Multiple sequence alignment - TraesCS5A01G415300

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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 TraesCS5A01G415300 chr5A 100.000 2639 0 0 1 2639 603528522 603531160 0.000000e+00 4874.0
1 TraesCS5A01G415300 chr5A 83.715 829 122 10 856 1682 603503340 603504157 0.000000e+00 771.0
2 TraesCS5A01G415300 chr5A 85.083 181 24 2 693 872 603503142 603503320 5.800000e-42 182.0
3 TraesCS5A01G415300 chr5A 79.126 206 23 13 747 939 613465934 613465736 9.920000e-25 124.0
4 TraesCS5A01G415300 chr5B 92.610 1042 68 4 641 1682 592836321 592837353 0.000000e+00 1489.0
5 TraesCS5A01G415300 chr5B 91.495 388 27 4 2207 2590 592837898 592838283 1.800000e-146 529.0
6 TraesCS5A01G415300 chr5B 88.235 340 39 1 2 341 592835862 592836200 3.160000e-109 405.0
7 TraesCS5A01G415300 chr5B 78.087 575 78 25 974 1521 606821934 606822487 1.180000e-83 320.0
8 TraesCS5A01G415300 chr5B 78.889 360 56 12 1295 1640 605531394 605531041 2.640000e-55 226.0
9 TraesCS5A01G415300 chr5B 95.455 44 1 1 2594 2636 592853620 592853663 4.710000e-08 69.4
10 TraesCS5A01G415300 chr5D 93.765 818 44 3 998 1811 482907143 482907957 0.000000e+00 1221.0
11 TraesCS5A01G415300 chr5D 84.660 691 99 6 993 1682 482900664 482901348 0.000000e+00 682.0
12 TraesCS5A01G415300 chr5D 93.077 390 14 6 1802 2191 482908367 482908743 2.290000e-155 558.0
13 TraesCS5A01G415300 chr5D 91.288 264 15 3 690 953 482906880 482907135 1.160000e-93 353.0
14 TraesCS5A01G415300 chr5D 93.333 225 15 0 2415 2639 482908904 482909128 1.510000e-87 333.0
15 TraesCS5A01G415300 chr5D 92.558 215 16 0 2 216 482903626 482903840 2.550000e-80 309.0
16 TraesCS5A01G415300 chr5D 93.023 172 11 1 2206 2377 482908729 482908899 1.570000e-62 250.0
17 TraesCS5A01G415300 chr5D 86.188 181 22 3 693 872 482900365 482900543 2.680000e-45 193.0
18 TraesCS5A01G415300 chr5D 79.902 204 24 10 747 939 490977609 490977412 1.650000e-27 134.0
19 TraesCS5A01G415300 chr5D 87.097 62 5 3 747 806 491727314 491727374 1.700000e-07 67.6
20 TraesCS5A01G415300 chr2A 85.833 120 17 0 227 346 194180252 194180371 7.670000e-26 128.0
21 TraesCS5A01G415300 chr7D 83.333 120 20 0 227 346 613409470 613409351 7.720000e-21 111.0
22 TraesCS5A01G415300 chr1D 85.185 108 15 1 227 334 109929072 109929178 2.780000e-20 110.0
23 TraesCS5A01G415300 chr7A 82.500 120 21 0 227 346 731973703 731973822 3.590000e-19 106.0
24 TraesCS5A01G415300 chr7B 82.203 118 21 0 405 522 419416838 419416955 4.650000e-18 102.0
25 TraesCS5A01G415300 chr6B 81.667 120 22 0 227 346 422362176 422362295 1.670000e-17 100.0
26 TraesCS5A01G415300 chr3B 80.000 140 22 5 407 542 737609958 737609821 6.010000e-17 99.0
27 TraesCS5A01G415300 chr6D 83.750 80 7 4 537 610 391697622 391697543 1.310000e-08 71.3
28 TraesCS5A01G415300 chr2B 80.198 101 13 2 537 631 491005118 491005019 4.710000e-08 69.4


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 TraesCS5A01G415300 chr5A 603528522 603531160 2638 False 4874.000000 4874 100.0000 1 2639 1 chr5A.!!$F1 2638
1 TraesCS5A01G415300 chr5A 603503142 603504157 1015 False 476.500000 771 84.3990 693 1682 2 chr5A.!!$F2 989
2 TraesCS5A01G415300 chr5B 592835862 592838283 2421 False 807.666667 1489 90.7800 2 2590 3 chr5B.!!$F3 2588
3 TraesCS5A01G415300 chr5B 606821934 606822487 553 False 320.000000 320 78.0870 974 1521 1 chr5B.!!$F2 547
4 TraesCS5A01G415300 chr5D 482900365 482909128 8763 False 487.375000 1221 90.9865 2 2639 8 chr5D.!!$F2 2637

