Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 84 of 444
Found at i:19819172 original size:19 final size:21
Alignment explanation
Indices: 19819131--19819178 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
19819121 TTAAAATTTT
19819131 AACTAAAAATATTAAAATAAA
1 AACTAAAAATATTAAAATAAA
* *
19819152 AA-TAAAAAT-TTAGAATCAA
1 AACTAAAAATATTAAAATAAA
19819171 AACTAAAA
1 AACTAAAA
19819179 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (21 bp):
AACTAAAAATATTAAAATAAA
Found at i:19822231 original size:40 final size:40
Alignment explanation
Indices: 19822150--19822235 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 40
19822140 CTAAGTGAAA
* * *
19822150 TAATTTTTTACGGCGTTTTTATAAAAAATGCCGTTATAAT
1 TAATTTTTTACGGCGTTTTTATAAAAAATGCCATAAAAAT
** *
19822190 TAATTTTTTATTGCGTTTTTATAAAAAA-GCTATAAAAAAT
1 TAATTTTTTACGGCGTTTTTATAAAAAATGCCAT-AAAAAT
19822230 T-ATTTT
1 TAATTTT
19822236 ATTTTAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
39 8 0.21
40 31 0.79
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (40 bp):
TAATTTTTTACGGCGTTTTTATAAAAAATGCCATAAAAAT
Found at i:19822329 original size:14 final size:14
Alignment explanation
Indices: 19822310--19822359 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
19822300 AGTTAAGTGA
19822310 TTTTATAAAATATT
1 TTTTATAAAATATT
* *
19822324 TTTTAT-TACTATT
1 TTTTATAAAATATT
* *
19822337 TTTTATAAATTAGT
1 TTTTATAAAATATT
19822351 TTTTATAAA
1 TTTTATAAA
19822360 TAAAAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 11 0.37
14 19 0.63
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTTATAAAATATT
Found at i:19822867 original size:32 final size:32
Alignment explanation
Indices: 19822831--19822901 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
19822821 ATCTTAACTT
19822831 TAAATCCTAAACCATTTAATATATATAAAGCC
1 TAAATCCTAAACCATTTAATATATATAAAGCC
*
19822863 TAAATCCTAAACCATTTAATATATATAAAGTC
1 TAAATCCTAAACCATTTAATATATATAAAGCC
19822895 T-AATCCT
1 TAAATCCT
19822902 TAAGTAAACC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 6 0.16
32 32 0.84
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (32 bp):
TAAATCCTAAACCATTTAATATATATAAAGCC
Found at i:19822934 original size:21 final size:21
Alignment explanation
Indices: 19822910--19822952 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
19822900 CTTAAGTAAA
19822910 CCTAACACTT-AACCCCTAACC
1 CCTAACACTTAAACCCC-AACC
*
19822931 CCTAACCCTTAAACCCCAACC
1 CCTAACACTTAAACCCCAACC
19822952 C
1 C
19822953 TTAAATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.33, C:0.51, G:0.00, T:0.16
Consensus pattern (21 bp):
CCTAACACTTAAACCCCAACC
Found at i:19822947 original size:15 final size:14
Alignment explanation
Indices: 19822927--19822957 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
19822917 CTTAACCCCT
19822927 AACCCCTAACCCTTA
1 AACCCC-AACCCTTA
19822942 AACCCCAACCCTTA
1 AACCCCAACCCTTA
19822956 AA
1 AA
19822958 TCATAATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.16
Consensus pattern (14 bp):
AACCCCAACCCTTA
Found at i:19824299 original size:40 final size:41
Alignment explanation
Indices: 19824143--19824310 Score: 189
Period size: 41 Copynumber: 4.1 Consensus size: 41
19824133 GCCACATGAC
* *
19824143 TTTTAGTGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTGT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTTGT
* * *
19824184 CTTTAGCGGTGTTTTACCAAAAGCGCCGCTAATGCTCTTGT
1 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTTGT
* * * *
19824225 CTTTAGCGGCGTTTTAACAAAAAACGCCGCTATTGCTC-AGT
1 TTTTAGCGGCGTTTT-ACCAAAAACGCCGCTAATGCTCTTGT
* * *
19824266 TTTTAGTGGCGTTTTGA-CAAAAACGCCACTATTGCTC-TGT
1 TTTTAGCGGCGTTTT-ACCAAAAACGCCGCTAATGCTCTTGT
19824306 TTTTA
1 TTTTA
19824311 TAATTTTTGC
Statistics
Matches: 112, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
40 25 0.22
41 68 0.61
42 19 0.17
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTTGT
Found at i:19825813 original size:21 final size:21
Alignment explanation
Indices: 19825789--19825842 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
19825779 TACCATTGTT
**
19825789 TCTAATCTCACTGCTACAGTA
1 TCTAATCTCACCACTACAGTA
*
19825810 TCTAATCTCACCATTACAGTA
1 TCTAATCTCACCACTACAGTA
*
19825831 ACTAATCTCACC
1 TCTAATCTCACC
19825843 GCCACCGCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.31
Consensus pattern (21 bp):
TCTAATCTCACCACTACAGTA
Found at i:19845661 original size:22 final size:22
Alignment explanation
Indices: 19845636--19845690 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
19845626 ATGTTTAATA
*
19845636 ATATTGAAA-ATTATAATATTTT
1 ATATTAAAATATTA-AATATTTT
19845658 ATATTAAAATATTAAATATTTTT
1 ATATTAAAATATTAAATA-TTTT
19845681 AATATTAAAA
1 -ATATTAAAA
19845691 ATAAAACTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 12 0.41
23 8 0.28
24 9 0.31
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATTAAAATATTAAATATTTT
Found at i:19845695 original size:22 final size:22
Alignment explanation
Indices: 19845634--19845710 Score: 68
Period size: 25 Copynumber: 3.3 Consensus size: 22
19845624 GTATGTTTAA
*
19845634 TAATATTGAAAATTATAATA-TTT
1 TAATATT-AAAAATA-AATATTTT
19845657 T-ATATTAAAATATTAAATATTTT
1 TAATATTAAAA-A-TAAATATTTT
19845680 TAATATTAAAAATAAAACTTATTTT
1 TAATATTAAAAAT-AAA--TATTTT
19845705 TAATAT
1 TAATAT
19845711 AATAATATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
21 4 0.09
22 10 0.22
23 11 0.24
24 9 0.20
25 12 0.26
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
TAATATTAAAAATAAATATTTT
Found at i:19846375 original size:41 final size:41
Alignment explanation
Indices: 19846329--19846410 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
19846319 GTCTTATATT
19846329 TCCACAATAAATATCAGATACTAATAGTTGTTTAGCATAAA
1 TCCACAATAAATATCAGATACTAATAGTTGTTTAGCATAAA
19846370 TCCACAATAAATATCAGATACTAATAGTTGTTTAGCATAAA
1 TCCACAATAAATATCAGATACTAATAGTTGTTTAGCATAAA
19846411 AGAAAGGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (41 bp):
TCCACAATAAATATCAGATACTAATAGTTGTTTAGCATAAA
Found at i:19857456 original size:57 final size:57
Alignment explanation
Indices: 19857393--19857533 Score: 205
Period size: 57 Copynumber: 2.5 Consensus size: 57
19857383 CAATTTCACT
* *
19857393 TAACTCATCACAATGTTATAATT-TATCATCAATCCATGAATTTATATCAAATACACA
1 TAACTCATCACAATGTCAT-ATTCTATCATCAATCCATAAATTTATATCAAATACACA
* *
19857450 TAACTCAT-ATCAATGTCATATTCTATCATCTATCCATAAATTTATATCAAATATACA
1 TAACTCATCA-CAATGTCATATTCTATCATCAATCCATAAATTTATATCAAATACACA
*
19857507 TAACTCATCTCAATGTCATATTCTATC
1 TAACTCATCACAATGTCATATTCTATC
19857534 CATGAATTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
56 4 0.05
57 72 0.95
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.38
Consensus pattern (57 bp):
TAACTCATCACAATGTCATATTCTATCATCAATCCATAAATTTATATCAAATACACA
Found at i:19890796 original size:26 final size:26
Alignment explanation
Indices: 19890767--19890869 Score: 179
Period size: 26 Copynumber: 4.0 Consensus size: 26
19890757 AATTCCCATA
*
19890767 ATGGAACATTTACCTAAACCATTATC
1 ATGGAACATTTACCTAACCCATTATC
19890793 ATGGAACATTTACCTAACCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
* *
19890819 ATGGAATATTTACCTAATCCATTATC
1 ATGGAACATTTACCTAACCCATTATC
19890845 ATGGAACATTTACCTAACCCATTAT
1 ATGGAACATTTACCTAACCCATTAT
19890870 TAATTTGTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (26 bp):
ATGGAACATTTACCTAACCCATTATC
Found at i:19892993 original size:130 final size:130
Alignment explanation
Indices: 19892755--19892994 Score: 291
Period size: 130 Copynumber: 1.8 Consensus size: 130
19892745 AAACAACTCA
* * * * * * * * * * *
19892755 TTGATTTAAGATCGTAGCTTAAGTTCATTTGATTTAATATCATGAACAGTTTTTTCTGAGTTAGC
1 TTGACTTAAGATCGCAACCTAAGCTCATTCGATTTAACATCATGAACAATCTTATCTAAGTTAGC
* * *
19892820 TGATTTACTATCACTAATCTAAACAGCTCATTGATTTAAGATCGCAATTGATATCAATAAGCTCG
66 TGATTTAATATCACTAATCCAAACAGCTCACTGATTTAAGATCGCAATTGATATCAATAAGCTCG
* *
19892885 TTGACTTAAGATCGCAACCTAAGCTCATTCGATTTAACATCATGAGCAATCTTATCTAAGTTAGG
1 TTGACTTAAGATCGCAACCTAAGCTCATTCGATTTAACATCATGAACAATCTTATCTAAGTTAGC
* ** * *
19892950 TGATTTAATATCGCTGCTCCAAACTGTTCACTGATTTAAGATCGC
66 TGATTTAATATCACTAATCCAAACAGCTCACTGATTTAAGATCGC
19892995 GGCCTATGTT
Statistics
Matches: 89, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
130 89 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (130 bp):
TTGACTTAAGATCGCAACCTAAGCTCATTCGATTTAACATCATGAACAATCTTATCTAAGTTAGC
TGATTTAATATCACTAATCCAAACAGCTCACTGATTTAAGATCGCAATTGATATCAATAAGCTCG
Found at i:19893008 original size:95 final size:95
Alignment explanation
Indices: 19892886--19893145 Score: 290
Period size: 95 Copynumber: 2.7 Consensus size: 95
19892876 ATAAGCTCGT
* * * *
19892886 TGACTTAAGATCGCAACCTAAGCTCATTCGATTTAACATCATGAGCAATCTTATCTAAGTTAGGT
1 TGACTTAAGATCGCAGCCTAAGTTCATTCGATTTAACATCATGAACAATCTTATCTAAGTTAGCT
* *
19892951 GATTTAATATCGCTGCTCCAAACT-GTTCAC
66 GATTTAACATCGCTGCTCCAAA-TGGCTCAC
* * * * * * *
19892981 TGATTTAAGATCGCGGCCTATGTTCATTCAATTTAACATCATGAACAAACTTATTTAAGTTAACT
1 TGACTTAAGATCGCAGCCTAAGTTCATTCGATTTAACATCATGAACAATCTTATCTAAGTTAGCT
* * *
19893046 GATTCAACATTGCTGCTTCAAATGGCTCAC
66 GATTTAACATCGCTGCTCCAAATGGCTCAC
* * * * * *
19893076 TGACTTAAGATTGCAGCATAAGTTCATTTGATTT-ACTATCATGAAAAATCTTATCTATGTTAGT
1 TGACTTAAGATCGCAGCCTAAGTTCATTCGATTTAAC-ATCATGAACAATCTTATCTAAGTTAGC
19893140 TGATTT
65 TGATTT
19893146 CCTAATTGCT
Statistics
Matches: 133, Mismatches: 30, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
94 3 0.02
95 130 0.98
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (95 bp):
TGACTTAAGATCGCAGCCTAAGTTCATTCGATTTAACATCATGAACAATCTTATCTAAGTTAGCT
