Multiple sequence alignment - TraesCS4B01G045700

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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 TraesCS4B01G045700 chr4B 100.000 3517 0 0 1 3517 32895637 32899153 0.000000e+00 6495.0
1 TraesCS4B01G045700 chr4B 84.112 107 15 2 322 427 87399483 87399378 6.210000e-18 102.0
2 TraesCS4B01G045700 chr4D 92.496 3145 149 45 424 3517 21777355 21774247 0.000000e+00 4420.0
3 TraesCS4B01G045700 chr4D 82.569 218 34 4 213 427 116251594 116251810 4.630000e-44 189.0
4 TraesCS4B01G045700 chr4D 97.778 45 1 0 132 176 246865371 246865327 1.050000e-10 78.7
5 TraesCS4B01G045700 chr4A 92.525 3144 117 38 440 3517 580736557 580733466 0.000000e+00 4396.0
6 TraesCS4B01G045700 chr4A 85.167 209 13 2 3 211 580736749 580736559 7.700000e-47 198.0
7 TraesCS4B01G045700 chr7D 86.792 212 24 4 218 427 608181400 608181191 2.110000e-57 233.0
8 TraesCS4B01G045700 chr7D 94.853 136 5 2 2194 2328 167229395 167229529 9.890000e-51 211.0
9 TraesCS4B01G045700 chr6D 91.613 155 11 2 2200 2354 382588762 382588610 2.750000e-51 213.0
10 TraesCS4B01G045700 chr6D 100.000 42 0 0 138 179 405582421 405582380 1.050000e-10 78.7
11 TraesCS4B01G045700 chr7B 94.853 136 5 2 2194 2328 131377843 131377977 9.890000e-51 211.0
12 TraesCS4B01G045700 chr7B 84.444 135 18 3 215 347 361168550 361168683 2.850000e-26 130.0
13 TraesCS4B01G045700 chr7A 94.853 136 5 2 2194 2328 168813528 168813662 9.890000e-51 211.0
14 TraesCS4B01G045700 chr6B 88.485 165 16 3 2200 2362 572392567 572392404 2.770000e-46 196.0
15 TraesCS4B01G045700 chr5B 83.810 210 29 5 218 424 85562912 85563119 9.960000e-46 195.0
16 TraesCS4B01G045700 chr1B 82.895 152 20 6 222 369 587659866 587660015 7.920000e-27 132.0
17 TraesCS4B01G045700 chr1B 84.426 122 7 6 314 424 465090894 465091014 3.710000e-20 110.0
18 TraesCS4B01G045700 chr3A 84.127 126 16 2 303 424 14854858 14854983 6.170000e-23 119.0
19 TraesCS4B01G045700 chr2A 91.667 72 2 1 108 179 44088711 44088778 2.890000e-16 97.1
20 TraesCS4B01G045700 chr2A 87.037 54 6 1 3140 3192 724019310 724019257 3.790000e-05 60.2
21 TraesCS4B01G045700 chr3B 79.259 135 15 7 303 424 769189012 769189146 8.090000e-12 82.4
22 TraesCS4B01G045700 chr3B 85.897 78 5 4 108 179 819286282 819286205 1.050000e-10 78.7
23 TraesCS4B01G045700 chr3B 79.279 111 11 6 326 424 769159981 769159871 2.270000e-07 67.6
24 TraesCS4B01G045700 chr5A 85.366 82 7 4 103 179 27695165 27695246 2.910000e-11 80.5
25 TraesCS4B01G045700 chr2D 87.500 72 5 2 104 173 352203232 352203163 2.910000e-11 80.5
26 TraesCS4B01G045700 chr5D 85.526 76 8 2 109 181 39012539 39012614 3.760000e-10 76.8
27 TraesCS4B01G045700 chrUn 78.740 127 15 6 310 424 333456426 333456552 1.350000e-09 75.0
28 TraesCS4B01G045700 chr1D 85.294 68 7 3 113 179 219475914 219475979 2.270000e-07 67.6
29 TraesCS4B01G045700 chr2B 97.368 38 1 0 252 289 41537799 41537762 8.150000e-07 65.8


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 TraesCS4B01G045700 chr4B 32895637 32899153 3516 False 6495 6495 100.000 1 3517 1 chr4B.!!$F1 3516
1 TraesCS4B01G045700 chr4D 21774247 21777355 3108 True 4420 4420 92.496 424 3517 1 chr4D.!!$R1 3093
2 TraesCS4B01G045700 chr4A 580733466 580736749 3283 True 2297 4396 88.846 3 3517 2 chr4A.!!$R1 3514

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
435 436 0.320771 AACTGGCCTTAGCGTGTGAG 60.321 55.0 3.32 0.0 41.24 3.51 F
1069 1075 0.250166 TCGTGTCTGACCTGACGAGA 60.250 55.0 15.17 0.0 39.64 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2035 2.071540 GGACAAGTGCTTACCGGTAAC 58.928 52.381 23.17 18.72 0.00 2.50 R
2822 2899 1.672363 AGGCATGCATTGACATACACG 59.328 47.619 21.36 0.00 34.87 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
27 28 3.733727 CGTGGTTTGTAGGATTTTTGCAC 59.266 43.478 0.00 0.00 0.00 4.57
47 48 8.908786 TTGCACTATTCCTATAGGATTTCTTG 57.091 34.615 22.30 15.53 44.98 3.02
65 66 1.917872 TGCTGCGGGATTTTTACCTT 58.082 45.000 0.00 0.00 0.00 3.50
74 75 1.982913 GATTTTTACCTTTGTGCGGCG 59.017 47.619 0.51 0.51 0.00 6.46
85 86 2.254918 TGTGCGGCGTTCATTTTATG 57.745 45.000 9.37 0.00 0.00 1.90
100 101 4.871871 TTTTATGGGAATGGAGGCACTA 57.128 40.909 0.00 0.00 41.55 2.74
