Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 21 of 325
Found at i:4980580 original size:54 final size:55
Alignment explanation
Indices: 4980495--4980634 Score: 194
Period size: 54 Copynumber: 2.6 Consensus size: 55
4980485 GAGGAAGCGT
* * *
4980495 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTATGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACAAATATCTGTA
* * *
4980549 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACAAATATCTGTA
* *
4980604 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
4980635 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 59 0.77
55 18 0.23
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTATGCCACAAATATCTGTA
Found at i:4980624 original size:27 final size:28
Alignment explanation
Indices: 4980495--4980634 Score: 166
Period size: 27 Copynumber: 5.2 Consensus size: 28
4980485 GAGGAAGCGT
* *
4980495 TCTGGTGGCTATGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAATTATCTGTA
* *
4980522 TCTGGTGGCTATGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACAATTATCTGTA
4980549 TCTGGTGGCTCTGCCAC-ATATATCTGT-
1 TCTGGTGGCTCTGCCACAAT-TATCTGTA
*
4980576 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAATTATCTGTA
* *
4980604 TCTGGTGACTCTGTCAC-ATTATCTGT-
1 TCTGGTGGCTCTGCCACAATTATCTGTA
4980630 TCTGG
1 TCTGG
4980635 CAGCCATGCT
Statistics
Matches: 105, Mismatches: 4, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
26 6 0.06
27 82 0.78
28 17 0.16
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (28 bp):
TCTGGTGGCTCTGCCACAATTATCTGTA
Found at i:4982130 original size:2 final size:2
Alignment explanation
Indices: 4982123--4982171 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
4982113 TGTACGTAAA
4982123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4982165 AT AT AT A
1 AT AT AT A
4982172 GTAATAGTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4982599 original size:22 final size:24
Alignment explanation
Indices: 4982551--4982605 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
4982541 TATTATATAT
*
4982551 ATATATATATAACATAGTAATTGAAA
1 ATATATACATAACATAGTAA-T-AAA
4982577 ATATATACATAACATA-TAA-AAA
1 ATATATACATAACATAGTAATAAA
4982599 ATATATA
1 ATATATA
4982606 ATGTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 10 0.36
25 3 0.11
26 15 0.54
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (24 bp):
ATATATACATAACATAGTAATAAA
Found at i:4982826 original size:26 final size:26
Alignment explanation
Indices: 4982778--4982827 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4982768 ATACATAATA
*
4982778 GTATATAAAAACATAATATAAAAAAC
1 GTATATAAAAACATAATAAAAAAAAC
*
4982804 GTATATACATAACAT-ATAAAAAAA
1 GTATATA-AAAACATAATAAAAAAA
4982828 GCAATATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.64, C:0.08, G:0.04, T:0.24
Consensus pattern (26 bp):
GTATATAAAAACATAATAAAAAAAAC
Found at i:4982943 original size:3 final size:3
Alignment explanation
Indices: 4982937--4982988 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
4982927 AAACATATAC
4982937 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4982985 TAA T
1 TAA T
4982989 TTGGGATACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4983093 original size:3 final size:3
Alignment explanation
Indices: 4983079--4983122 Score: 70
Period size: 3 Copynumber: 14.0 Consensus size: 3
4983069 AAGTATACTC
4983079 TAA TACA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAGA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
4983123 AAAAAAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4985755 original size:27 final size:27
Alignment explanation
Indices: 4985715--4985883 Score: 225
Period size: 27 Copynumber: 6.3 Consensus size: 27
4985705 AGCATGGCTG
* *
4985715 CCAGAACAGATA-ATGTGACAGAGTCA
1 CCAGAACAGATATATGTGGCAGAGCCA
*
4985741 CCAGATACAAATA-ATTGTGGCAGAGCCA
1 CCAGA-ACAGATATA-TGTGGCAGAGCCA
4985769 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
4985796 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* * *
4985823 CCAGATCAGATATTTATGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* * *
4985850 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
4985877 CCAGAAC
1 CCAGAAC
4985884 GCTTCCTCCA
Statistics
Matches: 130, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.04
27 108 0.83
28 17 0.13
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATATATGTGGCAGAGCCA
Found at i:4985850 original size:81 final size:81
Alignment explanation
Indices: 4985715--4985883 Score: 250
Period size: 81 Copynumber: 2.1 Consensus size: 81
4985705 AGCATGGCTG
* *
4985715 CCAGAACAGATAATGTGACAGAGTCACCAGATACAAATAATTGTGGCAGAGCCACCAGAACAGAT
1 CCAGAACAGATAATGTGACAGAGCCACCAGATACAAATAATTATGGCAGAGCCACCAGAACAGAT
4985780 ATATGTGGCAGAGCCA
66 ATATGTGGCAGAGCCA
* * * *
4985796 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATATTTATGGCAGAGCCACCAGATCAGA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATACAAATAATTATGGCAGAGCCACCAGAACAGA
* *
4985860 TATTTGTGGCATAGCCA
65 TATATGTGGCAGAGCCA
4985877 CCAGAAC
1 CCAGAAC
4985884 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 61 0.77
82 18 0.23
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (81 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATACAAATAATTATGGCAGAGCCACCAGAACAGAT
ATATGTGGCAGAGCCA
Found at i:4987501 original size:26 final size:26
Alignment explanation
Indices: 4987465--4987546 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
4987455 TGAAATTCCA
*
4987465 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCTATT
*
4987491 ATCATGAAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCTATT
4987517 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCTATT
4987543 ATCA
1 ATCA
4987547 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCTATT
Found at i:4988835 original size:25 final size:27
Alignment explanation
Indices: 4988798--4988850 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
4988788 TCAAACATGC
4988798 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* **
4988824 ATTTCGGT-AATTTTGCACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
4988850 A
1 A
4988851 AACAGTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:4990393 original size:25 final size:26
Alignment explanation
Indices: 4990332--4990412 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
4990322 TGAAATTCCA
4990332 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
4990358 ATCATGAAACATTTACCTAACCCA-T
1 ATCATGGAACATTTACCTAACCCATT
4990383 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
4990409 ATCA
1 ATCA
4990413 ATTTGTATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
25 24 0.46
26 28 0.54
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:4992872 original size:24 final size:24
Alignment explanation
Indices: 4992845--4992896 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
4992835 ATAGCAAGTC
** *
4992845 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTACACTAATAAATACT
* *
4992869 AAATACATTACACTAATAAATACT
1 AAATAAACTACACTAATAAATACT
4992893 AAAT
1 AAAT
4992897 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.29
Consensus pattern (24 bp):
AAATAAACTACACTAATAAATACT
Found at i:4995804 original size:41 final size:41
Alignment explanation
Indices: 4995528--4995785 Score: 426
Period size: 41 Copynumber: 6.3 Consensus size: 41
4995518 GACTTTGTAT
4995528 CGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTGTGC
1 CGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTGTGC
*
4995569 CGGTGTATTATATCAGGCTTATTGCCTAGTAGGCTTTGTGC
1 CGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTGTGC
* * *
4995610 CGGTGTTTTAAATCAGGCTTATTGCCTAGTAGGCTTTGTGC
1 CGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTGTGC
* * *
4995651 CGGTGTTTTAAATCAGGCTTATTGCCTAGTAGGCTTTGTGC
1 CGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTGTGC
* *
4995692 CGGTGTATTAAATCAGGTTTATTGCCTAGCAGGCTTTGTGC
1 CGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTGTGC
*
4995733 CGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTCTGTGC
1 CGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTGTGC
4995774 CGGTGTATTATA
1 CGGTGTATTATA
4995786 CTGGGCTTTA
Statistics
Matches: 208, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 208 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (41 bp):
CGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTGTGC
Found at i:5000916 original size:26 final size:26
Alignment explanation
Indices: 5000880--5001011 Score: 219
Period size: 26 Copynumber: 5.1 Consensus size: 26
5000870 ACAAATTGAC
5000880 AATAGGTTAGGTAAATGTTCCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
