Multiple sequence alignment - TraesCS1D01G278500

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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 TraesCS1D01G278500 chr1D 100.000 4241 0 0 1 4241 375988586 375992826 0.000000e+00 7832.0
1 TraesCS1D01G278500 chr1A 91.924 3368 175 42 1 3337 474790539 474793840 0.000000e+00 4623.0
2 TraesCS1D01G278500 chr1A 93.642 1384 85 3 1461 2843 59211692 59210311 0.000000e+00 2065.0
3 TraesCS1D01G278500 chr1A 84.015 807 65 30 3446 4218 474793935 474794711 0.000000e+00 717.0
4 TraesCS1D01G278500 chr1B 92.250 2400 82 18 1043 3367 502217887 502220257 0.000000e+00 3306.0
5 TraesCS1D01G278500 chr1B 87.690 788 31 27 3367 4106 502220292 502221061 0.000000e+00 857.0
6 TraesCS1D01G278500 chr1B 93.605 172 9 2 845 1015 502217146 502217316 5.440000e-64 255.0
7 TraesCS1D01G278500 chr5D 94.483 1885 94 5 1461 3345 42725376 42727250 0.000000e+00 2896.0
8 TraesCS1D01G278500 chr5D 94.164 1885 85 5 1461 3345 249912085 249913944 0.000000e+00 2848.0
9 TraesCS1D01G278500 chr5D 94.340 159 9 0 1465 1623 42727402 42727244 1.180000e-60 244.0
10 TraesCS1D01G278500 chr5D 92.683 164 11 1 1461 1623 249914101 249913938 7.090000e-58 235.0
11 TraesCS1D01G278500 chr2D 93.489 1889 88 12 1461 3342 185365795 185367655 0.000000e+00 2774.0
12 TraesCS1D01G278500 chr2D 92.593 54 4 0 3882 3935 185369104 185369157 1.260000e-10 78.7
13 TraesCS1D01G278500 chr2D 90.741 54 5 0 3882 3935 185365768 185365715 5.880000e-09 73.1
14 TraesCS1D01G278500 chr2A 93.114 1888 107 8 1459 3345 768058800 768060665 0.000000e+00 2745.0
15 TraesCS1D01G278500 chr2A 92.593 54 4 0 3882 3935 768058792 768058739 1.260000e-10 78.7
16 TraesCS1D01G278500 chr3A 76.797 1892 304 92 1139 2938 615938599 615940447 0.000000e+00 937.0
17 TraesCS1D01G278500 chr3B 76.072 2052 335 92 1145 3088 629195163 629193160 0.000000e+00 926.0
18 TraesCS1D01G278500 chr3D 76.054 2063 331 103 1142 3088 473482304 473484319 0.000000e+00 922.0
19 TraesCS1D01G278500 chr4A 80.303 132 21 4 587 715 66761933 66762062 1.260000e-15 95.3


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 TraesCS1D01G278500 chr1D 375988586 375992826 4240 False 7832.000000 7832 100.000000 1 4241 1 chr1D.!!$F1 4240
1 TraesCS1D01G278500 chr1A 474790539 474794711 4172 False 2670.000000 4623 87.969500 1 4218 2 chr1A.!!$F1 4217
2 TraesCS1D01G278500 chr1A 59210311 59211692 1381 True 2065.000000 2065 93.642000 1461 2843 1 chr1A.!!$R1 1382
3 TraesCS1D01G278500 chr1B 502217146 502221061 3915 False 1472.666667 3306 91.181667 845 4106 3 chr1B.!!$F1 3261
4 TraesCS1D01G278500 chr5D 42725376 42727250 1874 False 2896.000000 2896 94.483000 1461 3345 1 chr5D.!!$F1 1884
5 TraesCS1D01G278500 chr5D 249912085 249913944 1859 False 2848.000000 2848 94.164000 1461 3345 1 chr5D.!!$F2 1884
6 TraesCS1D01G278500 chr2D 185365795 185369157 3362 False 1426.350000 2774 93.041000 1461 3935 2 chr2D.!!$F1 2474
7 TraesCS1D01G278500 chr2A 768058800 768060665 1865 False 2745.000000 2745 93.114000 1459 3345 1 chr2A.!!$F1 1886
8 TraesCS1D01G278500 chr3A 615938599 615940447 1848 False 937.000000 937 76.797000 1139 2938 1 chr3A.!!$F1 1799
9 TraesCS1D01G278500 chr3B 629193160 629195163 2003 True 926.000000 926 76.072000 1145 3088 1 chr3B.!!$R1 1943
10 TraesCS1D01G278500 chr3D 473482304 473484319 2015 False 922.000000 922 76.054000 1142 3088 1 chr3D.!!$F1 1946

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
41 42 0.743345 GTCTATGTCGGGGTTGTGCC 60.743 60.000 0.00 0.0 0.00 5.01 F
789 818 1.004161 TGCACATTCGAAAGATGGGGA 59.996 47.619 7.49 0.0 41.60 4.81 F
