Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 116 of 175
Found at i:36476142 original size:50 final size:50
Alignment explanation
Indices: 36476034--36476231 Score: 207
Period size: 50 Copynumber: 3.8 Consensus size: 50
36476024 ATTTGGGTAA
* * *
36476034 AGAGATCCCATGTAAGACCATGTCTGAGACATGACATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATG
* *
36476090 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
** * * *
36476140 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATAGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
** * * *
36476190 AGAACTACCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
36476232 GTACAAGAAA
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 80 0.66
53 4 0.03
55 1 0.01
56 37 0.30
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
Found at i:36479373 original size:25 final size:25
Alignment explanation
Indices: 36479339--36479386 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
36479329 TTTTAATTCG
36479339 AAAACGTGCTATTAGAAGCAGACTC
1 AAAACGTGCTATTAGAAGCAGACTC
*
36479364 AAAACGTGCTATTAGAAGTAGAC
1 AAAACGTGCTATTAGAAGCAGAC
36479387 AATATGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (25 bp):
AAAACGTGCTATTAGAAGCAGACTC
Found at i:36493643 original size:16 final size:15
Alignment explanation
Indices: 36493624--36493659 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
36493614 TATTTTTGAA
36493624 AAAAATGATTTTTTTT
1 AAAAAT-ATTTTTTTT
36493640 AAAAATATTTTTTTT
1 AAAAATATTTTTTTT
36493655 AAAAA
1 AAAAA
36493660 AAGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
AAAAATATTTTTTTT
Found at i:36494700 original size:18 final size:17
Alignment explanation
Indices: 36494670--36494734 Score: 76
Period size: 18 Copynumber: 3.5 Consensus size: 17
36494660 TTTGGGAATA
36494670 ATTTTTGGATTTTTGTCC
1 ATTTTT-GATTTTTGTCC
36494688 ATTATTTGATTTTTGTCC
1 ATT-TTTGATTTTTGTCC
36494706 ATTTTTGTCCATTTTTGTCC
1 ATTTTTG---ATTTTTGTCC
36494726 ATTGTTTGA
1 ATT-TTTGA
36494735 GAAATTATTG
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.10
18 18 0.43
19 3 0.07
20 13 0.31
21 4 0.10
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.60
Consensus pattern (17 bp):
ATTTTTGATTTTTGTCC
Found at i:36494720 original size:9 final size:10
Alignment explanation
Indices: 36494678--36494733 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
36494668 TAATTTTTGG
36494678 ATTTTTGTCC
1 ATTTTTGTCC
36494688 ATTATTTG---
1 ATT-TTTGTCC
36494696 ATTTTTGTCC
1 ATTTTTGTCC
36494706 ATTTTTGTCC
1 ATTTTTGTCC
36494716 ATTTTTGTCC
1 ATTTTTGTCC
36494726 ATTGTTTG
1 ATT-TTTG
36494734 AGAAATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
7 4 0.10
8 3 0.07
10 26 0.63
11 8 0.20
ACGTcount: A:0.12, C:0.14, G:0.12, T:0.61
Consensus pattern (10 bp):
ATTTTTGTCC
Found at i:36501117 original size:76 final size:76
Alignment explanation
Indices: 36501025--36501178 Score: 290
Period size: 76 Copynumber: 2.0 Consensus size: 76
36501015 CCAAACTAAT
36501025 AAGATATCTAAAGGTTTATTGCATCTATCACAAAAGAATATTATATCTTTTCATAATCAATACTA
1 AAGATATCTAAAGGTTTATTGCATCTATCACAAAAGAATATTATATCTTTTCATAATCAATACTA
*
36501090 GGACTTAACGA
66 AGACTTAACGA
36501101 AAGATATCTAAAGGTTTATTGCATCTATCACAAAAGAATATTATATCTTTTCATAATCAATACTA
1 AAGATATCTAAAGGTTTATTGCATCTATCACAAAAGAATATTATATCTTTTCATAATCAATACTA
*
36501166 AGATTTAACGA
66 AGACTTAACGA
36501177 AA
1 AA
36501179 AAAAAGCTTC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (76 bp):
AAGATATCTAAAGGTTTATTGCATCTATCACAAAAGAATATTATATCTTTTCATAATCAATACTA
AGACTTAACGA
Found at i:36506862 original size:22 final size:24
Alignment explanation
Indices: 36506826--36506871 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
36506816 CAACCAATCA
*
36506826 AATTTCAACACA-TTTCT-TCCTT
1 AATTTCAACAAATTTTCTCTCCTT
*
36506848 AATTTCCACAAATTTTCTCTCCTT
1 AATTTCAACAAATTTTCTCTCCTT
36506872 TACACCCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 5 0.25
24 5 0.25
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTTCAACAAATTTTCTCTCCTT
Found at i:36511284 original size:26 final size:23
Alignment explanation
Indices: 36511255--36511324 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
36511245 GACTCACCAT
36511255 AGCTAGTATGAGCTTACCGATATATC
1 AGCTAGTATGAGCTTACCG-T-T-TC
** *
36511281 AGCTCTTATGAGCTGACCGTTTC
1 AGCTAGTATGAGCTTACCGTTTC
*
36511304 AACTAG-ATAGAGCTTACCGTT
1 AGCTAGTAT-GAGCTTACCGTT
36511325 CTTCAGCTGG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
22 2 0.06
23 16 0.44
24 1 0.03
25 1 0.03
26 16 0.44
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (23 bp):
AGCTAGTATGAGCTTACCGTTTC
Found at i:36511827 original size:30 final size:30
Alignment explanation
Indices: 36511791--36511852 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
36511781 TAATTCTTAC
36511791 TCAGTTTATTTCTTCGTGTTTTATAGAGGT
1 TCAGTTTATTTCTTCGTGTTTTATAGAGGT
*
36511821 TCAGTTTGTTTCTTCGTGTTTTATAGAGGT
1 TCAGTTTATTTCTTCGTGTTTTATAGAGGT
36511851 TC
1 TC
36511853 GTTATCTAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.15, C:0.11, G:0.21, T:0.53
Consensus pattern (30 bp):
TCAGTTTATTTCTTCGTGTTTTATAGAGGT
Found at i:36518198 original size:15 final size:15
Alignment explanation
Indices: 36518178--36518208 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
36518168 GAATCAAACG
36518178 AATCTCATTGAATTA
1 AATCTCATTGAATTA
36518193 AATCTCATTGAATTA
1 AATCTCATTGAATTA
36518208 A
1 A
36518209 TACAATTAAC
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:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (15 bp):
AATCTCATTGAATTA
Found at i:36524297 original size:131 final size:131
Alignment explanation
Indices: 36524055--36524316 Score: 318
Period size: 131 Copynumber: 2.0 Consensus size: 131
36524045 TTTGTCCTCC
* *
36524055 ATAAAACCTTAACTAGAGGAATCATTTTCTTTCTCAAAACTTTTACCTCATGATCCAAAATCTAA
1 ATAAAACCTTAACTAGAGGAATCATTTTCTTTCTCAAAAATTTTACCTCATGATCAAAAATCTAA
* * * *
36524120 ACTGACTCCTCCTCAAAAGACAAATTCGGATTTACATCGATCTCCTCAATCAAAACCACATAAGA
66 ACTGACTCCTCCTCAAAAGACAAATTCGAACTCACATCAATCTCCTCAATCAAAACCACATAAGA
36524185 T
131 T
36524186 ATAAAACCTTAACTAGAGGAAT-ATTCTTCTTTCT-AAACAATTTTACCTCAT-ATTCAAAAATC
1 ATAAAACCTTAACTAGAGGAATCATT-TTCTTTCTCAAA-AATTTTACCTCATGA-TCAAAAATC
* ** * * **
36524248 TGAACTGGTTCCTCCTCAAAAGATAAATTC-AACCTCACCA-CAATTTCCTCAATCGGAACCACA
63 TAAACTGACTCCTCCTCAAAAGACAAATTCGAA-CTCA-CATCAATCTCCTCAATCAAAACCACA
*
36524311 TGAGAT
126 TAAGAT
36524317 GGACCAGATC
Statistics
Matches: 112, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
130 8 0.07
131 102 0.91
132 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.29
Consensus pattern (131 bp):
ATAAAACCTTAACTAGAGGAATCATTTTCTTTCTCAAAAATTTTACCTCATGATCAAAAATCTAA
ACTGACTCCTCCTCAAAAGACAAATTCGAACTCACATCAATCTCCTCAATCAAAACCACATAAGA
T
Found at i:36530388 original size:44 final size:43
Alignment explanation
Indices: 36530328--36530454 Score: 125
Period size: 44 Copynumber: 2.9 Consensus size: 43
36530318 AGGATTATGT
*
36530328 TATGTG-TTATCGTGTAAGACCACATCTGGGACATTGGCATCGA
1 TATGTGATTA-CGTGTAAGACCACGTCTGGGACATTGGCATCGA
* * *
36530371 CT-TGTGACTTACGTGTAAGACC-CTGTTTGGGATAGTGGCATCGA
1 -TATGTGA-TTACGTGTAAGACCAC-GTCTGGGACATTGGCATCGA
** * *
36530415 TATGTGATTAAATATAAGACCACGTCTGGGACGTTGGCAT
1 TATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCAT
36530455 TGTACAAAAT
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
43 30 0.45
44 34 0.51
45 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (43 bp):
TATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCATCGA
Found at i:36534050 original size:30 final size:30
Alignment explanation
Indices: 36533980--36534061 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
36533970 AGTAACCTCG
* * *
36533980 ATATAATGTTAGA-TTGTGTGAGCAATTATG
1 ATATAATGTCA-ACTTGTGTGAGCAATCATA
* *
36534010 TTATAATGTCAACTTGTGTGAGCAATCCTA
1 ATATAATGTCAACTTGTGTGAGCAATCATA
* *
36534040 ATATATTGTCATCTTGTGTGAG
1 ATATAATGTCAACTTGTGTGAG
36534062 AAACTTATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (30 bp):
ATATAATGTCAACTTGTGTGAGCAATCATA
Found at i:36546634 original size:15 final size:16
Alignment explanation
Indices: 36546614--36546652 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
36546604 TTTAATTGTT
36546614 TTATAAAATTATA-AA
1 TTATAAAATTATATAA
36546629 TTATAAAA-TATATAA
1 TTATAAAATTATATAA
36546644 TT-TAAAATT
1 TTATAAAATT
36546653 TCAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTATAAAATTATATAA
Found at i:36553474 original size:235 final size:235
Alignment explanation
Indices: 36553047--36553515 Score: 823
Period size: 235 Copynumber: 2.0 Consensus size: 235
36553037 TCAAACATCC
* *
36553047 GATAATTTGTAAAGTCAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATAAAC
1 GATAATCTGTAAAGTAAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATAAAC
* *
36553112 TATAAACATAACATTTCATTTTAATAATGAAACTTTATGGCGTAATTATAAACTTATACTAATGC
66 TATAAACATAACATTTCATTTTAATAATGAAACTTTATGGCGTAATTATAAACCTATACCAATGC
* *
36553177 CATGGGATTAATATATAGGAATGCATCTAAAACACACATATACCTAAACTTATACATATTTGACC
131 CATGGGATTAATATATAAGAATGCATCTAAAACACACATATACCTAAACTTAAACATATTTGACC
36553242 ATAAGTCATCCATATATATATAAACATAACATTTAATTCT
196 ATAAGTCATCCATATATATATAAACATAACATTTAATTCT
*
36553282 GATAATCTGTTAAGTAAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATAAAC
1 GATAATCTGTAAAGTAAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATAAAC
* *
36553347 TTTAAACATAACATTTCATTTTAATAATGAAACTTTATGGGGTAATTATAAACCTATACCAATGC
66 TATAAACATAACATTTCATTTTAATAATGAAACTTTATGGCGTAATTATAAACCTATACCAATGC
* *
36553412 CATAGGG-TTAATATATAAGAGTGCATCTAAAACACATATATACCTAAACTTAAACATATTTGAC
131 CAT-GGGATTAATATATAAGAATGCATCTAAAACACACATATACCTAAACTTAAACATATTTGAC
36553476 CATAAGTCATCCATATATATATAAACATAACATTTAATTC
195 CATAAGTCATCCATATATATATAAACATAACATTTAATTC
36553516 ATCATTGTTA
Statistics
Matches: 222, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
235 219 0.99
236 3 0.01
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (235 bp):
GATAATCTGTAAAGTAAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATAAAC
TATAAACATAACATTTCATTTTAATAATGAAACTTTATGGCGTAATTATAAACCTATACCAATGC
CATGGGATTAATATATAAGAATGCATCTAAAACACACATATACCTAAACTTAAACATATTTGACC
ATAAGTCATCCATATATATATAAACATAACATTTAATTCT
Found at i:36557170 original size:35 final size:35
Alignment explanation
Indices: 36557114--36557224 Score: 141
