Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 184 of 189
Found at i:54889697 original size:5 final size:5
Alignment explanation
Indices: 54889687--54889711 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54889677 AAGTTCAGAG
54889687 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
54889712 GAGAGAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:54890959 original size:34 final size:35
Alignment explanation
Indices: 54890908--54891000 Score: 91
Period size: 34 Copynumber: 2.6 Consensus size: 35
54890898 CAGTAGACAG
* **
54890908 TTGGGG-AAAATCAAAGGGATTTCAAGATTTTAA-T
1 TTGGGGAAAAAT-TAAGGGATTTCAAGATTCCAATT
* *
54890942 TTGGGGAAAAATTAAGGGATTTGATGATTCCAATTT
1 TTGGGGAAAAATTAAGGGATTTCAAGATTCCAA-TT
*
54890978 TTAGGGGAAAAAATAAGGGATTT
1 TT-GGGGAAAAATTAAGGGATTT
54891001 TGGGGTTATA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 22 0.45
35 5 0.10
36 3 0.06
37 19 0.39
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (35 bp):
TTGGGGAAAAATTAAGGGATTTCAAGATTCCAATT
Found at i:54891034 original size:34 final size:34
Alignment explanation
Indices: 54890977--54891069 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 34
54890967 GATTCCAATT
* *
54890977 TTTAGGGGAAAAAATAAGGGATTTTGGGGTTATAG
1 TTTA-GGGAAAAAATAAGAGATTTTAGGGTTATAG
* *
54891012 TTTAGGGATAAAATAAGAGATTTTAGGGTTATGG
1 TTTAGGGAAAAAATAAGAGATTTTAGGGTTATAG
**
54891046 TTTAGGGGGAAAATAAGAGATTTT
1 TTTAGGGAAAAAATAAGAGATTTT
54891070 TAGCATAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 48 0.92
35 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.33
Consensus pattern (34 bp):
TTTAGGGAAAAAATAAGAGATTTTAGGGTTATAG
Found at i:54891166 original size:39 final size:39
Alignment explanation
Indices: 54891114--54891208 Score: 111
Period size: 41 Copynumber: 2.4 Consensus size: 39
54891104 AAAATGATAC
* *
54891114 TTTGCAGCGTTTTT-GATAAACGCCGCTAATGCTTGACTT
1 TTTGCAGCATTTTTCG-TAAACGCCGCTAATGCTTGACCT
* *
54891153 TTTGCAGCATTTTTCTCGTAAGCGCCGCTACTGCTTGACCT
1 TTTGCAGCA-TTTT-TCGTAAACGCCGCTAATGCTTGACCT
*
54891194 TTTGCGGCATTTTTC
1 TTTGCAGCATTTTTC
54891209 TTATAAACAC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
39 10 0.21
40 8 0.17
41 29 0.60
42 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (39 bp):
TTTGCAGCATTTTTCGTAAACGCCGCTAATGCTTGACCT
Found at i:54891222 original size:41 final size:41
Alignment explanation
Indices: 54891129--54891249 Score: 143
Period size: 41 Copynumber: 3.0 Consensus size: 41
54891119 AGCGTTTTTG
* * *
54891129 ATAAACGCCGCTAATGCTTGACTTTTTGCAGCATTTTTCTC
1 ATAAACGCCGCTACTGCTTGACCTTTTGCGGCATTTTTCTC
* * *
54891170 GTAAGCGCCGCTACTGCTTGACCTTTTGCGGCATTTTTCTT
1 ATAAACGCCGCTACTGCTTGACCTTTTGCGGCATTTTTCTC
* * * * *
54891211 ATAAACACCGCTACTGATTTACCTATTGCGGCGTTTTTC
1 ATAAACGCCGCTACTGCTTGACCTTTTGCGGCATTTTTC
54891250 CGTTAGTGCC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (41 bp):
ATAAACGCCGCTACTGCTTGACCTTTTGCGGCATTTTTCTC
Found at i:54894797 original size:14 final size:15
Alignment explanation
Indices: 54894773--54894801 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54894763 TTGTTAATAT
54894773 CCATTTGTCTGCAAA
1 CCATTTGTCTGCAAA
54894788 CCATTT-TCTGCAAA
1 CCATTTGTCTGCAAA
54894802 ATTGTGCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (15 bp):
CCATTTGTCTGCAAA
Found at i:54897109 original size:15 final size:16
Alignment explanation
Indices: 54897080--54897123 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
54897070 TATTAAATGT
*
54897080 ATATAAATATTTAAAA
1 ATATAAATATATAAAA
54897096 ATAT-AATATATAAAA
1 ATATAAATATATAAAA
* *
54897111 ATGTAAAAATATA
1 ATATAAATATATA
54897124 TATATAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATATAAATATATAAAA
Found at i:54897109 original size:23 final size:22
Alignment explanation
Indices: 54897079--54897130 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
54897069 TTATTAAATG
* *
54897079 TATATAAATATTTAAAAATATAA
1 TATATAAAAATGTAAAAATAT-A
54897102 TATATAAAAATGTAAAAATATA
1 TATATAAAAATGTAAAAATATA
54897124 TATATAA
1 TATATAA
54897131 TCTAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TATATAAAAATGTAAAAATATA
Found at i:54897308 original size:12 final size:12
Alignment explanation
Indices: 54897285--54897320 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
54897275 TATAAAACTT
54897285 TTATATTTTAATA
1 TTATA-TTTAATA
54897298 TTATATTTAATA
1 TTATATTTAATA
54897310 TTATATTTAAT
1 TTATATTTAAT
54897321 TTTTAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATTTAATA
Found at i:54897518 original size:19 final size:19
Alignment explanation
Indices: 54897506--54897557 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
54897496 TTTTTCTAGA
54897506 TTTTATATATTTTTTGAAT
1 TTTTATATATTTTTTGAAT
**
54897525 TTTTATATATTTATTTCCAT
1 TTTTATATATTT-TTTGAAT
54897545 TTTTATAT-TTTTT
1 TTTTATATATTTTT
54897558 AATGTGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 15 0.50
20 13 0.43
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTATATATTTTTTGAAT
Found at i:54910248 original size:18 final size:18
Alignment explanation
Indices: 54910213--54910254 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
54910203 GTTATAATAC
*
54910213 TTTATTTTATATTTTATT
1 TTTATTTTATATTCTATT
54910231 TTTATTTT-TATTACTATT
1 TTTATTTTATATT-CTATT
*
54910249 TCTATT
1 TTTATT
54910255 ACTATTCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTATATTCTATT
Found at i:54912306 original size:21 final size:21
Alignment explanation
Indices: 54912280--54912321 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54912270 CTAAGTACAT
* *
54912280 GGGCGTGTGGAGTAGCCACAC
1 GGGCGTGTGGAATAGACACAC
54912301 GGGCGTGTGGAATAGACACAC
1 GGGCGTGTGGAATAGACACAC
54912322 AATCTGGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.40, T:0.14
Consensus pattern (21 bp):
GGGCGTGTGGAATAGACACAC
Found at i:54913488 original size:18 final size:18
Alignment explanation
Indices: 54913465--54913499 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
54913455 AGCCTAGTAC
54913465 CCAAAC-TAAAGCCCAAAA
1 CCAAACTTAAA-CCCAAAA
54913483 CCAAACTTAAACCCAAA
1 CCAAACTTAAACCCAAA
54913500 CCTACCCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.54, C:0.34, G:0.03, T:0.09
Consensus pattern (18 bp):
CCAAACTTAAACCCAAAA
Found at i:54916618 original size:23 final size:24
Alignment explanation
Indices: 54916565--54916623 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
54916555 ATGTTTTGTA
* *
54916565 TTTTATTTAATATTAGTATACTTAT
1 TTTTATTTAATATTAATATAC-AAT
54916590 TTTTATTTAATATTAATATA-AAT
1 TTTTATTTAATATTAATATACAAT
54916613 TTTTATTTAAT
1 TTTTATTTAAT
54916624 TAGATTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 13 0.41
25 19 0.59
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTATTTAATATTAATATACAAT
Found at i:54917235 original size:29 final size:29
Alignment explanation
Indices: 54917185--54917244 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
54917175 TAATGTTCTT
* ** * *
54917185 ATCTCCCCAAGTATCTTGCTTCTTCTGAA
1 ATCTCCCCAAATAAATTCCTTCCTCTGAA
54917214 ATCTCCCCAAATAAATTCCTTCCTCTGAA
1 ATCTCCCCAAATAAATTCCTTCCTCTGAA
54917243 AT
1 AT
54917245 TTCCATGTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.35
Consensus pattern (29 bp):
ATCTCCCCAAATAAATTCCTTCCTCTGAA
Found at i:54921422 original size:25 final size:24
Alignment explanation
Indices: 54921368--54921420 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
54921358 GAACTCGTTA
*
54921368 TTTTTGCACATGTTATTTTTAAAT
1 TTTTTACACATGTTATTTTTAAAT
*
54921392 TTTTTACACATGTTATTTTTTAAT
1 TTTTTACACATGTTATTTTTAAAT
54921416 TTTTT
1 TTTTT
54921421 TATTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.08, G:0.06, T:0.64
Consensus pattern (24 bp):
TTTTTACACATGTTATTTTTAAAT
Found at i:54923557 original size:14 final size:14
Alignment explanation
Indices: 54923540--54923567 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54923530 GTTTAAAATT
54923540 TTTAATTAATTAAA
1 TTTAATTAATTAAA
54923554 TTTAATTAATTAAA
1 TTTAATTAATTAAA
54923568 AATCTATTCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:54930408 original size:68 final size:68
Alignment explanation
Indices: 54930268--54930411 Score: 157
Period size: 68 Copynumber: 2.1 Consensus size: 68
54930258 TTAATCACTT
*
54930268 TAATATTAAATTAATATAATACTTATGAAGATAAATATTAAATTTAACTTAATATAAGATAATCA
1 TAATATTAAATTAATAAAATACTTATGAAGATAAATATTAAATTTAACTTAATATAAGATAATCA
***
54930333 CTT
66 AAA
* * * * * *
54930336 TAATATTAAATTAATAAAAT-GTTATTAAGATAAGTATTGAATTTAATTTAATATTAA-ATTTAT
1 TAATATTAAATTAATAAAATACTTATGAAGATAAATATTAAATTTAACTTAATA-TAAGA-TAAT
*
54930399 TAAAA
64 CAAAA
54930404 TAATATTA
1 TAATATTA
54930412 TTTTTTAAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
67 29 0.46
68 34 0.54
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (68 bp):
TAATATTAAATTAATAAAATACTTATGAAGATAAATATTAAATTTAACTTAATATAAGATAATCA
AAA
Found at i:54932212 original size:18 final size:19
Alignment explanation
Indices: 54932191--54932228 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
54932181 AAAAAAATTT
54932191 AAAG-TTATGAAAATA-AAA
1 AAAGATTAT-AAAATAGAAA