102 103 6.523035 TTTTATGGGAATGGAGGCACTATA 57.477 37.500 0.00 0.00 41.55 1.31
104 105 6.718593 TTATGGGAATGGAGGCACTATATT 57.281 37.500 0.00 0.00 41.55 1.28
105 106 5.605540 ATGGGAATGGAGGCACTATATTT 57.394 39.130 0.00 0.00 41.55 1.40
107 108 4.665009 TGGGAATGGAGGCACTATATTTCT 59.335 41.667 0.00 0.00 41.55 2.52
108 109 5.134339 TGGGAATGGAGGCACTATATTTCTT 59.866 40.000 0.00 0.00 41.55 2.52
109 110 6.071320 GGGAATGGAGGCACTATATTTCTTT 58.929 40.000 0.00 0.00 41.55 2.52
110 111 6.551227 GGGAATGGAGGCACTATATTTCTTTT 59.449 38.462 0.00 0.00 41.55 2.27
111 112 7.069950 GGGAATGGAGGCACTATATTTCTTTTT 59.930 37.037 0.00 0.00 41.55 1.94
209 210 2.435372 TGTCCAAAACTGTGGCTTCT 57.565 45.000 0.00 0.00 38.68 2.85
210 211 2.023673 TGTCCAAAACTGTGGCTTCTG 58.976 47.619 0.00 0.00 38.68 3.02
211 212 2.024414 GTCCAAAACTGTGGCTTCTGT 58.976 47.619 0.00 0.00 38.68 3.41
212 213 2.023673 TCCAAAACTGTGGCTTCTGTG 58.976 47.619 0.00 0.00 38.68 3.66
213 214 2.023673 CCAAAACTGTGGCTTCTGTGA 58.976 47.619 0.00 0.00 0.00 3.58
214 215 2.223572 CCAAAACTGTGGCTTCTGTGAC 60.224 50.000 0.00 0.00 0.00 3.67
215 216 2.684881 CAAAACTGTGGCTTCTGTGACT 59.315 45.455 0.00 0.00 0.00 3.41
216 217 2.717639 AACTGTGGCTTCTGTGACTT 57.282 45.000 0.00 0.00 0.00 3.01
217 218 3.838244 AACTGTGGCTTCTGTGACTTA 57.162 42.857 0.00 0.00 0.00 2.24
218 219 3.393089 ACTGTGGCTTCTGTGACTTAG 57.607 47.619 0.00 0.00 0.00 2.18
219 220 2.037772 ACTGTGGCTTCTGTGACTTAGG 59.962 50.000 0.00 0.00 0.00 2.69
220 221 2.037772 CTGTGGCTTCTGTGACTTAGGT 59.962 50.000 0.00 0.00 0.00 3.08
221 222 2.037251 TGTGGCTTCTGTGACTTAGGTC 59.963 50.000 0.00 0.00 42.42 3.85
222 223 1.623811 TGGCTTCTGTGACTTAGGTCC 59.376 52.381 2.10 0.00 41.47 4.46
223 224 1.623811 GGCTTCTGTGACTTAGGTCCA 59.376 52.381 2.10 0.00 41.47 4.02
224 225 2.354203 GGCTTCTGTGACTTAGGTCCAG 60.354 54.545 13.71 13.71 41.47 3.86
225 226 2.300437 GCTTCTGTGACTTAGGTCCAGT 59.700 50.000 17.12 0.00 41.47 4.00
226 227 3.244249 GCTTCTGTGACTTAGGTCCAGTT 60.244 47.826 17.12 0.00 41.47 3.16
227 228 4.561105 CTTCTGTGACTTAGGTCCAGTTC 58.439 47.826 17.12 1.13 41.47 3.01
228 229 3.845860 TCTGTGACTTAGGTCCAGTTCT 58.154 45.455 17.12 0.00 41.47 3.01
229 230 4.223953 TCTGTGACTTAGGTCCAGTTCTT 58.776 43.478 17.12 0.00 41.47 2.52
230 231 4.654262 TCTGTGACTTAGGTCCAGTTCTTT 59.346 41.667 17.12 0.00 41.47 2.52
231 232 5.130477 TCTGTGACTTAGGTCCAGTTCTTTT 59.870 40.000 17.12 0.00 41.47 2.27
232 233 5.123227 TGTGACTTAGGTCCAGTTCTTTTG 58.877 41.667 2.10 0.00 41.47 2.44
233 234 4.515567 GTGACTTAGGTCCAGTTCTTTTGG 59.484 45.833 2.10 0.00 41.47 3.28
234 235 4.165372 TGACTTAGGTCCAGTTCTTTTGGT 59.835 41.667 2.10 0.00 41.47 3.67
235 236 5.367352 TGACTTAGGTCCAGTTCTTTTGGTA 59.633 40.000 2.10 0.00 41.47 3.25
236 237 5.866207 ACTTAGGTCCAGTTCTTTTGGTAG 58.134 41.667 0.00 0.00 37.02 3.18
237 238 3.141767 AGGTCCAGTTCTTTTGGTAGC 57.858 47.619 0.00 0.00 37.02 3.58
238 239 2.160205 GGTCCAGTTCTTTTGGTAGCC 58.840 52.381 0.00 0.00 37.02 3.93
239 240 2.224793 GGTCCAGTTCTTTTGGTAGCCT 60.225 50.000 0.00 0.00 37.02 4.58
240 241 3.487372 GTCCAGTTCTTTTGGTAGCCTT 58.513 45.455 0.00 0.00 37.02 4.35
241 242 3.889538 GTCCAGTTCTTTTGGTAGCCTTT 59.110 43.478 0.00 0.00 37.02 3.11
242 243 4.341235 GTCCAGTTCTTTTGGTAGCCTTTT 59.659 41.667 0.00 0.00 37.02 2.27
243 244 4.959839 TCCAGTTCTTTTGGTAGCCTTTTT 59.040 37.500 0.00 0.00 37.02 1.94
244 245 6.040054 GTCCAGTTCTTTTGGTAGCCTTTTTA 59.960 38.462 0.00 0.00 37.02 1.52
245 246 6.264518 TCCAGTTCTTTTGGTAGCCTTTTTAG 59.735 38.462 0.00 0.00 37.02 1.85
246 247 6.447162 CAGTTCTTTTGGTAGCCTTTTTAGG 58.553 40.000 0.00 0.00 0.00 2.69
247 248 6.040504 CAGTTCTTTTGGTAGCCTTTTTAGGT 59.959 38.462 0.00 0.00 0.00 3.08
248 249 6.610020 AGTTCTTTTGGTAGCCTTTTTAGGTT 59.390 34.615 0.00 0.00 0.00 3.50
249 250 7.125204 AGTTCTTTTGGTAGCCTTTTTAGGTTT 59.875 33.333 0.00 0.00 0.00 3.27
250 251 8.415553 GTTCTTTTGGTAGCCTTTTTAGGTTTA 58.584 33.333 0.00 0.00 0.00 2.01
251 252 8.715190 TCTTTTGGTAGCCTTTTTAGGTTTAT 57.285 30.769 0.00 0.00 0.00 1.40
252 253 9.810870 TCTTTTGGTAGCCTTTTTAGGTTTATA 57.189 29.630 0.00 0.00 0.00 0.98
254 255 9.810870 TTTTGGTAGCCTTTTTAGGTTTATAGA 57.189 29.630 0.00 0.00 0.00 1.98
255 256 9.810870 TTTGGTAGCCTTTTTAGGTTTATAGAA 57.189 29.630 0.00 0.00 0.00 2.10
