Multiple sequence alignment - TraesCS6A01G272200

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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 TraesCS6A01G272200 chr6A 100.000 4860 0 0 1 4860 499002622 499007481 0.000000e+00 8975.0
1 TraesCS6A01G272200 chr6D 96.068 2747 78 11 1546 4279 356594567 356597296 0.000000e+00 4447.0
2 TraesCS6A01G272200 chr6D 97.340 639 15 2 910 1548 356593427 356594063 0.000000e+00 1085.0
3 TraesCS6A01G272200 chr6D 94.265 558 29 1 21 578 356555292 356555846 0.000000e+00 850.0
4 TraesCS6A01G272200 chr6D 90.353 425 22 6 4444 4860 356597442 356597855 1.540000e-149 540.0
5 TraesCS6A01G272200 chr6D 81.211 644 91 16 24 643 78251264 78250627 4.370000e-135 492.0
6 TraesCS6A01G272200 chr6D 83.065 496 79 5 21 515 163143289 163143780 3.450000e-121 446.0
7 TraesCS6A01G272200 chr6D 76.396 394 66 14 311 677 368731324 368731717 2.310000e-43 187.0
8 TraesCS6A01G272200 chr6B 96.258 2699 88 6 1546 4234 537554302 537556997 0.000000e+00 4412.0
9 TraesCS6A01G272200 chr6B 95.659 645 24 2 907 1548 537553193 537553836 0.000000e+00 1033.0
10 TraesCS6A01G272200 chr6B 84.241 863 95 15 30 860 537551806 537552659 0.000000e+00 802.0
11 TraesCS6A01G272200 chr6B 88.947 380 23 8 4497 4860 537578067 537578443 7.420000e-123 451.0
12 TraesCS6A01G272200 chr6B 95.349 43 2 0 862 904 537553125 537553167 8.730000e-08 69.4
13 TraesCS6A01G272200 chr1B 80.910 681 101 14 25 682 579967007 579967681 1.210000e-140 510.0
14 TraesCS6A01G272200 chr5D 80.556 648 91 13 25 644 526037600 526038240 2.650000e-127 466.0
15 TraesCS6A01G272200 chr5D 83.333 492 74 5 26 514 392068492 392068006 9.600000e-122 448.0
16 TraesCS6A01G272200 chr1A 79.624 692 106 12 21 682 524386625 524387311 9.530000e-127 464.0
17 TraesCS6A01G272200 chr1A 74.216 287 59 11 4348 4624 481687138 481686857 6.650000e-19 106.0
18 TraesCS6A01G272200 chr3B 79.678 684 105 17 26 683 383837609 383838284 3.430000e-126 462.0
19 TraesCS6A01G272200 chr3B 75.901 527 99 20 156 666 771397083 771396569 1.350000e-60 244.0
20 TraesCS6A01G272200 chr7D 83.773 493 70 7 26 515 424105933 424105448 4.430000e-125 459.0
21 TraesCS6A01G272200 chr2B 83.164 493 76 5 26 515 412750518 412751006 1.240000e-120 444.0
22 TraesCS6A01G272200 chr2B 80.791 177 25 2 510 683 506573981 506573811 3.950000e-26 130.0
23 TraesCS6A01G272200 chr7A 75.660 682 104 32 35 682 701595983 701595330 2.860000e-72 283.0
24 TraesCS6A01G272200 chr4D 84.186 215 32 2 267 480 443223206 443222993 1.770000e-49 207.0


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 TraesCS6A01G272200 chr6A 499002622 499007481 4859 False 8975.0 8975 100.00000 1 4860 1 chr6A.!!$F1 4859
1 TraesCS6A01G272200 chr6D 356593427 356597855 4428 False 2024.0 4447 94.58700 910 4860 3 chr6D.!!$F4 3950
2 TraesCS6A01G272200 chr6D 356555292 356555846 554 False 850.0 850 94.26500 21 578 1 chr6D.!!$F2 557
3 TraesCS6A01G272200 chr6D 78250627 78251264 637 True 492.0 492 81.21100 24 643 1 chr6D.!!$R1 619
4 TraesCS6A01G272200 chr6B 537551806 537556997 5191 False 1579.1 4412 92.87675 30 4234 4 chr6B.!!$F2 4204
5 TraesCS6A01G272200 chr1B 579967007 579967681 674 False 510.0 510 80.91000 25 682 1 chr1B.!!$F1 657
6 TraesCS6A01G272200 chr5D 526037600 526038240 640 False 466.0 466 80.55600 25 644 1 chr5D.!!$F1 619
