Multiple sequence alignment - TraesCS5D01G253100

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 TraesCS5D01G253100 chr5D 100.000 2891 0 0 1 2891 359473816 359476706 0.000000e+00 5339.0
1 TraesCS5D01G253100 chr5D 100.000 28 0 0 388 415 353475660 353475633 5.000000e-03 52.8
2 TraesCS5D01G253100 chr5B 94.388 2477 82 22 452 2891 425093060 425095516 0.000000e+00 3751.0
3 TraesCS5D01G253100 chr5B 89.965 289 11 5 13 286 425092769 425093054 9.850000e-95 357.0
4 TraesCS5D01G253100 chr5A 91.436 2534 86 53 443 2886 459776906 459774414 0.000000e+00 3356.0
5 TraesCS5D01G253100 chr5A 88.559 236 22 4 3 234 459777171 459776937 6.100000e-72 281.0
6 TraesCS5D01G253100 chr6B 81.250 208 28 9 1661 1861 539195275 539195072 1.070000e-34 158.0
7 TraesCS5D01G253100 chr6D 82.065 184 24 7 1683 1861 357592095 357591916 6.450000e-32 148.0
8 TraesCS5D01G253100 chr6A 81.579 190 26 7 1677 1861 499955472 499955657 6.450000e-32 148.0
9 TraesCS5D01G253100 chr7D 96.875 64 1 1 381 443 30266637 30266700 3.940000e-19 106.0
10 TraesCS5D01G253100 chr7D 91.071 56 3 2 388 441 538491889 538491944 1.110000e-09 75.0
11 TraesCS5D01G253100 chr4B 96.552 58 2 0 386 443 42132353 42132410 2.370000e-16 97.1
12 TraesCS5D01G253100 chr7A 96.429 56 1 1 388 442 64316641 64316586 1.100000e-14 91.6
13 TraesCS5D01G253100 chr1D 86.842 76 10 0 293 368 10985620 10985695 5.130000e-13 86.1
14 TraesCS5D01G253100 chr1B 78.788 132 22 4 1733 1861 185184929 185184801 1.850000e-12 84.2
15 TraesCS5D01G253100 chr2D 80.508 118 14 6 1760 1874 578306522 578306633 6.640000e-12 82.4
16 TraesCS5D01G253100 chr2D 91.379 58 3 2 388 443 634903981 634904038 8.590000e-11 78.7
17 TraesCS5D01G253100 chr3B 86.207 58 5 3 388 442 454518016 454517959 3.110000e-05 60.2


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 TraesCS5D01G253100 chr5D 359473816 359476706 2890 False 5339.0 5339 100.0000 1 2891 1 chr5D.!!$F1 2890
1 TraesCS5D01G253100 chr5B 425092769 425095516 2747 False 2054.0 3751 92.1765 13 2891 2 chr5B.!!$F1 2878
2 TraesCS5D01G253100 chr5A 459774414 459777171 2757 True 1818.5 3356 89.9975 3 2886 2 chr5A.!!$R1 2883

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
299 318 0.029834 CTGCTGGAACACTTGCACAC 59.97 55.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 2022 0.251519 CTGGCCCAGGAGCTCTTTTT 60.252 55.0 14.64 0.0 0.0 1.94 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
168 172 0.620556 TCTGGGGAAAGGCTAGCTTG 59.379 55.000 15.72 0.00 0.00 4.01
210 214 1.671845 CGACCCGGAAAACAGTTTTGA 59.328 47.619 16.21 0.00 31.94 2.69
216 220 4.261447 CCCGGAAAACAGTTTTGAGTTAGG 60.261 45.833 16.21 9.16 31.94 2.69
218 222 4.617959 GGAAAACAGTTTTGAGTTAGGGC 58.382 43.478 16.21 0.00 31.94 5.19
228 232 8.711457 CAGTTTTGAGTTAGGGCAAATAAATTG 58.289 33.333 0.00 0.00 42.21 2.32
241 245 6.859715 CAAATAAATTGCTCGAGAGGTTTG 57.140 37.500 18.75 11.90 31.00 2.93
243 247 1.168714 AATTGCTCGAGAGGTTTGGC 58.831 50.000 18.75 0.00 0.00 4.52
282 301 5.579511 GCCTTCATGAATTTCATTTCACCTG 59.420 40.000 8.96 0.00 38.37 4.00
283 302 5.579511 CCTTCATGAATTTCATTTCACCTGC 59.420 40.000 8.96 0.00 38.37 4.85
284 303 5.988310 TCATGAATTTCATTTCACCTGCT 57.012 34.783 9.19 0.00 38.37 4.24