Period size: 35 Copynumber: 3.1 Consensus size: 35
36557104 AAACCACCCA
*
36557114 AACACACCAGATGCTCATAAGAGCCAATCCAACTGT
1 AACACACCA-ATGCTCATAAGAGCTAATCCAACTGT
** * *
36557150 AACATGCCAATGCTCATAAGAGTTAATCCAACCGT
1 AACACACCAATGCTCATAAGAGCTAATCCAACTGT
* * *
36557185 AACACATCAATGCTCATAAAAGCTAATCCAACTGA
1 AACACACCAATGCTCATAAGAGCTAATCCAACTGT
36557220 AACAC
1 AACAC
36557225 GTCAAACATA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 56 0.89
36 7 0.11
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (35 bp):
AACACACCAATGCTCATAAGAGCTAATCCAACTGT
Found at i:36560669 original size:40 final size:39
Alignment explanation
Indices: 36560615--36560746 Score: 138
Period size: 40 Copynumber: 3.5 Consensus size: 39
36560605 AAATATATTT
* *
36560615 ATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
36560654 ATTTTTTTAAATTTTAAAATATTTTT-AAA-A------T-
1 ATTTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTA
36560685 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTA
*
36560725 ATTTTTTAAAATTTTTAAAATA
1 ATTTTTT-TAA-TTTTAAAATA
36560747 AAAATGGGCT
Statistics
Matches: 78, Mismatches: 2, Indels: 23
0.76 0.02 0.22
Matches are distributed among these distances:
30 17 0.22
31 11 0.14
32 2 0.03
38 1 0.01
39 11 0.14
40 24 0.31
41 2 0.03
42 10 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:36560688 original size:70 final size:72
Alignment explanation
Indices: 36560614--36560746 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 72
36560604 TAAATATATT
* * *
36560614 TATTTTTTTAATTTTAAAATATTTTTTACATAC-TTTTTTAATTTTTTTAAA-TTTTAAAATATT
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAATATT
36560677 TTTAAAA
66 TTTAAAA
36560684 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAATA
36560747 AAAATGGGCT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 31 0.53
71 17 0.29
72 10 0.17
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (72 bp):
TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTAAAATTTTTAAAATATT
TTTAAAA
Found at i:36560690 original size:30 final size:31
Alignment explanation
Indices: 36560656--36560746 Score: 132
Period size: 30 Copynumber: 3.0 Consensus size: 31
36560646 CTTTTTTAAT
36560656 TTTTTTAAATTTTAAAATATTTTTAAAATA-
1 TTTTTTAAATTTTAAAATATTTTTAAAATAC
*
36560686 TTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAAATTTTAAAATATTTTTAAAATAC
* *
36560717 TTTTTTTAATTTTTTAAA-ATTTTTAAAATA
1 -TTTTTTAAATTTTAAAATATTTTTAAAATA
36560747 AAAATGGGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
30 29 0.53
31 12 0.22
32 14 0.25
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTTAAATTTTAAAATATTTTTAAAATAC
Found at i:36560692 original size:31 final size:31
Alignment explanation
Indices: 36560654--36560746 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
36560644 TACTTTTTTA
36560654 ATTTTTTTAAATTTTAAAATATTTTTAAAAT
1 ATTTTTTTAAATTTTAAAATATTTTTAAAAT
36560685 ATTTTTTT-AATTTTAAAATATTTTTAAAAT
1 ATTTTTTTAAATTTTAAAATATTTTTAAAAT
* *
36560715 ACTTTTTTTAATTTTTTAAA-ATTTTTAAAAT
1 A-TTTTTTTAAATTTTAAAATATTTTTAAAAT
36560746 A
1 A
36560747 AAAATGGGCT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
30 23 0.40
31 27 0.47
32 8 0.14
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
ATTTTTTTAAATTTTAAAATATTTTTAAAAT
Found at i:36560693 original size:13 final size:11
Alignment explanation
Indices: 36560665--36560746 Score: 77
Period size: 11 Copynumber: 7.9 Consensus size: 11
36560655 TTTTTTTAAA
36560665 TTTTAAAATAT
1 TTTTAAAATAT
36560676 TTTTAAAATAT
1 TTTTAAAATAT
* *
36560687 TTTT---TTAA
1 TTTTAAAATAT
36560695 TTTTAAAATAT
1 TTTTAAAATAT
36560706 TTTTAAAATACT
1 TTTTAAAATA-T
**
36560718 TTTTTTAAT-T
1 TTTTAAAATAT
36560728 TTTT-AAA-AT
1 TTTTAAAATAT
36560737 TTTTAAAATA
1 TTTTAAAATA
36560747 AAAATGGGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
8 6 0.11
9 7 0.12
10 8 0.14
11 28 0.49
12 8 0.14
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:36565998 original size:21 final size:21
Alignment explanation
Indices: 36565966--36566006 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
36565956 GAACATTTGG
36565966 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
36565987 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
36566007 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:36574438 original size:23 final size:23
Alignment explanation
Indices: 36574394--36574438 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
36574384 TCTTATTTTG
* *
36574394 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
36574417 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
36574439 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:36574675 original size:3 final size:3
Alignment explanation
Indices: 36574667--36574707 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
36574657 ATCTTGTATC
*
36574667 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
36574708 ATTCATGCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:36579865 original size:14 final size:15
Alignment explanation
Indices: 36579839--36579871 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
36579829 TCCCAAGCTG
36579839 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
36579854 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
36579868 GGAA
1 GGAA
36579872 AAGTGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:36581363 original size:43 final size:43
Alignment explanation
Indices: 36581222--36581363 Score: 104
Period size: 43 Copynumber: 3.3 Consensus size: 43
36581212 CCTGCACCGA
*
36581222 CAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
1 CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
* * ** * **** * * * ****
36581265 CAGCGGAGCAGGTTAAAAATTGTAGATCTTGCCTTCTTGCACCG
1 CAGCGAAGCAGATCGAAGACACCAG-CCTTGCCTCCCTGGGTTG
36581309 ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
1 -CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
*
36581353 CAGCGGAGCAG
1 CAGCGAAGCAG
36581364 GTTAAAAATA
Statistics
Matches: 63, Mismatches: 34, Indels: 4
0.62 0.34 0.04
Matches are distributed among these distances:
43 25 0.40
44 22 0.35
45 16 0.25
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (43 bp):
CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
Found at i:36581384 original size:44 final size:44
Alignment explanation
Indices: 36581248--36581391 Score: 119
Period size: 44 Copynumber: 3.3 Consensus size: 44
36581238 AGACACCAGC
* *
36581248 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATTGTAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* * **** * * ** * * * *
36581292 CTTGCCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACCAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
36581336 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
*
36581380 CTTGCCTTCCTG
1 CTTGCCTCCCTG
36581392 CACCGATAGC
Statistics
Matches: 67, Mismatches: 31, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
43 18 0.27
44 33 0.49
45 16 0.24
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:36581454 original size:88 final size:88
Alignment explanation
Indices: 36581192--36581413 Score: 399
Period size: 88 Copynumber: 2.5 Consensus size: 88
36581182 CAGATCAGTG
*
36581192 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
36581257 CTGGGTTGCAGCGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* * *
36581280 AAAATTGTAGATCTTGCCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
1 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
36581345 CTGGGTTGCAGCGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
*
36581368 AAAATAGCAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGA
1 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
36581414 TGACCCTGGC
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 126 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (88 bp):
AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
CTGGGTTGCAGCGGAGCAGGTTA
Found at i:36581490 original size:44 final size:43
Alignment explanation
Indices: 36581425--36581545 Score: 163
Period size: 44 Copynumber: 2.7 Consensus size: 43
36581415 GACCCTGGCT
* *
36581425 CTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGT-AAGTC
1 CTATCTCCCTAG-CAGCAGTGGAATAGGTTGAAGATTGTGAA-TC
36581469 CTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAATC
1 CTATCTCCCTAG-CAGCAGTGGAATAGGTTGAAGATTGTGAATC
* *
36581513 CTATCTCCCTGAGCAACAGTGGAGTAGGTTGAA
1 CTATCTCCCT-AGCAGCAGTGGAATAGGTTGAA
36581546 AATAGCTGAT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
44 66 0.94
45 4 0.06
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (43 bp):
CTATCTCCCTAGCAGCAGTGGAATAGGTTGAAGATTGTGAATC
Found at i:36582158 original size:45 final size:43
Alignment explanation
Indices: 36581909--36582340 Score: 195
Period size: 44 Copynumber: 10.0 Consensus size: 43
36581899 GAAGATGACG
* * **
36581909 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGATAAT
* * * * * * * * *
36581953 AATCCTATCTCTCTGAAGTTGTAGTGAAGTAGATTAAAATCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAAT
* * * * *
36581996 AGATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T-CGCAT-CT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-ATAAT
* * * *
36582037 AGTCTTATCTCCCTAAAGTTCCAGTGGAGCAAACTAAG-TAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAAT
* * * **
36582079 CAAGTCTTATC-CTCCTAAAGTTACCGT-GAGGCAGACTGAAGATGGT
1 -AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGATAAT
*
36582125 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-ATCCAAT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAT--AAT
* * * * * **
36582170 AATCCTATCTCCTTGAAGTTGCAGTAGAGCAGATTAAAACCAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAAT
* * * * * **
36582213 AGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGA-TCACAT-CG
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAAT
** * *
36582255 GGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAGA-AAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGATAA-T
* * * *
36582299 AAGTCTTATCCCCCTGAAATTACAGTGGGGCAGACTAA-ATAA
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAA
36582341 ACAAATTCTG
Statistics
Matches: 293, Mismatches: 71, Indels: 48
0.71 0.17 0.12
Matches are distributed among these distances:
40 19 0.06
41 37 0.13
42 6 0.02
43 25 0.09
