Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 48 of 279
Found at i:16054894 original size:47 final size:47
Alignment explanation
Indices: 16054838--16055006 Score: 257
Period size: 47 Copynumber: 3.6 Consensus size: 47
16054828 CATGTCTTGG
* * *
16054838 CATGGTCTTACATGATATCTTTATATTACCAAATGCCATGTTCAAAA
1 CATGGTCTTACATGATATCCTTGTATTACCAAATGCCATGTTCCAAA
* * *
16054885 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCCAA
1 CATGGTCTTACATGATATCCTTGTATTACCAAATGCCATGTTCCAAA
*
16054932 CATGGTCTTACATGATATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGATATCCTTGTATTACCAAATGCCATGTTCCAAA
* *
16054979 CATGGCCTTACATGGTATCCTTGTATTA
1 CATGGTCTTACATGATATCCTTGTATTA
16055007 GTGCCAATGC
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 111 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (47 bp):
CATGGTCTTACATGATATCCTTGTATTACCAAATGCCATGTTCCAAA
Found at i:16057412 original size:15 final size:17
Alignment explanation
Indices: 16057377--16057416 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
16057367 AACATACATA
*
16057377 CAACTCAATCAATTACT
1 CAACTAAATCAATTACT
16057394 CAACTAAATCAA-T-CT
1 CAACTAAATCAATTACT
16057409 CAACTAAA
1 CAACTAAA
16057417 AGACAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
16 1 0.05
17 11 0.50
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (17 bp):
CAACTAAATCAATTACT
Found at i:16060379 original size:39 final size:39
Alignment explanation
Indices: 16060215--16060397 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
16060205 TTGAATGCTG
* * * * * * *
16060215 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
16060255 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
16060295 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
16060335 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
16060374 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
16060398 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:16060417 original size:79 final size:80
Alignment explanation
Indices: 16060251--16060432 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
16060241 GCTAAGTGAA
* * * *
16060251 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
16060315 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
16060331 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
16060395 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
16060410 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
16060433 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:16072222 original size:40 final size:40
Alignment explanation
Indices: 16072191--16072402 Score: 243
Period size: 40 Copynumber: 5.3 Consensus size: 40
16072181 GGACTAAGAT
16072191 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
16072231 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
* *
16072271 CCGAAGGCCTTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
* * ** * *
16072311 CCGAAGGCATTCGTGCGAGTTGTTAAA-TCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCC
* * * * * *
16072351 CCGAAGGCA-TTGTGTGAGTTACTAAA-ACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
16072390 CCGAAGGCATTTG
1 CCGAAGGCATTTG
16072403 AACGAGGAGC
Statistics
Matches: 154, Mismatches: 14, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
39 32 0.21
40 119 0.77
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
Found at i:16072275 original size:80 final size:80
Alignment explanation
Indices: 16072138--16072402 Score: 272
Period size: 80 Copynumber: 3.3 Consensus size: 80
16072128 TAGAATGCTG
* * ** **
16072138 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGA-ATATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TGACA-A-ATCCGGGTTAAGCCCCGAAGGCA
16072200 TTTGTGCGAGATAC-AAA
63 TTTGTGCGAGATACTAAA
* *
16072217 TTCCGGGTTAAGCCCCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCCT
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATGACAAA-TCCGGGTTAAGCCCCGAAGGCAT
16072281 TTGTGCGAGATACTAAA
64 TTGTGCGAGATACTAAA
* * ** * *
16072298 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCA-TT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTT
* *
16072362 GTGTGAGTTACTAAA
66 GTGCGAGATACTAAA
* * *
16072377 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
16072403 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
79 38 0.24
80 102 0.65
81 16 0.10
82 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:16074143 original size:50 final size:49
Alignment explanation
Indices: 16074065--16074163 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 49
16074055 AAGAAATTCC
*
16074065 TTCCGTTTTTGATCAATGAATCTTTGACTGATATACTT-TTTCCGAAACT
1 TTCCGTTTTTGATCAATGAATCTCTGACTGATATACTTCTTT-CGAAACT
*
16074114 NTTCCGTTTTTGGTCAATGAATCTCTGACTGATATACTTCTTTCGAAACT
1 -TTCCGTTTTTGATCAATGAATCTCTGACTGATATACTTCTTTCGAAACT
16074164 CGGTTTGGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 43 0.93
51 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.43
Consensus pattern (49 bp):
TTCCGTTTTTGATCAATGAATCTCTGACTGATATACTTCTTTCGAAACT
Found at i:16075083 original size:35 final size:35
Alignment explanation
Indices: 16075043--16075113 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 35
16075033 AGACTCATAT
*
16075043 ATCCATCCACAAATT-TGTTTCTAGAATTTTTGGTC
1 ATCCATCCAAAAATTGT-TTTCTAGAATTTTTGGTC
16075078 ATCCATCCAAAAATTGTTTTCTAGAATTTTTGGTC
1 ATCCATCCAAAAATTGTTTTCTAGAATTTTTGGTC
16075113 A
1 A
16075114 GGCCAATTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 33 0.97
36 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.42
Consensus pattern (35 bp):
ATCCATCCAAAAATTGTTTTCTAGAATTTTTGGTC
Found at i:16076313 original size:40 final size:40
Alignment explanation
Indices: 16076232--16076369 Score: 208
Period size: 40 Copynumber: 3.5 Consensus size: 40
16076222 AAACCAAGTA
* * * *
16076232 CCTTCGGGATTTAG-CCAGATATAGCT-ACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
16076271 CCTTCGGGACTTAGCCCGGAGATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
16076311 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
16076351 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
16076370 TTATCATCCG
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 14 0.15
40 77 0.85
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:16083562 original size:40 final size:40
Alignment explanation
Indices: 16083496--16083666 Score: 281
Period size: 40 Copynumber: 4.3 Consensus size: 40
16083486 CAAGTACCTA
* * ** * *
16083496 CGGGATTTAGCC-GGATATAGCCACTCGCTCAACTGCCTT
1 CGGGACTTAGCCTAGATATAGTAACTCGCACAAATGCCTT
16083535 CGGGACTTAGCCTAGATATAGTAACTCGCACAAATGCCTT
1 CGGGACTTAGCCTAGATATAGTAACTCGCACAAATGCCTT
16083575 CGGGACTTAGCCTAGATATAGTAACTCGCACAAATGCCTT
1 CGGGACTTAGCCTAGATATAGTAACTCGCACAAATGCCTT
16083615 CGGGACTTAGCCTAGATATAGTAACTCGCACAAATGCCTT
1 CGGGACTTAGCCTAGATATAGTAACTCGCACAAATGCCTT
16083655 CGGGACTTAGCC
1 CGGGACTTAGCC
16083667 CGGTTATCAT
Statistics
Matches: 125, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
39 11 0.09
40 114 0.91
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CGGGACTTAGCCTAGATATAGTAACTCGCACAAATGCCTT
Found at i:16085334 original size:38 final size:38
Alignment explanation
Indices: 16085287--16085371 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 38
16085277 GGCTTAAAGA
* *
16085287 CCCGTAGGCTTCGTGCTGGTAAAATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGATAAAT
** *
16085325 CCCGCAGGCTTCGTGCTGGTATTATATCTGGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGATAAAT
*
16085363 CCTGCAGGC
1 CCCGCAGGC
16085372 CTAGTATTGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTAAAATATCCGGGATAAAT
Found at i:16085464 original size:43 final size:43
Alignment explanation
Indices: 16085387--16085468 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
16085377 ATTGGTATTA
* **
16085387 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCATAATGCCGGTGATGTG
16085430 TATTCGGGCCTTCGTGCCTAGCAGGCATAATGCCGGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGGCATAATGCCGGTGA
16085469 AATGATATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.33, T:0.28
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCATAATGCCGGTGATGTG
Found at i:16087445 original size:13 final size:12
Alignment explanation
Indices: 16087415--16087449 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
16087405 AATTATTCTA
16087415 TAAAAATTTT-T
1 TAAAAATTTTGT
16087426 TAAAAATTTTGT
1 TAAAAATTTTGT
16087438 TAAAAAATTTTG
1 T-AAAAATTTTG
16087450 ACATTTGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.45
12 2 0.09
13 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (12 bp):
TAAAAATTTTGT
Found at i:16089302 original size:47 final size:45
Alignment explanation
Indices: 16089227--16089598 Score: 243
Period size: 47 Copynumber: 7.9 Consensus size: 45
16089217 GGGTTATTAT
* *
16089227 AAGCCAGTGTAAGACCATGTCTGGGACATAGCATTGGCATTGAGACG
1 AAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGACG
*
16089274 AGAGCTAGTGTAAGACATGTTTGGGACATGGCATCGGCATTGAGACG
1 A-AGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCATTGAGACG
* * * * *
16089321 AAAGCTAGTATAAGACGTGTCTGGGACATGCATCAGCCTCGAGACG
1 -AAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACG
* * *
16089367 TAAGCTAGTGTAAGACATGTCTGGGACATGCATCAGC-TACGAGATG
1 -AAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-TGAGACG
* * * ** * *
16089413 -TG-TCAGTTTAAGACCATGTCTGGGACATGGCATCGACACGGATATGTG
1 AAGCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGA--CG
* * * ** *
16089461 AGAGCTAGTGTAAGACCATGTCTGGGATATGGCATCAGCCTCAATGATG
1 A-AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGA-GACG
* *
16089510 ATAG-TCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTGAGA-T
1 A-AGCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGACG
*
16089556 ATGAGCTAGTGTAAGACCATATCTGGGACATGGCATCGGCATT
1 A--AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATT
16089599 CTACCCCATG
Statistics
Matches: 267, Mismatches: 41, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.00
44 9 0.03
45 15 0.06
46 64 0.24
47 89 0.33
48 21 0.08
49 35 0.13
50 31 0.12
51 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (45 bp):
AAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACG
Found at i:16089527 original size:99 final size:93
Alignment explanation
Indices: 16089231--16089592 Score: 303
Period size: 96 Copynumber: 3.8 Consensus size: 93
16089221 TATTATAAGC
* * * * *
