Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 16 of 203
Found at i:5182156 original size:85 final size:79
Alignment explanation
Indices: 5182049--5182404 Score: 310
Period size: 85 Copynumber: 4.3 Consensus size: 79
5182039 TAACATAATT
*
5182049 TAATTAAATTAAAAACCCTAACCTTATTTAATTAAATTAAAAACCCTAACCCTAACCTAATTTAA
1 TAATTTAATTAAAAACCCTAACC-----TAATTAAATTAAAAACCCTAA-CCTAACCTAATTTAA
5182114 TTAAATTAAAAACCCTAACC
60 TTAAATTAAAAACCCTAACC
** *
5182134 TAATTTAATTAAAAACCCTAACCTAATTTAATTAAATTAAAAACCCTAACCCTAACCTAACCTAC
1 TAATTTAATTAAAAACCCTAACC-----TAATTAAATTAAAAACCCTAA-CCTAACCTAATTTAA
5182199 TTAAATTAAAAACCCTAACC
60 TTAAATTAAAAACCCTAACC
* * * ** *
5182219 TTATTTAATTTAATTAAAAACCCTAACCTACTTAAATTAAAAATCCTAACCTTATTTAATTAAAT
1 -----TAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAACCTAATTTAAT
* *
5182284 TAAAAACCCTAACCCTAACCCTAACC
61 T--AAA--TTAA---AAACCCTAACC
* * *
5182310 TAATTAAATTAAAAATCCTAACCTAATTTAATTAAAAACCCTAACCT----T-ATTTAATTAAAT
1 TAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAACCTAATTTAATTAAAT
5182370 TAAAAACCCTAACCC
66 TAAAAACCCTAA-CC
5182385 T-ATTTAATTAAAAACCCTAA
1 TAATTTAATTAAAAACCCTAA
5182405 TTAAATTGTA
Statistics
Matches: 232, Mismatches: 26, Indels: 37
0.79 0.09 0.13
Matches are distributed among these distances:
74 25 0.11
75 3 0.01
77 3 0.01
79 3 0.01
81 7 0.03
82 1 0.00
84 10 0.04
85 99 0.43
86 45 0.19
88 3 0.01
90 23 0.10
91 10 0.04
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (79 bp):
TAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAACCTAATTTAATTAAAT
TAAAAACCCTAACC
Found at i:5182168 original size:113 final size:112
Alignment explanation
Indices: 5181984--5182368 Score: 384
Period size: 113 Copynumber: 3.4 Consensus size: 112
5181974 AATTAAAAAC
* *
5181984 CCTAATTTAATTAAATTAAAAACCCTAAACCCT-ACTTAATTAGAAACCCTAACCCTAACATAAT
1 CCTAATTTAATTAAATTAAAAACCCT-AA-CCTAATTTAATT--AAA----AACCCTAACCTAAT
**
5182048 TTAATTAAATTAAAAACCCTAACCT-T-ATTTAATTAAATTAAAAACCCTAACCCT
58 TTAATTAAATTAAAAACCCTAACCTATAACCTAATTAAATTAAAAACCCTAA-CCT
5182102 AACCTAATTTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATT
1 --CCTAATTTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATT
*
5182167 AAATTAAAAACCCTAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACCT
64 AAATTAAAAACCCTAA-CCT-A--TAACCTAATTAAATTAAAAACCCTAACCT
* * * * *
5182220 --T-ATTTAATTTAATTAAAAACCCTAACCTACTTAAATTAAAAATCCTAACCTTATTTAATTAA
1 CCTAATTTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAA
*
5182282 ATTAAAAACCCTAACCCTAACCCTAACCTAATTAAATTAAAAATCCTAA---
66 ATTAAAAACCCTAA-CCT-A---TAACCTAATTAAATTAAAAACCCTAACCT
*
5182331 CCTAA--T--TT-AATTAAAAACCCTAACCTTATTTAATTAAA
1 CCTAATTTAATTAAATTAAAAACCCTAACCTAATTTAATTAAA
5182369 TTAAAAACCC
Statistics
Matches: 239, Mismatches: 15, Indels: 33
0.83 0.05 0.11
Matches are distributed among these distances:
109 27 0.11
110 2 0.01
112 1 0.00
113 112 0.47
114 31 0.13
117 3 0.01
118 7 0.03
119 30 0.13
120 26 0.11
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.31
Consensus pattern (112 bp):
CCTAATTTAATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAA
ATTAAAAACCCTAACCTATAACCTAATTAAATTAAAAACCCTAACCT
Found at i:5182333 original size:23 final size:23
Alignment explanation
Indices: 5182300--5182404 Score: 122
Period size: 23 Copynumber: 4.3 Consensus size: 23
5182290 CCCTAACCCT
5182300 AACCCTAACCTAATTAAATTAAA
1 AACCCTAACCTAATTAAATTAAA
* *
5182323 AATCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTAAATTAAA
5182346 AACCCTAACCTTATTTAATTAAATTAAA
1 AACCCTAACC-----TAATTAAATTAAA
*
5182374 AACCCTAACCCT-ATTTAATTAAA
1 AACCCTAA-CCTAATTAAATTAAA
5182397 AACCCTAA
1 AACCCTAA
5182405 TTAAATTGTA
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
23 48 0.68
24 1 0.01
28 20 0.28
29 2 0.03
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (23 bp):
AACCCTAACCTAATTAAATTAAA
Found at i:5182344 original size:86 final size:86
Alignment explanation
Indices: 5182224--5182386 Score: 281
Period size: 86 Copynumber: 1.9 Consensus size: 86
5182214 TAACCTTATT
* * *
5182224 TAATTTAATTAAAAACCCTAACCTACTTAAATTAAAAATCCTAACCTTATTTAATTAAATTAAAA
1 TAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTTATTTAATTAAATTAAAA
5182289 ACCCTAACCCTAACCCTAACC
66 ACCCTAACCCTAACCCTAACC
* *
5182310 TAATTAAATTAAAAATCCTAACCTAATTTAATTAAAAACCCTAACCTTATTTAATTAAATTAAAA
1 TAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTTATTTAATTAAATTAAAA
5182375 ACCCTAACCCTA
66 ACCCTAACCCTA
5182387 TTTAATTAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 72 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (86 bp):
TAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTTATTTAATTAAATTAAAA
ACCCTAACCCTAACCCTAACC
Found at i:5187968 original size:20 final size:21
Alignment explanation
Indices: 5187921--5187980 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
5187911 AAAAGTGAAT
* *
5187921 ATGTACA-A-AAAAACAACAA
1 ATGTACATATAAAAATAAAAA
* *
5187940 ATGTACATATATAGATAAAAA
1 ATGTACATATAAAAATAAAAA
5187961 AT-TACATATAAAAATAAAAA
1 ATGTACATATAAAAATAAAAA
5187981 TAATAATTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.21
20 17 0.52
21 9 0.27
ACGTcount: A:0.65, C:0.08, G:0.05, T:0.22
Consensus pattern (21 bp):
ATGTACATATAAAAATAAAAA
Found at i:5189152 original size:18 final size:18
Alignment explanation
Indices: 5189129--5189163 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5189119 TTTTGGGCCG
* *
5189129 CGTTTGTAATTGGGCCAC
1 CGTTTGAAATCGGGCCAC
5189147 CGTTTGAAATCGGGCCA
1 CGTTTGAAATCGGGCCA
5189164 TGTGTTTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (18 bp):
CGTTTGAAATCGGGCCAC
Found at i:5189631 original size:44 final size:44
Alignment explanation
Indices: 5189577--5190245 Score: 323
Period size: 44 Copynumber: 15.3 Consensus size: 44
5189567 CTACTGTGAT
* * *
5189577 TTCAGCGAGATAAGATCCATGATTTTAATCCGCTCCACTGCAAC
1 TTCAGGGAGATAAGATCTATGATTTTAATCTGCTCCACTGCAAC
* **
5189621 TTCAGGGAGATAGGAT-TATTGACCTTAATCTGCTCCACTGCAAC
1 TTCAGGGAGATAAGATCTA-TGATTTTAATCTGCTCCACTGCAAC
* ** * * * *
5189665 TTCAGGGAGATAAGAT-T-CGCCCTTCAGTCTGC-CTCACGGAAAC
1 TTCAGGGAGATAAGATCTATG-ATTTTAATCTGCTC-CACTGCAAC
* * * * *
5189708 CTCAGGGGGATAAGAT-TATAAGCTTAAATCTGCTCCACTGCAAC
1 TTCAGGGAGATAAGATCTATGA-TTTTAATCTGCTCCACTGCAAC
* * ** * *
5189752 TTTAGAGAGATAAG-T-T-TCGCCATTTTGGGTCCGCCCCACTGCAAC
1 TTCAGGGAGATAAGATCTAT-G--ATTTT-AATCTGCTCCACTGCAAC
* * *
5189797 TTCAGGGAGATAAGA-CTA-GA-TATGATCTGCT-CTCTGCAAC
1 TTCAGGGAGATAAGATCTATGATTTTAATCTGCTCCACTGCAAC
* * *
5189837 TTCAGAGAGATAAGATCTGTGATTTTAAT-TCACTCCACTGCAAC
1 TTCAGGGAGATAAGATCTATGATTTTAATCT-GCTCCACTGCAAC
* * ** * *
5189881 TTTAGGGAGATAGGAT-TATAGGCTTAAATCTGCTCTACTGCAA-
1 TTCAGGGAGATAAGATCTAT-GATTTTAATCTGCTCCACTGCAAC
* * *
5189924 TTCTAGGGAGATAATAT-T-TGCCATTTTAGGTCTGCCCCACTGCAAC
1 TTC-AGGGAGATAAGATCTATG--ATTTTA-ATCTGCTCCACTGCAAC
* * * *
5189970 TTCAGGGGGATAAGA-C-CTGCTTATTCAGTCTGCTCCACTGCAAC
1 TTCAGGGAGATAAGATCTATGATT-TT-AATCTGCTCCACTGCAAC
* * **
5190014 TTCAGGGAGATAAGA-CTA-GA-TGTGATCTGCT-CTTTGCAAC
1 TTCAGGGAGATAAGATCTATGATTTTAATCTGCTCCACTGCAAC
* * *
5190054 TTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGCAAC
1 TTCAGGGAGATAAGATCTATGATTTTAATCTGCTCCACTGCAAC
* * * ** * * * *
5190098 TTTAAGGAGATAGGAT-TATAGGCTTAAATATGTTCCATTGCAAC
1 TTCAGGGAGATAAGATCTAT-GATTTTAATCTGCTCCACTGCAAC
** * ** *
5190142 TTTTGGGAGATAAGAT-T-CGCCATTTTGGGTCTGCCCCACTGCAAC
1 TTCAGGGAGATAAGATCTATG--ATTTT-AATCTGCTCCACTGCAAC
* * * *
5190187 TTCAGGGGGATAAGA-C-CTGCTTATTCAGTCTGCTCCACTGCAAC
1 TTCAGGGAGATAAGATCTATGATT-TT-AATCTGCTCCACTGCAAC
5190231 TTCAGGGAGATAAGA
1 TTCAGGGAGATAAGA
5190246 CTGGATGTCT
Statistics
Matches: 466, Mismatches: 118, Indels: 82
0.70 0.18 0.12
Matches are distributed among these distances:
40 43 0.09
41 15 0.03
42 13 0.03
43 60 0.13
44 250 0.54
45 81 0.17
46 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
TTCAGGGAGATAAGATCTATGATTTTAATCTGCTCCACTGCAAC
Found at i:5190042 original size:217 final size:217
Alignment explanation
Indices: 5189787--5190253 Score: 792
Period size: 217 Copynumber: 2.2 Consensus size: 217
5189777 TGGGTCCGCC
*
5189787 CCACTGCAACTTCAGGGAGATAAGACTAGATATGATCTGCTCTCTGCAACTTCAGAGAGATAAGA
1 CCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCTGCTCTCTGCAACTTCAGAGAGATAAGA
* * * *
5189852 TCTGTGATTTTAATTCACTCCACTGCAACTTTAGGGAGATAGGATTATAGGCTTAAATCTGCTCT
66 TCTGTGATTTTAATCCACTCCACTGCAACTTTAAGGAGATAGGATTATAGGCTTAAATATGCTCC
* *
5189917 ACTGCAA-TTCTAGGGAGATAATATTTGCCATTTTAGGTCTGCCCCACTGCAACTTCAGGGGGAT
131 ACTGCAACTT-TAGGGAGATAAGATTCGCCATTTTAGGTCTGCCCCACTGCAACTTCAGGGGGAT
5189981 AAGACCTGCTTATTCAGTCTGCT
195 AAGACCTGCTTATTCAGTCTGCT
*
5190004 CCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCTGCTCTTTGCAACTTCAGAGAGATAAGA
1 CCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCTGCTCTCTGCAACTTCAGAGAGATAAGA
* *
5190069 TCTGTGATTTTAATCCGCTCCACTGCAACTTTAAGGAGATAGGATTATAGGCTTAAATATGTTCC
66 TCTGTGATTTTAATCCACTCCACTGCAACTTTAAGGAGATAGGATTATAGGCTTAAATATGCTCC
* * *
5190134 ATTGCAACTTTTGGGAGATAAGATTCGCCATTTTGGGTCTGCCCCACTGCAACTTCAGGGGGATA
131 ACTGCAACTTTAGGGAGATAAGATTCGCCATTTTAGGTCTGCCCCACTGCAACTTCAGGGGGATA
5190199 AGACCTGCTTATTCAGTCTGCT
196 AGACCTGCTTATTCAGTCTGCT
*
5190221 CCACTGCAACTTCAGGGAGATAAGACTGGATGT
1 CCACTGCAACTTCAGGGAGATAAGACTAGATGT
5190254 CTTCGATCTG
Statistics
Matches: 235, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
217 233 0.99
218 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (217 bp):
CCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCTGCTCTCTGCAACTTCAGAGAGATAAGA
TCTGTGATTTTAATCCACTCCACTGCAACTTTAAGGAGATAGGATTATAGGCTTAAATATGCTCC
ACTGCAACTTTAGGGAGATAAGATTCGCCATTTTAGGTCTGCCCCACTGCAACTTCAGGGGGATA
AGACCTGCTTATTCAGTCTGCT
Found at i:5190055 original size:173 final size:173
Alignment explanation
Indices: 5189709--5190028 Score: 412
Period size: 173 Copynumber: 1.8 Consensus size: 173
5189699 CACGGAAACC
*
5189709 TCAGGGGGATAAGATTATAAGCTTAAATCTGCTCCACTGCAACTTTAGAGAGATAAGTTTCGCCA
1 TCAGGGAGATAAGATTATAAGCTTAAATCTGCTCCACTGCAACTTTAGAGAGATAAGTTTCGCCA
* * *
5189774 TTTTGGGTCCGCCCCACTGCAACTTCAGGGAGATAAGACTAGATATGATCTGCTCTCTGCAACTT
66 TTTTAGGTCCGCCCCACTGCAACTTCAGGGAGATAAGACTAGATATCATCTGCTCACTGCAACTT
* *
5189839 CAGAGAGATAAGATCTGTGATTTTAATTCACTCCACTGCAACT
131 CAGAGAGATAAGATCTGAGATTGTAATTCACTCCACTGCAACT
* * * * * *
5189882 TTAGGGAGATAGGATTATAGGCTTAAATCTGCTCTACTGCAA-TTCTAGGGAGATAA-TATTTGC
1 TCAGGGAGATAAGATTATAAGCTTAAATCTGCTCCACTGCAACTT-TAGAGAGATAAGT-TTCGC
* * *
5189945 CATTTTAGGTCTGCCCCACTGCAACTTCAGGGGGATAAGACCT-GCTTATTCAGTCTGCTCCACT
