:13
Alignment explanation
Indices: 241342--241366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
241332 TTCTACGGTC
241342 TTAGTGGCTGCTG
1 TTAGTGGCTGCTG
241355 TTAGTGGCTGCT
1 TTAGTGGCTGCT
241367 AGCTTCAGCC
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:0.08, C:0.16, G:0.36, T:0.40
Consensus pattern (13 bp):
TTAGTGGCTGCTG
Found at i:243009 original size:38 final size:38
Alignment explanation
Indices: 242958--243835 Score: 1340
Period size: 38 Copynumber: 23.2 Consensus size: 38
242948 ACATTTTGAA
* *
242958 TATGTAGTCTATTCTATAGTCCGTGTCTTCATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
242996 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* *
243034 TATGAGATCTATTCTATAGTCCGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
243072 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
243110 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* *
243148 TATGTGGTCTATTCTATAGT-CGTGTCCACATATAGAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* *
243185 TATGTGGTCTATTCTCA-CGTCCGTGTCCACATATAAAG
1 TATGTGGTCTATTCT-ATAGTCCGTGTCTACATATAAAG
**
243223 TATGTGGTCTATTCTATACCCCGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
243261 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* * *
243299 TACGTGGTCTATTCTATAGT-CGTGTCCACATATAGAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* *
243336 TATGTGGTCTATTCTCA-CGTCCGTGTCCACATATAAAG
1 TATGTGGTCTATTCT-ATAGTCCGTGTCTACATATAAAG
**
243374 TATGTGGTCTATTCTATACCCCGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
243412 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* * *
243450 TACGTGGTCTATTCTATAGT-CGTGTCCACATATAGAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* *
243487 TATGTGGTCTATTCTCA-CGTCCGTGTCCACATATAAAG
1 TATGTGGTCTATTCT-ATAGTCCGTGTCTACATATAAAG
243525 TATGTGGTCTATTCTATAGT-CGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* * *
243562 TATGTGGTCTATTCTATAGTCCGTGCCCACAAATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* *
243600 TATGTGGTCTATTCAATAGTCCGTGTCTACATATTAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
243638 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
*
243676 TACGTGGTCTATTCTATAGT-CGTGTCTACATATAAAG
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
*
243713 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAA
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* * *
243751 AATGTGGTCTATTCTATAGTCTGTGTCTACATATAAAC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* * * *
243789 TACGTGGTCTATTCTATAGTCTGTGTCTACATCTAAAC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
*
243827 AATGTGGTC
1 TATGTGGTC
243836 CCTATCCACA
Statistics
Matches: 772, Mismatches: 57, Indels: 22
0.91 0.07 0.03
Matches are distributed among these distances:
37 169 0.22
38 603 0.78
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (38 bp):
TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
Found at i:243238 original size:113 final size:114
Alignment explanation
Indices: 242958--243835 Score: 1340
Period size: 113 Copynumber: 7.7 Consensus size: 114
242948 ACATTTTGAA
* *
242958 TATGTAGTCTATTCTATAGTCCGTGTCTTCATATAAAGTATGTGGTCTATTCTATAGTCCGTGTC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTC
* *
243023 TACATATAAAGTATGAGATCTATTCTATAGTCCGTGTCTACATATAAAG
66 TACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
243072 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTC
* *
243137 TACATATAAAGTATGTGGTCTATTCTATAGT-CGTGTCCACATATAGAG
66 TACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* * **
