Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 19 of 320
Found at i:5409442 original size:43 final size:43
Alignment explanation
Indices: 5409381--5409466 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
5409371 TATCCGGCCT
5409381 AAACGTTAAGACTAAGTCTGGAGGTTACATAAAAACGTTTAAG
1 AAACGTTAAGACTAAGTCTGGAGGTTACATAAAAACGTTTAAG
5409424 AAACGTTAAGACTAAGTCTGGAGGTTACATAAAAACGTTTAAG
1 AAACGTTAAGACTAAGTCTGGAGGTTACATAAAAACGTTTAAG
5409467 GGAAAAACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.26
Consensus pattern (43 bp):
AAACGTTAAGACTAAGTCTGGAGGTTACATAAAAACGTTTAAG
Found at i:5411307 original size:32 final size:33
Alignment explanation
Indices: 5411250--5411311 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
5411240 AAAAAATAGT
** *
5411250 AAAAAGAAATAGGGAAAGAATGAAAGAAAACAC
1 AAAAAGAAATAGAAAAAGAAAGAAAGAAAACAC
5411283 AAAAAGAAA-AGAAAAAGAAAGAAAGAAAA
1 AAAAAGAAATAGAAAAAGAAAGAAAGAAAA
5411312 AAAATTAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.74, C:0.03, G:0.19, T:0.03
Consensus pattern (33 bp):
AAAAAGAAATAGAAAAAGAAAGAAAGAAAACAC
Found at i:5412494 original size:19 final size:18
Alignment explanation
Indices: 5412454--5412502 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
5412444 AACACAATTA
* * *
5412454 AACAAATTAAATGGCTGT
1 AACAAATTAATTAGCTGG
5412472 AACAAATTAATTAAGCTGG
1 AACAAATTAATT-AGCTGG
*
5412491 AACATATTAATT
1 AACAAATTAATT
5412503 GCCGAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (18 bp):
AACAAATTAATTAGCTGG
Found at i:5414235 original size:40 final size:40
Alignment explanation
Indices: 5414180--5414296 Score: 189
Period size: 40 Copynumber: 2.9 Consensus size: 40
5414170 CGTTTGGAGC
* * * **
5414180 AAAAGCGCCGGTAAAGAGTGAGCAATAGCGGCGTTTAATT
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
5414220 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
5414260 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTA
1 AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTA
5414297 TAGATAACGC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (40 bp):
AAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAAGG
Found at i:5414441 original size:112 final size:112
Alignment explanation
Indices: 5414244--5414945 Score: 1201
Period size: 112 Copynumber: 6.3 Consensus size: 112
5414234 AGAGTGAGCA
** * *
5414244 TTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCG
5414309 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
*
5414356 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCG
*
5414421 CAAACAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
* *
5414468 TTAGTGGCATTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGCGGCGTTTATAAATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCG
5414533 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
* *
5414580 TTAGTGGCGTTTATTGCAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAGATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCG
5414645 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT-GGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
5414691 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCG
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCG
5414756 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
66 CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
* ** * * *
5414803 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGCTTATAAAAAAATGCC
1 TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTAT-AAATAACGCC
* *
5414868 GCAAATAATACTCCCAGACGGTGCCGTTTTGTGTCCTTTGGGGGGG-C
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
*
5414915 ATTAGTGGCGTTTTTTGTAAAGCGCCGCTAA
1 -TTAGTGGCGTTTATTGTAAAGCGCCGCTAA
5414946 TCTAGGTGTT
Statistics
Matches: 564, Mismatches: 23, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
111 109 0.19
112 374 0.66
113 81 0.14
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (112 bp):
TTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAGCATTAGTGGCGTTTATAAATAACGCCG
CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGAC
Found at i:5415575 original size:12 final size:12
Alignment explanation
Indices: 5415558--5415583 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5415548 ATATATAATT
5415558 GTAAAAGAGGTC
1 GTAAAAGAGGTC
5415570 GTAAAAGAGGTC
1 GTAAAAGAGGTC
5415582 GT
1 GT
5415584 GCTATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.35, T:0.19
Consensus pattern (12 bp):
GTAAAAGAGGTC
Found at i:5416061 original size:84 final size:83
Alignment explanation
Indices: 5415966--5416166 Score: 321
Period size: 84 Copynumber: 2.4 Consensus size: 83
5415956 TAGTTAAACT
* * *
5415966 TTTAGTGGCGTTTTTAAGAAAATGCCACAAATAATGCAATTCCAGACCATGAAAACGGTGTCGTT
1 TTTAGTGGCGTTTTTAA-AAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
5416031 TCTGTTCACAGCTGTAATA
65 TCTGTTCACAGCTGTAATA
* *
5416050 TTTAGTGGCGTTTTTCTAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTTGTT
1 TTTAGTGGCGTTTTT-AAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTT
5416115 TCTGTTCACAGCTGTAATA
65 TCTGTTCACAGCTGTAATA
5416134 TTTAGTGGCGTTTTTACCAAAAACGCCACAAAA
1 TTTAGTGGCGTTTTTA--AAAAACGCCACAAAA
5416167 CGGTGTTAAT
Statistics
Matches: 108, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
84 92 0.85
85 16 0.15
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (83 bp):
TTTAGTGGCGTTTTTAAAAAACGCCACAAAAAATGCAATTCCAGACCACGAAAACGGTGTCGTTT
CTGTTCACAGCTGTAATA
Found at i:5419482 original size:40 final size:40
Alignment explanation
Indices: 5419426--5419706 Score: 319
Period size: 40 Copynumber: 6.5 Consensus size: 40
5419416 AATACATTAC
*
5419426 TTACTAAAATAAATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
*
5419466 TTACTAAAATACATTACTTACTAAAATACATTACTTACATAAATTTGTTTAAA
1 TTACTAAAATACATTACTTACTAAAAT---TT-GTT---TAAA----TTT--A
5419519 TTTATTTCTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 -TTA---CTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
5419563 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTAA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAA--T-TT-A
*
5419607 TTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
5419647 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
* **
5419687 TTACTTAAATATGTTACTTA
1 TTACTAAAATACATTACTTA
5419707 AATTTATTAC
Statistics
Matches: 212, Mismatches: 8, Indels: 42
0.81 0.03 0.16
Matches are distributed among these distances:
40 116 0.55
41 2 0.01
42 2 0.01
43 7 0.03
44 39 0.18
46 3 0.01
47 4 0.02
50 4 0.02
51 3 0.01
53 3 0.01
54 5 0.02
57 24 0.11
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (40 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
Found at i:5419488 original size:57 final size:57
Alignment explanation
Indices: 5419400--5419673 Score: 288
Period size: 57 Copynumber: 4.6 Consensus size: 57
5419390 CGATTGAATG
5419400 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
*
5419457 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTAC-ATAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTA-AAATTTGT
*
5419514 TTAAATTTATTTCTAAAATACATTACTTACTAAAATTTGTTTAAATTTA-TTACTAAAATACATT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAA------TAAA-TTACTTACTAAAAT---TT
*
5419578 ACT
56 -GT
* * ** * * *
5419581 TACTAAAATT-TGT--TTAAATTTATTAATTACTTAAATACATTACTTACTAAAATTTGT
1 T--TAAATTTAT-TACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
5419638 TTAAATTTATTACTAAAATACATTACTTACTAAAAT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAAT
5419674 TTGTTTAAAT
Statistics
Matches: 179, Mismatches: 18, Indels: 40
0.76 0.08 0.17
Matches are distributed among these distances:
55 7 0.04
56 2 0.01
57 108 0.60
58 2 0.01
60 3 0.02
61 13 0.07
63 11 0.06
64 4 0.02
66 2 0.01
67 19 0.11
68 1 0.01
69 7 0.04
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (57 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
Found at i:5419509 original size:17 final size:17
Alignment explanation
Indices: 5419409--5419508 Score: 103
Period size: 17 Copynumber: 5.5 Consensus size: 17
5419399 GTTAAATTTA
5419409 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
5419426 TTACTAAAATAAATTAC
1 TTACTAAAATACATTAC
*
5419443 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
5419466 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
5419483 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
5419500 TTACATAAA
1 TTAC-TAAA
5419509 TTTGTTTAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 17
0.79 0.02 0.19
Matches are distributed among these distances:
16 3 0.04
17 49 0.68
18 4 0.06
23 13 0.18
24 3 0.04
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (17 bp):
TTACTAAAATACATTAC
Found at i:5419632 original size:84 final size:82
Alignment explanation
Indices: 5419483--5419689 Score: 357
Period size: 84 Copynumber: 2.5 Consensus size: 82
5419473 AATACATTAC
5419483 TTACTAAAATACATTACTTAC-ATAAATTTGTTTAAATTTA-T-TTCTAAAATACATTACTTACT
1 TTACTAAAATACATTACTTACTA-AAATTTGTTTAAATTTATTATTCTAAAATACATTACTTACT
5419545 AAAATTTGTTTAAATTTA
65 AAAATTTGTTTAAATTTA
*
5419563 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTAATTACTTAAATACATTACTTAC
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATT-ATT-CTAAAATACATTACTTAC
5419628 TAAAATTTGTTTAAATTTA
64 TAAAATTTGTTTAAATTTA
5419647 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTA
5419690 CTTAAATATG
Statistics
Matches: 121, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
80 38 0.31
81 2 0.02
83 3 0.02
84 78 0.64
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (82 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTATTCTAAAATACATTACTTACTA
AAATTTGTTTAAATTTA
Found at i:5419634 original size:124 final size:124
Alignment explanation
Indices: 5419478--5419706 Score: 388
Period size: 124 Copynumber: 1.8 Consensus size: 124
5419468 ACTAAAATAC
* *
5419478 ATTACTTACTAAAATACATTACTTACATAAATTTGTTTAAATTTATTTCTAAAATACATTACTTA
1 ATTAATTACTAAAATACATTACTTACATAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
5419543 CTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
66 CTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
*
5419602 ATTAATTACTTAAATACATTACTTAC-TAAAATTTGTTTAAATTTATTACTAAAATACATTACTT
1 ATTAATTACTAAAATACATTACTTACAT-AAATTTGTTTAAATTTATTACTAAAATACATTACTT
* **
5419666 ACTAAAATTTGTTTAAATTTATTACTTAAATATGTTACTTA
65 ACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
5419707 AATTTATTAC
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
123 1 0.01
124 97 0.99
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (124 bp):
ATTAATTACTAAAATACATTACTTACATAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
CTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
Found at i:5419696 original size:13 final size:13
Alignment explanation
Indices: 5419678--5419722 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
5419668 TAAAATTTGT
5419678 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