64 CATTTTAGGTCCGCCCCACTGCAACTTCAGGGAGATAAGA-CTAG-ATA-TCA-TCTGCT-CACT
*
5190009 GCAACTTCAGGGAGATAAGA
124 GCAACTTCAGAGAGATAAGA
5190029 CTAGATGTGA
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
172 3 0.02
173 89 0.71
174 4 0.03
175 2 0.02
176 6 0.05
177 22 0.17
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (173 bp):
TCAGGGAGATAAGATTATAAGCTTAAATCTGCTCCACTGCAACTTTAGAGAGATAAGTTTCGCCA
TTTTAGGTCCGCCCCACTGCAACTTCAGGGAGATAAGACTAGATATCATCTGCTCACTGCAACTT
CAGAGAGATAAGATCTGAGATTGTAATTCACTCCACTGCAACT
Found at i:5190357 original size:88 final size:88
Alignment explanation
Indices: 5190246--5190469 Score: 322
Period size: 88 Copynumber: 2.5 Consensus size: 88
5190236 GGAGATAAGA
*
5190246 CTGGATGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAGCCTGCT
1 CTGG-TGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCT
*
5190311 CCGCTACAACCTAGGGAGGCAAGG
65 CCGCTACAACCCAGGGAGGCAAGG
* * * * * * *
5190335 CTGGTGTCTTCGATTTGTTTCGCTGTTGATGCAGGAAGGCAAGATCTGTTATTTTTAACCTGCTT
1 CTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTC
*
5190400 CGCTGCAACCCAGGGAGGCAAGG
66 CGCTACAACCCAGGGAGGCAAGG
* * *
5190423 CTGGTGTCTTCGATCTGCTTCACTATCAGTGTAGGAAGGCAAGATCT
1 CTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCT
5190470 ACTCTCTTCA
Statistics
Matches: 117, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
88 113 0.97
89 4 0.03
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (88 bp):
CTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTC
CGCTACAACCCAGGGAGGCAAGG
Found at i:5190443 original size:43 final size:43
Alignment explanation
Indices: 5190306--5190443 Score: 105
Period size: 44 Copynumber: 3.2 Consensus size: 43
5190296 TATTTTTAGC
* * *
5190306 CTGCTCCGCTACAACCTAGGGAGGCAAGGCTGGTGTCTTCGAT
1 CTGCTTCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
* * ** ** * * * * * ** *
5190349 TTGTTTCGCTGTTGATGCAGGAAGGCAAGATCTGTTATTTTTAAC
1 CTGCTTCGCTG-CAACCCAGGGAGGCAAG-GCTGGTGTCTTCGAT
5190394 CTGCTTCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
1 CTGCTTCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
5190437 CTGCTTC
1 CTGCTTC
5190444 ACTATCAGTG
Statistics
Matches: 62, Mismatches: 31, Indels: 4
0.64 0.32 0.04
Matches are distributed among these distances:
43 22 0.35
44 23 0.37
45 17 0.27
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.30
Consensus pattern (43 bp):
CTGCTTCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGAT
Found at i:5191731 original size:5 final size:5
Alignment explanation
Indices: 5191723--5191751 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5191713 TTCTTCCTTT
5191723 TTTTG TTTTG TTTTG TTTTG TTTT- TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
5191752 AAATATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:5191850 original size:14 final size:15
Alignment explanation
Indices: 5191827--5191859 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5191817 ATCGACGCTT
5191827 TTCCAAATAAGGT-C
1 TTCCAAATAAGGTCC
*
5191841 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
5191856 TTCC
1 TTCC
5191860 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.30
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:5196991 original size:21 final size:22
Alignment explanation
Indices: 5196962--5197005 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5196952 AAAAAACAAC
* *
5196962 AAATGTACATATATAGATAAAA
1 AAATGTACATATAAAAATAAAA
5196984 AAAT-TACATATAAAAATAAAA
1 AAATGTACATATAAAAATAAAA
5197005 A
1 A
5197006 TAATAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (22 bp):
AAATGTACATATAAAAATAAAA
Found at i:5200249 original size:45 final size:45
Alignment explanation
Indices: 5200175--5200268 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 45
5200165 AAACCCTCCA
* *
5200175 AAACTTTTTTCCTTTTATTTTCCCTCAAAACCTTTACTT-TCCCC
1 AAACTTTTTTCCTTTTACTTTCCCTCAAAACCTTTACTTCCCCCC
* *
5200219 AAACTTTTTTCCTTTTACTTTCTCTCCAAAACTTTTACTTCCCCCC
1 AAACTTTTTTCCTTTTACTTTCCCT-CAAAACCTTTACTTCCCCCC
5200265 AAAC
1 AAAC
5200269 CCAATTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 23 0.52
45 13 0.30
46 8 0.18
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.45
Consensus pattern (45 bp):
AAACTTTTTTCCTTTTACTTTCCCTCAAAACCTTTACTTCCCCCC
Found at i:5203218 original size:50 final size:50
Alignment explanation
Indices: 5203105--5203401 Score: 321
Period size: 50 Copynumber: 5.8 Consensus size: 50
5203095 ATTTGGGTAA
* *
5203105 AGAGATCCCATGTAAGACTATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* * *
5203161 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
5203211 AGAGGTCCCATGTAAGGCCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
5203261 AGAGGTCCTC-TGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCC-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
5203311 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
5203360 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
5203402 TGTTATTATC
Statistics
Matches: 210, Mismatches: 28, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
48 1 0.00
49 40 0.19
50 125 0.60
51 1 0.00
53 3 0.01
55 2 0.01
56 38 0.18
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:5213483 original size:26 final size:26
Alignment explanation
Indices: 5213447--5213500 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
5213437 GGAAGTTAGT
5213447 TGATCATTTTGACCAAATTGAGTACA
1 TGATCATTTTGACCAAATTGAGTACA
5213473 TGATCATTTTGACCAAATTGAGTACA
1 TGATCATTTTGACCAAATTGAGTACA
5213499 TG
1 TG
5213501 GTTATACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (26 bp):
TGATCATTTTGACCAAATTGAGTACA
Found at i:5219967 original size:31 final size:31
Alignment explanation
Indices: 5219927--5220075 Score: 126
Period size: 31 Copynumber: 4.9 Consensus size: 31
5219917 CTAATGCTCT
*
5219927 AATC-AATTCAGCAATATATATTCATATACG
1 AATCAAATTCGGCAATATATATTCATATACG
** * *
5219957 AATCAAATTCAACAATGA-ATATTGATATACC
1 AATCAAATTCGGCAAT-ATATATTCATATACG
* ** *
5219988 AAGC-AATTCGGCAATATATAACCATATAAG
1 AATCAAATTCGGCAATATATATTCATATACG
* * * *
5220018 AATCAAATTTGGCAATGTATAATCATATACA
1 AATCAAATTCGGCAATATATATTCATATACG
*
5220049 AATCAAATTCGGC-ATCCTATATTCATA
1 AATCAAATTCGGCAAT-ATATATTCATA
5220076 AACAATTTAA
Statistics
Matches: 94, Mismatches: 20, Indels: 9
0.76 0.16 0.07
Matches are distributed among these distances:
29 1 0.01
30 26 0.28
31 66 0.70
32 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (31 bp):
AATCAAATTCGGCAATATATATTCATATACG
Found at i:5220034 original size:61 final size:61
Alignment explanation
Indices: 5219930--5220062 Score: 149
Period size: 61 Copynumber: 2.2 Consensus size: 61
5219920 ATGCTCTAAT
* ** * * * *
5219930 CAATTCAGCAATATATATTCATATACGAATCAAATTCAACAATGAATATTGATATACCAAG
1 CAATTCGGCAATATATAACCATATAAGAATCAAATTCAACAATGAATAATCATATACAAAG
*** * *
5219991 CAATTCGGCAATATATAACCATATAAGAATCAAATTTGGCAATGTATAATCATATACAAAT
1 CAATTCGGCAATATATAACCATATAAGAATCAAATTCAACAATGAATAATCATATACAAAG
5220052 CAAATTCGGCA
1 C-AATTCGGCA
5220063 TCCTATATTC
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
61 50 0.85
62 9 0.15
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.29
Consensus pattern (61 bp):
CAATTCGGCAATATATAACCATATAAGAATCAAATTCAACAATGAATAATCATATACAAAG
Found at i:5220121 original size:31 final size:31
Alignment explanation
Indices: 5220086--5220220 Score: 136
Period size: 31 Copynumber: 4.4 Consensus size: 31
5220076 AACAATTTAA
*
5220086 TTTCAACAATGTATAACCATATAAAAATTAT
1 TTTCAGCAATGTATAACCATATAAAAATTAT
** *
5220117 TTTCAGCAATGT-TCAACCATATACGAATCA-
1 TTTCAGCAATGTAT-AACCATATAAAAATTAT
* *
5220147 TTTCAGCAACT-TATATACC-TAT-ATAATTCAA
1 TTTCAGCAA-TGTATA-ACCATATAAAAATT-AT
*
5220178 TTTCAGCAATGAATAACCATATAAAAATTAT
1 TTTCAGCAATGTATAACCATATAAAAATTAT
5220209 TTTCAGCAATGT
1 TTTCAGCAATGT
5220221 TCAGCCATAT
Statistics
Matches: 84, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
29 3 0.04
30 20 0.24
31 56 0.67
32 5 0.06
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TTTCAGCAATGTATAACCATATAAAAATTAT
Found at i:5220202 original size:92 final size:92
Alignment explanation
Indices: 5220079--5220252 Score: 294
Period size: 92 Copynumber: 1.9 Consensus size: 92
5220069 ATTCATAAAC
* *
5220079 AATTTAATTTCAACAATGTATAACCATATAAAAATTATTTTCAGCAATGTTCAACCATATACGAA
1 AATTCAATTTCAACAATGAATAACCATATAAAAATTATTTTCAGCAATGTTCAACCATATACGAA
5220144 TCATTTCAGCAACTTATATACCTATAT
66 TCATTTCAGCAACTTATATACCTATAT
* * *
5220171 AATTCAATTTCAGCAATGAATAACCATATAAAAATTATTTTCAGCAATGTTCAGCCATATATGAA
1 AATTCAATTTCAACAATGAATAACCATATAAAAATTATTTTCAGCAATGTTCAACCATATACGAA
*
5220236 TCATTTCGGCAACTTAT
66 TCATTTCAGCAACTTAT
5220253 GTAATATACA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 76 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (92 bp):
AATTCAATTTCAACAATGAATAACCATATAAAAATTATTTTCAGCAATGTTCAACCATATACGAA
TCATTTCAGCAACTTATATACCTATAT
Found at i:5224069 original size:31 final size:31
Alignment explanation
Indices: 5224026--5224123 Score: 115
Period size: 31 Copynumber: 3.2 Consensus size: 31
5224016 TATAGTAGGC
*
5224026 ACTATGTGCTGATGTTTATATTTTAGCAGGT
1 ACTATGTGCTGATGTTTATATTTTATCAGGT
* * * *
5224057 ACTATGTACTGATGTTTTTATTGTATCAGGC
1 ACTATGTGCTGATGTTTATATTTTATCAGGT
* * * *
5224088 ACAATGTGTTGGTGTTTATATTTTATTAGGT
1 ACTATGTGCTGATGTTTATATTTTATCAGGT
5224119 ACTAT
1 ACTAT
5224124 TTACCGGTGT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.47
Consensus pattern (31 bp):
ACTATGTGCTGATGTTTATATTTTATCAGGT
Found at i:5225072 original size:24 final size:24
Alignment explanation
Indices: 5225045--5225093 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5225035 ATGGCCATAG
5225045 ACTTGTCTTCAAAATGGTCGTATC
1 ACTTGTCTTCAAAATGGTCGTATC
*
5225069 ACTTGTCTTCAGAATGGTCGTATC
1 ACTTGTCTTCAAAATGGTCGTATC
5225093 A
1 A
5225094 TAATTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (24 bp):
ACTTGTCTTCAAAATGGTCGTATC
Found at i:5225597 original size:18 final size:18
Alignment explanation
Indices: 5225574--5225613 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5225564 GATAATATAC
5225574 TAACCAAGTTAGCTATTG
1 TAACCAAGTTAGCTATTG
*
5225592 TAACCAAGTTAGTTATTG
1 TAACCAAGTTAGCTATTG
5225610 TAAC
1 TAAC
5225614 GACCTGGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (18 bp):
TAACCAAGTTAGCTATTG
Found at i:5228088 original size:54 final size:54
Alignment explanation
Indices: 5228001--5228111 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
5227991 ATGACCCAGT
* *
5228001 GACACGGCCGTGTGACCCACCTCAAACGAGCTTAGCTCTCGCACACGATTAGGG
