Multiple sequence alignment - TraesCS5A01G189100

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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 TraesCS5A01G189100 chr5A 100.000 4346 0 0 150 4495 391547124 391542779 0.000000e+00 8026.0
1 TraesCS5A01G189100 chr5A 100.000 41 0 0 1 41 391547273 391547233 4.820000e-10 76.8
2 TraesCS5A01G189100 chr5D 92.835 4103 192 52 417 4477 306190951 306194993 0.000000e+00 5854.0
3 TraesCS5A01G189100 chr5B 92.155 4219 204 61 354 4495 351473926 351478094 0.000000e+00 5840.0
4 TraesCS5A01G189100 chr5B 96.875 32 1 0 690 721 351474342 351474373 2.000000e-03 54.7
5 TraesCS5A01G189100 chr3A 97.487 199 5 0 153 351 489168116 489168314 1.550000e-89 340.0
6 TraesCS5A01G189100 chr3A 88.235 204 20 4 3822 4023 562982041 562982242 1.620000e-59 241.0
7 TraesCS5A01G189100 chr6B 96.135 207 8 0 150 356 402580112 402579906 5.570000e-89 339.0
8 TraesCS5A01G189100 chr7A 97.015 201 3 3 153 353 69160972 69160775 7.200000e-88 335.0
9 TraesCS5A01G189100 chr2B 96.985 199 5 1 153 351 138630803 138630606 2.590000e-87 333.0
10 TraesCS5A01G189100 chr1A 96.078 204 8 0 150 353 321772688 321772891 2.590000e-87 333.0
11 TraesCS5A01G189100 chr1A 96.500 200 6 1 153 352 521869216 521869414 3.350000e-86 329.0
12 TraesCS5A01G189100 chr6A 96.517 201 6 1 153 353 564852439 564852240 9.320000e-87 331.0
13 TraesCS5A01G189100 chr6A 84.038 213 21 9 3822 4023 561434044 561434254 4.590000e-45 193.0
14 TraesCS5A01G189100 chr6A 83.796 216 22 9 3822 4026 561619832 561619619 4.590000e-45 193.0
15 TraesCS5A01G189100 chr4A 95.215 209 7 3 150 358 311489834 311489629 1.210000e-85 327.0
16 TraesCS5A01G189100 chr7B 94.313 211 11 1 150 360 497919213 497919422 5.610000e-84 322.0
17 TraesCS5A01G189100 chr7B 88.571 140 15 1 3822 3960 44379273 44379134 7.730000e-38 169.0
18 TraesCS5A01G189100 chr3D 85.657 251 25 4 3823 4073 443308466 443308705 2.080000e-63 254.0
19 TraesCS5A01G189100 chr1D 85.657 251 24 6 3823 4073 126870500 126870262 2.080000e-63 254.0
20 TraesCS5A01G189100 chrUn 84.722 216 20 8 3822 4026 302550458 302550245 2.120000e-48 204.0


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 TraesCS5A01G189100 chr5A 391542779 391547273 4494 True 4051.40 8026 100.000 1 4495 2 chr5A.!!$R1 4494
1 TraesCS5A01G189100 chr5D 306190951 306194993 4042 False 5854.00 5854 92.835 417 4477 1 chr5D.!!$F1 4060
2 TraesCS5A01G189100 chr5B 351473926 351478094 4168 False 2947.35 5840 94.515 354 4495 2 chr5B.!!$F1 4141

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
348 349 0.104120 AAACGCCCAAAAGAACTGGC 59.896 50.000 0.00 0.00 40.54 4.85 F
352 353 0.251608 GCCCAAAAGAACTGGCCCTA 60.252 55.000 0.00 0.00 37.94 3.53 F
1956 1979 1.762957 TGGTTAGTGCAGGATCCTAGC 59.237 52.381 15.67 19.84 0.00 3.42 F
3221 3299 2.426738 CTCTCAGTCCAGTGATCCTGAC 59.573 54.545 11.48 8.37 44.49 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1427 0.607489 CTCTTTGCTCCACCCAGGTG 60.607 60.000 10.00 10.0 45.02 4.00 R
2037 2061 2.551270 GCACCAAGCGACAAGACG 59.449 61.111 0.00 0.0 0.00 4.18 R
3269 3347 0.096628 CAGCACGCATCTGCTTCTTC 59.903 55.000 0.09 0.0 45.64 2.87 R
4379 4490 0.458370 TCGATCATCTGTGCCACACG 60.458 55.000 0.00 0.0 37.14 4.49 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
32 33 2.668625 GGAAGATTCCGGAGTAGGTCT 58.331 52.381 3.34 1.94 37.65 3.85
33 34 3.032459 GGAAGATTCCGGAGTAGGTCTT 58.968 50.000 3.34 10.60 37.65 3.01
34 35 3.181474 GGAAGATTCCGGAGTAGGTCTTG 60.181 52.174 17.21 0.00 37.65 3.02
35 36 2.389715 AGATTCCGGAGTAGGTCTTGG 58.610 52.381 3.34 0.00 0.00 3.61
36 37 1.413077 GATTCCGGAGTAGGTCTTGGG 59.587 57.143 3.34 0.00 0.00 4.12
37 38 0.616679 TTCCGGAGTAGGTCTTGGGG 60.617 60.000 3.34 0.00 0.00 4.96
38 39 1.001248 CCGGAGTAGGTCTTGGGGA 59.999 63.158 0.00 0.00 0.00 4.81
39 40 1.043673 CCGGAGTAGGTCTTGGGGAG 61.044 65.000 0.00 0.00 0.00 4.30
40 41 1.043673 CGGAGTAGGTCTTGGGGAGG 61.044 65.000 0.00 0.00 0.00 4.30
