Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 169 of 325
Found at i:53360899 original size:54 final size:54
Alignment explanation
Indices: 53360789--53360903 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
53360779 TGGAGGAAGC
*
53360789 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATAACT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATAACT
* * * * * *
53360843 GTTCTGGTGGCTCTGCCGCGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATAACT
53360897 GTTCTGG
1 GTTCTGG
53360904 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATAACT
Found at i:53366245 original size:20 final size:19
Alignment explanation
Indices: 53366222--53366286 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
53366212 AAGCTCAAAC
53366222 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
53366242 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
53366262 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
53366282 GAGCT
1 GAGCT
53366287 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:53368100 original size:33 final size:33
Alignment explanation
Indices: 53368062--53368124 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
53368052 GATTACTCAC
53368062 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
53368095 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
53368125 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:53368151 original size:14 final size:14
Alignment explanation
Indices: 53368127--53368180 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
53368117 TCTCTTTCAA
*
53368127 TTTCTTTTTTCTCTT
1 TTTC-TTTTTCTCAT
*
53368142 TTTCTTTTTC-AAT
1 TTTCTTTTTCTCAT
53368155 TTTC-TTTTCTTCAT
1 TTTCTTTTTC-TCAT
53368169 TTTCTTTTTCTC
1 TTTCTTTTTCTC
53368181 TCACTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 5 0.15
13 5 0.15
14 14 0.42
15 9 0.27
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTTTTTCTCAT
Found at i:53368151 original size:27 final size:27
Alignment explanation
Indices: 53368121--53368178 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
53368111 TCAAGCTCTC
* *
53368121 TTTCAA-TTTCTTTTTTCTCTTTTTCTT
1 TTTCAATTTTCTTTTCT-TCATTTTCTT
53368148 TTTCAATTTTCTTTTCTTCATTTTCTT
1 TTTCAATTTTCTTTTCTTCATTTTCTT
53368175 TTTC
1 TTTC
53368179 TCTCACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTCAATTTTCTTTTCTTCATTTTCTT
Found at i:53368177 original size:15 final size:15
Alignment explanation
Indices: 53368122--53368179 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
53368112 CAAGCTCTCT
*
53368122 TTCAATTTCTTTTT-
1 TTCATTTTCTTTTTC
*
53368136 TCTCTTTTTCTTTTTC
1 T-TCATTTTCTTTTTC
*
53368152 --AATTTTC-TTTTC
1 TTCATTTTCTTTTTC
53368164 TTCATTTTCTTTTTC
1 TTCATTTTCTTTTTC
53368179 T
1 T
53368180 CTCACTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
12 5 0.15
13 5 0.15
14 7 0.21
15 17 0.50
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (15 bp):
TTCATTTTCTTTTTC
Found at i:53368229 original size:6 final size:6
Alignment explanation
Indices: 53368133--53368216 Score: 53
Period size: 6 Copynumber: 13.5 Consensus size: 6
53368123 TCAATTTCTT
* * * **
53368133 TTTTCTC TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC
1 TTTT-TC TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC
** *
53368185 TTTTTC GATTTC TTTTTC TTTTT- GTTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT
53368217 CAATTTCTTT
Statistics
Matches: 57, Mismatches: 17, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
5 4 0.07
6 37 0.65
7 13 0.23
8 3 0.05
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:53368248 original size:51 final size:51
Alignment explanation
Indices: 53368134--53368248 Score: 124
Period size: 51 Copynumber: 2.3 Consensus size: 51
53368124 CAATTTCTTT
* * **
53368134 TTTCTCTTTTTCTTTTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCAC
1 TTTCTCCTTTTCTTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCAC
* ** * * *
53368185 TTTTTCGATTTCTTTTTC-TTTTTGTTTTCTTTCAATTTCTTTTTCAATCTC
1 TTTCTCCTTTTCTTTTTCAATTTTCTTTTC-TTCAATTTCTTTTTCAATCAC
53368236 TTTCTCCTTTTCT
1 TTTCTCCTTTTCT
53368249 CGCTCAATGG
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
50 9 0.18
51 42 0.82
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (51 bp):
TTTCTCCTTTTCTTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCAC
Found at i:53370919 original size:20 final size:19
Alignment explanation
Indices: 53370896--53370960 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
53370886 AAGCTCAAAC
53370896 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
53370916 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
53370936 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
53370956 GAGCT
1 GAGCT
53370961 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:53377446 original size:23 final size:22
Alignment explanation
Indices: 53377394--53377446 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53377384 TCCACGTCTT
*
53377394 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53377416 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53377439 TTTCTTTT
1 TTTCTTTT
53377447 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53391525 original size:42 final size:42
Alignment explanation
Indices: 53391466--53391613 Score: 287
Period size: 42 Copynumber: 3.5 Consensus size: 42
53391456 CATTTAAGCC
53391466 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
53391508 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
53391550 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
53391592 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
53391614 TATTTAATGA
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
42 95 0.90
43 10 0.10
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:53391615 original size:14 final size:14
Alignment explanation
Indices: 53391596--53391640 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
53391586 AACTCATCTT
*
53391596 AGTTTAATTAAATG
1 AGTTTAATTTAATG
53391610 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
53391623 AATTTAATTTAATG
1 AGTTTAATTTAATG
53391637 AGTT
1 AGTT
53391641 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:53393510 original size:14 final size:14
Alignment explanation
Indices: 53393491--53393524 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53393481 CAATCCATTG
53393491 AAAGAGAAAAAGAA
1 AAAGAGAAAAAGAA
* *
53393505 AAAGAGCAAAATAA
1 AAAGAGAAAAAGAA
53393519 AAAGAG
1 AAAGAG
53393525 TGGAAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (14 bp):
AAAGAGAAAAAGAA
Found at i:53401565 original size:23 final size:22
Alignment explanation
Indices: 53401513--53401565 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53401503 TCCACGTCTT
*
53401513 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53401535 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53401558 TTTCTTTT
