Multiple sequence alignment - TraesCS2D01G345400

Loading Multiple Alignment...

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 TraesCS2D01G345400 chr2D 100.000 2794 0 0 1 2794 441563342 441566135 0.000000e+00 5160.0
1 TraesCS2D01G345400 chr2D 77.358 318 48 9 1491 1799 2098358 2098660 1.720000e-37 167.0
2 TraesCS2D01G345400 chr2D 87.097 93 7 4 1176 1264 2098123 2098214 1.770000e-17 100.0
3 TraesCS2D01G345400 chr2B 91.247 2045 92 35 494 2502 519123965 519125958 0.000000e+00 2704.0
4 TraesCS2D01G345400 chr2B 94.915 59 3 0 2719 2777 519176291 519176349 2.960000e-15 93.5
5 TraesCS2D01G345400 chr2A 93.051 849 45 7 1343 2179 585196002 585196848 0.000000e+00 1229.0
6 TraesCS2D01G345400 chr2A 93.301 836 26 11 490 1306 585195181 585196005 0.000000e+00 1206.0
7 TraesCS2D01G345400 chr2A 89.421 397 32 5 2402 2794 585197822 585198212 2.500000e-135 492.0
8 TraesCS2D01G345400 chr2A 90.323 372 26 3 1847 2208 585196848 585197219 1.950000e-131 479.0
9 TraesCS2D01G345400 chr2A 91.878 197 13 3 2199 2392 585197406 585197602 3.550000e-69 272.0
10 TraesCS2D01G345400 chr2A 74.941 427 75 15 1388 1799 2051129 2051538 1.720000e-37 167.0
11 TraesCS2D01G345400 chr2A 76.299 308 59 10 1388 1683 2106317 2106622 4.820000e-33 152.0
12 TraesCS2D01G345400 chr2A 84.906 106 12 3 1163 1264 2106157 2106262 1.370000e-18 104.0
13 TraesCS2D01G345400 chr2A 83.962 106 13 3 1163 1264 2050969 2051074 6.370000e-17 99.0
14 TraesCS2D01G345400 chr6B 89.542 153 8 4 1244 1391 255821920 255822069 1.320000e-43 187.0
15 TraesCS2D01G345400 chrUn 74.473 427 77 15 1388 1799 239586434 239586843 3.730000e-34 156.0
16 TraesCS2D01G345400 chrUn 76.299 308 59 10 1388 1683 395278688 395278993 4.820000e-33 152.0
17 TraesCS2D01G345400 chrUn 81.169 154 13 8 2475 2624 236183161 236183020 2.940000e-20 110.0
18 TraesCS2D01G345400 chrUn 78.395 162 27 7 271 426 45985359 45985518 6.370000e-17 99.0
19 TraesCS2D01G345400 chrUn 83.962 106 13 3 1163 1264 239586274 239586379 6.370000e-17 99.0
20 TraesCS2D01G345400 chrUn 83.962 106 13 3 1163 1264 395278528 395278633 6.370000e-17 99.0
21 TraesCS2D01G345400 chr3D 80.864 162 24 4 270 425 379001352 379001512 1.360000e-23 121.0
22 TraesCS2D01G345400 chr7D 81.699 153 19 8 276 422 616859429 616859578 4.890000e-23 119.0
23 TraesCS2D01G345400 chr5A 88.525 61 5 2 2564 2624 571459753 571459695 3.860000e-09 73.1
24 TraesCS2D01G345400 chr5A 85.938 64 5 4 294 355 462158683 462158622 6.460000e-07 65.8
25 TraesCS2D01G345400 chr4B 79.464 112 16 3 320 425 532580798 532580688 3.860000e-09 73.1


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 TraesCS2D01G345400 chr2D 441563342 441566135 2793 False 5160.0 5160 100.0000 1 2794 1 chr2D.!!$F1 2793
1 TraesCS2D01G345400 chr2B 519123965 519125958 1993 False 2704.0 2704 91.2470 494 2502 1 chr2B.!!$F1 2008
2 TraesCS2D01G345400 chr2A 585195181 585198212 3031 False 735.6 1229 91.5948 490 2794 5 chr2A.!!$F3 2304

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
122 123 0.040067 CCGAAGGCAAAGTGCTTGTC 60.040 55.0 0.0 0.0 46.14 3.18 F
291 292 0.322546 CTCCCTCCGGTCCTTTTTGG 60.323 60.0 0.0 0.0 37.10 3.28 F
293 294 0.608308 CCCTCCGGTCCTTTTTGGTC 60.608 60.0 0.0 0.0 37.07 4.02 F
1146 1162 0.628668 AGCAAGGGGAAGGGGATGAT 60.629 55.0 0.0 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 1144 0.468771 CATCATCCCCTTCCCCTTGC 60.469 60.000 0.00 0.0 0.0 4.01 R
1310 1330 0.669077 AGGATGACGTCGGATGTAGC 59.331 55.000 11.62 0.0 0.0 3.58 R
1406 1438 1.999735 TCATCATCGTTTTCCAGCGTC 59.000 47.619 0.00 0.0 0.0 5.19 R
2760 3562 0.793250 GTGAAGCAGAAGAACGAGGC 59.207 55.000 0.00 0.0 0.0 4.70 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
24 25 7.669089 AAACCCAATTTGTCTTCTCCTAAAA 57.331 32.000 0.00 0.00 0.00 1.52
25 26 7.855784 AACCCAATTTGTCTTCTCCTAAAAT 57.144 32.000 0.00 0.00 0.00 1.82
26 27 7.855784 ACCCAATTTGTCTTCTCCTAAAATT 57.144 32.000 0.00 0.00 32.20 1.82
27 28 7.670364 ACCCAATTTGTCTTCTCCTAAAATTG 58.330 34.615 10.66 10.66 43.17 2.32
28 29 7.508977 ACCCAATTTGTCTTCTCCTAAAATTGA 59.491 33.333 16.63 0.00 44.92 2.57
29 30 8.367156 CCCAATTTGTCTTCTCCTAAAATTGAA 58.633 33.333 16.63 0.00 44.92 2.69
30 31 9.415544 CCAATTTGTCTTCTCCTAAAATTGAAG 57.584 33.333 16.63 0.00 44.92 3.02
31 32 9.415544 CAATTTGTCTTCTCCTAAAATTGAAGG 57.584 33.333 11.76 0.69 44.92 3.46
32 33 8.712228 ATTTGTCTTCTCCTAAAATTGAAGGT 57.288 30.769 6.30 0.00 37.21 3.50
33 34 8.533569 TTTGTCTTCTCCTAAAATTGAAGGTT 57.466 30.769 6.30 0.00 37.21 3.50
