Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002340.1 Hibiscus syriacus cultivar Beakdansim tig00004777_pilon, whole genome shotgun sequence
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: 583550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:229340 original size:3 final size:3
Alignment explanation
Indices: 229334--229396 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
229324 ATTATTTTTT
* *
229334 TAA TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
*
229379 TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
229397 AATGGGTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:229360 original size:18 final size:19
Alignment explanation
Indices: 229336--229396 Score: 92
Period size: 18 Copynumber: 3.4 Consensus size: 19
229326 TATTTTTTTA
*
229336 ATAATAATAATAATAATAT
1 ATAATAATAATTATAATAT
229355 AT-ATAATAATTATAAT-T
1 ATAATAATAATTATAATAT
229372 ATAATAATAATTATAATA-
1 ATAATAATAATTATAATAT
229390 ATAATAA
1 ATAATAA
229397 AATGGGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
17 3 0.08
18 34 0.87
19 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATAATAATTATAATAT
Found at i:231103 original size:196 final size:185
Alignment explanation
Indices: 230846--231252 Score: 467
Period size: 196 Copynumber: 2.1 Consensus size: 185
230836 ACATATCTAG
* * * * * * *
230846 TAGCGCTTTACCGGTTTTGTCAAAATGAAACTGGTTTTGTCATATTTCAACATGTTATATTGTCA
1 TAGCTCTTTACCGATTTTGTCAAATTAAAACTGGTTTTGTCAAACTTCAACATATTATATTGTCA
* * *
230911 TGTATCGATACATGTGTCTAAGGTATAGATAC-TTTATAGGCGCTATTATTGCACTTCTTTTAAA
66 TATATCGATACATGTGT-T----T-TAGAGACATTT-T---C-CT-TT-TTGCACTTATTTTAAA
* *
230975 TCCCTAAAGTACAAATACTTTGGTGCATATACTTATAAAAGTATCGATACAA-TATCAACCATTC
118 TCCCTAAAGTACAAATACTTTGGTACATATACTTATAAAAGTATCGATACAATTATCAACAATTC
231039 CAA
183 CAA
* *
231042 TATCTCTTTACCGATTTTGTCAAATTAAAACTGGTTTTGTCAAACTTCAACCTATTATATTGTCA
1 TAGCTCTTTACCGATTTTGTCAAATTAAAACTGGTTTTGTCAAACTTCAACATATTATATTGTCA
* * * * * *
231107 TATATCGATACATGTGTTTTCGAGACATTTTCCTTTTTTCATTTATTTTAAATTCCTACAGTACC
66 TATATCGATACATGTGTTTTAGAGACATTTTCCTTTTTGCACTTATTTTAAATCCCTAAAGTACA
* * *
231172 AATACTTTGGTACATATATTTATAAACGTATCGATACAATTTTCAACAATTCCAA
131 AATACTTTGGTACATATACTTATAAAAGTATCGATACAATTATCAACAATTCCAA
*
231227 TAGCTCTTTACCGATTTTCTCAAATT
1 TAGCTCTTTACCGATTTTGTCAAATT
231253 TAAATCAGTT
Statistics
Matches: 184, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
184 59 0.32
185 39 0.21
186 2 0.01
187 1 0.01
190 6 0.03
191 4 0.02
195 1 0.01
196 72 0.39
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (185 bp):
TAGCTCTTTACCGATTTTGTCAAATTAAAACTGGTTTTGTCAAACTTCAACATATTATATTGTCA
TATATCGATACATGTGTTTTAGAGACATTTTCCTTTTTGCACTTATTTTAAATCCCTAAAGTACA
AATACTTTGGTACATATACTTATAAAAGTATCGATACAATTATCAACAATTCCAA
Found at i:231298 original size:20 final size:20
Alignment explanation
Indices: 231241--231299 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
231231 TCTTTACCGA
* *
231241 TTTTCTCAAATTTAAATCAG
1 TTTTGTCAAATTTAAATCGG
*
231261 TTTTGTTAAATTTAAATCGG
1 TTTTGTCAAATTTAAATCGG
* *
231281 TTTTGTCAATTTTTAATCG
1 TTTTGTCAAATTTAAATCG
231300 TTAAAGTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTTGTCAAATTTAAATCGG
Found at i:231853 original size:2 final size:2
Alignment explanation
Indices: 231846--231872 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
231836 TGAAGTTGGA
231846 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
231873 AGTCAACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:238461 original size:23 final size:23
Alignment explanation
Indices: 238433--238508 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
238423 TCCCAAATGA
238433 CCACATAGGTTTGCACCGAAGTG
1 CCACATAGGTTTGCACCGAAGTG
* *
238456 ACACATAAGTTTGCACCGAAGTG
1 CCACATAGGTTTGCACCGAAGTG
* *
238479 CCACATAGGTTTGCATCAAAGTG
1 CCACATAGGTTTGCACCGAAGTG
238502 CCACATA
1 CCACATA
238509 ATTGTCCCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
CCACATAGGTTTGCACCGAAGTG
Found at i:242680 original size:31 final size:31
Alignment explanation
Indices: 242642--242766 Score: 205
Period size: 31 Copynumber: 4.0 Consensus size: 31
242632 CCCGAAGGAC
* * * *
242642 CAGTCCATATATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
242673 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
242704 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
242735 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
242766 C
1 C
242767 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:246062 original size:31 final size:30
Alignment explanation
Indices: 246024--246148 Score: 153
Period size: 31 Copynumber: 4.0 Consensus size: 30
246014 CCCGAAGGAC
* *
246024 CAGTCCATA-GATTCTGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTC-GAAGAACATAGGTAAA
*
246055 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGT-TCGAAGAACATAGGTAAA
*
246086 CAATCCATATGTATCGAAGAACATAGGTAAA
1 CAGTCCATATGT-TCGAAGAACATAGGTAAA
*
246117 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGT-TCGAAGAACATAGGTAAA
246148 C
1 C
246149 CCTCGACCCT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
31 81 0.98
32 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (30 bp):
CAGTCCATATGTTCGAAGAACATAGGTAAA
Found at i:249623 original size:3 final size:3
Alignment explanation
Indices: 249615--249643 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
249605 TTATATGTAT
249615 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
249644 GTTTTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:249635 original size:14 final size:14
Alignment explanation
Indices: 249599--249643 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
249589 AATTATACTA
*
249599 ATTAAATTA-TATGT
1 ATTATATTATTAT-T
249613 ATT-TATTATTATT
1 ATTATATTATTATT
249626 ATTATATTATTATT
1 ATTATATTATTATT
249640 ATTA
1 ATTA
249644 GTTTTTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 8 0.29
14 20 0.71
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTATATTATTATT
Found at i:252014 original size:17 final size:17
Alignment explanation
Indices: 251992--252025 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
251982 TTTAGGGAAC
* *
251992 ACTTTTTAATTGCAGAA
1 ACTTTTAAATAGCAGAA
252009 ACTTTTAAATAGCAGAA
1 ACTTTTAAATAGCAGAA
252026 CAGTGAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
ACTTTTAAATAGCAGAA
Found at i:252799 original size:21 final size:21
Alignment explanation
Indices: 252775--252821 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
252765 ATAATTTTGA
252775 AAAATTAA-AAGCTTAGGTACT
1 AAAATTAATAA-CTTAGGTACT
* *
252796 AAAACTAATAATTTAGGTACT
1 AAAATTAATAACTTAGGTACT
252817 AAAAT
1 AAAAT
252822 CATAGTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (21 bp):
AAAATTAATAACTTAGGTACT
Found at i:256761 original size:18 final size:18
Alignment explanation
Indices: 256733--256775 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
256723 TCTTCTTATT
*
256733 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
*
256752 TTTATTTAATCGCTTTTA
1 TTTATTTAATCACTTTTA
256770 -TTATTT
1 TTTATTT
256776 TAATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:261209 original size:15 final size:16
Alignment explanation
Indices: 261184--261224 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
261174 AGGGCTGTTC
*
261184 GAAAG-AAAAAGAGA-
1 GAAAGAAAAAAGACAT
*
261198 GAGAGAAAAAAGACAT
1 GAAAGAAAAAAGACAT
261214 GAAAGAAAAAA
1 GAAAGAAAAAA
261225 ATGGAAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 4 0.18
15 8 0.36
16 10 0.45
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (16 bp):
GAAAGAAAAAAGACAT
Found at i:262867 original size:18 final size:18
Alignment explanation
Indices: 262839--262881 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
262829 CTTCTTATTT
*
262839 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
*
262858 TTTATTTAATCGCTTTTA
1 TTTATTTAATCACTTTTA
262876 -TTATTT
1 TTTATTT
262882 TAATATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:271323 original size:12 final size:12
Alignment explanation
Indices: 271307--271353 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
271297 TGAACGGTGG
*
271307 TGAACAATACCG
1 TGAACAATACCA
*
271319 TGAACAATGCCA
1 TGAACAATACCA
* *
271331 TGAACAGTACAA
1 TGAACAATACCA
271343 TGAACAATACC
1 TGAACAATACC
271354 CAAATGCTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (12 bp):
TGAACAATACCA
Found at i:272170 original size:31 final size:31
Alignment explanation
Indices: 272147--272256 Score: 175
Period size: 31 Copynumber: 3.5 Consensus size: 31
272137 CATAGATTCT
* *
272147 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
272178 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
* *
272209 GAAGAATATAGGTAAACAGTCTATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
272240 GAAGAACATAGATAAAC
1 GAAGAACATAGGTAAAC
272257 CCTCGACCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:275851 original size:84 final size:83
Alignment explanation
Indices: 275703--275994 Score: 379
Period size: 83 Copynumber: 3.5 Consensus size: 83
275693 CTGAGTTGAA
* * * *
275703 TGTAATCGAACTCGAAGGTCTTTGATGACAGATCACCCTTCTAACCTTGAGTTATGCTACAAATG
1 TGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATG
* *
275768 ATATGCCTTGGAGTTAAG
66 ATGTGCCTTGGAGCTAAG
* * * * *
275786 CGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGTTATGTTACAAAT
1 TGTAGTCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTACAAAT
*
275851 GATGTGCCTTTGAGCTAAG
65 GATGTGCCTTGGAGCTAAG
* * * **
275870 TGTAGTCGAACTCGAAGGTCTTTGCTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGGAAATG
1 TGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATG
* *
275935 ATGCGCCTTGGAGCTGAG
66 ATGTGCCTTGGAGCTAAG
*
275953 TGTAATCGAACTCGAAGGTCTTTGTTGACAGAT-ACTCCTTCT
1 TGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAAC-CCTTCT
275995 TTGAGTTGGA
Statistics
Matches: 179, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
82 1 0.01
83 106 0.59
84 72 0.40
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (83 bp):
TGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATG
ATGTGCCTTGGAGCTAAG
Found at i:276357 original size:106 final size:106