1 TTTCTTTT
53401566 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53408470 original size:23 final size:22
Alignment explanation
Indices: 53408419--53408470 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
53408409 CCTCGTCTTT
*
53408419 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
53408441 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
53408464 TTCTTTT
1 TTCTTTT
53408471 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:53411985 original size:29 final size:29
Alignment explanation
Indices: 53411952--53412011 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
53411942 ATAACCAAAC
* *
53411952 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
53411981 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
53412010 CT
1 CT
53412012 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:53412004 original size:15 final size:15
Alignment explanation
Indices: 53411958--53412005 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53411948 AAACCTACAA
*
53411958 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
53411973 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
53411987 AAACTTCATATCCAT
1 AAACTTCATATCCAT
53412002 AAAC
1 AAAC
53412006 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:53412272 original size:15 final size:15
Alignment explanation
Indices: 53412252--53412299 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53412242 TCAAAGATGG
53412252 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
53412267 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
53412281 GTTTATGGATATAAA
1 GTTTATGGATATGAA
53412296 GTTT
1 GTTT
53412300 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:53412286 original size:14 final size:14
Alignment explanation
Indices: 53412246--53412289 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
53412236 AAGGATTCAA
53412246 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
53412260 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
53412275 AGATGGGTTTATGG
1 AGATGGGTTTATGG
53412289 A
1 A
53412290 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:53412315 original size:29 final size:29
Alignment explanation
Indices: 53412246--53412305 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
53412236 AAGGATTCAA
*
53412246 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
53412275 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
53412304 AG
1 AG
53412306 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:53413323 original size:14 final size:14
Alignment explanation
Indices: 53413281--53413325 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
53413271 TTAAAGAAGC
53413281 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
53413295 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
53413308 AACTCATTTAATTA
1 AACTCATTAAATTA
53413322 AACT
1 AACT
53413326 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:53415770 original size:18 final size:18
Alignment explanation
Indices: 53415747--53415792 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
53415737 TTTATCTCAA
53415747 TTTCTTTTTC-CACTCTTT
1 TTTCTTTTTCACACTC-TT
* *
53415765 TTTCTTGTTCACATTCTT
1 TTTCTTTTTCACACTCTT
53415783 TTTCTTTTTC
1 TTTCTTTTTC
53415793 GCTTCTCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.07, C:0.24, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTCTTTTTCACACTCTT
Found at i:53419305 original size:27 final size:27
Alignment explanation
Indices: 53419275--53419331 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
53419265 TATGGCCGAA
53419275 CATAGACATAGCAAATCAGCTCCCATT
1 CATAGACATAGCAAATCAGCTCCCATT
53419302 CATAGACATAGCAAATCAGCTCCCATT
1 CATAGACATAGCAAATCAGCTCCCATT
53419329 CAT
1 CAT
53419332 TCTAATTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.23
Consensus pattern (27 bp):
CATAGACATAGCAAATCAGCTCCCATT
Found at i:53422855 original size:30 final size:30
Alignment explanation
Indices: 53422821--53422905 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
53422811 TAAACTAAAA
* *
53422821 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCATGAGCTAAAGC
* * * * *
53422851 TGAGCTGAGATTAAACTCCTAAGCTAAAGC
1 TGAGCTAAGATTTAGCTCATGAGCTAAAGC
* *
53422881 TGAGCTAAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCATGAGCT
53422906 GAATATGAGC
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCATGAGCTAAAGC
Found at i:53425220 original size:30 final size:30
Alignment explanation
Indices: 53425149--53425231 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
53425139 CTTTTGTTTC
* *
53425149 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
53425180 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
53425209 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
53425232 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:53425231 original size:18 final size:18
Alignment explanation
Indices: 53425182--53425237 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
53425172 CACTCTCAAA
* *
53425182 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
53425199 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
53425217 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
53425236 TT
1 TT
53425238 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:53425238 original size:12 final size:12
Alignment explanation
Indices: 53425207--53425231 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53425197 TTTTTCAATC
53425207 TCATTTTCTTTT
1 TCATTTTCTTTT
53425219 TCATTTTCTTTT
1 TCATTTTCTTTT
53425231 T
1 T
53425232 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:53425310 original size:5 final size:5
Alignment explanation
Indices: 53425300--53425362 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
53425290 CTCTTGCCTC
*
53425300 TCTTT TCTTT T-TATT TCATTT TCTTTT TCTTT T-TCT TCTTT TGCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT T-C-TTT
53425348 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
53425363 ATTTTCTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
4 4 0.08
5 29 0.59
6 11 0.22
7 5 0.10
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:53425322 original size:6 final size:6
Alignment explanation
Indices: 53425313--53425362 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
53425303 TTTCTTTTTA
*
53425313 TTTCAT TTTCTT TTTCTT TTTCTTCT TTTGCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTC-T-T TTT-CTT TTTCTT TTTCTT TTTCTT
53425362 T
1 T
53425363 ATTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 18 0.46
7 5 0.13
8 5 0.13
9 1 0.03
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:53425346 original size:21 final size:20
Alignment explanation
Indices: 53425302--53425362 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 20
53425292 CTTGCCTCTC
53425302 TTTTCTTTTTATTTCATTTTCT
1 TTTTCTTTTT-TTTC-TTTTCT
*