167 168 3.948735 TAGGGGCCAGTTCTTTTCG 57.051 52.632 4.39 0.00 0.00 3.46
168 169 0.326927 TAGGGGCCAGTTCTTTTCGG 59.673 55.000 4.39 0.00 0.00 4.30
169 170 2.636412 GGGGCCAGTTCTTTTCGGC 61.636 63.158 4.39 0.00 44.10 5.54
170 171 2.561373 GGCCAGTTCTTTTCGGCG 59.439 61.111 0.00 0.00 45.85 6.46
171 172 1.964373 GGCCAGTTCTTTTCGGCGA 60.964 57.895 4.99 4.99 45.85 5.54
172 173 1.305930 GGCCAGTTCTTTTCGGCGAT 61.306 55.000 11.76 0.00 45.85 4.58
173 174 0.521735 GCCAGTTCTTTTCGGCGATT 59.478 50.000 11.76 0.00 34.26 3.34
174 175 1.465856 GCCAGTTCTTTTCGGCGATTC 60.466 52.381 11.76 0.00 34.26 2.52
175 176 2.076863 CCAGTTCTTTTCGGCGATTCT 58.923 47.619 11.76 0.35 0.00 2.40
176 177 2.094417 CCAGTTCTTTTCGGCGATTCTC 59.906 50.000 11.76 0.00 0.00 2.87
177 178 2.094417 CAGTTCTTTTCGGCGATTCTCC 59.906 50.000 11.76 0.00 0.00 3.71
178 179 1.397343 GTTCTTTTCGGCGATTCTCCC 59.603 52.381 11.76 0.00 0.00 4.30
179 180 0.611200 TCTTTTCGGCGATTCTCCCA 59.389 50.000 11.76 0.00 0.00 4.37
180 181 1.009829 CTTTTCGGCGATTCTCCCAG 58.990 55.000 11.76 0.00 0.00 4.45
181 182 0.611200 TTTTCGGCGATTCTCCCAGA 59.389 50.000 11.76 0.00 0.00 3.86
182 183 0.611200 TTTCGGCGATTCTCCCAGAA 59.389 50.000 11.76 0.00 38.78 3.02
183 184 0.830648 TTCGGCGATTCTCCCAGAAT 59.169 50.000 11.76 0.00 46.84 2.40
189 190 1.839894 ATTCTCCCAGAATCGCCCC 59.160 57.895 0.00 0.00 40.75 5.80
190 191 1.709994 ATTCTCCCAGAATCGCCCCC 61.710 60.000 0.00 0.00 40.75 5.40
191 192 2.770048 CTCCCAGAATCGCCCCCT 60.770 66.667 0.00 0.00 0.00 4.79
192 193 2.286121 TCCCAGAATCGCCCCCTT 60.286 61.111 0.00 0.00 0.00 3.95
193 194 2.193248 CCCAGAATCGCCCCCTTC 59.807 66.667 0.00 0.00 0.00 3.46
194 195 2.193248 CCAGAATCGCCCCCTTCC 59.807 66.667 0.00 0.00 0.00 3.46
195 196 2.193248 CAGAATCGCCCCCTTCCC 59.807 66.667 0.00 0.00 0.00 3.97
196 197 3.097162 AGAATCGCCCCCTTCCCC 61.097 66.667 0.00 0.00 0.00 4.81
197 198 3.416880 GAATCGCCCCCTTCCCCA 61.417 66.667 0.00 0.00 0.00 4.96
198 199 3.420482 AATCGCCCCCTTCCCCAG 61.420 66.667 0.00 0.00 0.00 4.45
202 203 4.448976 GCCCCCTTCCCCAGCTTC 62.449 72.222 0.00 0.00 0.00 3.86
203 204 2.615288 CCCCCTTCCCCAGCTTCT 60.615 66.667 0.00 0.00 0.00 2.85
204 205 2.684499 CCCCCTTCCCCAGCTTCTC 61.684 68.421 0.00 0.00 0.00 2.87
205 206 2.684499 CCCCTTCCCCAGCTTCTCC 61.684 68.421 0.00 0.00 0.00 3.71
206 207 2.684499 CCCTTCCCCAGCTTCTCCC 61.684 68.421 0.00 0.00 0.00 4.30
207 208 1.925455 CCTTCCCCAGCTTCTCCCA 60.925 63.158 0.00 0.00 0.00 4.37
208 209 1.606531 CTTCCCCAGCTTCTCCCAG 59.393 63.158 0.00 0.00 0.00 4.45
209 210 0.911525 CTTCCCCAGCTTCTCCCAGA 60.912 60.000 0.00 0.00 0.00 3.86
210 211 0.475632 TTCCCCAGCTTCTCCCAGAA 60.476 55.000 0.00 0.00 32.50 3.02
211 212 0.253347 TCCCCAGCTTCTCCCAGAAT 60.253 55.000 0.00 0.00 33.13 2.40
212 213 0.182299 CCCCAGCTTCTCCCAGAATC 59.818 60.000 0.00 0.00 33.13 2.52
213 214 0.179062 CCCAGCTTCTCCCAGAATCG 60.179 60.000 0.00 0.00 33.13 3.34
214 215 0.813210 CCAGCTTCTCCCAGAATCGC 60.813 60.000 0.00 0.00 33.13 4.58
215 216 0.813210 CAGCTTCTCCCAGAATCGCC 60.813 60.000 0.00 0.00 33.13 5.54
216 217 1.221840 GCTTCTCCCAGAATCGCCA 59.778 57.895 0.00 0.00 33.13 5.69
217 218 1.092345 GCTTCTCCCAGAATCGCCAC 61.092 60.000 0.00 0.00 33.13 5.01
218 219 0.539051 CTTCTCCCAGAATCGCCACT 59.461 55.000 0.00 0.00 33.13 4.00
219 220 1.757118 CTTCTCCCAGAATCGCCACTA 59.243 52.381 0.00 0.00 33.13 2.74
220 221 1.112113 TCTCCCAGAATCGCCACTAC 58.888 55.000 0.00 0.00 0.00 2.73
221 222 0.824109 CTCCCAGAATCGCCACTACA 59.176 55.000 0.00 0.00 0.00 2.74
222 223 1.414181 CTCCCAGAATCGCCACTACAT 59.586 52.381 0.00 0.00 0.00 2.29
223 224 2.628178 CTCCCAGAATCGCCACTACATA 59.372 50.000 0.00 0.00 0.00 2.29
224 225 3.239449 TCCCAGAATCGCCACTACATAT 58.761 45.455 0.00 0.00 0.00 1.78
225 226 3.646162 TCCCAGAATCGCCACTACATATT 59.354 43.478 0.00 0.00 0.00 1.28
226 227 4.102524 TCCCAGAATCGCCACTACATATTT 59.897 41.667 0.00 0.00 0.00 1.40
227 228 4.821805 CCCAGAATCGCCACTACATATTTT 59.178 41.667 0.00 0.00 0.00 1.82
