Multiple sequence alignment - TraesCS7B01G351500

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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 TraesCS7B01G351500 chr7B 100.000 2746 0 0 1 2746 608379045 608381790 0.000000e+00 5072.0
1 TraesCS7B01G351500 chr7B 84.875 1924 217 45 880 2746 608392190 608394096 0.000000e+00 1873.0
2 TraesCS7B01G351500 chr7B 85.019 1602 171 41 815 2367 608405134 608406715 0.000000e+00 1565.0
3 TraesCS7B01G351500 chr7B 87.274 1108 103 29 880 1972 608415009 608416093 0.000000e+00 1230.0
4 TraesCS7B01G351500 chr7B 95.455 198 9 0 625 822 608404914 608405111 1.590000e-82 316.0
5 TraesCS7B01G351500 chr7B 92.647 68 3 1 814 879 608392097 608392164 2.250000e-16 97.1
6 TraesCS7B01G351500 chr7D 96.480 1449 42 7 1300 2746 560590254 560591695 0.000000e+00 2385.0
7 TraesCS7B01G351500 chr7D 85.714 1652 173 38 880 2486 560597154 560598787 0.000000e+00 1685.0
8 TraesCS7B01G351500 chr7D 84.597 1649 191 32 880 2486 560603047 560604674 0.000000e+00 1580.0
9 TraesCS7B01G351500 chr7D 86.871 1112 103 29 880 1972 560701832 560702919 0.000000e+00 1205.0
10 TraesCS7B01G351500 chr7D 87.407 1072 98 21 880 1932 560682867 560683920 0.000000e+00 1197.0
11 TraesCS7B01G351500 chr7D 90.458 262 24 1 18 278 560602446 560602707 7.280000e-91 344.0
12 TraesCS7B01G351500 chr7D 91.500 200 8 2 629 822 560602735 560602931 1.620000e-67 267.0
13 TraesCS7B01G351500 chr7D 92.857 70 4 1 814 883 560602954 560603022 1.740000e-17 100.0
14 TraesCS7B01G351500 chr7D 93.651 63 2 2 814 874 560597061 560597123 2.910000e-15 93.5
15 TraesCS7B01G351500 chr7A 94.753 1296 53 7 563 1845 644710145 644711438 0.000000e+00 2002.0
16 TraesCS7B01G351500 chr7A 84.331 1921 223 40 880 2746 644768558 644770454 0.000000e+00 1808.0
17 TraesCS7B01G351500 chr7A 84.142 1545 159 39 814 2296 644721845 644723365 0.000000e+00 1417.0
18 TraesCS7B01G351500 chr7A 86.279 1341 127 30 880 2181 644735019 644736341 0.000000e+00 1404.0
19 TraesCS7B01G351500 chr7A 92.123 914 63 8 1840 2746 644715158 644716069 0.000000e+00 1280.0
20 TraesCS7B01G351500 chr7A 99.234 261 2 0 306 566 291622319 291622579 3.200000e-129 472.0
21 TraesCS7B01G351500 chr7A 98.859 263 3 0 304 566 9210448 9210710 1.150000e-128 470.0
22 TraesCS7B01G351500 chr7A 98.485 264 4 0 303 566 139051941 139052204 1.490000e-127 466.0
23 TraesCS7B01G351500 chr7A 98.127 267 5 0 303 569 404836931 404836665 1.490000e-127 466.0
24 TraesCS7B01G351500 chr7A 98.127 267 5 0 303 569 463707870 463707604 1.490000e-127 466.0
25 TraesCS7B01G351500 chr7A 94.137 307 14 1 1 307 644709846 644710148 5.360000e-127 464.0
26 TraesCS7B01G351500 chr7A 83.571 420 38 15 2328 2718 644723487 644723904 5.590000e-97 364.0
27 TraesCS7B01G351500 chr7A 95.455 198 9 0 625 822 644768245 644768442 1.590000e-82 316.0
28 TraesCS7B01G351500 chr7A 86.937 222 24 4 2261 2481 644736385 644736602 7.600000e-61 244.0
29 TraesCS7B01G351500 chr7A 91.549 71 4 2 814 883 644768464 644768533 2.250000e-16 97.1
30 TraesCS7B01G351500 chr3A 98.864 264 3 0 303 566 58274811 58275074 3.200000e-129 472.0
31 TraesCS7B01G351500 chr3A 97.464 276 5 2 304 579 739283831 739283558 1.150000e-128 470.0
32 TraesCS7B01G351500 chrUn 98.485 264 4 0 303 566 1525428 1525691 1.490000e-127 466.0