53425324 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTTTTCTTTT-CT
53425345 TTTTCTTTTCTTTTCTTT
1 TTTTCTTTT-TTTTCTTT
53425363 ATTTTCTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 17 0.49
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTCTTTTTTTTCTTTTCT
Found at i:53426596 original size:11 final size:10
Alignment explanation
Indices: 53426571--53426631 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
53426561 ACCAATAAAA
53426571 TAAA-TGAGC
1 TAAATTGAGC
*
53426580 TGAATTGTAGC
1 TAAATTG-AGC
53426591 TAAATTGAGC
1 TAAATTGAGC
**
53426601 TCGATTGAGC
1 TAAATTGAGC
53426611 TGAAA-TGAGC
1 T-AAATTGAGC
*
53426621 TCAATTGAGC
1 TAAATTGAGC
53426631 T
1 T
53426632 GGTCAGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:53426632 original size:20 final size:20
Alignment explanation
Indices: 53426572--53426632 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
53426562 CCAATAAAAT
*
53426572 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
53426592 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
53426613 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
53426633 GTCAGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:53427162 original size:10 final size:11
Alignment explanation
Indices: 53427139--53427167 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
53427129 TATTAATATG
53427139 TTTT-ATGCAT
1 TTTTAATGCAT
53427149 TTTTAATGCAT
1 TTTTAATGCAT
53427160 TTTTAATG
1 TTTTAATG
53427168 AGTCAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.59
Consensus pattern (11 bp):
TTTTAATGCAT
Found at i:53427796 original size:22 final size:22
Alignment explanation
Indices: 53427768--53427811 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53427758 TTTTGAACCA
53427768 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
53427790 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
53427812 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:53430364 original size:24 final size:25
Alignment explanation
Indices: 53430331--53430383 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
53430321 AAATGAGAGA
*
53430331 AAAAGAAAAAACGAAAATACAAAAG
1 AAAAGAAAAAACGAAAAAACAAAAG
* *
53430356 AAAAG-AAAAATGAAAAAAGAAAAG
1 AAAAGAAAAAACGAAAAAACAAAAG
53430380 AAAA
1 AAAA
53430384 TTCAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (25 bp):
AAAAGAAAAAACGAAAAAACAAAAG
Found at i:53430390 original size:18 final size:18
Alignment explanation
Indices: 53430338--53430391 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
53430328 AGAAAAAGAA
53430338 AAAACGAAAATAC-AAAAG
1 AAAA-GAAAATACAAAAAG
53430356 AAAAGAAAAATGA-AAAAAG
1 AAAAG-AAAAT-ACAAAAAG
*
53430375 AAAAGAAAATTCAAAAA
1 AAAAGAAAATACAAAAA
53430392 AAGAGAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 1 0.03
18 19 0.61
19 11 0.35
ACGTcount: A:0.76, C:0.06, G:0.11, T:0.07
Consensus pattern (18 bp):
AAAAGAAAATACAAAAAG
Found at i:53430390 original size:19 final size:19
Alignment explanation
Indices: 53430351--53430392 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
53430341 ACGAAAATAC
*
53430351 AAAAGAAAAGAAAAATGAA
1 AAAAGAAAAGAAAAATCAA
*
53430370 AAAAGAAAAGAAAATTCAA
1 AAAAGAAAAGAAAAATCAA
53430389 AAAA
1 AAAA
53430393 AGAGAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAAGAAAAGAAAAATCAA
Found at i:53434743 original size:20 final size:19
Alignment explanation
Indices: 53434720--53434784 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
53434710 AAGCTCAAAC
53434720 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
53434740 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
53434760 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
53434780 GAGCT
1 GAGCT
53434785 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:53436697 original size:18 final size:18
Alignment explanation
Indices: 53436676--53436732 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
53436666 TTTTCTCTCA
53436676 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
53436694 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
53436712 CTTTTT-G-TTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
53436728 GTTTT
1 CTTTT
53436733 CTTTCAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 13 0.38
18 21 0.62
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.74
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:53436733 original size:11 final size:11
Alignment explanation
Indices: 53436708--53436736 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
53436698 TGCAATTTCT
53436708 TTTTCTTTTTG
1 TTTTCTTTTTG
53436719 -TTTCTTTTTG
1 TTTTCTTTTTG
53436729 TTTTCTTT
1 TTTTCTTT
53436737 CAATTTCTTT
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:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:53437774 original size:14 final size:13
Alignment explanation
Indices: 53437756--53437802 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
53437746 TTTTAAACTG
53437756 ATTTTTTTTGCTC
1 ATTTTTTTTGCTC
53437769 ACTTTTTTTT-CT-
1 A-TTTTTTTTGCTC
*
53437781 TTTTTTTTTGCTC
1 ATTTTTTTTGCTC
53437794 GATTTTTTT
1 -ATTTTTTT
53437803 CACTTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
11 8 0.29
12 2 0.07
13 3 0.11
14 15 0.54
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.74
Consensus pattern (13 bp):
ATTTTTTTTGCTC
Found at i:53437809 original size:24 final size:24
Alignment explanation
Indices: 53437757--53437810 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
53437747 TTTAAACTGA
**
53437757 TTTTTTTTGCTCACTTTTTTTTCTT
1 TTTTTTTTGCTCAC-TTTTTTTCAC
53437782 TTTTTTTTGCTCGA-TTTTTTTCAC
1 TTTTTTTTGCTC-ACTTTTTTTCAC
53437806 TTTTT
1 TTTTT
53437811 GAATTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 13 0.50
25 12 0.46
26 1 0.04
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (24 bp):
TTTTTTTTGCTCACTTTTTTTCAC
Found at i:53437809 original size:25 final size:24
Alignment explanation
Indices: 53437757--53437810 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
53437747 TTTAAACTGA
*
53437757 TTTTTTTTGCTCACTTTTTTTTCTT
1 TTTTTTTTGCTCAC-TTTTTTTCCT
53437782 TTTTTTTTGCTCGA-TTTTTTTCACT
1 TTTTTTTTGCTC-ACTTTTTTTC-CT
53437807 TTTT
1 TTTT
53437811 GAATTTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 8 0.31
25 17 0.65
26 1 0.04
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (24 bp):
TTTTTTTTGCTCACTTTTTTTCCT
Found at i:53437842 original size:11 final size:11
Alignment explanation
Indices: 53437826--53437855 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
53437816 TTTTCAATCA
53437826 AATTTTTTTTG
1 AATTTTTTTTG
53437837 AATTTTTTTTG
1 AATTTTTTTTG
53437848 -ATTTTTTT
1 AATTTTTTT
53437856 GTTACTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:53438765 original size:15 final size:15
Alignment explanation
Indices: 53438734--53438812 Score: 69
Period size: 15 Copynumber: 5.4 Consensus size: 15
53438724 AAAAATAGCA
53438734 AAAAAG-AAG-AATG
