Multiple sequence alignment - TraesCS5A01G239400

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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 TraesCS5A01G239400 chr5A 100.000 2795 0 0 1 2795 455509011 455506217 0.000000e+00 5162.0
1 TraesCS5A01G239400 chr5B 90.215 2841 185 49 5 2795 418912227 418909430 0.000000e+00 3620.0
2 TraesCS5A01G239400 chr5D 90.922 2093 105 38 379 2427 354513283 354511232 0.000000e+00 2734.0
3 TraesCS5A01G239400 chr5D 89.189 185 19 1 1 184 354513465 354513281 2.170000e-56 230.0
4 TraesCS5A01G239400 chr2B 85.315 143 19 2 2653 2794 195696500 195696359 2.240000e-31 147.0
5 TraesCS5A01G239400 chr2B 84.211 133 14 4 2665 2795 647095382 647095255 3.780000e-24 122.0
6 TraesCS5A01G239400 chr1B 84.444 135 19 2 2662 2795 649032549 649032416 6.280000e-27 132.0
7 TraesCS5A01G239400 chr2A 82.734 139 15 7 2662 2793 683567189 683567053 6.330000e-22 115.0
8 TraesCS5A01G239400 chr2A 81.818 132 19 2 2665 2795 684950853 684950726 3.810000e-19 106.0
9 TraesCS5A01G239400 chr4D 83.582 134 7 5 2662 2795 417670276 417670158 8.180000e-21 111.0
10 TraesCS5A01G239400 chr4D 95.082 61 3 0 2735 2795 401202217 401202157 2.290000e-16 97.1
11 TraesCS5A01G239400 chr2D 81.538 130 19 2 2666 2794 542136001 542135876 4.930000e-18 102.0


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 TraesCS5A01G239400 chr5A 455506217 455509011 2794 True 5162 5162 100.0000 1 2795 1 chr5A.!!$R1 2794
1 TraesCS5A01G239400 chr5B 418909430 418912227 2797 True 3620 3620 90.2150 5 2795 1 chr5B.!!$R1 2790
2 TraesCS5A01G239400 chr5D 354511232 354513465 2233 True 1482 2734 90.0555 1 2427 2 chr5D.!!$R1 2426

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
208 210 0.035056 ACATTGGCGGAGAAAGGAGG 60.035 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2173 0.033504 AGTTCACATTCGCGACCTGT 59.966 50.0 9.15 13.38 0.0 4.0 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
29 31 3.181487 GCAATGGCGGTAATGAATCAACT 60.181 43.478 0.00 0.00 0.00 3.16
100 102 5.750524 CTTAGAGATCAGATCTATCGGGGA 58.249 45.833 13.26 0.00 40.38 4.81
105 107 4.709397 AGATCAGATCTATCGGGGAACATC 59.291 45.833 11.57 0.00 38.00 3.06
107 109 1.546476 AGATCTATCGGGGAACATCGC 59.454 52.381 0.00 0.00 0.00 4.58
108 110 1.546476 GATCTATCGGGGAACATCGCT 59.454 52.381 0.00 0.00 0.00 4.93
126 128 0.251916 CTGGCCCGACTTGGTATCAA 59.748 55.000 0.00 0.00 35.15 2.57
148 150 2.667470 AGTAGGTAGATGATGCGGTGT 58.333 47.619 0.00 0.00 0.00 4.16
166 168 2.112190 TGTGTCTTGGTAGTGGTGACA 58.888 47.619 0.00 0.00 35.62 3.58
179 181 0.602638 GGTGACAGGTGACAATGCGA 60.603 55.000 0.00 0.00 0.00 5.10
181 183 0.943835 TGACAGGTGACAATGCGACG 60.944 55.000 0.00 0.00 0.00 5.12
182 184 0.666274 GACAGGTGACAATGCGACGA 60.666 55.000 0.00 0.00 0.00 4.20
183 185 0.037326 ACAGGTGACAATGCGACGAT 60.037 50.000 0.00 0.00 0.00 3.73
184 186 0.371301 CAGGTGACAATGCGACGATG 59.629 55.000 0.00 0.00 0.00 3.84
185 187 0.740868 AGGTGACAATGCGACGATGG 60.741 55.000 0.00 0.00 0.00 3.51
186 188 0.739462 GGTGACAATGCGACGATGGA 60.739 55.000 0.00 0.00 0.00 3.41
187 189 1.290203 GTGACAATGCGACGATGGAT 58.710 50.000 0.00 0.00 0.00 3.41
188 190 1.004610 GTGACAATGCGACGATGGATG 60.005 52.381 0.00 0.00 0.00 3.51
189 191 1.134848 TGACAATGCGACGATGGATGA 60.135 47.619 0.00 0.00 0.00 2.92
190 192 1.258982 GACAATGCGACGATGGATGAC 59.741 52.381 0.00 0.00 0.00 3.06
191 193 1.289276 CAATGCGACGATGGATGACA 58.711 50.000 0.00 0.00 0.00 3.58
192 194 1.869132 CAATGCGACGATGGATGACAT 59.131 47.619 0.00 0.00 44.18 3.06
193 195 2.245159 ATGCGACGATGGATGACATT 57.755 45.000 0.00 0.00 40.72 2.71
194 196 1.289276 TGCGACGATGGATGACATTG 58.711 50.000 0.00 0.00 45.03 2.82
195 197 0.583438 GCGACGATGGATGACATTGG 59.417 55.000 0.00 0.00 44.00 3.16
196 198 0.583438 CGACGATGGATGACATTGGC 59.417 55.000 0.00 0.00 44.42 4.52
197 199 0.583438 GACGATGGATGACATTGGCG 59.417 55.000 0.00 0.00 44.00 5.69
198 200 0.815213 ACGATGGATGACATTGGCGG 60.815 55.000 0.00 0.00 44.00 6.13
199 201 0.532640 CGATGGATGACATTGGCGGA 60.533 55.000 0.00 0.00 40.72 5.54
200 202 1.233019 GATGGATGACATTGGCGGAG 58.767 55.000 0.00 0.00 40.72 4.63
201 203 0.839277 ATGGATGACATTGGCGGAGA 59.161 50.000 0.00 0.00 35.97 3.71
202 204 0.617935 TGGATGACATTGGCGGAGAA 59.382 50.000 0.00 0.00 0.00 2.87
203 205 1.004161 TGGATGACATTGGCGGAGAAA 59.996 47.619 0.00 0.00 0.00 2.52
204 206 1.672881 GGATGACATTGGCGGAGAAAG 59.327 52.381 0.00 0.00 0.00 2.62
205 207 1.672881 GATGACATTGGCGGAGAAAGG 59.327 52.381 0.00 0.00 0.00 3.11
206 208 0.690192 TGACATTGGCGGAGAAAGGA 59.310 50.000 0.00 0.00 0.00 3.36
207 209 1.339055 TGACATTGGCGGAGAAAGGAG 60.339 52.381 0.00 0.00 0.00 3.69
208 210 0.035056 ACATTGGCGGAGAAAGGAGG 60.035 55.000 0.00 0.00 0.00 4.30
209 211 0.253044 CATTGGCGGAGAAAGGAGGA 59.747 55.000 0.00 0.00 0.00 3.71
210 212 0.543749 ATTGGCGGAGAAAGGAGGAG 59.456 55.000 0.00 0.00 0.00 3.69
211 213 0.544357 TTGGCGGAGAAAGGAGGAGA 60.544 55.000 0.00 0.00 0.00 3.71
212 214 0.544357 TGGCGGAGAAAGGAGGAGAA 60.544 55.000 0.00 0.00 0.00 2.87
213 215 0.176910 GGCGGAGAAAGGAGGAGAAG 59.823 60.000 0.00 0.00 0.00 2.85
214 216 1.187087 GCGGAGAAAGGAGGAGAAGA 58.813 55.000 0.00 0.00 0.00 2.87
