Multiple sequence alignment - TraesCS4A01G162600

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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 TraesCS4A01G162600 chr4A 100.000 2431 0 0 1 2431 358841615 358839185 0.000000e+00 4490
1 TraesCS4A01G162600 chr1A 94.436 2013 83 11 425 2431 311065488 311063499 0.000000e+00 3070
2 TraesCS4A01G162600 chr1A 87.205 508 37 12 424 930 235654387 235653907 9.820000e-154 553
3 TraesCS4A01G162600 chr1D 93.747 2015 103 10 421 2431 164438080 164440075 0.000000e+00 3001
4 TraesCS4A01G162600 chr1D 91.588 2021 141 11 425 2431 204020331 204018326 0.000000e+00 2763
5 TraesCS4A01G162600 chr2B 93.700 2016 98 18 425 2430 335503505 335501509 0.000000e+00 2992
6 TraesCS4A01G162600 chr6A 94.647 1943 81 10 494 2431 161373958 161372034 0.000000e+00 2990
7 TraesCS4A01G162600 chr5B 93.682 2010 105 16 425 2431 153181506 153179516 0.000000e+00 2988
8 TraesCS4A01G162600 chr2A 93.483 2010 111 8 429 2431 457930305 457928309 0.000000e+00 2968
9 TraesCS4A01G162600 chr6B 93.539 2012 98 18 425 2430 175724798 175722813 0.000000e+00 2966
10 TraesCS4A01G162600 chr4D 93.134 2010 121 6 425 2431 395951942 395953937 0.000000e+00 2931
11 TraesCS4A01G162600 chr4D 95.765 425 13 2 1 424 235516948 235517368 0.000000e+00 680
12 TraesCS4A01G162600 chr6D 93.030 2023 113 14 425 2431 237744155 237746165 0.000000e+00 2929
13 TraesCS4A01G162600 chr6D 92.717 508 24 4 424 931 194186382 194185888 0.000000e+00 721
14 TraesCS4A01G162600 chr2D 90.945 508 31 8 424 931 472776398 472775906 0.000000e+00 669
15 TraesCS4A01G162600 chr4B 98.106 264 5 0 1 264 249050806 249050543 6.120000e-126 460
16 TraesCS4A01G162600 chr4B 92.778 180 8 2 246 424 249050052 249049877 3.100000e-64 255


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 TraesCS4A01G162600 chr4A 358839185 358841615 2430 True 4490.0 4490 100.000 1 2431 1 chr4A.!!$R1 2430
1 TraesCS4A01G162600 chr1A 311063499 311065488 1989 True 3070.0 3070 94.436 425 2431 1 chr1A.!!$R2 2006
2 TraesCS4A01G162600 chr1D 164438080 164440075 1995 False 3001.0 3001 93.747 421 2431 1 chr1D.!!$F1 2010
3 TraesCS4A01G162600 chr1D 204018326 204020331 2005 True 2763.0 2763 91.588 425 2431 1 chr1D.!!$R1 2006
4 TraesCS4A01G162600 chr2B 335501509 335503505 1996 True 2992.0 2992 93.700 425 2430 1 chr2B.!!$R1 2005
5 TraesCS4A01G162600 chr6A 161372034 161373958 1924 True 2990.0 2990 94.647 494 2431 1 chr6A.!!$R1 1937
6 TraesCS4A01G162600 chr5B 153179516 153181506 1990 True 2988.0 2988 93.682 425 2431 1 chr5B.!!$R1 2006
7 TraesCS4A01G162600 chr2A 457928309 457930305 1996 True 2968.0 2968 93.483 429 2431 1 chr2A.!!$R1 2002
8 TraesCS4A01G162600 chr6B 175722813 175724798 1985 True 2966.0 2966 93.539 425 2430 1 chr6B.!!$R1 2005
9 TraesCS4A01G162600 chr4D 395951942 395953937 1995 False 2931.0 2931 93.134 425 2431 1 chr4D.!!$F2 2006
10 TraesCS4A01G162600 chr6D 237744155 237746165 2010 False 2929.0 2929 93.030 425 2431 1 chr6D.!!$F1 2006
11 TraesCS4A01G162600 chr4B 249049877 249050806 929 True 357.5 460 95.442 1 424 2 chr4B.!!$R1 423

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
339 340 0.523072 AATGCTGCAACGACACATCC 59.477 50.0 6.36 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2383 0.179009 ATCGCCTTCACCATCATGGG 60.179 55.0 9.04 0.0 43.37 4.0 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 8.443176 ACTCAATATGACATAATCCCTGACAAT 58.557 33.333 0.00 0.00 0.00 2.71
188 189 6.753279 TGACAATGAAAAGAGTTTTGCTCAAG 59.247 34.615 0.00 0.00 46.47 3.02
