Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397273.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.1, whole genome shotgun sequence
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: 3496717
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 46782 characters in sequence are not A, C, G, or T
File 4 of 9
Found at i:1017192 original size:21 final size:21
Alignment explanation
Indices: 1017157--1017202 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1017147 CTCTTAAAGT
1017157 AATTTAAAATAAAATAATCTAA
1 AATTTAAAATAAAATAA-CTAA
* *
1017179 AATTT-AACTAAAATAACTTA
1 AATTTAAAATAAAATAACTAA
1017199 AATT
1 AATT
1017203 AATCACTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 10 0.45
22 5 0.23
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTTAAAATAAAATAACTAA
Found at i:1018065 original size:15 final size:15
Alignment explanation
Indices: 1018040--1018079 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1018030 TTAATTTATA
1018040 AATAAATAATAATAAG
1 AATAAA-AATAATAAG
* *
1018056 AATAAAAATAATTAT
1 AATAAAAATAATAAG
1018071 AATAAAAAT
1 AATAAAAAT
1018080 TAGCAATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AATAAAAATAATAAG
Found at i:1018451 original size:253 final size:249
Alignment explanation
Indices: 1018000--1018847 Score: 939
Period size: 252 Copynumber: 3.4 Consensus size: 249
1017990 AACAGTGTTT
* * ** * *
1018000 AAGCTAAAAATACTTAATGGTTTACAAATTTTAATTTATAAATAAATAATAATAAGAATAAAAAT
1 AAGCTAAAAGTATTTAATAATTTACAAATTTTAATTTATAAATGAATAATAATAAGGATAAAAAT
* * * * *
1018065 AATTATAATAAAAATTAGCAATTGAAAAACTTTGATGTAAACCTATAAGAATTAACATAAAAAAT
66 AATTATAGTGAAAATTAGCAATTGAAAAA-TTTGAAGTAAACTTGTAAGAATT-ACATAAAAAAT
* * * *
1018130 TATAAAAATGTAACAA-ACATTTTTAAAATATTGACGTCAATGTGTGAGATTTAATGTCACA-AG
129 TATAAAAGTGAAACAAGA-ATTGTTAAAATATTGACGTAAATGTGTGAGATTTAATG-CA-ATAG
* *
1018193 TCAATTAAGTTAAAATAAATATATATTTTGTAAAAAATTAAATATTAAAATTTATGTTATC
191 TCAATTAAGTTAAAATAAATATA-ATTTTGT-AAAAATTAAATATTTAAATTTATATTATC
* *
1018254 AAGCTAAAAGTATTTAATAATTTACAAATTTTAATATATAAATGAATAAAAATAAGGATAAAAAT
1 AAGCTAAAAGTATTTAATAATTTACAAATTTTAATTTATAAATGAATAATAATAAGGATAAAAAT
* * * * *
1018319 AATTATAGTGAAAATTACCAATAGAAAAAGTTTGACG-AAATTTGTAAGAATTAGCGTAAAAAAT
66 AATTATAGTGAAAATTAGCAATTGAAAAA-TTTGAAGTAAACTTGTAAGAATTA-CATAAAAAAT
* * * * ** * *
1018383 TATAAAGGTGGAATAAGTATTGTTAAAATATTGGTGAAAATGTGTAAGATTTAATGCAATAGGTC
129 TATAAAAGTGAAACAAGAATTGTTAAAATATTGACGTAAATGTGTGAGATTTAATGCAATA-GTC
* * * * *
1018448 AATTAGGTCAAAATAAATATAATTTTAGTGAAAATTAAACATTTAAATTTATATTCTC
193 AATTAAGTTAAAATAAATATAATTTT-GTAAAAATTAAATATTTAAATTTATATTATC
* * * * * *
1018506 GAGCTAAAAGAATTTAACAATTTATAAATTTTAATTTATAAATGAATAATAAGAAAGATAAAAAT
1 AAGCTAAAAGTATTTAATAATTTACAAATTTTAATTTATAAATGAATAATAATAAGGATAAAAAT
* * *
1018571 AATTATAGTGAAAATTAGCAATTGAAAAATCTCT-AAGTAAACTTGTAAAAATTACCTTAAAAAT
66 AATTATAGTGAAAATTAGCAATTGAAAAAT-T-TGAAGTAAACTTGTAAGAATTACATAAAAAAT
* * * * * *** * *
1018635 CATAAATGTGAAACAAGAATTGTTAAAAGATTGACGTATATGTATGAGATTTAACATAATAAATT
129 TATAAAAGTGAAACAAGAATTGTTAAAATATTGACGTAAATGTGTGAGATTTAATGCAAT-AGTC
* *
1018700 AATTAAATTAAAATAAATATAATTTTTGTAAAAATTAAATATTTAAATTTATATTATT
193 AATTAAGTTAAAATAAATATAA-TTTTGTAAAAATTAAATATTTAAATTTATATTATC
* * * *
1018758 GAGCTAAAAGTATTTAATGATTTATAAATTTTAATTTATAAATGAACAATAATAAGGATAAAAAT
1 AAGCTAAAAGTATTTAATAATTTACAAATTTTAATTTATAAATGAATAATAATAAGGATAAAAAT
* * * *
1018823 AGTTATAGTGTATATTAACAATTGA
66 AATTATAGTGAAAATTAGCAATTGA
1018848 TAAACCTAGA
Statistics
Matches: 499, Mismatches: 85, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
251 2 0.00
252 300 0.60
253 109 0.22
254 88 0.18
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (249 bp):
AAGCTAAAAGTATTTAATAATTTACAAATTTTAATTTATAAATGAATAATAATAAGGATAAAAAT
AATTATAGTGAAAATTAGCAATTGAAAAATTTGAAGTAAACTTGTAAGAATTACATAAAAAATTA
TAAAAGTGAAACAAGAATTGTTAAAATATTGACGTAAATGTGTGAGATTTAATGCAATAGTCAAT
TAAGTTAAAATAAATATAATTTTGTAAAAATTAAATATTTAAATTTATATTATC
Found at i:1019842 original size:16 final size:14
Alignment explanation
Indices: 1019820--1019862 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 14
1019810 GAAAATAACT
1019820 AATTAACTAATTTA
1 AATTAACTAATTTA
1019834 ATTATTAACTAATTTA
1 A--ATTAACTAATTTA
*
1019850 AATTAATTAATTT
1 AATTAACTAATTT
1019863 CATTGATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 12 0.46
16 14 0.54
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTAACTAATTTA
Found at i:1019942 original size:21 final size:21
Alignment explanation
Indices: 1019904--1019944 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1019894 AATGGAATTT
*
1019904 TAATTTAATTAATTATTTAAC
1 TAATTTAATTAATAATTTAAC
1019925 TAATTTAATT-ATAAATTTAA
1 TAATTTAATTAAT-AATTTAA
1019945 AAAAATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATTTAATTAATAATTTAAC
Found at i:1020122 original size:34 final size:34
Alignment explanation
Indices: 1020083--1020160 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
1020073 AAATTTCATT
* *
1020083 TAATTAATTA-TTACTT-TAAATTAACTTAATTAAC
1 TAATTAATTAGTTA-TTGAAAAATAAC-TAATTAAC
1020117 TAATTAATTAGTTATTGAAAAATAACTAATTAAC
1 TAATTAATTAGTTATTGAAAAATAACTAATTAAC
1020151 TAATTCAATT
1 TAATT-AATT
1020161 GTAAACTAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 25 0.64
35 14 0.36
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (34 bp):
TAATTAATTAGTTATTGAAAAATAACTAATTAAC
Found at i:1034119 original size:32 final size:32
Alignment explanation
Indices: 1034083--1034207 Score: 126
Period size: 32 Copynumber: 3.8 Consensus size: 32
1034073 GAAAAATACT
*
1034083 TTTTAAGGTTCAAGCATAACCTTTACAATGCC
1 TTTTAAGGTTCAAGCACAACCTTTACAATGCC
*
1034115 TTTTAAGGATT-AAGCACAACCTCTTAATACAATACC
1 TTTTAAGG-TTCAAGCACAA-C-CTT--TACAATGCC
* * *
1034151 TTTTATGGATCAAGCACAACCTTCACAATGCC
1 TTTTAAGGTTCAAGCACAACCTTTACAATGCC
* *
1034183 TTTTAAAGGCTAAAGCACAACCTTT
1 TTTT-AAGGTTCAAGCACAACCTTT
1034208 TATCTTTGAC
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
32 26 0.34
33 19 0.25
34 6 0.08
35 2 0.03
36 23 0.30
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (32 bp):
TTTTAAGGTTCAAGCACAACCTTTACAATGCC
Found at i:1034164 original size:68 final size:69
Alignment explanation
Indices: 1034077--1034205 Score: 188
Period size: 68 Copynumber: 1.9 Consensus size: 69
1034067 CACTATGAAA
* * * * *
1034077 AATACTTTTTAAGGTTCAAGCATAACCTTTACAATGCCTTTT-AAGGATTAAGCACAACCTCTTA
1 AATACCTTTTAAGGATCAAGCACAACCTTCACAATGCCTTTTAAAGGATAAAGCACAACCTCTTA
1034141 ATAC
66 ATAC
* *
1034145 AATACCTTTTATGGATCAAGCACAACCTTCACAATGCCTTTTAAAGGCTAAAGCACAACCT
1 AATACCTTTTAAGGATCAAGCACAACCTTCACAATGCCTTTTAAAGGATAAAGCACAACCT
1034206 TTTATCTTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
68 37 0.70
69 16 0.30
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (69 bp):
AATACCTTTTAAGGATCAAGCACAACCTTCACAATGCCTTTTAAAGGATAAAGCACAACCTCTTA
ATAC
Found at i:1034686 original size:21 final size:22
Alignment explanation
Indices: 1034648--1034734 Score: 88
Period size: 21 Copynumber: 4.0 Consensus size: 22
1034638 TGGCACTTCC
* * *
1034648 AAACTTATTTAAAAAAGTTTAA
1 AAACTAATTCAAACAAGTTTAA
*
1034670 AAACT-ATTCAAACAAGTTCAA
1 AAACTAATTCAAACAAGTTTAA
* * *
1034691 AAACTCATTCAAACAACTTTAG
1 AAACTAATTCAAACAAGTTTAA
*
1034713 AAA-TAATTCAAACAATTTTAA
1 AAACTAATTCAAACAAGTTTAA
1034734 A
1 A
1034735 GATCATTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
21 34 0.62
22 21 0.38
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.30
Consensus pattern (22 bp):
AAACTAATTCAAACAAGTTTAA
Found at i:1034874 original size:21 final size:21
Alignment explanation
Indices: 1034840--1034904 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1034830 CAAAAACATT
* *
1034840 TTCAAACAACTTCAAAAATCA
1 TTCAAACAAGTTCAAAGATCA
* *
1034861 TTCCAACTAGTTCAAAGATCA
1 TTCAAACAAGTTCAAAGATCA
* *
1034882 CTCAAAGAAGTTCAAAGATCA
1 TTCAAACAAGTTCAAAGATCA
1034903 TT
1 TT
1034905 GAAGCAATTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.26
Consensus pattern (21 bp):
TTCAAACAAGTTCAAAGATCA
Found at i:1038016 original size:67 final size:67
Alignment explanation
Indices: 1037897--1038025 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 67
1037887 TTTCTCTAGA
* *
1037897 TGATGATTGTGATGCCACCTATAGAGAATACTCCGAATGATGCCGTTTGTTGGCATATTGCCTTA
1 TGATGATTGTGATGCCACCTATAGAGAATACTCCGAATGATACCGTTCGTTGGCATATTGCCTTA
1037962 GG
66 GG
* * * * * ** *
1037964 TGATGATTGTGATGCCACTTGTGGAGAATACTCTGAGTGATATTGTTCGTTGGGATATTGCC
1 TGATGATTGTGATGCCACCTATAGAGAATACTCCGAATGATACCGTTCGTTGGCATATTGCC
1038026 CTAAACGAGG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
67 52 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (67 bp):
TGATGATTGTGATGCCACCTATAGAGAATACTCCGAATGATACCGTTCGTTGGCATATTGCCTTA
GG
Found at i:1043692 original size:16 final size:17
Alignment explanation
Indices: 1043661--1043693 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1043651 TACTTAGGTT
1043661 CATCAAAAACTGCTTAA
1 CATCAAAAACTGCTTAA
*
1043678 CATCATAAA-TGCTTAA
1 CATCAAAAACTGCTTAA
1043694 AAACTCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.27
Consensus pattern (17 bp):
CATCAAAAACTGCTTAA
Found at i:1046493 original size:28 final size:28
Alignment explanation
Indices: 1046454--1046734 Score: 307
Period size: 28 Copynumber: 10.1 Consensus size: 28
1046444 GTGCAACAAC
* * *
1046454 TTTTTCATCATGACGTGTAACAACTAAA
1 TTTTTCAACATGACATGTAACAACTACA
* *
1046482 TTTTTTAACATGACGTGTAACAACTA-A
1 TTTTTCAACATGACATGTAACAACTACA
* * * * *
1046509 ATCTTCAACATGGCATATAATAACTACA
1 TTTTTCAACATGACATGTAACAACTACA
* *
1046537 TTTTTCAACATGACATATAACAACTATA
1 TTTTTCAACATGACATGTAACAACTACA
* *
1046565 -TTTTCAACATAACGTGTAACAACTACA
1 TTTTTCAACATGACATGTAACAACTACA
* *
1046592 TTTTTCAATATGACGTGTAACAACTA-A
1 TTTTTCAACATGACATGTAACAACTACA
* * * * *
1046619 ATCTTCAACGTGGCATATAACAACTACA
1 TTTTTCAACATGACATGTAACAACTACA
* *
1046647 TTTTTCAACATGGCATGTAACAATTACA
1 TTTTTCAACATGACATGTAACAACTACA
* *
1046675 TTTTTCAACATGACATATAACAATTACA
1 TTTTTCAACATGACATGTAACAACTACA
*
1046703 TTTTTCAACATGACATGTAACAAATACA
1 TTTTTCAACATGACATGTAACAACTACA
1046731 TTTT
1 TTTT
1046735 CAAAGTGATT
Statistics
Matches: 214, Mismatches: 36, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
27 63 0.29
28 151 0.71
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (28 bp):
TTTTTCAACATGACATGTAACAACTACA
Found at i:1046547 original size:55 final size:55
Alignment explanation
Indices: 1046457--1046725 Score: 322
Period size: 55 Copynumber: 4.9 Consensus size: 55
1046447 CAACAACTTT
* * * * * *
1046457 TTCATCATGACGTGTAACAACTAAATTTTTTAACATGACGTGTAACAACTAAATC
1 TTCAACATGACATATAACAACTACATTTTTCAACATGACATGTAACAACTAAATC
* * * * *
1046512 TTCAACATGGCATATAATAACTACATTTTTCAACATGACATATAACAACTATATT
1 TTCAACATGACATATAACAACTACATTTTTCAACATGACATGTAACAACTAAATC
* * * * *
1046567 TTCAACATAACGTGTAACAACTACATTTTTCAATATGACGTGTAACAACTAAATC
1 TTCAACATGACATATAACAACTACATTTTTCAACATGACATGTAACAACTAAATC
* * * * * *
1046622 TTCAACGTGGCATATAACAACTACATTTTTCAACATGGCATGTAACAATTACATTT
1 TTCAACATGACATATAACAACTACATTTTTCAACATGACATGTAACAACTA-AATC
*
1046678 TTCAACATGACATATAACAATTACATTTTTCAACATGACATGTAACAA
