Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 8 of 310
Found at i:1906488 original size:10 final size:10
Alignment explanation
Indices: 1906473--1906497 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1906463 GTTGAATATG
1906473 TTAAAAATGC
1 TTAAAAATGC
1906483 TTAAAAATGC
1 TTAAAAATGC
1906493 TTAAA
1 TTAAA
1906498 TTATAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (10 bp):
TTAAAAATGC
Found at i:1908833 original size:16 final size:16
Alignment explanation
Indices: 1908812--1908842 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1908802 ATTATTTTTC
*
1908812 TTTATGTATGTATGTG
1 TTTATGAATGTATGTG
1908828 TTTATGAATGTATGT
1 TTTATGAATGTATGT
1908843 AGGTATGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (16 bp):
TTTATGAATGTATGTG
Found at i:1913261 original size:16 final size:17
Alignment explanation
Indices: 1913240--1913272 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1913230 CACATTGAAG
1913240 TGTTTT-TTGAAAACCA
1 TGTTTTATTGAAAACCA
1913256 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
1913273 CTTCTTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TGTTTTATTGAAAACCA
Found at i:1913974 original size:28 final size:27
Alignment explanation
Indices: 1913924--1913976 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
1913914 CTATTCAGAA
*
1913924 ATCAATATTAACTGGGCCTTAGCCCAT
1 ATCAATATTAACTGGGCCATAGCCCAT
1913951 ATCAATATTAATCTGGGCCATAGCCC
1 ATCAATATTAA-CTGGGCCATAGCCC
1913977 CTTACAGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (27 bp):
ATCAATATTAACTGGGCCATAGCCCAT
Found at i:1918063 original size:49 final size:49
Alignment explanation
Indices: 1917961--1918089 Score: 152
Period size: 49 Copynumber: 2.6 Consensus size: 49
1917951 ATCAAAGTCG
* * * *
1917961 ATGCCATGTCCCAGACAGGTCTTACATTGACTTTCATATATCGAGGCCG
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATAGAGGCCA
* * * *
1918010 ATGCCATGTCCAAGACAGGTCTTACACTGGCTCTCATTTATAG-GTGTCA
1 ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATAGAG-GCCA
* *
1918059 ATGCCATGCCCCAGACAAGTCTTACACTGAC
1 ATGCCATGTCCCAGACAGGTCTTACACTGAC
1918090 ACACAACAAG
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
48 1 0.01
49 66 0.99
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (49 bp):
ATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATAGAGGCCA
Found at i:1918184 original size:46 final size:48
Alignment explanation
Indices: 1918117--1918242 Score: 186
Period size: 48 Copynumber: 2.7 Consensus size: 48
1918107 CATGTCCCAA
* * *
1918117 ATGCATGTCCCAGACATGTCTTACACTAGCTCT-C-GTCTCAATGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCTGCAATCTCAAGGCCG
*
1918163 ATGCATGTCCCAGACATGTCTTACACTGGCT-TGCATATCTCGAGGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCTGCA-ATCTCAAGGCCG
1918211 ATGCATGTCCCAGACATGTCTTACACTGGCTC
1 ATGCATGTCCCAGACATGTCTTACACTGGCTC
1918243 CCGTAATGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
45 1 0.01
46 31 0.43
48 40 0.56
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (48 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCTCTGCAATCTCAAGGCCG
Found at i:1918294 original size:94 final size:93
Alignment explanation
Indices: 1918117--1918295 Score: 218
Period size: 94 Copynumber: 1.9 Consensus size: 93
1918107 CATGTCCCAA
* *
1918117 ATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCCGATGCATGTCCCAGACATGT
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCCCG-CTCAATGCCGATGCATGTCCCAAACATGT
* ***
1918182 CTTACACTGGCTTGCATATCTCGAGGCCG
65 CTTACACTAGCACACATATCTCGAGGCCG
* ** *
1918211 ATGCATGTCCCAGACATGTCTTACACTGGCTCCCG-T-AATGTGGCCGATGCATGTTTCAAATAT
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCCCGCTCAA--T-GCCGATGCATGTCCCAAACAT
1918274 GTCTTACACTAGCACACATATC
63 GTCTTACACTAGCACACATATC
1918296 ACCCAATGTC
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
91 2 0.03
92 1 0.01
93 1 0.01
94 68 0.94
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (93 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTCCCGCTCAATGCCGATGCATGTCCCAAACATGTC
TTACACTAGCACACATATCTCGAGGCCG
Found at i:1936519 original size:21 final size:22
Alignment explanation
Indices: 1936480--1936520 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1936470 AACTCCTCCA
*
1936480 ATTCTTATTCAAATGTTAAAAT
1 ATTCTTATTCAAATATTAAAAT
1936502 ATTCTTATT-AAATATTAAA
1 ATTCTTATTCAAATATTAAA
1936521 GTAATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTCTTATTCAAATATTAAAAT
Found at i:1940155 original size:19 final size:20
Alignment explanation
Indices: 1940133--1940181 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1940123 ATTATATATA
*
1940133 TTTAAAAAAATTAT-TAAAT
1 TTTAAAAAAATTATAAAAAT
*
1940152 TTTATAAAACATTATAAAAAT
1 TTTA-AAAAAATTATAAAAAT
*
1940173 TATAAAAAA
1 TTTAAAAAA
1940182 GAGAGAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.17
20 13 0.54
21 7 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTAAAAAAATTATAAAAAT
Found at i:1940174 original size:9 final size:9
Alignment explanation
Indices: 1940138--1940180 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1940128 ATATATTTAA
1940138 AAAAATTATT
1 AAAAATTA-T
**
1940148 AAATTTTAT
1 AAAAATTAT
1940157 AAAACATTAT
1 AAAA-ATTAT
1940167 AAAAATTAT
1 AAAAATTAT
1940176 AAAAA
1 AAAAA
1940181 AGAGAGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 14 0.50
10 14 0.50
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:1940570 original size:29 final size:29
Alignment explanation
Indices: 1940528--1940584 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
1940518 TCATTTCTTT
1940528 TTTATAATGTTTTACAACTTTAAAAAAAA
1 TTTATAATGTTTTACAACTTTAAAAAAAA
1940557 TTTATAATGTTTTACAACTTTAAAAAAA
1 TTTATAATGTTTTACAACTTTAAAAAAA
1940585 TATATAGTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTATAATGTTTTACAACTTTAAAAAAAA
Found at i:1947335 original size:41 final size:41
Alignment explanation
Indices: 1947262--1947452 Score: 199
Period size: 40 Copynumber: 4.7 Consensus size: 41
1947252 CTCGATATCA
** * *
1947262 CGCACACTAAGTGCCAATACATAGTTGAAGCTATTTTAATCT
1 CGCACACTAAGTGCC-ATACATAGCCGAAGCTATCTCAATCT
* * * *
1947304 CGCACATTAAGTGCCTTACATAGCCGAAGCTAACTCGATCT
1 CGCACACTAAGTGCCATACATAGCCGAAGCTATCTCAATCT
* * * * *
1947345 CGCACACTAAGTTCCATATATAGCTGAAGCTATCCCAA-AT
1 CGCACACTAAGTGCCATACATAGCCGAAGCTATCTCAATCT
*
1947385 CACACACTAAGTGCCATACATAGCCGAAGCTATCTCGAA--T
1 CGCACACTAAGTGCCATACATAGCCGAAGCTATCTC-AATCT
**
1947425 CAAACACTAAGTGCCATACATAGCCGAA
1 CGCACACTAAGTGCCATACATAGCCGAA
1947453 TTATCGTCAA
Statistics
Matches: 125, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
40 60 0.48
41 51 0.41
42 14 0.11
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24
Consensus pattern (41 bp):
CGCACACTAAGTGCCATACATAGCCGAAGCTATCTCAATCT
Found at i:1951218 original size:50 final size:50
Alignment explanation
Indices: 1951138--1951247 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 50
1951128 TACGGTGCAG
* * *
1951138 GGGTCACACGAGTGTGTGCCCAGGCTGTGTAACTCACTGACTTT-GGATTT
1 GGGTCACACGAGCGTGTGCCCAGGCCGTGTAACTCACTGA-TTTCAGATTT
* * * *
1951188 GGGTTACACGAGCGTGTGTCGAGGCCGTGTAGCTCACTGATTTCAGATTT
1 GGGTCACACGAGCGTGTGCCCAGGCCGTGTAACTCACTGATTTCAGATTT
1951238 GGGTCACACG
1 GGGTCACACG
1951248 GGCAAGCCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 3 0.06
50 48 0.94
ACGTcount: A:0.18, C:0.22, G:0.32, T:0.28
Consensus pattern (50 bp):
GGGTCACACGAGCGTGTGCCCAGGCCGTGTAACTCACTGATTTCAGATTT
Found at i:1962427 original size:86 final size:86
Alignment explanation
Indices: 1962211--1962742 Score: 532
Period size: 86 Copynumber: 6.2 Consensus size: 86
1962201 AACATCGGGA
* * ** *
1962211 AATTACAGATCTTGTCTCACTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAGCCTTAACCCCCA
1 AATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATGAGCCTTAACCCCCT
*
1962276 AAGCAGTAGGGTAACAGGCTG
66 AAGCAGTAAGGTAACAGGCTG
* * * *
1962297 AAAATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATCGAAGATGATGAGCCTTAACCCC
1 --AATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATGAGCCTTAACCCC
* *
1962362 CTAAGCAGTAGGGCAACAGG-TCG
64 CTAAGCAGTAAGGTAACAGGCT-G
* * * *
1962385 AATTACAAATCTTGTCTCCCTGAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCTCT
1 AATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATGAGCCTTAACCCCCT
* *
1962450 AAGTAGTAAGGTAACAGGCTA
66 AAGCAGTAAGGTAACAGGCTG
* * *
1962471 AATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGTCTTAACCCCCT
1 AATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATGAGCCTTAACCCCCT
* *
1962536 AAACAATAAGGTAACAGGCTG
66 AAGCAGTAAGGTAACAGGCTG
* * *
1962557 AATTACAGAACTTGTCTCCCTAAGCAATAGT-G-G-AGA-C----A--ATGAGCCTTAACCCTCT
1 AATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATGAGCCTTAACCCCCT
* *
1962612 AAGTAGTAGGGTAACAGGCTG
66 AAGCAGTAAGGTAACAGGCTG
* * * * * * *
1962633 AAAAGTATAGATCTTATCTCCCTAAGCAATAGTGGAGTAGATC-AAGTACGGTAAGCCTTAACCC
1 --AATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAG-ACGATGAGCCTTAACCC
* * * *
1962697 CTTAAGCA-TAGGGTAATAGGTTGGG
63 CCTAAGCAGTAAGGTAACAGGCT--G
* *
1962722 AATTACAAATCTTTTCTCCCT
1 AATTACAGATCTTGTCTCCCT
1962743 GAAATGGCGT
Statistics
Matches: 371, Mismatches: 57, Indels: 33
0.80 0.12 0.07
Matches are distributed among these distances:
76 32 0.09
78 28 0.08
79 1 0.00
80 1 0.00
81 3 0.01
82 2 0.01
83 3 0.01
84 1 0.00
85 1 0.00
86 176 0.47
87 31 0.08
88 91 0.25
89 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (86 bp):
AATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGATGAGCCTTAACCCCCT
AAGCAGTAAGGTAACAGGCTG
Found at i:1962536 original size:44 final size:44
Alignment explanation
Indices: 1962230--1962537 Score: 141
Period size: 44 Copynumber: 7.1 Consensus size: 44
1962220 TCTTGTCTCA
* * ** *
1962230 CTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAGCCTTAACCCC
1 CTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGTCTTAACCCC
* * * * * * * *
1962274 CAAAGCAGTAG-GGTAACAG-GCTGAAAATTA-CAGATCTTATCTCC
1 CTAAGCAGTAGTGG-AGCAGATC-GAAGATGATGAG-TCTTAACCCC
* * *
1962318 TTAAGCAGTAGTGGAGCAAATCGAAGATGATGAGCCTTAACCCC
1 CTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGTCTTAACCCC
* * * ** * ** *
1962362 CTAAGCAGTAG-GGCAACAGGTCG-A-ATTACAAATCTTGTCTCC
1 CTAAGCAGTAGTGG-AGCAGATCGAAGATGATGAGTCTTAACCCC
* * * * *
1962404 CTGAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCT
1 CTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGTCTTAACCCC
* * * * * * * * *
1962448 CTAAGTAGTAAG-GTAACAG-GCTAA-ATTA-CAGATCTTATCTCC
1 CTAAGCAGT-AGTGGAGCAGATCGAAGATGATGAG-TCTTAACCCC
1962490 CTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGTCTTAACCCC
1 CTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGTCTTAACCCC
1962534 CTAA
1 CTAA
1962538 ACAATAAGGT
Statistics
Matches: 176, Mismatches: 72, Indels: 32
0.63 0.26 0.11
Matches are distributed among these distances:
41 4 0.02
42 47 0.27
43 17 0.10
44 99 0.56
45 9 0.05
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (44 bp):
CTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGTCTTAACCCC
Found at i:1962562 original size:172 final size:172
Alignment explanation