16089231 CAGTGTAAGACCATGTCTGGGACATAGCATTGGCATTGAGACGA-GAGCTAGTGTAAGA-CATGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACA-CGAGA-TATGAGCTAGTGTAAGACCATGT
* * * * **
16089294 TTGGGACATGGCATCGGCATTGAGACGA-AAG-
64 CTGGGACATGGCATCAGC--T-ACAAGATGTGT
* * * * ** *
16089325 CTAGTATAAGA-CGTGTCTGGGACAT-GCATCAGCCTCGAGACGTAAGCTAGTGTAAGA-CATGT
1 C-AGTGTAAGACCATGTCTGGGACATGGCATC-GACACGAGATATGAGCTAGTGTAAGACCATGT
*
16089387 CTGGGACAT-GCATCAGCTACGAGATGTGT
64 CTGGGACATGGCATCAGCTACAAGATGTGT
*
16089416 CAGTTTAAGACCATGTCTGGGACATGGCATCGACACG-GATATGTGAGAGCTAGTGTAAGACCAT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACACGAGATA--T--GAGCTAGTGTAAGACCAT
*
16089480 GTCTGGGATATGGCATCAGCCT-CAATGATGATAGT
62 GTCTGGGACATGGCATCAG-CTACAA-GATG-T-GT
** *
16089515 CAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATATGAGCTAGTGTAAGACCATATCT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACACGAGATATGAGCTAGTGTAAGACCATGTCT
16089580 GGGACATGGCATC
66 GGGACATGGCATC
16089593 GGCATTCTAC
Statistics
Matches: 220, Mismatches: 30, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
89 3 0.01
90 12 0.05
91 18 0.08
92 13 0.06
93 34 0.15
94 29 0.13
95 21 0.10
96 42 0.19
97 6 0.03
98 2 0.01
99 36 0.16
100 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (93 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGACACGAGATATGAGCTAGTGTAAGACCATGTCT
GGGACATGGCATCAGCTACAAGATGTGT
Found at i:16089888 original size:27 final size:27
Alignment explanation
Indices: 16089850--16089905 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
16089840 TTATATTTAT
16089850 TTGCATGCAACTTACTAAGTTTTGTGC
1 TTGCATGCAACTTACTAAGTTTTGTGC
16089877 TTGCATGCAACTTACTAAGTTTTGTGC
1 TTGCATGCAACTTACTAAGTTTTGTGC
16089904 TT
1 TT
16089906 ACTTCCTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (27 bp):
TTGCATGCAACTTACTAAGTTTTGTGC
Found at i:16091607 original size:48 final size:48
Alignment explanation
Indices: 16091536--16091671 Score: 182
Period size: 48 Copynumber: 2.8 Consensus size: 48
16091526 CATTAGGGTT
* * *
16091536 ATATGGGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATTG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* **
16091584 ATATGAGATCCCATGTAAGACCATATCTGGGATTTGGCATTGGCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* ** *
16091632 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATGGCAT
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCAT
16091672 CGATATGAGA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (48 bp):
ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
Found at i:16091622 original size:42 final size:42
Alignment explanation
Indices: 16091575--16091760 Score: 106
Period size: 48 Copynumber: 4.2 Consensus size: 42
16091565 GGACATGGCA
16091575 TTGGCATTGATATGAGATCCCATGTAAGACCATATCTGGGAT
1 TTGGCATTGATATGAGATCCCATGTAAGACCATATCTGGGAT
* ** * * *
16091617 TTGGCATTGGCATCGATATGTGATTTCGTGTAAGACCATGTCTGGGAC
1 TTGGCA-T----T-GATATGAGATCCCATGTAAGACCATATCTGGGAT
* * * * *
16091665 ATGGCATCGATATGAGA-CATCGTGTAAGACCATAGT-TGGGCT
1 TTGGCATTGATATGAGATC-CCATGTAAGACCATA-TCTGGGAT
* * * * *
16091707 ATTGGCATCAGTATGTGTGATCCCAGGTAATACCATATCTGGGAT
1 -TTGGCAT-TG-ATATGAGATCCCATGTAAGACCATATCTGGGAT
*
16091752 ATGGCATTG
1 TTGGCATTG
16091761 GCATCTTACT
Statistics
Matches: 107, Mismatches: 24, Indels: 25
0.69 0.15 0.16
Matches are distributed among these distances:
42 32 0.30
43 9 0.08
44 8 0.07
45 22 0.21
46 1 0.01
47 2 0.02
48 33 0.31
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (42 bp):
TTGGCATTGATATGAGATCCCATGTAAGACCATATCTGGGAT
Found at i:16107899 original size:45 final size:45
Alignment explanation
Indices: 16107832--16107923 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
16107822 AGGATGAGAT
* *
16107832 TGCATAAATTTTGTTTTCCGATCCTAGGGACAAAATTTTCATTTA
1 TGCATAAATTTTATTTTCCGATCCTAGGGACAAAATTGTCATTTA
* *
16107877 TGCATGAATTTTATTTTTCGATCCTAGGGACAAAATTGTCATTTA
1 TGCATAAATTTTATTTTCCGATCCTAGGGACAAAATTGTCATTTA
16107922 TG
1 TG
16107924 AAAAGTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (45 bp):
TGCATAAATTTTATTTTCCGATCCTAGGGACAAAATTGTCATTTA
Found at i:16112275 original size:79 final size:81
Alignment explanation
Indices: 16112139--16112323 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
16112129 TTGAATGATG
*
16112139 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
16112203 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
16112218 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
16112280 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
16112298 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
16112324 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:16112337 original size:40 final size:40
Alignment explanation
Indices: 16112140--16112323 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
16112130 TGAATGATGT
* * * *
16112140 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
16112180 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
16112220 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
16112258 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
16112299 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
16112324 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:16112345 original size:79 final size:79
Alignment explanation
Indices: 16112140--16112346 Score: 199
Period size: 79 Copynumber: 2.6 Consensus size: 79
16112130 TGAATGATGT
** * * * **
16112140 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
*
16112203 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** *
16112220 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
*
16112285 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* *
16112299 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAA
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAA
16112347 ATTCTGAAGG
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 64 0.59
80 42 0.39
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:16119218 original size:72 final size:72
Alignment explanation
Indices: 16119096--16119245 Score: 266
Period size: 72 Copynumber: 2.1 Consensus size: 72
16119086 TGGAAAGGAG
* *
16119096 AAGAGGAAGGCTGAATTTGAAGCTAGAGATTATCGTAAAAGATCGACGGGTAAAGCTCCGTTCTC
1 AAGAAGAAGGCTGAATTTGAAGCTAGAGACTATCGTAAAAGATCGACGGGTAAAGCTCCGTTCTC
16119161 AG-CTGTA
66 AGTC-GTA
16119168 AAGAAGAAGGCTGAATTTGAAGCTAGAGACTATCGTAAAAGATCGACGGGTAAAGCTCCGTTCTC
1 AAGAAGAAGGCTGAATTTGAAGCTAGAGACTATCGTAAAAGATCGACGGGTAAAGCTCCGTTCTC
16119233 AGTCGTA
66 AGTCGTA
16119240 AAGAAG
1 AAGAAG
16119246 TTCAGGGAGG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
72 74 0.99
73 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.22
Consensus pattern (72 bp):
AAGAAGAAGGCTGAATTTGAAGCTAGAGACTATCGTAAAAGATCGACGGGTAAAGCTCCGTTCTC
AGTCGTA
Found at i:16119827 original size:63 final size:63
Alignment explanation
Indices: 16119725--16119850 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
16119715 TTGACCCTGG
16119725 CTCTACTCATTCATATGTATGCGAAACCTTAGCAACCAGTAAGACTCTACCTGTTGAGTCTAC
1 CTCTACTCATTCATATGTATGCGAAACCTTAGCAACCAGTAAGACTCTACCTGTTGAGTCTAC
* *
16119788 CTCTACTCATTCATATGTATGTGAAACCTTAGCATCCAGTAAGACTCTACCTGTTGAGTCTAC
1 CTCTACTCATTCATATGTATGCGAAACCTTAGCAACCAGTAAGACTCTACCTGTTGAGTCTAC
16119851 TGAGTTCGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (63 bp):
CTCTACTCATTCATATGTATGCGAAACCTTAGCAACCAGTAAGACTCTACCTGTTGAGTCTAC
Found at i:16121107 original size:84 final size:84
Alignment explanation
Indices: 16120966--16121133 Score: 291
Period size: 84 Copynumber: 2.0 Consensus size: 84
16120956 GTTGACCCGA
* * *
16120966 ACAAAATTTCAGCCATACTTGACTGGAAACCTCCGAGAAATGTTACTGAAGTTCGGAGCTTTTTG
1 ACAAAATCTCAGCCATACTTAACTGGAAACCTCCGAGAAATATTACTGAAGTTCGGAGCTTTTTG
*
16121031 GGGCTCGCCGGTTATTACC
66 GGACTCGCCGGTTATTACC
*
16121050 ACAAAATCTCAGCCATACTTAACTGGAAACCTCCGAGAAATATTACTGAGGTTCGGAGCTTTTTG
1 ACAAAATCTCAGCCATACTTAACTGGAAACCTCCGAGAAATATTACTGAAGTTCGGAGCTTTTTG
16121115 GGACTCGCCGGTTATTACC
66 GGACTCGCCGGTTATTACC
16121134 GACGATTTGT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (84 bp):
ACAAAATCTCAGCCATACTTAACTGGAAACCTCCGAGAAATATTACTGAAGTTCGGAGCTTTTTG
GGACTCGCCGGTTATTACC
Found at i:16124803 original size:29 final size:28
Alignment explanation
Indices: 16124767--16124844 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
16124757 TCATGAGATT
16124767 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
16124797 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
16124824 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
16124845 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:16125062 original size:174 final size:174
Alignment explanation
Indices: 16124797--16125124 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
16124787 AAATTGTACA
*
16124797 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
16124862 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
16124927 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
16124971 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
16125036 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
16125101 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
16125125 ACCTTGAGTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:16133053 original size:39 final size:40
Alignment explanation
Indices: 16132958--16133219 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
16132948 TTGAATGATG
*
16132958 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
16132996 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
16133037 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
16133076 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
16133115 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
16133154 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
16133193 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
16133220 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:16134788 original size:342 final size:343
Alignment explanation
Indices: 16134159--16134844 Score: 1223
Period size: 342 Copynumber: 2.0 Consensus size: 343
16134149 AAATTCATTA
*
16134159 TAAATTAACCAGAGATAATTAGGAGTCATACCATATATGGATAGATTCCTCCCTGAGTCTAGTTT
1 TAAATTAACCAGAGACAATTAGGAGTCATACCATATATGGATAGATTCCTCCCTGAGTCTAGTTT
* *
16134224 CTATAGAAATAAACGGCATCAGTATTGGAGCCCTGTACAAGGAGATATCCAAGTCGTAATGCGCA
66 CTATAGAAACAAACGGCATCAGTATTGAAGCCCTGTACAAGGAGATATCCAAGTCGTAATGCGCA
16134289 AAGGTCAGGGTAGTCGATCCCTGTAACATGGGAGACTTTGACTAATAAACTGTACTAATTGGCCC
