Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 59 of 213
Found at i:15991541 original size:23 final size:23
Alignment explanation
Indices: 15991510--15991573 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
15991500 TAAAGACACT
* *
15991510 AACCCTAACCTAATTTAATTCAA
1 AACCCTAACCTAAATTAATTAAA
* *
15991533 AACCTTAACCTAAATTATTTAAA
1 AACCCTAACCTAAATTAATTAAA
* *
15991556 AACCCTAAACTAAGTTAA
1 AACCCTAACCTAAATTAA
15991574 CAATATTACA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.30
Consensus pattern (23 bp):
AACCCTAACCTAAATTAATTAAA
Found at i:15991726 original size:116 final size:116
Alignment explanation
Indices: 15991570--15991794 Score: 337
Period size: 116 Copynumber: 1.9 Consensus size: 116
15991560 CTAAACTAAG
*
15991570 TTAACAATATTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAACAATATTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
* *
15991635 T-AATTT-TACATAATTTGATAGTTTTACTAACCATTAACACAATTTTTTGAC
66 TAAATTTATAC-T-ATTTGATAATTTTACTAACAATTAACACAATTTTTTGAC
* * * *
15991686 TTAATAATTTTACATTCATATAATGTTAGATTTGGTAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAACAATATTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
* *
15991751 TAAATTTATACTATTTGATAATTTTAGTAACAATTAATACAATT
66 TAAATTTATACTATTTGATAATTTTACTAACAATTAACACAATT
15991795 ATCAAATAAT
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
116 89 0.91
117 6 0.06
118 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (116 bp):
TTAACAATATTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
TAAATTTATACTATTTGATAATTTTACTAACAATTAACACAATTTTTTGAC
Found at i:15995043 original size:125 final size:125
Alignment explanation
Indices: 15994817--15995182 Score: 536
Period size: 126 Copynumber: 2.9 Consensus size: 125
15994807 CCCAAACATG
* **
15994817 CTACTGTAGCAAAATCGCGTCCACGACGACT-CGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGA-GGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
*
15994881 CTAGAAGCGATTTTACACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCGGGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCGGGAC
** *
15994942 CTGTTGTAGCAAAAGCGCGTCCACGAGGGTGCGATATCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *** * *
15995007 TACAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCAA-AATTATTTCTTCCGGGAC
* * *
15995068 CTACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTTATAAATTCTTCTCAAATAGCATCCTGT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
15995133 TAGAAGCAATTTTATACTATTTGATCAGAAACGTCAACTCAAAATTATTT
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTT
15995183 ATTCTAGGAC
Statistics
Matches: 212, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
124 2 0.01
125 100 0.47
126 110 0.52
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCGGGAC
Found at i:15995208 original size:126 final size:123
Alignment explanation
Indices: 15994817--15995195 Score: 508
Period size: 125 Copynumber: 3.0 Consensus size: 123
15994807 CCCAAACATG
* **
15994817 CTACTGTAGCAAAATCGCGTCCACGACGACT-CGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTA-CAAAAGCGCGTCCACGA-GGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* *
15994881 CTAGAAGCGATTTTACACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCGGGAC
64 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTT-CTGGAC
** *
15994942 CTGTTGTAGCAAAAGCGCGTCCACGAGGGTGCGATATCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTA-CAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * ***
15995007 TACAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
65 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCAA-AATTATTTCTTCTG-GAC
* * *
15995068 CTACTGTAGCAAAAGCGCGTCCACGAGGGTGCGATTTTATAAATTCTTCTCAAATAGCATCCTGT
1 CTACTGTA-CAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
15995133 TAGAAGCAATTTTATACTATTTGATCAGAAACGTCAACTCAAAATTATTTATTCTAGGAC
65 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCT-GGAC
15995193 CTA
1 CTA
15995196 AAACCCTAAA
Statistics
Matches: 223, Mismatches: 27, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
124 2 0.01
125 112 0.50
126 109 0.49
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (123 bp):
CTACTGTACAAAAGCGCGTCCACGAGGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCT
AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCTGGAC
Found at i:16006976 original size:41 final size:40
Alignment explanation
Indices: 16006861--16006996 Score: 127
Period size: 41 Copynumber: 3.5 Consensus size: 40
16006851 ACCAGTTTGG
* * * *
16006861 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATCGAATAATCCGAAGTAGTAAATTGA
* * * * *
16006901 CACCTAGTGTCTCATC-AGCTAAACCG-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGA-ATAATCCGAAGTAGTAAATTGA
*
16006938 CACTCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCCGAAGTAGTAAATTGA
*
16006979 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
16006997 CTCGAAGTCG
Statistics
Matches: 73, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
37 20 0.27
38 7 0.10
39 2 0.03
40 19 0.26
41 25 0.34
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATCCGAAGTAGTAAATTGA
Found at i:16008344 original size:59 final size:59
Alignment explanation
Indices: 16008281--16008407 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 59
16008271 TCGTTACACT
* *
16008281 TTTTTTTTGTCAAATTTGGTACTTTAACTTGACACTTTTT-CCTAATTTGGTACCTAAAC
1 TTTTTTTTGCCAAATTTGGTACTTGAACTTGACA-TTTTTCCCTAATTTGGTACCTAAAC
** * ** * *
16008340 TTTTTTAGGCCCAATTTGGTACTTGAACTTGGTATTTTTCCCCTAGTTTGGTACCTAAGC
1 TTTTTTTTGCCAAATTTGGTACTTGAACTTGACATTTTT-CCCTAATTTGGTACCTAAAC
*
16008400 TATTTTTT
1 TTTTTTTT
16008408 AGGTTCAATT
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
58 5 0.09
59 27 0.50
60 22 0.41
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.49
Consensus pattern (59 bp):
TTTTTTTTGCCAAATTTGGTACTTGAACTTGACATTTTTCCCTAATTTGGTACCTAAAC
Found at i:16008396 original size:60 final size:60
Alignment explanation
Indices: 16008293--16008406 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 60
16008283 TTTTTTGTCA
*
16008293 AATTTGGTACTTTAACTTGACACTTTTTCCTAATTTGGTACCTAAACT-TTTTTAGGCCC
1 AATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTATTTTTAGGCCC
** * *
16008352 AATTTGGTACTTGAACTTGGTA-TTTTTCCCCTAGTTTGGTACCTAAGCTATTTTT
1 AATTTGGTACTTGAACTTGACACTTTTT--CCTAATTTGGTACCTAAACTATTTTT
16008407 TAGGTTCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 5 0.11
59 19 0.40
60 18 0.38
61 5 0.11
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (60 bp):
AATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTATTTTTAGGCCC
Found at i:16008925 original size:28 final size:29
Alignment explanation
Indices: 16008886--16008971 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 29
16008876 CCAACTTTTA
*
16008886 AAAAATTGTCAAGTTTATGTACCAAATT-
1 AAAAAGTGTCAAGTTTATGTACCAAATTG
* ** *
16008914 AAGAAGTGTCAAGTTTGGGTACTAAATTAGG
1 AAAAAGTGTCAAGTTTATGTACCAAATT--G
* *
16008945 AAAAAGTGTCAAGTTCATATACCAAAT
1 AAAAAGTGTCAAGTTTATGTACCAAAT
16008972 GTTATATTAA
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
28 23 0.52
31 21 0.48
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (29 bp):
AAAAAGTGTCAAGTTTATGTACCAAATTG
Found at i:16010363 original size:26 final size:26
Alignment explanation
Indices: 16010334--16010394 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
16010324 TAGGTTAATT
* *
16010334 TTAAAATAAGTAATATGTAAAATAAC
1 TTAAAATAAATAATATATAAAATAAC
*
16010360 TTAAAATAAATAATATATAAAGTAAC
1 TTAAAATAAATAATATATAAAATAAC
16010386 TTAAAATAA
1 TTAAAATAA
16010395 TTAGTCTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:16010442 original size:21 final size:21
Alignment explanation
Indices: 16010413--16010452 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16010403 ATAAGTTAGG
16010413 TTAAAATAATAAATAAAAGGT
1 TTAAAATAATAAATAAAAGGT
* **
16010434 TTAATATAATCTATAAAAG
1 TTAAAATAATAAATAAAAG
16010453 AGAAAATTGG
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:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAAATAATAAATAAAAGGT
Found at i:16010522 original size:16 final size:16
Alignment explanation
Indices: 16010503--16010545 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
16010493 TTAAAATAAC
16010503 ATATATAAAGTGATA-T
1 ATATATAAAGT-ATATT
*
16010519 ATATATAAACATATATT
1 ATATATAAA-GTATATT
16010536 ATATATAAAG
1 ATATATAAAG
16010546 GTTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (16 bp):
ATATATAAAGTATATT
Found at i:16011805 original size:21 final size:20
Alignment explanation
Indices: 16011772--16011811 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
16011762 AATCGGGTTT
16011772 GGGTTAGGCTAATTTGGGCTG
1 GGGTTAGGCTAA-TTGGGCTG
16011793 GGGTT-GGCTTAATTGGGCT
1 GGGTTAGGC-TAATTGGGCT
16011812 TAGTTCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.12, C:0.10, G:0.42, T:0.35
Consensus pattern (20 bp):
GGGTTAGGCTAATTGGGCTG
Found at i:16015505 original size:30 final size:31
Alignment explanation
Indices: 16015479--16015535 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
16015469 AATAAAATTT
16015479 TATAT-ATT-TCAAGTTCAAATATTAAAATA
1 TATATAATTGTCAAGTTCAAATATTAAAATA
* *
16015508 TATCTAATTGTCAAGTTCAATTATTAAA
1 TATATAATTGTCAAGTTCAAATATTAAA
16015536 GTGTTATGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 3 0.12
31 17 0.71
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (31 bp):
TATATAATTGTCAAGTTCAAATATTAAAATA
Found at i:16015547 original size:77 final size:77
Alignment explanation
Indices: 16015454--16015615 Score: 315
Period size: 77 Copynumber: 2.1 Consensus size: 77
16015444 TGAGATAATC
*
16015454 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAATATTAAAATATATCTAATTGT
1 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
16015519 CAAGTTCAATTA
66 CAAGTTCAATTA
16015531 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
1 TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
16015596 CAAGTTCAATTA
66 CAAGTTCAATTA
16015608 TTAAAGTG
1 TTAAAGTG
16015616 GACAAAAAAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 84 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.42
Consensus pattern (77 bp):
TTAAAGTGTTATGTCAATAAAATTTTATATATTTCAAGTTCAAAGATTAAAATATATCTAATTGT
CAAGTTCAATTA
Found at i:16016081 original size:61 final size:60
Alignment explanation
Indices: 16015908--16016203 Score: 174
Period size: 61 Copynumber: 4.9 Consensus size: 60
16015898 TTATATTATT
*
16015908 ATATATTATGATTTTAGTAAATTAATATAAGAATAATT-A-TATTAAGAATTTTATTA-AAT-
1 ATATATTATGA-TTTAGTAAATTCATATAAGAAT-ATTAATTATTAAGAATTTTA-TAGAATC
** * * *
16015967 -TATA-TAT-ATTT--T-AATTACAATATACCTAATAATAATTATGTTAATTTATATTTTATAGC
1 ATATATTATGATTTAGTAAATT-C-ATATA-AGAATATTAATTA--TTAA--GA-ATTTTATAGA
16016026 ATC
58 ATC
* *
16016029 ATATATTATGATTTGGGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTA-AATT
1 ATATATTATGATTT-AGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA-TAGAATC
* * * * * * * *
16016090 ATATATTTTAATTATAATATATTTAATAATAA-ATATGTTAA-T-TT-A-TATTTTATAGTATC