Indices: 1962211--1962742 Score: 642
Period size: 172 Copynumber: 3.1 Consensus size: 172
1962201 AACATCGGGA
* * * * *
1962211 AATTACAGATCTTGTCTCACTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAGCCTTAACCCCCA
1 AATTACAAATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATC-AAGACGGTGAGCCTTAACCCTCT
* * *
1962276 AAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAAATCG
65 AAGTAGTAGGGTAACAGGCT-AAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
* * *
1962341 AAGATGATGAGCCTTAACCCCCTAAGCAGTAGGGCAACAGGTCG
129 AAGATGATGAGCCTTAACCCCCTAAGCAATAGGGTAACAGGTGG
*
1962385 AATTACAAATCTTGTCTCCCTGAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCTCT
1 AATTACAAATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATC-AAGACGGTGAGCCTTAACCCTCT
*
1962450 AAGTAGTAAGGTAACAGGCT-AAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGA
65 AAGTAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGA
* * *
1962514 AGATGATGAGTCTTAACCCCCTAAACAATAAGGTAACAGGCT-G
130 AGATGATGAGCCTTAACCCCCTAAGCAATAGGGTAACAGG-TGG
*
1962557 AATTACAGAA-CTTGTCTCCCTAAGCAATAGT-G-G-AGA-C-A-A---TGAGCCTTAACCCTCT
1 AATTACA-AATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAGACGGTGAGCCTTAACCCTCT
* * * *
1962612 AAGTAGTAGGGTAACAGGCTGAAAAGTATAGATCTTATCTCCCTAAGCAATAGTGGAGTAGATC-
65 AAGTAGTAGGGTAACAGGCT-AAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
* * * * *
1962676 AAGTACGGTAAGCCTTAACCCCTTAAGC-ATAGGGTAATAGGTTGGG
129 AAG-ATGATGAGCCTTAACCCCCTAAGCAATAGGGTAACAGG-T-GG
*
1962722 AATTACAAATCTTTTCTCCCT
1 AATTACAAATCTTGTCTCCCT
1962743 GAAATGGCGT
Statistics
Matches: 317, Mismatches: 33, Indels: 25
0.85 0.09 0.07
Matches are distributed among these distances:
162 35 0.11
163 15 0.05
164 58 0.18
165 19 0.06
166 1 0.00
168 1 0.00
169 3 0.01
170 1 0.00
171 1 0.00
172 104 0.33
173 3 0.01
174 76 0.24
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (172 bp):
AATTACAAATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAGACGGTGAGCCTTAACCCTCTA
AGTAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA
GATGATGAGCCTTAACCCCCTAAGCAATAGGGTAACAGGTGG
Found at i:1962844 original size:68 final size:68
Alignment explanation
Indices: 1962730--1963138 Score: 507
Period size: 68 Copynumber: 6.0 Consensus size: 68
1962720 GGAATTACAA
* *
1962730 ATCTTTTCTCCCTGAAATGGCGTTGGAGCGGCTCGAAGCCACAGCAGATCTCCTTGAAGTTTTAG
1 ATCTTTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAG
1962795 CGG
66 CGG
* * * * *
1962798 ATCTATTCTCCCTAAAATGGCGTTGAAACGGCTAGAAACCACAGCAGATCTCCTTGAAGTTTCAG
1 ATCTTTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAG
**
1962863 CAA
66 CGG
* * * * * * **
1962866 ATTTTTTCCCCCTGAAATAGCGTTGGAGTGGCCCA-AAGACACAGCAGATCTCCTCAAAGTTTCA
1 ATCTTTTCTCCCTGAAATGGCGTTGGAGCGG-CTAGAAGCCACAGCAGATCTCCTTGAAGTTTCA
*
1962930 GCAG
65 GCGG
* * * * *
1962934 ATCTTTTCTCCCTGGAATGGCGTTGGAGTGACTCGAAGCCACAGCAGATCTCCTTGAAGTGTCAG
1 ATCTTTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAG
1962999 CGG
66 CGG
* * * * *
1963002 ATCTCTTCTCCCTAAAATGGCGTTGAAGCGGCTAGAAGCTACAGTAGATCTCCTTGAAGTTTCAG
1 ATCTTTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAG
1963067 CGG
66 CGG
* * *
1963070 ATCTCTTCTCCCTGAAATGACGTTGGAGCGGCTCA-AAGCTACAGCAGATCTCCTTGAAGTTTCA
1 ATCTTTTCTCCCTGAAATGGCGTTGGAGCGGCT-AGAAGCCACAGCAGATCTCCTTGAAGTTTCA
1963134 GCGG
65 GCGG
1963138 A
1 A
1963139 GTAGATTGGA
Statistics
Matches: 289, Mismatches: 49, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
67 1 0.00
68 285 0.99
69 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (68 bp):
ATCTTTTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAG
CGG
Found at i:1963085 original size:204 final size:204
Alignment explanation
Indices: 1962730--1963135 Score: 609
Period size: 204 Copynumber: 2.0 Consensus size: 204
1962720 GGAATTACAA
* * *
1962730 ATCTTTTCTCCCTGAAATGGCGTTGGAGCGGCTCGAAGCCACAGCAGATCTCCTTGAAGTTTTAG
1 ATCTTTTCTCCCTGAAATGGCGTTGGAGCGACTCGAAGCCACAGCAGATCTCCTTGAAGTGTCAG
1962795 CGGATCTATTCTCCCTAAAATGGCGTTGAAACGGCTAGAAACCACAGCAGATCTCCTTGAAGTTT
66 CGGATCTATTCTCCCTAAAATGGCGTTGAAACGGCTAGAAACCACAGCAGATCTCCTTGAAGTTT
* * *
1962860 CAGCAAATTTTTTCCCCCTGAAAT-AGCGTTGGAGTGGCCCAAAGAC-ACAGCAGATCTCCTCAA
131 CAGCAAATCTCTTCCCCCTGAAATGA-CGTTGGAGCGGCCCAAAG-CTACAGCAGATCTCCTCAA
1962923 AGTTTCAGCAG
194 AGTTTCAGCAG
* *
1962934 ATCTTTTCTCCCTGGAATGGCGTTGGAGTGACTCGAAGCCACAGCAGATCTCCTTGAAGTGTCAG
1 ATCTTTTCTCCCTGAAATGGCGTTGGAGCGACTCGAAGCCACAGCAGATCTCCTTGAAGTGTCAG
* * * * *
1962999 CGGATCTCTTCTCCCTAAAATGGCGTTGAAGCGGCTAGAAGCTACAGTAGATCTCCTTGAAGTTT
66 CGGATCTATTCTCCCTAAAATGGCGTTGAAACGGCTAGAAACCACAGCAGATCTCCTTGAAGTTT
** * * **
1963064 CAGCGGATCTCTTCTCCCTGAAATGACGTTGGAGCGGCTCAAAGCTACAGCAGATCTCCTTGAAG
131 CAGCAAATCTCTTCCCCCTGAAATGACGTTGGAGCGGCCCAAAGCTACAGCAGATCTCCTCAAAG
1963129 TTTCAGC
196 TTTCAGC
1963136 GGAGTAGATT
Statistics
Matches: 181, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
203 1 0.01
204 179 0.99
205 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (204 bp):
ATCTTTTCTCCCTGAAATGGCGTTGGAGCGACTCGAAGCCACAGCAGATCTCCTTGAAGTGTCAG
CGGATCTATTCTCCCTAAAATGGCGTTGAAACGGCTAGAAACCACAGCAGATCTCCTTGAAGTTT
CAGCAAATCTCTTCCCCCTGAAATGACGTTGGAGCGGCCCAAAGCTACAGCAGATCTCCTCAAAG
TTTCAGCAG
Found at i:1963213 original size:45 final size:45
Alignment explanation
Indices: 1963117--1963674 Score: 315
Period size: 44 Copynumber: 12.4 Consensus size: 45
1963107 GCTACAGCAG
* * * * * * * *
1963117 ATCTCCTTGAAGTTTCAGCGGAGTAGATTGGAG-TCACTAGTCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAACAAATCTT
* *
1963161 ATCTCCCTGAAGTTGCAGTGGAGCATACTGAAGATAACAAATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAACAAATCTT
* * *
1963206 ATTTCCCTGAAGTCGCAGTGGAACAGATTGAAGCTATAAATCACTAATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT-AA-CA--AATCTT
* * ** * * *
1963257 ATCTCTCTGAAGTTGCAGT--AG-AG-TAGACCAAAAGAAACCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAACAAATCTT
* ** * * * *
1963298 ATCTCCCTGAAGTTACAGACGAGCAGGTTGAAG-TAGCTAGTCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAACAAATCTT
* *
1963342 ATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGA-AAATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-ACAAATCTT
* * * * *
1963387 ATTTCCCTGAAGTTACAGTGGAACAGATTAAAGCTATAAATCACTGATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT-AA-CA--AATCTT
* * * * *
1963438 ATCTCTCTGAAGTTGCATTAGAGCAGA-T-CA-A-AACAAA-CCT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAACAAATCTT
* * ** *
1963478 -TCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAG-TCGCTAATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAACAAATCTT
* *
1963521 ATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATCACAGATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT-AA-CA-A-ATCTT
* * * * *
1963572 ATCTCTCTGAAGTTGCAGTAGAGTAGA-T-AA-A-AAAAACACCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAACAA-ATCTT
* *
1963614 ATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAACAAATCTT
* *
1963659 ATTTCCCTAAAGTTGC
1 ATCTCCCTGAAGTTGC
1963675 CGTAGAATAG
Statistics
Matches: 386, Mismatches: 91, Indels: 73
0.70 0.17 0.13
Matches are distributed among these distances:
39 21 0.05
40 3 0.01
41 23 0.06
42 32 0.08
43 9 0.02
44 98 0.25
45 95 0.25
46 5 0.01
47 9 0.02
48 5 0.01
49 8 0.02
50 3 0.01
51 75 0.19
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (45 bp):
ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAACAAATCTT
Found at i:1963346 original size:44 final size:45
Alignment explanation
Indices: 1963157--1963404 Score: 150
Period size: 45 Copynumber: 5.5 Consensus size: 45
1963147 GAGTCACTAG
* ** *
1963157 TCTTATCTCCCTGAAGTTGCAGTGGAGCATACTGAAGATA-ACAAA
1 TCTTATCTCCCTGAAGTTACAGACGAGCAGACTGAAGATAGA-AAA
* ** ** * * *
1963202 TCTTATTTCCCTGAAGTCGCAGTGGAACAGATTGAAGCTATAAATCACTAA
1 TCTTATCTCCCTGAAGTTACAGACGAGCAGACTGAAG--ATAGA--A--AA
* * * *
1963253 TCTTATCTCTCTGAAGTTGCAGTA-GAGTAGAC-CAA-A-AG-AAA
1 TCTTATCTCCCTGAAGTTACAG-ACGAGCAGACTGAAGATAGAAAA
* ** ** *
1963294 CCTTATCTCCCTGAAGTTACAGACGAGCAGGTTGAAG-TAGCTAG
1 TCTTATCTCCCTGAAGTTACAGACGAGCAGACTGAAGATAGAAAA
**
1963338 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGAAAA
1 TCTTATCTCCCTGAAGTTACAGACGAGCAGACTGAAGATAGAAAA
*
1963383 TCTTATTTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAAGTTACAG
1963405 TGGAACAGAT
Statistics
Matches: 158, Mismatches: 32, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
40 1 0.01
41 26 0.16
42 2 0.01
43 3 0.02
44 33 0.21
45 57 0.36
46 1 0.01
47 4 0.03
48 1 0.01
49 2 0.01
50 2 0.01
51 26 0.16
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTACAGACGAGCAGACTGAAGATAGAAAA
Found at i:1963428 original size:181 final size:179
Alignment explanation
Indices: 1963153--1963553 Score: 597
Period size: 181 Copynumber: 2.2 Consensus size: 179
1963143 ATTGGAGTCA
*
1963153 CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCATACTGAAGATAACAAATCTTATTTCCCTGAAG
1 CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTGAAG
* * *
1963218 TCGCAGTGGAACAGATTGAAGCTATAAATCACTAATCTTATCTCTCTGAAGTTGCAGTAGAGTAG
66 TCACAGTGGAACAGATTAAAGCTATAAATCACTAATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
*
1963283 ACCAAAAGAAACCTTATCTCCCTGAAGTTACAGACGAGCAGGTTGAAGTAG
131 ACCAAAACAAACC-T-TCTCCCTGAAGTTACAGACGAGCAGGTTGAAGTAG
*
1963334 CTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGA-AAATCTTATTTCCCTGAA
1 CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-ACAAATCTTATTTCCCTGAA
* * *
1963398 GTTACAGTGGAACAGATTAAAGCTATAAATCACTGATCTTATCTCTCTGAAGTTGCATTAGAGCA
65 GTCACAGTGGAACAGATTAAAGCTATAAATCACTAATCTTATCTCTCTGAAGTTGCAGTAGAGCA
* * ** * *
1963463 GATCAAAACAAACCTTCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGTCG
130 GACCAAAACAAACCTTCTCCCTGAAGTTACAGACGAGCAGGTTGAAGTAG
* * * *
1963513 CTAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAG
1 CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
1963554 CTATAAATCA
Statistics
Matches: 199, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
179 66 0.33
180 1 0.01
181 131 0.66
182 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (179 bp):
CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTGAAG
TCACAGTGGAACAGATTAAAGCTATAAATCACTAATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
ACCAAAACAAACCTTCTCCCTGAAGTTACAGACGAGCAGGTTGAAGTAG
Found at i:1963541 original size:134 final size:138
Alignment explanation
Indices: 1963339--1963729 Score: 556
Period size: 134 Copynumber: 2.9 Consensus size: 138
1963329 AGTAGCTAGT
* * *
1963339 CTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGAAAATCTTATTTCCCTGAAGTTACA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
* * * *
1963404 GTGGAACAGATTAAAGCTATAAATCACTGATCTTATCTCTCTGAAGTTGCATTAGAGCAGATCAA
66 GTGGAACAGATTGAAGCTATAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAA
*
1963469 AACAA-AC
131 AAAAACAC
* ** * *
1963476 C-T-TCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAG-TCGCTAATCTTATTTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
*
1963538 GTGGAACAGATTGAAGCTATAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATAAA
66 GTGGAACAGATTGAAGCTATAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAA
1963603 AAAAACAC
131 AAAAACAC
* *
1963611 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTGCC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
* * * * *
1963676 GTAGAATAGATTGAAGCTATGAATAAACAGATCTTATTTCTCTGAAGTTGCAGT
66 GTGGAACAGATTGAAGCTATAAAT-CACAGATCTTATCTCTCTGAAGTTGCAGT
1963730 GGAGTGGATC
Statistics
Matches: 223, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
134 88 0.39
135 31 0.14
136 2 0.01
137 30 0.13
138 45 0.20
139 27 0.12
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (138 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
GTGGAACAGATTGAAGCTATAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATAAA
AAAAACAC
Found at i:1964861 original size:78 final size:78
Alignment explanation
Indices: 1964732--1964889 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 78
1964722 GCCGACCCGA
1964732 ATCCGACCCGACCCGCCTCAGGATCCGCGTGTTTTTTAACGGAAGGGCTAATTGCACTTTTAGCC
1 ATCCGACCCGACCCGCCTCAGGATCCGCGTGTTTTTTAACGGAAGGGCTAATTGCACTTTTAGCC
1964797 CTTCTGCTTTTTT
66 CTTCTGCTTTTTT
*
1964810 ATCCGCCCCGACCCGCCTCAGGATCCGCGTGTTTTTTAACGGAAGGGCTAATTGCACTTTTAGCC
1 ATCCGACCCGACCCGCCTCAGGATCCGCGTGTTTTTTAACGGAAGGGCTAATTGCACTTTTAGCC
1964875 CTTCTGCTTTTTT
66 CTTCTGCTTTTTT
1964888 AT
1 AT
1964890 AGTTTTATAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.16, C:0.30, G:0.20, T:0.34
Consensus pattern (78 bp):
ATCCGACCCGACCCGCCTCAGGATCCGCGTGTTTTTTAACGGAAGGGCTAATTGCACTTTTAGCC
CTTCTGCTTTTTT
Found at i:1965261 original size:21 final size:22
Alignment explanation
Indices: 1965237--1965291 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
1965227 TTAATGTATT
*
1965237 ATTATTATTACTT-TCATTTTC
1 ATTATTATTACTTATCATTTTA
*
1965258 ATTATTATTA-TTATCCTTTTA
1 ATTATTATTACTTATCATTTTA
1965279 ATATATTATTACT
1 AT-TATTATTACT
1965292 ATTTTTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 18 0.62
22 8 0.28
23 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTATTATTACTTATCATTTTA
Found at i:1965289 original size:3 final size:3
Alignment explanation
Indices: 1965147--1965271 Score: 53
Period size: 3 Copynumber: 41.0 Consensus size: 3
1965137 TAATTTAATC
* * *
1965147 TAT TAT TAT TAT TAT TATT TAT T-T TAC TAT TAT TAT CTAA TA- TGT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT TAT
* * * * * * *
1965192 TAT CAT TAT CAC TAT TAT TAC T-T TAC TAT TGT AACT TAAT GTAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T T-AT -TAT TAT
*
1965239 TAT TAT TACT T-T CAT T-T TCAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT T-AT TAT TAT TAT TAT
1965272 CCTTTTAATA
Statistics
Matches: 89, Mismatches: 21, Indels: 24
0.66 0.16 0.18
Matches are distributed among these distances:
2 7 0.08
3 67 0.75
4 13 0.15
5 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:1965397 original size:14 final size:15
Alignment explanation
Indices: 1965368--1965471 Score: 75
Period size: 15 Copynumber: 6.6 Consensus size: 15
1965358 GTTATTAACA
1965368 ATTATTATTATTACT
1 ATTATTATTATTACT
*
1965383 ATTATTGTT-TTACT
1 ATTATTATTATTACT
*
1965397 ATTATTATCTAATGTATT
1 ATTATTAT-T-AT-TACT
* * *
1965415 TTTATTATCATTAATT
1 ATTATTATTATT-ACT
* *
1965431 ATTATTACTACTACT
1 ATTATTATTATTACT
*
1965446 ATTATTCTTATTAACAT
1 ATTATTATTATT-AC-T
1965463 ATTATTATT
1 ATTATTATT
1965472 TCCTTTTTTA
Statistics
Matches: 68, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
14 12 0.18
15 21 0.31
16 15 0.22
17 10 0.15
18 10 0.15
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.58
Consensus pattern (15 bp):
ATTATTATTATTACT
Found at i:1965490 original size:3 final size:3
Alignment explanation
Indices: 1965368--1965471 Score: 59
Period size: 3 Copynumber: 34.0 Consensus size: 3
1965358 GTTATTAACA
* * *
1965368 ATT ATT ATT ATT ACT ATT ATT GTT -TT ACT ATT ATT ATCT AATGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T -AT-T ATT
* * * * * * **
1965415 TTT ATT ATC ATT AATT ATT ATT ACT ACT ACT ATT ATT CTT ATT AAC
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1965461 A-T ATT ATT ATT
1 ATT ATT ATT ATT
1965472 TCCTTTTTTA
Statistics
Matches: 79, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
2 3 0.04
3 67 0.85
4 6 0.08
5 3 0.04
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1971174 original size:31 final size:31
Alignment explanation
Indices: 1971136--1971199 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1971126 CCTTTTCATA
*
1971136 TTTCATATTTCATAAGACTGGGTCGAAGCCT
1 TTTCATATTTCATAAGACTGGGCCGAAGCCT
***
1971167 TTTCATATTTCATATTTCTGGGCCGAAGCCT
1 TTTCATATTTCATAAGACTGGGCCGAAGCCT
1971198 TT
1 TT
1971200 ACTATAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (31 bp):
TTTCATATTTCATAAGACTGGGCCGAAGCCT
Found at i:1971451 original size:26 final size:26
Alignment explanation
Indices: 1971421--1971493 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
1971411 CTCTTTTAAT
*
1971421 AACTGGGGCATAACCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* *
1971447 AACTGGGGCATAAGCCATTTTCGTTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
1971473 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
1971494 GCCCTTCCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:1971565 original size:9 final size:9
Alignment explanation
Indices: 1971551--1971607 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
1971541 ACATCATGTG
1971551 CATATCATA
1 CATATCATA
*
1971560 CATATCATGTG
1 CATATCA--TA
*
1971571 CATATCGTA
1 CATATCATA
*
1971580 CATATCATGTG
1 CATATCA--TA
1971591 CATATCATA
1 CATATCATA
1971600 CATATCAT
1 CATATCAT
1971608 GTGCATATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:1971568 original size:20 final size:20
Alignment explanation
Indices: 1971543--1971619 Score: 145
Period size: 20 Copynumber: 3.9 Consensus size: 20
1971533 TTATGAATAC
1971543 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
1971563 ATCATGTGCATATCGTACAT
1 ATCATGTGCATATCATACAT
1971583 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
1971603 ATCATGTGCATATCATA
1 ATCATGTGCATATCATA
1971620 ATAATATTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:1971574 original size:11 final size:11
Alignment explanation
Indices: 1971543--1971618 Score: 83
Period size: 11 Copynumber: 7.5 Consensus size: 11
1971533 TTATGAATAC
1971543 ATCATGTGCAT
1 ATCATGTGCAT
*
1971554 ATCA--TACAT
1 ATCATGTGCAT
1971563 ATCATGTGCAT
1 ATCATGTGCAT
*
1971574 ATC--GTACAT
1 ATCATGTGCAT
1971583 ATCATGTGCAT
1 ATCATGTGCAT
*
1971594 ATCA--TACAT
1 ATCATGTGCAT
1971603 ATCATGTGCAT
1 ATCATGTGCAT
1971614 ATCAT
1 ATCAT
1971619 AATAATATTG
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
9 24 0.45
11 29 0.55
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:1980423 original size:25 final size:25
Alignment explanation
Indices: 1980393--1980498 Score: 117
Period size: 25 Copynumber: 4.2 Consensus size: 25
1980383 TATAAACAGA
1980393 AAGCTCCTCCGAGCTGAATAACGGT
1 AAGCTCCTCCGAGCTGAATAACGGT
*
1980418 AAGCTCCTCTC-AGCTGAATAACGAT
1 AAGCTCCTC-CGAGCTGAATAACGGT
* * ** *
1980443 GA-CCCCATGTGAGCTGAATCACGGT
1 AAGCTCC-TCCGAGCTGAATAACGGT
*
1980468 AAGCTCCTCCGAGCTGAATAACTGT
1 AAGCTCCTCCGAGCTGAATAACGGT
1980493 AAGCTC
1 AAGCTC
1980499 ATATGATCTA
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
24 3 0.05
25 57 0.89
26 4 0.06
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (25 bp):
AAGCTCCTCCGAGCTGAATAACGGT
Found at i:1980899 original size:15 final size:17
Alignment explanation
Indices: 1980874--1980907 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1980864 GCTAAGGACT
1980874 AAATTAGAAAG-TGATA
1 AAATTAGAAAGATGATA
1980890 AAATTA-AAAGATGATA
1 AAATTAGAAAGATGATA
1980906 AA
1 AA
1980908 TAATTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (17 bp):
AAATTAGAAAGATGATA
Found at i:1982074 original size:57 final size:58
Alignment explanation
Indices: 1981934--1982077 Score: 157
Period size: 57 Copynumber: 2.5 Consensus size: 58
1981924 ACCTCATTAA
* * *
1981934 AAAAAGGATTTAGCCTGGACTGGTAATCCAGATATAAGTCCTCTCGAGCATATGTTAT
1 AAAAAGGATTTAGCCTGGACTGGTAATCCAGATACAAGTCCTCTAGAGCATATGTCAT
** ** * * * * *
1981992 TGATTGGATTTAGCCCGGGCGGGTAATCCAGAT-CAAG-CTTTTTAGAGCATATGTCAT
1 AAAAAGGATTTAGCCTGGACTGGTAATCCAGATACAAGTC-CTCTAGAGCATATGTCAT
1982049 AAAAAGGATTTAGCCTGGACTGGTAATCC
1 AAAAAGGATTTAGCCTGGACTGGTAATCC
1982078 TATTTTATAC
Statistics
Matches: 66, Mismatches: 19, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
56 1 0.02
57 39 0.59
58 26 0.39
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (58 bp):
AAAAAGGATTTAGCCTGGACTGGTAATCCAGATACAAGTCCTCTAGAGCATATGTCAT
Found at i:1983483 original size:21 final size:22
Alignment explanation
Indices: 1983457--1983509 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1983447 ACGGCCTGCA
* *
1983457 ACACGGGCATG-TCCTAGGGTC
1 ACACGGGCATGCCCCTAGGATC
* *
1983478 ACACGGGCGTGCCCCTTGGATC
1 ACACGGGCATGCCCCTAGGATC
1983500 ACACGGGCAT
1 ACACGGGCAT
1983510 ATCAGCCCTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.17
Consensus pattern (22 bp):
ACACGGGCATGCCCCTAGGATC
Found at i:1985409 original size:158 final size:158
Alignment explanation
Indices: 1985121--1985437 Score: 526
Period size: 158 Copynumber: 2.0 Consensus size: 158
1985111 CACGACCGTG
* * * * *
1985121 TGTCTACTTGTGTGGACAAAATAAAGGCTATTTATCGAGCCATTTGTCACCCTCTTTTACCCCTG
1 TGTCTACTCGTGTGGACAAAATAAAGGCTATTTACCAAGCCATTTGTCACCCTCTTTTACACCTA
* * * * * *
1985186 TATACTCACAAATTCAATGCAATAATCCATGACATGTTTTAGCAATGAAAACATTCATAAACAAG
66 CATACACACAAATTCAATGCAATAATCCATAACATGTTTAAGCAACGAAAACATCCATAAACAAG
1985251 GCTAAATCATATCATTCATTACCAACAC
131 GCTAAATCATATCATTCATTACCAACAC
*
1985279 TGTCTGCTCGTGTGGACAAAATAAAGGCTATTTACCAAGCCATTTGTCACCCTCTTTTACACCTA
1 TGTCTACTCGTGTGGACAAAATAAAGGCTATTTACCAAGCCATTTGTCACCCTCTTTTACACCTA
1985344 CATACACACAAATTCAATGCAATAATCCATAACATGTTTAAGCAACGAAAACATCCATAAACAAG
66 CATACACACAAATTCAATGCAATAATCCATAACATGTTTAAGCAACGAAAACATCCATAAACAAG
1985409 GCTAAATCATATCATTCATTACCAACAC
131 GCTAAATCATATCATTCATTACCAACAC
1985437 T
1 T
1985438 TAACATATTT
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
158 147 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (158 bp):
TGTCTACTCGTGTGGACAAAATAAAGGCTATTTACCAAGCCATTTGTCACCCTCTTTTACACCTA
CATACACACAAATTCAATGCAATAATCCATAACATGTTTAAGCAACGAAAACATCCATAAACAAG
GCTAAATCATATCATTCATTACCAACAC
Found at i:1985480 original size:15 final size:17
Alignment explanation
Indices: 1985462--1985493 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1985452 TAGCATAATT
1985462 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
1985477 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
1985494 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:1992664 original size:25 final size:25
Alignment explanation
Indices: 1992587--1992666 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
1992577 GCTCTTTTTT
* *
1992587 GAGCTGAATAACGGTAAGCTCTTCC
1 GAGCTGAATAACGGTAAGCTCATAC
* * * *
1992612 AAGCTGAATAACGGTAAGGTCGTGC
1 GAGCTGAATAACGGTAAGCTCATAC
*
1992637 GAGCTGAATAATGGTAAGCTCATAC
1 GAGCTGAATAACGGTAAGCTCATAC
1992662 GAGCT
1 GAGCT