7 TraesCS6A01G272200 chr1A 524386625 524387311 686 False 464.0 464 79.62400 21 682 1 chr1A.!!$F1 661
8 TraesCS6A01G272200 chr3B 383837609 383838284 675 False 462.0 462 79.67800 26 683 1 chr3B.!!$F1 657
9 TraesCS6A01G272200 chr3B 771396569 771397083 514 True 244.0 244 75.90100 156 666 1 chr3B.!!$R1 510
10 TraesCS6A01G272200 chr7A 701595330 701595983 653 True 283.0 283 75.66000 35 682 1 chr7A.!!$R1 647


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
700 747 0.037326 TGATCCACGTCTGCAAGGAC 60.037 55.0 0.0 0.0 32.04 3.85 F
715 762 0.179045 AGGACCGCCAGTATCATTGC 60.179 55.0 0.0 0.0 36.29 3.56 F
905 1419 0.395312 ACGAGGACAAAATGGACCGT 59.605 50.0 0.0 0.0 0.00 4.83 F
2505 3555 0.178909 TGATGTTTGGGGTTGGGCAT 60.179 50.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 2922 1.298859 ATTGACGGCTTGGCGAAGAC 61.299 55.000 22.62 8.69 33.25 3.01 R
2505 3555 3.066621 GGATTGTGTGCAAGTGAGTTCAA 59.933 43.478 0.00 0.00 38.10 2.69 R
2753 3804 2.034812 GGTGTTTTCAATACGCCCAACA 59.965 45.455 0.00 0.00 39.68 3.33 R
4001 5054 0.033504 AACGAGGCTTTTCTGCTCGA 59.966 50.000 12.26 0.00 37.20 4.04 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
347 360 3.186702 TGCCCTTGTAAAACTTTTGGC 57.813 42.857 5.85 5.85 38.13 4.52
421 434 5.551233 TCAACCTCTTACTTCAGACATTGG 58.449 41.667 0.00 0.00 0.00 3.16
608 643 5.073144 TGGTAACTGGAGAACTCAATCCTTT 59.927 40.000 4.23 0.00 36.50 3.11
630 671 7.093596 CCTTTCCAAGGCATTCTTCTTTAAGAT 60.094 37.037 0.00 0.00 42.78 2.40
687 734 9.912634 GAAACAATAGAAGACATTTTTGATCCA 57.087 29.630 0.00 0.00 0.00 3.41
689 736 7.530010 ACAATAGAAGACATTTTTGATCCACG 58.470 34.615 0.00 0.00 0.00 4.94
700 747 0.037326 TGATCCACGTCTGCAAGGAC 60.037 55.000 0.00 0.00 32.04 3.85
703 750 3.414700 CACGTCTGCAAGGACCGC 61.415 66.667 0.86 0.00 33.07 5.68
707 754 3.241530 TCTGCAAGGACCGCCAGT 61.242 61.111 8.34 0.00 36.29 4.00
714 761 1.942657 CAAGGACCGCCAGTATCATTG 59.057 52.381 0.00 0.00 36.29 2.82
715 762 0.179045 AGGACCGCCAGTATCATTGC 60.179 55.000 0.00 0.00 36.29 3.56
717 764 1.498865 GACCGCCAGTATCATTGCCG 61.499 60.000 0.00 0.00 0.00 5.69
725 772 3.062763 CAGTATCATTGCCGTCTCATCC 58.937 50.000 0.00 0.00 0.00 3.51
734 781 1.403780 GCCGTCTCATCCGTGTAGTTT 60.404 52.381 0.00 0.00 0.00 2.66
736 783 3.323243 CCGTCTCATCCGTGTAGTTTTT 58.677 45.455 0.00 0.00 0.00 1.94
739 786 4.684703 CGTCTCATCCGTGTAGTTTTTCTT 59.315 41.667 0.00 0.00 0.00 2.52
754 801 9.366513 GTAGTTTTTCTTATCAAACGACTCAAC 57.633 33.333 0.00 0.00 37.85 3.18
758 805 8.835467 TTTTCTTATCAAACGACTCAACAAAG 57.165 30.769 0.00 0.00 0.00 2.77
767 814 4.569943 ACGACTCAACAAAGTGCTCATAT 58.430 39.130 0.00 0.00 0.00 1.78
769 816 6.341316 ACGACTCAACAAAGTGCTCATATAT 58.659 36.000 0.00 0.00 0.00 0.86
770 817 6.256539 ACGACTCAACAAAGTGCTCATATATG 59.743 38.462 6.36 6.36 0.00 1.78
771 818 6.256539 CGACTCAACAAAGTGCTCATATATGT 59.743 38.462 12.42 0.00 0.00 2.29
772 819 7.435192 CGACTCAACAAAGTGCTCATATATGTA 59.565 37.037 12.42 0.00 0.00 2.29
773 820 9.265901 GACTCAACAAAGTGCTCATATATGTAT 57.734 33.333 12.42 0.00 0.00 2.29
799 846 8.687292 TGTACTACATATCCGAATCAGTTACT 57.313 34.615 0.00 0.00 0.00 2.24
803 850 8.692710 ACTACATATCCGAATCAGTTACTTCAA 58.307 33.333 0.00 0.00 0.00 2.69
807 854 9.098355 CATATCCGAATCAGTTACTTCAAAGAA 57.902 33.333 0.00 0.00 0.00 2.52
