Multiple sequence alignment - TraesCS1D01G376800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G376800 chr1D 100.000 2804 0 0 1 2804 453212139 453209336 0.000000e+00 5179
1 TraesCS1D01G376800 chr1D 85.823 656 57 19 1001 1650 453199621 453200246 0.000000e+00 664
2 TraesCS1D01G376800 chr1D 85.061 656 59 21 1001 1650 453181698 453182320 1.420000e-177 632
3 TraesCS1D01G376800 chr1D 84.441 662 61 22 1001 1654 453134659 453135286 5.130000e-172 614
4 TraesCS1D01G376800 chr1A 89.147 2414 99 68 429 2778 547909033 547906719 0.000000e+00 2856
5 TraesCS1D01G376800 chr1A 85.312 674 53 32 995 1659 547886727 547887363 0.000000e+00 654
6 TraesCS1D01G376800 chr1A 84.629 566 41 22 1095 1650 547863992 547864521 3.200000e-144 521
7 TraesCS1D01G376800 chr1A 83.908 261 19 13 247 490 547914448 547914194 7.810000e-56 228
8 TraesCS1D01G376800 chr1B 84.025 2529 202 99 288 2733 623690131 623687722 0.000000e+00 2246
9 TraesCS1D01G376800 chr1B 83.333 660 72 18 995 1650 623672554 623673179 2.420000e-160 575
10 TraesCS1D01G376800 chr1B 86.004 543 52 15 1123 1650 623679684 623680217 6.780000e-156 560


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G376800 chr1D 453209336 453212139 2803 True 5179 5179 100.000 1 2804 1 chr1D.!!$R1 2803
1 TraesCS1D01G376800 chr1D 453199621 453200246 625 False 664 664 85.823 1001 1650 1 chr1D.!!$F3 649
2 TraesCS1D01G376800 chr1D 453181698 453182320 622 False 632 632 85.061 1001 1650 1 chr1D.!!$F2 649
3 TraesCS1D01G376800 chr1D 453134659 453135286 627 False 614 614 84.441 1001 1654 1 chr1D.!!$F1 653
4 TraesCS1D01G376800 chr1A 547906719 547909033 2314 True 2856 2856 89.147 429 2778 1 chr1A.!!$R1 2349
5 TraesCS1D01G376800 chr1A 547886727 547887363 636 False 654 654 85.312 995 1659 1 chr1A.!!$F2 664
6 TraesCS1D01G376800 chr1A 547863992 547864521 529 False 521 521 84.629 1095 1650 1 chr1A.!!$F1 555
7 TraesCS1D01G376800 chr1B 623687722 623690131 2409 True 2246 2246 84.025 288 2733 1 chr1B.!!$R1 2445
8 TraesCS1D01G376800 chr1B 623672554 623673179 625 False 575 575 83.333 995 1650 1 chr1B.!!$F1 655
9 TraesCS1D01G376800 chr1B 623679684 623680217 533 False 560 560 86.004 1123 1650 1 chr1B.!!$F2 527

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
988 1032 0.104855 AGAACACAAGAGCACGCAGA 59.895 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2622 2767 0.170561 TAGCGCAGAGAAAGGACGAC 59.829 55.0 11.47 0.0 0.0 4.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.049708 AGTGTGCGGATGATCATATGG 57.950 47.619 8.54 2.01 0.00 2.74
22 23 2.369860 AGTGTGCGGATGATCATATGGT 59.630 45.455 8.54 0.00 0.00 3.55
23 24 2.738846 GTGTGCGGATGATCATATGGTC 59.261 50.000 8.54 9.17 0.00 4.02
24 25 2.289631 TGTGCGGATGATCATATGGTCC 60.290 50.000 13.46 5.15 0.00 4.46
25 26 1.977129 TGCGGATGATCATATGGTCCA 59.023 47.619 13.46 0.00 0.00 4.02
26 27 2.371510 TGCGGATGATCATATGGTCCAA 59.628 45.455 13.46 0.00 0.00 3.53
27 28 2.744202 GCGGATGATCATATGGTCCAAC 59.256 50.000 13.46 4.84 0.00 3.77
28 29 3.557898 GCGGATGATCATATGGTCCAACT 60.558 47.826 13.46 0.00 0.00 3.16
29 30 4.645535 CGGATGATCATATGGTCCAACTT 58.354 43.478 13.46 0.00 0.00 2.66
30 31 5.065914 CGGATGATCATATGGTCCAACTTT 58.934 41.667 13.46 0.00 0.00 2.66
31 32 6.230472 CGGATGATCATATGGTCCAACTTTA 58.770 40.000 13.46 0.00 0.00 1.85
32 33 6.710295 CGGATGATCATATGGTCCAACTTTAA 59.290 38.462 13.46 0.00 0.00 1.52
33 34 7.228507 CGGATGATCATATGGTCCAACTTTAAA 59.771 37.037 13.46 0.00 0.00 1.52
34 35 9.082313 GGATGATCATATGGTCCAACTTTAAAT 57.918 33.333 13.46 0.00 0.00 1.40
36 37 8.153479 TGATCATATGGTCCAACTTTAAATCG 57.847 34.615 13.46 0.00 0.00 3.34
37 38 7.773224 TGATCATATGGTCCAACTTTAAATCGT 59.227 33.333 13.46 0.00 0.00 3.73
38 39 7.315247 TCATATGGTCCAACTTTAAATCGTG 57.685 36.000 2.13 0.00 0.00 4.35
39 40 7.106890 TCATATGGTCCAACTTTAAATCGTGA 58.893 34.615 2.13 0.00 0.00 4.35
40 41 7.608376 TCATATGGTCCAACTTTAAATCGTGAA 59.392 33.333 2.13 0.00 0.00 3.18
41 42 5.682943 TGGTCCAACTTTAAATCGTGAAG 57.317 39.130 0.00 0.00 0.00 3.02
42 43 4.517453 TGGTCCAACTTTAAATCGTGAAGG 59.483 41.667 0.00 0.00 0.00 3.46
43 44 4.758165 GGTCCAACTTTAAATCGTGAAGGA 59.242 41.667 0.00 0.00 0.00 3.36
44 45 5.414765 GGTCCAACTTTAAATCGTGAAGGAT 59.585 40.000 0.00 0.00 0.00 3.24
45 46 6.314784 GTCCAACTTTAAATCGTGAAGGATG 58.685 40.000 0.00 0.00 0.00 3.51
46 47 6.148811 GTCCAACTTTAAATCGTGAAGGATGA 59.851 38.462 0.00 0.00 0.00 2.92
47 48 6.712998 TCCAACTTTAAATCGTGAAGGATGAA 59.287 34.615 0.00 0.00 0.00 2.57
48 49 7.229707 TCCAACTTTAAATCGTGAAGGATGAAA 59.770 33.333 0.00 0.00 0.00 2.69
49 50 7.865385 CCAACTTTAAATCGTGAAGGATGAAAA 59.135 33.333 0.00 0.00 0.00 2.29
50 51 9.243637 CAACTTTAAATCGTGAAGGATGAAAAA 57.756 29.630 0.00 0.00 0.00 1.94
75 76 7.756395 AAGTCAGATGGCATAGAATAATTGG 57.244 36.000 0.00 0.00 0.00 3.16
76 77 7.083062 AGTCAGATGGCATAGAATAATTGGA 57.917 36.000 0.00 0.00 0.00 3.53
77 78 6.939163 AGTCAGATGGCATAGAATAATTGGAC 59.061 38.462 0.00 0.00 0.00 4.02
78 79 5.934043 TCAGATGGCATAGAATAATTGGACG 59.066 40.000 0.00 0.00 0.00 4.79
79 80 5.122869 CAGATGGCATAGAATAATTGGACGG 59.877 44.000 0.00 0.00 0.00 4.79
80 81 4.698201 TGGCATAGAATAATTGGACGGA 57.302 40.909 0.00 0.00 0.00 4.69
81 82 5.042463 TGGCATAGAATAATTGGACGGAA 57.958 39.130 0.00 0.00 0.00 4.30
82 83 4.819630 TGGCATAGAATAATTGGACGGAAC 59.180 41.667 0.00 0.00 0.00 3.62
83 84 4.819630 GGCATAGAATAATTGGACGGAACA 59.180 41.667 0.00 0.00 0.00 3.18