33 TraesCS7B01G351500 chr1A 98.485 264 4 0 303 566 358543290 358543553 1.490000e-127 466.0
34 TraesCS7B01G351500 chr6A 88.889 54 4 2 838 890 16449536 16449484 6.350000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G351500 chr7B 608379045 608381790 2745 False 5072.000000 5072 100.000000 1 2746 1 chr7B.!!$F1 2745
1 TraesCS7B01G351500 chr7B 608415009 608416093 1084 False 1230.000000 1230 87.274000 880 1972 1 chr7B.!!$F2 1092
2 TraesCS7B01G351500 chr7B 608392097 608394096 1999 False 985.050000 1873 88.761000 814 2746 2 chr7B.!!$F3 1932
3 TraesCS7B01G351500 chr7B 608404914 608406715 1801 False 940.500000 1565 90.237000 625 2367 2 chr7B.!!$F4 1742
4 TraesCS7B01G351500 chr7D 560590254 560591695 1441 False 2385.000000 2385 96.480000 1300 2746 1 chr7D.!!$F1 1446
5 TraesCS7B01G351500 chr7D 560701832 560702919 1087 False 1205.000000 1205 86.871000 880 1972 1 chr7D.!!$F3 1092
6 TraesCS7B01G351500 chr7D 560682867 560683920 1053 False 1197.000000 1197 87.407000 880 1932 1 chr7D.!!$F2 1052
7 TraesCS7B01G351500 chr7D 560597061 560604674 7613 False 678.250000 1685 89.796167 18 2486 6 chr7D.!!$F4 2468
8 TraesCS7B01G351500 chr7A 644709846 644716069 6223 False 1248.666667 2002 93.671000 1 2746 3 chr7A.!!$F4 2745
9 TraesCS7B01G351500 chr7A 644721845 644723904 2059 False 890.500000 1417 83.856500 814 2718 2 chr7A.!!$F5 1904
10 TraesCS7B01G351500 chr7A 644735019 644736602 1583 False 824.000000 1404 86.608000 880 2481 2 chr7A.!!$F6 1601
11 TraesCS7B01G351500 chr7A 644768245 644770454 2209 False 740.366667 1808 90.445000 625 2746 3 chr7A.!!$F7 2121

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
317 5692 0.395448 GCACTAGTACTCCCTCCGGT 60.395 60.0 0.00 0.00 0.00 5.28 F
542 5917 0.527113 TCGGCAAATCCAATGTGCAG 59.473 50.0 4.59 0.65 40.12 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 6805 2.277692 CCGATCTGCGCGACGTTA 60.278 61.111 12.1 0.0 39.11 3.18 R
1850 11061 5.067936 AGGACACAATATCCTCGACTTACAG 59.932 44.000 0.0 0.0 43.49 2.74 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
19 20 2.448926 TGGTCTTCACGTGTATGGTG 57.551 50.000 16.51 1.11 36.74 4.17
20 21 1.689813 TGGTCTTCACGTGTATGGTGT 59.310 47.619 16.51 0.00 36.76 4.16
34 5406 0.679321 TGGTGTGTGTGTGTGTGCAT 60.679 50.000 0.00 0.00 0.00 3.96
191 5563 6.114187 TCTTATTCTCGCATATGTCCCAAT 57.886 37.500 4.29 1.67 0.00 3.16
192 5564 6.166279 TCTTATTCTCGCATATGTCCCAATC 58.834 40.000 4.29 0.00 0.00 2.67
297 5672 2.869233 ATTGCAATGCACGGGTATTC 57.131 45.000 12.09 0.00 38.71 1.75
307 5682 2.724349 CACGGGTATTCGCACTAGTAC 58.276 52.381 0.00 0.00 0.00 2.73
308 5683 2.357009 CACGGGTATTCGCACTAGTACT 59.643 50.000 0.00 0.00 0.00 2.73
309 5684 2.615912 ACGGGTATTCGCACTAGTACTC 59.384 50.000 0.00 0.00 0.00 2.59
310 5685 2.031333 CGGGTATTCGCACTAGTACTCC 60.031 54.545 0.00 0.00 0.00 3.85
311 5686 2.295629 GGGTATTCGCACTAGTACTCCC 59.704 54.545 0.00 0.00 0.00 4.30
312 5687 3.220940 GGTATTCGCACTAGTACTCCCT 58.779 50.000 0.00 0.00 0.00 4.20
313 5688 3.252944 GGTATTCGCACTAGTACTCCCTC 59.747 52.174 0.00 0.00 0.00 4.30
314 5689 1.760192 TTCGCACTAGTACTCCCTCC 58.240 55.000 0.00 0.00 0.00 4.30
315 5690 0.463295 TCGCACTAGTACTCCCTCCG 60.463 60.000 0.00 0.00 0.00 4.63