1992667 AAAATTGATA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.23
Consensus pattern (25 bp):
GAGCTGAATAACGGTAAGCTCATAC
Found at i:1993553 original size:23 final size:23
Alignment explanation
Indices: 1993514--1993558 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1993504 TGAAGAAGAA
*
1993514 AACCTTTGTTTTATTATTTTATT
1 AACCTTTATTTTATTATTTTATT
1993537 AACCTTTATTTCT-TTATTTTAT
1 AACCTTTATTT-TATTATTTTAT
1993559 CTTTTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.64
Consensus pattern (23 bp):
AACCTTTATTTTATTATTTTATT
Found at i:1993612 original size:19 final size:20
Alignment explanation
Indices: 1993566--1993618 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
1993556 TATCTTTTTC
*
1993566 AATTAATAATAACATTATAA
1 AATTAAAAATAACATTATAA
* *
1993586 TA-TAAAAATCAC-TTATAA
1 AATTAAAAATAACATTATAA
*
1993604 AATTAAAAAGAACAT
1 AATTAAAAATAACAT
1993619 AAAGCTTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
18 7 0.28
19 16 0.64
20 2 0.08
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (20 bp):
AATTAAAAATAACATTATAA
Found at i:1997878 original size:37 final size:37
Alignment explanation
Indices: 1997835--1997913 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
1997825 TTATTACGAA
* * * *
1997835 GTCTTACCCGGACATAATCTCCACACGAAGTTATTGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
1997872 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
1997909 GTCTT
1 GTCTT
1997914 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:1998153 original size:37 final size:37
Alignment explanation
Indices: 1998110--1998188 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
1998100 TTATTACGAA
* * * *
1998110 GTCTTACCCGGACATAATCTCCACACGAAGTTATTGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
1998147 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
1998184 GTCTT
1 GTCTT
1998189 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:1998298 original size:275 final size:275
Alignment explanation
Indices: 1997807--1998357 Score: 1093
Period size: 275 Copynumber: 2.0 Consensus size: 275
1997797 TCGCATTGAA
1997807 TATATTTATAAGCAATTCTTATTACGAAGTCTTACCCGGACATAATCTCCACACGAAGTTATTGG
1 TATATTTATAAGCAATTCTTATTACGAAGTCTTACCCGGACATAATCTCCACACGAAGTTATTGG
1997872 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGGGTCTTTAGAGCTCGGATATAGTACGAGC
66 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGGGTCTTTAGAGCTCGGATATAGTACGAGC
1997937 ACGAAGCTTACGGACATTAATCAGTGATAATATTCTCGCATAAAGCCTGCGGGGGTTTAACCCGG
131 ACGAAGCTTACGGACATTAATCAGTGATAATATTCTCGCATAAAGCCTGCGGGGGTTTAACCCGG
1998002 ATATAGTACTGACACAAATGCCCTCGGGACTTATCACATTTATACACTTTCACATCCATCACGTT
196 ATATAGTACTGACACAAATGCCCTCGGGACTTATCACATTTATACACTTTCACATCCATCACGTT
1998067 GGCCACTCGGCCCTG
261 GGCCACTCGGCCCTG
1998082 TATATTTATAAGCAATTCTTATTACGAAGTCTTACCCGGACATAATCTCCACACGAAGTTATTGG
1 TATATTTATAAGCAATTCTTATTACGAAGTCTTACCCGGACATAATCTCCACACGAAGTTATTGG
1998147 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGGGTCTTTAGAGCTCGGATATAGTACGAGC
66 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGGGTCTTTAGAGCTCGGATATAGTACGAGC
*
1998212 ACGAAGCTTACGGACATTAATCAGTGATAATATTCTCGCATAAAGCCTGCGGGGTTTTAACCCGG
131 ACGAAGCTTACGGACATTAATCAGTGATAATATTCTCGCATAAAGCCTGCGGGGGTTTAACCCGG
1998277 ATATAGTACTGACACAAATGCCCTCGGGACTTATCACATTTATACACTTTCACATCCATCACGTT
196 ATATAGTACTGACACAAATGCCCTCGGGACTTATCACATTTATACACTTTCACATCCATCACGTT
1998342 GGCCACTCGGCCCTG
261 GGCCACTCGGCCCTG
1998357 T
1 T
1998358 CACATATATA
Statistics
Matches: 275, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
275 275 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (275 bp):
TATATTTATAAGCAATTCTTATTACGAAGTCTTACCCGGACATAATCTCCACACGAAGTTATTGG
GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGGGTCTTTAGAGCTCGGATATAGTACGAGC
ACGAAGCTTACGGACATTAATCAGTGATAATATTCTCGCATAAAGCCTGCGGGGGTTTAACCCGG
ATATAGTACTGACACAAATGCCCTCGGGACTTATCACATTTATACACTTTCACATCCATCACGTT
GGCCACTCGGCCCTG
Found at i:1998369 original size:47 final size:47
Alignment explanation
Indices: 1998306--1998484 Score: 268
Period size: 47 Copynumber: 3.8 Consensus size: 47
1998296 GCCCTCGGGA
* * * * * *
1998306 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
1998353 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1998400 CTTATCACATATATAAACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1998447 CTTATCACATATATACACTTTCACATTCATCACATCGG
1 CTTATCACATATATACACTTTCACATTCATCACATCGG
1998485 ATCCTAAATC
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 118 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:2001537 original size:47 final size:47
Alignment explanation
Indices: 2001471--2001596 Score: 139
Period size: 47 Copynumber: 2.7 Consensus size: 47
2001461 GATGTGTGCT
* ** *
2001471 AGTGTAAGACATGTTTGGGACATGCATCGGCCA-CATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCATCAAGACGAGAGCC
* * *
2001517 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CATTAAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCATCAAGACGAGAGCC
* *
2001565 AGTGTAAGACATGTCTAGGATATGCATCGGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC
2001597 TCGAGATATG
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
46 15 0.23
47 28 0.42
48 23 0.35
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCATCAAGACGAGAGCC
Found at i:2001740 original size:142 final size:140
Alignment explanation
Indices: 2001516--2001782 Score: 333
Period size: 142 Copynumber: 1.9 Consensus size: 140
2001506 TTATGAGAGC
** *
2001516 CAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTAAGACGAGAGCTAGTGTAAGACATGTCT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGAAGACGAGAGCCAGTGTAAGACATGTCT
* * * *
2001581 AGGATATGCATCGGCCTCGAGATATGCAAG-CTAGTGTAAGACCTATTTGGGACACGACATCGTC
66 AGGACATGCATCAGCCTCGAGATATGAAAGTC-AGTGTAAGACCTATCTGGGACACGACATCGTC
2001645 TTGACATGTGT
130 TTGACATGTGT
* * *
2001656 CAGTGTAAGA-CTTGTCTGGGACATGGCATC-GACACCGATAGATGAGAGCCAGTGTAAGACTTG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAG-CA-CGA-AGACGAGAGCCAGTGTAAGACATG
* * * * *
2001719 TCTGGGACATGGCATTAGCCTCGATATGTGAAAGTCAGTGTAAGACCTATCTGGGACATGACAT
63 TCTAGGACAT-GCATCAGCCTCGAGATATGAAAGTCAGTGTAAGACCTATCTGGGACACGACAT
2001783 TGACTTAGAT
Statistics
Matches: 107, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
138 1 0.01
139 21 0.20
140 11 0.10
141 29 0.27
142 44 0.41
143 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (140 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGAAGACGAGAGCCAGTGTAAGACATGTCT
AGGACATGCATCAGCCTCGAGATATGAAAGTCAGTGTAAGACCTATCTGGGACACGACATCGTCT
TGACATGTGT
Found at i:2001744 original size:49 final size:50
Alignment explanation
Indices: 2001656--2001783 Score: 156
Period size: 49 Copynumber: 2.6 Consensus size: 50
2001646 TGACATGTGT
* *
2001656 CAGTGTAAGACTTGTCTGGGACATGGCA-TCGACACCGATA-GATGAGAGC
1 CAGTGTAAGACTTGTCTGGGACATGGCATTAGACACCGATATG-TGAAAGC
*
2001705 CAGTGTAAGACTTGTCTGGGACATGGCATTAG-C-CTCGATATGTGAAAGT
1 CAGTGTAAGACTTGTCTGGGACATGGCATTAGACAC-CGATATGTGAAAGC
* * *
2001754 CAGTGTAAGACCTATCTGGGACATGACATT
1 CAGTGTAAGACTTGTCTGGGACATGGCATT
2001784 GACTTAGATG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
48 1 0.01
49 66 0.94
50 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (50 bp):
CAGTGTAAGACTTGTCTGGGACATGGCATTAGACACCGATATGTGAAAGC
Found at i:2001799 original size:98 final size:97
Alignment explanation
Indices: 2001654--2001830 Score: 214
Period size: 98 Copynumber: 1.8 Consensus size: 97
2001644 CTTGACATGT
* * * * * *
2001654 GTCAGTGTAAGACTTGTCTGGGACATGGCATCGACACCGATAGATGAGAGCCAGTGTAAGA-CTT
1 GTCAGTGTAAGACCTATCTGGGACATGACATCGACACAGATAGAT--GAGCCAATGTAAGACCAT
*
2001718 GTCTGGGACATGGCATTAGCCTCGATATGTGAAA
64 GTCTGGAACATGGCATTAGCCTCGATATGTGAAA
* **
2001752 GTCAGTGTAAGACCTATCTGGGACATGACATTGACTTAGAT-GTATGAGCCAATGTAAGACCATG
1 GTCAGTGTAAGACCTATCTGGGACATGACATCGACACAGATAG-ATGAGCCAATGTAAGACCATG
*
2001816 TTTGGAACATGGCAT
65 TCTGGAACATGGCAT
2001831 GGGCATCGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
96 13 0.20
97 17 0.26
98 36 0.55
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.26
Consensus pattern (97 bp):
GTCAGTGTAAGACCTATCTGGGACATGACATCGACACAGATAGATGAGCCAATGTAAGACCATGT
CTGGAACATGGCATTAGCCTCGATATGTGAAA
Found at i:2006763 original size:27 final size:27
Alignment explanation
Indices: 2006658--2006855 Score: 193
Period size: 27 Copynumber: 7.3 Consensus size: 27
2006648 TTAGTTTACC
* *
2006658 AAATTACCAAAATACCACTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
**
2006685 AAATTACCAAAATACCCCT-AGTTTACA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* *
2006712 AAATTATCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
*
2006739 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGATTTGTA
*** * **
2006766 AAATTATTGAAATACCCTTGACCTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
*** *
2006793 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
* *
2006820 AAATTACCAAAGTACCCCTGATTTATA
1 AAATTACCAAAATACCCCTGATTTGTA
2006847 AAATTACCA
1 AAATTACCA
2006856 TTTTACCCTC
Statistics
Matches: 141, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
26 3 0.02
27 134 0.95
28 4 0.03
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:2006877 original size:81 final size:80
Alignment explanation
Indices: 2006658--2006893 Score: 233
Period size: 81 Copynumber: 2.9 Consensus size: 80
2006648 TTAGTTTACC
* * * **
2006658 AAATTACCAAAATACCACTGGTTTGTAAAATTACCAAAATACCC-CTAGTTTACAAAATTATCAA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTACC-AAATACCCTCGA-TTTACAAAATTATTGA
**
2006722 AATACCCCTGGTTTGTA
64 AATACCCCTGACTTGTA
* ** * ** **
2006739 AAATTACCAAAATACCCCTGATTTGTGAAATTATTGAAATACCCTTGACCTGTAAAATTATTGAA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTA-CCAAATACCCTCGATTTACAAAATTATTGAA
2006804 ATA-CCCTCGACTTGTA
65 ATACCCCT-GACTTGTA
* * ** *
2006820 AAATTACCAAAGTACCCCTGATTTATAAAATTACCATTTTACCCTCGATTTACAAAATGATTGAA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTACCA-AATACCCTCGATTTACAAAATTATTGAA
2006885 ATACCCCTG
65 ATACCCCTG
2006894 TAGGGTAGAA
Statistics
Matches: 122, Mismatches: 28, Indels: 10
0.76 0.17 0.06
Matches are distributed among these distances:
80 5 0.04
81 112 0.92
82 5 0.04
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (80 bp):
AAATTACCAAAATACCCCTGATTTGTAAAATTACCAAATACCCTCGATTTACAAAATTATTGAAA
TACCCCTGACTTGTA
Found at i:2006909 original size:27 final size:27
Alignment explanation
Indices: 2006881--2007338 Score: 553
Period size: 27 Copynumber: 17.0 Consensus size: 27
2006871 ACAAAATGAT
*
2006881 TGAAATACCCCTGTAGGGTAGAATTAT
1 TGAAATACCCCTGTAGGGTAGAATTAC
* * *
2006908 TGAAATACCCTTGTAGGGTAAAAATAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
*
2006935 TGAAATACCCCTGTAGGGTAGAAATA-
1 TGAAATACCCCTGTAGGGTAGAATTAC
2006961 TCGAAATACCCCTGTAGGGTAGAATTAC
1 T-GAAATACCCCTGTAGGGTAGAATTAC
* *
2006989 TGAAATACCCCTATAAGGTAGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
* * *
2007016 TGAAATACCCCTTTAAGTTAGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
* * * *
2007043 TTAAATACCCTTATAAGGTAGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