84 85 5.473504 GGCATAGAATAATTGGACGGAACAT 59.526 40.000 0.00 0.00 0.00 2.71
85 86 6.653320 GGCATAGAATAATTGGACGGAACATA 59.347 38.462 0.00 0.00 0.00 2.29
86 87 7.174253 GGCATAGAATAATTGGACGGAACATAA 59.826 37.037 0.00 0.00 0.00 1.90
87 88 8.015658 GCATAGAATAATTGGACGGAACATAAC 58.984 37.037 0.00 0.00 0.00 1.89
88 89 6.937436 AGAATAATTGGACGGAACATAACC 57.063 37.500 0.00 0.00 0.00 2.85
89 90 5.826208 AGAATAATTGGACGGAACATAACCC 59.174 40.000 0.00 0.00 0.00 4.11
97 98 3.629438 CGGAACATAACCCGTGTTTTT 57.371 42.857 0.00 0.00 39.72 1.94
129 130 9.925545 TTGGTATATACTACTACCTCAGTTCAA 57.074 33.333 12.54 1.05 38.57 2.69
130 131 9.925545 TGGTATATACTACTACCTCAGTTCAAA 57.074 33.333 12.54 0.00 38.57 2.69
138 139 9.490379 ACTACTACCTCAGTTCAAAATTAAGTG 57.510 33.333 0.00 0.00 38.80 3.16
139 140 9.490379 CTACTACCTCAGTTCAAAATTAAGTGT 57.510 33.333 0.00 0.00 38.80 3.55
140 141 8.379457 ACTACCTCAGTTCAAAATTAAGTGTC 57.621 34.615 0.00 0.00 31.59 3.67
141 142 6.300354 ACCTCAGTTCAAAATTAAGTGTCG 57.700 37.500 0.00 0.00 0.00 4.35
142 143 5.147162 CCTCAGTTCAAAATTAAGTGTCGC 58.853 41.667 0.00 0.00 0.00 5.19
143 144 5.049405 CCTCAGTTCAAAATTAAGTGTCGCT 60.049 40.000 0.00 0.00 0.00 4.93
144 145 5.747565 TCAGTTCAAAATTAAGTGTCGCTG 58.252 37.500 0.00 0.00 0.00 5.18
145 146 5.525745 TCAGTTCAAAATTAAGTGTCGCTGA 59.474 36.000 0.00 0.00 0.00 4.26
146 147 6.037720 TCAGTTCAAAATTAAGTGTCGCTGAA 59.962 34.615 0.00 0.00 0.00 3.02
147 148 6.690957 CAGTTCAAAATTAAGTGTCGCTGAAA 59.309 34.615 0.00 0.00 0.00 2.69
148 149 7.379529 CAGTTCAAAATTAAGTGTCGCTGAAAT 59.620 33.333 0.00 0.00 0.00 2.17
149 150 7.379529 AGTTCAAAATTAAGTGTCGCTGAAATG 59.620 33.333 0.00 0.00 0.00 2.32
150 151 6.964908 TCAAAATTAAGTGTCGCTGAAATGA 58.035 32.000 0.00 0.00 0.00 2.57
151 152 7.077605 TCAAAATTAAGTGTCGCTGAAATGAG 58.922 34.615 0.00 0.00 0.00 2.90
152 153 6.560253 AAATTAAGTGTCGCTGAAATGAGT 57.440 33.333 0.00 0.00 0.00 3.41
153 154 4.990543 TTAAGTGTCGCTGAAATGAGTG 57.009 40.909 0.00 0.00 0.00 3.51
154 155 2.533266 AGTGTCGCTGAAATGAGTGT 57.467 45.000 0.00 0.00 0.00 3.55
155 156 3.660501 AGTGTCGCTGAAATGAGTGTA 57.339 42.857 0.00 0.00 0.00 2.90
156 157 4.193826 AGTGTCGCTGAAATGAGTGTAT 57.806 40.909 0.00 0.00 0.00 2.29
157 158 4.177026 AGTGTCGCTGAAATGAGTGTATC 58.823 43.478 0.00 0.00 0.00 2.24
158 159 4.081972 AGTGTCGCTGAAATGAGTGTATCT 60.082 41.667 0.00 0.00 0.00 1.98
159 160 5.125578 AGTGTCGCTGAAATGAGTGTATCTA 59.874 40.000 0.00 0.00 0.00 1.98
160 161 5.457148 GTGTCGCTGAAATGAGTGTATCTAG 59.543 44.000 0.00 0.00 0.00 2.43
161 162 5.357032 TGTCGCTGAAATGAGTGTATCTAGA 59.643 40.000 0.00 0.00 0.00 2.43
162 163 6.127730 TGTCGCTGAAATGAGTGTATCTAGAA 60.128 38.462 0.00 0.00 0.00 2.10
163 164 6.416455 GTCGCTGAAATGAGTGTATCTAGAAG 59.584 42.308 0.00 0.00 0.00 2.85
164 165 6.095580 TCGCTGAAATGAGTGTATCTAGAAGT 59.904 38.462 0.00 0.00 0.00 3.01
165 166 6.416455 CGCTGAAATGAGTGTATCTAGAAGTC 59.584 42.308 0.00 0.00 0.00 3.01
166 167 7.261325 GCTGAAATGAGTGTATCTAGAAGTCA 58.739 38.462 0.00 0.00 0.00 3.41
167 168 7.761704 GCTGAAATGAGTGTATCTAGAAGTCAA 59.238 37.037 0.00 0.00 0.00 3.18
168 169 8.988064 TGAAATGAGTGTATCTAGAAGTCAAC 57.012 34.615 0.00 0.00 0.00 3.18
169 170 8.807118 TGAAATGAGTGTATCTAGAAGTCAACT 58.193 33.333 0.00 0.00 0.00 3.16
170 171 9.296400 GAAATGAGTGTATCTAGAAGTCAACTC 57.704 37.037 0.00 6.95 0.00 3.01
171 172 7.946381 ATGAGTGTATCTAGAAGTCAACTCA 57.054 36.000 20.18 20.18 35.42 3.41
172 173 7.946381 TGAGTGTATCTAGAAGTCAACTCAT 57.054 36.000 16.69 0.00 0.00 2.90
173 174 8.354711 TGAGTGTATCTAGAAGTCAACTCATT 57.645 34.615 16.69 0.00 0.00 2.57
174 175 8.807118 TGAGTGTATCTAGAAGTCAACTCATTT 58.193 33.333 16.69 0.00 0.00 2.32
175 176 9.646427 GAGTGTATCTAGAAGTCAACTCATTTT 57.354 33.333 14.55 0.00 0.00 1.82
176 177 9.429359 AGTGTATCTAGAAGTCAACTCATTTTG 57.571 33.333 0.00 0.00 0.00 2.44
177 178 9.424319 GTGTATCTAGAAGTCAACTCATTTTGA 57.576 33.333 0.00 0.00 32.94 2.69
178 179 9.996554 TGTATCTAGAAGTCAACTCATTTTGAA 57.003 29.630 0.00 0.00 37.24 2.69
181 182 8.964476 TCTAGAAGTCAACTCATTTTGAAGTT 57.036 30.769 0.00 0.00 37.24 2.66
182 183 9.396022 TCTAGAAGTCAACTCATTTTGAAGTTT 57.604 29.630 0.00 0.00 37.24 2.66
183 184 9.657121 CTAGAAGTCAACTCATTTTGAAGTTTC 57.343 33.333 0.00 0.00 37.24 2.78
184 185 7.189512 AGAAGTCAACTCATTTTGAAGTTTCG 58.810 34.615 0.00 0.00 37.24 3.46
185 186 5.273944 AGTCAACTCATTTTGAAGTTTCGC 58.726 37.500 0.00 0.00 37.24 4.70
186 187 5.034152 GTCAACTCATTTTGAAGTTTCGCA 58.966 37.500 0.00 0.00 37.24 5.10
187 188 5.172053 GTCAACTCATTTTGAAGTTTCGCAG 59.828 40.000 0.00 0.00 37.24 5.18
188 189 5.065859 TCAACTCATTTTGAAGTTTCGCAGA 59.934 36.000 0.00 0.00 32.42 4.26
189 190 5.499139 ACTCATTTTGAAGTTTCGCAGAA 57.501 34.783 0.00 0.00 45.90 3.02
190 191 5.890334 ACTCATTTTGAAGTTTCGCAGAAA 58.110 33.333 0.55 0.55 45.90 2.52
191 192 6.507023 ACTCATTTTGAAGTTTCGCAGAAAT 58.493 32.000 6.93 0.00 45.90 2.17
192 193 6.418819 ACTCATTTTGAAGTTTCGCAGAAATG 59.581 34.615 6.93 0.00 45.90 2.32
193 194 6.502652 TCATTTTGAAGTTTCGCAGAAATGA 58.497 32.000 14.45 14.45 45.90 2.57
194 195 6.638063 TCATTTTGAAGTTTCGCAGAAATGAG 59.362 34.615 14.45 0.00 45.90 2.90
195 196 5.499139 TTTGAAGTTTCGCAGAAATGAGT 57.501 34.783 6.93 0.00 45.90 3.41
196 197 6.612247 TTTGAAGTTTCGCAGAAATGAGTA 57.388 33.333 6.93 0.00 45.90 2.59
197 198 6.801539 TTGAAGTTTCGCAGAAATGAGTAT 57.198 33.333 6.93 0.00 45.90 2.12
