Multiple sequence alignment - TraesCS2D01G392200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G392200 chr2D 100.000 2695 0 0 1 2695 499731419 499734113 0.000000e+00 4977.0
1 TraesCS2D01G392200 chr2D 96.309 867 18 7 1839 2695 4177049 4177911 0.000000e+00 1411.0
2 TraesCS2D01G392200 chr2D 97.732 485 5 4 2211 2695 640263757 640264235 0.000000e+00 830.0
3 TraesCS2D01G392200 chr2D 96.825 378 10 2 2300 2677 295803105 295802730 4.900000e-177 630.0
4 TraesCS2D01G392200 chr2D 96.154 390 6 1 1840 2220 640259395 640259784 1.760000e-176 628.0
5 TraesCS2D01G392200 chr2D 81.818 77 10 3 1763 1835 640021231 640021307 8.060000e-06 62.1
6 TraesCS2D01G392200 chr2B 89.617 1435 68 32 453 1839 587247066 587248467 0.000000e+00 1749.0
7 TraesCS2D01G392200 chr3D 97.015 871 13 8 1835 2695 426982966 426982099 0.000000e+00 1452.0
8 TraesCS2D01G392200 chr3D 93.995 383 18 4 2301 2680 15961162 15961542 2.330000e-160 575.0
9 TraesCS2D01G392200 chr3D 94.231 52 1 1 1763 1812 511735235 511735184 8.000000e-11 78.7
10 TraesCS2D01G392200 chr3D 86.364 66 4 4 1763 1823 430303268 430303333 1.730000e-07 67.6
11 TraesCS2D01G392200 chr7D 96.544 868 17 5 1838 2695 529451635 529450771 0.000000e+00 1424.0
12 TraesCS2D01G392200 chr7D 90.674 386 25 8 2301 2681 192985756 192985377 1.110000e-138 503.0
13 TraesCS2D01G392200 chr7D 95.745 47 2 0 1767 1813 413730973 413731019 2.880000e-10 76.8
14 TraesCS2D01G392200 chr7D 83.544 79 9 3 1763 1837 83871351 83871429 1.340000e-08 71.3
15 TraesCS2D01G392200 chr2A 92.657 926 43 8 800 1718 644253581 644254488 0.000000e+00 1310.0
16 TraesCS2D01G392200 chr2A 85.836 353 25 16 457 794 644252834 644253176 4.270000e-93 351.0
17 TraesCS2D01G392200 chr4B 95.096 469 14 1 1840 2299 483915085 483915553 0.000000e+00 730.0
18 TraesCS2D01G392200 chr4B 76.842 190 31 8 1837 2021 546115298 546115479 7.940000e-16 95.3
19 TraesCS2D01G392200 chr4A 93.603 469 21 7 1840 2299 564641717 564642185 0.000000e+00 691.0
20 TraesCS2D01G392200 chr7B 93.807 436 17 2 1838 2263 103102147 103101712 0.000000e+00 647.0
21 TraesCS2D01G392200 chr7B 90.256 390 22 12 2301 2678 22683790 22684175 1.860000e-136 496.0
22 TraesCS2D01G392200 chr1B 91.885 382 22 8 2301 2676 474603501 474603123 2.380000e-145 525.0
23 TraesCS2D01G392200 chr1B 93.182 44 3 0 1839 1882 623285263 623285306 6.230000e-07 65.8
24 TraesCS2D01G392200 chr5A 86.207 87 12 0 2157 2243 328949091 328949005 7.940000e-16 95.3
25 TraesCS2D01G392200 chr5A 81.818 77 10 3 1763 1835 1773442 1773518 8.060000e-06 62.1
26 TraesCS2D01G392200 chr1D 85.714 77 8 2 1763 1837 193500111 193500036 8.000000e-11 78.7
27 TraesCS2D01G392200 chrUn 84.211 76 9 2 1763 1836 60959676 60959750 1.340000e-08 71.3
28 TraesCS2D01G392200 chr5B 82.667 75 10 2 1763 1835 699778368 699778441 2.240000e-06 63.9


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 TraesCS2D01G392200 chr2D 499731419 499734113 2694 False 4977.0 4977 100.0000 1 2695 1 chr2D.!!$F2 2694
1 TraesCS2D01G392200 chr2D 4177049 4177911 862 False 1411.0 1411 96.3090 1839 2695 1 chr2D.!!$F1 856
2 TraesCS2D01G392200 chr2D 640259395 640264235 4840 False 729.0 830 96.9430 1840 2695 2 chr2D.!!$F4 855
3 TraesCS2D01G392200 chr2B 587247066 587248467 1401 False 1749.0 1749 89.6170 453 1839 1 chr2B.!!$F1 1386
4 TraesCS2D01G392200 chr3D 426982099 426982966 867 True 1452.0 1452 97.0150 1835 2695 1 chr3D.!!$R1 860
5 TraesCS2D01G392200 chr7D 529450771 529451635 864 True 1424.0 1424 96.5440 1838 2695 1 chr7D.!!$R2 857
6 TraesCS2D01G392200 chr2A 644252834 644254488 1654 False 830.5 1310 89.2465 457 1718 2 chr2A.!!$F1 1261

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
588 603 0.319555 TCTAAGCGTGACACCTGCAC 60.320 55.0 7.99 0.00 0.0 4.57 F
873 1287 0.593128 ATGAAAGCGCGCTCAAAAGT 59.407 45.0 36.57 15.57 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1516 1930 1.001406 AGCTTCTTCCACGACTTCCTG 59.999 52.381 0.00 0.0 0.00 3.86 R
1739 2177 1.028330 ATGTCGACTGCATGGCAAGG 61.028 55.000 17.92 0.0 38.41 3.61 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
85 86 2.595124 CCGCTTTGGTTTTTCCTTGT 57.405 45.000 0.00 0.00 37.07 3.16
86 87 3.719173 CCGCTTTGGTTTTTCCTTGTA 57.281 42.857 0.00 0.00 37.07 2.41
87 88 3.377439 CCGCTTTGGTTTTTCCTTGTAC 58.623 45.455 0.00 0.00 37.07 2.90
88 89 3.067601 CCGCTTTGGTTTTTCCTTGTACT 59.932 43.478 0.00 0.00 37.07 2.73
89 90 4.440940 CCGCTTTGGTTTTTCCTTGTACTT 60.441 41.667 0.00 0.00 37.07 2.24
90 91 5.106442 CGCTTTGGTTTTTCCTTGTACTTT 58.894 37.500 0.00 0.00 37.07 2.66
91 92 5.579119 CGCTTTGGTTTTTCCTTGTACTTTT 59.421 36.000 0.00 0.00 37.07 2.27
92 93 6.091577 CGCTTTGGTTTTTCCTTGTACTTTTT 59.908 34.615 0.00 0.00 37.07 1.94
93 94 7.461107 GCTTTGGTTTTTCCTTGTACTTTTTC 58.539 34.615 0.00 0.00 37.07 2.29
94 95 7.413657 GCTTTGGTTTTTCCTTGTACTTTTTCC 60.414 37.037 0.00 0.00 37.07 3.13
95 96 6.860790 TGGTTTTTCCTTGTACTTTTTCCT 57.139 33.333 0.00 0.00 37.07 3.36
96 97 7.247456 TGGTTTTTCCTTGTACTTTTTCCTT 57.753 32.000 0.00 0.00 37.07 3.36
97 98 7.681679 TGGTTTTTCCTTGTACTTTTTCCTTT 58.318 30.769 0.00 0.00 37.07 3.11