Alignment explanation
Indices: 276172--277552 Score: 2145
Period size: 106 Copynumber: 13.0 Consensus size: 106
276162 TGTACTGTTC
* * * * * *
276172 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAATTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
276237 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
276278 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
276343 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
276384 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
276449 ACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
276490 -AAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
276554 ACCA-CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
276594 CGAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * *
276659 ACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
276700 TGAGTCCAATATCATTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGATA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
276765 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
276806 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * *
276871 ACCAGCGGTCCTTTCGTAGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* ** ** *
276912 GGAGTCCAATATCCTTCTATGTGAAGTTGAAATTATCTTTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
276977 ACCAGCCGTTCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
277018 CGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
277083 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
277124 GGTGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
277189 ACCAGCCGTCCCTTCGGTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
277230 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * *
277295 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTTTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
277336 GGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTCGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
277401 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
277442 CGAGTCCAATATCCTTCGCTGTGAAGTTGAATTTGGCTCTGAAATTGGGAAGTTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
277507 ACCAGTCGTCCCTTCATTGTGAAGTTGAACTTATGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
277548 CGAGT
1 CGAGT
277553 GGCACGATAT
Statistics
Matches: 1162, Mismatches: 111, Indels: 4
0.91 0.09 0.00
Matches are distributed among these distances:
104 33 0.03
105 128 0.11
106 1001 0.86
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:278524 original size:22 final size:22
Alignment explanation
Indices: 278498--278552 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
278488 TTGTGTTTGG
*
278498 TCAAAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
278520 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
278542 TCAAAGGTTTG
1 TCAAAGGTTTG
278553 ATGGGGTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:279211 original size:13 final size:12
Alignment explanation
Indices: 279195--279250 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 12
279185 TTTCTTTCGA
279195 TTTTTGTTCTTT
1 TTTTTGTTCTTT
279207 CTTTTTGTTCTTT
1 -TTTTTGTTCTTT
*
279220 TGTTTT-TTCCTT
1 T-TTTTGTTCTTT
279232 TTTTTGTTTCTTT
1 TTTTTG-TTCTTT
279245 TCTTTT
1 T-TTTT
279251 TTATTTTTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
11 4 0.11
12 7 0.19
13 22 0.59
14 4 0.11
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTGTTCTTT
Found at i:279236 original size:16 final size:17
Alignment explanation
Indices: 279217--279252 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
279207 CTTTTTGTTC
279217 TTTTGTTT-TTTCCTTT
1 TTTTGTTTCTTTCCTTT
*
279233 TTTTGTTTCTTTTCTTT
1 TTTTGTTTCTTTCCTTT
279250 TTT
1 TTT
279253 ATTTTTACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTGTTTCTTTCCTTT
Found at i:279236 original size:25 final size:26
Alignment explanation
Indices: 279196--279252 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
279186 TTCTTTCGAT
* *
279196 TTTTGTTCTTTCTTTTTG-TTCTTTTG
1 TTTT-TTCCTTCTTTTTGTTTCTTTTC
279222 TTTTTTCCTT-TTTTTGTTTCTTTTC
1 TTTTTTCCTTCTTTTTGTTTCTTTTC
279247 TTTTTT
1 TTTTTT
279253 ATTTTTACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 18 0.64
26 4 0.14
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (26 bp):
TTTTTTCCTTCTTTTTGTTTCTTTTC
Found at i:279258 original size:25 final size:24
Alignment explanation
Indices: 279208--279258 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
279198 TTGTTCTTTC
* *
279208 TTTTTGTTCTTTTGTTTTTTCCTT
1 TTTTTGTTCTTTTCTTTTTTACTT
279232 TTTTTGTTTCTTTTCTTTTTTA-TT
1 TTTTTG-TTCTTTTCTTTTTTACTT
279256 TTT
1 TTT
279259 ACCCTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.82
Consensus pattern (24 bp):
TTTTTGTTCTTTTCTTTTTTACTT
Found at i:282773 original size:24 final size:24
Alignment explanation
Indices: 282738--282783 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
282728 TAACGCAAAA
282738 AAATGAAAAAAAGAGAATTATAAT
1 AAATGAAAAAAAGAGAATTATAAT
* *
282762 AAAT-AAATAAAATATAATTATA
1 AAATGAAA-AAAAGAGAATTATA
282784 TATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATGAAAAAAAGAGAATTATAAT
Found at i:283303 original size:37 final size:36
Alignment explanation
Indices: 283250--283351 Score: 122
Period size: 34 Copynumber: 2.8 Consensus size: 36
283240 ATGCTTATGG
* *
283250 ATCCTATCTTTGGGAGTTTGAATCATAGTAGAACTT-T
1 ATCCTATTTTTAGGAGTTTGAATC-TAGTAGAA-TTCT
283287 ATCCTATTTTTAGGAGTTTGAATTCTA--A-AATTCT
1 ATCCTATTTTTAGGAGTTTGAA-TCTAGTAGAATTCT
283321 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAAT-CTAGTAG
283352 GACGAAAAGG
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
33 3 0.05
34 28 0.49
35 1 0.02
36 1 0.02
37 22 0.39
38 2 0.04
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCTAGTAGAATTCT
Found at i:285090 original size:13 final size:13
Alignment explanation
Indices: 285072--285097 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
285062 AATGGGGTTT
285072 TGTTTTTCTTGGC
1 TGTTTTTCTTGGC
285085 TGTTTTTCTTGGC
1 TGTTTTTCTTGGC
285098 ATGGATTGAA
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:0.00, C:0.15, G:0.23, T:0.62
Consensus pattern (13 bp):
TGTTTTTCTTGGC
Found at i:286069 original size:60 final size:60
Alignment explanation
Indices: 285996--286125 Score: 174
Period size: 60 Copynumber: 2.1 Consensus size: 60
285986 CTTGGGTGAT
* * *
285996 CATTTTCTAACTTTTAATAG-TCGAGAGACTCAACAAAGCAACT-CCCTATAGTCGAGGGGC
1 CATTTTGTAACTTTTAATAGTTCG-GAGACTCAACAAAGCAA-TACCCTATAGTCAAGGGAC
* *
286056 CATTTTGTAACTTTTAATAGTTCGGAGACTTAACAAAGCAATATCCTATAGTCAAGGGAC
1 CATTTTGTAACTTTTAATAGTTCGGAGACTCAACAAAGCAATACCCTATAGTCAAGGGAC
286116 CATTTATGTA
1 CATTT-TGTA
286126 TTTTACCCTT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
59 1 0.02
60 54 0.87
61 7 0.11
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTTCGGAGACTCAACAAAGCAATACCCTATAGTCAAGGGAC
Found at i:293893 original size:45 final size:44
Alignment explanation
Indices: 293826--293920 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 44
293816 TTTTCTGGTC
293826 TACTGTGAAGGCTTTTATGGCAGGGGGTGTTTTTAAGTTTTATG
1 TACTGTGAAGGCTTTTATGGCAGGGGGTGTTTTTAAGTTTTATG
*
293870 TACTGTGAAGGATTTTTATGGCAGGGGGTGTTTTTAAGTTTTATG
1 TACTGTGAAGG-CTTTTATGGCAGGGGGTGTTTTTAAGTTTTATG
293915 TACTGT
1 TACTGT
293921 TTTTGGTGTA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 11 0.22
45 38 0.78
ACGTcount: A:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (44 bp):
TACTGTGAAGGCTTTTATGGCAGGGGGTGTTTTTAAGTTTTATG
Found at i:297610 original size:20 final size:20
Alignment explanation
Indices: 297571--297610 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
297561 ATTATTGAGC
* *
297571 TGGTTTTTATGTTCTGTGTT
1 TGGTTTTTAAGTTCTATGTT
*
297591 TGGTTTTTAAGTTTTATGTT
1 TGGTTTTTAAGTTCTATGTT
297611 GTAACAGAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.23, T:0.65
Consensus pattern (20 bp):
TGGTTTTTAAGTTCTATGTT
Found at i:309435 original size:156 final size:157
Alignment explanation
Indices: 309142--309444 Score: 554
Period size: 156 Copynumber: 1.9 Consensus size: 157
309132 TTGAATGCTA
* *
309142 TCAATTGTCAGTCGAAATTGATTGCTTATTCTTTTTTAATCCAATGTTGTCAAGGGCACACTTTA
1 TCAATTGTCAATCGAAATTGATTGCTTATTCTTTATTAATCCAATGTTGTCAAGGGCACACTTTA
* *
309207 GGCACTAGAATCCGTATATTGCCTCAGGCACAAGGCGCAAAGAAAGCGCTAACTTGAGTGATAAA
66 GGCACTAGAAGCCGTATATTGCCTCAGGAACAAGGCGCAAAGAAAGCGCTAACTTGAGTGATAAA
309272 GTGAAATATTTTTGGACGTATGTGATT
131 GTGAAATATTTTTGGACGTATGTGATT
309299 TCAATTGTCAATCGAAATTGATTGCTTATTCTTTATTAATCCAATGTTGTCAAGGGCACACTTTA
1 TCAATTGTCAATCGAAATTGATTGCTTATTCTTTATTAATCCAATGTTGTCAAGGGCACACTTTA
*
309364 GGC-CTAGAAGCCGTATATTGCCTCAGGAACAAGGTGCAAAGAAAGCGCTAACTTGAGTGATAAA
66 GGCACTAGAAGCCGTATATTGCCTCAGGAACAAGGCGCAAAGAAAGCGCTAACTTGAGTGATAAA
309428 GTGAAATATTTTTGGAC
131 GTGAAATATTTTTGGAC
309445 ATACATACAT
Statistics
Matches: 141, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
156 75 0.53
157 66 0.47
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (157 bp):
TCAATTGTCAATCGAAATTGATTGCTTATTCTTTATTAATCCAATGTTGTCAAGGGCACACTTTA
GGCACTAGAAGCCGTATATTGCCTCAGGAACAAGGCGCAAAGAAAGCGCTAACTTGAGTGATAAA
GTGAAATATTTTTGGACGTATGTGATT
Found at i:309452 original size:4 final size:4
Alignment explanation
Indices: 309443--309502 Score: 75
Period size: 4 Copynumber: 15.0 Consensus size: 4
309433 ATATTTTTGG
* * * *
309443 ACAT ACAT ACAT ACAT ACAT GCAT ACAT GCAT ACAT GCAT ACAT GCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
309491 ACAT GCAT ACAT
1 ACAT ACAT ACAT
309503 CCAAAAAGCT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:309456 original size:8 final size:8
Alignment explanation
Indices: 309443--309502 Score: 102
Period size: 8 Copynumber: 7.5 Consensus size: 8
309433 ATATTTTTGG
*
309443 ACATACAT
1 ACATGCAT
*
309451 ACATACAT
1 ACATGCAT
309459 ACATGCAT
1 ACATGCAT
309467 ACATGCAT
1 ACATGCAT
309475 ACATGCAT
1 ACATGCAT
309483 ACATGCAT
1 ACATGCAT
309491 ACATGCAT
1 ACATGCAT
309499 ACAT
1 ACAT
309503 CCAAAAAGCT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 51 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (8 bp):
ACATGCAT