34 35 7.510549 TGTCTTCTCCTAAAATTGAAGGTTG 57.489 36.000 6.30 2.56 37.21 3.77
35 36 6.016276 TGTCTTCTCCTAAAATTGAAGGTTGC 60.016 38.462 6.30 0.00 37.21 4.17
36 37 6.016276 GTCTTCTCCTAAAATTGAAGGTTGCA 60.016 38.462 6.30 0.00 37.21 4.08
37 38 6.549364 TCTTCTCCTAAAATTGAAGGTTGCAA 59.451 34.615 0.00 0.00 37.21 4.08
38 39 6.916360 TCTCCTAAAATTGAAGGTTGCAAT 57.084 33.333 0.59 0.00 37.56 3.56
39 40 8.415950 TTCTCCTAAAATTGAAGGTTGCAATA 57.584 30.769 0.59 0.00 35.06 1.90
40 41 8.593945 TCTCCTAAAATTGAAGGTTGCAATAT 57.406 30.769 0.59 0.00 35.06 1.28
41 42 9.034800 TCTCCTAAAATTGAAGGTTGCAATATT 57.965 29.630 0.59 0.00 35.06 1.28
42 43 9.657419 CTCCTAAAATTGAAGGTTGCAATATTT 57.343 29.630 0.59 0.00 35.06 1.40
101 102 7.690952 TTGTTGGGTATTACTTGTATCAACC 57.309 36.000 0.00 0.00 34.23 3.77
102 103 5.875910 TGTTGGGTATTACTTGTATCAACCG 59.124 40.000 0.00 0.00 34.23 4.44
103 104 4.444536 TGGGTATTACTTGTATCAACCGC 58.555 43.478 0.00 0.00 0.00 5.68
104 105 3.811497 GGGTATTACTTGTATCAACCGCC 59.189 47.826 0.00 0.00 0.00 6.13
105 106 3.492011 GGTATTACTTGTATCAACCGCCG 59.508 47.826 0.00 0.00 0.00 6.46
106 107 3.530265 ATTACTTGTATCAACCGCCGA 57.470 42.857 0.00 0.00 0.00 5.54
107 108 3.316071 TTACTTGTATCAACCGCCGAA 57.684 42.857 0.00 0.00 0.00 4.30
108 109 1.722011 ACTTGTATCAACCGCCGAAG 58.278 50.000 0.00 0.00 0.00 3.79
120 121 4.950744 CCGAAGGCAAAGTGCTTG 57.049 55.556 0.00 0.00 46.14 4.01
121 122 2.032981 CCGAAGGCAAAGTGCTTGT 58.967 52.632 0.00 0.00 46.14 3.16
122 123 0.040067 CCGAAGGCAAAGTGCTTGTC 60.040 55.000 0.00 0.00 46.14 3.18
123 124 0.662619 CGAAGGCAAAGTGCTTGTCA 59.337 50.000 0.00 0.00 42.48 3.58
124 125 1.334419 CGAAGGCAAAGTGCTTGTCAG 60.334 52.381 0.00 0.00 42.48 3.51
125 126 0.386838 AAGGCAAAGTGCTTGTCAGC 59.613 50.000 0.00 0.00 42.48 4.26
152 153 5.659440 AAAATGGGAAACATAGAATGCGT 57.341 34.783 0.00 0.00 39.40 5.24
153 154 5.659440 AAATGGGAAACATAGAATGCGTT 57.341 34.783 0.00 0.00 39.40 4.84
154 155 6.767524 AAATGGGAAACATAGAATGCGTTA 57.232 33.333 0.00 0.00 39.40 3.18
155 156 6.767524 AATGGGAAACATAGAATGCGTTAA 57.232 33.333 0.00 0.00 39.40 2.01
156 157 6.767524 ATGGGAAACATAGAATGCGTTAAA 57.232 33.333 0.00 0.00 38.26 1.52
157 158 6.767524 TGGGAAACATAGAATGCGTTAAAT 57.232 33.333 0.00 0.00 0.00 1.40
158 159 7.164230 TGGGAAACATAGAATGCGTTAAATT 57.836 32.000 0.00 0.00 0.00 1.82
159 160 7.032580 TGGGAAACATAGAATGCGTTAAATTG 58.967 34.615 0.00 0.00 0.00 2.32
160 161 7.033185 GGGAAACATAGAATGCGTTAAATTGT 58.967 34.615 0.00 0.00 0.00 2.71
161 162 7.009174 GGGAAACATAGAATGCGTTAAATTGTG 59.991 37.037 0.00 0.00 0.00 3.33
162 163 7.009174 GGAAACATAGAATGCGTTAAATTGTGG 59.991 37.037 0.00 0.00 0.00 4.17
163 164 5.339990 ACATAGAATGCGTTAAATTGTGGC 58.660 37.500 0.00 0.00 0.00 5.01
164 165 3.932545 AGAATGCGTTAAATTGTGGCA 57.067 38.095 0.00 0.00 38.09 4.92
165 166 3.574614 AGAATGCGTTAAATTGTGGCAC 58.425 40.909 11.55 11.55 36.31 5.01
166 167 3.005261 AGAATGCGTTAAATTGTGGCACA 59.995 39.130 17.96 17.96 36.31 4.57
167 168 2.871182 TGCGTTAAATTGTGGCACAA 57.129 40.000 32.77 32.77 44.16 3.33
168 169 2.736978 TGCGTTAAATTGTGGCACAAG 58.263 42.857 33.41 21.41 44.16 3.16
169 170 2.099921 TGCGTTAAATTGTGGCACAAGT 59.900 40.909 33.41 29.85 44.16 3.16
170 171 3.120041 GCGTTAAATTGTGGCACAAGTT 58.880 40.909 37.45 37.45 46.35 2.66
171 172 3.553917 GCGTTAAATTGTGGCACAAGTTT 59.446 39.130 39.51 32.54 42.80 2.66
172 173 4.317769 GCGTTAAATTGTGGCACAAGTTTC 60.318 41.667 39.51 30.86 42.80 2.78
173 174 4.800993 CGTTAAATTGTGGCACAAGTTTCA 59.199 37.500 39.51 27.55 42.80 2.69
174 175 5.276161 CGTTAAATTGTGGCACAAGTTTCAC 60.276 40.000 39.51 32.90 42.80 3.18
175 176 4.470334 AAATTGTGGCACAAGTTTCACT 57.530 36.364 32.90 16.48 42.80 3.41
176 177 5.590530 AAATTGTGGCACAAGTTTCACTA 57.409 34.783 32.90 12.24 42.80 2.74
177 178 5.590530 AATTGTGGCACAAGTTTCACTAA 57.409 34.783 33.41 11.19 44.16 2.24
178 179 5.590530 ATTGTGGCACAAGTTTCACTAAA 57.409 34.783 33.41 10.67 44.16 1.85
179 180 5.590530 TTGTGGCACAAGTTTCACTAAAT 57.409 34.783 28.09 0.00 44.16 1.40
180 181 4.930963 TGTGGCACAAGTTTCACTAAATG 58.069 39.130 19.74 0.00 44.16 2.32
181 182 4.202101 TGTGGCACAAGTTTCACTAAATGG 60.202 41.667 19.74 0.00 44.16 3.16
182 183 3.320541 TGGCACAAGTTTCACTAAATGGG 59.679 43.478 0.00 0.00 31.92 4.00
183 184 3.572255 GGCACAAGTTTCACTAAATGGGA 59.428 43.478 0.00 0.00 0.00 4.37
184 185 4.220602 GGCACAAGTTTCACTAAATGGGAT 59.779 41.667 0.00 0.00 0.00 3.85
185 186 5.417580 GGCACAAGTTTCACTAAATGGGATA 59.582 40.000 0.00 0.00 0.00 2.59