5000906 AATAGGTTAGGTAAATGTTCCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
*
5000932 AATAGGTTAGGTAAATGTTCCATAAT
1 AATAGGTTAGGTAAATGTTCCATGAT
* *
5000958 AATGGGTTAGGTAAATGTTTCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
* *
5000984 AATGGGTTAGGTAAATGTTTCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
5001010 AA
1 AA
5001012 GAATTTCATG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 102 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (26 bp):
AATAGGTTAGGTAAATGTTCCATGAT
Found at i:5002493 original size:28 final size:26
Alignment explanation
Indices: 5002451--5002520 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
5002441 AAAAGTAGCT
* *
5002451 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGGA
* *
5002479 AAATTACTGTTATA-CCCTAGGTGTA
1 AAATTACTGTTATACCCCTAGATGGA
*
5002504 AAATTACCGTTATACCC
1 AAATTACTGTTATACCC
5002521 TAGGGTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 16 0.44
26 3 0.08
27 5 0.14
28 12 0.33
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGGA
Found at i:5002669 original size:27 final size:27
Alignment explanation
Indices: 5002631--5002780 Score: 212
Period size: 27 Copynumber: 5.5 Consensus size: 27
5002621 AAGCGTTCTA
*
5002631 GTGGCTATGCCACAAATATCTGATCTG
1 GTGGCTCTGCCACAAATATCTGATCTG
5002658 GTGGCTCTGCCACAAATATCTGATCTG
1 GTGGCTCTGCCACAAATATCTGATCTG
5002685 GTGGCTCTGCCACAAATATCTGATCTG
1 GTGGCTCTGCCACAAATATCTGATCTG
* *
5002712 GTGGCTCTGCCACATATATCTGTTCTG
1 GTGGCTCTGCCACAAATATCTGATCTG
* *
5002739 GTGG-TCCTGCCACGATTATCTGTATCTG
1 GTGGCT-CTGCCACAAATATCTG-ATCTG
* *
5002767 GTGACTCTGTCACA
1 GTGGCTCTGCCACA
5002781 TTATCTGTTT
Statistics
Matches: 110, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
26 1 0.01
27 95 0.86
28 13 0.12
29 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
GTGGCTCTGCCACAAATATCTGATCTG
Found at i:5005189 original size:25 final size:25
Alignment explanation
Indices: 5005161--5005208 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5005151 TTATACCATG
* * *
5005161 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
5005186 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
5005209 GTTTATGTAT
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:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:5005276 original size:19 final size:19
Alignment explanation
Indices: 5005252--5005313 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
5005242 TAAATATGGT
5005252 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
5005271 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
5005290 TATGTATGATATGCACATG-
1 -ATGTATGATATGCACATGA
5005309 ATGTA
1 ATGTA
5005314 ATCATAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 5 0.12
19 19 0.45
20 18 0.43
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (19 bp):
ATGTATGATATGCACATGA
Found at i:5005289 original size:11 final size:11
Alignment explanation
Indices: 5005256--5005310 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
5005246 TATGGTATGT
5005256 ATGATATGCAC
1 ATGATATGCAC
*
5005267 ATGA-ATG--T
1 ATGATATGCAC
5005275 ATGATATGCAC
1 ATGATATGCAC
*
5005286 ATGATATG--T
1 ATGATATGCAC
5005295 ATGATATGCAC
1 ATGATATGCAC
5005306 ATGAT
1 ATGAT
5005311 GTAATCATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
8 4 0.11
9 11 0.31
10 3 0.09
11 17 0.49
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:5005296 original size:20 final size:20
Alignment explanation
Indices: 5005251--5005310 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
5005241 ATAAATATGG
5005251 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
5005271 -ATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
5005290 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
5005310 T
1 T
5005311 GTAATCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.49
20 20 0.51
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:5005387 original size:24 final size:24
Alignment explanation
Indices: 5005360--5005502 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
5005350 GAGGAAGTGA
5005360 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
5005384 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
5005408 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
5005431 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
5005455 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
5005479 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
5005503 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:5005453 original size:47 final size:47
Alignment explanation
Indices: 5005360--5005502 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
5005350 GAGGAAGTGA
5005360 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
5005408 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
5005455 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
5005503 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:5005476 original size:71 final size:72
Alignment explanation
Indices: 5005360--5005503 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
5005350 GAGGAAGTGA
*
5005360 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
5005423 CCAGTTAT
65 CCAGTTAT
** * *
5005431 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
5005496 CAGTTAT
66 CAGTTAT
5005503 A
1 A
5005504 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:5005753 original size:30 final size:31
Alignment explanation
Indices: 5005693--5005755 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
5005683 CGTTTACAGT
5005693 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
5005724 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
5005754 AA
1 AA
5005756 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:5013294 original size:25 final size:25
Alignment explanation
Indices: 5013265--5013312 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5013255 CCTTATAATG
* * *
5013265 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
5013290 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
5013313 GTTTATGTAT
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:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:5013415 original size:20 final size:20
Alignment explanation
Indices: 5013355--5013415 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
5013345 ATAAATATGG
*
5013355 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
5013375 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
5013395 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
5013415 T
1 T
5013416 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:5013492 original size:24 final size:24
Alignment explanation
Indices: 5013465--5013607 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
5013455 GAGGAAGTGA
5013465 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
5013489 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
5013513 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
5013536 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
5013560 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
5013584 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
5013608 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:5013558 original size:47 final size:47
Alignment explanation
Indices: 5013465--5013607 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
5013455 GAGGAAGTGA
5013465 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
5013513 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
5013560 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
5013608 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:5013581 original size:71 final size:72
Alignment explanation
Indices: 5013465--5013608 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
5013455 GAGGAAGTGA
*
5013465 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
5013528 CCAGTTAT
65 CCAGTTAT
** * *
5013536 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
5013601 CAGTTAT
66 CAGTTAT
5013608 A
1 A
5013609 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:5013858 original size:30 final size:31
Alignment explanation
Indices: 5013798--5013860 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
5013788 CGTTTACAGT
5013798 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
5013829 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
5013859 AA
1 AA
5013861 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:5015095 original size:2 final size:2
Alignment explanation
Indices: 5015088--5015139 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5015078 CATGGTATCG
5015088 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5015130 TA TA TA TA TA