228 229 5.299279 CCCAGAATCGCCACTACATATTTTT 59.701 40.000 0.00 0.00 0.00 1.94
270 271 9.214962 AGTTAAGGTCTAATTAGCTAGGATTGT 57.785 33.333 7.67 0.00 0.00 2.71
297 298 7.578310 AAAACATATGGAGTGATGATTCTGG 57.422 36.000 7.80 0.00 0.00 3.86
298 299 5.238624 ACATATGGAGTGATGATTCTGGG 57.761 43.478 7.80 0.00 0.00 4.45
299 300 4.909695 ACATATGGAGTGATGATTCTGGGA 59.090 41.667 7.80 0.00 0.00 4.37
300 301 5.012871 ACATATGGAGTGATGATTCTGGGAG 59.987 44.000 7.80 0.00 0.00 4.30
301 302 3.120468 TGGAGTGATGATTCTGGGAGA 57.880 47.619 0.00 0.00 0.00 3.71
302 303 3.453868 TGGAGTGATGATTCTGGGAGAA 58.546 45.455 0.00 0.00 38.78 2.87
303 304 3.453717 TGGAGTGATGATTCTGGGAGAAG 59.546 47.826 0.00 0.00 37.69 2.85
304 305 3.465871 GAGTGATGATTCTGGGAGAAGC 58.534 50.000 0.00 0.00 40.77 3.86
305 306 3.113824 AGTGATGATTCTGGGAGAAGCT 58.886 45.455 3.49 0.00 40.96 3.74
306 307 3.118334 AGTGATGATTCTGGGAGAAGCTG 60.118 47.826 3.49 0.00 40.96 4.24
307 308 2.172082 TGATGATTCTGGGAGAAGCTGG 59.828 50.000 3.49 0.00 40.96 4.85
308 309 0.914644 TGATTCTGGGAGAAGCTGGG 59.085 55.000 3.49 0.00 40.96 4.45
309 310 0.182299 GATTCTGGGAGAAGCTGGGG 59.818 60.000 0.00 0.00 37.62 4.96
310 311 0.253347 ATTCTGGGAGAAGCTGGGGA 60.253 55.000 0.00 0.00 37.69 4.81
311 312 0.911525 TTCTGGGAGAAGCTGGGGAG 60.912 60.000 0.00 0.00 29.50 4.30
312 313 2.285668 TGGGAGAAGCTGGGGAGG 60.286 66.667 0.00 0.00 0.00 4.30
313 314 3.093172 GGGAGAAGCTGGGGAGGG 61.093 72.222 0.00 0.00 0.00 4.30
314 315 3.093172 GGAGAAGCTGGGGAGGGG 61.093 72.222 0.00 0.00 0.00 4.79
315 316 3.093172 GAGAAGCTGGGGAGGGGG 61.093 72.222 0.00 0.00 0.00 5.40
329 330 3.965660 GGGGGCGATTCTGGTAGA 58.034 61.111 0.00 0.00 0.00 2.59
330 331 2.218066 GGGGGCGATTCTGGTAGAA 58.782 57.895 0.00 0.00 38.78 2.10
331 332 0.544697 GGGGGCGATTCTGGTAGAAA 59.455 55.000 0.00 0.00 37.82 2.52
332 333 1.664873 GGGGCGATTCTGGTAGAAAC 58.335 55.000 0.00 0.00 37.82 2.78
336 337 1.287425 CGATTCTGGTAGAAACGCCC 58.713 55.000 8.00 0.00 42.03 6.13
337 338 1.404986 CGATTCTGGTAGAAACGCCCA 60.405 52.381 8.00 0.00 42.03 5.36
338 339 2.706890 GATTCTGGTAGAAACGCCCAA 58.293 47.619 0.00 0.00 37.82 4.12
339 340 2.642154 TTCTGGTAGAAACGCCCAAA 57.358 45.000 0.00 0.00 29.99 3.28
340 341 2.642154 TCTGGTAGAAACGCCCAAAA 57.358 45.000 0.00 0.00 0.00 2.44
341 342 2.500229 TCTGGTAGAAACGCCCAAAAG 58.500 47.619 0.00 0.00 0.00 2.27
342 343 2.105134 TCTGGTAGAAACGCCCAAAAGA 59.895 45.455 0.00 0.00 0.00 2.52
343 344 2.882137 CTGGTAGAAACGCCCAAAAGAA 59.118 45.455 0.00 0.00 0.00 2.52
344 345 2.619646 TGGTAGAAACGCCCAAAAGAAC 59.380 45.455 0.00 0.00 0.00 3.01
345 346 2.882761 GGTAGAAACGCCCAAAAGAACT 59.117 45.455 0.00 0.00 0.00 3.01
346 347 3.304458 GGTAGAAACGCCCAAAAGAACTG 60.304 47.826 0.00 0.00 0.00 3.16
347 348 1.681264 AGAAACGCCCAAAAGAACTGG 59.319 47.619 0.00 0.00 0.00 4.00
348 349 0.104120 AAACGCCCAAAAGAACTGGC 59.896 50.000 0.00 0.00 40.54 4.85
349 350 1.744320 AACGCCCAAAAGAACTGGCC 61.744 55.000 0.00 0.00 40.87 5.36
350 351 2.931068 CGCCCAAAAGAACTGGCCC 61.931 63.158 0.00 0.00 40.87 5.80
351 352 1.533994 GCCCAAAAGAACTGGCCCT 60.534 57.895 0.00 0.00 37.94 5.19
352 353 0.251608 GCCCAAAAGAACTGGCCCTA 60.252 55.000 0.00 0.00 37.94 3.53
359 360 2.942604 AGAACTGGCCCTAGGTTAGA 57.057 50.000 8.29 0.00 0.00 2.10
362 363 4.892198 AGAACTGGCCCTAGGTTAGATAA 58.108 43.478 8.29 0.00 0.00 1.75
415 416 7.105588 TCACATAAATATGAACTCAGTGCTGT 58.894 34.615 7.40 0.00 37.15 4.40
467 468 7.383029 CGTCCTTGTCACTTTAGTGTACATTTA 59.617 37.037 9.53 0.00 45.76 1.40
493 494 6.407202 ACTCGTTAGATGGAATTTTGCTAGT 58.593 36.000 0.00 0.00 0.00 2.57
529 533 6.496565 AGGCTATATATCTATCACCCATGCTC 59.503 42.308 0.00 0.00 0.00 4.26
568 572 2.356535 CCCTTGCACCTCTTTGCTAGAT 60.357 50.000 7.93 0.00 45.00 1.98
631 635 2.472695 TGGGTGAATCTCACTTTCCG 57.527 50.000 6.74 0.00 46.19 4.30
746 753 7.284919 ACTTGTTCAATACCCAAACTTAAGG 57.715 36.000 7.53 0.00 0.00 2.69
859 882 5.894298 AATGATCTGGTGGACTATGCTAA 57.106 39.130 0.00 0.00 0.00 3.09