316 5691 1.445716 CGCACTAGTACTCCCTCCGG 61.446 65.000 0.00 0.00 0.00 5.14
317 5692 0.395448 GCACTAGTACTCCCTCCGGT 60.395 60.000 0.00 0.00 0.00 5.28
318 5693 1.677942 CACTAGTACTCCCTCCGGTC 58.322 60.000 0.00 0.00 0.00 4.79
319 5694 1.064906 CACTAGTACTCCCTCCGGTCA 60.065 57.143 0.00 0.00 0.00 4.02
320 5695 1.851653 ACTAGTACTCCCTCCGGTCAT 59.148 52.381 0.00 0.00 0.00 3.06
321 5696 2.244252 ACTAGTACTCCCTCCGGTCATT 59.756 50.000 0.00 0.00 0.00 2.57
322 5697 2.249309 AGTACTCCCTCCGGTCATTT 57.751 50.000 0.00 0.00 0.00 2.32
323 5698 2.547990 AGTACTCCCTCCGGTCATTTT 58.452 47.619 0.00 0.00 0.00 1.82
324 5699 2.910977 AGTACTCCCTCCGGTCATTTTT 59.089 45.455 0.00 0.00 0.00 1.94
325 5700 4.098894 AGTACTCCCTCCGGTCATTTTTA 58.901 43.478 0.00 0.00 0.00 1.52
326 5701 3.345508 ACTCCCTCCGGTCATTTTTAC 57.654 47.619 0.00 0.00 0.00 2.01
327 5702 2.910977 ACTCCCTCCGGTCATTTTTACT 59.089 45.455 0.00 0.00 0.00 2.24
328 5703 3.055312 ACTCCCTCCGGTCATTTTTACTC 60.055 47.826 0.00 0.00 0.00 2.59
329 5704 3.178865 TCCCTCCGGTCATTTTTACTCT 58.821 45.455 0.00 0.00 0.00 3.24
330 5705 3.055385 TCCCTCCGGTCATTTTTACTCTG 60.055 47.826 0.00 0.00 0.00 3.35
331 5706 2.678336 CCTCCGGTCATTTTTACTCTGC 59.322 50.000 0.00 0.00 0.00 4.26
332 5707 3.334691 CTCCGGTCATTTTTACTCTGCA 58.665 45.455 0.00 0.00 0.00 4.41
333 5708 3.941483 CTCCGGTCATTTTTACTCTGCAT 59.059 43.478 0.00 0.00 0.00 3.96
334 5709 5.092554 TCCGGTCATTTTTACTCTGCATA 57.907 39.130 0.00 0.00 0.00 3.14
335 5710 5.680619 TCCGGTCATTTTTACTCTGCATAT 58.319 37.500 0.00 0.00 0.00 1.78
336 5711 6.119536 TCCGGTCATTTTTACTCTGCATATT 58.880 36.000 0.00 0.00 0.00 1.28
337 5712 7.276658 TCCGGTCATTTTTACTCTGCATATTA 58.723 34.615 0.00 0.00 0.00 0.98
338 5713 7.441157 TCCGGTCATTTTTACTCTGCATATTAG 59.559 37.037 0.00 0.00 0.00 1.73
339 5714 7.307989 CCGGTCATTTTTACTCTGCATATTAGG 60.308 40.741 0.00 0.00 0.00 2.69
340 5715 7.226720 CGGTCATTTTTACTCTGCATATTAGGT 59.773 37.037 0.00 0.00 0.00 3.08
341 5716 8.903820 GGTCATTTTTACTCTGCATATTAGGTT 58.096 33.333 0.00 0.00 0.00 3.50
346 5721 7.859325 TTTACTCTGCATATTAGGTTTGTCC 57.141 36.000 0.00 0.00 0.00 4.02
347 5722 4.442706 ACTCTGCATATTAGGTTTGTCCG 58.557 43.478 0.00 0.00 41.99 4.79
348 5723 4.161565 ACTCTGCATATTAGGTTTGTCCGA 59.838 41.667 0.00 0.00 41.99 4.55
349 5724 5.092554 TCTGCATATTAGGTTTGTCCGAA 57.907 39.130 0.00 0.00 41.99 4.30
350 5725 5.116180 TCTGCATATTAGGTTTGTCCGAAG 58.884 41.667 0.00 0.00 41.99 3.79
351 5726 4.839121 TGCATATTAGGTTTGTCCGAAGT 58.161 39.130 0.00 0.00 41.99 3.01
352 5727 4.873827 TGCATATTAGGTTTGTCCGAAGTC 59.126 41.667 0.00 0.00 41.99 3.01
353 5728 4.873827 GCATATTAGGTTTGTCCGAAGTCA 59.126 41.667 0.00 0.00 41.99 3.41
354 5729 5.353123 GCATATTAGGTTTGTCCGAAGTCAA 59.647 40.000 0.00 0.00 41.99 3.18
355 5730 6.038271 GCATATTAGGTTTGTCCGAAGTCAAT 59.962 38.462 0.00 0.00 41.99 2.57
356 5731 7.630924 CATATTAGGTTTGTCCGAAGTCAATC 58.369 38.462 0.00 0.00 41.99 2.67
357 5732 3.771577 AGGTTTGTCCGAAGTCAATCT 57.228 42.857 0.00 0.00 41.99 2.40
358 5733 3.665190 AGGTTTGTCCGAAGTCAATCTC 58.335 45.455 0.00 0.00 41.99 2.75
359 5734 3.071023 AGGTTTGTCCGAAGTCAATCTCA 59.929 43.478 0.00 0.00 41.99 3.27
360 5735 4.003648 GGTTTGTCCGAAGTCAATCTCAT 58.996 43.478 0.00 0.00 0.00 2.90
361 5736 4.093556 GGTTTGTCCGAAGTCAATCTCATC 59.906 45.833 0.00 0.00 0.00 2.92