131 AAGGTCAGGGTAGTCGATCCCTGTAACATGGGAGACTTTGACTAATAAACTGTACTAATTGGCCC
16134354 GACCAAAAATTCTAGAAAAAAATATGTAGATGGGCATATGAGTCTAGTTTCAGGGAAAAATCACG
196 GACCAAAAATTCTAGAAAAAAATATGTAGATGGGCATATGAGTCTAGTTTCAGGGAAAAATCACG
*
16134419 AAACTGATTTTCGAGTTGTGAAACTCAAGATATGATTTTTAAAGCGACTATTACGCAGATTGGCA
261 AAACTGATTTTCGAGTTGTGAAACTCAAGATATGATTTTTAAAGCGACTAGTACGCAGATTGGCA
16134484 GTGTCTG-GAAA-ATTTT
326 GTGTCTGAGAAATATTTT
*
16134500 TAAANTTAACCAGAGACAATTAGGAGTCATACCATATATGGATAGATTCCTCTCTGAGTCTAGTT
1 TAAA-TTAACCAGAGACAATTAGGAGTCATACCATATATGGATAGATTCCTCCCTGAGTCTAGTT
* * * *
16134565 TCTATAGAAACAAACGGCATCAGTATTGAAGCTCTGTGCAGGGAGATATCCAGGTCGTAATGCGC
65 TCTATAGAAACAAACGGCATCAGTATTGAAGCCCTGTACAAGGAGATATCCAAGTCGTAATGCGC
* *
16134630 AAAGTTCAGTGTAGTCGATCCCTGTAACATGGGAGACTTTGACTAATAAACTGTACTAATTGGCC
130 AAAGGTCAGGGTAGTCGATCCCTGTAACATGGGAGACTTTGACTAATAAACTGTACTAATTGGCC
* *
16134695 TGACCAAAAATTCTAGAAAAAAATATGTAGATGGGCATATGAGTCTAGTTTTAGGGAAAAATCAC
195 CGACCAAAAATTCTAGAAAAAAATATGTAGATGGGCATATGAGTCTAGTTTCAGGGAAAAATCAC
*
16134760 GAAACTGATTTTTGAGTTGTGAAACTCAAGATATGATTTTTAAAGCGACTAGTACGCAGATTGGC
260 GAAACTGATTTTCGAGTTGTGAAACTCAAGATATGATTTTTAAAGCGACTAGTACGCAGATTGGC
16134825 AGTGTCTGAGAAATATTTT
325 AGTGTCTGAGAAATATTTT
16134844 T
1 T
16134845 TATAAAGGGT
Statistics
Matches: 328, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
341 4 0.01
342 314 0.96
343 4 0.01
344 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (343 bp):
TAAATTAACCAGAGACAATTAGGAGTCATACCATATATGGATAGATTCCTCCCTGAGTCTAGTTT
CTATAGAAACAAACGGCATCAGTATTGAAGCCCTGTACAAGGAGATATCCAAGTCGTAATGCGCA
AAGGTCAGGGTAGTCGATCCCTGTAACATGGGAGACTTTGACTAATAAACTGTACTAATTGGCCC
GACCAAAAATTCTAGAAAAAAATATGTAGATGGGCATATGAGTCTAGTTTCAGGGAAAAATCACG
AAACTGATTTTCGAGTTGTGAAACTCAAGATATGATTTTTAAAGCGACTAGTACGCAGATTGGCA
GTGTCTGAGAAATATTTT
Found at i:16140657 original size:17 final size:19
Alignment explanation
Indices: 16140615--16140658 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
16140605 ATGAAATTTT
*
16140615 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
16140634 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
16140652 AA-TATTA
1 AATTATTA
16140659 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:16146464 original size:21 final size:20
Alignment explanation
Indices: 16146440--16146485 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
16146430 CGAAATGAAA
16146440 TCAACCTAAAATGAATTAAAT
1 TCAACCTAAAATG-ATTAAAT
* *
16146461 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAAATGATTAAAT
16146481 T-AACC
1 TCAACC
16146486 GTTCCAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 3 0.14
20 8 0.36
21 11 0.50
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAAATGATTAAAT
Found at i:16149465 original size:25 final size:25
Alignment explanation
Indices: 16149437--16149484 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
16149427 TTATAATATG
* * *
16149437 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACTATTATACCCCTAGGTA
16149462 AAAATGACTATTATACCCCTAGG
1 AAAATGACTATTATACCCCTAGG
16149485 GTTTAATTAT
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:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (25 bp):
AAAATGACTATTATACCCCTAGGTA
Found at i:16149545 original size:20 final size:20
Alignment explanation
Indices: 16149510--16149558 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
16149500 TGATACGTGG
16149510 GATATGATAT-ACATGA-AT
1 GATATGATATGACATGATAT
16149528 GATATGATATGCACATGATAT
1 GATATGATATG-ACATGATAT
16149549 G-TATGATATG
1 GATATGATATG
16149559 TATGAAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.36
20 15 0.54
21 3 0.11
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (20 bp):
GATATGATATGACATGATAT
Found at i:16149546 original size:29 final size:29
Alignment explanation
Indices: 16149513--16149575 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
16149503 TACGTGGGAT
*
16149513 ATGATATACATGA-ATGATATGATATGCAC
1 ATGATATACATGATATG-TATGAAATGCAC
**
16149542 ATGATATGTATGATATGTATGAAATGCAC
1 ATGATATACATGATATGTATGAAATGCAC
16149571 ATGAT
1 ATGAT
16149576 GTAATCATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (29 bp):
ATGATATACATGATATGTATGAAATGCAC
Found at i:16149666 original size:26 final size:26
Alignment explanation
Indices: 16149626--16149760 Score: 172
Period size: 26 Copynumber: 5.3 Consensus size: 26
16149616 AGGAAGTGCG
16149626 AAAGGGC-TATGCCCCAGTTTATTGA
1 AAAGGGCTTATGCCCCAGTTTATTGA
**
16149651 AAAGGGCTTATGCCCCAGTTTACCGA
1 AAAGGGCTTATGCCCCAGTTTATTGA
16149677 AAAGGGCTTATGCCCCAGTTTATTGA
1 AAAGGGCTTATGCCCCAGTTTATTGA
* *
16149703 AAAGGGCTTATGCCCTAGTTTACCT-A
1 AAAGGGCTTATGCCCCAGTTTA-TTGA
*
16149729 AAAGGGCTT-TTCCCCAG-TTATT-A
1 AAAGGGCTTATGCCCCAGTTTATTGA
16149752 AAAGAGGCT
1 AAAG-GGCT
16149761 AGGCCTCCAG
Statistics
Matches: 98, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
23 6 0.06
24 7 0.07
25 13 0.13
26 71 0.72
27 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAGGGCTTATGCCCCAGTTTATTGA
Found at i:16149700 original size:52 final size:52
Alignment explanation
Indices: 16149626--16149760 Score: 206
Period size: 52 Copynumber: 2.7 Consensus size: 52
16149616 AGGAAGTGCG
16149626 AAAGGGC-TATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGA
1 AAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGA
* *
16149677 AAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCTAGTTTACCTA
1 AAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGA
*
16149729 AAAGGGCTT-TTCCCCAG-TTATT-AAAAGAGGCT
1 AAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
16149761 AGGCCTCCAG
Statistics
Matches: 79, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
49 5 0.06
50 9 0.11
51 14 0.18
52 51 0.65
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGA
Found at i:16151798 original size:18 final size:17
Alignment explanation
Indices: 16151758--16151798 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
16151748 AATTTGAGGG
*
16151758 TGTGGGCCACATGGGCC
1 TGTGGGCCACATGGGCA
*
16151775 TATGGGCCCACATGGGCA
1 TGTGGG-CCACATGGGCA
16151793 TGTGGG
1 TGTGGG
16151799 TGTACCTAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.15, C:0.24, G:0.41, T:0.20
Consensus pattern (17 bp):
TGTGGGCCACATGGGCA
Found at i:16152621 original size:18 final size:19
Alignment explanation
Indices: 16152600--16152635 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16152590 GTCTTTGAAC
16152600 AAACA-AACTGATTTCCTT
1 AAACACAACTGATTTCCTT
*
16152618 AAACACAACTGTTTTCCT
1 AAACACAACTGATTTCCT
16152636 AAGCTTCCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (19 bp):
AAACACAACTGATTTCCTT
Found at i:16157140 original size:40 final size:40
Alignment explanation
Indices: 16157089--16157232 Score: 166
Period size: 40 Copynumber: 3.6 Consensus size: 40
16157079 TTAACAATGA
* *
16157089 TTCGAATATATATGGCACTTAGTGTGCGATTTGAGATAAC
1 TTCGACTATATATGGCACTTAGTGTGCGATTTGAGATAGC
*
16157129 TTCGACTATATATGGCACTTAATGTGCGATTTG-GAATAGC
1 TTCGACTATATATGGCACTTAGTGTGCGATTTGAG-ATAGC
* * ** *
16157169 TTCGGCTATATATGACACTTAGTGTGCGAGACTGAGATAGT
1 TTCGACTATATATGGCACTTAGTGTGCGA-TTTGAGATAGC
*
16157210 TTC-AGCTATATAAGGCACTTAGT
1 TTCGA-CTATATATGGCACTTAGT
16157233 CTGCAAGAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 61 0.69
41 25 0.28
42 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (40 bp):
TTCGACTATATATGGCACTTAGTGTGCGATTTGAGATAGC
Found at i:16162512 original size:40 final size:40
Alignment explanation
Indices: 16162475--16162659 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
16162465 GCTACTCGTT
* *
16162475 CAAACGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
16162515 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
16162555 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
16162594 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
16162635 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
16162660 CATCATTCAA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 76 0.61
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:16162577 original size:79 final size:80
Alignment explanation
Indices: 16162475--16162659 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 80
16162465 GCTACTCGTT
* * *
16162475 CAAACGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAA-GCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
16162538 GGATTTAGTAAC-TCGCA
63 GGATATAGTAACTTAGCA
* **
16162555 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
16162619 ATATGGTCACTTAGCA
65 ATATAGTAACTTAGCA
16162635 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
16162660 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.60
80 33 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:16166718 original size:27 final size:27
Alignment explanation
Indices: 16166678--16166790 Score: 140
Period size: 27 Copynumber: 4.2 Consensus size: 27
16166668 AGGAAGCGTC
*
16166678 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
16166705 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
16166732 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
16166760 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
16166786 CTGGT
1 CTGGT
16166791 AGCCATGCTG
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 9 0.12
27 49 0.64
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:16166784 original size:54 final size:54
Alignment explanation
Indices: 16166678--16166790 Score: 165
Period size: 54 Copynumber: 2.1 Consensus size: 54
16166668 AGGAAGCGTC
* *
16166678 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
16166732 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
16166786 CTGGT
1 CTGGT
16166791 AGCCATGCTG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:16174441 original size:27 final size:27
Alignment explanation
Indices: 16174401--16174512 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
16174391 AGGAAGCGTC
*
16174401 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* * *
16174428 CTGGTGGCTCTGCCACATTTTTCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
**
16174455 CTGGTGGCTCTGCCATTATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
16174483 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
16174509 CTGG
1 CTGG
16174513 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
26 5 0.07
27 52 0.73
28 14 0.20
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.40
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:16174507 original size:54 final size:54