867 890 7.801104 TCTGGTGGACTATGCTAATTCAAATA 58.199 34.615 0.00 0.00 0.00 1.40
931 954 5.483811 TCGTTTTGCTGATACTATGGTTGA 58.516 37.500 0.00 0.00 0.00 3.18
987 1010 7.187824 TCTGACTAAGGAAGCACATAAGATT 57.812 36.000 0.00 0.00 0.00 2.40
1404 1427 5.186215 AGTTGAACTCTTAAGAGGTAGGCTC 59.814 44.000 30.98 16.21 43.22 4.70
1716 1739 5.789643 TTGCATTTAAGCCTGAGTTTCTT 57.210 34.783 0.00 0.00 0.00 2.52
1737 1760 4.004196 TCATGATATCTGCAAGCCTGAG 57.996 45.455 3.98 0.00 0.00 3.35
1930 1953 4.444536 GCAATACATGGCCATTGATTGTT 58.555 39.130 31.56 15.76 34.69 2.83
1956 1979 1.762957 TGGTTAGTGCAGGATCCTAGC 59.237 52.381 15.67 19.84 0.00 3.42
2046 2070 7.223058 AGAATTCTAATTTAGCGTCTTGTCG 57.777 36.000 6.06 0.00 0.00 4.35
2079 2103 6.782000 CCCATTCCCATGTCCTAATTGAAATA 59.218 38.462 0.00 0.00 0.00 1.40
2129 2153 7.219726 GCTTGAGCTTTAAAGATATTGACAAGC 59.780 37.037 26.88 26.88 44.61 4.01
2141 2165 7.743749 AGATATTGACAAGCATCTGTTATCCT 58.256 34.615 12.15 0.00 0.00 3.24
2226 2250 5.183140 ACATTAGGAAATGAAGGGTTGAACG 59.817 40.000 5.18 0.00 44.50 3.95
2231 2255 4.153655 GGAAATGAAGGGTTGAACGAGTAC 59.846 45.833 0.00 0.00 0.00 2.73
2240 2264 4.553323 GGTTGAACGAGTACTTTGAGCTA 58.447 43.478 0.00 0.00 0.00 3.32
2374 2398 6.882656 TGAAGAGCTGAGTATTTTGAGCTAT 58.117 36.000 0.00 0.00 41.88 2.97
2376 2400 5.852827 AGAGCTGAGTATTTTGAGCTATCC 58.147 41.667 0.00 0.00 41.88 2.59
2384 2408 7.500227 TGAGTATTTTGAGCTATCCATTTCTGG 59.500 37.037 0.00 0.00 44.64 3.86
2392 2416 8.593945 TGAGCTATCCATTTCTGGTTATTTTT 57.406 30.769 0.00 0.00 43.61 1.94
2444 2519 4.337555 GGATGCTGCATCTATTGTCTGTTT 59.662 41.667 33.94 2.48 40.39 2.83
2474 2549 4.082625 TCAGATATTGTTTGGTGCAAGCTG 60.083 41.667 0.00 0.00 33.76 4.24
2475 2550 2.437200 TATTGTTTGGTGCAAGCTGC 57.563 45.000 0.00 0.00 45.29 5.25
2520 2595 8.604890 GTTAATGCTAGTTCAGAATGGTTACTC 58.395 37.037 0.00 0.00 36.16 2.59
2527 2602 4.890158 TCAGAATGGTTACTCTTGCTGA 57.110 40.909 0.00 0.00 36.16 4.26
2567 2645 3.526931 ATCATTACTGTGGTCCTGTCG 57.473 47.619 0.00 0.00 0.00 4.35
2813 2891 7.143514 AGAAGAAATTGATGAACTCTTGAGC 57.856 36.000 0.00 0.00 0.00 4.26
3107 3185 3.766151 TCATAGTCCGTTGAATCGACAC 58.234 45.455 1.14 0.00 0.00 3.67
3131 3209 3.243535 CCAAAAGTTTGTGGAGAAGAGCC 60.244 47.826 9.83 0.00 37.03 4.70
3221 3299 2.426738 CTCTCAGTCCAGTGATCCTGAC 59.573 54.545 11.48 8.37 44.49 3.51
3479 3557 1.545428 GGTGGTCACAGGAAAGATGCA 60.545 52.381 3.40 0.00 0.00 3.96
3485 3563 3.932710 GTCACAGGAAAGATGCATACGAA 59.067 43.478 0.00 0.00 0.00 3.85
3652 3754 8.574196 AAATTAAACAACTTTTCTCACCATCG 57.426 30.769 0.00 0.00 0.00 3.84
3698 3800 3.265737 TGGTGTAGTGGGCAAATAGTGAT 59.734 43.478 0.00 0.00 0.00 3.06
3753 3863 4.317671 AGATTGTATGTACCGTAGCCAC 57.682 45.455 0.00 0.00 0.00 5.01
3777 3887 8.981659 CACCCCCAAGATATTCTTTAAGAAAAT 58.018 33.333 11.63 0.00 37.82 1.82
3816 3927 5.512749 CCTGCCTCAGTGCTCAATCTATATT 60.513 44.000 0.00 0.00 0.00 1.28
3817 3928 6.295518 CCTGCCTCAGTGCTCAATCTATATTA 60.296 42.308 0.00 0.00 0.00 0.98
3844 3955 7.042119 TGGTACACATGTAATCATTAGCAATCG 60.042 37.037 0.00 0.00 31.52 3.34
3846 3957 5.822519 ACACATGTAATCATTAGCAATCGGT 59.177 36.000 0.00 0.00 31.15 4.69
3969 4080 5.221224 TGTCTTTCAGGTTTTGGTGCTATTG 60.221 40.000 0.00 0.00 0.00 1.90
3993 4104 5.385509 TTGTTATTTGGTAAGCTTGCTCC 57.614 39.130 14.47 11.51 0.00 4.70
4115 4226 6.324819 TGCTACTGAAAGCTCATAAAAATGC 58.675 36.000 0.00 0.00 43.19 3.56
4133 4244 7.790823 AAAATGCAGCTTTCAAAAGTATGTT 57.209 28.000 4.54 0.00 38.28 2.71
4203 4314 0.960364 GCCCTCGCCATGTTCTTTGA 60.960 55.000 0.00 0.00 0.00 2.69
4244 4355 6.091441 GTGACAGACTATTGAGAATGTTGTCC 59.909 42.308 0.00 0.00 33.37 4.02
4324 4435 7.033791 ACATCATCAATTTGTGAATGAGCTTC 58.966 34.615 11.69 0.00 40.50 3.86
4379 4490 4.545610 TGTGCGTCTTGAAATTTCCATTC 58.454 39.130 15.48 3.63 0.00 2.67
4454 4565 9.160496 CAGTTTACTCTTTGAGATATCTTTGCT 57.840 33.333 6.70 0.00 33.32 3.91
4477 4588 5.252547 TCTATTTGCAGTGCAGTGGAATAA 58.747 37.500 26.42 14.86 40.61 1.40