285 304 5.716094 TCATGAATTTCATTTCACCTGCTG 58.284 37.500 9.19 0.00 38.37 4.41
286 305 4.524316 TGAATTTCATTTCACCTGCTGG 57.476 40.909 8.29 8.29 39.83 4.85
287 306 4.151121 TGAATTTCATTTCACCTGCTGGA 58.849 39.130 17.64 0.00 37.04 3.86
288 307 4.588106 TGAATTTCATTTCACCTGCTGGAA 59.412 37.500 17.64 0.26 37.04 3.53
289 308 4.525912 ATTTCATTTCACCTGCTGGAAC 57.474 40.909 17.64 0.00 37.04 3.62
290 309 2.655090 TCATTTCACCTGCTGGAACA 57.345 45.000 17.64 0.00 37.04 3.18
291 310 2.229792 TCATTTCACCTGCTGGAACAC 58.770 47.619 17.64 0.00 37.04 3.32
292 311 2.158623 TCATTTCACCTGCTGGAACACT 60.159 45.455 17.64 0.00 37.04 3.55
293 312 2.435372 TTTCACCTGCTGGAACACTT 57.565 45.000 17.64 0.00 37.04 3.16
294 313 1.679139 TTCACCTGCTGGAACACTTG 58.321 50.000 17.64 2.93 37.04 3.16
295 314 0.819259 TCACCTGCTGGAACACTTGC 60.819 55.000 17.64 0.00 37.04 4.01
296 315 1.102809 CACCTGCTGGAACACTTGCA 61.103 55.000 17.64 0.00 37.04 4.08
297 316 1.103398 ACCTGCTGGAACACTTGCAC 61.103 55.000 17.64 0.00 37.04 4.57
298 317 1.102809 CCTGCTGGAACACTTGCACA 61.103 55.000 2.92 0.00 34.57 4.57
299 318 0.029834 CTGCTGGAACACTTGCACAC 59.970 55.000 0.00 0.00 0.00 3.82
300 319 1.360192 GCTGGAACACTTGCACACC 59.640 57.895 0.00 0.00 0.00 4.16
301 320 2.032981 CTGGAACACTTGCACACCC 58.967 57.895 0.00 0.00 0.00 4.61
302 321 1.454847 TGGAACACTTGCACACCCC 60.455 57.895 0.00 0.00 0.00 4.95
303 322 2.200337 GGAACACTTGCACACCCCC 61.200 63.158 0.00 0.00 0.00 5.40
319 338 4.653888 CCCCGCCCGTCTTTTGGT 62.654 66.667 0.00 0.00 0.00 3.67
320 339 2.596338 CCCGCCCGTCTTTTGGTT 60.596 61.111 0.00 0.00 0.00 3.67
321 340 2.197605 CCCGCCCGTCTTTTGGTTT 61.198 57.895 0.00 0.00 0.00 3.27
322 341 0.890090 CCCGCCCGTCTTTTGGTTTA 60.890 55.000 0.00 0.00 0.00 2.01
323 342 1.170442 CCGCCCGTCTTTTGGTTTAT 58.830 50.000 0.00 0.00 0.00 1.40
324 343 1.542472 CCGCCCGTCTTTTGGTTTATT 59.458 47.619 0.00 0.00 0.00 1.40
325 344 2.029739 CCGCCCGTCTTTTGGTTTATTT 60.030 45.455 0.00 0.00 0.00 1.40
326 345 3.553302 CCGCCCGTCTTTTGGTTTATTTT 60.553 43.478 0.00 0.00 0.00 1.82
327 346 3.671459 CGCCCGTCTTTTGGTTTATTTTC 59.329 43.478 0.00 0.00 0.00 2.29
328 347 4.623002 GCCCGTCTTTTGGTTTATTTTCA 58.377 39.130 0.00 0.00 0.00 2.69
329 348 4.684242 GCCCGTCTTTTGGTTTATTTTCAG 59.316 41.667 0.00 0.00 0.00 3.02
330 349 5.737922 GCCCGTCTTTTGGTTTATTTTCAGT 60.738 40.000 0.00 0.00 0.00 3.41
331 350 5.918576 CCCGTCTTTTGGTTTATTTTCAGTC 59.081 40.000 0.00 0.00 0.00 3.51
332 351 5.623673 CCGTCTTTTGGTTTATTTTCAGTCG 59.376 40.000 0.00 0.00 0.00 4.18
333 352 5.623673 CGTCTTTTGGTTTATTTTCAGTCGG 59.376 40.000 0.00 0.00 0.00 4.79
334 353 6.500910 GTCTTTTGGTTTATTTTCAGTCGGT 58.499 36.000 0.00 0.00 0.00 4.69
335 354 6.416750 GTCTTTTGGTTTATTTTCAGTCGGTG 59.583 38.462 0.00 0.00 0.00 4.94
336 355 5.838531 TTTGGTTTATTTTCAGTCGGTGT 57.161 34.783 0.00 0.00 0.00 4.16
337 356 5.427036 TTGGTTTATTTTCAGTCGGTGTC 57.573 39.130 0.00 0.00 0.00 3.67
338 357 3.816523 TGGTTTATTTTCAGTCGGTGTCC 59.183 43.478 0.00 0.00 0.00 4.02
339 358 4.070009 GGTTTATTTTCAGTCGGTGTCCT 58.930 43.478 0.00 0.00 0.00 3.85
340 359 4.083484 GGTTTATTTTCAGTCGGTGTCCTG 60.083 45.833 0.00 0.00 0.00 3.86
341 360 2.930826 ATTTTCAGTCGGTGTCCTGT 57.069 45.000 0.00 0.00 0.00 4.00