1 TTCAACATGACATATAACAACTACATTTTTCAACATGACATGTAACAA
1046726 ATACATTTTC
Statistics
Matches: 177, Mismatches: 36, Indels: 1
0.83 0.17 0.00
Matches are distributed among these distances:
55 131 0.74
56 46 0.26
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (55 bp):
TTCAACATGACATATAACAACTACATTTTTCAACATGACATGTAACAACTAAATC
Found at i:1046644 original size:110 final size:111
Alignment explanation
Indices: 1046454--1046725 Score: 402
Period size: 110 Copynumber: 2.5 Consensus size: 111
1046444 GTGCAACAAC
* * *
1046454 TTTTTCATCATGACGTGTAACAACTAAATTTTTTAACATGACGTGTAACAACTAAATCTTCAACA
1 TTTTTCAACATGACGTGTAACAACTACATTTTTCAACATGACGTGTAACAACTAAATCTTCAACA
* *
1046519 TGGCATATAATAACTACATTTTTCAACATGACATATAACAACTATA
66 TGGCATATAACAACTACATTTTTCAACATGACATATAACAACTACA
* * *
1046565 -TTTTCAACATAACGTGTAACAACTACATTTTTCAATATGACGTGTAACAACTAAATCTTCAACG
1 TTTTTCAACATGACGTGTAACAACTACATTTTTCAACATGACGTGTAACAACTAAATCTTCAACA
* * *
1046629 TGGCATATAACAACTACATTTTTCAACATGGCATGTAACAATTACA
66 TGGCATATAACAACTACATTTTTCAACATGACATATAACAACTACA
* * * *
1046675 TTTTTCAACATGACATATAACAATTACATTTTTCAACATGACATGTAACAA
1 TTTTTCAACATGACGTGTAACAACTACATTTTTCAACATGACGTGTAACAA
1046726 ATACATTTTC
Statistics
Matches: 143, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
110 99 0.69
111 44 0.31
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (111 bp):
TTTTTCAACATGACGTGTAACAACTACATTTTTCAACATGACGTGTAACAACTAAATCTTCAACA
TGGCATATAACAACTACATTTTTCAACATGACATATAACAACTACA
Found at i:1050839 original size:29 final size:30
Alignment explanation
Indices: 1050785--1050842 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1050775 GGATCGATTT
*
1050785 TGTGAAGTAGAAATTTAGGGGTAAATAATC
1 TGTGAAGTAGAAATTTAGGGGCAAATAATC
*
1050815 TGTGAAGTA-AAGTTTAGGGGCAAATAAT
1 TGTGAAGTAGAAATTTAGGGGCAAATAAT
1050843 AACACTGGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.29
Consensus pattern (30 bp):
TGTGAAGTAGAAATTTAGGGGCAAATAATC
Found at i:1052400 original size:49 final size:49
Alignment explanation
Indices: 1052334--1052567 Score: 213
Period size: 49 Copynumber: 4.7 Consensus size: 49
1052324 TGTTAAGGAA
* * *
1052334 TATGTTTCACCCATAGATGATTCCAAACAATGATATGATGTAGATTATG
1 TATGTTCCATCCATAGATGATTCCAGACAATGATATGATGTAGATTATG
* * * * * * *
1052383 TATGTTCCA-CCAGTAGATAATTTCGGACGATGATAGGATATGAGA-CATG
1 TATGTTCCATCCA-TAGATGATTCCAGACAATGATATGATGT-AGATTATG
* *
1052432 TATGTTCCATCCATAGATGATTCTAGACAATGATATGATGT-GAAGTATG
1 TATGTTCCATCCATAGATGATTCCAGACAATGATATGATGTAG-ATTATG
* * * *
1052481 TATGTTCCATCCATGGATGATTTCAGACAATGTTATGATGTTGATTATG
1 TATGTTCCATCCATAGATGATTCCAGACAATGATATGATGTAGATTATG
* * * * *
1052530 CATGTTCCGTCCATGGAGGAATTCCAGCCAATGGATAT
1 TATGTTCCATCCATAGATG-ATTCCAGACAAT-GATAT
1052568 TATAAGGTTG
Statistics
Matches: 149, Mismatches: 28, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
47 1 0.01
48 4 0.03
49 123 0.83
50 17 0.11
51 4 0.03
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (49 bp):
TATGTTCCATCCATAGATGATTCCAGACAATGATATGATGTAGATTATG
Found at i:1058591 original size:2 final size:2
Alignment explanation
Indices: 1058584--1058628 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1058574 AGAGATATTT
*
1058584 AC AC AC AC AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1058626 AC A
1 AC A
1058629 TATAGATTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.49, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1062896 original size:16 final size:16
Alignment explanation
Indices: 1062858--1062902 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1062848 ATGAAAATTT
1062858 GAAA-TAAAA-AAATA
1 GAAACTAAAAGAAATA
*
1062872 -AATCTAAAAGAAATA
1 GAAACTAAAAGAAATA
1062887 GAAACTAAAAGAAATA
1 GAAACTAAAAGAAATA
1062903 ATCAAAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 2 0.08
14 5 0.19
15 5 0.19
16 14 0.54
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (16 bp):
GAAACTAAAAGAAATA
Found at i:1062896 original size:30 final size:29
Alignment explanation
Indices: 1062858--1062916 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
1062848 ATGAAAATTT
1062858 GAAATAAAA-AAATAAATCTAAA-AGAAATA
1 GAAATAAAAGAAAT-AATC-AAAGAGAAATA
1062887 GAAACTAAAAGAAATAATCAAAGAGAAATA
1 GAAA-TAAAAGAAATAATCAAAGAGAAATA
1062917 ATTAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 7 0.26
30 16 0.59
31 4 0.15
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (29 bp):
GAAATAAAAGAAATAATCAAAGAGAAATA
Found at i:1064093 original size:25 final size:25
Alignment explanation
Indices: 1064059--1064108 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1064049 CATATACCTT
1064059 GGTCATTCCAAAGTTATTTTTGCCA
1 GGTCATTCCAAAGTTATTTTTGCCA
1064084 GGTCATTCCAAAGTTATTTTTGCCA
1 GGTCATTCCAAAGTTATTTTTGCCA
1064109 ACTAAACACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (25 bp):
GGTCATTCCAAAGTTATTTTTGCCA
Found at i:1069669 original size:174 final size:173
Alignment explanation
Indices: 1069325--1069825 Score: 662
Period size: 174 Copynumber: 2.9 Consensus size: 173
1069315 ACAAGAGTGG
* * * * * ** * *
1069325 TCATAGTAATGAAATTGTCTTGAAGGAAAGCGAAATTGTGAGCGGACAAAATGGCCATAGGAGGA
1 TCATAGTAATGAAATGGTTTTGAA-GAAAG-GAGA-TGTTAACAAACAAAATGGCAAGAGGAGGA
* * * * *
1069390 GAGCAGATGTGCAAGTACCAAGGGTCTCTCCTTATTTTCAGTCAAGTGGAGAAAAACAAGAAATG
63 GAGCAGATGCGCAAGTTCTAAAGGTCTCTCCTTATTTTCAGACAAGTGGAGAAAAACAAGAAATG
* * *
1069455 TCAAGTGGAAACTGCAAACCAAAAGTCAGTTTGCTTTCACAAGTTGC
128 TAAAGTGGAAACTGCAAACC-AAAGTCAATTTGATTTCACAAGTTGC
1069502 TCATAGTAATGAAATGGTTTTGAAGAAAGGAGATGTTAACAAACAAAATGGCAAGAGGAGGAGAG
1 TCATAGTAATGAAATGGTTTTGAAGAAAGGAGATGTTAACAAACAAAATGGCAAGAGGAGGAGAG
* * * *
1069567 CAGATGCGCAAGTTCTAAAGGTTTCTCCTCATTTTCAGACAAGTGGAGAAAAACAAGATATGTTA
66 CAGATGCGCAAGTTCTAAAGGTCTCTCCTTATTTTCAGACAAGTGGAGAAAAACAAGAAATGTAA
*
1069632 AGTGGAAACTGCAAACCAAAGCTCAATTTGATTTCACAAGTTGT
131 AGTGGAAACTGCAAACCAAAG-TCAATTTGATTTCACAAGTTGC
* *
1069676 TCATAGTAATAAAAGGGTTTTGAAGAAAGGAGATGTTAACAAACAAAATGGCAAGAGGAGGAGAG
1 TCATAGTAATGAAATGGTTTTGAAGAAAGGAGATGTTAACAAACAAAATGGCAAGAGGAGGAGAG
* * * * * *
1069741 CAAATGCGCAAGTTCTAAAGGTCTCTCCTTATTTCCTGAGAAGTGGAGAAAAACAAGACATGGAA
66 CAGATGCGCAAGTTCTAAAGGTCTCTCCTTATTTTCAGACAAGTGGAGAAAAACAAGAAATGTAA
*
1069806 AGTGG-TACTAGCAAACCAAA
131 AGTGGAAACT-GCAAACCAAA
1069826 ACACAAAGTG
Statistics
Matches: 289, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
173 7 0.02
174 252 0.87
175 3 0.01
176 5 0.02
177 22 0.08
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (173 bp):
TCATAGTAATGAAATGGTTTTGAAGAAAGGAGATGTTAACAAACAAAATGGCAAGAGGAGGAGAG
CAGATGCGCAAGTTCTAAAGGTCTCTCCTTATTTTCAGACAAGTGGAGAAAAACAAGAAATGTAA
AGTGGAAACTGCAAACCAAAGTCAATTTGATTTCACAAGTTGC
Found at i:1073582 original size:48 final size:48
Alignment explanation
Indices: 1073511--1073602 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
1073501 CAGAATGGAT
1073511 CAGTTTTAGAAGCATCAAATGCAAGTAACAGGCTCAGTCATAACGGAG
1 CAGTTTTAGAAGCATCAAATGCAAGTAACAGGCTCAGTCATAACGGAG
1073559 CAGTTTTAGAAGCATCAAATGCAAGTAACAGGCTCAGTCATAAC
1 CAGTTTTAGAAGCATCAAATGCAAGTAACAGGCTCAGTCATAAC
1073603 CCAGCATGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (48 bp):
CAGTTTTAGAAGCATCAAATGCAAGTAACAGGCTCAGTCATAACGGAG
Found at i:1076423 original size:17 final size:16
Alignment explanation
Indices: 1076371--1076427 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
1076361 ATTGAATCGT
* *
1076371 TAATATTCTTATACATA
1 TAATTTTCTTTTA-ATA
* *
1076388 TAATTGTCTTTCAATTA
1 TAATTTTCTTTTAA-TA
1076405 TAATTTTCTTTTATATA
1 TAATTTTCTTTTA-ATA
1076422 TAATTT
1 TAATTT
1076428 ATTTAAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 1 0.03
17 30 0.94
18 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (16 bp):
TAATTTTCTTTTAATA
Found at i:1078629 original size:33 final size:33
Alignment explanation
Indices: 1078574--1078637 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
1078564 AAATGTGTTC
* *
1078574 TATTGTTTGGATGACAAGGTG-AATAATATTTTT
1 TATTATTTAGATGACAAGGTGAAAT-ATATTTTT
**
1078607 TATTATTTAGATGACATTGTGAAATATATTT
1 TATTATTTAGATGACAAGGTGAAATATATTT
1078638 CTCATTCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (33 bp):
TATTATTTAGATGACAAGGTGAAATATATTTTT
Found at i:1088619 original size:12 final size:12
Alignment explanation
Indices: 1088571--1088624 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
1088561 TACAGCTTAA
1088571 ATTTTATTAATT
1 ATTTTATTAATT
*
1088583 -TTTTA-AAATT
1 ATTTTATTAATT
1088593 A--TTATTATATAT
1 ATTTTATTA-AT-T
1088605 ATTTTATTAATT
1 ATTTTATTAATT
1088617 ATTTTATT
1 ATTTTATT
1088625 TTTTTTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
9 3 0.09
10 5 0.15
11 7 0.21
12 11 0.32
13 2 0.06
14 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTATTAATT
Found at i:1088774 original size:15 final size:16
Alignment explanation
Indices: 1088754--1088791 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
1088744 TAACCTCATC
1088754 TGTCGATTGGTTCAA-
1 TGTCGATTGGTTCAAT
1088769 TGTCGATTGGTTCAAT
1 TGTCGATTGGTTCAAT
1088785 TGTCGAT
1 TGTCGAT
1088792 CGAGAAACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.42
Consensus pattern (16 bp):
TGTCGATTGGTTCAAT
Found at i:1089348 original size:85 final size:85
Alignment explanation
Indices: 1089247--1089932 Score: 947
Period size: 85 Copynumber: 8.1 Consensus size: 85
1089237 GATTAAAGTT
* * *** *
1089247 TGCTAGAATTAAATATTAAAAATTATATTTAAAAATTAATGTTTAGAATTATTATTTAGATTTTC
1 TGCTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTGTTTAGATTTTC
*
1089312 AATGAAAATGATTGGCAATA
66 AATTAAAATGATTGGCAATA
* * * *
1089332 TGTTAAAATTAAATATTAAGAATTATGTTTGGGAATTAATAG-TTAGAATTATTGTTTAGATTTT
1 TGCTAGAATTAAACATTAAAAATTATGTTTGGGAATTAAT-GTTTAGAATTATTGTTTAGATTTT
* **
1089396 TAATTAAAATGATTGATAATA
65 CAATTAAAATGATTGGCAATA
* * *
1089417 TGCTAGAATTAAACATTAAAAATTATGTTTGAGAATTAACGTTTAGAATTATTGTTTGGATTTTC
1 TGCTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTGTTTAGATTTTC
1089482 AATTAAAATGATTGGCAATA
66 AATTAAAATGATTGGCAATA
* * * * *
1089502 TGCTTGAATTAAACATTAAGAATTATGTTT-GAAATTAATGTTTAGAATTATTGTTTTGGTTTTC
1 TGCTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTGTTTAGATTTTC
*
1089566 AATTAAAATGATTGGTAATA
66 AATTAAAATGATTGGCAATA
* * * *
1089586 TGCTAGAA-T---CATTAACAATTATATTTAGGAATTAGTGTTTAGAATTATTGTTT-GAATTTT
1 TGCTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTGTTTAG-ATTTT
1089646 CAATTAAAATGATTGGCAATA
65 CAATTAAAATGATTGGCAATA
* * *
1089667 TGCTAGAATTAAACATTAAGAATTATGTTTGGGAACTATTGTTTAGAATTATTGTTTAGATTTTC
1 TGCTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTGTTTAGATTTTC
*
1089732 AATTAAAATGATTGGTAATA
66 AATTAAAATGATTGGCAATA
* * *
1089752 TTCTAGAATTAAACATTAAAAATTATGTTTGGAAATTAATGTTTAGAATTATTGTTTGGATTTTC
1 TGCTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTGTTTAGATTTTC
1089817 AATTAAAATGATTGGCAATA
66 AATTAAAATGATTGGCAATA
* * * *
1089837 TACTAAAATTAAACA-TAAAAATTATGTTTGGGAATTAATATTTAGAATTATTATTTAGATTTTC
1 TGCTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTGTTTAGATTTTC
1089901 AATTAAAATGATTGGCAATA
66 AATTAAAATGATTGGCAATA
*
1089921 TGCTAAAATTAA