186 187 6.096846 GGCACAAGTTTCACTAAATGGGATAT 59.903 38.462 0.00 0.00 0.00 1.63
187 188 7.284489 GGCACAAGTTTCACTAAATGGGATATA 59.716 37.037 0.00 0.00 0.00 0.86
188 189 8.682710 GCACAAGTTTCACTAAATGGGATATAA 58.317 33.333 0.00 0.00 0.00 0.98
242 243 8.827177 ATCTGTCATAAACGTAAAACTTGAGA 57.173 30.769 0.00 0.00 0.00 3.27
243 244 8.827177 TCTGTCATAAACGTAAAACTTGAGAT 57.173 30.769 0.00 0.00 0.00 2.75
244 245 9.917129 TCTGTCATAAACGTAAAACTTGAGATA 57.083 29.630 0.00 0.00 0.00 1.98
280 281 9.512588 TTTACTCTACTTAATATACTCCCTCCG 57.487 37.037 0.00 0.00 0.00 4.63
281 282 6.483405 ACTCTACTTAATATACTCCCTCCGG 58.517 44.000 0.00 0.00 0.00 5.14
282 283 6.045341 ACTCTACTTAATATACTCCCTCCGGT 59.955 42.308 0.00 0.00 0.00 5.28
283 284 6.479884 TCTACTTAATATACTCCCTCCGGTC 58.520 44.000 0.00 0.00 0.00 4.79
284 285 4.414677 ACTTAATATACTCCCTCCGGTCC 58.585 47.826 0.00 0.00 0.00 4.46
285 286 4.107636 ACTTAATATACTCCCTCCGGTCCT 59.892 45.833 0.00 0.00 0.00 3.85
286 287 3.632420 AATATACTCCCTCCGGTCCTT 57.368 47.619 0.00 0.00 0.00 3.36
287 288 3.632420 ATATACTCCCTCCGGTCCTTT 57.368 47.619 0.00 0.00 0.00 3.11
288 289 2.265526 ATACTCCCTCCGGTCCTTTT 57.734 50.000 0.00 0.00 0.00 2.27
289 290 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
290 291 0.400594 ACTCCCTCCGGTCCTTTTTG 59.599 55.000 0.00 0.00 0.00 2.44
291 292 0.322546 CTCCCTCCGGTCCTTTTTGG 60.323 60.000 0.00 0.00 37.10 3.28
292 293 1.063654 TCCCTCCGGTCCTTTTTGGT 61.064 55.000 0.00 0.00 37.07 3.67
293 294 0.608308 CCCTCCGGTCCTTTTTGGTC 60.608 60.000 0.00 0.00 37.07 4.02
294 295 0.608308 CCTCCGGTCCTTTTTGGTCC 60.608 60.000 0.00 0.00 40.08 4.46
297 298 4.167597 GGTCCTTTTTGGTCCGCA 57.832 55.556 0.00 0.00 34.50 5.69
298 299 2.653557 GGTCCTTTTTGGTCCGCAT 58.346 52.632 0.00 0.00 34.50 4.73
299 300 1.828979 GGTCCTTTTTGGTCCGCATA 58.171 50.000 0.00 0.00 34.50 3.14
300 301 2.375146 GGTCCTTTTTGGTCCGCATAT 58.625 47.619 0.00 0.00 34.50 1.78
301 302 3.547746 GGTCCTTTTTGGTCCGCATATA 58.452 45.455 0.00 0.00 34.50 0.86
302 303 3.949113 GGTCCTTTTTGGTCCGCATATAA 59.051 43.478 0.00 0.00 34.50 0.98
303 304 4.036380 GGTCCTTTTTGGTCCGCATATAAG 59.964 45.833 0.00 0.00 34.50 1.73
304 305 4.638865 GTCCTTTTTGGTCCGCATATAAGT 59.361 41.667 0.00 0.00 37.07 2.24
305 306 5.124936 GTCCTTTTTGGTCCGCATATAAGTT 59.875 40.000 0.00 0.00 37.07 2.66
306 307 5.712917 TCCTTTTTGGTCCGCATATAAGTTT 59.287 36.000 0.00 0.00 37.07 2.66
307 308 6.209788 TCCTTTTTGGTCCGCATATAAGTTTT 59.790 34.615 0.00 0.00 37.07 2.43
308 309 7.393796 TCCTTTTTGGTCCGCATATAAGTTTTA 59.606 33.333 0.00 0.00 37.07 1.52
309 310 8.194769 CCTTTTTGGTCCGCATATAAGTTTTAT 58.805 33.333 0.00 0.00 0.00 1.40
310 311 9.233232 CTTTTTGGTCCGCATATAAGTTTTATC 57.767 33.333 0.00 0.00 0.00 1.75
311 312 6.870971 TTGGTCCGCATATAAGTTTTATCC 57.129 37.500 0.00 0.00 0.00 2.59
312 313 4.992319 TGGTCCGCATATAAGTTTTATCCG 59.008 41.667 0.00 0.00 0.00 4.18
313 314 5.221481 TGGTCCGCATATAAGTTTTATCCGA 60.221 40.000 0.00 0.00 0.00 4.55
314 315 5.697633 GGTCCGCATATAAGTTTTATCCGAA 59.302 40.000 0.00 0.00 0.00 4.30
315 316 6.128634 GGTCCGCATATAAGTTTTATCCGAAG 60.129 42.308 0.00 0.00 0.00 3.79
316 317 6.423001 GTCCGCATATAAGTTTTATCCGAAGT 59.577 38.462 0.00 0.00 0.00 3.01
317 318 6.643770 TCCGCATATAAGTTTTATCCGAAGTC 59.356 38.462 0.00 0.00 0.00 3.01
318 319 6.422701 CCGCATATAAGTTTTATCCGAAGTCA 59.577 38.462 0.00 0.00 0.00 3.41
319 320 7.042321 CCGCATATAAGTTTTATCCGAAGTCAA 60.042 37.037 0.00 0.00 0.00 3.18
320 321 8.332464 CGCATATAAGTTTTATCCGAAGTCAAA 58.668 33.333 0.00 0.00 0.00 2.69
321 322 9.651718 GCATATAAGTTTTATCCGAAGTCAAAG 57.348 33.333 0.00 0.00 0.00 2.77
322 323 9.651718 CATATAAGTTTTATCCGAAGTCAAAGC 57.348 33.333 0.00 0.00 0.00 3.51
323 324 7.681939 ATAAGTTTTATCCGAAGTCAAAGCA 57.318 32.000 0.00 0.00 0.00 3.91
324 325 6.575162 AAGTTTTATCCGAAGTCAAAGCAT 57.425 33.333 0.00 0.00 0.00 3.79
325 326 6.183309 AGTTTTATCCGAAGTCAAAGCATC 57.817 37.500 0.00 0.00 0.00 3.91
326 327 5.940470 AGTTTTATCCGAAGTCAAAGCATCT 59.060 36.000 0.00 0.00 0.00 2.90
327 328 6.092807 AGTTTTATCCGAAGTCAAAGCATCTC 59.907 38.462 0.00 0.00 0.00 2.75
328 329 3.902881 ATCCGAAGTCAAAGCATCTCT 57.097 42.857 0.00 0.00 0.00 3.10
329 330 6.465439 TTATCCGAAGTCAAAGCATCTCTA 57.535 37.500 0.00 0.00 0.00 2.43
330 331 4.111375 TCCGAAGTCAAAGCATCTCTAC 57.889 45.455 0.00 0.00 0.00 2.59
331 332 3.764434 TCCGAAGTCAAAGCATCTCTACT 59.236 43.478 0.00 0.00 0.00 2.57
332 333 4.220821 TCCGAAGTCAAAGCATCTCTACTT 59.779 41.667 0.00 0.00 0.00 2.24
333 334 4.932200 CCGAAGTCAAAGCATCTCTACTTT 59.068 41.667 0.00 0.00 36.56 2.66