1020 1050 1.070445 CGCCCCCTCATCAGTCATC 59.930 63.158 0.00 0.0 0.00 2.92 F
2297 3005 1.134946 CCAAATTCCGGTGGAAGATGC 59.865 52.381 0.00 0.0 45.48 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1015 1045 1.302752 TGCAGGCTGGTGTGATGAC 60.303 57.895 17.64 0.0 0.00 3.06 R
2286 2994 1.817099 CTGCGAGGCATCTTCCACC 60.817 63.158 0.00 0.0 38.13 4.61 R
2434 3142 4.211330 TGGCTTTGGGTCGGGCAA 62.211 61.111 0.00 0.0 32.76 4.52 R
4050 6040 0.249699 TTTCTCGTGCACATGTCCGT 60.250 50.000 18.64 0.0 0.00 4.69 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
41 42 0.743345 GTCTATGTCGGGGTTGTGCC 60.743 60.000 0.00 0.00 0.00 5.01
57 58 3.799753 CCAGTGTGTGGCTATCGC 58.200 61.111 0.00 0.00 40.39 4.58
79 80 1.195448 GTGTGGTGATCTCGCTTTGTG 59.805 52.381 0.00 0.00 0.00 3.33
91 92 1.983605 CGCTTTGTGGTAGTGACTACG 59.016 52.381 15.83 3.08 39.82 3.51
96 97 5.636543 GCTTTGTGGTAGTGACTACGTTTAT 59.363 40.000 15.83 0.00 39.82 1.40
98 99 7.410800 TTTGTGGTAGTGACTACGTTTATTG 57.589 36.000 15.83 0.00 39.82 1.90
111 112 2.093783 CGTTTATTGGAAGCGAGGTCAC 59.906 50.000 0.00 0.00 0.00 3.67
158 159 5.452077 GGAAGTGAAGCCGACAATATAGAGT 60.452 44.000 0.00 0.00 0.00 3.24
164 165 4.938080 AGCCGACAATATAGAGTGACTTG 58.062 43.478 0.00 0.00 0.00 3.16
172 173 8.764524 ACAATATAGAGTGACTTGAGTTTGAC 57.235 34.615 0.00 0.00 0.00 3.18
207 208 3.512033 ACATGGTCTCGAGTTCTAAGC 57.488 47.619 13.13 2.67 0.00 3.09
210 211 4.245660 CATGGTCTCGAGTTCTAAGCAAA 58.754 43.478 13.13 0.00 0.00 3.68
211 212 4.330944 TGGTCTCGAGTTCTAAGCAAAA 57.669 40.909 13.13 0.00 0.00 2.44
212 213 4.699637 TGGTCTCGAGTTCTAAGCAAAAA 58.300 39.130 13.13 0.00 0.00 1.94
213 214 4.750098 TGGTCTCGAGTTCTAAGCAAAAAG 59.250 41.667 13.13 0.00 0.00 2.27
219 221 6.285990 TCGAGTTCTAAGCAAAAAGTTAGGT 58.714 36.000 0.00 0.00 0.00 3.08
228 230 5.314529 AGCAAAAAGTTAGGTCTAACCCTC 58.685 41.667 14.99 2.72 44.79 4.30
229 231 4.153655 GCAAAAAGTTAGGTCTAACCCTCG 59.846 45.833 14.99 4.65 44.79 4.63
230 232 5.303165 CAAAAAGTTAGGTCTAACCCTCGT 58.697 41.667 14.99 0.00 44.79 4.18
290 292 2.208431 CTTTGTTGCGGGCATTTTTGA 58.792 42.857 0.00 0.00 0.00 2.69
296 298 4.218635 TGTTGCGGGCATTTTTGAACTATA 59.781 37.500 0.00 0.00 0.00 1.31
343 345 2.945008 TGCACAGTCTAGCCATTATTGC 59.055 45.455 0.00 0.00 0.00 3.56
356 358 6.229733 AGCCATTATTGCTAGATGAGAAGAC 58.770 40.000 0.00 0.00 37.28 3.01
362 364 4.991153 TGCTAGATGAGAAGACGACATT 57.009 40.909 0.00 0.00 0.00 2.71
382 384 1.194547 TGCTCGCACGTCATTTTCTTC 59.805 47.619 0.00 0.00 0.00 2.87
391 393 4.444388 CACGTCATTTTCTTCTCGAAGACA 59.556 41.667 8.78 0.34 46.13 3.41
408 410 2.368875 AGACATCGTTGTTGGAGAACCT 59.631 45.455 0.00 0.00 35.79 3.50
424 426 6.987403 GAGAACCTCTCTCTTATTATGGGT 57.013 41.667 0.00 0.00 46.32 4.51
433 435 8.183104 TCTCTCTTATTATGGGTATCACACTG 57.817 38.462 0.00 0.00 0.00 3.66
473 475 3.439293 CGTAGATCGCTTTGACATGACT 58.561 45.455 0.00 0.00 0.00 3.41
579 581 8.875803 CGACTAGCCTTTAACATTGTGTTTATA 58.124 33.333 0.20 0.00 41.45 0.98
653 656 7.609760 TCGGATGCATATGAATGTATTTACC 57.390 36.000 6.97 0.00 38.39 2.85
654 657 7.164803 TCGGATGCATATGAATGTATTTACCA 58.835 34.615 6.97 0.00 38.39 3.25
660 663 9.747293 TGCATATGAATGTATTTACCATGTTTG 57.253 29.630 6.97 0.00 35.38 2.93
755 774 5.237815 AGAAAACATCGAACATCTACTGCA 58.762 37.500 0.00 0.00 0.00 4.41
757 776 7.041721 AGAAAACATCGAACATCTACTGCATA 58.958 34.615 0.00 0.00 0.00 3.14
758 777 6.834959 AAACATCGAACATCTACTGCATAG 57.165 37.500 0.00 0.00 0.00 2.23
764 793 4.271049 CGAACATCTACTGCATAGTTTGGG 59.729 45.833 0.00 0.00 38.36 4.12