243185 TATGTGGTCTATTCTCA-CGTCCGTGTCCACATATAAAGTATGTGGTCTATTCTATACCCCGTGT
1 TATGTGGTCTATTCT-ATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGT
243249 CTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
65 CTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* * * *
243299 TACGTGGTCTATTCTATAGT-CGTGTCCACATATAGAGTATGTGGTCTATTCTCA-CGTCCGTGT
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCT-ATAGTCCGTGT
* **
243362 CCACATATAAAGTATGTGGTCTATTCTATACCCCGTGTCTACATATAAAG
65 CTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
*
243412 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTACGTGGTCTATTCTATAGT-CGTGTC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTC
* * * *
243476 CACATATAGAGTATGTGGTCTATTCTCA-CGTCCGTGTCCACATATAAAG
66 TACATATAAAGTATGTGGTCTATTCT-ATAGTCCGTGTCTACATATAAAG
*
243525 TATGTGGTCTATTCTATAGT-CGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGCC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTC
* * * *
243589 CACAAATAAAGTATGTGGTCTATTCAATAGTCCGTGTCTACATATTAAG
66 TACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
*
243638 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTACGTGGTCTATTCTATAGT-CGTGTC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTC
*
243702 TACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAA
66 TACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
* * * * *
243751 AATGTGGTCTATTCTATAGTCTGTGTCTACATATAAACTACGTGGTCTATTCTATAGTCTGTGTC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTC
* **
243816 TACATCTAAACAATGTGGTC
66 TACATATAAAGTATGTGGTC
243836 CCTATCCACA
Statistics
Matches: 700, Mismatches: 53, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
112 37 0.05
113 448 0.64
114 215 0.31
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (114 bp):
TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTC
TACATATAAAGTATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAG
Found at i:243239 original size:151 final size:151
Alignment explanation
Indices: 242958--243803 Score: 1351
Period size: 151 Copynumber: 5.6 Consensus size: 151
242948 ACATTTTGAA
* *
242958 TATGTAGTCTATTCTATAGTCCGTGTCTTCATATAAAGTATGTGGTCTATTCTATAGTCCGTGTC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGT-CGTGTC
* * * * * *
243023 TACATATAAAGTATGAGATCTATTCT-ATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCT
65 CACATATAGAGTATGTGGTCTATTCTCA-CGTCCGTGTCCACATATAAAGTATGTGGTCTATTCT
243087 ATAGTCCGTGTCTACATATAAAG
129 ATAGTCCGTGTCTACATATAAAG
243110 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCGTGTCC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCGTGTCC
243175 ACATATAGAGTATGTGGTCTATTCTCACGTCCGTGTCCACATATAAAGTATGTGGTCTATTCTAT
66 ACATATAGAGTATGTGGTCTATTCTCACGTCCGTGTCCACATATAAAGTATGTGGTCTATTCTAT
**
243240 ACCCCGTGTCTACATATAAAG
131 AGTCCGTGTCTACATATAAAG
*
243261 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTACGTGGTCTATTCTATAGTCGTGTCC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCGTGTCC
243326 ACATATAGAGTATGTGGTCTATTCTCACGTCCGTGTCCACATATAAAGTATGTGGTCTATTCTAT
66 ACATATAGAGTATGTGGTCTATTCTCACGTCCGTGTCCACATATAAAGTATGTGGTCTATTCTAT
**
243391 ACCCCGTGTCTACATATAAAG
131 AGTCCGTGTCTACATATAAAG
*
243412 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTACGTGGTCTATTCTATAGTCGTGTCC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCGTGTCC
243477 ACATATAGAGTATGTGGTCTATTCTCACGTCCGTGTCCACATATAAAGTATGTGGTCTATTCTAT
66 ACATATAGAGTATGTGGTCTATTCTCACGTCCGTGTCCACATATAAAGTATGTGGTCTATTCTAT
243542 AGT-CGTGTCTACATATAAAG