5419691 TTAAATATGTTAC
1 TTAAATTTATTAC
5419704 TTAAATTTATTAC
1 TTAAATTTATTAC
5419717 TTAAAT
1 TTAAAT
5419723 AATTATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (13 bp):
TTAAATTTATTAC
Found at i:5420065 original size:73 final size:73
Alignment explanation
Indices: 5419869--5420092 Score: 439
Period size: 73 Copynumber: 3.1 Consensus size: 73
5419859 TAAAATAAAA
5419869 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
5419934 TTAATAAT
66 TTAATAAT
5419942 TATAAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATT
1 TAT-AAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATT
5420007 ATTAATAAT
65 ATTAATAAT
5420016 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
1 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
5420081 TTAATAAT
66 TTAATAAT
5420089 TATA
1 TATA
5420093 TTAGTAATGT
Statistics
Matches: 150, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
73 77 0.51
74 73 0.49
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (73 bp):
TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
TTAATAAT
Found at i:5420212 original size:26 final size:26
Alignment explanation
Indices: 5420129--5420552 Score: 568
Period size: 26 Copynumber: 17.1 Consensus size: 26
5420119 ATTTTATTAA
5420129 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420155 ATAATACAT-TTAACTTACATTACTTAC
1 ATAATACATAATAACTTACA--ACTTAC
5420182 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420208 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420233 ATAATAC---AT---TT--AACTGAC
1 ATAATACATAATAACTTACAACTTAC
*
5420251 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420276 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420302 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420328 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
5420354 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420380 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420405 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
5420430 ATAATAC---AT---TT--AACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420448 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420473 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
5420499 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
5420525 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
5420551 AT
1 AT
5420553 TTAACTTACA
Statistics
Matches: 363, Mismatches: 16, Indels: 38
0.87 0.04 0.09
Matches are distributed among these distances:
18 27 0.07
20 6 0.02
23 6 0.02
25 107 0.29
26 193 0.53
27 15 0.04
28 9 0.02
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.32
Consensus pattern (26 bp):
ATAATACATAATAACTTACAACTTAC
Found at i:5420468 original size:197 final size:198
Alignment explanation
Indices: 5420131--5420552 Score: 776
Period size: 197 Copynumber: 2.1 Consensus size: 198
5420121 TTTATTAAAT
*
5420131 AATACATAATAACTTACAACTTACATAATACATTTAACTTACATTACTTACATAATACATAATAA
1 AATACATAATAACTTACAACTTACATAATACATATAACTTACA-TACTTACATAATACATAATAA
5420196 CTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATTTAACTGACATAATACATT
65 CTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATTTAACTGACATAATACATT
5420261 TAACTTACAACTTACACAATACATAATAACTTACAACTTACACAATACATAATAACTTACAACTT
130 TAACTTACAACTTACACAATACATAATAACTTACAACTTACACAATACATAATAACTTACAACTT
5420326 ACAC
195 ACAC
*
5420330 AATACATAATAACTTACAACTTACATAATACATAATAACTTACA-ACTTACATAATACAT-TTAA
1 AATACATAATAACTTACAACTTACATAATACAT-ATAACTTACATACTTACATAATACATAATAA
*
5420393 CTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATTTAACTTACATAATACATT
65 CTTACAACTTACATAATACATTTAACTTACAACTTACATAATACATTTAACTGACATAATACATT
5420458 TAACTTACAACTTACACAATACATAATAACTTACAACTTACACAATACATAATAACTTACAACTT
130 TAACTTACAACTTACACAATACATAATAACTTACAACTTACACAATACATAATAACTTACAACTT
*
5420523 ACAT
195 ACAC
5420527 AATACATAATAACTTACAACTTACAT
1 AATACATAATAACTTACAACTTACAT
5420553 TTAACTTACA
Statistics
Matches: 218, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
197 161 0.74
198 15 0.07
199 33 0.15
200 9 0.04
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.32
Consensus pattern (198 bp):
AATACATAATAACTTACAACTTACATAATACATATAACTTACATACTTACATAATACATAATAAC
TTACAACTTACATAATACATTTAACTTACAACTTACATAATACATTTAACTGACATAATACATTT
AACTTACAACTTACACAATACATAATAACTTACAACTTACACAATACATAATAACTTACAACTTA
CAC
Found at i:5420560 original size:11 final size:10
Alignment explanation
Indices: 5420544--5420597 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
5420534 AATAACTTAC
5420544 AACTTACATTT
1 AACTTACA-TT
5420555 AACTTACA-T
1 AACTTACATT
5420564 AA--TACATTT
1 AACTTACA-TT
5420573 AACTTACA-T
1 AACTTACATT
5420582 AACTTACA-T
1 AACTTACATT
5420591 AACTTAC
1 AACTTAC
5420598 CATTGCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:5426085 original size:21 final size:21
Alignment explanation
Indices: 5426054--5426109 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
5426044 CAGAGGCGGA
*
5426054 AGCGA-GGAAGCAGCGACTGC
1 AGCGAGGGAAGCAGAGACTGC
* *
5426074 AGCGAGGGAAGCGGAGGCTGC
1 AGCGAGGGAAGCAGAGACTGC
* *
5426095 AGCAAGAGAAGCAGA
1 AGCGAGGGAAGCAGA
5426110 ACAGAGCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.34, C:0.20, G:0.43, T:0.04
Consensus pattern (21 bp):
AGCGAGGGAAGCAGAGACTGC
Found at i:5441618 original size:21 final size:21
Alignment explanation
Indices: 5441592--5441661 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
5441582 CTACAACTTA
* *
5441592 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
5441613 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
5441634 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
5441655 AAGCAGA
1 AAGCAGA
5441662 ACAGAGCAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.34, C:0.19, G:0.44, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:5441905 original size:14 final size:14
Alignment explanation
Indices: 5441886--5441919 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
5441876 ATTGCTATTG
5441886 GTTGCTTTTGAAAT
1 GTTGCTTTTGAAAT
5441900 GTTGCTTTTGAAAT
1 GTTGCTTTTGAAAT
*
5441914 TTTGCT
1 GTTGCT
5441920 ACAGGAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.21, T:0.53
Consensus pattern (14 bp):
GTTGCTTTTGAAAT
Found at i:5442039 original size:41 final size:42
Alignment explanation
Indices: 5441986--5442274 Score: 186
Period size: 42 Copynumber: 6.9 Consensus size: 42
5441976 GTTTTTGTAT
* * *
5441986 AAAAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTG-TA
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
* *
5442027 AAAAATGCCACTAAAGAACATGTTCTTTAGCGGCGATTAGAAA
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG-TTTGAAA
* * ****
5442070 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCC
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
** * * ****
5442112 TTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTC
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
** * * * * * ****
5442154 CTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
* * ****
5442196 ACAAACGCCGCTAAAGAACATGTTCTTTAGCGGC-TTTTTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
** * * *
5442237 CTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTT
5442275 TTTTTCTAAG
Statistics
Matches: 212, Mismatches: 33, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
41 69 0.33
42 110 0.52
43 33 0.16
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (42 bp):
AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
Found at i:5442139 original size:42 final size:42
Alignment explanation
Indices: 5442075--5442361 Score: 400
Period size: 42 Copynumber: 6.8 Consensus size: 42
5442065 AGAAAAAAAA
**
5442075 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCTTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCTTAAG
* *
5442117 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCTTAAG
* * * * *
5442159 CGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTT-TACAAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT-TAAG
* *
5442201 CGCCGCTAAAGAACATGTTCTTTAGCGGCTTTTTTTC-TAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCTTAAG
*
5442242 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT-TAAG
5442285 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT-TAAG
* *
5442327 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
5442362 GTTTGTAAAC
Statistics
Matches: 221, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
41 36 0.16
42 145 0.66
43 40 0.18
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCTTAAG
Found at i:5442163 original size:84 final size:82
Alignment explanation
Indices: 5441988--5442361 Score: 426
Period size: 84 Copynumber: 4.5 Consensus size: 82
5441978 TTTTGTATAA
* * * *** ** *
5441988 AAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTGTAAAAAATGCCACTAAAGAACATGTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TTTTAAGCGCCGCTAAAGAACATGTTCT
*******
5442053 TTAGCGGCGATTAGAAAAA
65 TTAGCGGCG-TTTTTTTCT
* *
5442072 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCTTAAGCGCCGCTAAAGAACATGTTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT--TTTAAGCGCCGCTAAAGAACATGTTC
*
5442137 TTTAGCGGCGTTTTTTCCT
64 TTTAGCGGCGTTTTTTTCT
* * * *
5442156 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTACAAACGCCGCTAAAGAACATGTTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT--AAGCGCCGCTAAAGAACATGTTC
5442221 TTTAGCGGC-TTTTTTTCT
64 TTTAGCGGCGTTTTTTTCT
*
5442239 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCG--TTTTTT-TAAGCGCCGCTAAAGAACATGTT
5442304 CTTTAGCGGCGTTTTTTTCT
63 CTTTAGCGGCGTTTTTTTCT
* *
5442324 AAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
5442362 GTTTGTAAAC
Statistics
Matches: 251, Mismatches: 31, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
82 2 0.01
83 44 0.18
84 128 0.51
85 76 0.30
86 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (82 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTAAGCGCCGCTAAAGAACATGTTCTT
TAGCGGCGTTTTTTTCT
Found at i:5443296 original size:86 final size:86
Alignment explanation
Indices: 5443183--5443353 Score: 342
Period size: 86 Copynumber: 2.0 Consensus size: 86
5443173 AAACTGTCGT
5443183 TTTTTTTTTTACTTTTTCTCAAATATAATATTAAATGAAAGATTAGAAACGATAAGATTTGAATT
1 TTTTTTTTTTACTTTTTCTCAAATATAATATTAAATGAAAGATTAGAAACGATAAGATTTGAATT
5443248 CATATCATTTAGATATCTTAC
66 CATATCATTTAGATATCTTAC
5443269 TTTTTTTTTTACTTTTTCTCAAATATAATATTAAATGAAAGATTAGAAACGATAAGATTTGAATT
1 TTTTTTTTTTACTTTTTCTCAAATATAATATTAAATGAAAGATTAGAAACGATAAGATTTGAATT
5443334 CATATCATTTAGATATCTTA
66 CATATCATTTAGATATCTTA
5443354 ACGTGTTTTA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (86 bp):
TTTTTTTTTTACTTTTTCTCAAATATAATATTAAATGAAAGATTAGAAACGATAAGATTTGAATT
CATATCATTTAGATATCTTAC
Found at i:5445475 original size:21 final size:23
Alignment explanation
Indices: 5445449--5445496 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 23