1 AAAAAGAAAGAAATG
*
53438747 AAAAAGAAAGAAATT
1 AAAAAGAAAGAAATG
53438762 AAAAAGAAAG-AATGG
1 AAAAAGAAAGAAAT-G
* *
53438777 AAAGAGAATAGAAAAAG
1 AAAAAGAA-AG-AAATG
53438794 AAAAAG-AA-AAATG
1 AAAAAGAAAGAAATG
53438807 AAAAAG
1 AAAAAG
53438813 TTGAAGTGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
13 16 0.30
14 6 0.11
15 21 0.39
16 3 0.06
17 6 0.11
18 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (15 bp):
AAAAAGAAAGAAATG
Found at i:53438812 original size:13 final size:13
Alignment explanation
Indices: 53438734--53438811 Score: 54
Period size: 13 Copynumber: 5.8 Consensus size: 13
53438724 AAAAATAGCA
*
53438734 AAAAAGAAGAATG
1 AAAAAGAAAAATG
*
53438747 AAAAAGAAAGAAATT
1 AAAAAG-AA-AAATG
53438762 AAAAAGAAAGAATG
1 AAAAAGAAA-AATG
* *
53438776 -GAAAG-AGAATAG
1 AAAAAGAAAAAT-G
53438788 AAAAAGAAAAA-G
1 AAAAAGAAAAATG
53438800 AAAAATGAAAAA
1 AAAAA-GAAAAA
53438812 GTTGAAGTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
11 3 0.06
12 8 0.16
13 21 0.41
14 10 0.20
15 9 0.18
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (13 bp):
AAAAAGAAAAATG
Found at i:53443126 original size:20 final size:19
Alignment explanation
Indices: 53443103--53443167 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
53443093 AAGCTCAAAC
53443103 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
53443123 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
53443143 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
53443163 GAGCT
1 GAGCT
53443168 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:53444981 original size:33 final size:33
Alignment explanation
Indices: 53444943--53445005 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
53444933 GATTACTCAC
53444943 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
53444976 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
53445006 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:53445032 original size:21 final size:21
Alignment explanation
Indices: 53445003--53445058 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
53444993 CAAGCTCTCT
*
53445003 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
53445024 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
53445045 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
53445059 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:53445051 original size:14 final size:14
Alignment explanation
Indices: 53445002--53445058 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
53444992 TCAAGCTCTC
53445002 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
53445015 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
53445029 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
53445043 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
53445057 TT
1 TT
53445059 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:53445086 original size:17 final size:17
Alignment explanation
Indices: 53445066--53445136 Score: 63
Period size: 17 Copynumber: 4.0 Consensus size: 17
53445056 TTTCTCTCAC
*
53445066 TTTTTCGATTTCTTTTT
1 TTTTTCAATTTCTTTTT
*
53445083 TTTTGCAATTTCTTTTT
1 TTTTTCAATTTCTTTTT
**
53445100 CTTTTT-GTTTTCTTTTGTT
1 -TTTTTCAATTTC-TTT-TT
53445119 TTCTTTCAATTTCTTTTT
1 TT-TTTCAATTTCTTTTT
53445137 CAATCTCTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
17 19 0.45
18 11 0.26
19 8 0.19
20 4 0.10
ACGTcount: A:0.07, C:0.13, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTTCAATTTCTTTTT
Found at i:53445112 original size:11 final size:11
Alignment explanation
Indices: 53445096--53445124 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
53445086 TGCAATTTCT
53445096 TTTTCTTTTTG
1 TTTTCTTTTTG
53445107 TTTTC-TTTTG
1 TTTTCTTTTTG
53445117 TTTTCTTT
1 TTTTCTTT
53445125 CAATTTCTTT
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:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:53445137 original size:6 final size:6
Alignment explanation
Indices: 53445020--53445115 Score: 52
Period size: 6 Copynumber: 15.8 Consensus size: 6
53445010 TCTTTTTTCG
* * * **
53445020 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
53445071 CGATTT CTTTTT -TTTTG CAATTT CTTTTT CTTTTT -GTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
53445116 GTTTTCTTTC
Statistics
Matches: 63, Mismatches: 23, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
5 8 0.13
6 43 0.68
7 9 0.14
8 3 0.05
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:53446213 original size:11 final size:11
Alignment explanation
Indices: 53446198--53446232 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
53446188 TTTTTGCTCG
53446198 ATTTTTTTTCA
1 ATTTTTTTTCA
* *
53446209 CTTTTTTTTGA
1 ATTTTTTTTCA
53446220 ATTTTTTTTCA
1 ATTTTTTTTCA
53446231 AT
1 AT
53446233 CAAATTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:53448355 original size:18 final size:18
Alignment explanation
Indices: 53448334--53448368 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53448324 TTTTTCTTTT
53448334 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
53448352 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
53448369 TTTCTTTTCT
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:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:53450665 original size:11 final size:10
Alignment explanation
Indices: 53450640--53450700 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
53450630 ACCAATAAAA
53450640 TAAA-TGAGC
1 TAAATTGAGC
*
53450649 TGAATTGTAGC
1 TAAATTG-AGC
53450660 TAAATTGAGC
1 TAAATTGAGC
**
53450670 TCGATTGAGC
1 TAAATTGAGC
53450680 TGAAA-TGAGC
1 T-AAATTGAGC
*
53450690 TCAATTGAGC
1 TAAATTGAGC
53450700 T
1 T
53450701 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:53450701 original size:20 final size:20
Alignment explanation
Indices: 53450641--53450701 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
53450631 CCAATAAAAT
*
53450641 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
53450661 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
53450682 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
53450702 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:53451846 original size:14 final size:12
Alignment explanation
Indices: 53451827--53451897 Score: 90
Period size: 13 Copynumber: 5.6 Consensus size: 12
53451817 GCACAAATCT
53451827 TTTTTTTTTGAAA
1 TTTTTTTTTG-AA
53451840 CTTTTTTTTTGAA
1 -TTTTTTTTTGAA
53451853 TTTTTTTTTCGAA
1 TTTTTTTTT-GAA
53451866 TTTTTTTTTCCGAA
1 TTTTTTTTT--GAA
53451880 -TTTTTTTTGAA
1 TTTTTTTTTGAA
53451891 TTTTTTT
1 TTTTTTT
53451898 ATACTTGTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.06
12 15 0.28
13 22 0.41
14 14 0.26
ACGTcount: A:0.15, C:0.06, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:53454258 original size:20 final size:20
Alignment explanation
Indices: 53454235--53454281 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
53454225 GGGTTAAGAT
* *