Alignment explanation
Indices: 16174401--16174512 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
16174391 AGGAAGCGTC
* *
16174401 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATTTTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATTTATCTGTT
* ** *
16174455 CTGGTGGCTCTGCCATTATTATCTGTATCTGGTGACTCTGTCACA-TTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATTTATCTGTT
16174509 CTGG
1 CTGG
16174513 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.40
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATTTATCTGTT
Found at i:16181301 original size:64 final size:64
Alignment explanation
Indices: 16181222--16181344 Score: 246
Period size: 64 Copynumber: 1.9 Consensus size: 64
16181212 CATTGCTGTT
16181222 ACTATAATGTAACCCTTGAGAAATCCCGGTTGGACCTTTGGAAGTACCTAGGATACGGGATTTG
1 ACTATAATGTAACCCTTGAGAAATCCCGGTTGGACCTTTGGAAGTACCTAGGATACGGGATTTG
16181286 ACTATAATGTAACCCTTGAGAAATCCCGGTTGGACCTTTGGAAGTACCTAGGATACGGG
1 ACTATAATGTAACCCTTGAGAAATCCCGGTTGGACCTTTGGAAGTACCTAGGATACGGG
16181345 CATCGAGACA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (64 bp):
ACTATAATGTAACCCTTGAGAAATCCCGGTTGGACCTTTGGAAGTACCTAGGATACGGGATTTG
Found at i:16181481 original size:44 final size:45
Alignment explanation
Indices: 16181363--16181484 Score: 167
Period size: 46 Copynumber: 2.7 Consensus size: 45
16181353 CATTGCTGTT
*
16181363 ATGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGTCACGAG
1 ATGT-AGCTAGTGTAAGATATGTCTGGGACATGCATCAGTCACGAG
* * *
16181409 ATGTAAGCCAGTGTAAGATATGTTTGGGACATGCATC-GGCTACGAG
1 ATGT-AGCTAGTGTAAGATATGTCTGGGACATGCATCAGTC-ACGAG
16181455 ATGT-GCTAGTGTAAGATATGTCTGGGACAT
1 ATGTAGCTAGTGTAAGATATGTCTGGGACAT
16181485 ACGTTGGAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 24 0.35
45 2 0.03
46 42 0.62
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (45 bp):
ATGTAGCTAGTGTAAGATATGTCTGGGACATGCATCAGTCACGAG
Found at i:16184847 original size:43 final size:42
Alignment explanation
Indices: 16184786--16184891 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 42
16184776 CCAATACCAA
* *
16184786 GTCCCAGAC-GTGGTCTTACATGTAATCAAATATCGATGCC-ACT
1 GTCCCAGACAG-GGTCTTACACGAAATCAAATAT-GATGCCGA-T
16184829 GTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGAT
1 GTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGAT
* * *
16184871 GTCCCAAACATGTTCTTACAC
1 GTCCCAGACAGGGTCTTACAC
16184892 ATAAATCTCA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
42 25 0.45
43 30 0.54
44 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
GTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGAT
Found at i:16184888 original size:42 final size:43
Alignment explanation
Indices: 16184797--16184891 Score: 122
Period size: 42 Copynumber: 2.2 Consensus size: 43
16184787 TCCCAGACGT
* * *
16184797 GGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAG
1 GGTCTTACACGAAATCAAATATCGATGCCACTGTCCCAAACAG
*
16184840 GGTCTTACACGAAATCAAATAT-GATGCCGA-TGTCCCAAACAT
1 GGTCTTACACGAAATCAAATATCGATGCC-ACTGTCCCAAACAG
*
16184882 GTTCTTACAC
1 GGTCTTACAC
16184892 ATAAATCTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 25 0.54
43 21 0.46
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGCCACTGTCCCAAACAG
Found at i:16187009 original size:16 final size:16
Alignment explanation
Indices: 16186990--16187020 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16186980 ATCGACAAAA
16186990 GCTGAAATCCCGAAAT
1 GCTGAAATCCCGAAAT
*
16187006 GCTGAAATGCCGAAA
1 GCTGAAATCCCGAAA
16187021 AGCTAAAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (16 bp):
GCTGAAATCCCGAAAT
Found at i:16195225 original size:13 final size:14
Alignment explanation
Indices: 16195195--16195222 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16195185 GCTAAATCGG
16195195 CATTCGTAGGGCCC
1 CATTCGTAGGGCCC
16195209 CATTCGTAGGGCCC
1 CATTCGTAGGGCCC
16195223 ATTAGGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.29, T:0.21
Consensus pattern (14 bp):
CATTCGTAGGGCCC
Found at i:16195469 original size:10 final size:11
Alignment explanation
Indices: 16195451--16195525 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 11
16195441 ATATTATTAT
16195451 ACATGATATG-
1 ACATGATATGC
*
16195461 ACATAATATGC
1 ACATGATATGC
16195472 ACATGATATG-
1 ACATGATATGC
** *
16195482 TTATGAGATGC
1 ACATGATATGC
16195493 ACATGATATGC
1 ACATGATATGC
* *
16195504 -TATGATATAC
1 ACATGATATGC
* *
16195514 TCATTATATGC
1 ACATGATATGC
16195525 A
1 A
16195526 TGGATTGGGT
Statistics
Matches: 48, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
10 24 0.50
11 24 0.50
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (11 bp):
ACATGATATGC
Found at i:16195507 original size:21 final size:21
Alignment explanation
Indices: 16195451--16195508 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
16195441 ATATTATTAT
* *
16195451 ACATGATATGAC-ATAATATGC
1 ACATGATATG-CTATGAGATGC
*
16195472 ACATGATATGTTATGAGATGC
1 ACATGATATGCTATGAGATGC
16195493 ACATGATATGCTATGA
1 ACATGATATGCTATGA
16195509 TATACTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (21 bp):
ACATGATATGCTATGAGATGC
Found at i:16196850 original size:29 final size:28
Alignment explanation
Indices: 16196815--16196890 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
16196805 GCGACTAACG
16196815 GGCCATATAAATGTGATTTGGGCCTAAT
1 GGCCATATAAATGTGATTTGGGCCTAAT
* *
16196843 AGGCCATATACAGGTGATTTGGGCCTAAT
1 -GGCCATATAAATGTGATTTGGGCCTAAT
* *
16196872 GAGCCATATGAATATGATT
1 G-GCCATATAAATGTGATT
16196891 GGGGATGGGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (28 bp):
GGCCATATAAATGTGATTTGGGCCTAAT
Found at i:16198013 original size:17 final size:17
Alignment explanation
Indices: 16197991--16198031 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
16197981 GTTTTCAATG
*
16197991 AAAACATAGTTTTCGCT
1 AAAACACAGTTTTCGCT
*
16198008 AAAACACGGTTTTCGCT
1 AAAACACAGTTTTCGCT
16198025 AAAACAC
1 AAAACAC
16198032 TTCAATGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (17 bp):
AAAACACAGTTTTCGCT
Found at i:16207194 original size:17 final size:18
Alignment explanation
Indices: 16207164--16207197 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16207154 AGAAAAAAGT
16207164 AGAAGAGAAAAGGAGAAA
1 AGAAGAGAAAAGGAGAAA
*
16207182 AGAA-AGAAGAGGAGAA
1 AGAAGAGAAAAGGAGAA
16207198 TGGCCAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
AGAAGAGAAAAGGAGAAA
Found at i:16207335 original size:24 final size:24
Alignment explanation
Indices: 16207296--16207401 Score: 149
Period size: 24 Copynumber: 4.4 Consensus size: 24
16207286 GCCGGCCAAC
*
16207296 TCCTGCTCCTTGATCAGCTCCTAAA
1 TCCT-CTCCTTTATCAGCTCCTAAA
*
16207321 TCTTCTCCTTTATCAGCTCCTAAA
1 TCCTCTCCTTTATCAGCTCCTAAA
* *
16207345 TCCTCTCCCTTATCAACTCCTAAA
1 TCCTCTCCTTTATCAGCTCCTAAA
*
16207369 TCCTCTCCCTTATCAGCTCCTAAA
1 TCCTCTCCTTTATCAGCTCCTAAA
*
16207393 TCTTCTCCT
1 TCCTCTCCT
16207402 GATAGCCTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
24 70 0.96
25 3 0.04
ACGTcount: A:0.20, C:0.39, G:0.05, T:0.37
Consensus pattern (24 bp):
TCCTCTCCTTTATCAGCTCCTAAA
Found at i:16213575 original size:32 final size:33
Alignment explanation
Indices: 16213539--16213624 Score: 86
Period size: 32 Copynumber: 2.6 Consensus size: 33
16213529 ATCGGGCCTA
*
16213539 AGCCC-ATTCAGATAACAGTGATACTGGGCCAG
1 AGCCCTATTCAGATAACAGTGAAACTGGGCCAG
* * * **
16213571 AGCCCTTTTCAGATTACA-TTAAACTGGGCCTT
1 AGCCCTATTCAGATAACAGTGAAACTGGGCCAG
16213603 AGCCCATTATTCAGATAACAGT
1 AGCCC--TATTCAGATAACAGT
16213625 ATGGCCCATA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
32 20 0.48
33 10 0.24
34 11 0.26
35 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (33 bp):
AGCCCTATTCAGATAACAGTGAAACTGGGCCAG
Found at i:16213919 original size:22 final size:21
Alignment explanation
Indices: 16213883--16213923 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
16213873 CCAGCCCCAT
16213883 GCATCAGAAAATAACAACATG
1 GCATCAGAAAATAACAACATG
*
16213904 GCATGCAGTAAATAACAACA
1 GCAT-CAGAAAATAACAACA
16213924 ATCCAACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.51, C:0.20, G:0.15, T:0.15
Consensus pattern (21 bp):
GCATCAGAAAATAACAACATG
Found at i:16213964 original size:26 final size:26
Alignment explanation
Indices: 16213935--16213987 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
16213925 TCCAACATGC
16213935 ATTTAGGTCAATTTA-CTCCTAGGGGT
1 ATTTAGGT-AATTTATCTCCTAGGGGT
* *
16213961 ATTTTGGTACTTTATCTCCTAGGGGT
1 ATTTAGGTAATTTATCTCCTAGGGGT
16213987 A
1 A
16213988 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.42
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAGGGGT
Found at i:16215277 original size:24 final size:24
Alignment explanation
Indices: 16215243--16215319 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
16215233 CCAACTCCTG
*
16215243 CTCCTTGATCAGCTCCTAAATCTT
1 CTCCTTTATCAGCTCCTAAATCTT
*
16215267 CTCCTTTATCAGCTCCTAAATCCT
1 CTCCTTTATCAGCTCCTAAATCTT
*
16215291 CTCCCTTATCAGCTCCTAAATCTT
1 CTCCTTTATCAGCTCCTAAATCTT
16215315 CTCCT
1 CTCCT
16215320 GATAGCCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.19, C:0.38, G:0.05, T:0.38
Consensus pattern (24 bp):
CTCCTTTATCAGCTCCTAAATCTT
Found at i:16218172 original size:34 final size:34
Alignment explanation
Indices: 16218122--16218186 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
16218112 ATAGAGAGAA
*
16218122 TGTGGAACATACGTAGTGTATTACCCTTAACCCG
1 TGTGGAACATACGTAGTGTATCACCCTTAACCCG
* *
16218156 TGTGGAACGTATGTAGTGTATCACCCTTAAC
1 TGTGGAACATACGTAGTGTATCACCCTTAAC
16218187 TCGTATCCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (34 bp):
TGTGGAACATACGTAGTGTATCACCCTTAACCCG
Found at i:16220007 original size:36 final size:37
Alignment explanation
Indices: 16219900--16220048 Score: 210
Period size: 37 Copynumber: 4.1 Consensus size: 37
16219890 CTTTAGCTCA
* * * *
16219900 GACAAAATCTCCACATGAAGTTATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
16219937 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
* *
16219974 GGCATACTCTCCACACGTAGTC-TCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
* *
16220010 GACATAATCTCCACACATAGTCATCGGGTCTCACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
16220047 GA
1 GA
16220049 ATATATTTCC
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
36 33 0.33
37 68 0.67
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (37 bp):
GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:16220317 original size:47 final size:47