192 193 5.331902 TGAAAAGAGTTTTGCTCAAGAACG 58.668 37.500 0.00 0.00 46.47 3.95
272 273 7.548196 TTGTTAGGTAGTGCATATAAAGTGC 57.452 36.000 0.00 0.00 42.81 4.40
286 287 9.185192 GCATATAAAGTGCAATAGAAATTGGTC 57.815 33.333 0.00 0.00 42.39 4.02
287 288 9.385902 CATATAAAGTGCAATAGAAATTGGTCG 57.614 33.333 0.00 0.00 42.39 4.79
288 289 5.705609 AAAGTGCAATAGAAATTGGTCGT 57.294 34.783 0.00 0.00 42.39 4.34
289 290 4.946784 AGTGCAATAGAAATTGGTCGTC 57.053 40.909 0.00 0.00 42.39 4.20
290 291 4.323417 AGTGCAATAGAAATTGGTCGTCA 58.677 39.130 0.00 0.00 42.39 4.35
291 292 4.759693 AGTGCAATAGAAATTGGTCGTCAA 59.240 37.500 0.00 0.00 42.39 3.18
292 293 5.240623 AGTGCAATAGAAATTGGTCGTCAAA 59.759 36.000 0.00 0.00 42.39 2.69
293 294 5.918011 GTGCAATAGAAATTGGTCGTCAAAA 59.082 36.000 0.00 0.00 42.39 2.44
294 295 6.419413 GTGCAATAGAAATTGGTCGTCAAAAA 59.581 34.615 0.00 0.00 42.39 1.94
295 296 6.640499 TGCAATAGAAATTGGTCGTCAAAAAG 59.360 34.615 0.72 0.00 42.39 2.27
296 297 6.640907 GCAATAGAAATTGGTCGTCAAAAAGT 59.359 34.615 0.72 0.00 42.39 2.66
297 298 7.148967 GCAATAGAAATTGGTCGTCAAAAAGTC 60.149 37.037 0.72 0.00 42.39 3.01
298 299 5.828299 AGAAATTGGTCGTCAAAAAGTCA 57.172 34.783 0.00 0.00 39.05 3.41
299 300 6.391227 AGAAATTGGTCGTCAAAAAGTCAT 57.609 33.333 0.00 0.00 39.05 3.06
300 301 6.208644 AGAAATTGGTCGTCAAAAAGTCATG 58.791 36.000 0.00 0.00 39.05 3.07
301 302 5.514274 AATTGGTCGTCAAAAAGTCATGT 57.486 34.783 0.00 0.00 39.05 3.21
302 303 4.974368 TTGGTCGTCAAAAAGTCATGTT 57.026 36.364 0.00 0.00 31.46 2.71
303 304 4.974368 TGGTCGTCAAAAAGTCATGTTT 57.026 36.364 0.00 0.00 0.00 2.83
304 305 5.317733 TGGTCGTCAAAAAGTCATGTTTT 57.682 34.783 0.00 0.00 0.00 2.43
305 306 5.098893 TGGTCGTCAAAAAGTCATGTTTTG 58.901 37.500 11.77 11.77 43.99 2.44
306 307 5.099575 GGTCGTCAAAAAGTCATGTTTTGT 58.900 37.500 15.60 2.36 43.40 2.83
307 308 6.127980 TGGTCGTCAAAAAGTCATGTTTTGTA 60.128 34.615 15.60 4.85 43.40 2.41
308 309 6.915843 GGTCGTCAAAAAGTCATGTTTTGTAT 59.084 34.615 15.60 0.00 43.40 2.29
309 310 8.071368 GGTCGTCAAAAAGTCATGTTTTGTATA 58.929 33.333 15.60 4.49 43.40 1.47
310 311 9.440784 GTCGTCAAAAAGTCATGTTTTGTATAA 57.559 29.630 15.60 0.00 43.40 0.98
311 312 9.440784 TCGTCAAAAAGTCATGTTTTGTATAAC 57.559 29.630 15.60 8.61 43.40 1.89
312 313 9.227490 CGTCAAAAAGTCATGTTTTGTATAACA 57.773 29.630 15.60 0.00 43.40 2.41
328 329 8.900983 TTGTATAACATGTAGATAATGCTGCA 57.099 30.769 4.13 4.13 35.02 4.41
329 330 8.900983 TGTATAACATGTAGATAATGCTGCAA 57.099 30.769 6.36 0.00 34.23 4.08
330 331 8.773645 TGTATAACATGTAGATAATGCTGCAAC 58.226 33.333 6.36 0.00 34.23 4.17
331 332 4.801147 ACATGTAGATAATGCTGCAACG 57.199 40.909 6.36 0.00 34.23 4.10
332 333 4.441792 ACATGTAGATAATGCTGCAACGA 58.558 39.130 6.36 0.00 34.23 3.85
333 334 4.271049 ACATGTAGATAATGCTGCAACGAC 59.729 41.667 6.36 6.17 34.23 4.34
334 335 3.855858 TGTAGATAATGCTGCAACGACA 58.144 40.909 6.36 8.58 0.00 4.35
335 336 3.616821 TGTAGATAATGCTGCAACGACAC 59.383 43.478 6.36 1.67 0.00 3.67
336 337 2.698803 AGATAATGCTGCAACGACACA 58.301 42.857 6.36 0.00 0.00 3.72
337 338 3.273434 AGATAATGCTGCAACGACACAT 58.727 40.909 6.36 0.00 0.00 3.21
338 339 3.310774 AGATAATGCTGCAACGACACATC 59.689 43.478 6.36 2.34 0.00 3.06
339 340 0.523072 AATGCTGCAACGACACATCC 59.477 50.000 6.36 0.00 0.00 3.51
340 341 0.606130 ATGCTGCAACGACACATCCA 60.606 50.000 6.36 0.00 0.00 3.41
341 342 0.817229 TGCTGCAACGACACATCCAA 60.817 50.000 0.00 0.00 0.00 3.53
342 343 0.523072 GCTGCAACGACACATCCAAT 59.477 50.000 0.00 0.00 0.00 3.16