362 5737 3.526931 TGTCCGAAGTCAATCTCATCC 57.473 47.619 0.00 0.00 0.00 3.51
363 5738 2.831526 TGTCCGAAGTCAATCTCATCCA 59.168 45.455 0.00 0.00 0.00 3.41
364 5739 3.260632 TGTCCGAAGTCAATCTCATCCAA 59.739 43.478 0.00 0.00 0.00 3.53
365 5740 3.619038 GTCCGAAGTCAATCTCATCCAAC 59.381 47.826 0.00 0.00 0.00 3.77
366 5741 3.515502 TCCGAAGTCAATCTCATCCAACT 59.484 43.478 0.00 0.00 0.00 3.16
367 5742 4.020218 TCCGAAGTCAATCTCATCCAACTT 60.020 41.667 0.00 0.00 0.00 2.66
368 5743 4.697352 CCGAAGTCAATCTCATCCAACTTT 59.303 41.667 0.00 0.00 0.00 2.66
369 5744 5.391310 CCGAAGTCAATCTCATCCAACTTTG 60.391 44.000 0.00 0.00 0.00 2.77
370 5745 5.409520 CGAAGTCAATCTCATCCAACTTTGA 59.590 40.000 0.00 0.00 32.33 2.69
371 5746 6.566197 AAGTCAATCTCATCCAACTTTGAC 57.434 37.500 5.67 5.67 41.88 3.18
372 5747 5.006386 AGTCAATCTCATCCAACTTTGACC 58.994 41.667 9.31 0.00 42.29 4.02
373 5748 4.761739 GTCAATCTCATCCAACTTTGACCA 59.238 41.667 0.00 0.00 37.86 4.02
374 5749 5.241506 GTCAATCTCATCCAACTTTGACCAA 59.758 40.000 0.00 0.00 37.86 3.67
375 5750 5.474532 TCAATCTCATCCAACTTTGACCAAG 59.525 40.000 0.00 0.00 38.64 3.61
414 5789 9.679661 ATTATAGACATTCACATAACAACACCA 57.320 29.630 0.00 0.00 0.00 4.17
415 5790 7.994425 ATAGACATTCACATAACAACACCAA 57.006 32.000 0.00 0.00 0.00 3.67
416 5791 6.899393 AGACATTCACATAACAACACCAAT 57.101 33.333 0.00 0.00 0.00 3.16
417 5792 7.994425 AGACATTCACATAACAACACCAATA 57.006 32.000 0.00 0.00 0.00 1.90
418 5793 8.579850 AGACATTCACATAACAACACCAATAT 57.420 30.769 0.00 0.00 0.00 1.28
419 5794 8.677300 AGACATTCACATAACAACACCAATATC 58.323 33.333 0.00 0.00 0.00 1.63
420 5795 8.347004 ACATTCACATAACAACACCAATATCA 57.653 30.769 0.00 0.00 0.00 2.15
421 5796 8.970020 ACATTCACATAACAACACCAATATCAT 58.030 29.630 0.00 0.00 0.00 2.45
422 5797 9.806203 CATTCACATAACAACACCAATATCATT 57.194 29.630 0.00 0.00 0.00 2.57
425 5800 9.898152 TCACATAACAACACCAATATCATTAGA 57.102 29.630 0.00 0.00 0.00 2.10
432 5807 9.857656 ACAACACCAATATCATTAGATTCATCT 57.142 29.630 0.00 0.00 40.86 2.90
435 5810 9.293404 ACACCAATATCATTAGATTCATCTTGG 57.707 33.333 0.00 0.00 38.32 3.61
436 5811 9.511272 CACCAATATCATTAGATTCATCTTGGA 57.489 33.333 0.00 0.00 38.32 3.53
527 5902 5.758924 ACTTATCAAAGTTTGACTTTCGGC 58.241 37.500 20.26 0.00 44.47 5.54
528 5903 5.298276 ACTTATCAAAGTTTGACTTTCGGCA 59.702 36.000 20.26 0.00 44.47 5.69
529 5904 4.647424 ATCAAAGTTTGACTTTCGGCAA 57.353 36.364 20.26 0.00 44.47 4.52
530 5905 4.442375 TCAAAGTTTGACTTTCGGCAAA 57.558 36.364 14.35 0.00 44.47 3.68
531 5906 5.004922 TCAAAGTTTGACTTTCGGCAAAT 57.995 34.783 14.35 0.00 44.47 2.32
532 5907 5.040635 TCAAAGTTTGACTTTCGGCAAATC 58.959 37.500 14.35 0.00 44.47 2.17
533 5908 3.643159 AGTTTGACTTTCGGCAAATCC 57.357 42.857 0.00 0.00 36.51 3.01
534 5909 2.955660 AGTTTGACTTTCGGCAAATCCA 59.044 40.909 0.00 0.00 36.51 3.41
535 5910 3.383185 AGTTTGACTTTCGGCAAATCCAA 59.617 39.130 0.00 0.00 36.51 3.53
536 5911 4.039124 AGTTTGACTTTCGGCAAATCCAAT 59.961 37.500 0.00 0.00 36.51 3.16
537 5912 3.574284 TGACTTTCGGCAAATCCAATG 57.426 42.857 0.00 0.00 34.01 2.82
538 5913 2.890311 TGACTTTCGGCAAATCCAATGT 59.110 40.909 0.00 0.00 34.01 2.71
539 5914 3.244976 GACTTTCGGCAAATCCAATGTG 58.755 45.455 0.00 0.00 34.01 3.21
540 5915 1.994779 CTTTCGGCAAATCCAATGTGC 59.005 47.619 0.00 0.00 37.55 4.57