1 ATATATTATGATT-TAGTA-AATTCAT-ATAAGA-ATATTAATTATTAAGAATTTTATAGAATC
16016149 ATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTAT
1 ATATATTATGATTT-AGTAAATTCATATAAGAATATTAATTATTAAGAATTTTAT
16016204 TAAATTATAT
Statistics
Matches: 177, Mismatches: 29, Indels: 60
0.67 0.11 0.23
Matches are distributed among these distances:
52 4 0.02
53 1 0.01
54 7 0.04
55 7 0.04
56 3 0.02
57 13 0.07
58 18 0.10
59 24 0.14
60 5 0.03
61 38 0.21
62 11 0.06
63 14 0.08
64 7 0.04
65 4 0.02
66 10 0.06
67 5 0.03
68 2 0.01
69 4 0.02
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (60 bp):
ATATATTATGATTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATAGAATC
Found at i:16016116 original size:15 final size:15
Alignment explanation
Indices: 16016081--16016132 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
16016071 TTAAGAATTT
*
16016081 TATTAAATTAT-ATA
1 TATTTAATTATAATA
16016095 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
16016109 TATTTAATAATAA-A
1 TATTTAATTATAATA
16016123 TATGTTAATT
1 TAT-TTAATT
16016133 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 9 0.28
15 15 0.47
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:16016131 original size:120 final size:120
Alignment explanation
Indices: 16015908--16016246 Score: 542
Period size: 120 Copynumber: 2.8 Consensus size: 120
16015898 TTATATTATT
* *
16015908 ATATATTATGATTTTAGTAAATTAATATAAGAATAATT-A-TATTAAGAATTTTATTAAATTATA
1 ATATATTATGATTTCAGTAAATTCATATAAGAAT-ATTAATTATTAAGAATTTTATTAAA-T-TA
* **
16015971 TATATTTTAATTACAATATACCTAATAATAATTATGTTAATTTATATTTTATAGCATC
63 TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGCATC
**
16016029 ATATATTATGATTTGGGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
1 ATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
* *
16016094 ATTTTAATTATAATATATTTAATAATAAATATGTTAATTTATATTTTATAGTATC
66 ATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGCATC
16016149 ATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAA-T-TAT
1 ATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
16016212 ATTTTAATTATAATATATTTAATAATAATTATGTT
66 ATTTTAATTATAATATATTTAATAATAATTATGTT
16016247 TAAATATGAT
Statistics
Matches: 205, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
118 37 0.18
119 1 0.00
120 115 0.56
121 33 0.16
122 19 0.09
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTATGATTTCAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
ATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGCATC
Found at i:16016153 original size:59 final size:59
Alignment explanation
Indices: 16015970--16016155 Score: 139
Period size: 59 Copynumber: 3.1 Consensus size: 59
16015960 ATTAAATTAT
* ** * *
16015970 ATATATTTTAATTACAATATACCTAATAATAATTATGTTAATTTATATTTTATAGCATC
1 ATATATTTTAATTATAATATAATTAATAATAAATATGTTAATTTATATTTTATAGAATC
* * ** * * *
16016029 ATATATTATGATT-TGGGTA-AATTCAT-ATAAGA-ATATTAATTATTAAGAATTTTATTA-AAT
1 ATATATTTTAATTAT-AATATAATTAATAATAA-ATATGTTAA-T-TT-A-TATTTTA-TAGAAT
*
16016089 T
59 C
* *
16016090 ATATATTTTAATTATAATATATTTAATAATAAATATGTTAATTTATATTTTATAGTATC
1 ATATATTTTAATTATAATATAATTAATAATAAATATGTTAATTTATATTTTATAGAATC
16016149 ATATATT
1 ATATATT
16016156 ATGATTTCAG
Statistics
Matches: 92, Mismatches: 23, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
57 10 0.11
58 7 0.08
59 30 0.33
60 2 0.02
61 23 0.25
62 10 0.11
63 10 0.11
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (59 bp):
ATATATTTTAATTATAATATAATTAATAATAAATATGTTAATTTATATTTTATAGAATC
Found at i:16016184 original size:59 final size:58
Alignment explanation
Indices: 16016003--16016184 Score: 156
Period size: 59 Copynumber: 3.1 Consensus size: 58
16015993 TAATAATAAT
* *
16016003 TATGTTAATTTATATTTTATAGCATCATATATTATGATTTGGGTAAATTCATATAAGAA
1 TATGTTAATTTATATTTTATAGAATCATATATTATGATTT-AGTAAATTCATATAAGAA
* * * * * * * *
16016062 TA--TTAATTATTAAGAATTTTATTA-AATTATATATTTTAATTATAATATATTTA-ATAATAAA
1 TATGTTAA-T-TT-A-TATTTTA-TAGAATCATATATTATGATT-TAGTAAATTCATATAA-GAA
*
16016123 TATGTTAATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAA
1 TATGTTAATTTATATTTTATAGAATCATATATTATGATTT-AGTAAATTCATATAAGAA
16016182 TAT
1 TAT
16016185 TAATTATTAA
Statistics
Matches: 92, Mismatches: 19, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
57 4 0.04
58 4 0.04
59 35 0.38
60 10 0.11
61 31 0.34
62 4 0.04
63 4 0.04
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (58 bp):
TATGTTAATTTATATTTTATAGAATCATATATTATGATTTAGTAAATTCATATAAGAA
Found at i:16016228 original size:16 final size:16
Alignment explanation
Indices: 16016184--16016249 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 16
16016174 TATAAGAATA
*
16016184 TTAATTATTAAGA-ATT
1 TTAATTA-TAATATATT
16016200 TT-ATTA-AATTATATT
1 TTAATTATAA-TATATT
16016215 TTAATTATAATATA-T
1 TTAATTATAATATATT
*
16016230 TTAATAATAAT-TATGT
1 TTAATTATAATATAT-T
16016246 TTAA
1 TTAA
16016250 ATATGATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
13 2 0.05
14 3 0.07
15 20 0.48
16 15 0.36
17 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTAATTATAATATATT
Found at i:16016521 original size:16 final size:16
Alignment explanation
Indices: 16016463--16016527 Score: 76
Period size: 16 Copynumber: 4.1 Consensus size: 16
16016453 TTGATTTGCT
* *
16016463 ATTACACCTCTAATCC
1 ATTACGCCTCTATTCC
* *
16016479 ATTACACCTCTATCCC
1 ATTACGCCTCTATTCC
*
16016495 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
*
16016511 ATTATGCCTCTATTCC
1 ATTACGCCTCTATTCC
16016527 A
1 A
16016528 ATACAGCGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.25, C:0.35, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:16020481 original size:30 final size:30
Alignment explanation
Indices: 16020432--16020499 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
16020422 ATAGTTGAAC
*
16020432 CTAAATT-TTGGAATTTAAAAAGTA-AAGAAA
1 CTAAATTCTTGGAATGT-AAAAGTATAA-AAA
*
16020462 CTAAATTCTTGGAA-GTAAAAGTATAATAA
1 CTAAATTCTTGGAATGTAAAAGTATAAAAA
16020491 CTAAATTCT
1 CTAAATTCT
16020500 AAATTATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 18 0.53
30 10 0.29
31 6 0.18
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (30 bp):
CTAAATTCTTGGAATGTAAAAGTATAAAAA
Found at i:16022152 original size:23 final size:23
Alignment explanation
Indices: 16022109--16022157 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
16022099 AACTTTTTAA
*
16022109 AAATAAAATCTAAAAATATATAAC
1 AAATAAAATCTAAAAAAATAT-AC
16022133 AAATAAAAT-TAAAAAAATATAC
1 AAATAAAATCTAAAAAAATATAC
16022155 AAA
1 AAA
16022158 AAAGATAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
23 10 0.42
24 9 0.38
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAAATCTAAAAAAATATAC
Found at i:16022465 original size:24 final size:24
Alignment explanation
Indices: 16022437--16022509 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 24
16022427 AAATTTGTTA
16022437 TTTTATTTTCAATTTATATATATT
1 TTTTATTTTCAATTTATATATATT
16022461 CTTTATATTTATTTCAA-TT-T-TATATT
1 -TTT-TA--T-TTTCAATTTATATATATT
*
16022487 TTATATTTTCAATTTATATATAT
1 TTTTATTTTCAATTTATATATAT
16022510 ACATTAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
21 6 0.15
22 3 0.08
23 1 0.03
24 7 0.17
25 5 0.12
26 8 0.20
27 1 0.03
28 3 0.08
29 6 0.15
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATTTTCAATTTATATATATT
Found at i:16022502 original size:50 final size:52
Alignment explanation
Indices: 16022440--16022546 Score: 148
Period size: 50 Copynumber: 2.1 Consensus size: 52
16022430 TTTGTTATTT
* *
16022440 TATTTTCAATTTATATATATTCTTTATATTTATTTCAA-TTTTAT-ATTT-TA
1 TATTTTCAATTTATATATATACATTA-ATTTATTTCAAGTTTTATGATTTATA
* *
16022490 TATTTTCAATTTATATATATACATTAATTTTTTTGAAGTTTTATGATTTATA
1 TATTTTCAATTTATATATATACATTAATTTATTTCAAGTTTTATGATTTATA
16022542 TATTT
1 TATTT
16022547 CTTATATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 9 0.18
50 30 0.60
51 4 0.08
52 7 0.14
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (52 bp):
TATTTTCAATTTATATATATACATTAATTTATTTCAAGTTTTATGATTTATA
Found at i:16034643 original size:12 final size:13
Alignment explanation
Indices: 16034626--16034656 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16034616 AGAAATAGTG
16034626 AAATTGGA-TTTT
1 AAATTGGAGTTTT
16034638 AAATTGGAGTTTT
1 AAATTGGAGTTTT
16034651 AAATTG
1 AAATTG
16034657 AAAGATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (13 bp):
AAATTGGAGTTTT
Found at i:16040506 original size:44 final size:44
Alignment explanation
Indices: 16040443--16041253 Score: 311
Period size: 44 Copynumber: 18.6 Consensus size: 44
16040433 CTTGGGTCTA
*
16040443 CTCCACTGCAACTTTAGGGAGATAAGATTATCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTG
* ** ** * * *
16040487 CTCCACTGCATCTTCAGGGAGATAAGATCTGCCATCTTCAGTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TATCGGCTTTAATCTG
* *** *
16040532 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGTTTAC-TTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGA-TTATCGGCTTTAATCTG
* * * ***
16040576 CTCCACTACAACTTCAGGGAGATAAGACTA---GATGCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTG
* * * * * * * *
16040617 -TTCTCTACAACTTCAGAGAGATAAGATCCA-AGGTTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TATCGGCTTTAATCTG
* *
16040660 CTCCACTGTAACTTCAGGGAGATAGGATTATCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTG
* *
16040704 CTCCACTGCAACTTCAGGGAGATAAGATT-T-GCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGC-T-TT-AATCTG
* * *** *
16040749 C-CTCACTGCAACTTTA-GGAGGATAAGACTTGTTTAC-TTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGA-TTATCGGCTTTAATCTG
* * ** * *
16040793 CTCCACTGCAACTTCAGGGAGATAAAACTATATGC---GATATG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTG
* * * * * * *
16040834 CT-CTCTGTAACTTCAGAGAGATAAGATCCA-AGGTTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TATCGGCTTTAATCTG
* * * *
16040877 CTCCACTACAACTTCAGGGAAATAGGATTATCAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTG
* *
16040921 CTCCACTGCAACTTCAGGGAGATAAGATT-T-GCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGC-T-TT-AATCTG
* *** *
16040966 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGTTTAC-TTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGA-TTATCGGCTTTAATCTG
* * * *** *
16041010 CTCCACTGCAACTTCAAGGAGATAAGACTA---GATGCGATCAG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTG
*** * * * * * * * *
16041051 CT-TTTTGTAACTTTAGAGAGGTAAGATCCA-AGGTTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TATCGGCTTTAATCTG
* * * *
16041094 CTCCACTGCAACTTTAGGGAAATAGGATTATCAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTG
* * * *
16041138 CTCTACTGCAACTTCAGGGATATAAGATT-T-GCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTATCGGC-T-TT-AATCTG
* *** *
16041183 -TCTCACTGCAACTTCA-GGAGGATAAGAATTGTTTAC-TTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAG-ATTATCGGCTTTAATCTG
* *
16041227 CTCCACTGCAATTTTAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
16041254 CTAGATGCGA
Statistics
Matches: 572, Mismatches: 141, Indels: 109
0.70 0.17 0.13