131 AGTCCGTGTCTACATATAAAG
* * * *
243562 TATGTGGTCTATTCTATAGTCCGTGCCCACAAATAAAGTATGTGGTCTATTCAATAGTCCGTGTC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGT-CGTGTC
* * * *
243627 TACATATTA-AGTATGTGGTCTATTCT-ATAGTCCGTGTCTACATATAAAGTACGTGGTCTATTC
65 CACATA-TAGAGTATGTGGTCTATTCTCA-CGTCCGTGTCCACATATAAAGTATGTGGTCTATTC
243690 TATAGT-CGTGTCTACATATAAAG
128 TATAGTCCGTGTCTACATATAAAG
**
243713 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAAAATGTGGTCTATTCTATAGTCTGTGTC
1 TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTC-GTGTC
* * * *
243778 TACATATAAACTACGTGGTCTATTCT
65 CACATATAGAGTATGTGGTCTATTCT
243804 ATAGTCTGTG
Statistics
Matches: 658, Mismatches: 30, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
150 74 0.11
151 525 0.80
152 59 0.09
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (151 bp):
TATGTGGTCTATTCTATAGTCCGTGTCTACATATAAAGTATGTGGTCTATTCTATAGTCGTGTCC
ACATATAGAGTATGTGGTCTATTCTCACGTCCGTGTCCACATATAAAGTATGTGGTCTATTCTAT
AGTCCGTGTCTACATATAAAG
Found at i:246230 original size:12 final size:12
Alignment explanation
Indices: 246213--246240 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
246203 ATTTCACGTC
246213 ATTTCCATCTTT
1 ATTTCCATCTTT
246225 ATTTCCATCTTT
1 ATTTCCATCTTT
246237 ATTT
1 ATTT
246241 TTAAGAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTCCATCTTT
Found at i:248315 original size:30 final size:30
Alignment explanation
Indices: 248281--248362 Score: 146
Period size: 30 Copynumber: 2.7 Consensus size: 30
248271 ATAACAATAC
248281 TAAATATACGCCCATTACAACAAGGAAGTG
1 TAAATATACGCCCATTACAACAAGGAAGTG
248311 TAAATATACGCCCATTACAACAAGGAAGTG
1 TAAATATACGCCCATTACAACAAGGAAGTG
* *
248341 TAAATATACCCCCTTTACAACA
1 TAAATATACGCCCATTACAACA
248363 TACCCCTTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.22
Consensus pattern (30 bp):
TAAATATACGCCCATTACAACAAGGAAGTG
Found at i:253937 original size:2 final size:2
Alignment explanation
Indices: 253930--253975 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
253920 NNNNNNNNNN
253930 GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA G- GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
253970 GA GA GA
1 GA GA GA
253976 TGTAAAACAG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:259594 original size:2 final size:2
Alignment explanation
Indices: 259587--259639 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
259577 AAAGGATTTT
259587 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
259629 AG AG AG AG AG A
1 AG AG AG AG AG A
259640 ATATATAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:269348 original size:145 final size:146
Alignment explanation
Indices: 269117--269572 Score: 650
Period size: 146 Copynumber: 3.1 Consensus size: 146
269107 CTTTCTCAAT
* * * *
269117 TGACCTTGGGTCAAGGTCATGGCACACCCTCAGGGT-ATAAGCAATC-TTGATGTGAATTAAGAA
1 TGACCTTGGGTCAAGGTCATGACACACCCT-AAGGTCATAAGCAATCTTTG-TGTGAACTGAGAA
* * * **
269180 CTTCCAATATTTGTCCAGT-AGAAAGATATGGACTGGACATGAATTTTGCACTTTTT-TGCCAGT
64 CTTCCAATGTTTCTCCA-TAAGAAAGATATGGACTGGACACGAATTTTGCACTTTTTCAACCAGT
* **
269243 GACCTTGGCCTTGCCAAAA
128 GACCTTGACCTTGCCCGAA
* * *
269262 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAACAATCTTTGTGCGAACTGAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTAAGGTCATAAGCAATCTTTGTGTGAACTGAGAACT
* *
269327 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCACTTTTTCAACCAATGAC
66 TCCAATGTTTCTCCATAAGAAAGATATGGACTGGACACGAATTTTGCACTTTTTCAACCAGTGAC
269392 CTTGACCTTGCCCGAA
131 CTTGACCTTGCCCGAA
* * *