Found at i:319693 original size:20 final size:20
Alignment explanation
Indices: 319668--319759 Score: 83
Period size: 20 Copynumber: 5.0 Consensus size: 20
319658 AGCGACAGAA
319668 TAAAACTGATTCTATCTAAT
1 TAAAACTGATTCTATCTAAT
319688 TAAAACTGATTCTATCTAA-
1 TAAAACTGATTCTATCTAAT
* *
319707 T--AACT-A-AC-A--GAAT
1 TAAAACTGATTCTATCTAAT
* *
319720 AAAAATTGATTCTATCTAAT
1 TAAAACTGATTCTATCTAAT
*
319740 TAAAACTGATCCTATCTAAT
1 TAAAACTGATTCTATCTAAT
319760 AACTAACAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
12 2 0.04
14 1 0.02
15 4 0.07
16 2 0.04
17 5 0.09
18 1 0.02
19 1 0.02
20 39 0.71
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.36
Consensus pattern (20 bp):
TAAAACTGATTCTATCTAAT
Found at i:319736 original size:52 final size:52
Alignment explanation
Indices: 319662--319775 Score: 203
Period size: 52 Copynumber: 2.2 Consensus size: 52
319652 AAAATTAGCG
*
319662 ACAGAAT-AAAACTGATTCTATCTAATTAAAACTGATTCTATCTAATAACTA
1 ACAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATAACTA
*
319713 ACAGAATAAAAATTGATTCTATCTAATTAAAACTGATCCTATCTAATAACTA
1 ACAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATAACTA
319765 ACAGAATAAAA
1 ACAGAATAAAA
319776 TATCTAGTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 7 0.12
52 53 0.88
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (52 bp):
ACAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATAACTA
Found at i:325141 original size:20 final size:20
Alignment explanation
Indices: 325116--325207 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 20
325106 AGCAACAGAA
*
325116 TAAAACTGATTCTATCTAAT
1 TAAAACTGATCCTATCTAAT
325136 TAAAACTGATCCTATCTAA-
1 TAAAACTGATCCTATCTAAT
* *
325155 T--AACT-A-AC-A--GAAT
1 TAAAACTGATCCTATCTAAT
* * *
325168 AAAAAGTGATTCTATCTAAT
1 TAAAACTGATCCTATCTAAT
325188 TAAAACTGATCCTATCTAAT
1 TAAAACTGATCCTATCTAAT
325208 AACTAACAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
12 2 0.04
14 1 0.02
15 4 0.07
16 2 0.04
17 5 0.09
18 1 0.02
19 1 0.02
20 38 0.70
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (20 bp):
TAAAACTGATCCTATCTAAT
Found at i:325185 original size:52 final size:52
Alignment explanation
Indices: 325109--325223 Score: 214
Period size: 52 Copynumber: 2.2 Consensus size: 52
325099 TAAAATTAGC
325109 AACAGAAT-AAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATAACT
1 AACAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATAACT
*
325160 AACAGAATAAAAAGTGATTCTATCTAATTAAAACTGATCCTATCTAATAACT
1 AACAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATAACT
325212 AACAGAATAAAA
1 AACAGAATAAAA
325224 TATCTAGTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
51 8 0.13
52 54 0.87
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.29
Consensus pattern (52 bp):
AACAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATAACT
Found at i:329137 original size:32 final size:31
Alignment explanation
Indices: 329100--329169 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
329090 GGTATTAATT
*
329100 TTTTAAAATAAAA-AATAGTATATGAACTT-AA
1 TTTTAAAATAAAATAA-AGTACATGAA-TTAAA
*
329131 TCTTTAAATTAAAATAAAGTACATGAATTAAA
1 T-TTTAAAATAAAATAAAGTACATGAATTAAA
329163 TTTTAAA
1 TTTTAAA
329170 TAGTATATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 9 0.26
32 23 0.68
33 2 0.06
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (31 bp):
TTTTAAAATAAAATAAAGTACATGAATTAAA
Found at i:332005 original size:22 final size:22
Alignment explanation
Indices: 331954--332048 Score: 98
Period size: 22 Copynumber: 4.7 Consensus size: 22
331944 ACATAGAATT
*
331954 TGTCCCGTAGGACCAC--TA-A
1 TGTCCCGAAGGACCACTGTATA
331973 -GTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTGTATA
* *
331994 TGTCTCGAAGGACCATTGTATA
1 TGTCCCGAAGGACCACTGTATA
*
332016 TGTCCCAAAGGACCAC----TA
1 TGTCCCGAAGGACCACTGTATA
332034 TGTCCCGAAGGACCA
1 TGTCCCGAAGGACCA
332049 TTGATAATCC
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
18 30 0.46
20 2 0.03
21 1 0.02
22 32 0.49
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGTATA
Found at i:332037 original size:18 final size:18
Alignment explanation
Indices: 332014--332048 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
332004 GACCATTGTA
332014 TATGTCCCAAAGGACCAC
1 TATGTCCCAAAGGACCAC
*
332032 TATGTCCCGAAGGACCA
1 TATGTCCCAAAGGACCA
332049 TTGATAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.17
Consensus pattern (18 bp):
TATGTCCCAAAGGACCAC
Found at i:341357 original size:23 final size:24
Alignment explanation
Indices: 341331--341386 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
341321 CAGCTCGTAT
341331 AATTGCACCGA-AGTGCCACCTAG
1 AATTGCACCGAGAGTGCCACCTAG
* *
341354 AATTGCACC-AGAGTGCCGCGTAG
1 AATTGCACCGAGAGTGCCACCTAG
341377 AATTGCACCG
1 AATTGCACCG
341387 TTGTGCCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.18
Consensus pattern (24 bp):
AATTGCACCGAGAGTGCCACCTAG
Found at i:345959 original size:18 final size:18
Alignment explanation
Indices: 345936--345981 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
345926 CCAAGTTTAT
345936 CTCTTGTTCTTCAAGCAG
1 CTCTTGTTCTTCAAGCAG
*
345954 CTCTTGTTCTTCAAGCTG
1 CTCTTGTTCTTCAAGCAG
345972 CTCTTAGTTC
1 CTCTT-GTTC
345982 CAATCCTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.13, C:0.28, G:0.15, T:0.43
Consensus pattern (18 bp):
CTCTTGTTCTTCAAGCAG
Found at i:347725 original size:20 final size:20
Alignment explanation
Indices: 347700--347748 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
347690 GGATTAGCAC
347700 AGAACCGGTAAAGAACCGG-A
1 AGAACCGGTAAA-AACCGGCA
*
347720 AGAACCGGCTGAAAACCGGCA
1 AGAACCGG-TAAAAACCGGCA
347741 A-AACCGGT
1 AGAACCGGT
347749 TTGAACTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 5 0.19
ACGTcount: A:0.41, C:0.24, G:0.29, T:0.06
Consensus pattern (20 bp):
AGAACCGGTAAAAACCGGCA
Found at i:348012 original size:24 final size:24
Alignment explanation
Indices: 347982--348037 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
347972 TAGAAGTTCG
347982 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
348006 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
348030 ATTGAAGC
1 ATTGAAGC
348038 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:348469 original size:19 final size:19
Alignment explanation
Indices: 348445--348484 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
348435 AAACAGAAAA
348445 CCACGCCCAAATCCCCTTC
1 CCACGCCCAAATCCCCTTC
348464 CCACGCCCAAATCCCCTTC
1 CCACGCCCAAATCCCCTTC
348483 CC
1 CC
348485 CTACGTCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.60, G:0.05, T:0.15
Consensus pattern (19 bp):
CCACGCCCAAATCCCCTTC
Found at i:349018 original size:11 final size:10
Alignment explanation
Indices: 348967--349027 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
348957 ACTGCTGGAA
348967 AACCGGTTTG
1 AACCGGTTTG
*
348977 -ACCAGTTTTG
1 AACC-GGTTTG
348987 AACCGGTTTG
1 AACCGGTTTG
*
348997 -ACCGGTCTG
1 AACCGGTTTG
349006 AACCGGTTCTG
1 AACCGGTT-TG
*
349017 AACCGGGTTG
1 AACCGGTTTG
349027 A
1 A
349028 CCCGACCCGA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 11 0.26
10 19 0.45
11 12 0.29
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:349045 original size:17 final size:17
Alignment explanation
Indices: 349023--349063 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
349013 TCTGAACCGG
*
349023 GTTGACCCGACCCGACC
1 GTTGACCCGACCAGACC
349040 GTTGACCCGACCAGACC
1 GTTGACCCGACCAGACC
349057 GTTGACC
1 GTTGACC
349064 GTTGACCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.41, G:0.24, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCAGACC
Found at i:349077 original size:6 final size:7
Alignment explanation
Indices: 349053--349082 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
349043 GACCCGACCA
349053 GACCGTT
1 GACCGTT
349060 GACCGTT
1 GACCGTT
349067 GACCG-T
1 GACCGTT
349073 GACCGTT
1 GACCGTT
349080 GAC
1 GAC
349083 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:349077 original size:13 final size:14
Alignment explanation
Indices: 349053--349082 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
349043 GACCCGACCA
349053 GACCGTTGACCGTT
1 GACCGTTGACCGTT
349067 GACCG-TGACCGTT
1 GACCGTTGACCGTT
349080 GAC
1 GAC
349083 TTTCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:350021 original size:63 final size:63
Alignment explanation
Indices: 349953--350076 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
349943 CTAATGTGAC
** * *
349953 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
350016 TCTTAGGTAGGCTCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCTCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
350077 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 1 0.02
63 51 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCTCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:350036 original size:32 final size:32
Alignment explanation
Indices: 349953--350076 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
349943 CTAATGTGAC
* * *
349953 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
349983 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
350016 TCTTAGGTAGGCTC-CACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
350047 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
350077 TCCCTTAGGG
Statistics
Matches: 71, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.59
32 19 0.27
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:355003 original size:5 final size:5
Alignment explanation
Indices: 354973--355067 Score: 53
Period size: 5 Copynumber: 20.4 Consensus size: 5
354963 TCTTCTCTTC
* * * * *
354973 ATTTT GTTTT GTTTT ATTTT -TATTT ATTTT A--TT ATTTC GTTTT GTTTT
1 ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT ATTTT ATTTT
* * *
355021 A--TT ATTTT A-TTT ATTTT AATTT GTTTT CTTTT A--TT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
355066 AT
1 AT
355068 ATCTTAGCCA
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
3 9 0.13
4 5 0.07
5 55 0.79
6 1 0.01
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:355009 original size:18 final size:18
Alignment explanation
Indices: 354986--355064 Score: 71