381 382 8.845413 ACCAACATTTACAATGCAATATTGTT 57.155 26.923 16.61 1.58 41.81 2.83
382 383 9.935241 ACCAACATTTACAATGCAATATTGTTA 57.065 25.926 16.61 7.10 41.81 2.41
489 490 6.842676 ACAAAGTAAAAAGATCAGAGGGAGT 58.157 36.000 0.00 0.00 0.00 3.85
490 491 7.974504 ACAAAGTAAAAAGATCAGAGGGAGTA 58.025 34.615 0.00 0.00 0.00 2.59
491 492 8.097662 ACAAAGTAAAAAGATCAGAGGGAGTAG 58.902 37.037 0.00 0.00 0.00 2.57
492 493 8.314751 CAAAGTAAAAAGATCAGAGGGAGTAGA 58.685 37.037 0.00 0.00 0.00 2.59
493 494 8.616799 AAGTAAAAAGATCAGAGGGAGTAGAT 57.383 34.615 0.00 0.00 0.00 1.98
494 495 8.616799 AGTAAAAAGATCAGAGGGAGTAGATT 57.383 34.615 0.00 0.00 0.00 2.40
495 496 8.700973 AGTAAAAAGATCAGAGGGAGTAGATTC 58.299 37.037 0.00 0.00 0.00 2.52
510 511 5.385198 AGTAGATTCCTTTCCAAAGCACAA 58.615 37.500 0.00 0.00 34.69 3.33
541 542 1.731720 AGATCCTTGCTCTCGTTTGC 58.268 50.000 0.00 0.00 0.00 3.68
542 543 0.729690 GATCCTTGCTCTCGTTTGCC 59.270 55.000 0.00 0.00 0.00 4.52
543 544 0.678048 ATCCTTGCTCTCGTTTGCCC 60.678 55.000 0.00 0.00 0.00 5.36
544 545 2.680913 CCTTGCTCTCGTTTGCCCG 61.681 63.158 0.00 0.00 0.00 6.13
545 546 1.961277 CTTGCTCTCGTTTGCCCGT 60.961 57.895 0.00 0.00 0.00 5.28
688 697 3.514309 ACTATTTAGCCCTGTCGTCAAGT 59.486 43.478 0.00 0.00 0.00 3.16
735 744 2.357637 GCTGCTACGCCATTTTTGGATA 59.642 45.455 0.00 0.00 0.00 2.59
747 756 1.659022 TTTGGATACCCCGTCCTCAA 58.341 50.000 0.00 0.00 37.93 3.02
1143 1159 1.544917 ACAGCAAGGGGAAGGGGAT 60.545 57.895 0.00 0.00 0.00 3.85
1146 1162 0.628668 AGCAAGGGGAAGGGGATGAT 60.629 55.000 0.00 0.00 0.00 2.45
1160 1176 1.642037 GATGATGGCGCCATGGATCG 61.642 60.000 44.96 12.02 36.70 3.69
1206 1222 4.038042 TCGTTGCTCTCCAAGGTATCTATG 59.962 45.833 0.00 0.00 39.63 2.23
1208 1224 5.293560 GTTGCTCTCCAAGGTATCTATGTC 58.706 45.833 0.00 0.00 33.21 3.06
1214 1234 3.898123 TCCAAGGTATCTATGTCTCTGCC 59.102 47.826 0.00 0.00 0.00 4.85
1310 1330 5.732528 GCTGCAATTACCTGACATTCATCTG 60.733 44.000 0.00 0.00 0.00 2.90
1311 1331 4.096833 TGCAATTACCTGACATTCATCTGC 59.903 41.667 0.00 0.00 0.00 4.26
1312 1332 4.337555 GCAATTACCTGACATTCATCTGCT 59.662 41.667 0.00 0.00 0.00 4.24
1317 1337 4.701765 ACCTGACATTCATCTGCTACATC 58.298 43.478 0.00 0.00 0.00 3.06
1322 1342 2.492019 TTCATCTGCTACATCCGACG 57.508 50.000 0.00 0.00 0.00 5.12
1330 1350 1.067212 GCTACATCCGACGTCATCCTT 59.933 52.381 17.16 0.00 0.00 3.36
1368 1393 5.685954 CCTGCTTCATTCATTTCATCATTCG 59.314 40.000 0.00 0.00 0.00 3.34
1370 1395 6.623486 TGCTTCATTCATTTCATCATTCGTT 58.377 32.000 0.00 0.00 0.00 3.85
1378 1403 6.951643 TCATTTCATCATTCGTTAGATGCAG 58.048 36.000 0.00 0.00 41.02 4.41
1380 1405 5.973651 TTCATCATTCGTTAGATGCAGAC 57.026 39.130 0.00 0.00 41.02 3.51
1391 1416 5.760253 CGTTAGATGCAGACCCTGAATTTAT 59.240 40.000 0.00 0.00 28.32 1.40
1406 1438 7.599998 CCCTGAATTTATTTTCAACAGTTGGAG 59.400 37.037 13.52 0.00 35.31 3.86
1423 1455 1.671850 GGAGACGCTGGAAAACGATGA 60.672 52.381 0.00 0.00 0.00 2.92
1424 1456 2.271800 GAGACGCTGGAAAACGATGAT 58.728 47.619 0.00 0.00 0.00 2.45
1512 1544 1.006571 GACGTGGCGAAAGACCTGA 60.007 57.895 0.00 0.00 39.67 3.86
1856 1889 2.044793 TGTGTTCTCCCCTCCAGATT 57.955 50.000 0.00 0.00 0.00 2.40
1857 1890 3.199442 TGTGTTCTCCCCTCCAGATTA 57.801 47.619 0.00 0.00 0.00 1.75
1861 1894 4.654262 GTGTTCTCCCCTCCAGATTATGTA 59.346 45.833 0.00 0.00 0.00 2.29
1869 1902 5.765182 CCCCTCCAGATTATGTAATGTTGTC 59.235 44.000 0.00 0.00 0.00 3.18
1871 1904 6.356556 CCTCCAGATTATGTAATGTTGTCCA 58.643 40.000 0.00 0.00 0.00 4.02
1881 2256 7.849804 ATGTAATGTTGTCCATCTTGTCTAC 57.150 36.000 0.00 0.00 31.75 2.59
1986 2367 7.558161 TTGATCTCTGCACCATTTATTACTG 57.442 36.000 0.00 0.00 0.00 2.74
1987 2368 6.057533 TGATCTCTGCACCATTTATTACTGG 58.942 40.000 0.00 0.00 38.55 4.00
1988 2369 5.692115 TCTCTGCACCATTTATTACTGGA 57.308 39.130 0.00 0.00 36.35 3.86
1990 2371 5.189736 TCTCTGCACCATTTATTACTGGAGT 59.810 40.000 0.00 0.00 36.35 3.85
1997 2382 8.850156 GCACCATTTATTACTGGAGTAATCATT 58.150 33.333 14.02 0.34 45.22 2.57
2038 2423 4.352595 TGGGAAGGTTGAACCATCTCTTAA 59.647 41.667 19.00 0.00 37.36 1.85
2087 2472 2.814336 GGAGTGGAGGAATGTGTTTGAC 59.186 50.000 0.00 0.00 0.00 3.18
2110 2495 6.299141 ACTGATTTCCATGTGTAGTTTCAGT 58.701 36.000 0.00 0.00 37.16 3.41
2136 2524 6.163135 ACTCTTTGTACTACTGAAGCAAGT 57.837 37.500 0.00 0.00 0.00 3.16
2151 2539 2.103094 AGCAAGTGTGTCTGTAGCTGAA 59.897 45.455 0.00 0.00 31.62 3.02
2182 2570 4.713553 TGCAGTTACACTTCATTTCTCCA 58.286 39.130 0.00 0.00 0.00 3.86
2237 2821 5.997732 CAAATTCTGCTGGTATCGTTTTG 57.002 39.130 0.00 0.00 0.00 2.44