** *
2007070 CAAAATATCCCTGTAGGGTAGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
**
2007097 TGAAATACCCCTGTAAAGTAGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
*
2007124 CGAAATACCCCTGTAGGGTAGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
* * *
2007151 CGAAATACCCTTGTAGGGTAGAATCA-
1 TGAAATACCCCTGTAGGGTAGAATTAC
2007177 TCGAAATACCCCTGTAGGGTAGAATTAC
1 T-GAAATACCCCTGTAGGGTAGAATTAC
* *
2007205 CGAAATACCCCTATAGGGTAGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
*
2007232 TGAAATACCCTTGTAGGGTAGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
** *
2007259 CAAAATACTCCTGTAGGGTAGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
* * *
2007286 TAAAATACCCCTGCAGGGTGGAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
* * * *
2007313 CGAGATA-CCTTGTAGGGTAAAATTAC
1 TGAAATACCCCTGTAGGGTAGAATTAC
2007339 CATTTTACCC
Statistics
Matches: 373, Mismatches: 54, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
26 16 0.04
27 356 0.95
28 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (27 bp):
TGAAATACCCCTGTAGGGTAGAATTAC
Found at i:2007809 original size:22 final size:22
Alignment explanation
Indices: 2007766--2007830 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
2007756 TTAAAGCCTT
* * **
2007766 CTGATTATGGCTTTGTGTCAAC
1 CTGAATATGGCTGTGTACCAAC
2007788 CT-ACATATGGCTGTGTACCAAC
1 CTGA-ATATGGCTGTGTACCAAC
* *
2007810 CTGATTATGGCTGTGTGCCAA
1 CTGAATATGGCTGTGTACCAA
2007831 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.34
Consensus pattern (22 bp):
CTGAATATGGCTGTGTACCAAC
Found at i:2008019 original size:27 final size:27
Alignment explanation
Indices: 2007989--2008090 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
2007979 ATTCTGTTAA
*
2007989 GTGGCTTTGCCACAATATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
2008016 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
*
2008043 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* **
2008070 GTGACTCTATCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
2008091 ATAACTGAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 8 0.12
27 51 0.76
28 8 0.12
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.35
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:2008265 original size:6 final size:6
Alignment explanation
Indices: 2008227--2008307 Score: 58
Period size: 6 Copynumber: 13.0 Consensus size: 6
2008217 TTGCATTCAT
* * *
2008227 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
2008277 -TTACCTG ATACTG ATTTTG ATTCTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
2008308 TCACCTAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
5 4 0.07
6 41 0.71
7 11 0.19
8 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.51
Consensus pattern (6 bp):
ATTCTG
Found at i:2008273 original size:31 final size:31
Alignment explanation
Indices: 2008227--2008337 Score: 152
Period size: 31 Copynumber: 3.5 Consensus size: 31
2008217 TTGCATTCAT
2008227 ATTCTGATTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
2008259 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * * *
2008290 ATTTTGATTCTGATTCTGTCACCTAATTCT-
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
2008320 AGTTCTGATTTTGATTCT
1 A-TTCTGATTTTGATTCT
2008338 AGTTCTGATA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
30 1 0.01
31 63 0.89
32 7 0.10
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.50
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:2008355 original size:18 final size:18
Alignment explanation
Indices: 2008315--2008367 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
2008305 CTGTCACCTA
**
2008315 ATTCTAGTTCTGATTTTG
1 ATTCTAGTTCTGATAATG
2008333 ATTCTAGTTCTGATAATG
1 ATTCTAGTTCTGATAATG
*
2008351 TTTCTTA-TTCTG-TAATG
1 ATTC-TAGTTCTGATAATG
2008368 GGTTAAAGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.16
18 24 0.77
19 2 0.06
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.53
Consensus pattern (18 bp):
ATTCTAGTTCTGATAATG
Found at i:2009024 original size:25 final size:25
Alignment explanation
Indices: 2008989--2009038 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2008979 GAGTGTTACA
*
2008989 GTTGGCGTAAAAAGAATATGAATGT
1 GTTGGCATAAAAAGAATATGAATGT
*
2009014 GTTGGCATAAAACGAATATGAATGT
1 GTTGGCATAAAAAGAATATGAATGT
2009039 CAGTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28
Consensus pattern (25 bp):
GTTGGCATAAAAAGAATATGAATGT
Found at i:2012184 original size:37 final size:37
Alignment explanation
Indices: 2012134--2012212 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
2012124 TTATTACGAA
* * *
2012134 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
2012171 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
2012208 GTCTT
1 GTCTT
2012213 TAGATCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:2012407 original size:49 final size:47
Alignment explanation
Indices: 2012330--2012438 Score: 182
Period size: 49 Copynumber: 2.3 Consensus size: 47
2012320 GCCCTTCGGG
2012330 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCCTATCAC--ATATATAC
*
2012380 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
2012427 ACTTTCACATTC
1 ACTTTCACATTC
2012439 TCAAAGTAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
47 20 0.34
49 34 0.59
50 4 0.07
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.32
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAC
Found at i:2012757 original size:24 final size:23
Alignment explanation
Indices: 2012709--2012766 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
2012699 TAATCAAACA
2012709 TTATTATATATATATCATATCATT
1 TTATTAT-TATATATCATATCATT
*
2012733 TTATTATTAT-TATCATTATTTATT
1 TTATTATTATATATCA-TA-TCATT
2012757 TTATT-TTATA
1 TTATTATTATA
2012767 CTTTTCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.17
23 9 0.30
24 16 0.53
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTATTATATATCATATCATT
Found at i:2017177 original size:47 final size:47
Alignment explanation
Indices: 2017116--2017239 Score: 144
Period size: 47 Copynumber: 2.6 Consensus size: 47
2017106 TGTGTGCTAG
** *
2017116 TGTAAGACATGTCTGGGACATGCATCGGCCA-CATTATGAGAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCGGCCATCAAGATAAGAGCCAA
* * ** *
2017162 TGTAAGACCATGTCTGGGACATGGCATCAG-CATTAAGATAAGAGTTAG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCATCAAGATAAGAGCCAA
2017210 TGTAAGACATGTCTGGGACATGCATCGGCC
1 TGTAAGACATGTCTGGGACATGCATCGGCC
2017240 TTGAGATATG
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
46 13 0.20
47 31 0.48
48 21 0.32
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (47 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCATCAAGATAAGAGCCAA
Found at i:2017441 original size:49 final size:48
Alignment explanation
Indices: 2017114--2017441 Score: 200
Period size: 49 Copynumber: 6.9 Consensus size: 48
2017104 GATGTGTGCT
* * *** * *
2017114 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCACAT-TATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTGATGTATGAAAGTC
* * *
2017160 AATGTAAGACCATGTCTGGGACATGGCATC-AGCATT-AAG-AT-AAGAGTT
1 AGTGTAAGACC-TGTCTGGGACATGGCATCGA-C-TTGATGTATGAA-AGTC
* * *
2017208 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTTGA-GATATGCAAG-C
1 AGTGTAAGACCTGTCTGGGACATGGCATC-GACTTGATG-TATGAAAGTC
* * * * * *
2017255 TAGTGTAAAACCTATCTGGGACACGGCATCGGCTTGA--CATG--TGTC
1 -AGTGTAAGACCTGTCTGGGACATGGCATCGACTTGATGTATGAAAGTC
** *
2017300 AGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAG-ATGAGA-TCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC-TTGAT-GTATGAAAGT-C
* * *
2017349 AATGTAAGACCTGTCTGGGACATGGCATCGGCCTTGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATC-GACTTGATGTATGAAAGTC
* *
2017398 AGTGTAAGACCTGTCTGGGACATGACATTGACTTAGATGTATGA
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTT-GATGTATGA
2017442 GCCAATGTAA
Statistics
Matches: 217, Mismatches: 39, Indels: 49
0.71 0.13 0.16
Matches are distributed among these distances:
44 29 0.13
45 3 0.01
46 20 0.09
47 30 0.14
48 54 0.25
49 78 0.36
50 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACTTGATGTATGAAAGTC
Found at i:2019218 original size:20 final size:21
Alignment explanation
Indices: 2019190--2019228 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2019180 GTGTCATGGA
*
2019190 AAAATTTTCTAA-GTTTTCCC
1 AAAACTTTCTAAGGTTTTCCC
2019210 AAAACTTTCTAAGGTTTTC
1 AAAACTTTCTAAGGTTTTC
2019229 GGCTTAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.44
Consensus pattern (21 bp):
AAAACTTTCTAAGGTTTTCCC
Found at i:2020294 original size:30 final size:30
Alignment explanation
Indices: 2020260--2020320 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2020250 TTCCCGAGCC
2020260 TAGGGCCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGCCAAAAGTGTAAATATGCAAAAGTT
* * * *
2020290 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGCCAAAAGTGTAAATATGCAAAAGTT
2020320 T
1 T
2020321 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGCCAAAAGTGTAAATATGCAAAAGTT
Found at i:2020910 original size:68 final size:68
Alignment explanation
Indices: 2020830--2020981 Score: 177
Period size: 64 Copynumber: 2.2 Consensus size: 68
2020820 CATCATGTGT
* * * *
2020830 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACTA
1 ACAAGAGAGCTACGAGACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACTAGTGAAGGACACCA
2020893 TGTAG
64 TGTAG
* * *
2020898 ACAAGAGAGCTACG-G-GATATATGTAGCTAGGTCGCATGCGTGGTTCTAGGTGAAGGACACCAT
1 ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCGTGATACTA-GTGAAGGACACCAT
2020961 GTAG
65 GTAG
*
2020965 ACAAGAGAGGTACGAGA
1 ACAAGAGAGCTACGAGA
2020982 TAAACTGGCT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
64 25 0.35
65 3 0.04
66 3 0.04
67 25 0.35
68 15 0.21
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCGTGATACTAGTGAAGGACACCATG
TAG
Found at i:2028446 original size:67 final size:67
Alignment explanation
Indices: 2028371--2028523 Score: 288
Period size: 67 Copynumber: 2.3 Consensus size: 67
2028361 CATCATGTGT
2028371 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGTATGCGTGGTTCTAGGTAAAGGACACCATGT
1 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGTATGCGTGGTTCTAGGTAAAGGACACCATGT
2028436 AG
66 AG
2028438 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGTATGCGTGGTTCTAGGTAAAGGACACCATGT
1 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGTATGCGTGGTTCTAGGTAAAGGACACCATGT
2028503 AG
66 AG
* *
2028505 ACAAGAGAGGTACGAGATA
1 ACAAGAGAGCTACGGGATA
2028524 AACTGGCTAG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 84 1.00
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.22
Consensus pattern (67 bp):
ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGTATGCGTGGTTCTAGGTAAAGGACACCATGT
AG
Found at i:2032592 original size:41 final size:41
Alignment explanation
Indices: 2032505--2032644 Score: 142
Period size: 41 Copynumber: 3.4 Consensus size: 41
2032495 TGATATAATA
* * *
2032505 TCAGGCTTATTACCTAGCAGGCTTTGATGCCGATGTATGATA-
1 TCAGGCTTAATGCCTAGCAGGCTTT-ATGCCG-TGTATTATAC
*
2032547 TCAGGCTTAATGTCTAGCAGGCTTTATGCCAGTGTATTA-AC
1 TCAGGCTTAATGCCTAGCAGGCTTTATGCC-GTGTATTATAC