769 798 6.891908 ACATCTACTGCATAGTTTGGGAAAAT 59.108 34.615 0.00 0.00 38.36 1.82
778 807 3.652274 AGTTTGGGAAAATGCACATTCG 58.348 40.909 0.00 0.00 0.00 3.34
787 816 3.788333 AATGCACATTCGAAAGATGGG 57.212 42.857 7.49 0.85 41.60 4.00
789 818 1.004161 TGCACATTCGAAAGATGGGGA 59.996 47.619 7.49 0.00 41.60 4.81
790 819 2.091541 GCACATTCGAAAGATGGGGAA 58.908 47.619 7.49 0.00 41.60 3.97
793 822 4.560513 GCACATTCGAAAGATGGGGAAAAA 60.561 41.667 7.49 0.00 41.60 1.94
794 823 5.163513 CACATTCGAAAGATGGGGAAAAAG 58.836 41.667 7.49 0.00 41.60 2.27
795 824 3.934457 TTCGAAAGATGGGGAAAAAGC 57.066 42.857 0.00 0.00 41.60 3.51
796 825 2.167662 TCGAAAGATGGGGAAAAAGCC 58.832 47.619 0.00 0.00 33.31 4.35
797 826 1.892474 CGAAAGATGGGGAAAAAGCCA 59.108 47.619 0.00 0.00 0.00 4.75
799 828 3.244044 CGAAAGATGGGGAAAAAGCCAAA 60.244 43.478 0.00 0.00 0.00 3.28
800 829 4.713553 GAAAGATGGGGAAAAAGCCAAAA 58.286 39.130 0.00 0.00 0.00 2.44
801 830 3.769739 AGATGGGGAAAAAGCCAAAAC 57.230 42.857 0.00 0.00 0.00 2.43
802 831 3.044894 AGATGGGGAAAAAGCCAAAACA 58.955 40.909 0.00 0.00 0.00 2.83
803 832 2.700722 TGGGGAAAAAGCCAAAACAC 57.299 45.000 0.00 0.00 0.00 3.32
804 833 1.210722 TGGGGAAAAAGCCAAAACACC 59.789 47.619 0.00 0.00 0.00 4.16
805 834 1.488812 GGGGAAAAAGCCAAAACACCT 59.511 47.619 0.00 0.00 0.00 4.00
806 835 2.484770 GGGGAAAAAGCCAAAACACCTC 60.485 50.000 0.00 0.00 0.00 3.85
807 836 2.434336 GGGAAAAAGCCAAAACACCTCT 59.566 45.455 0.00 0.00 0.00 3.69
808 837 3.639561 GGGAAAAAGCCAAAACACCTCTA 59.360 43.478 0.00 0.00 0.00 2.43
809 838 4.100344 GGGAAAAAGCCAAAACACCTCTAA 59.900 41.667 0.00 0.00 0.00 2.10
810 839 5.395879 GGGAAAAAGCCAAAACACCTCTAAA 60.396 40.000 0.00 0.00 0.00 1.85
811 840 5.522460 GGAAAAAGCCAAAACACCTCTAAAC 59.478 40.000 0.00 0.00 0.00 2.01
812 841 4.665833 AAAGCCAAAACACCTCTAAACC 57.334 40.909 0.00 0.00 0.00 3.27
813 842 2.594131 AGCCAAAACACCTCTAAACCC 58.406 47.619 0.00 0.00 0.00 4.11
814 843 1.616865 GCCAAAACACCTCTAAACCCC 59.383 52.381 0.00 0.00 0.00 4.95
815 844 2.952116 CCAAAACACCTCTAAACCCCA 58.048 47.619 0.00 0.00 0.00 4.96
816 845 3.301274 CCAAAACACCTCTAAACCCCAA 58.699 45.455 0.00 0.00 0.00 4.12
817 846 3.320826 CCAAAACACCTCTAAACCCCAAG 59.679 47.826 0.00 0.00 0.00 3.61
818 847 4.211920 CAAAACACCTCTAAACCCCAAGA 58.788 43.478 0.00 0.00 0.00 3.02
819 848 3.790089 AACACCTCTAAACCCCAAGAG 57.210 47.619 0.00 0.00 39.19 2.85
834 863 4.828072 CCAAGAGGGTAGTAGAAAGCTT 57.172 45.455 0.00 0.00 0.00 3.74
838 867 5.669164 AGAGGGTAGTAGAAAGCTTGAAG 57.331 43.478 0.00 0.00 0.00 3.02
839 868 5.088026 AGAGGGTAGTAGAAAGCTTGAAGT 58.912 41.667 0.00 0.00 0.00 3.01
855 884 3.792401 TGAAGTCTTGAACGAAGCAGAA 58.208 40.909 0.00 0.00 0.00 3.02
931 960 5.178996 CCTTTCACTTTCATCTCTGTGTCTG 59.821 44.000 0.00 0.00 0.00 3.51
932 961 4.944619 TCACTTTCATCTCTGTGTCTGT 57.055 40.909 0.00 0.00 0.00 3.41
933 962 4.625028 TCACTTTCATCTCTGTGTCTGTG 58.375 43.478 0.00 0.00 0.00 3.66
934 963 4.100035 TCACTTTCATCTCTGTGTCTGTGT 59.900 41.667 0.00 0.00 0.00 3.72
938 967 2.029918 TCATCTCTGTGTCTGTGTTCCG 60.030 50.000 0.00 0.00 0.00 4.30
985 1015 1.074889 TCTAAAACCAGAACCAGCCCC 59.925 52.381 0.00 0.00 0.00 5.80
1015 1045 2.362369 ACTCACGCCCCCTCATCAG 61.362 63.158 0.00 0.00 0.00 2.90
1016 1046 2.284625 TCACGCCCCCTCATCAGT 60.285 61.111 0.00 0.00 0.00 3.41
1017 1047 2.187946 CACGCCCCCTCATCAGTC 59.812 66.667 0.00 0.00 0.00 3.51
1018 1048 2.284625 ACGCCCCCTCATCAGTCA 60.285 61.111 0.00 0.00 0.00 3.41
1019 1049 1.690633 ACGCCCCCTCATCAGTCAT 60.691 57.895 0.00 0.00 0.00 3.06
1020 1050 1.070445 CGCCCCCTCATCAGTCATC 59.930 63.158 0.00 0.00 0.00 2.92