Alignment explanation
Indices: 16220254--16220568 Score: 495
Period size: 47 Copynumber: 6.7 Consensus size: 47
16220244 ATATATATTT
* * * *
16220254 CACATTGACCATTCGGCTTTACCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* * *
16220301 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
*
16220348 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* *
16220395 CACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
* * *
16220442 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
*
16220489 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
*
16220536 CACATTGGCCATTCGGCCTTATCACACATATGC
1 CACATTGGCCATTCGGCCTTATCACATATATGC
16220569 TGTAACACCC
Statistics
Matches: 246, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 246 1.00
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.32
Consensus pattern (47 bp):
CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAC
Found at i:16220422 original size:141 final size:141
Alignment explanation
Indices: 16220253--16220568 Score: 569
Period size: 141 Copynumber: 2.2 Consensus size: 141
16220243 TATATATATT
* * *
16220253 TCACATTGACCATTCGGCTTTACCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGC
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGC
16220318 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
66 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
16220383 GTTCACATTCA
131 GTTCACATTCA
*
16220394 TCACATAGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGC
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGC
16220459 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
66 CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
*
16220524 GTTCATATTCA
131 GTTCACATTCA
* *
16220535 CCACATTGGCCATTCGGCCTTATCACACATATGC
1 TCACATTGGCCATTCGGCCTTATCACATATATGC
16220569 TGTAACACCC
Statistics
Matches: 167, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
141 167 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (141 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGC
CTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
GTTCACATTCA
Found at i:16221987 original size:40 final size:40
Alignment explanation
Indices: 16221950--16222134 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
16221940 GCTACTCGTT
*
16221950 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
16221990 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
16222030 CCAATGCCTTCGGG-CTTAGCCCAGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
16222069 AAAATGCCTTC-AGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
16222110 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
16222135 CATCATTCGA
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.01
39 31 0.25
40 79 0.65
41 11 0.09
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:16222061 original size:79 final size:80
Alignment explanation
Indices: 16221952--16222132 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 80
16221942 TACTCGTTCA
* ** * *
16221952 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCAAAAATGCCTTC-AGATCTTAACCCGGA
* *
16222016 TTTAGTAAC-TCGCACC
65 TATAGTAACTTAGCA-C
**
16222032 AATGCCTTCGGG-CTTAGCCCAGAAT-TAGTAACTCGCAAAAATGCCTTCAGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCC-GAATATAGTAACTCGCAAAAATGCCTTCAGATCTTAACCCGGA
*
16222095 TATAGTCACTTAGCAC
65 TATAGTAACTTAGCAC
*
16222111 AAAGCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
16222133 GACATCATTC
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
78 2 0.02
79 58 0.67
80 26 0.30
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCAAAAATGCCTTCAGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:16230116 original size:206 final size:205
Alignment explanation
Indices: 16229748--16230503 Score: 1101
Period size: 206 Copynumber: 3.7 Consensus size: 205
16229738 CTGCTTCTTT
* * * *
16229748 GATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCAACATAAGCACGCGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* * * *
16229813 AA-ACAAATCAGCTATGTCTTTGATTTGCTCCTTGTAAGCACAAGGATACCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* * * ** *
16229877 CTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTTTGCCTTCTGTCGAATATGGAGA
131 CTGCTTCA-TGTAAACATATGAAGGCCAGATCTGCTATGTGTATGCCTTCTGTCGAATATGGAGA
16229942 CGCCAAACTTC
195 CGCCAAACTTC
* *
16229953 AATTTGTTCTCTGGCAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* *
16230018 AAGCCAAATCAGCTATGAT-TTCGATTTGTTCCTTGTAAACACAAGGATTG-CAAATCATCTTGG
66 AAGCCAAATCAGCTATG-TCTTCGATTTGTTCCTTGTAAGCACAAGGA-TGCCAAACCATCTTGG
* *
16230081 ATCTGCTTCGATGTAAACATATGAAGGCCAGATCTGCTATGTGTCTG-CTCTCCGTCGAATATGG
129 ATCTGCTTC-ATGTAAACATATGAAGGCCAGATCTGCTATGTGTATGCCT-TCTGTCGAATATGG
*
16230145 AGACGCCAAAATTC
192 AGACGCCAAACTTC
*
16230159 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTAA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* *
16230224 AAGCCAAATTAGCTATGAT-TTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGA
66 AAGCCAAATCAGCTATG-TCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGA
* *
16230288 TATGCTTCAATGTAAACATATGAAGGCCAGATCTACTATGTGTATGCTCTT-TGTCGAATATGGA
130 TCTGCTTC-ATGTAAACATATGAAGGCCAGATCTGCTATGTGTATGC-CTTCTGTCGAATATGGA
* *
16230352 GAGGCCAAACTTT
193 GACGCCAAACTTC
* *
16230365 GATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTCGATTTGCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* *
16230430 AAGCCAAATCAGCTATGTCTTTGACTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
16230495 CTTGCTTCA
131 C-TGCTTCA
16230504 GCCAGATCTA
Statistics
Matches: 500, Mismatches: 41, Indels: 19
0.89 0.07 0.03
Matches are distributed among these distances:
205 66 0.13
206 422 0.84
207 10 0.02
208 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (205 bp):
GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
CTGCTTCATGTAAACATATGAAGGCCAGATCTGCTATGTGTATGCCTTCTGTCGAATATGGAGAC
GCCAAACTTC
Found at i:16234671 original size:39 final size:40
Alignment explanation
Indices: 16234589--16234703 Score: 119
Period size: 40 Copynumber: 2.9 Consensus size: 40
16234579 CGGATGATAA
* * * * * *
16234589 CCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGACCCGAAGGCATTGGTGCGAGTTATTATA-T
16234629 CCGGGCTAA-ACCCGAAGGCAATT-GTGCGAGTTATTATAT
1 CCGGGCTAAGACCCGAAGGC-ATTGGTGCGAGTTATTATAT
* *
16234668 CCGGGCTAAGTCCGGAAGGCATTGGTGCGAGTTATT
1 CCGGGCTAAGACCCGAAGGCATTGGTGCGAGTTATT
16234704 GAACCGGGCT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
39 31 0.48
40 33 0.52
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTGGTGCGAGTTATTATAT
Found at i:16234711 original size:39 final size:38
Alignment explanation
Indices: 16234589--16234714 Score: 130
Period size: 39 Copynumber: 3.2 Consensus size: 38
16234579 CGGATGATAA
* * * *
16234589 CCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTATTAA-T
*
16234629 CCGGGCTAA-ACCCGAAGGCAATTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGC-ATTGTGCGAGTTATTA-AT
*
16234668 CCGGGCTAAGTCCGGAAGGCATTGGTGCGAGTTATTGAA-
1 CCGGGCTAAGTCCCGAAGGCATT-GTGCGAGTTATT-AAT
16234707 CCGGGCTA
1 CCGGGCTA
16234715 GCTATTGAGC
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
39 41 0.55
40 32 0.43
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (38 bp):
CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTATTAAT
Found at i:16234898 original size:243 final size:243
Alignment explanation
Indices: 16234470--16234957 Score: 976
Period size: 243 Copynumber: 2.0 Consensus size: 243
16234460 CTCCTGTATG
16234470 TAGCTATTGAGCCGAAATGATAATGCTTGATAAGTGACTTGTGTTTGAATTCTAGTCATGAAATT
1 TAGCTATTGAGCCGAAATGATAATGCTTGATAAGTGACTTGTGTTTGAATTCTAGTCATGAAATT
16234535 GAAATAGAGATGTGTCATGATTTATTGATATGTGCATGGATATTCGGATGATAACCGGGCTAAGT
66 GAAATAGAGATGTGTCATGATTTATTGATATGTGCATGGATATTCGGATGATAACCGGGCTAAGT
16234600 CCTGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAACCCGAAGGCAATTGTGCGAGTTATTA
131 CCTGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAACCCGAAGGCAATTGTGCGAGTTATTA
16234665 TATCCGGGCTAAGTCCGGAAGGCATTGGTGCGAGTTATTGAACCGGGC
196 TATCCGGGCTAAGTCCGGAAGGCATTGGTGCGAGTTATTGAACCGGGC
16234713 TAGCTATTGAGCCGAAATGATAATGCTTGATAAGTGACTTGTGTTTGAATTCTAGTCATGAAATT
1 TAGCTATTGAGCCGAAATGATAATGCTTGATAAGTGACTTGTGTTTGAATTCTAGTCATGAAATT
16234778 GAAATAGAGATGTGTCATGATTTATTGATATGTGCATGGATATTCGGATGATAACCGGGCTAAGT
66 GAAATAGAGATGTGTCATGATTTATTGATATGTGCATGGATATTCGGATGATAACCGGGCTAAGT
16234843 CCTGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAACCCGAAGGCAATTGTGCGAGTTATTA
131 CCTGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAACCCGAAGGCAATTGTGCGAGTTATTA
16234908 TATCCGGGCTAAGTCCGGAAGGCATTGGTGCGAGTTATTGAACCGGGC
196 TATCCGGGCTAAGTCCGGAAGGCATTGGTGCGAGTTATTGAACCGGGC
16234956 TA
1 TA
16234958 AGTCCCGAAG
Statistics
Matches: 245, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
243 245 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (243 bp):
TAGCTATTGAGCCGAAATGATAATGCTTGATAAGTGACTTGTGTTTGAATTCTAGTCATGAAATT
GAAATAGAGATGTGTCATGATTTATTGATATGTGCATGGATATTCGGATGATAACCGGGCTAAGT
CCTGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAACCCGAAGGCAATTGTGCGAGTTATTA
TATCCGGGCTAAGTCCGGAAGGCATTGGTGCGAGTTATTGAACCGGGC
Found at i:16234939 original size:40 final size:39
Alignment explanation
Indices: 16234832--16235014 Score: 210
Period size: 39 Copynumber: 4.6 Consensus size: 39
16234822 CGGATGATAA
* * *
16234832 CCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA-T
* * *
16234872 CCGGGCTAA-ACCCGAAGGCAATTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AT
* * *
16234911 CCGGGCTAAGTCCGGAAGGCATTGGTGCGAGTTATTGAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAT
*
16234950 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AT
16234990 CCGGG-TCAAGTCCCGAAGGCATTTG
1 CCGGGCT-AAGTCCCGAAGGCATTTG
16235015 AGCAAGTAGT
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 1 0.01
39 66 0.53
40 56 0.45
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:16234965 original size:79 final size:78
Alignment explanation
Indices: 16234828--16235012 Score: 230
Period size: 79 Copynumber: 2.3 Consensus size: 78
16234818 TATTCGGATG
* * *
16234828 ATAACCGGGCTAAGTCCTGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAACCCGAAGGCAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTGACTAA-TCCGGGCTAAACCCGAAGGCAA
*
16234893 TTGTGCGAGTTATT
65 TTGTGCGAGTTACT
* * * * *
16234907 ATATCCGGGCTAAGTCCGGAAGGCATTGGTGCGAGTTATTGAA-CCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTGACT-AATCCGGGCTAA-ACCCGAAGGCA