215 217 1.136110 GCGGAGAAAGGAGGAGAAGAG 59.864 57.143 0.00 0.00 0.00 2.85
216 218 1.754226 CGGAGAAAGGAGGAGAAGAGG 59.246 57.143 0.00 0.00 0.00 3.69
217 219 2.115427 GGAGAAAGGAGGAGAAGAGGG 58.885 57.143 0.00 0.00 0.00 4.30
218 220 2.292587 GGAGAAAGGAGGAGAAGAGGGA 60.293 54.545 0.00 0.00 0.00 4.20
219 221 3.632385 GGAGAAAGGAGGAGAAGAGGGAT 60.632 52.174 0.00 0.00 0.00 3.85
220 222 3.383223 AGAAAGGAGGAGAAGAGGGATG 58.617 50.000 0.00 0.00 0.00 3.51
221 223 3.013417 AGAAAGGAGGAGAAGAGGGATGA 59.987 47.826 0.00 0.00 0.00 2.92
222 224 2.773525 AGGAGGAGAAGAGGGATGAG 57.226 55.000 0.00 0.00 0.00 2.90
223 225 2.222271 AGGAGGAGAAGAGGGATGAGA 58.778 52.381 0.00 0.00 0.00 3.27
224 226 2.177669 AGGAGGAGAAGAGGGATGAGAG 59.822 54.545 0.00 0.00 0.00 3.20
225 227 2.091333 GGAGGAGAAGAGGGATGAGAGT 60.091 54.545 0.00 0.00 0.00 3.24
226 228 3.629796 GGAGGAGAAGAGGGATGAGAGTT 60.630 52.174 0.00 0.00 0.00 3.01
227 229 4.386986 GGAGGAGAAGAGGGATGAGAGTTA 60.387 50.000 0.00 0.00 0.00 2.24
228 230 4.542697 AGGAGAAGAGGGATGAGAGTTAC 58.457 47.826 0.00 0.00 0.00 2.50
229 231 4.017037 AGGAGAAGAGGGATGAGAGTTACA 60.017 45.833 0.00 0.00 0.00 2.41
230 232 4.712337 GGAGAAGAGGGATGAGAGTTACAA 59.288 45.833 0.00 0.00 0.00 2.41
231 233 5.187967 GGAGAAGAGGGATGAGAGTTACAAA 59.812 44.000 0.00 0.00 0.00 2.83
232 234 6.295916 GGAGAAGAGGGATGAGAGTTACAAAA 60.296 42.308 0.00 0.00 0.00 2.44
233 235 7.264294 AGAAGAGGGATGAGAGTTACAAAAT 57.736 36.000 0.00 0.00 0.00 1.82
234 236 8.380742 AGAAGAGGGATGAGAGTTACAAAATA 57.619 34.615 0.00 0.00 0.00 1.40
235 237 8.826765 AGAAGAGGGATGAGAGTTACAAAATAA 58.173 33.333 0.00 0.00 0.00 1.40
236 238 9.449719 GAAGAGGGATGAGAGTTACAAAATAAA 57.550 33.333 0.00 0.00 0.00 1.40
237 239 9.807921 AAGAGGGATGAGAGTTACAAAATAAAA 57.192 29.630 0.00 0.00 0.00 1.52
238 240 9.454859 AGAGGGATGAGAGTTACAAAATAAAAG 57.545 33.333 0.00 0.00 0.00 2.27
239 241 8.581253 AGGGATGAGAGTTACAAAATAAAAGG 57.419 34.615 0.00 0.00 0.00 3.11
240 242 8.390921 AGGGATGAGAGTTACAAAATAAAAGGA 58.609 33.333 0.00 0.00 0.00 3.36
241 243 9.020731 GGGATGAGAGTTACAAAATAAAAGGAA 57.979 33.333 0.00 0.00 0.00 3.36
244 246 8.404107 TGAGAGTTACAAAATAAAAGGAAGGG 57.596 34.615 0.00 0.00 0.00 3.95
245 247 8.002459 TGAGAGTTACAAAATAAAAGGAAGGGT 58.998 33.333 0.00 0.00 0.00 4.34
246 248 8.777578 AGAGTTACAAAATAAAAGGAAGGGTT 57.222 30.769 0.00 0.00 0.00 4.11
247 249 8.638873 AGAGTTACAAAATAAAAGGAAGGGTTG 58.361 33.333 0.00 0.00 0.00 3.77
248 250 8.541899 AGTTACAAAATAAAAGGAAGGGTTGA 57.458 30.769 0.00 0.00 0.00 3.18
249 251 9.154632 AGTTACAAAATAAAAGGAAGGGTTGAT 57.845 29.630 0.00 0.00 0.00 2.57
250 252 9.419297 GTTACAAAATAAAAGGAAGGGTTGATC 57.581 33.333 0.00 0.00 0.00 2.92
251 253 7.855784 ACAAAATAAAAGGAAGGGTTGATCT 57.144 32.000 0.00 0.00 0.00 2.75
252 254 7.896811 ACAAAATAAAAGGAAGGGTTGATCTC 58.103 34.615 0.00 0.00 0.00 2.75
253 255 6.759497 AAATAAAAGGAAGGGTTGATCTCG 57.241 37.500 0.00 0.00 0.00 4.04
254 256 5.693769 ATAAAAGGAAGGGTTGATCTCGA 57.306 39.130 0.00 0.00 0.00 4.04
255 257 3.618690 AAAGGAAGGGTTGATCTCGAG 57.381 47.619 5.93 5.93 0.00 4.04
256 258 1.490574 AGGAAGGGTTGATCTCGAGG 58.509 55.000 13.56 0.00 0.00 4.63
257 259 0.179070 GGAAGGGTTGATCTCGAGGC 60.179 60.000 13.56 5.92 0.00 4.70
258 260 0.179070 GAAGGGTTGATCTCGAGGCC 60.179 60.000 13.56 0.00 0.00 5.19
259 261 0.909610 AAGGGTTGATCTCGAGGCCA 60.910 55.000 13.56 8.06 0.00 5.36
260 262 0.909610 AGGGTTGATCTCGAGGCCAA 60.910 55.000 13.56 13.67 0.00 4.52
261 263 0.744771 GGGTTGATCTCGAGGCCAAC 60.745 60.000 27.51 27.51 38.42 3.77
262 264 1.084370 GGTTGATCTCGAGGCCAACG 61.084 60.000 27.85 11.10 39.62 4.10
263 265 1.084370 GTTGATCTCGAGGCCAACGG 61.084 60.000 24.24 11.69 31.16 4.44
273 275 3.195698 GCCAACGGCGATGGAGAC 61.196 66.667 36.01 17.21 39.62 3.36
274 276 3.950794 GCCAACGGCGATGGAGACA 62.951 63.158 36.01 0.00 42.31 3.41
284 286 2.989639 TGGAGACAATGGGCGAGG 59.010 61.111 0.00 0.00 37.44 4.63
285 287 1.918293 TGGAGACAATGGGCGAGGT 60.918 57.895 0.00 0.00 37.44 3.85
286 288 1.153349 GGAGACAATGGGCGAGGTC 60.153 63.158 0.00 0.00 0.00 3.85
287 289 1.617947 GGAGACAATGGGCGAGGTCT 61.618 60.000 6.37 6.37 42.90 3.85
288 290 1.112113 GAGACAATGGGCGAGGTCTA 58.888 55.000 6.60 0.00 40.48 2.59
289 291 0.824759 AGACAATGGGCGAGGTCTAC 59.175 55.000 5.09 0.00 38.74 2.59
290 292 0.527817 GACAATGGGCGAGGTCTACG 60.528 60.000 0.00 0.00 0.00 3.51
291 293 1.255667 ACAATGGGCGAGGTCTACGT 61.256 55.000 0.00 0.00 0.00 3.57
292 294 0.806102 CAATGGGCGAGGTCTACGTG 60.806 60.000 0.00 0.00 0.00 4.49
293 295 1.255667 AATGGGCGAGGTCTACGTGT 61.256 55.000 0.00 0.00 0.00 4.49
294 296 0.394762 ATGGGCGAGGTCTACGTGTA 60.395 55.000 0.00 0.00 0.00 2.90
295 297 1.308069 TGGGCGAGGTCTACGTGTAC 61.308 60.000 0.00 0.00 0.00 2.90
296 298 1.431036 GGCGAGGTCTACGTGTACC 59.569 63.158 12.00 12.00 35.91 3.34
297 299 1.308069 GGCGAGGTCTACGTGTACCA 61.308 60.000 19.61 0.00 38.30 3.25
298 300 0.523072 GCGAGGTCTACGTGTACCAA 59.477 55.000 19.61 0.00 38.30 3.67
299 301 1.730446 GCGAGGTCTACGTGTACCAAC 60.730 57.143 19.61 13.11 38.30 3.77
307 309 2.029369 GTGTACCAACGCGGGTGA 59.971 61.111 16.20 1.30 42.39 4.02
308 310 1.375013 GTGTACCAACGCGGGTGAT 60.375 57.895 16.20 0.55 42.39 3.06