1 TA TA TA TA TA
5015140 ATCATATCAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5018487 original size:20 final size:20
Alignment explanation
Indices: 5018464--5018505 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5018454 CCAGTTTTAC
5018464 TTTATTTTTAATTCTTGCTT
1 TTTATTTTTAATTCTTGCTT
5018484 TTTATTTTTAATTCTTGCTT
1 TTTATTTTTAATTCTTGCTT
5018504 TT
1 TT
5018506 AAAAGTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.10, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTATTTTTAATTCTTGCTT
Found at i:5019350 original size:2 final size:2
Alignment explanation
Indices: 5019343--5019388 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
5019333 CAAAAGGGTT
*
5019343 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5019385 TA TA
1 TA TA
5019389 CATTGATTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5020774 original size:2 final size:2
Alignment explanation
Indices: 5020769--5020795 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5020759 CCCCCCCAAA
5020769 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5020796 ATACACCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5024573 original size:13 final size:13
Alignment explanation
Indices: 5024532--5024573 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
5024522 AACTTAAAAC
5024532 TTGTAATTCAAAT
1 TTGTAATTCAAAT
5024545 TTGGCTAATT-AAAT
1 TT-G-TAATTCAAAT
5024559 TTGTAATTCAAAT
1 TTGTAATTCAAAT
5024572 TT
1 TT
5024574 TATAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 7 0.27
15 5 0.19
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (13 bp):
TTGTAATTCAAAT
Found at i:5031506 original size:16 final size:16
Alignment explanation
Indices: 5031487--5031533 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
5031477 CATAATTTAC
5031487 AAATAAAAATATATAA
1 AAATAAAAATATATAA
*
5031503 AAATAAAATTATAT-A
1 AAATAAAAATATATAA
*
5031518 ATATAAAAATATATAA
1 AAATAAAAATATATAA
5031534 TATGATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAATATATAA
Found at i:5031511 original size:21 final size:21
Alignment explanation
Indices: 5031487--5031528 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5031477 CATAATTTAC
5031487 AAATAAAA-ATATATAAAAATA
1 AAATAAAATA-ATATAAAAATA
* *
5031508 AAATTATATAATATAAAAATA
1 AAATAAAATAATATAAAAATA
5031529 TATAATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAAAATAATATAAAAATA
Found at i:5031543 original size:12 final size:13
Alignment explanation
Indices: 5031488--5031632 Score: 59
Period size: 15 Copynumber: 10.8 Consensus size: 13
5031478 ATAATTTACA
*
5031488 AATAAAAATATAT
1 AATATAAATATAT
*
5031501 AAAAATAAAATTATAT
1 -AATAT-AAA-TATAT
5031517 AATATAAAAATATAT
1 AATAT--AAATATAT
*
5031532 AATATGATATATAT
1 AATAT-AAATATAT
5031546 AATAT-AATATAT
1 AATATAAATATAT
5031558 AA-A-AAA-ATAT
1 AATATAAATATAT
* * * *
5031568 TATGACAGATAGTAA
1 AAT-ATAAATA-TAT
*
5031583 AATAT-AATATGT
1 AATATAAATATAT
* *
5031595 AATAAAAATACAT
1 AATATAAATATAT
5031608 AA-ATAAATATAAT
1 AATATAAATAT-AT
*
5031621 AAAATATAATAT
1 AATATA-AATAT
5031633 GACATATGTA
Statistics
Matches: 99, Mismatches: 19, Indels: 25
0.69 0.13 0.17
Matches are distributed among these distances:
10 5 0.05
11 3 0.03
12 20 0.20
13 16 0.16
14 20 0.20
15 26 0.26
16 9 0.09
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (13 bp):
AATATAAATATAT
Found at i:5031544 original size:29 final size:31
Alignment explanation
Indices: 5031489--5031566 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 31
5031479 TAATTTACAA
5031489 ATAAAAATATATAAAAATAAAATTATATAAT
1 ATAAAAATATATAAAAATAAAATTATATAAT
* * *
5031520 ATAAAAATATAT-AATATGATA-TATATAAT
1 ATAAAAATATATAAAAATAAAATTATATAAT
* *
5031549 AT-AATATATAAAAAAATA
1 ATAAAAATATATAAAAATA
5031567 TTATGACAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 7 0.18
29 14 0.36
30 6 0.15
31 12 0.31
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (31 bp):
ATAAAAATATATAAAAATAAAATTATATAAT
Found at i:5036308 original size:38 final size:38
Alignment explanation
Indices: 5036257--5036330 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
5036247 GACTACCTAT
5036257 AAGTTGCTGATACATCAACCAATCTTTTAAGTCTTTAC
1 AAGTTGCTGATACATCAACCAATCTTTTAAGTCTTTAC
*
5036295 AAGTTGCTGATACATCAACCAATTTTTTAAGTCTTT
1 AAGTTGCTGATACATCAACCAATCTTTTAAGTCTTT
5036331 CCCTTCATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (38 bp):
AAGTTGCTGATACATCAACCAATCTTTTAAGTCTTTAC
Found at i:5040479 original size:25 final size:25
Alignment explanation
Indices: 5040445--5040497 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
5040435 CAAGTTAAGA
5040445 AAGAATTTTGAATGATCTTACTCAT
1 AAGAATTTTGAATGATCTTACTCAT
5040470 AAGAATTTTGAATGATCTTACTCAT
1 AAGAATTTTGAATGATCTTACTCAT
5040495 AAG
1 AAG
5040498 CTTAAACCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (25 bp):
AAGAATTTTGAATGATCTTACTCAT
Found at i:5055756 original size:24 final size:24
Alignment explanation
Indices: 5055729--5055780 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5055719 ATAGCAAGTC
* *
5055729 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
5055753 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
5055777 AAAT
1 AAAT
5055781 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:5057725 original size:24 final size:24
Alignment explanation
Indices: 5057698--5057745 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5057688 ATAGCAAGTC
*
5057698 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATGCT
* *
5057722 AAATATATTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATGCT
5057746 GAATCTTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATGCT
Found at i:5060880 original size:2 final size:2
Alignment explanation
Indices: 5060873--5060910 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5060863 TATGATCTAC
5060873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5060911 TCGAGTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5066488 original size:53 final size:53
Alignment explanation
Indices: 5066373--5066604 Score: 191
Period size: 53 Copynumber: 4.4 Consensus size: 53
5066363 ATGACTTCTC
*
5066373 ATGGTCTTACATGGTATCC-T---TT-TGAAACTTACCATTGCCATG-TCT-CAA
1 ATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCT-TGC-A
*
5066421 CATGGTCTTACATGGTATCCTTGCCTTATG-AACTCACCAATGCCATGCCTTGCA
1 -ATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATG-CTTGCA
* * * *
5066475 ATGGTCTTACATGGGA-CCTTTGCCTTATGGTAACTTATCAATGCCATGTTTG-A
1 ATGGTCTTACATGGTATCC-TTGCCTTAT-GAAACTTACCAATGCCATGCTTGCA
* * * *
5066528 CATGGTCTTACATGATTTACTTGCCTTA-GAAACCTTACCAATTGCAATGACTTGGC-
1 -ATGGTCTTACATGGTATCCTTGCCTTATGAAA-CTTACCAA-TGCCATG-CTT-GCA
5066584 ATGGTCTTACATGGTATCCTT
1 ATGGTCTTACATGGTATCCTT
5066605 AAACCCTAAT
Statistics
Matches: 148, Mismatches: 17, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
49 19 0.13
50 1 0.01
52 5 0.03
53 49 0.33
54 35 0.24
55 38 0.26
56 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (53 bp):
ATGGTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCTTGCA
Found at i:5066552 original size:54 final size:52
Alignment explanation
Indices: 5066420--5066596 Score: 137
Period size: 55 Copynumber: 3.3 Consensus size: 52
5066410 CCATGTCTCA
*
5066420 ACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
1 ACATGGTCTTACAT-GTATACTTGCCTTATGAACTCACCAATGCCATGCCTTG
* * * * *
5066473 -CAATGGTCTTACATGGGA-CCTTTGCCTTATGGTAACTTATCAATGCCATG-TTTG
1 AC-ATGGTCTTACAT-GTATAC-TTGCCTTAT-G-AACTCACCAATGCCATGCCTTG
* * * *
5066527 ACATGGTCTTACATGATTTACTTGCCTTA-GAAACCTTACCAATTGCAATGACTTG
1 ACATGGTCTTACATG-TATACTTGCCTTATG-AA-CTCACCAA-TGCCATGCCTTG
*
5066582 GCATGGTCTTACATG
1 ACATGGTCTTACATG
5066597 GTATCCTTAA
Statistics
Matches: 102, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
52 6 0.06
53 32 0.31
54 30 0.29
55 34 0.33
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (52 bp):
ACATGGTCTTACATGTATACTTGCCTTATGAACTCACCAATGCCATGCCTTG
Found at i:5075427 original size:21 final size:20
Alignment explanation
Indices: 5075383--5075427 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5075373 CCTTTTTTTA
*
5075383 AAAAATAAAAGAATAAATGG
1 AAAAATAAAAGAATAAATGC
5075403 AAAAATGAAAAGAATAGAAT-C
1 AAAAAT-AAAAGAATA-AATGC
5075424 AAAA
1 AAAA
5075428 GAACCACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 13 0.59
22 3 0.14
ACGTcount: A:0.71, C:0.02, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAAATAAAAGAATAAATGC
Found at i:5075758 original size:17 final size:18
Alignment explanation
Indices: 5075736--5075777 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
5075726 ATTGGGCTTA
**
5075736 GGGTTTTTTTTTGTT-TT
1 GGGTTTTTAATTGTTATT
*