54932209 AAAGATTATAAAATAGAAA
1 AAAGATTATAAAATAGAAA
54932228 A
1 A
54932229 TTGAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AAAGATTATAAAATAGAAA
Found at i:54936149 original size:17 final size:18
Alignment explanation
Indices: 54936120--54936153 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
54936110 ATTTTTAATA
54936120 TTTTAATACATTTATTTC
1 TTTTAATACATTTATTTC
54936138 TTTTAATA-ATTTATTT
1 TTTTAATACATTTATTT
54936154 AATCATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTAATACATTTATTTC
Found at i:54938897 original size:24 final size:24
Alignment explanation
Indices: 54938845--54938899 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
54938835 AAACTCATGC
* * *
54938845 GAGCCAATAACGGGTAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCCAAA
*
54938869 GAGCCATTAACGGGAAGCTCTAAA
1 GAGCCATTAACGGGAAGCTCCAAA
*
54938893 TAGCCAT
1 GAGCCAT
54938900 ATATCGGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCCAAA
Found at i:54939473 original size:10 final size:11
Alignment explanation
Indices: 54939450--54939478 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
54939440 GAATTTAACA
54939450 TCAATTCATAT
1 TCAATTCATAT
54939461 TCAATTC-TAT
1 TCAATTCATAT
54939471 TCAATTCA
1 TCAATTCA
54939479 CATCCTAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (11 bp):
TCAATTCATAT
Found at i:54944168 original size:51 final size:52
Alignment explanation
Indices: 54944052--54944181 Score: 192
Period size: 51 Copynumber: 2.5 Consensus size: 52
54944042 ACTAGTGACT
*
54944052 CAAGTGTGGTACTATGTGAAAGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
*
54944104 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTTGG-CTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTC-A
* * *
54944155 CAAGGGTGGTACTATGTGCAGGTCACT
1 CAAGTGTGGTACTATGTGAAGGCCACT
54944182 GGGTATCCAT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
50 1 0.01
51 37 0.51
52 34 0.47
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
Found at i:54944534 original size:14 final size:14
Alignment explanation
Indices: 54944515--54944542 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54944505 TAGAAGAAAT
54944515 GGTGTAAGCAAGAG
1 GGTGTAAGCAAGAG
54944529 GGTGTAAGCAAGAG
1 GGTGTAAGCAAGAG
54944543 AATTTCATAT
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:0.36, C:0.07, G:0.43, T:0.14
Consensus pattern (14 bp):
GGTGTAAGCAAGAG
Found at i:54955411 original size:19 final size:19
Alignment explanation
Indices: 54955382--54955430 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
54955372 TCATTTCTCT
54955382 TTTTCTATTCATTCTGTTCA
1 TTTT-TATTCATTCTGTTCA
54955402 TTTTTATTCATTCTGTTCA
1 TTTTTATTCATTCTGTTCA
*
54955421 TTTCTATTCA
1 TTTTTATTCA
54955431 AACACGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTTATTCATTCTGTTCA
Found at i:54957867 original size:27 final size:27
Alignment explanation
Indices: 54957833--54957888 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
54957823 AAAAAATTTG
54957833 GTTGAAATGATTTCTTGAAATAAAAAA
1 GTTGAAATGATTTCTTGAAATAAAAAA
54957860 GTTGAAATGATTTCTTGAAATAAAAAA
1 GTTGAAATGATTTCTTGAAATAAAAAA
54957887 GT
1 GT
54957889 GCAACTTGAA
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:0.46, C:0.04, G:0.16, T:0.34
Consensus pattern (27 bp):
GTTGAAATGATTTCTTGAAATAAAAAA
Found at i:54969078 original size:31 final size:31
Alignment explanation
Indices: 54969043--54969102 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
54969033 ATTGTCACTA
*
54969043 AACTA-TTCAAAAGTTTTCATTTAAGTCATTG
1 AACTATTTCAAAA-TTTTCACTTAAGTCATTG
*
54969074 AACTATTTGAAAATTTTCACTTAAGTCAT
1 AACTATTTCAAAATTTTCACTTAAGTCAT
54969103 CAAGCTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (31 bp):
AACTATTTCAAAATTTTCACTTAAGTCATTG
Found at i:54969111 original size:31 final size:32
Alignment explanation
Indices: 54969043--54969111 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
54969033 ATTGTCACTA
* * *
54969043 AACTA-TTCAAAAGTTTTCATTTAAGTCATTG
1 AACTATTTGAAAAGTTTTCACTTAAGTCATTC
54969074 AACTATTTGAAAA-TTTTCACTTAAGTCA-TC
1 AACTATTTGAAAAGTTTTCACTTAAGTCATTC
54969104 AAGCTATT
1 AA-CTATT
54969112 AAGTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 3 0.09
31 24 0.73
32 6 0.18
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (32 bp):
AACTATTTGAAAAGTTTTCACTTAAGTCATTC
Found at i:54974187 original size:193 final size:196
Alignment explanation
Indices: 54973703--54974293 Score: 786
Period size: 200 Copynumber: 3.0 Consensus size: 196
54973693 GATAAAGTTT
*
54973703 GTTATCTTTTCTTTTTAGCTACATTTTTTTTCTTAAATTAGTTACTAAATATTTCTATAGATTTG
1 GTTATCTTTTCTTTTTAGCTACA---TTTTCCTTAAATTAGTTACTAAATATTTCTATAGATTTG
*
54973768 AAAATTAGAGAAATTACTATGCCTCTTTCTGAATTATGATCTTGATCATCATAATCATGAAGTGT
63 AAAATTAGAGAAATTATTATGCCTCTTTCTGAATTATGATCTTGATCATCATAATCATGAAGTGT
* * ***** * *
54973833 TTCTGTTAAATGTTAATCTCTTTTTTATATTCTTTATTAATTTATTTTTGCAGGGAGAAGTGAAC
128 TTTTGTT-AATCTT--T-T-TAAAAAATATTCTTTATTAATTTAATTTTGCAGGGAGAAGAGAAC
*
54973898 AGGTTTTCA
188 AAGTTTTCA
* * *
54973907 GTTAT-GTTTCTTTTTAGCTAAATTTTCCTTAAATTAGTTACTAAATCTTTCTATAGATTTGAAA
1 GTTATCTTTTCTTTTTAGCTACATTTTCCTTAAATTAGTTACTAAATATTTCTATAGATTTGAAA
* * * *
54973971 ATTAGAGAAATTATTATGCCTCTTTCTGAATTATGATCTTGATTATCATAATTACGAATTGTTTT
66 ATTAGAGAAATTATTATGCCTCTTTCTGAATTATGATCTTGATCATCATAATCATGAAGTGTTTT
* *
54974036 TGTTAATCTTTTTAAAAAATATTCTTTGTTAATTTAATTTTGCCGGGAGAAGAGAACAAGTTTTC
131 TGTTAATCTTTTTAAAAAATATTCTTTATTAATTTAATTTTGCAGGGAGAAGAGAACAAGTTTTC
54974101 A
196 A
54974102 GTTATCTTTTCTTTTTAGCTACATTTTCCTTAAATTAGTTACTAAAT-TTT-T-TAGATTTGAAA
1 GTTATCTTTTCTTTTTAGCTACATTTTCCTTAAATTAGTTACTAAATATTTCTATAGATTTGAAA
*
54974164 ATTAGAGAAATTATTATGCCTCTTTCTGAATTATGATCTTGATCATAATAATCATGAAGTGTTTT
66 ATTAGAGAAATTATTATGCCTCTTTCTGAATTATGATCTTGATCATCATAATCATGAAGTGTTTT
** * * * *
54974229 TGTTAATCTTTTT----TTTCTT-TTTATTTATTTATTTTTTGCAGGGAGAAGAGAACAGGTTTT
131 TGTTAATCTTTTTAAAAAATATTCTTTATTAATTTA-ATTTTGCAGGGAGAAGAGAACAAGTTTT
54974289 CA
195 CA
54974291 GTT
1 GTT
54974294 TATGTTCATT
Statistics
Matches: 349, Mismatches: 36, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
188 10 0.03
189 33 0.09
193 84 0.24
194 1 0.00
195 52 0.15
196 40 0.11
197 1 0.00
199 5 0.01
200 103 0.30
203 15 0.04
204 5 0.01
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (196 bp):
GTTATCTTTTCTTTTTAGCTACATTTTCCTTAAATTAGTTACTAAATATTTCTATAGATTTGAAA
ATTAGAGAAATTATTATGCCTCTTTCTGAATTATGATCTTGATCATCATAATCATGAAGTGTTTT
TGTTAATCTTTTTAAAAAATATTCTTTATTAATTTAATTTTGCAGGGAGAAGAGAACAAGTTTTC
A
Found at i:54983152 original size:19 final size:19
Alignment explanation
Indices: 54983128--54983167 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
54983118 ATAAATAAAA
54983128 TATATTAAAAAAATT-ATAT
1 TATATT-AAAAAATTAATAT
54983147 TATATTAAAAAATTAATAT
1 TATATTAAAAAATTAATAT
54983166 TA
1 TA
54983168 ATATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATTAAAAAATTAATAT
Found at i:54994843 original size:6 final size:7
Alignment explanation
Indices: 54994818--54994848 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
54994808 TTGAAAATCG
54994818 AAAATATT
1 AAAA-ATT
54994826 AAAAATT
1 AAAAATT
54994833 AAAAATT
1 AAAAATT
54994840 AAAAATT
1 AAAAATT
54994847 AA
1 AA
54994849 GAAAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAAATT
Found at i:54995620 original size:20 final size:20
Alignment explanation
Indices: 54995595--54995639 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
54995585 GTCCTAACCG
54995595 AATTAATTAG-GTCTTAG-TTT
1 AATTAATT-GTGTCTT-GTTTT
54995615 AATTAATTGTGTCTTGTTTT
1 AATTAATTGTGTCTTGTTTT
54995635 AATTA
1 AATTA
54995640 TTTGAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.53
Consensus pattern (20 bp):
AATTAATTGTGTCTTGTTTT
Found at i:54998172 original size:41 final size:41
Alignment explanation
Indices: 54998118--54998305 Score: 238
Period size: 41 Copynumber: 4.6 Consensus size: 41
54998108 TTAATTTAAA
* * *** * *
54998118 CAGATTCAACGGCACATAACCTGCTAAACTTATAGCATGATT
1 CAGA-TCACCGGCACATAGCCTGCTAGGTTTATAACCTGATT
*
54998160 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACATAGCCTGCTAGGTTTATAACCTGATT
*
54998201 CAGATCACCGG--CAT-GCTTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACATAGCCTGCTAGGTTTATAACCTGATT
*
54998239 CAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACATAGCCTGCTAGGTTTATAACCTGATT
* *
54998280 CAGATCACCGGCACGTAGCCTACTAG
1 CAGATCACCGGCACATAGCCTGCTAG
54998306 ACTTAAAGTC
Statistics
Matches: 130, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
38 34 0.26
39 2 0.02
40 2 0.02
41 88 0.68
42 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (41 bp):
CAGATCACCGGCACATAGCCTGCTAGGTTTATAACCTGATT
Found at i:54998231 original size:38 final size:40
Alignment explanation
Indices: 54998155--54998305 Score: 243
Period size: 41 Copynumber: 3.8 Consensus size: 40
54998145 ACTTATAGCA
54998155 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCAC-TAGCCTGCTAGGTTTATAACC
*
54998196 TGATTCAGATCACCGGCA-T-GCTTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACTAGCCTGCTAGGTTTATAACC
54998234 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCAC-TAGCCTGCTAGGTTTATAACC
*
54998275 TGATTCAGATCACCGGCACGTAGCCTACTAG
1 TGATTCAGATCACCGGCAC-TAGCCTGCTAG
54998306 ACTTAAAGTC
Statistics
Matches: 104, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
38 36 0.35
39 1 0.01
40 1 0.01
41 66 0.63
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
TGATTCAGATCACCGGCACTAGCCTGCTAGGTTTATAACC
Found at i:55003234 original size:24 final size:24
Alignment explanation
Indices: 55003202--55003250 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
55003192 TTCATCAGGT
55003202 AGCAGTTAGTTACTACTTTTGCTA
1 AGCAGTTAGTTACTACTTTTGCTA
*
55003226 AGCAGTTAGTTGCTACTTTTGCTA
1 AGCAGTTAGTTACTACTTTTGCTA
55003250 A
1 A
55003251 CTGTTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
AGCAGTTAGTTACTACTTTTGCTA
Found at i:55004448 original size:2 final size:2
Alignment explanation
Indices: 55004441--55004468 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55004431 TGAGGTTACA
55004441 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
55004469 CTTGTGTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:55017184 original size:312 final size:312
Alignment explanation
Indices: 55016619--55017247 Score: 988
Period size: 312 Copynumber: 2.0 Consensus size: 312
55016609 AAGTTGCTTC
* * *
55016619 TCTGAGGAAGACTGACCAGAAGCAATTTCTTTTTTTGTAACTAACTGAAGCTCATTTAGCTCTTC
1 TCTGAGGAAGACTGACCAGAAGCAATTTCTTCTCTAGTAACTAACTGAAGCTCATTTAGCTCTTC
* * * * *
55016684 TGTTACTCCAGCTGATGAGTCTTCATGGTTCCCATCGTGAAGCTTTTCGGTTTCTTTCCTTTTTT
66 TGTTACTCCAGCTGACGAGTCTTCACGGTTCCCATCGTCAAGCTTTTCGGCTTCTTTCCTTTTCT
* *
55016749 CTTTGTTTGCTTCAATCTCTTGTGATTCCTCTGTTAATGAAGCCTGAGCAATAATGGTTTCTTGA
131 CTTCGTTTGCTTCAATCTCTTGTGATTCCTCTGTTAATGAAGCCTGAACAATAATGGTTTCTTGA
* * *
55016814 TCTATAACAGCTTTAGGCTCCTGAGGTCCTTCCTTTTCGAGAAGTTCCACTTCCTTCACCTTTTC
196 TCCATAACAGCTTCAGGCTCCTGAGGTCCTTCCTTTTCAAGAAGTTCCACTTCCTTCACCTTTTC
** **
55016879 CCCCTCTTCTTCATTGGCCTCAGCTCCATGCTTTAGGTTCTCTTCAGTCAAT
261 CCCCTCTTCTTCATTGGCCTCAGCTCCACACTTTAGGTTCTCGACAGTCAAT
* *
55016931 TCTGAGGAAGACTGACCAGAAGCAATTTCTTCTCTAGTAACTAATTGAAGCTCATTTAGCTTTTC
1 TCTGAGGAAGACTGACCAGAAGCAATTTCTTCTCTAGTAACTAACTGAAGCTCATTTAGCTCTTC
* *
55016996 TGTTTCTCCAGCTGACGAGTCTTCACGGTTCCCATCGTCAAGCTTTTTGGCTTCTTTCCTTTTCT
66 TGTTACTCCAGCTGACGAGTCTTCACGGTTCCCATCGTCAAGCTTTTCGGCTTCTTTCCTTTTCT
* * *
55017061 CTTCGTTTGCTTCAATCTCTTGTGATTCTTCTGTTATTGAAGCCTGAACTATAATGGTTTCTTGA
131 CTTCGTTTGCTTCAATCTCTTGTGATTCCTCTGTTAATGAAGCCTGAACAATAATGGTTTCTTGA
* * *
55017126 TCCATAACAGCTTCAGGTTCCTGAGGTCTTTCCTTTTCAAGAATTTCCACTTCCTTCACCTTTTC
196 TCCATAACAGCTTCAGGCTCCTGAGGTCCTTCCTTTTCAAGAAGTTCCACTTCCTTCACCTTTTC
** *
55017191 TTCCTCTTTTTCATTGGCCTCAGCTCCACACTTTAGGTTCTCGACAGTCAAT
261 CCCCTCTTCTTCATTGGCCTCAGCTCCACACTTTAGGTTCTCGACAGTCAAT
55017243 TCTGA
1 TCTGA
55017248 AGGCAAAGAT
Statistics
Matches: 287, Mismatches: 30, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
312 287 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (312 bp):
TCTGAGGAAGACTGACCAGAAGCAATTTCTTCTCTAGTAACTAACTGAAGCTCATTTAGCTCTTC
TGTTACTCCAGCTGACGAGTCTTCACGGTTCCCATCGTCAAGCTTTTCGGCTTCTTTCCTTTTCT
CTTCGTTTGCTTCAATCTCTTGTGATTCCTCTGTTAATGAAGCCTGAACAATAATGGTTTCTTGA
TCCATAACAGCTTCAGGCTCCTGAGGTCCTTCCTTTTCAAGAAGTTCCACTTCCTTCACCTTTTC
CCCCTCTTCTTCATTGGCCTCAGCTCCACACTTTAGGTTCTCGACAGTCAAT
Found at i:55027717 original size:6 final size:6
Alignment explanation
Indices: 55027708--55027752 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
55027698 TCTTTTCTCT
* *
55027708 TTCAGC TTCAGC ATCAGC TTCAGC TTCAGC ATCAGC TTCAGC TTC
1 TTCAGC TTCAGC TTCAGC TTCAGC TTCAGC TTCAGC TTCAGC TTC
55027753 CTTTATGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (6 bp):
TTCAGC
Found at i:55027731 original size:18 final size:18
Alignment explanation
Indices: 55027708--55027752 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
55027698 TCTTTTCTCT
55027708 TTCAGCTTCAGCATCAGC
1 TTCAGCTTCAGCATCAGC
55027726 TTCAGCTTCAGCATCAGC
1 TTCAGCTTCAGCATCAGC
55027744 TTCAGCTTC
1 TTCAGCTTC
55027753 CTTTATGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (18 bp):
TTCAGCTTCAGCATCAGC
Found at i:55036838 original size:12 final size:11
Alignment explanation
Indices: 55036819--55036848 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
55036809 CTTACACGAA
55036819 TCTGTTCATGT
1 TCTGTTCATGT
55036830 TCATGTTCATGT
1 TC-TGTTCATGT
55036842 TCTGTTC
1 TCTGTTC
55036849 TTGCTGAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.10, C:0.20, G:0.17, T:0.53
Consensus pattern (11 bp):
TCTGTTCATGT
Found at i:55052563 original size:2 final size:2
Alignment explanation
Indices: 55052558--55052584 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55052548 ACATACACAC
55052558 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
55052585 ATATGTACTT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55057795 original size:26 final size:26
Alignment explanation
Indices: 55057766--55057815 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
55057756 TTCGGTTTTA
*
55057766 TTTAAAAT-ATTTATTTCGATTTTAAT
1 TTTAAAATAATTT-CTTCGATTTTAAT
*
55057792 TTTAAATTAATTTCTTCGATTTTA
1 TTTAAAATAATTTCTTCGATTTTA
55057816 CCTTAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTAAAATAATTTCTTCGATTTTAAT
Found at i:55062303 original size:18 final size:18
Alignment explanation
Indices: 55062282--55062493 Score: 97
Period size: 18 Copynumber: 11.7 Consensus size: 18
55062272 ATACTAAGAA
55062282 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
*
55062300 TTTTGTTAAA-T-TATA-
1 TTTTATTAAATTATATAT
* *
55062315 -TTTAAT-AATAAT-TAT
1 TTTTATTAAATTATATAT
* * * *
55062330 TTTAAATTATATTTTATAG
1 TTT-TATTAAATTATATAT
* * *
55062349 TATTA-TATATTAT-GA-
1 TTTTATTAAATTATATAT
*
55062364 TTTTAGTAAATTCATATA-
1 TTTTATTAAATT-ATATAT
55062382 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
55062400 TTTTATTAAATTATAT-T
1 TTTTATTAAATTATATAT
* *
55062417 TAATAATAATTAGTATTATATATTAT
1 T--T--TTATTA--AAT-TATA-TAT
*
55062443 GATTTTAGTAAATTCATATA-
1 --TTTTATTAAATT-ATATAT
55062463 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
55062481 TTTTATTAAATTA
1 TTTTATTAAATTA
55062494 CATTTAATAA
Statistics
Matches: 146, Mismatches: 24, Indels: 48
0.67 0.11 0.22
Matches are distributed among these distances:
13 2 0.01
14 6 0.04
15 5 0.03
16 12 0.08
17 24 0.16
18 65 0.45
19 5 0.03
21 8 0.05
22 5 0.03
23 2 0.01
24 8 0.05
25 1 0.01
26 2 0.01
28 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:55062367 original size:233 final size:237
Alignment explanation
Indices: 55061952--55062381 Score: 751
Period size: 233 Copynumber: 1.8 Consensus size: 237
55061942 AAGTAGATTA
55061952 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATAGTATGATTTTAGT
1 TAAATTATATTTAATAATAATTA--TT--ATTATATTTTATAGTATTATATAGTATGATTTTAGT
55062017 AAATTCATATAAGAATATTTAATACTAAAGAATTTTATCAAATTATATATTTTTATTAAATTATA
62 AAATTCATATAAGAATATTTAATACTAAAGAATTTTATCAAATTATATATTTTTATTAAATTATA
55062082 TTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATA
127 TTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATA
55062147 TAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTAT
192 TAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTAT
* *
55062193 TAAATTATATTTAATAATAATTA-T-TT-TATTTTATAGTATTTTATATTATGATTTTAGTAAAT
1 TAAATTATATTTAATAATAATTATTATTATATTTTATAGTATTATATAGTATGATTTTAGTAAAT
* * *
55062255 TCATATAGGAATATTTAATACT-AAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTA
66 TCATATAAGAATATTTAATACTAAAGAATTTTATCAAATTATATATTTTTATTAAATTATATTTA
55062319 ATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATA
131 ATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATA
55062382 TTTTATTAAA
Statistics
Matches: 184, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
233 103 0.56
234 55 0.30
235 2 0.01
238 1 0.01
241 23 0.12
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (237 bp):
TAAATTATATTTAATAATAATTATTATTATATTTTATAGTATTATATAGTATGATTTTAGTAAAT
TCATATAAGAATATTTAATACTAAAGAATTTTATCAAATTATATATTTTTATTAAATTATATTTA
ATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAG
AATATTTAATACTAAGAATTTTATTAAATTATATATTTTTAT
Found at i:55062398 original size:100 final size:98
Alignment explanation
Indices: 55062168--55062493 Score: 291
Period size: 100 Copynumber: 3.3 Consensus size: 98
55062158 AATACTAAGA
* ** * * *
55062168 ATTTTATTAAATTATATATTTTTATTAAATTATAT-TTAATAAT-AATTAT-TTT-AT-TTTA-T
1 ATTTTAGTAAATTATATA-TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATT
* *
55062227 AGTATTTTATATTATGATTTTAGTAAATTCATAT
65 AGTATTATAAATTATGATTTTAGTAAATTCATAT
* * * * *
55062261 AGGAATATTTAAT-ACTAAGA-ATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAAT
1 ----AT-TTTAGTAAATTATATATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAAT
*
55062324 AATTA-T-TT-TAAATTAT-ATTTTATAGTATTATAT-ATTAT
61 AATTAGTATTATAAATTATGA-TTT-TAGTA-AAT-TCA-TAT
55062362 GATTTTAGTAAATTCATATATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAAT
1 -ATTTTAGTAAATT-ATATATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAAT
*
55062427 TAGTATTATATATTATGATTTTAGTAAATTCATAT