343 344 1.466360 GCTGCAACGACACATCCAATC 60.466 52.381 0.00 0.00 0.00 2.67
344 345 1.131126 CTGCAACGACACATCCAATCC 59.869 52.381 0.00 0.00 0.00 3.01
345 346 1.271325 TGCAACGACACATCCAATCCT 60.271 47.619 0.00 0.00 0.00 3.24
346 347 1.131126 GCAACGACACATCCAATCCTG 59.869 52.381 0.00 0.00 0.00 3.86
347 348 2.426522 CAACGACACATCCAATCCTGT 58.573 47.619 0.00 0.00 0.00 4.00
348 349 3.595173 CAACGACACATCCAATCCTGTA 58.405 45.455 0.00 0.00 0.00 2.74
349 350 3.526931 ACGACACATCCAATCCTGTAG 57.473 47.619 0.00 0.00 0.00 2.74
350 351 3.096852 ACGACACATCCAATCCTGTAGA 58.903 45.455 0.00 0.00 0.00 2.59
351 352 3.131223 ACGACACATCCAATCCTGTAGAG 59.869 47.826 0.00 0.00 0.00 2.43
352 353 3.381590 CGACACATCCAATCCTGTAGAGA 59.618 47.826 0.00 0.00 0.00 3.10
353 354 4.498850 CGACACATCCAATCCTGTAGAGAG 60.499 50.000 0.00 0.00 0.00 3.20
354 355 4.357325 ACACATCCAATCCTGTAGAGAGT 58.643 43.478 0.00 0.00 0.00 3.24
355 356 4.161189 ACACATCCAATCCTGTAGAGAGTG 59.839 45.833 0.00 0.00 0.00 3.51
356 357 4.403752 CACATCCAATCCTGTAGAGAGTGA 59.596 45.833 0.00 0.00 31.11 3.41
357 358 4.648762 ACATCCAATCCTGTAGAGAGTGAG 59.351 45.833 0.00 0.00 31.11 3.51
358 359 4.323569 TCCAATCCTGTAGAGAGTGAGT 57.676 45.455 0.00 0.00 31.11 3.41
359 360 4.678256 TCCAATCCTGTAGAGAGTGAGTT 58.322 43.478 0.00 0.00 31.11 3.01
360 361 4.707448 TCCAATCCTGTAGAGAGTGAGTTC 59.293 45.833 0.00 0.00 31.11 3.01
361 362 4.464244 CCAATCCTGTAGAGAGTGAGTTCA 59.536 45.833 0.00 0.00 31.11 3.18
362 363 5.128499 CCAATCCTGTAGAGAGTGAGTTCAT 59.872 44.000 0.00 0.00 31.11 2.57
363 364 6.351711 CCAATCCTGTAGAGAGTGAGTTCATT 60.352 42.308 0.00 0.00 31.11 2.57
364 365 5.906113 TCCTGTAGAGAGTGAGTTCATTC 57.094 43.478 0.00 0.00 33.41 2.67
365 366 5.325239 TCCTGTAGAGAGTGAGTTCATTCA 58.675 41.667 7.28 0.00 35.37 2.57
366 367 5.954752 TCCTGTAGAGAGTGAGTTCATTCAT 59.045 40.000 7.28 0.00 35.37 2.57
367 368 6.041511 CCTGTAGAGAGTGAGTTCATTCATG 58.958 44.000 7.28 0.00 35.37 3.07
368 369 6.350864 CCTGTAGAGAGTGAGTTCATTCATGT 60.351 42.308 7.28 0.00 35.37 3.21
369 370 7.148000 CCTGTAGAGAGTGAGTTCATTCATGTA 60.148 40.741 7.28 0.00 35.37 2.29
370 371 8.298729 TGTAGAGAGTGAGTTCATTCATGTAT 57.701 34.615 7.28 0.00 35.37 2.29
371 372 8.753133 TGTAGAGAGTGAGTTCATTCATGTATT 58.247 33.333 7.28 0.00 35.37 1.89
372 373 9.029243 GTAGAGAGTGAGTTCATTCATGTATTG 57.971 37.037 7.28 0.00 35.37 1.90
373 374 7.046652 AGAGAGTGAGTTCATTCATGTATTGG 58.953 38.462 7.28 0.00 35.37 3.16
374 375 6.715280 AGAGTGAGTTCATTCATGTATTGGT 58.285 36.000 7.28 0.00 35.37 3.67
375 376 7.170965 AGAGTGAGTTCATTCATGTATTGGTT 58.829 34.615 7.28 0.00 35.37 3.67
376 377 8.321353 AGAGTGAGTTCATTCATGTATTGGTTA 58.679 33.333 7.28 0.00 35.37 2.85
377 378 8.862325 AGTGAGTTCATTCATGTATTGGTTAA 57.138 30.769 0.00 0.00 0.00 2.01
378 379 8.950210 AGTGAGTTCATTCATGTATTGGTTAAG 58.050 33.333 0.00 0.00 0.00 1.85
379 380 8.730680 GTGAGTTCATTCATGTATTGGTTAAGT 58.269 33.333 0.00 0.00 0.00 2.24
380 381 8.946085 TGAGTTCATTCATGTATTGGTTAAGTC 58.054 33.333 0.00 0.00 0.00 3.01
381 382 9.167311 GAGTTCATTCATGTATTGGTTAAGTCT 57.833 33.333 0.00 0.00 0.00 3.24
382 383 8.950210 AGTTCATTCATGTATTGGTTAAGTCTG 58.050 33.333 0.00 0.00 0.00 3.51
383 384 7.864108 TCATTCATGTATTGGTTAAGTCTGG 57.136 36.000 0.00 0.00 0.00 3.86
384 385 6.318648 TCATTCATGTATTGGTTAAGTCTGGC 59.681 38.462 0.00 0.00 0.00 4.85
385 386 5.435686 TCATGTATTGGTTAAGTCTGGCT 57.564 39.130 0.00 0.00 0.00 4.75
386 387 5.185454 TCATGTATTGGTTAAGTCTGGCTG 58.815 41.667 0.00 0.00 0.00 4.85
387 388 4.634012 TGTATTGGTTAAGTCTGGCTGT 57.366 40.909 0.00 0.00 0.00 4.40