1021 1051 1.689243 CGCCCCCTCATCAGTCATCA 61.689 60.000 0.00 0.00 0.00 3.07
1136 1737 1.371267 CCGCGACAAGTGACGAAGA 60.371 57.895 8.23 0.00 35.37 2.87
2167 2875 3.427598 GACGGCTACCTCTTCGGCC 62.428 68.421 0.00 0.00 41.02 6.13
2286 2994 2.024918 CTCCGATGGCCAAATTCCG 58.975 57.895 10.96 8.69 0.00 4.30
2297 3005 1.134946 CCAAATTCCGGTGGAAGATGC 59.865 52.381 0.00 0.00 45.48 3.91
2307 3015 3.267860 GAAGATGCCTCGCAGCCG 61.268 66.667 0.00 0.00 46.90 5.52
2434 3142 1.272490 TGCTGAGAAGGTCGTTCGAAT 59.728 47.619 0.00 0.00 40.49 3.34
3094 3862 1.583495 CCGGCTGTACTGAGACGTGA 61.583 60.000 7.60 0.00 43.43 4.35
3108 3876 2.293677 AGACGTGACATCTCGTTTCACT 59.706 45.455 10.03 1.07 44.60 3.41
3109 3877 3.501062 AGACGTGACATCTCGTTTCACTA 59.499 43.478 10.03 0.00 44.60 2.74
3110 3878 3.562505 ACGTGACATCTCGTTTCACTAC 58.437 45.455 3.30 0.00 42.42 2.73
3157 3937 0.308993 AGTCGTTTCTTTGCAGCAGC 59.691 50.000 0.00 0.00 42.57 5.25
3273 4071 1.285280 TGGATGGAATGGAACGAGGT 58.715 50.000 0.00 0.00 0.00 3.85
3354 4152 1.033574 GTCGGTAGCTAGCTGTCCAT 58.966 55.000 27.68 1.87 0.00 3.41
3402 4235 6.152661 ACAAATCCCGATGTTCATATGTTGTT 59.847 34.615 1.90 0.00 0.00 2.83
3414 4247 6.474819 TCATATGTTGTTACTTTGGTGTCG 57.525 37.500 1.90 0.00 0.00 4.35
3425 4327 1.052124 TTGGTGTCGAAGTCTGGGGT 61.052 55.000 0.00 0.00 0.00 4.95
3446 4348 0.757561 GGGTCCTACTGCTCCTCCTC 60.758 65.000 0.00 0.00 0.00 3.71
3447 4349 0.260523 GGTCCTACTGCTCCTCCTCT 59.739 60.000 0.00 0.00 0.00 3.69
3448 4350 1.398692 GTCCTACTGCTCCTCCTCTG 58.601 60.000 0.00 0.00 0.00 3.35
3449 4351 0.260230 TCCTACTGCTCCTCCTCTGG 59.740 60.000 0.00 0.00 0.00 3.86
3450 4352 0.758685 CCTACTGCTCCTCCTCTGGG 60.759 65.000 0.00 0.00 0.00 4.45
3451 4353 0.260230 CTACTGCTCCTCCTCTGGGA 59.740 60.000 0.00 0.00 39.70 4.37
3452 4354 0.033011 TACTGCTCCTCCTCTGGGAC 60.033 60.000 0.00 0.00 36.57 4.46
3453 4355 1.001503 CTGCTCCTCCTCTGGGACT 59.998 63.158 0.00 0.00 36.57 3.85
3454 4356 1.305633 TGCTCCTCCTCTGGGACTG 60.306 63.158 0.00 0.00 36.57 3.51
3455 4357 2.063378 GCTCCTCCTCTGGGACTGG 61.063 68.421 0.00 0.00 36.57 4.00
3456 4358 1.382420 CTCCTCCTCTGGGACTGGG 60.382 68.421 0.00 0.00 36.57 4.45
3489 4393 3.242673 GGACCGTGTCTGTCGAATAGTAG 60.243 52.174 0.00 0.00 33.46 2.57
3490 4394 3.341823 ACCGTGTCTGTCGAATAGTAGT 58.658 45.455 0.00 0.00 0.00 2.73
3491 4395 4.507710 ACCGTGTCTGTCGAATAGTAGTA 58.492 43.478 0.00 0.00 0.00 1.82
3613 5150 2.711922 GCCACCTGACCGATCGACT 61.712 63.158 18.66 0.00 0.00 4.18
3614 5151 1.433879 CCACCTGACCGATCGACTC 59.566 63.158 18.66 11.10 0.00 3.36
3615 5152 1.313091 CCACCTGACCGATCGACTCA 61.313 60.000 18.66 15.14 0.00 3.41
3616 5153 0.741326 CACCTGACCGATCGACTCAT 59.259 55.000 18.66 0.05 0.00 2.90
3617 5154 1.025812 ACCTGACCGATCGACTCATC 58.974 55.000 18.66 6.52 0.00 2.92
3823 5364 2.352229 CGCCGTATTGCATTGCCG 60.352 61.111 6.12 2.07 0.00 5.69
3880 5828 1.396301 CTGCTGCTTCTTCATTCGTCC 59.604 52.381 0.00 0.00 0.00 4.79
3887 5851 1.079127 CTTCATTCGTCCGGCCACT 60.079 57.895 2.24 0.00 0.00 4.00
4050 6040 2.190313 GCCCTGGATGCGTGATCA 59.810 61.111 0.00 0.00 31.91 2.92
4078 6068 0.817634 TGCACGAGAAACCACAAGGG 60.818 55.000 0.00 0.00 44.81 3.95
4081 6071 0.535102 ACGAGAAACCACAAGGGCAG 60.535 55.000 0.00 0.00 42.05 4.85
4106 6096 1.335810 GTTGGTTCTTCAACGGGGTTC 59.664 52.381 0.00 0.00 37.80 3.62
4141 6131 3.052082 AGCTGCGTGGTGTGATGC 61.052 61.111 0.00 0.00 0.00 3.91
4142 6132 3.052082 GCTGCGTGGTGTGATGCT 61.052 61.111 0.00 0.00 0.00 3.79
4147 6137 1.737236 TGCGTGGTGTGATGCTATTTC 59.263 47.619 0.00 0.00 0.00 2.17