1 GACACGACCGTGTGACCCACCTCAAACGAGCTTAGCTCTCGCACAAGATTAGGG
* * * *
5228055 GACACGACCGTGTGACCCACCTCACACGGGCTTATCTCTCGCATAAGATTAGGG
1 GACACGACCGTGTGACCCACCTCAAACGAGCTTAGCTCTCGCACAAGATTAGGG
5228109 GAC
1 GAC
5228112 TGGTCGTGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.18
Consensus pattern (54 bp):
GACACGACCGTGTGACCCACCTCAAACGAGCTTAGCTCTCGCACAAGATTAGGG
Found at i:5242865 original size:18 final size:18
Alignment explanation
Indices: 5242842--5242888 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
5242832 CGCCCCATAG
5242842 CCAGATACAAATAGAATA
1 CCAGATACAAATAGAATA
*
5242860 CCAGATA-TAATAGAATA
1 CCAGATACAAATAGAATA
*
5242877 ACAGATAACAAA
1 CCAGAT-ACAAA
5242889 ATGTATGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 14 0.58
18 8 0.33
19 2 0.08
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (18 bp):
CCAGATACAAATAGAATA
Found at i:5247127 original size:22 final size:23
Alignment explanation
Indices: 5247101--5247144 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5247091 GTGATGAGGT
5247101 TATCTT-ATAAATATGTT-AAATC
1 TATCTTGA-AAATATGTTGAAATC
5247123 TATCTTGAAAATATGTTGAAAT
1 TATCTTGAAAATATGTTGAAAT
5247145 AAATTGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (23 bp):
TATCTTGAAAATATGTTGAAATC
Found at i:5249650 original size:16 final size:17
Alignment explanation
Indices: 5249608--5249643 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5249598 AGAGTAGAGC
*
5249608 AAAAAGTAAAAGAGAAG
1 AAAAAGAAAAAGAGAAG
5249625 AAAAAGAAAAAGA-AAG
1 AAAAAGAAAAAGAGAAG
5249641 AAA
1 AAA
5249644 CATAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAAGAGAAG
Found at i:5252121 original size:22 final size:22
Alignment explanation
Indices: 5252071--5252123 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
5252061 AAAATCATCT
*
5252071 TACATAAATTATATTGGCACAA
1 TACATCAATTATATTGGCACAA
*
5252093 T-CAATCAATTATATTGGCATAA
1 TAC-ATCAATTATATTGGCACAA
5252115 TACATCAAT
1 TACATCAAT
5252124 GGCAATAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (22 bp):
TACATCAATTATATTGGCACAA
Found at i:5257392 original size:40 final size:40
Alignment explanation
Indices: 5257344--5257731 Score: 722
Period size: 40 Copynumber: 9.7 Consensus size: 40
5257334 GCAAACACAT
* *
5257344 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
5257384 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
5257424 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
5257464 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
5257504 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
5257544 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
5257584 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
5257624 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
5257664 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
5257704 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
5257732 TCCAATGCTC
Statistics
Matches: 343, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 343 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:5267402 original size:176 final size:182
Alignment explanation
Indices: 5267078--5267430 Score: 459
Period size: 176 Copynumber: 1.9 Consensus size: 182
5267068 TAAGCTCACC
* * **
5267078 TATATTATTATTTTTAAATTCTTTTAAAAATTATATTATTTTTAATTTAATGTTTAAATTTTTTT
1 TATATTATTATTTTTAAATTCTTTAAAAAAGTATATTATTTTTAATTTAATGTTTAAAAATTTTT
** * * *
5267143 ATATGTTTTTTTGTTTTATGAAAATTTTAACCATAAACAATTTAACGCAATTTTTTTATATCTAT
66 ATA-----TTTCCTTTTATGAAAATTTTAACCAT-AACAA-TTAACACAATTTTTTTATATATAA
*
5267208 ATTGCACTATTATATATTTAATTTAATTTTATATAAATTATATAATACATAAAATAAAA
124 ATTGCAATATTATATATTTAATTTAATTTTATATAAATTATATAATACATAAAATAAAA
* *
5267267 TATA-TATTCTTTTTTAATTCTTTAAAAAAGTATATTATTTTTAATTTAATG-TTAAAAATTTTT
1 TATATTATTATTTTTAAATTCTTTAAAAAAGTATATTATTTTTAATTTAATGTTTAAAAATTTTT
*
5267330 ATA-TTCCTTTTATGAAAATTTTAACCAT-A-GA-TAACAC-ATCTTTTTTATATATAAATTGCA
66 ATATTTCCTTTTATGAAAATTTTAACCATAACAATTAACACAAT-TTTTTTATATATAAATTGCA
*
5267390 ATATTATATATTTAATTTAATTTTATATAAATTATTTAATA
130 ATATTATATATTTAATTTAATTTTATATAAATTATATAATA
5267431 TATGATAATA
Statistics
Matches: 149, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
175 2 0.01
176 62 0.42
178 1 0.01
179 1 0.01
181 23 0.15
187 13 0.09
188 43 0.29
189 4 0.03
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (182 bp):
TATATTATTATTTTTAAATTCTTTAAAAAAGTATATTATTTTTAATTTAATGTTTAAAAATTTTT
ATATTTCCTTTTATGAAAATTTTAACCATAACAATTAACACAATTTTTTTATATATAAATTGCAA
TATTATATATTTAATTTAATTTTATATAAATTATATAATACATAAAATAAAA
Found at i:5268622 original size:16 final size:16
Alignment explanation
Indices: 5268592--5268640 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5268582 CCTGACTTGT
* *
5268592 AGGTTTTTGGATTTTA
1 AGGTTTTAGGGTTTTA
*
5268608 AGGTTTTAGGGTTTTT
1 AGGTTTTAGGGTTTTA
5268624 AGGATTTTTAGGGTTTT
1 AGG--TTTTAGGGTTTT
5268641 GGAGAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 16 0.57
18 12 0.43
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (16 bp):
AGGTTTTAGGGTTTTA
Found at i:5268625 original size:9 final size:9
Alignment explanation
Indices: 5268611--5268640 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5268601 GATTTTAAGG
5268611 TTTTAGGGT
1 TTTTAGGGT
*
5268620 TTTTAGGAT
1 TTTTAGGGT
5268629 TTTTAGGGT
1 TTTTAGGGT
5268638 TTT
1 TTT
5268641 GGAGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (9 bp):
TTTTAGGGT
Found at i:5270330 original size:620 final size:620
Alignment explanation
Indices: 5269150--5270392 Score: 2459
Period size: 620 Copynumber: 2.0 Consensus size: 620
5269140 AAAAGCTGCA
5269150 AAACTTGCTAAAGTGAGTAAATAGTTTAACAATTAAATAAGGAAGGGCTAAAAGAGCAAATGGAC
1 AAACTTGCTAAAGTGAGTAAATAGTTTAACAATTAAATAAGGAAGGGCTAAAAGAGCAAATGGAC
5269215 AAATTTAAGTGGCTGAGATGGCATACCGTTAAAAAAATCTAGGATTTTTATGTATTTAAGGACAA
66 AAATTTAAGTGGCTGAGATGGCATACCGTTAAAAAAATCTAGGATTTTTATGTATTTAAGGACAA
5269280 AATTGGAATTACAAAAAAGTTTATGTGGCCAAATTTTATTTTAAGGATTTCAAGACCATTTCTTC
131 AATTGGAATTACAAAAAAGTTTATGTGGCCAAATTTTATTTTAAGGATTTCAAGACCATTTCTTC
5269345 TTGAAATTTTGGTGGGAAACAGCCATGGAAGAGGTTTGGAGCTGGTATTCCATATTTTGGCTTCA
196 TTGAAATTTTGGTGGGAAACAGCCATGGAAGAGGTTTGGAGCTGGTATTCCATATTTTGGCTTCA
5269410 AGTAAGTTTAATTCTTTCTTTTTCCTTGAAATTTTTATATTTTTGGACTTTTACAATTAGGTCCA
261 AGTAAGTTTAATTCTTTCTTTTTCCTTGAAATTTTTATATTTTTGGACTTTTACAATTAGGTCCA
5269475 ACTTAGTATTCTACTAGTTTCTCATTTAGTTGAAAGTTTTGGAAGATACCAATGATAAGTTCATA
326 ACTTAGTATTCTACTAGTTTCTCATTTAGTTGAAAGTTTTGGAAGATACCAATGATAAGTTCATA
5269540 TTATTTTTGTTATTTTATGATGAAATTGAGATGTTAATGGATGTTTAAAGGTGTTTTATTAAAGA
391 TTATTTTTGTTATTTTATGATGAAATTGAGATGTTAATGGATGTTTAAAGGTGTTTTATTAAAGA
* *
5269605 ATTTTGGATGAAAACATGTTTTAGGGATTAAGTTGAAAAGTATTGAAATTGTGGATAAATTCTGA
456 ATTTTGGATGAAAACATGTTTTAGGGATTAAATTGAAAAGTATTGAAATTGTGGATAAATTCTAA
5269670 AATTTCATGGAATCCATGGGCTGTTATTGATATGTATGAGAATTATTAGTCTTGAATAAAGGATT
521 AATTTCATGGAATCCATGGGCTGTTATTGATATGTATGAGAATTATTAGTCTTGAATAAAGGATT
5269735 ATATTGCAAGAATTTCATTTTCCGAGCCTAGGGAC
586 ATATTGCAAGAATTTCATTTTCCGAGCCTAGGGAC
5269770 AAACTTGCTAAAGTGAGTAAATAGTTTAACAATTAAATAAGGAAGGGCTAAAAGAGCAAATGGAC
1 AAACTTGCTAAAGTGAGTAAATAGTTTAACAATTAAATAAGGAAGGGCTAAAAGAGCAAATGGAC
5269835 AAATTTAAGTGGCTGAGATGGCATACCGTTAAAAAAATCTAGGATTTTTATGTATTTAAGGACAA
66 AAATTTAAGTGGCTGAGATGGCATACCGTTAAAAAAATCTAGGATTTTTATGTATTTAAGGACAA
5269900 AATTGGAATTACAAAAAAGTTTATGTGGCCAAATTTTATTTTAAGGATTTCAAGACCATTTCTTC
131 AATTGGAATTACAAAAAAGTTTATGTGGCCAAATTTTATTTTAAGGATTTCAAGACCATTTCTTC
5269965 TTGAAATTTTGGTGGGAAACAGCCATGGAAGAGGTTTGGAGCTGGTATTCCATATTTTGGCTTCA
196 TTGAAATTTTGGTGGGAAACAGCCATGGAAGAGGTTTGGAGCTGGTATTCCATATTTTGGCTTCA
5270030 AGTAAGTTTAATTCTTTCTTTTTCCTTGAAATTTTTATATTTTTGGACTTTTACAATTAGGTCCA
261 AGTAAGTTTAATTCTTTCTTTTTCCTTGAAATTTTTATATTTTTGGACTTTTACAATTAGGTCCA
5270095 ACTTAGTATTCTACTAGTTTCTCATTTAGTTGAAAGTTTTGGAAGATACCAATGATAAGTTCATA
326 ACTTAGTATTCTACTAGTTTCTCATTTAGTTGAAAGTTTTGGAAGATACCAATGATAAGTTCATA
5270160 TTATTTTTGTTATTTTATGATGAAATTGAGATGTTAATGGATGTTTAAAGGTGTTTTATTAAAGA
391 TTATTTTTGTTATTTTATGATGAAATTGAGATGTTAATGGATGTTTAAAGGTGTTTTATTAAAGA
*
5270225 ATTTTGGATGAAAACATGTTTTAGGGATTAAATTGAAAAGTATTGAAATTGTGGATAACTTCTAA
456 ATTTTGGATGAAAACATGTTTTAGGGATTAAATTGAAAAGTATTGAAATTGTGGATAAATTCTAA
5270290 AATTTCATGGAATCCATGGGCTGTTATTGATATGTATGAGAATTATTAGTCTTGAATAAAGGATT
521 AATTTCATGGAATCCATGGGCTGTTATTGATATGTATGAGAATTATTAGTCTTGAATAAAGGATT
5270355 ATATTGCAAGAATTTCATTTTCCGAGCCTAGGGAC
586 ATATTGCAAGAATTTCATTTTCCGAGCCTAGGGAC
5270390 AAA
1 AAA
5270393 GTTGTCATGT
Statistics
Matches: 620, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
620 620 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (620 bp):
AAACTTGCTAAAGTGAGTAAATAGTTTAACAATTAAATAAGGAAGGGCTAAAAGAGCAAATGGAC
AAATTTAAGTGGCTGAGATGGCATACCGTTAAAAAAATCTAGGATTTTTATGTATTTAAGGACAA
AATTGGAATTACAAAAAAGTTTATGTGGCCAAATTTTATTTTAAGGATTTCAAGACCATTTCTTC
TTGAAATTTTGGTGGGAAACAGCCATGGAAGAGGTTTGGAGCTGGTATTCCATATTTTGGCTTCA
AGTAAGTTTAATTCTTTCTTTTTCCTTGAAATTTTTATATTTTTGGACTTTTACAATTAGGTCCA
ACTTAGTATTCTACTAGTTTCTCATTTAGTTGAAAGTTTTGGAAGATACCAATGATAAGTTCATA
TTATTTTTGTTATTTTATGATGAAATTGAGATGTTAATGGATGTTTAAAGGTGTTTTATTAAAGA
ATTTTGGATGAAAACATGTTTTAGGGATTAAATTGAAAAGTATTGAAATTGTGGATAAATTCTAA
AATTTCATGGAATCCATGGGCTGTTATTGATATGTATGAGAATTATTAGTCTTGAATAAAGGATT
ATATTGCAAGAATTTCATTTTCCGAGCCTAGGGAC
Found at i:5271034 original size:576 final size:576
Alignment explanation
Indices: 5269942--5271093 Score: 2304
Period size: 576 Copynumber: 2.0 Consensus size: 576
5269932 ATTTTATTTT
5269942 AAGGATTTCAAGACCATTTCTTCTTGAAATTTTGGTGGGAAACAGCCATGGAAGAGGTTTGGAGC
1 AAGGATTTCAAGACCATTTCTTCTTGAAATTTTGGTGGGAAACAGCCATGGAAGAGGTTTGGAGC
5270007 TGGTATTCCATATTTTGGCTTCAAGTAAGTTTAATTCTTTCTTTTTCCTTGAAATTTTTATATTT
66 TGGTATTCCATATTTTGGCTTCAAGTAAGTTTAATTCTTTCTTTTTCCTTGAAATTTTTATATTT
5270072 TTGGACTTTTACAATTAGGTCCAACTTAGTATTCTACTAGTTTCTCATTTAGTTGAAAGTTTTGG
131 TTGGACTTTTACAATTAGGTCCAACTTAGTATTCTACTAGTTTCTCATTTAGTTGAAAGTTTTGG
5270137 AAGATACCAATGATAAGTTCATATTATTTTTGTTATTTTATGATGAAATTGAGATGTTAATGGAT
196 AAGATACCAATGATAAGTTCATATTATTTTTGTTATTTTATGATGAAATTGAGATGTTAATGGAT
5270202 GTTTAAAGGTGTTTTATTAAAGAATTTTGGATGAAAACATGTTTTAGGGATTAAATTGAAAAGTA
261 GTTTAAAGGTGTTTTATTAAAGAATTTTGGATGAAAACATGTTTTAGGGATTAAATTGAAAAGTA
5270267 TTGAAATTGTGGATAACTTCTAAAATTTCATGGAATCCATGGGCTGTTATTGATATGTATGAGAA
326 TTGAAATTGTGGATAACTTCTAAAATTTCATGGAATCCATGGGCTGTTATTGATATGTATGAGAA
5270332 TTATTAGTCTTGAATAAAGGATTATATTGCAAGAATTTCATTTTCCGAGCCTAGGGACAAAGTTG
391 TTATTAGTCTTGAATAAAGGATTATATTGCAAGAATTTCATTTTCCGAGCCTAGGGACAAAGTTG