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
652 6447 0.036164 TGTCCACGGATGTTTGAGGG 59.964 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 8604 0.035056 AAAGTCCAGGAGATTGGCGG 60.035 55.0 0.0 0.0 38.16 6.13 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
23 3284 5.644188 CCCATTTCCCATGGAGTGTATATT 58.356 41.667 15.22 0.00 41.64 1.28
81 3342 2.504996 TGATGTGATGTGCCACCTCATA 59.495 45.455 6.09 4.17 36.98 2.15
84 3345 2.504996 TGTGATGTGCCACCTCATATCA 59.495 45.455 6.09 0.00 40.62 2.15
115 3376 3.745799 TCTTCGGTGAACAAAGCCAATA 58.254 40.909 0.00 0.00 0.00 1.90
129 3390 4.118093 AGCCAATAACGTAAAATTGCCC 57.882 40.909 10.96 6.10 32.79 5.36
219 3480 6.480651 CCTCAGAACAAAGAGATCATCATCTG 59.519 42.308 0.00 0.00 39.71 2.90
231 3492 3.451526 TCATCATCTGCGCTTTGAGTAG 58.548 45.455 9.73 0.00 0.00 2.57
238 3499 3.159298 CGCTTTGAGTAGGGCATGT 57.841 52.632 0.00 0.00 0.00 3.21
243 3504 3.869912 GCTTTGAGTAGGGCATGTGAGAA 60.870 47.826 0.00 0.00 0.00 2.87
294 4280 3.901844 TCATAACCCATGCCCTACTCTAC 59.098 47.826 0.00 0.00 34.35 2.59
295 4281 2.570386 AACCCATGCCCTACTCTACT 57.430 50.000 0.00 0.00 0.00 2.57
298 4284 2.505819 ACCCATGCCCTACTCTACTTTG 59.494 50.000 0.00 0.00 0.00 2.77
307 4293 1.810030 CTCTACTTTGCCGGCGACC 60.810 63.158 23.90 0.00 0.00 4.79
312 4298 3.883744 CTTTGCCGGCGACCAGACT 62.884 63.158 23.90 0.00 0.00 3.24
320 4306 0.108756 GGCGACCAGACTAACACTCC 60.109 60.000 0.00 0.00 0.00 3.85
376 5161 6.258160 GCTTAAAGATCATTGTACGTTGCAT 58.742 36.000 0.00 0.00 0.00 3.96
377 5162 6.195244 GCTTAAAGATCATTGTACGTTGCATG 59.805 38.462 0.00 0.00 0.00 4.06
378 5163 5.627499 AAAGATCATTGTACGTTGCATGT 57.373 34.783 0.00 0.00 0.00 3.21
381 5166 6.925610 AGATCATTGTACGTTGCATGTAAT 57.074 33.333 0.00 0.00 0.00 1.89
382 5167 6.948353 AGATCATTGTACGTTGCATGTAATC 58.052 36.000 0.00 1.93 0.00 1.75
383 5168 6.538381 AGATCATTGTACGTTGCATGTAATCA 59.462 34.615 0.00 0.00 0.00 2.57
384 5169 6.487689 TCATTGTACGTTGCATGTAATCAA 57.512 33.333 0.00 4.58 0.00 2.57
385 5170 7.082700 TCATTGTACGTTGCATGTAATCAAT 57.917 32.000 0.00 6.48 0.00 2.57
387 5172 5.228579 TGTACGTTGCATGTAATCAATGG 57.771 39.130 0.00 0.00 34.45 3.16
388 5173 3.149436 ACGTTGCATGTAATCAATGGC 57.851 42.857 0.00 0.00 34.45 4.40
389 5174 2.110990 CGTTGCATGTAATCAATGGCG 58.889 47.619 0.00 0.00 0.00 5.69
390 5175 2.477694 CGTTGCATGTAATCAATGGCGT 60.478 45.455 0.00 0.00 0.00 5.68
391 5176 3.242576 CGTTGCATGTAATCAATGGCGTA 60.243 43.478 0.00 0.00 0.00 4.42
392 5177 4.282068 GTTGCATGTAATCAATGGCGTAG 58.718 43.478 0.00 0.00 0.00 3.51
407 5653 1.281656 GTAGCCAACACAACGCCAC 59.718 57.895 0.00 0.00 0.00 5.01
411 5657 4.622456 CAACACAACGCCACGCCC 62.622 66.667 0.00 0.00 0.00 6.13
426 5672 3.655211 CCCAGGGCCAGCTTCAGT 61.655 66.667 6.18 0.00 0.00 3.41
427 5673 2.360852 CCAGGGCCAGCTTCAGTG 60.361 66.667 6.18 0.00 0.00 3.66
429 5675 3.255397 AGGGCCAGCTTCAGTGCT 61.255 61.111 6.18 0.00 45.18 4.40
430 5676 1.920325 AGGGCCAGCTTCAGTGCTA 60.920 57.895 6.18 0.00 41.98 3.49
431 5677 1.746991 GGGCCAGCTTCAGTGCTAC 60.747 63.158 4.39 0.00 41.98 3.58
432 5678 1.003355 GGCCAGCTTCAGTGCTACA 60.003 57.895 0.00 0.00 41.98 2.74
433 5679 1.023513 GGCCAGCTTCAGTGCTACAG 61.024 60.000 0.00 0.00 41.98 2.74
434 5680 1.023513 GCCAGCTTCAGTGCTACAGG 61.024 60.000 0.00 0.00 41.98 4.00
436 5682 1.023513 CAGCTTCAGTGCTACAGGGC 61.024 60.000 0.00 0.00 41.98 5.19