541 5916 0.964700 TTCGGCAAATCCAATGTGCA 59.035 45.000 4.59 0.00 40.12 4.57
542 5917 0.527113 TCGGCAAATCCAATGTGCAG 59.473 50.000 4.59 0.65 40.12 4.41
543 5918 0.527113 CGGCAAATCCAATGTGCAGA 59.473 50.000 4.59 0.00 40.12 4.26
544 5919 1.468565 CGGCAAATCCAATGTGCAGAG 60.469 52.381 4.59 0.00 40.12 3.35
545 5920 1.547372 GGCAAATCCAATGTGCAGAGT 59.453 47.619 4.59 0.00 40.12 3.24
546 5921 2.754552 GGCAAATCCAATGTGCAGAGTA 59.245 45.455 4.59 0.00 40.12 2.59
547 5922 3.193267 GGCAAATCCAATGTGCAGAGTAA 59.807 43.478 4.59 0.00 40.12 2.24
548 5923 4.321899 GGCAAATCCAATGTGCAGAGTAAA 60.322 41.667 4.59 0.00 40.12 2.01
549 5924 5.229423 GCAAATCCAATGTGCAGAGTAAAA 58.771 37.500 0.00 0.00 38.19 1.52
550 5925 5.695816 GCAAATCCAATGTGCAGAGTAAAAA 59.304 36.000 0.00 0.00 38.19 1.94
551 5926 6.128742 GCAAATCCAATGTGCAGAGTAAAAAG 60.129 38.462 0.00 0.00 38.19 2.27
552 5927 5.649782 ATCCAATGTGCAGAGTAAAAAGG 57.350 39.130 0.00 0.00 0.00 3.11
553 5928 4.724399 TCCAATGTGCAGAGTAAAAAGGA 58.276 39.130 0.00 0.00 0.00 3.36
554 5929 4.518970 TCCAATGTGCAGAGTAAAAAGGAC 59.481 41.667 0.00 0.00 0.00 3.85
555 5930 4.321230 CCAATGTGCAGAGTAAAAAGGACC 60.321 45.833 0.00 0.00 0.00 4.46
556 5931 2.489971 TGTGCAGAGTAAAAAGGACCG 58.510 47.619 0.00 0.00 0.00 4.79
557 5932 1.804748 GTGCAGAGTAAAAAGGACCGG 59.195 52.381 0.00 0.00 0.00 5.28
558 5933 1.695242 TGCAGAGTAAAAAGGACCGGA 59.305 47.619 9.46 0.00 0.00 5.14
559 5934 2.289444 TGCAGAGTAAAAAGGACCGGAG 60.289 50.000 9.46 0.00 0.00 4.63
704 6079 3.795688 TGCTCTCTTGGATTCTTGGTT 57.204 42.857 0.00 0.00 0.00 3.67
709 6084 4.848357 TCTCTTGGATTCTTGGTTGATCC 58.152 43.478 0.00 0.00 0.00 3.36
809 6190 3.704231 ATCCTGCCGTCCCATGCAC 62.704 63.158 0.00 0.00 33.17 4.57
981 6441 4.761739 ACTGCTTGCAAATTTACTCTAGCA 59.238 37.500 16.18 16.18 36.31 3.49
1014 6474 2.388735 AGAGACATGGCCATTCGAGTA 58.611 47.619 17.92 0.00 0.00 2.59
1113 6573 1.956170 CTGCGTTGCCGACAAGACT 60.956 57.895 0.00 0.00 36.16 3.24
1137 6597 1.603456 CAGGTACAACATGCACACCA 58.397 50.000 0.00 0.00 0.00 4.17
1143 6607 6.094742 CAGGTACAACATGCACACCAATATAA 59.905 38.462 0.00 0.00 0.00 0.98
1160 6630 7.949565 ACCAATATAATCCATGGAATTGTAGCA 59.050 33.333 25.10 3.72 36.75 3.49
1317 6791 0.771127 AACCAACAAGCAGGGCTCTA 59.229 50.000 0.00 0.00 38.25 2.43
1715 7189 1.349357 GCCTTCCAGGTTGAGAAGAGT 59.651 52.381 1.42 0.00 41.69 3.24
1797 7279 8.734218 TGTCTATCGAGTCAATAGGTATATCC 57.266 38.462 0.00 0.00 0.00 2.59
2050 11274 7.934665 TGTTCTTTTCCTGTATAACTAGCACAA 59.065 33.333 0.00 0.00 0.00 3.33
2385 11749 8.723942 ACATCTAGAAACTGAATCATTACCAC 57.276 34.615 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.205911 CACACACACCATACACGTGAA 58.794 47.619 25.01 0.00 35.17 3.18
6 7 1.137282 ACACACACACCATACACGTGA 59.863 47.619 25.01 6.34 35.17 4.35
11 12 2.284190 CACACACACACACACCATACA 58.716 47.619 0.00 0.00 0.00 2.29
13 14 1.304254 GCACACACACACACACCATA 58.696 50.000 0.00 0.00 0.00 2.74
14 15 0.679321 TGCACACACACACACACCAT 60.679 50.000 0.00 0.00 0.00 3.55
15 16 0.679321 ATGCACACACACACACACCA 60.679 50.000 0.00 0.00 0.00 4.17
16 17 0.455410 AATGCACACACACACACACC 59.545 50.000 0.00 0.00 0.00 4.16
18 19 1.670295 GAGAATGCACACACACACACA 59.330 47.619 0.00 0.00 0.00 3.72