98 99 8.813951 TGGTTTTTCCTTGTACTTTTTCCTTTA 58.186 29.630 0.00 0.00 37.07 1.85
99 100 9.826574 GGTTTTTCCTTGTACTTTTTCCTTTAT 57.173 29.630 0.00 0.00 0.00 1.40
102 103 9.738832 TTTTCCTTGTACTTTTTCCTTTATTCG 57.261 29.630 0.00 0.00 0.00 3.34
103 104 7.443259 TCCTTGTACTTTTTCCTTTATTCGG 57.557 36.000 0.00 0.00 0.00 4.30
104 105 7.225725 TCCTTGTACTTTTTCCTTTATTCGGA 58.774 34.615 0.00 0.00 0.00 4.55
105 106 7.720515 TCCTTGTACTTTTTCCTTTATTCGGAA 59.279 33.333 0.00 0.00 38.71 4.30
106 107 8.520351 CCTTGTACTTTTTCCTTTATTCGGAAT 58.480 33.333 8.49 8.49 40.05 3.01
107 108 9.908152 CTTGTACTTTTTCCTTTATTCGGAATT 57.092 29.630 8.76 0.00 40.05 2.17
125 126 9.681062 TTCGGAATTTATCTATTTCAGTTTCCT 57.319 29.630 0.00 0.00 0.00 3.36
195 196 7.722949 ATGGCTTTATCTTCCAATTTTCTCA 57.277 32.000 0.00 0.00 33.04 3.27
196 197 7.537596 TGGCTTTATCTTCCAATTTTCTCAA 57.462 32.000 0.00 0.00 0.00 3.02
197 198 7.961351 TGGCTTTATCTTCCAATTTTCTCAAA 58.039 30.769 0.00 0.00 0.00 2.69
198 199 8.428063 TGGCTTTATCTTCCAATTTTCTCAAAA 58.572 29.630 0.00 0.00 34.41 2.44
199 200 8.929746 GGCTTTATCTTCCAATTTTCTCAAAAG 58.070 33.333 0.00 0.00 33.22 2.27
200 201 9.696917 GCTTTATCTTCCAATTTTCTCAAAAGA 57.303 29.630 0.00 0.00 33.22 2.52
232 233 8.421249 TCAAAAATTGAAAGATCCTGTATGGT 57.579 30.769 0.00 0.00 36.59 3.55
233 234 8.869109 TCAAAAATTGAAAGATCCTGTATGGTT 58.131 29.630 0.00 0.00 36.59 3.67
234 235 9.143631 CAAAAATTGAAAGATCCTGTATGGTTC 57.856 33.333 0.00 0.00 37.07 3.62
235 236 8.655935 AAAATTGAAAGATCCTGTATGGTTCT 57.344 30.769 0.00 0.00 44.47 3.01
241 242 4.848357 AGATCCTGTATGGTTCTTTGTGG 58.152 43.478 0.00 0.00 40.92 4.17
242 243 3.433306 TCCTGTATGGTTCTTTGTGGG 57.567 47.619 0.00 0.00 37.07 4.61
243 244 2.714250 TCCTGTATGGTTCTTTGTGGGT 59.286 45.455 0.00 0.00 37.07 4.51
244 245 3.139397 TCCTGTATGGTTCTTTGTGGGTT 59.861 43.478 0.00 0.00 37.07 4.11
245 246 3.255642 CCTGTATGGTTCTTTGTGGGTTG 59.744 47.826 0.00 0.00 0.00 3.77
246 247 3.226777 TGTATGGTTCTTTGTGGGTTGG 58.773 45.455 0.00 0.00 0.00 3.77
247 248 1.715785 ATGGTTCTTTGTGGGTTGGG 58.284 50.000 0.00 0.00 0.00 4.12
248 249 0.336737 TGGTTCTTTGTGGGTTGGGT 59.663 50.000 0.00 0.00 0.00 4.51
249 250 1.273324 TGGTTCTTTGTGGGTTGGGTT 60.273 47.619 0.00 0.00 0.00 4.11
250 251 1.138069 GGTTCTTTGTGGGTTGGGTTG 59.862 52.381 0.00 0.00 0.00 3.77
251 252 0.827368 TTCTTTGTGGGTTGGGTTGC 59.173 50.000 0.00 0.00 0.00 4.17
252 253 1.045911 TCTTTGTGGGTTGGGTTGCC 61.046 55.000 0.00 0.00 0.00 4.52
253 254 2.362329 CTTTGTGGGTTGGGTTGCCG 62.362 60.000 0.00 0.00 0.00 5.69
270 271 4.043200 GCTGCACCAAACCGCCTC 62.043 66.667 0.00 0.00 0.00 4.70
271 272 2.281761 CTGCACCAAACCGCCTCT 60.282 61.111 0.00 0.00 0.00 3.69
272 273 1.003839 CTGCACCAAACCGCCTCTA 60.004 57.895 0.00 0.00 0.00 2.43
273 274 1.298859 CTGCACCAAACCGCCTCTAC 61.299 60.000 0.00 0.00 0.00 2.59
274 275 1.302192 GCACCAAACCGCCTCTACA 60.302 57.895 0.00 0.00 0.00 2.74
275 276 0.676782 GCACCAAACCGCCTCTACAT 60.677 55.000 0.00 0.00 0.00 2.29
276 277 1.369625 CACCAAACCGCCTCTACATC 58.630 55.000 0.00 0.00 0.00 3.06
277 278 0.981183 ACCAAACCGCCTCTACATCA 59.019 50.000 0.00 0.00 0.00 3.07
278 279 1.559682 ACCAAACCGCCTCTACATCAT 59.440 47.619 0.00 0.00 0.00 2.45
279 280 2.213499 CCAAACCGCCTCTACATCATC 58.787 52.381 0.00 0.00 0.00 2.92
280 281 2.419990 CCAAACCGCCTCTACATCATCA 60.420 50.000 0.00 0.00 0.00 3.07
281 282 3.470709 CAAACCGCCTCTACATCATCAT 58.529 45.455 0.00 0.00 0.00 2.45
282 283 4.503123 CCAAACCGCCTCTACATCATCATA 60.503 45.833 0.00 0.00 0.00 2.15
283 284 4.527509 AACCGCCTCTACATCATCATAG 57.472 45.455 0.00 0.00 0.00 2.23
284 285 3.767711 ACCGCCTCTACATCATCATAGA 58.232 45.455 0.00 0.00 0.00 1.98
285 286 4.152647 ACCGCCTCTACATCATCATAGAA 58.847 43.478 0.00 0.00 0.00 2.10
286 287 4.588951 ACCGCCTCTACATCATCATAGAAA 59.411 41.667 0.00 0.00 0.00 2.52
287 288 4.926238 CCGCCTCTACATCATCATAGAAAC 59.074 45.833 0.00 0.00 0.00 2.78
288 289 4.926238 CGCCTCTACATCATCATAGAAACC 59.074 45.833 0.00 0.00 0.00 3.27
289 290 5.509670 CGCCTCTACATCATCATAGAAACCA 60.510 44.000 0.00 0.00 0.00 3.67
290 291 6.291377 GCCTCTACATCATCATAGAAACCAA 58.709 40.000 0.00 0.00 0.00 3.67
291 292 6.939163 GCCTCTACATCATCATAGAAACCAAT 59.061 38.462 0.00 0.00 0.00 3.16
292 293 7.446625 GCCTCTACATCATCATAGAAACCAATT 59.553 37.037 0.00 0.00 0.00 2.32
293 294 9.347240 CCTCTACATCATCATAGAAACCAATTT 57.653 33.333 0.00 0.00 0.00 1.82
295 296 9.904198 TCTACATCATCATAGAAACCAATTTCA 57.096 29.630 2.86 0.00 45.78 2.69
297 298 8.585471 ACATCATCATAGAAACCAATTTCAGT 57.415 30.769 2.86 0.00 45.78 3.41
298 299 8.464404 ACATCATCATAGAAACCAATTTCAGTG 58.536 33.333 2.86 1.58 45.78 3.66
299 300 7.395190 TCATCATAGAAACCAATTTCAGTGG 57.605 36.000 2.86 0.00 45.78 4.00
300 301 7.174413 TCATCATAGAAACCAATTTCAGTGGA 58.826 34.615 0.00 0.00 45.78 4.02
301 302 7.337689 TCATCATAGAAACCAATTTCAGTGGAG 59.662 37.037 0.00 0.00 45.78 3.86
302 303 5.945784 TCATAGAAACCAATTTCAGTGGAGG 59.054 40.000 0.00 0.00 45.78 4.30
303 304 2.893489 AGAAACCAATTTCAGTGGAGGC 59.107 45.455 0.00 0.00 45.78 4.70
304 305 2.380064 AACCAATTTCAGTGGAGGCA 57.620 45.000 0.00 0.00 39.62 4.75
305 306 2.380064 ACCAATTTCAGTGGAGGCAA 57.620 45.000 0.00 0.00 39.62 4.52