64 TAGTATTATAAATTATGATTTTAGTAAATTCATAT
*
55062462 ATTTTATTAAATTATATATTTTTATTAAATTA
1 ATTTTAGTAAATTATATA-TTTTATTAAATTA
55062494 CATTTAATAA
Statistics
Matches: 187, Mismatches: 21, Indels: 40
0.75 0.08 0.16
Matches are distributed among these distances:
95 16 0.09
96 5 0.03
97 18 0.10
98 27 0.14
99 36 0.19
100 57 0.30
101 10 0.05
102 7 0.04
103 10 0.05
104 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (98 bp):
ATTTTAGTAAATTATATATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTA
GTATTATAAATTATGATTTTAGTAAATTCATAT
Found at i:55062442 original size:113 final size:120
Alignment explanation
Indices: 55061952--55062381 Score: 730
Period size: 113 Copynumber: 3.6 Consensus size: 120
55061942 AAGTAGATTA
*
55061952 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATAGTATGATTTTAGT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
* *
55062017 AAATTCATATAAGAATATTTAATACTAAAGAATTTTATCAAATTATATATTTTTAT
66 AAATTCATATAAGAATATTAAATACT-AAGAATTTTATTAAATTATATATTTTTAT
55062073 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
*
55062138 AAATTCATATAAGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTAT
66 AAATTCATATAAGAATATTAAATACTAAGAATTTTATTAAATTATATATTTTTAT
*
55062193 TAAATTATATTTAATAATAATTA---T---TT-TATTTTATAGTATTTTATATTATGATTTTAGT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
* * *
55062251 AAATTCATATAGGAATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGT
66 AAATTCATATAAGAATATTAAATACTAAGAATTTTATTAAATTATATATTTTTAT
55062306 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
55062371 AAATTCATATA
66 AAATTCATATA
55062382 TTTTATTAAA
Statistics
Matches: 296, Mismatches: 6, Indels: 15
0.93 0.02 0.05
Matches are distributed among these distances:
113 107 0.36
114 2 0.01
116 1 0.00
117 1 0.00
119 2 0.01
120 93 0.31
121 90 0.30
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (120 bp):
TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
AAATTCATATAAGAATATTAAATACTAAGAATTTTATTAAATTATATATTTTTAT
Found at i:55062449 original size:81 final size:81
Alignment explanation
Indices: 55062346--55062509 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 81
55062336 TTATATTTTA
55062346 TAGTATTATATATTATGATTTTAGTAAATTCATATATTTTATTAAATTATATATTTTTATTAAAT
1 TAGTATTATATATTATGATTTTAGTAAATTCATATATTTTATTAAATTATATATTTTTATTAAAT
*
55062411 TATATTTAATAATAAT
66 TACATTTAATAATAAT
55062427 TAGTATTATATATTATGATTTTAGTAAATTCATATATTTTATTAAATTATATATTTTTATTAAAT
1 TAGTATTATATATTATGATTTTAGTAAATTCATATATTTTATTAAATTATATATTTTTATTAAAT
55062492 TACATTTAATAATAAT
66 TACATTTAATAATAAT
55062508 TA
1 TA
55062510 TGTTAAAATA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (81 bp):
TAGTATTATATATTATGATTTTAGTAAATTCATATATTTTATTAAATTATATATTTTTATTAAAT
TACATTTAATAATAAT
Found at i:55062750 original size:16 final size:16
Alignment explanation
Indices: 55062729--55062781 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
55062719 AGGATTACCT
*
55062729 ATTACGCCTTTATTAC
1 ATTACGCCTTTATTCC
*
55062745 ATTACGCATTTATTCC
1 ATTACGCCTTTATTCC
*
55062761 ATTACACCTTTATTCC
1 ATTACGCCTTTATTCC
55062777 ATTAC
1 ATTAC
55062782 AGCAAACCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.43
Consensus pattern (16 bp):
ATTACGCCTTTATTCC
Found at i:55065635 original size:97 final size:97
Alignment explanation
Indices: 55065529--55065732 Score: 252
Period size: 98 Copynumber: 2.1 Consensus size: 97
55065519 TCTGTCTTTT
* * *
55065529 TTTATTATTTGTTTTATAATATTTTAAATATATATATATTTTT-TGGAGTCATTCTAAATGGTAC
1 TTTATTATTTATTTTATAATATTTTAAATATATA-ATATTTTTATGGAGCCATTCTAAATGGCAC
* *
55065593 CACCGGTTCATTTAAACTTTTTTTTATTATTTG
65 CACCAGTTCATTTAAACATTTTTTTATTATTTG
* * * *
55065626 TTTATTATTTATTTTATAATGTTTTAAATGTATAATTTTTTTAGTGGAGCCATTCTAAATGGCGC
1 TTTATTATTTATTTTATAATATTTTAAATATATAATATTTTTA-TGGAGCCATTCTAAATGGCAC
* * * *
55065691 CATCAGTTTATTTAAACATTTTTTTA-AATTTT
65 CACCAGTTCATTTAAACATTTTTTTATTATTTG
55065723 TTTA-TATTTA
1 TTTATTATTTA
55065733 AAATTTTTAA
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
96 13 0.14
97 39 0.42
98 40 0.43
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.54
Consensus pattern (97 bp):
TTTATTATTTATTTTATAATATTTTAAATATATAATATTTTTATGGAGCCATTCTAAATGGCACC
ACCAGTTCATTTAAACATTTTTTTATTATTTG
Found at i:55065747 original size:28 final size:29
Alignment explanation
Indices: 55065699--55065757 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 29
55065689 GCCATCAGTT
**
55065699 TATTTAAACATTTTTTTAAAT-TTTTTTA
1 TATTTAAACATTTTTAAAAATATTTTTTA
55065727 TATTTAAA-ATTTTTAAAAAATAATTTTTTA
1 TATTTAAACATTTTT-AAAAAT-ATTTTTTA
55065757 T
1 T
55065758 TTTGTGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 6 0.23
28 12 0.46
30 8 0.31
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
TATTTAAACATTTTTAAAAATATTTTTTA
Found at i:55066181 original size:97 final size:97
Alignment explanation
Indices: 55066072--55066248 Score: 255
Period size: 97 Copynumber: 1.8 Consensus size: 97
55066062 AAAAAACATG
* * * * *
55066072 TTTAAATGAACTGATGACGCCATTTAGAATGACTCCACCAAAAAAATACACCTTTAAAATATTAT
1 TTTAAATAAACTGAGGACACAATTTAGAATGACTCCACCAAAAAAATACACATTTAAAATATTAT
*
55066137 AAAACAAATAATAAACAAATTTTAAAAAAAAA
66 AAAACAAACAATAAACAAATTTTAAAAAAAAA
* * * * *
55066169 TTTAAATAAACTGGGGGCACAATTTAGAATGACTCCTCCAAAAAAATATATATTTAAAATATTAT
1 TTTAAATAAACTGAGGACACAATTTAGAATGACTCCACCAAAAAAATACACATTTAAAATATTAT
55066234 AAAACAAACAATAAA
66 AAAACAAACAATAAA
55066249 AAAAAGACAG
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
97 69 1.00
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.27
Consensus pattern (97 bp):
TTTAAATAAACTGAGGACACAATTTAGAATGACTCCACCAAAAAAATACACATTTAAAATATTAT
AAAACAAACAATAAACAAATTTTAAAAAAAAA
Found at i:55072282 original size:11 final size:13
Alignment explanation
Indices: 55072262--55072293 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
55072252 AATAAAATAA
55072262 TAAAATATC-AAT
1 TAAAATATCAAAT
55072274 TAAAA-ATCAAAT
1 TAAAATATCAAAT
55072286 TAAAATAT
1 TAAAATAT
55072294 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 13 0.72
13 2 0.11
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAATATCAAAT
Found at i:55077980 original size:17 final size:17
Alignment explanation
Indices: 55077950--55077983 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55077940 CCTCGTTTAA
*
55077950 ATTTAAAATTAAAAAAT
1 ATTTAAAATAAAAAAAT
*
55077967 ATTTAGAATAAAAAAAT
1 ATTTAAAATAAAAAAAT
55077984 CTTCAAATGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATTTAAAATAAAAAAAT
Found at i:55079407 original size:19 final size:19
Alignment explanation
Indices: 55079383--55079428 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
55079373 TGAACTTAAC
*
55079383 TCACTTTAGTGATCCTAAT
1 TCACTTCAGTGATCCTAAT
*
55079402 TCACTTCAGTGATCTTAAT
1 TCACTTCAGTGATCCTAAT
*
55079421 TTACTTCA
1 TCACTTCA
55079429 AAACTCAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (19 bp):
TCACTTCAGTGATCCTAAT
Found at i:55081644 original size:13 final size:13
Alignment explanation
Indices: 55081594--55081654 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
55081584 ACACTTAAAT
55081594 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* * *
55081607 TTCTCTAAAGTAC
1 TTTTCAAAAGCAC
* *
55081620 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
*
55081633 TTTTCAAAAGCAT
1 TTTTCAAAAGCAC
55081646 TTTTCAAAA
1 TTTTCAAAA
55081655 TCAATGAAGA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:55085649 original size:27 final size:27
Alignment explanation
Indices: 55085616--55085680 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
55085606 GAGGGCCTGC
** *
55085616 CACAGGCGGCATCAGTGGTGCCAGTGA
1 CACAGGCGGCATCAAAGGTGCCACTGA
* * *
55085643 CAGAGGCAGCATCAAAGGTGCCACTGC
1 CACAGGCGGCATCAAAGGTGCCACTGA
55085670 CACAGGCGGCA
1 CACAGGCGGCA
55085681 CCAGCCCTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.29, G:0.34, T:0.11
Consensus pattern (27 bp):
CACAGGCGGCATCAAAGGTGCCACTGA
Found at i:55085745 original size:17 final size:16
Alignment explanation
Indices: 55085723--55085772 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
55085713 GCAGAAGGAG
55085723 AAGAAAAAAAGAGAACA
1 AAGAAAAAAAGAGAA-A
55085740 AAGAAAAACGAA-AGAAA
1 AAGAAAAA--AAGAGAAA
55085757 AAGAAAGAAAAG-GAAA
1 AAGAAA-AAAAGAGAAA
55085773 GGAGAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 6 0.21
17 15 0.52
18 6 0.21
19 2 0.07
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAGAGAAA
Found at i:55085762 original size:10 final size:10
Alignment explanation
Indices: 55085739--55085773 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
55085729 AAAAGAGAAC
55085739 AAAGAAAAACG
1 AAAGAAAAA-G
55085750 AAAGAAAAAG
1 AAAGAAAAAG
*
55085760 AAAGAAAAGG
1 AAAGAAAAAG
55085770 AAAG
1 AAAG
55085774 GAGAAGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:55085780 original size:20 final size:21
Alignment explanation
Indices: 55085733--55085781 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
55085723 AAGAAAAAAA
*
55085733 GAGAACAAAGAAAAACGAAAG
1 GAGAAGAAAGAAAAACGAAAG
* * *
55085754 AAAAAGAAAG-AAAAGGAAAG