269408 TGACCTTGGGTCAAGGTCATGACACACCCTAAGGTCATAAGCAAACTTTGTGTAAACCGAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTAAGGTCATAAGCAATCTTTGTGTGAACTGAGAACT
* **
269473 TCCAATGTTTCTCCATAAGAAAGATATGGAATCTACACGAATTTTGCACTTTTTCAACCAGTGAC
66 TCCAATGTTTCTCCATAAGAAAGATATGGACTGGACACGAATTTTGCACTTTTTCAACCAGTGAC
269538 CTTGACCTTGCCCGAA
131 CTTGACCTTGCCCGAA
269554 TGACCTTGGGTCAAGGTCA
1 TGACCTTGGGTCAAGGTCA
269573 AACTTCGTTT
Statistics
Matches: 279, Mismatches: 28, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
144 4 0.01
145 98 0.35
146 177 0.63
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (146 bp):
TGACCTTGGGTCAAGGTCATGACACACCCTAAGGTCATAAGCAATCTTTGTGTGAACTGAGAACT
TCCAATGTTTCTCCATAAGAAAGATATGGACTGGACACGAATTTTGCACTTTTTCAACCAGTGAC
CTTGACCTTGCCCGAA
Found at i:272024 original size:14 final size:14
Alignment explanation
Indices: 272007--272035 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
271997 ATTAAATTGG
272007 GGACCATCATCTGT
1 GGACCATCATCTGT
272021 GGACCATCATCTGT
1 GGACCATCATCTGT
272035 G
1 G
272036 AACTCATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.28
Consensus pattern (14 bp):
GGACCATCATCTGT
Found at i:274605 original size:15 final size:15
Alignment explanation
Indices: 274585--274615 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
274575 GTACCAACGT
274585 TAACGCAAGCAGGGA
1 TAACGCAAGCAGGGA
274600 TAACGCAAGCAGGGA
1 TAACGCAAGCAGGGA
274615 T
1 T
274616 GACCGCACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.32, T:0.10
Consensus pattern (15 bp):
TAACGCAAGCAGGGA
Found at i:275203 original size:166 final size:166
Alignment explanation
Indices: 274929--275863 Score: 1687
Period size: 166 Copynumber: 5.6 Consensus size: 166
274919 ACAATGTGAT
274929 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*
274994 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
66 CTGGCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
275059 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGG
131 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGG
*
275095 GTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
275160 CTGGCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
66 CTGGCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
275225 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGG
131 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGG
*
275261 GTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
275326 CTGGCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
66 CTGGCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
275391 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGG
131 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGG
275427 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * *
275492 CTGGCTGTTTAGTTTTTGAGGAGAAGATTTTTAAAGATTTACTCTATATGTTCCTATGTAAAACT
66 CTGGCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* *
275557 TCAATCCCCCATTGTGGCCCCACCCTACCCCCGGGG
131 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGG
*
275593 GTCATGAATTTCACAACTTAGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
275658 CTGGCTGTTTAGTTTCTGAGGAGAAGATTTTTAAAGATTTACTCTATATGTTCCTATGTAAAACT
66 CTGGCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* *
275723 TCAATCCCCCATTGTGGCCCCACCCTACCCCCGGGG
131 TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGG
*
275759 GTCATGAATTTCACAACTTAGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1 GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*
275824 CTGGCT-TTCT-GGTTCTTGAGAAGAAGATTTTTGAAA-ATTT
66 CTGGCTGTT-TAGTTTC-TGAGAAGAAGATTTTT-AAAGATTT