19 20 1.942657 AGAGAATGCACACACACACAC 59.057 47.619 0.00 0.00 0.00 3.82
20 21 2.330440 AGAGAATGCACACACACACA 57.670 45.000 0.00 0.00 0.00 3.72
191 5563 8.478877 GGAGATGTGGTAGAGATAAAAAGAAGA 58.521 37.037 0.00 0.00 0.00 2.87
192 5564 8.260818 TGGAGATGTGGTAGAGATAAAAAGAAG 58.739 37.037 0.00 0.00 0.00 2.85
278 5653 1.065401 CGAATACCCGTGCATTGCAAT 59.935 47.619 13.94 5.99 41.47 3.56
289 5664 2.031333 GGAGTACTAGTGCGAATACCCG 60.031 54.545 5.39 0.00 0.00 5.28
297 5672 2.023318 CGGAGGGAGTACTAGTGCG 58.977 63.158 5.39 0.00 0.00 5.34
311 5686 3.334691 TGCAGAGTAAAAATGACCGGAG 58.665 45.455 9.46 0.00 0.00 4.63
312 5687 3.410631 TGCAGAGTAAAAATGACCGGA 57.589 42.857 9.46 0.00 0.00 5.14
313 5688 6.377327 AATATGCAGAGTAAAAATGACCGG 57.623 37.500 0.00 0.00 0.00 5.28
314 5689 7.226720 ACCTAATATGCAGAGTAAAAATGACCG 59.773 37.037 0.00 0.00 0.00 4.79
315 5690 8.451908 ACCTAATATGCAGAGTAAAAATGACC 57.548 34.615 0.00 0.00 0.00 4.02
320 5695 8.736244 GGACAAACCTAATATGCAGAGTAAAAA 58.264 33.333 0.00 0.00 35.41 1.94
321 5696 7.065324 CGGACAAACCTAATATGCAGAGTAAAA 59.935 37.037 0.00 0.00 36.31 1.52
322 5697 6.537301 CGGACAAACCTAATATGCAGAGTAAA 59.463 38.462 0.00 0.00 36.31 2.01
323 5698 6.046593 CGGACAAACCTAATATGCAGAGTAA 58.953 40.000 0.00 0.00 36.31 2.24
324 5699 5.361571 TCGGACAAACCTAATATGCAGAGTA 59.638 40.000 0.00 0.00 36.31 2.59
325 5700 4.161565 TCGGACAAACCTAATATGCAGAGT 59.838 41.667 0.00 0.00 36.31 3.24
326 5701 4.693283 TCGGACAAACCTAATATGCAGAG 58.307 43.478 0.00 0.00 36.31 3.35
327 5702 4.746535 TCGGACAAACCTAATATGCAGA 57.253 40.909 0.00 0.00 36.31 4.26
328 5703 4.876107 ACTTCGGACAAACCTAATATGCAG 59.124 41.667 0.00 0.00 36.31 4.41
329 5704 4.839121 ACTTCGGACAAACCTAATATGCA 58.161 39.130 0.00 0.00 36.31 3.96
330 5705 4.873827 TGACTTCGGACAAACCTAATATGC 59.126 41.667 0.00 0.00 36.31 3.14
331 5706 6.978343 TTGACTTCGGACAAACCTAATATG 57.022 37.500 0.00 0.00 36.31 1.78
332 5707 7.565680 AGATTGACTTCGGACAAACCTAATAT 58.434 34.615 0.00 0.00 33.90 1.28
333 5708 6.942976 AGATTGACTTCGGACAAACCTAATA 58.057 36.000 0.00 0.00 33.90 0.98
334 5709 5.805728 AGATTGACTTCGGACAAACCTAAT 58.194 37.500 0.00 0.00 33.90 1.73
335 5710 5.221561 TGAGATTGACTTCGGACAAACCTAA 60.222 40.000 0.00 0.00 33.90 2.69
336 5711 4.282449 TGAGATTGACTTCGGACAAACCTA 59.718 41.667 0.00 0.00 33.90 3.08
337 5712 3.071023 TGAGATTGACTTCGGACAAACCT 59.929 43.478 0.00 0.00 33.90 3.50
338 5713 3.399330 TGAGATTGACTTCGGACAAACC 58.601 45.455 0.00 0.00 33.90 3.27
339 5714 4.093556 GGATGAGATTGACTTCGGACAAAC 59.906 45.833 0.00 0.00 33.90 2.93
340 5715 4.253685 GGATGAGATTGACTTCGGACAAA 58.746 43.478 0.00 0.00 33.90 2.83
341 5716 3.260632 TGGATGAGATTGACTTCGGACAA 59.739 43.478 0.00 0.00 34.59 3.18
342 5717 2.831526 TGGATGAGATTGACTTCGGACA 59.168 45.455 0.00 0.00 0.00 4.02
343 5718 3.526931 TGGATGAGATTGACTTCGGAC 57.473 47.619 0.00 0.00 0.00 4.79
344 5719 3.515502 AGTTGGATGAGATTGACTTCGGA 59.484 43.478 0.00 0.00 0.00 4.55
345 5720 3.866651 AGTTGGATGAGATTGACTTCGG 58.133 45.455 0.00 0.00 0.00 4.30
346 5721 5.409520 TCAAAGTTGGATGAGATTGACTTCG 59.590 40.000 0.00 0.00 0.00 3.79
347 5722 6.348868 GGTCAAAGTTGGATGAGATTGACTTC 60.349 42.308 13.97 0.00 43.66 3.01
348 5723 5.474876 GGTCAAAGTTGGATGAGATTGACTT 59.525 40.000 13.97 0.00 43.66 3.01