437 5683 1.746991 GCTTCAGTGCTACAGGGCC 60.747 63.158 0.00 0.00 0.00 5.80
438 5684 1.679311 CTTCAGTGCTACAGGGCCA 59.321 57.895 6.18 0.00 0.00 5.36
439 5685 0.036732 CTTCAGTGCTACAGGGCCAA 59.963 55.000 6.18 0.00 0.00 4.52
440 5686 0.476338 TTCAGTGCTACAGGGCCAAA 59.524 50.000 6.18 0.00 0.00 3.28
441 5687 0.250727 TCAGTGCTACAGGGCCAAAC 60.251 55.000 6.18 0.00 0.00 2.93
442 5688 0.537143 CAGTGCTACAGGGCCAAACA 60.537 55.000 6.18 0.00 0.00 2.83
443 5689 0.250901 AGTGCTACAGGGCCAAACAG 60.251 55.000 6.18 0.00 0.00 3.16
444 5690 0.537371 GTGCTACAGGGCCAAACAGT 60.537 55.000 6.18 0.00 0.00 3.55
445 5691 1.060729 TGCTACAGGGCCAAACAGTA 58.939 50.000 6.18 0.00 0.00 2.74
446 5692 1.271163 TGCTACAGGGCCAAACAGTAC 60.271 52.381 6.18 0.00 0.00 2.73
448 5694 1.349688 CTACAGGGCCAAACAGTACCA 59.650 52.381 6.18 0.00 0.00 3.25
449 5695 0.553819 ACAGGGCCAAACAGTACCAA 59.446 50.000 6.18 0.00 0.00 3.67
450 5696 1.063567 ACAGGGCCAAACAGTACCAAA 60.064 47.619 6.18 0.00 0.00 3.28
451 5697 1.339929 CAGGGCCAAACAGTACCAAAC 59.660 52.381 6.18 0.00 0.00 2.93
452 5698 0.677288 GGGCCAAACAGTACCAAACC 59.323 55.000 4.39 0.00 0.00 3.27
453 5699 0.312729 GGCCAAACAGTACCAAACCG 59.687 55.000 0.00 0.00 0.00 4.44
454 5700 1.026584 GCCAAACAGTACCAAACCGT 58.973 50.000 0.00 0.00 0.00 4.83
455 5701 1.002142 GCCAAACAGTACCAAACCGTC 60.002 52.381 0.00 0.00 0.00 4.79
456 5702 2.290464 CCAAACAGTACCAAACCGTCA 58.710 47.619 0.00 0.00 0.00 4.35
457 5703 2.882137 CCAAACAGTACCAAACCGTCAT 59.118 45.455 0.00 0.00 0.00 3.06
458 5704 4.066490 CCAAACAGTACCAAACCGTCATA 58.934 43.478 0.00 0.00 0.00 2.15
461 5707 6.372103 CCAAACAGTACCAAACCGTCATATTA 59.628 38.462 0.00 0.00 0.00 0.98
462 5708 7.066525 CCAAACAGTACCAAACCGTCATATTAT 59.933 37.037 0.00 0.00 0.00 1.28
463 5709 9.100554 CAAACAGTACCAAACCGTCATATTATA 57.899 33.333 0.00 0.00 0.00 0.98
464 5710 9.841295 AAACAGTACCAAACCGTCATATTATAT 57.159 29.630 0.00 0.00 0.00 0.86
466 5712 8.426489 ACAGTACCAAACCGTCATATTATATGT 58.574 33.333 11.44 0.00 0.00 2.29
467 5713 9.917129 CAGTACCAAACCGTCATATTATATGTA 57.083 33.333 11.44 0.00 0.00 2.29
469 5715 9.695526 GTACCAAACCGTCATATTATATGTACA 57.304 33.333 11.44 0.00 0.00 2.90
471 5717 9.787435 ACCAAACCGTCATATTATATGTACAAT 57.213 29.630 11.44 0.00 0.00 2.71
476 5722 9.135843 ACCGTCATATTATATGTACAATGAACG 57.864 33.333 11.44 10.64 0.00 3.95
477 5723 9.349145 CCGTCATATTATATGTACAATGAACGA 57.651 33.333 18.67 3.74 0.00 3.85
488 5734 7.079182 TGTACAATGAACGAAGAAAGTTGTT 57.921 32.000 0.00 0.00 31.57 2.83
489 5735 6.964370 TGTACAATGAACGAAGAAAGTTGTTG 59.036 34.615 0.00 0.00 33.63 3.33
490 5736 4.798387 ACAATGAACGAAGAAAGTTGTTGC 59.202 37.500 0.00 0.00 32.08 4.17
492 5738 2.750166 TGAACGAAGAAAGTTGTTGCCA 59.250 40.909 0.00 0.00 31.14 4.92
493 5739 2.844122 ACGAAGAAAGTTGTTGCCAC 57.156 45.000 0.00 0.00 0.00 5.01
494 5740 1.063469 ACGAAGAAAGTTGTTGCCACG 59.937 47.619 0.00 0.00 0.00 4.94
496 5742 0.102300 AAGAAAGTTGTTGCCACGCC 59.898 50.000 0.00 0.00 0.00 5.68
498 5744 1.734388 GAAAGTTGTTGCCACGCCCT 61.734 55.000 0.00 0.00 0.00 5.19
499 5745 2.015227 AAAGTTGTTGCCACGCCCTG 62.015 55.000 0.00 0.00 0.00 4.45
500 5746 3.977244 GTTGTTGCCACGCCCTGG 61.977 66.667 0.00 0.00 44.08 4.45
527 5773 4.404654 CTTGTTGCCCGGCTTCGC 62.405 66.667 11.61 0.00 0.00 4.70
528 5774 4.947147 TTGTTGCCCGGCTTCGCT 62.947 61.111 11.61 0.00 0.00 4.93
529 5775 3.538785 TTGTTGCCCGGCTTCGCTA 62.539 57.895 11.61 0.00 0.00 4.26
532 5778 4.752879 TGCCCGGCTTCGCTACAC 62.753 66.667 11.61 0.00 0.00 2.90