Matches are distributed among these distances:
40 61 0.11
41 17 0.03
42 4 0.01
43 35 0.06
44 313 0.55
45 128 0.22
46 8 0.01
47 3 0.01
48 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAATCTG
Found at i:16040830 original size:217 final size:217
Alignment explanation
Indices: 16040443--16041341 Score: 1447
Period size: 217 Copynumber: 4.1 Consensus size: 217
16040433 CTTGGGTCTA
* * * *
16040443 CTCCACTGCAACTTTAGGGAGATAAGATTATCGGCTTTAATCTGCTCCACTGCATCTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
* *
16040508 ATAAGATCTGCCATCTTCAGTTTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGT
66 ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGT
* * *
16040573 CTGCTCCACTACAACTTCAGGGAGATAAGACTAGATGCGATCTGTTCTCTACAACTTCAGAGAGA
131 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGA
16040638 TAAGATCCAAGGTTTTAATCCG
196 TAAGATCCAAGGTTTTAATCCG
* *
16040660 CTCCACTGTAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
*
16040725 ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACTTGTTTACTTAGT
66 ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGT
* * * *
16040790 CTGCTCCACTGCAACTTCAGGGAGATAAAACTATATGCGATATGCTCTCTGTAACTTCAGAGAGA
131 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGA
16040855 TAAGATCCAAGGTTTTAATCCG
196 TAAGATCCAAGGTTTTAATCCG
* *
16040877 CTCCACTACAACTTCAGGGAAATAGGATTATCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
16040942 ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGT
66 ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGT
* * * * * * *
16041007 CTGCTCCACTGCAACTTCAAGGAGATAAGACTAGATGCGATCAGCTTTTTGTAACTTTAGAGAGG
131 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGA
16041072 TAAGATCCAAGGTTTTAATCCG
196 TAAGATCCAAGGTTTTAATCCG
* * * *
16041094 CTCCACTGCAACTTTAGGGAAATAGGATTATCAGCTTTAATCTGCTCTACTGCAACTTCAGGGAT
1 CTCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
* *
16041159 ATAAGATTTGCCATCTTCAGTCTGTCTCACTGCAACTTCAGGAGGATAAGAATTGTTTACTTAGT
66 ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGT
* * * * *
16041224 CTGCTCCACTGCAATTTTAGGGAGATAAGACTAGATGCGATTTGCTCTTTGCAACTTCAGAGAGG
131 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGA
*
16041289 TAAGATCCAAGGTTTTAATCTG
196 TAAGATCCAAGGTTTTAATCCG
* *
16041311 CTCCACTGCAACTTAAGGGAGATATGATTAT
1 CTCCACTGCAACTTCAGGGAGATAGGATTAT
16041342 TGGCCACCGA
Statistics
Matches: 636, Mismatches: 46, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 636 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (217 bp):
CTCCACTGCAACTTCAGGGAGATAGGATTATCAGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
ATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAGT
CTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGA
TAAGATCCAAGGTTTTAATCCG
Found at i:16041013 original size:89 final size:88
Alignment explanation
Indices: 16040438--16041036 Score: 325
Period size: 89 Copynumber: 6.9 Consensus size: 88
16040428 TATTTCTTGG
* * * *** * *
16040438 GTCTACTCCACTGCAACTTTAGGGAGATAAGA-TTATCGGCTTTAATCTGCTCCACTGCATCTTC
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTAC-TTAGTCTGCTCCACTGCAACTTC
*
16040502 AGGGAGATAAGATCTGCCATCTTCA
65 AGGGAGATAAGATTTGCCAT-TTCA
* *
16040527 GTTTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTGTTTACTTAGTCTGCTCCACTACAACTT
1 GTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTT
* * *
16040590 CAGGGAGATAAGACTAG--A-TGC-
64 CAGGGAGATAAGATTTGCCATTTCA
* * * * ** * * * *
16040611 GATCTG-TTCTCTACAACTTCAGAGAGATAAGATCCAAGGTT--TTAATCCGCTCCACTGTAACT
1 G-TCTGCTCCACTGCAACTTCAGGGAGATAAGA--CTTGTTTACTTAGTCTGCTCCACTGCAACT
* *
16040673 TCAGGGAGATAGGATTATCGGC-TTT-A
63 TCAGGGAGATAAGATT-T-GCCATTTCA
* * **
16040699 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-CCATCTTCAGTCTGC-CTCACTGCAACT
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTA-CTT-AGTCTGCTC-CACTGCAACT
* * ** *
16040762 TTA-GGAGGATAAGACTTGTTTACTT-A
63 TCAGGGA-GATAAGATTTG-CCATTTCA
* * * * * * * *
16040788 GTCTGCTCCACTGCAACTTCAGGGAGATAAAAC-TATATGC-GA-TATGCT-CTCTGTAACTTCA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTTCA
* *
16040849 GAGAGATAAGA--T-CCAAGGTTTTA
66 GGGAGATAAGATTTGCC-A--TTTCA
* * * * * * * *
16040872 ATCCGCTCCACTACAACTTCAGGGAAATAGGA-TT-ATCAGCTTTAATCTGCTCCACTGCAACTT
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTA-C-TTAGTCTGCTCCACTGCAACTT
16040935 CAGGGAGATAAGATTTGCCATCTTCA
64 CAGGGAGATAAGATTTGCCAT-TTCA
16040961 GTCTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTT
1 GTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTT
*
16041024 CAAGGAGATAAGA
64 CAGGGAGATAAGA
16041037 CTAGATGCGA
Statistics
Matches: 376, Mismatches: 90, Indels: 88
0.68 0.16 0.16
Matches are distributed among these distances:
81 1 0.00
82 1 0.00
83 2 0.01
84 96 0.26
85 13 0.03
86 8 0.02
87 11 0.03
88 62 0.16
89 169 0.45
90 9 0.02
91 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (88 bp):
GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTTCA
GGGAGATAAGATTTGCCATTTCA
Found at i:16042168 original size:24 final size:27
Alignment explanation
Indices: 16042141--16042189 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
16042131 AGTGTCTTGA
16042141 AAAGAA-AAAGTA-TT-CAAGAACAGC
1 AAAGAATAAAGTATTTACAAGAACAGC
16042165 AAAGAATAAAGTATTTACAAGAACA
1 AAAGAATAAAGTATTTACAAGAACA
16042190 AACAAACTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 6 0.27
26 2 0.09
27 8 0.36
ACGTcount: A:0.59, C:0.10, G:0.14, T:0.16
Consensus pattern (27 bp):
AAAGAATAAAGTATTTACAAGAACAGC
Found at i:16058471 original size:46 final size:46
Alignment explanation
Indices: 16058371--16058742 Score: 466
Period size: 46 Copynumber: 8.6 Consensus size: 46
16058361 TACATATGAT
*
16058371 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
16058414 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
16058460 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
16058506 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-A-G----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
16058542 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
16058588 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A-G----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
16058624 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* * *
16058670 CACTTATCATTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
16058716 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
16058743 AGTACTCAAA
Statistics
Matches: 291, Mismatches: 15, Indels: 43
0.83 0.04 0.12
Matches are distributed among these distances:
36 57 0.20
38 5 0.02
39 1 0.00
40 4 0.01
41 4 0.01
42 4 0.01
43 11 0.04
44 10 0.03
45 19 0.07
46 176 0.60
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:16058547 original size:36 final size:36
Alignment explanation
Indices: 16058506--16058660 Score: 175
Period size: 36 Copynumber: 4.0 Consensus size: 36
16058496 CTAAGGCTAA
16058506 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
16058542 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* *
16058584 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
16058624 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
16058660 C
1 C
16058661 TAATGCTACC
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 64 0.62
38 3 0.03
40 3 0.03
42 3 0.03
44 2 0.02
46 28 0.27
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:16058597 original size:82 final size:82
Alignment explanation
Indices: 16058460--16058706 Score: 422
Period size: 82 Copynumber: 3.0 Consensus size: 82
16058450 CTAAGGCTAC
* * *
16058460 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
*
16058525 TGATCAGATAAGTATAG
66 TGATCAGATAAGTGTAG
*
16058542 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
16058607 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
* * *
16058624 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCATTTTCTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
16058689 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
16058706 C
1 C
16058707 TAATGCTACC
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 156 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
TGATCAGATAAGTGTAG
Found at i:16058609 original size:128 final size:123
Alignment explanation
Indices: 16058371--16058742 Score: 409
Period size: 128 Copynumber: 2.9 Consensus size: 123
16058361 TACATATGAT
* * * *
16058371 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAG-GTA-CTA--ATGCCACTTATCACTTTTTCACTT
* * *
16058434 GATCAGATAAGAGTAGCTAAGGCTACCACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTA
62 GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGATAA--GT-G-T-
16058499 AGG
122 A-G
16058502 CTAACACTTATCACTTTGTCACTTGATCAGATAA-GTA-T-A-G-CACTTATCACTTTTTCACTT
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGGTACTAATGCCACTTATCACTTTTTCACTT
* *
16058562 GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
62 GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
*
16058624 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCA-TTTTCTCAC
1 CACTTATCACTTTGTCACTTGATCAGATAAG-GTA-CTAATG---CCACTTATCACTTTT-TCAC
*
16058688 TTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTATCACTTGATCAGA
60 TTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGA
16058743 AGTACTCAAA
Statistics
Matches: 212, Mismatches: 12, Indels: 33
0.82 0.05 0.13
Matches are distributed among these distances:
118 29 0.14
120 3 0.01
122 2 0.01
123 2 0.01
124 2 0.01
125 1 0.00
126 2 0.01
127 4 0.02
128 136 0.64
133 1 0.00
135 13 0.06
136 5 0.02
137 12 0.06
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (123 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGGTACTAATGCCACTTATCACTTTTTCACTTGATC
AGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
Found at i:16061457 original size:27 final size:27
Alignment explanation
Indices: 16061394--16061475 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 27
16061384 CCCAAACTGA
* *
16061394 TATAAAATGACTGTTATGCCCCCACGT
1 TATAAAATGACTGTTATGCCCCTATGT
** *
16061421 GGTAATATGACTGTTATGCCCCTATGT
1 TATAAAATGACTGTTATGCCCCTATGT
* *
16061448 TATAAAATGACT-ATATG-CTCTATGT
1 TATAAAATGACTGTTATGCCCCTATGT
16061473 TAT
1 TAT
16061476 GTATGACTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
25 10 0.22
26 4 0.09
27 31 0.69
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (27 bp):
TATAAAATGACTGTTATGCCCCTATGT
Found at i:16062572 original size:36 final size:36
Alignment explanation
Indices: 16062449--16062684 Score: 134
Period size: 36 Copynumber: 6.6 Consensus size: 36
16062439 TTGGTTTTGA
* *
16062449 ACACTCATTTTTCAATTTTACCGACCAGCGCAGGAC
1 ACACTCATTTTTCAGTTTTACCGACCAGCGCAGGGC
* * * * * * *
16062485 GCACTTATTTGTT-GGTTATACCGACTAGTGCTGGGC
1 ACACTCATTT-TTCAGTTTTACCGACCAGCGCAGGGC
*
16062521 ACACTCATTTTTCAGTTTTATCGACCAGCGCAGGGC
1 ACACTCATTTTTCAGTTTTACCGACCAGCGCAGGGC
* * * * *****
16062557 ACACTTATTTATCAGTTATACCAACCAATATGGGGC
1 ACACTCATTTTTCAGTTTTACCGACCAGCGCAGGGC
* * * *
16062593 ACATTTATTTTTC-GATTTTACCGACCAGTGCAGGGT