306 307 2.893424 ACCAATTTCAGTGGAGGCAAT 58.107 42.857 0.00 0.00 39.62 3.56
307 308 2.564062 ACCAATTTCAGTGGAGGCAATG 59.436 45.455 0.00 0.00 39.62 2.82
308 309 2.827322 CCAATTTCAGTGGAGGCAATGA 59.173 45.455 0.00 0.00 38.54 2.57
309 310 3.258872 CCAATTTCAGTGGAGGCAATGAA 59.741 43.478 0.00 0.00 38.54 2.57
310 311 4.240096 CAATTTCAGTGGAGGCAATGAAC 58.760 43.478 0.00 0.00 38.61 3.18
311 312 2.957402 TTCAGTGGAGGCAATGAACT 57.043 45.000 0.00 0.00 34.77 3.01
312 313 2.189594 TCAGTGGAGGCAATGAACTG 57.810 50.000 0.00 0.00 39.66 3.16
313 314 1.699083 TCAGTGGAGGCAATGAACTGA 59.301 47.619 0.00 0.00 43.64 3.41
314 315 2.082231 CAGTGGAGGCAATGAACTGAG 58.918 52.381 0.00 0.00 40.54 3.35
315 316 1.701847 AGTGGAGGCAATGAACTGAGT 59.298 47.619 0.00 0.00 0.00 3.41
316 317 2.107204 AGTGGAGGCAATGAACTGAGTT 59.893 45.455 0.00 0.00 0.00 3.01
317 318 2.887152 GTGGAGGCAATGAACTGAGTTT 59.113 45.455 0.00 0.00 0.00 2.66
318 319 4.072131 GTGGAGGCAATGAACTGAGTTTA 58.928 43.478 0.00 0.00 0.00 2.01
319 320 4.154918 GTGGAGGCAATGAACTGAGTTTAG 59.845 45.833 0.00 0.00 0.00 1.85
320 321 4.041567 TGGAGGCAATGAACTGAGTTTAGA 59.958 41.667 0.00 0.00 0.00 2.10
321 322 4.393371 GGAGGCAATGAACTGAGTTTAGAC 59.607 45.833 0.00 0.00 0.00 2.59
322 323 3.997021 AGGCAATGAACTGAGTTTAGACG 59.003 43.478 0.00 0.00 0.00 4.18
323 324 3.125316 GGCAATGAACTGAGTTTAGACGG 59.875 47.826 0.00 0.00 0.00 4.79
324 325 3.746492 GCAATGAACTGAGTTTAGACGGT 59.254 43.478 0.00 0.00 0.00 4.83
325 326 4.213482 GCAATGAACTGAGTTTAGACGGTT 59.787 41.667 0.00 0.00 0.00 4.44
326 327 5.277828 GCAATGAACTGAGTTTAGACGGTTT 60.278 40.000 0.00 0.00 0.00 3.27
327 328 6.725246 CAATGAACTGAGTTTAGACGGTTTT 58.275 36.000 0.00 0.00 0.00 2.43
328 329 5.728351 TGAACTGAGTTTAGACGGTTTTG 57.272 39.130 0.00 0.00 0.00 2.44
329 330 5.421277 TGAACTGAGTTTAGACGGTTTTGA 58.579 37.500 0.00 0.00 0.00 2.69
330 331 5.292589 TGAACTGAGTTTAGACGGTTTTGAC 59.707 40.000 0.00 0.00 0.00 3.18
331 332 4.761975 ACTGAGTTTAGACGGTTTTGACA 58.238 39.130 0.00 0.00 0.00 3.58
332 333 5.180271 ACTGAGTTTAGACGGTTTTGACAA 58.820 37.500 0.00 0.00 0.00 3.18
333 334 5.644636 ACTGAGTTTAGACGGTTTTGACAAA 59.355 36.000 0.00 0.00 0.00 2.83
334 335 5.871539 TGAGTTTAGACGGTTTTGACAAAC 58.128 37.500 0.00 0.00 41.57 2.93
335 336 5.644636 TGAGTTTAGACGGTTTTGACAAACT 59.355 36.000 0.00 0.00 41.92 2.66
336 337 6.817641 TGAGTTTAGACGGTTTTGACAAACTA 59.182 34.615 0.00 0.00 41.92 2.24
337 338 7.333921 TGAGTTTAGACGGTTTTGACAAACTAA 59.666 33.333 0.00 2.39 41.92 2.24
338 339 7.691158 AGTTTAGACGGTTTTGACAAACTAAG 58.309 34.615 0.00 0.00 41.92 2.18
339 340 6.607735 TTAGACGGTTTTGACAAACTAAGG 57.392 37.500 0.00 0.00 41.92 2.69
340 341 4.773013 AGACGGTTTTGACAAACTAAGGA 58.227 39.130 0.00 0.00 41.92 3.36
341 342 5.187687 AGACGGTTTTGACAAACTAAGGAA 58.812 37.500 0.00 0.00 41.92 3.36
342 343 5.065602 AGACGGTTTTGACAAACTAAGGAAC 59.934 40.000 0.00 0.00 41.92 3.62
343 344 4.701171 ACGGTTTTGACAAACTAAGGAACA 59.299 37.500 0.00 0.00 41.92 3.18
344 345 5.183522 ACGGTTTTGACAAACTAAGGAACAA 59.816 36.000 0.00 0.00 41.92 2.83
345 346 6.094061 CGGTTTTGACAAACTAAGGAACAAA 58.906 36.000 0.00 0.00 41.92 2.83
346 347 6.754675 CGGTTTTGACAAACTAAGGAACAAAT 59.245 34.615 0.00 0.00 41.92 2.32
347 348 7.276878 CGGTTTTGACAAACTAAGGAACAAATT 59.723 33.333 0.00 0.00 41.92 1.82
348 349 8.941977 GGTTTTGACAAACTAAGGAACAAATTT 58.058 29.630 0.00 0.00 41.92 1.82
349 350 9.753669 GTTTTGACAAACTAAGGAACAAATTTG 57.246 29.630 16.67 16.67 39.49 2.32
350 351 9.495572 TTTTGACAAACTAAGGAACAAATTTGT 57.504 25.926 18.13 18.13 44.72 2.83
376 377 8.751215 TCCATATTGGAGGGTAGTAACATATT 57.249 34.615 0.00 0.00 42.67 1.28
377 378 9.177927 TCCATATTGGAGGGTAGTAACATATTT 57.822 33.333 0.00 0.00 42.67 1.40
378 379 9.231297 CCATATTGGAGGGTAGTAACATATTTG 57.769 37.037 0.00 0.00 40.96 2.32
379 380 9.793259 CATATTGGAGGGTAGTAACATATTTGT 57.207 33.333 0.00 0.00 37.82 2.83
382 383 8.570068 TTGGAGGGTAGTAACATATTTGTTTC 57.430 34.615 6.85 2.46 43.57 2.78
383 384 7.924541 TGGAGGGTAGTAACATATTTGTTTCT 58.075 34.615 6.85 9.62 43.57 2.52
384 385 8.387813 TGGAGGGTAGTAACATATTTGTTTCTT 58.612 33.333 12.07 0.00 43.57 2.52
385 386 9.239551 GGAGGGTAGTAACATATTTGTTTCTTT 57.760 33.333 12.07 0.00 43.57 2.52
426 427 8.225603 AGTTAAAAATGTGCTATGGAGTATGG 57.774 34.615 0.00 0.00 0.00 2.74
427 428 5.520376 AAAAATGTGCTATGGAGTATGGC 57.480 39.130 0.00 0.00 43.03 4.40
428 429 4.443978 AAATGTGCTATGGAGTATGGCT 57.556 40.909 0.00 0.00 43.13 4.75
429 430 2.916702 TGTGCTATGGAGTATGGCTG 57.083 50.000 0.00 0.00 43.13 4.85
430 431 2.118679 TGTGCTATGGAGTATGGCTGT 58.881 47.619 0.00 0.00 43.13 4.40
431 432 3.304829 TGTGCTATGGAGTATGGCTGTA 58.695 45.455 0.00 0.00 43.13 2.74
432 433 3.903714 TGTGCTATGGAGTATGGCTGTAT 59.096 43.478 0.00 0.00 43.13 2.29
433 434 4.248859 GTGCTATGGAGTATGGCTGTATG 58.751 47.826 0.00 0.00 43.13 2.39
434 435 3.261643 TGCTATGGAGTATGGCTGTATGG 59.738 47.826 0.00 0.00 43.13 2.74
435 436 3.369892 GCTATGGAGTATGGCTGTATGGG 60.370 52.174 0.00 0.00 39.90 4.00
436 437 0.764890 TGGAGTATGGCTGTATGGGC 59.235 55.000 0.00 0.00 0.00 5.36