5075753 GGGTTTGTAATTGTTATT
1 GGGTTTTTAATTGTTATT
5075771 GGGTTTT
1 GGGTTTT
5075778 GATTGGGCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.07, C:0.00, G:0.29, T:0.64
Consensus pattern (18 bp):
GGGTTTTTAATTGTTATT
Found at i:5076246 original size:88 final size:87
Alignment explanation
Indices: 5076110--5076574 Score: 311
Period size: 88 Copynumber: 5.3 Consensus size: 87
5076100 GACTTTATCG
** * * * *
5076110 CTTCAATCTATTCCACTACAACTTCA-GGAGTATAGGAATTGTTG-CTTCAGTCTGCTCCACTGC
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAG-ATAAG-ATTG-TGACTTCAGTCTACTCCACTAC
* *
5076173 AACTTCAGGGAGTTGAGATTCATAA
63 AACTTCAGGGAGATAAGATTCATAA
* *
5076198 CTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGACTTCAATCTACTCCACTACAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTGACTTCAGTCTACTCCACTACAA
* * *
5076263 CTTCAGGGAGATAAGGTTTATAG
65 CTTCAGGGAGATAAGATTCATAA
* * * * * *
5076286 CTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAG-TT-TTACTATCCCCGATCTACTCCCCTA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGACT-T--CAG-TCTACTCCACTA
*
5076349 CAACTTCAGGGAGACAAGA-TC-TAA
62 CAACTTCAGGGAGATAAGATTCATAA
* * * * * *
5076373 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGGTCTGCAATAACTTCAATCT-GTCCCACG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG---TGACTTCAGTCTACT-CCACT
* * *
5076437 ACAACTTCAGGGAGATAAGGTTTATAT
61 ACAACTTCAGGGAGATAAGATTCATAA
* * * * ** * * * * *
5076464 CTTTAATCTACTCTACTGCAACTTTAAAGAGATAAGATTTGTTA-TCCCCGATCTACTCCCCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTGACT-TCAG-TCTACTCCACTAC
* * *
5076528 AACTTTAGAGAGACAAGA-TC-TAA
63 AACTTCAGGGAGATAAGATTCATAA
* *
5076551 CTTCAATCTGCACCACCGCAACTT
1 CTTCAATCTGCTCCACTGCAACTT
5076575 TAGGAAGTTG
Statistics
Matches: 293, Mismatches: 64, Indels: 41
0.74 0.16 0.10
Matches are distributed among these distances:
85 4 0.01
86 3 0.01
87 59 0.20
88 105 0.36
89 78 0.27
90 3 0.01
91 35 0.12
92 2 0.01
93 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (87 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTCAGTCTACTCCACTACAAC
TTCAGGGAGATAAGATTCATAA
Found at i:5076262 original size:132 final size:130
Alignment explanation
Indices: 5076110--5076409 Score: 316
Period size: 132 Copynumber: 2.3 Consensus size: 130
5076100 GACTTTATCG
* * * *
5076110 CTTCAATCTATTCCACTACAACTTCAGGAG-TATAGGAATTGTTGCTTCAGTCTGCTCCACTGCA
1 CTTCAATCTACTCCACTACAACTTCAGGAGATA-AGG-ATTATAGCTTCAATCTGCTCCACTGCA
* * * ** * * *
5076174 ACTTCAGGGAGTTGAGATTCA-TAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGACTT
64 ACTTCAGAGAGATAAGATTCACTAACCCCAACCTACTCCACTACAACTTCAGGGAGACAAGA--T
* *
5076238 GTGA
127 CTAA
* * *
5076242 CTTCAATCTACTCCACTACAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTGCTCTACTGCAA
1 CTTCAATCTACTCCACTACAACTTCA-GGAGATAAGGATTATAGCTTCAATCTGCTCCACTGCAA
* * * * * *
5076307 CTTCAGAGAGATAAGTTTTACTATCCCCGATCTACTCCCCTACAACTTCAGGGAGACAAGATCTA
65 CTTCAGAGAGATAAGATTCACTAACCCCAACCTACTCCACTACAACTTCAGGGAGACAAGATCTA
5076372 A
130 A
*
5076373 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGG
1 CTTCAATCTACTCCACTACAACTTCA-GGAGATAAGG
5076410 TCTGCAATAA
Statistics
Matches: 141, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
131 39 0.28
132 62 0.44
133 38 0.27
134 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (130 bp):
CTTCAATCTACTCCACTACAACTTCAGGAGATAAGGATTATAGCTTCAATCTGCTCCACTGCAAC
TTCAGAGAGATAAGATTCACTAACCCCAACCTACTCCACTACAACTTCAGGGAGACAAGATCTAA
Found at i:5076273 original size:44 final size:43
Alignment explanation
Indices: 5076110--5076502 Score: 281
Period size: 44 Copynumber: 8.9 Consensus size: 43
5076100 GACTTTATCG
* * * * **
5076110 CTTCAATCTATTCCACTACAACTTCA-GGAGTATAGGAATTGTTG
1 CTTCAATCTACTCCACTGCAACTTCAGGGAG-ATAAG-ATTATAA
* * * *
5076154 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGTTGAGATTCATAA
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATT-ATAA
* * * *
5076198 CTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGA
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGA-TTATAA
* * *
5076242 CTTCAATCTACTCCACTACAACTTCAGGGAGATAAGGTTTATAG
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAA-GATTATAA
* * * * * *
5076286 CTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGTTTTACTAT
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG-ATTA-TAA
** * * * * *
5076331 CCCCGATCTACTCCCCTACAACTTCAGGGAGACAAGA-TCTAA
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATAA
*
5076373 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGGTCTGCAATAA
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGAT-T---ATAA
* * *
5076420 CTTCAATCT-GTCCCAC-GACAACTTCAGGGAGATAAGGTTTATAT
1 CTTCAATCTACT-CCACTG-CAACTTCAGGGAGATAA-GATTATAA
* * * **
5076464 CTTTAATCTACTCTACTGCAACTTTAAAGAGATAAGATT
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
5076503 TGTTATCCCC
Statistics
Matches: 273, Mismatches: 60, Indels: 33
0.75 0.16 0.09
Matches are distributed among these distances:
42 32 0.12
43 8 0.03
44 158 0.58
45 37 0.14
46 2 0.01
47 34 0.12
48 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (43 bp):
CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTATAA
Found at i:5076497 original size:178 final size:175
Alignment explanation
Indices: 5076172--5076574 Score: 540
Period size: 178 Copynumber: 2.3 Consensus size: 175
5076162 TGCTCCACTG
*** *
5076172 CAACTTCAGGGAGTTGAGATTCATAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 CAACTTCAGGGAGACAAGA-TC-TAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
* * *
5076237 TGTGACTTCAATCTACTCCACTACAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTGCTCTAC
64 TGTAACTTCAATCTACTCCACGACAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTACTCTAC
* *
5076302 TGCAACTTCAGAGAGATAAGTTTTACTATCCCCGATCTACTCCCCTA
129 TGCAACTTCAAAGAGATAAGATTTACTATCCCCGATCTACTCCCCTA
* *
5076349 CAACTTCAGGGAGACAAGATCTAACTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG-GTCT
1 CAACTTCAGGGAGACAAGATCTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-T
* *
5076413 GCAATAACTTCAATCT-GTCCCACGACAACTTCAGGGAGATAAGGTTTATATCTTTAATCTACTC
65 G---TAACTTCAATCTACT-CCACGACAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTACTC
* **
5076477 TACTGCAACTTTAAAGAGATAAGATTTGTTATCCCCGATCTACTCCCCTA
126 TACTGCAACTTCAAAGAGATAAGATTTACTATCCCCGATCTACTCCCCTA
* * * * *
5076527 TAACTTTAGAGAGACAAGATCTAACTTCAATCTGCACCACCGCAACTT
1 CAACTTCAGGGAGACAAGATCTAACTTCAATCTGCTCCACTGCAACTT
5076575 TAGGAAGTTG
Statistics
Matches: 199, Mismatches: 22, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
174 1 0.01
175 39 0.20
176 2 0.01
177 17 0.09
178 140 0.70
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (175 bp):
CAACTTCAGGGAGACAAGATCTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
TAACTTCAATCTACTCCACGACAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTACTCTACTG
CAACTTCAAAGAGATAAGATTTACTATCCCCGATCTACTCCCCTA
Found at i:5088969 original size:12 final size:12
Alignment explanation
Indices: 5088952--5089046 Score: 71
Period size: 12 Copynumber: 8.4 Consensus size: 12
5088942 TCTTAAAATT
5088952 ATAAATAATATA
1 ATAAATAATATA
5088964 ATAAATAATAT-
1 ATAAATAATATA
* *
5088975 AT-GATATACATA
1 ATAAATA-ATATA
*
5088987 ATATATAATA-A
1 ATAAATAATATA
5088998 A-AAATAATATA
1 ATAAATAATATA
*
5089009 ATAAGTAATAT-
1 ATAAATAATATA
5089020 ATATAATAA-A-A
1 ATA-AATAATATA
*
5089031 GTAAA-AATATA
1 ATAAATAATATA
5089042 ATAAA
1 ATAAA
5089047 ATGCTATATA
Statistics
Matches: 65, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
9 2 0.03
10 13 0.20
11 20 0.31
12 27 0.42
13 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (12 bp):
ATAAATAATATA
Found at i:5088971 original size:7 final size:7
Alignment explanation
Indices: 5088947--5089029 Score: 53
Period size: 7 Copynumber: 11.4 Consensus size: 7
5088937 ACAAATCTTA
*
5088947 AAATTAT
1 AAATAAT
5088954 AAATAAT
1 AAATAAT
5088961 --ATAAT
1 AAATAAT
5088966 AAATAAT
1 AAATAAT
*
5088973 ATATGATAT
1 AAAT-A-AT
*
5088982 ACATAAT
1 AAATAAT
*
5088989 ATATAAT
1 AAATAAT
*
5088996 AAAAAAT
1 AAATAAT
5089003 AATATAAT
1 AA-ATAAT
*
5089011 AAGTAAT
1 AAATAAT
5089018 ATATATAAT
1 A-A-ATAAT
5089027 AAA
1 AAA
5089030 AGTAAAAATA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
5 5 0.08
7 35 0.58
8 10 0.17
9 10 0.17
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (7 bp):
AAATAAT
Found at i:5089024 original size:33 final size:30
Alignment explanation
Indices: 5088954--5089045 Score: 73
Period size: 31 Copynumber: 2.9 Consensus size: 30
5088944 TTAAAATTAT
* *
5088954 AAATAATATAATAAATAAT-ATATGAT-ATAC
1 AAAT-ATATAATAAAAAATAATATAATAAT-C
5088984 ATAATATATAATAAAAAATAATATAATAAGT-
1 A-AATATATAATAAAAAATAATATAATAA-TC