44 142 0.48
45 57 0.19
46 7 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAAT
Found at i:36582371 original size:217 final size:217
Alignment explanation
Indices: 36581894--36582371 Score: 592
Period size: 217 Copynumber: 2.2 Consensus size: 217
36581884 GCAATTTAAA
* *
36581894 AGACTGAAGATGACGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
1 AGACTGAAGATAACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
* * *
36581959 ATCTCTCTGAAGTTGTAGTGAAGTAGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGA
66 ATCTCTCTGAAGTTGCAGTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGAGA
* * * *
36582024 GCAGATCGCATCTAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAAACTAAGTAATCAAGTCTTAT
131 GCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAAACTAAGAAAGCAAGTCTTAT
* *
36582089 CCTCCTAAAGTTACCGTGAGGC
196 CCCCCTAAAGTTACAGTGAGGC
**** * *
36582111 AGACTGAAGATGGTGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATCCAATAATCCT
1 AGACTGAAGATAACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
* *
36582176 ATCTC-CTTGAAGTTGCAGT-AGAGCAGATTAAAACCATAGATCTTATCTCTCTGAAGTTGCAGT
66 ATCTCTC-TGAAGTTGCAGTGA-AGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAG-
* * * * * *
36582239 AGAGTAGATCACATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAGAAAGCAAGTC
128 AGAGCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAAACT-AAGAAAGCAAGTC
*
36582304 TTATCCCCCTGAAA-TTACAGTGGGGC
192 TTATCCCCCT-AAAGTTACAGTGAGGC
* *
36582330 AGACT-AA-ATAAACAAAT-TCTGTCTCCCT-AAGTTGTAGTGGAG
1 AGACTGAAGAT-AACAAATCT-TATCTCCCTAAAGTTGCAGTGGAG
36582372 TGGATTAGAG
Statistics
Matches: 226, Mismatches: 28, Indels: 14
0.84 0.10 0.05
Matches are distributed among these distances:
216 2 0.01
217 130 0.58
218 56 0.25
219 35 0.15
220 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (217 bp):
AGACTGAAGATAACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
ATCTCTCTGAAGTTGCAGTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGAGA
GCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAAACTAAGAAAGCAAGTCTTAT
CCCCCTAAAGTTACAGTGAGGC
Found at i:36582420 original size:217 final size:216
Alignment explanation
Indices: 36581894--36582425 Score: 567
Period size: 217 Copynumber: 2.4 Consensus size: 216
36581884 GCAATTTAAA
* * * *
36581894 AGACTGAAGATGACGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCT
1 AGACTGAAGATAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-TCAATAATCCT
* * * *
36581959 ATCTCTCTGAAGTTGTAGTGAAGTAGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGA
65 ATCTCTCTGAAGTTGCAGTTAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGAGA
* * * *
36582024 GCAGATCGCATCTAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAAACTAAGTAATCAAGTCTTAT
130 GCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAAACTAAGAAAGCAAGTCTTAT
* *
36582089 CCTCCTAAAGTTACCGTGAGGC
195 CCCCCTAAAGTTACAGTGAGGC
****
36582111 AGACTGAAGATGGTGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATCCAATAATCCT
1 AGACTGAAGATAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAT-CAATAATCCT
* *
36582176 ATCTC-CTTGAAGTTGCAG-TAGAGCAGATTAAAACCATAGATCTTATCTCTCTGAAGTTGCAGT
65 ATCTCTC-TGAAGTTGCAGTTA-AGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAG-
* * * * * *
36582239 AGAGTAGATCACATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAGAAAGCAAGTC
127 AGAGCAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAAACT-AAGAAAGCAAGTC
*
36582304 TTATCCCCCTGAAA-TTACAGTGGGGC
191 TTATCCCCCT-AAAGTTACAGTGAGGC
* * ** * * *
36582330 AGACT-AA-ATAAACAAAT-TCTGTCTCCCT-AAGTTGTAGTGGAGTGGATTAGAGT-GATGGAT
1 AGACTGAAGAT-AACAAATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AATCAAT-AAT
** * *
36582390 TTTATCTCTCTGAAATTACAGTTAAGCAGATTAAAA
62 CCTATCTCTCTGAAGTTGCAGTTAAGCAGATTAAAA
36582426 GTTACGAGTC
Statistics
Matches: 265, Mismatches: 38, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
216 4 0.02
217 162 0.61
218 61 0.23
219 35 0.13
220 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (216 bp):
AGACTGAAGATAACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATCAATAATCCTA
TCTCTCTGAAGTTGCAGTTAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGAGAG
CAGATCACATCGAGTCTTATCTCCCTAAAGTTCCAGTGGAGCAAACTAAGAAAGCAAGTCTTATC
CCCCTAAAGTTACAGTGAGGC
Found at i:36582727 original size:21 final size:21
Alignment explanation
Indices: 36582682--36582757 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
36582672 ATCTTCAAGG
*
36582682 ATATGTAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
36582701 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
36582722 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
36582743 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
36582758 AGACATAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 18 0.33
21 36 0.67
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:36583255 original size:7 final size:7
Alignment explanation
Indices: 36583243--36583275 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
36583233 ATCATTATTA
36583243 TTATTTT
1 TTATTTT
36583250 TTATTTT
1 TTATTTT
36583257 TTA-TTT
1 TTATTTT
36583263 TTATTTT
1 TTATTTT
36583270 TATATT
1 T-TATT
36583276 CATGTGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 14 0.58
8 4 0.17
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTATTTT
Found at i:36583263 original size:13 final size:14
Alignment explanation
Indices: 36583237--36583275 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
36583227 TCTTGTATCA
*
36583237 TTATTATTAT-TTT
1 TTATTTTTATATTT
36583250 TTATTTTT-TATTT
1 TTATTTTTATATTT
36583263 TTATTTTTATATT
1 TTATTTTTATATT
36583276 CATGTGCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 1 0.04
13 18 0.78
14 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTTTATATTT
Found at i:36585006 original size:10 final size:11
Alignment explanation
Indices: 36584980--36585005 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
36584970 AAAAAAATAA
36584980 AAAAATATTTT
1 AAAAATATTTT
36584991 AAAAATATTTT
1 AAAAATATTTT
36585002 AAAA
1 AAAA
36585006 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:36585915 original size:28 final size:27
Alignment explanation
Indices: 36585829--36585915 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 27
36585819 GTATGTGGAA
*
36585829 AAAAATTTATAAAAATA-AAAATCA-AT
1 AAAATTTTATAAAAATATAAAAT-ATAT
* * *
36585855 AAAA-ATTATTAAAAATATAAAAAATTGT
1 AAAATTTTA-TAAAAATATAAAATA-TAT
*
36585883 CAAATTTTATAAAAATGATAAAATATAT
1 AAAATTTTATAAAAAT-ATAAAATATAT
36585911 AAAAT
1 AAAAT
36585916 GCATCAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
25 3 0.06
26 13 0.28
27 4 0.09
28 17 0.36
29 10 0.21
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAATTTTATAAAAATATAAAATATAT
Found at i:36586189 original size:19 final size:20
Alignment explanation
Indices: 36586167--36586213 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
36586157 TTTCTATATA
*
36586167 TTTTATAA-TTTTTTACTAT
1 TTTTATAATTTTTTTACGAT
*
36586186 TTTTATAATTTTTTTGCGAT
1 TTTTATAATTTTTTTACGAT
36586206 TTTTATAA
1 TTTTATAA
36586214 AAAAAATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (20 bp):
TTTTATAATTTTTTTACGAT
Found at i:36586199 original size:29 final size:29
Alignment explanation
Indices: 36586137--36586197 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
36586127 ACTTCATAAA
36586137 ATTTTATAATTTTTTCTATATTTCTATAT
1 ATTTTATAATTTTTTCTATATTTCTATAT
36586166 ATTTTATAATTTTTTACTAT-TTT-TATA-
1 ATTTTATAATTTTTT-CTATATTTCTATAT
36586193 ATTTT
1 ATTTT
36586198 TTTGCGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 5 0.16
28 4 0.13
29 18 0.58
30 4 0.13
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (29 bp):
ATTTTATAATTTTTTCTATATTTCTATAT
Found at i:36586269 original size:19 final size:19
Alignment explanation
Indices: 36586227--36586281 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
36586217 AAATTCTAAT
36586227 TTTTAATATTTTTATTAAA
1 TTTTAATATTTTTATTAAA
* *
36586246 ATTTAATAGTTTTTA-TAAG
1 TTTTAATA-TTTTTATTAAA
*
36586265 TTTTATTGATTTTTATT
1 TTTTAAT-ATTTTTATT
36586282 TTTTATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTAATATTTTTATTAAA
Found at i:36592743 original size:37 final size:37
Alignment explanation
Indices: 36592660--36592743 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
36592650 TGGTATAATG
36592660 GTAAGATTTGCTCAATTAAGTTCCATTCAATATAACA
1 GTAAGATTTGCTCAATTAAGTTCCATTCAATATAACA
* *
36592697 GTATGATTTGCTCAATTGAGCTT-CATTCAATATAACA
1 GTAAGATTTGCTCAATTAAG-TTCCATTCAATATAACA
*
36592734 GTAAAATTTG
1 GTAAGATTTG
36592744 GCTTGATAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 40 0.95
38 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (37 bp):
GTAAGATTTGCTCAATTAAGTTCCATTCAATATAACA
Found at i:36595573 original size:19 final size:19
Alignment explanation
Indices: 36595537--36595575 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
36595527 TATTATTAAT
**
36595537 ATATTTATAATTCTAATAA
1 ATATTTATAATTAAAATAA
*
36595556 ATATTTATTATTAAAATAA
1 ATATTTATAATTAAAATAA
36595575 A
1 A
36595576 ATTAAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:36595598 original size:12 final size:12
Alignment explanation
Indices: 36595578--36595625 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
36595568 AAAATAAAAT
*
36595578 TAAAATATTAAA
1 TAAATTATTAAA
36595590 TAAATTATTAAAA
1 TAAATTATT-AAA
*
36595603 TAAATTATATTAA
1 TAAATTAT-TAAA
*
36595616 TAATTTATTA
1 TAAATTATTA
36595626 TATGACTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 9 0.30
13 20 0.67
14 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATTATTAAA
Found at i:36595601 original size:26 final size:25
Alignment explanation
Indices: 36595572--36595625 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
36595562 ATTATTAAAA
36595572 TAAAATTAAA-ATATTAAATAAATTAT
1 TAAAA-TAAATATATT-AATAAATTAT
*
36595598 TAAAATAAATTATATTAATAATTTAT
1 TAAAATAAA-TATATTAATAAATTAT
36595624 TA
1 TA
36595626 TATGACTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 4 0.16
26 16 0.64
27 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAAATAAATATATTAATAAATTAT
Found at i:36595603 original size:13 final size:13
Alignment explanation
Indices: 36595572--36595610 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
36595562 ATTATTAAAA
*