309 311 0.108709 GTGTACCAACGCGGGTGATA 60.109 55.000 16.20 0.00 42.39 2.15
310 312 0.607112 TGTACCAACGCGGGTGATAA 59.393 50.000 16.20 0.00 42.39 1.75
311 313 1.283736 GTACCAACGCGGGTGATAAG 58.716 55.000 16.20 1.66 42.39 1.73
312 314 0.460635 TACCAACGCGGGTGATAAGC 60.461 55.000 16.20 0.00 42.39 3.09
313 315 1.743623 CCAACGCGGGTGATAAGCA 60.744 57.895 12.47 0.00 0.00 3.91
314 316 1.095228 CCAACGCGGGTGATAAGCAT 61.095 55.000 12.47 0.00 0.00 3.79
315 317 1.577468 CAACGCGGGTGATAAGCATA 58.423 50.000 12.47 0.00 0.00 3.14
316 318 2.143122 CAACGCGGGTGATAAGCATAT 58.857 47.619 12.47 0.00 0.00 1.78
317 319 2.543777 ACGCGGGTGATAAGCATATT 57.456 45.000 12.47 0.00 0.00 1.28
318 320 2.846193 ACGCGGGTGATAAGCATATTT 58.154 42.857 12.47 0.00 0.00 1.40
319 321 2.806244 ACGCGGGTGATAAGCATATTTC 59.194 45.455 12.47 0.00 0.00 2.17
320 322 3.067106 CGCGGGTGATAAGCATATTTCT 58.933 45.455 0.00 0.00 0.00 2.52
321 323 4.242475 CGCGGGTGATAAGCATATTTCTA 58.758 43.478 0.00 0.00 0.00 2.10
322 324 4.870426 CGCGGGTGATAAGCATATTTCTAT 59.130 41.667 0.00 0.00 0.00 1.98
323 325 5.220472 CGCGGGTGATAAGCATATTTCTATG 60.220 44.000 0.00 0.00 38.22 2.23
337 339 8.572828 CATATTTCTATGCTTAGGCTCTATCG 57.427 38.462 6.78 0.00 39.59 2.92
338 340 6.597832 ATTTCTATGCTTAGGCTCTATCGT 57.402 37.500 6.78 0.00 39.59 3.73
339 341 5.378292 TTCTATGCTTAGGCTCTATCGTG 57.622 43.478 6.78 0.00 39.59 4.35
340 342 3.759086 TCTATGCTTAGGCTCTATCGTGG 59.241 47.826 6.78 0.00 39.59 4.94
341 343 1.776662 TGCTTAGGCTCTATCGTGGT 58.223 50.000 0.00 0.00 39.59 4.16
342 344 1.681793 TGCTTAGGCTCTATCGTGGTC 59.318 52.381 0.00 0.00 39.59 4.02
343 345 1.335142 GCTTAGGCTCTATCGTGGTCG 60.335 57.143 0.00 0.00 35.43 4.79
344 346 1.948145 CTTAGGCTCTATCGTGGTCGT 59.052 52.381 0.00 0.00 38.33 4.34
345 347 2.048444 TAGGCTCTATCGTGGTCGTT 57.952 50.000 0.00 0.00 38.33 3.85
346 348 0.456221 AGGCTCTATCGTGGTCGTTG 59.544 55.000 0.00 0.00 38.33 4.10
347 349 0.454600 GGCTCTATCGTGGTCGTTGA 59.545 55.000 0.00 0.00 38.33 3.18
348 350 1.067212 GGCTCTATCGTGGTCGTTGAT 59.933 52.381 0.00 0.00 38.33 2.57
349 351 2.120232 GCTCTATCGTGGTCGTTGATG 58.880 52.381 0.00 0.00 38.33 3.07
350 352 2.120232 CTCTATCGTGGTCGTTGATGC 58.880 52.381 0.00 0.00 38.33 3.91
351 353 1.202371 TCTATCGTGGTCGTTGATGCC 60.202 52.381 0.00 0.00 38.33 4.40
352 354 0.179094 TATCGTGGTCGTTGATGCCC 60.179 55.000 0.00 0.00 38.33 5.36
353 355 1.899437 ATCGTGGTCGTTGATGCCCT 61.899 55.000 0.00 0.00 38.33 5.19
354 356 2.390599 CGTGGTCGTTGATGCCCTG 61.391 63.158 0.00 0.00 0.00 4.45
355 357 1.003839 GTGGTCGTTGATGCCCTGA 60.004 57.895 0.00 0.00 0.00 3.86
356 358 1.003839 TGGTCGTTGATGCCCTGAC 60.004 57.895 0.00 0.00 0.00 3.51
357 359 1.296715 GGTCGTTGATGCCCTGACT 59.703 57.895 0.00 0.00 0.00 3.41
358 360 0.321653 GGTCGTTGATGCCCTGACTT 60.322 55.000 0.00 0.00 0.00 3.01
359 361 0.798776 GTCGTTGATGCCCTGACTTG 59.201 55.000 0.00 0.00 0.00 3.16
360 362 0.321564 TCGTTGATGCCCTGACTTGG 60.322 55.000 0.00 0.00 0.00 3.61
361 363 0.606401 CGTTGATGCCCTGACTTGGT 60.606 55.000 0.00 0.00 0.00 3.67
362 364 1.338674 CGTTGATGCCCTGACTTGGTA 60.339 52.381 0.00 0.00 0.00 3.25
363 365 2.084546 GTTGATGCCCTGACTTGGTAC 58.915 52.381 0.00 0.00 0.00 3.34
364 366 1.357137 TGATGCCCTGACTTGGTACA 58.643 50.000 0.00 0.00 0.00 2.90
365 367 1.278985 TGATGCCCTGACTTGGTACAG 59.721 52.381 0.00 0.00 42.39 2.74
372 374 3.045601 CTGACTTGGTACAGGAAGTGG 57.954 52.381 8.44 0.35 42.39 4.00
373 375 2.632996 CTGACTTGGTACAGGAAGTGGA 59.367 50.000 8.44 0.00 42.39 4.02
374 376 2.367567 TGACTTGGTACAGGAAGTGGAC 59.632 50.000 8.44 0.00 42.39 4.02
375 377 1.343465 ACTTGGTACAGGAAGTGGACG 59.657 52.381 0.00 0.00 41.66 4.79
376 378 1.616865 CTTGGTACAGGAAGTGGACGA 59.383 52.381 0.00 0.00 41.66 4.20
377 379 1.707106 TGGTACAGGAAGTGGACGAA 58.293 50.000 0.00 0.00 41.66 3.85
383 385 2.232452 ACAGGAAGTGGACGAAGATCTG 59.768 50.000 0.00 0.00 0.00 2.90
386 388 2.611518 GAAGTGGACGAAGATCTGGTG 58.388 52.381 0.00 0.00 0.00 4.17
424 621 1.384222 GGGGTGGATTTGCGGTGATC 61.384 60.000 0.00 0.00 0.00 2.92
457 654 0.179108 AGAAACGAGTAGGGCGATGC 60.179 55.000 0.00 0.00 0.00 3.91
506 703 3.075148 GAGGAACGAGGAAAAAGGAAGG 58.925 50.000 0.00 0.00 0.00 3.46
510 707 0.251165 CGAGGAAAAAGGAAGGGGCA 60.251 55.000 0.00 0.00 0.00 5.36
519 716 0.783850 AGGAAGGGGCAGCCTAAAAA 59.216 50.000 12.43 0.00 0.00 1.94
520 717 1.186200 GGAAGGGGCAGCCTAAAAAG 58.814 55.000 12.43 0.00 0.00 2.27
528 725 1.852633 CAGCCTAAAAAGGGGAAGGG 58.147 55.000 0.00 0.00 0.00 3.95
546 743 2.110721 AGGGAGAAGAAAACCAAGGCAT 59.889 45.455 0.00 0.00 0.00 4.40
551 748 0.539438 AGAAAACCAAGGCATGCCGA 60.539 50.000 30.50 0.00 41.95 5.54
558 755 3.210012 AAGGCATGCCGACAGGGTT 62.210 57.895 30.50 14.95 41.95 4.11
582 779 2.609244 GGCATTTAAAAGCAAGCGACCA 60.609 45.455 16.47 0.00 0.00 4.02
586 783 5.610975 CATTTAAAAGCAAGCGACCAAATG 58.389 37.500 0.00 9.22 0.00 2.32
587 784 2.153366 AAAAGCAAGCGACCAAATGG 57.847 45.000 0.00 0.00 42.17 3.16
604 801 6.444633 CCAAATGGTTGCATTCAGATAGATC 58.555 40.000 0.00 0.00 33.01 2.75
605 802 6.264744 CCAAATGGTTGCATTCAGATAGATCT 59.735 38.462 0.00 0.00 33.56 2.75
608 805 6.737720 TGGTTGCATTCAGATAGATCTACT 57.262 37.500 4.10 1.96 34.85 2.57