4156 6146 1.139654 TGATGCTATTTCGCTGCTCCT 59.860 47.619 0.00 0.00 0.00 3.69
4172 6162 2.417379 GCTCCTCGACAAGCTCATGTTA 60.417 50.000 6.97 0.00 35.60 2.41
4173 6163 3.182967 CTCCTCGACAAGCTCATGTTAC 58.817 50.000 0.00 0.00 32.57 2.50
4174 6164 2.826128 TCCTCGACAAGCTCATGTTACT 59.174 45.455 0.00 0.00 32.57 2.24
4175 6165 4.014406 TCCTCGACAAGCTCATGTTACTA 58.986 43.478 0.00 0.00 32.57 1.82
4176 6166 4.096532 TCCTCGACAAGCTCATGTTACTAG 59.903 45.833 0.00 0.00 32.57 2.57
4177 6167 4.142359 CCTCGACAAGCTCATGTTACTAGT 60.142 45.833 0.00 0.00 32.57 2.57
4178 6168 5.066117 CCTCGACAAGCTCATGTTACTAGTA 59.934 44.000 0.00 0.00 32.57 1.82
4179 6169 6.120378 TCGACAAGCTCATGTTACTAGTAG 57.880 41.667 2.23 0.00 32.57 2.57
4180 6170 5.646793 TCGACAAGCTCATGTTACTAGTAGT 59.353 40.000 8.14 8.14 32.57 2.73
4183 6180 6.390721 ACAAGCTCATGTTACTAGTAGTGTG 58.609 40.000 13.29 6.75 0.00 3.82
4192 6189 5.232626 TGTTACTAGTAGTGTGTTGTTTGCG 59.767 40.000 13.29 0.00 0.00 4.85
4205 6202 5.615181 GTGTTGTTTGCGCAAAATATGTTTC 59.385 36.000 35.09 20.66 31.33 2.78
4206 6203 5.521735 TGTTGTTTGCGCAAAATATGTTTCT 59.478 32.000 35.09 0.00 31.33 2.52
4214 6211 6.644181 TGCGCAAAATATGTTTCTGAAATCAA 59.356 30.769 8.16 0.00 0.00 2.57
4221 6218 9.831737 AAATATGTTTCTGAAATCAACTTCGAG 57.168 29.630 6.06 0.00 0.00 4.04
4222 6219 5.095691 TGTTTCTGAAATCAACTTCGAGC 57.904 39.130 6.06 0.00 0.00 5.03
4223 6220 4.574421 TGTTTCTGAAATCAACTTCGAGCA 59.426 37.500 6.06 0.00 0.00 4.26
4224 6221 4.997905 TTCTGAAATCAACTTCGAGCAG 57.002 40.909 0.00 0.00 0.00 4.24
4225 6222 3.995199 TCTGAAATCAACTTCGAGCAGT 58.005 40.909 0.00 0.00 0.00 4.40
4226 6223 3.990469 TCTGAAATCAACTTCGAGCAGTC 59.010 43.478 0.00 0.00 0.00 3.51
4227 6224 3.727726 TGAAATCAACTTCGAGCAGTCA 58.272 40.909 0.00 0.00 0.00 3.41
4228 6225 3.494626 TGAAATCAACTTCGAGCAGTCAC 59.505 43.478 0.00 0.00 0.00 3.67
4229 6226 3.393089 AATCAACTTCGAGCAGTCACT 57.607 42.857 0.00 0.00 0.00 3.41
4230 6227 4.521130 AATCAACTTCGAGCAGTCACTA 57.479 40.909 0.00 0.00 0.00 2.74
4231 6228 3.560902 TCAACTTCGAGCAGTCACTAG 57.439 47.619 0.00 0.00 0.00 2.57
4232 6229 2.885266 TCAACTTCGAGCAGTCACTAGT 59.115 45.455 0.00 0.00 0.00 2.57
4233 6230 2.983136 CAACTTCGAGCAGTCACTAGTG 59.017 50.000 17.17 17.17 0.00 2.74
4234 6231 1.542030 ACTTCGAGCAGTCACTAGTGG 59.458 52.381 22.48 8.08 0.00 4.00
4235 6232 1.542030 CTTCGAGCAGTCACTAGTGGT 59.458 52.381 22.48 7.89 39.46 4.16
4236 6233 2.484742 TCGAGCAGTCACTAGTGGTA 57.515 50.000 22.48 1.20 36.90 3.25
4237 6234 2.786777 TCGAGCAGTCACTAGTGGTAA 58.213 47.619 22.48 0.39 36.90 2.85
4238 6235 2.486982 TCGAGCAGTCACTAGTGGTAAC 59.513 50.000 22.48 13.40 36.90 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.286751 CACACTGGCACAACCCCG 61.287 66.667 0.00 0.00 38.70 5.73
57 58 0.670546 AAAGCGAGATCACCACACGG 60.671 55.000 0.00 0.00 38.77 4.94
71 72 1.983605 CGTAGTCACTACCACAAAGCG 59.016 52.381 9.49 0.00 33.79 4.68
79 80 5.290400 GCTTCCAATAAACGTAGTCACTACC 59.710 44.000 9.49 0.00 45.00 3.18
91 92 3.071479 TGTGACCTCGCTTCCAATAAAC 58.929 45.455 0.00 0.00 0.00 2.01
96 97 0.179234 TGTTGTGACCTCGCTTCCAA 59.821 50.000 0.00 0.00 0.00 3.53
98 99 2.271800 CTATGTTGTGACCTCGCTTCC 58.728 52.381 0.00 0.00 0.00 3.46
134 135 4.945246 TCTATATTGTCGGCTTCACTTCC 58.055 43.478 0.00 0.00 0.00 3.46
142 143 4.645136 TCAAGTCACTCTATATTGTCGGCT 59.355 41.667 0.00 0.00 0.00 5.52
145 146 7.755373 TCAAACTCAAGTCACTCTATATTGTCG 59.245 37.037 0.00 0.00 0.00 4.35
158 159 3.132289 AGAGAACCGTCAAACTCAAGTCA 59.868 43.478 0.00 0.00 32.59 3.41
164 165 3.009301 TCGAAGAGAACCGTCAAACTC 57.991 47.619 0.00 0.00 0.00 3.01