1 GAGAAGAAAGAAAAACGAAAG
55085774 GAGAAGAA
1 GAGAAGAA
55085782 GAAGAAGAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.69, C:0.04, G:0.27, T:0.00
Consensus pattern (21 bp):
GAGAAGAAAGAAAAACGAAAG
Found at i:55085859 original size:43 final size:46
Alignment explanation
Indices: 55085760--55085859 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 46
55085750 AAAGAAAAAG
*
55085760 AAAGAAAAGGAAAGGAGAAGAAGAAGAAGAAGGAAGGAGGCGCAGGAA
1 AAAG-AAA-GAAAGGAGAAGAAGAAGAAGAAGGAAGGAGGCGAAGGAA
* *
55085808 AAAG--AGAAA-GAGAAGGAGAAGAAGAA-GAGGGAGG-GAAGGAA
1 AAAGAAAGAAAGGAGAAGAAGAAGAAGAAGGAAGGAGGCGAAGGAA
55085849 AAAGAAAGAAA
1 AAAGAAAGAAA
55085860 AAAAAAGGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
41 10 0.21
42 7 0.15
43 21 0.45
44 4 0.09
45 1 0.02
48 4 0.09
ACGTcount: A:0.59, C:0.02, G:0.39, T:0.00
Consensus pattern (46 bp):
AAAGAAAGAAAGGAGAAGAAGAAGAAGAAGGAAGGAGGCGAAGGAA
Found at i:55087350 original size:27 final size:26
Alignment explanation
Indices: 55087310--55087360 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
55087300 AAATTATAAA
*
55087310 ATATAGAAATATATATATATATGTAC
1 ATATAGAAAAATATATATATATGTAC
*
55087336 ATATAAGAAAAATATATATGTATGT
1 ATAT-AGAAAAATATATATATATGT
55087361 GAATTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (26 bp):
ATATAGAAAAATATATATATATGTAC
Found at i:55087373 original size:27 final size:26
Alignment explanation
Indices: 55087310--55087373 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
55087300 AAATTATAAA
* *
55087310 ATATAGAAATATATATATATATGTAC
1 ATATAAAAAAATATATATATATGTAC
*
55087336 ATATAAGAAAAATATATATGTATGTGA-
1 ATATAA-AAAAATATATATATATGT-AC
55087363 ATTATAAAAAA
1 A-TATAAAAAA
55087374 TAAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 5 0.16
27 21 0.66
28 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (26 bp):
ATATAAAAAAATATATATATATGTAC
Found at i:55087489 original size:36 final size:37
Alignment explanation
Indices: 55087449--55087529 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 37
55087439 TGAAACATAG
*
55087449 AAAATATATAAAAGTATGT-GTATATATATAT-TTATA
1 AAAATATA-AAAAATATGTAGTATATATATATATTATA
* *
55087485 AAAAT-TAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATATAAAAAATATGTA-GTATATATATATATTATA
55087522 AAACATAT
1 AAA-ATAT
55087530 GTATGTATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 8 0.22
35 2 0.05
36 16 0.43
37 8 0.22
38 2 0.05
39 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (37 bp):
AAAATATAAAAAATATGTAGTATATATATATATTATA
Found at i:55087887 original size:18 final size:19
Alignment explanation
Indices: 55087848--55087888 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
55087838 ACAAACCAAC
*
55087848 AAAATAAGAACAAGCCACAG
1 AAAATAAGAAC-AGCAACAG
55087868 AAAATAAGAAC-GCAACAG
1 AAAATAAGAACAGCAACAG
55087886 AAA
1 AAA
55087889 GAGAAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.63, C:0.17, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAATAAGAACAGCAACAG
Found at i:55088072 original size:22 final size:21
Alignment explanation
Indices: 55088037--55088094 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
55088027 AAATGGTATC
* * *
55088037 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
55088058 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
55088081 TGCATATCATATCT
1 TACAAATCATATCT
55088095 AAGATTGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:55088475 original size:13 final size:12
Alignment explanation
Indices: 55088457--55088506 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
55088447 ATACATTTCA
55088457 AAAATAATATAG
1 AAAATAATATAG
*
55088469 TAAAATAATATAA
1 -AAAATAATATAG
*
55088482 AATAATAAAATACG
1 AA-AATAATATA-G
55088496 AAAATAATATA
1 AAAATAATATA
55088507 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 27 0.87
14 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (12 bp):
AAAATAATATAG
Found at i:55088573 original size:159 final size:160
Alignment explanation
Indices: 55088281--55088742 Score: 727
Period size: 159 Copynumber: 2.9 Consensus size: 160
55088271 ATTACAACAA
55088281 TAAATGTATACATTTCAAACATAATGTAGTAAAATAATATAAAATAATAAAATACGAAAATAGA-
1 TAAATGTATACATTTCAAACATAATGTAGTAAAATAATATAAAATAATAAAATACGAAAATA-AT
* * * * * * *** *
55088345 AAACTTTTTGAAAGTAATAAAATTCAGGAAAAAAGAAAAATACGAAGAAAGGGAAAAAATAAGGA
65 ATATTTTTTGAAAGTAATAAAAATCGGGAAAAAAGAAAAATACGAACAAAGAGCCGAAATAAGGG
* *
55088410 TTTTTTACAAAATTTATTT-AAAACACACAC
130 TTTTTTACTAAATTTATTTAAAAAAACACAC
* *
55088440 TAAATGTATACATTTCAAAAATAATATAGTAAAATAATATAAAATAATAAAATACGAAAATAATA
1 TAAATGTATACATTTCAAACATAATGTAGTAAAATAATATAAAATAATAAAATACGAAAATAATA
*
55088505 TATTTTTTAAAAGTAATAAAAATCGGGAAAAAAGAAAAATACGAACAAAGAGCCGAAATAAGGG-
66 TATTTTTTGAAAGTAATAAAAATCGGGAAAAAAGAAAAATACGAACAAAGAGCCGAAATAAGGGT
55088569 TTTTTACTAAATTTATTTAAAAAAACACAC
131 TTTTTACTAAATTTATTTAAAAAAACACAC
55088599 TAAATGTATACATTTCAAACATAATGTAGTAAAATAATATAAAATAATAAAATACGAAAAT-ATC
1 TAAATGTATACATTTCAAACATAATGTAGTAAAATAATATAAAATAATAAAATACGAAAATAAT-
55088663 ATATTTTTTGAAAGTAAT-AAAATCTGGGAAAAAAGAAAAATACGAACAAAGAGCCGAAATAAGG
65 ATATTTTTTGAAAGTAATAAAAATC-GGGAAAAAAGAAAAATACGAACAAAGAGCCGAAATAAGG
55088727 GTTTTTTACTAAATTT
129 GTTTTTTACTAAATTT
55088743 GTTTTGAAGT
Statistics
Matches: 280, Mismatches: 18, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
158 26 0.09
159 240 0.86
160 14 0.05
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.27
Consensus pattern (160 bp):
TAAATGTATACATTTCAAACATAATGTAGTAAAATAATATAAAATAATAAAATACGAAAATAATA
TATTTTTTGAAAGTAATAAAAATCGGGAAAAAAGAAAAATACGAACAAAGAGCCGAAATAAGGGT
TTTTTACTAAATTTATTTAAAAAAACACAC
Found at i:55091041 original size:8 final size:8
Alignment explanation
Indices: 55091028--55091054 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
55091018 GGGTCTTACA
55091028 ACAACATT
1 ACAACATT
55091036 ACAACATT
1 ACAACATT
55091044 ACAACATT
1 ACAACATT
55091052 ACA
1 ACA
55091055 CATAACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (8 bp):
ACAACATT
Found at i:55093791 original size:79 final size:79
Alignment explanation
Indices: 55093699--55093857 Score: 318
Period size: 79 Copynumber: 2.0 Consensus size: 79
55093689 GTCAAATATA
55093699 CATCCAACAGTTGTTGTCAAGATGATTCCATCGAAATAAATGCATACAAAAAACTTATCATCCAT
1 CATCCAACAGTTGTTGTCAAGATGATTCCATCGAAATAAATGCATACAAAAAACTTATCATCCAT
55093764 CTTAAATATTCAAT
66 CTTAAATATTCAAT
55093778 CATCCAACAGTTGTTGTCAAGATGATTCCATCGAAATAAATGCATACAAAAAACTTATCATCCAT
1 CATCCAACAGTTGTTGTCAAGATGATTCCATCGAAATAAATGCATACAAAAAACTTATCATCCAT
55093843 CTTAAATATTCAAT
66 CTTAAATATTCAAT
55093857 C
1 C
55093858 TGTCAAAAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (79 bp):
CATCCAACAGTTGTTGTCAAGATGATTCCATCGAAATAAATGCATACAAAAAACTTATCATCCAT
CTTAAATATTCAAT
Found at i:55094036 original size:3 final size:3
Alignment explanation
Indices: 55094028--55094054 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55094018 AATAACTAAC
55094028 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
55094055 GTTTTTTACT
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:55094152 original size:76 final size:76
Alignment explanation
Indices: 55094062--55094203 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 76
55094052 ATAGTTTTTT
*
55094062 ACTAAAAATAATACTAACTAACAATAATAATTAGGG-TTTTACTAAAAATAATAACTAACAGTAA
1 ACTAAAAATAATACTAACTAA-AATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAA
55094126 TATAATGTAAAA
65 TATAATGTAAAA
* * ***
55094138 ACTAACAATCATACTAACTAAAATAATAATTAGGGTTTTTACTAATCCTAATAACTAACAATAAT
1 ACTAAAAATAATACTAACTAAAATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAAT
55094203 A
66 A
55094204 ATATTATTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 14 0.24
76 45 0.76
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (76 bp):
ACTAAAAATAATACTAACTAAAATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAAT
ATAATGTAAAA
Found at i:55094292 original size:50 final size:43
Alignment explanation
Indices: 55094238--55094342 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 43
55094228 TAATACTAAG
55094238 TAACAATAATTATTAACTAACAATAATAACTAAACTTATACAAAAATAAC
1 TAACAATAATTATTAACTAAC--TAA-AA-T-AA-TTATACAAAAAT-AC
*
55094288 TAACAATAGTTA-T-ACTAACTAAAATAATTATACAAAAATAC
1 TAACAATAATTATTAACTAACTAAAATAATTATACAAAAATAC
*
55094329 TAA-AATAATAATTA
1 TAACAATAATTATTA
55094343 CGGTTTTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
40 6 0.12
41 6 0.12
42 12 0.24
43 2 0.04
44 1 0.02
45 2 0.04
46 3 0.06
48 6 0.12
49 1 0.02
50 11 0.22
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (43 bp):
TAACAATAATTATTAACTAACTAAAATAATTATACAAAAATAC
Found at i:55094318 original size:18 final size:19
Alignment explanation
Indices: 55094230--55094320 Score: 60
Period size: 17 Copynumber: 5.2 Consensus size: 19
55094220 ACTAACAATA
*
55094230 ATACTAAGTAACAATAATT
1 ATACTAACTAACAATAATT
55094249 AT--TAACTAACAATAA-T
1 ATACTAACTAACAATAATT
55094265 A-ACTAAACTTATAC-A-AA--
1 ATACT-AAC-TA-ACAATAATT
*
55094282 A-A-TAACTAACAATAGTT
1 ATACTAACTAACAATAATT
55094299 ATACTAACTAA-AATAATT
1 ATACTAACTAACAATAATT
55094317 ATAC
1 ATAC
55094321 AAAAATACTA