5270397 TCATGTATTAAAAGTTTAGGGTCAAATTGGTAATCAATATTTTACACTAAAACAGTTTTGGGCAG
456 TCATGTATTAAAAGTTTAGGGTCAAATTGGTAATCAATATTTTACACTAAAACAGTTTTGGGCAG
5270462 CAGCAATGGTCTAAATTTGAAAAATCACCAAAAATTATGGGAATTTAATTAGAGGA
521 CAGCAATGGTCTAAATTTGAAAAATCACCAAAAATTATGGGAATTTAATTAGAGGA
5270518 AAGGATTTCAAGACCATTTCTTCTTGAAATTTTGGTGGGAAACAGCCATGGAAGAGGTTTGGAGC
1 AAGGATTTCAAGACCATTTCTTCTTGAAATTTTGGTGGGAAACAGCCATGGAAGAGGTTTGGAGC
5270583 TGGTATTCCATATTTTGGCTTCAAGTAAGTTTAATTCTTTCTTTTTCCTTGAAATTTTTATATTT
66 TGGTATTCCATATTTTGGCTTCAAGTAAGTTTAATTCTTTCTTTTTCCTTGAAATTTTTATATTT
5270648 TTGGACTTTTACAATTAGGTCCAACTTAGTATTCTACTAGTTTCTCATTTAGTTGAAAGTTTTGG
131 TTGGACTTTTACAATTAGGTCCAACTTAGTATTCTACTAGTTTCTCATTTAGTTGAAAGTTTTGG
5270713 AAGATACCAATGATAAGTTCATATTATTTTTGTTATTTTATGATGAAATTGAGATGTTAATGGAT
196 AAGATACCAATGATAAGTTCATATTATTTTTGTTATTTTATGATGAAATTGAGATGTTAATGGAT
5270778 GTTTAAAGGTGTTTTATTAAAGAATTTTGGATGAAAACATGTTTTAGGGATTAAATTGAAAAGTA
261 GTTTAAAGGTGTTTTATTAAAGAATTTTGGATGAAAACATGTTTTAGGGATTAAATTGAAAAGTA
5270843 TTGAAATTGTGGATAACTTCTAAAATTTCATGGAATCCATGGGCTGTTATTGATATGTATGAGAA
326 TTGAAATTGTGGATAACTTCTAAAATTTCATGGAATCCATGGGCTGTTATTGATATGTATGAGAA
5270908 TTATTAGTCTTGAATAAAGGATTATATTGCAAGAATTTCATTTTCCGAGCCTAGGGACAAAGTTG
391 TTATTAGTCTTGAATAAAGGATTATATTGCAAGAATTTCATTTTCCGAGCCTAGGGACAAAGTTG
5270973 TCATGTATTAAAAGTTTAGGGTCAAATTGGTAATCAATATTTTACACTAAAACAGTTTTGGGCAG
456 TCATGTATTAAAAGTTTAGGGTCAAATTGGTAATCAATATTTTACACTAAAACAGTTTTGGGCAG
5271038 CAGCAATGGTCTAAATTTGAAAAATCACCAAAAATTATGGGAATTTAATTAGAGGA
521 CAGCAATGGTCTAAATTTGAAAAATCACCAAAAATTATGGGAATTTAATTAGAGGA
5271094 TGAATAAAAT
Statistics
Matches: 576, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
576 576 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (576 bp):
AAGGATTTCAAGACCATTTCTTCTTGAAATTTTGGTGGGAAACAGCCATGGAAGAGGTTTGGAGC
TGGTATTCCATATTTTGGCTTCAAGTAAGTTTAATTCTTTCTTTTTCCTTGAAATTTTTATATTT
TTGGACTTTTACAATTAGGTCCAACTTAGTATTCTACTAGTTTCTCATTTAGTTGAAAGTTTTGG
AAGATACCAATGATAAGTTCATATTATTTTTGTTATTTTATGATGAAATTGAGATGTTAATGGAT
GTTTAAAGGTGTTTTATTAAAGAATTTTGGATGAAAACATGTTTTAGGGATTAAATTGAAAAGTA
TTGAAATTGTGGATAACTTCTAAAATTTCATGGAATCCATGGGCTGTTATTGATATGTATGAGAA
TTATTAGTCTTGAATAAAGGATTATATTGCAAGAATTTCATTTTCCGAGCCTAGGGACAAAGTTG
TCATGTATTAAAAGTTTAGGGTCAAATTGGTAATCAATATTTTACACTAAAACAGTTTTGGGCAG
CAGCAATGGTCTAAATTTGAAAAATCACCAAAAATTATGGGAATTTAATTAGAGGA
Found at i:5272383 original size:46 final size:46
Alignment explanation
Indices: 5272316--5272422 Score: 205
Period size: 46 Copynumber: 2.3 Consensus size: 46
5272306 TACTTCTGAT
*
5272316 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACA
1 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACA
5272362 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACA
1 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACA
5272408 AAGTGATAAGTGGTA
1 AAGTGATAAGTGGTA
5272423 ACCTAGGACA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (46 bp):
AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACA
Found at i:5275143 original size:37 final size:37
Alignment explanation
Indices: 5275102--5275172 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
5275092 GTTTTCCGGC
* * * *
5275102 TTAGACATCTTTTCTGTGAATATTTAAAGCATTCAAA
1 TTAGACATCTGTTCTATAAATATATAAAGCATTCAAA
5275139 TTAGACATCTGTTCTATAAATATATAAAGCATTC
1 TTAGACATCTGTTCTATAAATATATAAAGCATTC
5275173 GTATTTCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (37 bp):
TTAGACATCTGTTCTATAAATATATAAAGCATTCAAA
Found at i:5276824 original size:30 final size:31
Alignment explanation
Indices: 5276790--5276862 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
5276780 GATATGATAA
*
5276790 TTTTATAATTCTT-TTACGAATTT-TATATTT
1 TTTTATAATT-TTCTTACGAATTTATAAATTT
* *
5276820 TTTTATTATTTTCTTACGACTTTATAAATTT
1 TTTTATAATTTTCTTACGAATTTATAAATTT
*
5276851 TTTTATATTTTT
1 TTTTATAATTTT
5276863 GTATTTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.06
30 18 0.50
31 16 0.44
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.66
Consensus pattern (31 bp):
TTTTATAATTTTCTTACGAATTTATAAATTT
Found at i:5276882 original size:38 final size:38
Alignment explanation
Indices: 5276840--5276939 Score: 130
Period size: 38 Copynumber: 2.6 Consensus size: 38
5276830 TTCTTACGAC
*
5276840 TTTATAAATTTTTTTATATTTTTGTATT-TTTTATGATT
1 TTTATAAATTTTTTTA-ATTTTTATATTCTTTTATGATT
* ** *
5276878 TTTATAAAATTTTACAATTTTTATTTTCTTTTATGATT
1 TTTATAAATTTTTTTAATTTTTATATTCTTTTATGATT
5276916 TTTATAAATTTTTTCTAATTTTTA
1 TTTATAAATTTTTT-TAATTTTTA
5276940 ATAAAAATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
37 9 0.17
38 35 0.67
39 8 0.15
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (38 bp):
TTTATAAATTTTTTTAATTTTTATATTCTTTTATGATT
Found at i:5276928 original size:19 final size:19
Alignment explanation
Indices: 5276840--5276928 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
5276830 TTCTTACGAC
5276840 TTTATAAATTTTTTTAT-ATT
1 TTTATAAA--TTTTTATGATT
* *
5276860 TTTGT-ATTTTTTATGATT
1 TTTATAAATTTTTATGATT
* **
5276878 TTTATAAAATTTTACAATT
1 TTTATAAATTTTTATGATT
**
5276897 TTTAT-TTTCTTTTATGATT
1 TTTATAAAT-TTTTATGATT
5276916 TTTATAAATTTTT
1 TTTATAAATTTTT
5276929 TCTAATTTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
17 7 0.14
18 7 0.14
19 32 0.63
20 5 0.10
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATAAATTTTTATGATT
Found at i:5277358 original size:9 final size:9
Alignment explanation
Indices: 5277344--5277411 Score: 57
Period size: 9 Copynumber: 7.6 Consensus size: 9
5277334 TTTTGGTTAA
5277344 AAATTAACC
1 AAATTAACC
5277353 AAATTAACC
1 AAATTAACC
*
5277362 GAATT-ACC
1 AAATTAACC
**
5277370 AGAATTTTCC
1 A-AATTAACC
*
5277380 GAATTAACC
1 AAATTAACC
* *
5277389 GAATTACCC
1 AAATTAACC
*
5277398 GAATTAACC
1 AAATTAACC
5277407 AAATT
1 AAATT
5277412 GAATCACTAC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
8 3 0.06
9 43 0.90
10 2 0.04
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (9 bp):
AAATTAACC
Found at i:5277375 original size:18 final size:19
Alignment explanation
Indices: 5277345--5277411 Score: 79
Period size: 18 Copynumber: 3.7 Consensus size: 19
5277335 TTTGGTTAAA
5277345 AATTAACCA-AATTAACCG
1 AATTAACCAGAATTAACCG
**
5277363 AATT-ACCAGAATTTTCCG
1 AATTAACCAGAATTAACCG
*
5277381 AATTAACC-GAATTACCCG
1 AATTAACCAGAATTAACCG
5277399 AATTAACCA-AATT
1 AATTAACCAGAATT
5277412 GAATCACTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.10
18 35 0.83
19 3 0.07
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.27
Consensus pattern (19 bp):
AATTAACCAGAATTAACCG
Found at i:5277411 original size:27 final size:27
Alignment explanation
Indices: 5277345--5277411 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
5277335 TTTGGTTAAA
5277345 AATTAACCAAATTAACCGAATTACCAG
1 AATTAACCAAATTAACCGAATTACCAG
** * *
5277372 AATTTTCCGAATTAACCGAATTACCCG
1 AATTAACCAAATTAACCGAATTACCAG
5277399 AATTAACCAAATT
1 AATTAACCAAATT
5277412 GAATCACTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.27
Consensus pattern (27 bp):
AATTAACCAAATTAACCGAATTACCAG
Found at i:5282266 original size:22 final size:22
Alignment explanation
Indices: 5282241--5282292 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
5282231 GGTTCATAGT
* * *
5282241 GGTCAGTTGCTCTGGTTAGTAG
1 GGTCAGCTACTCTGGTTAGCAG
*
5282263 GGTCGGCTACTCTGGTTAGCAG
1 GGTCAGCTACTCTGGTTAGCAG
*
5282285 AGTCAGCT
1 GGTCAGCT
5282293 GCATTAGTAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.19, G:0.35, T:0.31
Consensus pattern (22 bp):
GGTCAGCTACTCTGGTTAGCAG
Found at i:5283965 original size:26 final size:25
Alignment explanation
Indices: 5283911--5283973 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
5283901 ACCCGATTTG
* **
5283911 TTATCCTTTTTATGAAGGGTTTTTTA
1 TTAT-CTTTTTATGAAGGGTTCTCGA
5283937 TTATCTTCTTTATGAAGGGTTCTCGA
1 TTATCTT-TTTATGAAGGGTTCTCGA
5283963 TTATCTATTTT
1 TTATCT-TTTT
5283974 TTTCAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 3 0.09
26 28 0.88
27 1 0.03
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (25 bp):
TTATCTTTTTATGAAGGGTTCTCGA
Found at i:5286458 original size:20 final size:18
Alignment explanation
Indices: 5286408--5286459 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
5286398 CTATAAGATA
5286408 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
5286425 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
5286445 AATATTAAATTAATA
1 AATATTAAATTAATA
5286460 AAATACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:5287574 original size:16 final size:16
Alignment explanation
Indices: 5287555--5287588 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5287545 ATATATTAAA
*
5287555 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
5287571 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
5287587 TA
1 TA
5287589 AATAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:5287576 original size:23 final size:24
Alignment explanation
Indices: 5287548--5287603 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
5287538 CATTTAAATA
* *
5287548 TATTAAATAT-TAAAATCAAACAT
1 TATTAAATATCAAAAATCAAACAG
* *
5287571 TATT-AATATCAAAAATTAAATAG
1 TATTAAATATCAAAAATCAAACAG
5287594 TATTAAATAT
1 TATTAAATAT
5287604 ATTAATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 17 0.63
24 5 0.19
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (24 bp):
TATTAAATATCAAAAATCAAACAG
Found at i:5290440 original size:7 final size:7
Alignment explanation
Indices: 5290428--5290531 Score: 63
Period size: 7 Copynumber: 15.0 Consensus size: 7
5290418 CTAGTTAATT
5290428 TAAACCC
1 TAAACCC
*
5290435 TAAACCA
1 TAAACCC
5290442 TAAA-CC
1 TAAACCC
5290448 T-AACCC
1 TAAACCC
5290454 TAAACCC
1 TAAACCC
* *
5290461 TTAACAC
1 TAAACCC
5290468 -ACAACCTC
1 TA-AACC-C
*
5290476 TAAACCT
1 TAAACCC
5290483 TAAACCC
1 TAAACCC
* *
5290490 T-AGCCTT
1 TAAACC-C
*
5290497 TAAACCA
1 TAAACCC
*
5290504 TAAACCA
1 TAAACCC
*
5290511 TAAACCA
1 TAAACCC
*
5290518 TAATCCC
1 TAAACCC
5290525 TAAACCC
1 TAAACCC
5290532 ATATTCCATA
Statistics
Matches: 75, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
5 2 0.03
6 8 0.11
7 56 0.75
8 8 0.11
9 1 0.01
ACGTcount: A:0.43, C:0.37, G:0.01, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:5290447 original size:14 final size:14
Alignment explanation
Indices: 5290428--5290608 Score: 86
Period size: 14 Copynumber: 12.9 Consensus size: 14
5290418 CTAGTTAATT
5290428 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
5290442 TAAA-CCT-AACCC
1 TAAACCCTAAACCA
*
5290454 TAAACCCTTAACACA
1 TAAACCCTAAAC-CA
* *
5290469 -CAACCTCTAAACCT
1 TAAACC-CTAAACCA