1 ACACTCATTTTTCAG-TTTTACCGACCAGCGCAGGGC
* * * * * ** **
16062629 GCACTTATTTGTCAGTTATACTGACCAATGTTGGGC
1 ACACTCATTTTTCAGTTTTACCGACCAGCGCAGGGC
* *
16062665 ACACTCATTTGTCAATTTTA
1 ACACTCATTTTTCAGTTTTA
16062685 TCGGCCAGTG
Statistics
Matches: 147, Mismatches: 49, Indels: 8
0.72 0.24 0.04
Matches are distributed among these distances:
35 3 0.02
36 141 0.96
37 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (36 bp):
ACACTCATTTTTCAGTTTTACCGACCAGCGCAGGGC
Found at i:16062703 original size:72 final size:72
Alignment explanation
Indices: 16062449--16062684 Score: 292
Period size: 72 Copynumber: 3.3 Consensus size: 72
16062439 TTGGTTTTGA
* ** * *
16062449 ACACTCATTTTTCAATTTTACCGACCAGCGCAGGACGCACTTATTTGTTGGTTATACCGACTAGT
1 ACACTCATTTTTCAATTTTACCGACCAGCGCAGGGCGCACTTATTTGTCAGTTATACCGACCAAT
*
16062514 GCTGGGC
66 GTTGGGC
* * * * *
16062521 ACACTCATTTTTCAGTTTTATCGACCAGCGCAGGGCACACTTATTTATCAGTTATACCAACCAAT
1 ACACTCATTTTTCAATTTTACCGACCAGCGCAGGGCGCACTTATTTGTCAGTTATACCGACCAAT
* *
16062586 ATGGGGC
66 GTTGGGC
* * * * * *
16062593 ACATTTATTTTTCGATTTTACCGACCAGTGCAGGGTGCACTTATTTGTCAGTTATACTGACCAAT
1 ACACTCATTTTTCAATTTTACCGACCAGCGCAGGGCGCACTTATTTGTCAGTTATACCGACCAAT
16062658 GTTGGGC
66 GTTGGGC
*
16062665 ACACTCATTTGTCAATTTTA
1 ACACTCATTTTTCAATTTTA
16062685 TCGGCCAGTG
Statistics
Matches: 134, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 134 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (72 bp):
ACACTCATTTTTCAATTTTACCGACCAGCGCAGGGCGCACTTATTTGTCAGTTATACCGACCAAT
GTTGGGC
Found at i:16069045 original size:43 final size:46
Alignment explanation
Indices: 16068941--16069061 Score: 133
Period size: 47 Copynumber: 2.7 Consensus size: 46
16068931 ATAGTTGAAG
*
16068941 GATGCCATAGTGTCTTTCAACCATGGTCTTATATATTTTTACGTCAT
1 GATGCCATA-TGTCTTTCAACCATGGTCTTATATATTTTGACGTCAT
* * *
16068988 GTTGTCATAGTGTCTTTCAACCATGGTCTTAT-T-TTTCTGA-TTCAT
1 GATGCCATA-TGTCTTTCAACCATGGTCTTATATATTT-TGACGTCAT
* *
16069033 GATGCCAT-TGTCTTTCAGCTATGGTCTTA
1 GATGCCATATGTCTTTCAACCATGGTCTTA
16069062 CTCGTTTTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 19 0.29
45 13 0.20
46 3 0.05
47 30 0.46
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.45
Consensus pattern (46 bp):
GATGCCATATGTCTTTCAACCATGGTCTTATATATTTTGACGTCAT
Found at i:16071488 original size:25 final size:25
Alignment explanation
Indices: 16071441--16071488 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
16071431 AACGTAATTC
*
16071441 GAACAGAACAAAATCGAATAGAGCA
1 GAACAGAACAAAATCGAACAGAGCA
* *
16071466 GAACAGAACAAGATGGAACAGAG
1 GAACAGAACAAAATCGAACAGAG
16071489 TAGAGCAATA
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:0.54, C:0.15, G:0.25, T:0.06
Consensus pattern (25 bp):
GAACAGAACAAAATCGAACAGAGCA
Found at i:16072581 original size:42 final size:41
Alignment explanation
Indices: 16072522--16072681 Score: 167
Period size: 42 Copynumber: 3.8 Consensus size: 41
16072512 GAGTTACATG
* *
16072522 GCTTGGACACACACCCATATCCTTGCCCGTGTGGCTCACAC
1 GCTTGGGCACACACCCATGTCCTTGCCCGTGTGGCTCACAC
*
16072563 AGCTTGGGCACACACCCATGTCCTTGCCAGTGTGGCTCACAC
1 -GCTTGGGCACACACCCATGTCCTTGCCCGTGTGGCTCACAC
* * * * * * *
16072605 GGTCTAGGCATACGCCGATGTCCTTGCCCGTGTAGCTCACATG
1 GCT-TGGGCACACACCCATGTCCTTGCCCGTGTGGCTCACA-C
* * * *
16072648 GCCTGGGCACACGCCCATGTCCCTGGCCGTGTGG
1 GCTTGGGCACACACCCATGTCCTTGCCCGTGTGG
16072682 TTCTAAAGCG
Statistics
Matches: 97, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
41 2 0.02
42 94 0.97
43 1 0.01
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (41 bp):
GCTTGGGCACACACCCATGTCCTTGCCCGTGTGGCTCACAC
Found at i:16073620 original size:17 final size:17
Alignment explanation
Indices: 16073566--16073626 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 17
16073556 AAAGGGTGAG
*
16073566 AAGTAAAAGTTTAGGGGAA
1 AAGTAAAAGTTT-GAGG-A
* *
16073585 AAATAAAAAGTTTTAGG-
1 AAGT-AAAAGTTTGAGGA
16073602 AAGTAAAAGTTTGAGGGA
1 AAGTAAAAGTTTGA-GGA
16073620 AAGTAAA
1 AAGTAAA
16073627 TAGGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 9 0.26
17 5 0.15
18 7 0.21
19 5 0.15
20 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (17 bp):
AAGTAAAAGTTTGAGGA
Found at i:16074860 original size:21 final size:19
Alignment explanation
Indices: 16074813--16074860 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 19
16074803 TTCGGTGTGC
16074813 TACAATTTTTTTAAAATTT
1 TACAATTTTTTTAAAATTT
16074832 TA-ATATTTTTTTACAATATTT
1 TACA-ATTTTTTTA-AA-ATTT
16074853 TACAATTT
1 TACAATTT
16074861 CTAATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.04
19 11 0.44
20 2 0.08
21 10 0.40
22 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (19 bp):
TACAATTTTTTTAAAATTT
Found at i:16074880 original size:30 final size:29
Alignment explanation
Indices: 16074821--16074880 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
16074811 GCTACAATTT
* *
16074821 TTTTAAAATTTTAATATTTTTTTACAATA
1 TTTTAAAATTTTAATAATTTATTACAATA
* *
16074850 TTTTACAATTTCTAATAATTTATTATAATA
1 TTTTAAAATTT-TAATAATTTATTACAATA
16074880 T
1 T
16074881 GTATAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTTAAAATTTTAATAATTTATTACAATA
Found at i:16074889 original size:39 final size:37
Alignment explanation
Indices: 16074846--16074929 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 37
16074836 ATTTTTTTAC
*
16074846 AATATTTTACAATTTCTAATAATTTATTATAATATGTAT
1 AATATTTTACAATTTCTAATAAATT-TTATAATAT-TAT
*
16074885 AATATTTTACAATTTCTAATAAATTTTATAATGTTAT
1 AATATTTTACAATTTCTAATAAATTTTATAATATTAT
*
16074922 GATATTTT
1 AATATTTT
16074930 TATTATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
37 10 0.24
38 8 0.19
39 24 0.57
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (37 bp):
AATATTTTACAATTTCTAATAAATTTTATAATATTAT
Found at i:16074904 original size:17 final size:17
Alignment explanation
Indices: 16074846--16074905 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
16074836 ATTTTTTTAC
16074846 AATATTTTACAATTTCT
1 AATATTTTACAATTTCT
* *
16074863 AATAATTTATTATAATATGTAT
1 AAT-A-TT-TTACAAT-T-TCT
16074885 AATATTTTACAATTTCT
1 AATATTTTACAATTTCT
16074902 AATA
1 AATA
16074906 AATTTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 9 0.26
18 2 0.06
19 8 0.24
20 8 0.24
21 2 0.06
22 5 0.15
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.50
Consensus pattern (17 bp):
AATATTTTACAATTTCT
Found at i:16074912 original size:19 final size:19
Alignment explanation
Indices: 16074849--16074912 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
16074839 TTTTTACAAT
16074849 ATTTTACAATTTCTAATAA
1 ATTTTACAATTTCTAATAA
* * * *
16074868 TTTATTATAATATGT-ATAA
1 ATT-TTACAATTTCTAATAA
16074887 TATTTTACAATTTCTAATAA
1 -ATTTTACAATTTCTAATAA
16074907 ATTTTA
1 ATTTTA
16074913 TAATGTTATG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTTACAATTTCTAATAA
Found at i:16087784 original size:15 final size:15
Alignment explanation
Indices: 16087766--16087796 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16087756 AAAAATTCCC
16087766 AATCAAAATAAAAAA
1 AATCAAAATAAAAAA
*
16087781 AATCGAAATAAAAAA
1 AATCAAAATAAAAAA
16087796 A
1 A
16087797 TAAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.13
Consensus pattern (15 bp):
AATCAAAATAAAAAA
Found at i:16087796 original size:23 final size:23
Alignment explanation
Indices: 16087770--16087866 Score: 92
Period size: 23 Copynumber: 4.2 Consensus size: 23
16087760 ATTCCCAATC
*
16087770 AAAATAAAAAAAATCGAAATAAA
1 AAAATAAAAAAAATCAAAATAAA
16087793 AAAATAAAAAAAATCAAAATAAA
1 AAAATAAAAAAAATCAAAATAAA
* * *
16087816 AAAACGGAAAAAAAAACAAAA-AAG
1 AAAA--TAAAAAAAATCAAAATAAA
* *
16087840 AAAGTAAAAAAGAA--AAAAGAAA
1 AAAATAAAAAA-AATCAAAATAAA
16087862 AAAAT
1 AAAAT
16087867 CAAATTGAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
21 4 0.06
22 12 0.19
23 28 0.45
24 5 0.08
25 13 0.21
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.08
Consensus pattern (23 bp):
AAAATAAAAAAAATCAAAATAAA
Found at i:16087877 original size:29 final size:28
Alignment explanation
Indices: 16087799--16087893 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
16087789 TAAAAAAATA
*
16087799 AAAAAAATCAAAATAAAAAAACGGAAAAAAA
1 AAAAAAATCAAAAT-AAAAAA--GAAAAAAG
** *
16087830 AACAAAAAAGAAAGTAAAAAAGAAAAAAG
1 AA-AAAAATCAAAATAAAAAAGAAAAAAG
* ** *
16087859 AAAAAAATCAAATTGAAAATGGCAAAAAG
1 AAAAAAATCAAAAT-AAAAAAGAAAAAAG
16087888 AAAAAA
1 AAAAAA
16087894 GGAAAGGAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
28 9 0.17
29 26 0.50
31 8 0.15
32 9 0.17
ACGTcount: A:0.77, C:0.05, G:0.11, T:0.07
Consensus pattern (28 bp):
AAAAAAATCAAAATAAAAAAGAAAAAAG
Found at i:16090163 original size:44 final size:44
Alignment explanation
Indices: 16090067--16090168 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
16090057 CTCTGGTCAG
* *
16090067 CAGTGGAGTAGATTGAAGCCAAAAATCTTATCTCCCTGAGGTTA
1 CAGTGGAGCAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTA
** * *
16090111 CAACGGAGCAGATTGAAGCCAATAAT-TCTATTTCCCTGAGATTA
1 CAGTGGAGCAGATTGAAGCCAAAAATCT-TATCTCCCTGAGATTA
*
16090155 CAGTGGAGCGGATT
1 CAGTGGAGCAGATT
16090169 AAAATAAAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
43 1 0.02
44 47 0.98
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (44 bp):
CAGTGGAGCAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTA
Found at i:16090445 original size:88 final size:88
Alignment explanation
Indices: 16090307--16090625 Score: 394
Period size: 88 Copynumber: 3.6 Consensus size: 88
16090297 TTGAAAATTA
* * * * *
16090307 CAGATCTTGCCTTCCTGCA-TCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGT
1 CAGATCTTGCCTTCTTGTACT-GACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCACTGGGT
16090371 TGCAGCGGAGCAGGTTGAAA-ATAG
65 TGCAGCGGAGCAGGTT-AAAGATAG
* * *
16090395 C-GCATCTTACCTTCTTGTACTGACAGTGAAGCAGATCGAAGACACTAGCCTTGCCTCACTCGGT
1 CAG-ATCTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCACTGGGT
*
16090459 TGCAGCGGGGCAGGTTAAAGATAG
65 TGCAGCGGAGCAGGTTAAAGATAG
* * *
16090483 CAGATCTCGCCTTCTTGCATTGACAGCGAAGCAGATCG-AGACACTAGCCTTGCCTCACTGGGTT
1 CAGATCTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCACTGGGTT
* ** *
16090547 ACAGTAGAGTAGGTTAAAGATAG
66 GCAGCGGAGCAGGTTAAAGATAG
* * * * *
16090570 CAGATCTTGCTTTCCTGTACTGACAGTGAAGTAGATCGAAGACATTAGCCTTGCCT
1 CAGATCTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
16090626 TCCTGTACTA
Statistics
Matches: 198, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
87 78 0.39
88 118 0.60
89 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (88 bp):
CAGATCTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCACTGGGTT
GCAGCGGAGCAGGTTAAAGATAG
Found at i:16090599 original size:175 final size:176
Alignment explanation
Indices: 16090307--16090625 Score: 464
Period size: 175 Copynumber: 1.8 Consensus size: 176
16090297 TTGAAAATTA
* *
16090307 CAGATCTTGCCTTCCTGCATCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTCGCCTTCCTGCATCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCACTGGGTT
* * *
16090372 GCAGCGGAGCAGGTTGAAAATAGCGCATCTTACCTTCTTGTACTGACAGTGAAGCAGATCGAAGA