* * * *
2032588 TCAGGTTTATTGCCTAGCAGGCTCTGTGCCGGTGTATTATAC
1 TCAGGCTTAATGCCTAGCAGGCTTTATGCC-GTGTATTATAC
*
2032630 T-AGGCTTCATGCCTA
1 TCAGGCTTAATGCCTA
2032645 ACAAATTTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
40 1 0.01
41 55 0.67
42 26 0.32
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (41 bp):
TCAGGCTTAATGCCTAGCAGGCTTTATGCCGTGTATTATAC
Found at i:2032655 original size:82 final size:83
Alignment explanation
Indices: 2032505--2032656 Score: 182
Period size: 82 Copynumber: 1.8 Consensus size: 83
2032495 TGATATAATA
* * * **
2032505 TCAGGCTTATTACCTAGCAGGCTTTGATGCCGATGTATGATATCAGGCTTAATGTCTAGCAGGCT
1 TCAGGCTTATTACCTAGCAGGCTCTGATGCCGATGTATGATATCAGGCTTAATGCCTAACAAACT
2032570 TTATGCCAGTGTATTAAC
66 TTATGCCAGTGTATTAAC
* * * * * *
2032588 TCAGGTTTATTGCCTAGCAGGCTCTG-TGCCGGTGTATTATA-CTAGGCTTCATGCCTAACAAAT
1 TCAGGCTTATTACCTAGCAGGCTCTGATGCCGATGTATGATATC-AGGCTTAATGCCTAACAAAC
2032651 TTTATG
65 TTTATG
2032657 TGAGCAACGA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
81 1 0.02
82 33 0.58
83 23 0.40
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (83 bp):
TCAGGCTTATTACCTAGCAGGCTCTGATGCCGATGTATGATATCAGGCTTAATGCCTAACAAACT
TTATGCCAGTGTATTAAC
Found at i:2056455 original size:42 final size:43
Alignment explanation
Indices: 2056331--2056456 Score: 159
Period size: 43 Copynumber: 3.0 Consensus size: 43
2056321 AAGTCTGAAC
* * **
2056331 TCAT-TCACTGGCATT-TCGCCTGCTAGGCTTGAAGCCCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
* * *
2056372 TCATTTCACCGGCATTATAGGCTACTAGGCCCGAAGCCCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
*
2056415 TTATCTCACCGGCATTA-AGCCTGCTAGGCCCGAAGCCCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
2056457 ATATTATTCA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
41 4 0.05
42 33 0.45
43 36 0.49
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (43 bp):
TCATCTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATA
Found at i:2056486 original size:44 final size:43
Alignment explanation
Indices: 2056348--2056501 Score: 147
Period size: 43 Copynumber: 3.6 Consensus size: 43
2056338 CTGGCATTTC
** * * *
2056348 GCCTGCTAGGCTTGAAGCCCG-ATATCATTTCACCGGCATTATA
1 GCCTGCTAGGCCCGAAGCCCGAATATTATCTCACCAGCATTA-A
* * *
2056391 GGCTACTAGGCCCGAAGCCCG-ATATTATCTCACCGGCATTAA
1 GCCTGCTAGGCCCGAAGCCCGAATATTATCTCACCAGCATTAA
2056433 GCCTGCTAGGCCCGAAGCCCGATAATATTAT-TCACCAGC-TTAAA
1 GCCTGCTAGGCCCGAAGCCCG--AATATTATCTCACCAGCATT-AA
* *
2056477 GCTTGCTAGG-CCGAGGCCCGAATAT
1 GCCTGCTAGGCCCGAAGCCCGAATAT
2056502 CACATTTCGA
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
41 5 0.05
42 20 0.21
43 46 0.48
44 18 0.19
45 7 0.07
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.23
Consensus pattern (43 bp):
GCCTGCTAGGCCCGAAGCCCGAATATTATCTCACCAGCATTAA
Found at i:2058190 original size:14 final size:15
Alignment explanation
Indices: 2058161--2058190 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2058151 AAAAATTTAG
2058161 ACATGATACTTTCAC
1 ACATGATACTTTCAC
2058176 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
2058190 A
1 A
2058191 TATAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:2067472 original size:21 final size:21
Alignment explanation
Indices: 2067448--2067487 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2067438 TTCTCCTTGC
*
2067448 CTCTTGCT-CCCTTTTTCTTTT
1 CTCTT-CTCCCCTTTCTCTTTT
2067469 CTCTTCTCCCCTTTCTCTT
1 CTCTTCTCCCCTTTCTCTT
2067488 AACTGGTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.00, C:0.40, G:0.03, T:0.57
Consensus pattern (21 bp):
CTCTTCTCCCCTTTCTCTTTT
Found at i:2068359 original size:27 final size:27
Alignment explanation
Indices: 2068342--2068540 Score: 272
Period size: 27 Copynumber: 7.4 Consensus size: 27
2068332 AAAGTGATTA
* * *
2068342 TTTTTCCCTTATGGGGTAAAATGACAG
1 TTTTGCCCTTATGAGGTAAAATGACTG
*
2068369 TTTTGCCCTTATGAGGTAAAATGATTG
1 TTTTGCCCTTATGAGGTAAAATGACTG
*
2068396 TTTTGCCCTTATGAGGTAAAAGGACTG
1 TTTTGCCCTTATGAGGTAAAATGACTG
* *
2068423 TTTTACCCTTATGTGGTAAAATGACTG
1 TTTTGCCCTTATGAGGTAAAATGACTG
* * *
2068450 TTTTGCCCTTATGTGGTAAAATAACTA
1 TTTTGCCCTTATGAGGTAAAATGACTG
* *
2068477 TTTTTCCCTTATGAGGTAAAATTACTG
1 TTTTGCCCTTATGAGGTAAAATGACTG
* *
2068504 TTTTGCCCTTATGTGGTAAAATGAATG
1 TTTTGCCCTTATGAGGTAAAATGACTG
2068531 TTTTGCCCTT
1 TTTTGCCCTT
2068541 TTATAGTAAG
Statistics
Matches: 152, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 152 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (27 bp):
TTTTGCCCTTATGAGGTAAAATGACTG
Found at i:2068558 original size:81 final size:81
Alignment explanation
Indices: 2068342--2068570 Score: 266
Period size: 81 Copynumber: 2.8 Consensus size: 81
2068332 AAAGTGATTA
* * * * *
2068342 TTTTTCCCTTATGGGGTAAAATGACA-GTTTTGCCC--TTATGAGGTAAAATGATTGTTTTGCCC
1 TTTTACCCTTATGTGGTAAAATGA-ATGTTTTGCCCTTTTAT-A-GTAAAATGACTATTTTACCC
2068404 TTATGAGGTAAAAGGACTG
63 TTATGAGGTAAAAGGACTG
* * * * * *
2068423 TTTTACCCTTATGTGGTAAAATGACTGTTTTGCCCTTATGTGGTAAAATAACTATTTTTCCCTTA
1 TTTTACCCTTATGTGGTAAAATGAATGTTTTGCCCTTTTATAGTAAAATGACTATTTTACCCTTA
**
2068488 TGAGGTAAAATTACTG
66 TGAGGTAAAAGGACTG
* * *
2068504 TTTTGCCCTTATGTGGTAAAATGAATGTTTTGCCCTTTTATAGTAAGATGACTATTTTACCCCTA
1 TTTTACCCTTATGTGGTAAAATGAATGTTTTGCCCTTTTATAGTAAAATGACTATTTTACCCTTA
2068569 TG
66 TG
2068571 TGATGTATGT
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
81 122 0.98
83 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (81 bp):
TTTTACCCTTATGTGGTAAAATGAATGTTTTGCCCTTTTATAGTAAAATGACTATTTTACCCTTA
TGAGGTAAAAGGACTG
Found at i:2068561 original size:27 final size:27
Alignment explanation
Indices: 2068357--2068561 Score: 173
Period size: 27 Copynumber: 7.6 Consensus size: 27
2068347 CCCTTATGGG
* *
2068357 GTAAAATGACAGTTTTGCCCTTATGA-G
1 GTAAAATGACTGTTTTGCCCTTAT-ATA
* *
2068384 GTAAAATGATTGTTTTGCCCTTATGA-G
1 GTAAAATGACTGTTTTGCCCTTAT-ATA
* * * *
2068411 GTAAAAGGACTGTTTTACCCTTATGTG
1 GTAAAATGACTGTTTTGCCCTTATATA
* *
2068438 GTAAAATGACTGTTTTGCCCTTATGTG
1 GTAAAATGACTGTTTTGCCCTTATATA
* * * *
2068465 GTAAAATAACTATTTTTCCCTTATGA-G
1 GTAAAATGACTGTTTTGCCCTTAT-ATA
* * *
2068492 GTAAAATTACTGTTTTGCCCTTATGTG
1 GTAAAATGACTGTTTTGCCCTTATATA
* *
2068519 GTAAAATGAATGTTTTGCCCTTTTATA
1 GTAAAATGACTGTTTTGCCCTTATATA
* *
2068546 GTAAGATGACTATTTT
1 GTAAAATGACTGTTTT
2068562 ACCCCTATGT
Statistics
Matches: 151, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
27 151 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (27 bp):
GTAAAATGACTGTTTTGCCCTTATATA
Found at i:2068910 original size:18 final size:18
Alignment explanation
Indices: 2068887--2068954 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
2068877 TTGCATACTG
*
2068887 TTTACTGTTACTGCATTA
1 TTTACTGTTACTGCACTA
* *
2068905 TTTACTATTATTGCACT-
1 TTTACTGTTACTGCACTA
* *
2068922 GTTATTGTTACTGCACTA
1 TTTACTGTTACTGCACTA
*
2068940 CTTACTGTTACTGCA
1 TTTACTGTTACTGCA
2068955 ATGGGCCAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 13 0.32
18 27 0.68
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (18 bp):
TTTACTGTTACTGCACTA
Found at i:2070305 original size:20 final size:20
Alignment explanation
Indices: 2070280--2070333 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2070270 AACAGGGGTC
2070280 ACACGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
*
2070300 ACACGCCCATGTGGCTTGGG
1 ACACGCCCGTGTGGCTTGGG
*
2070320 ACATGCCCGTGTGG
1 ACACGCCCGTGTGG
2070334 GTACGCTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.30, G:0.37, T:0.20
Consensus pattern (20 bp):
ACACGCCCGTGTGGCTTGGG
Found at i:2072987 original size:22 final size:22
Alignment explanation
Indices: 2072972--2073017 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2072962 ATTTTTTATG
2072972 TTATATTACTTCATTTTCTTTC
1 TTATATTACTTCATTTTCTTTC
2072994 TTATATTACTTCATTTTCTTTC
1 TTATATTACTTCATTTTCTTTC
2073016 TT
1 TT
2073018 TCATCTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATATTACTTCATTTTCTTTC
Found at i:2075018 original size:25 final size:25
Alignment explanation
Indices: 2074990--2075038 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2074980 CGATACTTAG
* **
2074990 CTCGCATGAGCTTACTGTTATTCAA
1 CTCGCAGGAGCTTACCATTATTCAA
*
2075015 CTCGGAGGAGCTTACCATTATTCA
1 CTCGCAGGAGCTTACCATTATTCA
2075039 GCTTGAAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (25 bp):
CTCGCAGGAGCTTACCATTATTCAA
Found at i:2075072 original size:24 final size:25
Alignment explanation
Indices: 2075022--2075074 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
2075012 CAACTCGGAG
* *
2075022 GAGCTTACCATTATTCAGCTTGAAA
1 GAGCTTACCATTATACAGCTCGAAA
* *
2075047 GAGCTTACCGTT-TACAGCTCGTAA
1 GAGCTTACCATTATACAGCTCGAAA
2075071 GAGC
1 GAGC
2075075 ATACTGGTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (25 bp):
GAGCTTACCATTATACAGCTCGAAA
Found at i:2078923 original size:46 final size:46
Alignment explanation
Indices: 2078856--2079165 Score: 303
Period size: 46 Copynumber: 6.7 Consensus size: 46
2078846 TAACCCACCT
* * * *
2078856 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCC
1 ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACGTTCACATCC
* * * *
2078902 ATAAGTGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCC
1 ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACGTTCACATCC
2078948 ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--
1 ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA---C--GTTCACATCC
* * * * * * *
2078996 TTCA-CGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCC
1 ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACGTTCACATCC
2079041 ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCCAGTT-ACAT-C
1 ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA----C-GTTCACATCC
* * *
2079090 -TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACGTTCGCATCC
1 ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACGTTCACATCC
*
2079134 ATAAGTGAACTCAGACTCAACTCAATGAGTTC
1 ATAAGTGAACTCAGACTCAACTCAACGAGTTC
2079166 CGATGCCCAA
Statistics
Matches: 216, Mismatches: 30, Indels: 36
0.77 0.11 0.13
Matches are distributed among these distances:
42 5 0.02
43 7 0.03
44 2 0.01
45 4 0.02
46 125 0.58
47 56 0.26
48 4 0.02
49 2 0.01
50 7 0.03
51 4 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
ATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACGTTCACATCC
Found at i:2079018 original size:47 final size:46
Alignment explanation
Indices: 2078954--2079122 Score: 193
Period size: 47 Copynumber: 3.6 Consensus size: 46
2078944 ATCCATAAGT
*
2078954 GAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCAGACTCAACTCAACGAGTTCGGATGCC-AGTTACATATCAC
* * * * *
2079001 GAACTCGGACTCAACTCAATGAGTTCGGA---CA-TTCGCATCCATAAGT
1 GAACTCAGACTCAACTCAACGAGTTCGGATGCCAGTT-ACAT--ATCA-C
*
2079047 GAACTCAGACTCAACTCAACGAGTTCGGATGCCCAGTTACATCTCAC
1 GAACTCAGACTCAACTCAACGAGTTCGGATG-CCAGTTACATATCAC
2079094 GAACTCAGACTCAACTCAACGAGTTCGGA
1 GAACTCAGACTCAACTCAACGAGTTCGGA
2079123 CGTTCGCATC
Statistics
Matches: 101, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 27 0.27
47 56 0.55
48 2 0.02
50 5 0.05
51 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.22