610 807 7.212976 TGGTTGCATTCAGATAGATCTACTTC 58.787 38.462 4.10 0.00 34.85 3.01
612 809 7.598493 GGTTGCATTCAGATAGATCTACTTCTC 59.402 40.741 4.10 0.00 34.85 2.87
614 811 6.072230 TGCATTCAGATAGATCTACTTCTCCG 60.072 42.308 4.10 0.00 34.85 4.63
615 812 6.150307 GCATTCAGATAGATCTACTTCTCCGA 59.850 42.308 4.10 0.00 34.85 4.55
963 1169 4.373116 CTGCCTACCACCACGCGT 62.373 66.667 5.58 5.58 0.00 6.01
964 1170 4.673298 TGCCTACCACCACGCGTG 62.673 66.667 31.77 31.77 42.62 5.34
1116 1328 2.425668 CGACTTCTCCTTCTCCTTCTCC 59.574 54.545 0.00 0.00 0.00 3.71
1151 1363 1.592223 CTCCACCTTCTCACGTCCC 59.408 63.158 0.00 0.00 0.00 4.46
1158 1370 3.214190 TTCTCACGTCCCCCTCCGA 62.214 63.158 0.00 0.00 0.00 4.55
1250 1462 0.951558 AACAACTACGCCAAAGCCAG 59.048 50.000 0.00 0.00 34.57 4.85
1795 2007 2.347490 CCGTGGCCAAGCAGTAGT 59.653 61.111 7.24 0.00 0.00 2.73
1796 2008 1.594833 CCGTGGCCAAGCAGTAGTA 59.405 57.895 7.24 0.00 0.00 1.82
1797 2009 0.739813 CCGTGGCCAAGCAGTAGTAC 60.740 60.000 7.24 0.00 0.00 2.73
1798 2010 0.246635 CGTGGCCAAGCAGTAGTACT 59.753 55.000 7.24 0.00 0.00 2.73
1799 2011 1.475280 CGTGGCCAAGCAGTAGTACTA 59.525 52.381 7.24 0.00 0.00 1.82
1800 2012 2.479730 CGTGGCCAAGCAGTAGTACTAG 60.480 54.545 7.24 0.00 0.00 2.57
1821 2033 0.251354 ACGTAGACTAGACTGCCGGA 59.749 55.000 5.05 0.00 0.00 5.14
1864 2076 4.502777 GGCTAGTGTAAATGGTAGGGTAGC 60.503 50.000 0.00 0.00 0.00 3.58
1868 2080 1.139455 GTAAATGGTAGGGTAGCGGCA 59.861 52.381 1.45 0.00 0.00 5.69
1872 2084 2.440817 GGTAGGGTAGCGGCATGGT 61.441 63.158 1.45 0.00 0.00 3.55
1894 2116 2.432628 GTCGTTGCACTCTCCCGG 60.433 66.667 0.00 0.00 0.00 5.73
1926 2151 1.226575 TGCGTACTGCTTCCGATCG 60.227 57.895 8.51 8.51 46.63 3.69
1927 2152 1.063649 GCGTACTGCTTCCGATCGA 59.936 57.895 18.66 0.00 41.73 3.59
1929 2154 1.864435 GCGTACTGCTTCCGATCGAAT 60.864 52.381 18.66 0.00 41.73 3.34
1932 2157 2.215907 ACTGCTTCCGATCGAATCAG 57.784 50.000 18.66 19.48 45.98 2.90
1947 2172 3.254892 GAATCAGAAGTTCTCGGTGGAC 58.745 50.000 1.26 0.00 0.00 4.02
1948 2173 1.699730 TCAGAAGTTCTCGGTGGACA 58.300 50.000 1.26 0.00 0.00 4.02
1958 2183 3.986006 GGTGGACACAGGTCGCGA 61.986 66.667 3.71 3.71 45.28 5.87
1985 2217 7.763172 GTGAACTTCACTCTGTTCCATATAG 57.237 40.000 13.77 0.00 43.73 1.31
1986 2218 7.324178 GTGAACTTCACTCTGTTCCATATAGT 58.676 38.462 13.77 0.00 43.73 2.12
1987 2219 8.467598 GTGAACTTCACTCTGTTCCATATAGTA 58.532 37.037 13.77 0.00 43.73 1.82
2115 2353 5.584253 ACTGATCATGTACTACTGTGTCC 57.416 43.478 0.00 0.00 0.00 4.02
2141 2379 9.766277 CTTGCAAGATTTTTCTCACTAATACTC 57.234 33.333 22.31 0.00 0.00 2.59
2157 2396 2.403252 ACTCCCGTGGAAGCTTATTG 57.597 50.000 0.00 0.00 0.00 1.90
2178 2417 6.538945 TTGCTCCTACTTGTGTATGTGATA 57.461 37.500 0.00 0.00 0.00 2.15
2192 2433 8.822855 TGTGTATGTGATATAATTGACCGAAAC 58.177 33.333 0.00 0.00 0.00 2.78
2259 2500 1.628846 ACACCGGCTGAGGTTATCTTT 59.371 47.619 0.00 0.00 43.00 2.52
2288 2529 5.961272 GGTTTTCATTGACCGGTTGAATAT 58.039 37.500 18.42 2.23 0.00 1.28
2341 2588 6.382859 TGATAGCCTGGTAGTAACTCAATTCA 59.617 38.462 0.00 0.00 0.00 2.57
2346 2593 8.934697 AGCCTGGTAGTAACTCAATTCATAATA 58.065 33.333 0.00 0.00 0.00 0.98
2419 2674 3.804325 CGCAACTCATTCGATCTAACCAT 59.196 43.478 0.00 0.00 0.00 3.55
2429 2684 0.107214 ATCTAACCATGCCACCACCG 60.107 55.000 0.00 0.00 0.00 4.94
2440 2703 3.326578 ACCACCGGCAGCCACATA 61.327 61.111 13.30 0.00 0.00 2.29
2464 2737 2.093306 TCACCAGCCACGATACAAAG 57.907 50.000 0.00 0.00 0.00 2.77
2468 2741 2.002586 CCAGCCACGATACAAAGTCAG 58.997 52.381 0.00 0.00 0.00 3.51
2509 2782 1.300931 GCAAGTGCACGAGTGGAGA 60.301 57.895 12.01 0.00 41.59 3.71
2518 2791 0.315568 ACGAGTGGAGACAAGCTCAC 59.684 55.000 0.00 0.00 45.81 3.51
2531 2804 1.558233 AGCTCACTAGTGGGTGTACC 58.442 55.000 23.56 6.90 38.28 3.34
2543 2816 1.574428 GTGTACCACGTACCGTCGT 59.426 57.895 0.00 0.00 45.10 4.34
2571 2844 1.968493 TCCAGCTTTCGTTGGTACTCT 59.032 47.619 0.00 0.00 41.76 3.24
2578 2851 4.377897 CTTTCGTTGGTACTCTGTCCTTT 58.622 43.478 0.00 0.00 0.00 3.11
2608 2881 2.736978 CCGATCCGATGTCTTTCTCTG 58.263 52.381 0.00 0.00 0.00 3.35
2646 2919 2.594592 AGTGGCCTTGTGCGTTCC 60.595 61.111 3.32 0.00 42.61 3.62
2647 2920 2.904866 GTGGCCTTGTGCGTTCCA 60.905 61.111 3.32 0.00 42.61 3.53
2651 2924 0.885196 GGCCTTGTGCGTTCCATTAA 59.115 50.000 0.00 0.00 42.61 1.40
2652 2925 1.402325 GGCCTTGTGCGTTCCATTAAC 60.402 52.381 0.00 0.00 42.61 2.01
2655 2928 3.189702 GCCTTGTGCGTTCCATTAACTTA 59.810 43.478 0.00 0.00 35.81 2.24
2656 2929 4.671766 GCCTTGTGCGTTCCATTAACTTAG 60.672 45.833 0.00 0.00 35.81 2.18
2657 2930 4.693566 CCTTGTGCGTTCCATTAACTTAGA 59.306 41.667 0.00 0.00 35.81 2.10
2658 2931 5.354234 CCTTGTGCGTTCCATTAACTTAGAT 59.646 40.000 0.00 0.00 35.81 1.98
2659 2932 6.128007 CCTTGTGCGTTCCATTAACTTAGATT 60.128 38.462 0.00 0.00 35.81 2.40
2698 2971 1.355210 CGTTGCTGCGGAAACTGTT 59.645 52.632 14.63 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.846007 TCATTACCGCCATTGCCTTT 58.154 45.000 0.00 0.00 0.00 3.11
16 17 7.256286 ACACGTAGACCTAGTTGATTCATTAC 58.744 38.462 0.00 0.00 0.00 1.89
29 31 3.359033 AGTGCCAATACACGTAGACCTA 58.641 45.455 0.00 0.00 45.45 3.08
100 102 3.254024 AAGTCGGGCCAGCGATGTT 62.254 57.895 4.39 0.60 0.00 2.71