256 257 9.984590 TTGGTAGCCTTTTTAGGTTTATAGAAT 57.015 29.630 0.00 0.00 0.00 2.40
267 268 9.623000 TTTAGGTTTATAGAATAAGTTGCCTCC 57.377 33.333 0.00 0.00 0.00 4.30
268 269 7.453141 AGGTTTATAGAATAAGTTGCCTCCT 57.547 36.000 0.00 0.00 0.00 3.69
269 270 8.562949 AGGTTTATAGAATAAGTTGCCTCCTA 57.437 34.615 0.00 0.00 0.00 2.94
270 271 8.430431 AGGTTTATAGAATAAGTTGCCTCCTAC 58.570 37.037 0.00 0.00 0.00 3.18
271 272 7.660617 GGTTTATAGAATAAGTTGCCTCCTACC 59.339 40.741 0.00 0.00 0.00 3.18
272 273 5.827326 ATAGAATAAGTTGCCTCCTACCC 57.173 43.478 0.00 0.00 0.00 3.69
273 274 3.460825 AGAATAAGTTGCCTCCTACCCA 58.539 45.455 0.00 0.00 0.00 4.51
274 275 3.456277 AGAATAAGTTGCCTCCTACCCAG 59.544 47.826 0.00 0.00 0.00 4.45
275 276 0.909623 TAAGTTGCCTCCTACCCAGC 59.090 55.000 0.00 0.00 0.00 4.85
276 277 0.842467 AAGTTGCCTCCTACCCAGCT 60.842 55.000 0.00 0.00 0.00 4.24
277 278 0.842467 AGTTGCCTCCTACCCAGCTT 60.842 55.000 0.00 0.00 0.00 3.74
278 279 0.909623 GTTGCCTCCTACCCAGCTTA 59.090 55.000 0.00 0.00 0.00 3.09
279 280 1.490910 GTTGCCTCCTACCCAGCTTAT 59.509 52.381 0.00 0.00 0.00 1.73
280 281 1.893315 TGCCTCCTACCCAGCTTATT 58.107 50.000 0.00 0.00 0.00 1.40
281 282 1.768870 TGCCTCCTACCCAGCTTATTC 59.231 52.381 0.00 0.00 0.00 1.75
282 283 2.050918 GCCTCCTACCCAGCTTATTCT 58.949 52.381 0.00 0.00 0.00 2.40
283 284 3.240302 GCCTCCTACCCAGCTTATTCTA 58.760 50.000 0.00 0.00 0.00 2.10
284 285 3.841255 GCCTCCTACCCAGCTTATTCTAT 59.159 47.826 0.00 0.00 0.00 1.98
285 286 5.024118 GCCTCCTACCCAGCTTATTCTATA 58.976 45.833 0.00 0.00 0.00 1.31
286 287 5.484290 GCCTCCTACCCAGCTTATTCTATAA 59.516 44.000 0.00 0.00 0.00 0.98
287 288 6.351456 GCCTCCTACCCAGCTTATTCTATAAG 60.351 46.154 2.75 2.75 0.00 1.73
381 382 8.561738 TTAGTTAGGCTTCAAGAATAAAGTGG 57.438 34.615 0.00 0.00 0.00 4.00
382 383 5.946377 AGTTAGGCTTCAAGAATAAAGTGGG 59.054 40.000 0.00 0.00 0.00 4.61
383 384 4.388577 AGGCTTCAAGAATAAAGTGGGT 57.611 40.909 0.00 0.00 0.00 4.51
384 385 5.514500 AGGCTTCAAGAATAAAGTGGGTA 57.486 39.130 0.00 0.00 0.00 3.69
385 386 5.501156 AGGCTTCAAGAATAAAGTGGGTAG 58.499 41.667 0.00 0.00 0.00 3.18
386 387 4.640647 GGCTTCAAGAATAAAGTGGGTAGG 59.359 45.833 0.00 0.00 0.00 3.18
387 388 4.640647 GCTTCAAGAATAAAGTGGGTAGGG 59.359 45.833 0.00 0.00 0.00 3.53
388 389 5.572885 GCTTCAAGAATAAAGTGGGTAGGGA 60.573 44.000 0.00 0.00 0.00 4.20
389 390 5.693769 TCAAGAATAAAGTGGGTAGGGAG 57.306 43.478 0.00 0.00 0.00 4.30
390 391 5.098663 TCAAGAATAAAGTGGGTAGGGAGT 58.901 41.667 0.00 0.00 0.00 3.85
391 392 6.266080 TCAAGAATAAAGTGGGTAGGGAGTA 58.734 40.000 0.00 0.00 0.00 2.59
392 393 6.383147 TCAAGAATAAAGTGGGTAGGGAGTAG 59.617 42.308 0.00 0.00 0.00 2.57
393 394 5.851418 AGAATAAAGTGGGTAGGGAGTAGT 58.149 41.667 0.00 0.00 0.00 2.73
394 395 6.269974 AGAATAAAGTGGGTAGGGAGTAGTT 58.730 40.000 0.00 0.00 0.00 2.24
395 396 6.734281 AGAATAAAGTGGGTAGGGAGTAGTTT 59.266 38.462 0.00 0.00 0.00 2.66
396 397 7.902941 AGAATAAAGTGGGTAGGGAGTAGTTTA 59.097 37.037 0.00 0.00 0.00 2.01
397 398 8.634188 AATAAAGTGGGTAGGGAGTAGTTTAT 57.366 34.615 0.00 0.00 31.63 1.40
398 399 6.964876 AAAGTGGGTAGGGAGTAGTTTATT 57.035 37.500 0.00 0.00 0.00 1.40
399 400 6.556974 AAGTGGGTAGGGAGTAGTTTATTC 57.443 41.667 0.00 0.00 0.00 1.75
400 401 5.851418 AGTGGGTAGGGAGTAGTTTATTCT 58.149 41.667 0.00 0.00 0.00 2.40
401 402 6.989894 AGTGGGTAGGGAGTAGTTTATTCTA 58.010 40.000 0.00 0.00 0.00 2.10
402 403 7.068061 AGTGGGTAGGGAGTAGTTTATTCTAG 58.932 42.308 0.00 0.00 0.00 2.43
403 404 7.065504 GTGGGTAGGGAGTAGTTTATTCTAGA 58.934 42.308 0.00 0.00 0.00 2.43
404 405 7.562821 GTGGGTAGGGAGTAGTTTATTCTAGAA 59.437 40.741 7.82 7.82 0.00 2.10
405 406 7.783596 TGGGTAGGGAGTAGTTTATTCTAGAAG 59.216 40.741 11.53 0.00 0.00 2.85
406 407 7.255906 GGGTAGGGAGTAGTTTATTCTAGAAGC 60.256 44.444 11.53 1.69 0.00 3.86
407 408 6.734502 AGGGAGTAGTTTATTCTAGAAGCC 57.265 41.667 11.53 0.00 0.00 4.35
408 409 6.203072 AGGGAGTAGTTTATTCTAGAAGCCA 58.797 40.000 11.53 0.00 0.00 4.75
409 410 6.325286 AGGGAGTAGTTTATTCTAGAAGCCAG 59.675 42.308 11.53 0.00 0.00 4.85
410 411 5.986741 GGAGTAGTTTATTCTAGAAGCCAGC 59.013 44.000 11.53 0.00 0.00 4.85
411 412 6.407074 GGAGTAGTTTATTCTAGAAGCCAGCA 60.407 42.308 11.53 0.00 0.00 4.41
412 413 6.947464 AGTAGTTTATTCTAGAAGCCAGCAA 58.053 36.000 11.53 0.00 0.00 3.91