809 856 5.932303 TCCGAATCAGTTACTTCAAAGAAGG 59.068 40.000 11.08 0.00 0.00 3.46
810 857 5.122396 CCGAATCAGTTACTTCAAAGAAGGG 59.878 44.000 11.08 0.00 0.00 3.95
811 858 5.932303 CGAATCAGTTACTTCAAAGAAGGGA 59.068 40.000 11.08 2.07 0.00 4.20
812 859 6.426937 CGAATCAGTTACTTCAAAGAAGGGAA 59.573 38.462 11.08 2.79 0.00 3.97
813 860 7.041372 CGAATCAGTTACTTCAAAGAAGGGAAA 60.041 37.037 11.08 0.83 0.00 3.13
845 895 0.611618 AACATTTCAGCCGGGCATGA 60.612 50.000 23.09 18.04 0.00 3.07
852 902 0.882042 CAGCCGGGCATGATGAGTAC 60.882 60.000 23.09 0.00 0.00 2.73
872 1386 1.823899 GTAAGGGGGCGCATTGAGG 60.824 63.158 10.83 0.00 0.00 3.86
904 1418 2.373540 TACGAGGACAAAATGGACCG 57.626 50.000 0.00 0.00 0.00 4.79
905 1419 0.395312 ACGAGGACAAAATGGACCGT 59.605 50.000 0.00 0.00 0.00 4.83
948 1485 4.215613 GGGCGAAGTGTAACAAAATTCTCT 59.784 41.667 0.00 0.00 41.43 3.10
1444 1981 8.005466 CGAAATTGATTTGACAAACAGGAAATG 58.995 33.333 1.94 0.00 33.44 2.32
1466 2006 6.860790 TGATAAGTTGTGACATGGTACCTA 57.139 37.500 14.36 0.00 0.00 3.08
1483 2023 4.942761 ACCTACCGTGAAACTTGAGTAA 57.057 40.909 0.00 0.00 31.75 2.24
1647 2696 6.042143 ACTTAGGTGTGCATTTCAAAAGTTG 58.958 36.000 0.00 0.00 0.00 3.16
1725 2774 4.099266 ACAACACTAAATTTCCTTGCAGCA 59.901 37.500 0.00 0.00 0.00 4.41
1873 2922 1.755179 AGGAAAGTCGATGGCAATGG 58.245 50.000 0.00 0.00 0.00 3.16
1908 2957 0.796312 CAATGAGGACCCGTGTTTCG 59.204 55.000 0.00 0.00 39.52 3.46
2189 3238 9.119329 GTAACGATTGCTATCTAGACATAACTG 57.881 37.037 6.58 0.00 0.00 3.16
2433 3483 2.682856 TGTTGTGGCAGTTTTCTCTGAC 59.317 45.455 0.00 0.00 43.20 3.51
2505 3555 0.178909 TGATGTTTGGGGTTGGGCAT 60.179 50.000 0.00 0.00 0.00 4.40
2632 3683 6.366061 TCACATTGTCTTTCTAACATCTCGTG 59.634 38.462 0.00 0.00 0.00 4.35
2753 3804 1.667724 GCGCTCACTATGCTTGAACAT 59.332 47.619 0.00 0.00 0.00 2.71
2759 3810 3.758023 TCACTATGCTTGAACATGTTGGG 59.242 43.478 17.58 6.74 0.00 4.12
2829 3880 1.622312 GTGGTTTCTTCTACGGGGACT 59.378 52.381 0.00 0.00 0.00 3.85
3000 4051 0.671251 GTGGAGATCGCTAGGAGTGG 59.329 60.000 0.00 0.00 0.00 4.00
3173 4224 9.741168 CTCTTGTTTTATACTGTCATTTACACG 57.259 33.333 0.00 0.00 33.45 4.49
3372 4423 5.927281 TTACTAGAAGTTGCCCGATAACT 57.073 39.130 0.00 0.00 39.92 2.24
3383 4434 3.635373 TGCCCGATAACTAGTCCTTGTAG 59.365 47.826 0.00 0.00 0.00 2.74
3395 4446 7.907389 ACTAGTCCTTGTAGTTCAATCATTCA 58.093 34.615 0.00 0.00 35.35 2.57
3409 4460 6.997655 TCAATCATTCACAGTCAGTAGTCTT 58.002 36.000 0.00 0.00 0.00 3.01
3413 4464 2.316108 TCACAGTCAGTAGTCTTGGCA 58.684 47.619 0.00 0.00 0.00 4.92
3506 4558 1.539157 CTGGTCCAAAAGCCTTCCTC 58.461 55.000 0.00 0.00 0.00 3.71
3548 4600 1.366435 AGAGGGGTGGAGGTAACAGAT 59.634 52.381 0.00 0.00 41.41 2.90
3824 4877 1.079127 AGCATGCGGTACTGTGTCC 60.079 57.895 13.01 0.00 0.00 4.02
3913 4966 3.379372 CGGATCTCCATGTTTCAAGCAAT 59.621 43.478 0.00 0.00 35.14 3.56
3951 5004 0.904649 TCATCTCCAATCACCGTGCT 59.095 50.000 0.00 0.00 0.00 4.40
4001 5054 2.282391 TCCAGCAATGCGGCTTGT 60.282 55.556 10.43 0.00 42.71 3.16
4100 5153 6.981559 GGTGCAAGAAAGGTATTTTTAACACA 59.018 34.615 0.00 0.00 0.00 3.72
4161 5215 4.829492 GGGCAGGAAATGTAGCTAATCAAT 59.171 41.667 0.00 0.00 0.00 2.57
4197 5257 3.204597 ACTCTTCTTAGAACGACGCTG 57.795 47.619 0.00 0.00 0.00 5.18
4207 5267 3.112075 CGACGCTGTTCGCCACAT 61.112 61.111 0.00 0.00 43.23 3.21
