Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 176 of 211
Found at i:52279523 original size:21 final size:22
Alignment explanation
Indices: 52279498--52279538 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
52279488 GGGGCTTAAG
*
52279498 GTTTAGGGTTTAA-AGTTTATA
1 GTTTAGAGTTTAAGAGTTTATA
52279519 GTTTAGAGTTTAAGAGTTTA
1 GTTTAGAGTTTAAGAGTTTA
52279539 GGATTTATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.46
Consensus pattern (22 bp):
GTTTAGAGTTTAAGAGTTTATA
Found at i:52282085 original size:9 final size:9
Alignment explanation
Indices: 52282073--52282128 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
52282063 AAATATATAT
52282073 CATAACTTA
1 CATAACTTA
52282082 CATAACTTA
1 CATAACTTA
*
52282091 CATAA-ATA
1 CATAACTTA
* * *
52282099 TATATCATA
1 CATAACTTA
*
52282108 TCAAAACTTA
1 -CATAACTTA
52282118 CATAACTTA
1 CATAACTTA
52282127 CA
1 CA
52282129 GAATTTTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
8 5 0.14
9 27 0.73
10 5 0.14
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (9 bp):
CATAACTTA
Found at i:52282203 original size:9 final size:9
Alignment explanation
Indices: 52282163--52282357 Score: 76
Period size: 9 Copynumber: 20.8 Consensus size: 9
52282153 CTTTGGATCT
52282163 TAACTTA-A
1 TAACTTATA
52282171 TAACTTATA
1 TAACTTATA
*
52282180 TATATCATATCA
1 TA-A-CTTAT-A
52282192 TAACTTATA
1 TAACTTATA
* *
52282201 TAACTCACA
1 TAACTTATA
* *
52282210 TAACATACA
1 TAACTTATA
52282219 TAACTTA-A
1 TAACTTATA
52282227 TAACTTATA
1 TAACTTATA
*
52282236 TATATCATATCA
1 TA-A-CTTAT-A
* *
52282248 TAACTCACA
1 TAACTTATA
52282257 TAACTTACATAA
1 TAACTT--AT-A
52282269 TAACTTATA
1 TAACTTATA
*
52282278 TATATCATATCA
1 TA-A-CTTAT-A
*
52282290 TAACTTACA
1 TAACTTATA
* *
52282299 TAACTCACA
1 TAACTTATA
*
52282308 TAACTTACA
1 TAACTTATA
*
52282317 TAA--TACA
1 TAACTTATA
*
52282324 TAA-ATATA
1 TAACTTATA
* *
52282332 TATCATATCA
1 TAACTTAT-A
*
52282342 TAACTTACA
1 TAACTTATA
52282351 TAACTTA
1 TAACTTA
52282358 ATTATACTTA
Statistics
Matches: 147, Mismatches: 23, Indels: 33
0.72 0.11 0.16
Matches are distributed among these distances:
7 7 0.05
8 20 0.14
9 68 0.46
10 20 0.14
11 16 0.11
12 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (9 bp):
TAACTTATA
Found at i:52282227 original size:56 final size:56
Alignment explanation
Indices: 52282163--52282268 Score: 185
Period size: 56 Copynumber: 1.9 Consensus size: 56
52282153 CTTTGGATCT
* *
52282163 TAACTTAATAACTTATATATATCATATCATAACTTATATAACTCACATAACATACA
1 TAACTTAATAACTTATATATATCATATCATAACTCACATAACTCACATAACATACA
*
52282219 TAACTTAATAACTTATATATATCATATCATAACTCACATAACTTACATAA
1 TAACTTAATAACTTATATATATCATATCATAACTCACATAACTCACATAA
52282269 TAACTTATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (56 bp):
TAACTTAATAACTTATATATATCATATCATAACTCACATAACTCACATAACATACA
Found at i:52282254 original size:47 final size:46
Alignment explanation
Indices: 52282200--52282355 Score: 185
Period size: 42 Copynumber: 3.3 Consensus size: 46
52282190 CATAACTTAT
52282200 ATAACTCACATAACATACATAACTTAATAACTTATATATATCATATC
1 ATAACTCACATAAC-TACATAACTTAATAACTTATATATATCATATC
*
52282247 ATAACTCACATAACT---T-ACATAATAACTTATATATATCATATC
1 ATAACTCACATAACTACATAACTTAATAACTTATATATATCATATC
* *
52282289 ATAACTTACATAACTCACATAACTTACATAATACATAAATATATATCATATC
1 ATAACTCACATAACT-ACATAACTTA-AT-A-AC-T-TATATATATCATATC
*
52282341 ATAACTTACATAACT
1 ATAACTCACATAACT
52282356 TAATTATACT
Statistics
Matches: 95, Mismatches: 4, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
42 39 0.41
43 1 0.01
46 2 0.02
47 18 0.19
48 2 0.02
49 1 0.01
50 2 0.02
51 1 0.01
52 29 0.31
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (46 bp):
ATAACTCACATAACTACATAACTTAATAACTTATATATATCATATC
Found at i:52282276 original size:98 final size:93
Alignment explanation
Indices: 52282168--52282369 Score: 300
Period size: 98 Copynumber: 2.1 Consensus size: 93
52282158 GATCTTAACT
*
52282168 TAATAACTTATATATATCATATCATAACTTATATAACTCACATAACATACATAACTTA-ATAACT
1 TAATAACTTATATATATCATATCATAACTTACATAACTCACATAACATACATAA--TACATAA--
52282232 TATATATATCATATCATAACTCACATAACTTACA
62 -ATATATATCATATCATAACTCACATAACTTA-A
*
52282266 TAATAACTTATATATATCATATCATAACTTACATAACTCACATAACTTACATAATACATAAATAT
1 TAATAACTTATATATATCATATCATAACTTACATAACTCACATAACATACATAATACATAAATAT
*
52282331 ATATCATATCATAACTTACATAACTTAA
66 ATATCATATCATAACTCACATAACTTAA
*
52282359 TTAT-ACTTATA
1 TAATAACTTATA
52282370 AATAAACAAC
Statistics
Matches: 99, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
92 7 0.07
93 4 0.04
94 30 0.30
96 2 0.02
97 4 0.04
98 52 0.53
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (93 bp):
TAATAACTTATATATATCATATCATAACTTACATAACTCACATAACATACATAATACATAAATAT
ATATCATATCATAACTCACATAACTTAA
Found at i:52284784 original size:43 final size:42
Alignment explanation
Indices: 52284737--52284872 Score: 115
Period size: 43 Copynumber: 3.3 Consensus size: 42
52284727 TTTAGCGACG
*
52284737 TTTGTGATAAAAGCGCTGTTAAAGATCATGTTCTTTAACGGTA
1 TTTGTGATAAAAGCGCTGTTAAAG-TCATGTTCTTTAGCGGTA
* * * *
52284780 TTTGTG---AAATCGC--TAAAAGTCAT-TCTCTATAGCGGCA
1 TTTGTGATAAAAGCGCTGTTAAAGTCATGT-TCTTTAGCGGTA
* * *
52284817 TTTGTGATAAAAGCG-TCGCTAAAGGTCATGTTCTTTAGCGATG
1 TTTGTGATAAAAGCGCT-GTTAAA-GTCATGTTCTTTAGCGGTA
52284860 TTTGTGATAAAAG
1 TTTGTGATAAAAG
52284873 TACCGCTAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
36 1 0.01
37 19 0.26
38 5 0.07
40 11 0.15
42 3 0.04
43 32 0.44
44 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.35
Consensus pattern (42 bp):
TTTGTGATAAAAGCGCTGTTAAAGTCATGTTCTTTAGCGGTA
Found at i:52286686 original size:16 final size:17
Alignment explanation
Indices: 52286656--52286688 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52286646 ATTGTATAAC
*
52286656 AATTTTTTCTTTTTGTT
1 AATTTTTTCTATTTGTT
52286673 AATTTTTT-TATTTGTT
1 AATTTTTTCTATTTGTT
52286689 TTAGAGACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (17 bp):
AATTTTTTCTATTTGTT
Found at i:52286839 original size:11 final size:11
Alignment explanation
Indices: 52286823--52286853 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
52286813 TATATACATT
52286823 TAAAAATTATA
1 TAAAAATTATA
*
52286834 TAAAAATAATA
1 TAAAAATTATA
52286845 TAAAAATTA
1 TAAAAATTA
52286854 ATACAAGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:52296621 original size:27 final size:27
Alignment explanation
Indices: 52296552--52296759 Score: 220
Period size: 27 Copynumber: 7.7 Consensus size: 27
52296542 AGATATGTCA
* * *
52296552 GAAATGAAAGCCTTTATGGTGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* * *
52296579 GAAGAGAGAGCATTTGTGGCGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* *
52296606 GAAAAGAAAGCTTTTGTGGTGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* *
52296633 GAAATA-AGAGCCTTGGTGGCGAACCAT
1 GAAA-AGAAAGCCTTTGTGGCGAACCAT
**
52296660 GAAAAGAAAGCCTTTGTGGAAAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* * *
52296687 GAAAAGAAAGTCTTTATGGTGAACCAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* * *
52296714 GAAAAGAAATCCTTTGTGGCAAACAAT
1 GAAAAGAAAGCCTTTGTGGCGAACCAT
* *
52296741 GAAATGAAAACCTTTGTGG
1 GAAAAGAAAGCCTTTGTGG
52296760 AAAATCCTGG
Statistics
Matches: 149, Mismatches: 30, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
26 1 0.01
27 147 0.99
28 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (27 bp):
GAAAAGAAAGCCTTTGTGGCGAACCAT
Found at i:52296733 original size:81 final size:81
Alignment explanation
Indices: 52296552--52296763 Score: 248
Period size: 81 Copynumber: 2.6 Consensus size: 81
52296542 AGATATGTCA
* * * * * * **
52296552 GAAATGAAAGCCTTTATGGTGAACCATGAAGAGAGAGCATTTGTGGCGAACCATGAAAAGAAAGC
1 GAAAAGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCCTTTGTGGAAAACCATGAAAAGAAAGC
*
52296617 TTTTGTGGTGAACCAT
66 TTTTATGGTGAACCAT
* *
52296633 GAAATA-AGAGCCTTGGTGGCGAACCATGAAAAGAAAGCCTTTGTGGAAAACCATGAAAAGAAAG
1 GAAA-AGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCCTTTGTGGAAAACCATGAAAAGAAAG
52296697 -TCTTTATGGTGAACCAT
65 CT-TTTATGGTGAACCAT
* * * * *
52296714 GAAAAGAAATCCTTTGTGGCAAACAATGAAATGAAAACCTTTGTGGAAAA
1 GAAAAGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCCTTTGTGGAAAA
52296764 TCCTGGAAGG
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
80 2 0.02
81 108 0.98
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.22
Consensus pattern (81 bp):
GAAAAGAAAGCCTTTGTGGCGAACCATGAAAAGAAAGCCTTTGTGGAAAACCATGAAAAGAAAGC
TTTTATGGTGAACCAT
Found at i:52296918 original size:27 final size:27
Alignment explanation
Indices: 52296888--52296939 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
52296878 AAAGGAACAA
* * *
52296888 TACTCATGGTGAACTTTAAAAGAATGG
1 TACTCATAGCGAACTCTAAAAGAATGG
*
52296915 TACTCATAGCGAACTCTAAAGGAAT
1 TACTCATAGCGAACTCTAAAAGAAT
52296940 TGTATACATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (27 bp):
TACTCATAGCGAACTCTAAAAGAATGG
Found at i:52298741 original size:5 final size:5
Alignment explanation
Indices: 52298728--52298760 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
52298718 AAATGAATTG
*
52298728 TATGG TATGA TATGA TATGA TATGA TATGA TAT
1 TATGA TATGA TATGA TATGA TATGA TATGA TAT
52298761 AGTGGATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (5 bp):
TATGA
Found at i:52299059 original size:36 final size:37
Alignment explanation
Indices: 52299016--52299108 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 37
52299006 AACCTATTAA
*
52299016 GGCGTGTTATTGGTTGGATTGGCCCTTATAAACATTT
1 GGCGTGTTATTGGTTGGATTAGCCCTTATAAACATTT
* * * *
52299053 GG-GTGTTATTGGTTGTATTAGCTCTTATGAGCATTT
1 GGCGTGTTATTGGTTGGATTAGCCCTTATAAACATTT
*
52299089 GGCGTGTT-TCGGTTGGATTA
1 GGCGTGTTATTGGTTGGATTA
52299109 CTTGTGTACT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 41 0.85
37 7 0.15
ACGTcount: A:0.16, C:0.11, G:0.30, T:0.43
Consensus pattern (37 bp):
GGCGTGTTATTGGTTGGATTAGCCCTTATAAACATTT
Found at i:52305371 original size:50 final size:50
Alignment explanation
Indices: 52305315--52305414 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
52305305 AAATATAAAA
* * *
52305315 CCGGTCAGCATGCAAAATTGAAAAGATGTGGTGCCAAATATATAAAGTGT
1 CCGGTCAGCATGCAAAATAGAAAAGATATGGTGCCAAATATACAAAGTGT
* **
52305365 CCGGTCAGCATGCGAAATAGGGAAGATATGGTGCCAAATATACAAAGTGT
1 CCGGTCAGCATGCAAAATAGAAAAGATATGGTGCCAAATATACAAAGTGT
52305415 GGAAGACTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (50 bp):
CCGGTCAGCATGCAAAATAGAAAAGATATGGTGCCAAATATACAAAGTGT
Found at i:52311574 original size:11 final size:11
Alignment explanation
Indices: 52311549--52311582 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
52311539 ATTATTTCTG
52311549 TTGTTTTATCTA
1 TTGTTTTA-CTA
52311561 TTGTTTTACTA
1 TTGTTTTACTA
52311572 TTGTGTTTACT
1 TTGT-TTTACT
52311583 GTTGCTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.65
Consensus pattern (11 bp):
TTGTTTTACTA
Found at i:52329242 original size:71 final size:71
Alignment explanation
Indices: 52329156--52329297 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
52329146 GAGTTCTTTT
*
52329156 TATTTGGGTTATGACTAGTTTCTTTATAATAAGGAACTAACTTTTTGTTGACATATTTTCTAGGT
1 TATTTGGGTTATGACTAGTTTCTTTATAATAAGAAACTAACTTTTTGTTGACATATTTTCTAGGT
52329221 TGAAAA
66 TGAAAA
*
52329227 TATTTGGGTTATGACTGGTTTCTTTATAATAAGAAACTAACTTTTTGTTGACATATTTTCTAGGT
1 TATTTGGGTTATGACTAGTTTCTTTATAATAAGAAACTAACTTTTTGTTGACATATTTTCTAGGT
52329292 TGAAAA
66 TGAAAA
52329298 AGGAAGGGGC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (71 bp):
TATTTGGGTTATGACTAGTTTCTTTATAATAAGAAACTAACTTTTTGTTGACATATTTTCTAGGT
TGAAAA
Found at i:52329957 original size:39 final size:39
Alignment explanation
Indices: 52329892--52330042 Score: 151
Period size: 39 Copynumber: 3.7 Consensus size: 39
52329882 ACGTTGTTTG
* * *
52329892 AAATTATA-TTTAAGTCTTTAAATAAATTATATTAAGTT
1 AAATTATATTTTAAGCCTCTAATTAAATTATATTAAGTT
* * *
52329930 AAATTATATTTTAAACCTCTAAGTAAATTATGTTAAGTT