534 5780 4.077184 CCCGGCTTCGCTACACCA 62.077 66.667 0.00 0.00 0.00 4.17
535 5781 2.813908 CCGGCTTCGCTACACCAC 60.814 66.667 0.00 0.00 0.00 4.16
536 5782 2.261671 CGGCTTCGCTACACCACT 59.738 61.111 0.00 0.00 0.00 4.00
572 5818 8.716674 ATATGGATTTGAGATTTGCAGGTATT 57.283 30.769 0.00 0.00 0.00 1.89
574 5820 5.951148 TGGATTTGAGATTTGCAGGTATTCA 59.049 36.000 0.00 0.00 0.00 2.57
581 5827 4.885907 AGATTTGCAGGTATTCAGATGTGG 59.114 41.667 0.00 0.00 0.00 4.17
597 5843 8.750515 TCAGATGTGGAATGCATTATTTAAGA 57.249 30.769 12.97 1.68 0.00 2.10
599 5845 7.588854 CAGATGTGGAATGCATTATTTAAGACG 59.411 37.037 12.97 0.00 0.00 4.18
602 5848 6.372937 TGTGGAATGCATTATTTAAGACGTGA 59.627 34.615 12.97 0.00 0.00 4.35
603 5849 6.687105 GTGGAATGCATTATTTAAGACGTGAC 59.313 38.462 12.97 0.00 0.00 3.67
604 5850 6.183360 TGGAATGCATTATTTAAGACGTGACC 60.183 38.462 12.97 4.56 0.00 4.02
606 5852 3.619483 TGCATTATTTAAGACGTGACCGG 59.381 43.478 0.00 0.00 38.78 5.28
607 5853 3.619929 GCATTATTTAAGACGTGACCGGT 59.380 43.478 6.92 6.92 38.78 5.28
608 5854 4.260091 GCATTATTTAAGACGTGACCGGTC 60.260 45.833 28.17 28.17 38.78 4.79
609 5855 4.517952 TTATTTAAGACGTGACCGGTCA 57.482 40.909 33.23 33.23 38.78 4.02
610 5856 2.886862 TTTAAGACGTGACCGGTCAA 57.113 45.000 37.75 19.46 41.85 3.18
611 5857 3.389925 TTTAAGACGTGACCGGTCAAT 57.610 42.857 37.75 28.23 41.85 2.57
612 5858 2.357327 TAAGACGTGACCGGTCAATG 57.643 50.000 37.75 31.97 41.85 2.82
614 5860 0.391597 AGACGTGACCGGTCAATGTT 59.608 50.000 37.75 23.26 41.85 2.71
652 6447 0.036164 TGTCCACGGATGTTTGAGGG 59.964 55.000 0.00 0.00 0.00 4.30
659 6454 0.392595 GGATGTTTGAGGGGTCGGAC 60.393 60.000 0.00 0.00 0.00 4.79
688 6483 2.355244 GGCGGTAGATGCTCTCGC 60.355 66.667 0.00 0.00 44.80 5.03
728 6576 1.552792 TCTGCACCGATGACACCAATA 59.447 47.619 0.00 0.00 0.00 1.90
729 6577 2.170397 TCTGCACCGATGACACCAATAT 59.830 45.455 0.00 0.00 0.00 1.28
796 6644 1.750778 CCCATACAATTGCCACCACTC 59.249 52.381 5.05 0.00 0.00 3.51
810 6658 3.309506 ACTCGCCAGCTGCTGTCT 61.310 61.111 26.41 0.00 38.05 3.41
818 6666 1.180907 CAGCTGCTGTCTCTACCTCA 58.819 55.000 21.21 0.00 0.00 3.86
828 6676 1.856259 TCTCTACCTCAGGCCAGAGAT 59.144 52.381 25.74 12.47 38.47 2.75
834 6682 3.663198 ACCTCAGGCCAGAGATAAGAAT 58.337 45.455 25.74 0.31 37.87 2.40
867 6716 5.506317 GGCAACGGTGATAACTACGTATACT 60.506 44.000 3.55 0.00 38.79 2.12
880 6765 2.465855 CGTATACTTACGTGCCATGCA 58.534 47.619 0.00 0.00 44.84 3.96
881 6766 3.057019 CGTATACTTACGTGCCATGCAT 58.943 45.455 0.00 0.00 44.84 3.96
1162 7048 2.507484 CTGAGGCCAATCAGTTTGTGA 58.493 47.619 12.79 0.00 41.52 3.58
1251 7166 0.978385 CTTCTCTGCGACGAGAAACG 59.022 55.000 14.90 0.00 46.19 3.60
1268 7183 4.220602 AGAAACGAATTAAATTGCCTGCCT 59.779 37.500 0.00 0.00 0.00 4.75
1292 7207 5.139435 TCCCTCATGCTAATTATGTCGAG 57.861 43.478 0.00 0.00 0.00 4.04
1374 7289 3.741476 GCTTGCAACCAGCCGGAG 61.741 66.667 5.05 0.00 44.83 4.63
1447 7362 2.664851 CGCGGTGGTTCTTCTGCA 60.665 61.111 0.00 0.00 35.91 4.41
1674 7589 7.595502 CCATCGACAAGGTTTCTACTACATATC 59.404 40.741 0.00 0.00 0.00 1.63
1682 7597 6.551601 AGGTTTCTACTACATATCTGACCCAG 59.448 42.308 0.00 0.00 0.00 4.45
1688 7611 1.683917 ACATATCTGACCCAGCGAGAC 59.316 52.381 0.00 0.00 0.00 3.36
1964 8353 9.057089 AGTGTACAGAGATTAACTTTCCAAAAG 57.943 33.333 0.00 0.00 0.00 2.27
1995 8392 1.981495 AGAGTCTAAAGCCTGCTTGGT 59.019 47.619 4.95 0.00 36.26 3.67
2083 8480 4.965814 TCTTAGCTAGAGAATGGGCAATG 58.034 43.478 0.00 0.00 0.00 2.82