388 389 5.748670 TGTATTGGTTAAGTCTGGCTGTA 57.251 39.130 0.00 0.00 0.00 2.74
389 390 6.116711 TGTATTGGTTAAGTCTGGCTGTAA 57.883 37.500 0.00 0.00 0.00 2.41
390 391 6.717289 TGTATTGGTTAAGTCTGGCTGTAAT 58.283 36.000 0.00 0.00 0.00 1.89
391 392 6.597672 TGTATTGGTTAAGTCTGGCTGTAATG 59.402 38.462 0.00 0.00 0.00 1.90
392 393 4.634012 TGGTTAAGTCTGGCTGTAATGT 57.366 40.909 0.00 0.00 0.00 2.71
393 394 4.575885 TGGTTAAGTCTGGCTGTAATGTC 58.424 43.478 0.00 0.00 0.00 3.06
394 395 4.286032 TGGTTAAGTCTGGCTGTAATGTCT 59.714 41.667 0.00 0.00 0.00 3.41
395 396 5.482526 TGGTTAAGTCTGGCTGTAATGTCTA 59.517 40.000 0.00 0.00 0.00 2.59
396 397 6.156256 TGGTTAAGTCTGGCTGTAATGTCTAT 59.844 38.462 0.00 0.00 0.00 1.98
397 398 7.048512 GGTTAAGTCTGGCTGTAATGTCTATT 58.951 38.462 0.00 0.00 0.00 1.73
398 399 7.553044 GGTTAAGTCTGGCTGTAATGTCTATTT 59.447 37.037 0.00 0.00 0.00 1.40
399 400 9.595823 GTTAAGTCTGGCTGTAATGTCTATTTA 57.404 33.333 0.00 0.00 0.00 1.40
402 403 8.668510 AGTCTGGCTGTAATGTCTATTTATTG 57.331 34.615 0.00 0.00 0.00 1.90
403 404 8.267894 AGTCTGGCTGTAATGTCTATTTATTGT 58.732 33.333 0.00 0.00 0.00 2.71
404 405 8.338259 GTCTGGCTGTAATGTCTATTTATTGTG 58.662 37.037 0.00 0.00 0.00 3.33
405 406 7.498900 TCTGGCTGTAATGTCTATTTATTGTGG 59.501 37.037 0.00 0.00 0.00 4.17
406 407 6.545666 TGGCTGTAATGTCTATTTATTGTGGG 59.454 38.462 0.00 0.00 0.00 4.61
407 408 6.770785 GGCTGTAATGTCTATTTATTGTGGGA 59.229 38.462 0.00 0.00 0.00 4.37
408 409 7.041098 GGCTGTAATGTCTATTTATTGTGGGAG 60.041 40.741 0.00 0.00 0.00 4.30
409 410 7.499232 GCTGTAATGTCTATTTATTGTGGGAGT 59.501 37.037 0.00 0.00 0.00 3.85
410 411 8.958119 TGTAATGTCTATTTATTGTGGGAGTC 57.042 34.615 0.00 0.00 0.00 3.36
411 412 7.990886 TGTAATGTCTATTTATTGTGGGAGTCC 59.009 37.037 0.00 0.00 0.00 3.85
412 413 6.575244 ATGTCTATTTATTGTGGGAGTCCA 57.425 37.500 12.30 0.00 41.58 4.02
413 414 5.989477 TGTCTATTTATTGTGGGAGTCCAG 58.011 41.667 12.30 0.00 45.05 3.86
414 415 5.724370 TGTCTATTTATTGTGGGAGTCCAGA 59.276 40.000 12.30 0.00 45.05 3.86
415 416 6.049790 GTCTATTTATTGTGGGAGTCCAGAC 58.950 44.000 12.30 7.56 45.05 3.51
416 417 3.328382 TTTATTGTGGGAGTCCAGACG 57.672 47.619 12.30 0.00 45.05 4.18
417 418 0.535335 TATTGTGGGAGTCCAGACGC 59.465 55.000 12.30 0.74 45.05 5.19
418 419 1.480212 ATTGTGGGAGTCCAGACGCA 61.480 55.000 12.30 3.68 45.05 5.24
419 420 2.099652 TTGTGGGAGTCCAGACGCAG 62.100 60.000 12.30 0.00 45.05 5.18
446 447 8.583296 TGTATGATGAGGAACAATAGATGAGAG 58.417 37.037 0.00 0.00 0.00 3.20
492 502 7.301068 CAAATCTGTTTGGCTACTTCTAGAG 57.699 40.000 0.00 0.00 40.78 2.43
511 521 3.704061 AGAGTTCTAGATGCTTCCACTCC 59.296 47.826 12.69 0.00 31.35 3.85
555 565 6.847421 TTCTTTTCTACCCTACCTACTGTC 57.153 41.667 0.00 0.00 0.00 3.51
599 609 5.536538 TGAGTAGCTATGAGTAGAATGGTGG 59.463 44.000 0.00 0.00 0.00 4.61
699 719 3.830755 GGTCCTCACCTCTACTTTGTACA 59.169 47.826 0.00 0.00 40.00 2.90
709 729 6.037098 CCTCTACTTTGTACACAGACTATGC 58.963 44.000 15.81 0.00 0.00 3.14
722 742 3.068307 CAGACTATGCACCCACTACCTAC 59.932 52.174 0.00 0.00 0.00 3.18
732 752 5.661458 CACCCACTACCTACAATAGAACTG 58.339 45.833 0.00 0.00 0.00 3.16
836 856 8.800370 ACATTCATCTCTAGAGCGATATCTAA 57.200 34.615 15.35 1.34 31.51 2.10
938 959 0.815734 GTGCTGCTTCAGATGGCATT 59.184 50.000 0.00 0.00 37.83 3.56
1025 1048 2.091994 AGCAATTGGAGAAGAGGATGGG 60.092 50.000 7.72 0.00 0.00 4.00
1248 1274 5.793817 AGAAGGCCAATTTATGTTGAAACC 58.206 37.500 5.01 0.00 0.00 3.27
1316 1504 2.239400 TGCATATCGGAGAGTACCCAG 58.761 52.381 0.00 0.00 43.63 4.45