342 361 5.471556 TTATTTTCAGTCGGTGTCCTGTA 57.528 39.130 0.00 0.00 0.00 2.74
343 362 3.380479 TTTTCAGTCGGTGTCCTGTAG 57.620 47.619 0.00 0.00 0.00 2.74
344 363 0.601558 TTCAGTCGGTGTCCTGTAGC 59.398 55.000 0.00 0.00 0.00 3.58
345 364 0.251209 TCAGTCGGTGTCCTGTAGCT 60.251 55.000 0.00 0.00 0.00 3.32
346 365 0.171455 CAGTCGGTGTCCTGTAGCTC 59.829 60.000 0.00 0.00 0.00 4.09
347 366 0.251209 AGTCGGTGTCCTGTAGCTCA 60.251 55.000 0.00 0.00 0.00 4.26
348 367 0.601558 GTCGGTGTCCTGTAGCTCAA 59.398 55.000 0.00 0.00 0.00 3.02
349 368 0.888619 TCGGTGTCCTGTAGCTCAAG 59.111 55.000 0.00 0.00 0.00 3.02
350 369 0.888619 CGGTGTCCTGTAGCTCAAGA 59.111 55.000 0.00 0.00 0.00 3.02
351 370 1.272490 CGGTGTCCTGTAGCTCAAGAA 59.728 52.381 0.00 0.00 0.00 2.52
352 371 2.689646 GGTGTCCTGTAGCTCAAGAAC 58.310 52.381 0.00 0.00 0.00 3.01
353 372 2.329379 GTGTCCTGTAGCTCAAGAACG 58.671 52.381 0.00 0.00 0.00 3.95
354 373 1.961394 TGTCCTGTAGCTCAAGAACGT 59.039 47.619 0.00 0.00 0.00 3.99
355 374 2.288213 TGTCCTGTAGCTCAAGAACGTG 60.288 50.000 0.00 0.00 0.00 4.49
356 375 1.961394 TCCTGTAGCTCAAGAACGTGT 59.039 47.619 0.00 0.00 0.00 4.49
357 376 2.364324 TCCTGTAGCTCAAGAACGTGTT 59.636 45.455 0.00 0.00 0.00 3.32
358 377 2.476619 CCTGTAGCTCAAGAACGTGTTG 59.523 50.000 0.00 4.83 0.00 3.33
359 378 2.476619 CTGTAGCTCAAGAACGTGTTGG 59.523 50.000 10.21 3.96 0.00 3.77
360 379 2.159014 TGTAGCTCAAGAACGTGTTGGT 60.159 45.455 10.21 0.78 0.00 3.67
361 380 2.038387 AGCTCAAGAACGTGTTGGTT 57.962 45.000 10.21 0.00 0.00 3.67
362 381 2.365582 AGCTCAAGAACGTGTTGGTTT 58.634 42.857 10.21 0.00 0.00 3.27
363 382 2.752903 AGCTCAAGAACGTGTTGGTTTT 59.247 40.909 10.21 0.00 0.00 2.43
364 383 3.105937 GCTCAAGAACGTGTTGGTTTTC 58.894 45.455 10.21 0.00 0.00 2.29
365 384 3.350912 CTCAAGAACGTGTTGGTTTTCG 58.649 45.455 10.21 0.00 0.00 3.46
366 385 2.743126 TCAAGAACGTGTTGGTTTTCGT 59.257 40.909 10.21 0.00 38.15 3.85
367 386 3.188873 TCAAGAACGTGTTGGTTTTCGTT 59.811 39.130 10.21 0.00 46.51 3.85
368 387 3.835378 AGAACGTGTTGGTTTTCGTTT 57.165 38.095 0.00 0.00 44.47 3.60
369 388 4.163458 AGAACGTGTTGGTTTTCGTTTT 57.837 36.364 0.00 0.00 44.47 2.43
370 389 4.548494 AGAACGTGTTGGTTTTCGTTTTT 58.452 34.783 0.00 0.00 44.47 1.94
395 414 4.886247 TTGTAGGAAGTGTTGGTTTTCG 57.114 40.909 0.00 0.00 0.00 3.46
396 415 3.876341 TGTAGGAAGTGTTGGTTTTCGT 58.124 40.909 0.00 0.00 0.00 3.85
397 416 4.263435 TGTAGGAAGTGTTGGTTTTCGTT 58.737 39.130 0.00 0.00 0.00 3.85
398 417 5.426504 TGTAGGAAGTGTTGGTTTTCGTTA 58.573 37.500 0.00 0.00 0.00 3.18
399 418 5.879223 TGTAGGAAGTGTTGGTTTTCGTTAA 59.121 36.000 0.00 0.00 0.00 2.01
400 419 6.543100 TGTAGGAAGTGTTGGTTTTCGTTAAT 59.457 34.615 0.00 0.00 0.00 1.40
401 420 5.827666 AGGAAGTGTTGGTTTTCGTTAATG 58.172 37.500 0.00 0.00 0.00 1.90
402 421 5.591067 AGGAAGTGTTGGTTTTCGTTAATGA 59.409 36.000 0.00 0.00 0.00 2.57
403 422 6.095720 AGGAAGTGTTGGTTTTCGTTAATGAA 59.904 34.615 6.00 6.00 0.00 2.57
404 423 6.752815 GGAAGTGTTGGTTTTCGTTAATGAAA 59.247 34.615 17.06 17.06 36.12 2.69
405 424 7.275999 GGAAGTGTTGGTTTTCGTTAATGAAAA 59.724 33.333 24.96 24.96 43.52 2.29
406 425 8.710835 AAGTGTTGGTTTTCGTTAATGAAAAT 57.289 26.923 29.08 14.78 46.22 1.82
407 426 8.347729 AGTGTTGGTTTTCGTTAATGAAAATC 57.652 30.769 29.08 28.56 46.22 2.17