2084 8481 4.655649 TCTTAGCTAGAGAATGGGCAATGA 59.344 41.667 0.00 0.00 0.00 2.57
2085 8482 3.488778 AGCTAGAGAATGGGCAATGAG 57.511 47.619 0.00 0.00 0.00 2.90
2086 8483 2.776536 AGCTAGAGAATGGGCAATGAGT 59.223 45.455 0.00 0.00 0.00 3.41
2087 8484 3.137533 GCTAGAGAATGGGCAATGAGTC 58.862 50.000 0.00 0.00 0.00 3.36
2088 8485 3.432749 GCTAGAGAATGGGCAATGAGTCA 60.433 47.826 0.00 0.00 0.00 3.41
2089 8486 3.726557 AGAGAATGGGCAATGAGTCAA 57.273 42.857 0.00 0.00 0.00 3.18
2090 8487 4.246712 AGAGAATGGGCAATGAGTCAAT 57.753 40.909 0.00 0.00 0.00 2.57
2182 8579 7.553881 TTAGCAACTATTGTTCTTATCTGCC 57.446 36.000 0.00 0.00 33.52 4.85
2183 8580 5.500234 AGCAACTATTGTTCTTATCTGCCA 58.500 37.500 0.00 0.00 33.52 4.92
2184 8581 5.945784 AGCAACTATTGTTCTTATCTGCCAA 59.054 36.000 0.00 0.00 33.52 4.52
2185 8582 6.604795 AGCAACTATTGTTCTTATCTGCCAAT 59.395 34.615 0.00 0.00 33.52 3.16
2186 8583 6.914757 GCAACTATTGTTCTTATCTGCCAATC 59.085 38.462 0.00 0.00 33.52 2.67
2187 8584 7.201767 GCAACTATTGTTCTTATCTGCCAATCT 60.202 37.037 0.00 0.00 33.52 2.40
2188 8585 8.341173 CAACTATTGTTCTTATCTGCCAATCTC 58.659 37.037 0.00 0.00 33.52 2.75
2189 8586 6.995091 ACTATTGTTCTTATCTGCCAATCTCC 59.005 38.462 0.00 0.00 0.00 3.71
2190 8587 5.441718 TTGTTCTTATCTGCCAATCTCCT 57.558 39.130 0.00 0.00 0.00 3.69
2191 8588 5.441718 TGTTCTTATCTGCCAATCTCCTT 57.558 39.130 0.00 0.00 0.00 3.36
2192 8589 5.819991 TGTTCTTATCTGCCAATCTCCTTT 58.180 37.500 0.00 0.00 0.00 3.11
2193 8590 6.248433 TGTTCTTATCTGCCAATCTCCTTTT 58.752 36.000 0.00 0.00 0.00 2.27
2194 8591 6.375455 TGTTCTTATCTGCCAATCTCCTTTTC 59.625 38.462 0.00 0.00 0.00 2.29
2195 8592 6.065976 TCTTATCTGCCAATCTCCTTTTCA 57.934 37.500 0.00 0.00 0.00 2.69
2196 8593 6.484288 TCTTATCTGCCAATCTCCTTTTCAA 58.516 36.000 0.00 0.00 0.00 2.69
2197 8594 6.947733 TCTTATCTGCCAATCTCCTTTTCAAA 59.052 34.615 0.00 0.00 0.00 2.69
2198 8595 7.451255 TCTTATCTGCCAATCTCCTTTTCAAAA 59.549 33.333 0.00 0.00 0.00 2.44
2199 8596 5.867903 TCTGCCAATCTCCTTTTCAAAAA 57.132 34.783 0.00 0.00 0.00 1.94
2225 8622 0.909610 TCCGCCAATCTCCTGGACTT 60.910 55.000 0.00 0.00 38.96 3.01
2306 8703 3.054802 CAGAACAGTCCCATCCTAAAGCT 60.055 47.826 0.00 0.00 0.00 3.74
2347 8744 7.495901 TGATAGAGTTAATCCAAGAGCTTCAG 58.504 38.462 0.00 0.00 0.00 3.02
2348 8745 5.753721 AGAGTTAATCCAAGAGCTTCAGT 57.246 39.130 0.00 0.00 0.00 3.41
2380 8777 3.188048 AGAAGAAACATTTCTCGCAGCTG 59.812 43.478 10.11 10.11 46.22 4.24
2475 8872 1.210478 ACCGGATTGTAAGCAGCATCT 59.790 47.619 9.46 0.00 0.00 2.90
2489 8886 3.657634 CAGCATCTCTATACGCCACAAT 58.342 45.455 0.00 0.00 0.00 2.71
2494 8891 5.105877 GCATCTCTATACGCCACAATACCTA 60.106 44.000 0.00 0.00 0.00 3.08
2590 8990 2.057654 ATTGTGCGTCGCAACTGCAA 62.058 50.000 23.58 20.98 41.47 4.08
2591 8991 2.722188 GTGCGTCGCAACTGCAAC 60.722 61.111 23.58 3.46 41.47 4.17
2592 8992 2.894879 TGCGTCGCAACTGCAACT 60.895 55.556 19.38 0.00 42.21 3.16
2615 9015 8.261492 ACTATTATATCTACTGCATTGCAAGC 57.739 34.615 13.18 9.48 38.41 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.600448 ATACACTCCATGGGAAATGGG 57.400 47.619 13.02 1.23 39.60 4.00
5 6 7.663905 CGGAAATAAATATACACTCCATGGGAA 59.336 37.037 13.02 0.00 0.00 3.97
81 3342 5.389859 TCACCGAAGAAAAATTGCATGAT 57.610 34.783 0.00 0.00 0.00 2.45
84 3345 4.942852 TGTTCACCGAAGAAAAATTGCAT 58.057 34.783 0.00 0.00 0.00 3.96
191 3452 5.246883 TGATGATCTCTTTGTTCTGAGGTGA 59.753 40.000 0.00 0.00 0.00 4.02