413 414 7.394816 AGTAGTTTATTCTAGAAGCCAGCAAA 58.605 34.615 11.53 2.09 0.00 3.68
414 415 7.883311 AGTAGTTTATTCTAGAAGCCAGCAAAA 59.117 33.333 11.53 0.86 0.00 2.44
415 416 7.150783 AGTTTATTCTAGAAGCCAGCAAAAG 57.849 36.000 11.53 0.00 0.00 2.27
416 417 6.942576 AGTTTATTCTAGAAGCCAGCAAAAGA 59.057 34.615 11.53 0.00 0.00 2.52
417 418 7.448469 AGTTTATTCTAGAAGCCAGCAAAAGAA 59.552 33.333 11.53 0.00 0.00 2.52
418 419 5.635417 ATTCTAGAAGCCAGCAAAAGAAC 57.365 39.130 11.53 0.00 0.00 3.01
419 420 4.357918 TCTAGAAGCCAGCAAAAGAACT 57.642 40.909 0.00 0.00 0.00 3.01
420 421 4.067896 TCTAGAAGCCAGCAAAAGAACTG 58.932 43.478 0.00 0.00 0.00 3.16
424 425 2.737503 CCAGCAAAAGAACTGGCCT 58.262 52.632 3.32 0.00 46.50 5.19
425 426 1.043022 CCAGCAAAAGAACTGGCCTT 58.957 50.000 3.32 0.00 46.50 4.35
426 427 2.238521 CCAGCAAAAGAACTGGCCTTA 58.761 47.619 3.32 0.00 46.50 2.69
427 428 2.229784 CCAGCAAAAGAACTGGCCTTAG 59.770 50.000 3.32 0.00 46.50 2.18
428 429 1.889170 AGCAAAAGAACTGGCCTTAGC 59.111 47.619 3.32 0.00 38.76 3.09
435 436 0.320771 AACTGGCCTTAGCGTGTGAG 60.321 55.000 3.32 0.00 41.24 3.51
459 464 0.453793 ATCTCGTGCACTCTCCTTCG 59.546 55.000 16.19 0.00 0.00 3.79
480 485 6.020971 TCGCTTCACAAAGAGTCTTATGTA 57.979 37.500 5.65 1.49 34.30 2.29
505 510 3.643763 ACTTGTCGAGTCAAGCTAACTG 58.356 45.455 13.95 0.00 45.86 3.16
507 512 4.277672 ACTTGTCGAGTCAAGCTAACTGTA 59.722 41.667 13.95 0.00 45.86 2.74
532 537 1.338655 GGCGCCCTAACAAGTTTGAAA 59.661 47.619 18.11 0.00 0.00 2.69
551 556 7.749539 TTGAAACTTGTTCGAAAAAGATTCC 57.250 32.000 31.86 21.12 35.48 3.01
576 581 6.484364 AAAAAGGGCTCATTTCAAAAGAGA 57.516 33.333 6.56 0.00 0.00 3.10
578 583 6.484364 AAAGGGCTCATTTCAAAAGAGAAA 57.516 33.333 6.56 0.00 41.31 2.52
581 586 6.519382 AGGGCTCATTTCAAAAGAGAAAAAG 58.481 36.000 6.56 0.00 40.54 2.27
624 630 1.135721 TGATGAGTCACCAGCGATCAG 59.864 52.381 0.00 0.00 0.00 2.90
718 724 2.092968 ACAGCTCGCCCAATAGAATTCA 60.093 45.455 8.44 0.00 0.00 2.57
719 725 3.144506 CAGCTCGCCCAATAGAATTCAT 58.855 45.455 8.44 0.00 0.00 2.57
973 979 1.152247 TCTCACCCCACACTGCTCT 60.152 57.895 0.00 0.00 0.00 4.09
975 981 2.033141 CACCCCACACTGCTCTGG 59.967 66.667 0.00 0.00 0.00 3.86
1057 1063 4.104417 GCTCGGTCGCTCGTGTCT 62.104 66.667 0.00 0.00 0.00 3.41
1061 1067 2.126424 GGTCGCTCGTGTCTGACC 60.126 66.667 5.17 8.98 43.60 4.02
1062 1068 2.627737 GGTCGCTCGTGTCTGACCT 61.628 63.158 5.17 0.00 45.86 3.85
1063 1069 1.442857 GTCGCTCGTGTCTGACCTG 60.443 63.158 5.17 0.00 0.00 4.00
1064 1070 1.599797 TCGCTCGTGTCTGACCTGA 60.600 57.895 5.17 2.29 0.00 3.86
1065 1071 1.442857 CGCTCGTGTCTGACCTGAC 60.443 63.158 5.17 0.00 37.47 3.51
1066 1072 1.442857 GCTCGTGTCTGACCTGACG 60.443 63.158 11.54 11.54 39.64 4.35
1067 1073 1.853114 GCTCGTGTCTGACCTGACGA 61.853 60.000 17.28 17.28 39.64 4.20
1068 1074 2.244946 TCGTGTCTGACCTGACGAG 58.755 57.895 15.17 0.73 39.64 4.18
1069 1075 0.250166 TCGTGTCTGACCTGACGAGA 60.250 55.000 15.17 0.00 39.64 4.04
1070 1076 0.805614 CGTGTCTGACCTGACGAGAT 59.194 55.000 12.20 0.00 39.64 2.75
1071 1077 1.202087 CGTGTCTGACCTGACGAGATC 60.202 57.143 12.20 0.00 39.64 2.75
1582 1588 3.069318 GACGAGTTCCGGGAGCCT 61.069 66.667 7.32 2.61 43.93 4.58
1597 1603 2.498726 CCTCTCGAGCAGAAGCCC 59.501 66.667 7.81 0.00 43.56 5.19
1598 1604 2.103934 CTCTCGAGCAGAAGCCCG 59.896 66.667 7.81 0.00 43.97 6.13
1627 1633 1.784062 CTTCTCGTCGCTTGCCAAG 59.216 57.895 0.00 0.00 0.00 3.61
1877 1883 4.421479 CGCCGGAGCAAGAGTCGT 62.421 66.667 5.05 0.00 39.83 4.34
2041 2047 0.461516 GGCTGGAGTTACCGGTAAGC 60.462 60.000 27.20 24.16 46.24 3.09
2044 2050 1.549170 CTGGAGTTACCGGTAAGCACT 59.451 52.381 27.20 21.04 42.61 4.40
2047 2053 2.289257 GGAGTTACCGGTAAGCACTTGT 60.289 50.000 27.20 6.26 0.00 3.16
2051 2057 0.763035 ACCGGTAAGCACTTGTCCTT 59.237 50.000 4.49 0.00 0.00 3.36
2052 2058 1.156736 CCGGTAAGCACTTGTCCTTG 58.843 55.000 0.00 0.00 0.00 3.61
2058 2064 1.352083 AGCACTTGTCCTTGCTCCTA 58.648 50.000 0.00 0.00 46.31 2.94
2072 2085 5.699915 CCTTGCTCCTAACATGTGATCTATG 59.300 44.000 0.00 8.42 0.00 2.23
2092 2109 8.703604 TCTATGCACTTATTTCACTTCTGTAC 57.296 34.615 0.00 0.00 0.00 2.90
2094 2111 6.539649 TGCACTTATTTCACTTCTGTACAC 57.460 37.500 0.00 0.00 0.00 2.90
2322 2347 2.046314 ATGAAGGGCCGGTTCGTG 60.046 61.111 1.90 0.00 0.00 4.35