1 TGCTAGAATTAA
1089933 TTATTGAAAT
Statistics
Matches: 535, Mismatches: 57, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
80 16 0.03
81 56 0.10
82 1 0.00
83 1 0.00
84 132 0.25
85 327 0.61
86 2 0.00
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (85 bp):
TGCTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTGTTTAGATTTTC
AATTAAAATGATTGGCAATA
Found at i:1089721 original size:13 final size:13
Alignment explanation
Indices: 1089685--1089726 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1089675 TTAAACATTA
1089685 AGAATTA-TGTTT
1 AGAATTATTGTTT
* *
1089697 GGGAACTATTGTTT
1 -AGAATTATTGTTT
1089711 AGAATTATTGTTT
1 AGAATTATTGTTT
1089724 AGA
1 AGA
1089727 TTTTCAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (13 bp):
AGAATTATTGTTT
Found at i:1089793 original size:14 final size:14
Alignment explanation
Indices: 1089771--1089811 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
1089761 TAAACATTAA
1089771 AAATT-ATGTTTGG
1 AAATTAATGTTTGG
*
1089784 AAATTAATGTTTAG
1 AAATTAATGTTTGG
*
1089798 -AATTATTGTTTGG
1 AAATTAATGTTTGG
1089811 A
1 A
1089812 TTTTCAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (14 bp):
AAATTAATGTTTGG
Found at i:1089883 original size:335 final size:335
Alignment explanation
Indices: 1089261--1089925 Score: 1041
Period size: 335 Copynumber: 2.0 Consensus size: 335
1089251 AGAATTAAAT
1089261 ATTAAAAATTATATTTAAAAATTAATGTTTAGAATTATTATTTAGATTTTCAATGAAAATGATTG
1 ATTAAAAATTATATTTAAAAATTAATGTTTAGAATTATTATTTAGATTTTCAATGAAAATGATTG
* * *
1089326 GCAATATGTTAAAATTAAATATTAAGAATTATGTTTGGGAATTAATAGTTAGAATTATTGTTTAG
66 GCAATATGCTAAAATTAAACATTAAGAATTATGTTTGGGAACTAATAGTTAGAATTATTGTTTAG
*
1089391 ATTTTTAATTAAAATGATTGATAATATGCTAGAATTAAACATTAAAAATTATGTTTGAGAATTAA
131 ATTTTCAATTAAAATGATTGATAATATGCTAGAATTAAACATTAAAAATTATGTTTGAGAATTAA
* **
1089456 CGTTTAGAATTATTGTTTGGATTTTCAATTAAAATGATTGGCAATATGCTTGAATTAAACATTAA
196 CGTTTAGAATTATTGTTTGGATTTTCAATTAAAATGATTGGCAATATACTAAAATTAAACATTAA
* * * * * *
1089521 GAATTATGTTTGAAATTAATGTTTAGAATTATTGTTTTGGTTTTCAATTAAAATGATTGGTAATA
261 AAATTATGTTTGAAATTAATATTTAGAATTATTATTTAGATTTTCAATTAAAATGATTGGCAATA
1089586 TGCTAGAATC
326 TGCTAGAATC
* ** * * *
1089596 ATTAACAATTATATTTAGGAATTAGTGTTTAGAATTATTGTTT-GAATTTTCAATTAAAATGATT
1 ATTAAAAATTATATTTAAAAATTAATGTTTAGAATTATTATTTAG-ATTTTCAATGAAAATGATT
* *
1089660 GGCAATATGCTAGAATTAAACATTAAGAATTATGTTTGGGAACT-ATTGTTTAGAATTATTGTTT
65 GGCAATATGCTAAAATTAAACATTAAGAATTATGTTTGGGAACTAATAG-TTAGAATTATTGTTT
* *
1089724 AGATTTTCAATTAAAATGATTGGTAATATTCTAGAATTAAACATTAAAAATTATGTTTG-GAAAT
129 AGATTTTCAATTAAAATGATTGATAATATGCTAGAATTAAACATTAAAAATTATGTTTGAG-AAT
*
1089788 TAATGTTTAGAATTATTGTTTGGATTTTCAATTAAAATGATTGGCAATATACTAAAATTAAACA-
193 TAACGTTTAGAATTATTGTTTGGATTTTCAATTAAAATGATTGGCAATATACTAAAATTAAACAT
*
1089852 TAAAAATTATGTTTGGGAATTAATATTTAGAATTATTATTTAGATTTTCAATTAAAATGATTGGC
258 TAAAAATTATGTTT-GAAATTAATATTTAGAATTATTATTTAGATTTTCAATTAAAATGATTGGC
1089917 AATATGCTA
322 AATATGCTA
1089926 AAATTAATTA
Statistics
Matches: 301, Mismatches: 25, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
334 18 0.06
335 283 0.94
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.42
Consensus pattern (335 bp):
ATTAAAAATTATATTTAAAAATTAATGTTTAGAATTATTATTTAGATTTTCAATGAAAATGATTG
GCAATATGCTAAAATTAAACATTAAGAATTATGTTTGGGAACTAATAGTTAGAATTATTGTTTAG
ATTTTCAATTAAAATGATTGATAATATGCTAGAATTAAACATTAAAAATTATGTTTGAGAATTAA
CGTTTAGAATTATTGTTTGGATTTTCAATTAAAATGATTGGCAATATACTAAAATTAAACATTAA
AAATTATGTTTGAAATTAATATTTAGAATTATTATTTAGATTTTCAATTAAAATGATTGGCAATA
TGCTAGAATC
Found at i:1097858 original size:13 final size:13
Alignment explanation
Indices: 1097840--1097864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1097830 CATATTTTTA
1097840 TTTTTTTCTAATC
1 TTTTTTTCTAATC
1097853 TTTTTTTCTAAT
1 TTTTTTTCTAAT
1097865 TTATTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTCTAATC
Found at i:1098787 original size:9 final size:9
Alignment explanation
Indices: 1098758--1098788 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1098748 GGTTTAGGGT
1098758 TTTTTATTA
1 TTTTTATTA
*
1098767 TTCTTATTA
1 TTTTTATTA
1098776 TTTTTATTA
1 TTTTTATTA
1098785 TTTT
1 TTTT
1098789 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTATTA
Found at i:1101053 original size:21 final size:20
Alignment explanation
Indices: 1101016--1101058 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1101006 AGTTGAAAAT
* * *
1101016 TGTGTAAATTTGGATGATGA
1 TGTGAAAATTTGAATGAGGA
1101036 TGTGAAAATTTTGAATGAGGA
1 TGTGAAAA-TTTGAATGAGGA
1101057 TG
1 TG
1101059 AAATTCCCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (20 bp):
TGTGAAAATTTGAATGAGGA
Found at i:1103369 original size:16 final size:16
Alignment explanation
Indices: 1103348--1103397 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
1103338 TTGAAACTTT
1103348 ATTTATGTTTAGTGTA
1 ATTTATGTTTAGTGTA
*
1103364 ATTTAT-TTT--T-TT
1 ATTTATGTTTAGTGTA
1103376 ATTTATGTTTAGTGTA
1 ATTTATGTTTAGTGTA
1103392 ATTTAT
1 ATTTAT
1103398 TTGTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
15 4 0.14
16 13 0.46
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (16 bp):
ATTTATGTTTAGTGTA
Found at i:1103377 original size:28 final size:29
Alignment explanation
Indices: 1103345--1103413 Score: 115
Period size: 28 Copynumber: 2.4 Consensus size: 29
1103335 TGATTGAAAC
1103345 TTTATTTATGTTTAGTGTAATTTATTT-T
1 TTTATTTATGTTTAGTGTAATTTATTTGT
1103373 TTTATTTATGTTTAGTGTAATTTATTTGT
1 TTTATTTATGTTTAGTGTAATTTATTTGT
*
1103402 TTTA-ATATGTTT
1 TTTATTTATGTTT
1103414 TTATTATTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 34 0.87
29 5 0.13
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.67
Consensus pattern (29 bp):
TTTATTTATGTTTAGTGTAATTTATTTGT
Found at i:1104682 original size:26 final size:26
Alignment explanation
Indices: 1104628--1104682 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1104618 AAGGAAATGA
* *
1104628 AAATGAAATGCAATAAAATACATGTG
1 AAATGAAATGCAATAAAATACAAGGG
*
1104654 AAATGTAATGCAAATAAAATA-AAGGG
1 AAATGAAATGC-AATAAAATACAAGGG
1104680 AAA
1 AAA
1104683 CATTGCATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.20
Consensus pattern (26 bp):
AAATGAAATGCAATAAAATACAAGGG
Found at i:1108134 original size:22 final size:22
Alignment explanation
Indices: 1108108--1108150 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1108098 GTGATTAACT
1108108 AAAAGCAAAACTAAAACTAAAC
1 AAAAGCAAAACTAAAACTAAAC
* * *
1108130 AAAAGCTAAACTGAATCTAAA
1 AAAAGCAAAACTAAAACTAAA
1108151 AGCTAACAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.16, G:0.07, T:0.14
Consensus pattern (22 bp):
AAAAGCAAAACTAAAACTAAAC
Found at i:1108138 original size:11 final size:12
Alignment explanation
Indices: 1108104--1108141 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
1108094 TAAAGTGATT
*
1108104 AACTAAAAGCAA
1 AACTAAAAGCTA
1108116 AACTAAAA-CTA
1 AACTAAAAGCTA
1108127 AAC-AAAAGCTA
1 AACTAAAAGCTA
1108138 AACT
1 AACT
1108142 GAATCTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 4 0.17
11 11 0.48
12 8 0.35
ACGTcount: A:0.63, C:0.18, G:0.05, T:0.13
Consensus pattern (12 bp):
AACTAAAAGCTA
Found at i:1110556 original size:19 final size:19
Alignment explanation
Indices: 1110532--1110571 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1110522 CCCAATATGA
1110532 TTGAATGATGACAGAAGGC
1 TTGAATGATGACAGAAGGC
1110551 TTGAATGATGACAGAAGGC
1 TTGAATGATGACAGAAGGC
1110570 TT
1 TT
1110572 ACTAGGATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.25
Consensus pattern (19 bp):
TTGAATGATGACAGAAGGC
Found at i:1113023 original size:15 final size:15
Alignment explanation
Indices: 1112993--1113057 Score: 85
Period size: 15 Copynumber: 4.3 Consensus size: 15
1112983 CGTTTGGTAC
*
1112993 ATTACAATGCAATGTG
1 ATTACAA-GTAATGTG
*
1113009 ATTACAGGTAATGTG
1 ATTACAAGTAATGTG
*
1113024 ATTGCAAGTAATGTG
1 ATTACAAGTAATGTG
*
1113039 ATTACAAGCAATGTG
1 ATTACAAGTAATGTG
1113054 ATTA
1 ATTA
1113058 TAGGGAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 37 0.86
16 6 0.14
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (15 bp):
ATTACAAGTAATGTG
Found at i:1113291 original size:6 final size:6
Alignment explanation
Indices: 1113280--1113354 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
1113270 ATATCATATA
* * * *
1113280 TTTTAT TTTTAT TTATTAT TGTAAT ATTTTAT ATTTTAT TTTTA- ATATAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT -TTTTAT -TTTTAT TTTTAT TTTTAT
* *
1113330 TTATAT TTTTAT TATTAAT TTTTAT
1 TTTTAT TTTTAT T-TTTAT TTTTAT
1113355 ATAATATCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 3 0.05
6 31 0.56
7 21 0.38
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (6 bp):
TTTTAT
Found at i:1113329 original size:23 final size:23
Alignment explanation
Indices: 1113310--1113461 Score: 67
Period size: 23 Copynumber: 6.7 Consensus size: 23
1113300 GTAATATTTT
1113310 ATATTTTATTTTTAATATA-TTT
1 ATATTTTATTTTTAATATATTTT
*
1113332 ATATTTTTATTATTAAT-T-TTTAT
1 ATA-TTTTATTTTTAATATATTT-T
* *
1113355 ATAATATCATTTCTTAAATATATTTT
1 AT-ATTTTATTT-TT-AATATATTTT
* *
1113381 -TAATGTCATATATTT--TAT-TTTT
1 AT-AT-T-TTATTTTTAATATATTTT
*
1113403 AT-TTATTA-TTATAA--TATTTT
1 ATATT-TTATTTTTAATATATTTT
1113423 ATATTTTATTTTTAATATA-TTT
1 ATATTTTATTTTTAATATATTTT
*
1113445 ATATTTATATTATTAAT
1 ATATTT-TATTTTTAAT
1113462 TTTTATATAA
Statistics
Matches: 97, Mismatches: 14, Indels: 37
0.66 0.09 0.25
Matches are distributed among these distances:
19 3 0.03
20 12 0.12
21 8 0.08
22 19 0.20
23 35 0.36
24 3 0.03
25 7 0.07
26 4 0.04
27 6 0.06
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (23 bp):
ATATTTTATTTTTAATATATTTT
Found at i:1113354 original size:113 final size:113
Alignment explanation
Indices: 1113206--1113547 Score: 616
Period size: 113 Copynumber: 3.0 Consensus size: 113
1113196 AAAATATAAG
1113206 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
*
1113271 TATCATATATTTTATTTTTATTTATTATTGTAATATTTTATATTTTATT
65 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
1113320 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
*
1113385 GTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
66 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
*
1113433 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAA
1113497 TATCATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTATT
65 TATCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTATT
1113546 TT
1 TT
1113548 CATTTCTTTA
Statistics
Matches: 222, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
112 3 0.01
113 202 0.91
114 17 0.08
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (113 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:1113409 original size:15 final size:15
Alignment explanation
Indices: 1113275--1113547 Score: 126
Period size: 15 Copynumber: 16.9 Consensus size: 15
1113265 TTTTAATATC
1113275 ATATATTTTATTTTT
1 ATATATTTTATTTTT
* *
1113290 ATTTATTATTGTAATATTT
1 A--TA-TATT-TTATTTTT
1113309 -TATATTTTATTTTT
1 ATATATTTTATTTTT
1113323 AATATATTTATATTTTT
1 -ATATATTT-TATTTTT
*
1113340 AT-TA-TTAATTTTT