1 AAATTATATTTTAAGCCTCTAATTAAATTATATTAAGTT
* *
52329969 AACAATTAAATTATGTTGAACCCTCTAATTAAATTATATTAAGTT
1 -A-AATT--A-TAT-TTTAAGCCTCTAATTAAATTATATTAAGTT
* *
52330014 ACATTATATTTTAAGTCTCTAATTAAATT
1 AAATTATATTTTAAGCCTCTAATTAAATT
52330043 TGTGTGATGA
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
38 8 0.09
39 42 0.45
40 4 0.04
41 5 0.05
43 4 0.04
44 4 0.04
45 26 0.28
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (39 bp):
AAATTATATTTTAAGCCTCTAATTAAATTATATTAAGTT
Found at i:52345361 original size:7 final size:7
Alignment explanation
Indices: 52345350--52345390 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
52345340 GTTTTGTTAT
*
52345350 AAAATTT
1 AAAATTC
52345357 AAAATTC
1 AAAATTC
52345364 AAAATTC
1 AAAATTC
52345371 AAAATTC
1 AAAATTC
52345378 AAAATTC
1 AAAATTC
52345385 AAAATT
1 AAAATT
52345391 TTTTTGTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAATTC
Found at i:52349805 original size:18 final size:16
Alignment explanation
Indices: 52349776--52349898 Score: 56
Period size: 17 Copynumber: 7.2 Consensus size: 16
52349766 TCCCATATCC
52349776 TTTAATTAAATTCTATT
1 TTTAATTAAATT-TATT
52349793 TTTAATATAAATTTATT
1 TTTAAT-TAAATTTATT
* *
52349810 ACTTTAAATATAA-TTATCC
1 --TTTAATTA-AATTTAT-T
*
52349829 TATAATT-AA-TTA-T
1 TTTAATTAAATTTATT
*
52349842 TTTAATTTTAATTTATT
1 TTTAA-TTAAATTTATT
* *
52349859 GCTTTAAATATAATTTATCA
1 --TTTAATTA-AATTTAT-T
52349879 TTTAATTAAATTCTATT
1 TTTAATTAAATT-TATT
52349896 TTT
1 TTT
52349899 TATTTTAAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
13 4 0.05
14 2 0.02
15 7 0.09
16 3 0.04
17 23 0.28
18 23 0.28
19 19 0.23
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (16 bp):
TTTAATTAAATTTATT
Found at i:52349824 original size:19 final size:18
Alignment explanation
Indices: 52349775--52349876 Score: 60
Period size: 19 Copynumber: 5.9 Consensus size: 18
52349765 GTCCCATATC
*
52349775 CTTTAATTA-AATTCTATT
1 CTTTAAATATAATT-TATT
52349793 -TTT-AATATAAATTTATT
1 CTTTAAATAT-AATTTATT
*
52349810 ACTTTAAATATAA-TTATC
1 -CTTTAAATATAATTTATT
*
52349828 CTAT-AAT-TAA-TTA-T
1 CTTTAAATATAATTTATT
* *
52349842 -TTTAATTTTAATTTATT
1 CTTTAAATATAATTTATT
52349859 GCTTTAAATATAATTTAT
1 -CTTTAAATATAATTTAT
52349877 CATTTAATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
13 2 0.03
14 2 0.03
15 9 0.14
16 9 0.14
17 11 0.17
18 8 0.12
19 19 0.29
20 5 0.08
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (18 bp):
CTTTAAATATAATTTATT
Found at i:52349900 original size:55 final size:53
Alignment explanation
Indices: 52349771--52349923 Score: 188
Period size: 49 Copynumber: 2.9 Consensus size: 53
52349761 GCCCGTCCCA
* * *
52349771 TATCCTTTAATTAAATTCTATTTTTAATATAAATTTATTACTTTAAATATAAT
1 TATCCTTTAATTAAATTCTATTTTTAATTTTAATTTATTGCTTTAAATATAAT
*
52349824 TATCCTATAATT-AA-T-TA-TTTTAATTTTAATTTATTGCTTTAAATATAATT
1 TATCCTTTAATTAAATTCTATTTTTAATTTTAATTTATTGCTTTAAATATAA-T
* * * *
52349874 TATCATTTAATTAAATTCTATTTTTTATTTTAAATTTCTTGTTTTAAATA
1 TATCCTTTAATTAAATTCTATTTTTAATTTT-AATTTATTGCTTTAAATA
52349924 ATTTTTTAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
49 28 0.33
50 13 0.15
51 3 0.04
52 3 0.04
53 13 0.15
54 9 0.11
55 16 0.19
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (53 bp):
TATCCTTTAATTAAATTCTATTTTTAATTTTAATTTATTGCTTTAAATATAAT
Found at i:52350407 original size:18 final size:19
Alignment explanation
Indices: 52350365--52350409 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
52350355 TCAATATCTT
52350365 AAATTAATGTGGTCCAAAG
1 AAATTAATGTGGTCCAAAG
52350384 AAATTAATGTGGTCCAAA-
1 AAATTAATGTGGTCCAAAG
52350402 AAATTAAT
1 AAATTAAT
52350410 TAGTACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.29
Consensus pattern (19 bp):
AAATTAATGTGGTCCAAAG
Found at i:52351614 original size:11 final size:11
Alignment explanation
Indices: 52351598--52351649 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
52351588 TATCTTTAAT
52351598 AATAATAATAC
1 AATAATAATAC
52351609 AATAATAATAC
1 AATAATAATAC
* **
52351620 TTATAAT-ATTT
1 -AATAATAATAC
52351631 AATAATAATAC
1 AATAATAATAC
52351642 AATAATAA
1 AATAATAA
52351650 AAATATGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 5 0.15
11 23 0.70
12 5 0.15
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAATAATAC
Found at i:52351639 original size:33 final size:34
Alignment explanation
Indices: 52351574--52351649 Score: 111
Period size: 33 Copynumber: 2.2 Consensus size: 34
52351564 TATGTTGAAT
*
52351574 AATAATAATACTTATATCTTTAATAATAATAATAC
1 AATAATAATACTTATATCATT-ATAATAATAATAC
52351609 AATAATAATACTTATAAT-ATT-TAATAATAATAC
1 AATAATAATACTTAT-ATCATTATAATAATAATAC
52351642 AATAATAA
1 AATAATAA
52351650 AAATATGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
33 20 0.51
35 17 0.44
36 2 0.05
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (34 bp):
AATAATAATACTTATATCATTATAATAATAATAC
Found at i:52352430 original size:14 final size:14
Alignment explanation
Indices: 52352411--52352438 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52352401 ACGAAATCCC
52352411 ATATGTTCTTGCAT
1 ATATGTTCTTGCAT
52352425 ATATGTTCTTGCAT
1 ATATGTTCTTGCAT
52352439 TCGACCAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
ATATGTTCTTGCAT
Found at i:52356210 original size:22 final size:22
Alignment explanation
Indices: 52356184--52356237 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
52356174 CTTGTTTATT
52356184 TTATTTTTTTCCATTATTAATG
1 TTATTTTTTTCCATTATTAATG
* *
52356206 TTATTTTATTCCATTATTAGTG
1 TTATTTTTTTCCATTATTAATG
52356228 TTATTTTTTT
1 TTATTTTTTT
52356238 TAAATACTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.07, G:0.06, T:0.67
Consensus pattern (22 bp):
TTATTTTTTTCCATTATTAATG
Found at i:52366881 original size:143 final size:142
Alignment explanation
Indices: 52366562--52367008 Score: 603
Period size: 143 Copynumber: 3.1 Consensus size: 142
52366552 ACTACGGTGA
* *
52366562 ATCTTATC-TCCTTGAAGTTGCAGTAGAGCAGATTTAAGCCACCAGCCTTATCTTCCTGAAGTCG
1 ATCTTATCTTCC-TGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATC-TCCTGAAGTTG
* * * *
52366626 CAGCAGAGCAGACTGAAGGTAATGAATCTTATTTCCCTGACGTTGTAGT-GAACAGATTAAAGCT
64 CAGCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCT
**
52366690 ACAAATTATGATGG
129 ACAAATTATGGCGG
*
52366704 ATCTTATCTTCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACCAGCCTTATCTCCGTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCC-TGAAGTTGC
* * * * *
52366769 AGCGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACATATTAAAGCTA
65 AGCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTA
52366834 CAAATTATGGCGG
130 CAAATTATGGCGG
* * * ** *
52366847 ATCTTATC-TCCTTGAAGTTGTAATAGAGCAGATTGATGTTACCAGCCTTATCTCCCTGAAATTG
1 ATCTTATCTTCC-TGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCT-CCTGAAGTTG
* * * *
52366911 CAGCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCGTTGTAGTGGAATAGATTAAAGCT
64 CAGCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCT
52366976 ACAAATTATGGCGG
129 ACAAATTATGGCGG
*
52366990 ACCTTATCTTCCTGAAGTT
1 ATCTTATCTTCCTGAAGTT
52367009 ATAGCGGAGC
Statistics
Matches: 269, Mismatches: 30, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
141 3 0.01
142 97 0.36
143 164 0.61
144 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (142 bp):
ATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCCTGAAGTTGCA
GCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTAC
AAATTATGGCGG
Found at i:52367023 original size:99 final size:99
Alignment explanation
Indices: 52366892--52367120 Score: 332
Period size: 99 Copynumber: 2.3 Consensus size: 99
52366882 ATGTTACCAG
* * * * *
52366892 CCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCGTTGT
1 CCTTATCTTCCTGAAGTTACAGCGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGGCATTGT
*
52366957 AGTGGAATAGATTAAAGCTACAAATTATGGCGGA
66 AATGGAATAGATTAAAGCTACAAATTATGGCGGA
* * *
52366991 CCTTATCTTCCTGAAGTTATAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGTATTGT
1 CCTTATCTTCCTGAAGTTACAGCGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGGCATTGT
*
52367056 AATGGAATAGATTAAAGCTACAAATTATGGTGGA
66 AATGGAATAGATTAAAGCTACAAATTATGGCGGA
* * * *
52367090 TCTTATCTTCCTAAAGTTGCAGTGGAGCAGA
1 CCTTATCTTCCTGAAGTTACAGCGGAGCAGA
52367121 TCGAAACCAC
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
99 115 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (99 bp):
CCTTATCTTCCTGAAGTTACAGCGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGGCATTGT
AATGGAATAGATTAAAGCTACAAATTATGGCGGA
Found at i:52367154 original size:44 final size:45
Alignment explanation
Indices: 52367091--52367196 Score: 133
Period size: 44 Copynumber: 2.4 Consensus size: 45
52367081 TATGGTGGAT
* *
52367091 CTTATCTTCCTAAAGTTGCAGTGGAGCAGATCGAAACCAC-AATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAACCACTAATC
* * **
52367135 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACTAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAACCACTAATC
* *
52367180 CGTATCTCCTTGAAGTT
1 CTTATCTCCCTGAAGTT
52367197 ATAGCGGAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 34 0.64
45 19 0.36
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAACCACTAATC
Found at i:52367219 original size:242 final size:242
Alignment explanation
Indices: 52366749--52367221 Score: 531
Period size: 242 Copynumber: 2.0 Consensus size: 242
52366739 AAGCCACCAG
* * *
52366749 CCTTATCTCCGTGAAGTTGCAGCGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGGCATTGC
1 CCTTATCTCCGTGAAGTTACAGCGGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCATTGC
* * * *
52366814 AGTGGAACATATTAAAGCTACAAATTATGGCGGATCTTATCTCCTTGAAGTTGTAATAGAGCAGA
66 AATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTCCTTAAAGTTGCAATAGAGCAGA
* **** * * *
52366879 TTGATGTTACCAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCTTATT
131 TCGAAACCACAAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCGTATC
** * * *
52366944 TCCCTGGCGTTGTAGTGGAATAGATTAAAGCTACAAATTATGGCGGA
196 TCCCTGAAGTTATAGCGGAATAGATCAAAGCTACAAATTATGGCGGA
* * *
52366991 CCTTATCTTCC-TGAAGTTATAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGTATTG
1 CCTTATC-TCCGTGAAGTTACAGCGGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCATTG
* * * * *
52367055 TAATGGAATAGATTAAAGCTACAAATTATGGTGGATCTTATCTTCC-TAAAGTTGCAGTGGAGCA
65 CAATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATC-TCCTTAAAGTTGCAATAGAGCA
* * * ** * *
52367119 GATCGAAACCACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-A-TTACTAATCCG
129 GATCGAAACCACAAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACAT-CAAAT-CG
* * * *
52367182 TATCTCCTTGAAGTTATAGCGGAGTGGATCGAAGCTACAA
192 TATCTCCCTGAAGTTATAGCGGAATAGATCAAAGCTACAA
52367222 GTCTCTTTTC
Statistics
Matches: 188, Mismatches: 39, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
240 1 0.01
241 5 0.03
242 176 0.94
243 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (242 bp):
CCTTATCTCCGTGAAGTTACAGCGGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCATTGC
AATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTCCTTAAAGTTGCAATAGAGCAGA
TCGAAACCACAAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCGTATC
TCCCTGAAGTTATAGCGGAATAGATCAAAGCTACAAATTATGGCGGA
Found at i:52368684 original size:21 final size:22
Alignment explanation
Indices: 52368660--52368700 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52368650 TTAAGTTAAT
52368660 ATTATTT-TTATTTTTATATCC
1 ATTATTTATTATTTTTATATCC
*
52368681 ATTATTTATTTTTTTTATAT
1 ATTATTTATTATTTTTATAT
52368701 ATCTAAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTATTTATTATTTTTATATCC
Found at i:52368936 original size:18 final size:17
Alignment explanation
Indices: 52368906--52368939 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52368896 TAAATCTATC
52368906 TTATATTAGTTTTTATT
1 TTATATTAGTTTTTATT
*
52368923 TTATCATTATTTTTTAT
1 TTAT-ATTAGTTTTTAT
52368940 ATTGGCTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTATATTAGTTTTTATT
Found at i:52370557 original size:41 final size:41
Alignment explanation
Indices: 52370512--52370605 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 41
52370502 CATTAGTGGT
* * * * *
52370512 GTTTTTTCTATAAACGCTGTAAAAGGTAAAACAATAATGGC
1 GTTTTTCCTATAAAAGCAGCAAAAGGTAAAACAATAACGGC
* * **
52370553 GTTTTACCTATAAAAGCAGCAAAAGTTAAAGTAATAACGGC
1 GTTTTTCCTATAAAAGCAGCAAAAGGTAAAACAATAACGGC
*
52370594 GTTTTTCATATA
1 GTTTTTCCTATA
52370606 GCGCGAATTT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (41 bp):
GTTTTTCCTATAAAAGCAGCAAAAGGTAAAACAATAACGGC
Found at i:52374511 original size:7 final size:7
Alignment explanation
Indices: 52374499--52374524 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52374489 AAAATAATTA
52374499 GATACTT
1 GATACTT
52374506 GATACTT
1 GATACTT
52374513 GATACTT
1 GATACTT
52374520 GATAC
1 GATAC
52374525 ATATTATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (7 bp):
GATACTT
Found at i:52374784 original size:90 final size:90
Alignment explanation
Indices: 52374631--52374807 Score: 354
Period size: 90 Copynumber: 2.0 Consensus size: 90
52374621 AATGGATAAG
52374631 AATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAATTT
1 AATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAATTT
52374696 TGCATTTCAAAATGCAAGCCAAAAT
66 TGCATTTCAAAATGCAAGCCAAAAT
52374721 AATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAATTT
1 AATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAATTT
52374786 TGCATTTCAAAATGCAAGCCAA
66 TGCATTTCAAAATGCAAGCCAA
52374808 GAGAATATGA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (90 bp):
AATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAATTT
TGCATTTCAAAATGCAAGCCAAAAT
Found at i:52389229 original size:143 final size:142
Alignment explanation
Indices: 52388910--52389356 Score: 603
Period size: 143 Copynumber: 3.1 Consensus size: 142
52388900 ACTACGGTGA
* *
52388910 ATCTTATC-TCCTTGAAGTTGCAGTAGAGCAGATTTAAGCCACCAGCCTTATCTTCCTGAAGTCG
1 ATCTTATCTTCC-TGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATC-TCCTGAAGTTG
* * * *
52388974 CAGCAGAGCAGACTGAAGGTAATGAATCTTATTTCCCTGACGTTGTAGT-GAACAGATTAAAGCT
64 CAGCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCT
**
52389038 ACAAATTATGATGG
129 ACAAATTATGGCGG
*
52389052 ATCTTATCTTCCTGAAGTTGCAGTAGAGTAGATTGAAGCCACCAGCCTTATCTCCGTGAAGTTGC
1 ATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCC-TGAAGTTGC
* * * * *
52389117 AGCGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACATATTAAAGCTA
65 AGCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTA
52389182 CAAATTATGGCGG
130 CAAATTATGGCGG
* * * ** *
52389195 ATCTTATC-TCCTTGAAGTTGTAATAGAGCAGATTGATGTTACCAGCCTTATCTCCCTGAAATTG
1 ATCTTATCTTCC-TGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCT-CCTGAAGTTG
* * * *
52389259 CAGCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCGTTGTAGTGGAATAGATTAAAGCT
64 CAGCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCT
52389324 ACAAATTATGGCGG
129 ACAAATTATGGCGG
*
52389338 ACCTTATCTTCCTGAAGTT
1 ATCTTATCTTCCTGAAGTT
52389357 ATAGCGGAGC
Statistics
Matches: 269, Mismatches: 30, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
141 3 0.01
142 97 0.36
143 164 0.61
144 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (142 bp):
ATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTCCTGAAGTTGCA
GCGGAGCAGACTGAAGATAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAGCTAC
AAATTATGGCGG
Found at i:52389371 original size:99 final size:99
Alignment explanation
Indices: 52389240--52389468 Score: 332
Period size: 99 Copynumber: 2.3 Consensus size: 99
52389230 ATGTTACCAG
* * * * *
52389240 CCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCGTTGT
1 CCTTATCTTCCTGAAGTTACAGCGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGGCATTGT
*
52389305 AGTGGAATAGATTAAAGCTACAAATTATGGCGGA
66 AATGGAATAGATTAAAGCTACAAATTATGGCGGA
* * *
52389339 CCTTATCTTCCTGAAGTTATAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGTATTGT
1 CCTTATCTTCCTGAAGTTACAGCGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGGCATTGT
*
52389404 AATGGAATAGATTAAAGCTACAAATTATGGTGGA
66 AATGGAATAGATTAAAGCTACAAATTATGGCGGA
* * * *
52389438 TCTTATCTTCCTAAAGTTGCAGTGGAGCAGA
1 CCTTATCTTCCTGAAGTTACAGCGGAGCAGA
52389469 TCGAAACCAC
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
99 115 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (99 bp):
CCTTATCTTCCTGAAGTTACAGCGGAGCAGACTGAAGACAACAAATCTTATTTCCCTGGCATTGT
AATGGAATAGATTAAAGCTACAAATTATGGCGGA
Found at i:52389502 original size:44 final size:45
Alignment explanation
Indices: 52389439--52389544 Score: 133
Period size: 44 Copynumber: 2.4 Consensus size: 45
52389429 TATGGTGGAT
* *
52389439 CTTATCTTCCTAAAGTTGCAGTGGAGCAGATCGAAACCAC-AATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAACCACTAATC
* * **
52389483 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACTAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAACCACTAATC
* *
52389528 CGTATCTCCTTGAAGTT
1 CTTATCTCCCTGAAGTT
52389545 ATAGCGGAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 34 0.64
45 19 0.36
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAACCACTAATC
Found at i:52389567 original size:242 final size:242
Alignment explanation
Indices: 52389097--52389569 Score: 531
Period size: 242 Copynumber: 2.0 Consensus size: 242
52389087 AAGCCACCAG
* * *
52389097 CCTTATCTCCGTGAAGTTGCAGCGGAGCAGACTAAAGATAGCGAATCTTATTTCCCTGGCATTGC
1 CCTTATCTCCGTGAAGTTACAGCGGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCATTGC
* * * *
52389162 AGTGGAACATATTAAAGCTACAAATTATGGCGGATCTTATCTCCTTGAAGTTGTAATAGAGCAGA
66 AATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTCCTTAAAGTTGCAATAGAGCAGA
* **** * * *
52389227 TTGATGTTACCAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCTTATT
131 TCGAAACCACAAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCGTATC
** * * *
52389292 TCCCTGGCGTTGTAGTGGAATAGATTAAAGCTACAAATTATGGCGGA
196 TCCCTGAAGTTATAGCGGAATAGATCAAAGCTACAAATTATGGCGGA
* * *
52389339 CCTTATCTTCC-TGAAGTTATAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGGTATTG
1 CCTTATC-TCCGTGAAGTTACAGCGGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCATTG
* * * * *
52389403 TAATGGAATAGATTAAAGCTACAAATTATGGTGGATCTTATCTTCC-TAAAGTTGCAGTGGAGCA
65 CAATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATC-TCCTTAAAGTTGCAATAGAGCA
* * * ** * *
52389467 GATCGAAACCACAATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-A-TTACTAATCCG
129 GATCGAAACCACAAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACAT-CAAAT-CG
* * * *
52389530 TATCTCCTTGAAGTTATAGCGGAGTGGATCGAAGCTACAA
192 TATCTCCCTGAAGTTATAGCGGAATAGATCAAAGCTACAA
52389570 GTCTCTTTTC
Statistics
Matches: 188, Mismatches: 39, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
240 1 0.01
241 5 0.03
242 176 0.94
243 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (242 bp):
CCTTATCTCCGTGAAGTTACAGCGGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCATTGC
AATGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTCCTTAAAGTTGCAATAGAGCAGA
TCGAAACCACAAGCCTTATCTCCCTGAAATTGCAGCGGAGCAGACTGAAGACATCAAATCGTATC
TCCCTGAAGTTATAGCGGAATAGATCAAAGCTACAAATTATGGCGGA
Found at i:52391032 original size:21 final size:21
Alignment explanation
Indices: 52391008--52391047 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
52390998 TTAAGTTAAT
52391008 ATTATTT-TTATTTTTATATCC
1 ATTATTTATT-TTTTTATATCC
52391029 ATTATTTATTTTTTTATAT
1 ATTATTTATTTTTTTATAT
52391048 ATCTAAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTATTTATTTTTTTATATCC
Found at i:52391283 original size:18 final size:17
Alignment explanation
Indices: 52391253--52391286 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52391243 TAAATCTATC
52391253 TTATATTAGTTTTTATT
1 TTATATTAGTTTTTATT
*
52391270 TTATCATTATTTTTTAT
1 TTAT-ATTAGTTTTTAT
52391287 ATTGGCTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTATATTAGTTTTTATT
Found at i:52392903 original size:41 final size:41
Alignment explanation
Indices: 52392858--52392951 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 41
52392848 CATTAGTGGT
* * * * *
52392858 GTTTTTTCTATAAACGCTGTAAAAGGTAAAACAATAATGGC
1 GTTTTTCCTATAAAAGCAGCAAAAGGTAAAACAATAACGGC
* * **
52392899 GTTTTACCTATAAAAGCAGCAAAAGTTAAAGTAATAACGGC
1 GTTTTTCCTATAAAAGCAGCAAAAGGTAAAACAATAACGGC
*
52392940 GTTTTTCATATA
1 GTTTTTCCTATA
52392952 GCGCGAATTT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (41 bp):
GTTTTTCCTATAAAAGCAGCAAAAGGTAAAACAATAACGGC
Found at i:52397124 original size:90 final size:90
Alignment explanation
Indices: 52396971--52397147 Score: 354
Period size: 90 Copynumber: 2.0 Consensus size: 90
52396961 AATGGATAAG
52396971 AATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAATTT
1 AATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAATTT
52397036 TGCATTTCAAAATGCAAGCCAAAAT
66 TGCATTTCAAAATGCAAGCCAAAAT
52397061 AATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAATTT
1 AATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAATTT
52397126 TGCATTTCAAAATGCAAGCCAA
66 TGCATTTCAAAATGCAAGCCAA
52397148 GAGAATATGA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (90 bp):
AATTGGATGGATTTGTCAAGGGTAAGCAACTACTATCGAAATGGAGTACAAACTTTTCTAAATTT
TGCATTTCAAAATGCAAGCCAAAAT
Found at i:52404353 original size:43 final size:44
Alignment explanation
Indices: 52404292--52404383 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 44
52404282 GCATTTTCCC
* * * *
52404292 ACAAACACTGCTATAGAACATGATCTTTAGCGGCACTTTTA-CT
1 ACAAACACCGCTAAAGAACATGATCTTTAGCGGCAATTCTAGCT
* *
52404335 ACAAACGCCGCTAAAGAACATGATCTTTTGCGGCAATTCTAGCT
1 ACAAACACCGCTAAAGAACATGATCTTTAGCGGCAATTCTAGCT
52404379 ACAAA
1 ACAAA
52404384 TGCCACAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 35 0.83
44 7 0.17
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (44 bp):
ACAAACACCGCTAAAGAACATGATCTTTAGCGGCAATTCTAGCT
Found at i:52407980 original size:35 final size:35
Alignment explanation
Indices: 52407941--52408012 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
52407931 GAGAGAAAGA
52407941 AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
1 AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
52407976 AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
1 AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
52408011 AA
1 AA
52408013 TAATCATATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (35 bp):
AAATCAACACAAGTTTGTTAACACAGTTTGAATTT
Found at i:52408763 original size:31 final size:30
Alignment explanation
Indices: 52408706--52408764 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
52408696 GTAAATACTC
* *
52408706 AAAATTTGAAGGGTTAAAATGTAAATATGA
1 AAAATTTGAAGGATCAAAATGTAAATATGA
*
52408736 AAAATTTGAAGGATCAATAGTGTAAATAT
1 AAAATTTGAAGGATCAA-AATGTAAATAT
52408765 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.49, C:0.02, G:0.19, T:0.31
Consensus pattern (30 bp):
AAAATTTGAAGGATCAAAATGTAAATATGA
Found at i:52410362 original size:26 final size:26
Alignment explanation
Indices: 52410319--52410375 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
52410309 GCATGAAATG
* *
52410319 AATAGCTTGTTGTGAGTAAATAAGTA
1 AATAGCTTGTAGTAAGTAAATAAGTA
52410345 AATAGCTTGTAGTAAGTAAATAAGTA
1 AATAGCTTGTAGTAAGTAAATAAGTA
52410371 AATAG
1 AATAG
52410376 TGGTAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.32
Consensus pattern (26 bp):
AATAGCTTGTAGTAAGTAAATAAGTA
Found at i:52410534 original size:249 final size:250
Alignment explanation
Indices: 52410088--52410570 Score: 869
Period size: 249 Copynumber: 1.9 Consensus size: 250
52410078 ACCATGACTG
* * *
52410088 AAGTGAATAGCTTGTTGTGAGTAAATAAGTAAATAGTGGTAATATATATATCAAGGATGTGGAAT
1 AAGTAAATAGCTTGTAGTAAGTAAATAAGTAAATAGTGGTAATATATATATCAAGGATGTGGAAT
52410153 GGAGTGGAGGAGGAGGAAAAATAATATATGTGAATATTCAGCTAATATGAGTTTAATTTAAAATA