207 208 5.303165 ACGAGGGTTAGACCTAACTTTTTG 58.697 41.667 16.63 10.25 43.58 2.44
228 230 5.276207 CGACCATTGCTATGTACAACTAACG 60.276 44.000 0.00 0.00 0.00 3.18
229 231 5.579511 ACGACCATTGCTATGTACAACTAAC 59.420 40.000 0.00 0.00 0.00 2.34
230 232 5.579119 CACGACCATTGCTATGTACAACTAA 59.421 40.000 0.00 0.00 0.00 2.24
240 242 3.190535 GTGGAAAACACGACCATTGCTAT 59.809 43.478 0.00 0.00 40.85 2.97
343 345 4.930963 AGCAATGTCGTCTTCTCATCTAG 58.069 43.478 0.00 0.00 0.00 2.43
349 351 0.642800 GCGAGCAATGTCGTCTTCTC 59.357 55.000 6.97 0.00 42.17 2.87
356 358 1.686566 ATGACGTGCGAGCAATGTCG 61.687 55.000 19.66 13.22 43.08 4.35
362 364 1.194547 GAAGAAAATGACGTGCGAGCA 59.805 47.619 0.00 0.00 0.00 4.26
382 384 7.068457 GTTCTCCAACAACGATGTCTTCGAG 62.068 48.000 14.43 8.87 40.18 4.04
391 393 2.900546 AGAGAGGTTCTCCAACAACGAT 59.099 45.455 2.60 0.00 44.42 3.73
408 410 8.004801 TCAGTGTGATACCCATAATAAGAGAGA 58.995 37.037 0.00 0.00 0.00 3.10
415 417 7.223584 CAACCATCAGTGTGATACCCATAATA 58.776 38.462 0.00 0.00 34.28 0.98
424 426 4.758688 CAGTAGCAACCATCAGTGTGATA 58.241 43.478 0.00 0.00 34.28 2.15
425 427 3.603532 CAGTAGCAACCATCAGTGTGAT 58.396 45.455 0.00 0.00 37.65 3.06
452 454 3.439293 AGTCATGTCAAAGCGATCTACG 58.561 45.455 0.00 0.00 45.66 3.51
534 536 1.134280 CGAGGCAGGGAGATTGAACAT 60.134 52.381 0.00 0.00 0.00 2.71
708 721 2.199236 GCGTCCGTTCCGAAATAAGAT 58.801 47.619 0.00 0.00 0.00 2.40
726 744 4.327357 AGATGTTCGATGTTTTCTACTGCG 59.673 41.667 0.00 0.00 0.00 5.18
755 774 5.184864 TCGAATGTGCATTTTCCCAAACTAT 59.815 36.000 0.00 0.00 0.00 2.12
757 776 3.320541 TCGAATGTGCATTTTCCCAAACT 59.679 39.130 0.00 0.00 0.00 2.66
758 777 3.648009 TCGAATGTGCATTTTCCCAAAC 58.352 40.909 0.00 0.00 0.00 2.93
764 793 4.563976 CCCATCTTTCGAATGTGCATTTTC 59.436 41.667 10.48 0.00 0.00 2.29
769 798 1.004161 TCCCCATCTTTCGAATGTGCA 59.996 47.619 10.48 0.00 0.00 4.57
778 807 4.350368 TTTGGCTTTTTCCCCATCTTTC 57.650 40.909 0.00 0.00 0.00 2.62
787 816 3.819564 AGAGGTGTTTTGGCTTTTTCC 57.180 42.857 0.00 0.00 0.00 3.13
789 818 5.424757 GGTTTAGAGGTGTTTTGGCTTTTT 58.575 37.500 0.00 0.00 0.00 1.94
790 819 4.141801 GGGTTTAGAGGTGTTTTGGCTTTT 60.142 41.667 0.00 0.00 0.00 2.27
793 822 2.594131 GGGTTTAGAGGTGTTTTGGCT 58.406 47.619 0.00 0.00 0.00 4.75
794 823 1.616865 GGGGTTTAGAGGTGTTTTGGC 59.383 52.381 0.00 0.00 0.00 4.52
795 824 2.952116 TGGGGTTTAGAGGTGTTTTGG 58.048 47.619 0.00 0.00 0.00 3.28
796 825 4.211920 TCTTGGGGTTTAGAGGTGTTTTG 58.788 43.478 0.00 0.00 0.00 2.44
797 826 4.470602 CTCTTGGGGTTTAGAGGTGTTTT 58.529 43.478 0.00 0.00 35.37 2.43
799 828 3.790089 CTCTTGGGGTTTAGAGGTGTT 57.210 47.619 0.00 0.00 35.37 3.32
813 842 4.223032 TCAAGCTTTCTACTACCCTCTTGG 59.777 45.833 0.00 0.00 41.37 3.61
814 843 5.407407 TCAAGCTTTCTACTACCCTCTTG 57.593 43.478 0.00 0.00 0.00 3.02
815 844 5.544562 ACTTCAAGCTTTCTACTACCCTCTT 59.455 40.000 0.00 0.00 0.00 2.85
816 845 5.088026 ACTTCAAGCTTTCTACTACCCTCT 58.912 41.667 0.00 0.00 0.00 3.69
817 846 5.186215 AGACTTCAAGCTTTCTACTACCCTC 59.814 44.000 0.00 0.00 0.00 4.30
818 847 5.088026 AGACTTCAAGCTTTCTACTACCCT 58.912 41.667 0.00 0.00 0.00 4.34
819 848 5.408880 AGACTTCAAGCTTTCTACTACCC 57.591 43.478 0.00 0.00 0.00 3.69
820 849 6.456501 TCAAGACTTCAAGCTTTCTACTACC 58.543 40.000 0.00 0.00 0.00 3.18
821 850 7.358517 CGTTCAAGACTTCAAGCTTTCTACTAC 60.359 40.741 0.00 0.00 0.00 2.73
822 851 6.641314 CGTTCAAGACTTCAAGCTTTCTACTA 59.359 38.462 0.00 0.00 0.00 1.82
823 852 5.463724 CGTTCAAGACTTCAAGCTTTCTACT 59.536 40.000 0.00 0.00 0.00 2.57