1343 1534 7.568349 CCTACATATGCAAGGGATACATACAT 58.432 38.462 14.37 0.00 39.74 2.29
1368 1559 4.074970 TGAAAGCTGAGATCCCAACTTTC 58.925 43.478 20.29 20.29 43.84 2.62
1500 1719 3.978571 GAAAGGAGGAGCCGGTGCC 62.979 68.421 1.90 4.75 43.43 5.01
1522 1741 0.447801 GTGGCATCGCGTTCAAGAAT 59.552 50.000 5.77 0.00 0.00 2.40
1853 2155 3.045601 CGAGAGGTTTGTGAGGACAAT 57.954 47.619 0.00 0.00 41.77 2.71
1913 2215 2.611518 CAAAGGCTTGTCTAGGAGTCG 58.388 52.381 0.00 0.00 0.00 4.18
2013 2315 1.185315 CCAATGAAGGCCCGAAATGT 58.815 50.000 0.00 0.00 0.00 2.71
2015 2317 2.028203 CCAATGAAGGCCCGAAATGTTT 60.028 45.455 0.00 0.00 0.00 2.83
2117 2419 4.523173 AGGCGATGAGGAAGAATACGAATA 59.477 41.667 0.00 0.00 0.00 1.75
2418 2726 3.244181 GGATCACCAAACAATGCAACCTT 60.244 43.478 0.00 0.00 35.97 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 5.331902 CGTTCTTGAGCAAAACTCTTTTCA 58.668 37.500 0.00 0.00 46.41 2.69
188 189 3.747099 ATAGTTTGACTGCATGCGTTC 57.253 42.857 14.09 12.13 0.00 3.95
247 248 7.981142 GCACTTTATATGCACTACCTAACAAA 58.019 34.615 0.00 0.00 42.88 2.83
260 261 9.185192 GACCAATTTCTATTGCACTTTATATGC 57.815 33.333 0.00 0.00 43.68 3.14
261 262 9.385902 CGACCAATTTCTATTGCACTTTATATG 57.614 33.333 0.00 0.00 39.87 1.78
262 263 9.120538 ACGACCAATTTCTATTGCACTTTATAT 57.879 29.630 0.00 0.00 39.87 0.86
263 264 8.500753 ACGACCAATTTCTATTGCACTTTATA 57.499 30.769 0.00 0.00 39.87 0.98
264 265 7.120579 TGACGACCAATTTCTATTGCACTTTAT 59.879 33.333 0.00 0.00 39.87 1.40
265 266 6.428465 TGACGACCAATTTCTATTGCACTTTA 59.572 34.615 0.00 0.00 39.87 1.85
266 267 5.240623 TGACGACCAATTTCTATTGCACTTT 59.759 36.000 0.00 0.00 39.87 2.66
267 268 4.759693 TGACGACCAATTTCTATTGCACTT 59.240 37.500 0.00 0.00 39.87 3.16
268 269 4.323417 TGACGACCAATTTCTATTGCACT 58.677 39.130 0.00 0.00 39.87 4.40
269 270 4.678509 TGACGACCAATTTCTATTGCAC 57.321 40.909 0.00 0.00 39.87 4.57
270 271 5.697473 TTTGACGACCAATTTCTATTGCA 57.303 34.783 0.00 0.00 39.87 4.08
271 272 6.640907 ACTTTTTGACGACCAATTTCTATTGC 59.359 34.615 0.00 0.00 39.87 3.56
272 273 7.860373 TGACTTTTTGACGACCAATTTCTATTG 59.140 33.333 0.00 0.00 40.70 1.90
273 274 7.936584 TGACTTTTTGACGACCAATTTCTATT 58.063 30.769 0.00 0.00 34.23 1.73
274 275 7.504924 TGACTTTTTGACGACCAATTTCTAT 57.495 32.000 0.00 0.00 34.23 1.98
275 276 6.928979 TGACTTTTTGACGACCAATTTCTA 57.071 33.333 0.00 0.00 34.23 2.10
276 277 5.828299 TGACTTTTTGACGACCAATTTCT 57.172 34.783 0.00 0.00 34.23 2.52
277 278 5.977129 ACATGACTTTTTGACGACCAATTTC 59.023 36.000 0.00 0.00 34.23 2.17
278 279 5.901552 ACATGACTTTTTGACGACCAATTT 58.098 33.333 0.00 0.00 34.23 1.82
279 280 5.514274 ACATGACTTTTTGACGACCAATT 57.486 34.783 0.00 0.00 34.23 2.32
280 281 5.514274 AACATGACTTTTTGACGACCAAT 57.486 34.783 0.00 0.00 34.23 3.16
281 282 4.974368 AACATGACTTTTTGACGACCAA 57.026 36.364 0.00 0.00 0.00 3.67
282 283 4.974368 AAACATGACTTTTTGACGACCA 57.026 36.364 0.00 0.00 0.00 4.02
283 284 5.099575 ACAAAACATGACTTTTTGACGACC 58.900 37.500 20.65 0.00 43.67 4.79
284 285 7.908193 ATACAAAACATGACTTTTTGACGAC 57.092 32.000 20.65 0.00 43.67 4.34
285 286 9.440784 GTTATACAAAACATGACTTTTTGACGA 57.559 29.630 20.65 9.94 43.67 4.20
286 287 9.227490 TGTTATACAAAACATGACTTTTTGACG 57.773 29.630 20.65 2.48 43.67 4.35
302 303 9.336171 TGCAGCATTATCTACATGTTATACAAA 57.664 29.630 2.30 0.00 0.00 2.83
303 304 8.900983 TGCAGCATTATCTACATGTTATACAA 57.099 30.769 2.30 0.00 0.00 2.41
304 305 8.773645 GTTGCAGCATTATCTACATGTTATACA 58.226 33.333 2.30 0.00 0.00 2.29