*
5089015 AATATATATAATAAAAGTAAAAATATAATAA
1 AA-ATATATAATAAAA--AATAATATAATAA
5089046 AATGCTATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
30 15 0.29
31 23 0.44
32 1 0.02
33 13 0.25
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATATATAATAAAAAATAATATAATAATC
Found at i:5089070 original size:15 final size:15
Alignment explanation
Indices: 5088989--5089072 Score: 71
Period size: 15 Copynumber: 5.4 Consensus size: 15
5088979 TATACATAAT
* *
5088989 ATATAATAAAAAATA
1 ATATAATAAAATACA
*
5089004 ATATAATAAGTAATA-T
1 ATATAATAA--AATACA
*
5089020 ATATAATAAAAGTAAAA
1 ATATAATAAAA-T-ACA
* *
5089037 ATATAATAAAATGCT
1 ATATAATAAAATACA
5089052 ATATAATAAAATACA
1 ATATAATAAAATACA
5089067 ATATAA
1 ATATAA
5089073 ATATATATAG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
14 2 0.04
15 29 0.52
16 11 0.20
17 14 0.25
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (15 bp):
ATATAATAAAATACA
Found at i:5089079 original size:25 final size:25
Alignment explanation
Indices: 5089034--5089081 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5089024 AATAAAAGTA
* *
5089034 AAAATATAATAAAATGCTATATAAT
1 AAAATACAATAAAATGATATATAAT
5089059 AAAATACAATATAAAT-ATATATA
1 AAAATACAATA-AAATGATATATA
5089082 GGAGAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAATACAATAAAATGATATATAAT
Found at i:5092231 original size:18 final size:18
Alignment explanation
Indices: 5092196--5092250 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
5092186 TATATTATAC
5092196 ATTATAAG-ATTA-TTTT
1 ATTATAAGTATTATTTTT
*
5092212 ATTATAAGTGTTATTTTT
1 ATTATAAGTATTATTTTT
* *
5092230 ATTATATGTATTATTATT
1 ATTATAAGTATTATTTTT
5092248 ATT
1 ATT
5092251 TGTTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 8 0.24
17 3 0.09
18 22 0.67
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTATAAGTATTATTTTT
Found at i:5092241 original size:15 final size:16
Alignment explanation
Indices: 5092208--5092260 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
5092198 TATAAGATTA
5092208 TTTTATTATAAGTGTTAT
1 TTTTATTAT-A-TGTTAT
5092226 TTTTATTATATG-TAT
1 TTTTATTATATGTTAT
* *
5092241 TATTATTATTTGTTAT
1 TTTTATTATATGTTAT
5092257 TTTT
1 TTTT
5092261 CTCAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 13 0.42
16 8 0.26
17 1 0.03
18 9 0.29
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.68
Consensus pattern (16 bp):
TTTTATTATATGTTAT
Found at i:5092515 original size:7 final size:7
Alignment explanation
Indices: 5092503--5092532 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5092493 TTATTCTTGT
5092503 TATTATA
1 TATTATA
5092510 TATTATA
1 TATTATA
5092517 TATTATA
1 TATTATA
5092524 TATTATA
1 TATTATA
5092531 TA
1 TA
5092533 CTATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATTATA
Found at i:5113083 original size:119 final size:119
Alignment explanation
Indices: 5112875--5113468 Score: 992
Period size: 119 Copynumber: 5.0 Consensus size: 119
5112865 TAAATTGAAG
*
5112875 ATAGCAGATCTAGA-CTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTG
1 ATAGCAGATCTA-ACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTG
* * *
5112939 TTTACAAGAAACAAGTCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAG
65 TTTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
5112994 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
5113059 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
5113113 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
*
5113178 TTACAAGGAAAAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
* * *
5113232 ATAACAGATCTAGCCTTCAGATGTTTATACTGAAGCAAATCCAAGATGATTTGGTATTCTTGTGT
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
* *
5113297 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGAT
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
* * * * * *
5113351 ATAGCAGATCTAACCTTCAGATGATTATACTGAAACAGATCCAAGATGATTTAGAATTCTTATGC
1 ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
* * * *
5113416 TTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAA
66 TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAA
5113469 CAGACTCAAA
Statistics
Matches: 450, Mismatches: 24, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
118 1 0.00
119 449 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (119 bp):
ATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGT
TTACAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAAT
Found at i:5113528 original size:83 final size:83
Alignment explanation
Indices: 5113413--5113658 Score: 384
Period size: 83 Copynumber: 3.0 Consensus size: 83
5113403 AGAATTCTTA
* * * * * *
5113413 TGCTTACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAACAGACTCAA
1 TGCTTACAAAGAACAAATCAAGGACGTAGCAGATTTGACTCTCAGATGTTCTCAAACAGACTCAA
5113478 AATGGTTTGGCATCTTTG
66 AATGGTTTGGCATCTTTG
5113496 TGCTTACAAAGAACAAATCAAGGACGTAGCAGATTTGACTCTCAGATGTTCTCAAACAGACTCAA
1 TGCTTACAAAGAACAAATCAAGGACGTAGCAGATTTGACTCTCAGATGTTCTCAAACAGACTCAA
*
5113561 AATGGTGTGGCATCTTTG
66 AATGGTTTGGCATCTTTG
*
5113579 TGCTTACAAAGAACAAATCAAGGACGTAGCAGATTTGACTCTCAGATGTTCTCAAAACAGATTCA
1 TGCTTACAAAGAACAAATCAAGGACGTAGCAGATTTGACTCTCAGATGTTCTC-AAACAGACTCA
** *
5113644 AGTTGATTTGGCATC
65 AAATGGTTTGGCATC
5113659 CCCACAAATC
Statistics
Matches: 150, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
83 129 0.86
84 21 0.14
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (83 bp):
TGCTTACAAAGAACAAATCAAGGACGTAGCAGATTTGACTCTCAGATGTTCTCAAACAGACTCAA
AATGGTTTGGCATCTTTG
Found at i:5115203 original size:2 final size:2
Alignment explanation
Indices: 5115196--5115222 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5115186 TTTATTATCC
5115196 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5115223 TTTTATTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5115300 original size:18 final size:18
Alignment explanation
Indices: 5115265--5115319 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
5115255 TATATTATAC
5115265 ATTATAAG-ATTA-TTTT
1 ATTATAAGTATTATTTTT
*
5115281 ATTATAAGTGTTATTTTT
1 ATTATAAGTATTATTTTT
* *
5115299 ATTATATGTATTATTATT
1 ATTATAAGTATTATTTTT
5115317 ATT
1 ATT
5115320 TGTTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 8 0.24
17 3 0.09
18 22 0.67
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTATAAGTATTATTTTT
Found at i:5115310 original size:15 final size:16
Alignment explanation
Indices: 5115277--5115329 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
5115267 TATAAGATTA
5115277 TTTTATTATAAGTGTTAT
1 TTTTATTAT-A-TGTTAT
5115295 TTTTATTATATG-TAT
1 TTTTATTATATGTTAT
* *
5115310 TATTATTATTTGTTAT
1 TTTTATTATATGTTAT
5115326 TTTT
1 TTTT
5115330 CTCAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 13 0.42
16 8 0.26
17 1 0.03
18 9 0.29
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.68
Consensus pattern (16 bp):
TTTTATTATATGTTAT
Found at i:5115584 original size:7 final size:7
Alignment explanation
Indices: 5115572--5115597 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5115562 TTATTCTTGT
5115572 TATTATA
1 TATTATA
5115579 TATTATA
1 TATTATA
5115586 TATTATA
1 TATTATA
5115593 TATTA
1 TATTA
5115598 AATACTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATTATA
Found at i:5115880 original size:2 final size:2
Alignment explanation
Indices: 5115873--5115905 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5115863 CAATACATGC
5115873 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5115906 TTTGTTTGCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5118303 original size:26 final size:26
Alignment explanation
Indices: 5118274--5118381 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
5118264 TGATACAAAT
5118274 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5118300 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5118326 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5118352 TGATAGTGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5118378 TGAT
1 TGAT
5118382 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5120399 original size:137 final size:136
Alignment explanation
Indices: 5120154--5120436 Score: 530
Period size: 137 Copynumber: 2.1 Consensus size: 136
5120144 TAGTCTCCCC
*
5120154 AAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
1 AAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
5120219 ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTG
66 ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTG
5120284 TTACCT
131 TTACCT
5120290 AAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGT
1 AAATGGGCTTGCATATG-TTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGT
*
5120355 TATCTGAATAAGGGGCTAAGGCCCTGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACT
65 TATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACT
5120420 GTTACCT
130 GTTACCT
*
5120427 GAATGGGCTT
1 AAATGGGCTT
5120437 AAGCCCAATA
Statistics
Matches: 143, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 17 0.12
137 126 0.88
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (136 bp):
AAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGTT
ATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACTG
TTACCT
Found at i:5124801 original size:3 final size:3
Alignment explanation
Indices: 5124793--5124826 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5124783 ACTAACAAAG
5124793 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5124827 ATGAGAGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5126470 original size:17 final size:18
Alignment explanation
Indices: 5126448--5126492 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
5126438 TAATAGTAAC
5126448 TATTTATTTTTTAC-TTT
1 TATTTATTTTTTACTTTT
5126465 TATTTA-TTTTTACTTTT
1 TATTTATTTTTTACTTTT
5126482 TATTT-TTTTTT
1 TATTTATTTTTT
5126493 TGTTCTGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (18 bp):
TATTTATTTTTTACTTTT
Found at i:5127170 original size:13 final size:13
Alignment explanation
Indices: 5127154--5127200 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
5127144 TTTTGATACT
*
5127154 ACACGGCCTAGCT
1 ACACGGCCTAGCC
5127167 ACACGGCCTAGCC
1 ACACGGCCTAGCC
*
5127180 ATACGGCCTAGCC
1 ACACGGCCTAGCC
5127193 ACACGGCC
1 ACACGGCC
5127201 GTGTGGCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.11
Consensus pattern (13 bp):
ACACGGCCTAGCC
Found at i:5127254 original size:21 final size:21
Alignment explanation
Indices: 5127230--5127278 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5127220 TTAGGGATCC
* *
5127230 CACACGGGAATGTGTTTTGGA
1 CACACGGGAATGTCTATTGGA
*
5127251 CACACGGGAATGTCTATTGGG
1 CACACGGGAATGTCTATTGGA
5127272 CACACGG
1 CACACGG
5127279 CCGTGTCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (21 bp):
CACACGGGAATGTCTATTGGA
Found at i:5129439 original size:19 final size:19
Alignment explanation
Indices: 5129415--5129453 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5129405 CCATGAAAAT
*
5129415 TTATTAACTACTTTC-TCCC
1 TTATTAA-TACATTCTTCCC
5129434 TTATTAATACATTCTTCCC
1 TTATTAATACATTCTTCCC
5129453 T
1 T
5129454 AATTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTAATACATTCTTCCC
Found at i:5132908 original size:5 final size:5
Alignment explanation
Indices: 5132898--5132929 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5132888 TTGTGTGTTC
5132898 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
5132930 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:5132912 original size:9 final size:9
Alignment explanation
Indices: 5132898--5132928 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
5132888 TTGTGTGTTC
5132898 TTTATTTTA
1 TTTATTTTA
5132907 TTTATTTTA
1 TTTATTTTA
5132916 TTTTATTTTA
1 -TTTATTTTA
5132926 TTT
1 TTT
5132929 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:5135949 original size:40 final size:39
Alignment explanation
Indices: 5135904--5136030 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 39
5135894 CGGAACATAA
5135904 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
5135944 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
5135984 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
5136024 CCGGATA
1 CCGGATA
5136031 AAATTTCCAG
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
38 1 0.01
40 67 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:5136048 original size:40 final size:40
Alignment explanation
Indices: 5135920--5136070 Score: 137
Period size: 40 Copynumber: 3.8 Consensus size: 40
5135910 ATAACCATGT
* * *
5135920 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAAAATCTC-CA
** ** * *
5135960 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATAAAATCTCCA
* *
5136000 GCACAATTGCCTTCGGGTCTTAACCCGGATAAAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAAAATCTCCA
* *
5136040 GCATAATTGTCTTCGGGAT-TTAGCCCGGATA
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATA
5136071 TCATTCAATT
Statistics
Matches: 89, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
39 2 0.02
40 84 0.94
41 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATAAAATCTCCA
Found at i:5136054 original size:80 final size:80
Alignment explanation
Indices: 5135920--5136069 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
5135910 ATAACCATGT
* *
5135920 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
5135984 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * *
5136000 GCACAATTGCCTTCGGGTCTTAACCCGGATAAAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
5136063 CCCGGAT
64 CCCGGAT
5136070 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAAAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:5140593 original size:5 final size:5
Alignment explanation
Indices: 5140576--5140616 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
5140566 TTGTGTGTTC
*
5140576 TTTAC TTTA- TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
5140617 TCACAGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.24
5 26 0.76
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:5140593 original size:9 final size:9
Alignment explanation
Indices: 5140576--5140615 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
5140566 TTGTGTGTTC
*
5140576 TTTACTTTA
1 TTTATTTTA
5140585 TTTATTTTA
1 TTTATTTTA
5140594 TTTATTTTA
1 TTTATTTTA
5140603 TTTTATTTTA
1 -TTTATTTTA
5140613 TTT
1 TTT
5140616 TTCACAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:5140602 original size:14 final size:15
Alignment explanation
Indices: 5140576--5140616 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
5140566 TTGTGTGTTC
5140576 TTTACTTTA-TTTAT
1 TTTACTTTATTTTAT
5140590 TTTA-TTTATTTTAT
1 TTTACTTTATTTTAT
*
5140604 TTTATTTTATTTT
1 TTTACTTTATTTT
5140617 TCACAGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.16
14 13 0.52
15 8 0.32
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTACTTTATTTTAT
Found at i:5143945 original size:5 final size:5
Alignment explanation
Indices: 5143935--5143967 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
5143925 TTGTGTGTTC
5143935 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
5143968 CACACAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:5147033 original size:18 final size:18
Alignment explanation
Indices: 5147010--5147051 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
5147000 TTAGTTGGGC
5147010 AAGAATCCATCTCGAGTT
1 AAGAATCCATCTCGAGTT
5147028 AAGAATCCATCTCGAGTT
1 AAGAATCCATCTCGAGTT
5147046 AAGAAT
1 AAGAAT
5147052 TTACTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (18 bp):
AAGAATCCATCTCGAGTT
Found at i:5149058 original size:21 final size:23
Alignment explanation
Indices: 5149034--5149079 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5149024 AATTTATATT
* *
5149034 TATA-ATAAA-ATAATTATATAA
1 TATATATAAATATAAGTATAAAA
5149055 TATATATAAATATAAGTATAAAA
1 TATATATAAATATAAGTATAAAA
5149078 TA
1 TA
5149080 AGTAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 5 0.24
23 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TATATATAAATATAAGTATAAAA
Found at i:5149994 original size:22 final size:21
Alignment explanation
Indices: 5149964--5150048 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 21
5149954 TACAAATTAA
5149964 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
5149986 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
5150007 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
5150026 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
5150045 ATCT
1 ATCT
5150049 AAGATTGCAT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
19 38 0.63
21 10 0.17
22 12 0.20
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:5150016 original size:19 final size:19
Alignment explanation
Indices: 5149981--5150061 Score: 144
Period size: 19 Copynumber: 4.2 Consensus size: 19
5149971 AGATTACAAG
5149981 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
5150002 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
5150021 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
5150040 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
5150059 ATC
1 ATC
5150062 CTTAAAGATT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
19 51 0.85
20 1 0.02
21 8 0.13
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:5151155 original size:205 final size:205
Alignment explanation
Indices: 5150422--5151132 Score: 1298
Period size: 205 Copynumber: 3.5 Consensus size: 205