4217 5277 3.941483 CTGTTCGCCACATTAAGAGGATT 59.059 43.478 0.00 0.00 33.76 3.01
4279 5341 0.693049 ATCCAGGAGTGAGGCGTTTT 59.307 50.000 0.00 0.00 0.00 2.43
4282 5361 0.868406 CAGGAGTGAGGCGTTTTGAC 59.132 55.000 0.00 0.00 0.00 3.18
4293 5372 5.169836 AGGCGTTTTGACTGACTAAAAAG 57.830 39.130 0.00 0.00 31.20 2.27
4362 5453 1.626654 GAAGTGCGTGATGTCCGTGG 61.627 60.000 0.00 0.00 0.00 4.94
4383 5474 4.020039 TGGCAAATTTCAGAGCATTTGGAT 60.020 37.500 14.67 0.00 39.71 3.41
4386 5477 5.063060 GCAAATTTCAGAGCATTTGGATGTC 59.937 40.000 14.67 0.66 39.71 3.06
4387 5478 4.996788 ATTTCAGAGCATTTGGATGTCC 57.003 40.909 0.00 0.00 35.63 4.02
4388 5479 3.438216 TTCAGAGCATTTGGATGTCCA 57.562 42.857 0.00 0.00 45.94 4.02
4401 5492 3.133003 TGGATGTCCAAGTAGCTCTTAGC 59.867 47.826 0.00 0.00 44.35 3.09
4402 5493 3.133003 GGATGTCCAAGTAGCTCTTAGCA 59.867 47.826 0.00 0.00 38.85 3.49
4403 5494 4.383118 GGATGTCCAAGTAGCTCTTAGCAA 60.383 45.833 0.00 0.00 38.85 3.91
4404 5495 4.617253 TGTCCAAGTAGCTCTTAGCAAA 57.383 40.909 0.00 0.00 45.56 3.68
4405 5496 4.968259 TGTCCAAGTAGCTCTTAGCAAAA 58.032 39.130 0.00 0.00 45.56 2.44
4406 5497 4.997395 TGTCCAAGTAGCTCTTAGCAAAAG 59.003 41.667 0.00 0.00 45.56 2.27
4407 5498 5.221641 TGTCCAAGTAGCTCTTAGCAAAAGA 60.222 40.000 0.00 2.04 45.56 2.52
4408 5499 5.350091 GTCCAAGTAGCTCTTAGCAAAAGAG 59.650 44.000 19.35 19.35 45.56 2.85
4409 5500 5.246203 TCCAAGTAGCTCTTAGCAAAAGAGA 59.754 40.000 25.01 8.82 45.56 3.10
4410 5501 6.070538 TCCAAGTAGCTCTTAGCAAAAGAGAT 60.071 38.462 25.01 22.20 45.56 2.75
4411 5502 7.124298 TCCAAGTAGCTCTTAGCAAAAGAGATA 59.876 37.037 25.01 21.37 45.56 1.98
4412 5503 7.766278 CCAAGTAGCTCTTAGCAAAAGAGATAA 59.234 37.037 25.01 11.36 43.99 1.75
4413 5504 9.155975 CAAGTAGCTCTTAGCAAAAGAGATAAA 57.844 33.333 25.01 8.59 43.99 1.40
4414 5505 9.898152 AAGTAGCTCTTAGCAAAAGAGATAAAT 57.102 29.630 25.01 15.43 43.99 1.40
4415 5506 9.898152 AGTAGCTCTTAGCAAAAGAGATAAATT 57.102 29.630 25.01 13.37 43.99 1.82
4418 5509 9.236006 AGCTCTTAGCAAAAGAGATAAATTTGA 57.764 29.630 25.01 0.00 45.56 2.69
4419 5510 9.500864 GCTCTTAGCAAAAGAGATAAATTTGAG 57.499 33.333 25.01 3.57 44.96 3.02
4421 5512 9.520515 TCTTAGCAAAAGAGATAAATTTGAGGT 57.479 29.630 0.00 0.00 0.00 3.85
4422 5513 9.780413 CTTAGCAAAAGAGATAAATTTGAGGTC 57.220 33.333 0.00 0.00 0.00 3.85
4423 5514 7.163001 AGCAAAAGAGATAAATTTGAGGTCC 57.837 36.000 0.00 0.00 0.00 4.46
4424 5515 6.030228 GCAAAAGAGATAAATTTGAGGTCCG 58.970 40.000 0.00 0.00 0.00 4.79
4425 5516 6.349363 GCAAAAGAGATAAATTTGAGGTCCGT 60.349 38.462 0.00 0.00 0.00 4.69
4426 5517 6.743575 AAAGAGATAAATTTGAGGTCCGTG 57.256 37.500 0.00 0.00 0.00 4.94
4427 5518 5.677319 AGAGATAAATTTGAGGTCCGTGA 57.323 39.130 0.00 0.00 0.00 4.35
4428 5519 6.049955 AGAGATAAATTTGAGGTCCGTGAA 57.950 37.500 0.00 0.00 0.00 3.18
4429 5520 6.472887 AGAGATAAATTTGAGGTCCGTGAAA 58.527 36.000 0.00 0.00 0.00 2.69
4430 5521 6.940298 AGAGATAAATTTGAGGTCCGTGAAAA 59.060 34.615 0.00 0.00 0.00 2.29
4431 5522 7.447238 AGAGATAAATTTGAGGTCCGTGAAAAA 59.553 33.333 0.00 0.00 0.00 1.94
4432 5523 7.368059 AGATAAATTTGAGGTCCGTGAAAAAC 58.632 34.615 0.00 0.00 0.00 2.43
4433 5524 5.592104 AAATTTGAGGTCCGTGAAAAACT 57.408 34.783 0.00 0.00 0.00 2.66
4434 5525 5.592104 AATTTGAGGTCCGTGAAAAACTT 57.408 34.783 0.00 0.00 0.00 2.66
4435 5526 5.592104 ATTTGAGGTCCGTGAAAAACTTT 57.408 34.783 0.00 0.00 0.00 2.66