66 GGAGT-G-GGAGGAGGAAAAATAATATATGTGAATATTCAGCTAATATGAGTTTAATTTAAAATA
*
52410218 GCTAATTTACATGTTTTAGGTTCAGGGACTAAATTGAATAAAATTAAAATTTTAAGGGTAATTTT
129 GCTAATTTACATGTTTTAGGTTCAGGGACTAAATTGAATAAAAGTAAAATTTTAAGGGTAATTTT
52410283 GTAAAAATGTCAAAAATGGCCAAATTGCATGAAATGAATAGCTTGTTGTGAGTAAAT
194 GTAAAAATGTCAAAAATGGCCAAATTGCATGAAATGAATAGCTTGTTGTGAGTAAAT
52410340 AAGTAAATAGCTTGTAGTAAGTAAATAAGTAAATAGTGGTAATATATATATCAAGGATGTGGAAT
1 AAGTAAATAGCTTGTAGTAAGTAAATAAGTAAATAGTGGTAATATATATATCAAGGATGTGGAAT
* *
52410405 GGAGT-GGAGGAGGAAAAATAATATATGTGAATATTCAGCTAATATGAGTTTATTTTACAATAGC
66 GGAGTGGGAGGAGGAAAAATAATATATGTGAATATTCAGCTAATATGAGTTTAATTTAAAATAGC
* *
52410469 TAATTTACATGTTTTTGGTTTAGGGACTAAATTGAATAAAAGTAAAATTTTAAGGGTAATTTTGT
131 TAATTTACATGTTTTAGGTTCAGGGACTAAATTGAATAAAAGTAAAATTTTAAGGGTAATTTTGT
52410534 AAAAATGTCAAAAATGGCCAAATTGCATGAAATGAAT
196 AAAAATGTCAAAAATGGCCAAATTGCATGAAATGAAT
52410571 TGTTTTATCA
Statistics
Matches: 223, Mismatches: 8, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
249 156 0.70
252 67 0.30
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (250 bp):
AAGTAAATAGCTTGTAGTAAGTAAATAAGTAAATAGTGGTAATATATATATCAAGGATGTGGAAT
GGAGTGGGAGGAGGAAAAATAATATATGTGAATATTCAGCTAATATGAGTTTAATTTAAAATAGC
TAATTTACATGTTTTAGGTTCAGGGACTAAATTGAATAAAAGTAAAATTTTAAGGGTAATTTTGT
AAAAATGTCAAAAATGGCCAAATTGCATGAAATGAATAGCTTGTTGTGAGTAAAT
Found at i:52411121 original size:67 final size:67
Alignment explanation
Indices: 52411005--52411130 Score: 209
Period size: 67 Copynumber: 1.9 Consensus size: 67
52410995 TAGGGTCTGA
* * *
52411005 ATTTAGCCTGGACTGGTAATCCCTCTGTAAGAAATGAGGTTCACGGGAGTGTGCTCTCTTGCAGG
1 ATTTAGCCTGGACTAGTAATCCCGCTGTAAGAAATGAGGTTCACAGGAGTGTGCTCTCTTGCAGG
52411070 GG
66 GG
52411072 ATTTAGCCTGGACTAGTAATCCCGCTGTAAGAAATGAGGTT-AGCAGGAGTGTGCTCTCT
1 ATTTAGCCTGGACTAGTAATCCCGCTGTAAGAAATGAGGTTCA-CAGGAGTGTGCTCTCT
52411131 GAATTGGGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 1 0.02
67 54 0.98
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (67 bp):
ATTTAGCCTGGACTAGTAATCCCGCTGTAAGAAATGAGGTTCACAGGAGTGTGCTCTCTTGCAGG
GG
Found at i:52411301 original size:26 final size:26
Alignment explanation
Indices: 52411243--52411301 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
52411233 ATAAAAATAG
52411243 AAAATGATAAGTACTTGAAATACATA
1 AAAATGATAAGTACTTGAAATACATA
* * * *
52411269 GAAATGATAATTATTTGATATAC-TA
1 AAAATGATAAGTACTTGAAATACATA
52411294 AAATATGA
1 AAA-ATGA
52411302 CATGGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 4 0.15
26 23 0.85
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (26 bp):
AAAATGATAAGTACTTGAAATACATA
Found at i:52412860 original size:49 final size:49
Alignment explanation
Indices: 52412714--52412860 Score: 195
Period size: 49 Copynumber: 3.0 Consensus size: 49
52412704 ACATGTGAAA
** * *
52412714 ATGTGATTATGTGATTTTTGTGTAAGGCCATAGCTGGACTATGGCATCAGT
1 ATGTGA-TATGTGA-TTACGTGTAAGACCATAGCTGGACTATGGCATCGGT
* * **
52412765 AAGTGATATGTGATTCCGTGTAAGACCATAGCTGGGTTATGGCATCGGT
1 ATGTGATATGTGATTACGTGTAAGACCATAGCTGGACTATGGCATCGGT
*
52412814 ATGTGATATGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 ATGTGATATGTGATTACGTGTAAGACCATAGCTGGACTATGGCATCG
52412861 AGAAAATAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
49 72 0.86
50 7 0.08
51 5 0.06
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (49 bp):
ATGTGATATGTGATTACGTGTAAGACCATAGCTGGACTATGGCATCGGT
Found at i:52416545 original size:67 final size:67
Alignment explanation
Indices: 52416437--52416564 Score: 220
Period size: 67 Copynumber: 1.9 Consensus size: 67
52416427 GTTTATATTA
* * *
52416437 TAGGGGATTTAGCCTGGACTGGTAATCCTGCTGTAAGAAATGAGGTTTGCGGGAGTATGCTCTCT
1 TAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTATGCTCTCT
52416502 TG
66 TG
*
52416504 TAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGCT
1 TAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTATGCT
52416565 ATCTGAATTG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.29
Consensus pattern (67 bp):
TAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTATGCTCTCT
TG
Found at i:52423512 original size:6 final size:6
Alignment explanation
Indices: 52423496--52423548 Score: 70
Period size: 6 Copynumber: 8.7 Consensus size: 6
52423486 TTTTGTTTCC
* * *
52423496 TTTATTT TTTATT TTTATT TTTATT TTTATT GTTATT TTAATT TTAATT
1 TTTA-TT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
52423545 TTTA
1 TTTA
52423549 GTATCACTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
6 38 0.90
7 4 0.10
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:52443382 original size:95 final size:94
Alignment explanation
Indices: 52443205--52443637 Score: 324
Period size: 95 Copynumber: 4.6 Consensus size: 94
52443195 CTTTACAAAT
* * * * **
52443205 TTTAGATAAGTGTCTTAAGTGGCTTAGCAGTGTATCTAG-TATTAGACTTAGCAAGCAGTTTCCT
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCT-GCTATTAGACTTAGTGAGCAGTTTCCT
* **
52443269 CTCAAG-TTGTCTGTTTTATAACTTCATTGA-A
65 CT-AAGAGTGTCTACTTTATAA-TT-ATTGACA
* * * *
52443300 TTTAGCTAAGTGCCCTAATAGGCTTAGCAGTATATCTGCTATTAGAATTAGTGAGTAGTTTCCTC
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAGACTTAGTGAGCAGTTTCCTC
* * *
52443365 TAAGAGTATCTACTTTATAAATATTGACT
66 TAAGAGTGTCTACTTTATAATTATTGACA
* * * * * ** *
52443394 TTTGGCTAAGTGCCTTAAGAGGC-TAGAAGCA-ATTCTTCTATTACACTTAGTGATTAGTTTCTT
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATA-TCTGCTATTAGACTTAGTGAGCAGTTTCCT
** * * *
52443457 CTCGGTGTGTCTACTTTAAAACTTTGTTGA-A
65 CTAAGAGTGTCTACTTTATAA--TTATTGACA
* * * * * *
52443488 TTTAGCTACGTGCCTTAAGAGGCTTAGCAATATATTTGCTGTTAGACTTAGTGAACAGTTCCCTC
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAGACTTAGTGAGCAGTTTCCTC
* * * * **
52443553 T-TGAATTGTCTGCTCTATAGA-TATTGATT
66 TAAG-AGTGTCTACTTTATA-ATTATTGACA
* * **
52443582 TTTGGCTAAGTGCCTTAAAAGGCTTAGCAGTATATCTGCTATTAGTTTTAGTGAGC
1 TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAGACTTAGTGAGC
52443638 TTGAAAGGCG
Statistics
Matches: 263, Mismatches: 64, Indels: 23
0.75 0.18 0.07
Matches are distributed among these distances:
92 1 0.00
93 57 0.22
94 94 0.36
95 109 0.41
96 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (94 bp):
TTTAGCTAAGTGCCTTAAGAGGCTTAGCAGTATATCTGCTATTAGACTTAGTGAGCAGTTTCCTC
TAAGAGTGTCTACTTTATAATTATTGACA
Found at i:52443683 original size:20 final size:20
Alignment explanation
Indices: 52443641--52443685 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
52443631 AGTGAGCTTG
* *
52443641 AAAGGCGATGTCGAGCATGA
1 AAAGGCAATGTCGAGCATAA
52443661 AAAGGCAATGTCGAGTC-TAA
1 AAAGGCAATGTCGAG-CATAA
52443681 AAAGG
1 AAAGG
52443686 TAGTGTCGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.31, T:0.16
Consensus pattern (20 bp):
AAAGGCAATGTCGAGCATAA
Found at i:52444715 original size:21 final size:21
Alignment explanation
Indices: 52444691--52444916 Score: 75
Period size: 21 Copynumber: 11.0 Consensus size: 21
52444681 GGAGATTAAT
52444691 AGTTTTCTCTAGGAGTTAAGC
1 AGTTTTCTCTAGGAGTTAAGC
* * *
52444712 AGTTTTCTTTAGGAATT-TGAC
1 AGTTTTCTCTAGGAGTTAAG-C
*
52444733 AGTCTTT-TCAAGGAGTTAAG-
1 AGT-TTTCTCTAGGAGTTAAGC
* * *
52444753 AGTTTTCCCTAGAAGTTTAGC
1 AGTTTTCTCTAGGAGTTAAGC
* * *
52444774 AATCTTTC-ATAGGAGTTAA-T
1 AGT-TTTCTCTAGGAGTTAAGC
*** * * *
52444794 AACATTCCCTAAGAGTTAA-T
1 AGTTTTCTCTAGGAGTTAAGC
* *
52444814 AGTTTT-TCCTAGTAGTTTAGC
1 AGTTTTCT-CTAGGAGTTAAGC
*
52444835 AGTCTTC-CTTA-GATGTTAA-C
1 AGTTTTCTC-TAGGA-GTTAAGC
*
52444855 AGTTTTCTCTAAGAGTT-A-C
1 AGTTTTCTCTAGGAGTTAAGC
*
52444874 AATTTT-TCCTAGGAGTTAAAGC
1 AGTTTTCT-CTAGGAGTT-AAGC
* *
52444896 AGTTTTC-CCAGGAGTTTAGC
1 AGTTTTCTCTAGGAGTTAAGC
52444916 A
1 A
52444917 ATCATCACAA
Statistics
Matches: 149, Mismatches: 37, Indels: 39
0.66 0.16 0.17
Matches are distributed among these distances:
18 1 0.01
19 21 0.14
20 54 0.36
21 59 0.40
22 14 0.09
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (21 bp):
AGTTTTCTCTAGGAGTTAAGC
Found at i:52444780 original size:41 final size:42
Alignment explanation
Indices: 52444700--52444792 Score: 104
Period size: 41 Copynumber: 2.2 Consensus size: 42
52444690 TAGTTTTCTC
** *
52444700 TAGGAGTTAAGCAGTTTTCTTTAGGAATTTGACAGTCTTTTCA
1 TAGGAGTTAAGCAGTTTTCCCTAGGAATTTGACAATC-TTTCA
52444743 -AGGAGTTAAG-AGTTTTCCCTA-GAAGTTT-AGCAATCTTTCA
1 TAGGAGTTAAGCAGTTTTCCCTAGGAA-TTTGA-CAATCTTTCA
52444783 TAGGAGTTAA
1 TAGGAGTTAA
52444793 TAACATTCCC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
40 9 0.20
41 25 0.57
42 10 0.23
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (42 bp):
TAGGAGTTAAGCAGTTTTCCCTAGGAATTTGACAATCTTTCA
Found at i:52444824 original size:20 final size:19
Alignment explanation
Indices: 52444801--52444903 Score: 66
Period size: 20 Copynumber: 5.1 Consensus size: 19
52444791 AATAACATTC
*
52444801 CCTAAGAGTTAATAGTTTTT
1 CCTAAGAGTTAACAG-TTTT
* *
52444821 CCT-AGTAGTTTAGCAGTCTT
1 CCTAAG-AG-TTAACAGTTTT
*
52444841 CCTTAGATGTTAACAGTTTT
1 CCTAAGA-GTTAACAGTTTT
*
52444861 CTCTAAGAGTT-ACAATTTTT
1 C-CTAAGAGTTAAC-AGTTTT
*
52444881 CCTAGGAGTTAAAGCAGTTTT
1 CCTAAGAGTT-AA-CAGTTTT
52444902 CC
1 CC
52444904 CAGGAGTTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
19 12 0.18
20 31 0.48
21 21 0.32
22 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (19 bp):
CCTAAGAGTTAACAGTTTT
Found at i:52452831 original size:27 final size:27
Alignment explanation
Indices: 52452773--52452831 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
52452763 CTCTAATTTG
* **
52452773 CCAAACAGACTAGTGAACCCTAGCTTG
1 CCAAACAGACTAGCGAACCCTAGCTCC
* * *
52452800 TCAAACAGATTGGCGAACCCTAGCTCC
1 CCAAACAGACTAGCGAACCCTAGCTCC
52452827 CCAAA
1 CCAAA
52452832 TAAACTGGAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (27 bp):
CCAAACAGACTAGCGAACCCTAGCTCC
Found at i:52457970 original size:137 final size:138
Alignment explanation
Indices: 52457723--52458028 Score: 461
Period size: 137 Copynumber: 2.2 Consensus size: 138
52457713 GTACACAAAT
* * * *
52457723 AATTAATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTTATACAAAATATTGATTG
1 AATTAATATTCTTTTGGAAAGAATATAATTAACATATGAATTTGATTCATACAAAATATTAACTG
* *
52457788 TATATATTTTACCAAATTTATTATTATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAA
66 TATATATTTTACCAAATTTATTAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAA
52457853 GAAATAGA
131 GAAATAGA
** **
52457861 AATTAATATTCTTACGGAAAGAATATAATTAACATATTCA-TTGATTCATACAAAATATTAACTG
1 AATTAATATTCTTTTGGAAAGAATATAATTAACATATGAATTTGATTCATACAAAATATTAACTG
* *
52457925 TATATATTTTATCGAATTTATTAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAA
66 TATATATTTTACCAAATTTATTAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAA
* **
52457990 GACATTTA
131 GAAATAGA
*
52457998 AATTAATATTCTTTTGGAAAGAATACAATTA
1 AATTAATATTCTTTTGGAAAGAATATAATTA
52458029 CTTTTTCCAA
Statistics
Matches: 150, Mismatches: 18, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
137 115 0.77
138 35 0.23
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.41
Consensus pattern (138 bp):
AATTAATATTCTTTTGGAAAGAATATAATTAACATATGAATTTGATTCATACAAAATATTAACTG
TATATATTTTACCAAATTTATTAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAA
GAAATAGA
Found at i:52458139 original size:75 final size:75
Alignment explanation
Indices: 52458003--52458149 Score: 199
Period size: 75 Copynumber: 2.0 Consensus size: 75
52457993 ATTTAAATTA
* * **
52458003 ATATTCTTTTGGAAAGAATACAATTACTTTTTCCAATTTTCCATTTGTCTTCTTTGTTAATAAGA
1 ATATTCTTTTGGAAAGAATACAATTACTTTTTCCAACTTTCCATTTGCCTTCTCAGTTAATAAGA
52458068 GAATAATCCT
66 GAATAATCCT
* *
52458078 ATATTCTTTTGGAAAGAATATAATT-CTTTTTTCTAACTTTCCATTTGCCTTCTCCAG-TAATAA
1 ATATTCTTTTGGAAAGAATACAATTAC-TTTTTCCAACTTTCCATTTGCCTTCT-CAGTTAATAA
*
52458141 GGGAATAAT
64 GAGAATAAT
52458150 AATGGTTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
74 1 0.02
75 61 0.97
76 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATACAATTACTTTTTCCAACTTTCCATTTGCCTTCTCAGTTAATAAGA
GAATAATCCT