Statistics
Matches: 58, Mismatches: 3, Indels: 23
0.69 0.04 0.27
Matches are distributed among these distances:
13 2 0.03
14 3 0.05
15 4 0.07
16 3 0.05
17 16 0.28
18 16 0.28
19 12 0.21
20 2 0.03
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACTAACTAACAATAATT
Found at i:55094333 original size:22 final size:22
Alignment explanation
Indices: 55094273--55094337 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
55094263 ATAACTAAAC
*
55094273 TTATACAAAAATAACTAACAATAG
1 TTATACAAAAAT-ACTAA-AATAA
*
55094297 TTATAC---TA-ACTAAAATAA
1 TTATACAAAAATACTAAAATAA
55094315 TTATACAAAAATACTAAAATAA
1 TTATACAAAAATACTAAAATAA
55094337 T
1 T
55094338 AATTACGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
18 10 0.29
19 5 0.15
21 2 0.06
22 11 0.32
24 6 0.18
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (22 bp):
TTATACAAAAATACTAAAATAA
Found at i:55094376 original size:60 final size:59
Alignment explanation
Indices: 55094303--55094488 Score: 203
Period size: 57 Copynumber: 3.2 Consensus size: 59
55094293 ATAGTTATAC
55094303 TAACTAA-AATAATTATACAAAAATACTAAAATAATAATTACGGTTTTTATTAATCTTAA
1 TAACTAACAATAATTATACAAAAATACTAAAATAATAATTA-GGTTTTTATTAATCTTAA
* * * *
55094362 TAACTAACAATAATTATACAAAAATACTAAGTAACAATAATTA----TTAACTAA-CAATAA
1 TAACTAACAATAATTATACAAAAATACTAA--AATAATAATTAGGTTTTTATTAATC-TTAA
* *
55094419 TAACTAACAATAATAATAC---TA-ACTAAAATAATAATTAGGGTTTTTATTAATCTTAA
1 TAACTAACAATAATTATACAAAAATACTAAAATAATAATTA-GGTTTTTATTAATCTTAA
55094475 TAACTAACAATAAT
1 TAACTAACAATAAT
55094489 AACTAAACTA
Statistics
Matches: 107, Mismatches: 10, Indels: 23
0.76 0.07 0.16
Matches are distributed among these distances:
51 10 0.09
53 5 0.05
54 1 0.01
56 24 0.22
57 28 0.26
59 7 0.07
60 22 0.21
62 10 0.09
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (59 bp):
TAACTAACAATAATTATACAAAAATACTAAAATAATAATTAGGTTTTTATTAATCTTAA
Found at i:55094422 original size:13 final size:13
Alignment explanation
Indices: 55094359--55094434 Score: 64
Period size: 13 Copynumber: 5.5 Consensus size: 13
55094349 TTATTAATCT
55094359 TAATAACTAACAA
1 TAATAACTAACAA
*
55094372 TAATTATAC-AAAAA
1 TAA-TA-ACTAACAA
* *
55094386 TACTAAGTAACAA
1 TAATAACTAACAA
55094399 TAATTATTAACTAACAA
1 T-A--A-TAACTAACAA
55094416 TAATAACTAACAA
1 TAATAACTAACAA
55094429 TAATAA
1 TAATAA
55094435 TACTAACTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
12 1 0.02
13 26 0.52
14 10 0.20
15 2 0.04
16 1 0.02
17 10 0.20
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.28
Consensus pattern (13 bp):
TAATAACTAACAA
Found at i:55094441 original size:19 final size:18
Alignment explanation
Indices: 55094414--55094453 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
55094404 ATTAACTAAC
55094414 AATAATAACTAACAATAAT
1 AATAATAACTAA-AATAAT
*
55094433 AATACTAACTAAAATAAT
1 AATAATAACTAAAATAAT
55094451 AAT
1 AAT
55094454 TAGGGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAATAACTAAAATAAT
Found at i:55097936 original size:30 final size:31
Alignment explanation
Indices: 55097898--55097984 Score: 101
Period size: 30 Copynumber: 2.9 Consensus size: 31
55097888 GGGTAATTTC
55097898 GATATAATGTCAGATTGTGTGAGCAATA-CT
1 GATATAATGTCAGATTGTGTGAGCAATACCT
*
55097928 -ATTATAATGTCA-ACTTGTGTGAACAA-ACCT
1 GA-TATAATGTCAGA-TTGTGTGAGCAATACCT
* *
55097958 GATATACTGTCAGCTTGTGTGAGCAAT
1 GATATAATGTCAGATTGTGTGAGCAAT
55097985 TTATCTCGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
29 3 0.06
30 43 0.91
31 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (31 bp):
GATATAATGTCAGATTGTGTGAGCAATACCT
Found at i:55103858 original size:17 final size:17
Alignment explanation
Indices: 55103836--55103868 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55103826 AAAATGAATA
*
55103836 TGATTGATATGTGATTC
1 TGATTGATATATGATTC
55103853 TGATTGATATATGATT
1 TGATTGATATATGATT
55103869 GATATGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.21, T:0.48
Consensus pattern (17 bp):
TGATTGATATATGATTC
Found at i:55108391 original size:13 final size:11
Alignment explanation
Indices: 55108363--55108405 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
55108353 AGTTAAATAT
55108363 TATTTTATTAA
1 TATTTTATTAA
55108374 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
55108387 TA-TTTATTAT
1 TATTTTATTAA
55108397 TATTTTATT
1 TATTTTATT
55108406 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:55108392 original size:23 final size:23
Alignment explanation
Indices: 55108366--55108409 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
55108356 TAAATATTAT
55108366 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
55108389 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
55108410 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:55109187 original size:20 final size:20
Alignment explanation
Indices: 55109162--55109258 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
55109152 AGGGGCACTG
55109162 AAGTGCAAACAGAGGCA-CA
1 AAGTGCAAACAGAGGCACCA
* * * *
55109181 AATGTGCAAGCAAAGGCATCG
1 AA-GTGCAAACAGAGGCACCA
* *
55109202 TAGTACAAACA-AGGACACCA
1 AAGTGCAAACAGAGG-CACCA
* * *
55109222 AAGTGTATACAGAAGCACCA
1 AAGTGCAAACAGAGGCACCA
55109242 AAGTGCAAACAGAGGCA
1 AAGTGCAAACAGAGGCA
55109259 TCGGAGTGCA
Statistics
Matches: 58, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
19 5 0.09
20 49 0.84
21 4 0.07
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (20 bp):
AAGTGCAAACAGAGGCACCA
Found at i:55114599 original size:56 final size:56
Alignment explanation
Indices: 55114530--55114680 Score: 239
Period size: 56 Copynumber: 2.7 Consensus size: 56
55114520 TCACAGAAGA
* * * *
55114530 TGCCATGGGTCTTAATCTCATGGTCTTACATACATTCATTCAATCATTTCATATCT
1 TGCCATAGGTCTTAACCACATGGTCTTACAAACATTCATTCAATCATTTCATATCT
* *
55114586 TGCCATAGATCTTAACCACATGGTCTTACAAACATTCATTCAGTCATTTCATATCT
1 TGCCATAGGTCTTAACCACATGGTCTTACAAACATTCATTCAATCATTTCATATCT
*
55114642 TGCCATAGGTCTTAACCACATGGTCTTATAAACATTCAT
1 TGCCATAGGTCTTAACCACATGGTCTTACAAACATTCAT
55114681 GTATCGCAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 87 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (56 bp):
TGCCATAGGTCTTAACCACATGGTCTTACAAACATTCATTCAATCATTTCATATCT
Found at i:55120668 original size:12 final size:12
Alignment explanation
Indices: 55120651--55120675 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55120641 TCTTTAAACT
55120651 TTCTTTTTTTTC
1 TTCTTTTTTTTC
55120663 TTCTTTTTTTTC
1 TTCTTTTTTTTC
55120675 T
1 T
55120676 ATTCTCTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCTTTTTTTTC
Found at i:55121593 original size:20 final size:21
Alignment explanation
Indices: 55121545--55121593 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
55121535 TTTTTGCAAT
*
55121545 AAAGAATATGAGAAGAGAGAA
1 AAAGAAAATGAGAAGAGAGAA
* *
55121566 AAA-TAAATGGGAAGA-AGAA
1 AAAGAAAATGAGAAGAGAGAA
55121585 AAAGAAAAT
1 AAAGAAAAT
55121594 AAAAAAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 7 0.30
20 13 0.57
21 3 0.13
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.10
Consensus pattern (21 bp):
AAAGAAAATGAGAAGAGAGAA
Found at i:55121703 original size:21 final size:21
Alignment explanation
Indices: 55121679--55121728 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
55121669 AAACTACGTT
* *
55121679 AAAAGAAATGGAGAAGAAAAG
1 AAAAGAAAGGGAGAAGAAAAA
* *
55121700 AAAACAGAGGGAGAAGAAAAA
1 AAAAGAAAGGGAGAAGAAAAA
55121721 AAAAGAAA
1 AAAAGAAA
55121729 ATTCAAAGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (21 bp):
AAAAGAAAGGGAGAAGAAAAA
Found at i:55131423 original size:18 final size:20
Alignment explanation
Indices: 55131400--55131437 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
55131390 TAAGTACTTG
55131400 AATTTGGT-TTTAAA-TTTT
1 AATTTGGTATTTAAAGTTTT
55131418 AATTTGGTATTTAAAGTTTT
1 AATTTGGTATTTAAAGTTTT
55131438 TTTTTATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (20 bp):
AATTTGGTATTTAAAGTTTT
Found at i:55132914 original size:23 final size:23
Alignment explanation
Indices: 55132888--55132951 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
55132878 GCCGATCAGA
55132888 CACTTTATGTGTCGTA-CATCAAG
1 CACTTTATGTGTCGTATC-TCAAG
* *
55132911 CACTTTATGTGTTGTATCTCACG
1 CACTTTATGTGTCGTATCTCAAG
55132934 CACTTTATGTGTCGTATC
1 CACTTTATGTGTCGTATC
55132952 AGGCACCTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (23 bp):
CACTTTATGTGTCGTATCTCAAG
Found at i:55133178 original size:6 final size:6
Alignment explanation
Indices: 55133167--55133196 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
55133157 AAATTATGGT
55133167 TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA
1 TTGAAA TTGAAA TTGAAA TTGAAA TTGAAA
55133197 GGCATGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
TTGAAA
Found at i:55137305 original size:13 final size:13
Alignment explanation
Indices: 55137287--55137311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55137277 ATTACGACTC
55137287 TAAAAATATTTAA
1 TAAAAATATTTAA
55137300 TAAAAATATTTA
1 TAAAAATATTTA
55137312 CAACCTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAAATATTTAA
Found at i:55142994 original size:21 final size:21