193 3454 5.752036 TGATGATCTCTTTGTTCTGAGGT 57.248 39.130 0.00 0.00 0.00 3.85
219 3480 1.026718 ACATGCCCTACTCAAAGCGC 61.027 55.000 0.00 0.00 0.00 5.92
231 3492 2.825836 CCGCCTTCTCACATGCCC 60.826 66.667 0.00 0.00 0.00 5.36
255 3516 1.519719 GAGCCGGCTCATGAGACTT 59.480 57.895 44.10 14.80 42.31 3.01
277 4263 2.505819 CAAAGTAGAGTAGGGCATGGGT 59.494 50.000 0.00 0.00 0.00 4.51
294 4280 2.501223 TAGTCTGGTCGCCGGCAAAG 62.501 60.000 28.98 17.14 0.00 2.77
295 4281 2.102109 TTAGTCTGGTCGCCGGCAAA 62.102 55.000 28.98 11.42 0.00 3.68
298 4284 2.508663 GTTAGTCTGGTCGCCGGC 60.509 66.667 19.07 19.07 0.00 6.13
307 4293 1.134560 GCTACCCGGAGTGTTAGTCTG 59.865 57.143 0.73 0.00 0.00 3.51
312 4298 1.978080 TGCGCTACCCGGAGTGTTA 60.978 57.895 9.73 0.00 37.44 2.41
320 4306 4.760047 AGTTGGCTGCGCTACCCG 62.760 66.667 9.73 0.00 40.75 5.28
359 5144 6.714492 TGATTACATGCAACGTACAATGATC 58.286 36.000 10.27 7.29 0.00 2.92
364 5149 5.635866 CCATTGATTACATGCAACGTACAA 58.364 37.500 0.00 0.00 0.00 2.41
366 5151 4.035017 GCCATTGATTACATGCAACGTAC 58.965 43.478 0.00 0.00 0.00 3.67
388 5173 2.248135 TGGCGTTGTGTTGGCTACG 61.248 57.895 0.00 0.00 39.74 3.51
389 5174 1.281656 GTGGCGTTGTGTTGGCTAC 59.718 57.895 0.00 0.00 0.00 3.58
390 5175 2.248135 CGTGGCGTTGTGTTGGCTA 61.248 57.895 0.00 0.00 0.00 3.93
391 5176 3.582120 CGTGGCGTTGTGTTGGCT 61.582 61.111 0.00 0.00 0.00 4.75
394 5179 4.622456 GGGCGTGGCGTTGTGTTG 62.622 66.667 0.00 0.00 0.00 3.33
409 5655 3.655211 ACTGAAGCTGGCCCTGGG 61.655 66.667 8.86 8.86 0.00 4.45
411 5657 2.189191 TAGCACTGAAGCTGGCCCTG 62.189 60.000 0.00 0.00 46.11 4.45
422 5668 0.250727 GTTTGGCCCTGTAGCACTGA 60.251 55.000 0.00 0.00 0.00 3.41
426 5672 1.060729 TACTGTTTGGCCCTGTAGCA 58.939 50.000 0.00 0.00 0.00 3.49
427 5673 1.450025 GTACTGTTTGGCCCTGTAGC 58.550 55.000 0.00 0.00 0.00 3.58
429 5675 1.436326 TGGTACTGTTTGGCCCTGTA 58.564 50.000 0.00 0.00 0.00 2.74
430 5676 0.553819 TTGGTACTGTTTGGCCCTGT 59.446 50.000 0.00 0.00 0.00 4.00
431 5677 1.339929 GTTTGGTACTGTTTGGCCCTG 59.660 52.381 0.00 0.00 0.00 4.45
432 5678 1.699730 GTTTGGTACTGTTTGGCCCT 58.300 50.000 0.00 0.00 0.00 5.19
433 5679 0.677288 GGTTTGGTACTGTTTGGCCC 59.323 55.000 0.00 0.00 0.00 5.80
434 5680 0.312729 CGGTTTGGTACTGTTTGGCC 59.687 55.000 0.00 0.00 0.00 5.36
436 5682 2.290464 TGACGGTTTGGTACTGTTTGG 58.710 47.619 0.00 0.00 46.41 3.28
437 5683 5.873179 ATATGACGGTTTGGTACTGTTTG 57.127 39.130 0.00 0.00 46.41 2.93
438 5684 9.841295 ATATAATATGACGGTTTGGTACTGTTT 57.159 29.630 0.00 0.00 46.41 2.83
439 5685 9.268268 CATATAATATGACGGTTTGGTACTGTT 57.732 33.333 0.00 0.00 46.41 3.16
441 5687 8.827177 ACATATAATATGACGGTTTGGTACTG 57.173 34.615 0.00 0.00 39.17 2.74
442 5688 9.918630 GTACATATAATATGACGGTTTGGTACT 57.081 33.333 0.00 0.00 0.00 2.73
443 5689 9.695526 TGTACATATAATATGACGGTTTGGTAC 57.304 33.333 0.00 0.00 0.00 3.34
445 5691 9.787435 ATTGTACATATAATATGACGGTTTGGT 57.213 29.630 0.00 0.00 0.00 3.67
450 5696 9.135843 CGTTCATTGTACATATAATATGACGGT 57.864 33.333 5.37 0.00 0.00 4.83
451 5697 9.349145 TCGTTCATTGTACATATAATATGACGG 57.651 33.333 17.65 9.79 0.00 4.79
461 5707 8.999431 ACAACTTTCTTCGTTCATTGTACATAT 58.001 29.630 0.00 0.00 0.00 1.78
462 5708 8.373048 ACAACTTTCTTCGTTCATTGTACATA 57.627 30.769 0.00 0.00 0.00 2.29
463 5709 7.259290 ACAACTTTCTTCGTTCATTGTACAT 57.741 32.000 0.00 0.00 0.00 2.29
464 5710 6.671614 ACAACTTTCTTCGTTCATTGTACA 57.328 33.333 0.00 0.00 0.00 2.90
466 5712 5.968848 GCAACAACTTTCTTCGTTCATTGTA 59.031 36.000 0.00 0.00 0.00 2.41