2450 2475 1.080093 GTTCGTCCGTGGATGCAGA 60.080 57.895 3.11 0.00 0.00 4.26
2451 2476 0.460284 GTTCGTCCGTGGATGCAGAT 60.460 55.000 3.11 0.00 0.00 2.90
2452 2477 0.460109 TTCGTCCGTGGATGCAGATG 60.460 55.000 3.11 0.00 0.00 2.90
2453 2478 2.528743 CGTCCGTGGATGCAGATGC 61.529 63.158 0.00 0.00 42.50 3.91
2531 2573 2.430465 TCACCTACGTAGCTCTCGTTT 58.570 47.619 17.41 5.08 41.72 3.60
2625 2688 7.431249 TGTGCAAAGTATAGTAGCTATGTACC 58.569 38.462 0.00 0.00 0.00 3.34
2626 2689 7.068962 TGTGCAAAGTATAGTAGCTATGTACCA 59.931 37.037 0.00 0.00 0.00 3.25
2631 2694 8.763984 AAGTATAGTAGCTATGTACCACAAGT 57.236 34.615 0.00 0.00 0.00 3.16
2632 2695 8.393671 AGTATAGTAGCTATGTACCACAAGTC 57.606 38.462 0.00 0.00 0.00 3.01
2634 2697 7.899648 ATAGTAGCTATGTACCACAAGTCTT 57.100 36.000 0.00 0.00 0.00 3.01
2645 2708 6.753279 TGTACCACAAGTCTTTGTATATACGC 59.247 38.462 8.33 0.00 45.53 4.42
2648 2711 6.040247 CCACAAGTCTTTGTATATACGCTCA 58.960 40.000 8.33 0.00 45.53 4.26
2694 2766 6.367686 ACTTTCGTCGTTTTTGTAAGGAAT 57.632 33.333 0.00 0.00 0.00 3.01
2695 2767 6.196571 ACTTTCGTCGTTTTTGTAAGGAATG 58.803 36.000 0.00 0.00 0.00 2.67
2710 2782 8.542497 TGTAAGGAATGTGTACTGATTACAAC 57.458 34.615 0.00 0.00 42.56 3.32
2762 2834 5.048921 ACGTAGGAGATACATTCATGGTACG 60.049 44.000 0.00 0.00 33.65 3.67
2780 2856 4.764308 GGTACGATAGAGTTAGGGTAAGGG 59.236 50.000 0.00 0.00 41.38 3.95
2803 2879 5.105310 GGCTTGTAACTGAGAATGGTAGAGA 60.105 44.000 0.00 0.00 0.00 3.10
2805 2881 6.531503 TTGTAACTGAGAATGGTAGAGAGG 57.468 41.667 0.00 0.00 0.00 3.69
2806 2882 5.827756 TGTAACTGAGAATGGTAGAGAGGA 58.172 41.667 0.00 0.00 0.00 3.71
2822 2899 4.649218 AGAGAGGAAGATCAAGCCTAGTTC 59.351 45.833 0.00 0.00 30.70 3.01
2845 2922 3.129113 GTGTATGTCAATGCATGCCTTCA 59.871 43.478 16.68 7.37 30.62 3.02
2895 2975 1.207089 CTCGAACCAGGGCACAATCTA 59.793 52.381 0.00 0.00 0.00 1.98
2923 3003 9.571810 GAATCACAATCACAATGTGCTTATTTA 57.428 29.630 8.78 0.00 46.05 1.40
2924 3004 8.915871 ATCACAATCACAATGTGCTTATTTAC 57.084 30.769 8.78 0.00 46.05 2.01
2932 3012 8.717821 TCACAATGTGCTTATTTACAAGTCTAC 58.282 33.333 8.78 0.00 32.98 2.59
2934 3014 9.231297 ACAATGTGCTTATTTACAAGTCTACAT 57.769 29.630 0.00 0.00 32.87 2.29
2973 3053 3.222173 ACTGGTGTAAAGGTTGCATGA 57.778 42.857 0.00 0.00 0.00 3.07
3007 3089 3.382227 TCGATCGAAGGCTTGTACCATTA 59.618 43.478 16.99 0.00 0.00 1.90
3159 3241 5.367945 TTCTAAGGGCTCATTCGGTTTAT 57.632 39.130 0.00 0.00 0.00 1.40
3209 3294 3.392616 AGTAATGATTAGGGTGGCCTCTG 59.607 47.826 3.32 0.00 0.00 3.35
3354 3440 2.658325 GCTGTGACAATGCATCGAAAAC 59.342 45.455 0.00 0.00 0.00 2.43
3356 3442 3.887741 TGTGACAATGCATCGAAAACTG 58.112 40.909 0.00 0.00 0.00 3.16
3358 3444 2.553602 TGACAATGCATCGAAAACTGCT 59.446 40.909 9.89 0.00 39.16 4.24
3459 3545 8.978539 GTGTTACAATTCTTTCAAAATTCCTCC 58.021 33.333 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.823790 AAATCCTACAAACCACGTGAAC 57.176 40.909 19.30 0.00 0.00 3.18
7 8 6.909550 ATAGTGCAAAAATCCTACAAACCA 57.090 33.333 0.00 0.00 0.00 3.67
15 16 8.045720 TCCTATAGGAATAGTGCAAAAATCCT 57.954 34.615 19.59 14.55 42.18 3.24
47 48 2.029380 ACAAAGGTAAAAATCCCGCAGC 60.029 45.455 0.00 0.00 0.00 5.25
65 66 2.590073 CATAAAATGAACGCCGCACAA 58.410 42.857 0.00 0.00 0.00 3.33
74 75 4.405358 TGCCTCCATTCCCATAAAATGAAC 59.595 41.667 0.00 0.00 36.43 3.18
85 86 5.248380 AGAAATATAGTGCCTCCATTCCC 57.752 43.478 0.00 0.00 0.00 3.97
143 144 9.692749 CATATTTGAAATTGAGCTATGATGCTT 57.307 29.630 0.00 0.00 44.17 3.91
155 156 9.985730 AGAAAGCAACTTCATATTTGAAATTGA 57.014 25.926 19.70 0.00 46.75 2.57
202 203 1.623811 GGACCTAAGTCACAGAAGCCA 59.376 52.381 0.00 0.00 45.48 4.75
203 204 1.623811 TGGACCTAAGTCACAGAAGCC 59.376 52.381 0.00 0.00 45.48 4.35
204 205 2.300437 ACTGGACCTAAGTCACAGAAGC 59.700 50.000 13.64 0.00 45.48 3.86
209 210 5.123227 CAAAAGAACTGGACCTAAGTCACA 58.877 41.667 0.00 0.00 45.48 3.58
210 211 4.515567 CCAAAAGAACTGGACCTAAGTCAC 59.484 45.833 0.00 0.00 45.48 3.67
211 212 4.165372 ACCAAAAGAACTGGACCTAAGTCA 59.835 41.667 0.00 0.00 45.48 3.41
212 213 4.715713 ACCAAAAGAACTGGACCTAAGTC 58.284 43.478 0.00 0.00 42.73 3.01
213 214 4.790718 ACCAAAAGAACTGGACCTAAGT 57.209 40.909 0.00 0.00 37.40 2.24
214 215 4.695928 GCTACCAAAAGAACTGGACCTAAG 59.304 45.833 0.00 0.00 37.40 2.18