36595572 TAAAATTAAAATAT
1 TAAAA-TAAATTAT
36595586 T-AAATAAATTAT
1 TAAAATAAATTAT
36595598 TAAAATAAATTAT
1 TAAAATAAATTAT
36595611 ATTAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 8 0.35
13 14 0.61
14 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAAATTAT
Found at i:36597918 original size:15 final size:16
Alignment explanation
Indices: 36597884--36597919 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
36597874 CTAAAATAAA
36597884 TAATT-ATAATTATTT
1 TAATTAATAATTATTT
36597899 T-ATTAATAA-TATTT
1 TAATTAATAATTATTT
36597913 TAATTAA
1 TAATTAA
36597920 AAAAATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTAATAATTATTT
Found at i:36600605 original size:47 final size:46
Alignment explanation
Indices: 36600490--36600614 Score: 135
Period size: 46 Copynumber: 2.7 Consensus size: 46
36600480 GGCAATTTAC
* * **
36600490 CTGCTCGACCAGTGGTTTATGCACAACGTATTTTACAGTAGTTTAT
1 CTGCTCGACCAGTGGTTTATCCACAACGTATTTTACAGGAGTCCAT
* * * *
36600536 CTGCTCAACCAGCGATTTATCCACAACGTATTTTAGTCGGGAG-CCAT
1 CTGCTCGACCAGTGGTTTATCCACAACGTATTTTA--CAGGAGTCCAT
* *
36600583 CTGCTCGACCAGTGGTTCATCCACAACATATT
1 CTGCTCGACCAGTGGTTTATCCACAACGTATT
36600615 AAACAACATT
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
46 31 0.48
47 29 0.45
48 4 0.06
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (46 bp):
CTGCTCGACCAGTGGTTTATCCACAACGTATTTTACAGGAGTCCAT
Found at i:36600694 original size:94 final size:94
Alignment explanation
Indices: 36600580--36600797 Score: 237
Period size: 93 Copynumber: 2.3 Consensus size: 94
36600570 AGTCGGGAGC
* * * ** *
36600580 CATCTGCTCGACCAGTGGTTCATCCACAACATATTAAACAACATTT-ATTTGCACCTATGGATGG
1 CATCTGCACGACCAGTGGTTCATCCACAACATATT-AAC-ACATTTGATATACACAAAAGGATGG
*
36600644 TTAATCCACCAATACTT-TTA-GTTGGCAGTT
64 TTAATCCACCAATA-TTCTTATGTTAGCAGTT
* ** * *
36600674 TATCTGCACGACCAGTGGTTCATCCACAATGTATTAGCATATTTGATATACACAAAAGGATGGTT
1 CATCTGCACGACCAGTGGTTCATCCACAACATATTAACACATTTGATATACACAAAAGGATGGTT
*
36600739 CATCCACCAATATTCTTATTGTTAGCAGTT
66 AATCCACCAATATTCTTA-TGTTAGCAGTT
*
36600769 CATCTGCAACGATCAGTGGTT-ATCCACAA
1 CATCTGC-ACGACCAGTGGTTCATCCACAA
36600798 TGTGGTGTGA
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
92 7 0.07
93 31 0.30
94 31 0.30
95 23 0.22
96 12 0.12
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (94 bp):
CATCTGCACGACCAGTGGTTCATCCACAACATATTAACACATTTGATATACACAAAAGGATGGTT
AATCCACCAATATTCTTATGTTAGCAGTT
Found at i:36618428 original size:20 final size:19
Alignment explanation
Indices: 36618400--36618439 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
36618390 TTGAACTTTG
36618400 TCAAAATTTTTCTAAG-TGT
1 TCAAAA-TTTTCTAAGATGT
36618419 TCAAACATTTTCTAAGATGT
1 TCAAA-ATTTTCTAAGATGT
36618439 T
1 T
36618440 TAGAAGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (19 bp):
TCAAAATTTTCTAAGATGT
Found at i:36644684 original size:84 final size:84
Alignment explanation
Indices: 36644596--36644825 Score: 218
Period size: 84 Copynumber: 2.7 Consensus size: 84
36644586 GTACTCCAAG
** *
36644596 GAGACTCAAGTTCA-AGCAAAG-GGTATATGTTAATAA-CATAAATGATGATAACCAAAACAGTA
1 GAGACTCAAGTTCAGA-CAAAGAGAAAT-TGTTAACAACCA-AAATGATGATAACCAAAACAGTA
*
36644658 GAGTCAAGGAGTTTACCCCGAA
63 AAGTCAAGGAGTTTACCCCGAA
* * * *
36644680 GAGACTCAAGTTCAGACGAAGAGAAATTGTTGACAACCAAAATGGTGATAACCAAAACGGTAAAG
1 GAGACTCAAGTTCAGACAAAGAGAAATTGTTAACAACCAAAATGATGATAACCAAAACAGTAAAG
* *
36644745 TCAAGGAGTGTACTCC-AA
66 TCAAGGAGTTTACCCCGAA
* * * * * * * *
36644763 TGAGACTGAAATTTC-GGCGAAGAGTAATTGTTGACAACCAAAATGGTGATAACAAAAACAGTA
1 -GAGACT-CAAGTTCAGACAAAGAGAAATTGTTAACAACCAAAATGATGATAACCAAAACAGTA
36644826 GAATCGAGGA
Statistics
Matches: 125, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
83 2 0.02
84 112 0.90
85 11 0.09
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (84 bp):
GAGACTCAAGTTCAGACAAAGAGAAATTGTTAACAACCAAAATGATGATAACCAAAACAGTAAAG
TCAAGGAGTTTACCCCGAA
Found at i:36644986 original size:81 final size:81
Alignment explanation
Indices: 36644926--36645262 Score: 584
Period size: 81 Copynumber: 4.2 Consensus size: 81
36644916 AGGAGTTTAG
* * *
36644926 TCCAAGGAAACTTGAGTCCTGCCAAAGAAATCTCGACAACAGAAATTCTGATGATCAAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
36644991 GAGGTGAGGACTCTGC
66 GAGGTGAGGACTCTGC
36645007 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
36645072 GAGGTGAGGACTCTGC
66 GAGGTGAGGACTCTGC
*
36645088 TCCAACGACACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
*
36645153 GAGGTGAGGACACTGC
66 GAGGTGAGGACTCTGC
* * *
36645169 TCCAACAAAACTTGAGTCCTGCCGAAGAGCTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
*
36645234 GAGGTGAGGACTCAGC
66 GAGGTGAGGACTCTGC
*
36645250 TCCAAGGAAACTT
1 TCCAACGAAACTT
36645263 ATCTTCAGGC
Statistics
Matches: 243, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 243 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (81 bp):
TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
GAGGTGAGGACTCTGC
Found at i:36657406 original size:24 final size:23
Alignment explanation
Indices: 36657347--36657418 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
36657337 GCGCATTCGT
*
36657347 ATATGAGAGTCCCTTGTGTGGGATG
1 ATATGAGAG-CCCTT-TATGGGATG
* *
36657372 -TATAAGAGCCCTTTTTGGGATG
1 ATATGAGAGCCCTTTATGGGATG
*
36657394 CATATGAGAGCCCCTTATGGGATG
1 -ATATGAGAGCCCTTTATGGGATG
36657418 A
1 A
36657419 ATGGAAGTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 8 0.20
23 6 0.15
24 26 0.65
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.31
Consensus pattern (23 bp):
ATATGAGAGCCCTTTATGGGATG
Found at i:36657499 original size:28 final size:28
Alignment explanation
Indices: 36657474--36657642 Score: 137
Period size: 28 Copynumber: 6.0 Consensus size: 28
36657464 TAGGATGATT
*
36657474 TTAAACGTGGAAGTCCGTCAGAATGATC
1 TTAAACGTGGAAGTCCGTCAGAACGATC
** * *
36657502 TTAAACGTGGAAGTTTG-CTAGGACAATC
1 TTAAACGTGGAAGTCCGTC-AGAACGATC
* * **
36657530 TTAAACGTGGAAGTCTGCCAGAATAATC
1 TTAAACGTGGAAGTCCGTCAGAACGATC
* * *
36657558 CTAAGCGTGGAAGTCC-TCCAGGACGATC
1 TTAAACGTGGAAGTCCGT-CAGAACGATC
* * * *
36657586 TTAAACATGGAAATTCATCAGAACGATC
1 TTAAACGTGGAAGTCCGTCAGAACGATC
*
36657614 TTAAATGTGGAAGTCCGTCATG-ACGATC
1 TTAAACGTGGAAGTCCGTCA-GAACGATC
36657642 T
1 T
36657643 AATGTGAAAG
Statistics
Matches: 110, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
27 1 0.01
28 106 0.96
29 3 0.03
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (28 bp):
TTAAACGTGGAAGTCCGTCAGAACGATC
Found at i:36657517 original size:56 final size:56
Alignment explanation
Indices: 36657453--36657627 Score: 190
Period size: 56 Copynumber: 3.1 Consensus size: 56
36657443 ACCATACACA
* *
36657453 TGGAAGTTTGCTAGGATGATTTTAAACGTGGAAGTCCGTCAGAATGATCTTAAACG
1 TGGAAGTTTGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAATGATCTTAAACG
* * * * * *
36657509 TGGAAGTTTGCTAGGACAATCTTAAACGTGGAAGTCTGCCAGAATAATCCTAAGCG
1 TGGAAGTTTGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAATGATCTTAAACG
* * * * * * * *
36657565 TGGAAGTCCT-CCAGGACGATCTTAAACATGGAAATTCATCAGAACGATCTTAAATG
1 TGGAAGT-TTGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAATGATCTTAAACG
36657621 TGGAAGT
1 TGGAAGT
36657628 CCGTCATGAC
Statistics
Matches: 96, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
56 95 0.99
57 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (56 bp):
TGGAAGTTTGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAATGATCTTAAACG
Found at i:36660631 original size:23 final size:24
Alignment explanation
Indices: 36660605--36660665 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
36660595 ACAAAAAATT
* *
36660605 TAAAGAAAAATAATTGAAATA-AA
1 TAAAGAAAAATAAGTAAAATAGAA
**
36660628 TAAACTAAAATAAGTAAAATAGAA
1 TAAAGAAAAATAAGTAAAATAGAA
*
36660652 TAATAGAACAATAA
1 TAA-AGAAAAATAA
36660666 ATAAGAAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
23 17 0.59
24 5 0.17
25 7 0.24
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.21
Consensus pattern (24 bp):
TAAAGAAAAATAAGTAAAATAGAA
Found at i:36673970 original size:20 final size:21
Alignment explanation
Indices: 36673947--36674001 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
36673937 TCTGGCAAAA
36673947 ACACTTGTTTTTTCATTT-TC
1 ACACTTGTTTTTTCATTTGTC
* *
36673967 ACACTCTTTTTTTTCTTTTGTC
1 ACACT-TGTTTTTTCATTTGTC
* *
36673989 GCTCTTGTTTTTT
1 ACACTTGTTTTTT
36674002 TTATCACTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 5 0.18
21 18 0.64
22 5 0.18
ACGTcount: A:0.09, C:0.20, G:0.07, T:0.64
Consensus pattern (21 bp):
ACACTTGTTTTTTCATTTGTC
Found at i:36674058 original size:14 final size:15
Alignment explanation
Indices: 36674017--36674071 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
36674007 ACTCTCATCA
*
36674017 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
36674032 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
36674047 TTCTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
36674061 TTCTCTTTCTC
1 TTCT-TTTCTC
36674072 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
14 10 0.29
15 23 0.66
16 2 0.06
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:36678931 original size:19 final size:19
Alignment explanation
Indices: 36678907--36678943 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
36678897 CTTGAAGACA
*
36678907 AGGCCCAATAAGATGTTCC
1 AGGCCCAATAAGAAGTTCC
36678926 AGGCCCAATAAGAAGTTC
1 AGGCCCAATAAGAAGTTC
36678944 AAACTAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (19 bp):
AGGCCCAATAAGAAGTTCC
Found at i:36681089 original size:17 final size:17
Alignment explanation
Indices: 36681067--36681101 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
36681057 GGAAGACAGA
36681067 AAAAGA-AATCGAAAAAG
1 AAAAGAGAAT-GAAAAAG
36681084 AAAAGAGAATGAAAAAG
1 AAAAGAGAATGAAAAAG
36681101 A
1 A
36681102 GCAAAAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.71, C:0.03, G:0.20, T:0.06
Consensus pattern (17 bp):
AAAAGAGAATGAAAAAG
Found at i:36682946 original size:34 final size:33
Alignment explanation
Indices: 36682871--36682946 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
36682861 GAGTTAGTTT
*
36682871 ATTAAATTTAGTTCAACTCAAATAAGTGTTAGA
1 ATTAATTTTAGTTCAACTCAAATAAGTGTTAGA
* * *
36682904 ATTAATTTTAGTTTAGCTTAAATAAGTGTTAGTA
1 ATTAATTTTAGTTCAACTCAAATAAGTGTTAG-A
36682938 ATTAATTTT
1 ATTAATTTT
36682947 TTTAAATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 28 0.74