437 438 0.764890 GGAGTATGGCTGTATGGGCA 59.235 55.000 0.00 0.00 45.45 5.36
441 442 2.123769 TGGCTGTATGGGCATGCC 60.124 61.111 29.47 29.47 43.49 4.40
442 443 2.196776 GGCTGTATGGGCATGCCT 59.803 61.111 34.70 19.81 40.36 4.75
443 444 1.456331 GGCTGTATGGGCATGCCTT 60.456 57.895 34.70 24.25 40.36 4.35
444 445 1.044790 GGCTGTATGGGCATGCCTTT 61.045 55.000 34.70 23.91 40.36 3.11
445 446 0.826062 GCTGTATGGGCATGCCTTTT 59.174 50.000 34.70 21.51 36.10 2.27
446 447 1.202452 GCTGTATGGGCATGCCTTTTC 60.202 52.381 34.70 22.14 36.10 2.29
447 448 2.381911 CTGTATGGGCATGCCTTTTCT 58.618 47.619 34.70 17.34 36.10 2.52
448 449 3.554934 CTGTATGGGCATGCCTTTTCTA 58.445 45.455 34.70 16.39 36.10 2.10
449 450 3.554934 TGTATGGGCATGCCTTTTCTAG 58.445 45.455 34.70 0.00 36.10 2.43
450 451 3.201930 TGTATGGGCATGCCTTTTCTAGA 59.798 43.478 34.70 15.01 36.10 2.43
451 452 3.607490 ATGGGCATGCCTTTTCTAGAT 57.393 42.857 34.70 11.85 36.10 1.98
452 453 2.936202 TGGGCATGCCTTTTCTAGATC 58.064 47.619 34.70 15.31 36.10 2.75
453 454 2.241941 TGGGCATGCCTTTTCTAGATCA 59.758 45.455 34.70 17.76 36.10 2.92
454 455 3.117398 TGGGCATGCCTTTTCTAGATCAT 60.117 43.478 34.70 0.00 36.10 2.45
455 456 3.255149 GGGCATGCCTTTTCTAGATCATG 59.745 47.826 34.70 4.50 37.53 3.07
456 457 3.255149 GGCATGCCTTTTCTAGATCATGG 59.745 47.826 29.98 9.30 36.26 3.66
457 458 4.139786 GCATGCCTTTTCTAGATCATGGA 58.860 43.478 6.36 1.18 36.26 3.41
458 459 4.581824 GCATGCCTTTTCTAGATCATGGAA 59.418 41.667 6.36 5.20 36.26 3.53
459 460 5.068198 GCATGCCTTTTCTAGATCATGGAAA 59.932 40.000 6.36 0.00 36.68 3.13
460 461 6.406177 GCATGCCTTTTCTAGATCATGGAAAA 60.406 38.462 6.36 14.88 43.63 2.29
461 462 7.549839 CATGCCTTTTCTAGATCATGGAAAAA 58.450 34.615 15.81 6.63 44.69 1.94
493 495 5.961396 AGCTTAGATCATGATCCAAATGC 57.039 39.130 28.23 24.14 38.58 3.56
500 502 3.293337 TCATGATCCAAATGCTCCCAAG 58.707 45.455 0.00 0.00 0.00 3.61
512 514 0.742281 CTCCCAAGTGACGAGCCATG 60.742 60.000 0.00 0.00 0.00 3.66
514 516 0.742281 CCCAAGTGACGAGCCATGAG 60.742 60.000 0.00 0.00 0.00 2.90
522 530 2.266554 GACGAGCCATGAGAAACAGAG 58.733 52.381 0.00 0.00 0.00 3.35
526 534 1.280421 AGCCATGAGAAACAGAGGACC 59.720 52.381 0.00 0.00 31.83 4.46
534 542 1.002087 GAAACAGAGGACCATCCACGT 59.998 52.381 0.00 0.00 39.61 4.49
535 543 0.321671 AACAGAGGACCATCCACGTG 59.678 55.000 9.08 9.08 39.61 4.49
536 544 0.541998 ACAGAGGACCATCCACGTGA 60.542 55.000 19.30 3.36 39.61 4.35
537 545 0.608130 CAGAGGACCATCCACGTGAA 59.392 55.000 19.30 0.00 39.61 3.18
539 547 1.697432 AGAGGACCATCCACGTGAAAA 59.303 47.619 19.30 2.00 39.61 2.29
541 549 2.484264 GAGGACCATCCACGTGAAAAAG 59.516 50.000 19.30 4.04 39.61 2.27
542 550 2.105821 AGGACCATCCACGTGAAAAAGA 59.894 45.455 19.30 5.40 39.61 2.52
546 554 4.678622 ACCATCCACGTGAAAAAGAAAAC 58.321 39.130 19.30 0.00 0.00 2.43
550 558 4.159857 TCCACGTGAAAAAGAAAACAACG 58.840 39.130 19.30 0.00 0.00 4.10
555 563 5.341196 ACGTGAAAAAGAAAACAACGACAAG 59.659 36.000 0.00 0.00 0.00 3.16
557 565 5.344933 GTGAAAAAGAAAACAACGACAAGCT 59.655 36.000 0.00 0.00 0.00 3.74
559 567 3.692791 AAGAAAACAACGACAAGCTCC 57.307 42.857 0.00 0.00 0.00 4.70
560 568 1.947456 AGAAAACAACGACAAGCTCCC 59.053 47.619 0.00 0.00 0.00 4.30
562 570 1.021968 AAACAACGACAAGCTCCCAC 58.978 50.000 0.00 0.00 0.00 4.61
563 571 1.157870 AACAACGACAAGCTCCCACG 61.158 55.000 0.00 0.00 0.00 4.94
583 598 1.918609 GACGAATCTAAGCGTGACACC 59.081 52.381 0.00 0.00 41.34 4.16
588 603 0.319555 TCTAAGCGTGACACCTGCAC 60.320 55.000 7.99 0.00 0.00 4.57
595 610 1.808512 CGTGACACCTGCACCACTTTA 60.809 52.381 0.00 0.00 32.74 1.85
603 618 2.632544 GCACCACTTTAACGCCCCC 61.633 63.158 0.00 0.00 0.00 5.40
604 619 1.074248 CACCACTTTAACGCCCCCT 59.926 57.895 0.00 0.00 0.00 4.79
606 621 1.131928 ACCACTTTAACGCCCCCTCT 61.132 55.000 0.00 0.00 0.00 3.69
648 663 2.609491 CGTCCTTCCACGACAATCTCAA 60.609 50.000 0.00 0.00 42.69 3.02
649 664 3.399330 GTCCTTCCACGACAATCTCAAA 58.601 45.455 0.00 0.00 0.00 2.69
650 665 3.813166 GTCCTTCCACGACAATCTCAAAA 59.187 43.478 0.00 0.00 0.00 2.44
651 666 4.065088 TCCTTCCACGACAATCTCAAAAG 58.935 43.478 0.00 0.00 0.00 2.27
652 667 3.365364 CCTTCCACGACAATCTCAAAAGC 60.365 47.826 0.00 0.00 0.00 3.51
653 668 2.151202 TCCACGACAATCTCAAAAGCC 58.849 47.619 0.00 0.00 0.00 4.35
681 696 4.308458 CCTCCCAACACGACGCCA 62.308 66.667 0.00 0.00 0.00 5.69
777 792 3.677648 AACGCTACGCCGACAGGT 61.678 61.111 0.00 0.00 40.50 4.00
817 1231 1.146774 TCCCCAATCTCTTTTGCACCA 59.853 47.619 0.00 0.00 0.00 4.17
822 1236 3.558505 CAATCTCTTTTGCACCAGAACG 58.441 45.455 0.00 0.00 0.00 3.95
826 1240 1.021202 CTTTTGCACCAGAACGGACA 58.979 50.000 0.00 0.00 38.63 4.02
845 1259 1.208052 CACCGAGTCTGGATCATGGTT 59.792 52.381 7.83 0.00 0.00 3.67
846 1260 1.909302 ACCGAGTCTGGATCATGGTTT 59.091 47.619 7.83 0.00 0.00 3.27
873 1287 0.593128 ATGAAAGCGCGCTCAAAAGT 59.407 45.000 36.57 15.57 0.00 2.66
971 1385 5.989777 CGCCTTTTAGCCTGTGTATATAAGT 59.010 40.000 0.00 0.00 0.00 2.24
976 1390 2.037251 AGCCTGTGTATATAAGTGCCGG 59.963 50.000 0.00 0.00 0.00 6.13
989 1403 2.588034 GCCGGGTATGCCGTTCTC 60.588 66.667 2.18 0.00 34.97 2.87
1058 1472 5.474578 TCTTGAAGACACACTGCTATTCT 57.525 39.130 0.00 0.00 0.00 2.40