198 199 7.899178 TTGAAGTTTCGCAGAAATGAGTATA 57.101 32.000 6.93 0.00 45.90 1.47
199 200 8.492673 TTGAAGTTTCGCAGAAATGAGTATAT 57.507 30.769 6.93 0.00 45.90 0.86
200 201 7.909267 TGAAGTTTCGCAGAAATGAGTATATG 58.091 34.615 6.93 0.00 45.90 1.78
201 202 7.549134 TGAAGTTTCGCAGAAATGAGTATATGT 59.451 33.333 6.93 0.00 45.90 2.29
202 203 8.942338 AAGTTTCGCAGAAATGAGTATATGTA 57.058 30.769 6.93 0.00 45.90 2.29
203 204 8.581057 AGTTTCGCAGAAATGAGTATATGTAG 57.419 34.615 6.93 0.00 45.90 2.74
204 205 8.414003 AGTTTCGCAGAAATGAGTATATGTAGA 58.586 33.333 6.93 0.00 45.90 2.59
205 206 9.031360 GTTTCGCAGAAATGAGTATATGTAGAA 57.969 33.333 6.93 0.00 45.90 2.10
206 207 8.803201 TTCGCAGAAATGAGTATATGTAGAAG 57.197 34.615 0.00 0.00 45.90 2.85
207 208 7.941919 TCGCAGAAATGAGTATATGTAGAAGT 58.058 34.615 0.00 0.00 0.00 3.01
208 209 8.076781 TCGCAGAAATGAGTATATGTAGAAGTC 58.923 37.037 0.00 0.00 0.00 3.01
209 210 7.862873 CGCAGAAATGAGTATATGTAGAAGTCA 59.137 37.037 0.00 0.00 0.00 3.41
210 211 9.534565 GCAGAAATGAGTATATGTAGAAGTCAA 57.465 33.333 0.00 0.00 0.00 3.18
230 231 2.393271 CTCATTTTGAGCGAGGGAGT 57.607 50.000 0.00 0.00 37.72 3.85
231 232 3.526931 CTCATTTTGAGCGAGGGAGTA 57.473 47.619 0.00 0.00 37.72 2.59
232 233 3.452474 CTCATTTTGAGCGAGGGAGTAG 58.548 50.000 0.00 0.00 37.72 2.57
233 234 3.096852 TCATTTTGAGCGAGGGAGTAGA 58.903 45.455 0.00 0.00 0.00 2.59
234 235 3.706594 TCATTTTGAGCGAGGGAGTAGAT 59.293 43.478 0.00 0.00 0.00 1.98
235 236 4.893524 TCATTTTGAGCGAGGGAGTAGATA 59.106 41.667 0.00 0.00 0.00 1.98
236 237 5.362717 TCATTTTGAGCGAGGGAGTAGATAA 59.637 40.000 0.00 0.00 0.00 1.75
237 238 5.871396 TTTTGAGCGAGGGAGTAGATAAT 57.129 39.130 0.00 0.00 0.00 1.28
238 239 6.971726 TTTTGAGCGAGGGAGTAGATAATA 57.028 37.500 0.00 0.00 0.00 0.98
239 240 6.971726 TTTGAGCGAGGGAGTAGATAATAA 57.028 37.500 0.00 0.00 0.00 1.40
240 241 6.576662 TTGAGCGAGGGAGTAGATAATAAG 57.423 41.667 0.00 0.00 0.00 1.73
241 242 5.632118 TGAGCGAGGGAGTAGATAATAAGT 58.368 41.667 0.00 0.00 0.00 2.24
242 243 5.473846 TGAGCGAGGGAGTAGATAATAAGTG 59.526 44.000 0.00 0.00 0.00 3.16
243 244 5.632118 AGCGAGGGAGTAGATAATAAGTGA 58.368 41.667 0.00 0.00 0.00 3.41
244 245 6.249951 AGCGAGGGAGTAGATAATAAGTGAT 58.750 40.000 0.00 0.00 0.00 3.06
245 246 6.722129 AGCGAGGGAGTAGATAATAAGTGATT 59.278 38.462 0.00 0.00 0.00 2.57
246 247 7.889073 AGCGAGGGAGTAGATAATAAGTGATTA 59.111 37.037 0.00 0.00 34.46 1.75
247 248 8.688151 GCGAGGGAGTAGATAATAAGTGATTAT 58.312 37.037 0.00 0.00 42.41 1.28
259 260 9.712305 ATAATAAGTGATTATCAACTTCCGGAG 57.288 33.333 3.34 1.34 36.16 4.63
260 261 5.677319 AAGTGATTATCAACTTCCGGAGA 57.323 39.130 3.34 0.00 0.00 3.71
261 262 5.269505 AGTGATTATCAACTTCCGGAGAG 57.730 43.478 3.34 8.16 0.00 3.20
262 263 4.956700 AGTGATTATCAACTTCCGGAGAGA 59.043 41.667 17.18 9.46 0.00 3.10
263 264 5.422331 AGTGATTATCAACTTCCGGAGAGAA 59.578 40.000 17.18 10.05 0.00 2.87
270 271 1.983972 CTTCCGGAGAGAAGTCAACG 58.016 55.000 3.34 0.00 38.76 4.10
271 272 0.601558 TTCCGGAGAGAAGTCAACGG 59.398 55.000 3.34 0.00 42.45 4.44
272 273 1.446272 CCGGAGAGAAGTCAACGGC 60.446 63.158 0.00 0.00 37.40 5.68
273 274 1.289066 CGGAGAGAAGTCAACGGCA 59.711 57.895 0.00 0.00 0.00 5.69
274 275 0.734253 CGGAGAGAAGTCAACGGCAG 60.734 60.000 0.00 0.00 0.00 4.85
275 276 0.603569 GGAGAGAAGTCAACGGCAGA 59.396 55.000 0.00 0.00 0.00 4.26
276 277 1.000955 GGAGAGAAGTCAACGGCAGAA 59.999 52.381 0.00 0.00 0.00 3.02
277 278 2.548067 GGAGAGAAGTCAACGGCAGAAA 60.548 50.000 0.00 0.00 0.00 2.52
278 279 3.131396 GAGAGAAGTCAACGGCAGAAAA 58.869 45.455 0.00 0.00 0.00 2.29
279 280 3.744660 AGAGAAGTCAACGGCAGAAAAT 58.255 40.909 0.00 0.00 0.00 1.82
280 281 3.499918 AGAGAAGTCAACGGCAGAAAATG 59.500 43.478 0.00 0.00 0.00 2.32
281 282 3.476552 AGAAGTCAACGGCAGAAAATGA 58.523 40.909 0.00 0.00 0.00 2.57
282 283 3.882888 AGAAGTCAACGGCAGAAAATGAA 59.117 39.130 0.00 0.00 0.00 2.57
283 284 4.338118 AGAAGTCAACGGCAGAAAATGAAA 59.662 37.500 0.00 0.00 0.00 2.69
284 285 4.853924 AGTCAACGGCAGAAAATGAAAT 57.146 36.364 0.00 0.00 0.00 2.17
285 286 5.200368 AGTCAACGGCAGAAAATGAAATT 57.800 34.783 0.00 0.00 38.98 1.82
286 287 5.222631 AGTCAACGGCAGAAAATGAAATTC 58.777 37.500 0.00 0.00 33.67 2.17
308 309 7.865706 TTCAAAGCCATCTAGAATAACTTCC 57.134 36.000 0.00 0.00 31.27 3.46
310 311 4.984146 AGCCATCTAGAATAACTTCCCC 57.016 45.455 0.00 0.00 31.27 4.81
312 313 3.071167 GCCATCTAGAATAACTTCCCCGT 59.929 47.826 0.00 0.00 31.27 5.28
313 314 4.799917 GCCATCTAGAATAACTTCCCCGTC 60.800 50.000 0.00 0.00 31.27 4.79
314 315 4.344102 CCATCTAGAATAACTTCCCCGTCA 59.656 45.833 0.00 0.00 31.27 4.35
315 316 5.509840 CCATCTAGAATAACTTCCCCGTCAG 60.510 48.000 0.00 0.00 31.27 3.51
316 317 4.863548 TCTAGAATAACTTCCCCGTCAGA 58.136 43.478 0.00 0.00 31.27 3.27
317 318 5.266788 TCTAGAATAACTTCCCCGTCAGAA 58.733 41.667 0.00 0.00 31.27 3.02
360 368 0.466543 AACGGTACCACACTTGCAGA 59.533 50.000 13.54 0.00 0.00 4.26
380 388 0.649993 CAAACGCCAACAAAACCAGC 59.350 50.000 0.00 0.00 0.00 4.85
390 398 0.385974 CAAAACCAGCTACTGTGCGC 60.386 55.000 0.00 0.00 38.13 6.09
391 399 1.515521 AAAACCAGCTACTGTGCGCC 61.516 55.000 4.18 0.00 38.13 6.53
503 511 1.585297 TTTCAACGGAAAGACGGACC 58.415 50.000 0.00 0.00 38.07 4.46
504 512 0.754472 TTCAACGGAAAGACGGACCT 59.246 50.000 0.00 0.00 38.39 3.85
505 513 0.316204 TCAACGGAAAGACGGACCTC 59.684 55.000 0.00 0.00 38.39 3.85
507 515 1.117142 AACGGAAAGACGGACCTCCA 61.117 55.000 0.00 0.00 38.39 3.86