Period size: 18 Copynumber: 4.7 Consensus size: 18
354976 TTGTTTTGTT
354986 TTATTTTTATTTATTTTA
1 TTATTTTTATTTATTTTA
* *
355004 TTATTTCGT-TTTGTTTTA
1 TTATTT-TTATTTATTTTA
355022 TTA-TTTTATTTATTTTA
1 TTATTTTTATTTATTTTA
* *
355039 --ATTTGT-TTTCTTTTA
1 TTATTTTTATTTATTTTA
355054 TTA-TTTTATTT
1 TTATTTTTATTT
355065 TATATCTTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
15 9 0.19
16 7 0.15
17 14 0.29
18 17 0.35
19 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.76
Consensus pattern (18 bp):
TTATTTTTATTTATTTTA
Found at i:355043 original size:27 final size:27
Alignment explanation
Indices: 354990--355066 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
354980 TTTGTTTTAT
***
354990 TTTTATTTATTTTA-TTATTTCGTTTTG
1 TTTTA-TTATTTTATTTATTTTAATTTG
355017 TTTTATTATTTTATTTATTTTAATTTG
1 TTTTATTATTTTATTTATTTTAATTTG
*
355044 TTTTCTT-TTATTATTTTATTTTA
1 TTTTATTATT-TTA-TTTATTTTA
355067 TATCTTAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
26 10 0.23
27 24 0.56
28 9 0.21
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTATTATTTTATTTATTTTAATTTG
Found at i:355053 original size:32 final size:33
Alignment explanation
Indices: 354975--355064 Score: 132
Period size: 32 Copynumber: 2.8 Consensus size: 33
354965 TTCTCTTCAT
354975 TTTGTTTTGTTTTA-T-TTTTATTTATTTTATTA
1 TTTGTTTTGTTTTATTATTTTATTTATTTTA-TA
355007 TTTCGTTTTGTTTTATTATTTTATTTATTTTA-A
1 TTT-GTTTTGTTTTATTATTTTATTTATTTTATA
*
355040 TTTGTTTTCTTTTATTATTTTATTT
1 TTTGTTTTGTTTTATTATTTTATTT
355065 TATATCTTAG
Statistics
Matches: 54, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
32 24 0.44
33 15 0.28
34 1 0.02
35 14 0.26
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.77
Consensus pattern (33 bp):
TTTGTTTTGTTTTATTATTTTATTTATTTTATA
Found at i:356115 original size:26 final size:26
Alignment explanation
Indices: 356084--356133 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
356074 ATGTTTCTTT
*
356084 TTTATTTTTCT-TTTCGTTATTTTATA
1 TTTATTTATCTATTT-GTTATTTTATA
*
356110 TTTATTTATCTATTTTTTATTTTA
1 TTTATTTATCTATTTGTTATTTTA
356134 CTAACTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTATTTATCTATTTGTTATTTTATA
Found at i:358434 original size:37 final size:37
Alignment explanation
Indices: 358376--358480 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
358366 CATTTTCGTC
*
358376 CTACTAGAATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
358413 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
358450 CTACTAAGATTTAAATTCCTAAATATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
358481 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:358941 original size:22 final size:22
Alignment explanation
Indices: 358916--358998 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 22
358906 TATTTTTTAC
358916 TATATTTAATTATTATTATATA
1 TATATTTAATTATTATTATATA
** * *
358938 TATATTTCTTTAATATTTTACTTA
1 TATATTTAATTATTATTATA--TA
* *
358962 TAAATCTAA-TATTACTATATATA
1 TATATTTAATTATTA-T-TATATA
358985 TATATTGTAATTAT
1 TATATT-TAATTAT
358999 CTTTATCTAG
Statistics
Matches: 43, Mismatches: 12, Indels: 9
0.67 0.19 0.14
Matches are distributed among these distances:
22 16 0.37
23 10 0.23
24 11 0.26
25 6 0.14
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (22 bp):
TATATTTAATTATTATTATATA
Found at i:359185 original size:20 final size:19
Alignment explanation
Indices: 359132--359186 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
359122 CTTTATAACT
359132 TTATATTATTTTTTTATTA
1 TTATATTATTTTTTTATTA
* * *
359151 TTTTCGTTTTTTTTTTATTA
1 TTAT-ATTATTTTTTTATTA
359171 TTATATTATTATTTTT
1 TTATATTATT-TTTTT
359187 TAAAAAAAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTATATTATTTTTTTATTA
Found at i:359378 original size:2 final size:2
Alignment explanation
Indices: 359371--359418 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
359361 TAATACTTTG
* *
359371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
359413 TT AT AT
1 AT AT AT
359419 TTTTTTCCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:359477 original size:20 final size:21
Alignment explanation
Indices: 359452--359497 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
359442 CTATATATAA
*
359452 TTATTA-CTTTAC-TATTTTTT
1 TTATTATC-TTACTTATTTATT
359472 TTATTATCTTACTTATTTATT
1 TTATTATCTTACTTATTTATT
359493 TTATT
1 TTATT
359498 TATTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATTATCTTACTTATTTATT
Found at i:361912 original size:12 final size:12
Alignment explanation
Indices: 361892--361928 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
361882 TCCAAAACTA
*
361892 ATCCTGATAATT
1 ATCCGGATAATT
361904 ATCCGGATAATT
1 ATCCGGATAATT
*
361916 ATCCGGATGATT
1 ATCCGGATAATT
361928 A
1 A
361929 CAGTATCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (12 bp):
ATCCGGATAATT
Found at i:363881 original size:183 final size:183
Alignment explanation
Indices: 363573--364110 Score: 943
Period size: 183 Copynumber: 2.9 Consensus size: 183
363563 AATTAAATCC
* *
363573 CTAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCTTGGCTTTATG
1 CTAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATG
* * *
363638 AATAGATTATGTTAAAACTATGACACTGCTCGGAAACTTGGCAATTCAGTGTTTGCTCCACTGCT
66 AATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
363703 TTTGTCAGGCCAAAGACTTTGTTATGAGATGAACCCTTCAGTGATTTGTCCCT
131 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCT
363756 CTAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATG
1 CTAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATG
363821 AATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 AATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
363886 TTTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCT
131 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCT
363939 CTAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATG
1 CTAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATG
* ** * *
364004 AATATATTACATTCAAA-TCATGACATTGCTCGGGCACTTGGCAATTCGGTGTTTGCTCCACTGC
66 AATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGC
*
364068 TTTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
364111 TAAACCTGAT
Statistics
Matches: 340, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 339 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
CTAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATG
AATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCT
Found at i:365328 original size:36 final size:36
Alignment explanation
Indices: 365288--365404 Score: 83
Period size: 36 Copynumber: 3.1 Consensus size: 36
365278 ATACTTTGTC
365288 TCACTTGAGACTTTTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGACTTTTTTTCTCGAAAGAAGATTTATT
** ** * * *
365324 TCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTC
1 TCACTTGAGACTT-TTTTTCTCGAAAGAAGATTTATT
* * **
365360 TCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TCACTTGAGA-CTTTTTTTCTCGAAAGAA-G-ATTT-ATT
365400 TCACT
1 TCACT
365405 CAAGGCTGTT
Statistics
Matches: 56, Mismatches: 19, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
35 2 0.04
36 33 0.59
37 10 0.18
38 2 0.04
39 4 0.07
40 5 0.09
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (36 bp):
TCACTTGAGACTTTTTTTCTCGAAAGAAGATTTATT
Found at i:365339 original size:72 final size:75
Alignment explanation
Indices: 365247--365421 Score: 209
Period size: 72 Copynumber: 2.4 Consensus size: 75
365237 ATGCAGATGA
* * * **
365247 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGA-CTTTTTTTCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
365309 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
365319 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
365384 AAGAAGGCAT
66 AAGAAGGCAT
**
365394 TTCATTTCACTCAAGGCTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
365422 GAAGATTTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 44 0.49
73 16 0.18
74 1 0.01
75 8 0.09
76 19 0.21
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:365456 original size:73 final size:72
Alignment explanation
Indices: 365263--365458 Score: 168
Period size: 72 Copynumber: 2.7 Consensus size: 72
365253 CACTCAAATT
* * * * **
365263 TGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGAC-TTTTTTTCTCGAAAGAAGATTTATTTC
1 TGTTTTTCTT-AAACA-AGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTC
*
365326 ACTCAAGAT
64 ACTCAAGAC
* *
365335 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TGTTTTTCTT-AAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAA-G-ATTT-ATT
*
365400 TCACTCAAGGC
62 TCACTCAAGAC
* * * *
365411 TGTTTTT-TT-AAGAAGATTTTATCTTGCTTGAGATAG-TTTCCCTCGAAA
1 TGTTTTTCTTAAACAAGA-TTTATCTCGCTTGAGACAGTTTTCACTCGAAA
365459 ACATTTCCTT
Statistics
Matches: 105, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
71 1 0.01
72 32 0.30
73 31 0.30
74 16 0.15
75 6 0.06
76 19 0.18
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (72 bp):
TGTTTTTCTTAAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCAC
TCAAGAC
Found at i:365519 original size:39 final size:39
Alignment explanation
Indices: 365476--365550 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
365466 CTTTGAAATT
* *
365476 AATTTTTTCTCTCC-TGAGATAGTTTCCCTCGAAACAGAA
1 AATTTTGTCTC-CCTTGAGACAGTTTCCCTCGAAACAGAA
* *
365515 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACA
365551 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.06
39 29 0.94
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (39 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAGAA
Found at i:365619 original size:105 final size:104
Alignment explanation
Indices: 365455--365771 Score: 500
Period size: 105 Copynumber: 3.1 Consensus size: 104
365445 AGTTTCCCTC
* *
365455 GAAAACATTTCCTTTGAAATTAATTTTTTCTCTCC-TGAGATAGTTTCCCTCGAAACAGAAAATT
1 GAAAACATTTCCCTTGAAA-TGATTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAATT
365519 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
65 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
365559 GAAAACATTTCCCTTGAAATGATTTTTTCTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATT
1 GAAAACATTTCCCTTGAAATGATTTTTTCTCTC-CTTGAGATAGTTTCCCTCGAAACAGAAAATT