4436 5527 6.702716 ATTTGAGGTCCGTGAAAAACTTTA 57.297 33.333 0.00 0.00 0.00 1.85
4437 5528 5.488645 TTGAGGTCCGTGAAAAACTTTAC 57.511 39.130 0.00 0.00 0.00 2.01
4438 5529 4.773013 TGAGGTCCGTGAAAAACTTTACT 58.227 39.130 0.00 0.00 0.00 2.24
4439 5530 4.573201 TGAGGTCCGTGAAAAACTTTACTG 59.427 41.667 0.00 0.00 0.00 2.74
4440 5531 3.314357 AGGTCCGTGAAAAACTTTACTGC 59.686 43.478 0.00 0.00 0.00 4.40
4441 5532 3.314357 GGTCCGTGAAAAACTTTACTGCT 59.686 43.478 0.00 0.00 0.00 4.24
4442 5533 4.201980 GGTCCGTGAAAAACTTTACTGCTT 60.202 41.667 0.00 0.00 0.00 3.91
4457 5548 0.109153 TGCTTGTGCACTGTCTGGAT 59.891 50.000 19.41 0.00 45.31 3.41
4459 5550 1.446907 CTTGTGCACTGTCTGGATCC 58.553 55.000 19.41 4.20 0.00 3.36
4478 5569 6.589523 TGGATCCGATTTTGTTTATTTTGCTG 59.410 34.615 7.39 0.00 0.00 4.41
4485 5576 8.755018 CGATTTTGTTTATTTTGCTGAGAACTT 58.245 29.630 0.00 0.00 0.00 2.66
4488 5579 8.856490 TTTGTTTATTTTGCTGAGAACTTCTC 57.144 30.769 11.37 11.37 43.65 2.87
4520 5611 8.309163 TCAAATGCTTTGAAATTTGACATACC 57.691 30.769 0.00 0.00 45.94 2.73
4521 5612 8.149647 TCAAATGCTTTGAAATTTGACATACCT 58.850 29.630 0.00 0.00 45.94 3.08
4522 5613 8.437742 CAAATGCTTTGAAATTTGACATACCTC 58.562 33.333 0.00 0.00 43.41 3.85
4544 5635 4.218635 TCACGCACTAAGTCATCTTTCTCT 59.781 41.667 0.00 0.00 35.36 3.10
4607 5700 0.250038 CATCAGGTGTAGATGCCCGG 60.250 60.000 0.00 0.00 36.77 5.73
4647 5746 5.243060 TCATCCAGAGACTCTAAACGTGAAA 59.757 40.000 4.22 0.00 0.00 2.69
4684 5783 1.226773 GCGTGATGCAAAGGGATGC 60.227 57.895 0.00 0.00 46.58 3.91
4685 5784 1.434696 CGTGATGCAAAGGGATGCC 59.565 57.895 0.00 0.00 45.83 4.40
4717 5816 9.985730 GATGAATAGAGAGAGAAAACTGATGAT 57.014 33.333 0.00 0.00 0.00 2.45
4803 5902 2.062971 ACACAGGATTCCATGATGGC 57.937 50.000 6.59 0.00 37.47 4.40
4814 5913 1.655484 CATGATGGCGACAACAGCTA 58.345 50.000 7.48 0.00 46.89 3.32
4815 5914 1.328680 CATGATGGCGACAACAGCTAC 59.671 52.381 7.48 0.00 46.89 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 157 3.973472 AAGGGAAAACTCCTCCTTGTT 57.027 42.857 0.00 0.00 38.11 2.83
347 360 2.686915 GCATTGGAGATGGAAGAACTGG 59.313 50.000 0.00 0.00 0.00 4.00
442 455 0.393077 CCCGAGAGAACCAACTGTGT 59.607 55.000 0.00 0.00 0.00 3.72
562 597 3.035727 TGCACGACAGCACTACGA 58.964 55.556 0.00 0.00 40.11 3.43
608 643 6.248433 ACATCTTAAAGAAGAATGCCTTGGA 58.752 36.000 0.00 0.00 44.85 3.53
630 671 3.064207 GTCCGTTGCTTTGATGACTACA 58.936 45.455 0.00 0.00 0.00 2.74
687 734 4.681978 GGCGGTCCTTGCAGACGT 62.682 66.667 0.00 0.00 37.66 4.34
689 736 2.167398 TACTGGCGGTCCTTGCAGAC 62.167 60.000 0.06 0.00 35.95 3.51
703 750 2.602257 TGAGACGGCAATGATACTGG 57.398 50.000 0.00 0.00 0.00 4.00
707 754 1.686587 ACGGATGAGACGGCAATGATA 59.313 47.619 0.00 0.00 35.23 2.15
714 761 0.172803 AACTACACGGATGAGACGGC 59.827 55.000 0.00 0.00 35.23 5.68
715 762 2.649331 AAACTACACGGATGAGACGG 57.351 50.000 0.00 0.00 35.23 4.79
717 764 7.544566 TGATAAGAAAAACTACACGGATGAGAC 59.455 37.037 0.00 0.00 0.00 3.36
725 772 7.561556 AGTCGTTTGATAAGAAAAACTACACG 58.438 34.615 5.95 0.00 35.53 4.49
734 781 7.908082 CACTTTGTTGAGTCGTTTGATAAGAAA 59.092 33.333 0.00 0.00 0.00 2.52
736 783 6.511121 GCACTTTGTTGAGTCGTTTGATAAGA 60.511 38.462 0.00 0.00 0.00 2.10
739 786 4.814234 AGCACTTTGTTGAGTCGTTTGATA 59.186 37.500 0.00 0.00 0.00 2.15