4480 4591 4.870123 TTGCAGTGCAGTGGAATAATTT 57.130 36.364 22.91 0.00 40.61 1.82
4481 4592 4.870123 TGCAGTGCAGTGGAATAATTTT 57.130 36.364 22.71 0.00 33.32 1.82
4482 4593 5.973899 TGCAGTGCAGTGGAATAATTTTA 57.026 34.783 22.71 0.00 33.32 1.52
4483 4594 6.528537 TGCAGTGCAGTGGAATAATTTTAT 57.471 33.333 22.71 0.00 33.32 1.40
4484 4595 6.331845 TGCAGTGCAGTGGAATAATTTTATG 58.668 36.000 22.71 0.00 33.32 1.90
4486 4597 7.035004 GCAGTGCAGTGGAATAATTTTATGAA 58.965 34.615 22.71 0.00 0.00 2.57
4487 4598 7.707893 GCAGTGCAGTGGAATAATTTTATGAAT 59.292 33.333 22.71 0.00 0.00 2.57
4488 4599 9.027129 CAGTGCAGTGGAATAATTTTATGAATG 57.973 33.333 14.08 0.00 0.00 2.67
4490 4601 7.439056 GTGCAGTGGAATAATTTTATGAATGGG 59.561 37.037 0.00 0.00 0.00 4.00
4491 4602 6.424812 GCAGTGGAATAATTTTATGAATGGGC 59.575 38.462 0.00 0.00 0.00 5.36
4492 4603 7.499292 CAGTGGAATAATTTTATGAATGGGCA 58.501 34.615 0.00 0.00 0.00 5.36
4493 4604 7.439056 CAGTGGAATAATTTTATGAATGGGCAC 59.561 37.037 0.00 0.00 0.00 5.01
4494 4605 6.420604 GTGGAATAATTTTATGAATGGGCACG 59.579 38.462 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.668625 AGACCTACTCCGGAATCTTCC 58.331 52.381 5.23 0.00 44.05 3.46
13 14 3.181474 CCAAGACCTACTCCGGAATCTTC 60.181 52.174 5.23 0.00 0.00 2.87
14 15 2.766828 CCAAGACCTACTCCGGAATCTT 59.233 50.000 5.23 7.15 0.00 2.40
15 16 2.389715 CCAAGACCTACTCCGGAATCT 58.610 52.381 5.23 0.61 0.00 2.40
16 17 1.413077 CCCAAGACCTACTCCGGAATC 59.587 57.143 5.23 0.00 0.00 2.52
17 18 1.497161 CCCAAGACCTACTCCGGAAT 58.503 55.000 5.23 0.00 0.00 3.01
18 19 0.616679 CCCCAAGACCTACTCCGGAA 60.617 60.000 5.23 0.00 0.00 4.30
19 20 1.001248 CCCCAAGACCTACTCCGGA 59.999 63.158 2.93 2.93 0.00 5.14
20 21 1.001248 TCCCCAAGACCTACTCCGG 59.999 63.158 0.00 0.00 0.00 5.14
21 22 1.043673 CCTCCCCAAGACCTACTCCG 61.044 65.000 0.00 0.00 0.00 4.63
22 23 2.917804 CCTCCCCAAGACCTACTCC 58.082 63.158 0.00 0.00 0.00 3.85
149 150 0.326927 CCGAAAAGAACTGGCCCCTA 59.673 55.000 0.00 0.00 0.00 3.53
150 151 1.074951 CCGAAAAGAACTGGCCCCT 59.925 57.895 0.00 0.00 0.00 4.79
151 152 2.636412 GCCGAAAAGAACTGGCCCC 61.636 63.158 0.00 0.00 41.70 5.80
152 153 2.962569 GCCGAAAAGAACTGGCCC 59.037 61.111 0.00 0.00 41.70 5.80
153 154 1.305930 ATCGCCGAAAAGAACTGGCC 61.306 55.000 0.00 0.00 44.71 5.36
154 155 0.521735 AATCGCCGAAAAGAACTGGC 59.478 50.000 0.00 0.00 44.09 4.85
155 156 2.076863 AGAATCGCCGAAAAGAACTGG 58.923 47.619 0.00 0.00 0.00 4.00
156 157 2.094417 GGAGAATCGCCGAAAAGAACTG 59.906 50.000 0.00 0.00 34.37 3.16
157 158 2.347731 GGAGAATCGCCGAAAAGAACT 58.652 47.619 0.00 0.00 34.37 3.01
158 159 1.397343 GGGAGAATCGCCGAAAAGAAC 59.603 52.381 0.00 0.00 43.06 3.01
159 160 1.734163 GGGAGAATCGCCGAAAAGAA 58.266 50.000 0.00 0.00 43.06 2.52
160 161 3.453559 GGGAGAATCGCCGAAAAGA 57.546 52.632 0.00 0.00 43.06 2.52
171 172 1.709994 GGGGGCGATTCTGGGAGAAT 61.710 60.000 0.00 0.00 46.84 2.40
172 173 2.375345 GGGGGCGATTCTGGGAGAA 61.375 63.158 0.00 0.00 38.78 2.87
173 174 2.768344 GGGGGCGATTCTGGGAGA 60.768 66.667 0.00 0.00 0.00 3.71
174 175 2.330924 GAAGGGGGCGATTCTGGGAG 62.331 65.000 0.00 0.00 0.00 4.30
175 176 2.286121 AAGGGGGCGATTCTGGGA 60.286 61.111 0.00 0.00 0.00 4.37
176 177 2.193248 GAAGGGGGCGATTCTGGG 59.807 66.667 0.00 0.00 0.00 4.45
177 178 2.193248 GGAAGGGGGCGATTCTGG 59.807 66.667 0.00 0.00 0.00 3.86
178 179 2.193248 GGGAAGGGGGCGATTCTG 59.807 66.667 0.00 0.00 0.00 3.02
179 180 3.097162 GGGGAAGGGGGCGATTCT 61.097 66.667 0.00 0.00 0.00 2.40
180 181 3.416880 TGGGGAAGGGGGCGATTC 61.417 66.667 0.00 0.00 0.00 2.52
181 182 3.420482 CTGGGGAAGGGGGCGATT 61.420 66.667 0.00 0.00 0.00 3.34
185 186 4.448976 GAAGCTGGGGAAGGGGGC 62.449 72.222 0.00 0.00 0.00 5.80
186 187 2.615288 AGAAGCTGGGGAAGGGGG 60.615 66.667 0.00 0.00 0.00 5.40
187 188 2.684499 GGAGAAGCTGGGGAAGGGG 61.684 68.421 0.00 0.00 0.00 4.79
188 189 2.684499 GGGAGAAGCTGGGGAAGGG 61.684 68.421 0.00 0.00 0.00 3.95
189 190 1.919600 CTGGGAGAAGCTGGGGAAGG 61.920 65.000 0.00 0.00 0.00 3.46