365624 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
65 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
* * *
365664 GAAAACATTTCCCTTGAAATGAATTTTATCTC-GCTTGAGATAGTTTCCCTTGAAAC-G--AATT
1 GAAAACATTTCCCTTGAAATG-ATTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAATT
** *
365725 TTGTCTCCCTTGAGACAGTTTCTCTCAAAACATAAACTTT
65 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
365765 GAAAACA
1 GAAAACA
365772 ATTTAACGAA
Statistics
Matches: 202, Mismatches: 8, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
101 48 0.24
103 14 0.07
104 41 0.20
105 90 0.45
106 9 0.04
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (104 bp):
GAAAACATTTCCCTTGAAATGATTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAATTT
TGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
Found at i:365718 original size:36 final size:36
Alignment explanation
Indices: 365671--365746 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
365661 ATTGAAAACA
* * *
365671 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
365707 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
365743 TTTC
1 TTTC
365747 TCTCAAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:366072 original size:105 final size:104
Alignment explanation
Indices: 365946--366368 Score: 568
Period size: 105 Copynumber: 4.1 Consensus size: 104
365936 ATATCGTGAC
* * * *
365946 ACTCGAGACAACACAATTTCAACTTCATGACGAAGGGACCGTTGCTTGTCAACAACAACTTCTCA
1 ACTC-AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
366011 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
366051 ACTTCAGACAACACAAGTTCAACATCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 AC-TCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
366116 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
366156 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAA-AA-AA-ATCTC-
1 ACT-CAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* * *
366217 A-TTCAAAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
366256 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTC-AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * * *
366321 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
64 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
366362 ACTCAGA
1 ACTCAGA
366369 ACAATGCTAC
Statistics
Matches: 280, Mismatches: 29, Indels: 18
0.86 0.09 0.06
Matches are distributed among these distances:
99 1 0.00
100 79 0.28
101 1 0.00
102 5 0.02
103 4 0.01
104 6 0.02
105 146 0.52
106 38 0.14
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (104 bp):
ACTCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAA
TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:366275 original size:205 final size:211
Alignment explanation
Indices: 365946--366365 Score: 595
Period size: 205 Copynumber: 2.0 Consensus size: 211
365936 ATATCGTGAC
* * * * * *
365946 ACTCGAGACAACACAATTTCAACTTCATGACGAAGGGACCGTTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACACAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAACAACATCTCA
*
366011 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACACAAGTTCAACAT
66 ATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACACAAGTTCAACAT
*
366076 CACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAA-TCTCAGAGCCAATTTCAACTTC
131 CACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTC-CAGAGCCAATTTCAACTTC
366139 ACAACGAAGGATATTGG
195 ACAACGAAGGATATTGG
*
366156 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAA-AA-AA-ATCTC-
1 ACTCCAGACAACACAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAACAACATCTCA
* * *
366217 A-TTCAAAGTCAATTTCAACTTCACAGCGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACT
66 ATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACACAAGTTCAACA
* * * **
366280 TCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTC
130 TCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTCCAGAGCCAATTTCAACTTC
* *
366345 ACGACGGAGGATATTGG
195 ACAACGAAGGATATTGG
366362 ACTC
1 ACTC
366366 AGAACAATGC
Statistics
Matches: 188, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
204 2 0.01
205 81 0.43
206 49 0.26
207 6 0.03
208 2 0.01
209 2 0.01
210 46 0.24
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (211 bp):
ACTCCAGACAACACAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAACAACATCTCA
ATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACACAAGTTCAACAT
CACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTCCAGAGCCAATTTCAACTTCA
CAACGAAGGATATTGG
Found at i:366961 original size:37 final size:37
Alignment explanation
Indices: 366908--367012 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
366898 CATTTTCGTC
366908 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
366945 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
366982 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
367013 CCATAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:367395 original size:17 final size:18
Alignment explanation
Indices: 367369--367408 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
367359 ATTATATGGA
367369 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
367385 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
367403 TATTAT
1 TATTAT
367409 ATGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:367480 original size:22 final size:22
Alignment explanation
Indices: 367452--367532 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
367442 ATTTTTTTAC
367452 TATATTTAATTATTATTATATA
1 TATATTTAATTATTATTATATA
** * *
367474 TATATTTCTTTAATATTTTACTTA
1 TATATTTAATTATTATTATA--TA
* * *
367498 TAAATCTAA-TATTACTATATA
1 TATATTTAATTATTATTATATA
367519 TATATTGTAATTAT
1 TATATT-TAATTAT
367533 CTTTATCTAG
Statistics
Matches: 42, Mismatches: 13, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
21 6 0.14
22 19 0.45
23 10 0.24
24 7 0.17
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (22 bp):
TATATTTAATTATTATTATATA
Found at i:372061 original size:21 final size:21
Alignment explanation
Indices: 372035--372084 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
372025 TGTGTGGGAT
372035 ATTTTCCTCTCACGCATACAC
1 ATTTTCCTCTCACGCATACAC
372056 ATTTTCCTCTCACGCATACAC
1 ATTTTCCTCTCACGCATACAC
372077 ATTTTCCT
1 ATTTTCCT
372085 TTCTTTCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.36, G:0.04, T:0.38
Consensus pattern (21 bp):
ATTTTCCTCTCACGCATACAC
Found at i:375638 original size:27 final size:25
Alignment explanation
Indices: 375608--375658 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
375598 CTCTAAACTG
** *
375608 AAAAAAATTAAAAAAGAGAAAAAAA
1 AAAAAAAAAAAAAAAAAGAAAAAAA
*
375633 AAAAAAAAAAAAAAAAAGAACAAAA
1 AAAAAAAAAAAAAAAAAGAAAAAAA
375658 A
1 A
375659 TAAGGTAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.88, C:0.02, G:0.06, T:0.04
Consensus pattern (25 bp):
AAAAAAAAAAAAAAAAAGAAAAAAA
Found at i:376277 original size:14 final size:14
Alignment explanation
Indices: 376258--376284 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
376248 GATCGAAACT
376258 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
376272 TCAAGATTCCAGA
1 TCAAGATTCCAGA
376285 CATGCAACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:378857 original size:2 final size:2
Alignment explanation
Indices: 378850--378880 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
378840 TCATCACGTT
378850 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
378881 TGTATTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:378951 original size:1 final size:1
Alignment explanation
Indices: 378940--379018 Score: 77
Period size: 1 Copynumber: 79.0 Consensus size: 1
378930 CTTCTCTTCA
* * * * * * * *
378940 TTTTGTTTTTTTTATTTTTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTATTTTTTTAT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
379005 TTTTTTATTTTTTT
1 TTTTTTTTTTTTTT
379019 ATTTCATTTT
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.10, C:0.00, G:0.01, T:0.89
Consensus pattern (1 bp):
T
Found at i:378951 original size:8 final size:8
Alignment explanation
Indices: 378946--379078 Score: 144
Period size: 8 Copynumber: 16.5 Consensus size: 8
378936 TTCATTTTGT
378946 TTTTTTTA
1 TTTTTTTA
378954 TTTTTTTTTA
1 --TTTTTTTA
378964 TTTTTTTA
1 TTTTTTTA
378972 TTTTTTTA
1 TTTTTTTA
378980 TTTTTTTA
1 TTTTTTTA
378988 TTTTTTTA
1 TTTTTTTA
378996 TTTTTTTA
1 TTTTTTTA
379004 TTTTTTTA
1 TTTTTTTA
379012 TTTTTTTA
1 TTTTTTTA
**
379020 TTTCATT-
1 TTTTTTTA
*
379027 TTGTTTTA
1 TTTTTTTA
*
379035 TTATTTTA
1 TTTTTTTA
*
379043 TTTAATTTA
1 TTT-TTTTA
* *
379052 ATTTGTT-
1 TTTTTTTA
*
379059 TTCTTTTA
1 TTTTTTTA
*
379067 TTATTTTA
1 TTTTTTTA
379075 TTTT
1 TTTT
379079 ATTTTATGTC
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
7 8 0.08
8 82 0.79
9 6 0.06
10 8 0.08
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:380686 original size:24 final size:23
Alignment explanation
Indices: 380642--380687 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
380632 GGAGCTAGGG
*
380642 CATCAGTTTTACATGAAGTTTTT
1 CATCAGTTTTACATCAAGTTTTT
* *
380665 CATCACGTTTTTCATCATGTTTT
1 CATCA-GTTTTACATCAAGTTTT
380688 ATTTAAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (23 bp):
CATCAGTTTTACATCAAGTTTTT
Found at i:383139 original size:102 final size:102
Alignment explanation
Indices: 382963--383173 Score: 341
Period size: 102 Copynumber: 2.1 Consensus size: 102
382953 CCTCAAACTC
382963 AGAAAGACCAACCTAAAGGACTCAAAAGTGAAAAACCAAAGGAATTTATCATAAATCCTCCTTTT
1 AGAAAGACCAACCTAAAGGACTCAAAAGTGAAAAACCAAAGGAATTTATCATAAATCCTCCTTTT
*
383028 CCCGCTAGATTCGCTAAGTCCAAGAAAGAAGCAGAAG
66 CCCGCTAGATTCGCTAAGTCCAAGAAAGAAGCAGAAA
*** * *
383065 AGAAAGACCAACCTAAAGGACTCAAAAGTGAAAAAGTGAAGGAATTTGTCATAGATCCTCCTTTT
1 AGAAAGACCAACCTAAAGGACTCAAAAGTGAAAAACCAAAGGAATTTATCATAAATCCTCCTTTT
* **
383130 CCCTCTAGATTCGCTAAGTTTAAGAAAGAAGCAGAAA
66 CCCGCTAGATTCGCTAAGTCCAAGAAAGAAGCAGAAA
383167 AGAAAGA
1 AGAAAGA
383174 AATTCTTGAG
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (102 bp):
AGAAAGACCAACCTAAAGGACTCAAAAGTGAAAAACCAAAGGAATTTATCATAAATCCTCCTTTT
CCCGCTAGATTCGCTAAGTCCAAGAAAGAAGCAGAAA