5150412 CTACTTCTTT
* *
5150422 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTTAACGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
5150487 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
*
5150552 CTGCTTCAGTATAAACATCTAAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
131 CTGCTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
5150617 -CTCAGACTTC
196 GC-CAGACTTC
5150627 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
*
5150692 AAGCCAAATTAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
*
5150757 CTGCTTCAGTATAAACATCTGAAGTTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
131 CTGCTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
5150822 GCCAGACTTC
196 GCCAGACTTC
* * *
5150832 GATTTGTTCTCTAACAATACAAAGATGCCAAATCATCTTAGATTTGTTTCAACGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
5150897 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
* *
5150962 CTACTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTTCGTCGAAGTGGAGAT
131 CTGCTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
5151027 GCCAGACTTC
196 GCCAGACTTC
*
5151037 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
*
5151102 AAGCCAAATCAGCTATGTCTTCGATCTGCTC
66 AAGCCAAATCAGCTATGTCTTCGATTTGCTC
5151133 TCCGCCAATA
Statistics
Matches: 488, Mismatches: 17, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
205 487 1.00
206 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (205 bp):
GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGAT
CTGCTTCAGTATAAACATCTGAAGGTTGGATCTGCTATGTGTCTGCCCTCCGTCGAAGTGGAGAT
GCCAGACTTC
Found at i:5151170 original size:44 final size:44
Alignment explanation
Indices: 5151104--5151211 Score: 162
Period size: 44 Copynumber: 2.4 Consensus size: 44
5151094 ACACGTGAAA
* *
5151104 GCCAAATCAGCTATGTCTTCGATCTGCTCTCCGCCAATACAGAGAT
1 GCCAAATCTGCTA--TCTTCGATCTGCTCTCCGACAATACAGAGAT
* *
5151150 GCCAAATCTGGTATCTTCGATCTGCTCTCTGACAATACAGAGAT
1 GCCAAATCTGCTATCTTCGATCTGCTCTCCGACAATACAGAGAT
5151194 GCCAAATCTGCTATCTTC
1 GCCAAATCTGCTATCTTC
5151212 AACTTGTTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 46 0.81
46 11 0.19
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (44 bp):
GCCAAATCTGCTATCTTCGATCTGCTCTCCGACAATACAGAGAT
Found at i:5151239 original size:44 final size:44
Alignment explanation
Indices: 5151142--5151595 Score: 322
Period size: 44 Copynumber: 10.3 Consensus size: 44
5151132 CTCCGCCAAT
* * * * * *
5151142 ACAGAGATGCCAAATCTGGTATCTTCGATCTGCTCTCTGA-CAAT
1 ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCT-ATAAAC
* *
5151186 ACAGAGATGCCAAATCTGCTATCTTC-AACTTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
** * * * *
5151230 ACAGGGATGCC--ATGCTGAAATCCTCGATCTGCTTCGCTGTAAGC
1 ACAGGGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAAAC
* * * **
5151274 ACA-AGAGTGTCAGATCTATTATCTTCGATCTGTTCCCTATAAAC
1 ACAGGGA-TGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
* *
5151318 ACAGGGATGCCAAATCTGCTATCTT-TAACTTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
** * *
5151362 ACAGGGATGCC--ATGCTGAAATCCTCGATCTGCTTCGCTATAAGTAC
1 ACAGGGATGCCAAAT-CTGCTATCTTCGATCTG-TTCCCTATAA--AC
* * * * * *
5151408 A-AGAG-TGTCAGATCTGTTATCTTTGATTTGTTCCCTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
* *
5151450 ACAGGGATGCCAAATCTGCTATCTTC-AACTTGTTCCCTATAAAT
1 ACAGGGATGCCAAATCTGCTATCTTCGATC-TGTTCCCTATAAAC
* * * * *
5151494 ACAGGGATGCCATA-CTG-AATCTTCGATCTGCTTCGCTGTAAGC
1 ACAGGGATGCCAAATCTGCTATCTTCGATCTG-TTCCCTATAAAC
* * * *
5151537 ACAGGAATGTCAGATCTGCTATCTTCGATCTGTTCCTTATAAAC
1 ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
*
5151581 ACAGGGATGCAAAAT
1 ACAGGGATGCCAAAT
5151596 GTTGTTTCTT
Statistics
Matches: 315, Mismatches: 71, Indels: 48
0.73 0.16 0.11
Matches are distributed among these distances:
42 15 0.05
43 54 0.17
44 197 0.63
45 42 0.13
46 7 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ACAGGGATGCCAAATCTGCTATCTTCGATCTGTTCCCTATAAAC
Found at i:5151398 original size:132 final size:132
Alignment explanation
Indices: 5151155--5151595 Score: 679
Period size: 132 Copynumber: 3.3 Consensus size: 132
5151145 GAGATGCCAA
* * * * * *
5151155 ATCTGGTATCTTCGATCTGCTCTCTGA-CAATACAGAGATGCCAAATCTGCTATCTTCAACTTGT
1 ATCTGTTATCTTCGATCTGTTCCCT-ATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGT
5151219 TCCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAAGAGTGT
65 TCCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAAGAGTGT
5151284 CAG
130 CAG
* *
5151287 ATCTATTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTTAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
* *
5151352 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTATAAGTACAAGAGTGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAAGAGTGTC
5151417 AG
131 AG
* *
5151419 ATCTGTTATCTTTGATTTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
* * * * *
5151484 CCCTATAAATACAGGGATGCCATACTG-AATCTTCGATCTGCTTCGCTGTAAGCACAGGAATGTC
66 CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAAGAGTGTC
5151548 AG
131 AG
* * *
5151550 ATCTGCTATCTTCGATCTGTTCCTTATAAACACAGGGATGCAAAAT
1 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAAT
5151596 GTTGTTTCTT
Statistics
Matches: 282, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
131 76 0.27
132 206 0.73
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (132 bp):
ATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAAATCTGCTATCTTCAACTTGTT
CCCTATAAACACAGGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCACAAGAGTGTC
AG
Found at i:5152491 original size:7 final size:7
Alignment explanation
Indices: 5152479--5152518 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
5152469 GGCCTCTCTA
5152479 TTTTTCT
1 TTTTTCT
5152486 TTTTTCT
1 TTTTTCT
5152493 TTTTTCTT
1 TTTTTC-T
5152501 TTTTTCT
1 TTTTTCT
5152508 TTTTT-T
1 TTTTTCT
5152514 TTTTT
1 TTTTT
5152519 GAAATAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 7 0.22
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTTCT
Found at i:5152498 original size:14 final size:14
Alignment explanation
Indices: 5152479--5152518 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
5152469 GGCCTCTCTA
5152479 TTTTTCTTTTTTCT
1 TTTTTCTTTTTTCT
5152493 TTTTTCTTTTTTTCT
1 TTTTTC-TTTTTTCT
5152508 TTTTT-TTTTTT
1 TTTTTCTTTTTT
5152519 GAAATAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 13 0.52
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTCTTTTTTCT
Found at i:5157443 original size:19 final size:19
Alignment explanation
Indices: 5157415--5157468 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
5157405 CGAAACCATT
* *
5157415 TCTAAAATTGCGTATCATA
1 TCTAAGATTGCATATCATA
5157434 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
5157453 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
5157469 CTTAAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5169924 original size:13 final size:13
Alignment explanation
Indices: 5169898--5169958 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 13
5169888 TAGGCGCGAC
5169898 ATATTTTTTATTA
1 ATATTTTTTATTA
5169911 ATAATTTTTT-TTA
1 AT-ATTTTTTATTA
5169924 ATATTTTATTATTA
1 ATATTTT-TTATTA
*
5169938 TTATTATTATTATT-
1 ATATT-TT-TTATTA
5169952 ATATTTT
1 ATATTTT
5169959 AAAAAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 5 0.12
13 11 0.26
14 18 0.43
15 8 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTTTTTATTA
Found at i:5169935 original size:3 final size:3
Alignment explanation
Indices: 5169925--5169953 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5169915 TTTTTTTTAA
5169925 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5169954 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:5173981 original size:20 final size:21
Alignment explanation
Indices: 5173956--5174005 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
5173946 ATGCAAAAAA
5173956 TAATTTACAT-AAAAATAAAG
1 TAATTTACATAAAAAATAAAG
5173976 TAATTTACATAAAAAATAAAG
1 TAATTTACATAAAAAATAAAG
5173997 TAATTTACA
1 TAATTTACA
5174006 ATACAAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (21 bp):
TAATTTACATAAAAAATAAAG
Found at i:5176649 original size:3 final size:3
Alignment explanation
Indices: 5176643--5176669 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5176633 TTTTTAAAAT
5176643 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
5176670 TATTAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5178009 original size:13 final size:13
Alignment explanation
Indices: 5177991--5178028 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5177981 TGATTAAGAT
5177991 TATTGAATATGTA
1 TATTGAATATGTA
*
5178004 TATTGAAT-TCTA
1 TATTGAATATGTA
*