190 191 0.911525 TCTGGGAGAAGCTGGGGAAG 60.912 60.000 0.00 0.00 0.00 3.46
191 192 0.475632 TTCTGGGAGAAGCTGGGGAA 60.476 55.000 0.00 0.00 29.50 3.97
192 193 0.253347 ATTCTGGGAGAAGCTGGGGA 60.253 55.000 0.00 0.00 37.69 4.81
193 194 0.182299 GATTCTGGGAGAAGCTGGGG 59.818 60.000 0.00 0.00 37.62 4.96
194 195 0.179062 CGATTCTGGGAGAAGCTGGG 60.179 60.000 0.00 0.00 38.40 4.45
195 196 0.813210 GCGATTCTGGGAGAAGCTGG 60.813 60.000 0.00 0.00 38.40 4.85
196 197 0.813210 GGCGATTCTGGGAGAAGCTG 60.813 60.000 0.00 0.00 38.40 4.24
197 198 1.267574 TGGCGATTCTGGGAGAAGCT 61.268 55.000 0.00 0.00 38.40 3.74
198 199 1.092345 GTGGCGATTCTGGGAGAAGC 61.092 60.000 0.00 0.00 37.69 3.86
199 200 0.539051 AGTGGCGATTCTGGGAGAAG 59.461 55.000 0.00 0.00 37.69 2.85
200 201 1.480954 GTAGTGGCGATTCTGGGAGAA 59.519 52.381 0.00 0.00 38.78 2.87
201 202 1.112113 GTAGTGGCGATTCTGGGAGA 58.888 55.000 0.00 0.00 0.00 3.71
202 203 0.824109 TGTAGTGGCGATTCTGGGAG 59.176 55.000 0.00 0.00 0.00 4.30
203 204 1.496060 ATGTAGTGGCGATTCTGGGA 58.504 50.000 0.00 0.00 0.00 4.37
204 205 3.685139 ATATGTAGTGGCGATTCTGGG 57.315 47.619 0.00 0.00 0.00 4.45
205 206 6.377327 AAAAATATGTAGTGGCGATTCTGG 57.623 37.500 0.00 0.00 0.00 3.86
244 245 9.214962 ACAATCCTAGCTAATTAGACCTTAACT 57.785 33.333 16.85 4.44 0.00 2.24
272 273 7.069085 CCCAGAATCATCACTCCATATGTTTTT 59.931 37.037 1.24 0.00 0.00 1.94
273 274 6.548622 CCCAGAATCATCACTCCATATGTTTT 59.451 38.462 1.24 0.00 0.00 2.43
274 275 6.066690 CCCAGAATCATCACTCCATATGTTT 58.933 40.000 1.24 0.00 0.00 2.83
275 276 5.370584 TCCCAGAATCATCACTCCATATGTT 59.629 40.000 1.24 0.00 0.00 2.71
276 277 4.909695 TCCCAGAATCATCACTCCATATGT 59.090 41.667 1.24 0.00 0.00 2.29
277 278 5.247792 TCTCCCAGAATCATCACTCCATATG 59.752 44.000 0.00 0.00 0.00 1.78
278 279 5.409712 TCTCCCAGAATCATCACTCCATAT 58.590 41.667 0.00 0.00 0.00 1.78
279 280 4.819610 TCTCCCAGAATCATCACTCCATA 58.180 43.478 0.00 0.00 0.00 2.74
280 281 3.662078 TCTCCCAGAATCATCACTCCAT 58.338 45.455 0.00 0.00 0.00 3.41
281 282 3.120468 TCTCCCAGAATCATCACTCCA 57.880 47.619 0.00 0.00 0.00 3.86
282 283 3.743899 GCTTCTCCCAGAATCATCACTCC 60.744 52.174 0.00 0.00 33.13 3.85
283 284 3.134442 AGCTTCTCCCAGAATCATCACTC 59.866 47.826 0.00 0.00 33.13 3.51
284 285 3.113824 AGCTTCTCCCAGAATCATCACT 58.886 45.455 0.00 0.00 33.13 3.41
285 286 3.204526 CAGCTTCTCCCAGAATCATCAC 58.795 50.000 0.00 0.00 33.13 3.06
286 287 2.172082 CCAGCTTCTCCCAGAATCATCA 59.828 50.000 0.00 0.00 33.13 3.07
287 288 2.486907 CCCAGCTTCTCCCAGAATCATC 60.487 54.545 0.00 0.00 33.13 2.92
288 289 1.493871 CCCAGCTTCTCCCAGAATCAT 59.506 52.381 0.00 0.00 33.13 2.45
289 290 0.914644 CCCAGCTTCTCCCAGAATCA 59.085 55.000 0.00 0.00 33.13 2.57
290 291 0.182299 CCCCAGCTTCTCCCAGAATC 59.818 60.000 0.00 0.00 33.13 2.52
291 292 0.253347 TCCCCAGCTTCTCCCAGAAT 60.253 55.000 0.00 0.00 33.13 2.40
292 293 0.911525 CTCCCCAGCTTCTCCCAGAA 60.912 60.000 0.00 0.00 32.50 3.02
293 294 1.306482 CTCCCCAGCTTCTCCCAGA 60.306 63.158 0.00 0.00 0.00 3.86
294 295 2.373707 CCTCCCCAGCTTCTCCCAG 61.374 68.421 0.00 0.00 0.00 4.45
295 296 2.285668 CCTCCCCAGCTTCTCCCA 60.286 66.667 0.00 0.00 0.00 4.37
296 297 3.093172 CCCTCCCCAGCTTCTCCC 61.093 72.222 0.00 0.00 0.00 4.30
297 298 3.093172 CCCCTCCCCAGCTTCTCC 61.093 72.222 0.00 0.00 0.00 3.71
298 299 3.093172 CCCCCTCCCCAGCTTCTC 61.093 72.222 0.00 0.00 0.00 2.87
312 313 0.544697 TTTCTACCAGAATCGCCCCC 59.455 55.000 0.00 0.00 33.67 5.40
313 314 1.664873 GTTTCTACCAGAATCGCCCC 58.335 55.000 0.00 0.00 33.67 5.80
314 315 1.287425 CGTTTCTACCAGAATCGCCC 58.713 55.000 6.48 0.00 39.54 6.13
317 318 1.287425 GGGCGTTTCTACCAGAATCG 58.713 55.000 12.68 12.68 45.27 3.34
318 319 2.396590 TGGGCGTTTCTACCAGAATC 57.603 50.000 0.00 0.00 33.67 2.52
319 320 2.871096 TTGGGCGTTTCTACCAGAAT 57.129 45.000 0.00 0.00 33.67 2.40
320 321 2.642154 TTTGGGCGTTTCTACCAGAA 57.358 45.000 0.00 0.00 35.37 3.02
321 322 2.105134 TCTTTTGGGCGTTTCTACCAGA 59.895 45.455 0.00 0.00 35.37 3.86