53454235 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTAAGCTCGAG
* *
53454255 TGAGTTGACTTAAGCTCGAG
1 TGAGCTGAATTAAGCTCGAG
53454275 TGAGCTG
1 TGAGCTG
53454282 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTAAGCTCGAG
Found at i:53456000 original size:48 final size:48
Alignment explanation
Indices: 53455948--53456053 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
53455938 TTGTCTTTTC
* *
53455948 TTTCTTTTTTAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
53455996 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
53456044 TTTCTTTTTC
1 TTTCTTTTTC
53456054 CATGACACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
48 39 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:53456146 original size:21 final size:21
Alignment explanation
Indices: 53456117--53456172 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
53456107 CAAGCTCTCT
*
53456117 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
53456138 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
53456159 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
53456173 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:53456165 original size:14 final size:14
Alignment explanation
Indices: 53456116--53456172 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
53456106 TCAAGCTCTC
53456116 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
53456129 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
53456143 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
53456157 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
53456171 TT
1 TT
53456173 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:53456200 original size:18 final size:18
Alignment explanation
Indices: 53456179--53456237 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
53456169 TTTTCTCTCA
53456179 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
53456197 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
53456215 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
53456233 GTTTT
1 CTTTT
53456238 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:53456254 original size:6 final size:6
Alignment explanation
Indices: 53456134--53456241 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
53456124 TCTTTTTTCG
* * * **
53456134 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
53456185 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
53456233 -GTTTT CTTT
1 CTTTTT CTTT
53456242 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:53457335 original size:12 final size:12
Alignment explanation
Indices: 53457320--53457344 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53457310 TTTGTTTTGA
53457320 TTTTTTTGAATT
1 TTTTTTTGAATT
53457332 TTTTTTTGAATT
1 TTTTTTTGAATT
53457344 T
1 T
53457345 ATTCTCTCTT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:53457436 original size:11 final size:11
Alignment explanation
Indices: 53457422--53457450 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
53457412 TCCAACTCAA
53457422 TTTTTTTTGA-
1 TTTTTTTTGAC
53457432 TTTTTTTTGAC
1 TTTTTTTTGAC
53457443 TTTTTTTT
1 TTTTTTTT
53457451 TACATTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:53458890 original size:24 final size:23
Alignment explanation
Indices: 53458836--53458891 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
53458826 GATTAATTAA
**
53458836 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
53458859 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
53458883 GAAATGGTA
1 GAAATGGTA
53458892 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:53462733 original size:30 final size:28
Alignment explanation
Indices: 53462699--53462755 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
53462689 AGTCGAAAAA
* *
53462699 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
53462729 GAAAAAGAGAGTGAGCAAAAAGAAAGT
1 GAAAAAGAGAGTGAGCAAAAAGAAAGT
53462756 GTGGAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 4 0.16
30 16 0.64
ACGTcount: A:0.53, C:0.04, G:0.30, T:0.14
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:53466024 original size:29 final size:29
Alignment explanation
Indices: 53465991--53466050 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
53465981 ATAACCAAAC
*
53465991 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
53466020 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
53466049 CT
1 CT
53466051 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:53466043 original size:15 final size:15
Alignment explanation
Indices: 53465997--53466044 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53465987 AAACCTACAA
*
53465997 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
53466012 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
53466026 AAACTTCATATCCAT
1 AAACTTCATATCCAT
53466041 AAAC
1 AAAC
53466045 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:53469494 original size:18 final size:17
Alignment explanation
Indices: 53469441--53469495 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
53469431 TGAATAAATT
53469441 ACTCATCTTAGTTAATTGA
1 ACTCATCTTAGTTAA-T-A
**
53469460 GTTCATCTTAGTTAATA
1 ACTCATCTTAGTTAATA
53469477 ACTCATCTTAGATTAATA
1 ACTCATCTTAG-TTAATA
53469495 A
1 A
53469496 ATGAGTTGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 10 0.32
18 8 0.26
19 13 0.42
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.42
Consensus pattern (17 bp):
ACTCATCTTAGTTAATA
Found at i:53474074 original size:9 final size:9
Alignment explanation
Indices: 53474060--53474094 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
53474050 GTAAGTTTTA
53474060 AAAAAAACG
1 AAAAAAACG
53474069 AAAAAAACG
1 AAAAAAACG
53474078 AAAAAAAACG
1 -AAAAAAACG
53474088 AAAAAAA
1 AAAAAAA
53474095 ATTCAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAACG
Found at i:53474074 original size:10 final size:10
Alignment explanation
Indices: 53474059--53474095 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
53474049 AGTAAGTTTT
53474059 AAAAAAAACG
1 AAAAAAAACG
53474069 -AAAAAAACG
1 AAAAAAAACG
53474078 AAAAAAAACG
1 AAAAAAAACG
53474088 AAAAAAAA
1 AAAAAAAA
53474096 TTCAAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAACG
Found at i:53475201 original size:30 final size:28
Alignment explanation
Indices: 53475165--53475220 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
53475155 AAGCGAAAAA
* *
53475165 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
53475195 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
53475221 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:53478760 original size:18 final size:18
Alignment explanation
Indices: 53478739--53478788 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
53478729 AAACTCTTTT
53478739 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
53478757 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