509 517 1.295746 GGAAAGACGGACCTCCACC 59.704 63.158 0.00 0.00 35.14 4.61
512 520 2.976284 AAAGACGGACCTCCACCCCA 62.976 60.000 0.00 0.00 35.14 4.96
514 522 4.250170 ACGGACCTCCACCCCACT 62.250 66.667 0.00 0.00 35.14 4.00
515 523 3.391382 CGGACCTCCACCCCACTC 61.391 72.222 0.00 0.00 35.14 3.51
516 524 3.009714 GGACCTCCACCCCACTCC 61.010 72.222 0.00 0.00 35.64 3.85
518 526 3.864983 GACCTCCACCCCACTCCCA 62.865 68.421 0.00 0.00 0.00 4.37
520 528 2.203998 CTCCACCCCACTCCCAGT 60.204 66.667 0.00 0.00 0.00 4.00
527 553 2.294078 CCCACTCCCAGTCTCCCAC 61.294 68.421 0.00 0.00 0.00 4.61
634 677 3.054166 GGCAACACCGGAAATAAACAAC 58.946 45.455 9.46 0.00 0.00 3.32
718 761 1.087771 CGTTAGCCTTAACCAGCGGG 61.088 60.000 0.00 0.00 36.60 6.13
729 772 1.584495 CCAGCGGGTTTGTTTAGCC 59.416 57.895 0.00 0.00 0.00 3.93
733 776 4.090723 GGGTTTGTTTAGCCGGCT 57.909 55.556 34.85 34.85 0.00 5.52
774 817 2.095604 TCCAACAAAAAGGGAAGGGG 57.904 50.000 0.00 0.00 0.00 4.79
781 825 2.231716 AAAAGGGAAGGGGATTTCCG 57.768 50.000 0.00 0.00 46.19 4.30
919 963 0.916086 AACCACCTGAACTCACCACA 59.084 50.000 0.00 0.00 0.00 4.17
922 966 1.691976 CCACCTGAACTCACCACACTA 59.308 52.381 0.00 0.00 0.00 2.74
928 972 2.224042 TGAACTCACCACACTACAGCAG 60.224 50.000 0.00 0.00 0.00 4.24
946 990 2.411904 CAGCTCTCAACCTCAAGTCAC 58.588 52.381 0.00 0.00 0.00 3.67
959 1003 2.958578 AAGTCACCGCCACCACCAAG 62.959 60.000 0.00 0.00 0.00 3.61
977 1021 3.192422 CCAAGAACACCACAAGAACACAA 59.808 43.478 0.00 0.00 0.00 3.33
978 1022 4.414852 CAAGAACACCACAAGAACACAAG 58.585 43.478 0.00 0.00 0.00 3.16
979 1023 3.950397 AGAACACCACAAGAACACAAGA 58.050 40.909 0.00 0.00 0.00 3.02
980 1024 3.941483 AGAACACCACAAGAACACAAGAG 59.059 43.478 0.00 0.00 0.00 2.85
981 1025 2.017049 ACACCACAAGAACACAAGAGC 58.983 47.619 0.00 0.00 0.00 4.09
982 1026 2.016318 CACCACAAGAACACAAGAGCA 58.984 47.619 0.00 0.00 0.00 4.26
983 1027 2.017049 ACCACAAGAACACAAGAGCAC 58.983 47.619 0.00 0.00 0.00 4.40
984 1028 1.003545 CCACAAGAACACAAGAGCACG 60.004 52.381 0.00 0.00 0.00 5.34
985 1029 0.657840 ACAAGAACACAAGAGCACGC 59.342 50.000 0.00 0.00 0.00 5.34
986 1030 0.657312 CAAGAACACAAGAGCACGCA 59.343 50.000 0.00 0.00 0.00 5.24
987 1031 0.940126 AAGAACACAAGAGCACGCAG 59.060 50.000 0.00 0.00 0.00 5.18
988 1032 0.104855 AGAACACAAGAGCACGCAGA 59.895 50.000 0.00 0.00 0.00 4.26
989 1033 0.510359 GAACACAAGAGCACGCAGAG 59.490 55.000 0.00 0.00 0.00 3.35
990 1034 0.104855 AACACAAGAGCACGCAGAGA 59.895 50.000 0.00 0.00 0.00 3.10
991 1035 0.598680 ACACAAGAGCACGCAGAGAC 60.599 55.000 0.00 0.00 0.00 3.36
992 1036 1.005630 ACAAGAGCACGCAGAGACC 60.006 57.895 0.00 0.00 0.00 3.85
993 1037 2.091112 CAAGAGCACGCAGAGACCG 61.091 63.158 0.00 0.00 0.00 4.79
994 1038 2.268802 AAGAGCACGCAGAGACCGA 61.269 57.895 0.00 0.00 0.00 4.69
995 1039 2.479412 AAGAGCACGCAGAGACCGAC 62.479 60.000 0.00 0.00 0.00 4.79
996 1040 3.268965 GAGCACGCAGAGACCGACA 62.269 63.158 0.00 0.00 0.00 4.35
997 1041 3.106407 GCACGCAGAGACCGACAC 61.106 66.667 0.00 0.00 0.00 3.67
998 1042 2.801162 CACGCAGAGACCGACACG 60.801 66.667 0.00 0.00 0.00 4.49
1308 1389 2.994995 TTCTTCGGAGCGGAGGCA 60.995 61.111 0.00 0.00 43.41 4.75
1794 1908 0.463654 TCCCGCCATCTGGAAATTCG 60.464 55.000 0.00 0.00 37.39 3.34
1823 1937 5.221722 ACTGAACTGAACCTGCTTGATTAGA 60.222 40.000 0.00 0.00 0.00 2.10
1824 1938 5.809001 TGAACTGAACCTGCTTGATTAGAT 58.191 37.500 0.00 0.00 0.00 1.98
1825 1939 5.877012 TGAACTGAACCTGCTTGATTAGATC 59.123 40.000 0.00 0.00 0.00 2.75
1826 1940 4.775236 ACTGAACCTGCTTGATTAGATCC 58.225 43.478 0.00 0.00 0.00 3.36
1827 1941 4.472833 ACTGAACCTGCTTGATTAGATCCT 59.527 41.667 0.00 0.00 0.00 3.24
1828 1942 5.663106 ACTGAACCTGCTTGATTAGATCCTA 59.337 40.000 0.00 0.00 0.00 2.94
1829 1943 6.166984 TGAACCTGCTTGATTAGATCCTAG 57.833 41.667 0.00 0.00 0.00 3.02
1830 1944 4.615588 ACCTGCTTGATTAGATCCTAGC 57.384 45.455 0.00 0.00 36.83 3.42
1831 1945 3.326297 ACCTGCTTGATTAGATCCTAGCC 59.674 47.826 0.00 0.00 36.00 3.93
1832 1946 3.583806 CTGCTTGATTAGATCCTAGCCG 58.416 50.000 0.00 0.00 36.00 5.52
1833 1947 2.965831 TGCTTGATTAGATCCTAGCCGT 59.034 45.455 0.00 0.00 36.00 5.68
1834 1948 3.388024 TGCTTGATTAGATCCTAGCCGTT 59.612 43.478 0.00 0.00 36.00 4.44
1835 1949 3.743396 GCTTGATTAGATCCTAGCCGTTG 59.257 47.826 0.00 0.00 32.82 4.10
1836 1950 4.310769 CTTGATTAGATCCTAGCCGTTGG 58.689 47.826 0.00 0.00 0.00 3.77
1837 1951 3.572642 TGATTAGATCCTAGCCGTTGGA 58.427 45.455 0.00 0.00 36.72 3.53
1838 1952 3.574396 TGATTAGATCCTAGCCGTTGGAG 59.426 47.826 0.00 0.00 35.63 3.86
1839 1953 3.308035 TTAGATCCTAGCCGTTGGAGA 57.692 47.619 0.00 0.00 35.63 3.71
1840 1954 2.390225 AGATCCTAGCCGTTGGAGAT 57.610 50.000 0.00 0.00 35.63 2.75
1841 1955 2.243810 AGATCCTAGCCGTTGGAGATC 58.756 52.381 0.00 0.00 35.63 2.75
1842 1956 1.273886 GATCCTAGCCGTTGGAGATCC 59.726 57.143 0.00 0.00 35.63 3.36
1843 1957 0.261991 TCCTAGCCGTTGGAGATCCT 59.738 55.000 0.00 0.00 36.82 3.24
1844 1958 1.497716 TCCTAGCCGTTGGAGATCCTA 59.502 52.381 0.00 0.00 36.82 2.94
1845 1959 2.091499 TCCTAGCCGTTGGAGATCCTAA 60.091 50.000 0.00 0.00 36.82 2.69
1846 1960 2.698797 CCTAGCCGTTGGAGATCCTAAA 59.301 50.000 0.00 0.00 36.82 1.85
1847 1961 3.134081 CCTAGCCGTTGGAGATCCTAAAA 59.866 47.826 0.00 0.00 36.82 1.52
1848 1962 3.713826 AGCCGTTGGAGATCCTAAAAA 57.286 42.857 0.00 0.00 36.82 1.94
1894 2008 4.536765 AGTGGACAAGACCATTTCACTTT 58.463 39.130 0.00 0.00 42.17 2.66