769 816 9.074576 ACTGATTCGGATATGTAGTACAATACA 57.925 33.333 7.16 0.00 39.85 2.29
770 817 9.909644 AACTGATTCGGATATGTAGTACAATAC 57.090 33.333 7.16 2.82 0.00 1.89
772 819 9.909644 GTAACTGATTCGGATATGTAGTACAAT 57.090 33.333 7.16 2.64 0.00 2.71
773 820 9.128404 AGTAACTGATTCGGATATGTAGTACAA 57.872 33.333 7.16 0.00 0.00 2.41
780 827 8.258007 TCTTTGAAGTAACTGATTCGGATATGT 58.742 33.333 0.00 0.00 0.00 2.29
813 860 6.074569 CGGCTGAAATGTTCGTGTTAATTTTT 60.075 34.615 0.00 0.00 0.00 1.94
816 863 4.472286 CGGCTGAAATGTTCGTGTTAATT 58.528 39.130 0.00 0.00 0.00 1.40
817 864 3.119990 CCGGCTGAAATGTTCGTGTTAAT 60.120 43.478 0.00 0.00 0.00 1.40
825 875 0.179129 CATGCCCGGCTGAAATGTTC 60.179 55.000 11.61 0.00 0.00 3.18
826 876 0.611618 TCATGCCCGGCTGAAATGTT 60.612 50.000 11.61 0.00 0.00 2.71
835 885 1.598130 GGTACTCATCATGCCCGGC 60.598 63.158 1.04 1.04 0.00 6.13
836 886 1.300931 CGGTACTCATCATGCCCGG 60.301 63.158 0.00 0.00 0.00 5.73
845 895 1.397390 CGCCCCCTTACGGTACTCAT 61.397 60.000 0.00 0.00 0.00 2.90
852 902 3.209097 CAATGCGCCCCCTTACGG 61.209 66.667 4.18 0.00 0.00 4.02
860 910 3.207669 CTCAGCCTCAATGCGCCC 61.208 66.667 4.18 0.00 36.02 6.13
861 911 1.308069 TTTCTCAGCCTCAATGCGCC 61.308 55.000 4.18 0.00 36.02 6.53
862 912 0.523072 TTTTCTCAGCCTCAATGCGC 59.477 50.000 0.00 0.00 36.02 6.09
863 913 2.995466 TTTTTCTCAGCCTCAATGCG 57.005 45.000 0.00 0.00 36.02 4.73
864 914 6.017934 TCGTATATTTTTCTCAGCCTCAATGC 60.018 38.462 0.00 0.00 0.00 3.56
872 1386 6.903883 TTGTCCTCGTATATTTTTCTCAGC 57.096 37.500 0.00 0.00 0.00 4.26
948 1485 2.816718 GGCGAGGGGCGTATGTAA 59.183 61.111 0.00 0.00 44.92 2.41
1086 1623 1.852626 AGGGTGGAAGAAGGGGGTG 60.853 63.158 0.00 0.00 0.00 4.61
1088 1625 2.309504 GGAGGGTGGAAGAAGGGGG 61.310 68.421 0.00 0.00 0.00 5.40
1444 1981 6.047231 GGTAGGTACCATGTCACAACTTATC 58.953 44.000 15.94 0.00 45.73 1.75
1466 2006 4.124970 GGAAGTTACTCAAGTTTCACGGT 58.875 43.478 0.00 0.00 0.00 4.83
1483 2023 2.208349 ACTGGGAGCCCTGGAAGT 59.792 61.111 15.71 4.18 39.05 3.01
1647 2696 2.227149 TCAACATTGCTCTGATGCACAC 59.773 45.455 0.00 0.00 43.20 3.82
1697 2746 9.906660 CTGCAAGGAAATTTAGTGTTGTTATTA 57.093 29.630 0.00 0.00 0.00 0.98
1698 2747 7.384932 GCTGCAAGGAAATTTAGTGTTGTTATT 59.615 33.333 0.00 0.00 0.00 1.40
1699 2748 6.868339 GCTGCAAGGAAATTTAGTGTTGTTAT 59.132 34.615 0.00 0.00 0.00 1.89
1725 2774 7.287696 TGAAGAAAATCCTTAGGAAGCTGTTTT 59.712 33.333 4.56 7.14 34.34 2.43
1873 2922 1.298859 ATTGACGGCTTGGCGAAGAC 61.299 55.000 22.62 8.69 33.25 3.01
1908 2957 5.836347 AGCAAGAAGAATCCTGTTTCAAAC 58.164 37.500 0.00 0.00 0.00 2.93
2189 3238 4.102649 GCACCACAGAAACAACAACTTAC 58.897 43.478 0.00 0.00 0.00 2.34
2427 3477 3.496130 ACAAATGAAGAAGCACGTCAGAG 59.504 43.478 0.00 2.12 39.96 3.35
2433 3483 6.573617 AAGAAAAACAAATGAAGAAGCACG 57.426 33.333 0.00 0.00 0.00 5.34
2505 3555 3.066621 GGATTGTGTGCAAGTGAGTTCAA 59.933 43.478 0.00 0.00 38.10 2.69
2632 3683 8.306761 AGTCCAAAATATCCTGTCAAAAATCAC 58.693 33.333 0.00 0.00 0.00 3.06
2753 3804 2.034812 GGTGTTTTCAATACGCCCAACA 59.965 45.455 0.00 0.00 39.68 3.33
2759 3810 3.636282 ACCTTGGTGTTTTCAATACGC 57.364 42.857 0.00 0.00 0.00 4.42
3173 4224 6.748333 TGAGATGTCCACAGATCAAAATTC 57.252 37.500 0.00 0.00 0.00 2.17
3372 4423 7.676004 TGTGAATGATTGAACTACAAGGACTA 58.324 34.615 0.00 0.00 42.02 2.59