1 ATATATTTTATTTTT
* *
1113353 ATATAATATCATTTCTT
1 ATAT-ATTTTATTT-TT
* * *
1113370 AAATATATTTTTAATGTC
1 --ATATA-TTTTATTTTT
1113388 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
1113403 ATTTATTATTATAATATTT
1 ATATATT-TTAT--T-TTT
1113422 -TATATTTTATTTTT
1 ATATATTTTATTTTT
*
1113436 A-ATATATTTATATTT
1 ATATAT-TTTATTTTT
*
1113451 ATAT-TATTAATTTTT
1 ATATAT-TTTATTTTT
* *
1113466 ATATAATATCATATTTTAA
1 ATAT-AT-T-TTATTTT-T
* * *
1113485 ATATATTTTTAATATC
1 ATATA-TTTTATTTTT
1113501 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
1113516 ATTTATTATTATAATTTT
1 ATATATT-TTAT--TTTT
1113534 ATATATTTTATTTT
1 ATATATTTTATTTT
1113548 CATTTCTTTA
Statistics
Matches: 197, Mismatches: 32, Indels: 58
0.69 0.11 0.20
Matches are distributed among these distances:
13 8 0.04
14 16 0.08
15 60 0.30
16 36 0.18
17 26 0.13
18 29 0.15
19 22 0.11
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (15 bp):
ATATATTTTATTTTT
Found at i:1113420 original size:21 final size:22
Alignment explanation
Indices: 1113396--1113469 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 22
1113386 TCATATATTT
1113396 TATTTT-TATTTATTATTATAA
1 TATTTTATATTTATTATTATAA
1113417 TATTTTATATTTTATT-TT-TAA
1 TATTTTATA-TTTATTATTATAA
1113438 TATATTTATATTTA-TATTATTAA
1 TAT-TTTATATTTATTATTA-TAA
1113461 T-TTTTATAT
1 TATTTTATAT
1113470 AATATCATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.02
21 25 0.53
22 11 0.23
23 10 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTTATATTTATTATTATAA
Found at i:1113538 original size:10 final size:9
Alignment explanation
Indices: 1113388--1113544 Score: 56
Period size: 9 Copynumber: 18.2 Consensus size: 9
1113378 TTTTAATGTC
1113388 ATATA-TTT
1 ATATATTTT
1113396 -TAT-TTTT
1 ATATATTTT
*
1113403 ATTTATTATT
1 ATATATT-TT
1113413 ATA-ATATTT
1 ATATAT-TTT
1113422 -TATATTTT
1 ATATATTTT
*
1113430 AT-T-TTTA
1 ATATATTTT
1113437 ATATATTTAT
1 ATATATTT-T
* *
1113447 ATTTATATT
1 ATATATTTT
1113456 AT-TAATTTT
1 ATAT-ATTTT
**
1113465 -TATATAAT
1 ATATATTTT
1113473 ATCATATTTT
1 AT-ATATTTT
1113483 AAATATATTTT
1 --ATATATTTT
* *
1113494 -TA-ATATC
1 ATATATTTT
1113501 ATATA-TTT
1 ATATATTTT
1113509 -TAT-TTTT
1 ATATATTTT
*
1113516 ATTTATTATT
1 ATATATT-TT
1113526 ATA-ATTTT
1 ATATATTTT
1113534 ATATATTTT
1 ATATATTTT
1113543 AT
1 AT
1113545 TTTCATTTCT
Statistics
Matches: 109, Mismatches: 17, Indels: 45
0.64 0.10 0.26
Matches are distributed among these distances:
7 20 0.18
8 26 0.24
9 34 0.31
10 20 0.18
11 7 0.06
12 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (9 bp):
ATATATTTT
Found at i:1113566 original size:33 final size:33
Alignment explanation
Indices: 1113501--1113567 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1113491 TTTTAATATC
* *
1113501 ATATATTTTATTTTTATTTATTATTATAATTTT
1 ATATATTTTATTTTCATTTATTAATATAATTTT
* *
1113534 ATATATTTTATTTTCATTTCTTTAATATATTTTT
1 ATATATTTTATTTTCATTT-ATTAATATAATTTT
1113568 TATGTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 18 0.62
34 11 0.38
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATATTTTATTTTCATTTATTAATATAATTTT
Found at i:1113669 original size:32 final size:33
Alignment explanation
Indices: 1113621--1113699 Score: 105
Period size: 32 Copynumber: 2.5 Consensus size: 33
1113611 AAATGTTAAT
1113621 TTTTATATT-T-TATTTTATTTT-A-ATTTTTA
1 TTTTATATTATATATTTTATTTTAATATTTTTA
1113650 TTCTTATATTATATATTTTATTTTAATATTTTTA
1 TT-TTATATTATATATTTTATTTTAATATTTTTA
1113684 TTTTA-ATTATAATATT
1 TTTTATATTAT-ATATT
1113700 ATAAAATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
29 2 0.05
30 7 0.16
31 1 0.02
32 16 0.36
33 9 0.20
34 9 0.20
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (33 bp):
TTTTATATTATATATTTTATTTTAATATTTTTA
Found at i:1113688 original size:51 final size:53
Alignment explanation
Indices: 1113577--1113688 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 53
1113567 TTATGTTATA
*
1113577 TATTTTATTTTAATTTGTTTTACCTATATTATATAAATGTTAATTTTTATATTT
1 TATTTTATTTTAATTTGTTTTACCTATATTATAT-AATGTTAATTTTAATATTT
* *
1113631 TATTTTATTTTAATTT-TTATT-CTTATATTATAT-AT-TTTATTTTAATATTTT
1 TATTTTATTTTAATTTGTT-TTACCTATATTATATAATGTTAATTTTAATA-TTT
1113682 TATTTTA
1 TATTTTA
1113689 ATTATAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
50 10 0.19
51 12 0.23
53 13 0.25
54 18 0.34
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (53 bp):
TATTTTATTTTAATTTGTTTTACCTATATTATATAATGTTAATTTTAATATTT
Found at i:1113689 original size:14 final size:15
Alignment explanation
Indices: 1113309--1113690 Score: 72
Period size: 15 Copynumber: 24.1 Consensus size: 15
1113299 TGTAATATTT
1113309 TATATTTTATTTTTAA
1 TATATTTTA-TTTTAA
*
1113325 TATATTTATATTTTTA
1 TATATTT-TATTTTAA
* *
1113341 T-TA-TTAATTTTTA
1 TATATTTTATTTTAA
* *
1113354 TATAATATCATTTCTTAAA
1 TAT-ATTTTA-TT-TT-AA
* * *
1113373 TATATTTTTAATGTCA
1 TATA-TTTTATTTTAA
*
1113389 TATATTTTATTTTTA
1 TATATTTTATTTTAA
* *
1113404 TTTATTATTATAATATT-T
1 TATATT-TTAT--T-TTAA
1113422 TATATTTTATTTTTAA
1 TATATTTTA-TTTTAA
1113438 TATA-TTTATATTT-A
1 TATATTTTAT-TTTAA
*
1113452 TAT-TATTAATTTTTATA
1 TATAT-TTTA-TTTTA-A
**
1113469 TAATATCATATTTTAAA
1 T-ATATTTTATTTT-AA
* * *
1113486 TATATTTTTAATATCA
1 TATA-TTTTATTTTAA
*
1113502 TATATTTTATTTTTA
1 TATATTTTATTTTAA
* *
1113517 TTTATTATTATAATTTTA
1 TATATT-TTAT--TTTAA
*
1113535 TATATTTTATTTTCA
1 TATATTTTATTTTAA
*
1113550 T-T-TCTTTA--AT-A
1 TATAT-TTTATTTTAA
* *
1113561 TATTTTTTATGTT-A
1 TATATTTTATTTTAA
1113575 TATATTTTATTTTAA
1 TATATTTTATTTTAA
* *
1113590 TTTGTTTTACCTATATTATA
1 TATATTTTA--T-T-TTA-A
* *
1113610 TAAATGTTAATTTTTATA
1 TATAT-TTTA-TTTTA-A
*
1113628 TTTTATTTTATTTTAA
1 -TATATTTTATTTTAA
* *
1113644 TTTTTATTCTTATATT-A
1 --TATATT-TTATTTTAA
1113661 TATATTTTATTTTAA
1 TATATTTTATTTTAA
1113676 TAT-TTTTATTTTAA
1 TATATTTTATTTTAA
1113690 T
1 T
1113691 TATAATATTA
Statistics
Matches: 274, Mismatches: 49, Indels: 88
0.67 0.12 0.21
Matches are distributed among these distances:
11 2 0.01
12 6 0.02
13 10 0.04
14 44 0.16
15 66 0.24
16 43 0.16
17 39 0.14
18 40 0.15
19 17 0.06
20 4 0.01
21 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (15 bp):
TATATTTTATTTTAA
Found at i:1120178 original size:27 final size:27
Alignment explanation
Indices: 1120119--1120178 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
1120109 TCTTAAATAA
* *
1120119 ATTTTTAATATCATATGTTTTATTTTT
1 ATTTATAATATCATATATTTTATTTTT
*
1120146 -TATTATAATTTCATATATTTTATTTTT
1 AT-TTATAATATCATATATTTTATTTTT
1120173 ATTTAT
1 ATTTAT
1120179 TGTAATACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 26 0.93
28 1 0.04
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (27 bp):
ATTTATAATATCATATATTTTATTTTT
Found at i:1121656 original size:21 final size:20
Alignment explanation
Indices: 1121630--1121673 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
1121620 TTAATTTCAG
1121630 TTATTTTAT-TTTAATTTTACT
1 TTATTTT-TCTTTAA-TTTACT
1121651 TTATTTTTCTTTAATTTACT
1 TTATTTTTCTTTAATTTACT
1121671 TTA
1 TTA
1121674 AAAATAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTTCTTTAATTTACT
Found at i:1121662 original size:10 final size:10
Alignment explanation
Indices: 1121630--1121673 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1121620 TTAATTTCAG
*
1121630 TTATTTTATT
1 TTATTTTACT
1121640 TTAATTTTACT
1 TT-ATTTTACT
*
1121651 TTATTTTTCT
1 TTATTTTACT
*
1121661 TTAATTTACT
1 TTATTTTACT
1121671 TTA
1 TTA
1121674 AAAATAGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATTTTACT
Found at i:1122181 original size:34 final size:34
Alignment explanation
Indices: 1122133--1122201 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1122123 CCATGACGCC
1122133 ACACAGCTTTCCGAAAATATTTTTTTATGCAAGA
1 ACACAGCTTTCCGAAAATATTTTTTTATGCAAGA
*
1122167 ACACTGCTTTCCGAAAATATTTTTTTATGCAAGA
1 ACACAGCTTTCCGAAAATATTTTTTTATGCAAGA
1122201 A
1 A
1122202 TAAGGAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (34 bp):
ACACAGCTTTCCGAAAATATTTTTTTATGCAAGA
Found at i:1122871 original size:21 final size:21
Alignment explanation
Indices: 1122845--1122893 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1122835 AAAGATGAAC
1122845 ATGTATCGATATATTGTCCAA
1 ATGTATCGATATATTGTCCAA
1122866 ATGTATCGATATATTGTCCAA
1 ATGTATCGATATATTGTCCAA
1122887 ATGTATC
1 ATGTATC
1122894 AATACATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (21 bp):
ATGTATCGATATATTGTCCAA
Found at i:1124100 original size:14 final size:14
Alignment explanation
Indices: 1124081--1124112 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1124071 AATCAAAATT
*
1124081 AATTAATTAACTAA
1 AATTAATTAACCAA
1124095 AATTAATTAACCAA
1 AATTAATTAACCAA
1124109 AATT
1 AATT
1124113 TAAACTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAATTAACCAA
Found at i:1138222 original size:33 final size:32
Alignment explanation
Indices: 1138150--1138225 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
1138140 TGTGATAATC
*
1138150 TTTGGAGAATTTGAGGATGATGATATGCCCTCA
1 TTTGGAG-ATTTGAGGATAATGATATGCCCTCA
*
1138183 TATTGGAGATTT-AGAGATAATGATATGCCCTGTA
1 T-TTGGAGATTTGAG-GATAATGATATGCCCT-CA
1138217 TTTGGAGAT
1 TTTGGAGAT
1138226 GTTTGTTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 2 0.05
33 28 0.74
34 8 0.21
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.36
Consensus pattern (32 bp):
TTTGGAGATTTGAGGATAATGATATGCCCTCA
Found at i:1144722 original size:21 final size:19
Alignment explanation
Indices: 1144698--1144739 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
1144688 TAATTGAAAA
1144698 TAAAATAATATAAAATTTAAC
1 TAAAATAAT-TAAAA-TTAAC
*
1144719 TAAAATAATTTAAATTAAC
1 TAAAATAATTAAAATTAAC
1144738 TA
1 TA
1144740 CTCAACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 9 0.45
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAATAATTAAAATTAAC
Found at i:1150513 original size:37 final size:37
Alignment explanation
Indices: 1150450--1150520 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
1150440 TAATAGTTTG
*
1150450 ACCAAAATCAAATAGAGCCCCTGTACAATATATGCCA
1 ACCAAAATCAAATAGAACCCCTGTACAATATATGCCA
1150487 ACCAAAATCAAATA-ATACCTCC-GTACAATATATG
1 ACCAAAATCAAATAGA-ACC-CCTGTACAATATATG
1150521 GCAATTACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 1 0.03
37 28 0.90
38 2 0.06
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.21
Consensus pattern (37 bp):
ACCAAAATCAAATAGAACCCCTGTACAATATATGCCA
Found at i:1151310 original size:24 final size:24
Alignment explanation
Indices: 1151283--1151329 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1151273 ACACCAACCA
1151283 CAGCTTCACTTGCTACACTAGTAG
1 CAGCTTCACTTGCTACACTAGTAG
*
1151307 CAGCTTCACTTGCTGCACTAGTA
1 CAGCTTCACTTGCTACACTAGTA
1151330 CCAATTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (24 bp):
CAGCTTCACTTGCTACACTAGTAG
Found at i:1151338 original size:24 final size:24
Alignment explanation
Indices: 1151286--1151340 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1151276 CCAACCACAG
* *
1151286 CTTCACTTGCTACACTAGTAGCAG
1 CTTCACTTGCTACACTAGTACCAA
*
1151310 CTTCACTTGCTGCACTAGTACCAA
1 CTTCACTTGCTACACTAGTACCAA
*
1151334 TTTCACT
1 CTTCACT