34 10 0.26
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (33 bp):
ATTAATTTTAGTTCAACTCAAATAAGTGTTAGA
Found at i:36694366 original size:4 final size:4
Alignment explanation
Indices: 36694357--36694383 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
36694347 TTAATTGGGA
36694357 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
36694384 GATGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:36698979 original size:26 final size:27
Alignment explanation
Indices: 36698945--36699097 Score: 78
Period size: 28 Copynumber: 5.3 Consensus size: 27
36698935 AATTGTTATA
36698945 AATATAATTTAATAAAATATATAATTT
1 AATATAATTTAATAAAATATATAATTT
36698972 AATA-AATTGTTAATAAATATTCTTATATGAATTT
1 AATATAA-T-TTAATAAA-A----TATAT-AATTT
* ** * * * **
36699006 ACTAATAAAATCATAATATATAATACTAC
1 AAT-ATAATTTAATAAAATAT-ATAATTT
* *
36699035 AATATAATTTAA-AATAAT-TATTATTA
1 AATATAATTTAATAA-AATATATAATTT
36699061 AATATAATTTAATAATAATATATAATTT
1 AATATAATTTAATAA-AATATATAATTT
*
36699089 AATAAAATT
1 AATATAATT
36699098 CTTATTCTTA
Statistics
Matches: 92, Mismatches: 20, Indels: 27
0.66 0.14 0.19
Matches are distributed among these distances:
26 17 0.18
27 14 0.15
28 30 0.33
29 8 0.09
30 2 0.02
33 6 0.07
34 12 0.13
35 1 0.01
36 2 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (27 bp):
AATATAATTTAATAAAATATATAATTT
Found at i:36699140 original size:108 final size:113
Alignment explanation
Indices: 36698927--36699184 Score: 354
Period size: 108 Copynumber: 2.3 Consensus size: 113
36698917 TTAATCATAT
* * *
36698927 TTTAACATAATTGTTA-TAAATATAATTTAATAA-AATATATAATTTAATAAATTGTTAATAAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAA-TATTAAT--AT
*
36698990 ATTCTTATATGAATTTACTAATAAAATCATAATATATAATAC-TACAATATAA
63 ATTCTTATATGAATTTAC--ATAAAATCATAATATATAATACATAAAATATAA
*
36699042 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAA-ATT-CT-TATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAATATTAATATATT
36699104 CTTATATGAATTTAC-TAAAATCATAATATATAATACTATAAAATATAA
66 CTTATATGAATTTACATAAAATCATAATATATAATAC-ATAAAATATAA
36699152 TTT-AAATAATTATTATTAAATATAATTT-ATAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAT
36699185 CTACTTTATT
Statistics
Matches: 134, Mismatches: 5, Indels: 15
0.87 0.03 0.10
Matches are distributed among these distances:
108 26 0.19
109 25 0.19
110 12 0.09
111 19 0.14
114 1 0.01
115 16 0.12
116 17 0.13
117 18 0.13
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (113 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAATATTAATATATT
CTTATATGAATTTACATAAAATCATAATATATAATACATAAAATATAA
Found at i:36699176 original size:32 final size:32
Alignment explanation
Indices: 36699140--36699203 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
36699130 TATATAATAC
*
36699140 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
** ** *
36699172 TATAATTTATAATCTACTTTATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
36699204 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATCTAAATAATTATTATTAAA
Found at i:36700645 original size:43 final size:47
Alignment explanation
Indices: 36700552--36700656 Score: 119
Period size: 49 Copynumber: 2.3 Consensus size: 47
36700542 GAAAAAAAAC
* *
36700552 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTAAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAA-G-AAACACTTCATA
*
36700601 AAATTAAAATTGAGTTCAATATCATGAAT-AAAA-AAA-AC-TCATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGAAACACTTCATA
*
36700644 AAGAATAAAATTA
1 AA-ATTAAAATTA
36700657 TAACACATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
43 6 0.12
44 10 0.20
45 3 0.06
48 4 0.08
49 27 0.54
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.30
Consensus pattern (47 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGAAACACTTCATA
Found at i:36701168 original size:64 final size:62
Alignment explanation
Indices: 36700829--36701166 Score: 586
Period size: 62 Copynumber: 5.4 Consensus size: 62
36700819 TAGAATCAAG
36700829 TTGATTATATCTAATGATCCAATTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
1 TTGATTATATCTAATGATCCAATTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
36700891 TTGATTATATCTAATGATCCAATTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
1 TTGATTATATCTAATGATCCAATTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
36700953 TTGATTATATCTAATGATCCAATTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
1 TTGATTATATCTAATGATCCAATTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
* *
36701015 TTGATTATATCTAATGATTCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
1 TTGATTATATCTAATGATCCAA--TTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
* *
36701079 TTGATTATATGTAATGATCCAATTTTAATATATTATCCATATGTTTTTTAATCAATTTGTTTAC
1 TTGATTATATCTAATGATCCAA--TTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
* *
36701143 TTGATTATATGTAATGATTCAATT
1 TTGATTATATCTAATGATCCAATT
36701167 TTTATTTTAT
Statistics
Matches: 269, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
62 147 0.55
64 122 0.45
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (62 bp):
TTGATTATATCTAATGATCCAATTAATATATTATCCATATGTTTTTTAATCAAGTTGTTTAC
Found at i:36701364 original size:32 final size:32
Alignment explanation
Indices: 36701284--36701365 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
36701274 TAGAAATATT
*
36701284 TTTAATTAATGAGTAGTATATGAATATACACA
1 TTTAATTAATGAGTTGTATATGAATATACACA
36701316 TTTAATTAATGAGTTGTATATGAATATACACA
1 TTTAATTAATGAGTTGTATATGAATATACACA
*
36701348 TTTAATTAATGCGTTGTA
1 TTTAATTAATGAGTTGTA
36701366 CACGTCTCGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.41
Consensus pattern (32 bp):
TTTAATTAATGAGTTGTATATGAATATACACA
Found at i:36701834 original size:12 final size:12
Alignment explanation
Indices: 36701817--36701863 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
36701807 GCCGCATTTT
36701817 AAGCAAAAGAAC
1 AAGCAAAAGAAC
36701829 AAGCAAAAGAAC
1 AAGCAAAAGAAC
*
36701841 GAGCAAAAGAA-
1 AAGCAAAAGAAC
36701852 AAG--AAAGAAC
1 AAGCAAAAGAAC
36701862 AA
1 AA
36701864 ATAACAAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 2 0.06
12 22 0.69
ACGTcount: A:0.68, C:0.13, G:0.19, T:0.00
Consensus pattern (12 bp):
AAGCAAAAGAAC
Found at i:36703910 original size:16 final size:16
Alignment explanation
Indices: 36703889--36703937 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
36703879 TTCGCTGTAT
36703889 TGGAATAGAGGCATAA
1 TGGAATAGAGGCATAA
36703905 TGGAATAGAGG-AGTAA
1 TGGAATAGAGGCA-TAA
*
36703921 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCATAA
36703937 T
1 T
36703938 AGCAAATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 1 0.03
16 29 0.97
ACGTcount: A:0.41, C:0.04, G:0.35, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCATAA
Found at i:36704289 original size:120 final size:120
Alignment explanation
Indices: 36704150--36704485 Score: 618
Period size: 120 Copynumber: 2.8 Consensus size: 120
36704140 TTAATCATAT
36704150 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
*
36704215 AAATATTCTTATATGAATTTTCTAAAATCATAGTATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
* *
36704270 TTTAACATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
36704335 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
*
36704390 TTTAACATAATTATTATTAATTATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
**
36704455 AAATATTCTTATATGAATTTAATAAAATCAT
66 AAATATTCTTATATGAATTTTCTAAAATCAT
36704486 GTAAAAAGAA
Statistics
Matches: 208, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 208 1.00
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
Found at i:36708138 original size:22 final size:24
Alignment explanation
Indices: 36708090--36708142 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
36708080 AATTTTGTGT
36708090 TATTTTTAAAATTATTAAATAATA
1 TATTTTTAAAATTATTAAATAATA
36708114 TATTTTTATAAATT-TTAAA-ATATA
1 TATTTTTA-AAATTATTAAATA-ATA
36708138 TATTT
1 TATTT
36708143 GCTAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 1 0.04
24 21 0.78
25 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTTTTAAAATTATTAAATAATA
Found at i:36713829 original size:19 final size:19
Alignment explanation
Indices: 36713805--36713848 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
36713795 AAAATTAGAA
36713805 AAAAATTGTTAAAAA-ATAT
1 AAAAATTG-TAAAAATATAT
*
36713824 AAAAATTGTAAAAATTTAT
1 AAAAATTGTAAAAATATAT
36713843 AAAAAT
1 AAAAAT
36713849 CATAAAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAAATTGTAAAAATATAT
Found at i:36713845 original size:28 final size:30
Alignment explanation
Indices: 36713805--36713876 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 30
36713795 AAAATTAGAA
*
36713805 AAAAATTGT-TAAAAAAT-ATAAAA-ATTGT
1 AAAAATT-TATAAAAAATCATAAAAGATTAT
36713833 AAAAATTTAT-AAAAATCATAAAAGATTAT
1 AAAAATTTATAAAAAATCATAAAAGATTAT
*
36713862 -AAAATGTATAAAAAA
1 AAAAATTTATAAAAAA
36713877 GCCCTTTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 7 0.18
28 22 0.58
29 9 0.24
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (30 bp):
AAAAATTTATAAAAAATCATAAAAGATTAT
Found at i:36713854 original size:19 final size:19
Alignment explanation
Indices: 36713821--36713865 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
36713811 TGTTAAAAAA
**
36713821 TATAAAAATTGTAAAA-ATT
1 TATAAAAATCATAAAAGA-T
36713840 TATAAAAATCATAAAAGAT
1 TATAAAAATCATAAAAGAT
36713859 TATAAAA
1 TATAAAA
36713866 TGTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
TATAAAAATCATAAAAGAT
Found at i:36713863 original size:10 final size:9
Alignment explanation
Indices: 36713739--36713875 Score: 64
Period size: 10 Copynumber: 14.6 Consensus size: 9
36713729 ACATGTGACA
36713739 AAAAATTAT
1 AAAAATTAT
36713748 AAAAA--AT
1 AAAAATTAT
* *
36713755 AGAAATCAAT
1 AAAAAT-TAT
*
36713765 AAAAAATAT
1 AAAAATTAT
*
36713774 AAAAGTTATT
1 AAAAATTA-T
**
36713784 AAATTTTATT
1 AAAAATTA-T
* *
36713794 CAAAATTAGAA
1 AAAAATT--AT
*
36713805 AAAAATTGTT
1 AAAAATT-AT
*
36713815 AAAAAATAT
1 AAAAATTAT
*
36713824 AAAAATTGT
1 AAAAATTAT
36713833 AAAAATTTAT
1 AAAAA-TTAT
*
36713843 AAAAATCAT
1 AAAAATTAT
36713852 AAAAGATTAT
1 AAAA-ATTAT
36713862 -AAAATGTAT
1 AAAAAT-TAT
36713871 AAAAA
1 AAAAA
36713876 AGCCCTTTAA
Statistics
Matches: 96, Mismatches: 22, Indels: 19
0.70 0.16 0.14