1059 1473 5.858381 TCTTGAAGACACACTGCTATTCTT 58.142 37.500 0.00 0.00 0.00 2.52
1060 1474 5.698089 TCTTGAAGACACACTGCTATTCTTG 59.302 40.000 0.00 0.00 0.00 3.02
1061 1475 5.213891 TGAAGACACACTGCTATTCTTGA 57.786 39.130 0.00 0.00 0.00 3.02
1062 1476 5.233225 TGAAGACACACTGCTATTCTTGAG 58.767 41.667 0.00 0.00 0.00 3.02
1063 1477 5.011023 TGAAGACACACTGCTATTCTTGAGA 59.989 40.000 0.00 0.00 0.00 3.27
1064 1478 5.070770 AGACACACTGCTATTCTTGAGAG 57.929 43.478 0.00 0.00 0.00 3.20
1065 1479 3.594134 ACACACTGCTATTCTTGAGAGC 58.406 45.455 0.00 0.00 42.94 4.09
1066 1480 3.260380 ACACACTGCTATTCTTGAGAGCT 59.740 43.478 0.00 0.00 43.05 4.09
1067 1481 4.464244 ACACACTGCTATTCTTGAGAGCTA 59.536 41.667 0.00 0.00 43.05 3.32
1068 1482 5.042593 CACACTGCTATTCTTGAGAGCTAG 58.957 45.833 0.00 0.00 43.05 3.42
1069 1483 4.709397 ACACTGCTATTCTTGAGAGCTAGT 59.291 41.667 0.00 6.86 43.05 2.57
1193 1607 3.854666 CGAGAAGAAGATCAAGAAGGCA 58.145 45.455 0.00 0.00 0.00 4.75
1205 1619 2.663826 AGAAGGCACTGTCGAATCTC 57.336 50.000 0.00 0.00 40.86 2.75
1231 1645 2.533266 ACGCATCATGTCATAGGACC 57.467 50.000 4.87 0.00 43.65 4.46
1243 1657 3.896272 GTCATAGGACCTTTCTACGGGAT 59.104 47.826 0.00 0.00 38.12 3.85
1244 1658 5.075493 GTCATAGGACCTTTCTACGGGATA 58.925 45.833 0.00 0.00 38.12 2.59
1263 1677 2.424842 AAACCGCCTGAGCAATGGGA 62.425 55.000 0.00 0.00 39.83 4.37
1366 1780 1.991167 GGTGACGGTGTGGGGGATA 60.991 63.158 0.00 0.00 0.00 2.59
1467 1881 3.522731 CGAGGACGCTAGGCTGCT 61.523 66.667 0.00 0.00 0.00 4.24
1468 1882 2.105930 GAGGACGCTAGGCTGCTG 59.894 66.667 0.00 0.00 0.00 4.41
1516 1930 4.789075 TTCGCCGCGTACAGGAGC 62.789 66.667 13.39 0.00 0.00 4.70
1592 2006 1.201704 CGAGCGTGATGTTTTGTCTCG 60.202 52.381 0.00 0.00 36.49 4.04
1754 2192 1.526575 AAACCCTTGCCATGCAGTCG 61.527 55.000 0.00 0.00 40.61 4.18
1756 2194 2.401766 CCCTTGCCATGCAGTCGAC 61.402 63.158 7.70 7.70 40.61 4.20
1757 2195 1.672030 CCTTGCCATGCAGTCGACA 60.672 57.895 19.50 0.00 40.61 4.35
1758 2196 1.028330 CCTTGCCATGCAGTCGACAT 61.028 55.000 19.50 0.00 40.61 3.06
1759 2197 1.655484 CTTGCCATGCAGTCGACATA 58.345 50.000 19.50 3.45 40.61 2.29
1778 2217 7.063074 TCGACATAGATTTTCGAGAAAACTTCC 59.937 37.037 12.51 4.19 42.32 3.46
1779 2218 7.148639 CGACATAGATTTTCGAGAAAACTTCCA 60.149 37.037 12.51 0.00 42.32 3.53
1792 2231 8.834465 CGAGAAAACTTCCAATCTATTCATCAT 58.166 33.333 0.00 0.00 0.00 2.45
1800 2239 6.844829 TCCAATCTATTCATCATGTCATGGT 58.155 36.000 12.90 2.38 0.00 3.55
1934 2384 9.826574 TGCTAATTAAATACACTTCCGTATCTT 57.173 29.630 0.00 0.00 30.73 2.40
2227 6659 2.673043 GCAACATGCAGACCATCCTTTG 60.673 50.000 0.00 0.00 44.26 2.77
2420 6854 4.195225 TGTCACATACAAATGCGACCTA 57.805 40.909 4.58 0.00 42.17 3.08
2440 6874 9.672086 CGACCTACAAATTTTGAGACAAAAATA 57.328 29.630 15.81 4.53 38.49 1.40
2500 6934 3.457749 ACCAAATGTCACCCCAAATTTGT 59.542 39.130 16.73 0.00 38.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 2.595124 ACAAGGAAAAACCAAAGCGG 57.405 45.000 0.00 0.00 42.04 5.52
67 68 4.301637 AGTACAAGGAAAAACCAAAGCG 57.698 40.909 0.00 0.00 42.04 4.68
68 69 6.978343 AAAAGTACAAGGAAAAACCAAAGC 57.022 33.333 0.00 0.00 42.04 3.51
69 70 7.822334 AGGAAAAAGTACAAGGAAAAACCAAAG 59.178 33.333 0.00 0.00 42.04 2.77
70 71 7.681679 AGGAAAAAGTACAAGGAAAAACCAAA 58.318 30.769 0.00 0.00 42.04 3.28
71 72 7.247456 AGGAAAAAGTACAAGGAAAAACCAA 57.753 32.000 0.00 0.00 42.04 3.67
72 73 6.860790 AGGAAAAAGTACAAGGAAAAACCA 57.139 33.333 0.00 0.00 42.04 3.67
73 74 9.826574 ATAAAGGAAAAAGTACAAGGAAAAACC 57.173 29.630 0.00 0.00 39.35 3.27
76 77 9.738832 CGAATAAAGGAAAAAGTACAAGGAAAA 57.261 29.630 0.00 0.00 0.00 2.29
77 78 8.354426 CCGAATAAAGGAAAAAGTACAAGGAAA 58.646 33.333 0.00 0.00 0.00 3.13
78 79 7.720515 TCCGAATAAAGGAAAAAGTACAAGGAA 59.279 33.333 0.00 0.00 34.33 3.36
79 80 7.225725 TCCGAATAAAGGAAAAAGTACAAGGA 58.774 34.615 0.00 0.00 34.33 3.36
80 81 7.443259 TCCGAATAAAGGAAAAAGTACAAGG 57.557 36.000 0.00 0.00 34.33 3.61
99 100 9.681062 AGGAAACTGAAATAGATAAATTCCGAA 57.319 29.630 0.00 0.00 41.13 4.30
169 170 9.425248 TGAGAAAATTGGAAGATAAAGCCATAT 57.575 29.630 0.00 0.00 0.00 1.78
170 171 8.821686 TGAGAAAATTGGAAGATAAAGCCATA 57.178 30.769 0.00 0.00 0.00 2.74
171 172 7.722949 TGAGAAAATTGGAAGATAAAGCCAT 57.277 32.000 0.00 0.00 0.00 4.40
172 173 7.537596 TTGAGAAAATTGGAAGATAAAGCCA 57.462 32.000 0.00 0.00 0.00 4.75
173 174 8.831715 TTTTGAGAAAATTGGAAGATAAAGCC 57.168 30.769 0.00 0.00 0.00 4.35
174 175 9.696917 TCTTTTGAGAAAATTGGAAGATAAAGC 57.303 29.630 0.00 0.00 0.00 3.51
180 181 9.942850 ACTTTTTCTTTTGAGAAAATTGGAAGA 57.057 25.926 13.27 0.00 44.21 2.87
183 184 9.717942 TGAACTTTTTCTTTTGAGAAAATTGGA 57.282 25.926 13.27 1.03 44.21 3.53
205 206 9.143631 CCATACAGGATCTTTCAATTTTTGAAC 57.856 33.333 2.31 0.00 44.30 3.18
206 207 8.869109 ACCATACAGGATCTTTCAATTTTTGAA 58.131 29.630 0.00 0.00 43.49 2.69
207 208 8.421249 ACCATACAGGATCTTTCAATTTTTGA 57.579 30.769 0.00 0.00 41.22 2.69
208 209 9.143631 GAACCATACAGGATCTTTCAATTTTTG 57.856 33.333 0.00 0.00 41.22 2.44
209 210 9.093458 AGAACCATACAGGATCTTTCAATTTTT 57.907 29.630 0.00 0.00 46.48 1.94