5445439 ATTTCACGTC
5445449 AAAAAATAATT-TAAAA-TTAT-
1 AAAAAATAATTCTAAAATTTATG
5445469 AAAAAA-AATTCTAAAATTTATG
1 AAAAAATAATTCTAAAATTTATG
5445491 AAAAAA
1 AAAAAA
5445497 ATTCTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.16
20 11 0.44
21 4 0.16
22 6 0.24
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAAAATAATTCTAAAATTTATG
Found at i:5445497 original size:21 final size:20
Alignment explanation
Indices: 5445449--5445501 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
5445439 ATTTCACGTC
5445449 AAAAAATAATT-TAAAATTAT
1 AAAAAA-AATTCTAAAATTAT
5445469 AAAAAAAATTCTAAAATTTAT
1 AAAAAAAATTCTAAAA-TTAT
*
5445490 GAAAAAAATTCT
1 AAAAAAAATTCT
5445502 TGAAAAACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.13
20 11 0.37
21 15 0.50
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAAAAAATTCTAAAATTAT
Found at i:5446588 original size:11 final size:11
Alignment explanation
Indices: 5446572--5446596 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5446562 GCCATTACCC
5446572 TATAAATATTT
1 TATAAATATTT
5446583 TATAAATATTT
1 TATAAATATTT
5446594 TAT
1 TAT
5446597 TTCTTCTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATAAATATTT
Found at i:5447211 original size:14 final size:14
Alignment explanation
Indices: 5447192--5447222 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5447182 CGGTGGTCTG
5447192 TTTCTTCTTCTTTT
1 TTTCTTCTTCTTTT
*
5447206 TTTCTTTTTCTTTT
1 TTTCTTCTTCTTTT
5447220 TTT
1 TTT
5447223 TTAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTCTTCTTCTTTT
Found at i:5452870 original size:26 final size:26
Alignment explanation
Indices: 5452841--5452898 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
5452831 CAAATACAAA
* * **
5452841 TACATTCTTTAACAAGAATAATTCAT
1 TACATTATTTAACAAAAATAATGAAT
5452867 TACATTATTTAACAAAAATAATGAAT
1 TACATTATTTAACAAAAATAATGAAT
5452893 TACATT
1 TACATT
5452899 GAATGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (26 bp):
TACATTATTTAACAAAAATAATGAAT
Found at i:5453659 original size:24 final size:23
Alignment explanation
Indices: 5453609--5453673 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
5453599 TTTAAATTTA
* * *
5453609 AATTAAAAAATTTAGAAATAAACT
1 AATT-AAAATTTTAAAAATAAAAT
5453633 AATTAAAATTTTAAAAATAAAAAT
1 AATTAAAATTTTAAAAAT-AAAAT
5453657 AATTCTAAAATTTTAAA
1 AA-T-TAAAATTTTAAA
5453674 GAATTGAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 12 0.34
24 10 0.29
25 1 0.03
26 12 0.34
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (23 bp):
AATTAAAATTTTAAAAATAAAAT
Found at i:5474499 original size:205 final size:205
Alignment explanation
Indices: 5473919--5474501 Score: 916
Period size: 205 Copynumber: 2.8 Consensus size: 205
5473909 TAGGCCGCAG
** *
5473919 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCTAGATCCAAGATGATTTGGCATCCTTGT
1 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAG-AAGATCCAAGATGATTTGGCATCCTTGT
* * *
5473984 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACAATGAAGCAAATC
65 GCTTACAAGGAGCGAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
* * * *
5474049 TAAGATGATGTGGCATCTCTGTATTGTCAGAGAACGAATCAAAATCTGGCATCTCCACTTCGACG
130 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAATCTGGCATCTCCACTTCAACG
5474114 GGGAACAGATA
195 GGGAACAGATA
* * *
5474125 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGGAGATCTAAGATGATTTGGCATTCTTGTG
1 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGTG
*
5474190 CTTGCAAGGAGCGAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCT
66 CTTACAAGGAGCGAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCT
* * * *
5474255 AAGATAATTTGGCATCTCTATATTGTTAGAGAACAAATCGAAATCTGGCATCTCCGCTTCAACGG
131 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAATCTGGCATCTCCACTTCAACGG
*
5474320 GGAGCAGATA
196 GGAACAGATA
* *
5474330 CATAGCAGATCTCACCTTTAGATGTTTATACTGAAGAAGATCCAAGATAATTTGGCATCCTTGTG
1 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGTG
* * * *
5474395 CTTACAAGGAGCGAATCGAAGACATTGTTG-TATTGGCTTTCATGTGTTTACGCTGAAGCAAATC
66 CTTACAAGGAGCGAATCGAAGACATAGCTGAT-TTGGCTTTCACGTGTTTACGATGAAGCAAATC
5474459 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAA
130 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAA
5474502 GAAGCAGATT
Statistics
Matches: 345, Mismatches: 31, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
204 1 0.00
205 310 0.90
206 34 0.10
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (205 bp):
CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGTG
CTTACAAGGAGCGAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCT
AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAATCTGGCATCTCCACTTCAACGG
GGAACAGATA
Found at i:5476304 original size:43 final size:43
Alignment explanation
Indices: 5476172--5476338 Score: 126
Period size: 46 Copynumber: 3.6 Consensus size: 43
5476162 AACATATATC
*
5476172 ATTACTTATTATTTATTATA-ATATATTTTTATCACA-TAATGTTATAT
1 ATTA-TTATTATTTATTATATAT-TATTTTTA-CAAACT-AT-TT-TAT
* *
5476219 ATCTTTATATTATATATTATATAATTA-TTTTACTATACACTATTTTAT
1 AT-TAT-TATTATTTATTATAT-ATTATTTTTAC-A-A-ACTATTTTAT
5476267 ATTATTATTATTTATTATATATTATTTTTACAAACTATTATTAT
1 ATTATTATTATTTATTATATATTATTTTTACAAACTATT-TTAT
*
5476311 TTTACATTATTATTTA-TATATTATTATT
1 ATT--ATTATTATTTATTATA-TATTATT
5476339 ATATTTTTAC
Statistics
Matches: 101, Mismatches: 6, Indels: 27
0.75 0.04 0.20
Matches are distributed among these distances:
43 6 0.06
44 7 0.07
45 9 0.09
46 38 0.38
47 6 0.06
48 25 0.25
49 4 0.04
50 5 0.05
51 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (43 bp):
ATTATTATTATTTATTATATATTATTTTTACAAACTATTTTAT
Found at i:5476321 original size:16 final size:16
Alignment explanation
Indices: 5476259--5476324 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
5476249 TACTATACAC
*
5476259 TATTTTATATTATTAT
1 TATTTTACATTATTAT
5476275 TA-TTT--ATTATATAT
1 TATTTTACATTAT-TAT
*
5476289 TATTTTTACAAACTATTAT
1 TA-TTTTAC--ATTATTAT
5476308 TATTTTACATTATTAT
1 TATTTTACATTATTAT
5476324 T
1 T
5476325 TATATATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
13 5 0.12
14 5 0.12
15 3 0.07
16 13 0.32
18 6 0.15
19 5 0.12
20 4 0.10
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTTACATTATTAT
Found at i:5483100 original size:50 final size:50
Alignment explanation
Indices: 5483025--5483126 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
5483015 TTCCTGGCCA
* * * *
5483025 TGTGACCCTAAATCCAAAACAGTGAGTTACACGGCTTGGACATACGCTCG
1 TGTGACCCTAAATCCAAAACAGTGAGTTACACAGCCTAGACATACGCCCG
*
5483075 TGTGACCTTAAATCCAAAACAGTGAGTTACACAGCCTAGACATACGCCCG
1 TGTGACCCTAAATCCAAAACAGTGAGTTACACAGCCTAGACATACGCCCG
5483125 TG
1 TG
5483127 CCTTTAGCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (50 bp):
TGTGACCCTAAATCCAAAACAGTGAGTTACACAGCCTAGACATACGCCCG
Found at i:5486513 original size:21 final size:22
Alignment explanation
Indices: 5486463--5486505 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5486453 TTTATGAATA
*
5486463 ATAAAATAAAACATAATTTATG
1 ATAAAATAAAACATAATATATG
5486485 ATAAAATAAAA-ATAATATATG
1 ATAAAATAAAACATAATATATG
5486506 GAATAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
ATAAAATAAAACATAATATATG
Found at i:5486539 original size:12 final size:12
Alignment explanation
Indices: 5486524--5486548 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5486514 TATAAAAATG
5486524 TATAATATATAA
1 TATAATATATAA
5486536 TATAATATATAA
1 TATAATATATAA
5486548 T
1 T
5486549 GGTATATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAATATATAA
Found at i:5486569 original size:12 final size:11
Alignment explanation
Indices: 5486494--5486577 Score: 58
Period size: 10 Copynumber: 8.3 Consensus size: 11
5486484 GATAAAATAA
5486494 AAATAATATAT
1 AAATAATATAT
*
5486505 GGAATAATATAT
1 -AAATAATATAT
*
5486517 AAA-AATGTAT
1 AAATAATATAT
5486527 -AAT-ATATA-
1 AAATAATATAT
*
5486535 ATATAATATAT
1 AAATAATATAT
**
5486546 -AATGGTATAT
1 AAATAATATAT
5486556 -AAT-A-ATAT
1 AAATAATATAT
5486564 AAATAATATAT
1 AAATAATATAT
5486575 AAA
1 AAA
5486578 GAAAAATAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
8 4 0.07
9 11 0.20
10 22 0.39
11 9 0.16
12 10 0.18
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (11 bp):
AAATAATATAT
Found at i:5486586 original size:29 final size:28
Alignment explanation
Indices: 5486492--5486592 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
5486482 ATGATAAAAT
*
5486492 AAAAATAATATATGGAATAATATATAAA-
1 AAAAATAATATAT-AAATAATATATAAAG
** *
5486520 AATGTATAATATATAATATAATATATAATG
1 AA-AAATAATATATAA-ATAATATATAAAG
** *
5486550 GTATATAATAATATAAATAATATATAAAG
1 AAAAATAAT-ATATAAATAATATATAAAG
5486579 AAAAATAATATATA
1 AAAAATAATATATA
5486593 CTATTTTACA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
28 8 0.14
29 44 0.76
30 6 0.10
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (28 bp):
AAAAATAATATATAAATAATATATAAAG
Found at i:5488197 original size:44 final size:44
Alignment explanation
Indices: 5488147--5488634 Score: 620
Period size: 44 Copynumber: 11.1 Consensus size: 44
5488137 CAAATGTCAG
* *
5488147 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * *
5488191 ATCTGCTATCTTCTAGCTGCTCTCTGACAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * *
5488235 ATCTGCTATCTTCTAGCTGCTCTCTGACAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * * *
5488279 ATCTGTCATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * *
5488323 ATCTATCATCTTCGATCTGCTCTCTGTCAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * * * *
5488367 ATCTGTCATCTTCGATTTGCTCTCAG-TAATGCAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * * *
5488410 ATCTGTTATGTTCGATCTGCTCTCTGTCAATATAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* **
5488454 ACCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACACCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * *
5488498 ACCTGTTATCTTCAATCTGCTCTCTGACAATATAGAG-TCGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAT-GCCAA
* * * *
5488542 ACCTGTTATCTTCGATCTGCTCTTTAACAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
* * *
5488586 ACCTGTTATCTTCGATTTGCTCTCTGACAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
5488630 ATCTG
1 ATCTG
5488635 CTTTCGGTGA
Statistics
Matches: 397, Mismatches: 44, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
43 37 0.09
44 360 0.91
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (44 bp):
ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGATGCCAA
Found at i:5488631 original size:263 final size:263
Alignment explanation
Indices: 5488147--5488634 Score: 717
Period size: 263 Copynumber: 1.9 Consensus size: 263
5488137 CAAATGTCAG
* * *
5488147 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGATGCCAAATCTGCTATCTTCTAGCTGCT
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAACCTGCTATCTTCGAGCTGCT
** * *
5488212 CTCTGACAATACAGAGATGCCAAATCTGCTATCTTCTAGCTGCTCTCTGACAATACAGAGATGCC
66 CTCTGACAATACAGAGACACCAAACCTGCTATCTTCAAGCTGCTCTCTGACAATACAGAGATGCC