53478775 TCAATCTCATTTTT
1 TCATTCTC-TTTTT
53478789 TTTTCTTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:53478853 original size:42 final size:42
Alignment explanation
Indices: 53478791--53478887 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
53478781 TCATTTTTTT
* * *
53478791 TTCTTTCA-TTTCTTTATTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTATTTCTTCTCTCGATTTCATTCAAAA
*
53478832 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTATTTCTTCTCTCGATTTCATTCAAAA
*
53478874 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
53478888 CTCATAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.15, C:0.24, G:0.04, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTATTTCTTCTCTCGATTTCATTCAAAA
Found at i:53481315 original size:10 final size:10
Alignment explanation
Indices: 53481302--53481336 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
53481292 AAGCTCGGTT
53481302 GAGCTCAAAC
1 GAGCTCAAAC
*
53481312 GAGCTAAAAC
1 GAGCTCAAAC
*
53481322 GAGCTCAAAT
1 GAGCTCAAAC
53481332 GAGCT
1 GAGCT
53481337 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:53481345 original size:20 final size:20
Alignment explanation
Indices: 53481299--53481346 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
53481289 AGTAAGCTCG
53481299 GTTGAGCTCAAACGAGCTAA
1 GTTGAGCTCAAACGAGCTAA
*** * *
53481319 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTAA
53481339 GTTGAGCT
1 GTTGAGCT
53481347 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTAA
Found at i:53489099 original size:23 final size:22
Alignment explanation
Indices: 53489047--53489099 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53489037 TCCACGTCTT
*
53489047 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53489069 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53489092 TTTCTTTT
1 TTTCTTTT
53489100 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53493999 original size:20 final size:20
Alignment explanation
Indices: 53493976--53494022 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
53493966 GGGTTAAGAT
*
53493976 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
53493996 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
53494016 TGAGCTG
1 TGAGCTG
53494023 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:53495353 original size:20 final size:20
Alignment explanation
Indices: 53495328--53495382 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
53495318 TGTGGTTCAA
*
53495328 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
53495348 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
53495368 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
53495383 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:53497195 original size:14 final size:13
Alignment explanation
Indices: 53497178--53497227 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
53497168 AAAAAAAAGG
53497178 AAAAAAAATTCAA
1 AAAAAAAATTCAA
53497191 AAAAAAAATTCAA
1 AAAAAAAATTCAA
53497204 AAAAAAAATTCAA
1 AAAAAAAATTCAA
53497217 AAAAAATAATT
1 AAAAAA-AATT
53497228 TTGTATTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 32 0.89
14 4 0.11
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:53497314 original size:17 final size:17
Alignment explanation
Indices: 53497278--53497315 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
53497268 TCAGTATTGG
*
53497278 AAAAAAAAGAGAAATTA
1 AAAAAAAAGAGAAATAA
53497295 AAAAAAAAGAAGAAA-AA
1 AAAAAAAAG-AGAAATAA
53497312 AAAA
1 AAAA
53497316 TGTTTCGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAAAAAAGAGAAATAA
Found at i:53498248 original size:17 final size:15
Alignment explanation
Indices: 53498228--53498266 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
53498218 GCGAGCGAGA
53498228 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
53498245 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
53498260 AAGATGA
1 AA-ATGA
53498267 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:53499603 original size:21 final size:21
Alignment explanation
Indices: 53499577--53499639 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
53499567 TTGGTATTTG
53499577 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
53499598 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
53499619 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
53499640 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:53501412 original size:20 final size:20
Alignment explanation
Indices: 53501387--53501441 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
53501377 TGTGGTTCAA
*
53501387 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
53501407 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
53501427 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
53501442 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:53512046 original size:18 final size:19
Alignment explanation
Indices: 53512023--53512061 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
53512013 TTTATCTCAA
*
53512023 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
53512041 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
53512060 TT
1 TT
53512062 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:53512076 original size:18 final size:18
Alignment explanation
Indices: 53512055--53512117 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
53512045 TTGTTCACAT
*
53512055 TCTTTTTCTCTCTCAAAC
1 TCTTTTTCTCTCTCAATC
** *
53512073 TCTTTTTCAT-TCTCTTTT
1 TCTTTTTC-TCTCTCAATC
*
53512091 TCTTTTTCACTCTCAATC
1 TCTTTTTCTCTCTCAATC
53512109 TCTTTTTCT
1 TCTTTTTCT
53512118 TTTTCTTTCA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
18 33 0.97
19 1 0.03
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTTTTCTCTCTCAATC
Found at i:53512079 original size:36 final size:35
Alignment explanation
Indices: 53512034--53512118 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
53512024 TTCTTTTTCC
* *
53512034 ACTCTTTTTTCTTGTTCACATTCTTTTTCTCTCTCAA
1 ACTC-TTTTTCTT-CTCACATTCTTTTTCACTCTCAA
***
53512071 ACTCTTTTTCATTCTCTTTTTCTTTTTCACTCTCAA
1 ACTCTTTTTC-TTCTCACATTCTTTTTCACTCTCAA
*
53512107 TCTCTTTTTCTT
1 ACTCTTTTTCTT
53512119 TTTCTTTCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 2 0.05
36 33 0.80
37 6 0.15
ACGTcount: A:0.12, C:0.27, G:0.01, T:0.60
Consensus pattern (35 bp):
ACTCTTTTTCTTCTCACATTCTTTTTCACTCTCAA
Found at i:53512125 original size:36 final size:36
Alignment explanation
Indices: 53512054--53512125 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
53512044 CTTGTTCACA
*
53512054 TTCTTTTTCTCTCTCAAACTCTTTTTCATTCTCTTT
1 TTCTTTTTCACTCTCAAACTCTTTTTCATTCTCTTT
* * *
53512090 TTCTTTTTCACTCTCAATCTCTTTTTCTTTTTCTTT
1 TTCTTTTTCACTCTCAAACTCTTTTTCATTCTCTTT
53512126 CATTTCTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (36 bp):
TTCTTTTTCACTCTCAAACTCTTTTTCATTCTCTTT
Found at i:53512151 original size:21 final size:21