Found at i:385424 original size:11 final size:11
Alignment explanation
Indices: 385408--385458 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
385398 TTCATTGAGG
*
385408 AAAAAAACAAA
1 AAAAAAAGAAA
*
385419 AAAAAAAG-GA
1 AAAAAAAGAAA
385429 AAAAAAAGAAA
1 AAAAAAAGAAA
*
385440 AGAAAAAGAAA
1 AAAAAAAGAAA
385451 AAGAAAAA
1 AA-AAAAA
385459 AAGTCGTGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
10 9 0.27
11 19 0.58
12 5 0.15
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:385430 original size:20 final size:21
Alignment explanation
Indices: 385405--385461 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
385395 TCATTCATTG
385405 AGGAAAAAAACA-AAAA-AAAA
1 AGGAAAAAAA-AGAAAAGAAAA
385425 AGGAAAAAAAAGAAAAGAAAA
1 AGGAAAAAAAAGAAAAGAAAA
385446 A-GAAAAAGAAA-AAAAG
1 AGGAAAAA-AAAGAAAAG
385462 TCGTGCAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.03
20 25 0.74
21 8 0.24
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (21 bp):
AGGAAAAAAAAGAAAAGAAAA
Found at i:386549 original size:12 final size:12
Alignment explanation
Indices: 386528--386573 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
386518 GGAGCTAGGG
386528 CATC-AGTTTTA
1 CATCAAGTTTTA
* *
386539 CATGAAGTTTTT
1 CATCAAGTTTTA
*
386551 CATCAGGTTTTA
1 CATCAAGTTTTA
386563 CATCAAGTTTT
1 CATCAAGTTTT
386574 CTTTAAGTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
11 3 0.11
12 25 0.89
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (12 bp):
CATCAAGTTTTA
Found at i:386574 original size:23 final size:23
Alignment explanation
Indices: 386528--386573 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
386518 GGAGCTAGGG
*
386528 CATCAGTTTTACATGAAGTTTTT
1 CATCAGTTTTACATCAAGTTTTT
386551 CATCAGGTTTTACATCAAGTTTT
1 CATCA-GTTTTACATCAAGTTTT
386574 CTTTAAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (23 bp):
CATCAGTTTTACATCAAGTTTTT
Found at i:389132 original size:97 final size:96
Alignment explanation
Indices: 388965--389254 Score: 361
Period size: 96 Copynumber: 3.0 Consensus size: 96
388955 TTAAAAACCC
* * * * * **
388965 CTTCATAATCTCCGCGGTACATAAGTACCTCAGCGGACATTGGAAGGATGAAAAGAGTGCCAGTA
1 CTTCATAACCGCCGCGGTACATAAGTACCTCAGCGGACATTGTAAGGAGGAAAAGAGTTCCAAAA
389030 ATTTTATTGCCAAAGAGAAATTACACCTCATA
66 ATTTTATTGCCAAA-AGAAATTACACCTCATA
* * * * *
389062 TTTCATAACTGTCGCGGTACATAAGTACCTCAGCGGACATTGTAAGGAGGATAAGAGTTCCACAA
1 CTTCATAACCGCCGCGGTACATAAGTACCTCAGCGGACATTGTAAGGAGGAAAAGAGTTCCAAAA
389127 ATTTTATTGCCTAAAAGAAATTACA-CTCATA
66 ATTTTATTGCC-AAAAGAAATTACACCTCATA
* ** *
389158 CTTCATAACCGCCACATTACATAAGTACCTCAGTGGACATT-TGAAGGAGGAAAAGAGTGT-CAA
1 CTTCATAACCGCCGCGGTACATAAGTACCTCAGCGGACATTGT-AAGGAGGAAAAGAGT-TCCAA
* *
389221 AAATTTTATTGCCAAAAAAAAGTACACCTCATA
64 AAATTTTATTGCCAAAAGAAATTACACCTCATA
389254 C
1 C
389255 AACAACAGGA
Statistics
Matches: 167, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
95 12 0.07
96 76 0.46
97 76 0.46
98 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (96 bp):
CTTCATAACCGCCGCGGTACATAAGTACCTCAGCGGACATTGTAAGGAGGAAAAGAGTTCCAAAA
ATTTTATTGCCAAAAGAAATTACACCTCATA
Found at i:391019 original size:31 final size:32
Alignment explanation
Indices: 390966--391083 Score: 161
Period size: 32 Copynumber: 3.8 Consensus size: 32
390956 GTTCTACGGA
390966 ACATATGGACAGAATTACCTATGTCTTTTGAG
1 ACATATGGACAGAATTACCTATGTCTTTTGAG
* ***
390998 ACATATGGACAGTA-TACCTATGTTCTACGGA-
1 ACATATGGACAGAATTACCTATG-TCTTTTGAG
391029 ACATATGGACAGAATTACCTATGTCTTTTGAG
1 ACATATGGACAGAATTACCTATGTCTTTTGAG
*
391061 ACATATGGACAGTA-TACCTATGT
1 ACATATGGACAGAATTACCTATGT
391084 TCTAAGGAAC
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
31 35 0.47
32 39 0.53
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTTGAG
Found at i:391024 original size:63 final size:63
Alignment explanation
Indices: 390946--391100 Score: 301
Period size: 63 Copynumber: 2.5 Consensus size: 63
390936 AGAGTCGAGG
390946 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
391009 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
*
391072 GTATACCTATGTTCTAAGGAACATATGGA
1 GTATACCTATGTTCTACGGAACATATGGA
391101 TAGTTTACCT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 91 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
Found at i:391096 original size:31 final size:31
Alignment explanation
Indices: 390946--391139 Score: 189
Period size: 31 Copynumber: 6.2 Consensus size: 31
390936 AGAGTCGAGG
390946 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* ***
390977 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTACGGA-ACATATGGACA
391009 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* ***
391040 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTACGGA-ACATATGGACA
* *
391072 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
391103 GTTTACCTAGGTTC-ATCGGAACCTATAGACA
1 GTATACCTATGTTCTA-CGGAACATATGGACA
391134 GT-TACC
1 GTATACC
391140 AAGGATCTTT
Statistics
Matches: 133, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
30 5 0.04
31 76 0.57
32 52 0.39
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:392695 original size:411 final size:414
Alignment explanation
Indices: 392128--392920 Score: 1499
Period size: 411 Copynumber: 1.9 Consensus size: 414
392118 AATGTATCAA
392128 ATTAGTTGATAAAGTTGCGAGCACCCAAGTTCAAGGGTGGATTGAGGAAGGTTCTATTGTTATAG
1 ATTAGTTGATAAAGTTGCGAGCACCCAAGTTCAAGGGTGGATTGAGGAAGGTTCTATTGTTATAG
392193 ACCTTTGGTTGAATGATATGATAGAAGTTTTCATTTCTTCAAAGTGGAGATGTTAAATTGAGTAG
66 ACCTTTGGTTGAATGATATGATAGAAGTTTTCATTTCTTCAAAGTGGAGATGTTAAATTGAGTAG
392258 TTTTGTTACTACTTTGGTAAGTTAGAGTATGGTGGACAATTGTCACCATAAGAACGTT-AAAGAT
131 TTTTGTTACTACTTTGGTAAGTTAGAGTATGGTGGACAATTGTCACCATAAGAACGTTAAAAGAT
392322 TAAATGATGTGATTAGAATTGTATAAGAGTTTCAAGAATAAGTGCATTGATGACCAGTTT-TAAG
196 TAAATGATGTGATTAGAATTGTATAAGAGTTT-AAGAATAAGTGCATTGATGACCAGTTTATAAG
392386 ACAGATGAAACTGGAAT-ACGAGCTTGAAACAAGGGAATTACACCTTGTATGAGTATGATTATAA
260 ACAGATGAAACTGGAATAACGAGCTTGAAACAAGGGAATTACACCTTGTATGAGTATGATTATAA
392450 -TTT-ATAAGCT-AGCAGAATTGCTGCTGAGTTAATTCCGACTGAAAATGATACATGATTTGTGT
325 GTTTAATAAGCTAAGCAGAATTGCTGCTGAGTTAATTCCGACTGAAAATGATACATGATTTGTGT
392512 TTAGGACTTGCGCCTAAATTAAAAG
390 TTAGGACTTGCGCCTAAATTAAAAG
392537 ATTAGTTGATAAAGTTGCGAGCACCCAAGTTCAAGGGTGGATTTGAGGAAGGTTCTATTGTTATA
1 ATTAGTTGATAAAGTTGCGAGCACCCAAGTTCAAGGGTGGA-TTGAGGAAGGTTCTATTGTTATA
*
392602 GACCTTTGGTTGAATGATATGATAGAAGGTTTTCATTTCTTCAAAGTGGAGATGTTGAATTGAGT
65 GACCTTTGGTTGAATGATATGATAGAA-GTTTTCATTTCTTCAAAGTGGAGATGTTAAATTGAGT
392667 AGTTTTGTTACTACTTTGGTAAGTTAGAGTATGGTGGACAATTGTCACCATAAGAACGTTAAAAG
129 AGTTTTGTTACTACTTTGGTAAGTTAGAGTATGGTGGACAATTGTCACCATAAGAACGTTAAAAG
392732 ATTAAATGATGTGATTAGAATTGTATAAGAGTTTAAGAATAAGTGCATTGATGACCAGTTTATAA
194 ATTAAATGATGTGATTAGAATTGTATAAGAGTTTAAGAATAAGTGCATTGATGACCAGTTTATAA
392797 GACAGATGAAACTGGAATACACGAGCTTGAAACAAGGGAATTACACCTTGTATGAGTATGATTAT
259 GACAGATGAAACTGGAATA-ACGAGCTTGAAACAAGGGAATTACACCTTGTATGAGTATGATTAT
392862 AAGTTTAATAAGCTAAGCAGAATTGCTGCTGAGTTAATTCCGACTGAAAATGATACATG
323 AAGTTTAATAAGCTAAGCAGAATTGCTGCTGAGTTAATTCCGACTGAAAATGATACATG
392921 TGACGAAATA
Statistics
Matches: 374, Mismatches: 1, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
409 41 0.11
410 50 0.13
411 123 0.33
412 59 0.16
414 47 0.13
415 3 0.01
416 7 0.02
417 44 0.12
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (414 bp):
ATTAGTTGATAAAGTTGCGAGCACCCAAGTTCAAGGGTGGATTGAGGAAGGTTCTATTGTTATAG
ACCTTTGGTTGAATGATATGATAGAAGTTTTCATTTCTTCAAAGTGGAGATGTTAAATTGAGTAG
TTTTGTTACTACTTTGGTAAGTTAGAGTATGGTGGACAATTGTCACCATAAGAACGTTAAAAGAT
TAAATGATGTGATTAGAATTGTATAAGAGTTTAAGAATAAGTGCATTGATGACCAGTTTATAAGA
CAGATGAAACTGGAATAACGAGCTTGAAACAAGGGAATTACACCTTGTATGAGTATGATTATAAG
TTTAATAAGCTAAGCAGAATTGCTGCTGAGTTAATTCCGACTGAAAATGATACATGATTTGTGTT
TAGGACTTGCGCCTAAATTAAAAG
Found at i:394967 original size:63 final size:63
Alignment explanation
Indices: 394889--395042 Score: 281
Period size: 63 Copynumber: 2.4 Consensus size: 63
394879 GAGTCGAGGG
394889 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACAA
1 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACAA
* *
394952 TATACCTATGTTCTACGGAACATATGGGCATAATTACCTATGTCTTTTGAGACATATGGACAA
1 TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACAA
*
395015 TATACCTATGTTCTAAGGAACATATGGA
1 TATACCTATGTTCTACGGAACATATGGA
395043 TAGTTTACCT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 87 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (63 bp):
TATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACAA
Found at i:395038 original size:31 final size:31
Alignment explanation
Indices: 394889--395042 Score: 154
Period size: 32 Copynumber: 4.9 Consensus size: 31
394879 GAGTCGAGGG
394889 TATACCTATGTTCTACGGAACATATGGACAGA
1 TATACCTATGTTCTACGGAACATATGGACA-A
***
394921 -ATTACCTATG-TCTTTTGAGACATATGGACAA
1 TA-TACCTATGTTCTACGGA-ACATATGGACAA
*
394952 TATACCTATGTTCTACGGAACATATGGGC-A
1 TATACCTATGTTCTACGGAACATATGGACAA
***
394982 TAATTACCTATG-TCTTTTGAGACATATGGACAA
1 T-A-TACCTATGTTCTACGGA-ACATATGGACAA
*
395015 TATACCTATGTTCTAAGGAACATATGGA
1 TATACCTATGTTCTACGGAACATATGGA
395043 TAGTTTACCT
Statistics
Matches: 99, Mismatches: 14, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
30 2 0.02
31 47 0.47
32 48 0.48
33 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (31 bp):
TATACCTATGTTCTACGGAACATATGGACAA
Found at i:395052 original size:31 final size:31
Alignment explanation
Indices: 394891--395075 Score: 151
Period size: 31 Copynumber: 5.9 Consensus size: 31
394881 GTCGAGGGTA
*
394891 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACA-ATT
*** *
394923 TACCTATG-TCTTTTGAGACATATGGACAATA
1 TACCTATGTTCTACGGA-ACATATGGACAATT
* *
394954 TACCTATGTTCTACGGAACATATGGGCATAAT
1 TACCTATGTTCTACGGAACATATGGACA-ATT
*** *
394986 TACCTATG-TCTTTTGAGACATATGGACAATA
1 TACCTATGTTCTACGGA-ACATATGGACAATT
* * *
395017 TACCTATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTACGGAACATATGGACAATT
* * *
395048 TACCTAGGTTC-ATCGGAACCTATAGACA
1 TACCTATGTTCTA-CGGAACATATGGACA
395076 GTTACCGAGG
Statistics
Matches: 119, Mismatches: 28, Indels: 13
0.74 0.17 0.08
Matches are distributed among these distances:
30 1 0.01
31 70 0.59