408 427 7.166804 AGTGTTGGTTTTCGTTAATGAAAATCG 59.833 33.333 29.08 6.04 46.90 3.34
409 428 6.418226 TGTTGGTTTTCGTTAATGAAAATCGG 59.582 34.615 29.08 0.00 46.90 4.18
410 429 6.315091 TGGTTTTCGTTAATGAAAATCGGA 57.685 33.333 29.08 16.49 46.90 4.55
411 430 6.375377 TGGTTTTCGTTAATGAAAATCGGAG 58.625 36.000 29.08 0.00 46.90 4.63
412 431 5.798434 GGTTTTCGTTAATGAAAATCGGAGG 59.202 40.000 29.08 0.00 46.22 4.30
413 432 5.554822 TTTCGTTAATGAAAATCGGAGGG 57.445 39.130 18.37 0.00 35.04 4.30
414 433 3.537580 TCGTTAATGAAAATCGGAGGGG 58.462 45.455 0.00 0.00 0.00 4.79
415 434 3.054948 TCGTTAATGAAAATCGGAGGGGT 60.055 43.478 0.00 0.00 0.00 4.95
416 435 3.064820 CGTTAATGAAAATCGGAGGGGTG 59.935 47.826 0.00 0.00 0.00 4.61
417 436 1.474330 AATGAAAATCGGAGGGGTGC 58.526 50.000 0.00 0.00 0.00 5.01
418 437 0.748005 ATGAAAATCGGAGGGGTGCG 60.748 55.000 0.00 0.00 0.00 5.34
419 438 1.078708 GAAAATCGGAGGGGTGCGA 60.079 57.895 0.00 0.00 0.00 5.10
420 439 1.078426 AAAATCGGAGGGGTGCGAG 60.078 57.895 0.00 0.00 0.00 5.03
421 440 3.682292 AAATCGGAGGGGTGCGAGC 62.682 63.158 0.00 0.00 0.00 5.03
429 448 2.034221 GGGTGCGAGCCCTTCTTT 59.966 61.111 7.39 0.00 45.22 2.52
430 449 1.603739 GGGTGCGAGCCCTTCTTTT 60.604 57.895 7.39 0.00 45.22 2.27
431 450 0.322187 GGGTGCGAGCCCTTCTTTTA 60.322 55.000 7.39 0.00 45.22 1.52
432 451 1.682087 GGGTGCGAGCCCTTCTTTTAT 60.682 52.381 7.39 0.00 45.22 1.40
433 452 2.092323 GGTGCGAGCCCTTCTTTTATT 58.908 47.619 0.00 0.00 0.00 1.40
434 453 3.275999 GGTGCGAGCCCTTCTTTTATTA 58.724 45.455 0.00 0.00 0.00 0.98
435 454 3.692593 GGTGCGAGCCCTTCTTTTATTAA 59.307 43.478 0.00 0.00 0.00 1.40
436 455 4.157105 GGTGCGAGCCCTTCTTTTATTAAA 59.843 41.667 0.00 0.00 0.00 1.52
437 456 5.336134 GGTGCGAGCCCTTCTTTTATTAAAA 60.336 40.000 1.85 1.85 0.00 1.52
438 457 6.153756 GTGCGAGCCCTTCTTTTATTAAAAA 58.846 36.000 3.37 0.00 33.58 1.94
462 485 1.490490 ACCTGCTGGAACACAAGAAGA 59.510 47.619 17.64 0.00 37.04 2.87
466 489 1.884067 GCTGGAACACAAGAAGAGGGG 60.884 57.143 0.00 0.00 0.00 4.79
469 492 1.608283 GGAACACAAGAAGAGGGGTCG 60.608 57.143 0.00 0.00 0.00 4.79
486 513 1.263217 GTCGTGTGTTGACCATGTTCC 59.737 52.381 0.00 0.00 0.00 3.62
502 529 4.126208 TGTTCCAGACACGAGTAACAAA 57.874 40.909 0.00 0.00 32.00 2.83
504 531 4.569162 TGTTCCAGACACGAGTAACAAAAG 59.431 41.667 0.00 0.00 32.00 2.27
507 534 5.421277 TCCAGACACGAGTAACAAAAGAAA 58.579 37.500 0.00 0.00 0.00 2.52
650 690 1.967319 AAGAACACACATCACGCCTT 58.033 45.000 0.00 0.00 0.00 4.35
912 964 3.056821 CCCAGTTTTAACCCTTGCTAAGC 60.057 47.826 0.00 0.00 0.00 3.09
943 1007 3.319198 GGCCTCCCCTCGACAACA 61.319 66.667 0.00 0.00 0.00 3.33
944 1008 2.047179 GCCTCCCCTCGACAACAC 60.047 66.667 0.00 0.00 0.00 3.32
945 1009 2.261671 CCTCCCCTCGACAACACG 59.738 66.667 0.00 0.00 0.00 4.49
946 1010 2.432628 CTCCCCTCGACAACACGC 60.433 66.667 0.00 0.00 0.00 5.34
947 1011 3.934391 CTCCCCTCGACAACACGCC 62.934 68.421 0.00 0.00 0.00 5.68
952 1016 4.893601 TCGACAACACGCCGGCAA 62.894 61.111 28.98 0.00 0.00 4.52
953 1017 3.943034 CGACAACACGCCGGCAAA 61.943 61.111 28.98 0.00 0.00 3.68
954 1018 2.353030 GACAACACGCCGGCAAAC 60.353 61.111 28.98 6.13 0.00 2.93
955 1019 3.817274 GACAACACGCCGGCAAACC 62.817 63.158 28.98 4.24 0.00 3.27