105 107 3.385749 ATACCAAGTCGGGCCAGCG 62.386 63.158 4.39 0.00 40.22 5.18
107 109 0.251916 TTGATACCAAGTCGGGCCAG 59.748 55.000 4.39 0.00 40.22 4.85
108 110 0.693622 TTTGATACCAAGTCGGGCCA 59.306 50.000 4.39 0.00 40.22 5.36
126 128 3.451178 ACACCGCATCATCTACCTACTTT 59.549 43.478 0.00 0.00 0.00 2.66
148 150 1.691976 CCTGTCACCACTACCAAGACA 59.308 52.381 0.00 0.00 37.61 3.41
166 168 0.740868 CCATCGTCGCATTGTCACCT 60.741 55.000 0.00 0.00 0.00 4.00
179 181 0.815213 CCGCCAATGTCATCCATCGT 60.815 55.000 0.00 0.00 31.75 3.73
181 183 1.202687 TCTCCGCCAATGTCATCCATC 60.203 52.381 0.00 0.00 31.75 3.51
182 184 0.839277 TCTCCGCCAATGTCATCCAT 59.161 50.000 0.00 0.00 34.36 3.41
183 185 0.617935 TTCTCCGCCAATGTCATCCA 59.382 50.000 0.00 0.00 0.00 3.41
184 186 1.672881 CTTTCTCCGCCAATGTCATCC 59.327 52.381 0.00 0.00 0.00 3.51
185 187 1.672881 CCTTTCTCCGCCAATGTCATC 59.327 52.381 0.00 0.00 0.00 2.92
186 188 1.281867 TCCTTTCTCCGCCAATGTCAT 59.718 47.619 0.00 0.00 0.00 3.06
187 189 0.690192 TCCTTTCTCCGCCAATGTCA 59.310 50.000 0.00 0.00 0.00 3.58
188 190 1.373570 CTCCTTTCTCCGCCAATGTC 58.626 55.000 0.00 0.00 0.00 3.06
189 191 0.035056 CCTCCTTTCTCCGCCAATGT 60.035 55.000 0.00 0.00 0.00 2.71
190 192 0.253044 TCCTCCTTTCTCCGCCAATG 59.747 55.000 0.00 0.00 0.00 2.82
191 193 0.543749 CTCCTCCTTTCTCCGCCAAT 59.456 55.000 0.00 0.00 0.00 3.16
192 194 0.544357 TCTCCTCCTTTCTCCGCCAA 60.544 55.000 0.00 0.00 0.00 4.52
193 195 0.544357 TTCTCCTCCTTTCTCCGCCA 60.544 55.000 0.00 0.00 0.00 5.69
194 196 0.176910 CTTCTCCTCCTTTCTCCGCC 59.823 60.000 0.00 0.00 0.00 6.13
195 197 1.136110 CTCTTCTCCTCCTTTCTCCGC 59.864 57.143 0.00 0.00 0.00 5.54
196 198 1.754226 CCTCTTCTCCTCCTTTCTCCG 59.246 57.143 0.00 0.00 0.00 4.63
197 199 2.115427 CCCTCTTCTCCTCCTTTCTCC 58.885 57.143 0.00 0.00 0.00 3.71
198 200 3.108847 TCCCTCTTCTCCTCCTTTCTC 57.891 52.381 0.00 0.00 0.00 2.87
199 201 3.013417 TCATCCCTCTTCTCCTCCTTTCT 59.987 47.826 0.00 0.00 0.00 2.52
200 202 3.379452 TCATCCCTCTTCTCCTCCTTTC 58.621 50.000 0.00 0.00 0.00 2.62
201 203 3.013417 TCTCATCCCTCTTCTCCTCCTTT 59.987 47.826 0.00 0.00 0.00 3.11
202 204 2.589664 TCTCATCCCTCTTCTCCTCCTT 59.410 50.000 0.00 0.00 0.00 3.36
203 205 2.177669 CTCTCATCCCTCTTCTCCTCCT 59.822 54.545 0.00 0.00 0.00 3.69
204 206 2.091333 ACTCTCATCCCTCTTCTCCTCC 60.091 54.545 0.00 0.00 0.00 4.30
205 207 3.312736 ACTCTCATCCCTCTTCTCCTC 57.687 52.381 0.00 0.00 0.00 3.71
206 208 3.774842 AACTCTCATCCCTCTTCTCCT 57.225 47.619 0.00 0.00 0.00 3.69
207 209 4.282496 TGTAACTCTCATCCCTCTTCTCC 58.718 47.826 0.00 0.00 0.00 3.71
208 210 5.923733 TTGTAACTCTCATCCCTCTTCTC 57.076 43.478 0.00 0.00 0.00 2.87
209 211 6.688073 TTTTGTAACTCTCATCCCTCTTCT 57.312 37.500 0.00 0.00 0.00 2.85
210 212 9.449719 TTTATTTTGTAACTCTCATCCCTCTTC 57.550 33.333 0.00 0.00 0.00 2.87
211 213 9.807921 TTTTATTTTGTAACTCTCATCCCTCTT 57.192 29.630 0.00 0.00 0.00 2.85
212 214 9.454859 CTTTTATTTTGTAACTCTCATCCCTCT 57.545 33.333 0.00 0.00 0.00 3.69
213 215 8.678199 CCTTTTATTTTGTAACTCTCATCCCTC 58.322 37.037 0.00 0.00 0.00 4.30
214 216 8.390921 TCCTTTTATTTTGTAACTCTCATCCCT 58.609 33.333 0.00 0.00 0.00 4.20
215 217 8.575649 TCCTTTTATTTTGTAACTCTCATCCC 57.424 34.615 0.00 0.00 0.00 3.85
218 220 9.025041 CCCTTCCTTTTATTTTGTAACTCTCAT 57.975 33.333 0.00 0.00 0.00 2.90
219 221 8.002459 ACCCTTCCTTTTATTTTGTAACTCTCA 58.998 33.333 0.00 0.00 0.00 3.27
220 222 8.405418 ACCCTTCCTTTTATTTTGTAACTCTC 57.595 34.615 0.00 0.00 0.00 3.20
221 223 8.638873 CAACCCTTCCTTTTATTTTGTAACTCT 58.361 33.333 0.00 0.00 0.00 3.24
222 224 8.635328 TCAACCCTTCCTTTTATTTTGTAACTC 58.365 33.333 0.00 0.00 0.00 3.01
223 225 8.541899 TCAACCCTTCCTTTTATTTTGTAACT 57.458 30.769 0.00 0.00 0.00 2.24
224 226 9.419297 GATCAACCCTTCCTTTTATTTTGTAAC 57.581 33.333 0.00 0.00 0.00 2.50
225 227 9.374711 AGATCAACCCTTCCTTTTATTTTGTAA 57.625 29.630 0.00 0.00 0.00 2.41
226 228 8.950007 AGATCAACCCTTCCTTTTATTTTGTA 57.050 30.769 0.00 0.00 0.00 2.41
227 229 7.309194 CGAGATCAACCCTTCCTTTTATTTTGT 60.309 37.037 0.00 0.00 0.00 2.83
228 230 7.029563 CGAGATCAACCCTTCCTTTTATTTTG 58.970 38.462 0.00 0.00 0.00 2.44
229 231 6.946009 TCGAGATCAACCCTTCCTTTTATTTT 59.054 34.615 0.00 0.00 0.00 1.82
230 232 6.481643 TCGAGATCAACCCTTCCTTTTATTT 58.518 36.000 0.00 0.00 0.00 1.40
231 233 6.062258 TCGAGATCAACCCTTCCTTTTATT 57.938 37.500 0.00 0.00 0.00 1.40
232 234 5.396884 CCTCGAGATCAACCCTTCCTTTTAT 60.397 44.000 15.71 0.00 0.00 1.40
233 235 4.081087 CCTCGAGATCAACCCTTCCTTTTA 60.081 45.833 15.71 0.00 0.00 1.52
234 236 3.307762 CCTCGAGATCAACCCTTCCTTTT 60.308 47.826 15.71 0.00 0.00 2.27
235 237 2.237392 CCTCGAGATCAACCCTTCCTTT 59.763 50.000 15.71 0.00 0.00 3.11
236 238 1.834263 CCTCGAGATCAACCCTTCCTT 59.166 52.381 15.71 0.00 0.00 3.36
237 239 1.490574 CCTCGAGATCAACCCTTCCT 58.509 55.000 15.71 0.00 0.00 3.36
238 240 0.179070 GCCTCGAGATCAACCCTTCC 60.179 60.000 15.71 0.00 0.00 3.46
239 241 0.179070 GGCCTCGAGATCAACCCTTC 60.179 60.000 15.71 0.00 0.00 3.46
240 242 0.909610 TGGCCTCGAGATCAACCCTT 60.910 55.000 15.71 0.00 0.00 3.95
241 243 0.909610 TTGGCCTCGAGATCAACCCT 60.910 55.000 15.71 0.00 0.00 4.34
242 244 0.744771 GTTGGCCTCGAGATCAACCC 60.745 60.000 26.26 13.77 34.97 4.11