32 48 0.40
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAATT
Found at i:404162 original size:41 final size:41
Alignment explanation
Indices: 404073--404164 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
404063 TAACCTTAGC
* * *
404073 GGCGTTTCTTTACAAACACCATAATAGGGTTCATCTATAGT
1 GGCGTTTTTTTACAAACACCACAATAGGGTCCATCTATAGT
* *
404114 GGCGTTTTTTTGACAAACGCCGCAATA-GGTCCATCTATAGT
1 GGCGTTTTTTT-ACAAACACCACAATAGGGTCCATCTATAGT
404155 GGCGTTTTTT
1 GGCGTTTTTT
404165 CAATAAACGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
41 33 0.73
42 12 0.27
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (41 bp):
GGCGTTTTTTTACAAACACCACAATAGGGTCCATCTATAGT
Found at i:404173 original size:41 final size:42
Alignment explanation
Indices: 404095--404179 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 42
404085 CAAACACCAT
* **
404095 AATAGGGTTCATCTATAGTGGCGTTTTTTTGACAAACGCCGC
1 AATAGGGTCCATCTATAGTGGCGTTTTTTCAACAAACGCCGC
* *
404137 AATA-GGTCCATCTATAGTGGCGTTTTTTCAATAAACGTCGC
1 AATAGGGTCCATCTATAGTGGCGTTTTTTCAACAAACGCCGC
404178 AA
1 AA
404180 CAGATTAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 34 0.89
42 4 0.11
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (42 bp):
AATAGGGTCCATCTATAGTGGCGTTTTTTCAACAAACGCCGC
Found at i:404381 original size:83 final size:83
Alignment explanation
Indices: 404242--404564 Score: 360
Period size: 83 Copynumber: 3.9 Consensus size: 83
404232 ATGCCACAAT
* * ** * *
404242 AGATTAGTACTTTAGCGGTATTTTTATATAAACGTTATAATAGGGTTCACCTATAGTGGCATTTT
1 AGATTAGAACTTTAGCGGTATTTTTATACAAACGCCACAATAGGATTCACCTATAGTGGCATTTT
*
404307 TTCAATAAACACCGTAAC
66 TTCAATAAACGCCGTAAC
* * * * **
404325 AGATTAGAACTTTAGCGGT-TATTTTATATAAATGCCATAATAGGGTTCACCTATAGTGGTGTTT
1 AGATTAGAACTTTAGCGGTAT-TTTTATACAAACGCCACAATAGGATTCACCTATAGTGGCATTT
*
404389 TTTCAATAAACGCCGCAAC
65 TTTCAATAAACGCCGTAAC
* ** * * * *
404408 AGATTATAACTTTAGCGGCGTTTTTATACAAAAGCCACAATAGTATTTACCTATAGTGGCGTTTT
1 AGATTAGAACTTTAGCGGTATTTTTATACAAACGCCACAATAGGATTCACCTATAGTGGCATTTT
*
404473 TTCAATAAACGTCGTAAC
66 TTCAATAAACGCCGTAAC
* * * * * * *
404491 ATATTAGAACTTTAGTGGCATTTTTATACAAACACCACAATAGTATTTATCTATAGTGGCATTTT
1 AGATTAGAACTTTAGCGGTATTTTTATACAAACGCCACAATAGGATTCACCTATAGTGGCATTTT
*
404556 TTAAATAAA
66 TTCAATAAA
404565 TGCTACAATT
Statistics
Matches: 210, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
82 1 0.00
83 208 0.99
84 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (83 bp):
AGATTAGAACTTTAGCGGTATTTTTATACAAACGCCACAATAGGATTCACCTATAGTGGCATTTT
TTCAATAAACGCCGTAAC
Found at i:404432 original size:42 final size:42
Alignment explanation
Indices: 404378--404515 Score: 122
Period size: 42 Copynumber: 3.3 Consensus size: 42
404368 GGTTCACCTA
*
404378 TAGTGGTGTTTTTTCAATAAACGCCGCAACAGATTATAACTT
1 TAGTGGCGTTTTTTCAATAAACGCCGCAACAGATTATAACTT
* * * * *
404420 TAGCGGCGTTTTTAT-ACA-AAA-GCCACAATAGTATT-TACCTA
1 TAGTGGCGTTTTT-TCA-ATAAACGCCGCAACAG-ATTATAACTT
* * * *
404461 TAGTGGCGTTTTTTCAATAAACGTCGTAACATATTAGAACTT
1 TAGTGGCGTTTTTTCAATAAACGCCGCAACAGATTATAACTT
*
404503 TAGTGGCATTTTT
1 TAGTGGCGTTTTT
404516 ATACAAACAC
Statistics
Matches: 73, Mismatches: 16, Indels: 14
0.71 0.16 0.14
Matches are distributed among these distances:
40 2 0.03
41 31 0.42
42 38 0.52
43 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (42 bp):
TAGTGGCGTTTTTTCAATAAACGCCGCAACAGATTATAACTT
Found at i:404469 original size:41 final size:41
Alignment explanation
Indices: 404414--404556 Score: 105
Period size: 41 Copynumber: 3.5 Consensus size: 41
404404 CAACAGATTA
* * *
404414 TAACTTTAGCGGCGTTTTTATACAAAAGCCACAATAGTATT
1 TAACTATAGTGGCATTTTTATACAAAAGCCACAATAGTATT
* * * ** *
404455 TACCTATAGTGGCGTTTTT-T-CAATAAACGTCGTAACA-TATT
1 TAACTATAGTGGCATTTTTATAC-A-AAA-GCCACAATAGTATT
* *
404496 AGAACTTTAGTGGCATTTTTATACAAACA-CCACAATAGTATT
1 -TAACTATAGTGGCATTTTTATACAAA-AGCCACAATAGTATT
*
404538 TATCTATAGTGGCATTTTT
1 TAACTATAGTGGCATTTTT
404557 TAAATAAATG
Statistics
Matches: 76, Mismatches: 18, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
39 1 0.01
40 2 0.03
41 43 0.57
42 26 0.34
43 3 0.04
44 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (41 bp):
TAACTATAGTGGCATTTTTATACAAAAGCCACAATAGTATT
Found at i:407010 original size:85 final size:85
Alignment explanation
Indices: 406845--407034 Score: 256
Period size: 85 Copynumber: 2.2 Consensus size: 85
406835 CAAAAGAGCC
* * * *
406845 GCTACAGATCTGACCTTTTGCGGTGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCG
1 GCTATAGATCTGACCTTTTACGGTGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTTACG
* *
406910 GCGTTTGTTAAAAAAA-ATT
66 ACGTTTGTTAAAAAAACACT
*
406929 GCTATAGATCTCGACCTTTTACGGTGTTTGTATACAAAAACGCCGCTATAGATCTGGCCTTTTAC
1 GCTATAGATCT-GACCTTTTACGGTGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTTAC
** *
406994 GACGTTTGTTTCAAAAACGCT
65 GACGTTTGTTAAAAAAACACT
*
407015 GCTATAGATCTTGACTTTTT
1 GCTATAGATC-TGACCTTTT
407035 GTGGCGTTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
84 10 0.11
85 63 0.68
86 18 0.20
87 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (85 bp):
GCTATAGATCTGACCTTTTACGGTGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTTACG
ACGTTTGTTAAAAAAACACT
Found at i:407043 original size:43 final size:43
Alignment explanation
Indices: 406825--407059 Score: 217
Period size: 43 Copynumber: 5.5 Consensus size: 43
406815 TAGAATTCGT
* * *
406825 CGTTTTTATCCAAAAGA-GCCGCTACAGATCTGACCTTTTGCGG
1 CGTTTGTATTCAAAA-ACGCCGCTATAGATCTGACCTTTTGCGG
* *
406868 TGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
1 CGTTTGTATTCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
* **** *
406911 CGTTTG--TTAAAAAAAATTGCTATAGATCTCGACCTTTTACGG
1 CGTTTGTATTCAAAAACGCCGCTATAGATCT-GACCTTTTGCGG
* * * * *
406953 TGTTTGTATACAAAAACGCCGCTATAGATCTGGCCTTTTACGA
1 CGTTTGTATTCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
* * *
406996 CGTTTGT-TTCAAAAACGCTGCTATAGATCTTGACTTTTTGTGG
1 CGTTTGTATTCAAAAACGCCGCTATAGATC-TGACCTTTTGCGG
* *
407039 CGTTTTTATTTCACAAACGCC
1 CGTTTGTA-TTCAAAAACGCC
407060 ACTAACATTA
Statistics
Matches: 154, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
41 17 0.11
42 37 0.24
43 73 0.47
44 17 0.11
45 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (43 bp):
CGTTTGTATTCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
Found at i:407089 original size:15 final size:15
Alignment explanation
Indices: 407071--407107 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
407061 CTAACATTAG
407071 CGGCACTGGTATGAC
1 CGGCACTGGTATGAC
407086 CGGCACTGGTATGAC
1 CGGCACTGGTATGAC
407101 CGGCACT
1 CGGCACT
407108 TCTTGCGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.30, G:0.32, T:0.19
Consensus pattern (15 bp):
CGGCACTGGTATGAC
Found at i:407818 original size:21 final size:21
Alignment explanation
Indices: 407775--407819 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
407765 TTAACTTTTT
* *
407775 CTTTTTCTCTTTTATTATTAA
1 CTTTTTCTCTTTCATTATGAA
*
407796 CTTTTTCTCTTTCATTCTGAA
1 CTTTTTCTCTTTCATTATGAA
407817 CTT
1 CTT
407820 ACTTTTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.62
Consensus pattern (21 bp):
CTTTTTCTCTTTCATTATGAA
Found at i:413229 original size:20 final size:20
Alignment explanation
Indices: 413204--413241 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
413194 TTTCAAAGTG
413204 ATGCATCGATGAACCAATCC
1 ATGCATCGATGAACCAATCC
*
413224 ATGCATCGATGCACCAAT
1 ATGCATCGATGAACCAAT
413242 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCATCGATGAACCAATCC
Found at i:413417 original size:19 final size:19
Alignment explanation
Indices: 413379--413417 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
413369 ATGCATTTTA
* *
413379 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCATAG
*
413398 TGCACCGATGCACTGATAG
1 TGCACCGATGCACTCATAG
413417 T
1 T
413418 CCAACGATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (19 bp):
TGCACCGATGCACTCATAG
Found at i:420836 original size:21 final size:21
Alignment explanation
Indices: 420794--420837 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
420784 ACCCCGGGAG
*
420794 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
420815 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
420836 CT
1 CT
420838 CCTCCTCCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:422083 original size:45 final size:46
Alignment explanation
Indices: 422034--422124 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
422024 AAACATCAAA
* *
422034 TGCATTTTATGCATCAATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAG
*
422079 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAG
422125 GTTTTTTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 20 0.48
46 22 0.52
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAG
Found at i:425553 original size:81 final size:84
Alignment explanation
Indices: 425461--425629 Score: 256
Period size: 81 Copynumber: 2.0 Consensus size: 84
425451 ATGAATGGAT
* * *
425461 TCAACGTAATATCCATATGGTTTTAAAATCAAACATATGATTTTAAAAGTACA-AT-TTTTTACT
1 TCAACGAAATATCCATATGATTTTAAAATCAAACATATGATTTTAAAAGTACATATATTTTTAAT
425524 GT-AACTCCTC-AGATGGTC
66 GTAAACTCCTCTA-ATGGTC
*
425542 TCAACGAAATATCCATATGATTTTAAAATCAAACATATGATTTTAAAAGTATATATATTTTTAAT
1 TCAACGAAATATCCATATGATTTTAAAATCAAACATATGATTTTAAAAGTACATATATTTTTAAT
*
425607 GTAAACTCTTCTAATGGTC
66 GTAAACTCCTCTAATGGTC
425626 TCAA
1 TCAA
425630 GGAAGAATCT
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
81 50 0.63
82 2 0.03
83 9 0.11
84 17 0.22
85 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.38
Consensus pattern (84 bp):
TCAACGAAATATCCATATGATTTTAAAATCAAACATATGATTTTAAAAGTACATATATTTTTAAT
GTAAACTCCTCTAATGGTC
Found at i:428076 original size:103 final size:103
Alignment explanation
Indices: 427887--428112 Score: 366
Period size: 103 Copynumber: 2.2 Consensus size: 103
427877 GTCGAGGATC
* *
427887 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGATGAGACACATAC
1 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCCGATGAGACACATAC
* *
427952 TTGATCCTTGGCATATATATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
*
427990 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCCGGTGAGACACATAC
1 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCCGATGAGACACATAC
*
428055 TTGATCCCTAGTATACT-TATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATA-TATATATGATTCTTAAGGAATGA
428093 TATGTGGTCCTTAT-GGACAT
1 TATGTGGTCCTT-TGGGACAT
428113 TATTATATGG
Statistics
Matches: 115, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
103 113 0.98
104 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCCGATGAGACACATAC
TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
Found at i:428154 original size:23 final size:23
Alignment explanation
Indices: 428121--428183 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
428111 ATTATTATAT
*
428121 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
428144 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
428167 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
428184 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:430521 original size:20 final size:20
Alignment explanation
Indices: 430461--430531 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
430451 TGGCCCATTA
* *
430461 ACTTTGACC-TGGCCTGTTG
1 ACTTTGACCTTTGACTGTTG
* *
430480 ACTTTTACCTGAGTTGATTGTTG
1 ACTTTGACCT---TTGACTGTTG
*
430503 ACTTTGACCTTTGACTGTTA
1 ACTTTGACCTTTGACTGTTG
*
430523 ACTTCGACC
1 ACTTTGACC
430532 CAAAAAGTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
19 8 0.20
20 16 0.40
23 16 0.40
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (20 bp):
ACTTTGACCTTTGACTGTTG
Found at i:435714 original size:30 final size:30
Alignment explanation
Indices: 435678--435759 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
435668 TTTGTACACG
435678 GTTACTCCTACTTATAATGTAACCGTTAAC
1 GTTACTCCTACTTATAATGTAACCGTTAAC
* *
435708 GTTACTCCTACTTGTAATGTAACTGTTAAC
1 GTTACTCCTACTTATAATGTAACCGTTAAC
* * *
435738 TTTACTCTTACTTATAAAGTAA
1 GTTACTCCTACTTATAATGTAA
435760 TCTTTTCGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (30 bp):
GTTACTCCTACTTATAATGTAACCGTTAAC
Found at i:435954 original size:54 final size:54
Alignment explanation
Indices: 435772--436254 Score: 388
Period size: 54 Copynumber: 8.9 Consensus size: 54
435762 TTTTCGCATC
* * * * *
435772 CGTTAACATTACTCCTACTTATAAGGTAATCGGTTAAAAATAACAAGACACAATA
1 CGTTAACGTTACTCCTACTTATAAGGTAACCGGTAAAAAATAACAAGGCATAA-A
* * *
435827 -GTTAACGTTACTCCTACTTATAAGGTAACCGGTAAAAACAAAACAAGGCGTAAC
1 CGTTAACGTTACTCCTACTTATAAGGTAACCGGTAAAAA-ATAACAAGGCATAAA
* *
435881 CGTAAACGTTACTCCTACTTATAAGGTAACCAGTAAAAAATAACAAGGCATAAA
1 CGTTAACGTTACTCCTACTTATAAGGTAACCGGTAAAAAATAACAAGGCATAAA
* * * * * * * * ** *
435935 TGTTAATGTTAATCCTACTTAAAAGGTAACCGATAAAAAACAAAAAAAAGACGCAAC
1 CGTTAACGTTACTCCTACTTATAAGGTAACCGGT--AAAA-AATAACAAGGCATAAA
* * * * *
435992 CGTAAACGTTACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGGC-GAAG
1 CGTTAACGTTACTCCTACTTATAAGGTAACCGGTAAAAAATAACAAGGCATAAA
* * * *
436045 CCTATAACATTACTCCTACTTATAAGGTAACCGGT---AAA-AA-AAGGCACAAC
1 CGT-TAACGTTACTCCTACTTATAAGGTAACCGGTAAAAAATAACAAGGCATAAA
* * * * * * *
436095 CGTAAACGTTACTCCTACTTATAAGGTAACTGGTTAGAAATAAAAAGTC-GAAA
1 CGTTAACGTTACTCCTACTTATAAGGTAACCGGTAAAAAATAACAAGGCATAAA
* * * * * *
436148 CCTATAATGTTACTCCTACTTATAAGGTAACTGGTAAAAAATAAAATAAGGCACAAC
1 CGT-TAACGTTACTCCTACTTATAAGGTAACCGGTAAAAAAT--AACAAGGCATAAA
* * * * * *
436205 CGTAAACGTTACTCATTCTTTTAAGGTAACTGGTTAAAAATAACAAGGCA
1 CGTTAACGTTACTCCTACTTATAAGGTAACCGGTAAAAAATAACAAGGCA
436255 CAATCTATGT
Statistics
Matches: 343, Mismatches: 69, Indels: 33
0.77 0.16 0.07
Matches are distributed among these distances:
49 33 0.10
50 6 0.02
51 3 0.01
52 3 0.01
53 10 0.03
54 156 0.45
55 49 0.14
56 42 0.12
57 41 0.12
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.24
Consensus pattern (54 bp):
CGTTAACGTTACTCCTACTTATAAGGTAACCGGTAAAAAATAACAAGGCATAAA
Found at i:436065 original size:220 final size:213
Alignment explanation
Indices: 435766--436257 Score: 583
Period size: 214 Copynumber: 2.3 Consensus size: 213
435756 GTAATCTTTT
* * * * * * *
435766 CGCATCCGTTAACATTACTCCTACTTATAAGGTAATCGGTTAAAAATAACAAGACACAATAGTTA
1 CGCAACCGTAAACGTTACTCCTACTTATAAGGTAACCGGTTAAAAATAACAAGGCACAAGACTTA
* **
435831 ACGTTACTCCTACTTATAAGGTAACCGGTAAAAACAAAACAAGGCGTAACCGTAAACGTTACTCC
66 ACATTACTCCTACTTATAAGGTAACCGGT----A-AAAA-AAGGCACAACCGTAAACGTTACTCC
* * **
435896 TACTTATAAGGTAACCAGTAAAAAATAACAAGGCATAAATGT-TAATGTTAATCCTACTTAAAAG
125 TACTTATAAGGTAACCAGTAAAAAATAAAAAGGC-GAAACCTATAATGTTAATCCTACTTAAAAG
435960 GTAACCGATAAAAAACAAAAAAAAGA
189 GTAACCGATAAAAAA-AAAAAAAAGA
* * *
435986 CGCAACCGTAAACGTTACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGGC-GAAGCCTAT
1 CGCAACCGTAAACGTTACTCCTACTTATAAGGTAACCGGTTAAAAATAACAAGGCACAAGACT-T
436050 AACATTACTCCTACTTATAAGGTAACCGGTAAAAAAAGGCACAACCGTAAACGTTACTCCTACTT
65 AACATTACTCCTACTTATAAGGTAACCGGTAAAAAAAGGCACAACCGTAAACGTTACTCCTACTT
** * * * * * *
436115 ATAAGGTAACTGGTTAGAAATAAAAAGTCGAAACCTATAATGTTACTCCTACTTATAAGGTAACT
130 ATAAGGTAACCAGTAAAAAATAAAAAGGCGAAACCTATAATGTTAATCCTACTTAAAAGGTAACC
* * * *
436180 GGTAAAAAATAAAATAAGG
195 GATAAAAAAAAAAAAAAGA
* * * * *
436199 CACAACCGTAAACGTTACTCATTCTTTTAAGGTAACTGGTTAAAAATAACAAGGCACAA
1 CGCAACCGTAAACGTTACTCCTACTTATAAGGTAACCGGTTAAAAATAACAAGGCACAA
436258 TCTATGTTAC
Statistics
Matches: 233, Mismatches: 36, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
213 60 0.26
214 86 0.37
215 4 0.02
216 1 0.00
219 3 0.01
220 79 0.34
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (213 bp):
CGCAACCGTAAACGTTACTCCTACTTATAAGGTAACCGGTTAAAAATAACAAGGCACAAGACTTA
ACATTACTCCTACTTATAAGGTAACCGGTAAAAAAAGGCACAACCGTAAACGTTACTCCTACTTA
TAAGGTAACCAGTAAAAAATAAAAAGGCGAAACCTATAATGTTAATCCTACTTAAAAGGTAACCG
ATAAAAAAAAAAAAAAGA
Found at i:436161 original size:103 final size:104
Alignment explanation
Indices: 435771--436253 Score: 411
Period size: 103 Copynumber: 4.5 Consensus size: 104
435761 CTTTTCGCAT
* * * *
435771 CCGTTAACATTACTCCTACTTATAAGGTAA-TCGGTTAAAAATAACAAGAC-ACAA--TAGTTAA
1 CCGTAAACGTTACTCCTACTTATAAGGTAACT-GGTTAAAAATAAAAAGGCGA-AACCTA--TAA
* **
435832 CGTTACTCCTACTTATAAGGTAACCGGTAAAAACAAAACAAGGCGTAA
62 CATTACTCCTACTTATAAGGTAACCGGT---AA-AAAA-AAGGCACAA
** * * * ** **
435880 CCGTAAACGTTACTCCTACTTATAAGGTAACCAGTAAAAAATAACAAGGCATAAATGT-TAATGT
1 CCGTAAACGTTACTCCTACTTATAAGGTAACTGGTTAAAAATAAAAAGGC-GAAACCTATAACAT
* * * * *
435944 TAATCCTACTTAAAAGGTAACCGATAAAAAACAAAAAAAAGACGCAA
65 TACTCCTACTTATAAGGTAACCGGT-------AAAAAAAAGGCACAA
** * *
435991 CCGTAAACGTTACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGGCGAAGCCTATAACATT
1 CCGTAAACGTTACTCCTACTTATAAGGTAACTGGTTAAAAATAAAAAGGCGAAACCTATAACATT
436056 ACTCCTACTTATAAGGTAACCGGT-AAAAAAAGGCACAA
66 ACTCCTACTTATAAGGTAACCGGTAAAAAAAAGGCACAA
* * **
436094 CCGTAAACGTTACTCCTACTTATAAGGTAACTGGTTAGAAATAAAAAGTCGAAACCTATAATGTT
1 CCGTAAACGTTACTCCTACTTATAAGGTAACTGGTTAAAAATAAAAAGGCGAAACCTATAACATT
*
436159 ACTCCTACTTATAAGGTAACTGGTAAAAAATAAAATAAGGCACAA
66 ACTCCTACTTATAAGGTAACCGGT----AA-AAAA-AAGGCACAA
* * * *
436204 CCGTAAACGTTACTCATTCTTTTAAGGTAACTGGTTAAAAATAACAAGGC
1 CCGTAAACGTTACTCCTACTTATAAGGTAACTGGTTAAAAATAAAAAGGC
436254 ACAATCTATG
Statistics
Matches: 317, Mismatches: 40, Indels: 33
0.81 0.10 0.08
Matches are distributed among these distances:
103 92 0.29
108 1 0.00
109 74 0.23
110 58 0.18
111 83 0.26
112 5 0.02
113 4 0.01
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.24
Consensus pattern (104 bp):
CCGTAAACGTTACTCCTACTTATAAGGTAACTGGTTAAAAATAAAAAGGCGAAACCTATAACATT
ACTCCTACTTATAAGGTAACCGGTAAAAAAAAGGCACAA
Found at i:436668 original size:3 final size:3
Alignment explanation
Indices: 436660--436686 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
436650 ATTGAGATAA
436660 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
436687 TTGAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:438045 original size:7 final size:7
Alignment explanation
Indices: 438033--438127 Score: 190
Period size: 7 Copynumber: 13.6 Consensus size: 7
438023 AAACTACCTT
438033 CTTCAAG
1 CTTCAAG
438040 CTTCAAG
1 CTTCAAG
438047 CTTCAAG
1 CTTCAAG
438054 CTTCAAG
1 CTTCAAG
438061 CTTCAAG
1 CTTCAAG
438068 CTTCAAG
1 CTTCAAG
438075 CTTCAAG
1 CTTCAAG
438082 CTTCAAG
1 CTTCAAG
438089 CTTCAAG
1 CTTCAAG
438096 CTTCAAG
1 CTTCAAG
438103 CTTCAAG
1 CTTCAAG
438110 CTTCAAG
1 CTTCAAG
438117 CTTCAAG
1 CTTCAAG
438124 CTTC
1 CTTC
438128 TGCAGGGGCT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 88 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.29
Consensus pattern (7 bp):
CTTCAAG
Found at i:438938 original size:60 final size:62
Alignment explanation
Indices: 438803--438949 Score: 164
Period size: 60 Copynumber: 2.4 Consensus size: 62
438793 AACATATTAA
** *
438803 ATAGTCGGGTGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGAAACACACTCT
1 ATAGTCGGGAAACCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAGAAACACACTCT
* * *
438865 A-A-TC--AAAGGACCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAGCATCA-AC-CT
1 ATAGTCGGGAA--ACCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAGAAACACACTCT
438923 ATAGTCGGGAAACCATTTGTGT-ACTTT
1 ATAGTCGGGAAACCATTT-TGTAACTTT
438950 ACCCAAGTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
58 3 0.04
59 3 0.04
60 58 0.82
61 4 0.06
62 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (62 bp):
ATAGTCGGGAAACCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAGAAACACACTCT
Found at i:439380 original size:30 final size:30
Alignment explanation
Indices: 439344--439405 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
439334 AATGCTAGGT
439344 AAAAGCATCATTGAAGACATTTGCAGATAA
1 AAAAGCATCATTGAAGACATTTGCAGATAA
439374 AAAAGCATCATTGAAGACATTTGCAGATAA
1 AAAAGCATCATTGAAGACATTTGCAGATAA
439404 AA
1 AA
439406 TTAACCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (30 bp):
AAAAGCATCATTGAAGACATTTGCAGATAA
Found at i:441905 original size:17 final size:17
Alignment explanation
Indices: 441878--441916 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
441868 AGTTTACAAT
441878 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
441894 TAATTATAAATAATATC
1 TAATTATAAATAATATC
441911 TAATTA
1 TAATTA
441917 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Done.