305 306 7.952101 CGTTGCAGCATTATCTACATGTTATAC 59.048 37.037 2.30 0.00 0.00 1.47
306 307 7.870445 TCGTTGCAGCATTATCTACATGTTATA 59.130 33.333 2.30 0.00 0.00 0.98
307 308 6.705825 TCGTTGCAGCATTATCTACATGTTAT 59.294 34.615 2.30 0.74 0.00 1.89
308 309 6.019075 GTCGTTGCAGCATTATCTACATGTTA 60.019 38.462 2.30 0.00 0.00 2.41
309 310 4.875536 TCGTTGCAGCATTATCTACATGTT 59.124 37.500 2.30 0.00 0.00 2.71
310 311 4.271049 GTCGTTGCAGCATTATCTACATGT 59.729 41.667 2.69 2.69 0.00 3.21
311 312 4.270808 TGTCGTTGCAGCATTATCTACATG 59.729 41.667 0.00 0.00 0.00 3.21
312 313 4.271049 GTGTCGTTGCAGCATTATCTACAT 59.729 41.667 0.00 0.00 0.00 2.29
313 314 3.616821 GTGTCGTTGCAGCATTATCTACA 59.383 43.478 0.00 0.00 0.00 2.74
314 315 3.616821 TGTGTCGTTGCAGCATTATCTAC 59.383 43.478 0.00 0.00 0.00 2.59
315 316 3.855858 TGTGTCGTTGCAGCATTATCTA 58.144 40.909 0.00 0.00 0.00 1.98
316 317 2.698803 TGTGTCGTTGCAGCATTATCT 58.301 42.857 0.00 0.00 0.00 1.98
317 318 3.546815 GGATGTGTCGTTGCAGCATTATC 60.547 47.826 0.00 0.00 0.00 1.75
318 319 2.355756 GGATGTGTCGTTGCAGCATTAT 59.644 45.455 0.00 0.00 0.00 1.28
319 320 1.737236 GGATGTGTCGTTGCAGCATTA 59.263 47.619 0.00 0.00 0.00 1.90
320 321 0.523072 GGATGTGTCGTTGCAGCATT 59.477 50.000 0.00 0.00 0.00 3.56
321 322 0.606130 TGGATGTGTCGTTGCAGCAT 60.606 50.000 0.00 0.00 0.00 3.79
322 323 0.817229 TTGGATGTGTCGTTGCAGCA 60.817 50.000 0.24 0.00 0.00 4.41
323 324 0.523072 ATTGGATGTGTCGTTGCAGC 59.477 50.000 0.00 0.00 0.00 5.25
324 325 1.131126 GGATTGGATGTGTCGTTGCAG 59.869 52.381 0.00 0.00 0.00 4.41
325 326 1.164411 GGATTGGATGTGTCGTTGCA 58.836 50.000 0.00 0.00 0.00 4.08
326 327 1.131126 CAGGATTGGATGTGTCGTTGC 59.869 52.381 0.00 0.00 0.00 4.17
327 328 2.426522 ACAGGATTGGATGTGTCGTTG 58.573 47.619 0.00 0.00 0.00 4.10
328 329 2.859165 ACAGGATTGGATGTGTCGTT 57.141 45.000 0.00 0.00 0.00 3.85
329 330 3.096852 TCTACAGGATTGGATGTGTCGT 58.903 45.455 0.00 0.00 0.00 4.34
330 331 3.381590 TCTCTACAGGATTGGATGTGTCG 59.618 47.826 0.00 0.00 0.00 4.35
331 332 4.404073 ACTCTCTACAGGATTGGATGTGTC 59.596 45.833 0.00 0.00 0.00 3.67
332 333 4.161189 CACTCTCTACAGGATTGGATGTGT 59.839 45.833 0.00 0.00 0.00 3.72
333 334 4.403752 TCACTCTCTACAGGATTGGATGTG 59.596 45.833 0.00 0.00 0.00 3.21
334 335 4.614475 TCACTCTCTACAGGATTGGATGT 58.386 43.478 0.00 0.00 0.00 3.06
335 336 4.648762 ACTCACTCTCTACAGGATTGGATG 59.351 45.833 0.00 0.00 0.00 3.51
336 337 4.877773 ACTCACTCTCTACAGGATTGGAT 58.122 43.478 0.00 0.00 0.00 3.41
337 338 4.323569 ACTCACTCTCTACAGGATTGGA 57.676 45.455 0.00 0.00 0.00 3.53
338 339 4.464244 TGAACTCACTCTCTACAGGATTGG 59.536 45.833 0.00 0.00 0.00 3.16
339 340 5.651387 TGAACTCACTCTCTACAGGATTG 57.349 43.478 0.00 0.00 0.00 2.67
340 341 6.438741 TGAATGAACTCACTCTCTACAGGATT 59.561 38.462 0.00 0.00 0.00 3.01
341 342 5.954752 TGAATGAACTCACTCTCTACAGGAT 59.045 40.000 0.00 0.00 0.00 3.24
342 343 5.325239 TGAATGAACTCACTCTCTACAGGA 58.675 41.667 0.00 0.00 0.00 3.86
343 344 5.651387 TGAATGAACTCACTCTCTACAGG 57.349 43.478 0.00 0.00 0.00 4.00
344 345 6.629128 ACATGAATGAACTCACTCTCTACAG 58.371 40.000 0.00 0.00 0.00 2.74
345 346 6.596309 ACATGAATGAACTCACTCTCTACA 57.404 37.500 0.00 0.00 0.00 2.74
346 347 9.029243 CAATACATGAATGAACTCACTCTCTAC 57.971 37.037 0.00 0.00 0.00 2.59
347 348 8.200120 CCAATACATGAATGAACTCACTCTCTA 58.800 37.037 0.00 0.00 0.00 2.43
348 349 7.046652 CCAATACATGAATGAACTCACTCTCT 58.953 38.462 0.00 0.00 0.00 3.10
349 350 6.820656 ACCAATACATGAATGAACTCACTCTC 59.179 38.462 0.00 0.00 0.00 3.20
350 351 6.715280 ACCAATACATGAATGAACTCACTCT 58.285 36.000 0.00 0.00 0.00 3.24