*
16234971 TTTGTGCGAGTTACT
64 ATTGTGCGAGTTACT
16234986 ATAACCGGG-TCAAGTCCCGAAGGCATT
1 ATAACCGGGCT-AAGTCCCGAAGGCATT
16235013 TGAGCAAGTA
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
78 10 0.11
79 80 0.87
80 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (78 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTGACTAATCCGGGCTAAACCCGAAGGCAAT
TGTGCGAGTTACT
Found at i:16243031 original size:19 final size:19
Alignment explanation
Indices: 16243007--16243043 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
16242997 ACTTGGGTTG
16243007 TGAATGGGCCAAATGGGCA
1 TGAATGGGCCAAATGGGCA
*
16243026 TGAATGGGCTAAATGGGC
1 TGAATGGGCCAAATGGGC
16243044 CCGATGGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.38, T:0.19
Consensus pattern (19 bp):
TGAATGGGCCAAATGGGCA
Found at i:16243203 original size:29 final size:27
Alignment explanation
Indices: 16243122--16243255 Score: 115
Period size: 29 Copynumber: 4.7 Consensus size: 27
16243112 CTGAGCATGA
* *
16243122 ATATAATGTGATTTGGGCCGGATGGGCC
1 ATATAA-GTGAATTGGGCCTGATGGGCC
* * *
16243150 ATATAAATGAGATTGGGCCTAATGGGTC
1 ATATAAGTGA-ATTGGGCCTGATGGGCC
*
16243178 ATATGAACGTGAATTGGGCCTGATGGTCC
1 ATAT-AA-GTGAATTGGGCCTGATGGGCC
* * *
16243207 ACATGAACGTGAATTGGGTCGGATGGGCC
1 ATAT-AA-GTGAATTGGGCCTGATGGGCC
*
16243236 ATATAAATGAGATTGGGCCT
1 ATATAAGTGA-ATTGGGCCT
16243256 AGTGGGCTAT
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
27 6 0.07
28 32 0.38
29 44 0.52
30 3 0.04
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (27 bp):
ATATAAGTGAATTGGGCCTGATGGGCC
Found at i:16249453 original size:16 final size:16
Alignment explanation
Indices: 16249432--16249462 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16249422 GTTGTAACAC
16249432 CCCAAAAATCACGAAG
1 CCCAAAAATCACGAAG
*
16249448 CCCAAAAATCCCGAA
1 CCCAAAAATCACGAA
16249463 ATCTTATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.35, G:0.10, T:0.06
Consensus pattern (16 bp):
CCCAAAAATCACGAAG
Found at i:16250844 original size:19 final size:19
Alignment explanation
Indices: 16250820--16250856 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16250810 CTTGGGTTGT
16250820 GAATGGGCCAAATGGGCCG
1 GAATGGGCCAAATGGGCCG
* *
16250839 GAATGGGCTAAGTGGGCC
1 GAATGGGCCAAATGGGCC
16250857 CAATGGGCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.19, G:0.43, T:0.14
Consensus pattern (19 bp):
GAATGGGCCAAATGGGCCG
Found at i:16250965 original size:28 final size:28
Alignment explanation
Indices: 16250934--16251019 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 28
16250924 GTGAGCATGA
**
16250934 ATAT-AATGTGATTTGGGCCGGATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
*
16250962 ATATAAATGAGATTGGGCCTAATGGG-C
1 ATATAAATGTGATTGGGCCTAATGGGCC
*
16250989 ATTATGAATGTGAATTGGGCCTAATGGGCC
1 A-TATAAATGTG-ATTGGGCCTAATGGGCC
16251019 A
1 A
16251020 CATGAACGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.04
28 24 0.49
29 21 0.43
30 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:16251024 original size:29 final size:29
Alignment explanation
Indices: 16250934--16251033 Score: 107
Period size: 29 Copynumber: 3.5 Consensus size: 29
16250924 GTGAGCATGA
* **
16250934 ATAT-AATGTGATTTGGGCCGGATGGGCC
1 ATATGAATGTGAATTGGGCCTAATGGGCC
* *
16250962 ATATAAATGAG-ATTGGGCCTAATGGG-C
1 ATATGAATGTGAATTGGGCCTAATGGGCC
16250989 ATTATGAATGTGAATTGGGCCTAATGGGCC
1 A-TATGAATGTGAATTGGGCCTAATGGGCC
* *
16251019 ACATGAACGTGAATT
1 ATATGAATGTGAATT
16251034 TGTAATGCCG
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 2 0.03
28 24 0.40
29 32 0.53
30 2 0.03
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.28
Consensus pattern (29 bp):
ATATGAATGTGAATTGGGCCTAATGGGCC
Found at i:16251168 original size:19 final size:19
Alignment explanation
Indices: 16251144--16251180 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16251134 CCTGGGTTGT
16251144 GAATGGGCCAAATAGGCCA
1 GAATGGGCCAAATAGGCCA
* *
16251163 GAATGGGCTAAATGGGCC
1 GAATGGGCCAAATAGGCC
16251181 CGATGGGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.35, T:0.14
Consensus pattern (19 bp):
GAATGGGCCAAATAGGCCA
Found at i:16251288 original size:28 final size:28
Alignment explanation
Indices: 16251269--16251344 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
16251259 ATAATGCGAT
*
16251269 TTGGGCC-AGATGGGCCATATAAATGAAA
1 TTGGGCCTAGATGGGCCATATAAATG-GA
16251297 TTGGGCCTA-ATGGGCCATATAAATGAGA
1 TTGGGCCTAGATGGGCCATATAAATG-GA
*
16251325 TTAGGCCTAG-TGGGCCATAT
1 TTGGGCCTAGATGGGCCATAT
16251345 GCATGTATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 43 0.98
29 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (28 bp):
TTGGGCCTAGATGGGCCATATAAATGGA
Found at i:16251309 original size:323 final size:323
Alignment explanation
Indices: 16250713--16251341 Score: 1019
Period size: 324 Copynumber: 1.9 Consensus size: 323
16250703 GAAATACCGA
* * *
16250713 AATGCTGAAAGTTTTGCTGCGGTAGTCTTGCAATTGTGCGAACACTCGTGAGGAGGAAACCGATA
1 AATGCCGAAAGTTTGGCTGCGGTAGTCTTGCAAGTGTGCGAACACTCGTGAGGAGGAAACCGATA
* * * *
16250778 GGTTACCTGAGGCCCATGGGCGATTCCATGGACTTGGGTTGTGAATGGGCCAAATGGGCCGGAAT
66 GGTTACCTGACGCCCATGGGCGATTCCATGGACCTGGGTTGTGAATGGGCCAAATAGGCCAGAAT
* * *
16250843 GGGCTAAGTGGGCCCAATGGGCTGTTGGGCCCATAGTAGGCAAAATTTGATAAGTGATGCTATGT
131 GGGCTAAATGGGCCCAATGGGCTGTTGGGCCCAAAATAGGCAAAATTTGATAAGTGATGCTATGT
* * *
16250908 GATAGAAAATTTGTGTGTGAGCATGAATATAATGTGATTTGGGCCGGATGGGCCATATAAATGAG
196 GATAGAAAATTTGTGTGTGAGCATGAATATAATGCGATTTGGGCCAGATGGGCCATATAAATGAA
* * *
16250973 ATTGGGCCTAATGGG-CATTATGAATGTGAATTGGGCCTAATGGGCCACATGAACGTGAATTTGT
261 ATTGGGCCTAATGGGCCA-TATAAATGAG-ATTAGGCCTAATGGGCCACATGAACGTGAATTTGT
* ** *
16251037 AATGCCGAAAGTTTGGTTGCGGTAGTCTTGTGAGTGTGCGAACACTTGTGAGGAGGAAACCGATA
1 AATGCCGAAAGTTTGGCTGCGGTAGTCTTGCAAGTGTGCGAACACTCGTGAGGAGGAAACCGATA
*
16251102 GGTTGCCTGACGCCCATGGGCGATTCCATGGACCTGGGTTGTGAATGGGCCAAATAGGCCAGAAT
66 GGTTACCTGACGCCCATGGGCGATTCCATGGACCTGGGTTGTGAATGGGCCAAATAGGCCAGAAT
*
16251167 GGGCTAAATGGGCCCGATGGG-TGTTGGGCCCAAAATAGGCAAAATTTGATAAGTGATGCTATGT
131 GGGCTAAATGGGCCCAATGGGCTGTTGGGCCCAAAATAGGCAAAATTTGATAAGTGATGCTATGT
16251231 GATAGAAAATTTGTGTGTGAGCATGAATATAATGCGATTTGGGCCAGATGGGCCATATAAATGAA
196 GATAGAAAATTTGTGTGTGAGCATGAATATAATGCGATTTGGGCCAGATGGGCCATATAAATGAA
*
16251296 ATTGGGCCTAATGGGCCATATAAATGAGATTAGGCCTAGTGGGCCA
261 ATTGGGCCTAATGGGCCATATAAATGAGATTAGGCCTAATGGGCCA
16251342 TATGCATGTA
Statistics
Matches: 281, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
322 16 0.06
323 126 0.45
324 139 0.49
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (323 bp):
AATGCCGAAAGTTTGGCTGCGGTAGTCTTGCAAGTGTGCGAACACTCGTGAGGAGGAAACCGATA
GGTTACCTGACGCCCATGGGCGATTCCATGGACCTGGGTTGTGAATGGGCCAAATAGGCCAGAAT
GGGCTAAATGGGCCCAATGGGCTGTTGGGCCCAAAATAGGCAAAATTTGATAAGTGATGCTATGT
GATAGAAAATTTGTGTGTGAGCATGAATATAATGCGATTTGGGCCAGATGGGCCATATAAATGAA
ATTGGGCCTAATGGGCCATATAAATGAGATTAGGCCTAATGGGCCACATGAACGTGAATTTGT
Found at i:16251357 original size:28 final size:28
Alignment explanation
Indices: 16251278--16251344 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
16251268 TTTGGGCCAG
* *
16251278 ATGGGCCATATAAATGAAATTGGGCCTA
1 ATGGGCCATATAAATGAGATTAGGCCTA
16251306 ATGGGCCATATAAATGAGATTAGGCCTA
1 ATGGGCCATATAAATGAGATTAGGCCTA
*
16251334 GTGGGCCATAT
1 ATGGGCCATAT
16251345 GCATGTATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (28 bp):
ATGGGCCATATAAATGAGATTAGGCCTA
Found at i:16255207 original size:44 final size:44
Alignment explanation
Indices: 16255157--16255244 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
16255147 ACATTAAGTT
*
16255157 CATTTCAATAATGCGGAATTGGAATGTTCTAGCGTGGTGTGAAA
1 CATTTCAATAATGCGGAATTGGAATGTTCTAGAGTGGTGTGAAA
* *
16255201 CATTTCAGTAATGTGGAATTGGAATGTTCTAGAGTGGTGTGAAA
1 CATTTCAATAATGCGGAATTGGAATGTTCTAGAGTGGTGTGAAA
16255245 TTGAAACAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (44 bp):
CATTTCAATAATGCGGAATTGGAATGTTCTAGAGTGGTGTGAAA
Found at i:16259606 original size:46 final size:46
Alignment explanation
Indices: 16259539--16259714 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
16259529 TGTAACCCGC
*
16259539 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
16259585 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-G--GAC--GTTCGCAT
* * * *
16259635 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
16259678 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
16259715 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 2 0.02
46 63 0.57
47 26 0.24
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:16259717 original size:93 final size:93
Alignment explanation
Indices: 16259547--16259717 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
16259537 GCCCATAAGT
* *
16259547 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
16259612 CGAGCTCAGATGCCTAGTTACATCTCAC
66 CAAGCTCAGATGCCTAGTTACATCTCAC
*
16259640 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
16259705 CAAGTTCGGATGC
66 CAAGCTCAGATGC
16259718 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CAAGCTCAGATGCCTAGTTACATCTCAC
Found at i:16273360 original size:55 final size:54
Alignment explanation
Indices: 16273234--16273437 Score: 203
Period size: 53 Copynumber: 3.8 Consensus size: 54
16273224 AGGGTTTAAG
* * *
16273234 GATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCAAA
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAA
* * * * * * *
16273288 AAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGCAAA
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGT-AAGTTCTATAAGGCAAA
* * * * * *
16273343 GATCCCATGTAAGACCATGCCAAGGCATCGCAATGGTGAGTTC-ATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAA
** * * *
16273396 GATACCACATAAGACCATGTCAAGACATGGAAATGGTAAGTT
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
16273438 TAAAAAGGAA
Statistics
Matches: 118, Mismatches: 31, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
53 43 0.36
54 33 0.28
55 42 0.36
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (54 bp):
GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGCAAA
Found at i:16275126 original size:28 final size:28
Alignment explanation
Indices: 16275071--16275159 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
16275061 AGCATGGCTG
* * *
16275071 CCAGAA-CAGATA-TTGTGACAGGGTCA
1 CCAGAATCAGATATTTGTGGCAGAGCCA
*
16275097 CCAG-ATACAGATATTTGTGGTAGAGCCA
1 CCAGAAT-CAGATATTTGTGGCAGAGCCA
*
16275125 CCAGAATCAGATATTTGTGGCATAGCCA