215 216 4.506095 GGCTACCAAAAGAACTGGACCTAA 60.506 45.833 0.00 0.00 37.40 2.69
216 217 3.008704 GGCTACCAAAAGAACTGGACCTA 59.991 47.826 0.00 0.00 37.40 3.08
217 218 2.224793 GGCTACCAAAAGAACTGGACCT 60.225 50.000 0.00 0.00 37.40 3.85
218 219 2.160205 GGCTACCAAAAGAACTGGACC 58.840 52.381 0.00 0.00 37.40 4.46
219 220 3.141767 AGGCTACCAAAAGAACTGGAC 57.858 47.619 0.00 0.00 37.40 4.02
220 221 3.876309 AAGGCTACCAAAAGAACTGGA 57.124 42.857 0.00 0.00 37.40 3.86
221 222 4.937201 AAAAGGCTACCAAAAGAACTGG 57.063 40.909 0.00 0.00 40.05 4.00
222 223 6.040504 ACCTAAAAAGGCTACCAAAAGAACTG 59.959 38.462 0.00 0.00 0.00 3.16
223 224 6.134055 ACCTAAAAAGGCTACCAAAAGAACT 58.866 36.000 0.00 0.00 0.00 3.01
224 225 6.401047 ACCTAAAAAGGCTACCAAAAGAAC 57.599 37.500 0.00 0.00 0.00 3.01
225 226 7.426606 AAACCTAAAAAGGCTACCAAAAGAA 57.573 32.000 0.00 0.00 0.00 2.52
226 227 8.715190 ATAAACCTAAAAAGGCTACCAAAAGA 57.285 30.769 0.00 0.00 0.00 2.52
228 229 9.810870 TCTATAAACCTAAAAAGGCTACCAAAA 57.189 29.630 0.00 0.00 0.00 2.44
229 230 9.810870 TTCTATAAACCTAAAAAGGCTACCAAA 57.189 29.630 0.00 0.00 0.00 3.28
230 231 9.984590 ATTCTATAAACCTAAAAAGGCTACCAA 57.015 29.630 0.00 0.00 0.00 3.67
259 260 0.909623 TAAGCTGGGTAGGAGGCAAC 59.090 55.000 0.00 0.00 0.00 4.17
260 261 1.893315 ATAAGCTGGGTAGGAGGCAA 58.107 50.000 0.00 0.00 0.00 4.52
261 262 1.768870 GAATAAGCTGGGTAGGAGGCA 59.231 52.381 0.00 0.00 0.00 4.75
262 263 2.050918 AGAATAAGCTGGGTAGGAGGC 58.949 52.381 0.00 0.00 0.00 4.70
263 264 6.351456 GCTTATAGAATAAGCTGGGTAGGAGG 60.351 46.154 19.55 0.00 44.64 4.30
264 265 6.351456 GGCTTATAGAATAAGCTGGGTAGGAG 60.351 46.154 23.65 0.00 46.58 3.69
265 266 5.484290 GGCTTATAGAATAAGCTGGGTAGGA 59.516 44.000 23.65 0.00 46.58 2.94
266 267 5.485708 AGGCTTATAGAATAAGCTGGGTAGG 59.514 44.000 23.65 0.00 46.58 3.18
267 268 6.613153 AGGCTTATAGAATAAGCTGGGTAG 57.387 41.667 23.65 0.00 46.58 3.18
268 269 7.511371 TGTTAGGCTTATAGAATAAGCTGGGTA 59.489 37.037 23.65 12.27 46.58 3.69
269 270 6.329197 TGTTAGGCTTATAGAATAAGCTGGGT 59.671 38.462 23.65 12.97 46.58 4.51
270 271 6.769512 TGTTAGGCTTATAGAATAAGCTGGG 58.230 40.000 23.65 0.00 46.58 4.45
271 272 8.677148 TTTGTTAGGCTTATAGAATAAGCTGG 57.323 34.615 23.65 0.00 46.58 4.85
355 356 9.010029 CCACTTTATTCTTGAAGCCTAACTAAA 57.990 33.333 0.00 0.00 0.00 1.85
356 357 7.610305 CCCACTTTATTCTTGAAGCCTAACTAA 59.390 37.037 0.00 0.00 0.00 2.24
357 358 7.110155 CCCACTTTATTCTTGAAGCCTAACTA 58.890 38.462 0.00 0.00 0.00 2.24
358 359 5.946377 CCCACTTTATTCTTGAAGCCTAACT 59.054 40.000 0.00 0.00 0.00 2.24
359 360 5.710567 ACCCACTTTATTCTTGAAGCCTAAC 59.289 40.000 0.00 0.00 0.00 2.34
360 361 5.887754 ACCCACTTTATTCTTGAAGCCTAA 58.112 37.500 0.00 0.00 0.00 2.69
361 362 5.514500 ACCCACTTTATTCTTGAAGCCTA 57.486 39.130 0.00 0.00 0.00 3.93
362 363 4.388577 ACCCACTTTATTCTTGAAGCCT 57.611 40.909 0.00 0.00 0.00 4.58
363 364 4.640647 CCTACCCACTTTATTCTTGAAGCC 59.359 45.833 0.00 0.00 0.00 4.35
364 365 4.640647 CCCTACCCACTTTATTCTTGAAGC 59.359 45.833 0.00 0.00 0.00 3.86
365 366 6.062258 TCCCTACCCACTTTATTCTTGAAG 57.938 41.667 0.00 0.00 0.00 3.02
366 367 5.550403 ACTCCCTACCCACTTTATTCTTGAA 59.450 40.000 0.00 0.00 0.00 2.69
367 368 5.098663 ACTCCCTACCCACTTTATTCTTGA 58.901 41.667 0.00 0.00 0.00 3.02
368 369 5.437191 ACTCCCTACCCACTTTATTCTTG 57.563 43.478 0.00 0.00 0.00 3.02
369 370 6.269974 ACTACTCCCTACCCACTTTATTCTT 58.730 40.000 0.00 0.00 0.00 2.52
370 371 5.851418 ACTACTCCCTACCCACTTTATTCT 58.149 41.667 0.00 0.00 0.00 2.40
371 372 6.556974 AACTACTCCCTACCCACTTTATTC 57.443 41.667 0.00 0.00 0.00 1.75
372 373 6.964876 AAACTACTCCCTACCCACTTTATT 57.035 37.500 0.00 0.00 0.00 1.40
373 374 8.634188 AATAAACTACTCCCTACCCACTTTAT 57.366 34.615 0.00 0.00 0.00 1.40
374 375 7.902941 AGAATAAACTACTCCCTACCCACTTTA 59.097 37.037 0.00 0.00 0.00 1.85
375 376 6.734281 AGAATAAACTACTCCCTACCCACTTT 59.266 38.462 0.00 0.00 0.00 2.66
376 377 6.269974 AGAATAAACTACTCCCTACCCACTT 58.730 40.000 0.00 0.00 0.00 3.16
377 378 5.851418 AGAATAAACTACTCCCTACCCACT 58.149 41.667 0.00 0.00 0.00 4.00
378 379 7.065504 TCTAGAATAAACTACTCCCTACCCAC 58.934 42.308 0.00 0.00 0.00 4.61
379 380 7.229951 TCTAGAATAAACTACTCCCTACCCA 57.770 40.000 0.00 0.00 0.00 4.51
380 381 7.255906 GCTTCTAGAATAAACTACTCCCTACCC 60.256 44.444 5.44 0.00 0.00 3.69