GATTTAACATCGCTGCTCCAAATGGCTCAC
Found at i:19897362 original size:21 final size:23
Alignment explanation
Indices: 19897336--19897381 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
19897326 TATTGAATCG
19897336 AGTCGAG-TG-AAATAAAATTAA
1 AGTCGAGTTGAAAATAAAATTAA
19897357 AGTCGAGTTGAAAAATAAAATTAA
1 AGTCGAGTTG-AAAATAAAATTAA
19897381 A
1 A
19897382 CCCCTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 2 0.09
24 13 0.59
ACGTcount: A:0.54, C:0.04, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTCGAGTTGAAAATAAAATTAA
Found at i:19916062 original size:202 final size:201
Alignment explanation
Indices: 19915717--19916120 Score: 754
Period size: 202 Copynumber: 2.0 Consensus size: 201
19915707 ATCACAATTA
*
19915717 AGGCAAGTGTACCTATCGAACAGTAGTATAGTTCAGCAAGACCGGATTGTCAAACCTAAGGGAAC
1 AGGCAAGTGTACCTATCGAACAGTAGTATAGTTCAGCAAGACCGGATTGTCAAACCCAAGGGAAC
19915782 CACGAGTACTAGTATTTACTTCATTTTTATTATCTAGCCTAAAAAAAATTAAGTGGTTTGGTTAT
66 CACGAGTACTAGTATTTACTTCATTTTTATTATCTAGCCTAAAAAAAATTAAGTGGTTTGGTTAT
19915847 TTAAACTAATTACTAAACTAAGAATGCACAGAAAGAAAATTTGAGAAAATACTTTTGGGAGAATT
131 TTAAACTAATTACTAAACTAAGAATGCACAGAAAGAAAATTTGAGAAAATACTTTTGGGAGAATT
19915912 CGATTG
196 CGATTG
* *
19915918 AGGCAAGTGTACCTATCGAAACATTAGTATAGTTCAGCAAGACCGGATTGTCGAACCCAAGGGAA
1 AGGCAAGTGTACCTATCG-AACAGTAGTATAGTTCAGCAAGACCGGATTGTCAAACCCAAGGGAA
* *
19915983 CCACGAGTACTAGTATTTACTTCCTTTTTATTATCTAGCCTGAAAAAAATTAAGTGGTTTGGTTA
65 CCACGAGTACTAGTATTTACTTCATTTTTATTATCTAGCCTAAAAAAAATTAAGTGGTTTGGTTA
19916048 TTTAAACTAATTACTAAACTAAGAATGCACAGAAAGAAAATTTGAGAAAATACTTTTGGGAGAAT
130 TTTAAACTAATTACTAAACTAAGAATGCACAGAAAGAAAATTTGAGAAAATACTTTTGGGAGAAT
19916113 TCGATTG
195 TCGATTG
19916120 A
1 A
19916121 TTAAGACAAT
Statistics
Matches: 197, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
201 18 0.09
202 179 0.91
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (201 bp):
AGGCAAGTGTACCTATCGAACAGTAGTATAGTTCAGCAAGACCGGATTGTCAAACCCAAGGGAAC
CACGAGTACTAGTATTTACTTCATTTTTATTATCTAGCCTAAAAAAAATTAAGTGGTTTGGTTAT
TTAAACTAATTACTAAACTAAGAATGCACAGAAAGAAAATTTGAGAAAATACTTTTGGGAGAATT
CGATTG
Found at i:19918472 original size:94 final size:94
Alignment explanation
Indices: 19918350--19918536 Score: 365
Period size: 94 Copynumber: 2.0 Consensus size: 94
19918340 AAATTGCAAA
19918350 GTAGTCAAAAGTATAGGGGCAAATGTATAATTTGGAAAGTATGTGCGAATTGAATTAAATGGTTA
1 GTAGTCAAAAGTATAGGGGCAAATGTATAATTTGGAAAGTATGTGCGAATTGAATTAAATGGTTA
19918415 CTAAAAATTTTGAATTTTTTAATATATAG
66 CTAAAAATTTTGAATTTTTTAATATATAG
*
19918444 GTAGTCAAAAGTATAGGGGCAAATGTATAATTTTGAAAGTATGTGCGAATTGAATTAAATGGTTA
1 GTAGTCAAAAGTATAGGGGCAAATGTATAATTTGGAAAGTATGTGCGAATTGAATTAAATGGTTA
19918509 CTAAAAATTTTGAATTTTTTAATATATA
66 CTAAAAATTTTGAATTTTTTAATATATA
19918537 AACCAAGATA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (94 bp):
GTAGTCAAAAGTATAGGGGCAAATGTATAATTTGGAAAGTATGTGCGAATTGAATTAAATGGTTA
CTAAAAATTTTGAATTTTTTAATATATAG
Found at i:19919121 original size:25 final size:26
Alignment explanation
Indices: 19919081--19919146 Score: 98
Period size: 25 Copynumber: 2.5 Consensus size: 26
19919071 GATCATATGA
*
19919081 TATAAGAGTTATATGATTTACATGAAT
1 TATAAGA-TTACATGATTTACATGAAT
19919108 TATAAGA-TACATGATTTACATGAAT
1 TATAAGATTACATGATTTACATGAAT
*
19919133 TATATGATTACATG
1 TATAAGATTACATG
19919147 GATATTATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 23 0.64
26 6 0.17
27 7 0.19
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (26 bp):
TATAAGATTACATGATTTACATGAAT
Found at i:19919145 original size:17 final size:17
Alignment explanation
Indices: 19919118--19919163 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
19919108 TATAAGATAC
19919118 ATGATTTACATGAAT-TAT
1 ATGA-TTACATGAATAT-T
*
19919136 ATGATTACATGGATATT
1 ATGATTACATGAATATT
19919153 ATGA-TACATGA
1 ATGATTACATGA
19919164 GATACTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 6 0.24
17 14 0.56
18 5 0.20
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (17 bp):
ATGATTACATGAATATT
Found at i:19919167 original size:17 final size:18
Alignment explanation
Indices: 19919135--19919172 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
19919125 ACATGAATTA
19919135 TATGATTACATGGATA-T
1 TATGATTACATGGATACT
19919152 TATGA-TACATGAGATACT
1 TATGATTACATG-GATACT
19919170 TAT
1 TAT
19919173 ATAATTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (18 bp):
TATGATTACATGGATACT
Found at i:19922648 original size:37 final size:37
Alignment explanation
Indices: 19922598--19922672 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
19922588 AATCTTGTAC
19922598 ATAAACTTTGATTTAACCTATGTACATGTCATAGCCT
1 ATAAACTTTGATTTAACCTATGTACATGTCATAGCCT
19922635 ATAAACTTTGATTTAACCTATGTACATGTCATAGCCT
1 ATAAACTTTGATTTAACCTATGTACATGTCATAGCCT
19922672 A
1 A
19922673 ATATTAAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (37 bp):
ATAAACTTTGATTTAACCTATGTACATGTCATAGCCT
Found at i:19932960 original size:31 final size:31
Alignment explanation
Indices: 19932924--19932990 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
19932914 TTTTACAGTT
* * * * *
19932924 AAATTTGACCCTCAACTTTTTTAAAAGAGTC
1 AAATTTAACCATCAAATTTTTAAAAAGAATC
*
19932955 AAATTTAACCATTAAATTTTTAAAAAGAATC
1 AAATTTAACCATCAAATTTTTAAAAAGAATC
19932986 AAATT
1 AAATT
19932991 GACGGGTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (31 bp):
AAATTTAACCATCAAATTTTTAAAAAGAATC
Found at i:19933647 original size:3 final size:3
Alignment explanation
Indices: 19933641--19933693 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
19933631 TTCAAGACGT
*
19933641 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19933689 TAA TA
1 TAA TA
19933694 GATACATCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:19933863 original size:16 final size:16
Alignment explanation
Indices: 19933844--19933878 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19933834 TGAAAATAAT
*
19933844 TATTATTTGGAACAAC
1 TATTATTTAGAACAAC
*
19933860 TATTATTTAGAATAAC
1 TATTATTTAGAACAAC
19933876 TAT
1 TAT
19933879 ATTCAAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (16 bp):
TATTATTTAGAACAAC
Found at i:19935465 original size:16 final size:17
Alignment explanation
Indices: 19935444--19935479 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
19935434 AATTAATTTA
*
19935444 AATTAATTAATTTT-TC
1 AATTAAATAATTTTCTC
19935460 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
19935477 AAT
1 AAT
19935480 CCAATTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:19938140 original size:33 final size:33
Alignment explanation
Indices: 19938103--19938246 Score: 128
Period size: 33 Copynumber: 4.4 Consensus size: 33
19938093 TGTCTCAACT
*
19938103 GACTATCTCTGTT-TTTCATTTACTATCCCAGCA
1 GACTATCTCTGTTATGT-ATTTACTATCCCAGCA
* *
19938136 GACTATCTTTGTTATGTATTTACTGTCCCAGCA
1 GACTATCTCTGTTATGTATTTACTATCCCAGCA
* * * * * *
19938169 GACTATCTCTGTTCTATGTTTACTGTCCCAACG
1 GACTATCTCTGTTATGTATTTACTATCCCAGCA
* * * * * *
19938202 GACTATCTCTATTCTATGTTTACTGTCGCAGCA
1 GACTATCTCTGTTATGTATTTACTATCCCAGCA
*
19938235 GACTATTTCTGT
1 GACTATCTCTGT
19938247 GGATGCCATG
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
33 93 0.98
34 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (33 bp):
GACTATCTCTGTTATGTATTTACTATCCCAGCA
Found at i:19938173 original size:66 final size:66
Alignment explanation
Indices: 19938088--19938246 Score: 167
Period size: 66 Copynumber: 2.4 Consensus size: 66
19938078 TTTATTTGTG
* * * * * * * *
19938088 TTTACTGTCTCAACTGACTATCTCTGTT-TTTCATTTACTATCCCAGCAGACTATCTTTGTTATG
1 TTTACTGTCCCAGCAGACTATCTCTGTTCTAT-ATTTACTATCCCAACAGACTATCTCTATTATA
19938152 TA
65 TA
* * * *
19938154 TTTACTGTCCCAGCAGACTATCTCTGTTCTATGTTTACTGTCCCAACGGACTATCTCTATTCTAT
1 TTTACTGTCCCAGCAGACTATCTCTGTTCTATATTTACTATCCCAACAGACTATCTCTATTATAT
*
19938219 G
66 A
* *
19938220 TTTACTGTCGCAGCAGACTATTTCTGT
1 TTTACTGTCCCAGCAGACTATCTCTGT
19938247 GGATGCCATG
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
66 75 0.97
67 2 0.03
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (66 bp):
TTTACTGTCCCAGCAGACTATCTCTGTTCTATATTTACTATCCCAACAGACTATCTCTATTATAT
A
Found at i:19961188 original size:6 final size:6
Alignment explanation
Indices: 19961177--19961248 Score: 128
Period size: 6 Copynumber: 12.2 Consensus size: 6
19961167 AAAAGAAAAT
*
19961177 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AGTAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
19961225 AATAAA AATAAA AAT-AA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
19961249 GATAGGAGGA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.08
6 58 0.92
ACGTcount: A:0.82, C:0.00, G:0.01, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:19964004 original size:16 final size:17
Alignment explanation
Indices: 19963973--19964005 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19963963 TTCATAAGTA
19963973 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
19963990 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
19964006 GCACCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:19964352 original size:46 final size:46
Alignment explanation
Indices: 19964302--19964560 Score: 358
Period size: 46 Copynumber: 5.6 Consensus size: 46
19964292 CCATAGTGTT
* * *
19964302 TTTCAACTATGGTCTTACTCATTTTC-TATCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTATTCA-TTTCATATCACGTTGCCATGGTATC
* * *
19964348 TTTCAACAATGGTCTTATTCATTTCATGTCACGCTGCCATGGTATC
1 TTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATC
* * * *
19964394 TTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGATATC
1 TTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATC
*
19964440 TTTCAACCATGGTGTTATTCATTTCATATCACGTTGCCATGGTATC
1 TTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATC
* * *
19964486 TTTCAACCATGGTCTTATACATTTCATATCAGGTTGTCATGGTATC
1 TTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATC
**
19964532 TTTCAACCATGGTCTTACACATTTCATAT
1 TTTCAACCATGGTCTTATTCATTTCATAT
19964561 AAGAGAGCAC
Statistics
Matches: 192, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 188 0.98
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (46 bp):
TTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATC
Found at i:19968882 original size:49 final size:49
Alignment explanation
Indices: 19968809--19969096 Score: 353
Period size: 49 Copynumber: 5.8 Consensus size: 49
19968799 TAGTCGAAGC
* *
19968809 TATCTGGTACGCGTAGTAGCCTGCACTTAGTACTACACATGCAACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * *
19968858 AATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAT
* * * *
19968909 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * *
19968958 TATCCGGTACACGTAATAGCCTGCACTTAGTACTACACACGTGATCATAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCA-A-T
* * *
19969009 T-TTTGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCT-GGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
*
19969058 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
19969097 CGTGACCTCA
Statistics
Matches: 199, Mismatches: 34, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
49 115 0.58
50 6 0.03
51 78 0.39
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:19968932 original size:100 final size:100
Alignment explanation
Indices: 19968814--19969101 Score: 513
Period size: 100 Copynumber: 2.9 Consensus size: 100
19968804 GAAGCTATCT
* * * *
19968814 GGTACGCGTAGTAGCCTGCACTTAGTACTACACATGCAACCAATAATCTGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
19968879 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
*
19968914 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAATAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
* *
19968979 TGCACTTAGTACTACACACGTGATCATAGTTTTTG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
19969014 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
19969079 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
19969102 CCTCACAATA
Statistics
Matches: 180, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 180 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTCG
Found at i:19972804 original size:13 final size:13
Alignment explanation
Indices: 19972786--19972813 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19972776 GTTCGTTTAT
19972786 TAAACTAATTAAC
1 TAAACTAATTAAC
19972799 TAAACTAATTAAC
1 TAAACTAATTAAC
19972812 TA
1 TA
19972814 CTTACTAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:19986682 original size:40 final size:40
Alignment explanation
Indices: 19986627--19986707 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
19986617 ATCAAAAGTG
19986627 TAGGAAAAGTAAAGATGAAAAATGAGATTATTTATGCAGT
1 TAGGAAAAGTAAAGATGAAAAATGAGATTATTTATGCAGT
19986667 TAGGAAAAGTAAAGATGAAAAATGAGATTATTTATGCAGT
1 TAGGAAAAGTAAAGATGAAAAATGAGATTATTTATGCAGT
19986707 T
1 T
19986708 TGACCTTAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.28
Consensus pattern (40 bp):
TAGGAAAAGTAAAGATGAAAAATGAGATTATTTATGCAGT
Found at i:19990032 original size:26 final size:26
Alignment explanation
Indices: 19989996--19990046 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
19989986 AAATCACTTC
19989996 GTCTTCATGTGTTGGGCTTTACTCAA
1 GTCTTCATGTGTTGGGCTTTACTCAA
19990022 GTCTTCATGTGTTGGGCTTTACTCA
1 GTCTTCATGTGTTGGGCTTTACTCA
19990047 TCCAATATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.43
Consensus pattern (26 bp):
GTCTTCATGTGTTGGGCTTTACTCAA
Found at i:19993742 original size:24 final size:26
Alignment explanation
Indices: 19993706--19993756 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
19993696 TCAAACATGC
19993706 ATTTAGGTCAATTTAACC-CTAGGGT
1 ATTTAGGTCAATTTAACCACTAGGGT
* *
19993731 ATTTCGGT-AATTTATCCACTAGGGT
1 ATTTAGGTCAATTTAACCACTAGGGT
19993756 A
1 A
19993757 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCACTAGGGT
Found at i:19995262 original size:26 final size:26
Alignment explanation
Indices: 19995231--19995338 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
19995221 TGAAATGCCC
*
19995231 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
19995257 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
19995283 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
19995309 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
19995335 ATCA
1 ATCA
19995339 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:20005085 original size:46 final size:46
Alignment explanation
Indices: 20005020--20005279 Score: 378
Period size: 46 Copynumber: 5.7 Consensus size: 46
20005010 CAACCTGAGT
* *
20005020 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGT
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGA
*
20005066 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGT
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGA
*
20005112 GTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGA
** *
20005158 ACAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGA
** * *
20005204 ACAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGA
1 GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAATGA
* * *
20005250 GTAAGACCATAGTTGAAAGACACTATGGCA
1 GTAAGACCATGGTTGAAAGATACCATGGCA
20005280 TCATGTCAAA
Statistics
Matches: 201, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 200 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
GTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGA
Found at i:20005210 original size:138 final size:130
Alignment explanation
Indices: 20004968--20005279 Score: 419
Period size: 138 Copynumber: 2.3 Consensus size: 130
20004958 AGTGTGCTCT
*
20004968 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
***
20005033 TGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACCTGATATAAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
*
20005098 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--A-G---TG--CAAG
* *
20005163 ACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAGACCATGGTTGAAAGATACC
58 ACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGAACAAGACCATGGTTGAAAGATACC
20005228 ATGGCAAC
123 ATGGCAAC
* * * * * *
20005236 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
20005280 TCATGTCAAA
Statistics
Matches: 160, Mismatches: 13, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
130 48 0.30
132 1 0.01
133 1 0.01
136 2 0.01
137 1 0.01
138 107 0.67
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (130 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
TGAAAGATACCATGGCAACCTGATATAAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:20005921 original size:26 final size:26
Alignment explanation
Indices: 20005885--20005995 Score: 195
Period size: 26 Copynumber: 4.3 Consensus size: 26
20005875 GGGTGTTACA
*
20005885 ATTATCATGGAACATTTACCTAAACC
1 ATTATCATGGAACATTTACCTAACCC
20005911 ATTATCATGGAACATTTACCTAACCC
1 ATTATCATGGAACATTTACCTAACCC
* *
20005937 ATTATCATGGAATATTTACCTAATCC
1 ATTATCATGGAACATTTACCTAACCC
20005963 ATTATCATGGAACATTTACCTAACCC
1 ATTATCATGGAACATTTACCTAACCC
20005989 ATTATCA
1 ATTATCA
20005996 ATTTGTACCA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATTATCATGGAACATTTACCTAACCC
Found at i:20012061 original size:28 final size:28
Alignment explanation
Indices: 20012013--20012072 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
20012003 TTTAATTTGA
* *
20012013 ATATATATTTTATGTTATTAAAATATTT
1 ATATATATTTTATGATATTAAAATATCT
* *
20012041 ATATATTTTTTATAGAT-TTAATATATCT
1 ATATATATTTTAT-GATATTAAAATATCT
20012069 ATAT
1 ATAT
20012073 TTCATATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (28 bp):
ATATATATTTTATGATATTAAAATATCT
Found at i:20012103 original size:24 final size:23
Alignment explanation
Indices: 20012039--20012103 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
20012029 ATTAAAATAT
*
20012039 TTATATATTTTTTATAGATTTAA
1 TTATATATTTTTTATATATTTAA
* * * *
20012062 TATATCTATATTTCATATTTTTATA
1 T-TATATATTTTTTATATATTTA-A
*
20012087 TTATTTATTTTTTATAT
1 TTATATATTTTTTATAT
20012104 CATTATTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
23 1 0.03
24 29 0.91
25 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (23 bp):
TTATATATTTTTTATATATTTAA
Found at i:20012114 original size:15 final size:16
Alignment explanation
Indices: 20012079--20012115 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
20012069 ATATTTCATA
*
20012079 TTTTTATATTATTTAT
1 TTTTTATATCATTTAT
20012095 TTTTTATATCA-TTAT
1 TTTTTATATCATTTAT
20012110 TTTTTA
1 TTTTTA
20012116 AGTTTCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTATATCATTTAT
Found at i:20014448 original size:20 final size:21
Alignment explanation
Indices: 20014418--20014457 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
20014408 AGCTGCCAGA
20014418 CAAATATTGCAGTAATACTGC
1 CAAATATTGCAGTAATACTGC
20014439 CAAA-ATTGCAGTAATACTG
1 CAAATATTGCAGTAATACTG
20014458 ACAGAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (21 bp):
CAAATATTGCAGTAATACTGC
Found at i:20016678 original size:24 final size:25
Alignment explanation
Indices: 20016651--20016706 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
20016641 TTTATCTTTA
*
20016651 AATTTTTGTAAATAT-ATATTTCTT
1 AATTTTTCTAAATATAATATTTCTT