66 ACAGCAGAGCAGGTTGAAAATAGCGCATCTTACCTTCCTGTACTGACAGTGAAGCAGATCGAAGA
16090437 CACTAGCCTTGCCTCACTCGGTTGCAGCGGGGCAGGTTAAAGATAG
131 CACTAGCCTTGCCTCACTCGGTTGCAGCGGGGCAGGTTAAAGATAG
* ** *
16090483 CAGATCTCGCCTTCTTGCATTGACAGCGAAGCAGATCG-AGACACTAGCCTTGCCTCACTGGGTT
1 CAGATCTCGCCTTCCTGCATCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCACTGGGTT
* * * * *
16090547 ACAGTAGAGTAGGTT-AAAGATAGCAG-ATCTTGCTTTCCTGTACTGACAGTGAAGTAGATCGAA
66 ACAGCAGAGCAGGTTGAAA-ATAGC-GCATCTTACCTTCCTGTACTGACAGTGAAGCAGATCGAA
*
16090610 GACATTAGCCTTGCCT
129 GACACTAGCCTTGCCT
16090626 TCCTGTACTA
Statistics
Matches: 126, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
174 3 0.02
175 88 0.70
176 35 0.28
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (176 bp):
CAGATCTCGCCTTCCTGCATCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCACTGGGTT
ACAGCAGAGCAGGTTGAAAATAGCGCATCTTACCTTCCTGTACTGACAGTGAAGCAGATCGAAGA
CACTAGCCTTGCCTCACTCGGTTGCAGCGGGGCAGGTTAAAGATAG
Found at i:16090869 original size:44 final size:45
Alignment explanation
Indices: 16090791--16090878 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
16090781 ATCGCATCAA
* *
16090791 GTCTTATCTCCCTGAGGTTGCAGCGGAGTGGACTGAGAA-AGCAG
1 GTCTTATCCCCCTGAAGTTGCAGCGGAGTGGACTGAGAATAGCAG
*
16090835 GTCTTATCCCCCTGAAGTTGCAG-TGAG-GCAGACTGAGAATAGCA
1 GTCTTATCCCCCTGAAGTTGCAGCGGAGTG--GACTGAGAATAGCA
16090879 AAACTTACGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
42 1 0.03
43 3 0.08
44 30 0.79
45 4 0.11
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.23
Consensus pattern (45 bp):
GTCTTATCCCCCTGAAGTTGCAGCGGAGTGGACTGAGAATAGCAG
Found at i:16091081 original size:99 final size:100
Alignment explanation
Indices: 16090900--16091270 Score: 505
Period size: 99 Copynumber: 3.7 Consensus size: 100
16090890 CTAGGCAGTA
* ** * * *
16090900 CAGTGGAACAGATTGAAGCCACAATAGCAAATATTGCTTCCCCAACATTGCAGTT-AAAAGATTA
1 CAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
16090964 AAGCTACAAC-AGCGAATCTTATTTCCCAGGCGGTG
66 AAGCTACAACGA-CGAATCTTATTTCCCAGGCGGTG
* * * *
16090999 CAGTGGAACAGTTTAAAGCCACAACGGCGAATCTTGCTTCCCTGACATTCCAGTTAAAAAGATTG
1 CAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
* * *
16091064 AAGCCACAACGAC-AATCTTACTTCTCAGGCGGTG
66 AAGCTACAACGACGAATCTTATTTCCCAGGCGGTG
* * * * * *
16091098 CAGTGAAACAGATTGAAGTCATAATGGCGAATCTTACTTCCCCGACATTGCAGTTAAAAAGATTA
1 CAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
*
16091163 AAGCTACAACGGCGAATCTTATTTCCCAGGCGGTG
66 AAGCTACAACGACGAATCTTATTTCCCAGGCGGTG
* * *
16091198 CAGTGGAACGGTTTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTG
1 CAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
16091263 AAGCTACA
66 AAGCTACA
16091271 GGCAACGAAT
Statistics
Matches: 233, Mismatches: 36, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
99 131 0.56
100 101 0.43
101 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (100 bp):
CAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
AAGCTACAACGACGAATCTTATTTCCCAGGCGGTG
Found at i:16091250 original size:50 final size:50
Alignment explanation
Indices: 16090900--16091266 Score: 281
Period size: 50 Copynumber: 7.4 Consensus size: 50
16090890 CTAGGCAGTA
* * ** * * *
16090900 CAGTGGAACAGATTGAAGCCACAATAGCAAATATTGCTTCCCCA-ACATTG
1 CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTACTT-CCCAGACATTG
* * * * * **
16090950 CAGTTAAA-AGATTAAAGCTACAACAGCGAATCTTATTTCCCAGGCGGTG
1 CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTACTTCCCAGACATTG
* * * * *
16090999 CAGTGGAACAGTTTAAAGCCACAACGGCGAATCTTGCTTCCCTGACATTC
1 CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTACTTCCCAGACATTG
* * * * * * **
16091049 CAGTTAAAAAGATTGAAGCCACAACGAC-AATCTTACTTCTCAGGCGGTG
1 CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTACTTCCCAGACATTG
* * * * *
16091098 CAGTGAAACAGATTGAAGTCATAATGGCGAATCTTACTTCCCCGACATTG
1 CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTACTTCCCAGACATTG
* * * * * **
16091148 CAGTTAAAAAGATTAAAGCTACAACGGCGAATCTTATTTCCCAGGCGGTG
1 CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTACTTCCCAGACATTG
* * * * *
16091198 CAGTGGAACGGTTTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTG
1 CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTACTTCCCAGACATTG
* * *
16091248 CAGTTAAAAAGATTGAAGC
1 CAGTGAAACAGATTAAAGC
16091267 TACAGGCAAC
Statistics
Matches: 236, Mismatches: 78, Indels: 6
0.74 0.24 0.02
Matches are distributed among these distances:
48 4 0.02
49 68 0.29
50 164 0.69
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (50 bp):
CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTACTTCCCAGACATTG
Found at i:16091254 original size:199 final size:198
Alignment explanation
Indices: 16090900--16091266 Score: 617
Period size: 199 Copynumber: 1.8 Consensus size: 198
16090890 CTAGGCAGTA
* *
16090900 CAGTGGAACAGATTGAAGCCACAATAGCAAATATTGCTTCCCCAACATTGCAGTTAAAAGATTAA
1 CAGTGAAACAGATTGAAGCCACAATAGCAAATATTACTTCCCCAACATTGCAGTTAAAAGATTAA
16090965 AGCTACAACAGCGAATCTTATTTCCCAGGCGGTGCAGTGGAACAGTTTAAAGCCACAACGGCGAA
66 AGCTACAACAGCGAATCTTATTTCCCAGGCGGTGCAGTGGAACAGTTTAAAGCCACAACGGCGAA
*
16091030 TCTTGCTTCCCTGACATTCCAGTTAAAAAGATTGAAGCCACAACGACAATCTTACTTCTCAGGCG
131 TCTTGCTTCCCCGACATTCCAGTTAAAAAGATTGAAGCCACAACGACAATCTTACTTCTCAGGCG
16091095 GTG
196 GTG
* * * * * *
16091098 CAGTGAAACAGATTGAAGTCATAATGGCGAATCTTACTTCCCCGACATTGCAGTTAAAAAGATTA
1 CAGTGAAACAGATTGAAGCCACAATAGCAAATATTACTTCCCCAACATTGCAGTT-AAAAGATTA
* *
16091163 AAGCTACAACGGCGAATCTTATTTCCCAGGCGGTGCAGTGGAACGGTTTAAAGCCACAACGGCGA
65 AAGCTACAACAGCGAATCTTATTTCCCAGGCGGTGCAGTGGAACAGTTTAAAGCCACAACGGCGA
*
16091228 ATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTGAAGC
130 ATCTTGCTTCCCCGACATTCCAGTTAAAAAGATTGAAGC
16091267 TACAGGCAAC
Statistics
Matches: 156, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
198 47 0.30
199 109 0.70
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (198 bp):
CAGTGAAACAGATTGAAGCCACAATAGCAAATATTACTTCCCCAACATTGCAGTTAAAAGATTAA
AGCTACAACAGCGAATCTTATTTCCCAGGCGGTGCAGTGGAACAGTTTAAAGCCACAACGGCGAA
TCTTGCTTCCCCGACATTCCAGTTAAAAAGATTGAAGCCACAACGACAATCTTACTTCTCAGGCG
GTG
Found at i:16093718 original size:122 final size:125
Alignment explanation
Indices: 16093411--16093761 Score: 494
Period size: 126 Copynumber: 2.8 Consensus size: 125
16093401 ATAATTTCAA
** *
16093411 TTTGACGTTTCTGATAAAATAGTATAAAATCACTTCTAGCAGGATGCTATTTGAGAAGAATTTGT
1 TTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGT
*
16093476 GAAATCGCGCCCTCGTGGA-TGCGCTTTTGCTATAGTAGGTCACGAAAGAAATAATTATTTT
66 GAAATCGCGCCCTCGTGGACT-CGCTTTTGCTACAGTAGGTCACGAAAGAAATAA-TATTTT
*
16093537 TTTGACGTTTCTGAGCAAATAGTACAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGT
1 TTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGT
* * * *
16093602 GAAATCGCGGCCTCGT-TACTCGCTTTTGCTACAGTAGGTCATGTAAGAAAT-A-ATTTT
66 GAAATCGCGCCCTCGTGGACTCGCTTTTGCTACAGTAGGTCACGAAAGAAATAATATTTT
* * * * * *
16093659 TTTGATGTTTTTGAGCAAATAATATAAAATCGCTTCTAGTAAGATTCTATTTGAGAAGAATTTGT
1 TTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGT
** *
16093724 GAAATCAAGCCCTCGTGGACGCGCTTTTGCTACAGTAG
66 GAAATCGCGCCCTCGTGGACTCGCTTTTGCTACAGTAG
16093762 CATGTTTGGG
Statistics
Matches: 202, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
122 76 0.38
123 19 0.09
124 1 0.00
125 29 0.14
126 77 0.38
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (125 bp):
TTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGT
GAAATCGCGCCCTCGTGGACTCGCTTTTGCTACAGTAGGTCACGAAAGAAATAATATTTT
Found at i:16096996 original size:116 final size:116
Alignment explanation
Indices: 16096792--16097029 Score: 413
Period size: 116 Copynumber: 2.1 Consensus size: 116
16096782 TGATAAATTG
16096792 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
*
16096857 TAGTACCAATCAAAACACTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAATCAAAACACTTTTCCAAATCTAACATTACGTGAATGTAAAAT
* *
16096908 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
* * *
16096973 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTACGTGAATGTAACAT
66 TAGTACCAATCAAAACACTTTTCCAAATCTAACATTACGTGAATGTAAAAT
*
16097024 TGTTAA
1 TATTAA
16097030 CTTAGTTTAG
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
TAGTACCAATCAAAACACTTTTCCAAATCTAACATTACGTGAATGTAAAAT
Found at i:16097052 original size:23 final size:23
Alignment explanation
Indices: 16097026--16097140 Score: 108
Period size: 23 Copynumber: 4.8 Consensus size: 23
16097016 TGTAACATTG
*
16097026 TTAACTTAGTTTAGGGTTTTTAA
1 TTAAATTAGTTTAGGGTTTTTAA
*
16097049 TTAAATTAGGTTAGGGTTTTTAA
1 TTAAATTAGTTTAGGGTTTTTAA
16097072 TTAAATTAGGTTAAGGTTAGGGTTTTTAA
1 TTAAATTA-G-T----TTAGGGTTTTTAA
**
16097101 GTT-AA-GGGTTTAGGGTTTTTAA
1 -TTAAATTAGTTTAGGGTTTTTAA
*
16097123 TTAAATTAGGTTAGGGTT
1 TTAAATTAGTTTAGGGTT
16097141 AGGATTTGTA
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
21 2 0.03
22 15 0.20
23 38 0.51
24 1 0.01
26 1 0.01
27 1 0.01
29 15 0.20
30 2 0.03
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.47
Consensus pattern (23 bp):
TTAAATTAGTTTAGGGTTTTTAA
Found at i:16097116 original size:22 final size:20
Alignment explanation
Indices: 16097081--16097126 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
16097071 ATTAAATTAG
16097081 GTTAAGGTTAGGGTTTTTAA
1 GTTAAGGTTAGGGTTTTTAA
16097101 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAA-GG-TTAGGGTTTTTAA
16097123 -TTAA
1 GTTAA
16097127 ATTAGGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 5 0.21
21 6 0.25
22 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (20 bp):
GTTAAGGTTAGGGTTTTTAA
Found at i:16097122 original size:51 final size:52
Alignment explanation
Indices: 16097057--16097263 Score: 204
Period size: 51 Copynumber: 3.8 Consensus size: 52
16097047 AATTAAATTA
*
16097057 GGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTA-AGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAGAGG
* * *
16097108 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGATTTGTAATTAATTTAGGTTAGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG-GTT-T--TTAAGTTA-G--AGG
*
16097167 GGTTAGGGTTTTTAATTAAATTAGG-TAGGGTTAGGGTTTTAAATTAAATTAG-GTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG-TTT---TTAAGTTAGAG---G
*
16097224 GGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTTAGGGTT
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTT
16097264 AATTAGGTTA
Statistics
Matches: 133, Mismatches: 8, Indels: 23
0.81 0.05 0.14
Matches are distributed among these distances:
51 34 0.26
52 2 0.02
53 1 0.01
54 1 0.01
55 7 0.05
57 27 0.20
58 28 0.21
59 33 0.25
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (52 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAGTTAGAGG
Found at i:16097152 original size:29 final size:29
Alignment explanation
Indices: 16097105--16097263 Score: 239
Period size: 29 Copynumber: 5.4 Consensus size: 29
16097095 TTTTAAGTTA
16097105 AGGGTTTAGGGTTTTTAATTAAATTAGGTT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTT
* * *
16097135 AGGGTTAGGATTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