Alignment explanation
Indices: 53512127--53512194 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
53512117 TTTTTCTTTC
*
53512127 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* ****
53512148 ATTTCATTGAAGATTCTCTC-
1 ATTTCTTTGTTTCTTCTCTCG
53512168 ATTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTTCTCTCG
53512190 ATTTC
1 ATTTC
53512195 ATTCAAAATC
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.12, C:0.21, G:0.09, T:0.59
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:53512175 original size:42 final size:42
Alignment explanation
Indices: 53512120--53512216 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
53512110 CTTTTTCTTT
* * * *
53512120 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTGAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
53512161 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
53512203 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
53512217 CTCATAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.14, C:0.23, G:0.06, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:53513263 original size:18 final size:17
Alignment explanation
Indices: 53513230--53513263 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53513220 ACAACTTGAA
*
53513230 TTTTTTTTAATTCGAAT
1 TTTTTTTTAATACGAAT
53513247 TTTTTTTTAACTACGAA
1 TTTTTTTTAA-TACGAA
53513264 CCTATTTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTTTTTTAATACGAAT
Found at i:53514367 original size:19 final size:19
Alignment explanation
Indices: 53514322--53514367 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
53514312 ATTAACACAC
*
53514322 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
53514341 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
53514359 AATTAATAA
1 AATTAATAA
53514368 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:53514625 original size:20 final size:21
Alignment explanation
Indices: 53514578--53514626 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
53514568 AGTAAGCTTG
53514578 GTTGAGCTCAAAACGAGCTGA
1 GTTGAGCTCAAAACGAGCTGA
*** *
53514599 AACGAGCTC-AAATGAGCTGA
1 GTTGAGCTCAAAACGAGCTGA
53514619 GTTGAGCT
1 GTTGAGCT
53514627 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 1
0.72 0.24 0.03
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (21 bp):
GTTGAGCTCAAAACGAGCTGA
Found at i:53515934 original size:28 final size:28
Alignment explanation
Indices: 53515891--53515979 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 28
53515881 GGAGGAAGCG
53515891 TTCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTGGTGGCTCTGCCACAAATATCTGT
*
53515919 TTCTGGTGGC-CTTGCCACAATTATCTGT
1 TTCTGGTGGCTC-TGCCACAAATATCTGT
* *
53515947 ATT-TGGTGACTCTGTCAC-AATATCTG-
1 -TTCTGGTGGCTCTGCCACAAATATCTGT
53515973 TTCTGGT
1 TTCTGGT
53515980 AGCCATGCTA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.04
26 4 0.08
27 8 0.15
28 36 0.68
29 3 0.06
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.39
Consensus pattern (28 bp):
TTCTGGTGGCTCTGCCACAAATATCTGT
Found at i:53516252 original size:14 final size:14
Alignment explanation
Indices: 53516212--53516255 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
53516202 AAGGATTCAA
53516212 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
53516226 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
53516241 AGATGGGTTTATGG
1 AGATGGGTTTATGG
53516255 A
1 A
53516256 TATAAAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:53516270 original size:29 final size:29
Alignment explanation
Indices: 53516212--53516271 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
53516202 AAGGATTCAA
* *
53516212 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAATTTATGT
*
53516241 AGATGGGTTTATGGATATAAAATTTTTGT
1 AGATGGGTTTATGGATATAAAATTTATGT
53516270 AG
1 AG
53516272 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAATTTATGT
Found at i:53519857 original size:22 final size:22
Alignment explanation
Indices: 53519829--53519875 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
53519819 CCTTTTTGAA
53519829 CCCTTACCATTTCGTACCAAAT
1 CCCTTACCATTTCGTACCAAAT
* *
53519851 CCCTTACCATTTTGTACCAATT
1 CCCTTACCATTTCGTACCAAAT
53519873 CCC
1 CCC
53519876 AAATACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.38, G:0.04, T:0.34
Consensus pattern (22 bp):
CCCTTACCATTTCGTACCAAAT
Found at i:53523639 original size:23 final size:22
Alignment explanation
Indices: 53523587--53523639 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53523577 TCCACGTCTT
*
53523587 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53523609 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53523632 TTTCTTTT
1 TTTCTTTT
53523640 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53534957 original size:12 final size:12
Alignment explanation
Indices: 53534942--53534973 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
53534932 ATTTTGTTTG
53534942 TTTTTTTTTCAA
1 TTTTTTTTTCAA
53534954 TTTTTTTTTCAA
1 TTTTTTTTTCAA
53534966 TTTTTTTT
1 TTTTTTTT
53534974 GAAACTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:53535214 original size:15 final size:15
Alignment explanation
Indices: 53535194--53535241 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53535184 TCAAAGATGG
53535194 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
53535209 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
53535223 GTTTATGGATATAAA
1 GTTTATGGATATGAA
53535238 GTTT
1 GTTT
53535242 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:53535228 original size:14 final size:14
Alignment explanation
Indices: 53535188--53535231 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
53535178 AAGGATTCAA
53535188 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
53535202 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
53535217 AGATGGGTTTATGG
1 AGATGGGTTTATGG
53535231 A
1 A
53535232 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:53535257 original size:29 final size:29
Alignment explanation
Indices: 53535188--53535247 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
53535178 AAGGATTCAA
*
53535188 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
53535217 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
53535246 AG
1 AG
53535248 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:53538753 original size:6 final size:6
Alignment explanation
Indices: 53538728--53538802 Score: 60
Period size: 6 Copynumber: 11.8 Consensus size: 6
53538718 AGTGTGAAAG
** **
53538728 AAAGCAA AAAGAGA ATAAGAA AAAGAA AAATGAA ATTGAA AAAGAA AGTGAA
1 AAAG-AA AAAGA-A A-AAGAA AAAGAA AAA-GAA AAAGAA AAAGAA AAAGAA
* *
53538780 AAAGAA AAAGAG AAGGAA AAAGA
1 AAAGAA AAAGAA AAAGAA AAAGA
53538803 GATCGAGATC
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
6 37 0.70
7 12 0.23
8 4 0.08