210 211 8.655935 AGAACCATACAGGATCTTTCAATTTT 57.344 30.769 0.00 0.00 46.48 1.82
220 221 3.947834 CCCACAAAGAACCATACAGGATC 59.052 47.826 0.00 0.00 41.22 3.36
221 222 3.333680 ACCCACAAAGAACCATACAGGAT 59.666 43.478 0.00 0.00 41.22 3.24
222 223 2.714250 ACCCACAAAGAACCATACAGGA 59.286 45.455 0.00 0.00 41.22 3.86
223 224 3.154827 ACCCACAAAGAACCATACAGG 57.845 47.619 0.00 0.00 45.67 4.00
224 225 3.255642 CCAACCCACAAAGAACCATACAG 59.744 47.826 0.00 0.00 0.00 2.74
225 226 3.226777 CCAACCCACAAAGAACCATACA 58.773 45.455 0.00 0.00 0.00 2.29
226 227 2.560981 CCCAACCCACAAAGAACCATAC 59.439 50.000 0.00 0.00 0.00 2.39
227 228 2.178106 ACCCAACCCACAAAGAACCATA 59.822 45.455 0.00 0.00 0.00 2.74
228 229 1.062505 ACCCAACCCACAAAGAACCAT 60.063 47.619 0.00 0.00 0.00 3.55
229 230 0.336737 ACCCAACCCACAAAGAACCA 59.663 50.000 0.00 0.00 0.00 3.67
230 231 1.138069 CAACCCAACCCACAAAGAACC 59.862 52.381 0.00 0.00 0.00 3.62
231 232 1.472552 GCAACCCAACCCACAAAGAAC 60.473 52.381 0.00 0.00 0.00 3.01
232 233 0.827368 GCAACCCAACCCACAAAGAA 59.173 50.000 0.00 0.00 0.00 2.52
233 234 1.045911 GGCAACCCAACCCACAAAGA 61.046 55.000 0.00 0.00 0.00 2.52
234 235 1.445518 GGCAACCCAACCCACAAAG 59.554 57.895 0.00 0.00 0.00 2.77
235 236 2.427245 CGGCAACCCAACCCACAAA 61.427 57.895 0.00 0.00 0.00 2.83
236 237 2.835431 CGGCAACCCAACCCACAA 60.835 61.111 0.00 0.00 0.00 3.33
253 254 4.043200 GAGGCGGTTTGGTGCAGC 62.043 66.667 9.47 9.47 0.00 5.25
254 255 1.003839 TAGAGGCGGTTTGGTGCAG 60.004 57.895 0.00 0.00 0.00 4.41
255 256 1.302192 GTAGAGGCGGTTTGGTGCA 60.302 57.895 0.00 0.00 0.00 4.57
256 257 0.676782 ATGTAGAGGCGGTTTGGTGC 60.677 55.000 0.00 0.00 0.00 5.01
257 258 1.338674 TGATGTAGAGGCGGTTTGGTG 60.339 52.381 0.00 0.00 0.00 4.17
258 259 0.981183 TGATGTAGAGGCGGTTTGGT 59.019 50.000 0.00 0.00 0.00 3.67
259 260 2.213499 GATGATGTAGAGGCGGTTTGG 58.787 52.381 0.00 0.00 0.00 3.28
260 261 2.905075 TGATGATGTAGAGGCGGTTTG 58.095 47.619 0.00 0.00 0.00 2.93
261 262 3.845781 ATGATGATGTAGAGGCGGTTT 57.154 42.857 0.00 0.00 0.00 3.27
262 263 4.152647 TCTATGATGATGTAGAGGCGGTT 58.847 43.478 0.00 0.00 0.00 4.44
263 264 3.767711 TCTATGATGATGTAGAGGCGGT 58.232 45.455 0.00 0.00 0.00 5.68
264 265 4.790765 TTCTATGATGATGTAGAGGCGG 57.209 45.455 0.00 0.00 0.00 6.13
265 266 4.926238 GGTTTCTATGATGATGTAGAGGCG 59.074 45.833 0.00 0.00 0.00 5.52
266 267 5.858381 TGGTTTCTATGATGATGTAGAGGC 58.142 41.667 0.00 0.00 0.00 4.70
267 268 8.915057 AATTGGTTTCTATGATGATGTAGAGG 57.085 34.615 0.00 0.00 0.00 3.69
269 270 9.904198 TGAAATTGGTTTCTATGATGATGTAGA 57.096 29.630 3.00 0.00 43.30 2.59
271 272 9.685276 ACTGAAATTGGTTTCTATGATGATGTA 57.315 29.630 3.00 0.00 43.30 2.29
272 273 8.464404 CACTGAAATTGGTTTCTATGATGATGT 58.536 33.333 3.00 0.00 43.30 3.06
273 274 7.919091 CCACTGAAATTGGTTTCTATGATGATG 59.081 37.037 3.00 0.00 43.30 3.07
274 275 7.835682 TCCACTGAAATTGGTTTCTATGATGAT 59.164 33.333 3.00 0.00 43.30 2.45
275 276 7.174413 TCCACTGAAATTGGTTTCTATGATGA 58.826 34.615 3.00 0.00 43.30 2.92
276 277 7.395190 TCCACTGAAATTGGTTTCTATGATG 57.605 36.000 3.00 0.00 43.30 3.07
277 278 6.604795 CCTCCACTGAAATTGGTTTCTATGAT 59.395 38.462 3.00 0.00 43.30 2.45
278 279 5.945784 CCTCCACTGAAATTGGTTTCTATGA 59.054 40.000 3.00 0.00 43.30 2.15
279 280 5.393461 GCCTCCACTGAAATTGGTTTCTATG 60.393 44.000 3.00 1.77 43.30 2.23
280 281 4.706962 GCCTCCACTGAAATTGGTTTCTAT 59.293 41.667 3.00 0.00 43.30 1.98
281 282 4.079253 GCCTCCACTGAAATTGGTTTCTA 58.921 43.478 3.00 0.00 43.30 2.10
282 283 2.893489 GCCTCCACTGAAATTGGTTTCT 59.107 45.455 3.00 0.00 43.30 2.52
283 284 2.627699 TGCCTCCACTGAAATTGGTTTC 59.372 45.455 0.00 0.00 43.22 2.78
284 285 2.676748 TGCCTCCACTGAAATTGGTTT 58.323 42.857 0.00 0.00 35.42 3.27
285 286 2.380064 TGCCTCCACTGAAATTGGTT 57.620 45.000 0.00 0.00 35.42 3.67
286 287 2.380064 TTGCCTCCACTGAAATTGGT 57.620 45.000 0.00 0.00 35.42 3.67
287 288 2.827322 TCATTGCCTCCACTGAAATTGG 59.173 45.455 0.00 0.00 35.18 3.16
288 289 4.021719 AGTTCATTGCCTCCACTGAAATTG 60.022 41.667 0.00 0.00 40.75 2.32
289 290 4.021719 CAGTTCATTGCCTCCACTGAAATT 60.022 41.667 0.00 0.00 40.75 1.82
290 291 3.508793 CAGTTCATTGCCTCCACTGAAAT 59.491 43.478 0.00 0.00 40.75 2.17
291 292 2.886523 CAGTTCATTGCCTCCACTGAAA 59.113 45.455 0.00 0.00 40.75 2.69
292 293 2.106338 TCAGTTCATTGCCTCCACTGAA 59.894 45.455 0.00 0.00 40.66 3.02
293 294 1.699083 TCAGTTCATTGCCTCCACTGA 59.301 47.619 0.00 0.00 41.21 3.41
294 295 2.082231 CTCAGTTCATTGCCTCCACTG 58.918 52.381 0.00 0.00 36.91 3.66
295 296 1.701847 ACTCAGTTCATTGCCTCCACT 59.298 47.619 0.00 0.00 0.00 4.00
296 297 2.191128 ACTCAGTTCATTGCCTCCAC 57.809 50.000 0.00 0.00 0.00 4.02
297 298 2.957402 AACTCAGTTCATTGCCTCCA 57.043 45.000 0.00 0.00 0.00 3.86
298 299 4.393371 GTCTAAACTCAGTTCATTGCCTCC 59.607 45.833 0.00 0.00 0.00 4.30
299 300 4.092091 CGTCTAAACTCAGTTCATTGCCTC 59.908 45.833 0.00 0.00 0.00 4.70
300 301 3.997021 CGTCTAAACTCAGTTCATTGCCT 59.003 43.478 0.00 0.00 0.00 4.75
301 302 3.125316 CCGTCTAAACTCAGTTCATTGCC 59.875 47.826 0.00 0.00 0.00 4.52
302 303 3.746492 ACCGTCTAAACTCAGTTCATTGC 59.254 43.478 0.00 0.00 0.00 3.56