16097164 AGGGGTTAGGGTTTTTAATTAAATTAGG-T
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTT
*
16097193 AGGGTTAGGGTTTTAAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
16097222 AGGGTTAGGGTTTTTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
16097251 AGGGTTTAGGGTT
1 AGGG-TTAGGGTT
16097264 AATTAGGTTA
Statistics
Matches: 117, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
28 25 0.21
29 57 0.49
30 35 0.30
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (29 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:16097221 original size:23 final size:26
Alignment explanation
Indices: 16097036--16097257 Score: 117
Period size: 29 Copynumber: 8.3 Consensus size: 26
16097026 TTAACTTAGT
*
16097036 TTAGGGTTTTTAATTAAA-T-TA-GG
1 TTAGGGTTTTAAATTAAATTGTAGGG
* *
16097059 TTAGGGTTTTTAATTAAATTAGGTTAAGG
1 TTAGGGTTTTAAATTAAATT--G-TAGGG
* *
16097088 TTAGGGTTTTTAAGTT-AA--G--GGT
1 TTAGGG-TTTTAAATTAAATTGTAGGG
*
16097110 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTAAATTAAATT--G-TAGGG
* *
16097139 TTAGGATTTGT-AATTAATTTAGGTTAGGGG
1 TTAGGGTTT-TAAATTAAATT--G-TA-GGG
*
16097169 TTAGGGTTTTTAATTAAATTAGGTAGGG
1 TTAGGGTTTTAAATTAAATT--GTAGGG
16097197 TTAGGGTTTTAAATTAAATTAGGTTAGGG
1 TTAGGGTTTTAAATTAAATT--G-TAGGG
*
16097226 TTAGGGTTTTTAATT-AATT-TA-GG
1 TTAGGGTTTTAAATTAAATTGTAGGG
16097249 TTAGGGTTT
1 TTAGGGTTT
16097258 AGGGTTAATT
Statistics
Matches: 167, Mismatches: 13, Indels: 38
0.77 0.06 0.17
Matches are distributed among these distances:
21 7 0.04
22 9 0.05
23 29 0.17
24 3 0.02
25 1 0.01
26 1 0.01
28 31 0.19
29 56 0.34
30 30 0.18
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (26 bp):
TTAGGGTTTTAAATTAAATTGTAGGG
Found at i:16097312 original size:25 final size:25
Alignment explanation
Indices: 16097278--16097390 Score: 96
Period size: 25 Copynumber: 4.7 Consensus size: 25
16097268 AGGTTAGGGT
16097278 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
16097303 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * *** *
16097326 --AAATAAC-TCGAAA-ATTTTTTTA
1 TTTTATTACATC-AAATAAACTTCTA
16097348 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
16097373 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
16097391 TATCAAAATA
Statistics
Matches: 66, Mismatches: 13, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
20 2 0.03
21 8 0.12
22 2 0.03
23 2 0.03
24 11 0.17
25 41 0.62
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.43
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:16097354 original size:70 final size:69
Alignment explanation
Indices: 16097278--16097434 Score: 260
Period size: 70 Copynumber: 2.3 Consensus size: 69
16097268 AGGTTAGGGT
**
16097278 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAATTT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTC-AAAACAT
*
16097343 TTTTA
65 TTCTA
16097348 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAACATT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAACATT
16097413 TCTA
66 TCTA
* *
16097417 TTTTTTTACATAAAATAA
1 TTTTATTACATCAAATAA
16097435 TATCAAAATA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 25 0.30
70 57 0.70
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (69 bp):
TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAACATT
TCTA
Found at i:16097396 original size:35 final size:35
Alignment explanation
Indices: 16097287--16097397 Score: 95
Period size: 35 Copynumber: 3.2 Consensus size: 35
16097277 TTTTTATTAC
16097287 ATCAAATAAACTTCTATTTTATTACATCAAATAAT
1 ATCAAATAAACTTCTATTTTATTACATCAAATAAT
* * *** * *
16097322 ATCAAA-ATAAC-TCGAAAATTTT-TT-TATTTTATTAC
1 ATCAAATA-AACTTC---TATTTTATTACATCAAATAAT
16097357 ATCAAATAAACTTCTATTTTATTACATCAAATAAT
1 ATCAAATAAACTTCTATTTTATTACATCAAATAAT
16097392 ATCAAA
1 ATCAAA
16097398 ATAACTCAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 16
0.64 0.17 0.19
Matches are distributed among these distances:
33 5 0.09
34 5 0.09
35 34 0.63
36 5 0.09
37 5 0.09
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.41
Consensus pattern (35 bp):
ATCAAATAAACTTCTATTTTATTACATCAAATAAT
Found at i:16098559 original size:7 final size:7
Alignment explanation
Indices: 16098549--16098573 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16098539 TTATATACAT
16098549 AATACTA
1 AATACTA
16098556 AATACTA
1 AATACTA
16098563 AATACTA
1 AATACTA
16098570 AATA
1 AATA
16098574 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:16099531 original size:12 final size:11
Alignment explanation
Indices: 16099497--16099531 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
16099487 GAATTTTGGA
16099497 AGGAAATTGAG
1 AGGAAATTGAG
16099508 AGG-AATTGAG
1 AGGAAATTGAG
16099518 AGGAAATATGAG
1 AGGAAAT-TGAG
16099530 AG
1 AG
16099532 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:16104441 original size:111 final size:112
Alignment explanation
Indices: 16104245--16104463 Score: 289
Period size: 111 Copynumber: 2.0 Consensus size: 112
16104235 AGGGGGTGAC
* * * * *
16104245 ATTCTAGGATCTTTTGCATGTTATAAAAAATATATGTAAATGAATGTTGATGAATTATATAGTTG
1 ATTCTAAGATCTTTTGCATGTTATAAAAAATACATCTAAATGAATGATGATGAATTATATAATTG
* * * *
16104310 TTATTATGTAATTTTGTCAAGGTTGT-GGTACCTAAAATTAGAACAAT
66 TTATTAGGTAATGTTATCAAGGTTGTAGGTA-CAAAAATTAGAACAAT
** * *
16104357 ATTCTAAGATCTTTTGCATGTTAT-TGAAATACATCTAAATGGATGATGATGAATTATGTAATTG
1 ATTCTAAGATCTTTTGCATGTTATAAAAAATACATCTAAATGAATGATGATGAATTATATAATTG
*
16104421 TTATTAGGTAATGTTATCAAGGTTGTAGTTACAAAAATTAGAA
66 TTATTAGGTAATGTTATCAAGGTTGTAGGTACAAAAATTAGAA
16104464 TAATTGTATT
Statistics
Matches: 92, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
111 66 0.72
112 26 0.28
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.40
Consensus pattern (112 bp):
ATTCTAAGATCTTTTGCATGTTATAAAAAATACATCTAAATGAATGATGATGAATTATATAATTG
TTATTAGGTAATGTTATCAAGGTTGTAGGTACAAAAATTAGAACAAT
Found at i:16107802 original size:17 final size:16
Alignment explanation
Indices: 16107780--16107820 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
16107770 ATAGTTTTAA
16107780 TTATTTAATTTAGATTT
1 TTATTTAATTTA-ATTT
*
16107797 TTATTTTATTTTAATTT
1 TTA-TTTAATTTAATTT
16107814 TTATTTA
1 TTATTTA
16107821 CCAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
18 8 0.36
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTAATTTAATTT
Found at i:16109953 original size:12 final size:12
Alignment explanation
Indices: 16109936--16109977 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
16109926 TCAAACAATA
16109936 TATAAATTTAAT
1 TATAAATTTAAT
16109948 TATAAAAATTT-A-
1 TAT--AAATTTAAT
16109960 TATAAATTTAAT
1 TATAAATTTAAT
16109972 TATAAA
1 TATAAA
16109978 AAGACTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 6 0.23
11 1 0.04
12 12 0.46
13 1 0.04
14 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATAAATTTAAT
Found at i:16109961 original size:24 final size:24
Alignment explanation
Indices: 16109934--16109979 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
16109924 ATTCAAACAA
16109934 TATATAAATTTAATTATAAAAATT
1 TATATAAATTTAATTATAAAAATT
16109958 TATATAAATTTAATTATAAAAA
1 TATATAAATTTAATTATAAAAA
16109980 GACTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TATATAAATTTAATTATAAAAATT
Found at i:16109987 original size:24 final size:24
Alignment explanation
Indices: 16109934--16109988 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
16109924 ATTCAAACAA
**
16109934 TATATAAATTTAATTATAAAAATT
1 TATATAAATTTAATTATAAAAAAC
16109958 TATATAAATTTAATTATAAAAAGAC
1 TATATAAATTTAATTATAAAAA-AC
16109983 TTATAT
1 -TATAT
16109989 TAACTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 22 0.81
26 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TATATAAATTTAATTATAAAAAAC
Found at i:16112481 original size:42 final size:42
Alignment explanation
Indices: 16112413--16112616 Score: 243
Period size: 42 Copynumber: 4.8 Consensus size: 42
16112403 GCGTTGCTAA
16112413 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA-CATGAC
* * *
16112456 ATTTAGCGGCGC-TTTCCCACAAACGCCACTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA-CATGAC
* * *
16112498 CTTTAGCGGCGC-TTCCCCACAAACGCCGCTAAAGATATTGAG
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACA-TGAC
* * *
16112540 CTTTAGCGGTGCTTTTTCCCACAAACGCCACTATAGA-ATAGAC
1 CTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAAGACAT-GAC
**
16112583 CTTTAGCGGCGCTTTTAACACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
16112617 AATATATCTT
Statistics
Matches: 138, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 92 0.67
43 25 0.18
44 20 0.14
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACATGAC
Found at i:16112613 original size:86 final size:84
Alignment explanation
Indices: 16112413--16112621 Score: 273
Period size: 86 Copynumber: 2.5 Consensus size: 84
16112403 GCGTTGCTAA
*
16112413 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-TGACATTTAGCGGCGCTTTCCCACA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA-TATTGACATTTAGCGGCGCTTTCCCACA
16112477 AACGCCACTAAAGACCAAGAC
65 AACGCCACTAAAGA-CAAGAC
* *
16112498 CTTTAGCGGCGC-TTCCCCACAAACGCCGCTAAAGATATTGAGC-TTTAGCGGTGCTTTTTCCCA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATATTGA-CATTTAGCGGCGC--TTTCCCA
*
16112561 CAAACGCCACTATAGA-ATAGAC
63 CAAACGCCACTAAAGACA-AGAC
** *
16112583 CTTTAGCGGCGCTTTTAACACAAACGCCGCTAAAAATAT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATAT
16112622 ATCTTTTAAA
Statistics
Matches: 110, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
83 1 0.01
84 36 0.33
85 29 0.26
86 44 0.40
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (84 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATATTGACATTTAGCGGCGCTTTCCCACAA
ACGCCACTAAAGACAAGAC
Found at i:16112955 original size:43 final size:43
Alignment explanation
Indices: 16112889--16112979 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
16112879 ACATATGCAA
* * * *
16112889 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
16112932 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
16112975 -GTAAT
1 GGTAAT
16112980 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:16116991 original size:13 final size:13
Alignment explanation
Indices: 16116973--16116997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16116963 TGTCAATCTT
16116973 TTACATTAATTTG
1 TTACATTAATTTG
16116986 TTACATTAATTT
1 TTACATTAATTT
16116998 ATTTATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TTACATTAATTTG
Found at i:16117493 original size:7 final size:7
Alignment explanation
Indices: 16117483--16117541 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
16117473 CACTAACTCT
*
16117483 TAACCTC
1 TAACCCC
**
16117490 TAACCTT
1 TAACCCC
16117497 TAACCCC
1 TAACCCC
16117504 TAACCCC
1 TAACCCC
16117511 TAACCCC
1 TAACCCC
16117518 TAACCCC
1 TAACCCC
**
16117525 TAACTAC
1 TAACCCC
16117532 TAACCCC
1 TAACCCC
16117539 TAA
1 TAA
16117542 ATCTTATTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.32, C:0.46, G:0.00, T:0.22
Consensus pattern (7 bp):
TAACCCC
Found at i:16117534 original size:14 final size:14