467 5713 4.798387 GCAACAACTTTCTTCGTTCATTGT 59.202 37.500 0.00 0.00 0.00 2.71
469 5715 4.359706 GGCAACAACTTTCTTCGTTCATT 58.640 39.130 0.00 0.00 0.00 2.57
470 5716 3.964909 GGCAACAACTTTCTTCGTTCAT 58.035 40.909 0.00 0.00 0.00 2.57
471 5717 3.414549 GGCAACAACTTTCTTCGTTCA 57.585 42.857 0.00 0.00 0.00 3.18
508 5754 3.373565 GAAGCCGGGCAACAAGGG 61.374 66.667 23.09 0.00 36.54 3.95
509 5755 3.737172 CGAAGCCGGGCAACAAGG 61.737 66.667 23.09 0.00 38.74 3.61
523 5769 4.787260 TTACATACAGTGGTGTAGCGAA 57.213 40.909 9.62 0.00 42.53 4.70
524 5770 4.994907 ATTACATACAGTGGTGTAGCGA 57.005 40.909 9.62 0.00 42.53 4.93
560 5806 4.858850 TCCACATCTGAATACCTGCAAAT 58.141 39.130 0.00 0.00 0.00 2.32
562 5808 3.998913 TCCACATCTGAATACCTGCAA 57.001 42.857 0.00 0.00 0.00 4.08
564 5810 3.004106 GCATTCCACATCTGAATACCTGC 59.996 47.826 0.00 0.00 31.42 4.85
565 5811 4.201657 TGCATTCCACATCTGAATACCTG 58.798 43.478 0.00 0.00 31.42 4.00
572 5818 8.623903 GTCTTAAATAATGCATTCCACATCTGA 58.376 33.333 16.86 3.79 0.00 3.27
574 5820 7.283127 ACGTCTTAAATAATGCATTCCACATCT 59.717 33.333 16.86 0.00 0.00 2.90
581 5827 5.901884 CGGTCACGTCTTAAATAATGCATTC 59.098 40.000 16.86 0.00 34.81 2.67
594 5840 0.391597 ACATTGACCGGTCACGTCTT 59.608 50.000 36.40 16.24 39.66 3.01
597 5843 1.938016 GCTAACATTGACCGGTCACGT 60.938 52.381 36.40 30.46 39.66 4.49
599 5845 0.719465 CGCTAACATTGACCGGTCAC 59.281 55.000 36.40 21.31 39.66 3.67
602 5848 0.390735 GTCCGCTAACATTGACCGGT 60.391 55.000 6.92 6.92 39.87 5.28
603 5849 1.418342 CGTCCGCTAACATTGACCGG 61.418 60.000 0.00 0.00 40.25 5.28
604 5850 1.995991 CGTCCGCTAACATTGACCG 59.004 57.895 0.00 0.00 0.00 4.79
606 5852 1.343821 CGCGTCCGCTAACATTGAC 59.656 57.895 10.21 0.00 39.32 3.18
607 5853 1.074319 GACGCGTCCGCTAACATTGA 61.074 55.000 28.61 0.00 39.32 2.57
608 5854 1.343821 GACGCGTCCGCTAACATTG 59.656 57.895 28.61 0.00 39.32 2.82
609 5855 1.808390 GGACGCGTCCGCTAACATT 60.808 57.895 39.77 0.00 40.36 2.71
610 5856 2.202703 GGACGCGTCCGCTAACAT 60.203 61.111 39.77 0.00 40.36 2.71
634 6429 0.676782 CCCCTCAAACATCCGTGGAC 60.677 60.000 0.00 0.00 0.00 4.02
636 6431 0.676782 GACCCCTCAAACATCCGTGG 60.677 60.000 0.00 0.00 0.00 4.94
637 6432 1.019278 CGACCCCTCAAACATCCGTG 61.019 60.000 0.00 0.00 0.00 4.94
639 6434 1.449601 CCGACCCCTCAAACATCCG 60.450 63.158 0.00 0.00 0.00 4.18
640 6435 0.392595 GTCCGACCCCTCAAACATCC 60.393 60.000 0.00 0.00 0.00 3.51
642 6437 1.064825 AAGTCCGACCCCTCAAACAT 58.935 50.000 0.00 0.00 0.00 2.71
643 6438 0.107831 CAAGTCCGACCCCTCAAACA 59.892 55.000 0.00 0.00 0.00 2.83
644 6439 0.108019 ACAAGTCCGACCCCTCAAAC 59.892 55.000 0.00 0.00 0.00 2.93
645 6440 0.395312 GACAAGTCCGACCCCTCAAA 59.605 55.000 0.00 0.00 0.00 2.69
659 6454 1.006832 CTACCGCCGGATTTGACAAG 58.993 55.000 11.71 0.00 0.00 3.16
688 6483 5.769367 CAGATGAATGGGCAGAACAATATG 58.231 41.667 0.00 0.00 0.00 1.78
691 6539 2.429610 GCAGATGAATGGGCAGAACAAT 59.570 45.455 0.00 0.00 0.00 2.71
728 6576 8.084073 GCCAAATGTGATGTATTTAGTATGCAT 58.916 33.333 3.79 3.79 0.00 3.96
729 6577 7.424803 GCCAAATGTGATGTATTTAGTATGCA 58.575 34.615 0.00 0.00 0.00 3.96
796 6644 1.518133 GTAGAGACAGCAGCTGGCG 60.518 63.158 26.38 1.62 45.59 5.69
810 6658 3.463704 TCTTATCTCTGGCCTGAGGTAGA 59.536 47.826 32.23 26.82 32.07 2.59
818 6666 2.294791 CGACGATTCTTATCTCTGGCCT 59.705 50.000 3.32 0.00 0.00 5.19
867 6716 2.682155 TCACTATGCATGGCACGTAA 57.318 45.000 10.16 0.00 43.04 3.18