275864 CTCGAAATTC
Statistics
Matches: 754, Mismatches: 12, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
165 6 0.01
166 745 0.99
167 3 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (166 bp):
GTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
CTGGCTGTTTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
TCGACCCCCCATTGTGGCCCCACCCTACCCCCGGGG
Found at i:276036 original size:8 final size:8
Alignment explanation
Indices: 276025--276073 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
276015 TGAAAAGTTT
276025 ACGGACAG
1 ACGGACAG
276033 ACGGACAG
1 ACGGACAG
*
276041 ACGGACGG
1 ACGGACAG
*
276049 ACGGACGG
1 ACGGACAG
* *
276057 ACAGACGG
1 ACGGACAG
276065 AC-GACAG
1 ACGGACAG
276072 AC
1 AC
276074 AAAATGTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
7 6 0.16
8 32 0.84
ACGTcount: A:0.35, C:0.27, G:0.39, T:0.00
Consensus pattern (8 bp):
ACGGACAG
Found at i:276049 original size:12 final size:12
Alignment explanation
Indices: 276025--276073 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
276015 TGAAAAGTTT
* *
276025 ACGGACAGACGG
1 ACGGACGGACAG
* *
276037 ACAGACGGACGG
1 ACGGACGGACAG
276049 ACGGACGGACAG
1 ACGGACGGACAG
276061 ACGGAC-GACAG
1 ACGGACGGACAG
276072 AC
1 AC
276074 AAAATGTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
11 7 0.21
12 26 0.79
ACGTcount: A:0.35, C:0.27, G:0.39, T:0.00
Consensus pattern (12 bp):
ACGGACGGACAG
Found at i:276074 original size:4 final size:4
Alignment explanation
Indices: 276025--276067 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
276015 TGAAAAGTTT
* * *
276025 ACGG ACAG ACGG ACAG ACGG ACGG ACGG ACGG ACAG ACGG ACG
1 ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACG
276068 ACAGACAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.42, T:0.00
Consensus pattern (4 bp):
ACGG
Found at i:283204 original size:23 final size:23
Alignment explanation
Indices: 283174--283427 Score: 508
Period size: 23 Copynumber: 11.0 Consensus size: 23
283164 GCACCAAAGT
283174 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283197 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283220 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283243 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283266 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283289 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283312 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283335 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283358 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283381 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283404 CCTAGGATAGCTTCTGGAACATG
1 CCTAGGATAGCTTCTGGAACATG
283427 C
1 C
283428 TTGCAGTTGA
Statistics
Matches: 231, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 231 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
CCTAGGATAGCTTCTGGAACATG
Found at i:286104 original size:18 final size:18
Alignment explanation
Indices: 286081--286136 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
286071 CCAAATTAGG
* *
286081 GGCCAGGCTAAAGTTTGA
1 GGCCAGGCCAAAATTTGA
*
286099 GGCCAGGCCAAAATTTGG
1 GGCCAGGCCAAAATTTGA
* *
286117 GGCCTGGCC-AATTTTGA
1 GGCCAGGCCAAAATTTGA
286134 GGC
1 GGC
286137 AAAAGTGAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 9 0.28
18 23 0.72
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.21
Consensus pattern (18 bp):
GGCCAGGCCAAAATTTGA
Found at i:292592 original size:5 final size:5
Alignment explanation
Indices: 292578--292668 Score: 69