1 CCAGAATCAGATATTTGTGGCAGAGCCA
*
16275153 CTAGAAT
1 CCAGAAT
16275160 GCATCCTCCA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 6 0.12
28 39 0.75
29 2 0.04
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (28 bp):
CCAGAATCAGATATTTGTGGCAGAGCCA
Found at i:16275258 original size:28 final size:28
Alignment explanation
Indices: 16275209--16275325 Score: 168
Period size: 28 Copynumber: 4.2 Consensus size: 28
16275199 AGCATGGCTG
* *
16275209 CCAGAA-CAGATA-TTGTGACAGAGTCA
1 CCAGAATCAGATATTTGTGGCAGAGCCA
16275235 CCAG-ATACAGATATTTGTGGCAGAGCCA
1 CCAGAAT-CAGATATTTGTGGCAGAGCCA
16275263 CCAGAATCAGATATTTGTGGCAGAGCCA
1 CCAGAATCAGATATTTGTGGCAGAGCCA
* *
16275291 CCAAAATCAGATATTTGTGGCATAGCCA
1 CCAGAATCAGATATTTGTGGCAGAGCCA
16275319 CCAGAAT
1 CCAGAAT
16275326 GCATCCTCCA
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
25 1 0.01
26 4 0.05
27 6 0.07
28 69 0.84
29 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (28 bp):
CCAGAATCAGATATTTGTGGCAGAGCCA
Found at i:16276854 original size:35 final size:35
Alignment explanation
Indices: 16276806--16276876 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
16276796 GCTTCGCCCG
* * * *
16276806 TGCTGCTGACCACTGTACCATGCTTCCTTCTTTAC
1 TGCTACTGACCACTGCACCACGCTTCCTTATTTAC
*
16276841 TGCTACTGGCCACTGCACCACGCTTCCTTATTTAC
1 TGCTACTGACCACTGCACCACGCTTCCTTATTTAC
16276876 T
1 T
16276877 AATATAGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.15, C:0.35, G:0.14, T:0.35
Consensus pattern (35 bp):
TGCTACTGACCACTGCACCACGCTTCCTTATTTAC
Found at i:16279954 original size:28 final size:27
Alignment explanation
Indices: 16279905--16279992 Score: 124
Period size: 28 Copynumber: 3.2 Consensus size: 27
16279895 AGCATGGCTG
* *
16279905 CCAGAACAGATA-TTGTGACAGAGTCA
1 CCAGAACAGATATTTGTGGCAGAGCCA
16279931 CCAGATACAGATATTTGTGGCAGAGCCA
1 CCAGA-ACAGATATTTGTGGCAGAGCCA
*
16279959 CCAGAATCAGATATTTGTGGCATAGCCA
1 CCAGAA-CAGATATTTGTGGCAGAGCCA
16279987 CCAGAA
1 CCAGAA
16279993 TGCTTCCTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
26 5 0.09
27 8 0.14
28 43 0.77
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (27 bp):
CCAGAACAGATATTTGTGGCAGAGCCA
Found at i:16282595 original size:30 final size:29
Alignment explanation
Indices: 16282556--16282621 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
16282546 CCTTATTACT
*
16282556 TTTAATTTTACTAAGATACT-TTATATATTA
1 TTTATTTTTA-TAA-ATACTATTATATATTA
*
16282586 TTTATTTTTATAAATATTAGTTATATATTA
1 TTTATTTTTATAAATACTA-TTATATATTA
*
16282616 TATATT
1 TTTATT
16282622 ATATATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 4 0.13
29 3 0.10
30 24 0.77
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTATTTTTATAAATACTATTATATATTA
Found at i:16282721 original size:29 final size:29
Alignment explanation
Indices: 16282613--16282721 Score: 79
Period size: 29 Copynumber: 3.9 Consensus size: 29
16282603 TAGTTATATA
* **
16282613 TTATATATTATATATTATT-TTTATCTCAT
1 TTATAAATTATATATTATTATTTAT-TTTT
* * *
16282642 CTATAAATTATATTTTATTA--TATTTTG
1 TTATAAATTATATATTATTATTTATTTTT
*
16282669 TTAT--A-TATAT-TTCCTTATATTATTTTT
1 TTATAAATTATATATT-ATTAT-TTATTTTT
16282696 TTATAAATTATATATTATTATTTATT
1 TTATAAATTATATATTATTATTTATT
16282722 AAATTTGTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
23 2 0.03
24 8 0.13
25 1 0.02
27 14 0.23
28 3 0.05
29 22 0.36
30 9 0.15
31 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (29 bp):
TTATAAATTATATATTATTATTTATTTTT
Found at i:16282724 original size:22 final size:22
Alignment explanation
Indices: 16282684--16282726 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16282674 TATATTTCCT
*
16282684 TATATTATTTTTTTATAAATTA
1 TATATTATTTTTATATAAATTA
16282706 TATATTATTATTTAT-TAAATT
1 TATATTATT-TTTATATAAATT
16282727 TGTAAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATATTATTTTTATATAAATTA
Found at i:16297493 original size:26 final size:26
Alignment explanation
Indices: 16297433--16297483 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
16297423 CATACTGATG
* *
16297433 AAATGACTGTTATACCCCTAGTGGTA
1 AAATGACTGATATACCCCTAGTGCTA
16297459 AAATGACTGATATACCCCTA-TGCTA
1 AAATGACTGATATACCCCTAGTGCTA
16297484 TATTTGACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (26 bp):
AAATGACTGATATACCCCTAGTGCTA
Found at i:16303529 original size:55 final size:55
Alignment explanation
Indices: 16303456--16303565 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
16303446 TGTAAGTCGC
* * * * *
16303456 TAACATATTTGGAGTTTCATTCTCGATCTTGATAAAAACATGTAATCTAGGGAAA
1 TAACATATTTGGAATTTCATCCTCGATCTTGATAAAAACAAGTAACCTAGAGAAA
16303511 TAACATATTTGGAATTTCATCCTCGATCTTGATAAAAACAAGTAACCTAGAGAAA
1 TAACATATTTGGAATTTCATCCTCGATCTTGATAAAAACAAGTAACCTAGAGAAA
16303566 GAAGAATAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (55 bp):
TAACATATTTGGAATTTCATCCTCGATCTTGATAAAAACAAGTAACCTAGAGAAA
Found at i:16316762 original size:37 final size:37
Alignment explanation
Indices: 16316703--16316848 Score: 256
Period size: 37 Copynumber: 3.9 Consensus size: 37
16316693 AGCTCAGACG
* *
16316703 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
16316740 AAATCTCCACACGTAGTCATCGGGTCTTACTCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
16316777 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
16316814 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
16316849 ATATATTTCC
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:16317120 original size:48 final size:49
Alignment explanation
Indices: 16316994--16317130 Score: 206
Period size: 50 Copynumber: 2.8 Consensus size: 49
16316984 GCACATCGCC
*
16316994 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA-A
* * *
16317044 TATATATTTCACATT-GACCATTCAGCTTTACCACATATGCATATCTC-A
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCAA
16317092 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
16317131 TGCATGTTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
48 35 0.45
49 2 0.03
50 41 0.53
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (49 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCAA
Found at i:16317162 original size:47 final size:47
Alignment explanation
Indices: 16317100--16317293 Score: 262
Period size: 47 Copynumber: 4.1 Consensus size: 47
16317090 CATACATATT
* * * *
16317100 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * *
16317147 CCACATTGGCCATTCGACCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
16317194 TCACATTGGTCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * * **
16317241 TCACATTGGTCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
16317288 TCACAT
1 TCACAT
16317294 AAAATCCTAA
Statistics
Matches: 130, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 130 1.00
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:16317220 original size:22 final size:22
Alignment explanation
Indices: 16317193--16317264 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
16317183 GCTCACATTC
16317193 ATCACATTGGTCATTCGGCCTT
1 ATCACATTGGTCATTCGGCCTT
* * *
16317215 ATCACATAT-ATGCATGTTC-ACATT
1 ATCACAT-TGGT-CA--TTCGGCCTT
16317239 CATCACATTGGTCATTCGGCCTT
1 -ATCACATTGGTCATTCGGCCTT
16317262 ATC
1 ATC
16317265 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 14 0.38
23 6 0.16
24 6 0.16
25 11 0.30
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (22 bp):
ATCACATTGGTCATTCGGCCTT
Found at i:16320597 original size:40 final size:40
Alignment explanation
Indices: 16320588--16321424 Score: 1586
Period size: 40 Copynumber: 20.9 Consensus size: 40
16320578 TAACACCAGA
*
16320588 ACGAATGCTCTTCG-GAACTTAGTTCGGATACATCACTAGC
1 ACGAATGCTCTTCGAG-ACTTAGTCCGGATACATCACTAGC
16320628 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
* *
16320668 ACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
* *
16320708 ACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16320748 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16320788 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16320828 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16320868 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16320908 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16320948 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16320988 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16321028 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16321068 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16321108 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16321148 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16321188 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16321228 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16321268 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16321308 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
16321348 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
* * *
16321388 ACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACT
16321425 CTCAATTTTC
Statistics
Matches: 788, Mismatches: 8, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
40 787 1.00
41 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
ACGAATGCTCTTCGAGACTTAGTCCGGATACATCACTAGC
Found at i:16321625 original size:48 final size:48
Alignment explanation
Indices: 16321554--16321650 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
16321544 ATAGTCATAA
*
16321554 CACTCTTTCAAAATTGCATCACTTATACCCTTATAATTCAATCCAAAT
1 CACTCTTTCAAAATTGCATCACTTACACCCTTATAATTCAATCCAAAT
16321602 CACTCTTTCAAAATTGCATCACTTACACCCTTATAATTCAATCCAAAT
1 CACTCTTTCAAAATTGCATCACTTACACCCTTATAATTCAATCCAAAT
16321650 C
1 C
16321651 GAAATTCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (48 bp):
CACTCTTTCAAAATTGCATCACTTACACCCTTATAATTCAATCCAAAT
Found at i:16321639 original size:23 final size:23
Alignment explanation
Indices: 16321565--16321639 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
16321555 ACTCTTTCAA
*
16321565 AATTGCATCACTTATACCCTTAT
1 AATTGCATCACTTACACCCTTAT
** * *
16321588 AATT-CAATC-CAAATCACTCTTTCAA
1 AATTGC-ATCACTTA-CAC-CCTT-AT
16321613 AATTGCATCACTTACACCCTTAT
1 AATTGCATCACTTACACCCTTAT
16321636 AATT
1 AATT
16321640 CAATCCAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 12
0.64 0.16 0.21
Matches are distributed among these distances:
22 3 0.08
23 14 0.38
24 6 0.16
25 11 0.30
26 3 0.08
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.36
Consensus pattern (23 bp):
AATTGCATCACTTACACCCTTAT
Found at i:16331876 original size:46 final size:46