Found at i:52466353 original size:34 final size:34
Alignment explanation
Indices: 52466292--52466358 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
52466282 ACAGTTAAAG
* **
52466292 CAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTAA
1 CAGTCTTGGGCCTAAGCCCATCCCAGTA-CAGTAA
*
52466327 CAGT-TTGGGCCTTAGCCCATCCCAGTACAGTA
1 CAGTCTTGGGCCTAAGCCCATCCCAGTACAGTA
52466359 TCAAATATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 5 0.18
34 19 0.68
35 4 0.14
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.28
Consensus pattern (34 bp):
CAGTCTTGGGCCTAAGCCCATCCCAGTACAGTAA
Found at i:52479359 original size:15 final size:16
Alignment explanation
Indices: 52479332--52479361 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52479322 AATTACAATT
52479332 AATATATATTATATAA
1 AATATATATTATATAA
52479348 AATATA-ATTATATA
1 AATATATATTATATA
52479362 TTAGTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:52479476 original size:27 final size:28
Alignment explanation
Indices: 52479423--52479478 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
52479413 TATTTTTAAA
*
52479423 AATATTTATAAAAAAAGACAACTAATTTT
1 AATATTTACAAAAAAAGACAAC-AATTTT
*
52479452 AATATTTACAAAAAAAGTCAA-AATTTT
1 AATATTTACAAAAAAAGACAACAATTTT
52479479 CAAATAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.24
29 19 0.76
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (28 bp):
AATATTTACAAAAAAAGACAACAATTTT
Found at i:52479484 original size:29 final size:29
Alignment explanation
Indices: 52479422--52479484 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
52479412 CTATTTTTAA
*
52479422 AAATATTTATAAAAAAAGACAACTAATTTT
1 AAATATTTACAAAAAAAGACAAC-AATTTT
*
52479452 -AATATTTACAAAAAAAGTCAA-AATTTT
1 AAATATTTACAAAAAAAGACAACAATTTT
52479479 CAAATA
1 -AAATA
52479485 ATTCAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 6 0.21
29 23 0.79
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (29 bp):
AAATATTTACAAAAAAAGACAACAATTTT
Found at i:52508334 original size:41 final size:41
Alignment explanation
Indices: 52508270--52508365 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
52508260 TCGGGTTTTT
* ** *
52508270 AGCCTAGCAGGCTTTATGCCGGTGAATTATTTCAGGCTTTA
1 AGCCTAGCAGGCTTAATGCCGGTGAACCATATCAGGCTTTA
* *
52508311 TA-CCTAGCAGGCTTAATGTCGGTGTACCATATCAGGCTTTA
1 -AGCCTAGCAGGCTTAATGCCGGTGAACCATATCAGGCTTTA
52508352 AGCCTAGCAGGCTT
1 AGCCTAGCAGGCTT
52508366 TGTGCCGATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.02
41 45 0.96
42 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (41 bp):
AGCCTAGCAGGCTTAATGCCGGTGAACCATATCAGGCTTTA
Found at i:52509453 original size:17 final size:18
Alignment explanation
Indices: 52509431--52509466 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
52509421 GACGTTGTTT
52509431 TGTGATATATAT-ATATA
1 TGTGATATATATGATATA
*
52509448 TGTGATATGTATGATATA
1 TGTGATATATATGATATA
52509466 T
1 T
52509467 TTGAACTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (18 bp):
TGTGATATATATGATATA
Found at i:52511712 original size:17 final size:17
Alignment explanation
Indices: 52511664--52511705 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
52511654 CCTAAAGGGA
52511664 TTATGAAAGAAAAATAT
1 TTATGAAAGAAAAATAT
52511681 TTATGAAAGAAAAATAT
1 TTATGAAAGAAAAATAT
52511698 TTATGAAA
1 TTATGAAA
52511706 TGTAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (17 bp):
TTATGAAAGAAAAATAT
Found at i:52514253 original size:27 final size:27
Alignment explanation
Indices: 52514199--52514267 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
52514189 AGATCGCCAA
* *
52514199 AAAGGTTATTCTTTCATAATTTTCCAC
1 AAAGGCTATTCTTTCATAATTATCCAC
52514226 AAAGGCTATTCTTTCATAATTCAT-CAC
1 AAAGGCTATTCTTTCATAATT-ATCCAC
*
52514253 AAAAGCTATTCTTTC
1 AAAGGCTATTCTTTC
52514268 CTGTCATGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (27 bp):
AAAGGCTATTCTTTCATAATTATCCAC
Found at i:52522445 original size:21 final size:21
Alignment explanation
Indices: 52522421--52522463 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
52522411 TCCGGGTGGA
52522421 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
*
52522442 TCAGCTTTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
52522463 T
1 T
52522464 GGAATGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:52525984 original size:22 final size:22
Alignment explanation
Indices: 52525931--52525984 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
52525921 ATGGTTATGC
*
52525931 ATTTAGAATTATAATTGTAATT
1 ATTTACAATTATAATTGTAATT
* * *
52525953 ATATT-TAATTTTAATTTTAATT
1 AT-TTACAATTATAATTGTAATT
52525975 ATTTACAATT
1 ATTTACAATT
52525985 CGATACAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
ATTTACAATTATAATTGTAATT
Found at i:52539336 original size:43 final size:43
Alignment explanation
Indices: 52539273--52539359 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
52539263 TTGCCAGATA
*
52539273 TAGAATTCGTGGTTTGTATTCTTTAACTATCGACCTAGATTCT
1 TAGAATTCGTGGTTTCTATTCTTTAACTATCGACCTAGATTCT
*
52539316 TAGAATTCGTGGTTTCTATTCTTTAACTATCGACTTAGATTCT
1 TAGAATTCGTGGTTTCTATTCTTTAACTATCGACCTAGATTCT
52539359 T
1 T
52539360 TCTTACTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (43 bp):
TAGAATTCGTGGTTTCTATTCTTTAACTATCGACCTAGATTCT
Found at i:52540902 original size:14 final size:13
Alignment explanation
Indices: 52540882--52540915 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
52540872 AATCAAGCAA
52540882 AAAAAATTAGAATT
1 AAAAAATTA-AATT
*
52540896 TAAAAATTAAATT
1 AAAAAATTAAATT
52540909 AAAAAAT
1 AAAAAAT
52540916 ATTAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
AAAAAATTAAATT
Found at i:52540919 original size:15 final size:15
Alignment explanation
Indices: 52540881--52540928 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
52540871 GAATCAAGCA
*
52540881 AAAAAAATTAGAATT
1 AAAAAAATTAAAATT
*
52540896 -TAAAAATT-AAATT
1 AAAAAAATTAAAATT
52540909 AAAAAATATTAAAATT
1 AAAAAA-ATTAAAATT
52540925 AAAA
1 AAAA
52540929 TTAAAATGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 4 0.15
14 11 0.41
15 3 0.11
16 9 0.33
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAAAAATTAAAATT
Found at i:52542667 original size:47 final size:48
Alignment explanation
Indices: 52542557--52542673 Score: 125
Period size: 47 Copynumber: 2.5 Consensus size: 48
52542547 TTAAAAATTG
* *
52542557 ATGAT-AATTTAAAAATAATAATACGTGATAAATTCAAAATAATAATAT
1 ATGATAAATTT-AAAATAATAATACATGATAAACTCAAAATAATAATAT
* * * **
52542605 ATGTTAACTTT-AAATAAAAATACATGATAAAC-CTAAAATAATGTTA-
1 ATGATAAATTTAAAATAATAATACATGATAAACTC-AAAATAATAATAT
52542651 ATGATAAATTTAAAATAATAATA
1 ATGATAAATTTAAAATAATAATA
52542674 TATTATAATA
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
46 10 0.18
47 38 0.68
48 4 0.07
49 4 0.07
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (48 bp):
ATGATAAATTTAAAATAATAATACATGATAAACTCAAAATAATAATAT
Found at i:52542687 original size:24 final size:23
Alignment explanation
Indices: 52542527--52542691 Score: 124
Period size: 24 Copynumber: 7.2 Consensus size: 23
52542517 ATAAATTTGG
*
52542527 AATAATAATACATGATAAATTTA
1 AATAATAATACATGATAAATTAA
* *
52542550 AA-AAT--T-GATGATAATTTAAA
1 AATAATAATACATGATAAATT-AA
*
52542570 AATAATAATACGTGATAAATTCAA
1 AATAATAATACATGATAAATT-AA
* * * *
52542594 AATAATAATATATGTTAACTTTA
1 AATAATAATACATGATAAATTAA
* *
52542617 AATAAAAATACATGATAAACCTAA
1 AATAATAATACATGATAAA-TTAA
**
52542641 AATAATGTTA-ATGATAAATTTAA
1 AATAATAATACATGATAAA-TTAA
* *
52542664 AATAATAATATATTATAATATTAA
1 AATAATAATACATGATAA-ATTAA
52542688 AATA
1 AATA
52542692 GTATTGATAA
Statistics
Matches: 108, Mismatches: 26, Indels: 15
0.72 0.17 0.10
Matches are distributed among these distances:
19 9 0.08
20 4 0.04
21 3 0.03
22 3 0.03
23 38 0.35
24 50 0.46
25 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (23 bp):
AATAATAATACATGATAAATTAA
Found at i:52544215 original size:45 final size:45
Alignment explanation
Indices: 52544166--52544269 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
52544156 TTAATCTACT
* *
52544166 CCACTATAACTTCAAGGACATAAGA-TTCACCATCTTTAGTCTGCC
1 CCACTGTAACTTCAAGGACATAAGACTT-ACCATCTTCAGTCTGCC
* * ** * * *
52544211 CCACTGCAACTTCAGGGGGATAAGACTTGCTATCTTCAGTCTGCT
1 CCACTGTAACTTCAAGGACATAAGACTTACCATCTTCAGTCTGCC
52544256 CCACTGTAACTTCA
1 CCACTGTAACTTCA
52544270 GGGAGATAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
45 46 0.96
46 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (45 bp):
CCACTGTAACTTCAAGGACATAAGACTTACCATCTTCAGTCTGCC
Found at i:52544466 original size:51 final size:51
Alignment explanation
Indices: 52544400--52544925 Score: 526
Period size: 51 Copynumber: 10.7 Consensus size: 51
52544390 CTATTGTAAT
* * * *
52544400 GCCAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTACAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAAC
* *
52544451 GCCAAGGAAATAAGATTCGCTGTCTTCAGCTCTAATC---T--ACTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAAC
* * *
52544497 GCC-AGAGAAATAAGATTTGCTGCCTTCAGCATTAATCTGTTCCACTGTAAC
1 GCCAAG-GAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAAC
* * * *
52544548 ACCAAGGAAACAAGATTCGCTGCCTTTAGCTTTAATC---T--ATTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAAC
* * * *
52544594 GCCAGGGAAACAAG--TCACTGCCTTCAGCTTTAATCTATTCCACTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAAC
* * * *
52544643 GGCAAGGAAATAAGATCCGTTGCCATT-AGCTTTAATC---T--ATTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCC-TTCAGCTTTAATCTGTTCCACTGCAAC
* * * * *
52544689 G-CAAGGGAAACAAGATTTGCTACCTTTAGCTTTAATCTGTTCCACTGCAAT
1 GCCAA-GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAAC
*
52544740 GCCAAGGAAATAAGATTCGCTGTCTTCAGCTTTAATCTGTTCCACTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAAC
* * * *
52544791 GCCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATCTATTGCACTACAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAAC
* *
52544842 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAA--T-AT--ATTGCAAC
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAAC
* * *
52544888 GCTAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCT
1 GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT
52544926 ATTGCAACGC
Statistics
Matches: 395, Mismatches: 55, Indels: 53
0.79 0.11 0.11
Matches are distributed among these distances:
44 19 0.05
45 7 0.02
46 125 0.32
47 1 0.00
48 5 0.01
49 21 0.05
51 210 0.53
52 7 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (51 bp):
GCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAAC
Found at i:52544532 original size:97 final size:97
Alignment explanation
Indices: 52544381--52544925 Score: 682
Period size: 97 Copynumber: 5.6 Consensus size: 97
52544371 TGTGACTTAT
** * * *
52544381 AGCTTTAGCCTATTGTAATGCCAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
* *
52544446 ACAACGCCAAGGAAATAAGATTCGCTGTCTTC
66 GCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* * * * * *
52544478 AGCTCTAATCTACTGCAACGCCAGAGAAATAAGATTTGCTGCCTTCAGCATTAATCTGTTCCACT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
* * * *
52544543 GTAACACCAAGGAAACAAGATTCGCTGCCTTT
66 GCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* *
52544575 AGCTTTAATCTATTGCAACGCCAGGGAAACAAG--TCACTGCCTTCAGCTTTAATCTATTCCACT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
* * *
52544638 GCAACGGCAAGGAAATAAGATCCGTTGCCATT-
66 GCAACGCCAAGGAAATAAGATTCGCTGCC-TTC
* * * *
52544670 AGCTTTAATCTATTGCAACGCAAGGGAAACAAGATTTGCTACCTTTAGCTTTAATCTGTTCCACT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
* *
52544735 GCAATGCCAAGGAAATAAGATTCGCTGTCTTC
66 GCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* * * * *
52544767 AGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATCTATT
1 AGCTTTAATC---T--ATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTT
* *
52544832 GCACTACAACGCCAAGGAAATAAGATTCGCTGCCTTC
61 CCACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTC
* *
52544869 AGCTTTAATATATTGCAACGCTAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCT
1 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCT
52544926 ATTGCAACGC
Statistics
Matches: 382, Mismatches: 57, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
95 81 0.21
96 4 0.01
97 211 0.55
99 1 0.00
100 1 0.00
102 84 0.22
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (97 bp):
AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACT
GCAACGCCAAGGAAATAAGATTCGCTGCCTTC
Found at i:52546684 original size:27 final size:27
Alignment explanation
Indices: 52546654--52546718 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
52546644 CCACAATGAA
* *
52546654 CATTTCTTTTAG-GTACGCCACGAAAG
1 CATTTCTTTTAGAGTACCCCACAAAAG
* *
52546680 CCA-TTCCTTCAGAGTACCCCACAAAAG
1 -CATTTCTTTTAGAGTACCCCACAAAAG
52546707 CATTTCTTTTAG
1 CATTTCTTTTAG
52546719 TTTATCGCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (27 bp):
CATTTCTTTTAGAGTACCCCACAAAAG
Found at i:52546787 original size:27 final size:27
Alignment explanation
Indices: 52546750--52546825 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
52546740 CTTTGAGAGA
* *
52546750 TCACCAAAAAGGTTATTCTTTCATAAT
1 TCACCACAAAGGCTATTCTTTCATAAT
** *
52546777 TTGCCACAAAGGCTATTCTTTTATAAT
1 TCACCACAAAGGCTATTCTTTCATAAT
*
52546804 TCATCACAAAGGCTATTCTTTC
1 TCACCACAAAGGCTATTCTTTC
52546826 CTGTCATGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (27 bp):
TCACCACAAAGGCTATTCTTTCATAAT
Found at i:52550003 original size:159 final size:160
Alignment explanation
Indices: 52549812--52550130 Score: 552
Period size: 159 Copynumber: 2.0 Consensus size: 160
52549802 TAATAGGCCA
* * *
52549812 TCACATGGGGTCTAAGATAATATTTTTGTTTTGCATTTTGATTATTTTTGTTGGATTAGGTTTAA
1 TCACATGGGGTCTAAGATAATATTTTTATTTTGCATTTTGATTAATTTTGTTGGATTAAGTTTAA
* * *
52549877 AAGAAATTTTTATTACTTAAATTATGTAAAACATAATATAAATCGATAT-AAAAAATGATAAAAG
66 AACAAATTTTTATTACTTAAATTATGAAAAACACAATATAAATCGATATAAAAAAATGATAAAAG
52549941 ATAAACTAAAACATAACATATCACAAAAAC
131 ATAAACTAAAACATAACATATCACAAAAAC
52549971 TCACATGGGGTTCTAAGATAATA-TTTTATTTTGCATTTTGATTAATTTTGTTGGATTAAGTTTA
1 TCACATGGGG-TCTAAGATAATATTTTTATTTTGCATTTTGATTAATTTTGTTGGATTAAGTTTA
*
52550035 AAACAAATTTTTATTACTTAAATTATGAAAAACACAATATAAATGGATATAAAAAAATGATAAAA
65 AAACAAATTTTTATTACTTAAATTATGAAAAACACAATATAAATCGATATAAAAAAATGATAAAA
52550100 GATAAACTAAAACATAACATATCACAAAAAC
130 GATAAACTAAAACATAACATATCACAAAAAC
52550131 AATAAAAACA
Statistics
Matches: 151, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
159 94 0.62
160 57 0.38
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (160 bp):
TCACATGGGGTCTAAGATAATATTTTTATTTTGCATTTTGATTAATTTTGTTGGATTAAGTTTAA
AACAAATTTTTATTACTTAAATTATGAAAAACACAATATAAATCGATATAAAAAAATGATAAAAG
ATAAACTAAAACATAACATATCACAAAAAC
Found at i:52552514 original size:21 final size:21
Alignment explanation
Indices: 52552490--52552532 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
52552480 TCCGGGTGGA
52552490 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
52552511 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
52552532 T
1 T
52552533 GGCATGTTTC
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:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:52572143 original size:25 final size:24
Alignment explanation
Indices: 52572115--52572161 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
52572105 TAAAAATTGA
*
52572115 TGATAATTTAAAAAATAATAATACG
1 TGATAAATT-AAAAATAATAATACG
*
52572140 TGATAAATTCAAAATAATAATA
1 TGATAAATTAAAAATAATAATA
52572162 TATGTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (24 bp):
TGATAAATTAAAAATAATAATACG
Found at i:52573738 original size:45 final size:45
Alignment explanation
Indices: 52573682--52573783 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 45
52573672 AATCTGCACT
*
52573682 ACTGCAACTTCAAGGACATAAG-GTTCACCATCTTCAGTCTGCCCC
1 ACTGCAACTTCAAGGACATAAGACTT-ACCATCTTCAGTCTGCCCC
* ** * * *
52573727 ACTGCAACTTCAGGGGGATAAGACTTGCTATCTTCAGTCTGCTCC
1 ACTGCAACTTCAAGGACATAAGACTTACCATCTTCAGTCTGCCCC
*
52573772 ACTGCCACTTCA
1 ACTGCAACTTCA
52573784 GGGAAATAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 46 0.96
46 2 0.04
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (45 bp):
ACTGCAACTTCAAGGACATAAGACTTACCATCTTCAGTCTGCCCC
Found at i:52573826 original size:44 final size:44
Alignment explanation
Indices: 52573624--52573869 Score: 167
Period size: 44 Copynumber: 5.6 Consensus size: 44
52573614 CGTCTTGTTT
** * *
52573624 CTTCAATCCACTCTACTGCAACTTCAAGGAGATAGGATTATTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGG
* * * * * ****
52573668 CTTTAATCTGCACTACTGCAACTTCAAGGACATAAGG-TTCACCAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGAT-AGGATT-ATTGG
* * * * ** **
52573713 CTTCAGTCTGCCCCACTGCAACTTCAGGGGGATAAGACTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGA-TTATTGG
* * *
52573758 CTTCAGTCTGCTCCACTGCCACTTCAGGGAAATAGGATTATTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGG
* * * *
52573802 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-TCGC
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGG
* *
52573844 CTTGAA-CTGCTCTACTGCAACTTCAG
1 CTTCAATCTGCTCCACTGCAACTTCAG
52573870 AGGGATAAGA
Statistics
Matches: 161, Mismatches: 37, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
41 19 0.12
42 7 0.04
43 1 0.01
44 67 0.42
45 65 0.40
46 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTGG
Found at i:52574035 original size:46 final size:46
Alignment explanation
Indices: 52573892--52574766 Score: 667
Period size: 46 Copynumber: 18.2 Consensus size: 46
52573882 TGTGACTTAT
* * * * *
52573892 AGCTTTAATCTATTGCAATGCCAGGGAAACAAGATTCGCTGCCTTT
1 AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
52573938 AGCTTTAATCTGTTCCACTACAACGCCAAGGAAATAAGATTCGCTGTCTTC
1 AGCTTTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
52573989 AGCTCTAATTTACTGCAACGCCAGGGAAATAAGATTTGCTGCCTTC
1 AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * ** **
52574035 AGCATTAATCTGTTCCACTGCAACACCAAGGAAATAAGATTTTCTATCTTC
1 AGCTTTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
52574086 AGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCACTGCCTTC
1 AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
52574132 AGCTTCAATCTATTGCAACGCCAGGGAAACAAG--TCGCTGCCTTC
1 AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * * *
52574176 AGCTTTAATCTGTTCCACTGCAACGGCAAGGAAATAAGATTCGTTTCCATC
1 AGCTTTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * * * *
52574227 AGCTTTAATCTATTGCAAAGCAAGGGAAACAAGATTTGCTGCCTTC
1 AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
52574273 AGCTTTAATTTGTTCCACTGCAACGCCAAGGACATAAGATTCGCTGCCTTC
1 AGCTTTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * * *
52574324 AGCTTTAATCTATTGCAACGCTAGGGAAACAAGA-TCTGCTACCTTC
1 AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTC-GCTGCCTTC
* * * *
52574370 AGCTTTAATCTATTCCACTGCAATGCCAAGGAAATAAGATTCACTACCTTC
1 AGCTTTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
52574421 AGCTTTAATCTGTTCCACTGCAATGCCAAGGAAATAAGATTCTCTGCCTTC
1 AGCTTTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * * * *
52574472 AGCTTTAATCTATTTCAACGCTAGGGAAACAAGATTCGCTGACTTC
1 AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * * * *
52574518 AGCTTTAATCTATTGGAACGCCAGAGAAACAAGATTTGCTGCCTTC
1 AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
52574564 AGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCACTGCCTTC
1 AGCTTTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
52574615 AACTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTC
1 AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * ** *
52574661 AGATTTAATCTGTTCCACTACAACGCCAAAGAAATAATATTCGCTGCCTTC
1 AGCTTTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * * *
52574712 AGGTTTAATCTATTGCAACGCCAGGGAGATAAGATTCGCTGCCTTC
1 AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
52574758 AGCTTTAAT
1 AGCTTTAAT
52574767 GTATTCCACT
Statistics
Matches: 666, Mismatches: 124, Indels: 78
0.77 0.14 0.09
Matches are distributed among these distances:
44 17 0.03
45 2 0.00
46 321 0.48
47 1 0.00
48 14 0.02
49 32 0.05
51 277 0.42
52 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (46 bp):
AGCTTTAATTTACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
Found at i:52574043 original size:97 final size:98
Alignment explanation
Indices: 52573905--52574798 Score: 722
Period size: 97 Copynumber: 9.2 Consensus size: 98
52573895 TTTAATCTAT
* * * *
52573905 TGCAATGCCAGGGAAACAAGATTCGCTGCCTTTAGCTTTAATCTGTTCCACTACAACGCCAAGGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTT--ACTGCAACGCCAAGGA
* * *
52573970 AATAAGATTCGCTGTCTTCAGCTCTAA-T-TT-AC
64 AACAAGATTCGCTGCCTTCAGCTTTAATTGTTCAC
* * *
52574002 TGCAACGCCAGGGAAATAAGATTTGCTGCCTTCAGCATTAATCTGTTCCACTGCAACACCAAGGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTT--ACTGCAACGCCAAGGA
* ** ** * *
52574067 AATAAGATTTTCTATCTTCAGCTTTAA-T-CT-AT
64 AACAAGATTCGCTGCCTTCAGCTTTAATTGTTCAC
* * * * *
52574099 TGCAACGCCAGGGAAACAAGATTCACTGCCTTCAGCTTCAATC---TATTGCAACGCCAGGGAAA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAGGAAA
52574161 CAAG--TCGCTGCCTTCAGCTTTAATCTGTTCCAC
66 CAAGATTCGCTGCCTTCAGCTTTAAT-TGTT-CAC
* * * * * * *
52574194 TGCAACGGCAAGGAAATAAGATTCGTTTCCATCAGCTTTAATC---TATTGCAAAG-CAAGGGAA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAA-GGAA
*
52574255 ACAAGATTTGCTGCCTTCAGCTTTAATTTGTTCCAC
65 ACAAGATTCGCTGCCTTCAGCTTTAA-TTGTT-CAC
* * * * *
52574291 TGCAACGCCAAGGACATAAGATTCGCTGCCTTCAGCTTTAATC---TATTGCAACGCTAGGGAAA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAGGAAA
* *
52574353 CAAGA-TCTGCTACCTTCAGCTTTAATCTATTCCAC
66 CAAGATTC-GCTGCCTTCAGCTTTAAT-TGTT-CAC
* * * * *
52574388 TGCAATGCCAAGGAAATAAGATTCACTACCTTCAGCTTTAATCTGTTCCACTGCAATGCCAAGGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTT--ACTGCAACGCCAAGGA
* * *
52574453 AATAAGATTCTCTGCCTTCAGCTTTAATCTATT---
64 AACAAGATTCGCTGCCTTCAGCTTTAAT-TGTTCAC
* * * * *
52574486 T-CAACGCTAGGGAAACAAGATTCGCTGACTTCAGCTTTAATC---TATTGGAACGCC-AGAGAA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAG-GAA
*
52574546 ACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCAC
65 ACAAGATTCGCTGCCTTCAGCTTTAAT-TGTT-CAC
* * * * *
52574582 TGCAACGCCAAGGAAATAAGATTCACTGCCTTCAACTTTAATC---TATTGCAACGCCAGGGAAA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAGGAAA
*
52574644 CAAGATTCGCTGCCTTCAGATTTAATCTGTTCCAC
66 CAAGATTCGCTGCCTTCAGCTTTAAT-TGTT-CAC
* ** * * * * *
52574679 TACAACGCCAAAGAAATAATATTCGCTGCCTTCAGGTTTAATC---TATTGCAACGCCAGGGAGA
1 TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAGGAAA
* *
52574741 TAAGATTCGCTGCCTTCAGCTTTAATGTATTCCAC
66 CAAGATTCGCTGCCTTCAGCTTTAAT-TGTT-CAC
* *
52574776 TGCAACACTC-GGGAAAAAAGATT
1 TGCAACGC-CAGGGAAATAAGATT
52574799 TGCCATAATG
Statistics
Matches: 669, Mismatches: 102, Indels: 52
0.81 0.12 0.06
Matches are distributed among these distances:
90 15 0.02
91 2 0.00
92 58 0.09
93 1 0.00
94 4 0.01
95 54 0.08
96 3 0.00
97 485 0.72
98 5 0.01
100 1 0.00
102 39 0.06
103 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (98 bp):
TGCAACGCCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTACTGCAACGCCAAGGAAA
CAAGATTCGCTGCCTTCAGCTTTAATTGTTCAC
Found at i:52574431 original size:194 final size:194
Alignment explanation
Indices: 52573905--52574781 Score: 871
Period size: 194 Copynumber: 4.5 Consensus size: 194
52573895 TTTAATCTAT
* * * * * *
52573905 TGCAATGCCAGGGAAACAAGATTCGCTGCCTTTAGCTTTAATCTGTTCCACTACAACGCCAAGGA
1 TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATC---T--ATTGCAACGCCAGGGA
* * * * **
52573970 AATAAGAT-TCGCTGTCTTCAGCTCTAA--T-TT--ACTGCAACGCCAGGGAAATAAGATTTGCT
61 AACAAGATCT-GCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCACT
* * * * * * **
52574029 GCCTTCAGCATTAATCTGTTCCACTGCAACACCAA-GGAAATAAGATTTTCTATCTTCAGCTTTA
