Multiple sequence alignment - TraesCS6B01G286000

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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 TraesCS6B01G286000 chr6B 100.000 3835 0 0 1 3835 515072534 515068700 0.000000e+00 7083.0
1 TraesCS6B01G286000 chr6B 85.279 197 25 3 364 560 11571600 11571792 2.340000e-47 200.0
2 TraesCS6B01G286000 chr6B 79.928 279 40 13 47 314 334468634 334468361 1.410000e-44 191.0
3 TraesCS6B01G286000 chr6B 84.466 103 7 6 216 314 550784038 550784135 4.080000e-15 93.5
4 TraesCS6B01G286000 chr6B 86.747 83 8 3 10 91 176771078 176770998 5.280000e-14 89.8
5 TraesCS6B01G286000 chr6D 93.360 1988 86 29 1 1954 311542065 311544040 0.000000e+00 2898.0
6 TraesCS6B01G286000 chr6D 90.212 756 48 14 3084 3830 311545152 311545890 0.000000e+00 963.0
7 TraesCS6B01G286000 chr6D 89.961 259 19 2 2114 2370 311544210 311544463 1.030000e-85 327.0
8 TraesCS6B01G286000 chr6D 81.111 360 47 14 216 557 427121118 427121474 6.320000e-68 268.0
9 TraesCS6B01G286000 chr6D 86.161 224 23 3 2460 2682 311544520 311544736 6.410000e-58 235.0
10 TraesCS6B01G286000 chr6D 83.744 203 28 4 360 557 448560300 448560502 1.820000e-43 187.0
11 TraesCS6B01G286000 chr6A 90.879 1831 79 32 885 2699 448217208 448218966 0.000000e+00 2375.0
12 TraesCS6B01G286000 chr6A 91.508 1048 49 18 2807 3835 448218993 448220019 0.000000e+00 1406.0
13 TraesCS6B01G286000 chr4D 82.335 334 42 15 1 323 307806539 307806866 1.360000e-69 274.0
14 TraesCS6B01G286000 chr7A 83.045 289 37 9 1 287 716249890 716249612 6.360000e-63 252.0
15 TraesCS6B01G286000 chr5D 82.642 265 34 10 1 258 520584040 520584299 1.390000e-54 224.0
16 TraesCS6B01G286000 chr2B 78.652 356 59 11 216 556 39783670 39784023 1.790000e-53 220.0
17 TraesCS6B01G286000 chr2B 85.167 209 27 3 357 563 165113725 165113519 1.080000e-50 211.0
18 TraesCS6B01G286000 chr2B 75.726 379 47 23 216 554 798806901 798807274 8.580000e-32 148.0
19 TraesCS6B01G286000 chr2B 89.011 91 6 4 228 314 668006148 668006058 4.050000e-20 110.0
20 TraesCS6B01G286000 chr3B 85.047 214 26 6 357 564 712526328 712526115 3.000000e-51 213.0
21 TraesCS6B01G286000 chr3B 89.412 85 7 2 7 91 133444640 133444558 5.240000e-19 106.0
22 TraesCS6B01G286000 chr2D 84.793 217 27 6 90 301 555225489 555225274 3.000000e-51 213.0
23 TraesCS6B01G286000 chr2D 80.836 287 42 12 30 307 609634136 609634418 3.000000e-51 213.0
24 TraesCS6B01G286000 chr7D 84.804 204 24 7 56 258 65621130 65620933 8.400000e-47 198.0
25 TraesCS6B01G286000 chr7D 84.577 201 29 2 360 558 575575736 575575936 8.400000e-47 198.0
26 TraesCS6B01G286000 chr5B 84.615 195 28 2 364 556 470406504 470406310 3.910000e-45 193.0
27 TraesCS6B01G286000 chr2A 80.784 255 35 12 9 258 13078533 13078778 1.820000e-43 187.0
28 TraesCS6B01G286000 chr7B 91.954 87 6 1 4 90 579829010 579828925 1.870000e-23 121.0


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 TraesCS6B01G286000 chr6B 515068700 515072534 3834 True 7083.00 7083 100.0000 1 3835 1 chr6B.!!$R3 3834
1 TraesCS6B01G286000 chr6D 311542065 311545890 3825 False 1105.75 2898 89.9235 1 3830 4 chr6D.!!$F3 3829
2 TraesCS6B01G286000 chr6A 448217208 448220019 2811 False 1890.50 2375 91.1935 885 3835 2 chr6A.!!$F1 2950