1932 2046 5.913137 TTACCTCTGTTGCATTATTTGGG 57.087 39.130 0.00 0.00 0.00 4.12
1963 2077 8.688151 ACAGAGTCTGTGAATTATAAGTAGGAC 58.312 37.037 24.93 0.00 43.63 3.85
2078 2192 9.165035 TCTTCGTTTTTACTCTTTGTTCCTTTA 57.835 29.630 0.00 0.00 0.00 1.85
2178 2292 4.278419 GGAAGGTTCAGCTTACATTGTTGT 59.722 41.667 0.00 0.00 39.98 3.32
2187 2301 9.891828 TTCAGCTTACATTGTTGTAAAATGTAG 57.108 29.630 8.51 5.69 46.03 2.74
2235 2352 6.889177 ACATCCACCATGTACAAACATTGATA 59.111 34.615 0.00 0.00 44.07 2.15
2236 2353 7.395772 ACATCCACCATGTACAAACATTGATAA 59.604 33.333 0.00 0.00 44.07 1.75
2278 2395 2.428890 CTCCTGTGGTACATCACTCTCC 59.571 54.545 0.00 0.00 44.52 3.71
2332 2453 6.128445 GGATAACAGATTGCATAACTGGATCG 60.128 42.308 15.88 2.91 36.17 3.69
2400 2521 2.284773 TAAGCCACCGGTAGCCCA 60.285 61.111 21.88 6.72 0.00 5.36
2461 2586 3.367025 GGTCGAAGTGTTGTTCTATTCCG 59.633 47.826 0.00 0.00 0.00 4.30
2622 2767 2.064242 AAAGTGTTCCCGACCCCCTG 62.064 60.000 0.00 0.00 0.00 4.45
2669 2832 0.468214 TCCATCCGCTGTCTCCCTAG 60.468 60.000 0.00 0.00 0.00 3.02
2726 2889 6.545298 GCAATCTTCTTCCTGATGGTCTAAAT 59.455 38.462 0.00 0.00 34.23 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.578282 ACCATATGATCATCCGCACACTA 59.422 43.478 12.53 0.00 0.00 2.74
1 2 2.369860 ACCATATGATCATCCGCACACT 59.630 45.455 12.53 0.00 0.00 3.55
4 5 2.289631 TGGACCATATGATCATCCGCAC 60.290 50.000 12.53 2.78 31.65 5.34
5 6 1.977129 TGGACCATATGATCATCCGCA 59.023 47.619 12.53 0.00 31.65 5.69
6 7 2.744202 GTTGGACCATATGATCATCCGC 59.256 50.000 12.53 1.55 31.65 5.54
7 8 4.277515 AGTTGGACCATATGATCATCCG 57.722 45.455 12.53 4.36 31.65 4.18
8 9 8.463930 TTTAAAGTTGGACCATATGATCATCC 57.536 34.615 12.53 8.46 0.00 3.51
10 11 8.786898 CGATTTAAAGTTGGACCATATGATCAT 58.213 33.333 13.81 13.81 0.00 2.45
11 12 7.773224 ACGATTTAAAGTTGGACCATATGATCA 59.227 33.333 3.65 0.00 0.00 2.92
12 13 8.070171 CACGATTTAAAGTTGGACCATATGATC 58.930 37.037 3.65 0.00 0.00 2.92
13 14 7.773224 TCACGATTTAAAGTTGGACCATATGAT 59.227 33.333 3.65 0.00 0.00 2.45
14 15 7.106890 TCACGATTTAAAGTTGGACCATATGA 58.893 34.615 3.65 0.00 0.00 2.15
15 16 7.315247 TCACGATTTAAAGTTGGACCATATG 57.685 36.000 0.00 0.00 0.00 1.78
16 17 7.067008 CCTTCACGATTTAAAGTTGGACCATAT 59.933 37.037 0.00 0.00 0.00 1.78
17 18 6.373216 CCTTCACGATTTAAAGTTGGACCATA 59.627 38.462 0.00 0.00 0.00 2.74
18 19 5.183140 CCTTCACGATTTAAAGTTGGACCAT 59.817 40.000 0.00 0.00 0.00 3.55
19 20 4.517453 CCTTCACGATTTAAAGTTGGACCA 59.483 41.667 0.00 0.00 0.00 4.02
20 21 4.758165 TCCTTCACGATTTAAAGTTGGACC 59.242 41.667 0.00 0.00 0.00 4.46
21 22 5.934935 TCCTTCACGATTTAAAGTTGGAC 57.065 39.130 0.00 0.00 0.00 4.02
22 23 6.234920 TCATCCTTCACGATTTAAAGTTGGA 58.765 36.000 0.00 0.00 0.00 3.53
23 24 6.494893 TCATCCTTCACGATTTAAAGTTGG 57.505 37.500 0.00 0.00 0.00 3.77
24 25 8.795786 TTTTCATCCTTCACGATTTAAAGTTG 57.204 30.769 0.00 0.00 0.00 3.16
49 50 8.636213 CCAATTATTCTATGCCATCTGACTTTT 58.364 33.333 0.00 0.00 0.00 2.27
50 51 8.000709 TCCAATTATTCTATGCCATCTGACTTT 58.999 33.333 0.00 0.00 0.00 2.66
51 52 7.446625 GTCCAATTATTCTATGCCATCTGACTT 59.553 37.037 0.00 0.00 0.00 3.01
52 53 6.939163 GTCCAATTATTCTATGCCATCTGACT 59.061 38.462 0.00 0.00 0.00 3.41
53 54 6.128445 CGTCCAATTATTCTATGCCATCTGAC 60.128 42.308 0.00 0.00 0.00 3.51
54 55 5.934043 CGTCCAATTATTCTATGCCATCTGA 59.066 40.000 0.00 0.00 0.00 3.27
55 56 5.122869 CCGTCCAATTATTCTATGCCATCTG 59.877 44.000 0.00 0.00 0.00 2.90
56 57 5.013079 TCCGTCCAATTATTCTATGCCATCT 59.987 40.000 0.00 0.00 0.00 2.90
57 58 5.245531 TCCGTCCAATTATTCTATGCCATC 58.754 41.667 0.00 0.00 0.00 3.51
58 59 5.241403 TCCGTCCAATTATTCTATGCCAT 57.759 39.130 0.00 0.00 0.00 4.40
59 60 4.698201 TCCGTCCAATTATTCTATGCCA 57.302 40.909 0.00 0.00 0.00 4.92
60 61 4.819630 TGTTCCGTCCAATTATTCTATGCC 59.180 41.667 0.00 0.00 0.00 4.40
61 62 6.560253 ATGTTCCGTCCAATTATTCTATGC 57.440 37.500 0.00 0.00 0.00 3.14
62 63 8.504005 GGTTATGTTCCGTCCAATTATTCTATG 58.496 37.037 0.00 0.00 0.00 2.23
63 64 7.664318 GGGTTATGTTCCGTCCAATTATTCTAT 59.336 37.037 0.00 0.00 0.00 1.98
64 65 6.993902 GGGTTATGTTCCGTCCAATTATTCTA 59.006 38.462 0.00 0.00 0.00 2.10
65 66 5.826208 GGGTTATGTTCCGTCCAATTATTCT 59.174 40.000 0.00 0.00 0.00 2.40
66 67 5.277634 CGGGTTATGTTCCGTCCAATTATTC 60.278 44.000 0.00 0.00 41.23 1.75
67 68 4.577283 CGGGTTATGTTCCGTCCAATTATT 59.423 41.667 0.00 0.00 41.23 1.40
68 69 4.131596 CGGGTTATGTTCCGTCCAATTAT 58.868 43.478 0.00 0.00 41.23 1.28
69 70 3.533547 CGGGTTATGTTCCGTCCAATTA 58.466 45.455 0.00 0.00 41.23 1.40
70 71 2.361789 CGGGTTATGTTCCGTCCAATT 58.638 47.619 0.00 0.00 41.23 2.32
71 72 2.032680 CGGGTTATGTTCCGTCCAAT 57.967 50.000 0.00 0.00 41.23 3.16
72 73 3.536548 CGGGTTATGTTCCGTCCAA 57.463 52.632 0.00 0.00 41.23 3.53
103 104 9.925545 TTGAACTGAGGTAGTAGTATATACCAA 57.074 33.333 9.32 0.00 43.33 3.67
104 105 9.925545 TTTGAACTGAGGTAGTAGTATATACCA 57.074 33.333 9.32 0.00 43.33 3.25
112 113 9.490379 CACTTAATTTTGAACTGAGGTAGTAGT 57.510 33.333 0.00 0.00 39.18 2.73
113 114 9.490379 ACACTTAATTTTGAACTGAGGTAGTAG 57.510 33.333 0.00 0.00 39.18 2.57
114 115 9.485206 GACACTTAATTTTGAACTGAGGTAGTA 57.515 33.333 0.00 0.00 39.18 1.82
115 116 7.170998 CGACACTTAATTTTGAACTGAGGTAGT 59.829 37.037 0.00 0.00 42.89 2.73
116 117 7.510630 CGACACTTAATTTTGAACTGAGGTAG 58.489 38.462 0.00 0.00 0.00 3.18
117 118 6.073440 GCGACACTTAATTTTGAACTGAGGTA 60.073 38.462 0.00 0.00 0.00 3.08