125 ACCTTCAGCTTTAATC---T--ATTGCAA-AGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTA
*
52574093 ATC---T--AT
184 ATCTGTTCCAC
* * *
52574099 TGCAACGCCAGGGAAACAAGATTCACTGCCTTCAGCTTCAATCTATTGCAACGCCAGGGAAACAA
1 TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAA
* * ** * *
52574164 G-TC-GCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGGCAAGGAAATAAGATTCGTTTCCATC
66 GATCTGCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCACTACCTTC
*
52574227 AGCTTTAATCTATTGCAAAGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATTTGTTCCAC
131 AGCTTTAATCTATTGCAAAGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCAC
* * *
52574291 TGCAACGCCAAGGACATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCTAGGGAAACAA
1 TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAA
* *
52574356 GATCTGCTACCTTCAGCTTTAATCTATTCCACTGCAATGCCAAGGAAATAAGATTCACTACCTTC
66 GATCTGCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCACTACCTTC
* * * *
52574421 AGCTTTAATCTGTTCCACTGCAATGCCAA-GGAAATAAGATTCT-CTGCCTTCAGCTTTAATCTA
131 AGCTTTAATC---T--ATTGCAAAG-CAAGGGAAACAAGATT-TGCTGCCTTCAGCTTTAATCTG
52574484 TT----
189 TTCCAC
* * * * *
52574486 T-CAACGCTAGGGAAACAAGATTCGCTGACTTCAGCTTTAATCTATTGGAACGCCAGAGAAACAA
1 TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAA
* * *
52574550 GATTTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCACTGCCTTC
66 GATCTGCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCACTACCTTC
* * * * *
52574615 AACTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTGCCTTCAGATTTAATCTGTTCCAC
131 AGCTTTAATCTATTGCAAAGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCAC
* * * * * * *
52574679 TACAACGCCAAAGAAATAATATTCGCTGCCTTCAGGTTTAATCTATTGCAACGCCAGGGAGATAA
1 TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAA
*
52574744 GAT-TCGCTGCCTTCAGCTTTAATGTATTCCACTGCAAC
66 GATCT-GCTGCCTTCAGCTTTAATCTATTCCACTGCAAC
52574782 ACTCGGGAAA
Statistics
Matches: 576, Mismatches: 78, Indels: 58
0.81 0.11 0.08
Matches are distributed among these distances:
186 4 0.01
187 48 0.08
188 3 0.01
189 58 0.10
190 3 0.01
191 2 0.00
192 99 0.17
193 4 0.01
194 311 0.54
195 1 0.00
197 1 0.00
199 38 0.07
200 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (194 bp):
TGCAACGCCAAGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAA
GATCTGCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAATAAGATTCACTACCTTC
AGCTTTAATCTATTGCAAAGCAAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCAC
Found at i:52576048 original size:14 final size:15
Alignment explanation
Indices: 52576024--52576059 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
52576014 GCCTCTCTAT
52576024 TTTTTACTTTTTTCA
1 TTTTTACTTTTTTCA
*
52576039 TTTTTA-TTTTTTTA
1 TTTTTACTTTTTTCA
52576053 TTTTTAC
1 TTTTTAC
52576060 GACTCAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTACTTTTTTCA
Found at i:52577183 original size:9 final size:8
Alignment explanation
Indices: 52577167--52577191 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
52577157 TTTTTAAATA
52577167 TATTTTTT
1 TATTTTTT
52577175 TATTTTTT
1 TATTTTTT
52577183 TATTTTTT
1 TATTTTTT
52577191 T
1 T
52577192 GAAACTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TATTTTTT
Found at i:52582373 original size:13 final size:14
Alignment explanation
Indices: 52582342--52582376 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
52582332 ATGAAACGAA
52582342 TTAAAATAAATCAAT
1 TTAAAA-AAATCAAT
52582357 TTAAAAAAATC-AT
1 TTAAAAAAATCAAT
52582370 TTAAAAA
1 TTAAAAA
52582377 TACATGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 5 0.25
15 6 0.30
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAAAAATCAAT
Found at i:52589343 original size:18 final size:19
Alignment explanation
Indices: 52589313--52589366 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 19
52589303 TTTACTTAGC
52589313 ATTTTA-TTAATTTAATTT
1 ATTTTACTTAATTTAATTT
*
52589331 ATTTTACTT-ATTTTA-TT
1 ATTTTACTTAATTTAATTT
* * *
52589348 ATTATGCTTCATTTAATTT
1 ATTTTACTTAATTTAATTT
52589367 TTATTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 9 0.31
18 16 0.55
19 4 0.14
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTACTTAATTTAATTT
Found at i:52589382 original size:21 final size:24
Alignment explanation
Indices: 52589341--52589383 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
52589331 ATTTTACTTA
52589341 TTTTATTATTATGCTTCATTTAAT
1 TTTTATTATTATGCTTCATTTAAT
52589365 TTTTATT-TTAT-CTT-ATTTA
1 TTTTATTATTATGCTTCATTTA
52589384 TGATATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 4 0.21
24 7 0.37
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTATTATTATGCTTCATTTAAT
Found at i:52590140 original size:25 final size:25
Alignment explanation
Indices: 52590106--52590153 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
52590096 ACCACATAAA
52590106 CAAAATTACTTTTAATGTTATCAGT
1 CAAAATTACTTTTAATGTTATCAGT
52590131 CAAAATTACTTTTAATGTTATCA
1 CAAAATTACTTTTAATGTTATCA
52590154 TATCATGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (25 bp):
CAAAATTACTTTTAATGTTATCAGT
Found at i:52595817 original size:17 final size:17
Alignment explanation
Indices: 52595777--52595818 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
52595767 TATAATTTAG
*
52595777 ATGTAAAATATACTAAA
1 ATGTAAAATAAACTAAA
*
52595794 ATATAAAATAAACTAGAA
1 ATGTAAAATAAACTA-AA
52595812 A-GTAAAA
1 ATGTAAAA
52595819 ATGGAGTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (17 bp):
ATGTAAAATAAACTAAA
Found at i:52595943 original size:17 final size:17
Alignment explanation
Indices: 52595917--52595961 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
52595907 TATAACTAAG
*
52595917 ATATAGATAAATAAAAA
1 ATATATATAAATAAAAA
52595934 ATATATAT-AATAAAAA
1 ATATATATAAATAAAAA
52595950 ATTATAATATAA
1 A-TAT-ATATAA
52595962 TGAATTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.38
17 10 0.42
18 4 0.17
19 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATATATATAAATAAAAA
Found at i:52595947 original size:16 final size:18
Alignment explanation
Indices: 52595926--52595962 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
52595916 GATATAGATA
52595926 AATAAAAAA-TAT-ATAT
1 AATAAAAAATTATAATAT
52595942 AATAAAAAATTATAATAT
1 AATAAAAAATTATAATAT
52595960 AAT
1 AAT
52595963 GAATTGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 3 0.16
18 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAAAAATTATAATAT
Found at i:52596427 original size:39 final size:39
Alignment explanation
Indices: 52596370--52596444 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
52596360 TAATTTGGCA
52596370 GAAGTTTGTTTGGCAGTTAAATTGCATTATCATAATAAG
1 GAAGTTTGTTTGGCAGTTAAATTGCATTATCATAATAAG
* *
52596409 GAAGTTTGTTTGGTAGTTAAATTGTATTATCATAAT
1 GAAGTTTGTTTGGCAGTTAAATTGCATTATCATAAT
52596445 TCGACAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (39 bp):
GAAGTTTGTTTGGCAGTTAAATTGCATTATCATAATAAG
Found at i:52599303 original size:24 final size:24
Alignment explanation
Indices: 52599276--52599325 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
52599266 ATCCTATCAG
52599276 TCATTCATTCTATCGGTTCCAAAA
1 TCATTCATTCTATCGGTTCCAAAA
* *
52599300 TCATTCATTCTATTGGTTCCCAAA
1 TCATTCATTCTATCGGTTCCAAAA
52599324 TC
1 TC
52599326 CTAACAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (24 bp):
TCATTCATTCTATCGGTTCCAAAA
Found at i:52602175 original size:69 final size:69
Alignment explanation
Indices: 52602050--52602528 Score: 415
Period size: 69 Copynumber: 6.9 Consensus size: 69
52602040 TTTATAGCTA
* * * * * ** *
52602050 GGAGCTTTGCTCTCGCTAGCTGTGCTAGAGGTCGTGGCTTTTTGCCTGGGGTCCTTAATGTTACA
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
*
52602115 GTTG
66 ATTG
* * * * * * *
52602119 GGAGCTTTGCCCTCGCTAACTGTGTTAGAGGTCATGGCACTTCACCTGCGAACCTTAGTTTTACA
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
52602184 GA-TG
66 -ATTG
* * * * **
52602188 GGAGCTTTGCTCTCACTAACTATGTTGCAGGTCGTGGCTCTTCGCCT-ATAGACCTTAATTTTAC
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGA-ACCTTAATTTTAC
52602252 AATTG
65 AATTG
* * * ***** *
52602257 AGAGCTTTACTCTTGCTAACTGTGCTGGAGGTTACACCTCTTCGCCTGTGAACCTTAATTTTACA
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
52602322 ATTG
66 ATTG
* * * * * *
52602326 GGAACTTTGCTCTCGCTACCTATGCTGGAGGTTGTGCCTCTTCGCCTGC-AACCCTTAATTTTAT
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAA-CCTTAATTTTAC
** *
52602390 AGCTA
65 AATTG
* * ** * * *
52602395 GGACCTTTGCTCTCGTTAGTTGTGCTGGAGGTCGCGGCTCTTCACCTGCAAACCTTAATTTTACA
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
*
52602460 ACTG
66 ATTG
* * * * * **
52602464 GGAGCTTTGCTCTTGCTAACCGTGCTGAAGGTTGCGGCTCTTCGCCTGTAAACCTTAATTTTACA
1 GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
52602529 GGTAACATTT
Statistics
Matches: 329, Mismatches: 75, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
68 4 0.01
69 322 0.98
70 3 0.01
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.34
Consensus pattern (69 bp):
GGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTTCGCCTGCGAACCTTAATTTTACA
ATTG
Found at i:52602275 original size:138 final size:137
Alignment explanation
Indices: 52602027--52602529 Score: 463
Period size: 138 Copynumber: 3.6 Consensus size: 137
52602017 CATTTTTTTA
** * * * * * *
52602027 TGCGAACCTTGGTTTTATAGCTAGGAGCTTTGCTCTCGCTAGCTGTGCTAGAGGTCGTGGCTTTT
1 TGCGAACCTTAATTTTACAACTGGGAGCTTTGCTCTCGCTAACTATGCT-GAGGTCGTGGCTCTT
* ** * * * * * * *
52602092 TGCCTGGGGTCCTTAATGTTACAGTTGGGAGCTTTGCCCTCGCTAACTGTGTTAGAGGTCATGGC
65 CGCCTGTAGACCTTAATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCACGGC
*
52602157 ACTTCACC
130 TCTTCACC
* * *
52602165 TGCGAACCTTAGTTTTACAGA-TGGGAGCTTTGCTCTCACTAACTATGTTGCAGGTCGTGGCTCT
1 TGCGAACCTTAATTTTACA-ACTGGGAGCTTTGCTCTCGCTAACTATGCTG-AGGTCGTGGCTCT
* * * * * **
52602229 TCGCCTATAGACCTTAATTTTACAATTGAGAGCTTTACTCTTGCTAACTGTGCTGGAGGTTACAC
64 TCGCCTGTAGACCTTAATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCACGG
*
52602294 CTCTTCGCC
129 CTCTTCACC
* * * * * *
52602303 TGTGAACCTTAATTTTACAATTGGGAACTTTGCTCTCGCTACCTATGCTGGAGGTTGTGCCTCTT
1 TGCGAACCTTAATTTTACAACTGGGAGCTTTGCTCTCGCTAACTATGCT-GAGGTCGTGGCTCTT
* * * * * ** *
52602368 CGCCTGCA-ACCCTTAATTTTATAGCT-AGGACCTTTGCTCTCGTTAGTTGTGCTGGAGGTCGCG
65 CGCCTGTAGA-CCTTAATTTTACAGTTGA-GAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCACG
52602431 GCTCTTCACC
128 GCTCTTCACC
* * ** * *
52602441 TGCAAACCTTAATTTTACAACTGGGAGCTTTGCTCTTGCTAACCGTGCTGAAGGTTGCGGCTCTT
1 TGCGAACCTTAATTTTACAACTGGGAGCTTTGCTCTCGCTAACTATGCTG-AGGTCGTGGCTCTT
*
52602506 CGCCTGTAAACCTTAATTTTACAG
65 CGCCTGTAGACCTTAATTTTACAG
52602530 GTAACATTTT
Statistics
Matches: 293, Mismatches: 64, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
137 5 0.02
138 286 0.98
139 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (137 bp):
TGCGAACCTTAATTTTACAACTGGGAGCTTTGCTCTCGCTAACTATGCTGAGGTCGTGGCTCTTC
GCCTGTAGACCTTAATTTTACAGTTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCACGGCT
CTTCACC
Found at i:52606898 original size:26 final size:25
Alignment explanation
Indices: 52606869--52606945 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 25
52606859 ACTAGCGATA
*
52606869 AACGGTAAGCTC-TTTCGAGCTGAAAT
1 AACGGTAAGCTCATAT-GAGCTG-AAT
*
52606895 AACGGTAAGCTCATATGAGCTGAGT
1 AACGGTAAGCTCATATGAGCTGAAT
* *
52606920 ATCGGTAAGCTCATAAGAGCTTGAAT
1 AACGGTAAGCTCATATGAGC-TGAAT
52606946 CGATAACCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
25 20 0.45
26 22 0.50
27 2 0.05
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (25 bp):
AACGGTAAGCTCATATGAGCTGAAT
Found at i:52606931 original size:25 final size:26
Alignment explanation
Indices: 52606869--52606940 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
52606859 ACTAGCGATA
*
52606869 AACGGTAAGCTC-TTTCGAGCTGAAAT
1 AACGGTAAGCTCATAT-GAGCTGAAAT
*
52606895 AACGGTAAGCTCATATGAGCTG-AGT
1 AACGGTAAGCTCATATGAGCTGAAAT