* * *
20016675 AATTTTTCTAATTTTAATATTTTTT
1 AATTTTTCTAAATATAATATTTCTT
20016700 AATTTTT
1 AATTTTT
20016707 TATGCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (25 bp):
AATTTTTCTAAATATAATATTTCTT
Found at i:20018561 original size:19 final size:20
Alignment explanation
Indices: 20018516--20018562 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
20018506 GATCAATTAA
* *
20018516 GTCTGATAGGGTTGTTTTAT
1 GTCTGTTAGGGTTGTTATAT
*
20018536 GTCTGTTAGGGTTGTTATCT
1 GTCTGTTAGGGTTGTTATAT
20018556 -TCTGTTA
1 GTCTGTTA
20018563 TACTGTTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.13, C:0.09, G:0.28, T:0.51
Consensus pattern (20 bp):
GTCTGTTAGGGTTGTTATAT
Found at i:20021810 original size:21 final size:21
Alignment explanation
Indices: 20021784--20021826 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
20021774 CACTGTGAGG
20021784 ATCAATGCTTACAATGAAAGA
1 ATCAATGCTTACAATGAAAGA
20021805 ATCAATGCTTACAATGAAAGA
1 ATCAATGCTTACAATGAAAGA
20021826 A
1 A
20021827 AAGTCATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (21 bp):
ATCAATGCTTACAATGAAAGA
Found at i:20029550 original size:14 final size:14
Alignment explanation
Indices: 20029531--20029557 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20029521 AAGAAAGATG
20029531 AAGAGCCATAATCA
1 AAGAGCCATAATCA
20029545 AAGAGCCATAATC
1 AAGAGCCATAATC
20029558 TTTTTCCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (14 bp):
AAGAGCCATAATCA
Found at i:20029636 original size:34 final size:34
Alignment explanation
Indices: 20029593--20029660 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
20029583 AGAGAAAAGA
20029593 AAGAAAAAAACTTTCTTTTCTTTATAATTTGGTC
1 AAGAAAAAAACTTTCTTTTCTTTATAATTTGGTC
20029627 AAGAAAAAAACTTTCTTTTCTTTATAATTTGGTC
1 AAGAAAAAAACTTTCTTTTCTTTATAATTTGGTC
20029661 CTTTCACCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (34 bp):
AAGAAAAAAACTTTCTTTTCTTTATAATTTGGTC
Found at i:20031274 original size:33 final size:33
Alignment explanation
Indices: 20031165--20031309 Score: 89
Period size: 33 Copynumber: 4.4 Consensus size: 33
20031155 AAAACATGGT
* *
20031165 TGGGCCATGGCAATATATGTGTAAGACCATAGC
1 TGGGCCATGGCAACATACGTGTAAGACCATAGC
* * * * * *
20031198 TAGGCAATGGCATCCT--GATGATAATACCATATC
1 TGGGCCATGGCAACATACG-TG-TAAGACCATAGC
* ** * *
20031231 TGAGATATGGCACCATGA-GTGTAAGACCATGGC
1 TGGGCCATGGCAACAT-ACGTGTAAGACCATAGC
* *
20031264 TGGGCCATGGCAATATACGTGTAAGACCATAGT
1 TGGGCCATGGCAACATACGTGTAAGACCATAGC
* *
20031297 TGGACTATGGCAA
1 TGGGCCATGGCAA
20031310 TCTGACGAGA
Statistics
Matches: 82, Mismatches: 25, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
31 1 0.01
32 3 0.04
33 75 0.91
34 2 0.02
35 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (33 bp):
TGGGCCATGGCAACATACGTGTAAGACCATAGC
Found at i:20031374 original size:46 final size:46
Alignment explanation
Indices: 20031303--20031498 Score: 268
Period size: 46 Copynumber: 4.3 Consensus size: 46
20031293 TAGTTGGACT
* *
20031303 ATGGCAATC-TGACGAGAAATGAATAAGACCATGGTTGAAAAATATC
1 ATGGCAA-CATGACAAGAAATGAATAAGACCATGGTTGAAAAATACC
* * * *
20031349 ATGGCAACATGACAGGAAATAAATAAGACCATGGGTGAAAGATACC
1 ATGGCAACATGACAAGAAATGAATAAGACCATGGTTGAAAAATACC
* *
20031395 ATGGCAACGTGACAAGAAATGAATAAGACCATGGTTGAAAGATACC
1 ATGGCAACATGACAAGAAATGAATAAGACCATGGTTGAAAAATACC
* * * *
20031441 ATGACAACGTGACAAGAAATGAATAAGACCATAGTTGGAAAATACC
1 ATGGCAACATGACAAGAAATGAATAAGACCATGGTTGAAAAATACC
20031487 ATGGCAACATGA
1 ATGGCAACATGA
20031499 GAGAAAATTA
Statistics
Matches: 133, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.01
46 132 0.99
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (46 bp):
ATGGCAACATGACAAGAAATGAATAAGACCATGGTTGAAAAATACC
Found at i:20031537 original size:46 final size:46
Alignment explanation
Indices: 20031303--20031561 Score: 265
Period size: 46 Copynumber: 5.7 Consensus size: 46
20031293 TAGTTGGACT
* * * *
20031303 ATGGCAATC-TGACGAGAAATGAATAAGACCATGGTTGAAAAATATC
1 ATGGCAA-CATGACAAGAAATGAATAAGACCATAGTTGAAAGATACC
* * * *
20031349 ATGGCAACATGACAGGAAATAAATAAGACCATGGGTGAAAGATACC
1 ATGGCAACATGACAAGAAATGAATAAGACCATAGTTGAAAGATACC
* *
20031395 ATGGCAACGTGACAAGAAATGAATAAGACCATGGTTGAAAGATACC
1 ATGGCAACATGACAAGAAATGAATAAGACCATAGTTGAAAGATACC
* *
20031441 ATGACAACGTGACAAGAAATGAATAAGACCATAGTTGGAAA-ATACC
1 ATGGCAACATGACAAGAAATGAATAAGACCATAGTT-GAAAGATACC
* * * * * *
20031487 ATGGCAACATGA-GAGAAAATTAGTAAGACTATAGTTGAAAGACACT
1 ATGGCAACATGACAAG-AAATGAATAAGACCATAGTTGAAAGATACC
* * * *
20031533 ATGGCATCATGTCAA-AGATAAATAAGACC
1 ATGGCAACATGACAAGAAATGAATAAGACC
20031562 GTGGATGGGA
Statistics
Matches: 181, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
45 17 0.09
46 159 0.88
47 5 0.03
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (46 bp):
ATGGCAACATGACAAGAAATGAATAAGACCATAGTTGAAAGATACC
Found at i:20032993 original size:16 final size:17
Alignment explanation
Indices: 20032974--20033006 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20032964 TCAAAATGAT
*
20032974 TGAAATTATAT-TTATA
1 TGAAATAATATATTATA
20032990 TGAAATAATATATTATA
1 TGAAATAATATATTATA
20033007 AATTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TGAAATAATATATTATA
Found at i:20033090 original size:22 final size:22
Alignment explanation
Indices: 20033056--20033097 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20033046 TAAGAAATTG
* *
20033056 TTAAAAAATATATTTATATTCA
1 TTAAAAAACATATTAATATTCA
*
20033078 TTAATAAACATATTAATATT
1 TTAAAAAACATATTAATATT
20033098 AACCTATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAAAACATATTAATATTCA
Found at i:20036701 original size:21 final size:21
Alignment explanation
Indices: 20036675--20036715 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20036665 AGACGAGCGA
* *
20036675 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
20036696 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
20036716 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:20040062 original size:50 final size:50
Alignment explanation
Indices: 20039991--20040090 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
20039981 TAAATTTTCA
20039991 AATGGGGATGAAAATAGATTTTTAATTAAATAAATTTAATTAATTAAAAT
1 AATGGGGATGAAAATAGATTTTTAATTAAATAAATTTAATTAATTAAAAT
*
20040041 AATGGGGATGAAAATATATTTTTAATTAAATAAATTTAATTAATTAAAAT
1 AATGGGGATGAAAATAGATTTTTAATTAAATAAATTTAATTAATTAAAAT
20040091 TTTTAAACAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (50 bp):
AATGGGGATGAAAATAGATTTTTAATTAAATAAATTTAATTAATTAAAAT
Found at i:20040105 original size:7 final size:7
Alignment explanation
Indices: 20040093--20040131 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
20040083 ATTAAAATTT
20040093 TTAAACA
1 TTAAACA
*
20040100 TTAAACC
1 TTAAACA
20040107 TT-AACA
1 TTAAACA
20040113 TTAAACA
1 TTAAACA
*
20040120 TTAAACC
1 TTAAACA
20040127 TTAAA
1 TTAAA
20040132 AAACTGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAACA
Found at i:20040116 original size:20 final size:20
Alignment explanation
Indices: 20040093--20040130 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
20040083 ATTAAAATTT
20040093 TTAAACATTAAACCTTAACA
1 TTAAACATTAAACCTTAACA
20040113 TTAAACATTAAACCTTAA
1 TTAAACATTAAACCTTAA
20040131 AAAACTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAAACATTAAACCTTAACA
Found at i:20040244 original size:18 final size:18
Alignment explanation
Indices: 20040221--20040255 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20040211 TGAAATATGT
20040221 ATAAACCCAAAACAAATC
1 ATAAACCCAAAACAAATC
20040239 ATAAACCCAAAACAAAT
1 ATAAACCCAAAACAAAT
20040256 GACGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.26, G:0.00, T:0.11
Consensus pattern (18 bp):
ATAAACCCAAAACAAATC
Found at i:20045965 original size:49 final size:49
Alignment explanation
Indices: 20045909--20046140 Score: 302
Period size: 49 Copynumber: 4.7 Consensus size: 49
20045899 TATGTACGCA
*
20045909 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
* ** * *
20045958 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATCCGGTACACG
* * * * *
20046008 TAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGTTATCGGGTACACA
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACG
* * *
20046059 TAGTAGCCTCCAGTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
*
20046108 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC
20046141 TCACAATAGA
Statistics
Matches: 155, Mismatches: 25, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
49 72 0.46
50 47 0.30
51 36 0.23
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACG
Found at i:20046137 original size:100 final size:99
Alignment explanation
Indices: 20045909--20046140 Score: 313
Period size: 100 Copynumber: 2.3 Consensus size: 99
20045899 TATGTACGCA
* * * *
20045909 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACATAGTAGCCTCCACTTA
* *
20045974 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACCTAACCATCCGATACACG
* * * *
20046008 TAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGTTATCGGGTACACATAGTAGCCTCCAGT
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACATAGTAGCCTCCACT
* ** *
20046073 TAGTACTACACATGCGACC-AATTATCCGGTACACG
64 TAGTACTACACACGCGACCTAACCATCCGATACACG
20046108 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
20046141 TCACAATAGA
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
99 29 0.25
100 45 0.39
101 41 0.36
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACATAGTAGCCTCCACTTA
GTACTACACACGCGACCTAACCATCCGATACACG
Found at i:20046751 original size:30 final size:30
Alignment explanation