2318 2906 0.599558 TGCAACTGATTTGGAGCAGC 59.400 50.000 0.00 0.00 43.01 5.25
2320 2908 1.668047 GCAACTGATTTGGAGCAGCAC 60.668 52.381 0.00 0.00 43.01 4.40
2469 3270 7.347222 TCCTTCAATAGGTGATGTACAATAGGT 59.653 37.037 0.00 0.00 45.03 3.08
2493 3294 5.777802 CACTACTAGTGCTCCAATAGATGG 58.222 45.833 5.39 0.00 44.30 3.51
2521 3322 6.949578 AAACAAGTTCATTCACACAAACAG 57.050 33.333 0.00 0.00 0.00 3.16
2605 3406 8.023128 ACAAACATTGCAATGACTACTTCATAC 58.977 33.333 38.99 0.00 44.86 2.39
2640 3441 7.727578 TGATCACCCTGAACATAAACTACTA 57.272 36.000 0.00 0.00 0.00 1.82
2643 3444 7.166691 TCACCCTGAACATAAACTACTAGTC 57.833 40.000 0.00 0.00 0.00 2.59
2649 3450 7.081526 TGAACATAAACTACTAGTCGGACTC 57.918 40.000 15.05 0.00 0.00 3.36
2678 3480 1.590259 GGATCGAGTTCCAGAGCGC 60.590 63.158 0.00 0.00 35.72 5.92
2680 3482 3.417275 ATCGAGTTCCAGAGCGCGG 62.417 63.158 8.83 0.00 35.79 6.46
2695 3497 2.878429 CGGTGGTCTCCTCGTCAG 59.122 66.667 0.00 0.00 0.00 3.51
2699 3501 1.249407 GTGGTCTCCTCGTCAGAACT 58.751 55.000 0.00 0.00 0.00 3.01
2712 3514 2.946329 GTCAGAACTATCGAGCTCCTCA 59.054 50.000 8.47 0.00 0.00 3.86
2715 3517 2.811431 AGAACTATCGAGCTCCTCATCG 59.189 50.000 8.47 0.00 40.26 3.84
2716 3518 2.264005 ACTATCGAGCTCCTCATCGT 57.736 50.000 8.47 0.00 39.86 3.73
2717 3519 2.147958 ACTATCGAGCTCCTCATCGTC 58.852 52.381 8.47 0.00 39.86 4.20
2718 3520 1.127766 CTATCGAGCTCCTCATCGTCG 59.872 57.143 8.47 0.00 39.86 5.12
2719 3521 0.816018 ATCGAGCTCCTCATCGTCGT 60.816 55.000 8.47 0.00 39.86 4.34
2720 3522 1.010574 CGAGCTCCTCATCGTCGTC 60.011 63.158 8.47 0.00 34.30 4.20
2721 3523 1.010574 GAGCTCCTCATCGTCGTCG 60.011 63.158 0.87 0.00 38.55 5.12
2726 3528 0.675837 TCCTCATCGTCGTCGTCCTT 60.676 55.000 1.33 0.00 38.33 3.36
2752 3554 1.064208 ACTCGATCTTGATCACCGTCG 59.936 52.381 13.65 13.65 0.00 5.12
2760 3562 3.432051 GATCACCGTCGAGGGCCAG 62.432 68.421 23.64 13.82 46.96 4.85
2770 3572 2.930562 AGGGCCAGCCTCGTTCTT 60.931 61.111 6.18 0.00 36.10 2.52
2783 3585 1.412710 TCGTTCTTCTGCTTCACCTGT 59.587 47.619 0.00 0.00 0.00 4.00
2784 3586 2.158957 TCGTTCTTCTGCTTCACCTGTT 60.159 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.669089 TTTTAGGAGAAGACAAATTGGGTTT 57.331 32.000 0.00 0.00 0.00 3.27
2 3 7.508977 TCAATTTTAGGAGAAGACAAATTGGGT 59.491 33.333 13.11 0.00 41.80 4.51
4 5 9.415544 CTTCAATTTTAGGAGAAGACAAATTGG 57.584 33.333 13.11 0.00 41.80 3.16
5 6 9.415544 CCTTCAATTTTAGGAGAAGACAAATTG 57.584 33.333 8.66 8.66 42.41 2.32
6 7 9.147732 ACCTTCAATTTTAGGAGAAGACAAATT 57.852 29.630 9.14 0.00 39.78 1.82
7 8 8.712228 ACCTTCAATTTTAGGAGAAGACAAAT 57.288 30.769 9.14 0.00 39.78 2.32
8 9 8.413229 CAACCTTCAATTTTAGGAGAAGACAAA 58.587 33.333 9.14 0.00 39.78 2.83
9 10 7.470009 GCAACCTTCAATTTTAGGAGAAGACAA 60.470 37.037 9.14 0.00 39.78 3.18
10 11 6.016276 GCAACCTTCAATTTTAGGAGAAGACA 60.016 38.462 9.14 0.00 39.78 3.41
11 12 6.016276 TGCAACCTTCAATTTTAGGAGAAGAC 60.016 38.462 9.14 0.00 39.78 3.01
12 13 6.068010 TGCAACCTTCAATTTTAGGAGAAGA 58.932 36.000 9.14 0.00 39.78 2.87
13 14 6.331369 TGCAACCTTCAATTTTAGGAGAAG 57.669 37.500 9.14 2.54 37.74 2.85
14 15 6.723298 TTGCAACCTTCAATTTTAGGAGAA 57.277 33.333 9.14 0.00 35.45 2.87
15 16 6.916360 ATTGCAACCTTCAATTTTAGGAGA 57.084 33.333 0.00 0.00 35.45 3.71
16 17 9.657419 AAATATTGCAACCTTCAATTTTAGGAG 57.343 29.630 0.00 3.58 35.87 3.69
75 76 8.745590 GGTTGATACAAGTAATACCCAACAATT 58.254 33.333 0.00 0.00 35.64 2.32
76 77 7.066525 CGGTTGATACAAGTAATACCCAACAAT 59.933 37.037 0.00 0.00 35.64 2.71
77 78 6.372103 CGGTTGATACAAGTAATACCCAACAA 59.628 38.462 0.00 0.00 35.64 2.83
78 79 5.875910 CGGTTGATACAAGTAATACCCAACA 59.124 40.000 0.00 0.00 35.64 3.33
79 80 5.220719 GCGGTTGATACAAGTAATACCCAAC 60.221 44.000 0.00 0.00 33.85 3.77
80 81 4.877251 GCGGTTGATACAAGTAATACCCAA 59.123 41.667 0.00 0.00 0.00 4.12
81 82 4.444536 GCGGTTGATACAAGTAATACCCA 58.555 43.478 0.00 0.00 0.00 4.51
82 83 3.811497 GGCGGTTGATACAAGTAATACCC 59.189 47.826 0.00 0.00 0.00 3.69
83 84 3.492011 CGGCGGTTGATACAAGTAATACC 59.508 47.826 0.00 0.00 0.00 2.73
84 85 4.362279 TCGGCGGTTGATACAAGTAATAC 58.638 43.478 7.21 0.00 0.00 1.89
85 86 4.652421 TCGGCGGTTGATACAAGTAATA 57.348 40.909 7.21 0.00 0.00 0.98
86 87 3.530265 TCGGCGGTTGATACAAGTAAT 57.470 42.857 7.21 0.00 0.00 1.89
87 88 3.255725 CTTCGGCGGTTGATACAAGTAA 58.744 45.455 7.21 0.00 0.00 2.24
88 89 2.417651 CCTTCGGCGGTTGATACAAGTA 60.418 50.000 7.21 0.00 0.00 2.24
89 90 1.674817 CCTTCGGCGGTTGATACAAGT 60.675 52.381 7.21 0.00 0.00 3.16