Alignment explanation
Indices: 16331733--16331876 Score: 113
Period size: 46 Copynumber: 3.1 Consensus size: 46
16331723 CCCGCCCATA
*
16331733 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGC-CTAGTTA-CATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC-CT
* * * * *
16331782 --CGAACTCGGACTCAACTCAACGAGTTCAGAAAT-TTGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTC-G-GATGCT-CAACCATCCT
16331826 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
16331872 AGTGA
1 AGTGA
16331877 CATGTCACTT
Statistics
Matches: 74, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 31 0.42
47 28 0.38
48 1 0.01
49 3 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
Found at i:16334536 original size:93 final size:93
Alignment explanation
Indices: 16334428--16334599 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
16334418 CGCCCATAAG
* *
16334428 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTTGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
16334492 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
16334521 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
16334586 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
16334600 TCAATCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:16334594 original size:46 final size:45
Alignment explanation
Indices: 16334421--16334596 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 45
16334411 TGTAACCCGC
* *
16334421 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGAC-ATTGCAT
* *
16334467 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTGCAT
*
16334517 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCAT
*
16334560 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
16334597 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
Found at i:16335679 original size:59 final size:59
Alignment explanation
Indices: 16335611--16335728 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
16335601 CCCTTACTAC
16335611 TAAACTTTCCAAAAATTCCTTCCATGTACTAATTTTGTCCATGAACTTAAAATTGGTCA
1 TAAACTTTCCAAAAATTCCTTCCATGTACTAATTTTGTCCATGAACTTAAAATTGGTCA
16335670 TAAACTTTCCAAAAATTCCTTCCATGTACTAATTTTGTCCATGAACTTAAAATTGGTCA
1 TAAACTTTCCAAAAATTCCTTCCATGTACTAATTTTGTCCATGAACTTAAAATTGGTCA
16335729 AATTGCTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.37
Consensus pattern (59 bp):
TAAACTTTCCAAAAATTCCTTCCATGTACTAATTTTGTCCATGAACTTAAAATTGGTCA
Found at i:16339904 original size:28 final size:28
Alignment explanation
Indices: 16339838--16339965 Score: 175
Period size: 28 Copynumber: 4.5 Consensus size: 28
16339828 CATGAGATTG
* * **
16339838 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
16339867 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
16339895 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
16339924 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
16339952 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
16339966 GACTTACTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 45 0.51
29 44 0.49
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:16339927 original size:57 final size:57
Alignment explanation
Indices: 16339838--16339965 Score: 186
Period size: 57 Copynumber: 2.2 Consensus size: 57
16339828 CATGAGATTG
*
16339838 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* * * *
16339895 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
*
16339952 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
16339966 GACTTACTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 61 0.95
58 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:16345122 original size:13 final size:13
Alignment explanation
Indices: 16345104--16345129 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16345094 ATTTTTATTT
16345104 TTAACATAAAATA
1 TTAACATAAAATA
16345117 TTAACATAAAATA
1 TTAACATAAAATA
16345130 ATTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:16351811 original size:40 final size:40
Alignment explanation
Indices: 16351747--16351847 Score: 150
Period size: 40 Copynumber: 2.5 Consensus size: 40
16351737 TGGATGTAAC
*
16351747 AACCAGCACGAATGCCTTCGGGACTTAGCCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* *
16351787 AACCCGCATGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
16351827 AACTAGCAC-AATTGCCTTCGG
1 AACCAGCACGAA-TGCCTTCGG
16351848 ATCTTAGTCC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 2 0.04
40 52 0.96
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:16351872 original size:40 final size:40
Alignment explanation
Indices: 16351828--16351903 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
16351818 GGTTATAATA
* *
16351828 ACTAGCACAATTGCCTTCGGATCTTAGTCCGGATATAGTG
1 ACTAGCACAAATGCCCTCGGATCTTAGTCCGGATATAGTG
16351868 ACTAGCACAAATGCCCTCGGATCTTAGTCCGGATAT
1 ACTAGCACAAATGCCCTCGGATCTTAGTCCGGATAT
16351904 CATCTGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (40 bp):
ACTAGCACAAATGCCCTCGGATCTTAGTCCGGATATAGTG
Found at i:16353422 original size:13 final size:13
Alignment explanation
Indices: 16353404--16353429 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16353394 ATTTTTATTT
16353404 TTAACATAAAATA
1 TTAACATAAAATA
16353417 TTAACATAAAATA
1 TTAACATAAAATA
16353430 ATTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:16359020 original size:37 final size:38
Alignment explanation
Indices: 16358979--16359059 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 38
16358969 AAAAGTTGTG
16358979 CTTCTGCATTGATTGCTATTCAAACCAAATTTGA-TTT
1 CTTCTGCATTGATTGCTATTCAAACCAAATTTGATTTT
* * * *
16359016 CTTCTGCATTGATTGTTGTTCAAATCATATTTGATTTT
1 CTTCTGCATTGATTGCTATTCAAACCAAATTTGATTTT
16359054 CTTCTG
1 CTTCTG
16359060 GGTTTAGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 30 0.77
38 9 0.23
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.48
Consensus pattern (38 bp):
CTTCTGCATTGATTGCTATTCAAACCAAATTTGATTTT
Found at i:16363596 original size:46 final size:46
Alignment explanation
Indices: 16363546--16363721 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
16363536 TGGTTGAGCA
* *
16363546 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
16363592 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
16363639 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
16363685 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
16363722 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 63 0.58
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:16363702 original size:93 final size:93
Alignment explanation
Indices: 16363543--16363714 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
16363533 GGATGGTTGA
* *
16363543 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
16363608 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
16363636 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
16363701 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
16363715 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:16369739 original size:39 final size:39
Alignment explanation
Indices: 16369696--16369890 Score: 302
Period size: 39 Copynumber: 5.0 Consensus size: 39
16369686 CAAGACACTA
* * * *
16369696 GAAATGTATCCGGGCTAAAGTCTCGCAGGCTTTGTGGTA
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
*
16369735 GAAATGTATCCGGGCTAAAGTCCCACAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
16369774 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* *
16369813 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCATGTTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
* *
16369852 GAAATGTATCC-GGCTAAAGTTCCGCAGGCTTTGTGCTG
1 GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
16369890 G
1 G
16369891 TAATATAATT
Statistics
Matches: 144, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
38 24 0.17
39 120 0.83
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.26
Consensus pattern (39 bp):
GAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
Found at i:16376685 original size:49 final size:49
Alignment explanation
Indices: 16376628--16376815 Score: 367
Period size: 49 Copynumber: 3.8 Consensus size: 49
16376618 GCCTAATGGC
16376628 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
16376677 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
16376726 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
16376775 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGATAAGT
1 TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGA-AAGT
16376816 CCCGAAGGGC
Statistics
Matches: 138, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
49 134 0.97
50 4 0.03
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (49 bp):
TGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
Found at i:16376991 original size:37 final size:37
Alignment explanation
Indices: 16376933--16377011 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
16376923 CCGAGCTCTA
* * * *
16376933 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
* *
16376970 AAGACCCGATAACTTCATGTGGAGATTATGTCTGGGT
1 AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
16377007 AAGAC
1 AAGAC
16377012 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
Found at i:16378079 original size:150 final size:150
Alignment explanation
Indices: 16377879--16378182 Score: 581
Period size: 150 Copynumber: 2.0 Consensus size: 150
16377869 TAAGAGATAT
16377879 TCAGCTTCTCGTGAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTCCGACTTTGGAAATTCAT
1 TCAGCTTCTCGTGAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTCCGACTTTGGAAATTCAT
16377944 TATAAATTAACCAGAGATAATTAGGAGTCATTCCATATATGTATAGATTTCTATATGAGTCTAGT
66 TATAAATTAACCAGAGATAATTAGGAGTCATTCCATATATGTATAGATTTCTATATGAGTCTAGT
16378009 TTCTATAGAAACAAACGGCA
131 TTCTATAGAAACAAACGGCA
*
16378029 TCAGGTTCTCGTGAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTCCGACTTTGGAAATTCAT
1 TCAGCTTCTCGTGAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTCCGACTTTGGAAATTCAT
* *
16378094 TATAAATTAACCAGAGATAATTAGGAGTCATTCCATATATGTATAGATTTCTCTCTGAGTCTAGT
66 TATAAATTAACCAGAGATAATTAGGAGTCATTCCATATATGTATAGATTTCTATATGAGTCTAGT
16378159 TTCTATAGAAACAAACGGCA
131 TTCTATAGAAACAAACGGCA
16378179 TCAG
1 TCAG
16378183 TATTGAAGCT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 151 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (150 bp):
TCAGCTTCTCGTGAGACAGGGCCAGAACGGTTTCTGGATTCCCTGTTCCGACTTTGGAAATTCAT
TATAAATTAACCAGAGATAATTAGGAGTCATTCCATATATGTATAGATTTCTATATGAGTCTAGT
TTCTATAGAAACAAACGGCA
Done.