Consensus pattern (46 bp):
GAACTCAGACTCAACTCAACGAGTTCGGATGCCAGTTACATATCAC
Found at i:2079027 original size:93 final size:93
Alignment explanation
Indices: 2078908--2079174 Score: 471
Period size: 93 Copynumber: 2.9 Consensus size: 93
2078898 ATCCATAAGT
2078908 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
* *
2078973 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCCAGTTACATCTCAC
2079001 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
2079066 CGAGTTCGGATGCCCAGTTACATCTCAC
66 CGAGTTCGGATGCCCAGTTACATCTCAC
* * *
2079094 GAACTCAGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
* *
2079159 TGAGTTCCGATGCCCA
66 CGAGTTCGGATGCCCA
2079175 AATATCTGAA
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 167 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCCAGTTACATCTCAC
Found at i:2079144 original size:139 final size:138
Alignment explanation
Indices: 2078856--2079165 Score: 344
Period size: 139 Copynumber: 2.2 Consensus size: 138
2078846 TAACCCACCT
* * * * *
2078856 ATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCA
1 ATAAGCGAACTCGGACTCAACTCAATGAGTTCGGACATTCACATCCATAAGTGAACTCAGACTCA
* * * *
2078921 ACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGC
66 ACTCAACGAGTTCGGACATTCACATCCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGACGC
*
2078986 CTAGTTAC
131 CTAGATAC
* *
2078994 ATTTCA-CGAACTCGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACT
1 A--TAAGCGAACTCGGACTCAACTCAATGAGTTCGGACATTCACATCCATAAGTGAACTCAGACT
*
2079058 CAACTCAACGAGTTCGGATGCCCAGTT-ACAT-C-TCA-CGAACTCAGACTCAACTCAACGAGTT
64 CAACTCAACGAGTTCGGA----CA-TTCACATCCATAAGCGAACTCAGACTCAACTCAACGAGTT
* * *
2079119 CGGACG-TTCGCATCC
124 CGGACGCCTAG-ATAC
* *
2079134 ATAAGTGAACTCAGACTCAACTCAATGAGTTC
1 ATAAGCGAACTCGGACTCAACTCAATGAGTTC
2079166 CGATGCCCAA
Statistics
Matches: 144, Mismatches: 19, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
138 3 0.02
139 96 0.67
140 35 0.24
141 2 0.01
142 1 0.01
143 5 0.03
144 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (138 bp):
ATAAGCGAACTCGGACTCAACTCAATGAGTTCGGACATTCACATCCATAAGTGAACTCAGACTCA
ACTCAACGAGTTCGGACATTCACATCCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGACGC
CTAGATAC
Found at i:2081923 original size:30 final size:29
Alignment explanation
Indices: 2081879--2081935 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
2081869 AAAGATAATA
*
2081879 AGAAAACCGAATAAAGAAATCCAAGATTG
1 AGAAAACCGAATAAAGAAACCCAAGATTG
*
2081908 AGAAACCCAGAATAAAGAAACCCAAGAT
1 AGAAAACC-GAATAAAGAAACCCAAGAT
2081936 ACGATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.56, C:0.18, G:0.16, T:0.11
Consensus pattern (29 bp):
AGAAAACCGAATAAAGAAACCCAAGATTG
Found at i:2083689 original size:5 final size:5
Alignment explanation
Indices: 2083679--2083749 Score: 62
Period size: 5 Copynumber: 14.6 Consensus size: 5
2083669 AAAAAAATAT
* *
2083679 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TCATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA T-ATTA
2083725 -A-TA TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT
2083750 ACATAAAACA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
3 4 0.07
4 8 0.15
5 32 0.58
6 10 0.18
7 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:2083731 original size:19 final size:19
Alignment explanation
Indices: 2083707--2083749 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2083697 ATTATGTTTT
2083707 TATATTATATTATCATTA-A
1 TATATTATATTAT-ATTATA
2083726 TATATTATATTATATTATA
1 TATATTATATTATATTATA
2083745 TATAT
1 TATAT
2083750 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:2083780 original size:16 final size:16
Alignment explanation
Indices: 2083759--2083791 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2083749 TACATAAAAC
*
2083759 AAAAGAAAGAATAGAA
1 AAAAGAAAGAAAAGAA
2083775 AAAAGAAAGAAAAGAA
1 AAAAGAAAGAAAAGAA
2083791 A
1 A
2083792 CAGAATAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAGAAAGAAAAGAA
Found at i:2084419 original size:29 final size:30
Alignment explanation
Indices: 2084360--2084417 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2084350 TCCGAGCCTT
**
2084360 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATCAAAAAGTTTA
* *
2084390 GGGGCAAAATTGTAATTTTCAAAAAGTT
1 GGGGCAAAAATGTAATTATCAAAAAGTT
2084418 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATCAAAAAGTTTA
Found at i:2084647 original size:13 final size:13
Alignment explanation
Indices: 2084629--2084660 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2084619 TTTCCAGCAA
2084629 TTATGAATTTATT
1 TTATGAATTTATT
2084642 TTATGAATTTATT
1 TTATGAATTTATT
*
2084655 TGATGA
1 TTATGA
2084661 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:2084868 original size:50 final size:50
Alignment explanation
Indices: 2084755--2085096 Score: 443
Period size: 50 Copynumber: 6.7 Consensus size: 50
2084745 ATTTGGGTAA
* * * *
2084755 AGAGATCCCATGTAAGACCATGCCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
2084811 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2084861 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* *
2084911 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2084961 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
2085011 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
2085061 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
2085097 TTTGGCATGT
Statistics
Matches: 255, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
49 1 0.00
50 181 0.71
51 29 0.11
52 1 0.00
53 3 0.01
55 2 0.01
56 38 0.15
ACGTcount: A:0.26, C:0.25, G:0.30, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:2084943 original size:100 final size:100
Alignment explanation
Indices: 2084755--2085103 Score: 538
Period size: 100 Copynumber: 3.4 Consensus size: 100
2084745 ATTTGGGTAA
* * *
2084755 AGAGATCCCATGTAAGACCATGCCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC----GA-GATGAGAGGTCCC
*
2084820 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
60 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
*
2084861 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAA
2084926 GACCATGTCTGGGACATGGCATGGGCACCGAGACG
66 GACCATGTCTGGGACATGGCATGGGCACCGAGACG
*
2084961 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAA
*
2085026 GACCATGTCTGGGACATGGCATGGGCACC-ATCACG
66 GACCATGTCTGGGACATGGCATGGGCACCGA-GACG
* *
2085061 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
2085104 TGTTATTATC
Statistics
Matches: 232, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
99 1 0.00
100 151 0.65
101 39 0.17
105 2 0.01
106 39 0.17
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.19
Consensus pattern (100 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAA
GACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:2088174 original size:93 final size:93
Alignment explanation
Indices: 2088059--2088233 Score: 287
Period size: 93 Copynumber: 1.9 Consensus size: 93
2088049 CACCCATAAG
* *
2088059 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAACAAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAACAAACTCAGACTCAACTCA
*
2088124 ATGAGTTCGGATGCCTAGGTACATCTCA
66 ACGAGTTCGGATGCCTAGGTACATCTCA
* ***
2088152 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAACAAACTCAGACTCAACTCA
2088217 ACGAGTTCGGATGCCTA
66 ACGAGTTCGGATGCCTA
2088234 AATATTTGAG
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCACATCCATAAACAAACTCAGACTCAACTCA
ACGAGTTCGGATGCCTAGGTACATCTCA
Found at i:2088227 original size:46 final size:46
Alignment explanation
Indices: 2088052--2088227 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
2088042 TGTAACCCAC
* *
2088052 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACAT
* * * *
2088098 CCATAAACAAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGGT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCACAT
*
2088148 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACAT
* *
2088191 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
2088228 TGCCTAAATA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.56
47 28 0.26
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCACAT
Found at i:2093424 original size:43 final size:43
Alignment explanation
Indices: 2093316--2093433 Score: 136
Period size: 42 Copynumber: 2.8 Consensus size: 43
2093306 GACTTGAGAT
*
2093316 TTACGTGTAAGACCATATCTGGGACA-TTGGCATCGTATATTA
1 TTACGTGTAAGACCATATCTGGGACAGTTAGCATCGTATATTA
* *
2093358 TTCCGTGTAAGACCCTATCTGGGACAGTT-GCATCG-ATATTTGA
1 TTACGTGTAAGACCATATCTGGGACAGTTAGCATCGTATA-TT-A
* * *
2093401 TTACATGTAAGACCATGTTTGGGA-AGTTAGCAT
1 TTACGTGTAAGACCATATCTGGGACAGTTAGCAT
2093434 TGTACGAGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
41 3 0.05
42 36 0.55
43 26 0.40
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (43 bp):
TTACGTGTAAGACCATATCTGGGACAGTTAGCATCGTATATTA
Found at i:2097244 original size:43 final size:43
Alignment explanation
Indices: 2097196--2097300 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 43
2097186 TAACGAGATA
2097196 TGATTATGTGTAAGACCATGTCTAGGAAATTGGCATCATTATG
1 TGATTATGTGTAAGACCATGTCTAGGAAATTGGCATCATTATG
* * * * *
2097239 TGATTATGTGTAAGACCAGGTCTGGGACATTGGCATCGTTATT
1 TGATTATGTGTAAGACCATGTCTAGGAAATTGGCATCATTATG
*
2097282 TGATT-TCGTGCAAGACCAT
1 TGATTAT-GTGTAAGACCAT
2097301 AGTTGGGCCA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.02
43 53 0.98
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
TGATTATGTGTAAGACCATGTCTAGGAAATTGGCATCATTATG
Found at i:2111028 original size:40 final size:40
Alignment explanation
Indices: 2110936--2111043 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 40
2110926 ACTCGATATC
* * * * *
2110936 TCGCACACTAAGTGCCGTACATAGTCGAGGCTATCTCAAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATATCAAA
** * *
2110976 TTACACAGTAAGTGCCATATATAGCCGAAGCTATATCGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATATCAAA
* *
2111016 TCGCACACTAAGTGTCATGTATAGCCGA
1 TCGCACACTAAGTGCCATATATAGCCGA
2111044 TCTAGCACAC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCTATATCAAA
Found at i:2115788 original size:27 final size:27
Alignment explanation
Indices: 2115729--2115781 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2115719 CATACATCTT
2115729 ATAGGGGCATAACAGTCATTTTATCAC
1 ATAGGGGCATAACAGTCATTTTATCAC
* *
2115756 ATAGGGGCATCATAGTCATTTTATCA
1 ATAGGGGCATAACAGTCATTTTATCA
2115782 GTTAGGGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (27 bp):
ATAGGGGCATAACAGTCATTTTATCAC
Found at i:2116015 original size:17 final size:17
Alignment explanation
Indices: 2115990--2116023 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2115980 GTTTACTCGA
* *
2115990 GTGGGGCCCACATGGCC
1 GTGGAGCCCACACGGCC
2116007 GTGGAGCCCACACGGCC
1 GTGGAGCCCACACGGCC
2116024 TAGTTCGACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.38, G:0.38, T:0.09
Consensus pattern (17 bp):
GTGGAGCCCACACGGCC
Found at i:2122557 original size:28 final size:28
Alignment explanation
Indices: 2122525--2122593 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
2122515 AATGAGATTG
*
2122525 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