118 119 5.277828 GCGACACTTAATTTTGAACTGAGGT 60.278 40.000 0.00 0.00 0.00 3.85
119 120 5.049405 AGCGACACTTAATTTTGAACTGAGG 60.049 40.000 0.00 0.00 0.00 3.86
120 121 5.848036 CAGCGACACTTAATTTTGAACTGAG 59.152 40.000 0.00 0.00 0.00 3.35
121 122 5.525745 TCAGCGACACTTAATTTTGAACTGA 59.474 36.000 0.00 0.00 0.00 3.41
122 123 5.747565 TCAGCGACACTTAATTTTGAACTG 58.252 37.500 0.00 0.00 0.00 3.16
123 124 6.371809 TTCAGCGACACTTAATTTTGAACT 57.628 33.333 0.00 0.00 0.00 3.01
124 125 7.378461 TCATTTCAGCGACACTTAATTTTGAAC 59.622 33.333 0.00 0.00 0.00 3.18
125 126 7.421599 TCATTTCAGCGACACTTAATTTTGAA 58.578 30.769 0.00 0.00 0.00 2.69
126 127 6.964908 TCATTTCAGCGACACTTAATTTTGA 58.035 32.000 0.00 0.00 0.00 2.69
127 128 6.857964 ACTCATTTCAGCGACACTTAATTTTG 59.142 34.615 0.00 0.00 0.00 2.44
128 129 6.857964 CACTCATTTCAGCGACACTTAATTTT 59.142 34.615 0.00 0.00 0.00 1.82
129 130 6.017109 ACACTCATTTCAGCGACACTTAATTT 60.017 34.615 0.00 0.00 0.00 1.82
130 131 5.470098 ACACTCATTTCAGCGACACTTAATT 59.530 36.000 0.00 0.00 0.00 1.40
131 132 4.997395 ACACTCATTTCAGCGACACTTAAT 59.003 37.500 0.00 0.00 0.00 1.40
132 133 4.377021 ACACTCATTTCAGCGACACTTAA 58.623 39.130 0.00 0.00 0.00 1.85
133 134 3.990092 ACACTCATTTCAGCGACACTTA 58.010 40.909 0.00 0.00 0.00 2.24
134 135 2.838736 ACACTCATTTCAGCGACACTT 58.161 42.857 0.00 0.00 0.00 3.16
135 136 2.533266 ACACTCATTTCAGCGACACT 57.467 45.000 0.00 0.00 0.00 3.55
136 137 4.177026 AGATACACTCATTTCAGCGACAC 58.823 43.478 0.00 0.00 0.00 3.67
137 138 4.456280 AGATACACTCATTTCAGCGACA 57.544 40.909 0.00 0.00 0.00 4.35
138 139 5.822278 TCTAGATACACTCATTTCAGCGAC 58.178 41.667 0.00 0.00 0.00 5.19
139 140 6.095580 ACTTCTAGATACACTCATTTCAGCGA 59.904 38.462 0.00 0.00 0.00 4.93
140 141 6.269315 ACTTCTAGATACACTCATTTCAGCG 58.731 40.000 0.00 0.00 0.00 5.18
141 142 7.261325 TGACTTCTAGATACACTCATTTCAGC 58.739 38.462 0.00 0.00 0.00 4.26
142 143 9.081997 GTTGACTTCTAGATACACTCATTTCAG 57.918 37.037 0.00 0.00 0.00 3.02
143 144 8.807118 AGTTGACTTCTAGATACACTCATTTCA 58.193 33.333 0.00 0.00 0.00 2.69
144 145 9.296400 GAGTTGACTTCTAGATACACTCATTTC 57.704 37.037 0.00 0.00 0.00 2.17
145 146 8.807118 TGAGTTGACTTCTAGATACACTCATTT 58.193 33.333 12.98 0.00 0.00 2.32
146 147 8.354711 TGAGTTGACTTCTAGATACACTCATT 57.645 34.615 12.98 0.00 0.00 2.57
147 148 7.946381 TGAGTTGACTTCTAGATACACTCAT 57.054 36.000 12.98 0.00 0.00 2.90
148 149 7.946381 ATGAGTTGACTTCTAGATACACTCA 57.054 36.000 16.72 16.72 35.42 3.41
149 150 9.646427 AAAATGAGTTGACTTCTAGATACACTC 57.354 33.333 0.00 2.60 0.00 3.51
150 151 9.429359 CAAAATGAGTTGACTTCTAGATACACT 57.571 33.333 0.00 0.00 0.00 3.55
151 152 9.424319 TCAAAATGAGTTGACTTCTAGATACAC 57.576 33.333 0.00 0.00 32.56 2.90
152 153 9.996554 TTCAAAATGAGTTGACTTCTAGATACA 57.003 29.630 0.00 0.00 37.24 2.29
155 156 9.566432 AACTTCAAAATGAGTTGACTTCTAGAT 57.434 29.630 0.00 0.00 37.24 1.98
156 157 8.964476 AACTTCAAAATGAGTTGACTTCTAGA 57.036 30.769 0.00 0.00 37.24 2.43
157 158 9.657121 GAAACTTCAAAATGAGTTGACTTCTAG 57.343 33.333 0.00 0.00 37.24 2.43
158 159 8.335356 CGAAACTTCAAAATGAGTTGACTTCTA 58.665 33.333 0.00 0.00 37.24 2.10
159 160 7.189512 CGAAACTTCAAAATGAGTTGACTTCT 58.810 34.615 0.00 0.00 37.24 2.85
160 161 6.075362 GCGAAACTTCAAAATGAGTTGACTTC 60.075 38.462 0.00 0.00 37.24 3.01
161 162 5.743872 GCGAAACTTCAAAATGAGTTGACTT 59.256 36.000 0.00 0.00 37.24 3.01
162 163 5.163663 TGCGAAACTTCAAAATGAGTTGACT 60.164 36.000 0.00 0.00 37.24 3.41
163 164 5.034152 TGCGAAACTTCAAAATGAGTTGAC 58.966 37.500 0.00 0.00 37.24 3.18
164 165 5.065859 TCTGCGAAACTTCAAAATGAGTTGA 59.934 36.000 0.00 0.00 35.72 3.18
165 166 5.273170 TCTGCGAAACTTCAAAATGAGTTG 58.727 37.500 0.00 0.00 0.00 3.16
166 167 5.499139 TCTGCGAAACTTCAAAATGAGTT 57.501 34.783 0.00 0.00 0.00 3.01
167 168 5.499139 TTCTGCGAAACTTCAAAATGAGT 57.501 34.783 0.00 0.00 0.00 3.41
168 169 6.638063 TCATTTCTGCGAAACTTCAAAATGAG 59.362 34.615 5.99 0.00 36.97 2.90
169 170 6.502652 TCATTTCTGCGAAACTTCAAAATGA 58.497 32.000 5.99 0.00 38.57 2.57
170 171 6.418819 ACTCATTTCTGCGAAACTTCAAAATG 59.581 34.615 5.99 0.00 35.17 2.32
171 172 6.507023 ACTCATTTCTGCGAAACTTCAAAAT 58.493 32.000 5.99 0.00 0.00 1.82
172 173 5.890334 ACTCATTTCTGCGAAACTTCAAAA 58.110 33.333 5.99 0.00 0.00 2.44
173 174 5.499139 ACTCATTTCTGCGAAACTTCAAA 57.501 34.783 5.99 0.00 0.00 2.69
174 175 6.801539 ATACTCATTTCTGCGAAACTTCAA 57.198 33.333 5.99 0.00 0.00 2.69
175 176 7.549134 ACATATACTCATTTCTGCGAAACTTCA 59.451 33.333 5.99 0.00 0.00 3.02
176 177 7.910304 ACATATACTCATTTCTGCGAAACTTC 58.090 34.615 5.99 0.00 0.00 3.01
177 178 7.849804 ACATATACTCATTTCTGCGAAACTT 57.150 32.000 5.99 0.00 0.00 2.66
178 179 8.414003 TCTACATATACTCATTTCTGCGAAACT 58.586 33.333 5.99 0.00 0.00 2.66
179 180 8.575565 TCTACATATACTCATTTCTGCGAAAC 57.424 34.615 5.99 0.00 0.00 2.78
180 181 9.249457 CTTCTACATATACTCATTTCTGCGAAA 57.751 33.333 6.26 6.26 0.00 3.46
181 182 8.414003 ACTTCTACATATACTCATTTCTGCGAA 58.586 33.333 0.00 0.00 0.00 4.70
182 183 7.941919 ACTTCTACATATACTCATTTCTGCGA 58.058 34.615 0.00 0.00 0.00 5.10
183 184 7.862873 TGACTTCTACATATACTCATTTCTGCG 59.137 37.037 0.00 0.00 0.00 5.18
184 185 9.534565 TTGACTTCTACATATACTCATTTCTGC 57.465 33.333 0.00 0.00 0.00 4.26
196 197 8.887717 GCTCAAAATGAGTTGACTTCTACATAT 58.112 33.333 8.97 0.00 45.94 1.78
197 198 7.063426 CGCTCAAAATGAGTTGACTTCTACATA 59.937 37.037 8.97 0.00 45.94 2.29