* * ** *
5488277 AAATCTGTCATTTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTATCATCTTCGATCTG
131 AAACCTGTCATCTTCGATCTGCTCTCTAACAATACAGAGACGCCAAACCTATCATCTTCGATCTG
* *
5488342 CTCTCTGTCAATACAGAGATGCCAAATCTGTCATCTTCGATTTGCTCTCAGTAATGCAGAGATGC
196 CTCTCTGACAATACAGAGACGCCAAATCTGTCATCTTCGATTTGCTCTCAGTAATGCAGAGATGC
5488407 CAA
261 CAA
* * * * *
5488410 ATCTGTTATGTTCGATCTGCTCTCTGTCAATATAGAGACGCCAAACCTGTTATCTTCGATCTGCT
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAACCTGCTATCTTCGAGCTGCT
* * *
5488475 CTCTGACAATACAGAGACACCAAACCTGTTATCTTCAATCTGCTCTCTGACAATATAGAG-TCGC
66 CTCTGACAATACAGAGACACCAAACCTGCTATCTTCAAGCTGCTCTCTGACAATACAGAGAT-GC
* * * * *
5488539 CAAACCTGTTATCTTCGATCTGCTCTTTAACAATACAGAGACGCCAAACCTGTTATCTTCGATTT
130 CAAACCTGTCATCTTCGATCTGCTCTCTAACAATACAGAGACGCCAAACCTATCATCTTCGATCT
5488604 GCTCTCTGACAATACAGAGACGCCAAATCTG
195 GCTCTCTGACAATACAGAGACGCCAAATCTG
5488635 CTTTCGGTGA
Statistics
Matches: 197, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
262 1 0.01
263 196 0.99
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (263 bp):
ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAACCTGCTATCTTCGAGCTGCT
CTCTGACAATACAGAGACACCAAACCTGCTATCTTCAAGCTGCTCTCTGACAATACAGAGATGCC
AAACCTGTCATCTTCGATCTGCTCTCTAACAATACAGAGACGCCAAACCTATCATCTTCGATCTG
CTCTCTGACAATACAGAGACGCCAAATCTGTCATCTTCGATTTGCTCTCAGTAATGCAGAGATGC
CAA
Found at i:5491387 original size:19 final size:19
Alignment explanation
Indices: 5491363--5491460 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
5491353 AATCTTTAAG
5491363 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5491382 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5491401 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5491418 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5491437 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
5491458 GAT
1 GAT
5491461 CTTGTAATCT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5491393 original size:36 final size:35
Alignment explanation
Indices: 5491353--5491460 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 35
5491343 ATGGAAATAT
5491353 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
5491389 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
5491425 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
5491461 CTTGTAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 28 0.46
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:5495624 original size:7 final size:7
Alignment explanation
Indices: 5495614--5495646 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5495604 CATCAATTTC
*
5495614 AAAAAAA
1 AAAAAAG
5495621 AAAAAAG
1 AAAAAAG
5495628 AAAAAAG
1 AAAAAAG
5495635 AAAAAAG
1 AAAAAAG
5495642 AAAAA
1 AAAAA
5495647 GAAGAAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:5497163 original size:9 final size:9
Alignment explanation
Indices: 5497146--5497195 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
5497136 CTTCTATTTC
*
5497146 AAAAAAAAA
1 AAAAAAAAG
5497155 AAGAAAAAAG
1 AA-AAAAAAG
5497165 AAAAAAAA-
1 AAAAAAAAG
* *
5497173 CAATAAAAG
1 AAAAAAAAG
5497182 AAAAAAAAG
1 AAAAAAAAG
5497191 AAAAA
1 AAAAA
5497196 TGGAGAGGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
8 6 0.18
9 20 0.59
10 8 0.24
ACGTcount: A:0.88, C:0.02, G:0.08, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:5497170 original size:17 final size:17
Alignment explanation
Indices: 5497148--5497195 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
5497138 TCTATTTCAA
5497148 AAAAAAAAAGAAAAAAG
1 AAAAAAAAAGAAAAAAG
*
5497165 AAAAAAAACA-ATAAAAG
1 AAAAAAAA-AGAAAAAAG
5497182 -AAAAAAAAGAAAAA
1 AAAAAAAAAGAAAAA
5497196 TGGAGAGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 1 0.04
16 11 0.41
17 14 0.52
18 1 0.04
ACGTcount: A:0.88, C:0.02, G:0.08, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAG
Found at i:5498326 original size:132 final size:132
Alignment explanation
Indices: 5498086--5499049 Score: 1604
Period size: 132 Copynumber: 7.3 Consensus size: 132
5498076 TAGAGAAACA
* * * * * *
5498086 AGATTTGGGATCCCTGTGTTTATAGGGAATAGATTGAAGATAGTAGATCTAACACTCTTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* *
5498151 ACAGCGAAGCAGATCGAAGATTTCAGGATGGCATCCCTGTGTTTATAGGGAACAAGTTGAATATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
*
5498216 GA
131 GC
* * *
5498218 AGATTTGGCATCCCTGTGTTTATAGGGAATAGATCGAAGATAGCAGATCTGATACTCCTGTGTTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
*
5498283 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTATGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
5498348 GC
131 GC
* *
5498350 AGATTTGGAATCCTTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
*
5498415 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAAAAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
5498480 GC
131 GC
* * *
5498482 AGATTTGGCATCCCTATGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTTCTGTACTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
5498547 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
5498612 GC
131 GC
5498614 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
*
5498679 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
5498744 GC
131 GC
* * * * * *
5498746 AGATTTAGCATCCCTGTGTTTATAGAGAACAAATCGAAGATAGCAGATCTAACACTCCTATGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* *
5498811 ACAGCGAAGCAGATCGAAGATTTCAGCATAGCATCCCTGTGTTTATAGGGAACAAATTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
5498876 GC
131 GC
* * * ** *
5498878 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGTAGATTTGACGTTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
5498943 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
*
5499008 GT
131 GC
*
5499010 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGA
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGA
5499050 GGATTCTATT
Statistics
Matches: 784, Mismatches: 48, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 784 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GC
Found at i:5499434 original size:14 final size:14
Alignment explanation
Indices: 5499415--5499443 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5499405 TTTTTTACTT
5499415 TGTTATATAGATTA
1 TGTTATATAGATTA
5499429 TGTTATATAGATTA
1 TGTTATATAGATTA
5499443 T
1 T
5499444 TATTTATCTA
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:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TGTTATATAGATTA
Found at i:5499544 original size:21 final size:21
Alignment explanation
Indices: 5499520--5499560 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5499510 AGATTGATTA
* *
5499520 TATAGATATATCCAACTTTTC
1 TATAGAGATATACAACTTTTC
*
5499541 TATAGAGATATAGAACTTTT
1 TATAGAGATATACAACTTTT
5499561 ATCAGTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (21 bp):
TATAGAGATATACAACTTTTC
Found at i:5499592 original size:21 final size:21
Alignment explanation
Indices: 5499568--5499607 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5499558 TTTATCAGTA
*
5499568 ATTCCATTTCATTTATATTAT
1 ATTCCATATCATTTATATTAT
*
5499589 ATTCTATATCATTTATATT
1 ATTCCATATCATTTATATT
5499608 TTGAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTCCATATCATTTATATTAT
Found at i:5499811 original size:44 final size:44
Alignment explanation
Indices: 5499763--5499857 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 44
5499753 GATTTCAGTA
* ** * *
5499763 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAACAGATC
*
5499807 TGGCATTCCTGTGTTTATAGGGAACAAATCAAAGATAACAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAACAGATC
5499851 TGGCATC
1 TGGCATC
5499858 TCCATTTCGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (44 bp):
TGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAACAGATC
Found at i:5500454 original size:19 final size:19
Alignment explanation
Indices: 5500430--5500527 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
5500420 AATCTTTAAG
5500430 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5500449 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5500468 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5500485 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5500504 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
5500525 GAT
1 GAT
5500528 CTTGTAATCT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5500460 original size:36 final size:35
Alignment explanation
Indices: 5500420--5500527 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 35
5500410 ATGGAAATAT
5500420 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
5500456 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
5500492 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
5500528 CTTGTAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 28 0.46
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:5508073 original size:39 final size:39
Alignment explanation
Indices: 5507998--5508323 Score: 438
Period size: 39 Copynumber: 8.3 Consensus size: 39
5507988 ATGGAATATC
* * * * *
5507998 GATTATACTGAATGATTTGTTCAAACGAACAATATCCACT
1 GATTATGCTGAATG-CTTGCTCAAACGAGCATTATCCACT
** * *
5508038 GATTATATTGAATGTTTGCTCAAATGAGCATTATCCACT
1 GATTATGCTGAATGCTTGCTCAAACGAGCATTATCCACT
*
5508077 GATTATACTGAATGCTTGCTCAAACGAG-ATTATCCACT
1 GATTATGCTGAATGCTTGCTCAAACGAGCATTATCCACT
* *
5508115 AATTATGTTGAATGCTTGCTCAAAACGAGCATTATCCACT
1 GATTATGCTGAATGCTTGCTC-AAACGAGCATTATCCACT
* *
5508155 AATTATGCTGAATGCTTGCTCAAACGAGCAATATCCACT
1 GATTATGCTGAATGCTTGCTCAAACGAGCATTATCCACT
* *
5508194 GATTATGCTGAATGCTTGCTCAAATGAGCAATATCCACT
1 GATTATGCTGAATGCTTGCTCAAACGAGCATTATCCACT
* *
5508233 GATTATGCTGAATGCTTGCTCAAACAAGCACTATCCACT
1 GATTATGCTGAATGCTTGCTCAAACGAGCATTATCCACT
* *
5508272 AATCATGCTGAATGCTTGCTCAAACGAGCATTATCCACT
1 GATTATGCTGAATGCTTGCTCAAACGAGCATTATCCACT
*
5508311 GATTATACTGAAT
1 GATTATGCTGAAT
5508324 AAGATTTTTT
Statistics
Matches: 259, Mismatches: 25, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
38 28 0.11
39 188 0.73
40 43 0.17
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (39 bp):
GATTATGCTGAATGCTTGCTCAAACGAGCATTATCCACT
Found at i:5512483 original size:46 final size:46
Alignment explanation
Indices: 5512417--5512536 Score: 161
Period size: 46 Copynumber: 2.6 Consensus size: 46
5512407 TGTTATACGT
*
5512417 GTAACGTGTTGCTAAGTGGATATACCACGATTACACATATTGA-TA
1 GTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATTA
* * * *
5512462 CGTAACGTGGTGCTAAATGGATATGCCACGGTTACATATATTGATTTA
1 -GTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTGA-TTA
*
5512510 TTAACGTGGTGCTAAGTGGATATACCA
1 GTAACGTGGTGCTAAGTGGATATACCA
5512537 TGGTTAAACA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
46 38 0.59
47 24 0.38
48 2 0.03
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (46 bp):
GTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTGATTA
Found at i:5512562 original size:38 final size:38
Alignment explanation
Indices: 5512511--5512587 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
5512501 ATTGATTTAT
*
5512511 TAACGTGGTGCTAAGTGGATATACCATGGTTAAACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
* *
5512549 TAACGTGGTGCTAAGTGGATATGCCACGGTTATACATG
1 TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
5512587 T
1 T
5512588 TAATTTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTAAACATG
Found at i:5512619 original size:131 final size:131
Alignment explanation
Indices: 5512385--5512621 Score: 316
Period size: 131 Copynumber: 1.8 Consensus size: 131
5512375 TGGAAAAACA
* * *
5512385 TGGTGCTAAGTGGATATACCACTGTTATACGTGTAACGTGTTGCTAAGTGGATATACCACGATTA
1 TGGTGCTAAGTGGATATACCACTGTTAAACATGTAACGTGGTGCTAAGTGGATATACCACGATTA
* * * *
5512450 CACATATTGATACGTAACGTGGTGCTAAATGGATATGCCACGGTTACATATATTGATTTATTAAC
66 CACATATTAATACGAAAAGTGGCGCTAAATGGATATGCCACGGTTACATATATTGATTTATTAAC
5512515 G
131 G
* *
5512516 TGGTGCTAAGTGGATATACCA-TGGTTAAACATGTAACGTGGTGCTAAGTGGATATGCCACGGTT
1 TGGTGCTAAGTGGATATACCACT-GTTAAACATGTAACGTGGTGCTAAGTGGATATACCACGATT
* * ** *
5512580 ATACATGTTAATTTGAAAAGTGGCGCTAAGTGCG-TATGCCAC
65 ACACATATTAATACGAAAAGTGGCGCTAAATG-GATATGCCAC
5512622 AATTTCATGT
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
130 1 0.01
131 88 0.98
132 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (131 bp):
TGGTGCTAAGTGGATATACCACTGTTAAACATGTAACGTGGTGCTAAGTGGATATACCACGATTA
CACATATTAATACGAAAAGTGGCGCTAAATGGATATGCCACGGTTACATATATTGATTTATTAAC
G
Found at i:5515014 original size:50 final size:50
Alignment explanation
Indices: 5514957--5515068 Score: 215
Period size: 50 Copynumber: 2.2 Consensus size: 50
5514947 TTATTTTATT
5514957 TTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGA
1 TTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGA
5515007 TTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGA
1 TTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGA
*
5515057 TTAGGATAAGGT
1 TTAGAATAAGGT
5515069 GTTTCAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (50 bp):
TTAGAATAAGGTTTTTTAAACCTTATTAAACTCCATCTATTTTATATTGA
Found at i:5515256 original size:5 final size:5
Alignment explanation
Indices: 5515222--5515255 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
5515212 TGTGTGTTCT
5515222 TTTTA TTTTTA TTTTA TTTTA TTTTA TTTT- TTTT
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5515256 TCACAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTA
Found at i:5530862 original size:18 final size:18
Alignment explanation
Indices: 5530841--5530879 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5530831 ATGGAAATAG
* *
5530841 AAATAAAAATAAAAGGAA
1 AAATAAAAACAAAAAGAA
5530859 AAATAAAAACAAAAAGAA
1 AAATAAAAACAAAAAGAA
5530877 AAA
1 AAA
5530880 GAACTAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (18 bp):
AAATAAAAACAAAAAGAA
Found at i:5533810 original size:17 final size:17
Alignment explanation
Indices: 5533790--5533823 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5533780 GTGGGTATGT
5533790 TTAGGTAGGTTCGCGGA
1 TTAGGTAGGTTCGCGGA
5533807 TTAGGTAGGTTCGCGGA
1 TTAGGTAGGTTCGCGGA
5533824 GCCATAGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.41, T:0.29
Consensus pattern (17 bp):
TTAGGTAGGTTCGCGGA
Found at i:5536994 original size:31 final size:31
Alignment explanation
Indices: 5536959--5537025 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
5536949 ACTCAGCGTA
*
5536959 TACTGGGCCGAAGCCTTTTCATATTTCATAT
1 TACTGGGCCGAAGCCTTTACATATTTCATAT
5536990 TACTGGGCCGAAGCCTTTACATATTTCATAT
1 TACTGGGCCGAAGCCTTTACATATTTCATAT
5537021 TACTG
1 TACTG
5537026 TAAACGGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (31 bp):
TACTGGGCCGAAGCCTTTACATATTTCATAT
Found at i:5537327 original size:26 final size:25
Alignment explanation
Indices: 5537230--5537327 Score: 110
Period size: 25 Copynumber: 3.9 Consensus size: 25
5537220 CTGGAGGCCT
*
5537230 AGCCTCTTTTAAT-AACTGGGG-AAA
1 AGCC-CTTTTGATAAACTGGGGCAAA
5537254 AGCCCTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
* * **
5537279 AGCCTTTTTAATAAACTAAGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
*
5537304 AGCCCTTTTCGGTAAACTGGGGCA
1 AGCCCTTTT-GATAAACTGGGGCA
5537328 TAGGCCTTCT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
23 7 0.11
24 12 0.20
25 32 0.52
26 10 0.16
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:5537428 original size:20 final size:20
Alignment explanation
Indices: 5537385--5537431 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5537375 TTATGAATAC
*
5537385 ATCATCTGCATACCATACAT
1 ATCATGTGCATACCATACAT
*
5537405 ATCATGTGCATATCATATCA-
1 ATCATGTGCATACCATA-CAT
5537425 ATCATGT
1 ATCATGT
5537432 ATATCAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATACCATACAT
Found at i:5543934 original size:18 final size:18
Alignment explanation
Indices: 5543911--5543948 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5543901 CGCAACGTCA
5543911 TAGCCTAGCTACAGTTCT
1 TAGCCTAGCTACAGTTCT
5543929 TAGCCTAGCTACAGTTCT
1 TAGCCTAGCTACAGTTCT
5543947 TA
1 TA
5543949 CTCCTACCGT
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:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (18 bp):
TAGCCTAGCTACAGTTCT
Found at i:5545167 original size:31 final size:31
Alignment explanation
Indices: 5545094--5545171 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
5545084 TTTCATATTT
** * *
5545094 CATATTTCATAACACTGGGCCGAAGCCTTTT
1 CATATTTCATATTACTAGGCCGAAGCCTTTA
5545125 CATATTTCATATTACTAGGCCGAAGCCTTTA
1 CATATTTCATATTACTAGGCCGAAGCCTTTA
5545156 CATATTTCATATTACT
1 CATATTTCATATTACT
5545172 GTAAACGGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (31 bp):
CATATTTCATATTACTAGGCCGAAGCCTTTA
Found at i:5545416 original size:24 final size:24
Alignment explanation
Indices: 5545376--5545456 Score: 121
Period size: 23 Copynumber: 3.4 Consensus size: 24
5545366 CTGGAGGCCT
5545376 AGCCTCTTTTAAT-AACTGGGGCAA
1 AGCC-CTTTTAATAAACTGGGGCAA
*
5545400 AGCCCTTTTGATAAACTGGGGCAA
1 AGCCCTTTTAATAAACTGGGGCAA
5545424 AG-CCTTTTAATAAACTGGGGCAAA
1 AGCCCTTTTAATAAACTGGGGC-AA
5545448 AGCCCTTTT
1 AGCCCTTTT
5545457 TCGGTAAACT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
23 25 0.48
24 21 0.40
25 6 0.12
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
AGCCCTTTTAATAAACTGGGGCAA
Found at i:5545646 original size:25 final size:25
Alignment explanation
Indices: 5545618--5545665 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5545608 ATAATTAAAC
* * *
5545618 CCTAGGGGTATAATAGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
5545643 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
5545666 CATAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:5557930 original size:18 final size:18
Alignment explanation
Indices: 5557907--5557944 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5557897 CGCAACGTCA
5557907 TAGCCTAGCTACAGTTCT
1 TAGCCTAGCTACAGTTCT
5557925 TAGCCTAGCTACAGTTCT
1 TAGCCTAGCTACAGTTCT
5557943 TA
1 TA
5557945 CTCCTACCGT
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:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (18 bp):
TAGCCTAGCTACAGTTCT
Found at i:5559166 original size:31 final size:31
Alignment explanation
Indices: 5559093--5559170 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
5559083 TTTCATATTT
** * *
5559093 CATATTTCATAACACTGGGCCGAAGCCTTTT
1 CATATTTCATATTACTAGGCCGAAGCCTTTA
5559124 CATATTTCATATTACTAGGCCGAAGCCTTTA
1 CATATTTCATATTACTAGGCCGAAGCCTTTA
5559155 CATATTTCATATTACT
1 CATATTTCATATTACT
5559171 GTAAACGGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (31 bp):
CATATTTCATATTACTAGGCCGAAGCCTTTA
Found at i:5559415 original size:24 final size:25
Alignment explanation
Indices: 5559388--5559483 Score: 115
Period size: 25 Copynumber: 3.8 Consensus size: 25
5559378 CCTCTTTAAT
5559388 AACTGGGGC-AAAGCCCTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTGATA
* *
5559412 AACTGGGGCAAAAGCCTTTTTAATA
1 AACTGGGGCAAAAGCCCTTTTGATA
*
5559437 AACTGGGGCAAAAGCCCTTTTTCGGTA
1 AACTGGGGCAAAAGCCC-TTTT-GATA
* *
5559464 AACTGAGGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
5559484 TGCACTTCCT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
24 9 0.15
25 33 0.53
26 10 0.16
27 10 0.16
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAAGCCCTTTTGATA
Found at i:5567301 original size:21 final size:21
Alignment explanation
Indices: 5567263--5567302 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5567253 TTGTATAAAT
* *
5567263 AGATGTCTGAGTTATTCAATA
1 AGATGTATGAATTATTCAATA
*
5567284 AGATGTATGAATTCTTCAA
1 AGATGTATGAATTATTCAA
5567303 GTTCTTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (21 bp):
AGATGTATGAATTATTCAATA
Found at i:5571606 original size:35 final size:37
Alignment explanation
Indices: 5571535--5571632 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
5571525 ATAATCTTCA
5571535 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
5571573 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
5571608 ATGATATGCAATCTTAGA-A-GATATG
1 ATGATA-GCAATCTTAGATATGATATG
5571633 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:5571632 original size:17 final size:19
Alignment explanation
Indices: 5571535--5571625 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
5571525 ATAATCTTCA
5571535 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5571554 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5571573 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5571590 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5571608 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
5571626 AGATATGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5571651 original size:22 final size:22
Alignment explanation
Indices: 5571535--5571648 Score: 96
Period size: 19 Copynumber: 5.8 Consensus size: 22
5571525 ATAATCTTCA
5571535 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
5571554 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
5571573 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
5571590 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
5571608 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
5571630 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
5571649 GATTTAATTT
Statistics
Matches: 86, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
17 16 0.19
18 16 0.19
19 34 0.40
22 8 0.09
23 12 0.14
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:5571937 original size:17 final size:17
Alignment explanation
Indices: 5571915--5571948 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5571905 TGTTTCCCTG
5571915 ATTTTTT-ATATATTTTA
1 ATTTTTTAATA-ATTTTA
5571932 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
5571949 GTATCACATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:5582710 original size:48 final size:51
Alignment explanation
Indices: 5582659--5582772 Score: 114