3383 4434 6.870965 AGACTACTGACTGTGAATGATTGAAC 59.129 38.462 0.00 0.00 0.00 3.18
3395 4446 2.039418 TGTGCCAAGACTACTGACTGT 58.961 47.619 0.00 0.00 0.00 3.55
3448 4500 1.434513 ATCCACCTGCAGGGACCAAA 61.435 55.000 35.42 15.28 40.27 3.28
3635 4687 5.132648 ACAATGATAGGGTAATCAAGCTCCA 59.867 40.000 0.00 0.00 39.25 3.86
3824 4877 9.489084 TCATATTTATTCAAGATTACCAGACCG 57.511 33.333 0.00 0.00 0.00 4.79
3913 4966 7.418368 GGAGATGATGATTCTAAGAGAACACCA 60.418 40.741 0.00 0.00 37.00 4.17
3951 5004 7.819415 CAGTAGATTACAACTCTGATTCAACCA 59.181 37.037 0.00 0.00 0.00 3.67
4001 5054 0.033504 AACGAGGCTTTTCTGCTCGA 59.966 50.000 12.26 0.00 37.20 4.04
4100 5153 6.665992 TCTGTAATACAGTGAAAGACCACT 57.334 37.500 18.71 0.00 46.03 4.00
4127 5180 5.490159 ACATTTCCTGCCCAATTGTTATTG 58.510 37.500 4.43 0.00 40.70 1.90
4161 5215 6.235231 AGAAGAGTTTGTTCTGTTGAGGTA 57.765 37.500 0.00 0.00 32.86 3.08
4197 5257 3.938963 TGAATCCTCTTAATGTGGCGAAC 59.061 43.478 0.00 0.00 0.00 3.95
4217 5277 8.595362 TTAATCTCTAGTCTCTTGGATTGTGA 57.405 34.615 0.00 0.00 0.00 3.58
4253 5315 1.306997 TCACTCCTGGATGGTCCCC 60.307 63.158 0.00 0.00 35.03 4.81
4255 5317 1.977293 GCCTCACTCCTGGATGGTCC 61.977 65.000 0.00 0.00 36.96 4.46
4325 5404 4.692625 CACTTCGTCATCTTTCTCCACAAT 59.307 41.667 0.00 0.00 0.00 2.71
4342 5433 1.733041 ACGGACATCACGCACTTCG 60.733 57.895 0.00 0.00 45.38 3.79
4347 5438 3.816367 TTGCCACGGACATCACGCA 62.816 57.895 0.00 0.00 34.00 5.24
4357 5448 0.597568 TGCTCTGAAATTTGCCACGG 59.402 50.000 0.00 0.00 0.00 4.94
4362 5453 4.933400 ACATCCAAATGCTCTGAAATTTGC 59.067 37.500 15.14 0.00 40.74 3.68
4383 5474 4.617253 TTTGCTAAGAGCTACTTGGACA 57.383 40.909 11.55 7.43 42.97 4.02
4386 5477 5.482908 TCTCTTTTGCTAAGAGCTACTTGG 58.517 41.667 18.62 6.75 42.97 3.61
4387 5478 8.709386 TTATCTCTTTTGCTAAGAGCTACTTG 57.291 34.615 18.62 1.96 42.97 3.16
4388 5479 9.898152 ATTTATCTCTTTTGCTAAGAGCTACTT 57.102 29.630 18.62 0.00 42.97 2.24
4389 5480 9.898152 AATTTATCTCTTTTGCTAAGAGCTACT 57.102 29.630 18.62 9.59 42.97 2.57
4392 5483 9.236006 TCAAATTTATCTCTTTTGCTAAGAGCT 57.764 29.630 18.62 13.99 42.97 4.09
4393 5484 9.500864 CTCAAATTTATCTCTTTTGCTAAGAGC 57.499 33.333 18.62 0.00 42.58 4.09
4395 5486 9.520515 ACCTCAAATTTATCTCTTTTGCTAAGA 57.479 29.630 0.00 2.59 31.88 2.10
4396 5487 9.780413 GACCTCAAATTTATCTCTTTTGCTAAG 57.220 33.333 0.00 0.00 31.88 2.18
4397 5488 8.739972 GGACCTCAAATTTATCTCTTTTGCTAA 58.260 33.333 0.00 0.00 31.88 3.09
4398 5489 7.065803 CGGACCTCAAATTTATCTCTTTTGCTA 59.934 37.037 0.00 0.00 31.88 3.49
4399 5490 6.127897 CGGACCTCAAATTTATCTCTTTTGCT 60.128 38.462 0.00 0.00 31.88 3.91
4400 5491 6.030228 CGGACCTCAAATTTATCTCTTTTGC 58.970 40.000 0.00 0.00 31.88 3.68
4401 5492 7.023575 CACGGACCTCAAATTTATCTCTTTTG 58.976 38.462 0.00 0.00 0.00 2.44
4402 5493 6.940298 TCACGGACCTCAAATTTATCTCTTTT 59.060 34.615 0.00 0.00 0.00 2.27
4403 5494 6.472887 TCACGGACCTCAAATTTATCTCTTT 58.527 36.000 0.00 0.00 0.00 2.52
4404 5495 6.049955 TCACGGACCTCAAATTTATCTCTT 57.950 37.500 0.00 0.00 0.00 2.85
4405 5496 5.677319 TCACGGACCTCAAATTTATCTCT 57.323 39.130 0.00 0.00 0.00 3.10
4406 5497 6.737254 TTTCACGGACCTCAAATTTATCTC 57.263 37.500 0.00 0.00 0.00 2.75
4407 5498 7.230712 AGTTTTTCACGGACCTCAAATTTATCT 59.769 33.333 0.00 0.00 0.00 1.98
4408 5499 7.368059 AGTTTTTCACGGACCTCAAATTTATC 58.632 34.615 0.00 0.00 0.00 1.75