878 6763 2.793790 CAGAGCTCGACAATCACTATGC 59.206 50.000 8.37 0.00 0.00 3.14
879 6764 4.039151 ACAGAGCTCGACAATCACTATG 57.961 45.455 8.37 0.00 0.00 2.23
880 6765 3.067461 GGACAGAGCTCGACAATCACTAT 59.933 47.826 8.37 0.00 0.00 2.12
881 6766 2.423892 GGACAGAGCTCGACAATCACTA 59.576 50.000 8.37 0.00 0.00 2.74
933 6819 5.483685 TCCTGACTTGTGTACTATGCTTT 57.516 39.130 0.00 0.00 0.00 3.51
939 6825 6.852420 ATAGCTTTCCTGACTTGTGTACTA 57.148 37.500 0.00 0.00 0.00 1.82
1220 7135 1.537990 GCAGAGAAGAAGGAGCGATCC 60.538 57.143 13.00 13.00 0.00 3.36
1251 7166 4.835056 AGGGATAGGCAGGCAATTTAATTC 59.165 41.667 0.00 0.00 0.00 2.17
1268 7183 6.628175 GCTCGACATAATTAGCATGAGGGATA 60.628 42.308 0.00 0.00 35.05 2.59
1292 7207 2.434134 CCGTACTCGAACACTGCGC 61.434 63.158 0.00 0.00 39.71 6.09
1447 7362 4.996434 GCAGTGCTGGTCCGTGCT 62.996 66.667 8.18 0.00 0.00 4.40
1674 7589 3.343788 GACGGTCTCGCTGGGTCAG 62.344 68.421 0.00 0.00 40.63 3.51
1688 7611 4.027458 CACAACGGTATAATAACACGACGG 60.027 45.833 0.00 0.00 0.00 4.79
1755 7724 7.062749 ACACTCACACCTTCATACTAAGAAA 57.937 36.000 0.00 0.00 0.00 2.52
1787 7756 9.405587 GCACTGTTTTTAAATGCTTCAGTAATA 57.594 29.630 3.94 0.00 34.11 0.98
1964 8353 7.386573 GCAGGCTTTAGACTCTATATCTTTTCC 59.613 40.741 0.00 0.00 0.00 3.13
2030 8427 8.723942 TTTATGCAAAGATCTTCTTCTAGTCC 57.276 34.615 8.78 0.00 35.27 3.85
2083 8480 3.755378 AGGACTTGCAATGTCATTGACTC 59.245 43.478 26.36 14.04 42.30 3.36
2084 8481 3.759581 AGGACTTGCAATGTCATTGACT 58.240 40.909 26.36 11.84 42.30 3.41
2085 8482 4.510038 AAGGACTTGCAATGTCATTGAC 57.490 40.909 26.36 17.85 42.25 3.18
2088 8485 2.564062 CCCAAGGACTTGCAATGTCATT 59.436 45.455 22.19 19.81 44.22 2.57
2089 8486 2.173519 CCCAAGGACTTGCAATGTCAT 58.826 47.619 22.19 16.34 42.30 3.06
2090 8487 1.144708 TCCCAAGGACTTGCAATGTCA 59.855 47.619 22.19 6.11 42.30 3.58
2159 8556 6.649155 TGGCAGATAAGAACAATAGTTGCTA 58.351 36.000 0.00 0.00 38.30 3.49
2201 8598 2.102578 CCAGGAGATTGGCGGATTTTT 58.897 47.619 0.00 0.00 0.00 1.94
2202 8599 1.284785 TCCAGGAGATTGGCGGATTTT 59.715 47.619 0.00 0.00 38.16 1.82
2203 8600 0.918983 TCCAGGAGATTGGCGGATTT 59.081 50.000 0.00 0.00 38.16 2.17
2204 8601 0.181350 GTCCAGGAGATTGGCGGATT 59.819 55.000 0.00 0.00 38.16 3.01
2205 8602 0.692419 AGTCCAGGAGATTGGCGGAT 60.692 55.000 0.00 0.00 38.16 4.18
2206 8603 0.909610 AAGTCCAGGAGATTGGCGGA 60.910 55.000 0.00 0.00 38.16 5.54
2207 8604 0.035056 AAAGTCCAGGAGATTGGCGG 60.035 55.000 0.00 0.00 38.16 6.13
2208 8605 1.373570 GAAAGTCCAGGAGATTGGCG 58.626 55.000 0.00 0.00 38.16 5.69
2209 8606 1.004745 TGGAAAGTCCAGGAGATTGGC 59.995 52.381 0.00 0.00 42.67 4.52
2225 8622 5.115480 GCAACAACAAGGAATCTTTTGGAA 58.885 37.500 3.87 0.00 31.52 3.53
2306 8703 6.303839 ACTCTATCAGCTTTGGTGGTTAAAA 58.696 36.000 0.00 0.00 0.00 1.52
2347 8744 6.753744 AGAAATGTTTCTTCTGTTTTGCAGAC 59.246 34.615 2.25 0.00 44.94 3.51
2348 8745 6.866480 AGAAATGTTTCTTCTGTTTTGCAGA 58.134 32.000 2.25 0.00 44.94 4.26
2475 8872 5.595542 AGTTGTAGGTATTGTGGCGTATAGA 59.404 40.000 0.00 0.00 0.00 1.98
2489 8886 8.148437 TCCAAATATACACCAAGTTGTAGGTA 57.852 34.615 1.45 1.97 35.44 3.08
2494 8891 5.479027 GGGTTCCAAATATACACCAAGTTGT 59.521 40.000 1.45 0.00 0.00 3.32
2590 8990 7.879677 TGCTTGCAATGCAGTAGATATAATAGT 59.120 33.333 16.36 0.00 42.52 2.12
2591 8991 8.260270 TGCTTGCAATGCAGTAGATATAATAG 57.740 34.615 16.36 0.00 42.52 1.73
2615 9015 3.254166 ACTGGCAAGCACACTCTAAAATG 59.746 43.478 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.