Indices: 20046716--20046775 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
20046706 CCAAAATCAT
*
20046716 ATTTTGAAAAAATTATAATTTTGCCCCTAA
1 ATTTTGAAAAAATTACAATTTTGCCCCTAA
** *
20046746 ATTTTGTCAAAATTACATTTTTGCCCCTAA
1 ATTTTGAAAAAATTACAATTTTGCCCCTAA
20046776 GCTCGTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.42
Consensus pattern (30 bp):
ATTTTGAAAAAATTACAATTTTGCCCCTAA
Found at i:20048667 original size:21 final size:20
Alignment explanation
Indices: 20048620--20048667 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
20048610 AAAAATAATT
**
20048620 AAAATAATATTTAATTTTAA
1 AAAATAATATTTAAAATTAA
20048640 AATAATAATATATTAAAATTAA
1 AA-AATAATAT-TTAAAATTAA
20048662 AAAATA
1 AAAATA
20048668 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 12 0.50
22 10 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATATTTAAAATTAA
Found at i:20055345 original size:6 final size:6
Alignment explanation
Indices: 20055329--20055363 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
20055319 ATTATGAATG
* *
20055329 GTTAAA ATTAAA GTTAAA GTTAAA GTTAAA ATTAA
1 GTTAAA GTTAAA GTTAAA GTTAAA GTTAAA GTTAA
20055364 TTTATACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (6 bp):
GTTAAA
Found at i:20055346 original size:12 final size:12
Alignment explanation
Indices: 20055329--20055363 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
20055319 ATTATGAATG
20055329 GTTAAAATTAAA
1 GTTAAAATTAAA
*
20055341 GTTAAAGTTAAA
1 GTTAAAATTAAA
20055353 GTTAAAATTAA
1 GTTAAAATTAA
20055364 TTTATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (12 bp):
GTTAAAATTAAA
Found at i:20056917 original size:2 final size:2
Alignment explanation
Indices: 20056912--20056947 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20056902 CTATATACAA
20056912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20056948 CATCTTAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20057240 original size:90 final size:90
Alignment explanation
Indices: 20057097--20057373 Score: 268
Period size: 90 Copynumber: 3.1 Consensus size: 90
20057087 AACCATAAAA
* *** * *
20057097 GTTGCAGGTTAATATGCTGCCAGATGGTTGTGAATGTATAACATATTTACAAATGAGAGCTGGC-
1 GTTGCAGGTTAATACGCTGCCAGATGGTTGTGAACACACAACATATTTACAAATGAAAGCT-GCT
* ** *
20057161 GGAATGTGGGTGGATGAACCACCAGT
65 AGAAAATCGGTGGATGAACCACCAGT
* * *
20057187 GTTGCAGGTTAATACGTTGCTAGATGGTTGTGAACACACAACGTATTTACAAATGAAAGCTGCTA
1 GTTGCAGGTTAATACGCTGCCAGATGGTTGTGAACACACAACATATTTACAAATGAAAGCTGCTA
20057252 GAAAATCGGTGGATGAACCACCAGT
66 GAAAATCGGTGGATGAACCACCAGT
* * *** * ** * ** * *
20057277 GATGCAGGTTAATAAGCTATTAGATGATTGTGAATGCAAAACATATTTGTAAATAAAAGCTGCCA
1 GTTGCAGGTTAATACGCTGCCAGATGGTTGTGAACACACAACATATTTACAAATGAAAGCTGCTA
* * * *
20057342 GATAATCTGTGGATGAACCACTAGG
66 GAAAATCGGTGGATGAACCACCAGT
20057367 GTTGCAG
1 GTTGCAG
20057374 ATTATTAATC
Statistics
Matches: 154, Mismatches: 32, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
89 2 0.01
90 152 0.99
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (90 bp):
GTTGCAGGTTAATACGCTGCCAGATGGTTGTGAACACACAACATATTTACAAATGAAAGCTGCTA
GAAAATCGGTGGATGAACCACCAGT
Found at i:20060146 original size:28 final size:28
Alignment explanation
Indices: 20060078--20060132 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
20060068 TTTCTTAGGC
* *
20060078 AAAACTGTAAAATCTAAAAAATAGGGGA
1 AAAAGTGTAAAATCTAAAAAATAGAGGA
20060106 AAAAGTGTAAAATCTAAAAAATAGAGG
1 AAAAGTGTAAAATCTAAAAAATAGAGG
20060133 CAACTTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.58, C:0.05, G:0.18, T:0.18
Consensus pattern (28 bp):
AAAAGTGTAAAATCTAAAAAATAGAGGA
Found at i:20060847 original size:24 final size:24
Alignment explanation
Indices: 20060819--20060871 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
20060809 ATTCGTAGGT
* *
20060819 TAAATAAATTATGCTAATAAATGC
1 TAAATAAATTATACTAATAAATAC
* *
20060843 TAAATATATTATACTAATTAATAC
1 TAAATAAATTATACTAATAAATAC
20060867 TAAAT
1 TAAAT
20060872 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
TAAATAAATTATACTAATAAATAC
Found at i:20065401 original size:14 final size:14
Alignment explanation
Indices: 20065365--20065408 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20065355 CCGGGCCCAT
20065365 AATTAAATAAATAAA
1 AATTAAA-AAATAAA
** *
20065380 AAACAAAAAACAAA
1 AATTAAAAAATAAA
20065394 AATTAAAAAATAAA
1 AATTAAAAAATAAA
20065408 A
1 A
20065409 GTTCATTTAC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (14 bp):
AATTAAAAAATAAA
Found at i:20066630 original size:17 final size:16
Alignment explanation
Indices: 20066602--20066640 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
20066592 TAAAATTAAA
*
20066602 TTAAATTAAATTTTTT
1 TTAAATTAAATTTATT
*
20066618 TTGAAATTCAATTTATT
1 TT-AAATTAAATTTATT
20066635 TTAAAT
1 TTAAAT
20066641 ACTATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (16 bp):
TTAAATTAAATTTATT
Found at i:20078762 original size:44 final size:44
Alignment explanation
Indices: 20078711--20079192 Score: 537
Period size: 44 Copynumber: 11.0 Consensus size: 44
20078701 AGCAGATCCA
* * *
20078711 AGCAGATTTGGCGTCTCTGTATTGTCAGGGAGCAGATCAAAGTT
1 AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT
* * *
20078755 AGCAGATTTGGCGTCTCTATATTGTCAGGGAGTAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT
* *
20078799 AGCAGATTTGGCGTCTCTGTATTGTTAGGGAGCAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT
* * *
20078843 AGCAGATTTGGTGTCTCTGTATTGTTAGAGAGTAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT
* * ** * *
20078887 AACAGATTTGGCATCTCCATATTCGACAGAGAGCAGATCCAAGAT
1 AGCAGATTTGGCGTCTCTGTATT-GTCAGAGAGCAGATCGAAGAT
** * * * *
20078932 ----GATTTGGTATCT-TCGTATT-TGACGAGGAGTAAATCCAAGA-
1 AGCAGATTTGGCGTCTCT-GTATTGTCA-GA-GAGCAGATCGAAGAT
* * *
20078972 AACAGATTTGGCGTCTCTGTATTGTCAAAGAGCAGATCAAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT
* * * * *
20079016 AGTAGATTTGGCGTCTTTGTATTGTCAGGGAGCAAATTGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT
* *
20079060 AGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGAC
1 AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT
*
20079104 AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGAAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT
** * *
20079148 AGCAGATTTGGTATCTTTGTATTGTTAGAGAGCAGATCGAAGAT
1 AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT
20079192 A
1 A
20079193 TCAACATGGC
Statistics
Matches: 371, Mismatches: 56, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 27 0.07
43 11 0.03
44 310 0.84
45 20 0.05
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (44 bp):
AGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGAT
Found at i:20079060 original size:173 final size:173
Alignment explanation
Indices: 20078783--20079102 Score: 444
Period size: 173 Copynumber: 1.8 Consensus size: 173
20078773 ATATTGTCAG
* * * * ** *
20078783 GGAGTAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTTAGGGAGCAGATCGAAGATAGCAG
1 GGAGTAAATCCAAGATAACAGATTTGGCGTCTCTGTATTGTCAAAGAGCAGATCAAAGATAGCAG
* * * *
20078848 ATTTGGTGTCTCTGTATTGTTAGAGAGTAGATCGAAGATAACAGATTTGGCATCTCCATATTCGA
66 ATTTGGCGTCTCTGTATTGTCAGAGAGCAAATCGAAGATAACAGATTTGGCATCTCCATATT-GA
20078913 CAGAGAGCAGATCCAAGATGATTTGGTATCTTCGTATTTGACGA
130 CAGAGAGCAGATCCAAGATGATTTGGTATCTTCGTATTTGACGA
*
20078957 GGAGTAAATCCAAGA-AACAGATTTGGCGTCTCTGTATTGTCAAAGAGCAGATCAAAGATAGTAG
1 GGAGTAAATCCAAGATAACAGATTTGGCGTCTCTGTATTGTCAAAGAGCAGATCAAAGATAGCAG
* * * * ** *
20079021 ATTTGGCGTCTTTGTATTGTCAGGGAGCAAATTGAAGATAGCAGATTTGGCATCTCTGTATTGTC
66 ATTTGGCGTCTCTGTATTGTCAGAGAGCAAATCGAAGATAACAGATTTGGCATCTCCATATTGAC
*
20079086 AGAGAGCAGATCGAAGA
131 AGAGAGCAGATCCAAGA
20079103 CAGCAGATTT
Statistics
Matches: 126, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
172 18 0.14
173 95 0.75
174 13 0.10
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (173 bp):
GGAGTAAATCCAAGATAACAGATTTGGCGTCTCTGTATTGTCAAAGAGCAGATCAAAGATAGCAG
ATTTGGCGTCTCTGTATTGTCAGAGAGCAAATCGAAGATAACAGATTTGGCATCTCCATATTGAC
AGAGAGCAGATCCAAGATGATTTGGTATCTTCGTATTTGACGA
Found at i:20080503 original size:7 final size:7
Alignment explanation
Indices: 20080491--20080531 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
20080481 CCTTCTGTGT
20080491 TTTTTAA
1 TTTTTAA
20080498 TTTTTAA
1 TTTTTAA
20080505 TTTTTAA
1 TTTTTAA
20080512 -TTTT-A
1 TTTTTAA
20080517 TTTTT-A
1 TTTTTAA
*
20080523 TTTTAAA
1 TTTTTAA
20080530 TT
1 TT
20080532 AGCCCTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 1 0.03
6 13 0.42
7 17 0.55
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTAA
Found at i:20080867 original size:10 final size:9
Alignment explanation
Indices: 20080853--20080951 Score: 52
Period size: 10 Copynumber: 11.1 Consensus size: 9
20080843 TTTTATAAAT
20080853 TTTATTATA
1 TTTATTATA
20080862 TGTTA-TAT-
1 T-TTATTATA
20080870 TTTATTATA
1 TTTATTATA
20080879 TGTTATT-TA
1 T-TTATTATA
20080888 TTCTATTTATA
1 TT-TA-TTATA
20080899 TTTTATTATA
1 -TTTATTATA
*
20080909 TATTGTTACTA
1 T-TTATTA-TA
20080920 --TA-TATA
1 TTTATTATA
*
20080926 TTGATTAT-
1 TTTATTATA
*
20080934 TTTACTATA
1 TTTATTATA
20080943 TTT-TTATA
1 TTTATTATA
20080951 T
1 T
20080952 GTAAATTTAC
Statistics
Matches: 70, Mismatches: 6, Indels: 29
0.67 0.06 0.28
Matches are distributed among these distances:
6 2 0.03
7 5 0.07
8 18 0.26
9 17 0.24
10 20 0.29
11 6 0.09
12 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTATTATA
Found at i:20080873 original size:17 final size:17
Alignment explanation
Indices: 20080851--20080909 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
20080841 TTTTTTATAA
20080851 ATTTTATTATATGTTAT