Period size: 50 Copynumber: 2.3 Consensus size: 51
5582649 AAATGACATA
* * * *
5582659 ATAATTTAAAATAAT-TAT-AAT-ATATAATATGAA-AGTATATATGTAAA-A
1 ATAATATAAAATAATATATAAATAATACAATAT-AATAATAT-TATATAAATA
*
5582707 ATAATATATAAT-ATATATAAATAATACAATATAATAATATTATATAAATA
1 ATAATATAAAATAATATATAAATAATACAATATAATAATATTATATAAATA
*
5582757 ATAATGTAAAATAATA
1 ATAATATAAAATAATA
5582773 CTAATTTGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
47 2 0.04
48 13 0.25
49 12 0.23
50 23 0.43
51 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.37
Consensus pattern (51 bp):
ATAATATAAAATAATATATAAATAATACAATATAATAATATTATATAAATA
Found at i:5582728 original size:20 final size:20
Alignment explanation
Indices: 5582667--5582849 Score: 71
Period size: 20 Copynumber: 9.8 Consensus size: 20
5582657 TAATAATTTA
5582667 AAATAAT-TATAATATATA-
1 AAATAATATATAATATATAT
* * *
5582685 ATATGAA-AGTAT-ATATGTAA
1 AAAT-AATA-TATAATATATAT
5582705 AAATAATATATAATATATAT
1 AAATAATATATAATATATAT
*
5582725 AAAT-A-ATACAATATA-AT
1 AAATAATATATAATATATAT
*
5582742 -AATATTATATAA-ATA-AT
1 AAATAATATATAATATATAT
*
5582759 AATGTAA-A-ATAATACTA-AT
1 AA-ATAATATATAATA-TATAT
*** *
5582778 TTGTGAA-AAATAATATATAGT
1 AAAT-AATATATAATATATA-T
*
5582799 AAATAATA-ATAATATAAAT
1 AAATAATATATAATATATAT
5582818 AATATAAT-TATAATATAT-T
1 AA-ATAATATATAATATATAT
5582837 --ATAATATATAATA
1 AAATAATATATAATA
5582850 CAAAGATATA
Statistics
Matches: 128, Mismatches: 17, Indels: 41
0.69 0.09 0.22
Matches are distributed among these distances:
16 8 0.06
17 18 0.14
18 22 0.17
19 29 0.23
20 48 0.38
21 3 0.02
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (20 bp):
AAATAATATATAATATATAT
Found at i:5582740 original size:14 final size:14
Alignment explanation
Indices: 5582721--5582759 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
5582711 TATATAATAT
5582721 ATATAAATAATACA
1 ATATAAATAATACA
**
5582735 ATAT-AATAATATT
1 ATATAAATAATACA
5582748 ATATAAATAATA
1 ATATAAATAATA
5582760 ATGTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATAAATAATACA
Found at i:5582756 original size:27 final size:25
Alignment explanation
Indices: 5582709--5582759 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 25
5582699 ATGTAAAAAT
5582709 AATATATAATATATATAAATAATAC
1 AATATATAATATATATAAATAATAC
5582734 AATATAATAATATTATATAAATAATA
1 AATAT-ATAATA-TATATAAATAATA
5582760 ATGTAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.21
26 6 0.25
27 13 0.54
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
AATATATAATATATATAAATAATAC
Found at i:5582758 original size:40 final size:41
Alignment explanation
Indices: 5582714--5582849 Score: 116
Period size: 40 Copynumber: 3.1 Consensus size: 41
5582704 AAAATAATAT
5582714 ATAATATATATAAATAATACAA-TATAATAATATTATATAA
1 ATAATATATATAAATAATACAATTATAATAATATTATATAA
* * *
5582754 ATAATA-ATGTAAAATAATACTAATTTGTGAAAAATAATATATAGTAA
1 ATAATATATAT-AAATAATAC-AA-TTAT-AATAAT-AT-TATA-TAA
* *
5582801 ATAATAATAATATAAATAATATAATTATAAT-ATATTATAATAT
1 ATAAT-AT-ATATAAATAATACAATTATAATAATATTAT-ATAA
5582844 ATAATA
1 ATAATA
5582850 CAAAGATATA
Statistics
Matches: 76, Mismatches: 8, Indels: 22
0.72 0.08 0.21
Matches are distributed among these distances:
39 3 0.04
40 15 0.20
41 2 0.03
42 1 0.01
43 12 0.16
44 8 0.11
45 4 0.05
46 6 0.08
47 11 0.14
48 3 0.04
49 8 0.11
50 3 0.04
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (41 bp):
ATAATATATATAAATAATACAATTATAATAATATTATATAA
Found at i:5582769 original size:27 final size:26
Alignment explanation
Indices: 5582714--5582772 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
5582704 AAAATAATAT
*
5582714 ATAATATATATAAATAATACAATATA
1 ATAATATATATAAATAATACAATAAA
*
5582740 ATAATATTATATAAATAATA-ATGTAAA
1 ATAATA-TATATAAATAATACA-ATAAA
5582767 ATAATA
1 ATAATA
5582773 CTAATTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
ATAATATATATAAATAATACAATAAA
Found at i:5585118 original size:206 final size:207
Alignment explanation
Indices: 5584670--5585220 Score: 813
Period size: 206 Copynumber: 2.7 Consensus size: 207
5584660 CTGCTTCTTT
* *
5584670 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTAGT-GTAAGCACGCG
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCA-TCGTAAGCACGTG
* * * * * *
5584734 AAAACCAAACCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATACCAAACCATCTTGGA
65 AAAGCCAAATCAGCTATGTCTTCGATTTGTTTCTTGTAAGTACAAGGATGCCAAACCATCTTGGA
* * ** * *
5584799 TCTTGCTTCAGTGAAATCATCTGAAGGTGAGATCTGCTATGTGTCTGCCCTCCGTCGAATATGGA
130 TCTTGCTTCAGTGAAAACATATGAAGGCCAGATCTGCTATGTGTCTACCCTCCATCGAATATGGA
5584864 GACGCCAAACTTC
195 GACGCCAAACTTC
*
5584877 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTTCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* * *
5584942 AAGCCAAATCAGCCATGAT-TTCGATTTGTTTCTTGTAAATACAAGGATGCCAAATCATCTTGGA
66 AAGCCAAATCAGCTATG-TCTTCGATTTGTTTCTTGTAAGTACAAGGATGCCAAACCATCTTGGA
*
5585006 TC-TGCTTCAGT-ATAAACATATGAAGGCCAGATCTGCTATGTGTCTACTCTCCATCGAATATGG
130 TCTTGCTTCAGTGA-AAACATATGAAGGCCAGATCTGCTATGTGTCTACCCTCCATCGAATATGG
5585069 AGACGCCAAACTTC
194 AGACGCCAAACTTC
* * * *
5585083 GATTTGTTCTTTGACAATACATAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* * *
5585148 AAGCCAAATCAGCTATGTCTTCGGTTTGTTTCTTGTAAGTACAAAGATGCCATACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTTCTTGTAAGTACAAGGATGCCAAACCATCTTGGAT
5585213 CTTGCTTC
131 CTTGCTTC
5585221 TGCCAGATCT
Statistics
Matches: 309, Mismatches: 30, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
205 2 0.01
206 185 0.60
207 121 0.39
208 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (207 bp):
GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGTTTCTTGTAAGTACAAGGATGCCAAACCATCTTGGAT
CTTGCTTCAGTGAAAACATATGAAGGCCAGATCTGCTATGTGTCTACCCTCCATCGAATATGGAG
ACGCCAAACTTC
Found at i:5587360 original size:45 final size:45
Alignment explanation
Indices: 5587296--5587384 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
5587286 GTCTTTCCGT
*
5587296 GTCTTGTACAAGATATCTCCGTCTGAGACATAGTCGCAAGCTAAA
1 GTCTTGTACAAGATATCTCCGTCTAAGACATAGTCGCAAGCTAAA
* *
5587341 GTCTTGTATAAGATATCTCCTTCTAAGACATAGTCGCAAGCTAA
1 GTCTTGTACAAGATATCTCCGTCTAAGACATAGTCGCAAGCTAA
5587385 CCTCCTCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (45 bp):
GTCTTGTACAAGATATCTCCGTCTAAGACATAGTCGCAAGCTAAA
Found at i:5593375 original size:14 final size:16
Alignment explanation
Indices: 5593340--5593376 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5593330 CAAACGATGC
5593340 GATG-AAATGCTATGA
1 GATGCAAATGCTATGA
5593355 GATGCAAATGC-ATGA
1 GATGCAAATGCTATGA
5593370 -ATGCAAA
1 GATGCAAA
5593377 AGGATATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GATGCAAATGCTATGA
Found at i:5593419 original size:14 final size:14
Alignment explanation
Indices: 5593396--5593425 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5593386 ATTCTGGTAC
5593396 AACTTCATTTAGAA
1 AACTTCATTTAGAA
*
5593410 AACTTTATTTAGAA
1 AACTTCATTTAGAA
5593424 AA
1 AA
5593426 ATAATATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
AACTTCATTTAGAA
Found at i:5597195 original size:18 final size:18
Alignment explanation
Indices: 5597145--5597195 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 18
5597135 TAATATACAA
* *
5597145 TATATAATATAAAA-AAT
1 TATATAAAACAAAATAAT
*
5597162 T-TATAAAAGAATAATAAT
1 TATATAAAACAA-AATAAT
5597180 TATATAAAACAAAATA
1 TATATAAAACAAAATA
5597196 TAATGATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 8 0.29
17 3 0.11
18 8 0.29
19 9 0.32
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
TATATAAAACAAAATAAT
Found at i:5597437 original size:23 final size:23
Alignment explanation
Indices: 5597378--5597437 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
5597368 GTAATAATAG
*
5597378 AATATAAG-TAAAATAATTATTA
1 AATATAAGTTAAAATAAGTATTA
* *
5597400 ACATATAAATAAAAATAAGTA-TA
1 A-ATATAAGTTAAAATAAGTATTA
5597423 TAATATAAGTTAAAA
1 -AATATAAGTTAAAA
5597438 CTTTTAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 19 0.63
24 10 0.33
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (23 bp):
AATATAAGTTAAAATAAGTATTA
Found at i:5597600 original size:27 final size:26
Alignment explanation
Indices: 5597545--5597603 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
5597535 GTAAAAAAAT
*
5597545 ATAATATATATAAATAATACAATATA
1 ATAATATATATAAATAATACAATAAA
*
5597571 ATAATATTATATAAATAATA-ATGTAAA
1 ATAATA-TATATAAATAATACA-ATAAA
5597598 ATAATA
1 ATAATA
5597604 CTAATTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
ATAATATATATAAATAATACAATAAA
Found at i:5597662 original size:27 final size:28
Alignment explanation
Indices: 5597616--5597670 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
5597606 AATTTGTGAA
5597616 AAATAATATATAGTAAATAATAATAATAC
1 AAATAATATATAG-AAATAATAATAATAC
* *
5597645 AAATAATATATA-ATATAATTATAATA
1 AAATAATATATAGAAATAATAATAATA
5597671 TATAATACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
29 12 0.50
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (28 bp):
AAATAATATATAGAAATAATAATAATAC
Found at i:5597669 original size:11 final size:12
Alignment explanation
Indices: 5597503--5597672 Score: 59
Period size: 13 Copynumber: 13.7 Consensus size: 12
5597493 ATAATTTAAA
5597503 ATAATTATAATAT
1 ATAA-TATAATAT
*
5597516 ATAATATGATAGT
1 ATAATATAATA-T
*
5597529 ATATATGTAA-A-
1 ATA-ATATAATAT
*
5597540 AAAATATAATAT
1 ATAATATAATAT
5597552 AT-ATA-AATAAT
1 ATAATATAAT-AT
*
5597563 ACAATATAATAAT
1 ATAATATAAT-AT
*
5597576 ATTATATAA-AT
1 ATAATATAATAT
*
5597587 AATAATGTAA-A-
1 -ATAATATAATAT
*
5597598 ATAATACTAATTT
1 ATAATA-TAATAT
* *
5597611 GTGAAAAATAATAT
1 AT--AATATAATAT
*
5597625 ATAGTAAATAATAAT
1 ATA--ATATAAT-AT
*
5597640 AATACAAATAATAT
1 -ATA-ATATAATAT
5597654 ATAATATAAT-T
1 ATAATATAATAT
5597665 ATAATATA
1 ATAATATA
5597673 TAATACAAAG
Statistics
Matches: 121, Mismatches: 19, Indels: 36
0.69 0.11 0.20
Matches are distributed among these distances:
10 13 0.11
11 23 0.19
12 25 0.21
13 26 0.21
14 19 0.16
15 12 0.10
16 3 0.02
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:5597676 original size:40 final size:39
Alignment explanation
Indices: 5597503--5597677 Score: 96
Period size: 40 Copynumber: 4.5 Consensus size: 39
5597493 ATAATTTAAA
* ** *
5597503 ATAATTATAATATATAAT-ATGATA-GTATATATGTAA-
1 ATAATTATAATATATAATAATAATACAAATATATATAAT
* *
5597539 AAAAATATAATATAT-ATAAATAATAC-AATATA-ATAAT
1 ATAATTATAATATATAAT-AATAATACAAATATATATAAT
* * * * * *
5597576 ATTATATAAATAATAATGTAA-AATAATACTAATTTGTGA-AAA
1 A-TA-AT-TATAAT-ATATAATAATAATACAAATATAT-ATAAT
* *
5597618 ATAATATATAGTAAATAATAATAATACAAATAATATATAAT
1 ATAAT-TATAATATATAATAATAATACAAAT-ATATATAAT
5597659 ATAATTATAATATATAATA
1 ATAATTATAATATATAATA
5597678 CAAAGATATA
Statistics
Matches: 102, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
35 2 0.02
36 16 0.16
37 11 0.11
38 1 0.01
39 5 0.05
40 44 0.43
41 18 0.18
42 4 0.04
43 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (39 bp):