* *
5290483 TAAACCCT-AGCCTT
1 TAAACCCTAAACC-A
*
5290497 TAAACCATAAACCA
1 TAAACCCTAAACCA
* * *
5290511 TAAACCATAATCCC
1 TAAACCCTAAACCA
**
5290525 TAAACCCATATTCCA
1 TAAACCC-TAAACCA
*
5290540 TAAACCTTAAA--A
1 TAAACCCTAAACCA
*
5290552 TAGTAACTCCTAAACCT
1 TA--AAC-CCTAAACCA
**
5290569 TAAACTGTAAACCA
1 TAAACCCTAAACCA
*
5290583 TATACCCTAAACCA
1 TAAACCCTAAACCA
* *
5290597 AAAACCTTAAAC
1 TAAACCCTAAAC
5290609 TATAGTGATA
Statistics
Matches: 125, Mismatches: 29, Indels: 26
0.69 0.16 0.14
Matches are distributed among these distances:
12 11 0.09
13 9 0.07
14 71 0.57
15 32 0.26
17 2 0.02
ACGTcount: A:0.45, C:0.32, G:0.02, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:5290550 original size:7 final size:7
Alignment explanation
Indices: 5290497--5290608 Score: 57
Period size: 7 Copynumber: 15.7 Consensus size: 7
5290487 CCCTAGCCTT
5290497 TAAACCA
1 TAAACCA
5290504 TAAACCA
1 TAAACCA
5290511 TAAACCA
1 TAAACCA
* *
5290518 TAATCCC
1 TAAACCA
5290525 TAAACCCA
1 TAAA-CCA
**
5290533 TATTCCA
1 TAAACCA
*
5290540 TAAACCT
1 TAAACCA
5290547 TAAA--A
1 TAAACCA
*
5290552 TAGTAACTCC
1 TA--AAC-CA
*
5290562 TAAACCT
1 TAAACCA
**
5290569 TAAACTG
1 TAAACCA
5290576 TAAACCA
1 TAAACCA
* *
5290583 TATACCC
1 TAAACCA
5290590 TAAACCA
1 TAAACCA
* *
5290597 AAAACCT
1 TAAACCA
5290604 TAAAC
1 TAAAC
5290609 TATAGTGATA
Statistics
Matches: 76, Mismatches: 23, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
5 2 0.03
7 65 0.86
8 7 0.09
10 2 0.03
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:5291005 original size:41 final size:41
Alignment explanation
Indices: 5290918--5291143 Score: 276
Period size: 41 Copynumber: 5.6 Consensus size: 41
5290908 TTTTTGTGTT
* **
5290918 GCTTTTTTAAAAACGCCGCTAAAG-ATCGAGCATTAGCGGC
1 GCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGC
* * * *
5290958 GCTTTTTCAAAAATGCCGTTAAAGCCCCGAGCATTAGTGGT
1 GCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGC
* *
5290999 GTTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGTGGC
1 GCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGC
* * * *
5291040 GC-TTTTCAAAAATGCCGCTAAAGCCCCAATCATTAGCAGC
1 GCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGC
* * **
5291080 GCTTTTTCAAAACCGCCGCTAAAGCCCCAAGCATTAGCGAT
1 GCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGC
*
5291121 GCTTTTTGAAAAACGCCGCTAAA
1 GCTTTTTCAAAAACGCCGCTAAA
5291144 ATCCCGAAAG
Statistics
Matches: 159, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
40 56 0.35
41 103 0.65
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (41 bp):
GCTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGC
Found at i:5291011 original size:81 final size:81
Alignment explanation
Indices: 5290920--5291143 Score: 263
Period size: 81 Copynumber: 2.8 Consensus size: 81
5290910 TTTGTGTTGC
* *
5290920 TTTTTT-AAAAACGCCGCTAAAG-ATCGAGCATTAGCGGCGCTTTTTCAAAAATGCCGTTAAAGC
1 TTTTTTCAAAAACGCCGCTAAAGCACCGAGCATTAGCGGCGC-TTTTCAAAAATGCCGCTAAAGC
* ** *
5290983 CCCGAGCATTAGTGGTG
65 CCCAAGCATTAGCAGCG
* *
5291000 TTTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGTGGCGCTTTTCAAAAATGCCGCTAAAGCC
1 TTTTTTCAAAAACGCCGCTAAAGCACCGAGCATTAGCGGCGCTTTTCAAAAATGCCGCTAAAGCC
*
5291065 CCAATCATTAGCAGCG
66 CCAAGCATTAGCAGCG
* * * * ** * *
5291081 CTTTTTCAAAACCGCCGCTAAAGCCCCAAGCATTAGCGATGCTTTTTGAAAAACGCCGCTAAA
1 TTTTTTCAAAAACGCCGCTAAAGCACCGAGCATTAGCGGCGC-TTTTCAAAAATGCCGCTAAA
5291144 ATCCCGAAAG
Statistics
Matches: 124, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
80 6 0.05
81 85 0.69
82 33 0.27
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (81 bp):
TTTTTTCAAAAACGCCGCTAAAGCACCGAGCATTAGCGGCGCTTTTCAAAAATGCCGCTAAAGCC
CCAAGCATTAGCAGCG
Found at i:5293220 original size:13 final size:13
Alignment explanation
Indices: 5293202--5293227 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5293192 TTTCTGTACG
5293202 TAGCCTTTCCCTA
1 TAGCCTTTCCCTA
5293215 TAGCCTTTCCCTA
1 TAGCCTTTCCCTA
5293228 CAAGTTTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (13 bp):
TAGCCTTTCCCTA
Found at i:5294906 original size:17 final size:16
Alignment explanation
Indices: 5294884--5294917 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5294874 TTAAAAACAA
5294884 AAGAGAAAGAAATGGAT
1 AAGAGAAAGAAA-GGAT
*
5294901 AAGAGAAATAAAGGAT
1 AAGAGAAAGAAAGGAT
5294917 A
1 A
5294918 TCAGTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (16 bp):
AAGAGAAAGAAAGGAT
Found at i:5295418 original size:29 final size:29
Alignment explanation
Indices: 5295372--5295433 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
5295362 TGTGTTCTGC
* *
5295372 GAGCTCCCATGCATACGAGCTATGAACTGT
1 GAGCTCCCATGCAGACGAGCAATGAA-TGT
* *
5295402 GAGCT-CCATGTAGACGAGCAATGCATGT
1 GAGCTCCCATGCAGACGAGCAATGAATGT
5295430 GAGC
1 GAGC
5295434 ATAGGGTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.25
29 16 0.57
30 5 0.18
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (29 bp):
GAGCTCCCATGCAGACGAGCAATGAATGT
Found at i:5301040 original size:6 final size:6
Alignment explanation
Indices: 5301029--5301083 Score: 74
Period size: 6 Copynumber: 8.5 Consensus size: 6
5301019 AAATCGAAAA
5301029 TCCACC TCCACC TCCACC TCCACC TCCACC TCCACC AATCCACC ATTCCACC
1 TCCACC TCCACC TCCACC TCCACC TCCACC TCCACC --TCCACC --TCCACC
5301081 TCC
1 TCC
5301084 GGTCCACCAC
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
6 33 0.72
8 13 0.28
ACGTcount: A:0.20, C:0.62, G:0.00, T:0.18
Consensus pattern (6 bp):
TCCACC
Found at i:5302173 original size:14 final size:14
Alignment explanation
Indices: 5302154--5302193 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5302144 TTGATTGCCA
5302154 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
5302168 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
5302182 GGAAAATGTTTT
1 GTAAAATGTTTT
5302194 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:5302202 original size:20 final size:20
Alignment explanation
Indices: 5302177--5302216 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5302167 CGTAAAATGA
*
5302177 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
5302197 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
5302217 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:5302206 original size:34 final size:35
Alignment explanation
Indices: 5302162--5302228 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
5302152 CAGTAAAATG
*
5302162 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
5302196 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
5302229 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:5302232 original size:14 final size:15
Alignment explanation
Indices: 5302156--5302232 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
5302146 GATTGCCAGT
* *
5302156 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
5302170 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
5302184 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
5302204 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
5302219 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
5302233 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:5302385 original size:22 final size:24
Alignment explanation
Indices: 5302360--5302410 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
5302350 TTATTTATAA
5302360 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
5302380 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
5302406 ATAAA
1 ATAAA
5302411 AGCATTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:5305433 original size:6 final size:6
Alignment explanation
Indices: 5305402--5305431 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5305392 GGTGTCAAGC
*
5305402 GAAGGG GAAGGG GAAGGG GAAGGG AAAGGG
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
5305432 AAGATCGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:5314361 original size:18 final size:18
Alignment explanation
Indices: 5314338--5314377 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5314328 ACTAGTATAG
5314338 TATTCTTTGCAACATCTT
1 TATTCTTTGCAACATCTT
* *
5314356 TATTCTTTGTAACATTTT
1 TATTCTTTGCAACATCTT
5314374 TATT
1 TATT
5314378 TACGTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.57
Consensus pattern (18 bp):
TATTCTTTGCAACATCTT
Found at i:5315598 original size:32 final size:32
Alignment explanation
Indices: 5315556--5315617 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
5315546 GATATAGGAA
*
5315556 AACTACGAGAGGGGGCCAGCAGACCCTAGTTT
1 AACTACGAGAGGGGGCCAGCAAACCCTAGTTT
* *
5315588 AACTAGGAGAGGGGGCTAGCAAACCCTAGT
1 AACTACGAGAGGGGGCCAGCAAACCCTAGT
5315618 GTCTCAGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.32, T:0.15
Consensus pattern (32 bp):
AACTACGAGAGGGGGCCAGCAAACCCTAGTTT
Found at i:5320932 original size:19 final size:18
Alignment explanation
Indices: 5320876--5320933 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
5320866 GTAAAAATAT
5320876 AAAAAGAAAA-ACAAAGGAA
1 AAAAAGAAAAGA-AAA-GAA
* *
5320895 ATAAAGAACAAGGAAAGAA
1 AAAAAGAA-AAGAAAAGAA
5320914 CAAAAAGAAAAGAAAAGAA
1 -AAAAAGAAAAGAAAAGAA
5320933 A
1 A
5320934 TGGTAGAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
18 1 0.03
19 19 0.59
20 12 0.38
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAGAA
Found at i:5326101 original size:29 final size:31
Alignment explanation
Indices: 5326044--5326109 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
5326034 TTTTATTATA
*
5326044 GTACTTGTACTTTCGTAAAATGTCCAATGTG
1 GTACATGTACTTTCGTAAAATGTCCAATGTG
* * *
5326075 TTACATGTACTTT-G-AAGATGTCTAATGTG
1 GTACATGTACTTTCGTAAAATGTCCAATGTG
5326104 GTACAT
1 GTACAT
5326110 TAATTATCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 18 0.60
30 1 0.03
31 11 0.37
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (31 bp):
GTACATGTACTTTCGTAAAATGTCCAATGTG
Found at i:5333815 original size:40 final size:40
Alignment explanation
Indices: 5333760--5333839 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
5333750 AGCTTGGCCA
*
5333760 ATTCTCTTCCCAAGGGCGTATAAAAGCTGTTCACACTATG
1 ATTCTCTTCCCAAGGGCATATAAAAGCTGTTCACACTATG
5333800 ATTCTCTTCCCAAGGGCATATAAAAGCTGTTCACACTATG
1 ATTCTCTTCCCAAGGGCATATAAAAGCTGTTCACACTATG
5333840 TCTATTCGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (40 bp):
ATTCTCTTCCCAAGGGCATATAAAAGCTGTTCACACTATG
Found at i:5334670 original size:12 final size:13
Alignment explanation
Indices: 5334653--5334685 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
5334643 TTGTAGATTC
5334653 AAAAAAAATCGA-
1 AAAAAAAATCGAG
5334665 AAAAAAAATCGAG