351 352 6.992063 ACCAATACATGAATGAACTCACTC 57.008 37.500 0.00 0.00 0.00 3.51
352 353 8.862325 TTAACCAATACATGAATGAACTCACT 57.138 30.769 0.00 0.00 0.00 3.41
353 354 8.730680 ACTTAACCAATACATGAATGAACTCAC 58.269 33.333 0.00 0.00 0.00 3.51
354 355 8.862325 ACTTAACCAATACATGAATGAACTCA 57.138 30.769 0.00 0.00 0.00 3.41
355 356 9.167311 AGACTTAACCAATACATGAATGAACTC 57.833 33.333 0.00 0.00 0.00 3.01
356 357 8.950210 CAGACTTAACCAATACATGAATGAACT 58.050 33.333 0.00 0.00 0.00 3.01
357 358 8.184192 CCAGACTTAACCAATACATGAATGAAC 58.816 37.037 0.00 0.00 0.00 3.18
358 359 7.148086 GCCAGACTTAACCAATACATGAATGAA 60.148 37.037 0.00 0.00 0.00 2.57
359 360 6.318648 GCCAGACTTAACCAATACATGAATGA 59.681 38.462 0.00 0.00 0.00 2.57
360 361 6.319658 AGCCAGACTTAACCAATACATGAATG 59.680 38.462 0.00 0.00 0.00 2.67
361 362 6.319658 CAGCCAGACTTAACCAATACATGAAT 59.680 38.462 0.00 0.00 0.00 2.57
362 363 5.647658 CAGCCAGACTTAACCAATACATGAA 59.352 40.000 0.00 0.00 0.00 2.57
363 364 5.185454 CAGCCAGACTTAACCAATACATGA 58.815 41.667 0.00 0.00 0.00 3.07
364 365 4.943705 ACAGCCAGACTTAACCAATACATG 59.056 41.667 0.00 0.00 0.00 3.21
365 366 5.179452 ACAGCCAGACTTAACCAATACAT 57.821 39.130 0.00 0.00 0.00 2.29
366 367 4.634012 ACAGCCAGACTTAACCAATACA 57.366 40.909 0.00 0.00 0.00 2.29
367 368 6.598064 ACATTACAGCCAGACTTAACCAATAC 59.402 38.462 0.00 0.00 0.00 1.89
368 369 6.717289 ACATTACAGCCAGACTTAACCAATA 58.283 36.000 0.00 0.00 0.00 1.90
369 370 5.570320 ACATTACAGCCAGACTTAACCAAT 58.430 37.500 0.00 0.00 0.00 3.16
370 371 4.980573 ACATTACAGCCAGACTTAACCAA 58.019 39.130 0.00 0.00 0.00 3.67
371 372 4.286032 AGACATTACAGCCAGACTTAACCA 59.714 41.667 0.00 0.00 0.00 3.67
372 373 4.833390 AGACATTACAGCCAGACTTAACC 58.167 43.478 0.00 0.00 0.00 2.85
373 374 8.494016 AAATAGACATTACAGCCAGACTTAAC 57.506 34.615 0.00 0.00 0.00 2.01
376 377 9.113838 CAATAAATAGACATTACAGCCAGACTT 57.886 33.333 0.00 0.00 0.00 3.01
377 378 8.267894 ACAATAAATAGACATTACAGCCAGACT 58.732 33.333 0.00 0.00 0.00 3.24
378 379 8.338259 CACAATAAATAGACATTACAGCCAGAC 58.662 37.037 0.00 0.00 0.00 3.51
379 380 7.498900 CCACAATAAATAGACATTACAGCCAGA 59.501 37.037 0.00 0.00 0.00 3.86
380 381 7.255242 CCCACAATAAATAGACATTACAGCCAG 60.255 40.741 0.00 0.00 0.00 4.85
381 382 6.545666 CCCACAATAAATAGACATTACAGCCA 59.454 38.462 0.00 0.00 0.00 4.75
382 383 6.770785 TCCCACAATAAATAGACATTACAGCC 59.229 38.462 0.00 0.00 0.00 4.85
383 384 7.499232 ACTCCCACAATAAATAGACATTACAGC 59.501 37.037 0.00 0.00 0.00 4.40
384 385 8.964476 ACTCCCACAATAAATAGACATTACAG 57.036 34.615 0.00 0.00 0.00 2.74
385 386 7.990886 GGACTCCCACAATAAATAGACATTACA 59.009 37.037 0.00 0.00 0.00 2.41
386 387 7.990886 TGGACTCCCACAATAAATAGACATTAC 59.009 37.037 0.00 0.00 37.58 1.89
387 388 8.096621 TGGACTCCCACAATAAATAGACATTA 57.903 34.615 0.00 0.00 37.58 1.90
388 389 6.969043 TGGACTCCCACAATAAATAGACATT 58.031 36.000 0.00 0.00 37.58 2.71
389 390 6.386927 TCTGGACTCCCACAATAAATAGACAT 59.613 38.462 0.00 0.00 37.58 3.06
390 391 5.724370 TCTGGACTCCCACAATAAATAGACA 59.276 40.000 0.00 0.00 37.58 3.41
391 392 6.049790 GTCTGGACTCCCACAATAAATAGAC 58.950 44.000 0.00 0.00 37.58 2.59
392 393 5.163447 CGTCTGGACTCCCACAATAAATAGA 60.163 44.000 0.00 0.00 37.58 1.98
393 394 5.050490 CGTCTGGACTCCCACAATAAATAG 58.950 45.833 0.00 0.00 37.58 1.73
394 395 4.682320 GCGTCTGGACTCCCACAATAAATA 60.682 45.833 0.00 0.00 37.58 1.40
395 396 3.873910 CGTCTGGACTCCCACAATAAAT 58.126 45.455 0.00 0.00 37.58 1.40
396 397 2.614481 GCGTCTGGACTCCCACAATAAA 60.614 50.000 0.00 0.00 37.58 1.40