349 5724 5.006386 GGTCAAAGTTGGATGAGATTGACT 58.994 41.667 13.97 0.00 43.66 3.41
350 5725 4.761739 TGGTCAAAGTTGGATGAGATTGAC 59.238 41.667 7.68 7.68 43.51 3.18
351 5726 4.984295 TGGTCAAAGTTGGATGAGATTGA 58.016 39.130 0.00 0.00 0.00 2.57
352 5727 5.706916 CTTGGTCAAAGTTGGATGAGATTG 58.293 41.667 0.00 0.00 0.00 2.67
353 5728 5.972107 CTTGGTCAAAGTTGGATGAGATT 57.028 39.130 0.00 0.00 0.00 2.40
388 5763 9.679661 TGGTGTTGTTATGTGAATGTCTATAAT 57.320 29.630 0.00 0.00 0.00 1.28
389 5764 9.508642 TTGGTGTTGTTATGTGAATGTCTATAA 57.491 29.630 0.00 0.00 0.00 0.98
390 5765 9.679661 ATTGGTGTTGTTATGTGAATGTCTATA 57.320 29.630 0.00 0.00 0.00 1.31
391 5766 7.994425 TTGGTGTTGTTATGTGAATGTCTAT 57.006 32.000 0.00 0.00 0.00 1.98
392 5767 7.994425 ATTGGTGTTGTTATGTGAATGTCTA 57.006 32.000 0.00 0.00 0.00 2.59
393 5768 6.899393 ATTGGTGTTGTTATGTGAATGTCT 57.101 33.333 0.00 0.00 0.00 3.41
394 5769 8.458052 TGATATTGGTGTTGTTATGTGAATGTC 58.542 33.333 0.00 0.00 0.00 3.06
395 5770 8.347004 TGATATTGGTGTTGTTATGTGAATGT 57.653 30.769 0.00 0.00 0.00 2.71
396 5771 9.806203 AATGATATTGGTGTTGTTATGTGAATG 57.194 29.630 0.00 0.00 0.00 2.67
399 5774 9.898152 TCTAATGATATTGGTGTTGTTATGTGA 57.102 29.630 0.00 0.00 0.00 3.58
406 5781 9.857656 AGATGAATCTAATGATATTGGTGTTGT 57.142 29.630 0.00 0.00 34.85 3.32
409 5784 9.293404 CCAAGATGAATCTAATGATATTGGTGT 57.707 33.333 0.00 0.00 35.76 4.16
410 5785 9.511272 TCCAAGATGAATCTAATGATATTGGTG 57.489 33.333 0.00 0.00 35.76 4.17
508 5883 9.508155 TGGATTTGCCGAAAGTCAAACTTTGAT 62.508 37.037 9.65 0.00 42.50 2.57
509 5884 8.293065 TGGATTTGCCGAAAGTCAAACTTTGA 62.293 38.462 9.65 0.00 42.50 2.69
510 5885 6.190408 TGGATTTGCCGAAAGTCAAACTTTG 61.190 40.000 9.65 0.00 42.50 2.77
511 5886 4.142049 TGGATTTGCCGAAAGTCAAACTTT 60.142 37.500 4.82 4.82 41.99 2.66
512 5887 3.383185 TGGATTTGCCGAAAGTCAAACTT 59.617 39.130 0.00 0.00 38.90 2.66
513 5888 2.955660 TGGATTTGCCGAAAGTCAAACT 59.044 40.909 0.00 0.00 40.66 2.66
514 5889 3.363341 TGGATTTGCCGAAAGTCAAAC 57.637 42.857 0.00 0.00 40.66 2.93
515 5890 4.202202 ACATTGGATTTGCCGAAAGTCAAA 60.202 37.500 0.00 0.00 40.66 2.69
516 5891 3.320541 ACATTGGATTTGCCGAAAGTCAA 59.679 39.130 0.00 0.00 40.66 3.18
517 5892 2.890311 ACATTGGATTTGCCGAAAGTCA 59.110 40.909 0.00 0.00 40.66 3.41
518 5893 3.244976 CACATTGGATTTGCCGAAAGTC 58.755 45.455 0.00 0.00 40.66 3.01
519 5894 2.610232 GCACATTGGATTTGCCGAAAGT 60.610 45.455 0.00 0.00 40.66 2.66
520 5895 1.994779 GCACATTGGATTTGCCGAAAG 59.005 47.619 0.00 0.00 40.66 2.62
521 5896 1.342496 TGCACATTGGATTTGCCGAAA 59.658 42.857 0.00 0.00 40.66 3.46
522 5897 0.964700 TGCACATTGGATTTGCCGAA 59.035 45.000 0.00 0.00 40.66 4.30
523 5898 0.527113 CTGCACATTGGATTTGCCGA 59.473 50.000 0.00 0.00 40.66 5.54
524 5899 0.527113 TCTGCACATTGGATTTGCCG 59.473 50.000 0.00 0.00 40.66 5.69
525 5900 1.547372 ACTCTGCACATTGGATTTGCC 59.453 47.619 0.00 0.00 35.26 4.52
526 5901 4.439305 TTACTCTGCACATTGGATTTGC 57.561 40.909 0.00 0.00 36.76 3.68
527 5902 6.366877 CCTTTTTACTCTGCACATTGGATTTG 59.633 38.462 0.00 0.00 0.00 2.32
528 5903 6.267471 TCCTTTTTACTCTGCACATTGGATTT 59.733 34.615 0.00 0.00 0.00 2.17
529 5904 5.774690 TCCTTTTTACTCTGCACATTGGATT 59.225 36.000 0.00 0.00 0.00 3.01
530 5905 5.183904 GTCCTTTTTACTCTGCACATTGGAT 59.816 40.000 0.00 0.00 0.00 3.41