1 AAAAAAAATCGAG
5334678 AAAAAAAA
1 AAAAAAAA
5334686 ATTGTATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (13 bp):
AAAAAAAATCGAG
Found at i:5340309 original size:23 final size:23
Alignment explanation
Indices: 5340283--5340349 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
5340273 ATATTACGAA
5340283 TCGTTATTTCATATGAAACGAGC
1 TCGTTATTTCATATGAAACGAGC
* * *
5340306 TCGTGA---AATAT--TACGA-C
1 TCGTTATTTCATATGAAACGAGC
*
5340323 TCGTTATTTCATACGAAACGAGC
1 TCGTTATTTCATATGAAACGAGC
5340346 TCGT
1 TCGT
5340350 ATCACCATTC
Statistics
Matches: 31, Mismatches: 7, Indels: 12
0.62 0.14 0.24
Matches are distributed among these distances:
17 6 0.19
18 4 0.13
20 7 0.23
22 4 0.13
23 10 0.32
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (23 bp):
TCGTTATTTCATATGAAACGAGC
Found at i:5340327 original size:40 final size:40
Alignment explanation
Indices: 5340271--5340349 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
5340261 TTCGATCGGA
*
5340271 AAATATTACGAATCGTTATTTCATATGAAACGAGCTCGTG
1 AAATATTACGAATCGTTATTTCATACGAAACGAGCTCGTG
*
5340311 AAATATTACGACTCGTTATTTCATACGAAACGAGCTCGT
1 AAATATTACGAATCGTTATTTCATACGAAACGAGCTCGT
5340350 ATCACCATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (40 bp):
AAATATTACGAATCGTTATTTCATACGAAACGAGCTCGTG
Found at i:5343888 original size:21 final size:21
Alignment explanation
Indices: 5343862--5343902 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5343852 TTAACCTCCT
5343862 AACTATATTTAACAACTAACC
1 AACTATATTTAACAACTAACC
*
5343883 AACTATATTTAATAACTAAC
1 AACTATATTTAACAACTAAC
5343903 ATCACTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (21 bp):
AACTATATTTAACAACTAACC
Found at i:5347442 original size:34 final size:34
Alignment explanation
Indices: 5347403--5347471 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
5347393 AATATAGAGA
*
5347403 AGTCATTTATAAAAGTGATAAAATATCATTTTCT
1 AGTCATCTATAAAAGTGATAAAATATCATTTTCT
5347437 AGTCATCTATAAAAGTGATAAAATATCATTTTCT
1 AGTCATCTATAAAAGTGATAAAATATCATTTTCT
5347471 A
1 A
5347472 TCTCTTGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (34 bp):
AGTCATCTATAAAAGTGATAAAATATCATTTTCT
Found at i:5349861 original size:25 final size:25
Alignment explanation
Indices: 5349833--5349885 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
5349823 GATGAACTAT
*
5349833 GTTCGCCAGGT-AAGTTGCAAACAGG
1 GTTCGCCA-GTCAAGGTGCAAACAGG
* *
5349858 GTTCGCTAGTCAAGGTGCAAACTGG
1 GTTCGCCAGTCAAGGTGCAAACAGG
5349883 GTT
1 GTT
5349886 GGCCGATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (25 bp):
GTTCGCCAGTCAAGGTGCAAACAGG
Found at i:5358080 original size:29 final size:29
Alignment explanation
Indices: 5358023--5358081 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
5358013 TGATTGCTCG
* *
5358023 ACTAACATAATATCAATGATGTTACCTCA
1 ACTAACATAATATCAATGATGTCAACTCA
*
5358052 ACTAACATAATATCTATGATGTCAACTCA
1 ACTAACATAATATCAATGATGTCAACTCA
5358081 A
1 A
5358082 GAATTAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (29 bp):
ACTAACATAATATCAATGATGTCAACTCA
Found at i:5370823 original size:23 final size:23
Alignment explanation
Indices: 5370779--5370823 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5370769 TCTTATTTTG
* *
5370779 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
*
5370802 TTGATTTGTATATTATTGATTT
1 TTGATTTGTATATAATTGATTT
5370824 CAAATCTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:5371276 original size:51 final size:51
Alignment explanation
Indices: 5371204--5371313 Score: 175
Period size: 51 Copynumber: 2.1 Consensus size: 51
5371194 TATATATACT
**
5371204 TTTATATTTAGTTTCAATTTTTTTTACTTTTGTATATATGTACATGTATGTA
1 TTTATA-TTAGTAACAATTTTTTTTACTTTTGTATATATGTACATGTATGTA
* *
5371256 TTTATATTAGTAACAATTTTTTTTATTTTTGTATGTATGTACATGTATGTA
1 TTTATATTAGTAACAATTTTTTTTACTTTTGTATATATGTACATGTATGTA
5371307 TTTATAT
1 TTTATAT
5371314 ATTTTTTCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
51 48 0.89
52 6 0.11
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (51 bp):
TTTATATTAGTAACAATTTTTTTTACTTTTGTATATATGTACATGTATGTA
Found at i:5375549 original size:79 final size:81
Alignment explanation
Indices: 5375447--5375630 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
5375437 GCTCCTCGTT
* *
5375447 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACC
*
5375509 CGGAT-TTAGTAAC-TCGCA
63 CGGATATT-GTAACTTAGCA
**
5375527 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
*
5375591 ATATTGTCACTTAGCA
66 ATATTGTAACTTAGCA
5375607 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5375631 CATCATTCAA
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 14 0.15
79 56 0.61
80 22 0.24
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATTGTAACTTAGCA
Found at i:5375564 original size:39 final size:41
Alignment explanation
Indices: 5375447--5375630 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 41
5375437 GCTCCTCGTT
* *
5375447 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCA
* *
5375487 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAA-CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
5375527 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * *
5375566 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
5375607 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5375631 CATCATTCAA
Statistics
Matches: 128, Mismatches: 7, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
38 3 0.02
39 48 0.38
40 66 0.52
41 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:5383443 original size:40 final size:40
Alignment explanation
Indices: 5383399--5383582 Score: 211
Period size: 40 Copynumber: 4.7 Consensus size: 40
5383389 GCTCCTCGTT
*
5383399 CAAATGCCTTCGGGACATAGCCC-GATTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAATTCGCA
* *
5383439 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
*
5383479 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAAT-TCGCA
* * *
5383518 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGT-AATTCGCA
5383559 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5383583 CATCATTCAA
Statistics
Matches: 125, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
38 3 0.02
39 47 0.38
40 63 0.50
41 11 0.09
42 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
Found at i:5383581 original size:79 final size:81
Alignment explanation
Indices: 5383399--5383582 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
5383389 GCTCCTCGTT
* *
5383399 CAAATGCCTTCGGGACATAGCCC-GATTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
*
5383463 GATTTAGTAACTCGCA
66 GATTTAGTAACTAGCA
**
5383479 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
*
5383540 CGGATATT-GTCACTTAGCA
64 CGGAT-TTAGTAAC-TAGCA
5383559 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5383583 CATCATTCAA
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 14 0.15
79 54 0.59
80 24 0.26
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
GATTTAGTAACTAGCA
Found at i:5385308 original size:16 final size:16
Alignment explanation
Indices: 5385277--5385306 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5385267 TGAATGCCTC
5385277 TTTTTTAAAATATTTA
1 TTTTTTAAAATATTTA
5385293 TTTTTT-AAATATTT
1 TTTTTTAAAATATTT
5385307 TACTTTGCCT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTAAAATATTTA
Found at i:5385588 original size:3 final size:3
Alignment explanation
Indices: 5385580--5385627 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
5385570 ATCATTGTCA
*
5385580 CAT CAT CAT CAT TAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
5385628 AATTACTACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:5395682 original size:21 final size:20
Alignment explanation
Indices: 5395658--5395696 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5395648 AGGTTAGAAT
*
5395658 TTTTCAGATCACAAACTATGC
1 TTTTCAAAT-ACAAACTATGC
*
5395679 TTTTGAAATACAAACTAT
1 TTTTCAAATACAAACTAT
5395697 CATCGAAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (20 bp):
TTTTCAAATACAAACTATGC
Found at i:5401094 original size:46 final size:48
Alignment explanation
Indices: 5401037--5401168 Score: 135
Period size: 46 Copynumber: 2.8 Consensus size: 48
5401027 GGTGGCATGT
* * *
5401037 GAGCCAGTGTAAGACATGTCTAGGACATGCATCGACATTGAGA-CGA-
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGATAGAC
* * * * *
5401083 GAGCTAGTGTAAGACATGTATGGGACGTGCATC-AGCCTTGGGATATAC
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGA-CATTGAGATAGAC
* *
5401131 AAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACA
1 GAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGACA
5401169 CCGATAGATG
Statistics
Matches: 68, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
45 1 0.01
46 35 0.51
47 1 0.01
48 24 0.35
49 6 0.09
50 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (48 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGATAGAC
Found at i:5401216 original size:97 final size:95
Alignment explanation
Indices: 5401041--5401264 Score: 238
Period size: 97 Copynumber: 2.3 Consensus size: 95
5401031 GCATGTGAGC
* * ** * * *
5401041 CAGTGTAAGACATGTCTAGGACAT-GCATCGACATTGAGACGAGAGCTAGTGTAAGACATGTATG
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGAGACGAGAGCCAGCGTAAGACATGTACG
* * * *
5401105 GGACGTGCATCAGCCTTGGGATATACAAG-
66 GGACATGCATCAGCCTCGAGATATAAAAGT
* *
5401134 CTAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAGCCAGCGTAAGACCTGT
1 C-AGTGTAAGACCTGTCTGGGACATGGCATCGACACCG--AGACGAGAGCCAGCGTAAGACATGT
*
5401199 -CGGGACATGGCATCAGCCTCGATATATAAAAGT
63 ACGGGACAT-GCATCAGCCTCGAGATATAAAAGT
* * *
5401232 CAATGTAAGACCTGTCTGGGACACGACATCGAC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC
5401265 TTTAATGTGC
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
93 1 0.01
94 21 0.19
95 10 0.09
96 6 0.06
97 69 0.64
98 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (95 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGAGACGAGAGCCAGCGTAAGACATGTACG
GGACATGCATCAGCCTCGAGATATAAAAGT
Found at i:5401222 original size:48 final size:49
Alignment explanation
Indices: 5401139--5401264 Score: 141
Period size: 48 Copynumber: 2.6 Consensus size: 49
5401129 ACAAGCTAGT
* * *
5401139 GTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAGCCAGC
1 GTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATAAAAGCCAAC
* * *
5401188 GTAAGACCTGTC-GGGACATGGCATC-AGC-CTCGATATATAAAAGTCAAT
1 GTAAGACCTGTCTGGGACATGGCATCGA-CAC-CGATAGATAAAAGCCAAC
* *
5401236 GTAAGACCTGTCTGGGACACGACATCGAC
1 GTAAGACCTGTCTGGGACATGGCATCGAC