ACGTcount: A:0.71, C:0.01, G:0.21, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:53538858 original size:30 final size:32
Alignment explanation
Indices: 53538824--53538884 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
53538814 AGATCGAGAG
53538824 TGAAAAAGA-ATGTGAG-AAGAA-AAAGAAAAT
1 TGAAAAAGAGA-GTGAGTAAGAAGAAAGAAAAT
*
53538854 TGAAAAAGAGAGTGAGTATGAAGAAAGAAAA
1 TGAAAAAGAGAGTGAGTAAGAAGAAAGAAAA
53538885 GATATTGATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 14 0.52
31 5 0.19
32 8 0.30
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (32 bp):
TGAAAAAGAGAGTGAGTAAGAAGAAAGAAAAT
Found at i:53540912 original size:21 final size:20
Alignment explanation
Indices: 53540888--53540927 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
53540878 AGCTCACTTG
*
53540888 AGCTCGTTTGAGCTTGATTTT
1 AGCTCGTTTCAGC-TGATTTT
53540909 AGCTCGTTTCAGCTGATTT
1 AGCTCGTTTCAGCTGATTT
53540928 CTTTTCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
AGCTCGTTTCAGCTGATTTT
Found at i:53542819 original size:20 final size:20
Alignment explanation
Indices: 53542794--53542848 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
53542784 TGTGGTTCAA
*
53542794 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
53542814 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
53542834 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
53542849 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:53547967 original size:13 final size:13
Alignment explanation
Indices: 53547949--53547979 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
53547939 GGTTGATATA
53547949 AACTCTGATAAAG
1 AACTCTGATAAAG
53547962 AACTCTGATAAAG
1 AACTCTGATAAAG
53547975 AACTC
1 AACTC
53547980 ACAAGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (13 bp):
AACTCTGATAAAG
Found at i:53559042 original size:23 final size:22
Alignment explanation
Indices: 53558990--53559042 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
53558980 TCCACGTCTT
*
53558990 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53559012 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53559035 TTTCTTTT
1 TTTCTTTT
53559043 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:53562812 original size:10 final size:10
Alignment explanation
Indices: 53562799--53562844 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
53562789 AGCTTACTTG
53562799 AGCTCGTTTT
1 AGCTCGTTTT
*
53562809 AGCTCGTTTG
1 AGCTCGTTTT
*
53562819 AGCTCGAATTT
1 AGCTCG-TTTT
*
53562830 AGCTCGTTTC
1 AGCTCGTTTT
53562840 AGCTC
1 AGCTC
53562845 ATTACTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:53562832 original size:21 final size:20
Alignment explanation
Indices: 53562796--53562844 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
53562786 ATCAGCTTAC
*
53562796 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
53562816 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
53562837 TTCAGCTC
1 TTGAGCTC
53562845 ATTACTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:53566684 original size:30 final size:30
Alignment explanation
Indices: 53566638--53566698 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53566628 AATTCCGAGC
*
53566638 TAGGAGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGAGAAAAAGTGTAAATATGCAAAAGTT
* * * *
53566668 TAGGAGAAAAATTGTAATTTTGCCAAAGTT
1 TAGGAGAAAAAGTGTAAATATGCAAAAGTT
53566698 T
1 T
53566699 GAGTTAAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.30
Consensus pattern (30 bp):
TAGGAGAAAAAGTGTAAATATGCAAAAGTT
Found at i:53569509 original size:14 final size:14
Alignment explanation
Indices: 53569492--53569531 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
53569482 CGAATGGAAT
*
53569492 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
53569506 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
53569520 GATATGAACAAA
1 GGTAGGAACAAA
53569532 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:53572235 original size:29 final size:30
Alignment explanation
Indices: 53572188--53572248 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
53572178 AAGGATTCAA
* *
53572188 AGATGGGTTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTTATGAATATAAAGTTTATGT
*
53572218 AGATGGG-TTTATGAATATAAAGTTTTTGT
1 AGATGGGTTTTATGAATATAAAGTTTATGT
53572247 AG
1 AG
53572249 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.43
Consensus pattern (30 bp):
AGATGGGTTTTATGAATATAAAGTTTATGT
Found at i:53581083 original size:20 final size:20
Alignment explanation
Indices: 53581058--53581112 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
53581048 TGTGGTTCAA
*
53581058 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
53581078 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
53581098 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
53581113 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:53588047 original size:25 final size:25
Alignment explanation
Indices: 53588002--53588049 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
53587992 ACAACTTCTA
* *
53588002 AAGAAAACTCAAGAGAGAATTCTTG
1 AAGAAAACCCAAGAGAAAATTCTTG
53588027 AAGAAAACCCCAA-AGAAAATTCT
1 AAGAAAA-CCCAAGAGAAAATTCT
53588050 GCACTCAACA
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:0.52, C:0.17, G:0.15, T:0.17
Consensus pattern (25 bp):
AAGAAAACCCAAGAGAAAATTCTTG
Found at i:53589736 original size:23 final size:22
Alignment explanation
Indices: 53589685--53589736 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
53589675 CCTCGTCTTT
*
53589685 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
53589707 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
53589730 TTCTTTT
1 TTCTTTT
53589737 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:53595006 original size:19 final size:19
Alignment explanation
Indices: 53594969--53595006 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
53594959 ACCTGATAGA
*
53594969 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
53594988 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
53595007 TAAATTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:53597900 original size:49 final size:49
Alignment explanation
Indices: 53597841--53598065 Score: 288
Period size: 49 Copynumber: 4.5 Consensus size: 49
53597831 CTGGTACGCA
* * * *
53597841 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
53597890 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
*** * *
53597939 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCCTCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * ** * *
53597989 TAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTTGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCGGTACACG
53598040 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
53598066 TGCGACCTCG
Statistics
Matches: 155, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
49 78 0.50
50 42 0.27
51 34 0.22
52 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Done.