ATAATTATAATATATAATAATAATACAAATATATATAAT
Found at i:5599546 original size:78 final size:77
Alignment explanation
Indices: 5599411--5600034 Score: 876
Period size: 78 Copynumber: 8.0 Consensus size: 77
5599401 GTGTTTACGC
* * * ** * * *
5599411 TGAAGCAGATCTAAGATGATATGGCTTCTCCATATTCGACGGAGAGCACATCAAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGG-GAGCAGATCGAAGACATAGCAG
5599476 ATCTGACCTTCAT
65 ATCTGACCTTCAT
* **
5599489 TGAAGCAGATCCAAGATGATTTAGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACACGGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAAGACATAGCAG
*
5599554 AT-TGGACCTTTAT
65 ATCT-GACCTTCAT
* ** *
5599567 TGAAGTAGATCCAAGATGATTTGGCATCTCCATATTTGACGGAGAGCAGATCGAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGG-GAGCAGATCGAAGACATAGCAG
5599632 ATCTGACCTTCAT
65 ATCTGACCTTCAT
* * *
5599645 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACATCAA
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAAGACATAGCAG
5599710 AT-TGCACCTTCAT
65 ATCTG-ACCTTCAT
** *
5599723 TGAAGCAGATCCAAGATGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGG-GAGCAGATCGAAGACATAGCAG
5599788 ATCTGACCTTCAT
65 ATCTGACCTTCAT
* *
5599801 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGTAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAAGACATAGCAG
5599866 ATCTGACCTTCAT
65 ATCTGACCTTCAT
* * *
5599879 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGGGAGCAGATCAAAGCCATAACAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAAGACATAGCAG
5599944 AT-TGGACCTTCAT
65 ATCT-GACCTTCAT
*
5599957 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAAACGGGGAGCAGATCGAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAAGACATAGCAG
5600022 ATCTGACCTTCAT
65 ATCTGACCTTCAT
5600035 GTGTTTACAT
Statistics
Matches: 486, Mismatches: 49, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
77 8 0.02
78 468 0.96
79 10 0.02
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (77 bp):
TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGAGCAGATCGAAGACATAGCAGA
TCTGACCTTCAT
Found at i:5599695 original size:156 final size:156
Alignment explanation
Indices: 5599411--5600034 Score: 977
Period size: 156 Copynumber: 4.0 Consensus size: 156
5599401 GTGTTTACGC
* * * *
5599411 TGAAGCAGATCTAAGATGATATGGCTTCTCCATATTCGACGGAGAGCACATCAAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCCATATTCGACGGAGAGCAGATCAAAGACATAGCAG
* *
5599476 ATCTGACCTTCATTGAAGCAGATCCAAGATGATTTAGCATCTCTGTATTAGACAGGGAGCAGATC
66 ATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
* *
5599541 GAAGACACGGCAGATTGGACCTTTAT
131 GAAGACACAGCAGATTGGACCTTCAT
* * *
5599567 TGAAGTAGATCCAAGATGATTTGGCATCTCCATATTTGACGGAGAGCAGATCGAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCCATATTCGACGGAGAGCAGATCAAAGACATAGCAG
5599632 ATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
66 ATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
* * *
5599697 GAAGACACATCAAATTGCACCTTCAT
131 GAAGACACAGCAGATTGGACCTTCAT
*
5599723 TGAAGCAGATCCAAGATGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCCATATTCGACGGAGAGCAGATCAAAGACATAGCAG
5599788 ATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
66 ATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
*
5599853 GAAGACACAGTAGATCT-GACCTTCAT
131 GAAGACACAGCAGAT-TGGACCTTCAT
** * * *
5599879 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGG-GAGCAGATCAAAGCCATAACA
1 TGAAGCAGATCCAAGATGATTTGGCATCTCCATATTCGAC-GGAGAGCAGATCAAAGACATAGCA
*
5599943 GAT-TGGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAAACGGGGAGCAGA
65 GATCT-GACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGA
*
5600007 TCGAAGACATAGCAGATCT-GACCTTCAT
129 TCGAAGACACAGCAGAT-TGGACCTTCAT
5600035 GTGTTTACAT
Statistics
Matches: 436, Mismatches: 29, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
155 1 0.00
156 432 0.99
157 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (156 bp):
TGAAGCAGATCCAAGATGATTTGGCATCTCCATATTCGACGGAGAGCAGATCAAAGACATAGCAG
ATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
GAAGACACAGCAGATTGGACCTTCAT
Found at i:5600174 original size:45 final size:44
Alignment explanation
Indices: 5599974--5600202 Score: 203
Period size: 45 Copynumber: 5.1 Consensus size: 44
5599964 GATCCAAGAT
* *
5599974 GATTTGGCATCTCTGTATTAAACGGGGAGCAGATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAAG--ATAACA
* * * * * * * *
5600021 GATCTGACCT-TCATGTGTTTACATC-GAAGCAGATCCAAGATGACA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGAGCAGATCGAAGATAACA
* * *
5600066 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATTGAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAAGATAACA
*
5600110 GATTTGGCATCTCTATATTAGACAGGGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCGAAGATAACA
* * *
5600155 GATTTGGCGTCTCTGTATTAGACGGAGAGCAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTAGACGG-GAGCAGATCGAAGATAACA
5600200 GAT
1 GAT
5600203 ATCGCCTTCT
Statistics
Matches: 145, Mismatches: 29, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
43 1 0.01
44 44 0.30
45 69 0.48
46 4 0.03
47 22 0.15
48 4 0.03
49 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTAGACGGGAGCAGATCGAAGATAACA
Found at i:5600230 original size:89 final size:88
Alignment explanation
Indices: 5599974--5600237 Score: 241
Period size: 89 Copynumber: 2.9 Consensus size: 88
5599964 GATCCAAGAT
* * * * *
5599974 GATTTGGCATCTCTGTATTAAACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATGTGT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATC-AA-AGATAGCAGATATG-CCTTCTTGAG-
* * *
5600039 TTACA-TCGAAGCAGATCCAAGATGACA
62 TTGCAGT-GAAGCAGATCGAAGATAACA
* ** * *
5600066 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATTGAAGA-AGCAGATTTGGCATCTCTAT-A-T
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATAT-GCCT-TCT-TGAGT
*
5600128 TAGACAG-GGAGCAGATCGAAGATAACA
63 T-G-CAGTGAAGCAGATCGAAGATAACA
* *
5600155 GATTTGGCGTCTCTGTATTAGACGGAGAGCAGATCAAAGATAGCAGATATCGCCTTCTTGAGTTG
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATAT-GCCTTCTTGAGTTG
*
5600220 CAGTGAAGCAGATTGAAG
65 CAGTGAAGCAGATCGAAG
5600238 CCGTCAAGAG
Statistics
Matches: 139, Mismatches: 23, Indels: 23
0.75 0.12 0.12
Matches are distributed among these distances:
88 6 0.04
89 79 0.57
90 20 0.14
91 2 0.01
92 32 0.23
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (88 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGATATGCCTTCTTGAGTTGC
AGTGAAGCAGATCGAAGATAACA
Found at i:5600577 original size:14 final size:15
Alignment explanation
Indices: 5600558--5600613 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
5600548 AATCTTTAAT
5600558 GATATG-CAATCTTA
1 GATATGACAATCTTA
5600572 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
5600589 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
5600607 GATATGA
1 GATATGA
5600614 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:5600580 original size:19 final size:19
Alignment explanation
Indices: 5600556--5600627 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
5600546 ATAATCTTTA
5600556 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5600575 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5600592 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5600610 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
5600628 ATATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5600602 original size:35 final size:37
Alignment explanation
Indices: 5600556--5600634 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
5600546 ATAATCTTTA
5600556 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
5600592 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
5600628 AT-ATATG
1 ATGATATG
5600635 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 21 0.52
36 9 0.22
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:5600866 original size:18 final size:19
Alignment explanation
Indices: 5600826--5600867 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5600816 TCCCTCTTAC
5600826 GTTCTTATTTTATACGGTTT
1 GTTCTTATTTTATAC-GTTT
*
5600846 GTTCTTATTTTATTC-TTT
1 GTTCTTATTTTATACGTTT
5600864 GTTC
1 GTTC
5600868 ATCTTCGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (19 bp):
GTTCTTATTTTATACGTTT
Found at i:5600941 original size:17 final size:17
Alignment explanation
Indices: 5600917--5600951 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5600907 TGTTTCCCTG
*
5600917 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
5600935 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
5600952 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:5603584 original size:28 final size:28
Alignment explanation
Indices: 5603553--5603621 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
5603543 TCCTTATTAA
*
5603553 TTTTATTTTATTTT-ATTTTACGACCCCT
1 TTTTATTTTATTTTAATTTTA-AACCCCT
* *
5603581 TTTTACTTTCTTTTAATTTTAAACCCCT
1 TTTTATTTTATTTTAATTTTAAACCCCT
*
5603609 TTAT-TTTTATTTT
1 TTTTATTTTATTTT
5603622 TATTAATGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 7 0.21
28 21 0.62
29 6 0.18
ACGTcount: A:0.19, C:0.16, G:0.01, T:0.64
Consensus pattern (28 bp):
TTTTATTTTATTTTAATTTTAAACCCCT
Found at i:5611358 original size:23 final size:23
Alignment explanation
Indices: 5611332--5611379 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5611322 TGAAGAGAAG
*
5611332 AAGCGTAAGGATTGAAAGGCGTT
1 AAGCGTAAGGATCGAAAGGCGTT
*
5611355 AAGCGTAAGGATCGAAAGGTGTT
1 AAGCGTAAGGATCGAAAGGCGTT
5611378 AA
1 AA
5611380 CACAATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (23 bp):
AAGCGTAAGGATCGAAAGGCGTT
Found at i:5621992 original size:83 final size:85
Alignment explanation
Indices: 5621903--5622101 Score: 212
Period size: 84 Copynumber: 2.4 Consensus size: 85
5621893 TAAAAAACAA
* ** * *
5621903 GAATAAATCCTAG-AATAGA-ATTATTTGA-TTAAGTCTTCGTTTGGAAA-AAAATTAATATTGA
1 GAATAAATCCTAGAAATAGATATTATTTAATTTAAGTC-TAATTTGAAAACAAAATTAA-ATCGA
5621964 ATAAAATCTTGTTAAACGACGG
64 ATAAAATCTTGTTAAACGACGG
* *
5621986 GAATAAATCCT-GAAATAGATTTTATTTAATTTAATTCTAATTTGAAAACAAAATTAAATCGAAT
1 GAATAAATCCTAGAAATAGATATTATTTAATTTAAGTCTAATTTGAAAACAAAATTAAATCGAAT
* * **
5622050 AGAATCTTGTTAATCGGTGG
66 AAAATCTTGTTAAACGACGG
* * *
5622070 GAATAAATCCTA-AAACATATTTTATTTAATTT
1 GAATAAATCCTAGAAATAGATATTATTTAATTT
5622102 TAATTTCTCG
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
82 1 0.01
83 17 0.17
84 66 0.67
85 14 0.14
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.37
Consensus pattern (85 bp):
GAATAAATCCTAGAAATAGATATTATTTAATTTAAGTCTAATTTGAAAACAAAATTAAATCGAAT
AAAATCTTGTTAAACGACGG
Found at i:5622062 original size:84 final size:85
Alignment explanation
Indices: 5621942--5622106 Score: 226
Period size: 84 Copynumber: 2.0 Consensus size: 85
5621932 TAAGTCTTCG
* * * *
5621942 TTTGGAAAAAAATTAATATTGAATAAAATCTTGTTAAACGACGGGAATAAATCCTGAAATAGATT
1 TTTGAAAAAAAATTAATATCGAATAAAATCTTGTTAAACGACGGGAATAAATCCTAAAACAGATT
5622007 TTATTTAA-TTTAATTCTAA
66 TTATTTAATTTTAATTCTAA