956 1020 4.639171 CAACACGCCGGCAAACCC 62.639 66.667 28.98 0.00 0.00 4.11
1644 1717 4.536316 CTGAGCAGCATGTCCCTC 57.464 61.111 0.00 0.00 39.31 4.30
1892 1965 4.133796 GCCGCCCAGCATTTGACC 62.134 66.667 0.00 0.00 0.00 4.02
1894 1967 3.814268 CGCCCAGCATTTGACCGG 61.814 66.667 0.00 0.00 0.00 5.28
1896 1969 3.814268 CCCAGCATTTGACCGGCG 61.814 66.667 0.00 0.00 0.00 6.46
1916 2013 2.359850 GCATGCAACCGGAGACCA 60.360 61.111 14.21 0.00 0.00 4.02
1918 2015 2.040544 CATGCAACCGGAGACCACC 61.041 63.158 9.46 0.00 0.00 4.61
1919 2016 3.268103 ATGCAACCGGAGACCACCC 62.268 63.158 9.46 0.00 0.00 4.61
1921 2018 3.246112 CAACCGGAGACCACCCCA 61.246 66.667 9.46 0.00 0.00 4.96
1922 2019 2.448931 AACCGGAGACCACCCCAA 60.449 61.111 9.46 0.00 0.00 4.12
1924 2021 2.606519 CCGGAGACCACCCCAAGA 60.607 66.667 0.00 0.00 0.00 3.02
1925 2022 2.221299 CCGGAGACCACCCCAAGAA 61.221 63.158 0.00 0.00 0.00 2.52
1926 2023 1.758592 CGGAGACCACCCCAAGAAA 59.241 57.895 0.00 0.00 0.00 2.52
1927 2024 0.109723 CGGAGACCACCCCAAGAAAA 59.890 55.000 0.00 0.00 0.00 2.29
1928 2025 1.477923 CGGAGACCACCCCAAGAAAAA 60.478 52.381 0.00 0.00 0.00 1.94
2279 2384 1.780025 GCTAGCTGGCGAGGAATTGC 61.780 60.000 6.22 0.00 0.00 3.56
2323 2428 4.256090 GCCATGGATTCCGTGCGC 62.256 66.667 18.40 17.56 39.07 6.09
2324 2429 2.514592 CCATGGATTCCGTGCGCT 60.515 61.111 18.02 0.00 39.07 5.92
2330 2435 1.590259 GATTCCGTGCGCTCTCCTC 60.590 63.158 9.73 0.00 0.00 3.71
2331 2436 3.417275 ATTCCGTGCGCTCTCCTCG 62.417 63.158 9.73 3.96 0.00 4.63
2333 2438 4.544689 CCGTGCGCTCTCCTCGAG 62.545 72.222 9.73 5.13 42.88 4.04
2500 2620 4.789012 TCTTTGCTTAGCCATTTTCCTG 57.211 40.909 0.29 0.00 0.00 3.86
2504 2627 0.740737 CTTAGCCATTTTCCTGCCCG 59.259 55.000 0.00 0.00 0.00 6.13
2712 2849 3.181397 CATGAATCAATGCAACCGTTCC 58.819 45.455 0.00 0.00 0.00 3.62
2718 2855 3.545124 ATGCAACCGTTCCCTCGCA 62.545 57.895 0.00 0.00 0.00 5.10
2742 2879 1.455032 CCCCCGCATTTAACTCCCC 60.455 63.158 0.00 0.00 0.00 4.81
2744 2881 1.304952 CCCGCATTTAACTCCCCCA 59.695 57.895 0.00 0.00 0.00 4.96
2769 2915 2.159627 CGCGAGCAATGTTAAGGTTCTT 59.840 45.455 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.427098 CGACCATGTAGTGTAGCGAAGAA 60.427 47.826 0.00 0.00 0.00 2.52
1 2 2.096980 CGACCATGTAGTGTAGCGAAGA 59.903 50.000 0.00 0.00 0.00 2.87
69 73 0.239879 ACGCAAGCATACAAAACCCG 59.760 50.000 0.00 0.00 45.62 5.28
168 172 1.063166 GATGCAAGCAACGCTAGCC 59.937 57.895 9.66 0.00 38.25 3.93
218 222 5.801947 CCAAACCTCTCGAGCAATTTATTTG 59.198 40.000 7.81 10.45 38.43 2.32
228 232 1.078143 ATGGCCAAACCTCTCGAGC 60.078 57.895 10.96 0.00 40.22 5.03
229 233 0.539051 AGATGGCCAAACCTCTCGAG 59.461 55.000 10.96 5.93 40.22 4.04
230 234 1.757118 CTAGATGGCCAAACCTCTCGA 59.243 52.381 10.96 0.00 40.22 4.04
231 235 1.808133 GCTAGATGGCCAAACCTCTCG 60.808 57.143 10.96 5.29 40.22 4.04
232 236 1.808133 CGCTAGATGGCCAAACCTCTC 60.808 57.143 10.96 0.30 40.22 3.20
233 237 0.179000 CGCTAGATGGCCAAACCTCT 59.821 55.000 10.96 11.15 40.22 3.69
234 238 0.815615 CCGCTAGATGGCCAAACCTC 60.816 60.000 10.96 1.72 40.22 3.85
235 239 1.224592 CCGCTAGATGGCCAAACCT 59.775 57.895 10.96 10.36 40.22 3.50
243 247 2.670934 GGCCATGCCGCTAGATGG 60.671 66.667 0.00 4.22 39.62 3.51
282 301 1.360192 GGTGTGCAAGTGTTCCAGC 59.640 57.895 0.00 0.00 0.00 4.85