322 323 2.500229 TCTTTTGGGCGTTTCTACCAG 58.500 47.619 0.00 0.00 35.37 4.00
323 324 2.619646 GTTCTTTTGGGCGTTTCTACCA 59.380 45.455 0.00 0.00 0.00 3.25
324 325 2.882761 AGTTCTTTTGGGCGTTTCTACC 59.117 45.455 0.00 0.00 0.00 3.18
325 326 3.304458 CCAGTTCTTTTGGGCGTTTCTAC 60.304 47.826 0.00 0.00 31.87 2.59
326 327 2.882137 CCAGTTCTTTTGGGCGTTTCTA 59.118 45.455 0.00 0.00 31.87 2.10
327 328 1.681264 CCAGTTCTTTTGGGCGTTTCT 59.319 47.619 0.00 0.00 31.87 2.52
328 329 1.868109 GCCAGTTCTTTTGGGCGTTTC 60.868 52.381 0.00 0.00 36.58 2.78
329 330 0.104120 GCCAGTTCTTTTGGGCGTTT 59.896 50.000 0.00 0.00 36.58 3.60
330 331 1.739667 GCCAGTTCTTTTGGGCGTT 59.260 52.632 0.00 0.00 36.58 4.84
331 332 3.443588 GCCAGTTCTTTTGGGCGT 58.556 55.556 0.00 0.00 36.58 5.68
334 335 1.616994 CCTAGGGCCAGTTCTTTTGGG 60.617 57.143 6.18 0.00 36.19 4.12
335 336 1.075536 ACCTAGGGCCAGTTCTTTTGG 59.924 52.381 14.81 0.00 38.78 3.28
336 337 2.586648 ACCTAGGGCCAGTTCTTTTG 57.413 50.000 14.81 0.00 0.00 2.44
337 338 3.914435 TCTAACCTAGGGCCAGTTCTTTT 59.086 43.478 14.81 0.00 0.00 2.27
338 339 3.527937 TCTAACCTAGGGCCAGTTCTTT 58.472 45.455 14.81 0.00 0.00 2.52
339 340 3.200958 TCTAACCTAGGGCCAGTTCTT 57.799 47.619 14.81 0.00 0.00 2.52
340 341 2.942604 TCTAACCTAGGGCCAGTTCT 57.057 50.000 14.81 0.00 0.00 3.01
341 342 5.625568 TTTATCTAACCTAGGGCCAGTTC 57.374 43.478 14.81 0.00 0.00 3.01
342 343 5.670361 TCATTTATCTAACCTAGGGCCAGTT 59.330 40.000 14.81 9.12 0.00 3.16
343 344 5.224441 TCATTTATCTAACCTAGGGCCAGT 58.776 41.667 14.81 0.00 0.00 4.00
344 345 5.799213 CTCATTTATCTAACCTAGGGCCAG 58.201 45.833 14.81 6.96 0.00 4.85
345 346 4.041691 GCTCATTTATCTAACCTAGGGCCA 59.958 45.833 14.81 0.00 0.00 5.36
346 347 4.565861 GGCTCATTTATCTAACCTAGGGCC 60.566 50.000 14.81 7.40 0.00 5.80
347 348 4.565861 GGGCTCATTTATCTAACCTAGGGC 60.566 50.000 14.81 1.31 0.00 5.19
348 349 4.322801 CGGGCTCATTTATCTAACCTAGGG 60.323 50.000 14.81 0.00 0.00 3.53
349 350 4.527038 TCGGGCTCATTTATCTAACCTAGG 59.473 45.833 7.41 7.41 0.00 3.02
350 351 5.477291 TCTCGGGCTCATTTATCTAACCTAG 59.523 44.000 0.00 0.00 0.00 3.02
351 352 5.391256 TCTCGGGCTCATTTATCTAACCTA 58.609 41.667 0.00 0.00 0.00 3.08
352 353 4.223953 TCTCGGGCTCATTTATCTAACCT 58.776 43.478 0.00 0.00 0.00 3.50
359 360 3.392616 ACCATCTTCTCGGGCTCATTTAT 59.607 43.478 0.00 0.00 0.00 1.40
362 363 1.207791 ACCATCTTCTCGGGCTCATT 58.792 50.000 0.00 0.00 0.00 2.57
412 413 7.907214 AGCAGTGAGTAAATTTAACCTACAG 57.093 36.000 0.00 0.00 0.00 2.74
415 416 7.389607 GTCCAAGCAGTGAGTAAATTTAACCTA 59.610 37.037 0.00 0.00 0.00 3.08
467 468 8.204836 ACTAGCAAAATTCCATCTAACGAGTAT 58.795 33.333 0.00 0.00 0.00 2.12
529 533 1.335872 GGGAACTGTGCATTTGGTTCG 60.336 52.381 13.60 0.00 38.94 3.95
568 572 9.421806 CAGGACATGTTCTATTTATTTGCAAAA 57.578 29.630 17.19 0.00 0.00 2.44
647 651 7.341446 GCAAAAATTACCAACACAACACATAC 58.659 34.615 0.00 0.00 0.00 2.39
648 652 6.480320 GGCAAAAATTACCAACACAACACATA 59.520 34.615 0.00 0.00 0.00 2.29
733 740 2.158519 CCACCACTCCTTAAGTTTGGGT 60.159 50.000 15.21 8.93 35.89 4.51
734 741 2.514803 CCACCACTCCTTAAGTTTGGG 58.485 52.381 15.21 8.42 35.89 4.12
746 753 0.264955 TATCTCCCCTCCCACCACTC 59.735 60.000 0.00 0.00 0.00 3.51
904 927 5.354234 ACCATAGTATCAGCAAAACGAAAGG 59.646 40.000 0.00 0.00 0.00 3.11
931 954 9.590451 CCAAATTATACTTCAAACTGCATCATT 57.410 29.630 0.00 0.00 0.00 2.57
987 1010 9.403583 GGTATTTTATCCATTAAGAACAGGTCA 57.596 33.333 0.00 0.00 0.00 4.02
1404 1427 0.607489 CTCTTTGCTCCACCCAGGTG 60.607 60.000 10.00 10.00 45.02 4.00
1716 1739 3.390311 ACTCAGGCTTGCAGATATCATGA 59.610 43.478 5.32 0.00 0.00 3.07
1836 1859 5.760253 AGAAATATTAGCAACATGACCTCGG 59.240 40.000 0.00 0.00 0.00 4.63
1893 1916 4.763073 TGTATTGCCAGTCATCTGAAGAG 58.237 43.478 0.00 0.00 43.76 2.85
1930 1953 3.451178 GGATCCTGCACTAACCAGAGTAA 59.549 47.826 3.84 0.00 32.03 2.24
1956 1979 9.559732 TTGGAATGTCTTACCTTATGATATGTG 57.440 33.333 0.00 0.00 0.00 3.21
2037 2061 2.551270 GCACCAAGCGACAAGACG 59.449 61.111 0.00 0.00 0.00 4.18