303 304 5.924475 AACCGTCTAAACTCAGTTCATTG 57.076 39.130 0.00 0.00 0.00 2.82
304 305 6.540914 TCAAAACCGTCTAAACTCAGTTCATT 59.459 34.615 0.00 0.00 0.00 2.57
305 306 6.018180 GTCAAAACCGTCTAAACTCAGTTCAT 60.018 38.462 0.00 0.00 0.00 2.57
306 307 5.292589 GTCAAAACCGTCTAAACTCAGTTCA 59.707 40.000 0.00 0.00 0.00 3.18
307 308 5.292589 TGTCAAAACCGTCTAAACTCAGTTC 59.707 40.000 0.00 0.00 0.00 3.01
308 309 5.180271 TGTCAAAACCGTCTAAACTCAGTT 58.820 37.500 0.00 0.00 0.00 3.16
309 310 4.761975 TGTCAAAACCGTCTAAACTCAGT 58.238 39.130 0.00 0.00 0.00 3.41
310 311 5.728351 TTGTCAAAACCGTCTAAACTCAG 57.272 39.130 0.00 0.00 0.00 3.35
311 312 5.644636 AGTTTGTCAAAACCGTCTAAACTCA 59.355 36.000 0.00 0.00 45.75 3.41
312 313 6.115450 AGTTTGTCAAAACCGTCTAAACTC 57.885 37.500 0.00 0.00 45.75 3.01
313 314 7.201670 CCTTAGTTTGTCAAAACCGTCTAAACT 60.202 37.037 0.00 0.00 45.75 2.66
314 315 6.908820 CCTTAGTTTGTCAAAACCGTCTAAAC 59.091 38.462 0.00 0.00 45.75 2.01
315 316 6.822676 TCCTTAGTTTGTCAAAACCGTCTAAA 59.177 34.615 0.00 0.00 45.75 1.85
316 317 6.347696 TCCTTAGTTTGTCAAAACCGTCTAA 58.652 36.000 0.00 2.93 45.75 2.10
317 318 5.916318 TCCTTAGTTTGTCAAAACCGTCTA 58.084 37.500 0.00 0.00 45.75 2.59
318 319 4.773013 TCCTTAGTTTGTCAAAACCGTCT 58.227 39.130 0.00 0.00 45.75 4.18
319 320 5.163733 TGTTCCTTAGTTTGTCAAAACCGTC 60.164 40.000 0.00 0.00 45.75 4.79
320 321 4.701171 TGTTCCTTAGTTTGTCAAAACCGT 59.299 37.500 0.00 0.00 45.75 4.83
321 322 5.238006 TGTTCCTTAGTTTGTCAAAACCG 57.762 39.130 0.00 0.00 45.75 4.44
322 323 8.487313 AATTTGTTCCTTAGTTTGTCAAAACC 57.513 30.769 0.00 0.00 45.75 3.27
323 324 9.753669 CAAATTTGTTCCTTAGTTTGTCAAAAC 57.246 29.630 10.15 0.00 45.09 2.43
324 325 9.495572 ACAAATTTGTTCCTTAGTTTGTCAAAA 57.504 25.926 18.13 0.00 38.47 2.44
351 352 8.751215 AATATGTTACTACCCTCCAATATGGA 57.249 34.615 0.00 0.00 45.98 3.41
352 353 9.231297 CAAATATGTTACTACCCTCCAATATGG 57.769 37.037 0.00 0.00 39.43 2.74
353 354 9.793259 ACAAATATGTTACTACCCTCCAATATG 57.207 33.333 0.00 0.00 35.91 1.78
400 401 8.686334 CCATACTCCATAGCACATTTTTAACTT 58.314 33.333 0.00 0.00 0.00 2.66
401 402 7.201821 GCCATACTCCATAGCACATTTTTAACT 60.202 37.037 0.00 0.00 0.00 2.24
402 403 6.918022 GCCATACTCCATAGCACATTTTTAAC 59.082 38.462 0.00 0.00 0.00 2.01
403 404 6.833416 AGCCATACTCCATAGCACATTTTTAA 59.167 34.615 0.00 0.00 0.00 1.52
404 405 6.262944 CAGCCATACTCCATAGCACATTTTTA 59.737 38.462 0.00 0.00 0.00 1.52
405 406 5.068198 CAGCCATACTCCATAGCACATTTTT 59.932 40.000 0.00 0.00 0.00 1.94
406 407 4.581824 CAGCCATACTCCATAGCACATTTT 59.418 41.667 0.00 0.00 0.00 1.82
407 408 4.139786 CAGCCATACTCCATAGCACATTT 58.860 43.478 0.00 0.00 0.00 2.32
408 409 3.137176 ACAGCCATACTCCATAGCACATT 59.863 43.478 0.00 0.00 0.00 2.71
409 410 2.707791 ACAGCCATACTCCATAGCACAT 59.292 45.455 0.00 0.00 0.00 3.21
410 411 2.118679 ACAGCCATACTCCATAGCACA 58.881 47.619 0.00 0.00 0.00 4.57
411 412 2.918712 ACAGCCATACTCCATAGCAC 57.081 50.000 0.00 0.00 0.00 4.40
412 413 3.261643 CCATACAGCCATACTCCATAGCA 59.738 47.826 0.00 0.00 0.00 3.49
413 414 3.369892 CCCATACAGCCATACTCCATAGC 60.370 52.174 0.00 0.00 0.00 2.97
414 415 3.369892 GCCCATACAGCCATACTCCATAG 60.370 52.174 0.00 0.00 0.00 2.23
415 416 2.571653 GCCCATACAGCCATACTCCATA 59.428 50.000 0.00 0.00 0.00 2.74
416 417 1.352352 GCCCATACAGCCATACTCCAT 59.648 52.381 0.00 0.00 0.00 3.41
417 418 0.764890 GCCCATACAGCCATACTCCA 59.235 55.000 0.00 0.00 0.00 3.86
418 419 0.764890 TGCCCATACAGCCATACTCC 59.235 55.000 0.00 0.00 0.00 3.85
419 420 2.430465 CATGCCCATACAGCCATACTC 58.570 52.381 0.00 0.00 0.00 2.59
420 421 1.546323 GCATGCCCATACAGCCATACT 60.546 52.381 6.36 0.00 0.00 2.12
421 422 0.883833 GCATGCCCATACAGCCATAC 59.116 55.000 6.36 0.00 0.00 2.39
422 423 0.251297 GGCATGCCCATACAGCCATA 60.251 55.000 27.24 0.00 44.59 2.74
423 424 1.532316 GGCATGCCCATACAGCCAT 60.532 57.895 27.24 0.00 44.59 4.40
424 425 2.123769 GGCATGCCCATACAGCCA 60.124 61.111 27.24 0.00 44.59 4.75
425 426 1.044790 AAAGGCATGCCCATACAGCC 61.045 55.000 33.14 4.77 45.54 4.85
426 427 0.826062 AAAAGGCATGCCCATACAGC 59.174 50.000 33.14 5.59 36.58 4.40
427 428 2.381911 AGAAAAGGCATGCCCATACAG 58.618 47.619 33.14 0.00 36.58 2.74
428 429 2.530460 AGAAAAGGCATGCCCATACA 57.470 45.000 33.14 0.00 36.58 2.29
429 430 3.820557 TCTAGAAAAGGCATGCCCATAC 58.179 45.455 33.14 21.04 36.58 2.39
430 431 4.104579 TGATCTAGAAAAGGCATGCCCATA 59.895 41.667 33.14 16.71 36.58 2.74
431 432 3.117398 TGATCTAGAAAAGGCATGCCCAT 60.117 43.478 33.14 19.90 36.58 4.00
432 433 2.241941 TGATCTAGAAAAGGCATGCCCA 59.758 45.455 33.14 16.45 36.58 5.36
433 434 2.936202 TGATCTAGAAAAGGCATGCCC 58.064 47.619 33.14 17.70 36.58 5.36
434 435 3.255149 CCATGATCTAGAAAAGGCATGCC 59.745 47.826 30.12 30.12 37.21 4.40
435 436 4.139786 TCCATGATCTAGAAAAGGCATGC 58.860 43.478 9.90 9.90 37.21 4.06
436 437 6.704289 TTTCCATGATCTAGAAAAGGCATG 57.296 37.500 0.00 6.28 37.76 4.06
437 438 7.722949 TTTTTCCATGATCTAGAAAAGGCAT 57.277 32.000 0.00 0.00 39.78 4.40
467 468 8.521176 GCATTTGGATCATGATCTAAGCTTTAT 58.479 33.333 29.85 18.84 39.05 1.40
493 495 0.742281 CATGGCTCGTCACTTGGGAG 60.742 60.000 0.00 0.00 0.00 4.30
500 502 1.728971 CTGTTTCTCATGGCTCGTCAC 59.271 52.381 0.00 0.00 0.00 3.67