283 302 1.455383 GGGGTGTGCAAGTGTTCCAG 61.455 60.000 0.00 0.00 0.00 3.86
284 303 1.454847 GGGGTGTGCAAGTGTTCCA 60.455 57.895 0.00 0.00 0.00 3.53
285 304 2.200337 GGGGGTGTGCAAGTGTTCC 61.200 63.158 0.00 0.00 0.00 3.62
286 305 3.443588 GGGGGTGTGCAAGTGTTC 58.556 61.111 0.00 0.00 0.00 3.18
302 321 4.653888 ACCAAAAGACGGGCGGGG 62.654 66.667 0.00 0.00 0.00 5.73
303 322 0.890090 TAAACCAAAAGACGGGCGGG 60.890 55.000 0.00 0.00 0.00 6.13
304 323 1.170442 ATAAACCAAAAGACGGGCGG 58.830 50.000 0.00 0.00 0.00 6.13
305 324 3.291809 AAATAAACCAAAAGACGGGCG 57.708 42.857 0.00 0.00 0.00 6.13
306 325 4.623002 TGAAAATAAACCAAAAGACGGGC 58.377 39.130 0.00 0.00 0.00 6.13
307 326 5.838529 ACTGAAAATAAACCAAAAGACGGG 58.161 37.500 0.00 0.00 0.00 5.28
308 327 5.623673 CGACTGAAAATAAACCAAAAGACGG 59.376 40.000 0.00 0.00 0.00 4.79
309 328 5.623673 CCGACTGAAAATAAACCAAAAGACG 59.376 40.000 0.00 0.00 0.00 4.18
310 329 6.416750 CACCGACTGAAAATAAACCAAAAGAC 59.583 38.462 0.00 0.00 0.00 3.01
311 330 6.095720 ACACCGACTGAAAATAAACCAAAAGA 59.904 34.615 0.00 0.00 0.00 2.52
312 331 6.270064 ACACCGACTGAAAATAAACCAAAAG 58.730 36.000 0.00 0.00 0.00 2.27
313 332 6.210287 ACACCGACTGAAAATAAACCAAAA 57.790 33.333 0.00 0.00 0.00 2.44
314 333 5.221087 GGACACCGACTGAAAATAAACCAAA 60.221 40.000 0.00 0.00 0.00 3.28
315 334 4.276431 GGACACCGACTGAAAATAAACCAA 59.724 41.667 0.00 0.00 0.00 3.67
316 335 3.816523 GGACACCGACTGAAAATAAACCA 59.183 43.478 0.00 0.00 0.00 3.67
317 336 4.070009 AGGACACCGACTGAAAATAAACC 58.930 43.478 0.00 0.00 0.00 3.27
318 337 4.514066 ACAGGACACCGACTGAAAATAAAC 59.486 41.667 0.00 0.00 38.09 2.01
319 338 4.710324 ACAGGACACCGACTGAAAATAAA 58.290 39.130 0.00 0.00 38.09 1.40
320 339 4.345859 ACAGGACACCGACTGAAAATAA 57.654 40.909 0.00 0.00 38.09 1.40
321 340 4.619863 GCTACAGGACACCGACTGAAAATA 60.620 45.833 0.00 0.00 38.09 1.40
322 341 2.930826 ACAGGACACCGACTGAAAAT 57.069 45.000 0.00 0.00 38.09 1.82
323 342 2.547218 GCTACAGGACACCGACTGAAAA 60.547 50.000 0.00 0.00 38.09 2.29
324 343 1.000506 GCTACAGGACACCGACTGAAA 59.999 52.381 0.00 0.00 38.09 2.69
325 344 0.601558 GCTACAGGACACCGACTGAA 59.398 55.000 0.00 0.00 38.09 3.02
326 345 0.251209 AGCTACAGGACACCGACTGA 60.251 55.000 0.00 0.00 38.09 3.41
327 346 0.171455 GAGCTACAGGACACCGACTG 59.829 60.000 0.00 0.00 40.48 3.51
328 347 0.251209 TGAGCTACAGGACACCGACT 60.251 55.000 0.00 0.00 0.00 4.18
329 348 0.601558 TTGAGCTACAGGACACCGAC 59.398 55.000 0.00 0.00 0.00 4.79
330 349 0.888619 CTTGAGCTACAGGACACCGA 59.111 55.000 0.00 0.00 0.00 4.69
331 350 0.888619 TCTTGAGCTACAGGACACCG 59.111 55.000 0.00 0.00 29.70 4.94
332 351 2.689646 GTTCTTGAGCTACAGGACACC 58.310 52.381 0.00 0.00 34.40 4.16
333 352 2.288273 ACGTTCTTGAGCTACAGGACAC 60.288 50.000 4.33 3.70 34.40 3.67
334 353 1.961394 ACGTTCTTGAGCTACAGGACA 59.039 47.619 4.33 0.00 34.40 4.02
335 354 2.288273 ACACGTTCTTGAGCTACAGGAC 60.288 50.000 0.00 0.00 34.40 3.85
336 355 1.961394 ACACGTTCTTGAGCTACAGGA 59.039 47.619 0.00 0.00 32.83 3.86
337 356 2.440539 ACACGTTCTTGAGCTACAGG 57.559 50.000 0.00 0.00 0.00 4.00
338 357 2.476619 CCAACACGTTCTTGAGCTACAG 59.523 50.000 4.58 0.00 0.00 2.74
339 358 2.159014 ACCAACACGTTCTTGAGCTACA 60.159 45.455 4.58 0.00 0.00 2.74