Alignment explanation
Indices: 16117473--16117541 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
16117463 AACCCTAAAT
* *
16117473 CACTAACTCTTAAC
1 CACTAACCCCTAAC
* **
16117487 CTCTAACCTTTAAC
1 CACTAACCCCTAAC
*
16117501 CCCTAACCCCTAAC
1 CACTAACCCCTAAC
*
16117515 CCCTAACCCCTAAC
1 CACTAACCCCTAAC
*
16117529 TACTAACCCCTAA
1 CACTAACCCCTAA
16117542 ATCTTATTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 47 1.00
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (14 bp):
CACTAACCCCTAAC
Found at i:16118268 original size:41 final size:41
Alignment explanation
Indices: 16118207--16118450 Score: 346
Period size: 41 Copynumber: 6.0 Consensus size: 41
16118197 TCAAAAGCGG
*
16118207 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* *
16118248 GCATTAGCGGCGCTTATTCAAAAACACCACTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* * *
16118289 GCATTAGCGGCGCTTCTTCCAAAACGCCGCTAAAGGCCTGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* *
16118330 GCATTAGCGGCGCTTATTCAAAAACACCGCTAAAGGCCCTA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
**
16118371 AAATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
* * * *
16118412 GAATTAGCGGCG-TTTTTGAAAAAACGCTGCTAAAGGCCC
1 GCATTAGCGGCGCTTATT-CAAAAACGCCGCTAAAGGCCC
16118451 CAAAAACTCA
Statistics
Matches: 181, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 4 0.02
41 177 0.98
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (41 bp):
GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
Found at i:16118612 original size:40 final size:39
Alignment explanation
Indices: 16118502--16118612 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
16118492 TTTGGAAAAA
* *
16118502 GCCGGTAATGCTT-ATTTTTAGCT-GCGTTTTCCAAAAAGC
1 GCCGCTAATGCTTGATTTTTAG-TGGCGTTTT-TAAAAAGC
* ** *
16118541 GCCGCTAATGCTCGACCTTTAGCGGCGTTTTTATAAAAGC
1 GCCGCTAATGCTTGATTTTTAGTGGCGTTTTTA-AAAAGC
16118581 GCCGCTAATGCTTGATTTTTAGTGGCGTTTTT
1 GCCGCTAATGCTTGATTTTTAGTGGCGTTTTT
16118613 TATCCAAACG
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
39 12 0.20
40 47 0.80
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (39 bp):
GCCGCTAATGCTTGATTTTTAGTGGCGTTTTTAAAAAGC
Found at i:16119567 original size:4 final size:4
Alignment explanation
Indices: 16119558--16119595 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
16119548 AGTAAGCAAT
16119558 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
16119596 GTGTTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:16119806 original size:3 final size:3
Alignment explanation
Indices: 16119798--16119845 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
16119788 TTGCAGCTCT
16119798 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16119846 GGATGAATGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16136590 original size:5 final size:5
Alignment explanation
Indices: 16136580--16136618 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
16136570 GTCTAAGATG
* *
16136580 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
16136619 GCTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:16136780 original size:22 final size:22
Alignment explanation
Indices: 16136753--16136804 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
16136743 TGAGAATTTA
16136753 TATGTGTTAATTGAATTGTATC
1 TATGTGTTAATTGAATTGTATC
*
16136775 TATGTGTTAATTGAATTGTATG
1 TATGTGTTAATTGAATTGTATC
16136797 TATGTGTT
1 TATGTGTT
16136805 TGTATTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.02, G:0.21, T:0.52
Consensus pattern (22 bp):
TATGTGTTAATTGAATTGTATC
Found at i:16137178 original size:23 final size:24
Alignment explanation
Indices: 16137150--16137215 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
16137140 TTCCTAATTA
*
16137150 ATGGCTCTCTAAAGCTTCTCG-AT
1 ATGGCTCTCTGAAGCTTCTCGAAT
*
16137173 ATGGCTCGCTTGAA-CTTCTCGATAT
1 ATGGCTCTC-TGAAGCTTCTCGA-AT
*
16137198 ATGGCTATCTGAAGCTTC
1 ATGGCTCTCTGAAGCTTC
16137216 CCGTTAATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 15 0.43
24 7 0.20
25 13 0.37
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (24 bp):
ATGGCTCTCTGAAGCTTCTCGAAT
Found at i:16137268 original size:24 final size:24
Alignment explanation
Indices: 16137241--16137345 Score: 59
Period size: 25 Copynumber: 4.3 Consensus size: 24
16137231 TGGAGCTACT
16137241 CGTTATTGGCTCGCATAAGCTTCC
1 CGTTATTGGCTCGCATAAGCTTCC
** *
16137265 CGTT-TATGGCTCTTATGAGCTTCC
1 CGTTAT-TGGCTCGCATAAGCTTCC
* ** * * *
16137289 TGTTATACAGCCCGGATAAGTTTCC
1 CGTTAT-TGGCTCGCATAAGCTTCC
* * *
16137314 CGTTACATGGCTCACATAATCTTCC
1 CGTTA-TTGGCTCGCATAAGCTTCC
*
16137339 CATTATT
1 CGTTATT
16137346 TAGCTTGAGA
Statistics
Matches: 56, Mismatches: 22, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
23 1 0.02
24 23 0.41
25 32 0.57
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (24 bp):
CGTTATTGGCTCGCATAAGCTTCC
Found at i:16148329 original size:24 final size:22
Alignment explanation
Indices: 16148290--16148350 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 22
16148280 ATCCAAAATA
16148290 ATAAATTTAAA-AATATTA-ATG
1 ATAAATTTAAATAATA-TACATG
16148311 ATAAATTTGAAATAGATATACATG
1 ATAAATTT-AAATA-ATATACATG
16148335 ATAAATTTAAAATAAT
1 ATAAATTT-AAATAAT
16148351 GTTAACAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 8 0.23
22 3 0.09
23 5 0.14
24 19 0.54
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (22 bp):
ATAAATTTAAATAATATACATG
Found at i:16148337 original size:59 final size:59
Alignment explanation
Indices: 16148233--16148350 Score: 143
Period size: 59 Copynumber: 2.0 Consensus size: 59
16148223 AATACATATA
* * *
16148233 AAATTTAAAAATTTTGATGATAATTATAGAATAATCATACGTGATAAATCCAAAATAAT
1 AAATTTAAAAATATTAATGATAATTATAGAATAATCATACATGATAAATCCAAAATAAT
**
16148292 AAATTTAAAAATATTAATGATAAATT-T-GAAATAGAT-ATACATGATAAATTTAAAATAAT
1 AAATTTAAAAATATTAATGAT-AATTATAG-AATA-ATCATACATGATAAATCCAAAATAAT
16148351 GTTAACAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
58 1 0.02
59 44 0.86
60 6 0.12
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (59 bp):
AAATTTAAAAATATTAATGATAATTATAGAATAATCATACATGATAAATCCAAAATAAT
Found at i:16148387 original size:23 final size:23
Alignment explanation
Indices: 16148361--16148425 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 23
16148351 GTTAACAATG
16148361 AATTTAAAATAATAATATTGAGA
1 AATTTAAAATAATAATATTGAGA
* * * *
16148384 AATTAAAAATAATAAAACATGATA
1 AATTTAAAATAATAATA-TTGAGA
*
16148408 AATCTAAAATAATAATAT
1 AATTTAAAATAATAATAT
16148426 ACAATACACT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (23 bp):
AATTTAAAATAATAATATTGAGA
Found at i:16148416 original size:24 final size:24
Alignment explanation
Indices: 16148308--16148422 Score: 94
Period size: 23 Copynumber: 4.9 Consensus size: 24
16148298 AAAAATATTA
* *
16148308 ATGATAAATTTGAAATAGAT-ATAC
1 ATGATAAATTTAAAATA-ATAAAAC
**
16148332 ATGATAAATTTAAAATAATGTTAAC
1 ATGATAAATTTAAAATAAT-AAAAC
* *
16148357 A--ATGAATTTAAAATAATAATA-
1 ATGATAAATTTAAAATAATAAAAC
* * *
16148378 TTGAGAAATTAAAAATAATAAAAC
1 ATGATAAATTTAAAATAATAAAAC
*
16148402 ATGATAAATCTAAAATAATAA
1 ATGATAAATTTAAAATAATAA
16148423 TATACAATAC
Statistics
Matches: 70, Mismatches: 16, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
22 1 0.01
23 33 0.47
24 33 0.47
25 3 0.04
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.31
Consensus pattern (24 bp):
ATGATAAATTTAAAATAATAAAAC
Found at i:16149272 original size:22 final size:21
Alignment explanation
Indices: 16149247--16149294 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
16149237 TACAAATTAA
16149247 ATCTCTAAGATTACAAAATCTT
1 ATCTCTAAGATTAC-AAATCTT
* * *
16149269 ATCTTTTAAGATTGCATATCTT
1 ATC-TCTAAGATTACAAATCTT
16149291 ATCT
1 ATCT
16149295 AAGATTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 12 0.55
23 9 0.41
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (21 bp):
ATCTCTAAGATTACAAATCTT
Found at i:16150038 original size:51 final size:51
Alignment explanation
Indices: 16149919--16150039 Score: 181
Period size: 51 Copynumber: 2.4 Consensus size: 51
16149909 ATATGCTATG
* * * *
16149919 ACGCCAGGGAAATAAGATTCGCTGCCCTCAGCTTCAATTTATTCCACTGCA
1 ACGCCAAGGAAATGAGATTCGCTGCCCTCAACTTCAATTTATACCACTGCA
16149970 ACGCCAAGGAAATGAGATTCGCTGCCCTCAACTTCAATCTT-TACCACTGCA
1 ACGCCAAGGAAATGAGATTCGCTGCCCTCAACTTCAAT-TTATACCACTGCA
*
16150021 ACGCCAAGGAAACGAGATT
1 ACGCCAAGGAAATGAGATT
16150040 GGTGTCTTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 62 0.97
52 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (51 bp):
ACGCCAAGGAAATGAGATTCGCTGCCCTCAACTTCAATTTATACCACTGCA
Found at i:16162142 original size:50 final size:50
Alignment explanation
Indices: 16162018--16162266 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
16162008 GATAATAACA
* * ** * *
16162018 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
16162069 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
16162119 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
16162169 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
16162224 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
16162267 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:16162196 original size:100 final size:104
Alignment explanation
Indices: 16162017--16162266 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
16162007 TGATAATAAC
**
16162017 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
16162082 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
16162119 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
16162182 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
16162224 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
16162267 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:16162382 original size:13 final size:13
Alignment explanation
Indices: 16162361--16162392 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16162351 GCTTGGATCA
*
16162361 TCATCAAATAAAT
1 TCATAAAATAAAT
16162374 TCATAAAATAAAT
1 TCATAAAATAAAT
16162387 TCATAA
1 TCATAA
16162393 TGGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:16162639 original size:30 final size:30
Alignment explanation
Indices: 16162604--16162661 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
16162594 CCTCGACTCT
*
16162604 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
16162634 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
16162662 AAGGCTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:16169735 original size:50 final size:50
Alignment explanation
Indices: 16169611--16169859 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
16169601 GATAATAACA
* * ** * *
16169611 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
16169662 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
16169712 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
16169762 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
16169817 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
16169860 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:16169789 original size:100 final size:104