508 510 3.539604 GATGGTCCTCTGTTTCTCATGG 58.460 50.000 0.00 0.00 0.00 3.66
512 514 2.675317 CGTGGATGGTCCTCTGTTTCTC 60.675 54.545 0.00 0.00 37.46 2.87
514 516 1.002087 ACGTGGATGGTCCTCTGTTTC 59.998 52.381 0.00 0.00 37.46 2.78
522 530 2.500229 TCTTTTTCACGTGGATGGTCC 58.500 47.619 17.00 0.00 36.96 4.46
526 534 5.275695 CGTTGTTTTCTTTTTCACGTGGATG 60.276 40.000 17.00 0.50 0.00 3.51
534 542 5.465935 AGCTTGTCGTTGTTTTCTTTTTCA 58.534 33.333 0.00 0.00 0.00 2.69
535 543 5.004440 GGAGCTTGTCGTTGTTTTCTTTTTC 59.996 40.000 0.00 0.00 0.00 2.29
536 544 4.862574 GGAGCTTGTCGTTGTTTTCTTTTT 59.137 37.500 0.00 0.00 0.00 1.94
537 545 4.421058 GGAGCTTGTCGTTGTTTTCTTTT 58.579 39.130 0.00 0.00 0.00 2.27
539 547 2.357952 GGGAGCTTGTCGTTGTTTTCTT 59.642 45.455 0.00 0.00 0.00 2.52
541 549 1.673920 TGGGAGCTTGTCGTTGTTTTC 59.326 47.619 0.00 0.00 0.00 2.29
542 550 1.404035 GTGGGAGCTTGTCGTTGTTTT 59.596 47.619 0.00 0.00 0.00 2.43
546 554 1.300620 TCGTGGGAGCTTGTCGTTG 60.301 57.895 0.00 0.00 0.00 4.10
550 558 0.389948 ATTCGTCGTGGGAGCTTGTC 60.390 55.000 0.00 0.00 0.00 3.18
555 563 1.841450 CTTAGATTCGTCGTGGGAGC 58.159 55.000 0.00 0.00 0.00 4.70
557 565 0.099968 CGCTTAGATTCGTCGTGGGA 59.900 55.000 0.00 0.00 0.00 4.37
559 567 0.914551 CACGCTTAGATTCGTCGTGG 59.085 55.000 5.31 0.00 44.47 4.94
562 570 1.578023 GTGTCACGCTTAGATTCGTCG 59.422 52.381 0.00 0.00 36.73 5.12
563 571 1.918609 GGTGTCACGCTTAGATTCGTC 59.081 52.381 0.00 0.00 36.73 4.20
583 598 1.579429 GGGCGTTAAAGTGGTGCAG 59.421 57.895 0.00 0.00 0.00 4.41
588 603 0.392595 GAGAGGGGGCGTTAAAGTGG 60.393 60.000 0.00 0.00 0.00 4.00
595 610 2.198304 GATTGGTGAGAGGGGGCGTT 62.198 60.000 0.00 0.00 0.00 4.84
603 618 2.943690 CTGATTGGCTGATTGGTGAGAG 59.056 50.000 0.00 0.00 0.00 3.20
604 619 2.356432 CCTGATTGGCTGATTGGTGAGA 60.356 50.000 0.00 0.00 0.00 3.27
606 621 2.133281 CCTGATTGGCTGATTGGTGA 57.867 50.000 0.00 0.00 0.00 4.02
648 663 1.625315 GGAGGATTTGGCTTTGGCTTT 59.375 47.619 0.00 0.00 38.73 3.51
649 664 1.269958 GGAGGATTTGGCTTTGGCTT 58.730 50.000 0.00 0.00 38.73 4.35
650 665 0.615827 GGGAGGATTTGGCTTTGGCT 60.616 55.000 0.00 0.00 38.73 4.75
651 666 0.904394 TGGGAGGATTTGGCTTTGGC 60.904 55.000 0.00 0.00 37.82 4.52
652 667 1.276138 GTTGGGAGGATTTGGCTTTGG 59.724 52.381 0.00 0.00 0.00 3.28
653 668 1.969923 TGTTGGGAGGATTTGGCTTTG 59.030 47.619 0.00 0.00 0.00 2.77
777 792 4.357947 GCGTGGAGTGAGTGGCGA 62.358 66.667 0.00 0.00 0.00 5.54
822 1236 1.115467 ATGATCCAGACTCGGTGTCC 58.885 55.000 6.59 0.00 46.46 4.02
826 1240 1.573108 AACCATGATCCAGACTCGGT 58.427 50.000 0.00 0.00 0.00 4.69
845 1259 1.662876 GCGCGCTTTCATTTCTGACAA 60.663 47.619 26.67 0.00 0.00 3.18
846 1260 0.110238 GCGCGCTTTCATTTCTGACA 60.110 50.000 26.67 0.00 0.00 3.58
873 1287 1.221566 CATGGCACCATCGACCTCA 59.778 57.895 0.00 0.00 33.90 3.86
914 1328 2.038952 TGGATAATCTTGCAGATCCCGG 59.961 50.000 0.00 0.00 37.63 5.73
976 1390 0.175073 AACCTCGAGAACGGCATACC 59.825 55.000 15.71 0.00 40.21 2.73
989 1403 0.999406 CGGTGTGCAGATAAACCTCG 59.001 55.000 0.00 0.00 0.00 4.63
1026 1440 4.508124 GTGTGTCTTCAAGAACTCGATGTT 59.492 41.667 0.00 0.71 42.38 2.71
1065 1479 6.259167 CCCATCGTATTCTAGCTAGCTACTAG 59.741 46.154 20.67 13.25 38.79 2.57
1066 1480 6.114089 CCCATCGTATTCTAGCTAGCTACTA 58.886 44.000 20.67 11.44 0.00 1.82
1067 1481 4.944930 CCCATCGTATTCTAGCTAGCTACT 59.055 45.833 20.67 10.56 0.00 2.57
1068 1482 4.701171 ACCCATCGTATTCTAGCTAGCTAC 59.299 45.833 20.67 16.81 0.00 3.58
1069 1483 4.700692 CACCCATCGTATTCTAGCTAGCTA 59.299 45.833 22.85 22.85 0.00 3.32
1193 1607 3.834610 CGTACCTTTGAGATTCGACAGT 58.165 45.455 0.00 0.00 0.00 3.55
1205 1619 4.212004 CCTATGACATGATGCGTACCTTTG 59.788 45.833 0.00 0.00 0.00 2.77
1243 1657 0.679640 CCCATTGCTCAGGCGGTTTA 60.680 55.000 0.00 0.00 42.25 2.01
1244 1658 1.978617 CCCATTGCTCAGGCGGTTT 60.979 57.895 0.00 0.00 42.25 3.27
1263 1677 3.055719 CATGGCCGCCTCAACGTT 61.056 61.111 11.61 0.00 0.00 3.99
1315 1729 1.056660 AATCCACCTGAACCGAGTGT 58.943 50.000 0.00 0.00 0.00 3.55
1366 1780 2.029964 ACGTCGTTCCGGTTGCAT 59.970 55.556 0.00 0.00 0.00 3.96
1516 1930 1.001406 AGCTTCTTCCACGACTTCCTG 59.999 52.381 0.00 0.00 0.00 3.86
1739 2177 1.028330 ATGTCGACTGCATGGCAAGG 61.028 55.000 17.92 0.00 38.41 3.61
1745 2183 4.504097 TCGAAAATCTATGTCGACTGCATG 59.496 41.667 17.92 2.96 38.78 4.06
1749 2187 6.871044 TTTCTCGAAAATCTATGTCGACTG 57.129 37.500 17.92 7.25 38.78 3.51
1754 2192 8.029642 TGGAAGTTTTCTCGAAAATCTATGTC 57.970 34.615 7.95 3.64 41.64 3.06
1756 2194 9.495754 GATTGGAAGTTTTCTCGAAAATCTATG 57.504 33.333 7.95 0.00 41.64 2.23
1757 2195 9.454859 AGATTGGAAGTTTTCTCGAAAATCTAT 57.545 29.630 7.95 2.55 41.64 1.98
1758 2196 8.848474 AGATTGGAAGTTTTCTCGAAAATCTA 57.152 30.769 7.95 0.00 41.64 1.98
1759 2197 7.751768 AGATTGGAAGTTTTCTCGAAAATCT 57.248 32.000 7.95 3.12 41.64 2.40
1778 2217 8.843885 ACTACCATGACATGATGAATAGATTG 57.156 34.615 17.24 0.00 0.00 2.67
1867 2308 4.501714 GTGGATACCGACCGCGCA 62.502 66.667 8.75 0.00 35.83 6.09
2227 6659 1.972660 ATTAGAGCTGCGGGGTGGAC 61.973 60.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.