1151341 CACTCTACCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.33
Consensus pattern (24 bp):
CTTCACTTGCTACACTAGTACCAA
Found at i:1154671 original size:21 final size:21
Alignment explanation
Indices: 1154601--1154671 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
1154591 ACAGCTTAAA
1154601 ATGGGCCTCTAGTAG-TTTCAG
1 ATGGGCCTCTAGTAGCTTT-AG
* * * * *
1154622 ATAGGCCACCAGTAACTTTAA
1 ATGGGCCTCTAGTAGCTTTAG
**
1154643 ATTTGCCTCTAGTAGCTTTAG
1 ATGGGCCTCTAGTAGCTTTAG
1154664 ATGGGCCT
1 ATGGGCCT
1154672 GTAATTGCTG
Statistics
Matches: 36, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
21 33 0.92
22 3 0.08
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (21 bp):
ATGGGCCTCTAGTAGCTTTAG
Found at i:1156582 original size:31 final size:30
Alignment explanation
Indices: 1156539--1156617 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
1156529 TCACTCTTAA
*
1156539 TTTAGTGTTTAGGCTGGGTTTAAAGTTTAGG
1 TTTAGTGTTTAGGCTGGGTTTAAA-TCTAGG
* * * *
1156570 TTTAATGTTTAGGCTAGGTTTCAATCTCGG
1 TTTAGTGTTTAGGCTGGGTTTAAATCTAGG
*
1156600 TTTAGTGTTTAGGTTGGG
1 TTTAGTGTTTAGGCTGGG
1156618 CTTCACTCTC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 19 0.47
31 21 0.52
ACGTcount: A:0.18, C:0.06, G:0.30, T:0.46
Consensus pattern (30 bp):
TTTAGTGTTTAGGCTGGGTTTAAATCTAGG
Found at i:1156628 original size:30 final size:30
Alignment explanation
Indices: 1156568--1156638 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
1156558 TTAAAGTTTA
*
1156568 GGTTTAATGTTTAGGCTAGGTTTCAATCTC
1 GGTTTAATGTTTAGGCTAGGCTTCAATCTC
* * * *
1156598 GGTTTAGTGTTTAGGTTGGGCTTCACTCTC
1 GGTTTAATGTTTAGGCTAGGCTTCAATCTC
* *
1156628 GATTTATTGTT
1 GGTTTAATGTT
1156639 CTCTCTTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.15, C:0.13, G:0.25, T:0.46
Consensus pattern (30 bp):
GGTTTAATGTTTAGGCTAGGCTTCAATCTC
Found at i:1159704 original size:20 final size:20
Alignment explanation
Indices: 1159672--1159728 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
1159662 TTCATTCATG
*
1159672 AAAATTAAA-AAACAAAAAA
1 AAAAATAAAGAAACAAAAAA
*
1159691 CAAAATAAAGAAACCAAAAAA
1 AAAAATAAAGAAA-CAAAAAA
*
1159712 AAAAAAAAAGAAACAAA
1 AAAAATAAAGAAACAAA
1159729 GAGCAAGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 7 0.22
20 7 0.22
21 18 0.56
ACGTcount: A:0.82, C:0.09, G:0.04, T:0.05
Consensus pattern (20 bp):
AAAAATAAAGAAACAAAAAA
Found at i:1161667 original size:244 final size:245
Alignment explanation
Indices: 1161238--1161705 Score: 764
Period size: 244 Copynumber: 1.9 Consensus size: 245
1161228 TAGTTACCTG
* * * *
1161238 ATTGTATGTGCTGATGATACTGTTTCGTATAAGATGGTGGCAAAGCTAGAGTGGAATGAAATTAA
1 ATTGTATGTGCTGATGATACTGTTTCATATAAGATGGTAGCAAAACTAGAGCGGAATGAAATTAA
*
1161303 TTTCAGGTTCAAACATCAAAATACTCCAAAAATGAGATTATACTTCAACGATATCTATGATTATG
66 TTTCAGGTTCAAACATCAAAATACTCCAAAAATGAGATTATACTTCAACGATATCTATGATGATG
* *
1161368 AAAATTTGACGCAATAGCATTTATTTGGAAAAATGTTGAGTTGGGCATGTAAAACACAACAATCA
131 AAAATTTGACACAATAGCATTCATTTGGAAAAATGTTGAGTTGGGCATGTAAAACACAACAATCA
1161433 TAGTCTGCAAAATC-C-CATAATGATATTTAAAAAGATTGTATTTTTGATT
196 TAGTCTGC-AAATCTCGCATAATGATATTTAAAAAGATTGTATTTTTGATT
1161482 ATTGTATGTGCTGATGATACTGTTTCATATAAGATGGTAGCAAAACTAGAGCGGAATGAAATTAA
1 ATTGTATGTGCTGATGATACTGTTTCATATAAGATGGTAGCAAAACTAGAGCGGAATGAAATTAA
* * *
1161547 TTTCATGTT-AAATCATCAAAATACTCCAAAAATGAGATTATGCTTGAAC-AGTATCTATGATGA
66 TTTCAGGTTCAAA-CATCAAAATACTCCAAAAATGAGATTATACTTCAACGA-TATCTATGATGA
*
1161610 TGAAAATTTGACACAATAGCATTCATTTGGAAAAATGTTGAGTTGGGTATGTAAAACACAACAAT
129 TGAAAATTTGACACAATAGCATTCATTTGGAAAAATGTTGAGTTGGGCATGTAAAACACAACAAT
* *
1161675 CATAGTGTGCAACTCTCGCATAATGATATTT
194 CATAGTCTGCAAATCTCGCATAATGATATTT
1161706 TGAAAAACGT
Statistics
Matches: 207, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
243 8 0.04
244 186 0.90
245 13 0.06
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (245 bp):
ATTGTATGTGCTGATGATACTGTTTCATATAAGATGGTAGCAAAACTAGAGCGGAATGAAATTAA
TTTCAGGTTCAAACATCAAAATACTCCAAAAATGAGATTATACTTCAACGATATCTATGATGATG
AAAATTTGACACAATAGCATTCATTTGGAAAAATGTTGAGTTGGGCATGTAAAACACAACAATCA
TAGTCTGCAAATCTCGCATAATGATATTTAAAAAGATTGTATTTTTGATT
Found at i:1166475 original size:32 final size:32
Alignment explanation
Indices: 1166439--1166504 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
1166429 GGCTCAAAAG
1166439 GGGTATACTAGGGATAAAAATTTAACAAGGTT
1 GGGTATACTAGGGATAAAAATTTAACAAGGTT
1166471 GGGTATACTAGGGATAAAAATTTAACAAGGTT
1 GGGTATACTAGGGATAAAAATTTAACAAGGTT
1166503 GG
1 GG
1166505 CCTTTTAGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.27
Consensus pattern (32 bp):
GGGTATACTAGGGATAAAAATTTAACAAGGTT
Found at i:1167976 original size:74 final size:72
Alignment explanation
Indices: 1167818--1168013 Score: 207
Period size: 74 Copynumber: 2.7 Consensus size: 72
1167808 TGGCCGGTCC
* * * *
1167818 AGAAACAGAAAAGACTTAGTCAACTAAGAAGCATCATTAGTCGACTAAGTGCTCACTATCAGAAA
1 AGAAACAGAAAAGACTTAGTCGACTAAGAAGCAT-GTTAGTCGACTAAGTGCTCACTACCACAAA
*
1167883 CTTCAATA
65 CTGCAATA
* * * *
1167891 AGAAAATAGAAAAGACTTAGTCGA-TCAAGGAGCATGGTTAGTCGACTAAGTGCTCATTGCCACA
1 AG-AAACAGAAAAGACTTAGTCGACT-AAGAAGCAT-GTTAGTCGACTAAGTGCTCACTACCACA
* *
1167955 AACTGGGAGT-
63 AACT-GCAATA
* *
1167965 AGAAGACAGAAAAGACTTAGTCGACTAAGAAGTATGTTAGTCAACTAAG
1 AGAA-ACAGAAAAGACTTAGTCGACTAAGAAGCATGTTAGTCGACTAAG
1168014 AGCACACGGT
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
73 18 0.18
74 81 0.79
75 3 0.03
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (72 bp):
AGAAACAGAAAAGACTTAGTCGACTAAGAAGCATGTTAGTCGACTAAGTGCTCACTACCACAAAC
TGCAATA
Found at i:1169525 original size:21 final size:20
Alignment explanation
Indices: 1169497--1169542 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1169487 CTGAAACTTA
1169497 AAGAAGAAGAAAAAAAAAAC
1 AAGAAGAAGAAAAAAAAAAC
* * *
1169517 AAGAGAGAAGCAAAAGAAAAG
1 AAGA-AGAAGAAAAAAAAAAC
1169538 AAGAA
1 AAGAA
1169543 AAACATTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (20 bp):
AAGAAGAAGAAAAAAAAAAC
Found at i:1170824 original size:11 final size:11
Alignment explanation
Indices: 1170808--1170840 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1170798 TAAAAAAAAA
*
1170808 TTTTTTGAATT
1 TTTTTTGAAAT
1170819 TTTTTTGAAAT
1 TTTTTTGAAAT
1170830 TTTTTTGAAAT
1 TTTTTTGAAAT
1170841 GTACCTGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (11 bp):
TTTTTTGAAAT
Found at i:1170899 original size:14 final size:14
Alignment explanation
Indices: 1170871--1170910 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1170861 GTTAATAATT
1170871 TAAAAATAA--AAA
1 TAAAAATAAGTAAA
1170883 TAAAAATAAGTAAA
1 TAAAAATAAGTAAA
1170897 T-AAAATAAAGTAAA
1 TAAAAAT-AAGTAAA
1170911 GTAAGTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.36
13 5 0.20
14 11 0.44
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (14 bp):
TAAAAATAAGTAAA
Found at i:1172281 original size:21 final size:21
Alignment explanation
Indices: 1172242--1172320 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
1172232 TGGAGGCACT
*
1172242 AGTCTTTATCAT-AATTGCATC
1 AGTCTTTGTCATGAA-TGCATC
* *
1172263 AATCTTTGTTATGAATGCATC
1 AGTCTTTGTCATGAATGCATC
1172284 AGTCTTTGTCATGAATGCATC
1 AGTCTTTGTCATGAATGCATC
1172305 AGTCTTTGTCATGAAT
1 AGTCTTTGTCATGAAT
1172321 TGCACGAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
21 50 0.96
22 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (21 bp):
AGTCTTTGTCATGAATGCATC
Found at i:1175022 original size:22 final size:23
Alignment explanation
Indices: 1174994--1175045 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1174984 ATTTTTATAC
*
1174994 ATTACTACAAGAACTAAG-CCAA
1 ATTACTACAAAAACTAAGCCCAA
* *
1175016 ATTACTATAAAAATTAAGCCCAA
1 ATTACTACAAAAACTAAGCCCAA
*
1175039 ATAACTA
1 ATTACTA
1175046 TATATCATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (23 bp):
ATTACTACAAAAACTAAGCCCAA
Found at i:1177625 original size:70 final size:70
Alignment explanation
Indices: 1177547--1177685 Score: 242
Period size: 70 Copynumber: 2.0 Consensus size: 70
1177537 AATGTATGAG
1177547 AGTTAAATCATTTCAAGAACTTGTCAAGGATCACTCAAATAATGTTCAAGTAAATTTGATAATTT
1 AGTTAAATCATTTCAAGAACTTGTCAAGGATCACTCAAATAATGTTCAAGTAAATTTGATAATTT
1177612 TGTCT
66 TGTCT
* * * *
1177617 AGTTAAATCATTTCAAGAACTTGTCCAGGATCAGTCAAATATTGTTCAAGTAAATTTGATCATTT
1 AGTTAAATCATTTCAAGAACTTGTCAAGGATCACTCAAATAATGTTCAAGTAAATTTGATAATTT
1177682 TGTC
66 TGTC
1177686 ATAATAAAAC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (70 bp):
AGTTAAATCATTTCAAGAACTTGTCAAGGATCACTCAAATAATGTTCAAGTAAATTTGATAATTT
TGTCT
Found at i:1177712 original size:44 final size:45
Alignment explanation
Indices: 1177664--1177754 Score: 157
Period size: 44 Copynumber: 2.0 Consensus size: 45
1177654 AATATTGTTC
1177664 AAGTAAATTTGATCATTTTGTCATAAT-AAAACTATAATAATTTT
1 AAGTAAATTTGATCATTTTGTCATAATCAAAACTATAATAATTTT
* *
1177708 AAGTAAATTTGATCATTTTGTTATAATCAAAACTATAATAGTTTT
1 AAGTAAATTTGATCATTTTGTCATAATCAAAACTATAATAATTTT
1177753 AA
1 AA
1177755 AGCTAACAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 26 0.59
45 18 0.41
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (45 bp):
AAGTAAATTTGATCATTTTGTCATAATCAAAACTATAATAATTTT
Found at i:1178476 original size:19 final size:19
Alignment explanation
Indices: 1178443--1178490 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1178433 TCAAGTGAGA
1178443 AGATA-TAATTCTAAAGCT
1 AGATACTAATTCTAAAGCT
* * *
1178461 TGATGCTAATTTTAAAGCT
1 AGATACTAATTCTAAAGCT
1178480 AGATACTAATT
1 AGATACTAATT
1178491 AAAAAAACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
AGATACTAATTCTAAAGCT
Found at i:1187672 original size:68 final size:68
Alignment explanation
Indices: 1187558--1187751 Score: 300
Period size: 68 Copynumber: 2.9 Consensus size: 68
1187548 GATGAATGCC
* * * *
1187558 ATAAGATTATGTATATGATGTAAATTCCATATATCATATGAGATAATTAAGTATGCATAATGTAT
1 ATAAGATTGTTTATATGATGTAAATTCCATATATCATATGAAATAATTAAATATGCATAATGTAT
1187623 ACT
66 ACT
*
1187626 ATAAGATTGTTTATATGATGTAAATTCCATATATCATTTGAAATAATTAAATATGCATAATGTAT
1 ATAAGATTGTTTATATGATGTAAATTCCATATATCATATGAAATAATTAAATATGCATAATGTAT
*
1187691 ATT
66 ACT
* *
1187694 ATAAGATTGTTTATATGATGTAAATTCCATATACCATAT-AAGATGATTAAATATGCAT
1 ATAAGATTGTTTATATGATGTAAATTCCATATATCATATGAA-ATAATTAAATATGCAT
1187752 GATAAATGCC
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
67 2 0.02
68 114 0.98
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (68 bp):
ATAAGATTGTTTATATGATGTAAATTCCATATATCATATGAAATAATTAAATATGCATAATGTAT
ACT
Found at i:1187769 original size:68 final size:68
Alignment explanation
Indices: 1187549--1187848 Score: 295
Period size: 68 Copynumber: 4.4 Consensus size: 68
1187539 GCTTGGTATG
* * *
1187549 ATGAATGCCATAAGATTATGTATATGATGTAAATTCCATATATCATATGAGATAATTAAGTATGC
1 ATGAATACCATAAGATTATGTATATGATGTAAATTCCATATATCATATAAGATAATTAAATATGC
1187614 ATA
66 ATA
* * * * *
1187617 ATGTATACTATAAGATTGTTTATATGATGTAAATTCCATATATCATTTGAA-ATAATTAAATATG
1 ATGAATACCATAAGATTATGTATATGATGTAAATTCCATATATCATAT-AAGATAATTAAATATG
1187681 CATA
65 CATA
* ** * * * *
1187685 ATGTATATTATAAGATTGTTTATATGATGTAAATTCCATATACCATATAAGATGATTAAATATGC