Period size: 5 Copynumber: 18.2 Consensus size: 5
292568 CTGTAAAGTG
* * * * * *
292578 CGAAA CGAAA TGAAA CAAAA CGAAA TC-TAC CGAAA CGAAA CGAAA TC-TAC
1 CGAAA CGAAA CGAAA CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA -CGAAA
* * *
292628 CGAAA CGAAA CAAAA CGAAA CAAAA CGAAA CGAAA CAAAA C
1 CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA C
292669 AAAATCGAGA
Statistics
Matches: 65, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
4 2 0.03
5 61 0.94
6 2 0.03
ACGTcount: A:0.59, C:0.22, G:0.13, T:0.05
Consensus pattern (5 bp):
CGAAA
Found at i:292612 original size:20 final size:20
Alignment explanation
Indices: 292589--292657 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
292579 GAAACGAAAT
292589 GAAACAAAACGAAATCTACC
1 GAAACAAAACGAAATCTACC
*
292609 GAAACGAAACGAAATCTACC
1 GAAACAAAACGAAATCTACC
*
292629 GAAACGAAAC-AAA---A-C
1 GAAACAAAACGAAATCTACC
292644 GAAACAAAACGAAA
1 GAAACAAAACGAAA
292658 CGAAACAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
15 10 0.22
16 4 0.09
19 3 0.07
20 29 0.63
ACGTcount: A:0.59, C:0.22, G:0.13, T:0.06
Consensus pattern (20 bp):
GAAACAAAACGAAATCTACC
Found at i:294787 original size:69 final size:69
Alignment explanation
Indices: 294664--294977 Score: 376
Period size: 69 Copynumber: 4.6 Consensus size: 69
294654 ATATTCCATT
* * * * * ** * *
294664 TATCCATGATACTTGATATAACACTAGCCTTGTCTTTAAGCTTACGATATTCCATTAGTCCCAGT
1 TATCAATGATACTTGATATAACGCTAGCCGTGTGTGTAAGCCAAAGATAATCCATTAGTCCCAGT
294729 AATG
66 AATG
* *
294733 TATCAATGATACTTGATATAACACTAGCCGTGTGTGTAAGCCAAAGATAATCCATTAGTCTCAGT
1 TATCAATGATACTTGATATAACGCTAGCCGTGTGTGTAAGCCAAAGATAATCCATTAGTCCCAGT
294798 AATG
66 AATG
* ** * * ** *
294802 TATCAATGATACTTGATGTAACGCTAGAAGTGTCTGTAAACCAAAGATAATTGATTAGTCCCAGG
1 TATCAATGATACTTGATATAACGCTAGCCGTGTGTGTAAGCCAAAGATAATCCATTAGTCCCAGT
294867 AATG
66 AATG
* * * * * *
294871 TATCAATGATACTTCATATAACGCTAGCAGTATGTGCAAGCCAATGATGATCCATTAGTCCCAGT
1 TATCAATGATACTTGATATAACGCTAGCCGTGTGTGTAAGCCAAAGATAATCCATTAGTCCCAGT
294936 AATG
66 AATG
* * *
294940 TATCAATGATACTTAAAATAACGCTAGGCGTGTGTGTA
1 TATCAATGATACTTGATATAACGCTAGCCGTGTGTGTA
294978 TGTAAACCAA
Statistics
Matches: 208, Mismatches: 37, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 208 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (69 bp):
TATCAATGATACTTGATATAACGCTAGCCGTGTGTGTAAGCCAAAGATAATCCATTAGTCCCAGT
AATG
Found at i:296607 original size:22 final size:22
Alignment explanation
Indices: 296579--296633 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
296569 TTATAAAAAG
*
296579 GCGAAGGCGAAAGCGCGAAGAT
1 GCGAAGGCGAAAGCGCAAAGAT
* * *
296601 GCGAAGGCGAGAGTGCAAAGTT
1 GCGAAGGCGAAAGCGCAAAGAT
*
296623 GCAAAGGCGAA
1 GCGAAGGCGAA
296634 TCTTCGCAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.40, T:0.07
Consensus pattern (22 bp):
GCGAAGGCGAAAGCGCAAAGAT
Found at i:300044 original size:12 final size:11
Alignment explanation
Indices: 300022--300076 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
300012 CCCCCCCCCC
300022 AAAAA-AAAAA
1 AAAAACAAAAA
*
300032 AAAAACGAAAA
1 AAAAACAAAAA
*
300043 AAAAACAAAAC
1 AAAAACAAAAA
300054 AAAAA-AAAAA
1 AAAAACAAAAA
* *
300064 ACAAACCAAAA
1 AAAAACAAAAA
300075 AA
1 AA
300077 CGAGTATCTC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 13 0.36
11 23 0.64
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:300044 original size:17 final size:16
Alignment explanation
Indices: 300021--300076 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
300011 CCCCCCCCCC