* * ** *
5622026 TTTGAAAACAAAATTAA-ATCGAATAGAATCTTGTTAATCGGTGGGAATAAATCCTAAAACATAT
1 TTTGAAAA-AAAATTAATATCGAATAAAATCTTGTTAAACGACGGGAATAAATCCTAAAACAGAT
5622090 TTTATTTAATTTTAATT
65 TTTATTTAATTTTAATT
5622107 TCTCGTTTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
84 55 0.79
85 15 0.21
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.38
Consensus pattern (85 bp):
TTTGAAAAAAAATTAATATCGAATAAAATCTTGTTAAACGACGGGAATAAATCCTAAAACAGATT
TTATTTAATTTTAATTCTAA
Found at i:5622448 original size:19 final size:20
Alignment explanation
Indices: 5622420--5622460 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
5622410 AAATAGATAA
5622420 ATATAAAT-AAAT-ATTTAT
1 ATATAAATAAAATAATTTAT
5622438 ATATAAAATAAAATAATTTAT
1 ATAT-AAATAAAATAATTTAT
5622459 AT
1 AT
5622461 TCCAATTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 4 0.20
20 4 0.20
21 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAAATAAAATAATTTAT
Found at i:5628309 original size:19 final size:19
Alignment explanation
Indices: 5628285--5628353 Score: 138
Period size: 19 Copynumber: 3.6 Consensus size: 19
5628275 AATCTTTAAG
5628285 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5628304 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5628323 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5628342 GATATGCAATCT
1 GATATGCAATCT
5628354 CGAAGATGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5628753 original size:4 final size:4
Alignment explanation
Indices: 5628744--5628772 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5628734 AAACAAAAGA
5628744 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
5628773 TCTATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:5630353 original size:25 final size:24
Alignment explanation
Indices: 5630325--5630377 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
5630315 ATATAAATTT
5630325 TATTA-TATGTTATATATATTTATTA
1 TATTACTATGTTAT-TATATTT-TTA
*
5630350 TATTACTTATTTTATTATATTTTTA
1 TATTAC-TATGTTATTATATTTTTA
5630375 TAT
1 TAT
5630378 GTAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 11 0.44
26 7 0.28
27 7 0.28
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTACTATGTTATTATATTTTTA
Found at i:5630375 original size:8 final size:9
Alignment explanation
Indices: 5630323--5630446 Score: 64
Period size: 9 Copynumber: 13.7 Consensus size: 9
5630313 ATATATAAAT
5630323 TTTATTATA
1 TTTATTATA
5630332 TGTTATATATA
1 T-TTAT-TATA
5630343 TTTATTATA
1 TTTATTATA
5630352 -TTACTTAT-
1 TTTA-TTATA
5630360 TTTATTATA
1 TTTATTATA
5630369 TTT-TTATA
1 TTTATTATA
* **
5630377 TGTAAAATA
1 TTTATTATA
* *
5630386 TTTGTTACA
1 TTTATTATA
5630395 -TTATTAT-
1 TTTATTATA
5630402 TATTATTAT-
1 T-TTATTATA
* *
5630411 TATA-CATA
1 TTTATTATA
5630419 TTTCATATTATA
1 -TT--TATTATA
5630431 TTTCATTATA
1 TTT-ATTATA
5630441 TTTATT
1 TTTATT
5630447 TAAGTTTTTC
Statistics
Matches: 87, Mismatches: 14, Indels: 28
0.67 0.11 0.22
Matches are distributed among these distances:
7 2 0.02
8 21 0.24
9 35 0.40
10 17 0.20
11 9 0.10
12 3 0.03
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTATTATA
Found at i:5630668 original size:19 final size:19
Alignment explanation
Indices: 5630646--5630684 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5630636 TTTGATATAT
5630646 TTATGTTACTATATTATTA
1 TTATGTTACTATATTATTA
* **
5630665 TTATTTTTTTATATTATTA
1 TTATGTTACTATATTATTA
5630684 T
1 T
5630685 CACATTTGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTATGTTACTATATTATTA
Found at i:5634400 original size:12 final size:12
Alignment explanation
Indices: 5634383--5634415 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
5634373 TAAAGTTATT
5634383 AAAAAGAGAAAG
1 AAAAAGAGAAAG
5634395 AAAAAGAGAAAG
1 AAAAAGAGAAAG
5634407 AGAAAAGAG
1 A-AAAAGAG
5634416 GGTCACCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAG
Found at i:5637001 original size:9 final size:9
Alignment explanation
Indices: 5636941--5636994 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 9
5636931 ACTTCTATTT
*
5636941 AAAAAAAGG
1 AAAAAAAGA
5636950 AAAAAAAGAA
1 AAAAAAAG-A
5636960 AAGAAAAAGA
1 AA-AAAAAGA
*
5636970 GAAAAAAATTA
1 -AAAAAAA-GA
5636981 AAAAAAAGA
1 AAAAAAAGA
5636990 AAAAA
1 AAAAA
5636995 GAAAAAATGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 14 0.37
10 15 0.39
11 9 0.24
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:5638003 original size:44 final size:44
Alignment explanation
Indices: 5637953--5638054 Score: 152
Period size: 44 Copynumber: 2.3 Consensus size: 44
5637943 AGCGCCTTAA
* *
5637953 TCCCCTAAGTAGTAGGGTAACAGGTTAAATTTACAGATCTTATC
1 TCCCCTAAGTAGTAGGGTAACAGGTCAAAATTACAGATCTTATC
* * *
5637997 TCCCCTAAGCAGTAGGGTAACAGGTCAAAATTGCGGATCTTATC
1 TCCCCTAAGTAGTAGGGTAACAGGTCAAAATTACAGATCTTATC
5638041 T-CCCTAAGTAGTAG
1 TCCCCTAAGTAGTAG
5638055 TGGAGTAGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 12 0.23
44 40 0.77
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (44 bp):
TCCCCTAAGTAGTAGGGTAACAGGTCAAAATTACAGATCTTATC
Found at i:5638444 original size:89 final size:87
Alignment explanation
Indices: 5638315--5638475 Score: 252
Period size: 89 Copynumber: 1.8 Consensus size: 87
5638305 ATTCGATGGA
* * *
5638315 GAGCAGATCGAAGACATAGCAGATCTGACCTTTGGATGTTTTCACATCGAAGCAGATCCAAGATG
1 GAGCAAATCAAAGACATAGCAGATCTGACCTTTGGATGTTTACAC-T-GAAGCAGATCCAAGATG
5638380 ATTTGGCATTCTTGTGTTTACAAG
64 ATTTGGCATTCTTGTGTTTACAAG
*
5638404 GAGCAAATCAAAGACATAGCAGATCTGATCTTTAGG-TGTTTACACTGAAGCAGATCCAAGATGA
1 GAGCAAATCAAAGACATAGCAGATCTGACCTTT-GGATGTTTACACTGAAGCAGATCCAAGATGA
5638468 TTTGGCAT
65 TTTGGCAT
5638476 CTCTGTATTG
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
87 26 0.39
88 1 0.01
89 38 0.57
90 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (87 bp):
GAGCAAATCAAAGACATAGCAGATCTGACCTTTGGATGTTTACACTGAAGCAGATCCAAGATGAT
TTGGCATTCTTGTGTTTACAAG
Found at i:5638525 original size:220 final size:220
Alignment explanation
Indices: 5638143--5638962 Score: 1300
Period size: 220 Copynumber: 3.7 Consensus size: 220
5638133 TGTTCATGCT
* *
5638143 GAAGCAGATCCAAGATGAGTTGGTATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
1 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
* * * *
5638208 TTGACCTTCAGGTGCTTACACTGAAGCAGATCCAAGATGATTTGGCATATCTGTATTGTCAGAGA
66 CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCAGAGA
*
5638273 AGAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAGACATAGCAGA
131 ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAGACATAGCAGA
5638338 TCTGACCTTTGGATGTTTTCACATC
196 TCTGACCTTTGGATGTTTTCACATC
5638363 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
1 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
* * *
5638428 CTGATCTTTAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTGTCAGAGA
66 CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCAGAGA
* * *
5638493 ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATAGAGAGCAGATCGAACACATAGCAGT
131 ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAGACATAGCAGA
5638558 TCTGACCTTTGGATGTTTTCACATC
196 TCTGACCTTTGGATGTTTTCACATC
* **
5638583 AAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCGTAGACATAGCAGAT
1 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
*
5638648 CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATGTCTGTATTGTCAGAGA
66 CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCAGAGA
* * * * * *
5638713 ACAAATTGAATAAACAGATTTGGCATCTCCATATTCGACGGAGAGTAGATTGAAGGCATAGCAGA
131 ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAGACATAGCAGA
* * *
5638778 TCTGACCTTCGGATATTTTCACATT
196 TCTGACCTTTGGATGTTTTCACATC
* * * *
5638803 GAAGCAGATCCAAGATGATTTAGCATCCTTGTGTTTACAAGGAGCAAATCGAAGACATAGTAGAT
1 GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
*
5638868 CTGACCTTCAGGTGTTTACGCTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCA-AGG
66 CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCAGA-G
* * * *
5638932 AACGAATCGAAGGTAGCAGATTTGACATCTC
130 AACAAATCGAA-GAAACAGATTTGGCATCTC
5638963 TGTATTTGAC
Statistics
Matches: 555, Mismatches: 43, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
219 1 0.00
220 539 0.97
221 15 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (220 bp):
GAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAGCAAATCAAAGACATAGCAGAT
CTGACCTTCAGGTGTTTACACTGAAGCAGATCCAAGATGATTTGACATCTCTGTATTGTCAGAGA
ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAGACATAGCAGA
TCTGACCTTTGGATGTTTTCACATC
Found at i:5639361 original size:16 final size:17
Alignment explanation
Indices: 5639311--5639361 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
5639301 ATGGAAATAT
*
5639311 AATCTTTAAGGATATGC
1 AATCTTGAAGGATATGC
*
5639328 AATCTTAGATATGATATGC
1 AATCTT-GA-AGGATATGC
5639347 AATCTTGAA-GATATG
1 AATCTTGAAGGATATG
5639362 ATCTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 3 0.10
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
AATCTTGAAGGATATGC
Found at i:5639380 original size:22 final size:21
Alignment explanation
Indices: 5639321--5639363 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
5639311 AATCTTTAAG
5639321 GATATGCAATCTT--AGATAT
1 GATATGCAATCTTGAAGATAT
5639340 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTTGAAGATAT
5639361 GAT
1 GAT
5639364 CTTGTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (21 bp):
GATATGCAATCTTGAAGATAT
Found at i:5639981 original size:21 final size:20
Alignment explanation
Indices: 5639949--5639995 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
5639939 TTTTTGCATG
5639949 TATTATGTTTTTCT-TTTAGTT
1 TATTATGTTTTT-TATTT-GTT
5639970 TATTCATG-TTTTTATTTGTT
1 TATT-ATGTTTTTTATTTGTT
5639990 TATTAT
1 TATTAT
5639996 CTTATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.08
20 8 0.33
21 11 0.46
22 3 0.12
ACGTcount: A:0.17, C:0.04, G:0.09, T:0.70
Consensus pattern (20 bp):
TATTATGTTTTTTATTTGTT
Found at i:5639992 original size:20 final size:21
Alignment explanation
Indices: 5639949--5639995 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
5639939 TTTTTGCATG
*
5639949 TATTATGTTTTTCTTTTAGTT
1 TATTATGTTTTTCATTTAGTT
5639970 TATTCATGTTTTT-ATTT-GTT
1 TATT-ATGTTTTTCATTTAGTT
5639990 TATTAT
1 TATTAT
5639996 CTTATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 7 0.29
21 7 0.29
22 8 0.33
ACGTcount: A:0.17, C:0.04, G:0.09, T:0.70
Consensus pattern (21 bp):
TATTATGTTTTTCATTTAGTT
Found at i:5641997 original size:28 final size:28
Alignment explanation
Indices: 5641957--5642045 Score: 115
Period size: 28 Copynumber: 3.2 Consensus size: 28
5641947 CCAAAGGTGG
*
5641957 GTGCAAGCCAAAGTGGTGGACAGTCTAA
1 GTGCAAGCCAAAGTGGCGGACAGTCTAA
* *
5641985 GTGCAAGCCAAAGTGGCGGAGATTCTAA
1 GTGCAAGCCAAAGTGGCGGACAGTCTAA
* * * *
5642013 ATGCAAGTCAAAGTGGCAGACAGTTTAA
1 GTGCAAGCCAAAGTGGCGGACAGTCTAA
5642041 GTGCA
1 GTGCA
5642046 CTCCAAAAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (28 bp):
GTGCAAGCCAAAGTGGCGGACAGTCTAA
Done.