381 382 7.255906 GGCTTCTAGAATAAACTACTCCCTACC 60.256 44.444 5.44 0.00 0.00 3.18
382 383 7.287235 TGGCTTCTAGAATAAACTACTCCCTAC 59.713 40.741 5.44 0.00 0.00 3.18
383 384 7.359849 TGGCTTCTAGAATAAACTACTCCCTA 58.640 38.462 5.44 0.00 0.00 3.53
384 385 6.203072 TGGCTTCTAGAATAAACTACTCCCT 58.797 40.000 5.44 0.00 0.00 4.20
385 386 6.481434 TGGCTTCTAGAATAAACTACTCCC 57.519 41.667 5.44 0.00 0.00 4.30
386 387 5.986741 GCTGGCTTCTAGAATAAACTACTCC 59.013 44.000 5.44 0.00 0.00 3.85
387 388 6.574350 TGCTGGCTTCTAGAATAAACTACTC 58.426 40.000 5.44 0.00 0.00 2.59
388 389 6.546428 TGCTGGCTTCTAGAATAAACTACT 57.454 37.500 5.44 0.00 0.00 2.57
389 390 7.611213 TTTGCTGGCTTCTAGAATAAACTAC 57.389 36.000 5.44 0.00 0.00 2.73
390 391 8.100791 TCTTTTGCTGGCTTCTAGAATAAACTA 58.899 33.333 5.44 0.00 0.00 2.24
391 392 6.942576 TCTTTTGCTGGCTTCTAGAATAAACT 59.057 34.615 5.44 0.00 0.00 2.66
392 393 7.145932 TCTTTTGCTGGCTTCTAGAATAAAC 57.854 36.000 5.44 0.00 0.00 2.01
393 394 7.448469 AGTTCTTTTGCTGGCTTCTAGAATAAA 59.552 33.333 5.44 0.00 0.00 1.40
394 395 6.942576 AGTTCTTTTGCTGGCTTCTAGAATAA 59.057 34.615 5.44 0.00 0.00 1.40
395 396 6.372659 CAGTTCTTTTGCTGGCTTCTAGAATA 59.627 38.462 5.44 0.00 0.00 1.75
396 397 5.182760 CAGTTCTTTTGCTGGCTTCTAGAAT 59.817 40.000 5.44 0.00 0.00 2.40
397 398 4.516698 CAGTTCTTTTGCTGGCTTCTAGAA 59.483 41.667 4.81 4.81 0.00 2.10
398 399 4.067896 CAGTTCTTTTGCTGGCTTCTAGA 58.932 43.478 0.00 0.00 0.00 2.43
399 400 3.190118 CCAGTTCTTTTGCTGGCTTCTAG 59.810 47.826 0.00 0.00 44.65 2.43
400 401 3.149196 CCAGTTCTTTTGCTGGCTTCTA 58.851 45.455 0.00 0.00 44.65 2.10
401 402 1.959282 CCAGTTCTTTTGCTGGCTTCT 59.041 47.619 0.00 0.00 44.65 2.85
402 403 2.428888 CCAGTTCTTTTGCTGGCTTC 57.571 50.000 0.00 0.00 44.65 3.86
407 408 2.352127 GCTAAGGCCAGTTCTTTTGCTG 60.352 50.000 5.01 0.00 0.00 4.41
408 409 1.889170 GCTAAGGCCAGTTCTTTTGCT 59.111 47.619 5.01 0.00 0.00 3.91
409 410 1.401539 CGCTAAGGCCAGTTCTTTTGC 60.402 52.381 5.01 0.54 34.44 3.68
410 411 1.880027 ACGCTAAGGCCAGTTCTTTTG 59.120 47.619 5.01 0.00 34.44 2.44
411 412 1.880027 CACGCTAAGGCCAGTTCTTTT 59.120 47.619 5.01 0.00 34.44 2.27
412 413 1.202770 ACACGCTAAGGCCAGTTCTTT 60.203 47.619 5.01 0.00 34.44 2.52
413 414 0.396811 ACACGCTAAGGCCAGTTCTT 59.603 50.000 5.01 0.00 34.44 2.52
414 415 0.320771 CACACGCTAAGGCCAGTTCT 60.321 55.000 5.01 0.00 34.44 3.01
415 416 0.320421 TCACACGCTAAGGCCAGTTC 60.320 55.000 5.01 0.00 34.44 3.01
416 417 0.320771 CTCACACGCTAAGGCCAGTT 60.321 55.000 5.01 0.00 34.44 3.16
417 418 1.293498 CTCACACGCTAAGGCCAGT 59.707 57.895 5.01 0.00 34.44 4.00
418 419 1.016130 CACTCACACGCTAAGGCCAG 61.016 60.000 5.01 0.00 34.44 4.85
419 420 1.005037 CACTCACACGCTAAGGCCA 60.005 57.895 5.01 0.00 34.44 5.36
420 421 0.245539 TACACTCACACGCTAAGGCC 59.754 55.000 0.00 0.00 34.44 5.19
421 422 2.074547 TTACACTCACACGCTAAGGC 57.925 50.000 0.00 0.00 0.00 4.35
422 423 4.106197 GAGATTACACTCACACGCTAAGG 58.894 47.826 0.00 0.00 36.95 2.69
423 424 3.786576 CGAGATTACACTCACACGCTAAG 59.213 47.826 0.00 0.00 36.80 2.18
424 425 3.189910 ACGAGATTACACTCACACGCTAA 59.810 43.478 0.00 0.00 36.80 3.09
425 426 2.745821 ACGAGATTACACTCACACGCTA 59.254 45.455 0.00 0.00 36.80 4.26
426 427 1.540267 ACGAGATTACACTCACACGCT 59.460 47.619 0.00 0.00 36.80 5.07
427 428 1.649171 CACGAGATTACACTCACACGC 59.351 52.381 0.00 0.00 36.80 5.34
428 429 1.649171 GCACGAGATTACACTCACACG 59.351 52.381 0.00 0.00 36.80 4.49
435 436 2.164624 AGGAGAGTGCACGAGATTACAC 59.835 50.000 12.01 0.00 0.00 2.90
459 464 7.834068 TGATACATAAGACTCTTTGTGAAGC 57.166 36.000 12.92 0.00 32.75 3.86
480 485 3.393089 AGCTTGACTCGACAAGTTGAT 57.607 42.857 10.54 0.00 45.98 2.57
505 510 0.321830 TTGTTAGGGCGCCAAGGTAC 60.322 55.000 30.85 17.88 0.00 3.34
507 512 1.303317 CTTGTTAGGGCGCCAAGGT 60.303 57.895 30.85 12.07 33.57 3.50
573 578 6.350974 CGCGTAGAATCATGATCTTTTTCTC 58.649 40.000 9.06 0.76 0.00 2.87
575 580 5.435557 CCGCGTAGAATCATGATCTTTTTC 58.564 41.667 9.06 3.19 0.00 2.29
576 581 4.273480 CCCGCGTAGAATCATGATCTTTTT 59.727 41.667 9.06 0.00 0.00 1.94
578 583 3.181465 ACCCGCGTAGAATCATGATCTTT 60.181 43.478 9.06 0.00 0.00 2.52
581 586 2.440539 ACCCGCGTAGAATCATGATC 57.559 50.000 9.06 2.96 0.00 2.92