1 ATGAATACCATAAGATTATGTATATGATGTAAATTCCATATATCATATAAGATAATTAAATATGC
*
1187750 ATG
66 ATA
* * * * * * * *
1187753 ATAAATGCCATGAGATTATGTATATGATGTATATTCCAT-TAACTACATGAA-ATGATTGTGAA-
1 ATGAATACCATAAGATTATGTATATGATGTAAATTCCATATATC-ATAT-AAGAT-AAT-TAAAT
1187815 A-GCATA
62 ATGCATA
*
1187821 ATGAATACCATGAGATTATGTATATGAT
1 ATGAATACCATAAGATTATGTATATGAT
1187849 ATATTTTCTA
Statistics
Matches: 196, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
67 5 0.03
68 183 0.93
69 5 0.03
70 3 0.02
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.37
Consensus pattern (68 bp):
ATGAATACCATAAGATTATGTATATGATGTAAATTCCATATATCATATAAGATAATTAAATATGC
ATA
Found at i:1195713 original size:68 final size:68
Alignment explanation
Indices: 1195507--1195713 Score: 238
Period size: 68 Copynumber: 3.0 Consensus size: 68
1195497 CATGTTTGGT
* ** * *
1195507 ATGATGAATGCCATAAGATTATGTGCATGATGTAAATTCCATATACCATATGAGATGATTAATTA
1 ATGATAAATGCCATAAGATTATGTATATGATGTAATTTCCATATACCATATGAGATGATTAAGTA
1195572 TGC
66 TGC
* * * * * *
1195575 ATAATATATACTATAAGATTGTGTATATGATGTAAATTT-CATATACCATATGAGGTGATTAAGT
1 ATGATAAATGCCATAAGATTATGTATATGATGT-AATTTCCATATACCATATGAGATGATTAAGT
1195639 ATGC
65 ATGC
* * * * *
1195643 ATGATAAATGCCATGAGATTATGTATATGATGTATTTTCCATATACC-TGATGAGTTGAGTAAGC
1 ATGATAAATGCCATAAGATTATGTATATGATGTAATTTCCATATACCAT-ATGAGATGATTAAGT
1195707 ATGC
65 ATGC
1195711 ATG
1 ATG
1195714 TAATGAACTT
Statistics
Matches: 115, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
67 5 0.04
68 106 0.92
69 4 0.03
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (68 bp):
ATGATAAATGCCATAAGATTATGTATATGATGTAATTTCCATATACCATATGAGATGATTAAGTA
TGC
Found at i:1196223 original size:20 final size:20
Alignment explanation
Indices: 1196191--1196243 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1196181 TTCACTAATT
*
1196191 TATCGATAGATTCTCGAAAG
1 TATCGATAGATTCTAGAAAG
* * *
1196211 TATTGATACATTCTAGAATG
1 TATCGATAGATTCTAGAAAG
1196231 TATCGATAGATTC
1 TATCGATAGATTC
1196244 ATTGTAGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (20 bp):
TATCGATAGATTCTAGAAAG
Found at i:1198125 original size:24 final size:24
Alignment explanation
Indices: 1198076--1198125 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1198066 CGGTTAACTA
*
1198076 AAGATTGCTTGGCTTTTCCCTTAC
1 AAGATTGCTTGGCTTTTCCCTAAC
*
1198100 AAGATTGCATT-GCTTTTCTCTAAC
1 AAGATTGC-TTGGCTTTTCCCTAAC
1198124 AA
1 AA
1198126 AATCAAGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (24 bp):
AAGATTGCTTGGCTTTTCCCTAAC
Found at i:1200646 original size:27 final size:27
Alignment explanation
Indices: 1200616--1201147 Score: 277
Period size: 27 Copynumber: 19.9 Consensus size: 27
1200606 TCTTGGGCGC
* * *
1200616 TTCTGTACTTGGAACGCCCTTAGGTGT
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* **
1200643 TTCTGTGTTTGGAACACCCCTAGGCACT
1 TTCTGTGCTTGGAACACCCCTAGG-TGT
* * * * * *
1200671 TT-TGTACTTAGAACGCCCTTGGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* * * * *
1200697 TTCTGCGCTTGGAACACCTCTGGGCGC
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* * *
1200724 TTCTATACTTGGAACA-CCCTAGGCGT
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* * *
1200750 TTTTGTGCTTCGAACACCCCTAGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* ** * *
1200777 TTCTGTACTTGGAATGCCCATGGGTGCT
1 TTCTGTGCTTGGAACACCCCTAGGTG-T
* * * * * **
1200805 TT-TGCGCTTGTAACGCCTCTGGGCAT
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* *
1200831 TTCTATGCTTGAAACACCCCTAGGTGT
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* * * *
1200858 TTTTGTACTTGTATCACCCCTAGGTGT
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* * * * *
1200885 TTCTGCGCTTGGAACTCCCCTGGGCGC
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* * * *
1200912 TTCTGTACTTGGAACA-CACTACGCGT
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* *
1200938 TTCTGTGGTTGGAACACCCCTAGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* * ** * * *
1200965 TTCTGTACTTGAAATGCCCTTGGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGTGT
** * * ***
1200992 TTCTGCACTTGGAACTCCCCTGGGCAC
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* * *
1201019 TACTGTACTTGGAACA-CCCTAGGCGT
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* *
1201045 TTCTGTGCTTAGAACA-CCCTAGGCGT
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* *
1201071 TTTTGTGCTTGGAACACCCTTAGGTGCT
1 TTCTGTGCTTGGAACACCCCTAGGTG-T
* * * *
1201099 TT-TGTGCTTGAAACGCCCCTGGGTGC
1 TTCTGTGCTTGGAACACCCCTAGGTGT
* *
1201125 TTCTGCGCTTGGAACTCCCCTAG
1 TTCTGTGCTTGGAACACCCCTAG
1201148 AAGCTTCTAT
Statistics
Matches: 375, Mismatches: 121, Indels: 18
0.73 0.24 0.04
Matches are distributed among these distances:
26 90 0.24
27 277 0.74
28 8 0.02
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (27 bp):
TTCTGTGCTTGGAACACCCCTAGGTGT
Found at i:1200685 original size:54 final size:54
Alignment explanation
Indices: 1200615--1201224 Score: 266
Period size: 54 Copynumber: 11.4 Consensus size: 54
1200605 CTCTTGGGCG
*
1200615 CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGTTTGGAACACCCCTAGGCA
1 CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGCTTGGAACACCCCTAGGCA
* * * * * * * *
1200669 CTTTTGTACTTAGAACGCCCTTGGGTGCTTCTGCGCTTGGAACACCTCTGGGCG
1 CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGCTTGGAACACCCCTAGGCA
* * * * * **
1200723 CTTCTATACTTGGAACACCC-TAGGCGTTTTTGTGCTTCGAACACCCCTAGGTG
1 CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGCTTGGAACACCCCTAGGCA
* * * * * * * *
1200776 CTTCTGTACTTGGAATGCCCATGGGTGCTTT-TGCGCTTGTAACGCCTCTGGGCA
1 CTTCTGTACTTGGAACGCCCTTAGGTG-TTTCTGTGCTTGGAACACCCCTAGGCA
* * * * * * * * * * **
1200830 TTTCTATGCTTGAAACACCCCTAGGTGTTTTTGTACTTGTATCACCCCTAGGTG
1 CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGCTTGGAACACCCCTAGGCA
* ** * * * * * * * * *
1200884 TTTCTGCGCTTGGAACTCCCCTGGGCGCTTCTGTACTTGGAACA-CACTACGCG
1 CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGCTTGGAACACCCCTAGGCA
* ** * * * * * ** * * **
1200937 TTTCTGTGGTTGGAACACCCCTAGGTGCTTCTGTACTTGAAATGCCCTTGGGTG
1 CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGCTTGGAACACCCCTAGGCA
* * * * *** * * *
1200991 CTTCTGCACTTGGAACTCCCCTGGGCACTACTGTACTTGGAACA-CCCTAGGCG
1 CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGCTTGGAACACCCCTAGGCA
* * * * * * * **
1201044 TTTCTGTGCTTAGAACACCC-TAGGCGTTTTTGTGCTTGGAACACCCTTAGGTG
1 CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGCTTGGAACACCCCTAGGCA
* * * * * * * * *
1201097 CTTTTGTGCTTGAAACGCCCCTGGGTGCTTCTGCGCTTGGAACTCCCCTA-GAA
1 CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGCTTGGAACACCCCTAGGCA
* ** * *
1201150 GCTTCTATACTTGGAACGCCCTCGGGCTG-TTCTGCGCTTGGAACA-CCCT-GAGCG
1 -CTTCTGTACTTGGAACGCCCTTAGG-TGTTTCTGTGCTTGGAACACCCCTAG-GCA
1201204 CTTCTGTACTTGGAACGCCCT
1 CTTCTGTACTTGGAACGCCCT
1201225 CGGGCGCTTC
Statistics
Matches: 417, Mismatches: 129, Indels: 21
0.74 0.23 0.04
Matches are distributed among these distances:
52 17 0.04
53 154 0.37
54 241 0.58
55 5 0.01
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (54 bp):
CTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGCTTGGAACACCCCTAGGCA
Found at i:1200804 original size:107 final size:107
Alignment explanation
Indices: 1200611--1201223 Score: 498
Period size: 107 Copynumber: 5.7 Consensus size: 107
1200601 AACTCTCTTG
* * * ** *
1200611 GGCGCTTCTGTACTTGGAACGCCCTTAGGTGTTTCTGTGTTTGGAACACCCCTAGGCACTTTTGT
1 GGCGCTTCTATACTTGGAACACCC-TAGGTGTTTCTGTGCTTGGAACACCCCTAGGTGCTTCTGT
* * *
1200676 ACTTAGAACGCCCTTGGGTGCTTCTGCGCTTGGAACACCTCTG
65 ACTTGGAACGCCCCTGGGTGCTTCTGCGCTTGGAACACCTCTA
* * *
1200719 GGCGCTTCTATACTTGGAACACCCTAGGCGTTTTTGTGCTTCGAACACCCCTAGGTGCTTCTGTA
1 GGCGCTTCTATACTTGGAACACCCTAGGTGTTTCTGTGCTTGGAACACCCCTAGGTGCTTCTGTA
* * * * * *
1200784 CTTGGAATGCCCATGGGTGCTTTTGCGCTTGTAACGCCTCTG
66 CTTGGAACGCCCCTGGGTGCTTCTGCGCTTGGAACACCTCTA
** * * * * * * * *
1200826 GGCATTTCTATGCTTGAAACACCCCTAGGTGTTTTTGTACTTGTATCACCCCTAGGTGTTTCTGC
1 GGCGCTTCTATACTTGGAACA-CCCTAGGTGTTTCTGTGCTTGGAACACCCCTAGGTGCTTCTGT
* * * ** *
1200891 GCTTGGAACTCCCCTGGGCGCTTCTGTACTTGGAACA-CACTA
65 ACTTGGAACGCCCCTGGGTGCTTCTGCGCTTGGAACACCTCTA
* * * ** * * * ** * * *
1200933 CGCGTTTCTGTGGTTGGAACACCCCTAGGTGCTTCTGTACTTGAAATGCCCTTGGGTGCTTCTGC
1 GGCGCTTCTATACTTGGAACA-CCCTAGGTGTTTCTGTGCTTGGAACACCCCTAGGTGCTTCTGT
* ** * **
1200998 ACTTGGAACTCCCCTGGGCACTACTGTACTTGGAACACC-CTA
65 ACTTGGAACGCCCCTGGGTGCTTCTGCGCTTGGAACACCTCTA
* * * * * * * * *
1201040 GGCGTTTCTGTGCTTAGAACACCCTAGGCGTTTTTGTGCTTGGAACACCCTTAGGTGCTTTTGTG
1 GGCGCTTCTATACTTGGAACACCCTAGGTGTTTCTGTGCTTGGAACACCCCTAGGTGCTTCTGTA
* * *
1201105 CTTGAAACGCCCCTGGGTGCTTCTGCGCTTGGAACTCCCCTA
66 CTTGGAACGCCCCTGGGTGCTTCTGCGCTTGGAACACCTCTA
** * * * *
1201147 GAAGCTTCTATACTTGGAACGCCCTCGG-GCTGTTCTGCGCTTGGAACA-CCCT-GAGCGCTTCT
1 GGCGCTTCTATACTTGGAACACCCTAGGTG-T-TTCTGTGCTTGGAACACCCCTAG-GTGCTTCT
1201209 GTACTTGGAACGCCC
63 GTACTTGGAACGCCC
1201224 TCGGGCGCTT
Statistics
Matches: 407, Mismatches: 92, Indels: 13
0.79 0.18 0.03
Matches are distributed among these distances:
106 65 0.16
107 242 0.59
108 100 0.25
ACGTcount: A:0.16, C:0.28, G:0.25, T:0.31
Consensus pattern (107 bp):
GGCGCTTCTATACTTGGAACACCCTAGGTGTTTCTGTGCTTGGAACACCCCTAGGTGCTTCTGTA
CTTGGAACGCCCCTGGGTGCTTCTGCGCTTGGAACACCTCTA
Found at i:1201037 original size:188 final size:188
Alignment explanation
Indices: 1200651--1201089 Score: 551
Period size: 188 Copynumber: 2.3 Consensus size: 188
1200641 GTTTCTGTGT
** * * * * *
1200651 TTGGAACACCCCTAGGCACTTTTGTACTTAGAACGCCCTTGGGTGCTTCTGCGCTTGGAACACCT
1 TTGGAACACCCCTAGGCGTTTTTGTACTTAGAACACCCCTAGGTGTTTCTGCGCTTGGAACACCC
* * *
1200716 CTGGGCGCTTCTATACTTGGAACACCCTAGGCGTTTTTGTGCTTCGAACACCCCTAGGTGCTTCT
66 CTGGGCGCTTCTATACTTGGAACACACTACGCGTTTCTGTGCTTCGAACACCCCTAGGTGCTTCT
* * * * * * * *
1200781 GTACTTGGAATGCCCATGGGTGCTTTTGCGCTTGTAACGCCTCTGGGCATTTCTATGC
131 GTACTTGAAATGCCCATGGGTGCTTCTGCACTTGGAACGCCCCTGGGCACTACTATAC
* * * *
1200839 TTGAAACACCCCTAGGTGTTTTTGTACTT-GTATCACCCCTAGGTGTTTCTGCGCTTGGAACTCC
1 TTGGAACACCCCTAGGCGTTTTTGTACTTAG-AACACCCCTAGGTGTTTCTGCGCTTGGAACACC
* * *
1200903 CCTGGGCGCTTCTGTACTTGGAACACACTACGCGTTTCTGTGGTTGGAACACCCCTAGGTGCTTC
65 CCTGGGCGCTTCTATACTTGGAACACACTACGCGTTTCTGTGCTTCGAACACCCCTAGGTGCTTC
* * *
1200968 TGTACTTGAAATGCCCTTGGGTGCTTCTGCACTTGGAACTCCCCTGGGCACTACTGTAC
130 TGTACTTGAAATGCCCATGGGTGCTTCTGCACTTGGAACGCCCCTGGGCACTACTATAC
* * * * *
1201027 TTGGAACA-CCCTAGGCGTTTCTGTGCTTAGAACA-CCCTAGGCGTTTTTGTGCTTGGAACACCC
1 TTGGAACACCCCTAGGCGTTTTTGTACTTAGAACACCCCTAGGTGTTTCTGCGCTTGGAACACCC
1201090 TTAGGTGCTT
Statistics
Matches: 212, Mismatches: 37, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
186 25 0.12
187 21 0.10
188 166 0.78
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.32
Consensus pattern (188 bp):
TTGGAACACCCCTAGGCGTTTTTGTACTTAGAACACCCCTAGGTGTTTCTGCGCTTGGAACACCC
CTGGGCGCTTCTATACTTGGAACACACTACGCGTTTCTGTGCTTCGAACACCCCTAGGTGCTTCT
GTACTTGAAATGCCCATGGGTGCTTCTGCACTTGGAACGCCCCTGGGCACTACTATAC
Found at i:1201161 original size:133 final size:133
Alignment explanation
Indices: 1200892--1201224 Score: 375