Matches are distributed among these distances:
7 6 0.06
8 2 0.02
9 39 0.41
10 42 0.44
11 6 0.06
12 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:36714060 original size:9 final size:9
Alignment explanation
Indices: 36714046--36714229 Score: 101
Period size: 9 Copynumber: 20.0 Consensus size: 9
36714036 TTTTGGAATG
36714046 ATAATTTTT
1 ATAATTTTT
36714055 ATAATTTTT
1 ATAATTTTT
* *
36714064 TTACGAATTTT
1 ATA--ATTTTT
*
36714075 ATATTTCTTT
1 ATAATT-TTT
*
36714085 AAAATTTTT
1 ATAATTTTT
36714094 ATAATTTTCTT
1 ATAA-TTT-TT
*
36714105 ATGA-TTTT
1 ATAATTTTT
*
36714113 ATAAAATTTT
1 AT-AATTTTT
*
36714123 AAAATTTTT
1 ATAATTTTT
36714132 AT-ATTTTT
1 ATAATTTTT
**
36714140 ACGATTTTT
1 ATAATTTTT
36714149 AT-ATTTTT
1 ATAATTTTT
36714157 -TAATTTTT
1 ATAATTTTT
*
36714165 AATTATTTATT
1 -ATAATTT-TT
* *
36714176 AAAATTTAAT
1 ATAATTT-TT
**
36714186 ATTTTTTTT
1 ATAATTTTT
*
36714195 ATAAATTTT
1 ATAATTTTT
36714204 ATAAATTTTT
1 AT-AATTTTT
36714214 AT--TTTTT
1 ATAATTTTT
36714221 ATAATTTTT
1 ATAATTTTT
36714230 TCCACACGTC
Statistics
Matches: 133, Mismatches: 27, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
7 8 0.06
8 23 0.17
9 49 0.37
10 39 0.29
11 14 0.11
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:36714093 original size:19 final size:19
Alignment explanation
Indices: 36714048--36714230 Score: 102
Period size: 19 Copynumber: 9.9 Consensus size: 19
36714038 TTGGAATGAT
*
36714048 AATTTTTATAATTTTTTTACG
1 AATTTTTATAA-TTTTTTA-A
36714069 AA-TTTTAT-ATTTCTTTAA
1 AATTTTTATAATTT-TTTAA
*
36714087 AATTTTTATAATTTTCTTAT
1 AATTTTTATAATTTT-TTAA
* **
36714107 GA-TTTTATAAAATTTTAA
1 AATTTTTATAATTTTTTAA
*
36714125 AATTTTTAT-A-TTTTTAC
1 AATTTTTATAATTTTTTAA
*
36714142 GATTTTTAT-ATTTTTT--
1 AATTTTTATAATTTTTTAA
* *
36714158 AATTTTTAATTATTTATTAA
1 AATTTTT-ATAATTTTTTAA
* *
36714178 AA-TTTAATATTTTTTTTATA
1 AATTTTTATA-ATTTTTTA-A
*
36714198 AA-TTTTATAAATTTTT--
1 AATTTTTATAATTTTTTAA
*
36714214 ATTTTTTATAATTTTTT
1 AATTTTTATAATTTTTT
36714231 CCACACGTCA
Statistics
Matches: 128, Mismatches: 21, Indels: 30
0.72 0.12 0.17
Matches are distributed among these distances:
16 7 0.05
17 29 0.23
18 23 0.18
19 42 0.33
20 25 0.20
21 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTTTTATAATTTTTTAA
Found at i:36714124 original size:38 final size:39
Alignment explanation
Indices: 36714048--36714151 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 39
36714038 TTGGAATGAT
* **
36714048 AATTTTTATAATTTTTTTACGAATTTTATATTTCTTTAA
1 AATTTTTATAATTTTCTTACGAATTTTATAAATCTTTAA
*
36714087 AATTTTTATAATTTTCTTATG-ATTTTATAAAAT-TTTAA
1 AATTTTTATAATTTTCTTACGAATTTTAT-AAATCTTTAA
*
36714125 AATTTTTAT-A-TTT-TTACGATTTTTATA
1 AATTTTTATAATTTTCTTACGAATTTTATA
36714152 TTTTTTAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
35 5 0.09
36 9 0.16
37 1 0.02
38 21 0.37
39 21 0.37
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (39 bp):
AATTTTTATAATTTTCTTACGAATTTTATAAATCTTTAA
Found at i:36714967 original size:20 final size:19
Alignment explanation
Indices: 36714925--36714968 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
36714915 CTAGTTATAG
* *
36714925 TTTTAGATTATTTTAGTGT
1 TTTTAGATTATTTTAATGC
*
36714944 TTTTATATTATTTTTAATGC
1 TTTTAGATTA-TTTTAATGC
36714964 TTTTA
1 TTTTA
36714969 AATAAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (19 bp):
TTTTAGATTATTTTAATGC
Found at i:36719680 original size:24 final size:26
Alignment explanation
Indices: 36719637--36719694 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
36719627 GTATTACACC
*
36719637 CAAACCCAAACAGCCCAAAACT-AAA
1 CAAACCCAAACAGCACAAAACTAAAA
*
36719662 CAAACCC-AACAGCATAAAACTAAAAA
1 CAAACCCAAACAGCACAAAACT-AAAA
36719688 CAAACCC
1 CAAACCC
36719695 TAGCCCCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 12 0.41
25 7 0.24
26 10 0.34
ACGTcount: A:0.57, C:0.34, G:0.03, T:0.05
Consensus pattern (26 bp):
CAAACCCAAACAGCACAAAACTAAAA
Found at i:36722838 original size:22 final size:22
Alignment explanation
Indices: 36722812--36722856 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
36722802 AGAGACAGGA
36722812 AGAGAAAGTCTACATGTTAAAC
1 AGAGAAAGTCTACATGTTAAAC
36722834 AGAGAAAGTCTACATGTTAAAC
1 AGAGAAAGTCTACATGTTAAAC
36722856 A
1 A
36722857 ATGCCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (22 bp):
AGAGAAAGTCTACATGTTAAAC
Found at i:36728589 original size:22 final size:23
Alignment explanation
Indices: 36728546--36728589 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
36728536 ATTCAAAATA
*
36728546 TTTATAAAAATTTCAAATATTTT
1 TTTATAAAAATTTCAAAAATTTT
36728569 TTTA-AAAAATTAT-AAAAATTT
1 TTTATAAAAATT-TCAAAAATTT
36728590 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTATAAAAATTTCAAAAATTTT
Found at i:36736407 original size:106 final size:106
Alignment explanation
Indices: 36736217--36736423 Score: 360
Period size: 106 Copynumber: 2.0 Consensus size: 106
36736207 TCGACTACAA
* *
36736217 AAAGAGAGCGTCGAAAAAACTACATTCTTAGATTTGGACTTAAAATGGAATTTATGAGACATACT
1 AAAGAGAGCATCCAAAAAACTACATTCTTAGATTTGGACTTAAAATGGAATTTATGAGACATACT
*
36736282 AACCTCTTTTTTTACGATTCGTGTGTCCAAATCATAGATCG
66 AACCTCTTTTTGTACGATTCGTGTGTCCAAATCATAGATCG
* *
36736323 AAAGAGAGCATCCAAATAACTACATTCTTAGATTTGGACTTAAGATGGAATTTATGAGACATACT
1 AAAGAGAGCATCCAAAAAACTACATTCTTAGATTTGGACTTAAAATGGAATTTATGAGACATACT
*
36736388 AACCTCTTTTTGTATGATTCGTGTGTCCAAATCATA
66 AACCTCTTTTTGTACGATTCGTGTGTCCAAATCATA
36736424 TATCTTCAAT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 95 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (106 bp):
AAAGAGAGCATCCAAAAAACTACATTCTTAGATTTGGACTTAAAATGGAATTTATGAGACATACT
AACCTCTTTTTGTACGATTCGTGTGTCCAAATCATAGATCG
Found at i:36738323 original size:54 final size:56
Alignment explanation
Indices: 36738257--36738362 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 56
36738247 TGTAAAGTTC
36738257 ATTGATTCTGTTAATTT-ATTT-TGTTTG-TAGAGAGTAGTGCATGACTCAAATTTA
1 ATTGATTCTGTTAATTTCATTTCTGTTTGCT-GAGAGTAGTGCATGACTCAAATTTA
* * * *
36738311 ATTGATTTTGTTAATTTCTTTTCTTTTTGCTGAGAGTAGTGTATGACTCAAA
1 ATTGATTCTGTTAATTTCATTTCTGTTTGCTGAGAGTAGTGCATGACTCAAA
36738363 CCGGTAATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
54 16 0.36
55 3 0.07
56 25 0.56
57 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.48
Consensus pattern (56 bp):
ATTGATTCTGTTAATTTCATTTCTGTTTGCTGAGAGTAGTGCATGACTCAAATTTA
Found at i:36741380 original size:27 final size:27
Alignment explanation
Indices: 36741348--36741414 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
36741338 CCTATCAGGT
*
36741348 AGGCGCCAATGAAGGTGCTTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
36741375 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
36741402 AGGCGCCAATGAA
1 AGGCGCCAATGAA
36741415 TATTGTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.22, G:0.33, T:0.13
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:36741434 original size:19 final size:19
Alignment explanation
Indices: 36741410--36741746 Score: 144
Period size: 19 Copynumber: 16.8 Consensus size: 19
36741400 AGAGGCGCCA
36741410 ATGAATATTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
*
36741429 ATGAATATTGTAATTATTTT
1 ATGAATATTGTAATT-TTGT
36741449 AT-AATTAAATTTGT-ATTTATAGTT
1 ATGAA-T--A-TTGTAATTT-T-G-T
* * *
36741473 TTGGAT-TAGT-ATTTTGT
1 ATGAATATTGTAATTTTGT
36741490 ATGAATATTGTAATTTTTTGT
1 ATGAATATTGTAA--TTTTGT
36741511 ATGAATATTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
*
36741530 ATGAATATTGTAA-TAT-T
1 ATGAATATTGTAATTTTGT
* *
36741547 AT-AATTTTGTATGAATATTG-
1 ATGAATATTG--T-AATTTTGT
*
36741567 -T-AATTTTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
* *
36741584 ATGAATATTGTAATGTCGGGATAT
1 ATGAATATTGTAAT-T----TTGT
*
36741608 ATTGTAATATTGTAATTTTTTGC
1 A-TG-AATATTGTAA--TTTTGT
*
36741631 ATGAATATTGTAATTATTTT
1 ATGAATATTGTAATT-TTGT
36741651 AT-AATTAAATTTGT-ATTTATAGTT
1 ATGAA-T--A-TTGTAATTT-T-G-T
* * *
36741675 TTGGAT-TAGT-ATTTTGT
1 ATGAATATTGTAATTTTGT
36741692 ATGAATATTGTAATTTTTTGT
1 ATGAATATTGTAA--TTTTGT
*
36741713 ATGAATATTGTAGTTTTGT
1 ATGAATATTGTAATTTTGT
36741732 ATGAATATTGTAATT
1 ATGAATATTGTAATT
36741747 ATTTTATAAT
Statistics
Matches: 245, Mismatches: 30, Indels: 86
0.68 0.08 0.24
Matches are distributed among these distances:
16 12 0.05
17 14 0.06
18 12 0.05
19 84 0.34
20 27 0.11
21 49 0.20
22 12 0.05
23 10 0.04
24 9 0.04
25 4 0.02
26 10 0.04
27 1 0.00
28 1 0.00
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.53
Consensus pattern (19 bp):
ATGAATATTGTAATTTTGT
Found at i:36741509 original size:21 final size:21
Alignment explanation
Indices: 36741484--36741573 Score: 112
Period size: 21 Copynumber: 4.1 Consensus size: 21
36741474 TGGATTAGTA
36741484 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
36741505 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
36741524 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
36741549 AATTTTGTATGAATATTGTAATT
1 --TTTTGTATGAATATTGTAATT
36741572 TT
1 TT
36741574 GTAATTTTGT
Statistics
Matches: 61, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.28
20 1 0.02
21 22 0.36
23 1 0.02
24 1 0.02
25 1 0.02
26 1 0.02
27 17 0.28
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:36741545 original size:27 final size:27
Alignment explanation
Indices: 36741493--36741597 Score: 150
Period size: 27 Copynumber: 4.1 Consensus size: 27
36741483 ATTTTGTATG
36741493 AATATTGTAATTTT-T-TG--TA-TG-
1 AATATTGTAATTTTGTATGAATATTGT
36741514 AATATTGTAATTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
*
36741541 AATATTATAATTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
*
36741568 AATTTTGTAATTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
36741595 AAT
1 AAT
36741598 GTCGGGATAT
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
21 14 0.19
22 1 0.01
23 2 0.03
25 2 0.03
26 2 0.03
27 54 0.72
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (27 bp):
AATATTGTAATTTTGTATGAATATTGT
Found at i:36741740 original size:101 final size:100
Alignment explanation
Indices: 36741410--36741764 Score: 456
Period size: 101 Copynumber: 3.5 Consensus size: 100
36741400 AGAGGCGCCA
36741410 ATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTT
1 ATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATT-AATTTGTATTTATAGTTTT
36741475 GGATTAGTATTTTGTATGAATATTGTAATTTTTTGT
65 GGATTAGTATTTTGTATGAATATTGTAATTTTTTGT