* *
52606920 ATCGGTAAGCTCATAAGAGCT
1 AACGGTAAGCTCATATGAGCT
52606941 TGAATCGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 21 0.51
26 18 0.44
27 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (26 bp):
AACGGTAAGCTCATATGAGCTGAAAT
Found at i:52614479 original size:25 final size:25
Alignment explanation
Indices: 52614431--52614522 Score: 98
Period size: 25 Copynumber: 3.7 Consensus size: 25
52614421 GTACATGTAT
*
52614431 GCTCATACGAGC-G-ATAAACGGTAA
1 GCTCATATGAGCTGAAT-AACGGTAA
* *
52614455 GCTCTTCTGAGCTGAATAACGGTAA
1 GCTCATATGAGCTGAATAACGGTAA
* *
52614480 GCTCATATGAGCTGAGTATCGGTAA
1 GCTCATATGAGCTGAATAACGGTAA
*
52614505 GCTCATAAGAGCTTGAAT
1 GCTCATATGAGC-TGAAT
52614523 CAATAACCCT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 9 0.16
25 41 0.73
26 6 0.11
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (25 bp):
GCTCATATGAGCTGAATAACGGTAA
Found at i:52619888 original size:111 final size:111
Alignment explanation
Indices: 52619694--52620023 Score: 642
Period size: 111 Copynumber: 3.0 Consensus size: 111
52619684 ATATAAAAAT
52619694 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
1 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
52619759 AAAGTATTAGTTACACGCTGTACCATTCAACCATCACATTTGAATC
66 AAAGTATTAGTTACACGCTGTACCATTCAACCATCACATTTGAATC
52619805 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
1 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
52619870 AAAGTATTAGTTACACGCTGTACCATTCAACCATCACATTTGAATC
66 AAAGTATTAGTTACACGCTGTACCATTCAACCATCACATTTGAATC
*
52619916 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTATAATTGAATCATT
1 ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
*
52619981 AAAGTATTAGTTACACGATGTACCATTCAACCATCACATTTGA
66 AAAGTATTAGTTACACGCTGTACCATTCAACCATCACATTTGA
52620024 CCTATCAGTT
Statistics
Matches: 217, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 217 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (111 bp):
ATTCTTCTATAATTAACATTTCATGCTTATAACTCTTAATTTCTGATATCTGTAATTGAATCATT
AAAGTATTAGTTACACGCTGTACCATTCAACCATCACATTTGAATC
Found at i:52627150 original size:33 final size:33
Alignment explanation
Indices: 52627113--52627178 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
52627103 TATCCTGATC
52627113 TATACTTTAAAATATAATTTGGATGACCAAAAT
1 TATACTTTAAAATATAATTTGGATGACCAAAAT
52627146 TATACTTTAAAATATAATTTGGATGACCAAAAT
1 TATACTTTAAAATATAATTTGGATGACCAAAAT
52627179 ATAGGAATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (33 bp):
TATACTTTAAAATATAATTTGGATGACCAAAAT
Found at i:52627244 original size:21 final size:21
Alignment explanation
Indices: 52627218--52627261 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
52627208 GGACGGGTAA
52627218 AATTAGAAACTATAAAACTAG
1 AATTAGAAACTATAAAACTAG
52627239 AATTAGAAACTATAAAACTAG
1 AATTAGAAACTATAAAACTAG
52627260 AA
1 AA
52627262 ACTCCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.23
Consensus pattern (21 bp):
AATTAGAAACTATAAAACTAG
Found at i:52629887 original size:84 final size:82
Alignment explanation
Indices: 52629705--52629933 Score: 296
Period size: 84 Copynumber: 2.7 Consensus size: 82
52629695 TAACTTTTGC
* * * * ** *
52629705 TTTAATTCGTCAATGAAACAGTGCCATTTTGTTAAATTTTTAATATATTTTTTACGGTATTTTTA
1 TTTAATTCATCAATGAAA-AGAGCCGTTTTGTTAAATTTTTAATATATTTTTTGCGGCGTTTGTA
* *
52629770 TAGAAAACGTCACTAATA
65 TACAAAACGCCACTAATA
*
52629788 TTTAATTCATCAATGAAAAGACGCCGTTTTATTAAATTTTTAATATATTTTTTTGCGGCGTTTGT
1 TTTAATTCATCAATGAAAAGA-GCCGTTTTGTTAAATTTTTAATATA-TTTTTTGCGGCGTTTGT
*
52629853 ATACAAAACGCCACTGATA
64 ATACAAAACGCCACTAATA
* * *
52629872 TTTAATTCATCAATGAAACGTATCCGTTTTGTTAAATTTTAAATATATTTTTTGCGGCGTTT
1 TTTAATTCATCAATGAAAAG-AGCCGTTTTGTTAAATTTTTAATATATTTTTTGCGGCGTTT
52629934 TTGACCAAAC
Statistics
Matches: 128, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
82 2 0.02
83 55 0.43
84 70 0.55
85 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (82 bp):
TTTAATTCATCAATGAAAAGAGCCGTTTTGTTAAATTTTTAATATATTTTTTGCGGCGTTTGTAT
ACAAAACGCCACTAATA
Found at i:52630105 original size:14 final size:14
Alignment explanation
Indices: 52630088--52630115 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52630078 ATGACATTAT
52630088 TAATATTATTTAAA
1 TAATATTATTTAAA
52630102 TAATATTATTTAAA
1 TAATATTATTTAAA
52630116 ATTTTGATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTATTTAAA
Found at i:52630639 original size:21 final size:20
Alignment explanation
Indices: 52630613--52630677 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
52630603 TAACAAATCA
*
52630613 TAAACCCTAAACTCTAAACTC
1 TAAACCCCAAACTCTAAAC-C
52630634 TAAACCCCAAACTCATAAACC
1 TAAACCCCAAACTC-TAAACC
** *
52630655 TTTTACCCCAAACACTAAACC
1 -TAAACCCCAAACTCTAAACC
52630676 TA
1 TA
52630678 CACCATAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 20 0.54
22 16 0.43
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAACCCCAAACTCTAAACC
Found at i:52631572 original size:41 final size:42
Alignment explanation
Indices: 52631524--52631910 Score: 349
Period size: 41 Copynumber: 9.5 Consensus size: 42
52631514 TGTTTTTTGA
*
52631524 GGCGCTTTCA-CAAAAACACCGCTAAAAACCCGAGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACCCGAGCATTAGC
* * * *
52631565 GGTGCTTT-TTCAAAAACGCTC-CTAAAAACCCAACCATTAGC
1 GGCGCTTTCATCAAAAACGC-CGCTAAAAACCCGAGCATTAGC
* * **
52631606 AGCACTTTC-TCAAAAACGCCGCT-AAAACCTAAAGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACC-CGAGCATTAGC
* * *
52631647 AGCGC-TTC-TCTAAAAACGCCGCTAAAACCCCCAGCATTAGC
1 GGCGCTTTCATC-AAAAACGCCGCTAAAAACCCGAGCATTAGC
* * *** *
52631688 GGTG-TTT-AGT-ATTAAATATCGCT-AAAACCCTAAGCATTAGC
1 GGCGCTTTCA-TCA-AAAACGCCGCTAAAAACCC-GAGCATTAGC
**
52631729 GGCGC-TTCATCAAAAACGCTACTAAAAACCCGAGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACCCGAGCATTAGC
*
52631770 GGCGC-TTCATCGAAAACGCCGCT-AAAACCCAGAGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACCC-GAGCATTAGC
* *
52631811 GGCGC-TTCATCGAAAACGCCGCTAAAATCCCGAGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACCCGAGCATTAGC
* *
52631852 GGCGCTTT-ATCAAAAATGCCGCTAAAACCCCGAGCATTAGC
1 GGCGCTTTCATCAAAAACGCCGCTAAAAACCCGAGCATTAGC
* *
52631893 GACGC-TTCATGAAAAACG
1 GGCGCTTTCATCAAAAACG
52631911 TCTCTAAAGC
Statistics
Matches: 286, Mismatches: 40, Indels: 40
0.78 0.11 0.11
Matches are distributed among these distances:
40 28 0.10
41 234 0.82
42 24 0.08
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.19
Consensus pattern (42 bp):
GGCGCTTTCATCAAAAACGCCGCTAAAAACCCGAGCATTAGC
Found at i:52631918 original size:82 final size:81
Alignment explanation
Indices: 52631524--52631918 Score: 388
Period size: 82 Copynumber: 4.8 Consensus size: 81
52631514 TGTTTTTTGA
* * **
52631524 GGCGCTTTCA-CAAAAACACCGCTAAAAACCC-GAGCATTAGCGGTGCTTTTTCAAAAACGCTCC
1 GGCGCTTT-ATCAAAAACGCCGCT-AAAACCCAGAGCATTAGCGGCGCTTCATCAAAAACGCT-C
* *
52631587 TAAAAACCCAACCATTAGC
63 TAAAAACCCGAGCATTAGC
* * * * * * *
52631606 AGCACTTTCTCAAAAACGCCGCTAAAACCTAAAGCATTAGCAGCGCTTC-TCTAAAAACGCCGCT
1 GGCGCTTTATCAAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCATC-AAAAACG-CTCT
* *
52631670 AAAACCCCCAGCATTAGC
64 AAAAACCCGAGCATTAGC
* * ***
52631688 GGTG-TTTAGT-ATTAAATATCGCTAAAACCCTA-AGCATTAGCGGCGCTTCATCAAAAACGCTA
1 GGCGCTTTA-TCA-AAAACGCCGCTAAAACCC-AGAGCATTAGCGGCGCTTCATCAAAAACGCT-
52631750 CTAAAAACCCGAGCATTAGC
62 CTAAAAACCCGAGCATTAGC
* * * *
52631770 GGCGCTTCATCGAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCATCGAAAACGCCGCTA
1 GGCGCTTTATCAAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCATCAAAAACG-CTCTA
*
52631835 AAATCCCGAGCATTAGC
65 AAAACCCGAGCATTAGC
* * * *
52631852 GGCGCTTTATCAAAAATGCCGCTAAAACCCCGAGCATTAGCGACGCTTCATGAAAAACGTCTCTA
1 GGCGCTTTATCAAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCATCAAAAACG-CTCTA
52631917 AA
65 AA
52631919 GCCCCCGATG
Statistics
Matches: 255, Mismatches: 45, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
81 14 0.05
82 233 0.91
83 8 0.03
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (81 bp):
GGCGCTTTATCAAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCATCAAAAACGCTCTAA
AAACCCGAGCATTAGC
Found at i:52631918 original size:123 final size:122
Alignment explanation
Indices: 52631535--52631910 Score: 388
Period size: 123 Copynumber: 3.1 Consensus size: 122
52631525 GCGCTTTCAC
* * *
52631535 AAAAACACCGCTAAAAACCCGAGCATTAGCGGTGCTTTTTCAAAAACGCTC-CTAAAAACCCAAC
1 AAAAACGCCGCT-AAAACCCGAGCATTAGCGGTGCTTTATCAAAAACGC-CGCT-AAAACCCAAG
* * * *** *
52631599 CATTAGCAGCACTTTCTCAAAAACGCCGCTAAAACCTAAAGCATTAGC-AGCGCTTC-TCT
63 CATTAGCGGCGCTTTATCAAAAACGCCGCTAAAACCCCGAGCATTAGCGA-CGCTTCATCG
* * ***
52631658 AAAAACGCCGCTAAAACCCCCAGCATTAGCGGTG-TTTAGT-ATTAAATATCGCTAAAACCCTAA
1 AAAAACGCCGCTAAAA-CCCGAGCATTAGCGGTGCTTTA-TCA-AAAACGCCGCTAAAACCC-AA
* ** * *
52631721 GCATTAGCGGCGCTTCATCAAAAACGCTACTAAAAACCCGAGCATTAGCGGCGCTTCATCG
62 GCATTAGCGGCGCTTTATCAAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCTTCATCG
* * * *
52631782 -AAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCATCGAAAACGCCGCTAAAATCCCGAGC
1 AAAAACGCCGCTAAAACCC-GAGCATTAGCGGTGCTTTATCAAAAACGCCGCTAAAA-CCCAAGC
*
52631846 ATTAGCGGCGCTTTATCAAAAATGCCGCTAAAACCCCGAGCATTAGCGACGCTTCAT-G
64 ATTAGCGGCGCTTTATCAAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCTTCATCG
52631904 AAAAACG
1 AAAAACG
52631911 TCTCTAAAGC
Statistics
Matches: 206, Mismatches: 35, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
122 20 0.10
123 178 0.86
124 8 0.04
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (122 bp):
AAAAACGCCGCTAAAACCCGAGCATTAGCGGTGCTTTATCAAAAACGCCGCTAAAACCCAAGCAT
TAGCGGCGCTTTATCAAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCTTCATCG
Found at i:52632038 original size:39 final size:38
Alignment explanation
Indices: 52631995--52632078 Score: 89
Period size: 40 Copynumber: 2.2 Consensus size: 38
52631985 GATAATGCTT
* *
52631995 TTTTTTAGAA-CGTCGCTAATGCACAATCTTTAGCGGCGA
1 TTTTTTA-AAGCGCCGCTAATGCACAATCTTTACCGGC-A
* * *
52632034 TTTTTGTAAAGCGCCGCTAATGCTCGATTTTTACCGGCA
1 TTTTT-TAAAGCGCCGCTAATGCACAATCTTTACCGGCA
52632073 TTTTTT
1 TTTTTT
52632079 GTCCAAACGT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
38 1 0.03
39 13 0.34
40 24 0.63
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (38 bp):
TTTTTTAAAGCGCCGCTAATGCACAATCTTTACCGGCA
Found at i:52641033 original size:26 final size:26
Alignment explanation
Indices: 52641004--52641060 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
52640994 AGTAATTATT
*
52641004 AATATATGTACCAAGTTGTTGATTTG
1 AATATATGTACAAAGTTGTTGATTTG
* *
52641030 AATATGTTTACAAAGTTGTTGATTTG
1 AATATATGTACAAAGTTGTTGATTTG
52641056 AATAT
1 AATAT
52641061 GTTTACATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (26 bp):
AATATATGTACAAAGTTGTTGATTTG
Found at i:52641061 original size:26 final size:26
Alignment explanation
Indices: 52641016--52641067 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
52641006 TATATGTACC
52641016 AAGTTGTTGATTTGAATATGTTTACA
1 AAGTTGTTGATTTGAATATGTTTACA
52641042 AAGTTGTTGATTTGAATATGTTTACA
1 AAGTTGTTGATTTGAATATGTTTACA
52641068 TGTAAGGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (26 bp):
AAGTTGTTGATTTGAATATGTTTACA
Found at i:52650512 original size:14 final size:16
Alignment explanation
Indices: 52650482--52650513 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
52650472 TTATAAGGCC
52650482 TTTATAATTTCTGGAT
1 TTTATAATTTCTGGAT
52650498 TTTA-AATTT-TGGAT
1 TTTATAATTTCTGGAT
52650512 TT
1 TT
52650514 GCTTTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTATAATTTCTGGAT
Found at i:52658538 original size:11 final size:11
Alignment explanation
Indices: 52658522--52658546 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52658512 AAACATGACA
52658522 AAATTAAGGAT
1 AAATTAAGGAT
52658533 AAATTAAGGAT
1 AAATTAAGGAT
52658544 AAA
1 AAA
52658547 CATCGCACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (11 bp):
AAATTAAGGAT
Done.