Period size: 133 Copynumber: 2.5 Consensus size: 133
1200882 TGTTTCTGCG
* * * * * * *
1200892 CTTGGAACTCCCCTGGGCGCTTCTGTACTTGGAACACACTACGCGTTTCTGTGGTTGGAACACCC
1 CTTGGAAC-ACCCTAGGCGTTTCTGTGCTTGGAACACCCTAGGCGTTTCTGTGCTTGGAACACCC
* * * * *
1200957 CTAGGTGCTTCTGTACTTGAAATGCCCTTGGGTGCTTCTGCACTTGGAACTCCCCTGGGCACTAC
65 TTAGGTGCTTCTGTACTTGAAACGCCCCTGGGTGCTTCTGCACTTGGAACTCCCCTGAGAACTAC
*
1201022 TGTA
130 TATA
* *
1201026 CTTGGAACACCCTAGGCGTTTCTGTGCTTAGAACACCCTAGGCGTTTTTGTGCTTGGAACACCCT
1 CTTGGAACACCCTAGGCGTTTCTGTGCTTGGAACACCCTAGGCGTTTCTGTGCTTGGAACACCCT
* * * *
1201091 TAGGTGCTTTTGTGCTTGAAACGCCCCTGGGTGCTTCTGCGCTTGGAACTCCCCT-AGAAGCTTC
66 TAGGTGCTTCTGTACTTGAAACGCCCCTGGGTGCTTCTGCACTTGGAACTCCCCTGAGAA-CTAC
1201155 TATA
130 TATA
* * * * * *
1201159 CTTGGAACGCCCTCGG-GCTGTTCTGCGCTTGGAACACCCT-GAGCGCTTCTGTACTTGGAACGC
1 CTTGGAACACCCTAGGCG-T-TTCTGTGCTTGGAACACCCTAG-GCGTTTCTGTGCTTGGAACAC
1201222 CCT
63 CCT
1201225 CGGGCGCTTC
Statistics
Matches: 168, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
132 3 0.02
133 119 0.71
134 46 0.27
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.30
Consensus pattern (133 bp):
CTTGGAACACCCTAGGCGTTTCTGTGCTTGGAACACCCTAGGCGTTTCTGTGCTTGGAACACCCT
TAGGTGCTTCTGTACTTGAAACGCCCCTGGGTGCTTCTGCACTTGGAACTCCCCTGAGAACTACT
ATA
Found at i:1201182 original size:27 final size:27
Alignment explanation
Indices: 1201150--1201246 Score: 108
Period size: 27 Copynumber: 3.6 Consensus size: 27
1201140 TCCCCTAGAA
1201150 GCTTCTATACTTGGAACGCCCTCGGGC
1 GCTTCTATACTTGGAACGCCCTCGGGC
*** * *
1201177 TG-TTCTGCGCTTGGAACACCCT-GAGC
1 -GCTTCTATACTTGGAACGCCCTCGGGC
*
1201203 GCTTCTGTACTTGGAACGCCCTCGGGC
1 GCTTCTATACTTGGAACGCCCTCGGGC
*
1201230 GCTTCTATACTTAGAAC
1 GCTTCTATACTTGGAAC
1201247 ACCTTGGGCG
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
25 1 0.02
26 20 0.36
27 34 0.61
28 1 0.02
ACGTcount: A:0.16, C:0.31, G:0.25, T:0.28
Consensus pattern (27 bp):
GCTTCTATACTTGGAACGCCCTCGGGC
Found at i:1201269 original size:53 final size:53
Alignment explanation
Indices: 1201158--1201272 Score: 124
Period size: 53 Copynumber: 2.2 Consensus size: 53
1201148 AAGCTTCTAT
* * * * *
1201158 ACTTGGAACGCCCTCGGGCTGTTCTGCGCTTGGAACACCCTGAGCGCTTCTGT
1 ACTTGGAACGCCCTCGGGCTGTTCTACACTTAGAACACCCTGAGCGCTTCAGC
* * * *
1201211 ACTTGGAACGCCCTCGGGC-GCTTCTATACTTAGAACACCTTGGGCGTTTCAGC
1 ACTTGGAACGCCCTCGGGCTG-TTCTACACTTAGAACACCCTGAGCGCTTCAGC
*
1201264 GCTTGGAAC
1 ACTTGGAAC
1201273 ATCCCAGGGA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
52 1 0.02
53 50 0.98
ACGTcount: A:0.17, C:0.30, G:0.27, T:0.26
Consensus pattern (53 bp):
ACTTGGAACGCCCTCGGGCTGTTCTACACTTAGAACACCCTGAGCGCTTCAGC
Found at i:1205510 original size:33 final size:33
Alignment explanation
Indices: 1205473--1205578 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 33
1205463 TTAACGATGG
**
1205473 TGATGTGGATGCTGCTGTTAGAGTTGGTGGTGA
1 TGATGTGGATGCTGCTACTAGAGTTGGTGGTGA
** * ** *
1205506 TGATGTCAATACTATTACTAGAGTTGG-GGATGG
1 TGATGTGGATGCTGCTACTAGAGTTGGTGG-TGA
* * *
1205539 CGATGTGGGTGCTGCTACTAGAGTTGGTGATGA
1 TGATGTGGATGCTGCTACTAGAGTTGGTGGTGA
1205572 TGATGTG
1 TGATGTG
1205579 AGTACCATTA
Statistics
Matches: 53, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
32 2 0.04
33 50 0.94
34 1 0.02
ACGTcount: A:0.20, C:0.08, G:0.38, T:0.34
Consensus pattern (33 bp):
TGATGTGGATGCTGCTACTAGAGTTGGTGGTGA
Found at i:1207192 original size:15 final size:15
Alignment explanation
Indices: 1207139--1207197 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
1207129 TATTATTTTC
* *
1207139 CCTGTAATCACATTG
1 CCTGCAATCACATTA
* *
1207154 CTTACAATCACATTA
1 CCTGCAATCACATTA
*
1207169 CTTGCAATCACATTA
1 CCTGCAATCACATTA
*
1207184 CCTGTAATCACATT
1 CCTGCAATCACATT
1207198 GCATTGTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (15 bp):
CCTGCAATCACATTA
Found at i:1208155 original size:14 final size:14
Alignment explanation
Indices: 1208136--1208164 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1208126 CTTTAAGTTA
1208136 ACATTAGAATGCAG
1 ACATTAGAATGCAG
1208150 ACATTAGAATGCAG
1 ACATTAGAATGCAG
1208164 A
1 A
1208165 GGCTTTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
ACATTAGAATGCAG
Found at i:1210610 original size:2 final size:2
Alignment explanation
Indices: 1210603--1210628 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1210593 ATGTCTCTGT
1210603 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1210629 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1219925 original size:12 final size:13
Alignment explanation
Indices: 1219895--1219925 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1219885 AGAGGAATAG
*
1219895 TAAAAAGTACAAT
1 TAAAAAGTACAAC
1219908 TAAAAAGTACAAC
1 TAAAAAGTACAAC
1219921 TAAAA
1 TAAAA
1219926 TACTTTTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (13 bp):
TAAAAAGTACAAC
Found at i:1232693 original size:30 final size:31
Alignment explanation
Indices: 1232641--1232703 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
1232631 AATGATTGAC
1232641 TTTGTCTGCAAGTTTGGGGGAAGTATGCTCT
1 TTTGTCTGCAAGTTTGGGGGAAGTATGCTCT
*
1232672 TTTGTCTGCAAGTTT-GGGGAAGTATTCTCT
1 TTTGTCTGCAAGTTTGGGGGAAGTATGCTCT
1232702 TT
1 TT
1232704 CTTTACTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.43
Consensus pattern (31 bp):
TTTGTCTGCAAGTTTGGGGGAAGTATGCTCT
Found at i:1236437 original size:26 final size:26
Alignment explanation
Indices: 1236407--1236461 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
1236397 GCGCTCCCTT
*
1236407 AGGTGTTCTAAGCGCT-GAAGCGTCCA
1 AGGTGTTCTAAG-GATAGAAGCGTCCA
*
1236433 AGGTGTTCTAAGTATAGAAGCGTCCA
1 AGGTGTTCTAAGGATAGAAGCGTCCA
1236459 AGG
1 AGG
1236462 GCGTTTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (26 bp):
AGGTGTTCTAAGGATAGAAGCGTCCA
Found at i:1236495 original size:26 final size:26
Alignment explanation
Indices: 1236459--1236587 Score: 125
Period size: 26 Copynumber: 4.9 Consensus size: 26
1236449 GAAGCGTCCA
1236459 AGGGCGTTTTAAGTGCAGAAGCACTC
1 AGGGCGTTTTAAGTGCAGAAGCACTC
* * *
1236485 AGGGTGTTTTAAGTGCAGAAGCGCCC
1 AGGGCGTTTTAAGTGCAGAAGCACTC
* **
1236511 AGAGGCGTTTTAAGTACAGAAGGGCTC
1 AG-GGCGTTTTAAGTGCAGAAGCACTC
* * *
1236538 AAGGGAGTTTCAAGCGCAGAAGCAC-C
1 -AGGGCGTTTTAAGTGCAGAAGCACTC
**
1236564 AGGGGCGTTTTAAGTATAGAAGCA
1 A-GGGCGTTTTAAGTGCAGAAGCA
1236588 TCTAAGGGTG
Statistics
Matches: 82, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
25 1 0.01
26 43 0.52
27 36 0.44
28 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.33, T:0.21
Consensus pattern (26 bp):
AGGGCGTTTTAAGTGCAGAAGCACTC
Found at i:1236542 original size:80 final size:79
Alignment explanation
Indices: 1236408--1236578 Score: 193
Period size: 80 Copynumber: 2.2 Consensus size: 79
1236398 CGCTCCCTTA
* * * * * * * * *
1236408 GGTGTTCTAAGCGCTGAAGCGTCCAAGGTGTTCTAAGTATAGAAGCGTCCAAGGGCGTTTTAAGT
1 GGTGTTTTAAGTGCAGAAGCGCCCAAGGCGTTCTAAGTACAGAAGCGTCCAAGGGAGTTTCAAGC
1236473 GCAGAAGCACTCA-G
66 GCAGAAGCAC-CAGG
* *
1236487 GGTGTTTTAAGTGCAGAAGCGCCCAGAGGCGTTTTAAGTACAGAAG-GGCTCAAGGGAGTTTCAA
1 GGTGTTTTAAGTGCAGAAGCGCCCA-AGGCGTTCTAAGTACAGAAGCGTC-CAAGGGAGTTTCAA
1236551 GCGCAGAAGCACCAGG
64 GCGCAGAAGCACCAGG
*
1236567 GGCGTTTTAAGT
1 GGTGTTTTAAGT
1236579 ATAGAAGCAT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
79 25 0.32
80 52 0.68
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (79 bp):
GGTGTTTTAAGTGCAGAAGCGCCCAAGGCGTTCTAAGTACAGAAGCGTCCAAGGGAGTTTCAAGC
GCAGAAGCACCAGG
Found at i:1236571 original size:53 final size:52
Alignment explanation
Indices: 1236460--1236686 Score: 165
Period size: 53 Copynumber: 4.3 Consensus size: 52
1236450 AAGCGTCCAA
* * * * *
1236460 GGGCGTTTTAAGTGCAGAAGCACTC-AGGGTGTTTTAAGTGCAGAAGCGCCCAG
1 GGGCGTTTTAAGTACAGAAG-ACTCAAGGGAGTTTCAAGCGCAGAAGC-ACCAG
* *
1236513 AGGCGTTTTAAGTACAGAAGGGCTCAAGGGAGTTTCAAGCGCAGAAGCACCAG
1 GGGCGTTTTAAGTACAGAA-GACTCAAGGGAGTTTCAAGCGCAGAAGCACCAG
* * * *
1236566 GGGCGTTTTAAGTATAGAAG-CATCTAAGGGTGTTTCAAGCACAGAAACACCTA-
1 GGGCGTTTTAAGTACAGAAGAC-TC-AAGGGAGTTTCAAGCGCAGAAGCACC-AG
* * * * * * * *
1236619 AGGTGTCTTAAGTACAAAAGTAC-CTAGGGAAGTTCCAAGCGCAAAAGCACTTAG
1 GGGCGTTTTAAGTACAGAAG-ACTCAAGGG-AGTTTCAAGCGCAGAAGCAC-CAG
*
1236673 GGGCGTTCTAAGTA
1 GGGCGTTTTAAGTA
1236687 TAAAAGCACT
Statistics
Matches: 136, Mismatches: 28, Indels: 19
0.74 0.15 0.10
Matches are distributed among these distances:
51 1 0.01
52 7 0.05
53 96 0.71
54 31 0.23
55 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (52 bp):
GGGCGTTTTAAGTACAGAAGACTCAAGGGAGTTTCAAGCGCAGAAGCACCAG
Found at i:1236611 original size:27 final size:26
Alignment explanation
Indices: 1236538--1236621 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 26
1236528 AGAAGGGCTC
* *
1236538 AAGGGAGTTTCAAGCGCAGAAGCACC
1 AAGGGAGTTTCAAGCACAGAAGCACT
* * * * *
1236564 AGGGGCGTTTTAAGTATAGAAGCATCT
1 AAGGGAGTTTCAAGCACAGAAGCA-CT
* *
1236591 AAGGGTGTTTCAAGCACAGAAACACCT
1 AAGGGAGTTTCAAGCACAGAAGCA-CT
1236618 AAGG
1 AAGG
1236622 TGTCTTAAGT
Statistics
Matches: 43, Mismatches: 14, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
26 18 0.42
27 25 0.58
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.19
Consensus pattern (26 bp):
AAGGGAGTTTCAAGCACAGAAGCACT
Found at i:1236680 original size:27 final size:27
Alignment explanation
Indices: 1236632--1236715 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 27
1236622 TGTCTTAAGT
* * *
1236632 ACAAAAGTACCTAGGGAAGTTCCAAGC
1 ACAAAAGCACTTAGGGACGTTCCAAGC
* * * *
1236659 GCAAAAGCACTTAGGGGCGTTCTAAGT
1 ACAAAAGCACTTAGGGACGTTCCAAGC
*
1236686 ATAAAAGCACTTAGGGACGTTCCAAGC
1 ACAAAAGCACTTAGGGACGTTCCAAGC
1236713 ACA
1 ACA
1236716 GAAACGCCTA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (27 bp):
ACAAAAGCACTTAGGGACGTTCCAAGC
Found at i:1236785 original size:107 final size:107
Alignment explanation
Indices: 1236522--1236793 Score: 284
Period size: 107 Copynumber: 2.6 Consensus size: 107
1236512 GAGGCGTTTT
* * * * *
1236522 AAGTACAGAAGGGCTCAAGGGAGTTTCAAGCGCAGAAGCA-CCAGGGGCGTTTTAAGTATAGAAG
1 AAGTACAGAAGTGCTCATGGGAGTTTCAAGCGCAAAAGCACCCAGGGGCGTTCTAAGTATAAAAG
* * *
1236586 CATCTAAGGGTGTTTCAAGCACAGAAACACCTAAGGTGTCTT
66 CATCTAAGGGCGTTCCAAGCACAGAAACACCTAAGGTGTCTC
* * * **
1236628 AAGTACAAAAGTAC-C-TAGGGAAGTTCCAAGCGCAAAAGCACTTAGGGGCGTTCTAAGTATAAA
1 AAGTACAGAAGTGCTCAT-GGG-AGTTTCAAGCGCAAAAGCACCCAGGGGCGTTCTAAGTATAAA
* * *
1236691 AGCA-CTTAGGGACGTTCCAAGCACAGAAACGCCTAGGGTGT-TCC
64 AGCATCTAAGGG-CGTTCCAAGCACAGAAACACCTAAGGTGTCT-C
* * ** *
1236735 AAGTATAGAAGTGCTCATGGGAGTTTCAAGCACAAAAGCACCCAAAGGCGTTCCAAGTA
1 AAGTACAGAAGTGCTCATGGGAGTTTCAAGCGCAAAAGCACCCAGGGGCGTTCTAAGTA
1236794 CATAAGTGCT
Statistics
Matches: 133, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
105 4 0.03
106 35 0.26
107 89 0.67
108 4 0.03
109 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (107 bp):
AAGTACAGAAGTGCTCATGGGAGTTTCAAGCGCAAAAGCACCCAGGGGCGTTCTAAGTATAAAAG
CATCTAAGGGCGTTCCAAGCACAGAAACACCTAAGGTGTCTC
Found at i:1236801 original size:54 final size:54
Alignment explanation
Indices: 1236730--1236853 Score: 176
Period size: 54 Copynumber: 2.3 Consensus size: 54