Alignment explanation
Indices: 16169610--16169859 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
16169600 TGATAATAAC
**
16169610 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
16169675 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
16169712 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
16169775 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
16169817 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
16169860 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:16169975 original size:13 final size:13
Alignment explanation
Indices: 16169954--16169985 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16169944 GCTTGGATCA
*
16169954 TCATCAAATAAAT
1 TCATAAAATAAAT
16169967 TCATAAAATAAAT
1 TCATAAAATAAAT
16169980 TCATAA
1 TCATAA
16169986 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:16170232 original size:30 final size:30
Alignment explanation
Indices: 16170197--16170254 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16170187 CCTCGACTCT
* *
16170197 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTACCCCTA
* *
16170227 AACTTTTACATAATTACATTTTTACCCC
1 AACTTTTACAAAATTACAATTTTACCCC
16170255 AAGGCTCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTACCCCTA
Found at i:16178423 original size:20 final size:22
Alignment explanation
Indices: 16178398--16178442 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16178388 GTAATGAACT
*
16178398 AAAACA-TTACTT-TAATAAAA
1 AAAACACTTAATTATAATAAAA
*
16178418 AAAACACTTAATTATATTAAAA
1 AAAACACTTAATTATAATAAAA
16178440 AAA
1 AAA
16178443 TACTATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 5 0.24
22 10 0.48
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAACACTTAATTATAATAAAA
Found at i:16185392 original size:21 final size:21
Alignment explanation
Indices: 16185330--16185436 Score: 101
Period size: 23 Copynumber: 5.0 Consensus size: 21
16185320 CTTGATCAGT
16185330 ATACGACACAT-AAGTG-CTTG
1 ATACGACACATAAAGTGTC-TG
* ** * *
16185350 AAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGTCTG
*
16185371 ATACAACACATAAAGTGTCTGAG
1 ATACGACACATAAAGTGTCT--G
16185394 ATACGACACATAAAGTGTCTG
1 ATACGACACATAAAGTGTCTG
16185415 ATGTACGACACATAAAGTGTCT
1 A--TACGACACATAAAGTGTCT
16185437 AATCGGCAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
20 9 0.13
21 22 0.31
22 1 0.01
23 39 0.55
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (21 bp):
ATACGACACATAAAGTGTCTG
Found at i:16185402 original size:23 final size:24
Alignment explanation
Indices: 16185369--16185436 Score: 113
Period size: 23 Copynumber: 2.9 Consensus size: 24
16185359 ACGAGGTGCC
*
16185369 TGATACAACACATAAAGTGTCTGA
1 TGATACGACACATAAAGTGTCTGA
16185393 -GATACGACACATAAAGTGTCTGA
1 TGATACGACACATAAAGTGTCTGA
16185416 TG-TACGACACATAAAGTGTCT
1 TGATACGACACATAAAGTGTCT
16185437 AATCGGCAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
23 41 0.98
24 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (24 bp):
TGATACGACACATAAAGTGTCTGA
Found at i:16186511 original size:17 final size:16
Alignment explanation
Indices: 16186486--16186521 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16186476 AACCCTAGTT
* *
16186486 TTTCCCTTTTCTTTTC
1 TTTCCCCTTTCCTTTC
16186502 TTTCCCCTTTCCTTTC
1 TTTCCCCTTTCCTTTC
16186518 TTTC
1 TTTC
16186522 TTTTTCGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTCCCCTTTCCTTTC
Found at i:16186775 original size:24 final size:25
Alignment explanation
Indices: 16186743--16186791 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
16186733 TATTTAAAAC
16186743 ATAATAATA-TAATATAATTAATTTA
1 ATAATAATACT-ATATAATTAATTTA
*
16186768 ATAA-AATACTTTATAATTAATTTA
1 ATAATAATACTATATAATTAATTTA
16186792 TATATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATAATAATACTATATAATTAATTTA
Found at i:16198609 original size:18 final size:18
Alignment explanation
Indices: 16198588--16198636 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
16198578 TTTTAACATA
*
16198588 ATTTATTTATTTTATAAT
1 ATTTAATTATTTTATAAT
16198606 ATTTAATTATTTTATAAT
1 ATTTAATTATTTTATAAT
16198624 ATTTAATTATTTT
1 ATTTAATTATTTT
16198637 TTGACAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTAATTATTTTATAAT
Found at i:16205035 original size:19 final size:19
Alignment explanation
Indices: 16204992--16205036 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
16204982 CACAAGGTAA
16204992 AATATATTTATTTTGATAAC
1 AATA-ATTTATTTTGATAAC
* *
16205012 CATAATTTATTTTGATAAT
1 AATAATTTATTTTGATAAC
16205031 AATAAT
1 AATAAT
16205037 AATAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (19 bp):
AATAATTTATTTTGATAAC
Found at i:16207176 original size:50 final size:50
Alignment explanation
Indices: 16207072--16207363 Score: 336
Period size: 50 Copynumber: 5.7 Consensus size: 50
16207062 GGGAATGAGA
16207072 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATGAGAGG
* *
16207128 TCCCATGTAAGACCATGTCTGGTACATGGCATTGGCACCGAGACGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
16207178 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * ** * **
16207228 TCCCCTGTAAGACCATGTCTAGGACATGGCAAGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * **
16207278 TCCCATGTAAGACCATATCTAGGATATGGCATTGGCA--GTACATGAAATA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* *
16207327 TCCCATGTAAGAACATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16207364 TGTTATTATC
Statistics
Matches: 208, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
48 1 0.00
49 38 0.18
50 128 0.62
53 3 0.01
55 2 0.01
56 36 0.17
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:16210910 original size:13 final size:13
Alignment explanation
Indices: 16210892--16210916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16210882 ATTTACAAGA
16210892 TTACATAATCAAT
1 TTACATAATCAAT
16210905 TTACATAATCAA
1 TTACATAATCAA
16210917 ATCAAATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:16216274 original size:20 final size:19
Alignment explanation
Indices: 16216249--16216298 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
16216239 TAATAGTATT
16216249 TTATTAATTTAATATTAAA
1 TTATTAATTTAATATTAAA
16216268 GTTATT-ATCTTAATATTAAA
1 -TTATTAAT-TTAATATTAAA
16216288 -T-TTAATTTAAT
1 TTATTAATTTAAT
16216299 GTTTATCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 7 0.25
18 3 0.11
19 2 0.07
20 16 0.57
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TTATTAATTTAATATTAAA
Found at i:16216357 original size:12 final size:12
Alignment explanation
Indices: 16216340--16216386 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
16216330 TTTTAAAAAG
16216340 ATTTAATATTAA
1 ATTTAATATTAA
*
16216352 ATTTAAT-CTAA
1 ATTTAATATTAA
16216363 TATTT-ATATT-A
1 -ATTTAATATTAA
16216374 ATTTAATATTAA
1 ATTTAATATTAA
16216386 A
1 A
16216387 GTGATTAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 4 0.14
11 11 0.38
12 14 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:16216365 original size:17 final size:18
Alignment explanation
Indices: 16216343--16216386 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
16216333 TAAAAAGATT
16216343 TAATATTAAAT-TTAATC
1 TAATATTAAATATTAATC
* *
16216360 TAATATT-TATATTAATT
1 TAATATTAAATATTAATC
16216377 TAATATTAAA
1 TAATATTAAA
16216387 GTGATTAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.86
18 1 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATTAAATATTAATC
Found at i:16219520 original size:17 final size:19
Alignment explanation
Indices: 16219498--16219545 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
16219488 AAAAAAGAAC
16219498 AATATATATATAAA-TAT-
1 AATATATATATAAACTATG
*
16219515 AATATATAAATAAACTATG
1 AATATATATATAAACTATG
*
16219534 AAAATATATATA
1 AATATATATATA
16219546 TGTGTGTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 13 0.50
18 3 0.12
19 10 0.38
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AATATATATATAAACTATG
Found at i:16219521 original size:13 final size:12
Alignment explanation
Indices: 16219498--16219546 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
16219488 AAAAAAGAAC
16219498 AATATATATATA
1 AATATATATATA
16219510 AATATAATATATA
1 AATAT-ATATATA
*
16219523 AATAAACTATGA-A
1 AATATA-TAT-ATA
16219536 AATATATATAT
1 AATATATATAT
16219547 GTGTGTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
11 1 0.03
12 9 0.29
13 20 0.65
14 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (12 bp):
AATATATATATA
Found at i:16219595 original size:12 final size:13
Alignment explanation
Indices: 16219580--16219608 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16219570 TAAAGGTATA
16219580 TATAAAATG-AAG
1 TATAAAATGTAAG
16219592 TATAAAATGTAAG
1 TATAAAATGTAAG
16219605 TATA
1 TATA
16219609 TATAAACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (13 bp):
TATAAAATGTAAG
Found at i:16227771 original size:13 final size:13
Alignment explanation
Indices: 16227753--16227780 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16227743 ACGGTTCAAA
16227753 AGTGTGTGAAATG
1 AGTGTGTGAAATG
16227766 AGTGTGTGAAATG
1 AGTGTGTGAAATG
16227779 AG
1 AG
16227781 CTTTAACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (13 bp):
AGTGTGTGAAATG
Found at i:16234508 original size:30 final size:30
Alignment explanation
Indices: 16234472--16234581 Score: 152
Period size: 30 Copynumber: 3.7 Consensus size: 30
16234462 CTCTAATTTC
16234472 CTAAAATTACATTTTGACCCCTAAACTTTT
1 CTAAAATTACATTTTGACCCCTAAACTTTT
*
16234502 CTAAAATTATATTTTGACCCCTCAAA-TTTT
1 CTAAAATTACATTTTGACCCCT-AAACTTTT
*
16234532 CTAAAATTACATTTTGACCCCTTAAC-TTT
1 CTAAAATTACATTTTGACCCCTAAACTTTT
* *
16234561 CTTAAAGTTACATTTTTACCC
1 C-TAAAATTACATTTTGACCC
16234582 TAGAAATTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
29 6 0.08
30 63 0.88
31 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (30 bp):
CTAAAATTACATTTTGACCCCTAAACTTTT
Found at i:16234591 original size:60 final size:60
Alignment explanation
Indices: 16234461--16234581 Score: 172
Period size: 60 Copynumber: 2.0 Consensus size: 60
16234451 TATATTTTCA
* * *
16234461 CCTCTAATTTCCTAAAATTACATTTTGACCCCTAAACTTTTCTAAAATTATATTTTGACC
1 CCTCAAATTTTCTAAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTGACC
* * *
16234521 CCTCAAATTTTCTAAAATTACATTTTGACCCCTTAAC-TTTCTTAAAGTTACATTTTTACC
1 CCTCAAATTTTCTAAAATTACATTTTGACCCCTAAACTTTTC-TAAAATTACATTTTGACC
16234581 C
1 C
16234582 TAGAAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (60 bp):
CCTCAAATTTTCTAAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTGACC
Found at i:16235286 original size:15 final size:13
Alignment explanation
Indices: 16235252--16235296 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
16235242 GAAGAAGGAG
16235252 AAAAAAGAGGAAAA
1 AAAAAAGA-GAAAA
16235266 ATAAAGAA-AGAAAA
1 A-AAA-AAGAGAAAA
16235280 AAAAAAGAGAAAA
1 AAAAAAGAGAAAA
16235293 AAAA
1 AAAA
16235297 GGGAAGAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.07
13 13 0.46
14 7 0.25
15 4 0.14
16 2 0.07
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Done.