243 245 1.084370 CGTTGGCCTCGAGATCAACC 61.084 60.000 28.34 17.49 36.95 3.77
244 246 1.084370 CCGTTGGCCTCGAGATCAAC 61.084 60.000 26.52 26.52 36.93 3.18
245 247 1.218047 CCGTTGGCCTCGAGATCAA 59.782 57.895 15.71 14.47 0.00 2.57
246 248 2.892640 CCGTTGGCCTCGAGATCA 59.107 61.111 15.71 8.81 0.00 2.92
247 249 2.586357 GCCGTTGGCCTCGAGATC 60.586 66.667 15.71 6.00 44.06 2.75
256 258 3.195698 GTCTCCATCGCCGTTGGC 61.196 66.667 9.34 0.00 46.75 4.52
257 259 0.744414 ATTGTCTCCATCGCCGTTGG 60.744 55.000 7.90 7.90 35.45 3.77
258 260 0.374758 CATTGTCTCCATCGCCGTTG 59.625 55.000 0.00 0.00 0.00 4.10
259 261 0.744414 CCATTGTCTCCATCGCCGTT 60.744 55.000 0.00 0.00 0.00 4.44
260 262 1.153369 CCATTGTCTCCATCGCCGT 60.153 57.895 0.00 0.00 0.00 5.68
261 263 1.889105 CCCATTGTCTCCATCGCCG 60.889 63.158 0.00 0.00 0.00 6.46
262 264 2.189499 GCCCATTGTCTCCATCGCC 61.189 63.158 0.00 0.00 0.00 5.54
263 265 2.537560 CGCCCATTGTCTCCATCGC 61.538 63.158 0.00 0.00 0.00 4.58
264 266 0.877649 CTCGCCCATTGTCTCCATCG 60.878 60.000 0.00 0.00 0.00 3.84
265 267 0.533755 CCTCGCCCATTGTCTCCATC 60.534 60.000 0.00 0.00 0.00 3.51
266 268 1.274703 ACCTCGCCCATTGTCTCCAT 61.275 55.000 0.00 0.00 0.00 3.41
267 269 1.899437 GACCTCGCCCATTGTCTCCA 61.899 60.000 0.00 0.00 0.00 3.86
268 270 1.153349 GACCTCGCCCATTGTCTCC 60.153 63.158 0.00 0.00 0.00 3.71
269 271 1.112113 TAGACCTCGCCCATTGTCTC 58.888 55.000 0.00 0.00 38.85 3.36
270 272 0.824759 GTAGACCTCGCCCATTGTCT 59.175 55.000 0.00 0.00 40.87 3.41
271 273 0.527817 CGTAGACCTCGCCCATTGTC 60.528 60.000 0.00 0.00 0.00 3.18
272 274 1.255667 ACGTAGACCTCGCCCATTGT 61.256 55.000 0.00 0.00 0.00 2.71
273 275 0.806102 CACGTAGACCTCGCCCATTG 60.806 60.000 0.00 0.00 0.00 2.82
274 276 1.255667 ACACGTAGACCTCGCCCATT 61.256 55.000 0.00 0.00 0.00 3.16
275 277 0.394762 TACACGTAGACCTCGCCCAT 60.395 55.000 0.00 0.00 0.00 4.00
276 278 1.002257 TACACGTAGACCTCGCCCA 60.002 57.895 0.00 0.00 0.00 5.36
277 279 1.431036 GTACACGTAGACCTCGCCC 59.569 63.158 0.00 0.00 0.00 6.13
278 280 1.308069 TGGTACACGTAGACCTCGCC 61.308 60.000 16.62 0.28 36.62 5.54
279 281 0.523072 TTGGTACACGTAGACCTCGC 59.477 55.000 16.62 0.00 39.29 5.03
280 282 1.464687 CGTTGGTACACGTAGACCTCG 60.465 57.143 16.62 15.97 39.29 4.63
281 283 1.730446 GCGTTGGTACACGTAGACCTC 60.730 57.143 16.62 10.13 39.29 3.85
282 284 0.242017 GCGTTGGTACACGTAGACCT 59.758 55.000 16.62 0.00 39.29 3.85
283 285 1.067199 CGCGTTGGTACACGTAGACC 61.067 60.000 10.44 10.44 39.29 3.85
284 286 1.067199 CCGCGTTGGTACACGTAGAC 61.067 60.000 4.92 0.00 39.29 2.59
285 287 1.209898 CCGCGTTGGTACACGTAGA 59.790 57.895 4.92 0.00 39.29 2.59
286 288 1.802715 CCCGCGTTGGTACACGTAG 60.803 63.158 4.92 2.99 39.29 3.51
287 289 2.257980 CCCGCGTTGGTACACGTA 59.742 61.111 4.92 0.00 39.29 3.57
288 290 3.915330 ACCCGCGTTGGTACACGT 61.915 61.111 4.92 0.00 39.29 4.49
289 291 3.408020 CACCCGCGTTGGTACACG 61.408 66.667 4.92 1.59 39.29 4.49
290 292 0.108709 TATCACCCGCGTTGGTACAC 60.109 55.000 4.92 0.00 39.29 2.90
291 293 0.607112 TTATCACCCGCGTTGGTACA 59.393 50.000 4.92 0.00 36.67 2.90
292 294 1.283736 CTTATCACCCGCGTTGGTAC 58.716 55.000 4.92 0.00 36.67 3.34
293 295 0.460635 GCTTATCACCCGCGTTGGTA 60.461 55.000 4.92 0.00 36.67 3.25
294 296 1.743995 GCTTATCACCCGCGTTGGT 60.744 57.895 4.92 2.60 39.96 3.67
295 297 1.095228 ATGCTTATCACCCGCGTTGG 61.095 55.000 4.92 1.79 37.55 3.77
296 298 1.577468 TATGCTTATCACCCGCGTTG 58.423 50.000 4.92 1.27 0.00 4.10
297 299 2.543777 ATATGCTTATCACCCGCGTT 57.456 45.000 4.92 0.00 0.00 4.84
298 300 2.543777 AATATGCTTATCACCCGCGT 57.456 45.000 4.92 0.00 0.00 6.01
299 301 3.067106 AGAAATATGCTTATCACCCGCG 58.933 45.455 0.00 0.00 0.00 6.46
300 302 5.447818 GCATAGAAATATGCTTATCACCCGC 60.448 44.000 11.93 0.00 46.78 6.13
301 303 6.111768 GCATAGAAATATGCTTATCACCCG 57.888 41.667 11.93 0.00 46.78 5.28
311 313 7.168972 CGATAGAGCCTAAGCATAGAAATATGC 59.831 40.741 11.39 11.39 45.94 3.14
312 314 8.194104 ACGATAGAGCCTAAGCATAGAAATATG 58.806 37.037 0.00 0.00 40.40 1.78
313 315 8.194104 CACGATAGAGCCTAAGCATAGAAATAT 58.806 37.037 0.00 0.00 40.40 1.28
314 316 7.363007 CCACGATAGAGCCTAAGCATAGAAATA 60.363 40.741 0.00 0.00 40.40 1.40
315 317 6.393990 CACGATAGAGCCTAAGCATAGAAAT 58.606 40.000 0.00 0.00 40.40 2.17
316 318 5.279006 CCACGATAGAGCCTAAGCATAGAAA 60.279 44.000 0.00 0.00 40.40 2.52
317 319 4.218635 CCACGATAGAGCCTAAGCATAGAA 59.781 45.833 0.00 0.00 40.40 2.10
318 320 3.759086 CCACGATAGAGCCTAAGCATAGA 59.241 47.826 0.00 0.00 40.40 1.98
319 321 3.508012 ACCACGATAGAGCCTAAGCATAG 59.492 47.826 0.00 0.00 40.40 2.23
320 322 3.497332 ACCACGATAGAGCCTAAGCATA 58.503 45.455 0.00 0.00 40.40 3.14
321 323 2.297597 GACCACGATAGAGCCTAAGCAT 59.702 50.000 0.00 0.00 40.40 3.79
322 324 1.681793 GACCACGATAGAGCCTAAGCA 59.318 52.381 0.00 0.00 40.40 3.91
323 325 1.335142 CGACCACGATAGAGCCTAAGC 60.335 57.143 0.00 0.00 42.66 3.09
324 326 1.948145 ACGACCACGATAGAGCCTAAG 59.052 52.381 0.00 0.00 42.66 2.18
325 327 2.048444 ACGACCACGATAGAGCCTAA 57.952 50.000 0.00 0.00 42.66 2.69
326 328 1.674441 CAACGACCACGATAGAGCCTA 59.326 52.381 0.00 0.00 42.66 3.93
327 329 0.456221 CAACGACCACGATAGAGCCT 59.544 55.000 0.00 0.00 42.66 4.58