531 5906 4.518970 GTCCTTTTTACTCTGCACATTGGA 59.481 41.667 0.00 0.00 0.00 3.53
532 5907 4.321230 GGTCCTTTTTACTCTGCACATTGG 60.321 45.833 0.00 0.00 0.00 3.16
533 5908 4.613622 CGGTCCTTTTTACTCTGCACATTG 60.614 45.833 0.00 0.00 0.00 2.82
534 5909 3.502211 CGGTCCTTTTTACTCTGCACATT 59.498 43.478 0.00 0.00 0.00 2.71
535 5910 3.074412 CGGTCCTTTTTACTCTGCACAT 58.926 45.455 0.00 0.00 0.00 3.21
536 5911 2.489971 CGGTCCTTTTTACTCTGCACA 58.510 47.619 0.00 0.00 0.00 4.57
537 5912 1.804748 CCGGTCCTTTTTACTCTGCAC 59.195 52.381 0.00 0.00 0.00 4.57
538 5913 1.695242 TCCGGTCCTTTTTACTCTGCA 59.305 47.619 0.00 0.00 0.00 4.41
539 5914 2.347731 CTCCGGTCCTTTTTACTCTGC 58.652 52.381 0.00 0.00 0.00 4.26
540 5915 2.354805 CCCTCCGGTCCTTTTTACTCTG 60.355 54.545 0.00 0.00 0.00 3.35
541 5916 1.907255 CCCTCCGGTCCTTTTTACTCT 59.093 52.381 0.00 0.00 0.00 3.24
542 5917 1.904537 TCCCTCCGGTCCTTTTTACTC 59.095 52.381 0.00 0.00 0.00 2.59
543 5918 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
544 5919 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
545 5920 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
546 5921 2.034436 TACTCCCTCCGGTCCTTTTT 57.966 50.000 0.00 0.00 0.00 1.94
547 5922 2.265526 ATACTCCCTCCGGTCCTTTT 57.734 50.000 0.00 0.00 0.00 2.27
548 5923 3.142407 AGATATACTCCCTCCGGTCCTTT 59.858 47.826 0.00 0.00 0.00 3.11
549 5924 2.723010 AGATATACTCCCTCCGGTCCTT 59.277 50.000 0.00 0.00 0.00 3.36
550 5925 2.309458 GAGATATACTCCCTCCGGTCCT 59.691 54.545 0.00 0.00 39.53 3.85
551 5926 2.309458 AGAGATATACTCCCTCCGGTCC 59.691 54.545 0.00 0.00 45.96 4.46
552 5927 3.724732 AGAGATATACTCCCTCCGGTC 57.275 52.381 0.00 0.00 45.96 4.79
553 5928 5.595814 TTTAGAGATATACTCCCTCCGGT 57.404 43.478 0.00 0.00 45.96 5.28
554 5929 8.591114 TTATTTTAGAGATATACTCCCTCCGG 57.409 38.462 0.00 0.00 45.96 5.14
594 5969 7.768582 ACAACCTTCTTTTTCCAGTAAAATTGG 59.231 33.333 0.00 0.00 36.94 3.16
595 5970 8.716646 ACAACCTTCTTTTTCCAGTAAAATTG 57.283 30.769 0.00 0.00 36.94 2.32
596 5971 7.985184 GGACAACCTTCTTTTTCCAGTAAAATT 59.015 33.333 0.00 0.00 36.94 1.82
603 5978 2.293399 CGGGACAACCTTCTTTTTCCAG 59.707 50.000 0.00 0.00 36.97 3.86
604 5979 2.303175 CGGGACAACCTTCTTTTTCCA 58.697 47.619 0.00 0.00 36.97 3.53
709 6084 5.188327 AGTCGACTGTACATATCCACATG 57.812 43.478 19.30 0.00 0.00 3.21
809 6190 3.181540 GCAGAGCGCGTGTATGTATAATG 60.182 47.826 8.43 0.00 0.00 1.90
967 6427 6.942576 TGCTTTCTCCTTGCTAGAGTAAATTT 59.057 34.615 0.00 0.00 32.93 1.82
981 6441 4.077822 CCATGTCTCTTTGCTTTCTCCTT 58.922 43.478 0.00 0.00 0.00 3.36
1113 6573 2.105649 TGTGCATGTTGTACCTGGAGAA 59.894 45.455 0.00 0.00 31.71 2.87
1143 6607 4.025360 TGCTTTGCTACAATTCCATGGAT 58.975 39.130 17.06 2.53 0.00 3.41
1160 6630 2.893424 ACCAAGATGGGTGATTGCTTT 58.107 42.857 0.87 0.00 43.37 3.51
1331 6805 2.277692 CCGATCTGCGCGACGTTA 60.278 61.111 12.10 0.00 39.11 3.18
1850 11061 5.067936 AGGACACAATATCCTCGACTTACAG 59.932 44.000 0.00 0.00 43.49 2.74
2159 11403 6.865834 TGGTTTTAAAATCCTGCATACCAT 57.134 33.333 8.70 0.00 0.00 3.55
2455 11819 6.529829 TGTGATTTGGTTTTCTCAAAAAGTCG 59.470 34.615 0.00 0.00 37.60 4.18
2684 12078 3.436700 AAGAAAACCTTTGCTTCACCG 57.563 42.857 0.00 0.00 30.06 4.94


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

AutoCloner maintained by Alex Coulton.