*
2122553 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
2122581 GCACTAAGTGTGC
1 GCACTAAGTGTGC
2122594 AAACTTACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:2124699 original size:25 final size:25
Alignment explanation
Indices: 2124666--2124715 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2124656 TGAATACGGC
*
2124666 TAAGGGGTGTTATAATATGAATTAA
1 TAAGCGGTGTTATAATATGAATTAA
2124691 TAAGCGGTGTTATAATATGAATTAA
1 TAAGCGGTGTTATAATATGAATTAA
2124716 AATGTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (25 bp):
TAAGCGGTGTTATAATATGAATTAA
Found at i:2132969 original size:27 final size:27
Alignment explanation
Indices: 2132939--2132993 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2132929 GTCGAGTGGA
2132939 GAGTGCCTAGTTCAACTACTAGAATTT
1 GAGTGCCTAGTTCAACTACTAGAATTT
2132966 GAGTGCCTAGTTCAACTACTAGAATTT
1 GAGTGCCTAGTTCAACTACTAGAATTT
2132993 G
1 G
2132994 TGTACTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (27 bp):
GAGTGCCTAGTTCAACTACTAGAATTT
Found at i:2133003 original size:24 final size:26
Alignment explanation
Indices: 2132939--2133006 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
2132929 GTCGAGTGGA
*
2132939 GAGTGCCTAGTTCAACTACTAGAATTT
1 GAGTGACTA-TTCAACTACTAGAATTT
*
2132966 GAGTGCCTAGTTCAACTACTAGAATTT
1 GAGTGACTA-TTCAACTACTAGAATTT
*
2132993 GTGT-ACT-TTCAACT
1 GAGTGACTATTCAACT
2133007 GGATAATATC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
24 7 0.18
26 2 0.05
27 30 0.77
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (26 bp):
GAGTGACTATTCAACTACTAGAATTT
Found at i:2135493 original size:15 final size:15
Alignment explanation
Indices: 2135475--2135508 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2135465 CTTTTATTTC
2135475 TTTTAACTTTCTTTT
1 TTTTAACTTTCTTTT
* *
2135490 TTTTCATTTTCTTTT
1 TTTTAACTTTCTTTT
2135505 TTTT
1 TTTT
2135509 TCTCTCTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTAACTTTCTTTT
Found at i:2150559 original size:29 final size:27
Alignment explanation
Indices: 2150522--2150590 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 27
2150512 TAGGCCCTCC
*
2150522 ATATTATTTTTAATTTTTTAAAAATATTT
1 ATATTATTTTTAA-TATTTAAAAAT-TTT
*
2150551 ATATTATTTTTTTAATATTTAATAATTTT
1 ATATTA--TTTTTAATATTTAAAAATTTT
2150580 ATA-TATTTTTA
1 ATATTATTTTTA
2150591 TATAGTCAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
26 6 0.17
28 2 0.06
29 12 0.33
30 9 0.25
31 7 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
ATATTATTTTTAATATTTAAAAATTTT
Found at i:2150566 original size:31 final size:28
Alignment explanation
Indices: 2150522--2150589 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 28
2150512 TAGGCCCTCC
*
2150522 ATATTATTTTTAATTTTTTAAAAATATTTAT
1 ATATT-TTTTTAA-TATTTAAAAAT-TTTAT
*
2150553 ATTATTTTTTTAATATTTAATAATTTTAT
1 A-TATTTTTTTAATATTTAAAAATTTTAT
2150582 ATATTTTT
1 ATATTTTT
2150590 ATATAGTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 7 0.21
29 6 0.18
30 9 0.26
31 8 0.24
32 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
ATATTTTTTTAATATTTAAAAATTTTAT
Found at i:2150749 original size:29 final size:30
Alignment explanation
Indices: 2150702--2150758 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
2150692 TTGATTTAAT
* *
2150702 GTGCAATTATATACATGAACTT-TAATTTG
1 GTGCAATTATACACATGAAATTCTAATTTG
**
2150731 GTGCAATTATACATGTGAAATTCTAATT
1 GTGCAATTATACACATGAAATTCTAATT
2150759 GTAGTTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (30 bp):
GTGCAATTATACACATGAAATTCTAATTTG
Found at i:2150865 original size:23 final size:21
Alignment explanation
Indices: 2150829--2150870 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
2150819 TAAAAGCGTC
2150829 AATTTATTTTTATTATGGATA
1 AATTTATTTTTATTATGGATA
2150850 AATTTAATTATTTATTATGGA
1 AATTT-ATT-TTTATTATGGA
2150871 ATATATGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (21 bp):
AATTTATTTTTATTATGGATA
Found at i:2152005 original size:15 final size:15
Alignment explanation
Indices: 2151985--2152038 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
2151975 ATAGTACAAA
2151985 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
2152000 ATATTTATAATTGCAAT
1 ATATTTATTATT--AAT
*
2152017 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
2152034 ATATT
1 ATATT
2152039 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 16 0.50
17 5 0.16
19 11 0.34
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:2152036 original size:19 final size:17
Alignment explanation
Indices: 2151983--2152032 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 17
2151973 TTATAGTACA
2151983 AAATATTTATTATTAAT
1 AAATATTTATTATTAAT
*
2152000 --ATATTTATAATTGCAAT
1 AAATATTTATTATT--AAT
2152017 AAATATTTATTATTAA
1 AAATATTTATTATTAA
2152033 AATATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 11 0.41
17 5 0.19
19 11 0.41
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AAATATTTATTATTAAT
Found at i:2152173 original size:16 final size:16
Alignment explanation
Indices: 2152152--2152184 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2152142 AATAAATTAT
*
2152152 ATTTATTATATTAATA
1 ATTTATTATATGAATA
2152168 ATTTATTATATGAATA
1 ATTTATTATATGAATA
2152184 A
1 A
2152185 ATATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
ATTTATTATATGAATA
Found at i:2167273 original size:2 final size:2
Alignment explanation
Indices: 2167266--2167291 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2167256 ATTTTGTTTC
2167266 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2167292 CTTTTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2167889 original size:131 final size:132
Alignment explanation
Indices: 2167623--2167915 Score: 392
Period size: 131 Copynumber: 2.2 Consensus size: 132
2167613 TTATTCATTC
* ** *
2167623 AAAAATTCTTCAAAACGAAGACGAGATTCGATGTTTGGCAATTCACGGAATCGTGCCCTAACGTG
1 AAAAATTCTTCAAAACGAAGACAAGATTCGATACTTAGCAATTCACGGAATCGTGCCCTAACGTG
* * *
2167688 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATAGCACTTTGAAATTTCACTCACGTCTT
66 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATAGCACTTTAAAACTTCACTCACATCTT
2167753 -T
131 CT
* *
2167754 TAAAATTCTTCAAAACGAAGACAAGATTCGATACTTAGCAATTCGCGGAATCGTGCCCTAACGTG
1 AAAAATTCTTCAAAACGAAGACAAGATTCGATACTTAGCAATTCACGGAATCGTGCCCTAACGTG
* * * * * *
2167819 TTGGGTTGCAATTTCGCGTTTGCTTAAAGTAATCGAGTATC-CTTTCAAAACTTCATTCATATCT
66 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATAGCACTTT-AAAACTTCACTCACATCT
2167883 TCT
130 TCT
* * * *
2167886 AAAAATTATTTAAAACGAAGGCAACATTCG
1 AAAAATTCTTCAAAACGAAGACAAGATTCG
2167916 GCATTTGACA
Statistics
Matches: 140, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
130 4 0.03
131 110 0.79
132 26 0.19
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (132 bp):
AAAAATTCTTCAAAACGAAGACAAGATTCGATACTTAGCAATTCACGGAATCGTGCCCTAACGTG
TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATAGCACTTTAAAACTTCACTCACATCTT
CT
Found at i:2167936 original size:131 final size:131
Alignment explanation
Indices: 2167623--2167976 Score: 354
Period size: 131 Copynumber: 2.7 Consensus size: 131
2167613 TTATTCATTC
* * * *** * * *
2167623 AAAAATTCTTCAAAACGAAGACGAGATTCGATGTTTGGCAATTCACGGAATCGTGCCCTAACGTG
1 AAAAATTATTCAAAACGAAGACAACATTCGACACTTAGCAATTCGCAGAATCGTGCCCTAACGTG
* * *
2167688 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATAGCACTTTGAAATTTCACTCACGTCTT
66 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATAGCACTTTAAAACTTCACTCACATCTT
2167753 T
131 T
* * * * *
2167754 TAAAATTCTTCAAAACGAAGACAAGATTCGATACTTAGCAATTCGCGGAATCGTGCCCTAACGTG
1 AAAAATTATTCAAAACGAAGACAACATTCGACACTTAGCAATTCGCAGAATCGTGCCCTAACGTG
* * * * * *
2167819 TTGGGTTGCAATTTCGCGTTTGCTTAAAGTAATCGAGTATC-CTTTCAAAACTTCATTCATATCT
66 TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATAGCACTTT-AAAACTTCACTCACATCT
2167883 TCT
130 T-T
* * * * * *
2167886 AAAAATTATTTAAAACGAAGGCAACATTCGGCA-TTTGACAATTCG-AGAATCATGCCCTATCGT
1 AAAAATTATTCAAAACGAAGACAACATTCGACACTTAG-CAATTCGCAGAATCGTGCCCTAACGT
* ** * *
2167949 GCTGGGTTGTGATTTCTCGTTTGTTCAA
65 GTTGGGTTGCAATTTCGCGTTTGCTCAA
2167977 TGATTGAATA
Statistics
Matches: 188, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
130 4 0.02
131 150 0.80
132 34 0.18
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (131 bp):
AAAAATTATTCAAAACGAAGACAACATTCGACACTTAGCAATTCGCAGAATCGTGCCCTAACGTG
TTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATAGCACTTTAAAACTTCACTCACATCTT
T
Found at i:2170403 original size:12 final size:11
Alignment explanation
Indices: 2170380--2170438 Score: 59
Period size: 12 Copynumber: 5.3 Consensus size: 11
2170370 GAAGTCTAAG
*
2170380 AAAATAACAAT
1 AAAATAAAAAT
2170391 AAACATAAAAAT
1 AAA-ATAAAAAT
*
2170403 AGAAATAAAACT
1 A-AAATAAAAAT
2170415 AAAACT-AAAA-
1 AAAA-TAAAAAT
2170425 AAAATAAAAAT
1 AAAATAAAAAT
2170436 AAA
1 AAA
2170439 TGAACTCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
9 1 0.03
10 8 0.20
11 12 0.30
12 17 0.43
13 2 0.05
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:2170403 original size:18 final size:16
Alignment explanation
Indices: 2170380--2170438 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 16
2170370 GAAGTCTAAG
2170380 AAAATAACAATAAACATA
1 AAAATAA-AATAAA-ATA
2170398 AAAATAGAAATAAAACTA
1 AAAATA-AAATAAAA-TA
*
2170416 AAACTAAAA-AAAATA
1 AAAATAAAATAAAATA
2170431 AAAATAAA
1 AAAATAAA
2170439 TGAACTCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
15 9 0.24
16 4 0.11
17 4 0.11
18 19 0.51
19 1 0.03
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:2170433 original size:6 final size:6
Alignment explanation
Indices: 2170380--2170438 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
2170370 GAAGTCTAAG
* * * * *
2170380 AAAATA ACAATA AACATA AAAATA GAAATA AAACTA AAACT- -AAA-A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
2170425 AAAATA AAAATA AA
1 AAAATA AAAATA AA
2170439 TGAACTCAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
4 2 0.05
5 3 0.07
6 37 0.88
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:2172134 original size:40 final size:38
Alignment explanation
Indices: 2172071--2172159 Score: 92
Period size: 40 Copynumber: 2.3 Consensus size: 38
2172061 GAAAATGAAC
*
2172071 AAATAACTTATAAAAATACTAATA-ATAAAGAAATAAAAT
1 AAATAACTAATAAAAATACTAATAGAT-AAG-AATAAAAT
* *
2172110 AATATAACTAATAATAACTA-TAATAGATAAGAATTAAAT
1 AA-ATAACTAATAA-AAATACTAATAGATAAGAATAAAAT
*
2172149 AAATAATTAAT
1 AAATAACTAAT
2172160 TAAATAAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
38 8 0.19
39 11 0.26
40 18 0.42
41 6 0.14
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.29
Consensus pattern (38 bp):
AAATAACTAATAAAAATACTAATAGATAAGAATAAAAT
Found at i:2172509 original size:24 final size:24
Alignment explanation
Indices: 2172482--2172529 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2172472 GGAGAAGGAA
* *
2172482 AGGGATGAATGGGCCAAGGGAGGG
1 AGGGACGAAAGGGCCAAGGGAGGG
2172506 AGGGACGAAAGGGCCAAGGGAGGG
1 AGGGACGAAAGGGCCAAGGGAGGG
2172530 GCGACGGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.10, G:0.54, T:0.04
Consensus pattern (24 bp):
AGGGACGAAAGGGCCAAGGGAGGG
Done.