340 359 2.480845 ACCAACACGTTCTTGAGCTAC 58.519 47.619 4.58 0.00 0.00 3.58
341 360 2.902705 ACCAACACGTTCTTGAGCTA 57.097 45.000 4.58 0.00 0.00 3.32
342 361 2.038387 AACCAACACGTTCTTGAGCT 57.962 45.000 4.58 0.00 0.00 4.09
343 362 2.844122 AAACCAACACGTTCTTGAGC 57.156 45.000 4.58 0.00 0.00 4.26
344 363 3.181514 ACGAAAACCAACACGTTCTTGAG 60.182 43.478 4.58 0.00 35.47 3.02
345 364 2.743126 ACGAAAACCAACACGTTCTTGA 59.257 40.909 4.58 0.00 35.47 3.02
346 365 3.125698 ACGAAAACCAACACGTTCTTG 57.874 42.857 0.00 0.00 35.47 3.02
347 366 3.835378 AACGAAAACCAACACGTTCTT 57.165 38.095 0.00 0.00 43.66 2.52
348 367 3.835378 AAACGAAAACCAACACGTTCT 57.165 38.095 0.00 0.00 45.71 3.01
349 368 4.889519 AAAAACGAAAACCAACACGTTC 57.110 36.364 0.00 0.00 45.71 3.95
371 390 6.094061 CGAAAACCAACACTTCCTACAAAAA 58.906 36.000 0.00 0.00 0.00 1.94
372 391 5.183522 ACGAAAACCAACACTTCCTACAAAA 59.816 36.000 0.00 0.00 0.00 2.44
373 392 4.701171 ACGAAAACCAACACTTCCTACAAA 59.299 37.500 0.00 0.00 0.00 2.83
374 393 4.263435 ACGAAAACCAACACTTCCTACAA 58.737 39.130 0.00 0.00 0.00 2.41
375 394 3.876341 ACGAAAACCAACACTTCCTACA 58.124 40.909 0.00 0.00 0.00 2.74
376 395 4.888038 AACGAAAACCAACACTTCCTAC 57.112 40.909 0.00 0.00 0.00 3.18
377 396 6.766944 TCATTAACGAAAACCAACACTTCCTA 59.233 34.615 0.00 0.00 0.00 2.94
378 397 5.591067 TCATTAACGAAAACCAACACTTCCT 59.409 36.000 0.00 0.00 0.00 3.36
379 398 5.823353 TCATTAACGAAAACCAACACTTCC 58.177 37.500 0.00 0.00 0.00 3.46
380 399 7.743520 TTTCATTAACGAAAACCAACACTTC 57.256 32.000 0.00 0.00 32.05 3.01
381 400 8.710835 ATTTTCATTAACGAAAACCAACACTT 57.289 26.923 11.29 0.00 45.09 3.16
382 401 7.166804 CGATTTTCATTAACGAAAACCAACACT 59.833 33.333 11.29 0.00 45.09 3.55
383 402 7.270834 CGATTTTCATTAACGAAAACCAACAC 58.729 34.615 11.29 0.64 45.09 3.32
384 403 6.418226 CCGATTTTCATTAACGAAAACCAACA 59.582 34.615 11.29 0.00 45.09 3.33
385 404 6.637658 TCCGATTTTCATTAACGAAAACCAAC 59.362 34.615 11.29 4.08 45.09 3.77
386 405 6.736123 TCCGATTTTCATTAACGAAAACCAA 58.264 32.000 11.29 0.00 45.09 3.67
387 406 6.315091 TCCGATTTTCATTAACGAAAACCA 57.685 33.333 11.29 0.00 45.09 3.67
388 407 5.798434 CCTCCGATTTTCATTAACGAAAACC 59.202 40.000 11.29 1.36 45.09 3.27
389 408 5.798434 CCCTCCGATTTTCATTAACGAAAAC 59.202 40.000 11.29 5.68 45.09 2.43
390 409 5.106078 CCCCTCCGATTTTCATTAACGAAAA 60.106 40.000 11.44 11.44 46.02 2.29
391 410 4.396790 CCCCTCCGATTTTCATTAACGAAA 59.603 41.667 0.00 0.00 33.12 3.46
392 411 3.942748 CCCCTCCGATTTTCATTAACGAA 59.057 43.478 0.00 0.00 0.00 3.85
393 412 3.054948 ACCCCTCCGATTTTCATTAACGA 60.055 43.478 0.00 0.00 0.00 3.85
394 413 3.064820 CACCCCTCCGATTTTCATTAACG 59.935 47.826 0.00 0.00 0.00 3.18
395 414 3.181490 GCACCCCTCCGATTTTCATTAAC 60.181 47.826 0.00 0.00 0.00 2.01
396 415 3.020984 GCACCCCTCCGATTTTCATTAA 58.979 45.455 0.00 0.00 0.00 1.40
397 416 2.650322 GCACCCCTCCGATTTTCATTA 58.350 47.619 0.00 0.00 0.00 1.90
398 417 1.474330 GCACCCCTCCGATTTTCATT 58.526 50.000 0.00 0.00 0.00 2.57
399 418 0.748005 CGCACCCCTCCGATTTTCAT 60.748 55.000 0.00 0.00 0.00 2.57
400 419 1.376683 CGCACCCCTCCGATTTTCA 60.377 57.895 0.00 0.00 0.00 2.69
401 420 1.078708 TCGCACCCCTCCGATTTTC 60.079 57.895 0.00 0.00 0.00 2.29