** *
36741511 ATGAATATTGTAATTTTGTATGAATATTGTAA-TA--TTATAA-T--TTTGTATGAATA-TTGT-
1 ATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTGTATTTATAGTTTTG
* * *** *
36741568 AATTTTGTAATTTTGTATGAATATTGTAATGTCGGGATAT
66 GA-TTAGT-ATTTTGTATGAATATTGTAAT-T--TTTTGT
*
36741608 ATTGTAATATTGTAATTTTTTGCATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAG
1 A-TG-AATATTGTAA--TTTTGTATGAATATTGTAATTATTTTATAATT-AATTTGTATTTATAG
36741673 TTTTGGATTAGTATTTTGTATGAATATTGTAATTTTTTGT
61 TTTTGGATTAGTATTTTGTATGAATATTGTAATTTTTTGT
*
36741713 ATGAATATTGTAGTTTTGTATGAATATTGTAATTATTTTATAATTAATTTGT
1 ATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTGT
36741765 TAGTAATTTA
Statistics
Matches: 215, Mismatches: 21, Indels: 37
0.79 0.08 0.14
Matches are distributed among these distances:
92 1 0.00
93 7 0.03
94 31 0.14
95 1 0.00
97 4 0.02
98 8 0.04
99 10 0.05
100 9 0.04
101 81 0.38
102 2 0.01
103 9 0.04
104 8 0.04
105 4 0.02
107 1 0.00
108 31 0.14
109 7 0.03
110 1 0.00
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (100 bp):
ATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTGTATTTATAGTTTTG
GATTAGTATTTTGTATGAATATTGTAATTTTTTGT
Found at i:36745822 original size:23 final size:24
Alignment explanation
Indices: 36745796--36745849 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
36745786 TTAACTAATA
* *
36745796 CTAAA-AGGTATTATTAAATGAAC
1 CTAAACAGATATTATTAAATAAAC
*
36745819 CTAAACATATATTATTAAATAAAC
1 CTAAACAGATATTATTAAATAAAC
36745843 CTAAACA
1 CTAAACA
36745850 TGTCCTTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.30
Consensus pattern (24 bp):
CTAAACAGATATTATTAAATAAAC
Found at i:36745836 original size:24 final size:24
Alignment explanation
Indices: 36745804--36745850 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
36745794 TACTAAAAGG
*
36745804 TATTATTAAATGAACCTAAACATA
1 TATTATTAAATAAACCTAAACATA
36745828 TATTATTAAATAAACCTAAACAT
1 TATTATTAAATAAACCTAAACAT
36745851 GTCCTTAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (24 bp):
TATTATTAAATAAACCTAAACATA
Found at i:36747491 original size:35 final size:35
Alignment explanation
Indices: 36747452--36747525 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
36747442 AGAATAACAA
*
36747452 TTTTACTGGTTTTTATTAAAGAAGAGAAATTTTCT
1 TTTTACTGGTTTCTATTAAAGAAGAGAAATTTTCT
36747487 TTTTACTGGTTTCTATTAAAGAAGAGAAATTTTCT
1 TTTTACTGGTTTCTATTAAAGAAGAGAAATTTTCT
36747522 TTTT
1 TTTT
36747526 CACCTCAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.50
Consensus pattern (35 bp):
TTTTACTGGTTTCTATTAAAGAAGAGAAATTTTCT
Found at i:36748824 original size:29 final size:29
Alignment explanation
Indices: 36748777--36748858 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
36748767 TTACCTCATG
* *
36748777 TTTATTGTCCTGACGGACTTTATCTTCTA
1 TTTATTGTCCCGACAGACTTTATCTTCTA
* * * *
36748806 TTTATTGTCCCGGCAGACTTTGTCTTGTG
1 TTTATTGTCCCGACAGACTTTATCTTCTA
* * *
36748835 TTTACTATCCCTACAGACTTTATC
1 TTTATTGTCCCGACAGACTTTATC
36748859 CCATGTTTAC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (29 bp):
TTTATTGTCCCGACAGACTTTATCTTCTA
Found at i:36748865 original size:29 final size:29
Alignment explanation
Indices: 36748819--36748927 Score: 130
Period size: 29 Copynumber: 3.8 Consensus size: 29
36748809 ATTGTCCCGG
* *
36748819 CAGACTTTGTCTTGTGTTTACTATCCCTA
1 CAGACTTTATCTCGTGTTTACTATCCCTA
* * *
36748848 CAGACTTTATCCCATGTTTACTAT-CTTGA
1 CAGACTTTATCTCGTGTTTACTATCCCT-A
* *
36748877 CAGACTTTATCTCGTGTTTACTGTCCCAA
1 CAGACTTTATCTCGTGTTTACTATCCCTA
*
36748906 CAAACTTTATCTCGTGTTTACT
1 CAGACTTTATCTCGTGTTTACT
36748928 GTCTCTACGA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 64 0.96
30 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (29 bp):
CAGACTTTATCTCGTGTTTACTATCCCTA
Found at i:36748902 original size:87 final size:86
Alignment explanation
Indices: 36748756--36748927 Score: 195
Period size: 87 Copynumber: 2.0 Consensus size: 86
36748746 GTTTCTCTTG
* * * * **
36748756 TCCCAACAGACTTACCTCATGTTTATTGTCCTGACGGACTTTATCTTCTATTTATTGTCCCGGCA
1 TCCCAACAGACTTACCTCATGTTTACTATCCTGACAGACTTTATCTTCTATTTACTGTCCCAACA
* * *
36748821 GACTTTGTCTTGTGTTTACTA
66 AACTTTATCTCGTGTTTACTA
* * *
36748842 TCCCTACAGACTTTATCC-CATGTTTACTATCTTGACAGACTTTATC-TCGTGTTTACTGTCCCA
1 TCCCAACAGAC-TTA-CCTCATGTTTACTATCCTGACAGACTTTATCTTC-TATTTACTGTCCCA
36748905 ACAAACTTTATCTCGTGTTTACT
63 ACAAACTTTATCTCGTGTTTACT
36748928 GTCTCTACGA
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
86 12 0.17
87 57 0.80
88 2 0.03
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (86 bp):
TCCCAACAGACTTACCTCATGTTTACTATCCTGACAGACTTTATCTTCTATTTACTGTCCCAACA
AACTTTATCTCGTGTTTACTA
Found at i:36750967 original size:19 final size:19
Alignment explanation
Indices: 36750939--36751049 Score: 159
Period size: 19 Copynumber: 5.8 Consensus size: 19
36750929 AATCTTCAGG
*
36750939 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
36750958 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
* *
36750977 AATATATAATCTTAGATAT
1 GATATACAATCTTAGATAT
* *
36750996 GATATGCAATTTTAGATAT
1 GATATACAATCTTAGATAT
*
36751015 GATATATAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
36751034 GATATGCAATCTTAGA
1 GATATACAATCTTAGA
36751050 AGATATGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.39
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:36750989 original size:38 final size:38
Alignment explanation
Indices: 36750946--36751049 Score: 181
Period size: 38 Copynumber: 2.7 Consensus size: 38
36750936 AGGGATATGC
*
36750946 AATCTTAGATATGATATACAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
* *
36750984 AATCTTAGATATGATATGCAATTTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
36751022 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
36751050 AGATATGATT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:36751075 original size:22 final size:21
Alignment explanation
Indices: 36750939--36751075 Score: 96
Period size: 19 Copynumber: 6.9 Consensus size: 21
36750929 AATCTTCAGG
*
36750939 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
**
36750958 GATATACAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
36750977 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
36750996 GATATGCAAT-TT-TAGATAT
1 GATATGTAATCTTAGAGATAT
*
36751015 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
36751034 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
36751056 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
36751076 TTAATTTGTA
Statistics
Matches: 100, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.02
19 73 0.73
20 2 0.02
22 12 0.12
23 11 0.11
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:36751618 original size:30 final size:29
Alignment explanation
Indices: 36751570--36751626 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
36751560 CTTTTTCATT
*
36751570 TTCTTTATTTTTTATTAATTAGTTTTTTTA
1 TTCTTTATTTTATATTAATTA-TTTTTTTA
36751600 TTCTTT-TTTTATATTTAATTATTTTTT
1 TTCTTTATTTTATA-TTAATTATTTTTT
36751627 AAAAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (29 bp):
TTCTTTATTTTATATTAATTATTTTTTTA
Found at i:36751732 original size:22 final size:21
Alignment explanation
Indices: 36751684--36751744 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
36751674 TTGTAGTATA
*
36751684 ATATAATTTTTT-TTATATGT
1 ATATATTTTTTTATTATATGT
36751704 A-ATTATTTTTTTATCTATATGT
1 ATA-TATTTTTTTAT-TATATGT
*
36751726 ATATATTTATTTTAGTATA
1 ATATATTT-TTTTATTATA
36751745 CATATGTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 1 0.03
20 9 0.26
21 1 0.03
22 17 0.50
23 6 0.18
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (21 bp):
ATATATTTTTTTATTATATGT
Found at i:36762968 original size:2 final size:2
Alignment explanation
Indices: 36762961--36762990 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
36762951 GAAGTACCTC
*
36762961 CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
36762991 ATGCATTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:36771759 original size:15 final size:15
Alignment explanation
Indices: 36771739--36771771 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
36771729 AAAGAAAATA
*
36771739 CTTGGTATGGAGATT
1 CTTGGTATAGAGATT
36771754 CTTGGTATAGAGATT
1 CTTGGTATAGAGATT
36771769 CTT
1 CTT
36771772 AGAGATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.27, T:0.42
Consensus pattern (15 bp):
CTTGGTATAGAGATT
Found at i:36773458 original size:13 final size:15
Alignment explanation
Indices: 36773430--36773473 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
36773420 TTTTATCAAT
*
36773430 AATTTATTCATTTTA
1 AATTTATTCTTTTTA
*
36773445 AGTTT-TT-TTTTTA
1 AATTTATTCTTTTTA
36773458 AATTTATTCTTTTTA
1 AATTTATTCTTTTTA
36773473 A
1 A
36773474 TTTCAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (15 bp):
AATTTATTCTTTTTA
Found at i:36773475 original size:14 final size:14
Alignment explanation
Indices: 36773429--36773476 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
36773419 CTTTTATCAA
*
36773429 TAATTTATTCATTT
1 TAATTTATTCTTTT
36773443 TAAGTTT-TT-TTTT
1 TAA-TTTATTCTTTT
36773456 TAAATTTATTCTTTT
1 T-AATTTATTCTTTT
36773471 TAATTT
1 TAATTT
36773477 CAAAAGTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 7 0.24
14 14 0.48
15 8 0.28
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (14 bp):
TAATTTATTCTTTT
Found at i:36780205 original size:33 final size:33
Alignment explanation
Indices: 36780163--36780318 Score: 108
Period size: 33 Copynumber: 4.6 Consensus size: 33
36780153 CCGTTACGGT
36780163 GGAATCAGCACTTAGCAACCACCAACGATTTGG
1 GGAATCAGCACTTAGCAACCACCAACGATTTGG
* * ***
36780196 GGAATCAGCAGTTAGCAACCCCTTTCATATCCGAAGACACGG
1 GGAATCAGCACTTAGCAACCAC---CA-A--C---GATTTGG
* *
36780238 TGGAATCAGCACTTAGCAACCACCGATGATTTGG
1 -GGAATCAGCACTTAGCAACCACCAACGATTTGG
*
36780272 GGAATCAGCACTTAGCAA-C-CC--C--TTGGG
1 GGAATCAGCACTTAGCAACCACCAACGATTTGG
36780299 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
36780319 CCCTTTTTTG
Statistics
Matches: 98, Mismatches: 14, Indels: 27
0.71 0.10 0.19
Matches are distributed among these distances:
27 22 0.22
28 1 0.01
31 2 0.02
32 1 0.01
33 38 0.39
34 4 0.04
36 2 0.02
37 1 0.01
39 2 0.02
40 1 0.01
42 4 0.04
43 20 0.20
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAACGATTTGG
Found at i:36783384 original size:69 final size:69
Alignment explanation