300021 CAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAA
* *
300037 CGAAAAAAAAACAAAA
1 CAAAAAAAAAAAAAAA
*
300053 CAAAAAAAAAAACAAA
1 CAAAAAAAAAAAAAAA
*
300069 CCAAAAAA
1 CAAAAAAA
300077 CGAGTATCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAAAAAAAA
Found at i:300076 original size:1 final size:1
Alignment explanation
Indices: 300022--300064 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
300012 CCCCCCCCCC
** * *
300022 AAAAAAAAAAAAAAACGAAAAAAAAACAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
300065 CAAACCAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.07, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:301498 original size:2 final size:2
Alignment explanation
Indices: 301491--301542 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
301481 CAAGTTGAAT
301491 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
301533 TC TC TC TC TC
1 TC TC TC TC TC
301543 AAAATCATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:304922 original size:21 final size:19
Alignment explanation
Indices: 304893--304931 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
304883 TTTGCTTTTT
304893 TTGTATTATATTTCAAAACAA
1 TTGTATTAT-TTT-AAAACAA
*
304914 TTGTTTTATTTTAAAACA
1 TTGTATTATTTTAAAACA
304932 GGGTATTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 3 0.18
21 8 0.47
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (19 bp):
TTGTATTATTTTAAAACAA
Found at i:307669 original size:14 final size:15
Alignment explanation
Indices: 307641--307669 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
307631 AATCAGTGTT
307641 ATTACTATGCAAGCA
1 ATTACTATGCAAGCA
307656 ATTACTAT-CAAGCA
1 ATTACTATGCAAGCA
307670 TCTTTAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (15 bp):
ATTACTATGCAAGCA
Found at i:320673 original size:12 final size:12
Alignment explanation
Indices: 320652--320683 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
320642 TTATTACTTG
*
320652 TATCACTATTAT
1 TATCATTATTAT
320664 TATCATTATTAT
1 TATCATTATTAT
320676 TATCATTA
1 TATCATTA
320684 CTACTGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (12 bp):
TATCATTATTAT
Found at i:333057 original size:6 final size:6
Alignment explanation
Indices: 333044--333075 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
333034 TGTAAAAATT
333044 AAAA-A AAAACA AAAACA AAAAC- AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
333076 AAACCTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 9 0.36
6 16 0.64
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:336651 original size:2 final size:2
Alignment explanation
Indices: 336644--336676 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
336634 AGACAAGCAT
*
336644 TA TA TA TA TA TA TA AA 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 TA T
336677 CTACTTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:336838 original size:27 final size:27
Alignment explanation
Indices: 336800--336856 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
336790 TAAATAAAAA
336800 AAATTCTAATGTAAAACTGTACGGTAT
1 AAATTCTAATGTAAAACTGTACGGTAT
*
336827 AAATTCTAATGTAAAACTGTACGTTAT
1 AAATTCTAATGTAAAACTGTACGGTAT
336854 AAA
1 AAA
336857 AAAAAATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (27 bp):
AAATTCTAATGTAAAACTGTACGGTAT
Found at i:355364 original size:2 final size:2
Alignment explanation
Indices: 355357--355412 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
355347 TTTCTAACAC
355357 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
355399 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