5178016 TAGTGAATATGTA
1 TATTGAATATGTA
5178029 ATTAAAGGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45
Consensus pattern (13 bp):
TATTGAATATGTA
Found at i:5181002 original size:18 final size:19
Alignment explanation
Indices: 5180969--5181006 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5180959 AATTTTGTTT
*
5180969 ATAATTTTTATGATTTTAA
1 ATAATTTTTATAATTTTAA
5180988 ATAATTTTTA-AATTTTAA
1 ATAATTTTTATAATTTTAA
5181006 A
1 A
5181007 AGGGTTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATAATTTTTATAATTTTAA
Found at i:5184520 original size:14 final size:14
Alignment explanation
Indices: 5184501--5184530 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5184491 GATAGTCTTT
5184501 CCTGATTAGCAAAA
1 CCTGATTAGCAAAA
5184515 CCTGATTAGCAAAA
1 CCTGATTAGCAAAA
5184529 CC
1 CC
5184531 AACACCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (14 bp):
CCTGATTAGCAAAA
Found at i:5186976 original size:2 final size:2
Alignment explanation
Indices: 5186969--5186994 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5186959 TATTTATAAT
5186969 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5186995 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5189656 original size:13 final size:14
Alignment explanation
Indices: 5189633--5189661 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5189623 TAAATTGATT
5189633 AAGATAATAAAATA
1 AAGATAATAAAATA
5189647 AAGA-AATAAAATA
1 AAGATAATAAAATA
5189660 AA
1 AA
5189662 TGGGTAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (14 bp):
AAGATAATAAAATA
Found at i:5190408 original size:23 final size:23
Alignment explanation
Indices: 5190382--5190433 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
5190372 TAGAATTTTA
5190382 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
5190405 CTAAATATTATCATTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
5190428 CAAAAT
1 CTAAAT
5190434 TTAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:5191176 original size:23 final size:24
Alignment explanation
Indices: 5191115--5191177 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
5191105 TAAAATTAAA
*
5191115 ATTTTGATATGTTTGTATATGATCAG
1 ATTTTGATAT-ATT-TATATGATCAG
*
5191141 ATTTGTG-TA-ATTTATGTGATC-G
1 ATTT-TGATATATTTATATGATCAG
5191163 ATTTTGATATATTTA
1 ATTTTGATATATTTA
5191178 GTTTCTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
21 2 0.06
22 7 0.22
23 13 0.41
24 2 0.06
26 6 0.19
27 2 0.06
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.52
Consensus pattern (24 bp):
ATTTTGATATATTTATATGATCAG
Found at i:5191625 original size:2 final size:2
Alignment explanation
Indices: 5191613--5191648 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5191603 GATATGAAGA
5191613 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5191649 AAAGATTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5193801 original size:2 final size:2
Alignment explanation
Indices: 5193794--5193825 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5193784 AATTTTAACC
5193794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5193826 AAGATGCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5194106 original size:3 final size:3
Alignment explanation
Indices: 5194098--5194130 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
5194088 GGTTGTTTCC
5194098 TTA TTA TTA TTA TTA TTA TTA TT- TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
5194131 ATTTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.86
4 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5198045 original size:29 final size:29
Alignment explanation
Indices: 5197967--5198034 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
5197957 ATACAAAGAC
*
5197967 AAAAAAAAGTGCCAGACAAAGCCCAAAGT
1 AAAAAAAAGTGCCAGGCAAAGCCCAAAGT
5197996 AAAAAAAAGTGCCAGGCAAAGCCCAAAGT
1 AAAAAAAAGTGCCAGGCAAAGCCCAAAGT
5198025 AAAAATAAAG
1 AAAAA-AAAG
5198035 ATTGCAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 33 0.89
30 4 0.11
ACGTcount: A:0.57, C:0.18, G:0.18, T:0.07
Consensus pattern (29 bp):
AAAAAAAAGTGCCAGGCAAAGCCCAAAGT
Found at i:5198860 original size:36 final size:36
Alignment explanation
Indices: 5198813--5198888 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
5198803 ACCAAAGTCC
5198813 ATCTAATTACCAAGCTCAGAGATAAAACATTTTATT
1 ATCTAATTACCAAGCTCAGAGATAAAACATTTTATT
5198849 ATCTAATTACCAAGCTCAGAGATAAAACATTTTATT
1 ATCTAATTACCAAGCTCAGAGATAAAACATTTTATT
5198885 ATCT
1 ATCT
5198889 CTTTTAAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (36 bp):
ATCTAATTACCAAGCTCAGAGATAAAACATTTTATT
Found at i:5199743 original size:45 final size:45
Alignment explanation
Indices: 5199692--5199781 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
5199682 TGTAAAATGT
*
5199692 ACCTATAGTCCTTGTACTTTTGGAAAATTAGGAATTTAGTTTTTC
1 ACCTATAGTCCTTGTACTTTTGGAAAATTAAGAATTTAGTTTTTC
5199737 ACCTATAGTCCTTGTACTTTTGGAAAATTAAGAATTTAGTTTTTC
1 ACCTATAGTCCTTGTACTTTTGGAAAATTAAGAATTTAGTTTTTC
5199782 TACTTTTCAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.44
Consensus pattern (45 bp):
ACCTATAGTCCTTGTACTTTTGGAAAATTAAGAATTTAGTTTTTC
Found at i:5200362 original size:15 final size:16
Alignment explanation
Indices: 5200331--5200363 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5200321 AAATCTTAAA
5200331 ATATTTACATATATTT
1 ATATTTACATATATTT
*
5200347 ATATTTA-ATATTTTT
1 ATATTTACATATATTT
5200362 AT
1 AT
5200364 GTGATTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTACATATATTT
Found at i:5200853 original size:14 final size:14
Alignment explanation
Indices: 5200834--5200863 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5200824 TTATTATTCA
5200834 TAAAAAATTAATAAT
1 TAAAAAA-TAATAAT
5200849 TAAAAAATAATAAT
1 TAAAAAATAATAAT
5200863 T
1 T
5200864 TTATCTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAAAATAATAAT
Found at i:5202187 original size:16 final size:16
Alignment explanation
Indices: 5202166--5202199 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5202156 ACATAATCGA
5202166 ATTAACATCATTTTAC
1 ATTAACATCATTTTAC
5202182 ATTAACATCATTTTAC
1 ATTAACATCATTTTAC
5202198 AT
1 AT
5202200 ACAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAACATCATTTTAC
Found at i:5206018 original size:15 final size:16
Alignment explanation
Indices: 5205998--5206027 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5205988 ATCTTTTAAC
5205998 AAAAAAAAGA-AAAAG
1 AAAAAAAAGAGAAAAG
5206013 AAAAAAAAGAGAAAA
1 AAAAAAAAGAGAAAA
5206028 CAATATGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAGAAAAG
Found at i:5208199 original size:72 final size:72
Alignment explanation
Indices: 5208076--5208209 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 72
5208066 GTGTTGAATC
*
5208076 TCTCCCAGAACAAGCTCTTTGGTGAACTGACTCCAGAATTAGCAAAACTTACAGATCTGGAATCG
1 TCTCCCAGAACAAGCTCTTTGGTGAACTGACTCCAGAATTAACAAAACTTACAGATCTGGAATCG
5208141 TTGGATG
66 TTGGATG
* * * **
5208148 TCTCCCATAACAAGCTCTTTGGTGAACT-ATGTCCAGAATTAACAAATCTTACATTTCTGGAA
1 TCTCCCAGAACAAGCTCTTTGGTGAACTGA-CTCCAGAATTAACAAAACTTACAGATCTGGAA
5208210 GTATTCAACG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 1 0.02
72 54 0.98
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (72 bp):
TCTCCCAGAACAAGCTCTTTGGTGAACTGACTCCAGAATTAACAAAACTTACAGATCTGGAATCG
TTGGATG
Found at i:5213878 original size:17 final size:18
Alignment explanation
Indices: 5213856--5213889 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5213846 TAAATGTAAA
5213856 TTAAAT-TATAATTATTT
1 TTAAATATATAATTATTT
*
5213873 TTAAATATGTAATTATT
1 TTAAATATATAATTATT
5213890 ATAATTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TTAAATATATAATTATTT
Found at i:5213887 original size:24 final size:23
Alignment explanation
Indices: 5213859--5213932 Score: 64
Period size: 24 Copynumber: 3.3 Consensus size: 23
5213849 ATGTAAATTA
5213859 AATTATAATTATTTTTAAATATGT
1 AATTATAATTATTTTTAAATAT-T
* * * *
5213883 AATTATTATAATTTCT--AT-TA
1 AATTATAATTATTTTTAAATATT
*
5213903 AATTATAATTATTATTAAATATAT
1 AATTATAATTATTTTTAAATAT-T
5213927 AATTAT
1 AATTAT
5213933 CACAAACAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
20 12 0.32
21 1 0.03
22 4 0.11
23 1 0.03
24 19 0.51
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (23 bp):
AATTATAATTATTTTTAAATATT
Found at i:5213892 original size:27 final size:26
Alignment explanation
Indices: 5213860--5213917 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
5213850 TGTAAATTAA
* *
5213860 ATTATAATTAT-TTTTAAATATGTAATT
1 ATTATAATT-TCTATTAAAT-TATAATT
5213887 ATTATAATTTCTATTAAATTATAATT
1 ATTATAATTTCTATTAAATTATAATT
5213913 ATTAT
1 ATTAT
5213918 TAAATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTATAATTTCTATTAAATTATAATT
Done.