198 199 6.128445 CGCTCAAAATGAGTTGACTTCTACAT 60.128 38.462 8.97 0.00 45.94 2.29
199 200 5.177511 CGCTCAAAATGAGTTGACTTCTACA 59.822 40.000 8.97 0.00 45.94 2.74
200 201 5.405571 TCGCTCAAAATGAGTTGACTTCTAC 59.594 40.000 8.97 0.00 45.94 2.59
201 202 5.538118 TCGCTCAAAATGAGTTGACTTCTA 58.462 37.500 8.97 0.00 45.94 2.10
202 203 4.380531 TCGCTCAAAATGAGTTGACTTCT 58.619 39.130 8.97 0.00 45.94 2.85
203 204 4.377841 CCTCGCTCAAAATGAGTTGACTTC 60.378 45.833 8.97 0.00 45.94 3.01
204 205 3.499918 CCTCGCTCAAAATGAGTTGACTT 59.500 43.478 8.97 0.00 45.94 3.01
205 206 3.070018 CCTCGCTCAAAATGAGTTGACT 58.930 45.455 8.97 0.00 45.94 3.41
206 207 2.160417 CCCTCGCTCAAAATGAGTTGAC 59.840 50.000 8.97 0.00 45.94 3.18
207 208 2.038426 TCCCTCGCTCAAAATGAGTTGA 59.962 45.455 8.97 6.72 45.94 3.18
208 209 2.417933 CTCCCTCGCTCAAAATGAGTTG 59.582 50.000 8.97 3.03 45.94 3.16
209 210 2.039084 ACTCCCTCGCTCAAAATGAGTT 59.961 45.455 8.97 0.00 45.94 3.01
210 211 1.625818 ACTCCCTCGCTCAAAATGAGT 59.374 47.619 8.97 0.00 45.94 3.41
211 212 2.393271 ACTCCCTCGCTCAAAATGAG 57.607 50.000 3.00 3.00 46.90 2.90
212 213 3.096852 TCTACTCCCTCGCTCAAAATGA 58.903 45.455 0.00 0.00 0.00 2.57
213 214 3.526931 TCTACTCCCTCGCTCAAAATG 57.473 47.619 0.00 0.00 0.00 2.32
214 215 5.871396 TTATCTACTCCCTCGCTCAAAAT 57.129 39.130 0.00 0.00 0.00 1.82
215 216 5.871396 ATTATCTACTCCCTCGCTCAAAA 57.129 39.130 0.00 0.00 0.00 2.44
216 217 6.550108 ACTTATTATCTACTCCCTCGCTCAAA 59.450 38.462 0.00 0.00 0.00 2.69
217 218 6.016192 CACTTATTATCTACTCCCTCGCTCAA 60.016 42.308 0.00 0.00 0.00 3.02
218 219 5.473846 CACTTATTATCTACTCCCTCGCTCA 59.526 44.000 0.00 0.00 0.00 4.26
219 220 5.706369 TCACTTATTATCTACTCCCTCGCTC 59.294 44.000 0.00 0.00 0.00 5.03
220 221 5.632118 TCACTTATTATCTACTCCCTCGCT 58.368 41.667 0.00 0.00 0.00 4.93
221 222 5.961396 TCACTTATTATCTACTCCCTCGC 57.039 43.478 0.00 0.00 0.00 5.03
233 234 9.712305 CTCCGGAAGTTGATAATCACTTATTAT 57.288 33.333 5.23 0.00 42.36 1.28
234 235 8.920174 TCTCCGGAAGTTGATAATCACTTATTA 58.080 33.333 5.23 0.00 34.56 0.98
235 236 7.792032 TCTCCGGAAGTTGATAATCACTTATT 58.208 34.615 5.23 0.00 0.00 1.40
236 237 7.287927 TCTCTCCGGAAGTTGATAATCACTTAT 59.712 37.037 5.23 0.00 0.00 1.73
237 238 6.605995 TCTCTCCGGAAGTTGATAATCACTTA 59.394 38.462 5.23 0.00 0.00 2.24
238 239 5.422331 TCTCTCCGGAAGTTGATAATCACTT 59.578 40.000 5.23 0.00 0.00 3.16
239 240 4.956700 TCTCTCCGGAAGTTGATAATCACT 59.043 41.667 5.23 0.00 0.00 3.41
240 241 5.263968 TCTCTCCGGAAGTTGATAATCAC 57.736 43.478 5.23 0.00 0.00 3.06
241 242 5.907207 CTTCTCTCCGGAAGTTGATAATCA 58.093 41.667 5.23 0.00 38.22 2.57
251 252 1.402984 CCGTTGACTTCTCTCCGGAAG 60.403 57.143 5.23 1.72 45.68 3.46
252 253 0.601558 CCGTTGACTTCTCTCCGGAA 59.398 55.000 5.23 0.00 34.25 4.30
253 254 1.874345 GCCGTTGACTTCTCTCCGGA 61.874 60.000 2.93 2.93 34.25 5.14
254 255 1.446272 GCCGTTGACTTCTCTCCGG 60.446 63.158 0.00 0.00 35.00 5.14
255 256 0.734253 CTGCCGTTGACTTCTCTCCG 60.734 60.000 0.00 0.00 0.00 4.63
256 257 0.603569 TCTGCCGTTGACTTCTCTCC 59.396 55.000 0.00 0.00 0.00 3.71
257 258 2.440539 TTCTGCCGTTGACTTCTCTC 57.559 50.000 0.00 0.00 0.00 3.20
258 259 2.910688 TTTCTGCCGTTGACTTCTCT 57.089 45.000 0.00 0.00 0.00 3.10
259 260 3.498397 TCATTTTCTGCCGTTGACTTCTC 59.502 43.478 0.00 0.00 0.00 2.87
260 261 3.476552 TCATTTTCTGCCGTTGACTTCT 58.523 40.909 0.00 0.00 0.00 2.85
261 262 3.896648 TCATTTTCTGCCGTTGACTTC 57.103 42.857 0.00 0.00 0.00 3.01
262 263 4.647424 TTTCATTTTCTGCCGTTGACTT 57.353 36.364 0.00 0.00 0.00 3.01
263 264 4.853924 ATTTCATTTTCTGCCGTTGACT 57.146 36.364 0.00 0.00 0.00 3.41
264 265 4.981674 TGAATTTCATTTTCTGCCGTTGAC 59.018 37.500 0.00 0.00 0.00 3.18
265 266 5.193663 TGAATTTCATTTTCTGCCGTTGA 57.806 34.783 0.00 0.00 0.00 3.18
266 267 5.903764 TTGAATTTCATTTTCTGCCGTTG 57.096 34.783 0.00 0.00 0.00 4.10
267 268 5.050159 GCTTTGAATTTCATTTTCTGCCGTT 60.050 36.000 0.00 0.00 0.00 4.44
268 269 4.448732 GCTTTGAATTTCATTTTCTGCCGT 59.551 37.500 0.00 0.00 0.00 5.68
269 270 4.143052 GGCTTTGAATTTCATTTTCTGCCG 60.143 41.667 0.00 0.00 31.11 5.69
270 271 4.756135 TGGCTTTGAATTTCATTTTCTGCC 59.244 37.500 0.00 8.39 36.35 4.85
271 272 5.927954 TGGCTTTGAATTTCATTTTCTGC 57.072 34.783 0.00 0.00 0.00 4.26
272 273 7.900782 AGATGGCTTTGAATTTCATTTTCTG 57.099 32.000 0.00 0.00 0.00 3.02
273 274 9.028284 TCTAGATGGCTTTGAATTTCATTTTCT 57.972 29.630 0.00 1.25 0.00 2.52
274 275 9.643693 TTCTAGATGGCTTTGAATTTCATTTTC 57.356 29.630 0.00 0.00 0.00 2.29
279 280 9.466497 AGTTATTCTAGATGGCTTTGAATTTCA 57.534 29.630 0.00 0.00 32.38 2.69
282 283 8.907885 GGAAGTTATTCTAGATGGCTTTGAATT 58.092 33.333 0.00 0.00 35.63 2.17
283 284 7.503902 GGGAAGTTATTCTAGATGGCTTTGAAT 59.496 37.037 0.00 0.00 35.63 2.57
284 285 6.828785 GGGAAGTTATTCTAGATGGCTTTGAA 59.171 38.462 0.00 0.00 35.63 2.69
285 286 6.357367 GGGAAGTTATTCTAGATGGCTTTGA 58.643 40.000 0.00 0.00 35.63 2.69
286 287 5.532779 GGGGAAGTTATTCTAGATGGCTTTG 59.467 44.000 0.00 0.00 35.63 2.77
344 345 1.961793 TTGTCTGCAAGTGTGGTACC 58.038 50.000 4.43 4.43 33.76 3.34
360 368 2.003196 CTGGTTTTGTTGGCGTTTGT 57.997 45.000 0.00 0.00 0.00 2.83
380 388 4.435436 TCGGCAGGCGCACAGTAG 62.435 66.667 12.43 0.00 41.24 2.57
499 507 3.009714 GGAGTGGGGTGGAGGTCC 61.010 72.222 0.00 0.00 0.00 4.46
503 511 2.203998 ACTGGGAGTGGGGTGGAG 60.204 66.667 0.00 0.00 0.00 3.86
504 512 2.203938 GACTGGGAGTGGGGTGGA 60.204 66.667 0.00 0.00 0.00 4.02