Indices: 36783273--36783409 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
36783263 TTTGTTCACG
* *
36783273 AATCATGTTTTGAGCGTATATTTAAGTTAGGGAAGCTTTATTCTATGCAAA-TCGTACTGTGTGG
1 AATCATGTTTTGAGCGTATATTTAAGTTACGGAAGCTTTATTCTATGCAAACT-ATACTGTGTGG
36783337 GATCA
65 GATCA
*
36783342 AATCATGTTTTGAGTGTATATTTAAGTTACGGAAGCTTTATTCTATGCAAACTATACTGTGTGGG
1 AATCATGTTTTGAGCGTATATTTAAGTTACGGAAGCTTTATTCTATGCAAACTATACTGTGTGGG
36783407 ATC
66 ATC
36783410 TCATCCCTCG
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 63 0.98
70 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.39
Consensus pattern (69 bp):
AATCATGTTTTGAGCGTATATTTAAGTTACGGAAGCTTTATTCTATGCAAACTATACTGTGTGGG
ATCA
Found at i:36789022 original size:3 final size:3
Alignment explanation
Indices: 36789014--36789044 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
36789004 GAAGTGGTAA
36789014 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
36789045 CAGAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:36791232 original size:41 final size:40
Alignment explanation
Indices: 36791187--36791272 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
36791177 AGCGGCACTT
* * *
36791187 TTAGCAGCCTTTGGACAAAAAACGCCAC-TAGTAATCGAGCA
1 TTAGCAGCATTT-GACAAAAAACGCCACAAAAT-ATCGAGCA
* * *
36791228 TTAGCGGCATTTTACGAAAAACGCCACAAAATATCGAGCA
1 TTAGCAGCATTTGACAAAAAACGCCACAAAATATCGAGCA
36791268 TTAGC
1 TTAGC
36791273 GGCGCTACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 26 0.68
41 12 0.32
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (40 bp):
TTAGCAGCATTTGACAAAAAACGCCACAAAATATCGAGCA
Found at i:36791445 original size:113 final size:111
Alignment explanation
Indices: 36791314--36791661 Score: 423
Period size: 113 Copynumber: 3.1 Consensus size: 111
36791304 AGCATTAACA
*
36791314 GCGTTTTACAAAAAGCGCCGCAATAGAGTCACACAGAACGACGCCGTTTTCATATAGTTGGGAAC
1 GCGTTTTAC-AAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATA-TTGGGAAC
36791379 ATTAGTGGCGGTTATTTCCAAGCGCCGCTAAAACTCCGTTCTACAGCG
64 ATTAGTGGCGGTTATTTCCAAGCGCCGCTAAAACTCCGTTCTACAGCG
* * *
36791427 GCGTTTTATACAAAGCGCCGCAATGGAGTAATACAGAACGACGCCGTTTTCATATATCTGGGAAC
1 GCGTTTTACA-AAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATAT-TGGGAAC
* * * *
36791492 ATTAGTGGCGGTT-TTGCCCAAGCGCCGCTAATACTCCATTCTTCAGCG
64 ATTAGTGGCGGTTATT-TCCAAGCGCCGCTAAAACTCCGTTCTACAGCG
* * ** *
36791540 GCGTTTTACAAAATGCGTCGCAAATACAGTAACACAGAACGACGCCGTTTTTGTATATTTTGGAA
1 GCGTTTTACAAAA-GCGCCGC-AATAGAGTAACACAGAACGACGCCGTTTTCATATA-TTGGGAA
* * * *
36791605 CACTAGTGGCAG-TATTTTCCCAAACGCCGCTAATAAC-CCGTTCTACAGCA
63 CATTAGTGGCGGTTA-TTT-CCAAGCGCCGCTAA-AACTCCGTTCTACAGCG
36791655 GCGTTTT
1 GCGTTTT
36791662 GCGTTAAGCG
Statistics
Matches: 201, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
112 7 0.03
113 114 0.57
114 45 0.22
115 33 0.16
116 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (111 bp):
GCGTTTTACAAAAGCGCCGCAATAGAGTAACACAGAACGACGCCGTTTTCATATATTGGGAACAT
TAGTGGCGGTTATTTCCAAGCGCCGCTAAAACTCCGTTCTACAGCG
Found at i:36791820 original size:41 final size:42
Alignment explanation
Indices: 36791765--36791866 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 42
36791755 CCGCTGATGC
* * *
36791765 TCCGCTCTAAAGCGGCGTTTATGGAGAATCGCCGCTAAAT-T
1 TCCGGTCTATAGCGGCGTTTATGGAGAAGCGCCGCTAAATCT
** *
36791806 TCCGGTCTATAGCGGCGTTCCTGGAGAAGCGCCGGTAAATCT
1 TCCGGTCTATAGCGGCGTTTATGGAGAAGCGCCGCTAAATCT
* *
36791848 T-GGGTCGATAGCGGCGTTT
1 TCCGGTCTATAGCGGCGTTT
36791867 GTGTAAGAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 49 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (42 bp):
TCCGGTCTATAGCGGCGTTTATGGAGAAGCGCCGCTAAATCT
Found at i:36793989 original size:16 final size:16
Alignment explanation
Indices: 36793965--36793995 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36793955 ATTTTCCCTA
36793965 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
*
36793981 TTCTGAAATCCCTAA
1 TTCTAAAATCCCTAA
36793996 CTCATAAACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:36795051 original size:2 final size:2
Alignment explanation
Indices: 36795039--36795072 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
36795029 AAGTATATGG
*
36795039 TA TA CTA TA TA TA TA TA TA AA 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
36795073 TTTGGTGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:36796572 original size:9 final size:9
Alignment explanation
Indices: 36796558--36796615 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
36796548 ACTTACAACT
36796558 TACATAACA
1 TACATAACA
36796567 TACATAATACA
1 TACAT-A-ACA
*
36796578 TA-ATAACT
1 TACATAACA
*
36796586 TAC--AACT
1 TACATAACA
36796593 TACATAACA
1 TACATAACA
*
36796602 TACATAACT
1 TACATAACA
36796611 TACAT
1 TACAT
36796616 TCATAACTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
7 7 0.17
8 4 0.10
9 22 0.54
10 3 0.07
11 5 0.12
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (9 bp):
TACATAACA
Found at i:36796620 original size:13 final size:13
Alignment explanation
Indices: 36796564--36796628 Score: 59
Period size: 13 Copynumber: 5.3 Consensus size: 13
36796554 AACTTACATA
36796564 ACATACATAA--T
1 ACATACATAACTT
36796575 ACATA-ATAACTT
1 ACATACATAACTT
* *
36796587 ACA-AC-TTACATA
1 ACATACATAAC-TT
36796599 ACATACATAACTT
1 ACATACATAACTT
*
36796612 ACATTCATAACTT
1 ACATACATAACTT
36796625 ACAT
1 ACAT
36796629 CAACTTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
10 4 0.09
11 9 0.21
12 8 0.19
13 19 0.44
14 3 0.07
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.31
Consensus pattern (13 bp):
ACATACATAACTT
Found at i:36796732 original size:19 final size:19
Alignment explanation
Indices: 36796710--36796770 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
36796700 GCATACATTT
36796710 ACTTACATAATACATAATA
1 ACTTACATAATACATAATA
*
36796729 ACTTAC---A-ACTTACATA
1 ACTTACATAATACATA-ATA
*
36796745 ACATACATAATACATAATA
1 ACTTACATAATACATAATA
36796764 ACTTACA
1 ACTTACA
36796771 ACTTACATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
15 4 0.12
16 9 0.27
19 16 0.48
20 4 0.12
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.30
Consensus pattern (19 bp):
ACTTACATAATACATAATA
Found at i:36796751 original size:16 final size:16
Alignment explanation
Indices: 36796726--36796786 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
36796716 ATAATACATA
*
36796726 ATAACTTACAACTTAC
1 ATAACATACAACTTAC
*
36796742 ATAACATACATA-ATAC
1 ATAACATACA-ACTTAC
*
36796758 ATAATAACTTACAACTTAC
1 ---ATAACATACAACTTAC
36796777 ATAACATACA
1 ATAACATACA
36796787 TTAATTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
16 21 0.60
17 1 0.03
18 1 0.03
19 12 0.34
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAACATACAACTTAC
Found at i:36796777 original size:19 final size:19
Alignment explanation
Indices: 36796720--36796780 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
36796710 ACTTACATAA
36796720 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
* *
36796739 TAC---ATAACATACATA-A
1 TACATAATAACTTACA-ACT
36796755 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
36796774 TACATAA
1 TACATAA
36796781 CATACATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
16 12 0.36
17 1 0.03
18 1 0.03
19 19 0.58
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.30
Consensus pattern (19 bp):
TACATAATAACTTACAACT
Found at i:36796803 original size:35 final size:35
Alignment explanation
Indices: 36796543--36796787 Score: 175
Period size: 35 Copynumber: 6.8 Consensus size: 35
36796533 TACACAGTTT
36796543 TAATAACTTACAACTTACATAACATACATAATACA
1 TAATAACTTACAACTTACATAACATACATAATACA
36796578 TAATAACTTACAACTTACATAACATACATAACTTACA
1 TAATAACTTACAACTTACATAACATACATAA--TACA
* * * *
36796615 TTCATAACTTACATCAACTTATATGTTACCTTACATAATACA
1 -TAATAACTT--A-CAACTTACA---TAACATACATAATACA
* ** * **
36796657 TAACTTATATTTATGATTTTTATATA-A-AC-T--TACA
1 TAA--TA-ACTTACAACTTACATA-ACATACATAATACA
* * *
36796691 TAAT-ACATAGC-A--TACATTTACTTACATAATACA
1 TAATAACTTA-CAACTTACA-TAACATACATAATACA
36796724 TAATAACTTACAACTTACATAACATACATAATACA
1 TAATAACTTACAACTTACATAACATACATAATACA
36796759 TAATAACTTACAACTTACATAACATACAT
1 TAATAACTTACAACTTACATAACATACAT
36796788 TAATTTTTTA
Statistics
Matches: 164, Mismatches: 22, Indels: 48
0.70 0.09 0.21
Matches are distributed among these distances:
28 3 0.02
29 1 0.01
30 6 0.04
31 1 0.01
32 1 0.01
33 9 0.05
34 12 0.07
35 74 0.45
36 5 0.03
37 6 0.04
38 10 0.06
40 1 0.01
41 15 0.09
42 5 0.03
43 2 0.01
44 13 0.08
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (35 bp):
TAATAACTTACAACTTACATAACATACATAATACA
Found at i:36796846 original size:60 final size:59
Alignment explanation
Indices: 36796761--36796888 Score: 193
Period size: 60 Copynumber: 2.2 Consensus size: 59
36796751 ATAATACATA
* ** * *
36796761 ATAACTTACAACTTACATAACATACATTAATTTTTTAAACTTATAGAAGTTACATAATAC
1 ATAACTTACAACTTACATAACATACATTAATATGAT-AACCTACAGAAGTTACATAATAC
*
36796821 ATAACTTACAACTTACATAACATACATTAATATGATAACCTACATAAGTTACATAATAC
1 ATAACTTACAACTTACATAACATACATTAATATGATAACCTACAGAAGTTACATAATAC
36796880 ATAACTTAC
1 ATAACTTAC
36796889 CACTGAACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 29 0.47
60 33 0.53
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (59 bp):
ATAACTTACAACTTACATAACATACATTAATATGATAACCTACAGAAGTTACATAATAC
Found at i:36802493 original size:87 final size:87
Alignment explanation
Indices: 36802355--36802532 Score: 261
Period size: 87 Copynumber: 2.0 Consensus size: 87
36802345 GAGGCAACAT
* *
36802355 CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAAAACTCCAGGTACAACTTAAAGCAGATGCGGCA
1 CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAAAACTCCAGGCACAACTTAAAGCAGATGCAGCA
36802420 ACGAGAGAAGCAGAGGCTGCAG
66 ACGAGAGAAGCAGAGGCTGCAG
* * * *
36802442 CGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTTCA-GCAGCAGCTTAAAGCAGATGCAG
1 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAAAACTCCAGGCA-CAACTTAAAGCAGATGCAG
*
36802505 CAGCGAGAGAAGCAGAGGCTGCAG
64 CAACGAGAGAAGCAGAGGCTGCAG
36802529 CGAG
1 CGAG
36802533 GGAATCAGAG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
86 2 0.02
87 76 0.93
88 4 0.05
ACGTcount: A:0.39, C:0.18, G:0.31, T:0.12
Consensus pattern (87 bp):
CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAAAACTCCAGGCACAACTTAAAGCAGATGCAGCA
ACGAGAGAAGCAGAGGCTGCAG
Done.