1236720 CGCCTAGGGT
* *
1236730 GTTCCAAGTATAGAAGTGCTCATGGGAGTTTCAAGCACAAAAGCACCCAAAGGC
1 GTTCCAAGTACAGAAGTGCTCATGGGAGTTTCAAGCACAAAAACACCCAAAGGC
* * * *
1236784 GTTCCAAGTACATAAGTGCTTATGGGTGTTTCAAGTACAAAAACACCCAAAGGC
1 GTTCCAAGTACAGAAGTGCTCATGGGAGTTTCAAGCACAAAAACACCCAAAGGC
* *
1236838 ATTCCAAGTATAGAAG
1 GTTCCAAGTACAGAAG
1236854 CGTCTAAGAG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (54 bp):
GTTCCAAGTACAGAAGTGCTCATGGGAGTTTCAAGCACAAAAACACCCAAAGGC
Found at i:1240829 original size:12 final size:12
Alignment explanation
Indices: 1240809--1240849 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1240799 AAATATTTAC
*
1240809 ATATGCATACAT
1 ATATACATACAT
1240821 ATATACATACAT
1 ATATACATACAT
* *
1240833 ATATATATATAT
1 ATATACATACAT
1240845 ATATA
1 ATATA
1240850 TAAGTTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (12 bp):
ATATACATACAT
Found at i:1250114 original size:35 final size:35
Alignment explanation
Indices: 1250039--1250293 Score: 284
Period size: 35 Copynumber: 7.3 Consensus size: 35
1250029 TCTCAAGCAC
*
1250039 TTGATTAAAATTGTTTAATTAAG---TTGTGCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
* *
1250072 TTCATTAAATTGTTTAATTAGGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* * *
1250107 TTGATTAAATTTATTTAATCAAGTTATTGGGCTTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
* * * *
1250143 TTAATCAAATTGTTTAATTAAGTTATTAGGCCTTA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
****
1250178 TTGATTAAATTAAAAAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* *
1250213 TTGATTAAATTTGTTTAATCAAATTATTGGGCCTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
* *
1250249 TTAATTAAATTG-TTAATTAAGTTATTGGACCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
*
1250283 TTAATTAAATT
1 TTGATTAAATT
1250294 AAATAATTAC
Statistics
Matches: 184, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
32 15 0.08
33 5 0.03
34 30 0.16
35 77 0.42
36 57 0.31
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:1250168 original size:71 final size:70
Alignment explanation
Indices: 1250066--1250293 Score: 287
Period size: 71 Copynumber: 3.2 Consensus size: 70
1250056 ATTAAGTTGT
* * * *
1250066 GCCTAATTCATTAAATTGTTTAATTAGGTTATTGGGCCTAATTGATTAAATTTATTTAATCAAGT
1 GCCTAATTAATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAA-TTAATTAATTAAGT
1250131 TATTGG
65 TATTGG
* * * * **
1250137 GCTTAATTAATCAAATTGTTTAATTAAGTTATTAGGCCTTATTGATTAAATTAAAAAATTAAGTT
1 GCCTAATTAATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAATTAATTAAGTT
1250202 ATTGG
66 ATTGG
* * * * *
1250207 GCCTAATTGATTAAATTTGTTTAATCAAATTATTGGGCCTAATTAATTAAATT-GTTAATTAAGT
1 GCCTAATTAATTAAA-TTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAATTAATTAAGT
1250271 TATTGG
65 TATTGG
*
1250277 ACCTAATTAATTAAATT
1 GCCTAATTAATTAAATT
1250294 AAATAATTAC
Statistics
Matches: 133, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
69 2 0.02
70 55 0.41
71 76 0.57
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (70 bp):
GCCTAATTAATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTAATTAATTAAGTT
ATTGG
Found at i:1250208 original size:106 final size:105
Alignment explanation
Indices: 1250087--1250314 Score: 341
Period size: 106 Copynumber: 2.2 Consensus size: 105
1250077 TAAATTGTTT
* * *
1250087 AATTAGGTTATTGGGCCTAATTGATTAAATTTATTTAATCAAGTTATTGGGCTTAATTAATCAAA
1 AATTAAGTTATTGGGCCTAATTGATTAAATTTATTTAATCAAATTATTGGGCCTAATTAATCAAA
* *
1250152 TTGTTTAATTAAGTTATTAGG-CCTTATTGATTAAATTAAAA
66 TTG-TTAATTAAGTTATT-GGACCTAATTAATTAAATTAAAA
* *
1250193 AATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATCAAATTATTGGGCCTAATTAATTAAA
1 AATTAAGTTATTGGGCCTAATTGATTAAATTTATTTAATCAAATTATTGGGCCTAATTAATCAAA
*
1250258 TTGTTAATTAAGTTATTGGACCTAATTAATTAAATTAAAT
66 TTGTTAATTAAGTTATTGGACCTAATTAATTAAATTAAAA
*
1250298 AATTACGTTAATTGGGC
1 AATTAAGTT-ATTGGGC
1250315 TTCTTAAGGA
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
104 2 0.02
105 39 0.35
106 70 0.63
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (105 bp):
AATTAAGTTATTGGGCCTAATTGATTAAATTTATTTAATCAAATTATTGGGCCTAATTAATCAAA
TTGTTAATTAAGTTATTGGACCTAATTAATTAAATTAAAA
Found at i:1253608 original size:12 final size:12
Alignment explanation
Indices: 1253578--1253612 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
1253568 CCAGAATAGT
1253578 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1253590 T-TTGCTGCCTC
1 TCTTGCTGCCTC
1253601 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1253613 GGCCATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.00, C:0.40, G:0.17, T:0.43
Consensus pattern (12 bp):
TCTTGCTGCCTC
Found at i:1262900 original size:21 final size:21
Alignment explanation
Indices: 1262849--1262897 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1262839 TACATGTTGA
*
1262849 TTAGTTTGA-TTTAAGTTATT
1 TTAGTTTAATTTTAAGTTATT
*
1262869 TTAGTTTAATTTTATGTTATT
1 TTAGTTTAATTTTAAGTTATT
1262890 TT-GTTTAA
1 TTAGTTTAA
1262898 ATTACTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.63
Consensus pattern (21 bp):
TTAGTTTAATTTTAAGTTATT
Found at i:1275161 original size:25 final size:25
Alignment explanation
Indices: 1275123--1275173 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1275113 TATAGTGATT
* * * *
1275123 TGGCTTTTTTGATACTAATATCCAC
1 TGGCCTTTTCGATACCAACATCCAC
1275148 TGGCCTTTTCGATACCAACATCCAC
1 TGGCCTTTTCGATACCAACATCCAC
1275173 T
1 T
1275174 CCCTTGGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (25 bp):
TGGCCTTTTCGATACCAACATCCAC
Found at i:1276605 original size:110 final size:105
Alignment explanation
Indices: 1276472--1276796 Score: 253
Period size: 110 Copynumber: 3.0 Consensus size: 105
1276462 CCATTTGTGG
* *
1276472 GGGAGTAGAAATACACTAGTGATTCCGAGAGTCCACCCAATGACTCATTCTGAGTGATGAATTAA
1 GGGAGTAAAAATACAC-AGTGATTCCGAGAGTCCACCCAATGACTCATTCTAAGTGATGAATTAA
1276537 CACCTTGTCTGGGGAGTAGAAAAGTACCAATATTACCCTTGACAA
65 CACCTTG-CTGGGGAGTAGAAAAGT--CAATATTACCCTT-ACAA
* * * ** *
1276582 TGGAGTAAAAATACATCAATGATTCTGGAAGAG--CACTTAATGACTCATTCCAAGTGATGAATT
1 GGGAGTAAAAATACA-CAGTGATTC-CG-AGAGTCCACCCAATGACTCATTCTAAGTGATGAATT
* * * * ***
1276645 AATATCGTTGGTGGGGAAAG-AGAATATGTCAATATTACCCTTAGTG
63 AACA-CCTTGCTGGGG--AGTAGAA-AAGTCAATATTACCCTTACAA
* * * * *
1276691 GGGAGTAAAAATACACCAGCGATTTCGAGAGTCCATCCGATGACTCATT-TCAAGTGATGAGTTA
1 GGGAGTAAAAATACA-CAGTGATTCCGAGAGTCCACCCAATGACTCATTCT-AAGTGATGAATTA
* * *
1276755 ACACTCTTGACGGGGGAGTAGAAATACGCCAACATTACCCTT
64 ACAC-CTTG-CTGGGGAGTAGAAA-A-GTCAATATTACCCTT
1276797 GGTGAAGGAG
Statistics
Matches: 166, Mismatches: 34, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
107 4 0.02
108 5 0.03
109 54 0.33
110 84 0.51
111 10 0.06
112 9 0.05
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (105 bp):
GGGAGTAAAAATACACAGTGATTCCGAGAGTCCACCCAATGACTCATTCTAAGTGATGAATTAAC
ACCTTGCTGGGGAGTAGAAAAGTCAATATTACCCTTACAA
Found at i:1283562 original size:2 final size:2
Alignment explanation
Indices: 1283555--1283585 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1283545 NNNNNNNNNN
1283555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1283586 GATGTATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1287677 original size:20 final size:20
Alignment explanation
Indices: 1287640--1287678 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1287630 AAAATTTCTT
**
1287640 GTTTAAGTAATCTTTGAATA
1 GTTTAAGTAATCCATGAATA
*
1287660 GTTTAAGTGATCCATGAAT
1 GTTTAAGTAATCCATGAAT
1287679 GCTTTCAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (20 bp):
GTTTAAGTAATCCATGAATA
Found at i:1288163 original size:63 final size:63
Alignment explanation
Indices: 1288064--1288217 Score: 184
Period size: 63 Copynumber: 2.4 Consensus size: 63
1288054 AATCAATGGT
* ** * *
1288064 TCAAGAATGCAAAGATTGATTCCTAGAAAACAGAAAGCTCTAAAGACACAAAGAATTGATTTC
1 TCAAGAATGCAATGATTGATTCCTTCAAAACAGAAAGCTCTAAAGACACAAAGAAATGACTTC
* * * *
1288127 TCAAGAATGCACTGATCGATTCCTTCAAAACAGAAAGCTTTAAAGGCACAAAGAAATGACTTC
1 TCAAGAATGCAATGATTGATTCCTTCAAAACAGAAAGCTCTAAAGACACAAAGAAATGACTTC
* * *
1288190 TC-TGAAATGCATTGATTGATTCTTTCAA
1 TCAAG-AATGCAATGATTGATTCCTTCAA
1288218 GGCATAAAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
62 1 0.01
63 76 0.99
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.26
Consensus pattern (63 bp):
TCAAGAATGCAATGATTGATTCCTTCAAAACAGAAAGCTCTAAAGACACAAAGAAATGACTTC
Found at i:1299692 original size:62 final size:63
Alignment explanation
Indices: 1299623--1299754 Score: 156
Period size: 63 Copynumber: 2.1 Consensus size: 63
1299613 CCCTTTCAAT
* * * * *
1299623 AATTTTTAAATTTTTATAACTTGCCTTTGCTTTTTAAAAATTTTATAATTTCACTACTACAAA
1 AATTTTAAAATTCTTATAACATACCTTTACTTTTTAAAAATTTTATAATTTCACTACTACAAA
* ** * * * *
1299686 AATTTTAAAATTCTTCTAACATATTTTTATTTTTTAAAAATTTTATAATTTTACTCCTACAAT
1 AATTTTAAAATTCTTATAACATACCTTTACTTTTTAAAAATTTTATAATTTCACTACTACAAA
1299749 AATTTT
1 AATTTT
1299755 TTGTTTAGTA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (63 bp):
AATTTTAAAATTCTTATAACATACCTTTACTTTTTAAAAATTTTATAATTTCACTACTACAAA
Found at i:1306097 original size:18 final size:18
Alignment explanation
Indices: 1306074--1306108 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1306064 TAGTTTATTT
* *
1306074 ATTTAACTTGTTTTCATC
1 ATTTAAATTGCTTTCATC
1306092 ATTTAAATTGCTTTCAT
1 ATTTAAATTGCTTTCAT
1306109 TTATGTTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTTAAATTGCTTTCATC
Found at i:1309552 original size:23 final size:23
Alignment explanation
Indices: 1309522--1309567 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1309512 ATTTGGTGTC
*
1309522 TTTAAAGTGCTGGAAAGAGAAAT
1 TTTAAAGTGCGGGAAAGAGAAAT
*
1309545 TTTAAAGTGCGGGAGAGAGAAAT
1 TTTAAAGTGCGGGAAAGAGAAAT
1309568 CAGGAGCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.04, G:0.30, T:0.24
Consensus pattern (23 bp):
TTTAAAGTGCGGGAAAGAGAAAT
Found at i:1312281 original size:12 final size:12
Alignment explanation
Indices: 1312264--1312290 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1312254 AATCTCATAT
1312264 ATATATATATAC
1 ATATATATATAC
1312276 ATATATATATAC
1 ATATATATATAC
1312288 ATA
1 ATA
1312291 CACATATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:1314148 original size:21 final size:21
Alignment explanation
Indices: 1314117--1314196 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
1314107 CTAGAAAAAT
*
1314117 TGTATCAATACATTATGAACA
1 TGTATCGATACATTATGAACA
* * ** *
1314138 TGTATTGATACATGA-CCATA
1 TGTATCGATACATTATGAACA
* *
1314158 TGTATCGATATATTATAAACA
1 TGTATCGATACATTATGAACA
1314179 TGTATCGATACATT-TGAA
1 TGTATCGATACATTATGAA
1314197 ACAAAATGTA
Statistics
Matches: 44, Mismatches: 14, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTATGAACA
Found at i:1316524 original size:18 final size:18
Alignment explanation
Indices: 1316503--1316540 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1316493 CAATACCTCA
1316503 TCTTGCAATGCAATTTTC
1 TCTTGCAATGCAATTTTC
1316521 TCTTGCAATGCAATTTTC
1 TCTTGCAATGCAATTTTC
1316539 TC
1 TC
1316541 CTACCTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (18 bp):
TCTTGCAATGCAATTTTC
Done.