Alignment explanation
Indices: 55142970--55143021 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
55142960 CCCTAAATCA
55142970 CTAACTCTTAACCT-CTAACCC
1 CTAACTCTTAA-CTACTAACCC
* *
55142991 CTAACCCCTAACTACTAACCC
1 CTAACTCTTAACTACTAACCC
*
55143012 CTAAATCTTA
1 CTAACTCTTA
55143022 TTTAATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (21 bp):
CTAACTCTTAACTACTAACCC
Found at i:55143107 original size:23 final size:23
Alignment explanation
Indices: 55143081--55143127 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
55143071 ACCCCTAAAC
55143081 CTTATTTAATATAAATTAAAATG
1 CTTATTTAATATAAATTAAAATG
55143104 CTTATTTAATATAAATTAAAATG
1 CTTATTTAATATAAATTAAAATG
55143127 C
1 C
55143128 ACTAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (23 bp):
CTTATTTAATATAAATTAAAATG
Found at i:55143142 original size:24 final size:23
Alignment explanation
Indices: 55143086--55143142 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
55143076 TAAACCTTAT
* *
55143086 TTAATATAAATTAAAATGCTTAT
1 TTAATATAAATTAAAATGCCTAA
55143109 TTAATATAAATTAAAATGCACTAA
1 TTAATATAAATTAAAATGC-CTAA
*
55143133 TTAATCTAAA
1 TTAATATAAA
55143143 CCCTAAACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.39
Consensus pattern (23 bp):
TTAATATAAATTAAAATGCCTAA
Found at i:55143767 original size:41 final size:40
Alignment explanation
Indices: 55143716--55143873 Score: 174
Period size: 41 Copynumber: 3.9 Consensus size: 40
55143706 GCTAAATCCC
**
55143716 AGCATTAGCGGCGCTTCTTGGAAAACGCCGCTAAAAGCCTG
1 AGCATTAGCGGCGCTT-TTTAAAAACGCCGCTAAAAGCCTG
*
55143757 AGCATTAGCGGCGCTTTTTTAAAACTGCCGCTAAAAGCCTG
1 AGCATTAGCGGCGCTTTTTAAAAAC-GCCGCTAAAAGCCTG
* * *
55143798 CGCATTAGCGGCGCTTTTTTAAAAATGCCGCT-AAAGCTCTA
1 AGCATTAGCGGCGC-TTTTTAAAAACGCCGCTAAAAGC-CTG
* * * *
55143839 AGCAATAGCAGTGCTTTTTAAAAAAAGCCGCTAAA
1 AGCATTAGCGGCGCTTTTT-AAAAACGCCGCTAAA
55143874 GCCCCGAAAG
Statistics
Matches: 101, Mismatches: 11, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
40 17 0.17
41 73 0.72
42 11 0.11
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (40 bp):
AGCATTAGCGGCGCTTTTTAAAAACGCCGCTAAAAGCCTG
Found at i:55143855 original size:82 final size:82
Alignment explanation
Indices: 55143717--55143873 Score: 199
Period size: 82 Copynumber: 1.9 Consensus size: 82
55143707 CTAAATCCCA
* * * * * *
55143717 GCATTAGCGGCGCTTCTTGGAAAACGCCGCTAAAAGCCTGAGCATTAGCGGCGCTTTTTTAAAAC
1 GCATTAGCGGCGCTTCTTGAAAAACGCCGCTAAAAGCCTAAGCAATAGCAGCGCTTTTTAAAAAA
*
55143782 TGCCGCTAAAAGCCTGC
66 AGCCGCTAAAAGCCTGC
* * * *
55143799 GCATTAGCGGCGCTTTTTTAAAAATGCCGCT-AAAGCTCTAAGCAATAGCAGTGCTTTTTAAAAA
1 GCATTAGCGGCGCTTCTTGAAAAACGCCGCTAAAAGC-CTAAGCAATAGCAGCGCTTTTTAAAAA
55143863 AAGCCGCTAAA
65 AAGCCGCTAAA
55143874 GCCCCGAAAG
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
81 5 0.08
82 58 0.92
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (82 bp):
GCATTAGCGGCGCTTCTTGAAAAACGCCGCTAAAAGCCTAAGCAATAGCAGCGCTTTTTAAAAAA
AGCCGCTAAAAGCCTGC
Found at i:55145120 original size:107 final size:107
Alignment explanation
Indices: 55144929--55145128 Score: 337
Period size: 107 Copynumber: 1.9 Consensus size: 107
55144919 ACAAAAATAA
* * * *
55144929 GTGTAAGGCTATGTGGTTGAGACCCTTGGCATAATATAATATAAAGACACTCATGGTGATGCCTC
1 GTGTAAGGCCATGTGGCTGAGACCCATGGCATAATATAATATAAAAACACTCATGGTGATGCCTC
*
55144994 TAGTAAGATGAAAGTTGGACTGGTAGATCACCACATGAGAAT
66 TAGTAAGATGAAAGCTGGACTGGTAGATCACCACATGAGAAT
* *
55145036 GTGTAAGTCCATGTGGCTGAGACCCATGGCATAATATGATATAAAAACACTCATGGTGATGCCTC
1 GTGTAAGGCCATGTGGCTGAGACCCATGGCATAATATAATATAAAAACACTCATGGTGATGCCTC
55145101 TAGTAAGATGAAAGCTGGACTGGTAGAT
66 TAGTAAGATGAAAGCTGGACTGGTAGAT
55145129 ATGATTGTAA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 86 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (107 bp):
GTGTAAGGCCATGTGGCTGAGACCCATGGCATAATATAATATAAAAACACTCATGGTGATGCCTC
TAGTAAGATGAAAGCTGGACTGGTAGATCACCACATGAGAAT
Found at i:55145979 original size:18 final size:18
Alignment explanation
Indices: 55145948--55145998 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 18
55145938 ATTGGGGGGT
55145948 TAAA-TTGT-GAAAATGC
1 TAAATTTGTGGAAAATGC
*
55145964 TAAATTTGTGGAAAATTC
1 TAAATTTGTGGAAAATGC
* *
55145982 TAATTTTTGTGAAAAAT
1 TAA-ATTTGTGGAAAAT
55145999 ATGTGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 10 0.34
19 11 0.38
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (18 bp):
TAAATTTGTGGAAAATGC
Found at i:55145986 original size:17 final size:17
Alignment explanation
Indices: 55145948--55145996 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
55145938 ATTGGGGGGT
55145948 TAAA-TTGTGAAAATGC
1 TAAATTTGTGAAAATGC
*
55145964 TAAATTTGTGGAAAATTC
1 TAAATTTGT-GAAAATGC
*
55145982 TAATTTTTGTGAAAA
1 TAA-ATTTGTGAAAA
55145997 ATATGTGCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 15 0.54
19 5 0.18
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (17 bp):
TAAATTTGTGAAAATGC
Found at i:55146775 original size:24 final size:25
Alignment explanation
Indices: 55146737--55146788 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
55146727 GCTATCCGAT
*
55146737 GCTTTCTGATTAAGTGCTCTTCAAA
1 GCTTTCCGATTAAGTGCTCTTCAAA
*
55146762 GCTTTCCG-TTAAGTGCTCTTCAGA
1 GCTTTCCGATTAAGTGCTCTTCAAA
55146786 GCT
1 GCT
55146789 ACTCATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (25 bp):
GCTTTCCGATTAAGTGCTCTTCAAA
Found at i:55154532 original size:84 final size:84
Alignment explanation
Indices: 55154387--55154544 Score: 214
Period size: 84 Copynumber: 1.9 Consensus size: 84
55154377 ATATGTGTTA
* * * *
55154387 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGA
1 TCGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
55154452 CATTGGCATCGTATTTGAT
66 CATTGGCATCGTATTTGAT
*
55154471 TCGTGTAAGACC-CTATCTGGGACAG-TGGCATTGA-TATGTGATTACATGTAAGACCACGTCTG
1 TCGTGTAAGACCAC-ATCTGGGAC-GTTGGCATCGACT-TGTGATTACATGTAAGACCACGTCTG
*
55154533 GGACGTTGGCAT
63 GGACATTGGCAT
55154545 TGTACGAGTC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
83 2 0.03
84 62 0.95
85 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (84 bp):
TCGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
CATTGGCATCGTATTTGAT
Found at i:55154546 original size:43 final size:43
Alignment explanation
Indices: 55154375--55154544 Score: 199
Period size: 43 Copynumber: 4.0 Consensus size: 43
55154365 ATAGGATTTC
55154375 CGATATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
55154418 CGACT-TGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCAT
1 CGA-TATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
* *
55154461 CG-TATTTGATT-CGTGTAAGACC-CTATCTGGGACAG-TGGCAT
1 CGATATGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
* *
55154502 TGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
55154545 TGTACGAGTC
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
41 27 0.25
42 14 0.13
43 61 0.57
44 5 0.05
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
CGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:55154734 original size:16 final size:17
Alignment explanation
Indices: 55154705--55154736 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
55154695 TGAATTGATG
55154705 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
55154722 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
55154737 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:55157581 original size:19 final size:19
Alignment explanation
Indices: 55157557--55157594 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55157547 TGATGGAAGG
55157557 AGTATGAGAATTTAGTTAA
1 AGTATGAGAATTTAGTTAA
55157576 AGTATGAGAATTTAGTTAA
1 AGTATGAGAATTTAGTTAA
55157595 GGCCCGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (19 bp):
AGTATGAGAATTTAGTTAA
Found at i:55167577 original size:25 final size:25
Alignment explanation
Indices: 55167526--55167582 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
55167516 TCAGAGTTTT
55167526 CCGTTA-AGTGCTCTTAGGAGCTAC
1 CCGTTATAGTGCTCTTAGGAGCTAC
* *
55167550 CCGTTATAG-GCTCTTTGTGAGCTTC
1 CCGTTATAGTGCTCTTAG-GAGCTAC
55167575 CCGTTATA
1 CCGTTATA
55167583 TTGTCCGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.35
Consensus pattern (25 bp):
CCGTTATAGTGCTCTTAGGAGCTAC
Found at i:55173136 original size:44 final size:44
Alignment explanation
Indices: 55173017--55173157 Score: 135
Period size: 44 Copynumber: 3.2 Consensus size: 44
55173007 TTGTCGCTTC
* * *
55173017 AATCTACTCCACTGCAACTTTGAGG-AGATAAGATTAGTATCTTT
1 AATCTGCTCCACTGCATCTTT-AGGAAGATAAGATTAGTAACTTT
* * * * * *
55173061 AATTTGCTCCGCTACATCTTCAAGAATATAAGATTAGTAACTTT
1 AATCTGCTCCACTGCATCTTTAGGAAGATAAGATTAGTAACTTT
* *
55173105 -ATCCTGCTCCACTGCATCTTTAGGAAGATAAGGTTTA-TAGCTTT
1 AAT-CTGCTCCACTGCATCTTTAGGAAGATAA-GATTAGTAACTTT
55173149 AATCTGCTC
1 AATCTGCTC
55173158 TATTGCAACT
Statistics
Matches: 76, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
43 4 0.05
44 66 0.87
45 6 0.08
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (44 bp):
AATCTGCTCCACTGCATCTTTAGGAAGATAAGATTAGTAACTTT
Found at i:55173212 original size:45 final size:44
Alignment explanation