1 ATTTTATTATATGTTAT
20080868 ATTTTATTATATG-T-T
1 ATTTTATTATATGTTAT
*
20080883 A-TTTATTCTAT-TTAT
1 ATTTTATTATATGTTAT
20080898 ATTTTATTATAT
1 ATTTTATTATAT
20080910 ATTGTTACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 10 0.27
15 4 0.11
16 10 0.27
17 13 0.35
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTTTATTATATGTTAT
Found at i:20080920 original size:27 final size:29
Alignment explanation
Indices: 20080864--20080927 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
20080854 TTATTATATG
* *
20080864 TTATATTTTATTATATGTTATTTATTCTAT
1 TTATATTTTATTATATATTAGTTA-TCTAT
20080894 TTATATTTTATTATATATT-GTTA-CTAT
1 TTATATTTTATTATATATTAGTTATCTAT
*
20080921 ATATATT
1 TTATATT
20080928 GATTATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.32
29 3 0.10
30 18 0.58
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (29 bp):
TTATATTTTATTATATATTAGTTATCTAT
Found at i:20082617 original size:28 final size:28
Alignment explanation
Indices: 20082577--20082646 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
20082567 AGGTAACATC
* *
20082577 TAAAATCTGAAAAATATGGATAATATTG
1 TAAAATCTGAAAAATATGGATAAAATTA
* *
20082605 TAAAATTTGAAAAATATGGGTAAAATTA
1 TAAAATCTGAAAAATATGGATAAAATTA
20082633 TAAAATCTGAAAAA
1 TAAAATCTGAAAAA
20082647 AGGGGCAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.30
Consensus pattern (28 bp):
TAAAATCTGAAAAATATGGATAAAATTA
Found at i:20085472 original size:92 final size:92
Alignment explanation
Indices: 20085314--20085966 Score: 492
Period size: 92 Copynumber: 7.2 Consensus size: 92
20085304 ATTGAGATTG
* * * * **
20085314 ACTGAACTGGCAGTTTTATTGCAATATAT-AGGTATAGCGAATTACCGTATTGCACTATACTACA
1 ACTGAACTGGCAGTTTTACTGCAATATATCA-GTATAGAGGATTACCGTATTGCACTGTACCGCA
* *
20085378 TGTACGTTAGCTACGCTATGTACCATTA
65 TGTACGTTAGATACGCTACGTACCATTA
* * *
20085406 ACTGAACTGGTAGTTTTACTGTAATATATCAGTATAGAGGATTATCGTATTGCACTGTACCGCAT
1 ACTGAACTGGCAGTTTTACTGCAATATATCAGTATAGAGGATTACCGTATTGCACTGTACCGCAT
* * *
20085471 GTACATTAGATACACTACGTACCATTG
66 GTACGTTAGATACGCTACGTACCATTA
* * * * **
20085498 GCTGAACTGGCAATTTTACTGCAATCTATCGGTATAGCA-GATTACCACATTGCACTGTACCGCA
1 ACTGAACTGGCAGTTTTACTGCAATATATCAGTATAG-AGGATTACCGTATTGCACTGTACCGCA
*
20085562 TGTACGTTAGATACGCTACGTACCACTA
65 TGTACGTTAGATACGCTACGTACCATTA
* * * * * * * * * * ** *
20085590 TCTGATCTGGTAGTTCATACTG---TATTTCAGTACATATA-CATAAAC-TATT---TTGGGCGG
1 ACTGAACTGGCAGTT-TTACTGCAATATATCAGT--ATAGAGGATTACCGTATTGCACTGTACCG
* ** * * * ** * *
20085647 GAT-TTTG-AAGAGAAGGGA-GATTGA-GATTG
63 CATGTACGTTAGATACGCTACG--T-ACCATTA
* * * * **
20085676 ACTGAACTGGCAGTTTTATTGCAATATAT-AGGTATAGCGAATTACCGTATTGCACTATACTACA
1 ACTGAACTGGCAGTTTTACTGCAATATATCA-GTATAGAGGATTACCGTATTGCACTGTACCGCA
* *
20085740 TGTACGTTAGCTACGCTATGTACCATTA
65 TGTACGTTAGATACGCTACGTACCATTA
* * *
20085768 ACTGAACTGGTAGTTTTACTGTAATATATCAGTATAGAGGATTATCGTATTGCACTGTACCGCAT
1 ACTGAACTGGCAGTTTTACTGCAATATATCAGTATAGAGGATTACCGTATTGCACTGTACCGCAT
* * *
20085833 GTACATTAGATACACTACGTACCATTG
66 GTACGTTAGATACGCTACGTACCATTA
* * * * **
20085860 GCTGAACTGGCAATTTTACTGCAATCTATCGGTATAGCA-GATTACCACATTGCACTGTACCGCA
1 ACTGAACTGGCAGTTTTACTGCAATATATCAGTATAG-AGGATTACCGTATTGCACTGTACCGCA
*
20085924 TGTACGTTAGATACGCTACGTACCACTA
65 TGTACGTTAGATACGCTACGTACCATTA
* * *
20085952 TCTGATCTGGTAGTT
1 ACTGAACTGGCAGTT
20085967 CATACTGTAT
Statistics
Matches: 424, Mismatches: 114, Indels: 46
0.73 0.20 0.08
Matches are distributed among these distances:
84 1 0.00
85 10 0.02
86 20 0.05
87 12 0.03
88 10 0.02
90 9 0.02
91 10 0.02
92 337 0.79
93 14 0.03
94 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (92 bp):
ACTGAACTGGCAGTTTTACTGCAATATATCAGTATAGAGGATTACCGTATTGCACTGTACCGCAT
GTACGTTAGATACGCTACGTACCATTA
Found at i:20085923 original size:362 final size:362
Alignment explanation
Indices: 20085258--20085984 Score: 1454
Period size: 362 Copynumber: 2.0 Consensus size: 362
20085248 CATATATGCA
20085258 TACATATACATAAACTATTTTGGGCGGGATTTTGAAGAGAAGGGAGATTGAGATTGACTGAACTG
1 TACATATACATAAACTATTTTGGGCGGGATTTTGAAGAGAAGGGAGATTGAGATTGACTGAACTG
20085323 GCAGTTTTATTGCAATATATAGGTATAGCGAATTACCGTATTGCACTATACTACATGTACGTTAG
66 GCAGTTTTATTGCAATATATAGGTATAGCGAATTACCGTATTGCACTATACTACATGTACGTTAG
20085388 CTACGCTATGTACCATTAACTGAACTGGTAGTTTTACTGTAATATATCAGTATAGAGGATTATCG
131 CTACGCTATGTACCATTAACTGAACTGGTAGTTTTACTGTAATATATCAGTATAGAGGATTATCG
20085453 TATTGCACTGTACCGCATGTACATTAGATACACTACGTACCATTGGCTGAACTGGCAATTTTACT
196 TATTGCACTGTACCGCATGTACATTAGATACACTACGTACCATTGGCTGAACTGGCAATTTTACT
20085518 GCAATCTATCGGTATAGCAGATTACCACATTGCACTGTACCGCATGTACGTTAGATACGCTACGT
261 GCAATCTATCGGTATAGCAGATTACCACATTGCACTGTACCGCATGTACGTTAGATACGCTACGT
20085583 ACCACTATCTGATCTGGTAGTTCATACTGTATTTCAG
326 ACCACTATCTGATCTGGTAGTTCATACTGTATTTCAG
20085620 TACATATACATAAACTATTTTGGGCGGGATTTTGAAGAGAAGGGAGATTGAGATTGACTGAACTG
1 TACATATACATAAACTATTTTGGGCGGGATTTTGAAGAGAAGGGAGATTGAGATTGACTGAACTG
20085685 GCAGTTTTATTGCAATATATAGGTATAGCGAATTACCGTATTGCACTATACTACATGTACGTTAG
66 GCAGTTTTATTGCAATATATAGGTATAGCGAATTACCGTATTGCACTATACTACATGTACGTTAG
20085750 CTACGCTATGTACCATTAACTGAACTGGTAGTTTTACTGTAATATATCAGTATAGAGGATTATCG
131 CTACGCTATGTACCATTAACTGAACTGGTAGTTTTACTGTAATATATCAGTATAGAGGATTATCG
20085815 TATTGCACTGTACCGCATGTACATTAGATACACTACGTACCATTGGCTGAACTGGCAATTTTACT
196 TATTGCACTGTACCGCATGTACATTAGATACACTACGTACCATTGGCTGAACTGGCAATTTTACT
20085880 GCAATCTATCGGTATAGCAGATTACCACATTGCACTGTACCGCATGTACGTTAGATACGCTACGT
261 GCAATCTATCGGTATAGCAGATTACCACATTGCACTGTACCGCATGTACGTTAGATACGCTACGT
20085945 ACCACTATCTGATCTGGTAGTTCATACTGTATTTCAG
326 ACCACTATCTGATCTGGTAGTTCATACTGTATTTCAG
20085982 TAC
1 TAC
20085985 TGCGGTTCAC
Statistics
Matches: 365, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
362 365 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (362 bp):
TACATATACATAAACTATTTTGGGCGGGATTTTGAAGAGAAGGGAGATTGAGATTGACTGAACTG
GCAGTTTTATTGCAATATATAGGTATAGCGAATTACCGTATTGCACTATACTACATGTACGTTAG
CTACGCTATGTACCATTAACTGAACTGGTAGTTTTACTGTAATATATCAGTATAGAGGATTATCG
TATTGCACTGTACCGCATGTACATTAGATACACTACGTACCATTGGCTGAACTGGCAATTTTACT
GCAATCTATCGGTATAGCAGATTACCACATTGCACTGTACCGCATGTACGTTAGATACGCTACGT
ACCACTATCTGATCTGGTAGTTCATACTGTATTTCAG
Found at i:20085928 original size:184 final size:185
Alignment explanation
Indices: 20085310--20085975 Score: 709
Period size: 184 Copynumber: 3.6 Consensus size: 185
20085300 GGAGATTGAG
* * ** *
20085310 ATTGACTGAACTGGCAGTTTTATTGCAATATATAGGTATAGCGAATTACCGTATTGCACTATACT
1 ATTGACTGAACTGGCAATTTTACTGCAATATATAGGTATAGCGAATTACCACATTGCACTATACC
* * * *
20085375 ACATGTACGTTAGCTACGCTATGTACCATTAACTGAACTGGTAGTT-TTACTGTAATATATCAGT
66 ACATGTACGTTAGATACGCTACGTACCACTAACTGAACTGGTAGTTCATACTGTAATATATCAGT
20085439 ATAGAGGATTATCGTATTGCACTGTACCGCATGTACATTAGATACACTACGTACC
131 ATAGAGGATTATCGTATTGCACTGTACCGCATGTACATTAGATACACTACGTACC
* * * *
20085494 ATTGGCTGAACTGGCAATTTTACTGCAATCTATCGGTATAGC-AGATTACCACATTGCACTGTAC
1 ATTGACTGAACTGGCAATTTTACTGCAATATATAGGTATAGCGA-ATTACCACATTGCACTATAC
* * *
20085558 CGCATGTACGTTAGATACGCTACGTACCACTATCTGATCTGGTAGTTCATACTGT-AT-T-TCAG
65 CACATGTACGTTAGATACGCTACGTACCACTAACTGAACTGGTAGTTCATACTGTAATATATCAG
* * * * * ** * * * ** * ** *
20085620 TACATATA-CATAAAC-TATT---TTGGGCGGGATTTTGA--AGAGA-AGGGA-GATTGA-G
130 T--ATAGAGGATTATCGTATTGCACTGTACCGCATGTACATTAGATACA-CTACG--T-ACC
* * ** *
20085672 ATTGACTGAACTGGCAGTTTTATTGCAATATATAGGTATAGCGAATTACCGTATTGCACTATACT
1 ATTGACTGAACTGGCAATTTTACTGCAATATATAGGTATAGCGAATTACCACATTGCACTATACC
* * * *
20085737 ACATGTACGTTAGCTACGCTATGTACCATTAACTGAACTGGTAGTT-TTACTGTAATATATCAGT
66 ACATGTACGTTAGATACGCTACGTACCACTAACTGAACTGGTAGTTCATACTGTAATATATCAGT
20085801 ATAGAGGATTATCGTATTGCACTGTACCGCATGTACATTAGATACACTACGTACC
131 ATAGAGGATTATCGTATTGCACTGTACCGCATGTACATTAGATACACTACGTACC
* * * *
20085856 ATTGGCTGAACTGGCAATTTTACTGCAATCTATCGGTATAGC-AGATTACCACATTGCACTGTAC
1 ATTGACTGAACTGGCAATTTTACTGCAATATATAGGTATAGCGA-ATTACCACATTGCACTATAC
* * *
20085920 CGCATGTACGTTAGATACGCTACGTACCACTATCTGATCTGGTAGTTCATACTGTA
65 CACATGTACGTTAGATACGCTACGTACCACTAACTGAACTGGTAGTTCATACTGTA
20085976 TTTCAGTACT
Statistics
Matches: 378, Mismatches: 80, Indels: 47
0.75 0.16 0.09
Matches are distributed among these distances:
176 2 0.01
177 11 0.03
178 101 0.27
179 15 0.04
180 9 0.02
182 9 0.02
183 16 0.04
184 195 0.52
185 18 0.05
186 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (185 bp):
ATTGACTGAACTGGCAATTTTACTGCAATATATAGGTATAGCGAATTACCACATTGCACTATACC
ACATGTACGTTAGATACGCTACGTACCACTAACTGAACTGGTAGTTCATACTGTAATATATCAGT
ATAGAGGATTATCGTATTGCACTGTACCGCATGTACATTAGATACACTACGTACC
Found at i:20090322 original size:10 final size:10
Alignment explanation
Indices: 20090309--20090385 Score: 59
Period size: 10 Copynumber: 7.7 Consensus size: 10
20090299 TCCTACTTTG
20090309 TTCTGTTCTA
1 TTCTGTTCTA
*
20090319 TTCTGTTCTG
1 TTCTGTTCTA
*
20090329 TAT-TGCTCTA
1 T-TCTGTTCTA
* * *
20090339 CTCTATTCCA
1 TTCTGTTCTA
20090349 -TCTTGTTCTA
1 TTC-TGTTCTA
*
20090359 TTCTGCTCTA
1 TTCTGTTCTA
20090369 TTCTGTTCTA
1 TTCTGTTCTA
*
20090379 TTTTGTT
1 TTCTGTT
20090386 TGAATTGTAT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
9 3 0.06
10 45 0.88
11 3 0.06
ACGTcount: A:0.10, C:0.22, G:0.10, T:0.57
Consensus pattern (10 bp):
TTCTGTTCTA
Found at i:20090385 original size:30 final size:30
Alignment explanation
Indices: 20090309--20090385 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
20090299 TCCTACTTTG
* *
20090309 TTCTGTTCTATTCTGTTCTGTATTGCTCTA
1 TTCTGTTCTATTTTGTTCTATATTGCTCTA
* * * *
20090339 CTCTATTCCATCTTGTTCTAT-TCTGCTCTA
1 TTCTGTTCTATTTTGTTCTATAT-TGCTCTA
20090369 TTCTGTTCTATTTTGTT
1 TTCTGTTCTATTTTGTT