4409 5500 7.284919 AGTTTTTCACGGACCTCAAATTTAT 57.715 32.000 0.00 0.00 0.00 1.40
4410 5501 6.702716 AGTTTTTCACGGACCTCAAATTTA 57.297 33.333 0.00 0.00 0.00 1.40
4411 5502 5.592104 AGTTTTTCACGGACCTCAAATTT 57.408 34.783 0.00 0.00 0.00 1.82
4412 5503 5.592104 AAGTTTTTCACGGACCTCAAATT 57.408 34.783 0.00 0.00 0.00 1.82
4413 5504 5.592104 AAAGTTTTTCACGGACCTCAAAT 57.408 34.783 0.00 0.00 0.00 2.32
4414 5505 5.648960 AGTAAAGTTTTTCACGGACCTCAAA 59.351 36.000 0.00 0.00 0.00 2.69
4415 5506 5.065474 CAGTAAAGTTTTTCACGGACCTCAA 59.935 40.000 0.00 0.00 0.00 3.02
4416 5507 4.573201 CAGTAAAGTTTTTCACGGACCTCA 59.427 41.667 0.00 0.00 0.00 3.86
4417 5508 4.554134 GCAGTAAAGTTTTTCACGGACCTC 60.554 45.833 0.00 0.00 0.00 3.85
4418 5509 3.314357 GCAGTAAAGTTTTTCACGGACCT 59.686 43.478 0.00 0.00 0.00 3.85
4419 5510 3.314357 AGCAGTAAAGTTTTTCACGGACC 59.686 43.478 0.00 0.00 0.00 4.46
4420 5511 4.547406 AGCAGTAAAGTTTTTCACGGAC 57.453 40.909 0.00 0.00 0.00 4.79
4421 5512 4.396790 ACAAGCAGTAAAGTTTTTCACGGA 59.603 37.500 0.00 0.00 0.00 4.69
4422 5513 4.499040 CACAAGCAGTAAAGTTTTTCACGG 59.501 41.667 0.00 0.00 0.00 4.94
4423 5514 4.027702 GCACAAGCAGTAAAGTTTTTCACG 60.028 41.667 0.00 0.00 41.58 4.35
4424 5515 5.375544 GCACAAGCAGTAAAGTTTTTCAC 57.624 39.130 0.00 0.00 41.58 3.18
4439 5530 0.801251 GATCCAGACAGTGCACAAGC 59.199 55.000 21.04 7.18 42.57 4.01
4440 5531 1.446907 GGATCCAGACAGTGCACAAG 58.553 55.000 21.04 13.67 0.00 3.16
4441 5532 0.320683 CGGATCCAGACAGTGCACAA 60.321 55.000 21.04 0.00 0.00 3.33
4442 5533 1.184970 TCGGATCCAGACAGTGCACA 61.185 55.000 21.04 0.00 0.00 4.57
4457 5548 6.976088 TCTCAGCAAAATAAACAAAATCGGA 58.024 32.000 0.00 0.00 0.00 4.55
4459 5550 8.285776 AGTTCTCAGCAAAATAAACAAAATCG 57.714 30.769 0.00 0.00 0.00 3.34
4478 5569 7.144000 AGCATTTGAACATTTGAGAAGTTCTC 58.856 34.615 23.53 23.53 43.65 2.87
4515 5606 3.503827 TGACTTAGTGCGTGAGGTATG 57.496 47.619 0.00 0.00 0.00 2.39
4516 5607 3.954904 AGATGACTTAGTGCGTGAGGTAT 59.045 43.478 0.00 0.00 0.00 2.73
4517 5608 3.353557 AGATGACTTAGTGCGTGAGGTA 58.646 45.455 0.00 0.00 0.00 3.08
4518 5609 2.171840 AGATGACTTAGTGCGTGAGGT 58.828 47.619 0.00 0.00 0.00 3.85
4519 5610 2.949451 AGATGACTTAGTGCGTGAGG 57.051 50.000 0.00 0.00 0.00 3.86
4520 5611 4.489810 AGAAAGATGACTTAGTGCGTGAG 58.510 43.478 0.00 0.00 35.05 3.51
4521 5612 4.218635 AGAGAAAGATGACTTAGTGCGTGA 59.781 41.667 0.00 0.00 35.05 4.35
4522 5613 4.489810 AGAGAAAGATGACTTAGTGCGTG 58.510 43.478 0.00 0.00 35.05 5.34
4607 5700 3.754188 GATGATATCCAATTCTGCGCC 57.246 47.619 4.18 0.00 0.00 6.53
4634 5733 6.764877 TGCTAGTTTCTTTCACGTTTAGAG 57.235 37.500 0.00 0.00 0.00 2.43
4647 5746 1.672881 GCCATCGCATTGCTAGTTTCT 59.327 47.619 7.12 0.00 34.03 2.52
4684 5783 4.071423 TCTCTCTCTATTCATCTCAGCGG 58.929 47.826 0.00 0.00 0.00 5.52
4685 5784 5.687770 TTCTCTCTCTATTCATCTCAGCG 57.312 43.478 0.00 0.00 0.00 5.18
4725 5824 3.793060 AGGAACGTCCTCACCTGG 58.207 61.111 0.00 0.00 45.66 4.45
4803 5902 0.662374 AACGTCCGTAGCTGTTGTCG 60.662 55.000 0.00 0.00 0.00 4.35
4814 5913 2.304751 AGTTTTCTGTGAACGTCCGT 57.695 45.000 0.00 0.00 32.38 4.69
4815 5914 4.377022 CCATTAGTTTTCTGTGAACGTCCG 60.377 45.833 0.00 0.00 32.38 4.79



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

AutoCloner maintained by Alex Coulton.