Indices: 55173013--55173407 Score: 128
Period size: 44 Copynumber: 8.8 Consensus size: 44
55173003 GAATTTGTCG
*
55173013 CTTCAATCTACTCCACTGCAACTT-TGAGGAGATAAGA-TTAGTAT
1 CTTCAATCTACTCCACTGCAACTTCAGA-GAGATAAGACTT-GTAT
* * * * * * * *
55173057 CTTTAATTTGCTCCGCTACATCTTCA-AGAATATAAGA-TTAGTAA
1 CTTCAATCTACTCCACTGCAACTTCAGAG-AGATAAGACTT-GTAT
* * * * ** * *
55173101 CTT-TATCCTGCTCCACTGCATCTTTAG-GAAGATAAGGTTTATAG
1 CTTCAAT-CTACTCCACTGCAACTTCAGAG-AGATAAGACTTGTAT
* * * *
55173145 CTTTAATCTGCTCTATTGCAACTTCAGAGAGATAAGA-TCTGCTAT
1 CTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGACT-TG-TAT
* *
55173190 CTTCAGTCTACTCCACTGCAACTTCA-AGTAGATATGACTTGTAT
1 CTTCAATCTACTCCACTGCAACTTCAGAG-AGATAAGACTTGTAT
* * * * **
55173234 CTTCAATCTGCTTCACTGCAATTTCAGGGAGATCCGA-TTGTAAT
1 CTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGACTTGT-AT
* ** * * * *
55173278 TTGTAGCCTTAATCTGTTCCACTGTAACTTCAGGGAAATAAGA-TTCACTAT
1 CT-T---C--AATCTACTCCACTGCAACTTCAGAGAGATAAGACTT--GTAT
* * * * * * *
55173329 CTTTAGTCTGCTCCACTGCAACATCAGGGAGATAAGACTCGTAA
1 CTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGACTTGTAT
* * *
55173373 CTTCAA-CTTGCCCCACTGCAACTTCAGGGAGATAA
1 CTTCAATC-TACTCCACTGCAACTTCAGAGAGATAA
55173408 TCTTTATAGC
Statistics
Matches: 266, Mismatches: 62, Indels: 46
0.71 0.17 0.12
Matches are distributed among these distances:
43 9 0.03
44 154 0.58
45 67 0.25
46 2 0.01
48 1 0.00
50 29 0.11
51 3 0.01
52 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGACTTGTAT
Found at i:55181771 original size:236 final size:237
Alignment explanation
Indices: 55181319--55181795 Score: 710
Period size: 236 Copynumber: 2.0 Consensus size: 237
55181309 CCTCATCCAC
* * * *
55181319 GTGCCCTAGTGCTTTAAGGAAAACAACCAGCCTTTAAATGCTTAAAGCGAAGACATTGACCCCTT
1 GTGCCCTAGTGCTTTAAGGAAAACAACCAGCCTATAAATGCTCAAAGCGAAGACATTCAACCCTT
* *
55181384 TTTTTCATATCTGGGTGTGTTAAAATCAAATCTCGCAAACTATTCCAAGGGATACATTTACCATC
66 TTTTTCATA--TGGGTGTGCTAAAATCAAATCTCGCAAACTATTCCAAGGAATACATTTACCATC
* *
55181449 TCCCTTTGCTTGATCCGGCCTACAACCCATTGCTCACTCATCCCTGTTATTTTCATTAGTTTCTT
129 TCCCTTTGCTTAATCCGGCCTACAACCCATTGCTCACTCATCCCTGTTATGTTCATTAGTTTCTT
* * * *
55181514 TAGGAAGGTCGGGATGTTGGCGGCTCTGGAATAAACCTTGTCAG
194 TAGAAAGGTCGAGACGTTGGCGGCTCTGAAATAAACCTTGTCAG
55181558 GTGCCCTAGTGCTTT-AGAGAAAACAACCAGCCTATAAATGCTCAAAGCGAAGACA-TCAACCCT
1 GTGCCCTAGTGCTTTAAG-GAAAACAACCAGCCTATAAATGCTCAAAGCGAAGACATTCAACCCT
* * *
55181621 TTTTTTCATA-GGGTGTGCTAAGATCAAATCTCGTAAACTATTCCAAGGAATACATTTACCATTT
65 TTTTTTCATATGGGTGTGCTAAAATCAAATCTCGCAAACTATTCCAAGGAATACATTTACCATCT
* * * *
55181685 CTCTTTTGCTTAATCCGGGCTGCAACTCATTGCTCACTCATCCCT-TTGATGTTCATTAGTTTCT
130 C-CCTTTGCTTAATCCGGCCTACAACCCATTGCTCACTCATCCCTGTT-ATGTTCATTAGTTTCT
55181749 TTAGAAAGGTCGAGACGTTGGCGGCTCTGAAATAAACCTTGTCAG
193 TTAGAAAGGTCGAGACGTTGGCGGCTCTGAAATAAACCTTGTCAG
55181794 GT
1 GT
55181796 TAAATTTTCA
Statistics
Matches: 216, Mismatches: 19, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
235 52 0.24
236 96 0.44
238 18 0.08
239 50 0.23
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (237 bp):
GTGCCCTAGTGCTTTAAGGAAAACAACCAGCCTATAAATGCTCAAAGCGAAGACATTCAACCCTT
TTTTTCATATGGGTGTGCTAAAATCAAATCTCGCAAACTATTCCAAGGAATACATTTACCATCTC
CCTTTGCTTAATCCGGCCTACAACCCATTGCTCACTCATCCCTGTTATGTTCATTAGTTTCTTTA
GAAAGGTCGAGACGTTGGCGGCTCTGAAATAAACCTTGTCAG
Found at i:55183864 original size:12 final size:12
Alignment explanation
Indices: 55183834--55183875 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
55183824 GATAAAATGG
55183834 AATA-ATAAAAA
1 AATATATAAAAA
55183845 ATATTATATAAAAA
1 A-A-TATATAAAAA
55183859 AATATATAAAAA
1 AATATATAAAAA
55183871 GAATA
1 -AATA
55183876 CACCATAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 11 0.41
13 7 0.26
14 8 0.30
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
AATATATAAAAA
Found at i:55191920 original size:18 final size:18
Alignment explanation
Indices: 55191894--55191929 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55191884 AAACTGAAAA
* *
55191894 AATTTGGTTAATTGATCG
1 AATTCGGTTAATCGATCG
55191912 AATTCGGTTAATCGATCG
1 AATTCGGTTAATCGATCG
55191930 GTTAACCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (18 bp):
AATTCGGTTAATCGATCG
Found at i:55192132 original size:13 final size:13
Alignment explanation
Indices: 55192116--55192142 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55192106 CAAGTATTCA
55192116 ACCCAACCCAATT
1 ACCCAACCCAATT
55192129 ACCCAACCCAATT
1 ACCCAACCCAATT
55192142 A
1 A
55192143 TAAAAATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:55192251 original size:9 final size:9
Alignment explanation
Indices: 55192237--55192303 Score: 82
Period size: 9 Copynumber: 7.4 Consensus size: 9
55192227 GTAGTGATTC
55192237 AATTCGGTT
1 AATTCGGTT
55192246 AATTCGGTT
1 AATTCGGTT
*
55192255 AATTCGGGT
1 AATTCGGTT
*
55192264 AA-TCTAGTT
1 AATTC-GGTT
*
55192273 AATTCTGTT
1 AATTCGGTT
*
55192282 AATTCGGGT
1 AATTCGGTT
55192291 AATTCGGTT
1 AATTCGGTT
55192300 AATT
1 AATT
55192304 TTTAACCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
8 2 0.04
9 45 0.92
10 2 0.04
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55192300 original size:27 final size:27
Alignment explanation
Indices: 55192237--55192303 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
55192227 GTAGTGATTC
55192237 AATTCGGTTAATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTCGGGT
* *
55192264 AA-TCTAGTTAATTCTGTTAATTCGGGT
1 AATTC-GGTTAATTCGGTTAATTCGGGT
55192291 AATTCGGTTAATT
1 AATTCGGTTAATT
55192304 TTTAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.06
27 31 0.89
28 2 0.06
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.43
Consensus pattern (27 bp):
AATTCGGTTAATTCGGTTAATTCGGGT
Found at i:55194436 original size:13 final size:13
Alignment explanation
Indices: 55194418--55194444 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55194408 TTAATTTATA
55194418 TGTGTGAAAATTT
1 TGTGTGAAAATTT
55194431 TGTGTGAAAATTT
1 TGTGTGAAAATTT
55194444 T
1 T
55194445 ATCGTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:55195691 original size:43 final size:42
Alignment explanation
Indices: 55195534--55195692 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 42
55195524 TATGTGATAT
* *
55195534 CGTGTAAGACCACGTCTGGGACGTTGACATCG-ATTTGATATTTA
1 CGTGTAAGACCACGTCTAGGACGTTGGCATCGTATTTG--A-TTA
* * * * *
55195578 CGTGTAAGACCATGTCTAGGACATTGGCATCATATATGATTT
1 CGTGTAAGACCACGTCTAGGACGTTGGCATCGTATTTGATTA
*
55195620 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGTTATTTGATTA
1 CGTGTAAGACCAC-GTCTAGGAC-GTTGGCATCG-TATTTGATTA
*
55195663 CATGTAAGACCACGTCTAGGACGTTGGCAT
1 CGTGTAAGACCACGTCTAGGACGTTGGCAT
55195693 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
42 29 0.31
43 33 0.35
44 28 0.30
45 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTAGGACGTTGGCATCGTATTTGATTA
Found at i:55200096 original size:21 final size:21
Alignment explanation
Indices: 55200070--55200111 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
55200060 AGAGAGAGAA
55200070 ATCTAGAAGGCGATGATGATG
1 ATCTAGAAGGCGATGATGATG
55200091 ATCTAGAAGGCGATGATGATG
1 ATCTAGAAGGCGATGATGATG
55200112 TTGGTGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.24
Consensus pattern (21 bp):
ATCTAGAAGGCGATGATGATG
Found at i:55200182 original size:11 final size:13
Alignment explanation
Indices: 55200158--55200189 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
55200148 TAGTTTATTA
55200158 ATATTTTAATATG
1 ATATTTTAATATG
55200171 AT-TTTTAA-ATG
1 ATATTTTAATATG
55200182 ATATTTTA
1 ATATTTTA
55200190 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:55212873 original size:13 final size:13
Alignment explanation
Indices: 55212855--55212879 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55212845 ATCTAATTTA
55212855 TGTAGTTTCTTTT
1 TGTAGTTTCTTTT
55212868 TGTAGTTTCTTT
1 TGTAGTTTCTTT
55212880 GATCTGTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.68
Consensus pattern (13 bp):
TGTAGTTTCTTTT
Found at i:55218994 original size:9 final size:9
Alignment explanation
Indices: 55218977--55219013 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55218967 TGAGTTTTCG
55218977 AATTCGAAT
1 AATTCGAAT
*
55218986 AACTCGAAT
1 AATTCGAAT
55218995 AATTCGAAT
1 AATTCGAAT
55219004 AATTCGAAT
1 AATTCGAAT
55219013 A
1 A
55219014 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55219102 original size:27 final size:27
Alignment explanation
Indices: 55219062--55219113 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
55219052 AAACCTTTTT
* *
55219062 ACTTTTCCCTCAAAACTTTTACTCCTC
1 ACTTTCCCCCCAAAACTTTTACTCCTC
55219089 ACTTTCCCCCCAAAACTTTTACTCC
1 ACTTTCCCCCCAAAACTTTTACTCC
55219114 CCTCCCCTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37
Consensus pattern (27 bp):
ACTTTCCCCCCAAAACTTTTACTCCTC
Found at i:55220030 original size:5 final size:5
Alignment explanation
Indices: 55220020--55220045 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
55220010 CTCGAAAATT
55220020 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
55220046 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Done.