824 853 5.462398 TCGTTCAAGACTTCAAGCTTTCTAC 59.538 40.000 0.00 0.00 0.00 2.59
825 854 5.597806 TCGTTCAAGACTTCAAGCTTTCTA 58.402 37.500 0.00 0.00 0.00 2.10
826 855 4.442706 TCGTTCAAGACTTCAAGCTTTCT 58.557 39.130 0.00 0.00 0.00 2.52
827 856 4.795970 TCGTTCAAGACTTCAAGCTTTC 57.204 40.909 0.00 0.00 0.00 2.62
828 857 4.496507 GCTTCGTTCAAGACTTCAAGCTTT 60.497 41.667 0.00 0.00 33.59 3.51
829 858 3.002759 GCTTCGTTCAAGACTTCAAGCTT 59.997 43.478 0.00 0.00 33.59 3.74
830 859 2.545946 GCTTCGTTCAAGACTTCAAGCT 59.454 45.455 0.00 0.00 33.59 3.74
831 860 2.287915 TGCTTCGTTCAAGACTTCAAGC 59.712 45.455 0.00 0.00 35.38 4.01
832 861 3.804325 TCTGCTTCGTTCAAGACTTCAAG 59.196 43.478 0.00 0.00 33.29 3.02
833 862 3.792401 TCTGCTTCGTTCAAGACTTCAA 58.208 40.909 0.00 0.00 33.29 2.69
834 863 3.452755 TCTGCTTCGTTCAAGACTTCA 57.547 42.857 0.00 0.00 33.29 3.02
838 867 3.131396 TCCTTTCTGCTTCGTTCAAGAC 58.869 45.455 0.00 0.00 33.29 3.01
839 868 3.069586 TCTCCTTTCTGCTTCGTTCAAGA 59.930 43.478 0.00 0.00 33.29 3.02
855 884 1.064979 GTCGTCTCTCTCCCTCTCCTT 60.065 57.143 0.00 0.00 0.00 3.36
931 960 4.517832 AGGTAAAAGGATGAAACGGAACAC 59.482 41.667 0.00 0.00 0.00 3.32
932 961 4.721132 AGGTAAAAGGATGAAACGGAACA 58.279 39.130 0.00 0.00 0.00 3.18
933 962 4.142966 CGAGGTAAAAGGATGAAACGGAAC 60.143 45.833 0.00 0.00 0.00 3.62
934 963 3.998341 CGAGGTAAAAGGATGAAACGGAA 59.002 43.478 0.00 0.00 0.00 4.30
938 967 3.751698 AGTGCGAGGTAAAAGGATGAAAC 59.248 43.478 0.00 0.00 0.00 2.78
985 1015 2.048503 GTGAGTGGACGGGTTCGG 60.049 66.667 0.00 0.00 41.39 4.30
1015 1045 1.302752 TGCAGGCTGGTGTGATGAC 60.303 57.895 17.64 0.00 0.00 3.06
1016 1046 1.302752 GTGCAGGCTGGTGTGATGA 60.303 57.895 17.64 0.00 0.00 2.92
1017 1047 2.338015 GGTGCAGGCTGGTGTGATG 61.338 63.158 17.64 0.00 0.00 3.07
1018 1048 2.034687 GGTGCAGGCTGGTGTGAT 59.965 61.111 17.64 0.00 0.00 3.06
1019 1049 3.487626 TGGTGCAGGCTGGTGTGA 61.488 61.111 17.64 0.00 0.00 3.58
1020 1050 3.289834 GTGGTGCAGGCTGGTGTG 61.290 66.667 17.64 0.00 0.00 3.82
1021 1051 3.482232 GAGTGGTGCAGGCTGGTGT 62.482 63.158 17.64 0.00 0.00 4.16
1302 1903 4.329545 GAGGTGGACTTGCGGCCA 62.330 66.667 2.24 0.00 0.00 5.36
1644 2308 3.020274 CTCGTCCTCCAAGAAGATCTCA 58.980 50.000 0.00 0.00 0.00 3.27
2067 2750 2.921221 TCAAGGGAGAATCTTGGGTCT 58.079 47.619 0.00 0.00 41.23 3.85
2286 2994 1.817099 CTGCGAGGCATCTTCCACC 60.817 63.158 0.00 0.00 38.13 4.61
2434 3142 4.211330 TGGCTTTGGGTCGGGCAA 62.211 61.111 0.00 0.00 32.76 4.52
3094 3862 3.056749 GGTCAGGTAGTGAAACGAGATGT 60.057 47.826 0.00 0.00 45.86 3.06
3108 3876 1.035932 GCCGAGCTACTGGTCAGGTA 61.036 60.000 2.87 0.00 40.44 3.08
3109 3877 2.352032 GCCGAGCTACTGGTCAGGT 61.352 63.158 2.87 0.00 40.44 4.00
3110 3878 2.351244 TGCCGAGCTACTGGTCAGG 61.351 63.158 2.87 0.00 40.44 3.86
3157 3937 2.119801 AGCCTTAATCACCACTGCTG 57.880 50.000 0.00 0.00 0.00 4.41
3158 3938 2.887151 AAGCCTTAATCACCACTGCT 57.113 45.000 0.00 0.00 0.00 4.24
3159 3939 3.610911 ACTAAGCCTTAATCACCACTGC 58.389 45.455 0.00 0.00 0.00 4.40
3160 3940 5.978814 ACTACTAAGCCTTAATCACCACTG 58.021 41.667 0.00 0.00 0.00 3.66
3161 3941 6.896307 ACTACTACTAAGCCTTAATCACCACT 59.104 38.462 0.00 0.00 0.00 4.00
3162 3942 7.110043 ACTACTACTAAGCCTTAATCACCAC 57.890 40.000 0.00 0.00 0.00 4.16
3163 3943 8.857098 CATACTACTACTAAGCCTTAATCACCA 58.143 37.037 0.00 0.00 0.00 4.17
3164 3944 9.075678 TCATACTACTACTAAGCCTTAATCACC 57.924 37.037 0.00 0.00 0.00 4.02
3273 4071 8.849168 ACAAACAAGTGATCACATGAGATAAAA 58.151 29.630 31.65 0.00 34.46 1.52
3354 4152 1.001633 GCTTCCTACCGAGGTGAACAA 59.998 52.381 4.80 0.00 44.19 2.83