90 91 1.006832 CCTTCGGCGGTTGATACAAG 58.993 55.000 7.21 0.00 0.00 3.16
91 92 1.022451 GCCTTCGGCGGTTGATACAA 61.022 55.000 7.21 0.00 39.62 2.41
92 93 1.448893 GCCTTCGGCGGTTGATACA 60.449 57.895 7.21 0.00 39.62 2.29
93 94 3.406559 GCCTTCGGCGGTTGATAC 58.593 61.111 7.21 0.00 39.62 2.24
103 104 0.040067 GACAAGCACTTTGCCTTCGG 60.040 55.000 0.00 0.00 46.52 4.30
104 105 0.662619 TGACAAGCACTTTGCCTTCG 59.337 50.000 0.00 0.00 46.52 3.79
105 106 2.412421 CTGACAAGCACTTTGCCTTC 57.588 50.000 0.00 0.00 46.52 3.46
129 130 6.036577 ACGCATTCTATGTTTCCCATTTTT 57.963 33.333 0.00 0.00 34.86 1.94
130 131 5.659440 ACGCATTCTATGTTTCCCATTTT 57.341 34.783 0.00 0.00 34.86 1.82
131 132 5.659440 AACGCATTCTATGTTTCCCATTT 57.341 34.783 0.00 0.00 34.86 2.32
132 133 6.767524 TTAACGCATTCTATGTTTCCCATT 57.232 33.333 0.00 0.00 34.86 3.16
133 134 6.767524 TTTAACGCATTCTATGTTTCCCAT 57.232 33.333 0.00 0.00 37.58 4.00
134 135 6.767524 ATTTAACGCATTCTATGTTTCCCA 57.232 33.333 0.00 0.00 0.00 4.37
135 136 7.009174 CACAATTTAACGCATTCTATGTTTCCC 59.991 37.037 0.00 0.00 0.00 3.97
136 137 7.009174 CCACAATTTAACGCATTCTATGTTTCC 59.991 37.037 0.00 0.00 0.00 3.13
137 138 7.462724 GCCACAATTTAACGCATTCTATGTTTC 60.463 37.037 0.00 0.00 0.00 2.78
138 139 6.310224 GCCACAATTTAACGCATTCTATGTTT 59.690 34.615 0.00 0.00 0.00 2.83
139 140 5.804979 GCCACAATTTAACGCATTCTATGTT 59.195 36.000 0.00 0.00 0.00 2.71
140 141 5.105957 TGCCACAATTTAACGCATTCTATGT 60.106 36.000 0.00 0.00 0.00 2.29
141 142 5.229887 GTGCCACAATTTAACGCATTCTATG 59.770 40.000 0.00 0.00 0.00 2.23
142 143 5.105957 TGTGCCACAATTTAACGCATTCTAT 60.106 36.000 0.00 0.00 0.00 1.98
143 144 4.216472 TGTGCCACAATTTAACGCATTCTA 59.784 37.500 0.00 0.00 0.00 2.10
144 145 3.005261 TGTGCCACAATTTAACGCATTCT 59.995 39.130 0.00 0.00 0.00 2.40
145 146 3.312828 TGTGCCACAATTTAACGCATTC 58.687 40.909 0.00 0.00 0.00 2.67
146 147 3.377346 TGTGCCACAATTTAACGCATT 57.623 38.095 0.00 0.00 0.00 3.56
147 148 3.243704 ACTTGTGCCACAATTTAACGCAT 60.244 39.130 11.26 0.00 37.48 4.73
148 149 2.099921 ACTTGTGCCACAATTTAACGCA 59.900 40.909 11.26 0.00 37.48 5.24
149 150 2.738135 ACTTGTGCCACAATTTAACGC 58.262 42.857 11.26 0.00 37.48 4.84
150 151 4.800993 TGAAACTTGTGCCACAATTTAACG 59.199 37.500 11.26 0.60 37.48 3.18
151 152 6.031549 GTGAAACTTGTGCCACAATTTAAC 57.968 37.500 11.26 12.31 37.48 2.01
216 217 9.917129 TCTCAAGTTTTACGTTTATGACAGATA 57.083 29.630 0.00 0.00 0.00 1.98
217 218 8.827177 TCTCAAGTTTTACGTTTATGACAGAT 57.173 30.769 0.00 0.00 0.00 2.90
218 219 8.827177 ATCTCAAGTTTTACGTTTATGACAGA 57.173 30.769 0.00 0.00 0.00 3.41
254 255 9.512588 CGGAGGGAGTATATTAAGTAGAGTAAA 57.487 37.037 0.00 0.00 0.00 2.01
276 277 2.942641 GGACCAAAAAGGACCGGAG 58.057 57.895 9.46 0.00 42.31 4.63
281 282 4.638865 ACTTATATGCGGACCAAAAAGGAC 59.361 41.667 0.00 0.00 41.22 3.85
282 283 4.850680 ACTTATATGCGGACCAAAAAGGA 58.149 39.130 0.00 0.00 41.22 3.36
283 284 5.576447 AACTTATATGCGGACCAAAAAGG 57.424 39.130 0.00 0.00 45.67 3.11
284 285 9.233232 GATAAAACTTATATGCGGACCAAAAAG 57.767 33.333 0.00 0.00 0.00 2.27
285 286 8.192110 GGATAAAACTTATATGCGGACCAAAAA 58.808 33.333 0.00 0.00 0.00 1.94
286 287 7.467539 CGGATAAAACTTATATGCGGACCAAAA 60.468 37.037 0.00 0.00 39.83 2.44
287 288 6.017770 CGGATAAAACTTATATGCGGACCAAA 60.018 38.462 0.00 0.00 39.83 3.28
288 289 5.467399 CGGATAAAACTTATATGCGGACCAA 59.533 40.000 0.00 0.00 39.83 3.67
289 290 4.992319 CGGATAAAACTTATATGCGGACCA 59.008 41.667 0.00 0.00 39.83 4.02
290 291 5.232463 TCGGATAAAACTTATATGCGGACC 58.768 41.667 7.43 0.00 42.55 4.46
291 292 6.423001 ACTTCGGATAAAACTTATATGCGGAC 59.577 38.462 7.43 0.00 42.55 4.79
292 293 6.518493 ACTTCGGATAAAACTTATATGCGGA 58.482 36.000 7.43 0.00 42.55 5.54
293 294 6.422701 TGACTTCGGATAAAACTTATATGCGG 59.577 38.462 7.43 0.00 42.55 5.69
294 295 7.402811 TGACTTCGGATAAAACTTATATGCG 57.597 36.000 1.71 1.71 43.31 4.73
295 296 9.651718 CTTTGACTTCGGATAAAACTTATATGC 57.348 33.333 0.00 0.00 0.00 3.14
296 297 9.651718 GCTTTGACTTCGGATAAAACTTATATG 57.348 33.333 0.00 0.00 0.00 1.78
297 298 9.391006 TGCTTTGACTTCGGATAAAACTTATAT 57.609 29.630 0.00 0.00 0.00 0.86
298 299 8.780846 TGCTTTGACTTCGGATAAAACTTATA 57.219 30.769 0.00 0.00 0.00 0.98
299 300 7.681939 TGCTTTGACTTCGGATAAAACTTAT 57.318 32.000 0.00 0.00 0.00 1.73
300 301 7.606456 AGATGCTTTGACTTCGGATAAAACTTA 59.394 33.333 0.00 0.00 0.00 2.24
301 302 6.431234 AGATGCTTTGACTTCGGATAAAACTT 59.569 34.615 0.00 0.00 0.00 2.66
302 303 5.940470 AGATGCTTTGACTTCGGATAAAACT 59.060 36.000 0.00 0.00 0.00 2.66