1057 1063 1.025041 CCATCGATCTCGTCAGGTCA 58.975 55.000 0.00 0.00 40.80 4.02
1061 1067 0.385348 CTCGCCATCGATCTCGTCAG 60.385 60.000 13.42 3.86 44.56 3.51
1062 1068 1.649267 CTCGCCATCGATCTCGTCA 59.351 57.895 13.42 0.00 44.56 4.35
1063 1069 1.727723 GCTCGCCATCGATCTCGTC 60.728 63.158 13.42 5.76 44.56 4.20
1064 1070 2.333225 GCTCGCCATCGATCTCGT 59.667 61.111 13.42 0.00 44.56 4.18
1065 1071 2.798675 CGCTCGCCATCGATCTCG 60.799 66.667 0.00 1.85 44.56 4.04
1066 1072 3.102668 GCGCTCGCCATCGATCTC 61.103 66.667 0.00 0.00 44.56 2.75
1267 1273 4.741239 TGGAGGGAGGAGGTGGCC 62.741 72.222 0.00 0.00 0.00 5.36
1598 1604 3.184683 CGAGAAGCAGCAGACGGC 61.185 66.667 0.00 0.00 45.30 5.68
1875 1881 3.955650 TCCTTTTCCTGTCCTCTAACG 57.044 47.619 0.00 0.00 0.00 3.18
1876 1882 4.004314 GCTTCCTTTTCCTGTCCTCTAAC 58.996 47.826 0.00 0.00 0.00 2.34
1877 1883 3.306780 CGCTTCCTTTTCCTGTCCTCTAA 60.307 47.826 0.00 0.00 0.00 2.10
1942 1948 2.446848 ATGGGCCCAGGAGTCGATG 61.447 63.158 31.97 0.00 0.00 3.84
2029 2035 2.071540 GGACAAGTGCTTACCGGTAAC 58.928 52.381 23.17 18.72 0.00 2.50
2041 2047 3.126001 TGTTAGGAGCAAGGACAAGTG 57.874 47.619 0.00 0.00 0.00 3.16
2044 2050 3.072330 TCACATGTTAGGAGCAAGGACAA 59.928 43.478 0.00 0.00 0.00 3.18
2047 2053 3.776969 AGATCACATGTTAGGAGCAAGGA 59.223 43.478 0.00 0.00 0.00 3.36
2051 2057 4.101430 TGCATAGATCACATGTTAGGAGCA 59.899 41.667 0.00 0.00 0.00 4.26
2052 2058 4.450419 GTGCATAGATCACATGTTAGGAGC 59.550 45.833 0.00 0.00 34.73 4.70
2058 2064 8.400947 GTGAAATAAGTGCATAGATCACATGTT 58.599 33.333 0.00 0.00 36.75 2.71
2072 2085 6.539649 TGTGTACAGAAGTGAAATAAGTGC 57.460 37.500 0.00 0.00 0.00 4.40
2092 2109 6.955963 GCTTGATTAGACGACAAGTTTATGTG 59.044 38.462 0.00 0.00 41.73 3.21
2094 2111 7.295952 AGCTTGATTAGACGACAAGTTTATG 57.704 36.000 0.00 0.00 41.73 1.90
2430 2455 3.186047 GCATCCACGGACGAACGG 61.186 66.667 0.00 0.00 38.39 4.44
2625 2688 7.520119 TTGAGCGTATATACAAAGACTTGTG 57.480 36.000 13.22 0.00 45.53 3.33
2631 2694 9.256477 CTAAACCATTGAGCGTATATACAAAGA 57.744 33.333 13.22 0.00 0.00 2.52
2632 2695 8.495949 CCTAAACCATTGAGCGTATATACAAAG 58.504 37.037 13.22 0.00 0.00 2.77
2634 2697 6.932400 CCCTAAACCATTGAGCGTATATACAA 59.068 38.462 13.22 0.27 0.00 2.41
2645 2708 5.163457 ACAACAACAACCCTAAACCATTGAG 60.163 40.000 0.00 0.00 0.00 3.02
2648 2711 5.685520 AACAACAACAACCCTAAACCATT 57.314 34.783 0.00 0.00 0.00 3.16
2694 2766 4.695396 ACAACCGTTGTAATCAGTACACA 58.305 39.130 15.36 0.00 42.56 3.72
2695 2767 5.922544 AGTACAACCGTTGTAATCAGTACAC 59.077 40.000 22.66 11.63 46.72 2.90
2710 2782 5.651530 AGATCAACATCTACAGTACAACCG 58.348 41.667 0.00 0.00 37.63 4.44
2762 2834 4.654724 ACAAGCCCTTACCCTAACTCTATC 59.345 45.833 0.00 0.00 0.00 2.08
2780 2856 5.967088 TCTCTACCATTCTCAGTTACAAGC 58.033 41.667 0.00 0.00 0.00 4.01
2803 2879 3.100671 ACGAACTAGGCTTGATCTTCCT 58.899 45.455 2.20 0.29 0.00 3.36
2805 2881 3.851098 ACACGAACTAGGCTTGATCTTC 58.149 45.455 2.20 0.00 0.00 2.87
2806 2882 3.963428 ACACGAACTAGGCTTGATCTT 57.037 42.857 2.20 0.00 0.00 2.40
2822 2899 1.672363 AGGCATGCATTGACATACACG 59.328 47.619 21.36 0.00 34.87 4.49
2845 2922 2.042162 ACACATCAGGAATGGAAGGCTT 59.958 45.455 0.00 0.00 39.90 4.35
2895 2975 5.654603 AGCACATTGTGATTGTGATTCAT 57.345 34.783 20.77 0.00 45.83 2.57
2938 3018 9.661563 CTTTACACCAGTAGAAAACACCATATA 57.338 33.333 0.00 0.00 0.00 0.86
2939 3019 7.610305 CCTTTACACCAGTAGAAAACACCATAT 59.390 37.037 0.00 0.00 0.00 1.78
2940 3020 6.938030 CCTTTACACCAGTAGAAAACACCATA 59.062 38.462 0.00 0.00 0.00 2.74
2941 3021 5.768164 CCTTTACACCAGTAGAAAACACCAT 59.232 40.000 0.00 0.00 0.00 3.55
2946 3026 5.066764 TGCAACCTTTACACCAGTAGAAAAC 59.933 40.000 0.00 0.00 0.00 2.43
3007 3089 6.231211 AGTGTCAAGACGTTTAGATCCAAAT 58.769 36.000 0.00 0.00 0.00 2.32
3159 3241 6.553476 TCCTGTTTCTATGATCGGAAATCCTA 59.447 38.462 10.13 0.00 34.60 2.94
3209 3294 6.584185 TTATTGAACCAAAGCCTAAGGAAC 57.416 37.500 0.00 0.00 0.00 3.62
3358 3444 3.260884 AGACGATCCAAAGAGCTGGTTTA 59.739 43.478 0.00 0.00 37.74 2.01
3377 3463 7.647715 TCAAATTTCCGTGAATTTCAAAGAGAC 59.352 33.333 0.00 0.00 37.17 3.36
3459 3545 4.730949 TCCTACTGGATAACTCAAACCG 57.269 45.455 0.00 0.00 37.46 4.44


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

AutoCloner maintained by Alex Coulton.