20090386 TGAATTGTAT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
29 1 0.03
30 35 0.97
ACGTcount: A:0.10, C:0.22, G:0.10, T:0.57
Consensus pattern (30 bp):
TTCTGTTCTATTTTGTTCTATATTGCTCTA
Found at i:20090424 original size:15 final size:15
Alignment explanation
Indices: 20090379--20090429 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
20090369 TTCTGTTCTA
*
20090379 TTTTG-TTTGAATTG
1 TTTTGTTTTGATTTG
* *
20090393 TATTGTTTTGATCTG
1 TTTTGTTTTGATTTG
*
20090408 TTTTGTTTTGCTTTG
1 TTTTGTTTTGATTTG
*
20090423 TTCTGTT
1 TTTTGTT
20090430 GTACTACCTC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 4 0.14
15 25 0.86
ACGTcount: A:0.08, C:0.06, G:0.20, T:0.67
Consensus pattern (15 bp):
TTTTGTTTTGATTTG
Found at i:20092093 original size:23 final size:23
Alignment explanation
Indices: 20092067--20092110 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
20092057 AGTAAAATAT
20092067 TTAATAAATATAG-TAATTTTTAA
1 TTAATAAATA-AGTTAATTTTTAA
*
20092090 TTAATATATAAGTTAATTTTT
1 TTAATAAATAAGTTAATTTTT
20092111 CTTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
TTAATAAATAAGTTAATTTTTAA
Found at i:20099370 original size:27 final size:26
Alignment explanation
Indices: 20099322--20099453 Score: 133
Period size: 27 Copynumber: 4.9 Consensus size: 26
20099312 GTGAGGCTGC
* *
20099322 CAGATATTGTGAC-GAAGTCACCAGAT
1 CAGATATTGTGGCAG-AGCCACCAGAT
*
20099348 ACAGATATTGTGGCAGAGCCACCAAAT
1 -CAGATATTGTGGCAGAGCCACCAGAT
*
20099375 CAGATAATTGTGGCATAGCCACCAGGA-
1 CAGAT-ATTGTGGCAGAGCCACCA-GAT
*
20099402 CAGATATATGTGGTAGAGCCACCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
* *
20099429 CAGATAATTGTAGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
20099454 GACGCTTCCT
Statistics
Matches: 89, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
26 9 0.10
27 76 0.85
28 4 0.04
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAT
Found at i:20099414 original size:54 final size:53
Alignment explanation
Indices: 20099348--20099456 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 53
20099338 GTCACCAGAT
*
20099348 ACAGATATTGTGGCAGAGCCACCAAATCAGATAATTGTGGCATAGCCACCAGG
1 ACAGATATTGTGGCAGAGCCACCAAATCAGATAATTGTAGCATAGCCACCAGG
* *
20099401 ACAGATATATGTGGTAGAGCCACCAGATCAGATAATTGTAGCATAGCCACCAGG
1 ACAGATAT-TGTGGCAGAGCCACCAAATCAGATAATTGTAGCATAGCCACCAGG
20099455 AC
1 AC
20099457 GCTTCCTCCA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 8 0.15
54 44 0.85
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (53 bp):
ACAGATATTGTGGCAGAGCCACCAAATCAGATAATTGTAGCATAGCCACCAGG
Found at i:20108463 original size:21 final size:21
Alignment explanation
Indices: 20108428--20108476 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
20108418 ATAAATAAAA
*
20108428 TCATTCA-TGTCAATTCCCTG
1 TCATTCACTATCAATTCCCTG
*
20108448 TCATTCACTATCAATTTCCTG
1 TCATTCACTATCAATTCCCTG
20108469 TCATTCAC
1 TCATTCAC
20108477 AACTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.41
Consensus pattern (21 bp):
TCATTCACTATCAATTCCCTG
Found at i:20112162 original size:20 final size:19
Alignment explanation
Indices: 20112117--20112163 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
20112107 GTAACATAGT
*
20112117 TATTATTTTAAATGTTTTGA
1 TATTA-TTTAAATGATTTGA
*
20112137 TGTTATTTAAATGATTTGA
1 TATTATTTAAATGATTTGA
20112156 TAATTATT
1 T-ATTATT
20112164 ATGAGATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (19 bp):
TATTATTTAAATGATTTGA
Found at i:20118348 original size:50 final size:50
Alignment explanation
Indices: 20118273--20118373 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
20118263 TACTTTTACT
20118273 CGTATTCTCGTAAACCTACCGATCCCCCTTAAGATCAAAGTAGTGTCATA
1 CGTATTCTCGTAAACCTACCGATCCCCCTTAAGATCAAAGTAGTGTCATA
* *
20118323 CGTATTCTTGTAAACTTACCGATCCCCCTTAAGATCAAAGTAGTGTCATA
1 CGTATTCTCGTAAACCTACCGATCCCCCTTAAGATCAAAGTAGTGTCATA
20118373 C
1 C
20118374 TCCATAAAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (50 bp):
CGTATTCTCGTAAACCTACCGATCCCCCTTAAGATCAAAGTAGTGTCATA
Found at i:20119074 original size:43 final size:43
Alignment explanation
Indices: 20119022--20119127 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 43
20119012 TTATCATATG
*
20119022 AAAATTATATATAAAT-T-TATAATACTCATTAACACACATAA
1 AAAAATATATATAAATATGTATAATACTCATTAACACACATAA
20119063 AAAAA-ACTATATTAAATATGGTATAATACTCATTAACACACATAA
1 AAAAATA-TATA-TAAATAT-GTATAATACTCATTAACACACATAA
20119108 AAAAATATATATGAAATATG
1 AAAAATATATAT-AAATATG
20119128 ATTTTACTTA
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
40 1 0.02
41 8 0.14
42 5 0.09
43 1 0.02
44 2 0.04
45 39 0.68
46 1 0.02
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (43 bp):
AAAAATATATATAAATATGTATAATACTCATTAACACACATAA
Found at i:20119089 original size:45 final size:45
Alignment explanation
Indices: 20119039--20119127 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
20119029 TATATAAATT
*
20119039 TATAATACTCATTAACACACATAAAAAAA-ACTATATTAAATATGG
1 TATAATACTCATTAACACACATAAAAAAATA-TATATGAAATATGG
20119084 TATAATACTCATTAACACACATAAAAAAATATATATGAAATATG
1 TATAATACTCATTAACACACATAAAAAAATATATATGAAATATG
20119128 ATTTTACTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.29
Consensus pattern (45 bp):
TATAATACTCATTAACACACATAAAAAAATATATATGAAATATGG
Found at i:20119532 original size:3 final size:3
Alignment explanation
Indices: 20119524--20119579 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
20119514 TAACCAAAGC
20119524 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20119572 TTA TTA TT
1 TTA TTA TT
20119580 TCAATGGTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20121344 original size:19 final size:19
Alignment explanation
Indices: 20121320--20121360 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
20121310 CTTTTTCATC
20121320 TTTTTAAGGGTAGTTTACT
1 TTTTTAAGGGTAGTTTACT
*
20121339 TTTTTAAGGTTAGTTTACT
1 TTTTTAAGGGTAGTTTACT
20121358 TTT
1 TTT
20121361 ATGATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.05, G:0.17, T:0.59
Consensus pattern (19 bp):
TTTTTAAGGGTAGTTTACT
Found at i:20125003 original size:133 final size:133
Alignment explanation
Indices: 20124855--20125129 Score: 514
Period size: 133 Copynumber: 2.1 Consensus size: 133
20124845 CATTTAGTTT
20124855 ATATATATATACATATATAATTTGTAGCATATAAGGAATTAAATATATATGGTACTATAATGTAA
1 ATATATATATACATATATAATTTGTAGCATATAAGGAATTAAATATATATGGTACTATAATGTAA
* *
20124920 ATGCTAAAAATATATTAAGTTATTTATGTTTAAAAATTTAATAAGCGAAAGGCATATAATGGTAG
66 ATGCTAAAAATATATTAAGTTATATATGTTTAAAAATTTAATAAGAGAAAGGCATATAATGGTAG
20124985 TAA
131 TAA
20124988 ATATATATATACATATATAATTTGTAGCATATAAGGAATTAAATATATATGGTACTATAATGTAA
1 ATATATATATACATATATAATTTGTAGCATATAAGGAATTAAATATATATGGTACTATAATGTAA
* *
20125053 ATGCTAAAAATATATTAAGTTATATATGTTTAGAAATTTAATAAGAGAAATGCATATAATGGTAG
66 ATGCTAAAAATATATTAAGTTATATATGTTTAAAAATTTAATAAGAGAAAGGCATATAATGGTAG
20125118 TAA
131 TAA
20125121 ATATATATA
1 ATATATATA
20125130 ACTAATTATT
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 138 1.00
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (133 bp):
ATATATATATACATATATAATTTGTAGCATATAAGGAATTAAATATATATGGTACTATAATGTAA
ATGCTAAAAATATATTAAGTTATATATGTTTAAAAATTTAATAAGAGAAAGGCATATAATGGTAG
TAA
Found at i:20130518 original size:24 final size:24
Alignment explanation
Indices: 20130490--20130541 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20130480 TTAGGAAGTC
* *
20130490 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
20130514 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
20130538 AAAT
1 AAAT
20130542 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:20132486 original size:24 final size:24
Alignment explanation
Indices: 20132458--20132509 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20132448 TTAGCAAGTC
* *
20132458 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
20132482 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
20132506 AAAT
1 AAAT
20132510 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:20133895 original size:16 final size:16
Alignment explanation
Indices: 20133861--20133904 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
20133851 ATCTTTTTAT
*
20133861 TTTTTTTACTTTTTGA
1 TTTTTTTACTTTTTCA
20133877 TTTTTTT-CTTATTTCA
1 TTTTTTTACTT-TTTCA
20133893 TTTTTTTA-TTTT
1 TTTTTTTACTTTT
20133905 GTTTTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTTTACTTTTTCA
Found at i:20133897 original size:17 final size:17
Alignment explanation
Indices: 20133853--20133899 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
20133843 TAAATTGTAT
20133853 CTTTTT-ATTTTTTTTA
1 CTTTTTCATTTTTTTTA
*
20133869 CTTTTTGA-TTTTTTT-
1 CTTTTTCATTTTTTTTA
20133884 CTTATTTCATTTTTTT
1 CTT-TTTCATTTTTTT
20133900 ATTTTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 3 0.11
16 17 0.63
17 7 0.26
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.79
Consensus pattern (17 bp):
CTTTTTCATTTTTTTTA
Found at i:20133905 original size:30 final size:31
Alignment explanation
Indices: 20133861--20133919 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
20133851 ATCTTTTTAT
20133861 TTTTTTTACTTTTTGATTTT-TTTCTTATTTCA
1 TTTTTTTAC-TTTTG-TTTTATTTCTTATTTCA
*
20133893 TTTTTTTA-TTTTGTTTTATTTTTTATT
1 TTTTTTTACTTTTGTTTTATTTCTTATT
20133920 ATTAACTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 4 0.16
30 13 0.52
32 8 0.32
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (31 bp):
TTTTTTTACTTTTGTTTTATTTCTTATTTCA
Found at i:20133973 original size:22 final size:22
Alignment explanation
Indices: 20133948--20134008 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