303 304 6.092807 AGAGATGCTTTGACTTCGGATAAAAC 59.907 38.462 0.00 0.00 0.00 2.43
304 305 6.173339 AGAGATGCTTTGACTTCGGATAAAA 58.827 36.000 0.00 0.00 0.00 1.52
305 306 5.734720 AGAGATGCTTTGACTTCGGATAAA 58.265 37.500 0.00 0.00 0.00 1.40
306 307 5.344743 AGAGATGCTTTGACTTCGGATAA 57.655 39.130 0.00 0.00 0.00 1.75
307 308 5.594725 AGTAGAGATGCTTTGACTTCGGATA 59.405 40.000 0.00 0.00 0.00 2.59
308 309 3.902881 AGAGATGCTTTGACTTCGGAT 57.097 42.857 0.00 0.00 0.00 4.18
309 310 3.764434 AGTAGAGATGCTTTGACTTCGGA 59.236 43.478 0.00 0.00 0.00 4.55
310 311 4.116747 AGTAGAGATGCTTTGACTTCGG 57.883 45.455 0.00 0.00 0.00 4.30
355 356 9.935241 AACAATATTGCATTGTAAATGTTGGTA 57.065 25.926 15.48 0.00 40.94 3.25
356 357 8.845413 AACAATATTGCATTGTAAATGTTGGT 57.155 26.923 15.48 13.62 40.94 3.67
463 464 8.606830 ACTCCCTCTGATCTTTTTACTTTGTAT 58.393 33.333 0.00 0.00 0.00 2.29
464 465 7.974504 ACTCCCTCTGATCTTTTTACTTTGTA 58.025 34.615 0.00 0.00 0.00 2.41
465 466 6.842676 ACTCCCTCTGATCTTTTTACTTTGT 58.157 36.000 0.00 0.00 0.00 2.83
466 467 8.314751 TCTACTCCCTCTGATCTTTTTACTTTG 58.685 37.037 0.00 0.00 0.00 2.77
467 468 8.437274 TCTACTCCCTCTGATCTTTTTACTTT 57.563 34.615 0.00 0.00 0.00 2.66
468 469 8.616799 ATCTACTCCCTCTGATCTTTTTACTT 57.383 34.615 0.00 0.00 0.00 2.24
469 470 8.616799 AATCTACTCCCTCTGATCTTTTTACT 57.383 34.615 0.00 0.00 0.00 2.24
470 471 7.929245 GGAATCTACTCCCTCTGATCTTTTTAC 59.071 40.741 0.00 0.00 0.00 2.01
471 472 7.846823 AGGAATCTACTCCCTCTGATCTTTTTA 59.153 37.037 0.00 0.00 35.95 1.52
472 473 6.676189 AGGAATCTACTCCCTCTGATCTTTTT 59.324 38.462 0.00 0.00 35.95 1.94
473 474 6.209026 AGGAATCTACTCCCTCTGATCTTTT 58.791 40.000 0.00 0.00 35.95 2.27
474 475 5.787327 AGGAATCTACTCCCTCTGATCTTT 58.213 41.667 0.00 0.00 35.95 2.52
475 476 5.417170 AGGAATCTACTCCCTCTGATCTT 57.583 43.478 0.00 0.00 35.95 2.40
476 477 5.417170 AAGGAATCTACTCCCTCTGATCT 57.583 43.478 0.00 0.00 35.95 2.75
477 478 5.011635 GGAAAGGAATCTACTCCCTCTGATC 59.988 48.000 0.00 0.00 35.95 2.92
478 479 4.904853 GGAAAGGAATCTACTCCCTCTGAT 59.095 45.833 0.00 0.00 35.95 2.90
479 480 4.264850 TGGAAAGGAATCTACTCCCTCTGA 60.265 45.833 0.00 0.00 35.95 3.27
480 481 4.033709 TGGAAAGGAATCTACTCCCTCTG 58.966 47.826 0.00 0.00 35.95 3.35
481 482 4.354208 TGGAAAGGAATCTACTCCCTCT 57.646 45.455 0.00 0.00 35.95 3.69
482 483 5.432645 CTTTGGAAAGGAATCTACTCCCTC 58.567 45.833 0.00 0.00 35.95 4.30
483 484 4.324641 GCTTTGGAAAGGAATCTACTCCCT 60.325 45.833 1.45 0.00 35.95 4.20
484 485 3.948473 GCTTTGGAAAGGAATCTACTCCC 59.052 47.826 1.45 0.00 35.95 4.30
485 486 4.396478 GTGCTTTGGAAAGGAATCTACTCC 59.604 45.833 1.45 0.00 38.11 3.85
486 487 5.003804 TGTGCTTTGGAAAGGAATCTACTC 58.996 41.667 1.45 0.00 38.11 2.59
487 488 4.985538 TGTGCTTTGGAAAGGAATCTACT 58.014 39.130 1.45 0.00 38.11 2.57
488 489 5.473504 TCTTGTGCTTTGGAAAGGAATCTAC 59.526 40.000 1.45 0.00 38.11 2.59
489 490 5.630121 TCTTGTGCTTTGGAAAGGAATCTA 58.370 37.500 1.45 0.00 38.11 1.98
490 491 4.473444 TCTTGTGCTTTGGAAAGGAATCT 58.527 39.130 1.45 0.00 38.11 2.40
491 492 4.853924 TCTTGTGCTTTGGAAAGGAATC 57.146 40.909 1.45 0.00 38.11 2.52
492 493 5.541484 AGATTCTTGTGCTTTGGAAAGGAAT 59.459 36.000 1.45 1.89 38.11 3.01
493 494 4.895297 AGATTCTTGTGCTTTGGAAAGGAA 59.105 37.500 1.45 0.00 38.11 3.36
494 495 4.473444 AGATTCTTGTGCTTTGGAAAGGA 58.527 39.130 1.45 0.00 36.53 3.36
495 496 4.861102 AGATTCTTGTGCTTTGGAAAGG 57.139 40.909 1.45 0.00 36.53 3.11
664 671 5.363005 ACTTGACGACAGGGCTAAATAGTAT 59.637 40.000 1.81 0.00 0.00 2.12
778 787 1.299468 GCGACGGCGAGATGAGATT 60.299 57.895 18.90 0.00 40.82 2.40
1023 1039 3.498071 CCACCACCACCACCACCT 61.498 66.667 0.00 0.00 0.00 4.00
1128 1144 0.468771 CATCATCCCCTTCCCCTTGC 60.469 60.000 0.00 0.00 0.00 4.01
1130 1146 1.659035 GCCATCATCCCCTTCCCCTT 61.659 60.000 0.00 0.00 0.00 3.95
1131 1147 2.087461 GCCATCATCCCCTTCCCCT 61.087 63.158 0.00 0.00 0.00 4.79
1132 1148 2.523016 GCCATCATCCCCTTCCCC 59.477 66.667 0.00 0.00 0.00 4.81
1133 1149 2.113986 CGCCATCATCCCCTTCCC 59.886 66.667 0.00 0.00 0.00 3.97
1134 1150 2.595754 GCGCCATCATCCCCTTCC 60.596 66.667 0.00 0.00 0.00 3.46
1135 1151 2.595754 GGCGCCATCATCCCCTTC 60.596 66.667 24.80 0.00 0.00 3.46
1143 1159 2.281002 CGATCCATGGCGCCATCA 60.281 61.111 38.60 27.43 33.90 3.07
1146 1162 3.738429 CTCACGATCCATGGCGCCA 62.738 63.158 34.80 34.80 0.00 5.69
1206 1222 3.944055 TGTACAAGAAGAGGCAGAGAC 57.056 47.619 0.00 0.00 0.00 3.36
1208 1224 4.159321 TCAGATGTACAAGAAGAGGCAGAG 59.841 45.833 0.00 0.00 0.00 3.35
1214 1234 8.777413 TGAAACAATTCAGATGTACAAGAAGAG 58.223 33.333 0.00 4.70 40.59 2.85