397 398 1.066430 GCGTCTGGACTCCCACAATAA 60.066 52.381 0.00 0.00 37.58 1.40
398 399 0.535335 GCGTCTGGACTCCCACAATA 59.465 55.000 0.00 0.00 37.58 1.90
399 400 1.296715 GCGTCTGGACTCCCACAAT 59.703 57.895 0.00 0.00 37.58 2.71
400 401 2.099652 CTGCGTCTGGACTCCCACAA 62.100 60.000 0.00 0.00 37.58 3.33
401 402 2.523168 TGCGTCTGGACTCCCACA 60.523 61.111 0.00 0.00 37.58 4.17
402 403 2.262915 CTGCGTCTGGACTCCCAC 59.737 66.667 0.00 0.00 37.58 4.61
403 404 2.203640 ACTGCGTCTGGACTCCCA 60.204 61.111 0.00 0.00 40.95 4.37
404 405 1.248785 TACACTGCGTCTGGACTCCC 61.249 60.000 0.00 0.00 0.00 4.30
405 406 0.818296 ATACACTGCGTCTGGACTCC 59.182 55.000 0.00 0.00 0.00 3.85
406 407 1.472878 TCATACACTGCGTCTGGACTC 59.527 52.381 0.00 0.00 0.00 3.36
407 408 1.545841 TCATACACTGCGTCTGGACT 58.454 50.000 0.00 0.00 0.00 3.85
408 409 2.159240 TCATCATACACTGCGTCTGGAC 60.159 50.000 0.00 0.00 0.00 4.02
409 410 2.099405 TCATCATACACTGCGTCTGGA 58.901 47.619 0.00 0.00 0.00 3.86
410 411 2.467838 CTCATCATACACTGCGTCTGG 58.532 52.381 0.00 0.00 0.00 3.86
411 412 2.099756 TCCTCATCATACACTGCGTCTG 59.900 50.000 0.00 0.00 0.00 3.51
412 413 2.379005 TCCTCATCATACACTGCGTCT 58.621 47.619 0.00 0.00 0.00 4.18
413 414 2.860735 GTTCCTCATCATACACTGCGTC 59.139 50.000 0.00 0.00 0.00 5.19
414 415 2.233676 TGTTCCTCATCATACACTGCGT 59.766 45.455 0.00 0.00 0.00 5.24
415 416 2.892374 TGTTCCTCATCATACACTGCG 58.108 47.619 0.00 0.00 0.00 5.18
416 417 6.283694 TCTATTGTTCCTCATCATACACTGC 58.716 40.000 0.00 0.00 0.00 4.40
417 418 8.146412 TCATCTATTGTTCCTCATCATACACTG 58.854 37.037 0.00 0.00 0.00 3.66
418 419 8.255111 TCATCTATTGTTCCTCATCATACACT 57.745 34.615 0.00 0.00 0.00 3.55
419 420 8.363390 TCTCATCTATTGTTCCTCATCATACAC 58.637 37.037 0.00 0.00 0.00 2.90
492 502 3.196685 ACTGGAGTGGAAGCATCTAGAAC 59.803 47.826 0.00 0.00 0.00 3.01
653 671 6.183361 CCTCTATTTATAGGGCTTTGGGAAGT 60.183 42.308 0.00 0.00 35.25 3.01
699 719 1.831736 GGTAGTGGGTGCATAGTCTGT 59.168 52.381 0.00 0.00 0.00 3.41
709 729 5.395324 CCAGTTCTATTGTAGGTAGTGGGTG 60.395 48.000 0.00 0.00 32.46 4.61
732 752 6.644347 TCCAAGATCTTAGATGAGAACAACC 58.356 40.000 7.86 0.00 0.00 3.77
818 838 5.410132 GCTGTGTTAGATATCGCTCTAGAGA 59.590 44.000 24.24 3.85 0.00 3.10
836 856 4.540153 AGCTTCAACGTGCTGTGT 57.460 50.000 0.00 0.00 38.21 3.72
938 959 2.029623 GTATGGGTCAACGAGGCTCTA 58.970 52.381 13.50 0.00 0.00 2.43
1025 1048 3.082698 TGATTTGTTGTTCTGCAGCAC 57.917 42.857 9.47 9.63 38.04 4.40
1248 1274 7.041916 GCTTCATCATATTCTTCACCTTCAGAG 60.042 40.741 0.00 0.00 0.00 3.35
1316 1504 2.887151 ATCCCTTGCATATGTAGGGC 57.113 50.000 27.51 7.43 46.82 5.19
1343 1534 1.361204 TGGGATCTCAGCTTTCACCA 58.639 50.000 0.00 0.00 0.00 4.17
1368 1559 7.493320 CACCCTTCAATATCAACATTTCCATTG 59.507 37.037 0.00 0.00 0.00 2.82
1500 1719 2.244436 CTTGAACGCGATGCCACCAG 62.244 60.000 15.93 0.00 0.00 4.00
1522 1741 2.043953 TCCTCTCAGCCTGCGCTA 60.044 61.111 9.73 0.00 46.25 4.26
1546 1768 1.891919 GCCGCCAAGTTCTCACACA 60.892 57.895 0.00 0.00 0.00 3.72
1853 2155 5.456186 GGATATGGAGCCTTAGTTGCCTTTA 60.456 44.000 0.00 0.00 0.00 1.85
1913 2215 5.818336 GTCTTTTCTTCCACTCTATTAGGCC 59.182 44.000 0.00 0.00 0.00 5.19
2013 2315 3.504520 GTCCCTCTTCGCCACATTTAAAA 59.495 43.478 0.00 0.00 0.00 1.52
2015 2317 2.039216 TGTCCCTCTTCGCCACATTTAA 59.961 45.455 0.00 0.00 0.00 1.52
2081 2383 0.179009 ATCGCCTTCACCATCATGGG 60.179 55.000 9.04 0.00 43.37 4.00
2117 2419 4.653341 CCTCTTGTCCCTCTACATCTTCAT 59.347 45.833 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.