328 330 0.454600 TCAACGACCACGATAGAGCC 59.545 55.000 0.00 0.00 42.66 4.70
329 331 2.120232 CATCAACGACCACGATAGAGC 58.880 52.381 0.00 0.00 42.66 4.09
330 332 2.120232 GCATCAACGACCACGATAGAG 58.880 52.381 0.00 0.00 42.66 2.43
331 333 1.202371 GGCATCAACGACCACGATAGA 60.202 52.381 0.00 0.00 42.66 1.98
332 334 1.209128 GGCATCAACGACCACGATAG 58.791 55.000 0.00 0.00 42.66 2.08
333 335 0.179094 GGGCATCAACGACCACGATA 60.179 55.000 0.00 0.00 42.66 2.92
334 336 1.449601 GGGCATCAACGACCACGAT 60.450 57.895 0.00 0.00 42.66 3.73
335 337 2.047655 GGGCATCAACGACCACGA 60.048 61.111 0.00 0.00 42.66 4.35
336 338 2.047274 AGGGCATCAACGACCACG 60.047 61.111 0.00 0.00 45.75 4.94
337 339 1.003839 TCAGGGCATCAACGACCAC 60.004 57.895 0.00 0.00 0.00 4.16
338 340 1.003839 GTCAGGGCATCAACGACCA 60.004 57.895 0.00 0.00 0.00 4.02
339 341 0.321653 AAGTCAGGGCATCAACGACC 60.322 55.000 0.00 0.00 0.00 4.79
340 342 0.798776 CAAGTCAGGGCATCAACGAC 59.201 55.000 0.00 0.00 0.00 4.34
341 343 0.321564 CCAAGTCAGGGCATCAACGA 60.322 55.000 0.00 0.00 0.00 3.85
342 344 0.606401 ACCAAGTCAGGGCATCAACG 60.606 55.000 0.00 0.00 0.00 4.10
343 345 2.084546 GTACCAAGTCAGGGCATCAAC 58.915 52.381 0.00 0.00 0.00 3.18
344 346 1.702401 TGTACCAAGTCAGGGCATCAA 59.298 47.619 0.00 0.00 0.00 2.57
345 347 1.278985 CTGTACCAAGTCAGGGCATCA 59.721 52.381 0.00 0.00 0.00 3.07
346 348 1.407437 CCTGTACCAAGTCAGGGCATC 60.407 57.143 3.58 0.00 45.11 3.91
347 349 0.620556 CCTGTACCAAGTCAGGGCAT 59.379 55.000 3.58 0.00 45.11 4.40
348 350 2.066340 CCTGTACCAAGTCAGGGCA 58.934 57.895 3.58 0.00 45.11 5.36
352 354 2.632996 TCCACTTCCTGTACCAAGTCAG 59.367 50.000 0.00 0.00 30.06 3.51
353 355 2.367567 GTCCACTTCCTGTACCAAGTCA 59.632 50.000 0.00 0.00 30.06 3.41
354 356 2.609737 CGTCCACTTCCTGTACCAAGTC 60.610 54.545 0.00 0.00 30.06 3.01
355 357 1.343465 CGTCCACTTCCTGTACCAAGT 59.657 52.381 0.00 0.00 32.87 3.16
356 358 1.616865 TCGTCCACTTCCTGTACCAAG 59.383 52.381 0.00 0.00 0.00 3.61
357 359 1.707106 TCGTCCACTTCCTGTACCAA 58.293 50.000 0.00 0.00 0.00 3.67
358 360 1.616865 CTTCGTCCACTTCCTGTACCA 59.383 52.381 0.00 0.00 0.00 3.25
359 361 1.891150 TCTTCGTCCACTTCCTGTACC 59.109 52.381 0.00 0.00 0.00 3.34
360 362 3.444388 AGATCTTCGTCCACTTCCTGTAC 59.556 47.826 0.00 0.00 0.00 2.90
361 363 3.444034 CAGATCTTCGTCCACTTCCTGTA 59.556 47.826 0.00 0.00 0.00 2.74
362 364 2.232452 CAGATCTTCGTCCACTTCCTGT 59.768 50.000 0.00 0.00 0.00 4.00
363 365 2.417924 CCAGATCTTCGTCCACTTCCTG 60.418 54.545 0.00 0.00 0.00 3.86
364 366 1.827969 CCAGATCTTCGTCCACTTCCT 59.172 52.381 0.00 0.00 0.00 3.36
365 367 1.550976 ACCAGATCTTCGTCCACTTCC 59.449 52.381 0.00 0.00 0.00 3.46
366 368 2.611518 CACCAGATCTTCGTCCACTTC 58.388 52.381 0.00 0.00 0.00 3.01
367 369 1.276421 CCACCAGATCTTCGTCCACTT 59.724 52.381 0.00 0.00 0.00 3.16
368 370 0.898320 CCACCAGATCTTCGTCCACT 59.102 55.000 0.00 0.00 0.00 4.00
369 371 0.608640 ACCACCAGATCTTCGTCCAC 59.391 55.000 0.00 0.00 0.00 4.02
370 372 1.348064 AACCACCAGATCTTCGTCCA 58.652 50.000 0.00 0.00 0.00 4.02
371 373 2.474410 AAACCACCAGATCTTCGTCC 57.526 50.000 0.00 0.00 0.00 4.79
372 374 3.058224 CCAAAAACCACCAGATCTTCGTC 60.058 47.826 0.00 0.00 0.00 4.20
373 375 2.884639 CCAAAAACCACCAGATCTTCGT 59.115 45.455 0.00 0.00 0.00 3.85
374 376 2.884639 ACCAAAAACCACCAGATCTTCG 59.115 45.455 0.00 0.00 0.00 3.79
375 377 5.048713 CACTACCAAAAACCACCAGATCTTC 60.049 44.000 0.00 0.00 0.00 2.87
376 378 4.827284 CACTACCAAAAACCACCAGATCTT 59.173 41.667 0.00 0.00 0.00 2.40
377 379 4.398319 CACTACCAAAAACCACCAGATCT 58.602 43.478 0.00 0.00 0.00 2.75
383 385 3.003585 CGTAACCACTACCAAAAACCACC 59.996 47.826 0.00 0.00 0.00 4.61
386 388 2.553602 CCCGTAACCACTACCAAAAACC 59.446 50.000 0.00 0.00 0.00 3.27
424 621 4.160626 ACTCGTTTCTCCTCCTCCTATTTG 59.839 45.833 0.00 0.00 0.00 2.32
457 654 5.105023 TCCTTCTTCCTCTCTCAATGTCATG 60.105 44.000 0.00 0.00 0.00 3.07
506 703 0.252057 TTCCCCTTTTTAGGCTGCCC 60.252 55.000 16.57 0.00 0.00 5.36
510 707 1.641192 CTCCCTTCCCCTTTTTAGGCT 59.359 52.381 0.00 0.00 0.00 4.58
519 716 1.711375 GGTTTTCTTCTCCCTTCCCCT 59.289 52.381 0.00 0.00 0.00 4.79
520 717 1.427753 TGGTTTTCTTCTCCCTTCCCC 59.572 52.381 0.00 0.00 0.00 4.81
528 725 2.353109 GGCATGCCTTGGTTTTCTTCTC 60.353 50.000 29.98 0.00 0.00 2.87
546 743 4.947147 GCCACAACCCTGTCGGCA 62.947 66.667 11.41 0.00 43.53 5.69
551 748 3.494223 GCTTTTAAATGCCACAACCCTGT 60.494 43.478 13.65 0.00 35.63 4.00
558 755 2.035193 TCGCTTGCTTTTAAATGCCACA 59.965 40.909 19.88 6.58 0.00 4.17
582 779 8.216423 AGTAGATCTATCTGAATGCAACCATTT 58.784 33.333 5.57 0.00 38.73 2.32
586 783 7.441017 AGAAGTAGATCTATCTGAATGCAACC 58.559 38.462 5.57 0.00 37.76 3.77
587 784 7.598493 GGAGAAGTAGATCTATCTGAATGCAAC 59.402 40.741 10.05 0.00 37.76 4.17
589 786 6.072230 CGGAGAAGTAGATCTATCTGAATGCA 60.072 42.308 10.05 0.00 37.76 3.96
590 787 6.150307 TCGGAGAAGTAGATCTATCTGAATGC 59.850 42.308 10.05 0.00 37.76 3.56
591 788 7.174080 TGTCGGAGAAGTAGATCTATCTGAATG 59.826 40.741 10.05 0.00 39.69 2.67
592 789 7.227873 TGTCGGAGAAGTAGATCTATCTGAAT 58.772 38.462 10.05 0.00 39.69 2.57
593 790 6.592870 TGTCGGAGAAGTAGATCTATCTGAA 58.407 40.000 10.05 2.30 39.69 3.02
594 791 6.176014 TGTCGGAGAAGTAGATCTATCTGA 57.824 41.667 10.05 8.99 39.69 3.27