1310 1330 0.669077 AGGATGACGTCGGATGTAGC 59.331 55.000 11.62 0.00 0.00 3.58
1311 1331 3.116300 CAAAGGATGACGTCGGATGTAG 58.884 50.000 11.62 0.00 0.00 2.74
1312 1332 2.494471 ACAAAGGATGACGTCGGATGTA 59.506 45.455 11.62 0.00 0.00 2.29
1317 1337 2.359792 CGACAAAGGATGACGTCGG 58.640 57.895 11.62 0.00 45.60 4.79
1330 1350 4.574892 TGAAGCAGGATTTGTATCGACAA 58.425 39.130 0.00 0.00 43.94 3.18
1350 1370 8.071967 GCATCTAACGAATGATGAAATGAATGA 58.928 33.333 16.00 0.00 41.69 2.57
1368 1393 7.573968 AATAAATTCAGGGTCTGCATCTAAC 57.426 36.000 0.00 0.00 0.00 2.34
1370 1395 7.833682 TGAAAATAAATTCAGGGTCTGCATCTA 59.166 33.333 0.00 0.00 34.50 1.98
1378 1403 7.384932 CCAACTGTTGAAAATAAATTCAGGGTC 59.615 37.037 21.49 0.00 40.21 4.46
1380 1405 7.441017 TCCAACTGTTGAAAATAAATTCAGGG 58.559 34.615 21.49 0.00 40.21 4.45
1391 1416 2.354510 CAGCGTCTCCAACTGTTGAAAA 59.645 45.455 21.49 6.15 0.00 2.29
1406 1438 1.999735 TCATCATCGTTTTCCAGCGTC 59.000 47.619 0.00 0.00 0.00 5.19
1423 1455 4.221422 CGGCACCGTCCGGATCAT 62.221 66.667 7.81 0.00 45.38 2.45
1512 1544 2.039480 TGTTCTGCCTCTTGATCTTGCT 59.961 45.455 0.00 0.00 0.00 3.91
1856 1889 8.536175 TGTAGACAAGATGGACAACATTACATA 58.464 33.333 0.00 0.00 40.72 2.29
1857 1890 7.394016 TGTAGACAAGATGGACAACATTACAT 58.606 34.615 0.00 0.00 40.72 2.29
1861 1894 6.114187 TCTGTAGACAAGATGGACAACATT 57.886 37.500 0.00 0.00 40.72 2.71
1869 1902 7.046652 ACAAATCTCATCTGTAGACAAGATGG 58.953 38.462 12.21 5.09 39.69 3.51
1871 1904 9.761504 CATACAAATCTCATCTGTAGACAAGAT 57.238 33.333 3.31 3.31 32.95 2.40
1881 2256 4.825634 ACATGGCCATACAAATCTCATCTG 59.174 41.667 20.30 4.63 0.00 2.90
1959 2340 9.193806 AGTAATAAATGGTGCAGAGATCAAAAT 57.806 29.630 0.00 0.00 0.00 1.82
1969 2350 7.807977 ATTACTCCAGTAATAAATGGTGCAG 57.192 36.000 9.79 0.00 46.15 4.41
1984 2365 8.737168 TTTTCAGGTGATAATGATTACTCCAG 57.263 34.615 0.00 0.00 0.00 3.86
1986 2367 9.956720 CATTTTTCAGGTGATAATGATTACTCC 57.043 33.333 8.56 0.00 32.66 3.85
1987 2368 9.455847 GCATTTTTCAGGTGATAATGATTACTC 57.544 33.333 14.72 0.00 32.66 2.59
1988 2369 8.416329 GGCATTTTTCAGGTGATAATGATTACT 58.584 33.333 14.72 0.00 32.66 2.24
1990 2371 8.415553 CAGGCATTTTTCAGGTGATAATGATTA 58.584 33.333 14.72 0.00 32.66 1.75
1997 2382 3.011144 TCCCAGGCATTTTTCAGGTGATA 59.989 43.478 0.00 0.00 0.00 2.15
2038 2423 4.469657 TGTCTGAAATACAGGGCTGTTTT 58.530 39.130 0.00 0.00 45.76 2.43
2087 2472 6.808008 ACTGAAACTACACATGGAAATCAG 57.192 37.500 0.00 4.35 38.14 2.90
2110 2495 8.202137 ACTTGCTTCAGTAGTACAAAGAGTTTA 58.798 33.333 15.76 0.00 0.00 2.01
2136 2524 3.321968 ACATCAGTTCAGCTACAGACACA 59.678 43.478 0.00 0.00 0.00 3.72
2182 2570 3.181429 ACATCCACACAACAGGATTCCTT 60.181 43.478 1.28 0.00 41.80 3.36
2260 2847 3.384789 AGCAGGCAGAATTGTATCGTCTA 59.615 43.478 0.00 0.00 0.00 2.59
2318 2906 5.181056 GGAAAATTAACAGGCCAATTTGGTG 59.819 40.000 16.62 10.38 40.46 4.17
2320 2908 5.559770 AGGAAAATTAACAGGCCAATTTGG 58.440 37.500 11.27 11.27 41.55 3.28
2417 3215 2.489938 TGTGATGTAGAAAGGCACCC 57.510 50.000 0.00 0.00 0.00 4.61
2493 3294 7.804614 TTGTGTGAATGAACTTGTTTTACAC 57.195 32.000 0.00 0.00 37.13 2.90
2502 3303 6.324819 CACTTCTGTTTGTGTGAATGAACTT 58.675 36.000 0.00 0.00 32.72 2.66
2521 3322 5.689383 TGAACTTGGTATCTTTGCACTTC 57.311 39.130 0.00 0.00 0.00 3.01
2577 3378 7.584108 TGAAGTAGTCATTGCAATGTTTGTAG 58.416 34.615 32.67 11.25 37.65 2.74
2580 3381 7.485913 GGTATGAAGTAGTCATTGCAATGTTTG 59.514 37.037 32.67 14.59 45.13 2.93
2605 3406 3.889538 TCAGGGTGATCAAGTAGTATCGG 59.110 47.826 0.00 0.00 0.00 4.18
2640 3441 4.680537 AGCACCCCGAGTCCGACT 62.681 66.667 0.00 0.00 38.22 4.18
2643 3444 4.135153 CAGAGCACCCCGAGTCCG 62.135 72.222 0.00 0.00 0.00 4.79
2649 3450 3.144120 CTCGATCCAGAGCACCCCG 62.144 68.421 0.00 0.00 0.00 5.73
2678 3480 1.241990 TTCTGACGAGGAGACCACCG 61.242 60.000 0.00 0.00 34.73 4.94
2680 3482 1.249407 AGTTCTGACGAGGAGACCAC 58.751 55.000 0.00 0.00 0.00 4.16
2695 3497 2.550606 ACGATGAGGAGCTCGATAGTTC 59.449 50.000 7.83 0.00 38.24 3.01
2699 3501 1.149148 CGACGATGAGGAGCTCGATA 58.851 55.000 7.83 0.00 38.24 2.92
2712 3514 1.134075 CGACAAGGACGACGACGAT 59.866 57.895 15.32 0.00 42.66 3.73
2715 3517 2.949106 TCCGACAAGGACGACGAC 59.051 61.111 0.00 0.00 45.98 4.34
2736 3538 1.269309 CCCTCGACGGTGATCAAGATC 60.269 57.143 0.00 3.12 38.29 2.75
2740 3542 2.577059 GCCCTCGACGGTGATCAA 59.423 61.111 0.00 0.00 0.00 2.57
2760 3562 0.793250 GTGAAGCAGAAGAACGAGGC 59.207 55.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.