2079 2103 7.070322 AGCAATTCAACAAATATAATCCAGGCT 59.930 33.333 0.00 0.00 0.00 4.58
2129 2153 8.616076 GTTATCAAGTCCAAAGGATAACAGATG 58.384 37.037 14.93 0.00 45.65 2.90
2226 2250 9.387123 CTCAAAAATTGTTAGCTCAAAGTACTC 57.613 33.333 0.00 0.00 0.00 2.59
2231 2255 8.749499 CAGTTCTCAAAAATTGTTAGCTCAAAG 58.251 33.333 0.00 0.00 0.00 2.77
2314 2338 9.601971 GTTTACGAAGAGTTATGTAATTTGCAA 57.398 29.630 0.00 0.00 0.00 4.08
2334 2358 5.048713 AGCTCTTCATTTCCAAAGGTTTACG 60.049 40.000 0.00 0.00 0.00 3.18
2444 2519 6.152492 TGCACCAAACAATATCTGAAATGCTA 59.848 34.615 0.00 0.00 0.00 3.49
2474 2549 3.179048 ACAAAAAGAAAGCAGACAACGC 58.821 40.909 0.00 0.00 0.00 4.84
2475 2550 6.862944 TTAACAAAAAGAAAGCAGACAACG 57.137 33.333 0.00 0.00 0.00 4.10
2543 2621 4.033709 ACAGGACCACAGTAATGATAGCT 58.966 43.478 0.00 0.00 0.00 3.32
2544 2622 4.372656 GACAGGACCACAGTAATGATAGC 58.627 47.826 0.00 0.00 0.00 2.97
2545 2623 4.499865 CCGACAGGACCACAGTAATGATAG 60.500 50.000 0.00 0.00 41.02 2.08
2567 2645 6.220726 ACAAACAATTATAGGTTGCATCCC 57.779 37.500 10.29 2.37 0.00 3.85
2651 2729 1.496060 AATCTATCAGTGTCGGGGCA 58.504 50.000 0.00 0.00 0.00 5.36
2825 2903 4.978580 GGCATATTCTTTTCCGATTTCAGC 59.021 41.667 0.00 0.00 0.00 4.26
2918 2996 4.275443 GCAGCTCCTTCAATATTTCCTGAG 59.725 45.833 0.00 0.00 0.00 3.35
3107 3185 2.357637 TCTTCTCCACAAACTTTTGGCG 59.642 45.455 6.65 0.00 42.34 5.69
3221 3299 4.708726 CTTGTTTTGCCTCAAGGATAGG 57.291 45.455 0.00 0.00 37.83 2.57
3269 3347 0.096628 CAGCACGCATCTGCTTCTTC 59.903 55.000 0.09 0.00 45.64 2.87
3485 3563 4.183865 GCAAACCTGTTTCTCAGCTTTTT 58.816 39.130 0.00 0.00 42.38 1.94
3539 3617 8.870116 AGAAGGAAACCACAGCTTAAATAAATT 58.130 29.630 0.00 0.00 0.00 1.82
3548 3626 6.431234 CACTTATTAGAAGGAAACCACAGCTT 59.569 38.462 0.00 0.00 0.00 3.74
3550 3628 5.705905 ACACTTATTAGAAGGAAACCACAGC 59.294 40.000 0.00 0.00 0.00 4.40
3652 3754 6.483640 CACTCCTGTTTGTAGGATAATTAGGC 59.516 42.308 0.00 0.00 45.44 3.93
3724 3834 7.866393 GCTACGGTACATACAATCTTTAGTCAT 59.134 37.037 0.00 0.00 0.00 3.06
3726 3836 6.640092 GGCTACGGTACATACAATCTTTAGTC 59.360 42.308 0.00 0.00 0.00 2.59
3733 3843 3.387397 GGTGGCTACGGTACATACAATC 58.613 50.000 0.00 0.00 0.00 2.67
3734 3844 2.103601 GGGTGGCTACGGTACATACAAT 59.896 50.000 0.00 0.00 0.00 2.71
3777 3887 7.554118 CACTGAGGCAGGAGAATTTCTAATTTA 59.446 37.037 0.00 0.00 35.51 1.40
3788 3898 0.833409 TGAGCACTGAGGCAGGAGAA 60.833 55.000 0.00 0.00 35.51 2.87
3790 3900 0.252479 ATTGAGCACTGAGGCAGGAG 59.748 55.000 0.00 0.00 35.51 3.69
3816 3927 9.791801 ATTGCTAATGATTACATGTGTACCATA 57.208 29.630 9.11 0.00 36.79 2.74
3817 3928 8.696043 ATTGCTAATGATTACATGTGTACCAT 57.304 30.769 9.11 3.98 36.79 3.55
3827 3938 7.066887 ACAAATCACCGATTGCTAATGATTACA 59.933 33.333 0.00 0.00 38.69 2.41
3828 3939 7.417612 ACAAATCACCGATTGCTAATGATTAC 58.582 34.615 0.00 0.00 38.69 1.89
3844 3955 6.040504 AGTCAGGAAAAGGTAAACAAATCACC 59.959 38.462 0.00 0.00 0.00 4.02
3846 3957 7.654022 AAGTCAGGAAAAGGTAAACAAATCA 57.346 32.000 0.00 0.00 0.00 2.57
3889 4000 3.440173 CCAGTTGTTTGTACCAGCCATAG 59.560 47.826 0.00 0.00 0.00 2.23
3969 4080 6.036470 GGAGCAAGCTTACCAAATAACAATC 58.964 40.000 0.00 0.00 0.00 2.67
3993 4104 0.948623 TCCGACGACAAGCACAATGG 60.949 55.000 0.00 0.00 0.00 3.16
4084 4195 3.249917 GAGCTTTCAGTAGCAGACTCAC 58.750 50.000 0.00 0.00 43.68 3.51
4115 4226 6.042143 ACACCAAACATACTTTTGAAAGCTG 58.958 36.000 3.48 4.69 38.54 4.24
4133 4244 1.605968 CGGACAATACGGTGACACCAA 60.606 52.381 24.18 11.97 38.47 3.67
4203 4314 2.158914 TGTCACAGCAACTCACACAGAT 60.159 45.455 0.00 0.00 0.00 2.90
4244 4355 5.437289 TTTACAACACCAATCAAGAGCAG 57.563 39.130 0.00 0.00 0.00 4.24
4324 4435 3.067180 ACTTGCATTGTGTCTTCAAGGTG 59.933 43.478 0.00 0.00 38.64 4.00
4379 4490 0.458370 TCGATCATCTGTGCCACACG 60.458 55.000 0.00 0.00 37.14 4.49
4454 4565 2.857186 TCCACTGCACTGCAAATAGA 57.143 45.000 4.99 0.00 38.41 1.98


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

AutoCloner maintained by Alex Coulton.