595 792 6.869315 TTGTCGGAGAAGTAGATCTATCTG 57.131 41.667 10.05 7.00 39.69 2.90
601 798 9.922305 CAAATATTTTTGTCGGAGAAGTAGATC 57.078 33.333 0.00 0.00 39.69 2.75
671 874 7.309770 GAGTACTCCCTCCATCAGAAAATAT 57.690 40.000 12.13 0.00 0.00 1.28
696 900 1.299541 AACGGTCAGCTTGACTTGTG 58.700 50.000 13.59 6.57 46.19 3.33
785 990 6.675002 GCAAGCTGATGAAGTGAGAAATGTAG 60.675 42.308 0.00 0.00 0.00 2.74
786 991 5.122869 GCAAGCTGATGAAGTGAGAAATGTA 59.877 40.000 0.00 0.00 0.00 2.29
787 992 4.082895 GCAAGCTGATGAAGTGAGAAATGT 60.083 41.667 0.00 0.00 0.00 2.71
1116 1328 2.193248 GGCGATGGAGGGAAAGGG 59.807 66.667 0.00 0.00 0.00 3.95
1151 1363 3.839432 GCGGAAGGACTCGGAGGG 61.839 72.222 10.23 0.00 0.00 4.30
1158 1370 4.083862 GCCGGAAGCGGAAGGACT 62.084 66.667 5.05 0.00 0.00 3.85
1250 1462 4.980805 TCGTGGCTTGACGGTGGC 62.981 66.667 0.00 0.00 39.88 5.01
1354 1566 4.828925 GTCTCTGCCCTCGCCTGC 62.829 72.222 0.00 0.00 0.00 4.85
1488 1700 4.016706 CCGTGCCGGGAGAAGGTT 62.017 66.667 2.18 0.00 44.15 3.50
1795 2007 5.506483 CGGCAGTCTAGTCTACGTACTAGTA 60.506 48.000 19.93 0.00 46.07 1.82
1796 2008 4.692228 GGCAGTCTAGTCTACGTACTAGT 58.308 47.826 19.93 0.00 46.07 2.57
1797 2009 3.735240 CGGCAGTCTAGTCTACGTACTAG 59.265 52.174 16.27 16.27 46.92 2.57
1798 2010 3.491619 CCGGCAGTCTAGTCTACGTACTA 60.492 52.174 10.58 0.00 0.00 1.82
1799 2011 2.548875 CGGCAGTCTAGTCTACGTACT 58.451 52.381 0.00 0.00 0.00 2.73
1800 2012 1.596727 CCGGCAGTCTAGTCTACGTAC 59.403 57.143 10.58 0.00 0.00 3.67
1868 2080 2.590291 TGCAACGACGCACACCAT 60.590 55.556 0.00 0.00 36.86 3.55
1926 2151 3.254892 GTCCACCGAGAACTTCTGATTC 58.745 50.000 0.00 0.00 0.00 2.52
1927 2152 2.632996 TGTCCACCGAGAACTTCTGATT 59.367 45.455 0.00 0.00 0.00 2.57
1929 2154 1.340248 GTGTCCACCGAGAACTTCTGA 59.660 52.381 0.00 0.00 0.00 3.27
1932 2157 1.605712 CCTGTGTCCACCGAGAACTTC 60.606 57.143 0.00 0.00 0.00 3.01
1947 2172 0.163788 GTTCACATTCGCGACCTGTG 59.836 55.000 30.90 30.90 41.24 3.66
1948 2173 0.033504 AGTTCACATTCGCGACCTGT 59.966 50.000 9.15 13.38 0.00 4.00
1982 2214 9.829507 CAAGAAAATCTGAGATGGAAGTACTAT 57.170 33.333 0.00 0.00 0.00 2.12
1983 2215 7.766278 GCAAGAAAATCTGAGATGGAAGTACTA 59.234 37.037 0.00 0.00 0.00 1.82
1984 2216 6.597280 GCAAGAAAATCTGAGATGGAAGTACT 59.403 38.462 0.00 0.00 0.00 2.73
1985 2217 6.597280 AGCAAGAAAATCTGAGATGGAAGTAC 59.403 38.462 0.00 0.00 0.00 2.73
1986 2218 6.715280 AGCAAGAAAATCTGAGATGGAAGTA 58.285 36.000 0.00 0.00 0.00 2.24
1987 2219 5.568392 AGCAAGAAAATCTGAGATGGAAGT 58.432 37.500 0.00 0.00 0.00 3.01
2091 2329 7.063593 AGGACACAGTAGTACATGATCAGTAT 58.936 38.462 0.00 0.00 0.00 2.12
2094 2332 5.843673 AGGACACAGTAGTACATGATCAG 57.156 43.478 0.00 0.00 0.00 2.90
2098 2336 3.576550 TGCAAGGACACAGTAGTACATGA 59.423 43.478 0.00 0.00 0.00 3.07
2108 2346 5.192327 AGAAAAATCTTGCAAGGACACAG 57.808 39.130 25.73 0.00 0.00 3.66
2109 2347 4.644234 TGAGAAAAATCTTGCAAGGACACA 59.356 37.500 25.73 6.94 0.00 3.72
2110 2348 4.978580 GTGAGAAAAATCTTGCAAGGACAC 59.021 41.667 25.73 17.59 0.00 3.67
2115 2353 9.766277 GAGTATTAGTGAGAAAAATCTTGCAAG 57.234 33.333 20.81 20.81 0.00 4.01
2157 2396 9.712305 AATTATATCACATACACAAGTAGGAGC 57.288 33.333 0.00 0.00 35.65 4.70
2259 2500 1.515081 GGTCAATGAAAACCGACGGA 58.485 50.000 23.38 0.00 0.00 4.69
2288 2529 3.411446 AGAAACGGTCAGCATCATCAAA 58.589 40.909 0.00 0.00 0.00 2.69
2393 2640 1.754803 AGATCGAATGAGTTGCGGGTA 59.245 47.619 0.00 0.00 0.00 3.69
2395 2642 2.509052 TAGATCGAATGAGTTGCGGG 57.491 50.000 0.00 0.00 0.00 6.13
2429 2684 0.734889 GTGATGTGTATGTGGCTGCC 59.265 55.000 12.87 12.87 0.00 4.85
2431 2686 2.011947 CTGGTGATGTGTATGTGGCTG 58.988 52.381 0.00 0.00 0.00 4.85
2432 2687 1.679944 GCTGGTGATGTGTATGTGGCT 60.680 52.381 0.00 0.00 0.00 4.75
2440 2703 0.901827 TATCGTGGCTGGTGATGTGT 59.098 50.000 0.00 0.00 0.00 3.72
2468 2741 6.368791 TGCATTCTCATGTAGACAGTTTGTAC 59.631 38.462 0.00 0.00 32.51 2.90
2509 2782 1.424638 ACACCCACTAGTGAGCTTGT 58.575 50.000 24.68 16.45 40.34 3.16
2543 2816 1.153449 CGAAAGCTGGATGGGCGTA 60.153 57.895 0.00 0.00 34.52 4.42
2571 2844 3.495434 TCGGCTTAAAAGGAAAGGACA 57.505 42.857 0.00 0.00 0.00 4.02
2578 2851 2.169769 ACATCGGATCGGCTTAAAAGGA 59.830 45.455 0.00 0.00 0.00 3.36
2625 2898 3.052082 CGCACAAGGCCACTCCTG 61.052 66.667 5.01 0.00 46.94 3.86
2628 2901 2.617274 GGAACGCACAAGGCCACTC 61.617 63.158 5.01 0.00 40.31 3.51
2632 2905 0.885196 TTAATGGAACGCACAAGGCC 59.115 50.000 0.00 0.00 40.31 5.19
2639 2912 8.556213 AGTTAAATCTAAGTTAATGGAACGCA 57.444 30.769 0.00 0.00 43.37 5.24
2655 2928 7.299586 GCGAGACGTATCATCTAGTTAAATCT 58.700 38.462 11.25 0.00 0.00 2.40
2656 2929 6.246748 CGCGAGACGTATCATCTAGTTAAATC 59.753 42.308 11.25 0.00 36.87 2.17
2657 2930 6.078479 CGCGAGACGTATCATCTAGTTAAAT 58.922 40.000 11.25 0.00 36.87 1.40
2658 2931 5.438117 CGCGAGACGTATCATCTAGTTAAA 58.562 41.667 11.25 0.00 36.87 1.52
2659 2932 5.015067 CGCGAGACGTATCATCTAGTTAA 57.985 43.478 11.25 0.00 36.87 2.01
2679 2952 2.427410 CAGTTTCCGCAGCAACGC 60.427 61.111 0.00 0.00 0.00 4.84
2688 2961 7.922505 TCAAATTATTTGTCAACAGTTTCCG 57.077 32.000 16.06 0.00 41.36 4.30


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

AutoCloner maintained by Alex Coulton.