402 421 1.078426 CTCGCACCCCTCCGATTTT 60.078 57.895 0.00 0.00 32.52 1.82
403 422 2.584608 CTCGCACCCCTCCGATTT 59.415 61.111 0.00 0.00 32.52 2.17
404 423 4.162690 GCTCGCACCCCTCCGATT 62.163 66.667 0.00 0.00 32.52 3.34
413 432 1.751437 ATAAAAGAAGGGCTCGCACC 58.249 50.000 0.00 0.00 0.00 5.01
414 433 4.957759 TTAATAAAAGAAGGGCTCGCAC 57.042 40.909 0.00 0.00 0.00 5.34
415 434 5.968528 TTTTAATAAAAGAAGGGCTCGCA 57.031 34.783 0.00 0.00 0.00 5.10
438 457 3.096092 TCTTGTGTTCCAGCAGGTTTTT 58.904 40.909 0.00 0.00 35.89 1.94
439 458 2.733956 TCTTGTGTTCCAGCAGGTTTT 58.266 42.857 0.00 0.00 35.89 2.43
440 459 2.435372 TCTTGTGTTCCAGCAGGTTT 57.565 45.000 0.00 0.00 35.89 3.27
441 460 2.092429 TCTTCTTGTGTTCCAGCAGGTT 60.092 45.455 0.00 0.00 35.89 3.50
442 461 1.490490 TCTTCTTGTGTTCCAGCAGGT 59.510 47.619 0.00 0.00 35.89 4.00
443 462 2.149578 CTCTTCTTGTGTTCCAGCAGG 58.850 52.381 0.00 0.00 0.00 4.85
444 463 2.149578 CCTCTTCTTGTGTTCCAGCAG 58.850 52.381 0.00 0.00 0.00 4.24
445 464 1.202806 CCCTCTTCTTGTGTTCCAGCA 60.203 52.381 0.00 0.00 0.00 4.41
446 465 1.528129 CCCTCTTCTTGTGTTCCAGC 58.472 55.000 0.00 0.00 0.00 4.85
462 485 2.826702 GGTCAACACACGACCCCT 59.173 61.111 0.00 0.00 46.12 4.79
466 489 1.263217 GGAACATGGTCAACACACGAC 59.737 52.381 13.90 0.00 0.00 4.34
469 492 2.290641 GTCTGGAACATGGTCAACACAC 59.709 50.000 13.90 0.00 38.20 3.82
486 513 7.305418 GCATTTTTCTTTTGTTACTCGTGTCTG 60.305 37.037 0.00 0.00 0.00 3.51
502 529 6.165700 ACATCTGGTCTTTGCATTTTTCTT 57.834 33.333 0.00 0.00 0.00 2.52
638 675 3.803082 CGGCCAAGGCGTGATGTG 61.803 66.667 2.24 0.00 46.33 3.21
650 690 4.248842 CTGTGTGTGTCCCGGCCA 62.249 66.667 2.24 0.00 0.00 5.36
750 798 1.216678 TCCCTCCCTAGCTTCTCTCTG 59.783 57.143 0.00 0.00 0.00 3.35
949 1013 2.677875 CCTCTGGGCTGGGTTTGC 60.678 66.667 0.00 0.00 0.00 3.68
1143 1207 3.825160 CTCACCACCACCACCACCG 62.825 68.421 0.00 0.00 0.00 4.94
1377 1447 2.291043 GGTGGGAGAGAAGGGCGAA 61.291 63.158 0.00 0.00 0.00 4.70
1925 2022 0.251519 CTGGCCCAGGAGCTCTTTTT 60.252 55.000 14.64 0.00 0.00 1.94
1926 2023 1.136329 TCTGGCCCAGGAGCTCTTTT 61.136 55.000 14.64 0.00 31.51 2.27
1927 2024 1.539869 TCTGGCCCAGGAGCTCTTT 60.540 57.895 14.64 0.00 31.51 2.52
1928 2025 1.994507 CTCTGGCCCAGGAGCTCTT 60.995 63.158 14.64 2.08 31.51 2.85
1929 2026 2.365370 CTCTGGCCCAGGAGCTCT 60.365 66.667 14.64 0.00 31.51 4.09
1930 2027 4.173924 GCTCTGGCCCAGGAGCTC 62.174 72.222 25.41 4.71 34.40 4.09
2065 2166 0.830648 TAAGCTAGCCATGAACCGCT 59.169 50.000 12.13 0.00 39.17 5.52
2071 2176 5.630415 AACCTAATGTAAGCTAGCCATGA 57.370 39.130 12.13 0.00 0.00 3.07
2173 2278 5.220739 GCTAGGAATTACATGAGCAACAGTG 60.221 44.000 0.00 0.00 0.00 3.66
2279 2384 2.851102 AGCCCCGATCCCCAGATG 60.851 66.667 0.00 0.00 30.90 2.90
2500 2620 2.032681 AAAGTGAGTGAGGCGGGC 59.967 61.111 0.00 0.00 0.00 6.13
2504 2627 0.610232 ATGCCCAAAGTGAGTGAGGC 60.610 55.000 0.00 0.00 40.87 4.70
2718 2855 0.755327 GTTAAATGCGGGGGCAGGAT 60.755 55.000 0.00 0.00 0.00 3.24
2742 2879 1.570813 TAACATTGCTCGCGAGATGG 58.429 50.000 38.74 24.51 40.84 3.51
2744 2881 2.205074 CCTTAACATTGCTCGCGAGAT 58.795 47.619 38.74 21.70 40.84 2.75
2769 2915 5.105146 GCAGAACTAATCAAGGAGGAGAAGA 60.105 44.000 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.