5401265 TTTAATGTGC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
47 2 0.03
48 38 0.58
49 24 0.37
50 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (49 bp):
GTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATAAAAGCCAAC
Found at i:5407790 original size:43 final size:43
Alignment explanation
Indices: 5407743--5407847 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
5407733 ATGCAACTAT
* * ** * *
5407743 AGAACATAACCTTTAGCGGAACTTTTCCCACAAATTCTGTTAA
1 AGAACATGACCTTTAGCGGAACTTTTCACACAAACGCCGCTAA
* **
5407786 AGAACATGACCTCTAGCGGTGCTTTTCACACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGAACTTTTCACACAAACGCCGCTAA
*
5407829 AGAACATGATCTTTAGCGG
1 AGAACATGACCTTTAGCGG
5407848 CGTTTTTAGT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
AGAACATGACCTTTAGCGGAACTTTTCACACAAACGCCGCTAA
Found at i:5418132 original size:29 final size:29
Alignment explanation
Indices: 5418093--5418307 Score: 204
Period size: 29 Copynumber: 7.6 Consensus size: 29
5418083 CCGTAACCGA
5418093 GCACTGTGTGTGCGAGATCGGTTGTTGAG
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
* * ****
5418122 GCACTGTGTGTGCGAGTTCCGTAACCGA-
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
* *
5418150 GCACTGTGTGTGCGAGATTGATTGTTGAG
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
* * ****
5418179 GCACTGTGTGTGCGAGTTC-CTAACCGA-
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
5418206 GCACTGTGTGTGCGAGATCGGTTGTTGAG
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
* * ** *
5418235 GCACTGTGTGTGCGAGTTCCGTAATCGA-
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
* *
5418263 GCATTGTGTGTACGAGATCGGTTGTTGAG
1 GCACTGTGTGTGCGAGATCGGTTGTTGAG
*
5418292 GCACTATGTGTGCGAG
1 GCACTGTGTGTGCGAG
5418308 TTCCATAACC
Statistics
Matches: 140, Mismatches: 42, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
27 18 0.13
28 47 0.34
29 75 0.54
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (29 bp):
GCACTGTGTGTGCGAGATCGGTTGTTGAG
Found at i:5418132 original size:57 final size:57
Alignment explanation
Indices: 5418063--5418362 Score: 476
Period size: 57 Copynumber: 5.2 Consensus size: 57
5418053 AAGTGAACAT
*
5418063 AGGCACTGTGTGTGTGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
* *
5418120 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATTGATTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
5418177 AGGCACTGTGTGTGCGAGTTCC-TAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
* * *
5418233 AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCATTGTGTGTACGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
* * * *
5418290 AGGCACTATGTGTGCGAGTTCCATAACCAAGCACTGTGTGTGCAAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
*
5418347 GGGCACTAAGTGTGTG
1 AGGCACT--GTGTGTG
5418363 AAATGAGATC
Statistics
Matches: 223, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
56 54 0.24
57 163 0.73
59 6 0.03
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (57 bp):
AGGCACTGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTG
Found at i:5418264 original size:113 final size:114
Alignment explanation
Indices: 5418063--5418362 Score: 476
Period size: 113 Copynumber: 2.6 Consensus size: 114
5418053 AAGTGAACAT
* *
5418063 AGGCACTGTGTGTGTGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTG
1 AGGCACTGTGTGTGCGAGTTCCATAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTG
* *
5418128 TGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGCGAGATTGATTGTTG
66 TGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTACGAGATCGATTGTTG
5418177 AGGCACTGTGTGTGCGAGTTCC-TAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTG
1 AGGCACTGTGTGTGCGAGTTCCATAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTG
* * *
5418241 TGTGTGCGAGTTCCGTAATCGAGCATTGTGTGTACGAGATCGGTTGTTG
66 TGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTACGAGATCGATTGTTG
* * * *
5418290 AGGCACTATGTGTGCGAGTTCCATAACCAAGCACTGTGTGTGCAAGATCGGTTGTTGGGGCACTA
1 AGGCACTGTGTGTGCGAGTTCCATAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACT-
5418355 AGTGTGTG
65 -GTGTGTG
5418363 AAATGAGATC
Statistics
Matches: 173, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
113 107 0.62
114 59 0.34
116 7 0.04
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (114 bp):
AGGCACTGTGTGTGCGAGTTCCATAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCACTG
TGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTACGAGATCGATTGTTG
Found at i:5422139 original size:48 final size:47
Alignment explanation
Indices: 5422066--5422210 Score: 159
Period size: 48 Copynumber: 3.0 Consensus size: 47
5422056 AAGAGGGTGA
* * * *
5422066 ATTGTCGATGTCATGTTCCAAACATGGTCTTACACTGGCTCTCGTCA-C
1 ATTGTCGATGCCATG-TCCAGACATGGTCTTACACTAGCTCTCAT-ATC
*
5422114 ATTGTCGATGCCATGTCCTAGACATGGTTTTACACTAGCTCTCATATC
1 ATTGTCGATGCCATGTCC-AGACATGGTCTTACACTAGCTCTCATATC
* * *
5422162 A-TGGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATC
1 ATTGTC-GATGCCATGT-CCAGACATGGTCTTACACTAGCTCTCATATC
5422210 A
1 A
5422211 CCCAAATATC
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
47 7 0.08
48 75 0.89
49 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (47 bp):
ATTGTCGATGCCATGTCCAGACATGGTCTTACACTAGCTCTCATATC
Found at i:5434034 original size:14 final size:14
Alignment explanation
Indices: 5434012--5434041 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5434002 GATAAATATT
*
5434012 TTATTTGTTCTTAA
1 TTATGTGTTCTTAA
5434026 TTATGTGTTCTTAA
1 TTATGTGTTCTTAA
5434040 TT
1 TT
5434042 CTTGTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (14 bp):
TTATGTGTTCTTAA
Found at i:5438395 original size:47 final size:47
Alignment explanation
Indices: 5438341--5438766 Score: 692
Period size: 47 Copynumber: 9.1 Consensus size: 47
5438331 TTAGGATTTT
** * * *
5438341 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
5438388 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
5438435 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
5438482 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
5438529 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
5438576 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
5438623 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
5438670 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * * * * * *
5438717 ATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATGTGTGATAAGGCCGAATGGCCA
5438764 ATG
1 ATG
5438767 CGAAATGTGT
Statistics
Matches: 364, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
47 361 0.99
48 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:5438796 original size:46 final size:46
Alignment explanation
Indices: 5438740--5438876 Score: 220
Period size: 46 Copynumber: 3.0 Consensus size: 46
5438730 GGAAGTGTAT
5438740 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* *
5438786 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * *
5438832 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
5438877 TGTATATATA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 83 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:5443515 original size:48 final size:48
Alignment explanation
Indices: 5443400--5443573 Score: 154
Period size: 48 Copynumber: 3.6 Consensus size: 48
5443390 GTGACTTGCT
* * * * * * *
5443400 GATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCGTCTTAAT-GTC
1 GATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCAT-ATCATGGAC
* *** * * * *
5443448 GATCCCATATTCCAAACATGGTCCTACATTGGCTCTCAT-TACATTGAC
1 GATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATAT-CATGGAC
* *
5443496 GATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATATCGTGGTC
1 GATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATATCATGGAC
*
5443544 GATGCCATGTCCCAGACATGGTCTTACACT
1 GATGCCATGCCCCAGACATGGTCTTACACT
5443574 AGCACACATC
Statistics
Matches: 101, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
46 1 0.01
47 2 0.02
48 97 0.96
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.30
Consensus pattern (48 bp):
GATGCCATGCCCCAGACATGGTCTTACACTGGCTCTCATATCATGGAC
Found at i:5446309 original size:32 final size:33
Alignment explanation
Indices: 5446239--5446312 Score: 105
Period size: 35 Copynumber: 2.2 Consensus size: 33
5446229 TTTTATATTT
*
5446239 TTTAAATGTTTATGTAAGTTATGATAATCATAAAC
1 TTTAAATGTTTATGTAAGTTATAATAATCAT--AC
*
5446274 TTTAAATGTTTATGTAAGTTATAATTATCAT-C
1 TTTAAATGTTTATGTAAGTTATAATAATCATAC
5446306 TTTAAAT
1 TTTAAAT
5446313 ATTGACTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 8 0.22
35 29 0.78
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.47
Consensus pattern (33 bp):
TTTAAATGTTTATGTAAGTTATAATAATCATAC
Found at i:5448447 original size:43 final size:42
Alignment explanation
Indices: 5448324--5448447 Score: 126
Period size: 41 Copynumber: 3.0 Consensus size: 42
5448314 TCTAGCATGT
*
5448324 TGGCATCGATATGCGATTACGTGTAAGACCATGTCTGGGACA
1 TGGCATCGATATGTGATTACGTGTAAGACCATGTCTGGGACA
* * * * ** *
5448366 TCGACATTG-TATTTGATT-TGTGTAAGACTTTGTGTGGGACA
1 T-GGCATCGATATGTGATTACGTGTAAGACCATGTCTGGGACA
* *
5448407 GTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGA
1 -TGGCATCGATATGTGATTACGTGTAAGACCATGTCTGGGA
5448448 TGTTCGCATT
Statistics
Matches: 61, Mismatches: 17, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
41 24 0.39
42 17 0.28
43 20 0.33
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.31
Consensus pattern (42 bp):
TGGCATCGATATGTGATTACGTGTAAGACCATGTCTGGGACA
Found at i:5456429 original size:49 final size:49
Alignment explanation
Indices: 5456338--5456434 Score: 115
Period size: 49 Copynumber: 2.0 Consensus size: 49
5456328 ATGTATTTAT
* * ** * *
5456338 AGGTTAAAAAACATTATTCTAATCAATGTCAAATGGATGAAGTGTAGTA
1 AGGTTAAAAAACATTATTCTAACCAATGTAAAATAAAAGAAGTATAGTA
*
5456387 AGGTTGAAAAATC-TTATTCTAACCAATGTAAAATAAAAGAAGTATAGT
1 AGGTT-AAAAAACATTATTCTAACCAATGTAAAATAAAAGAAGTATAGT
5456435 TCTGTATGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 34 0.85
50 6 0.15
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.30
Consensus pattern (49 bp):
AGGTTAAAAAACATTATTCTAACCAATGTAAAATAAAAGAAGTATAGTA
Found at i:5476291 original size:27 final size:27
Alignment explanation
Indices: 5476213--5476294 Score: 119
Period size: 27 Copynumber: 3.0 Consensus size: 27
5476203 TTATATTAAT
*
5476213 ATAATTTTAATGTGTCTAGTTTAGAAC
1 ATAATTTTAATGTGTCTAGTTTAGGAC
* *
5476240 ATAATTTTAATATGTCTAATTTAGGAC
1 ATAATTTTAATGTGTCTAGTTTAGGAC
* *
5476267 ATAATTTTAATGTGTCTGGTGTAGGAC
1 ATAATTTTAATGTGTCTAGTTTAGGAC