355413 TTTAATAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:356475 original size:21 final size:21
Alignment explanation
Indices: 356446--356513 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
356436 AATGCTATGC
* * *
356446 TATGGTATGCGATTTTAATGA
1 TATGCTATGAGATTTGAATGA
* *
356467 TATGCTATGAGATTTGCATGG
1 TATGCTATGAGATTTGAATGA
* *
356488 TATGCTATGAGATTTGTATGC
1 TATGCTATGAGATTTGAATGA
356509 TATGC
1 TATGC
356514 CATAAGAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (21 bp):
TATGCTATGAGATTTGAATGA
Found at i:356562 original size:10 final size:10
Alignment explanation
Indices: 356544--356576 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
356534 GGCTTAATGA
356544 TATGGTATGC
1 TATGGTATGC
*
356554 TATGCTATGC
1 TATGGTATGC
356564 TATGGTATGC
1 TATGGTATGC
356574 TAT
1 TAT
356577 CAGATTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.42
Consensus pattern (10 bp):
TATGGTATGC
Found at i:357490 original size:21 final size:21
Alignment explanation
Indices: 357453--357540 Score: 108
Period size: 21 Copynumber: 4.2 Consensus size: 21
357443 GAATGCGATT
357453 CTATGAGATTGT--ATGCTATG
1 CTATGAGATT-TCAATGCTATG
* * *
357473 GTATGAAATTCCAATGCTATG
1 CTATGAGATTTCAATGCTATG
* *
357494 ATATGAGATTTCAATGTTATG
1 CTATGAGATTTCAATGCTATG
357515 CTATGAGATTTCAATGCTATG
1 CTATGAGATTTCAATGCTATG
357536 CTATG
1 CTATG
357541 CTATGGTGTA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.14
21 49 0.86
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (21 bp):
CTATGAGATTTCAATGCTATG
Found at i:358799 original size:10 final size:10
Alignment explanation
Indices: 358786--358910 Score: 58
Period size: 10 Copynumber: 12.0 Consensus size: 10
358776 GTCAGTACCC
358786 TGTACAGTGG
1 TGTACAGTGG
*
358796 TGTATAGTGG
1 TGTACAGTGG
* *
358806 GGTACAGTGC
1 TGTACAGTGG
*
358816 TGGT-CAGTGCCC
1 T-GTACAGTG--G
* *
358828 CGTATAGTGG
1 TGTACAGTGG
358838 TGTACAGTGAG
1 TGTACAGTG-G
*
358849 -GTACAGTGC
1 TGTACAGTGG
358858 TGGT-CAGTGGG
1 T-GTACAGT-GG
*
358869 TAGGTACAGTGC
1 T--GTACAGTGG
*
358881 TGTCCAGTGG
1 TGTACAGTGG
*
358891 AGTACAGTGG
1 TGTACAGTGG
*
358901 AGTACAGTGG
1 TGTACAGTGG
358911 CTCTGTACAG
Statistics
Matches: 88, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
10 65 0.74
11 9 0.10
12 10 0.11
13 4 0.05
ACGTcount: A:0.20, C:0.14, G:0.39, T:0.26
Consensus pattern (10 bp):
TGTACAGTGG
Found at i:358856 original size:32 final size:32
Alignment explanation
Indices: 358797--358857 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
358787 GTACAGTGGT
*
358797 GTATAGTGGGGTACAGTGCTGGTCAGTGCCCC
1 GTATAGTGGGGTACAGTGCAGGTCAGTGCCCC
*
358829 GTATAGTGGTGTACAGTG-AGGTACAGTGC
1 GTATAGTGGGGTACAGTGCAGGT-CAGTGC
358858 TGGTCAGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.20, C:0.16, G:0.38, T:0.26
Consensus pattern (32 bp):
GTATAGTGGGGTACAGTGCAGGTCAGTGCCCC
Found at i:358866 original size:42 final size:41
Alignment explanation
Indices: 358745--358866 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 41
358735 AAAAACATTG
* * * *
358745 GTACAGTGG-GTTACAGTGGTGTACAGTGTTTGTCAGTACCCT
1 GTACAGTGGTG-TACAGTGG-GTACAGTGCTGGTCAGTGCCCC
*
358787 GTACAGTGGTGTATAGTGGGGTACAGTGCTGGTCAGTGCCCC
1 GTACAGTGGTGTACAGT-GGGTACAGTGCTGGTCAGTGCCCC
*
358829 GTATAGTGGTGTACAGTGAGGTACAGTGCTGGTCAGTG
1 GTACAGTGGTGTACAGTG-GGTACAGTGCTGGTCAGTG
358867 GGTAGGTACA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
41 1 0.01
42 66 0.94
43 3 0.04
ACGTcount: A:0.19, C:0.16, G:0.36, T:0.30
Consensus pattern (41 bp):
GTACAGTGGTGTACAGTGGGTACAGTGCTGGTCAGTGCCCC
Done.