505 513 2.203998 AGACTGGGAGTGGGGTGG 60.204 66.667 0.00 0.00 0.00 4.61
507 515 2.122954 GGAGACTGGGAGTGGGGT 59.877 66.667 0.00 0.00 0.00 4.95
509 517 2.122729 TGGGAGACTGGGAGTGGG 59.877 66.667 0.00 0.00 0.00 4.61
512 520 0.252284 AATCGTGGGAGACTGGGAGT 60.252 55.000 0.00 0.00 0.00 3.85
514 522 0.976073 GGAATCGTGGGAGACTGGGA 60.976 60.000 0.00 0.00 0.00 4.37
515 523 1.264749 TGGAATCGTGGGAGACTGGG 61.265 60.000 0.00 0.00 0.00 4.45
516 524 0.108138 GTGGAATCGTGGGAGACTGG 60.108 60.000 0.00 0.00 0.00 4.00
518 526 2.379972 CTAGTGGAATCGTGGGAGACT 58.620 52.381 0.00 0.00 0.00 3.24
520 528 1.112113 GCTAGTGGAATCGTGGGAGA 58.888 55.000 0.00 0.00 0.00 3.71
527 553 0.172578 TGGTGACGCTAGTGGAATCG 59.827 55.000 8.42 0.00 0.00 3.34
634 677 0.179234 GTTTGGGTTGGTTGGTTGGG 59.821 55.000 0.00 0.00 0.00 4.12
718 761 1.130561 CAGCTAGCCGGCTAAACAAAC 59.869 52.381 34.48 19.56 41.00 2.93
729 772 4.208686 GTCGGGGACAGCTAGCCG 62.209 72.222 12.13 3.05 32.09 5.52
733 776 4.371417 ACCGGTCGGGGACAGCTA 62.371 66.667 14.25 0.00 41.60 3.32
774 817 0.453390 CCTTTCTGCCTGCGGAAATC 59.547 55.000 22.49 0.00 46.33 2.17
781 825 0.679321 CTCTTCCCCTTTCTGCCTGC 60.679 60.000 0.00 0.00 0.00 4.85
919 963 1.548269 GAGGTTGAGAGCTGCTGTAGT 59.452 52.381 7.01 0.00 32.79 2.73
922 966 0.761187 TTGAGGTTGAGAGCTGCTGT 59.239 50.000 7.01 1.44 32.79 4.40
928 972 1.802069 GGTGACTTGAGGTTGAGAGC 58.198 55.000 0.00 0.00 0.00 4.09
946 990 2.203280 TGTTCTTGGTGGTGGCGG 60.203 61.111 0.00 0.00 0.00 6.13
959 1003 3.487544 GCTCTTGTGTTCTTGTGGTGTTC 60.488 47.826 0.00 0.00 0.00 3.18
977 1021 2.673341 TCGGTCTCTGCGTGCTCT 60.673 61.111 0.00 0.00 0.00 4.09
978 1022 2.505118 GTCGGTCTCTGCGTGCTC 60.505 66.667 0.00 0.00 0.00 4.26
979 1023 3.295273 TGTCGGTCTCTGCGTGCT 61.295 61.111 0.00 0.00 0.00 4.40
980 1024 3.106407 GTGTCGGTCTCTGCGTGC 61.106 66.667 0.00 0.00 0.00 5.34
981 1025 2.801162 CGTGTCGGTCTCTGCGTG 60.801 66.667 0.00 0.00 0.00 5.34
982 1026 4.702081 GCGTGTCGGTCTCTGCGT 62.702 66.667 0.00 0.00 0.00 5.24
983 1027 3.971453 ATGCGTGTCGGTCTCTGCG 62.971 63.158 0.00 0.00 0.00 5.18
984 1028 2.125912 ATGCGTGTCGGTCTCTGC 60.126 61.111 0.00 0.00 0.00 4.26
985 1029 1.073216 GTCATGCGTGTCGGTCTCTG 61.073 60.000 5.68 0.00 0.00 3.35
986 1030 1.213013 GTCATGCGTGTCGGTCTCT 59.787 57.895 5.68 0.00 0.00 3.10
987 1031 1.805945 GGTCATGCGTGTCGGTCTC 60.806 63.158 5.68 0.00 0.00 3.36
988 1032 1.816863 AAGGTCATGCGTGTCGGTCT 61.817 55.000 5.68 0.00 0.00 3.85
989 1033 1.352156 GAAGGTCATGCGTGTCGGTC 61.352 60.000 5.68 0.00 0.00 4.79
990 1034 1.374252 GAAGGTCATGCGTGTCGGT 60.374 57.895 5.68 0.00 0.00 4.69
991 1035 1.354337 CTGAAGGTCATGCGTGTCGG 61.354 60.000 5.68 0.00 0.00 4.79
992 1036 1.959899 GCTGAAGGTCATGCGTGTCG 61.960 60.000 5.68 0.00 0.00 4.35
993 1037 1.790387 GCTGAAGGTCATGCGTGTC 59.210 57.895 5.68 0.00 0.00 3.67
994 1038 2.029288 CGCTGAAGGTCATGCGTGT 61.029 57.895 5.68 0.00 38.36 4.49
995 1039 2.029288 ACGCTGAAGGTCATGCGTG 61.029 57.895 19.49 0.00 46.75 5.34
996 1040 2.343758 ACGCTGAAGGTCATGCGT 59.656 55.556 16.49 16.49 45.21 5.24
997 1041 1.416813 GAGACGCTGAAGGTCATGCG 61.417 60.000 15.56 15.56 43.94 4.73
998 1042 1.416813 CGAGACGCTGAAGGTCATGC 61.417 60.000 0.00 0.00 36.87 4.06
1386 1482 4.814771 CGGTACTTGTTCTTCTTGTTCCTT 59.185 41.667 0.00 0.00 0.00 3.36
1569 1665 2.530661 TGCTCGGGGAAGGGGAAA 60.531 61.111 0.00 0.00 0.00 3.13
1659 1773 3.729906 GACCCGGACATCGACGTCG 62.730 68.421 31.30 31.30 42.43 5.12
1662 1776 4.203076 GGGACCCGGACATCGACG 62.203 72.222 0.73 0.00 42.43 5.12
1794 1908 1.884235 CAGGTTCAGTTCAGTCCCAC 58.116 55.000 0.00 0.00 0.00 4.61
1823 1937 1.133009 AGGATCTCCAACGGCTAGGAT 60.133 52.381 0.00 0.00 38.89 3.24
1824 1938 0.261991 AGGATCTCCAACGGCTAGGA 59.738 55.000 0.00 0.00 38.89 2.94
1825 1939 1.996798 TAGGATCTCCAACGGCTAGG 58.003 55.000 0.00 0.00 38.89 3.02
1826 1940 4.402056 TTTTAGGATCTCCAACGGCTAG 57.598 45.455 0.00 0.00 38.89 3.42
1827 1941 4.829872 TTTTTAGGATCTCCAACGGCTA 57.170 40.909 0.00 0.00 38.89 3.93
1828 1942 3.713826 TTTTTAGGATCTCCAACGGCT 57.286 42.857 0.00 0.00 38.89 5.52
1848 1962 3.009143 ACTCCAACGGCTAGGATCTTTTT 59.991 43.478 0.00 0.00 32.53 1.94
1849 1963 2.572104 ACTCCAACGGCTAGGATCTTTT 59.428 45.455 0.00 0.00 32.53 2.27
1850 1964 2.093447 CACTCCAACGGCTAGGATCTTT 60.093 50.000 0.00 0.00 32.53 2.52
1851 1965 1.482593 CACTCCAACGGCTAGGATCTT 59.517 52.381 0.00 0.00 32.53 2.40
1852 1966 1.115467 CACTCCAACGGCTAGGATCT 58.885 55.000 0.00 0.00 32.53 2.75
1853 1967 1.067821 CTCACTCCAACGGCTAGGATC 59.932 57.143 0.00 0.00 32.53 3.36
1907 2021 7.330262 CCCAAATAATGCAACAGAGGTAAAAT 58.670 34.615 0.00 0.00 0.00 1.82
1932 2046 8.507249 ACTTATAATTCACAGACTCTGTTTTGC 58.493 33.333 9.11 0.00 42.59 3.68
2187 2301 8.142994 TGTCAAGTCACAAAACTTATTCTCTC 57.857 34.615 0.00 0.00 37.38 3.20
2324 2445 8.353684 CAGATACTTGTAAACTATCGATCCAGT 58.646 37.037 0.00 0.00 30.13 4.00
2332 2453 9.109393 TCATTTGCCAGATACTTGTAAACTATC 57.891 33.333 0.00 0.00 0.00 2.08
2400 2521 8.397906 CGTATCACTTTGTTGTTCCATATCAAT 58.602 33.333 0.00 0.00 0.00 2.57
2411 2532 6.965500 CGTCTCTATACGTATCACTTTGTTGT 59.035 38.462 12.24 0.00 38.07 3.32
2461 2586 1.847818 TCGTGCTCGGCATATACAAC 58.152 50.000 8.49 0.00 41.91 3.32
2622 2767 0.170561 TAGCGCAGAGAAAGGACGAC 59.829 55.000 11.47 0.00 0.00 4.34
2669 2832 3.746949 ATAGCCGTGCTGAGCAGGC 62.747 63.158 28.62 28.62 45.82 4.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.