5476294 A
1 A
5476295 AACTTATTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (27 bp):
ATAATTTTAATGTGTCTAGTTTAGGAC
Found at i:5480297 original size:20 final size:22
Alignment explanation
Indices: 5480264--5480304 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5480254 TTTTCAACTT
*
5480264 TTTTTTAGCATTAT-TAGAAGG
1 TTTTTTAACATTATCTAGAAGG
5480285 TTTTTTAAC-TTATCTAGAAG
1 TTTTTTAACATTATCTAGAAG
5480305 TTTCGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (22 bp):
TTTTTTAACATTATCTAGAAGG
Found at i:5480858 original size:14 final size:15
Alignment explanation
Indices: 5480841--5480869 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5480831 ATAATATGAA
5480841 TGATATGT-GATATG
1 TGATATGTGGATATG
5480855 TGATATGTGGATATG
1 TGATATGTGGATATG
5480870 GTGCTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (15 bp):
TGATATGTGGATATG
Found at i:5483840 original size:15 final size:16
Alignment explanation
Indices: 5483822--5483859 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5483812 CTACCGTTAG
*
5483822 TATTATTTTCATTAC-
1 TATTATTTTCAATACA
*
5483837 TATTATTTTTAATACA
1 TATTATTTTCAATACA
5483853 TATTATT
1 TATTATT
5483860 ACTAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATTTTCAATACA
Found at i:5496267 original size:14 final size:15
Alignment explanation
Indices: 5496243--5496271 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5496233 TTTTCTACTT
5496243 ATTATTATTACTATA
1 ATTATTATTACTATA
5496258 ATTATT-TTACTATA
1 ATTATTATTACTATA
5496272 CCATCTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATTATTACTATA
Found at i:5496461 original size:29 final size:27
Alignment explanation
Indices: 5496379--5496464 Score: 95
Period size: 26 Copynumber: 3.2 Consensus size: 27
5496369 TTTCCTTTAC
5496379 TATTATTTATT-ATTATTATTTATTAT
1 TATTATTTATTCATTATTATTTATTAT
* * **
5496405 TATTATTTTTTCCATTATAAATACATTAT
1 TATTATTTATT-CATTAT-TATTTATTAT
*
5496434 TATTATTTATTCATTATTA-TTGTTAT
1 TATTATTTATTCATTATTATTTATTAT
5496460 TATTA
1 TATTA
5496465 GAATTTACAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 19 0.40
27 1 0.02
28 11 0.23
29 17 0.35
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (27 bp):
TATTATTTATTCATTATTATTTATTAT
Found at i:5496484 original size:3 final size:3
Alignment explanation
Indices: 5496284--5496464 Score: 63
Period size: 3 Copynumber: 58.3 Consensus size: 3
5496274 ATCTAAATAC
* * * *
5496284 ATT ATT ATT GTC ACT ATT ATT ATT ATT ATT ATT ATT -TT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
5496331 A-C ATAT ACTC GTT AGT ATT ATT ATT AATT -TT ACCTT CATT -TCCT -TT
1 ATT AT-T A-TT ATT ATT ATT ATT ATT -ATT ATT A--TT -ATT AT--T ATT
* *
5496377 ACT ATT ATTT ATT ATT ATT ATTT ATT ATT ATT ATT -TT -TT CCATT ATA
1 ATT ATT A-TT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT --ATT ATT
* * *
5496424 AAT A-C ATT ATT ATT ATTT ATT CATT ATT ATT GTT ATT ATT A
1 ATT ATT ATT ATT ATT A-TT ATT -ATT ATT ATT ATT ATT ATT A
5496465 GAATTTACAT
Statistics
Matches: 133, Mismatches: 25, Indels: 40
0.67 0.13 0.20
Matches are distributed among these distances:
2 12 0.09
3 95 0.71
4 20 0.15
5 5 0.04
6 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:5496586 original size:28 final size:28
Alignment explanation
Indices: 5496555--5496630 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 28
5496545 ACATTATTAC
5496555 TATTTATTATTATTATTATATGCATATA
1 TATTTATTATTATTATTATATGCATATA
*** * *
5496583 TATTT-TTACCGTCATTAATTTGCATATA
1 TATTTATTATTATTATT-ATATGCATATA
5496611 TATATTATTATTCA-TATTAT
1 TAT-TTATTATT-ATTATTAT
5496631 TATTATTATT
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
27 7 0.20
28 18 0.51
29 4 0.11
30 6 0.17
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (28 bp):
TATTTATTATTATTATTATATGCATATA
Found at i:5496685 original size:3 final size:3
Alignment explanation
Indices: 5496679--5496789 Score: 61
Period size: 3 Copynumber: 37.3 Consensus size: 3
5496669 TAACCTCATT
* * * *
5496679 TTA TTA TTA TCA TTC TTA TTA ATA -CA TTA TTA TTA TT- TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * * *
5496723 TTA TTA TTG TTA TTA GCCTA -TA TTA TTA TTA AT- TTA TTA CTA TTT
1 TTA TTA TTA TTA TTA --TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5496768 TCTA TTA TT- TTA TTA CTA TTA T
1 T-TA TTA TTA TTA TTA TTA TTA T
5496790 CATTTTTAAA
Statistics
Matches: 81, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
2 8 0.10
3 66 0.81
4 5 0.06
5 2 0.02
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5496726 original size:12 final size:11
Alignment explanation
Indices: 5496682--5496787 Score: 52
Period size: 11 Copynumber: 9.0 Consensus size: 11
5496672 CCTCATTTTA
*
5496682 TTATTATCATT
1 TTATTATTATT
* **
5496693 CTTATTAATACA
1 -TTATTATTATT
5496705 TTATTATTATT
1 TTATTATTATT
5496716 TTATATATTATT
1 TTAT-TATTATT
*
5496728 ATTGTTATTAGCCTAT
1 -TTATTATTA---T-T
*
5496744 ATTATTATTAAT
1 -TTATTATTATT
*
5496756 TTATTACTATT
1 TTATTATTATT
*
5496767 TT-CTATTATT
1 TTATTATTATT
*
5496777 TTATTACTATT
1 TTATTATTATT
5496788 ATCATTTTTA
Statistics
Matches: 71, Mismatches: 16, Indels: 15
0.70 0.16 0.15
Matches are distributed among these distances:
10 8 0.11
11 29 0.41
12 20 0.28
13 3 0.04
15 1 0.01
16 10 0.14
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTATTATT
Found at i:5496912 original size:20 final size:20
Alignment explanation
Indices: 5496887--5496934 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
5496877 TGTATGTTTC
* *
5496887 TATTATATGTGTATATATAT
1 TATTATATATGTATATATAG
*
5496907 TATTATATATTTATATATAG
1 TATTATATATGTATATATAG
5496927 TATTATAT
1 TATTATAT
5496935 TTAATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
TATTATATATGTATATATAG
Found at i:5496953 original size:14 final size:14
Alignment explanation
Indices: 5496907--5496962 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
5496897 GTATATATAT
5496907 TATTATATATTTATATA
1 TATTAT-TATTT-TA-A
*
5496924 TAGTATTATATTTAA
1 TATTATTAT-TTTAA
5496939 TTATT-TTATTTTAA
1 -TATTATTATTTTAA
5496953 TATTATTATT
1 TATTATTATT
5496963 ATATTATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 4 0.12
14 10 0.29
15 5 0.15
16 8 0.24
17 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TATTATTATTTTAA
Found at i:5499385 original size:31 final size:31
Alignment explanation
Indices: 5499350--5499411 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5499340 TAATTAGAAA
5499350 GAAAATTTAATTAATAAACCTAGAGTTAGTT
1 GAAAATTTAATTAATAAACCTAGAGTTAGTT
*
5499381 GAAAATTTAATTAATAAACTTAGAGTTAGTT
1 GAAAATTTAATTAATAAACCTAGAGTTAGTT
5499412 TCTCTTACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (31 bp):
GAAAATTTAATTAATAAACCTAGAGTTAGTT
Found at i:5503448 original size:19 final size:19
Alignment explanation
Indices: 5503424--5503462 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5503414 TTGTAGAACG
5503424 TTGATGAAATCATAAGTTA
1 TTGATGAAATCATAAGTTA
5503443 TTGATGAAATCATAAGTTA
1 TTGATGAAATCATAAGTTA
5503462 T
1 T
5503463 CTTATAGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (19 bp):
TTGATGAAATCATAAGTTA
Found at i:5505466 original size:9 final size:10
Alignment explanation
Indices: 5505452--5505484 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5505442 ATATTATAAA
5505452 AAAATTA-TT
1 AAAATTATTT
5505461 AAAATTATTT
1 AAAATTATTT
*
5505471 AAAAATATTT
1 AAAATTATTT
5505481 AAAA
1 AAAA
5505485 AATAGGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAAATTATTT
Found at i:5505486 original size:11 final size:12
Alignment explanation
Indices: 5505439--5505488 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 12
5505429 ACTTGTTAGT
5505439 AAAATATTATAA
1 AAAATATTATAA
*
5505451 AAAA-ATTATTA
1 AAAATATTATAA
*
5505462 AAATTATT-T-A
1 AAAATATTATAA
5505472 AAAATATT-TAA
1 AAAATATTATAA
5505483 AAAATA
1 AAAATA
5505489 GGTTTAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 9 0.27
11 17 0.52
12 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATATTATAA
Found at i:5507131 original size:12 final size:11
Alignment explanation
Indices: 5507106--5507140 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
5507096 ATGTTTTTTC
5507106 AAAAA-AAAAA
1 AAAAAGAAAAA
5507116 AAAAAGAAAAA
1 AAAAAGAAAAA
5507127 GAAAAAGAAAAA
1 -AAAAAGAAAAA
5507139 AA
1 AA
5507141 GAATTAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 7 0.30
12 11 0.48
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:5507461 original size:16 final size:16
Alignment explanation
Indices: 5507411--5507461 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
5507401 TTTTATAATT
*
5507411 AAATTTATATAAAA-A
1 AAATTTATTTAAAATA
* * * *
5507426 TATTTTATTTATAATT
1 AAATTTATTTAAAATA
5507442 AAATTTATTTAAAATA
1 AAATTTATTTAAAATA
5507458 AAAT
1 AAAT
5507462 AAAAAATTGT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTATTTAAAATA
Found at i:5508160 original size:9 final size:9
Alignment explanation
Indices: 5508148--5508181 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5508138 AAATTAATTT
5508148 TTTTAATAA
1 TTTTAATAA
*
5508157 TTTTTATAA
1 TTTTAATAA
5508166 TTTTAATAA
1 TTTTAATAA
5508175 TATTTAA
1 T-TTTAA
5508182 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTAATAA
Found at i:5511529 original size:15 final size:15
Alignment explanation
Indices: 5511509--5511538 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5511499 TGTTATCTAA
5511509 GCTCCATTGATAATG
1 GCTCCATTGATAATG
5511524 GCTCCATTGATAATG
1 GCTCCATTGATAATG
5511539 AATTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (15 bp):
GCTCCATTGATAATG
Found at i:5516253 original size:43 final size:42
Alignment explanation
Indices: 5516061--5516264 Score: 135
Period size: 43 Copynumber: 4.8 Consensus size: 42
5516051 AGATGTGATT
* * *
5516061 ACATGTAAGACCATGT-TTGGACCATCGGCATTG-TATTGTGATT
1 ACATGTAAGACCATGTCTGGGA-CAT-GGCATTGATATT-CGATA
** * ** * * *
5516104 ATGTGTAAGACCATTTCTGGGACATCTACATCGTTATTCGATT
1 ACATGTAAGACCATGTCTGGGACAT-GGCATTGATATTCGATA
* * * * *
5516147 ACGTATAAGACCATGTCTGGGACATTGGCATCGTTATTCGATT
1 ACATGTAAGACCATGTCTGGGACA-TGGCATTGATATTCGATA
* * *
5516190 TCATGTAAGACCTTGCCTGGGACAGTGGCATTGATATGT-GATA
1 ACATGTAAGACCATGTCTGGGACA-TGGCATTGATAT-TCGATA
* *
5516233 ACATGTAAGACCATATCTGGGATATGGCATTG
1 ACATGTAAGACCATGTCTGGGACATGGCATTG
5516265 TACGAGCTTT
Statistics
Matches: 130, Mismatches: 27, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
42 8 0.06
43 112 0.86
44 10 0.08
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (42 bp):
ACATGTAAGACCATGTCTGGGACATGGCATTGATATTCGATA
Done.