3377 4210 5.652014 ACAACATATGAACATCGGGATTTGT 59.348 36.000 10.38 2.06 0.00 2.83
3402 4235 2.036733 CCCAGACTTCGACACCAAAGTA 59.963 50.000 0.00 0.00 35.90 2.24
3414 4247 2.657066 GGACCCGACCCCAGACTTC 61.657 68.421 0.00 0.00 0.00 3.01
3425 4327 1.076923 GAGGAGCAGTAGGACCCGA 60.077 63.158 0.00 0.00 0.00 5.14
3446 4348 2.366167 CCTCCCTCCCAGTCCCAG 60.366 72.222 0.00 0.00 0.00 4.45
3447 4349 4.024984 CCCTCCCTCCCAGTCCCA 62.025 72.222 0.00 0.00 0.00 4.37
3448 4350 3.695825 TCCCTCCCTCCCAGTCCC 61.696 72.222 0.00 0.00 0.00 4.46
3449 4351 2.041405 CTCCCTCCCTCCCAGTCC 60.041 72.222 0.00 0.00 0.00 3.85
3450 4352 2.041405 CCTCCCTCCCTCCCAGTC 60.041 72.222 0.00 0.00 0.00 3.51
3451 4353 3.700350 CCCTCCCTCCCTCCCAGT 61.700 72.222 0.00 0.00 0.00 4.00
3452 4354 3.368501 TCCCTCCCTCCCTCCCAG 61.369 72.222 0.00 0.00 0.00 4.45
3453 4355 3.695825 GTCCCTCCCTCCCTCCCA 61.696 72.222 0.00 0.00 0.00 4.37
3454 4356 4.500826 GGTCCCTCCCTCCCTCCC 62.501 77.778 0.00 0.00 0.00 4.30
3455 4357 4.862823 CGGTCCCTCCCTCCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
3456 4358 4.077180 ACGGTCCCTCCCTCCCTC 62.077 72.222 0.00 0.00 0.00 4.30
3489 4393 4.214119 TCTGCTTGTTCATGTCAAAGCTAC 59.786 41.667 21.10 0.00 0.00 3.58
3490 4394 4.388485 TCTGCTTGTTCATGTCAAAGCTA 58.612 39.130 21.10 12.02 0.00 3.32
3491 4395 3.216800 TCTGCTTGTTCATGTCAAAGCT 58.783 40.909 21.10 0.00 0.00 3.74
3613 5150 2.809174 CGCCGCAACTGTCGATGA 60.809 61.111 0.00 0.00 0.00 2.92
3614 5151 3.853330 CCGCCGCAACTGTCGATG 61.853 66.667 0.00 0.00 0.00 3.84
3834 5375 4.651008 CCACCGTACGTGCCGTGT 62.651 66.667 19.73 9.84 41.39 4.49
4010 5996 1.123077 CCCAAGTCGATCCAGATCCA 58.877 55.000 2.11 0.00 34.40 3.41
4050 6040 0.249699 TTTCTCGTGCACATGTCCGT 60.250 50.000 18.64 0.00 0.00 4.69
4131 6121 2.009051 CAGCGAAATAGCATCACACCA 58.991 47.619 0.00 0.00 40.15 4.17
4134 6124 1.935873 GAGCAGCGAAATAGCATCACA 59.064 47.619 0.00 0.00 40.15 3.58
4141 6131 1.202302 TGTCGAGGAGCAGCGAAATAG 60.202 52.381 0.00 0.00 38.36 1.73
4142 6132 0.815095 TGTCGAGGAGCAGCGAAATA 59.185 50.000 0.00 0.00 38.36 1.40
4147 6137 3.184683 GCTTGTCGAGGAGCAGCG 61.185 66.667 13.50 0.00 38.73 5.18
4156 6146 5.646793 ACTACTAGTAACATGAGCTTGTCGA 59.353 40.000 3.76 0.00 0.00 4.20
4172 6162 2.542595 GCGCAAACAACACACTACTAGT 59.457 45.455 0.30 0.00 0.00 2.57
4173 6163 2.542178 TGCGCAAACAACACACTACTAG 59.458 45.455 8.16 0.00 0.00 2.57
4174 6164 2.552031 TGCGCAAACAACACACTACTA 58.448 42.857 8.16 0.00 0.00 1.82
4175 6165 1.374560 TGCGCAAACAACACACTACT 58.625 45.000 8.16 0.00 0.00 2.57
4176 6166 2.181426 TTGCGCAAACAACACACTAC 57.819 45.000 22.78 0.00 0.00 2.73
4177 6167 2.921634 TTTGCGCAAACAACACACTA 57.078 40.000 30.63 5.54 0.00 2.74
4178 6168 2.071688 TTTTGCGCAAACAACACACT 57.928 40.000 33.73 0.00 0.00 3.55
4179 6169 4.026145 ACATATTTTGCGCAAACAACACAC 60.026 37.500 33.73 0.00 0.00 3.82
4180 6170 4.115516 ACATATTTTGCGCAAACAACACA 58.884 34.783 33.73 19.26 0.00 3.72
4183 6180 5.840267 CAGAAACATATTTTGCGCAAACAAC 59.160 36.000 33.73 17.96 0.00 3.32
4205 6202 3.742882 TGACTGCTCGAAGTTGATTTCAG 59.257 43.478 0.00 0.00 0.00 3.02
4206 6203 3.494626 GTGACTGCTCGAAGTTGATTTCA 59.505 43.478 0.00 0.00 0.00 2.69
4214 6211 1.542030 CCACTAGTGACTGCTCGAAGT 59.458 52.381 24.68 0.00 0.00 3.01
4218 6215 2.228103 TGTTACCACTAGTGACTGCTCG 59.772 50.000 24.68 7.91 36.00 5.03
4219 6216 3.576648 GTGTTACCACTAGTGACTGCTC 58.423 50.000 24.68 9.53 38.61 4.26
4220 6217 3.662247 GTGTTACCACTAGTGACTGCT 57.338 47.619 24.68 3.66 38.61 4.24


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

AutoCloner maintained by Alex Coulton.