20133938 GTAATGTATA
20133948 TTTAAAATGTTTTA-TAATATTT
1 TTTAAAAT-TTTTATTAATATTT
* *
20133970 TTTAAAATTTTAATTATTATTT
1 TTTAAAATTTTTATTAATATTT
*
20133992 TTAAAAATATTTT-TTAA
1 TTTAAAAT-TTTTATTAA
20134009 CTTTAGATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 4 0.12
22 25 0.78
23 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTAAAATTTTTATTAATATTT
Found at i:20134069 original size:36 final size:36
Alignment explanation
Indices: 20134028--20134107 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
20134018 TATATTTGTG
* *
20134028 AAATTAA-TTTTTATATATTTTAAAAATTTACTTTTA
1 AAATTAATTTTTTA-AAATTTTAAAAATTAACTTTTA
* *
20134064 AAATTAATTTTTTAAAATTTTAAATATTAATTTTTA
1 AAATTAATTTTTTAAAATTTTAAAAATTAACTTTTA
20134100 AATATTAA
1 AA-ATTAA
20134108 CCATATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 27 0.71
37 11 0.29
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (36 bp):
AAATTAATTTTTTAAAATTTTAAAAATTAACTTTTA
Found at i:20134098 original size:14 final size:14
Alignment explanation
Indices: 20134081--20134107 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20134071 TTTTTTAAAA
20134081 TTTTAAATATTAAT
1 TTTTAAATATTAAT
20134095 TTTTAAATATTAA
1 TTTTAAATATTAA
20134108 CCATATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAATATTAAT
Found at i:20134114 original size:23 final size:23
Alignment explanation
Indices: 20134061--20134107 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
20134051 AAATTTACTT
*
20134061 TTAAA-ATTAATTTTTTAAAATT
1 TTAAATATTAATTTTTTAAAATA
20134083 TTAAATATTAA-TTTTT-AAATA
1 TTAAATATTAATTTTTTAAAATA
20134104 TTAA
1 TTAA
20134108 CCATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 10 0.43
23 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAATATTAATTTTTTAAAATA
Found at i:20134389 original size:67 final size:67
Alignment explanation
Indices: 20134264--20134389 Score: 148
Period size: 67 Copynumber: 1.9 Consensus size: 67
20134254 CCATTTCAAA
* * ** *
20134264 TATTAAACATACATTTCAAATTGTTTGTAAAATAAAATTTAAAAAATTGTATGTAAAATTAATAA
1 TATTAAACATACATTTCAAATTGATTATAAAATAAAATTTAAAAAATAATATGAAAAATTAATAA
20134329 AG
66 AG
* * *
20134331 TATTAAACATACATTTCAAA-T-ATTATAAAACTAATAATTTCAAAACTAATTTGAAAAAT
1 TATTAAACATACATTTCAAATTGATTATAAAA-TAA-AATTTAAAAAATAATATGAAAAAT
20134390 ATATATTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
65 7 0.14
66 4 0.08
67 38 0.78
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.37
Consensus pattern (67 bp):
TATTAAACATACATTTCAAATTGATTATAAAATAAAATTTAAAAAATAATATGAAAAATTAATAA
AG
Found at i:20134418 original size:36 final size:35
Alignment explanation
Indices: 20134372--20134481 Score: 152
Period size: 34 Copynumber: 3.2 Consensus size: 35
20134362 TAATAATTTC
* *
20134372 AAAACTAATTTGAAAAATATATATTTAAAATTTATA
1 AAAAATAATTTCAAAAATATATATTTAAAATTTA-A
*
20134408 AAAAATAATTTCAAAAATATATATCT-AAATTTAA
1 AAAAATAATTTCAAAAATATATATTTAAAATTTAA
* *
20134442 AAAAATAATTTTAAAAATA-ATAATTAAAATTTAA
1 AAAAATAATTTCAAAAATATATATTTAAAATTTAA
20134476 AAAAAT
1 AAAAAT
20134482 TGTAAAACAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
33 4 0.06
34 33 0.49
35 7 0.10
36 23 0.34
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (35 bp):
AAAAATAATTTCAAAAATATATATTTAAAATTTAA
Found at i:20134456 original size:14 final size:15
Alignment explanation
Indices: 20134437--20134466 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
20134427 TATATCTAAA
20134437 TTTAAAAA-AATAAT
1 TTTAAAAATAATAAT
20134451 TTTAAAAATAATAAT
1 TTTAAAAATAATAAT
20134466 T
1 T
20134467 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTAAAAATAATAAT
Found at i:20134563 original size:36 final size:37
Alignment explanation
Indices: 20134523--20134597 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
20134513 TTTTAAAATT
20134523 AATAATAT-AAA-TTAAATAAACAAAATAAAA-TAAGAA
1 AATAATATAAAACTTAAA-AAACAAAA-AAAATTAAGAA
*
20134559 AATAATATAAAACTTAAAAAAGAAAAAAAATTAAGAA
1 AATAATATAAAACTTAAAAAACAAAAAAAATTAAGAA
20134596 AA
1 AA
20134598 AGACAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
36 12 0.34
37 18 0.51
38 5 0.14
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (37 bp):
AATAATATAAAACTTAAAAAACAAAAAAAATTAAGAA
Found at i:20134568 original size:18 final size:18
Alignment explanation
Indices: 20134518--20134570 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
20134508 AATTTTTTTA
* *
20134518 AAATTAATAATATAAATT
1 AAATAAATAATATAAAAT
* *
20134536 AAATAAACAAAATAAAAT
1 AAATAAATAATATAAAAT
20134554 AAGA-AAATAATATAAAA
1 AA-ATAAATAATATAAAA
20134571 CTTAAAAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
AAATAAATAATATAAAAT
Found at i:20134597 original size:19 final size:20
Alignment explanation
Indices: 20134573--20134627 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
20134563 ATATAAAACT
20134573 TAAAAAAGAAAAAAAATTAA
1 TAAAAAAGAAAAAAAATTAA
* * *
20134593 -GAAAAAG-ACAAAATTTAA
1 TAAAAAAGAAAAAAAATTAA
20134611 TAAAAAAGTAAAAAAAA
1 TAAAAAAG-AAAAAAAA
20134628 AAGGGTGGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
18 9 0.35
19 12 0.46
21 5 0.19
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (20 bp):
TAAAAAAGAAAAAAAATTAA
Found at i:20134829 original size:14 final size:14
Alignment explanation
Indices: 20134810--20134836 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20134800 AAAAATATGG
20134810 TTAATATTTAAAAA
1 TTAATATTTAAAAA
20134824 TTAATATTTAAAA
1 TTAATATTTAAAA
20134837 TTTTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATATTTAAAAA
Found at i:20134851 original size:37 final size:36
Alignment explanation
Indices: 20134810--20134952 Score: 132
Period size: 37 Copynumber: 4.0 Consensus size: 36
20134800 AAAAATATGG
20134810 TTAATATTTAAAAATTA-ATATTTAAAATTTTAAAAAA
1 TTAAT-TTTAAAAA-TACATATTTAAAATTTTAAAAAA
* * *
20134847 TTAATTTGAAAAATACATTTTTAAAATATATAAAAAA
1 TTAATTTTAAAAATACATATTTAAAAT-TTTAAAAAA
* * * * *
20134884 TTAATTTCACAAATATATATCT-AAA-GTTAAAAAA
1 TTAATTTTAAAAATACATATTTAAAATTTTAAAAAA
* * *
20134918 ATATTTTTAAAAATA-ATAATTAAAATTTTAAAAAA
1 TTAATTTTAAAAATACATATTTAAAATTTTAAAAAA
20134953 GTATTATAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
33 4 0.05
34 21 0.25
35 10 0.12
36 20 0.24
37 30 0.35
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (36 bp):
TTAATTTTAAAAATACATATTTAAAATTTTAAAAAA
Found at i:20135099 original size:22 final size:23
Alignment explanation
Indices: 20135074--20135117 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
20135064 TTAAGGAACA
20135074 AAATA-AAAAAGTAAAA-AAAAAG
1 AAATATAAAAA-TAAAAGAAAAAG
*
20135096 AAATATGAAAATAAAAGAAAAA
1 AAATATAAAAATAAAAGAAAAA
20135118 AACAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (23 bp):
AAATATAAAAATAAAAGAAAAAG
Found at i:20135106 original size:17 final size:16
Alignment explanation
Indices: 20135086--20135159 Score: 55
Period size: 17 Copynumber: 4.6 Consensus size: 16
20135076 ATAAAAAAGT
20135086 AAAAAAAAAGAAATATG
1 AAAAAAAAAGAAA-ATG
*
20135103 AAAATAAAAG-AAA--
1 AAAAAAAAAGAAAATG
*
20135116 AAAACAAAAGAAATATG
1 AAAAAAAAAGAAA-ATG
* * *
20135133 AAAATAAAACAAAAAG
1 AAAAAAAAAGAAAATG
20135149 AAAACAAAAAG
1 AAAA-AAAAAG
20135160 GTGTCAGAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 9 0.20
14 2 0.04
15 2 0.04
16 8 0.18
17 24 0.53
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.08
Consensus pattern (16 bp):
AAAAAAAAAGAAAATG
Found at i:20135107 original size:30 final size:30
Alignment explanation
Indices: 20135073--20135147 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
20135063 ATTAAGGAAC
20135073 AAAATAAAA-AAGTAAAAA-AAAAGAAATATG
1 AAAATAAAAGAA--AAAAACAAAAGAAATATG
20135103 AAAATAAAAGAAAAAAACAAAAGAAATATG
1 AAAATAAAAGAAAAAAACAAAAGAAATATG
*
20135133 AAAATAAAACAAAAA
1 AAAATAAAAGAAAAA
20135148 GAAAACAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 5 0.12
30 35 0.83
31 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.11
Consensus pattern (30 bp):
AAAATAAAAGAAAAAAACAAAAGAAATATG
Found at i:20135158 original size:22 final size:22
Alignment explanation
Indices: 20135116--20135158 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
20135106 ATAAAAGAAA
**
20135116 AAAACAAAAGAAATATGAAAAT
1 AAAACAAAAGAAATACAAAAAT
20135138 AAAACAAAAAGAAA-ACAAAAA
1 AAAAC-AAAAGAAATACAAAAA
20135159 GGTGTCAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (22 bp):
AAAACAAAAGAAATACAAAAAT
Found at i:20144990 original size:23 final size:23
Alignment explanation
Indices: 20144951--20144995 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20144941 ATATAAATCA
* *
20144951 TATAATAAATATAATATGTATTG
1 TATAATAAAAATAATATATATTG
20144974 TATAATTAAAAAT-ATATATATT
1 TATAA-TAAAAATAATATATATT
20144996 TAAATAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TATAATAAAAATAATATATATTG
Found at i:20157391 original size:5 final size:6
Alignment explanation
Indices: 20157366--20157390 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20157356 TTATTTCTTC
20157366 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
20157391 TGTGTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:20158371 original size:30 final size:30
Alignment explanation
Indices: 20158320--20158377 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
20158310 ATTTACGAGC
*
20158320 CTAGGGGTAAAATCGTGATTTTGTAAAAGT
1 CTAGGGGTAAAATCGTCATTTTGTAAAAGT
*
20158350 CTAGGGGTAAAAT-GATCATTTTTTAAAA
1 CTAGGGGTAAAATCG-TCATTTTGTAAAA
20158378 TATGAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.34
Consensus pattern (30 bp):
CTAGGGGTAAAATCGTCATTTTGTAAAAGT
Done.