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
395 422 0.031043 CCCAAAACGTCGAAAACCCC 59.969 55.000 0.00 0.00 0.00 4.95 F
1173 1201 1.226603 GTCCAAGTACGAGCGCGAT 60.227 57.895 19.05 1.23 41.64 4.58 F
1260 1288 1.626654 CCTACAACAGCTTCACCGCG 61.627 60.000 0.00 0.00 34.40 6.46 F
2783 2883 0.252103 AGGAAGAGGAGGTTACCGCA 60.252 55.000 7.54 0.00 34.73 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 2214 0.037326 TCCAGTTGCATCTGACGACC 60.037 55.000 23.46 0.0 37.61 4.79 R
2551 2645 0.030908 CTCCCGAATAGTCTGTCGCC 59.969 60.000 2.97 0.0 35.93 5.54 R
2788 2888 0.038343 TTAACTGTGCCCGACGGTAC 60.038 55.000 13.94 12.0 43.96 3.34 R
3687 3915 3.057033 GGAAGCATCTTGACAACAGCATT 60.057 43.478 5.02 0.0 0.00 3.56 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
78 79 3.181367 GCACAACCATGCCTCTCG 58.819 61.111 0.00 0.00 39.86 4.04
79 80 1.672356 GCACAACCATGCCTCTCGT 60.672 57.895 0.00 0.00 39.86 4.18
143 152 2.383527 CCGTGCCTCTCGTGAAAGC 61.384 63.158 2.99 2.99 0.00 3.51
157 166 0.586802 GAAAGCACAACCGTGTCTCC 59.413 55.000 0.00 0.00 45.50 3.71
167 176 2.511600 GTGTCTCCCGCGGAATGG 60.512 66.667 30.73 10.28 0.00 3.16
224 237 1.004440 GCACGGTCTTGCCTCTCTT 60.004 57.895 0.00 0.00 36.42 2.85
225 238 1.294659 GCACGGTCTTGCCTCTCTTG 61.295 60.000 0.00 0.00 36.42 3.02
258 271 0.953960 GCCTCTCGCGGAAGGAAAAA 60.954 55.000 25.65 0.00 0.00 1.94
259 272 1.079503 CCTCTCGCGGAAGGAAAAAG 58.920 55.000 19.22 0.77 0.00 2.27
272 285 6.756542 CGGAAGGAAAAAGAAACAGAAAACAT 59.243 34.615 0.00 0.00 0.00 2.71
312 325 4.595538 ACGGCCGTGACTTGCGAA 62.596 61.111 33.75 0.00 0.00 4.70
372 399 3.412237 TTTTCTAAAGGAGACCGGTGG 57.588 47.619 14.63 0.00 32.31 4.61
376 403 2.301009 TCTAAAGGAGACCGGTGGAAAC 59.699 50.000 14.63 0.00 0.00 2.78
384 411 1.360911 CCGGTGGAAACCCAAAACG 59.639 57.895 0.00 0.00 35.07 3.60
392 419 2.853594 GGAAACCCAAAACGTCGAAAAC 59.146 45.455 0.00 0.00 0.00 2.43
393 420 2.565210 AACCCAAAACGTCGAAAACC 57.435 45.000 0.00 0.00 0.00 3.27
395 422 0.031043 CCCAAAACGTCGAAAACCCC 59.969 55.000 0.00 0.00 0.00 4.95
396 423 0.031043 CCAAAACGTCGAAAACCCCC 59.969 55.000 0.00 0.00 0.00 5.40
462 489 2.198304 AAAATTCGGAGGGAGCGCCT 62.198 55.000 2.29 0.00 0.00 5.52
466 493 2.833582 CGGAGGGAGCGCCTAGAA 60.834 66.667 2.29 0.00 0.00 2.10
530 557 2.775911 TCATTGTGAGCCTCCTGAAG 57.224 50.000 0.00 0.00 0.00 3.02
544 571 1.471676 CCTGAAGGAGCGCTCGTTAAT 60.472 52.381 36.96 21.62 37.75 1.40
588 615 2.103153 TGAGAGGTTCTGGAGTTGGT 57.897 50.000 0.00 0.00 0.00 3.67
660 687 2.099405 CAACCGGCCCAAGTTTCATAT 58.901 47.619 0.00 0.00 0.00 1.78
810 838 2.573462 TGCCCTCTTGTTTATGAGCTCT 59.427 45.455 16.19 3.04 0.00 4.09
939 967 1.548081 CCACAATCACAAGGCCATCA 58.452 50.000 5.01 0.00 0.00 3.07
1173 1201 1.226603 GTCCAAGTACGAGCGCGAT 60.227 57.895 19.05 1.23 41.64 4.58
1196 1224 1.743252 CCTTCCAGAGCAACCTCGC 60.743 63.158 0.00 0.00 43.05 5.03
1260 1288 1.626654 CCTACAACAGCTTCACCGCG 61.627 60.000 0.00 0.00 34.40 6.46
1504 1532 1.911269 TACCGGAAGTGCAGCTCCA 60.911 57.895 9.46 0.00 0.00 3.86
1595 1623 2.436115 GGGGTACAAGCTGACCGC 60.436 66.667 12.24 12.24 40.92 5.68
1841 1877 6.150474 GTGGTACAATGCCAACTATGTTAAGT 59.850 38.462 0.00 0.00 44.16 2.24
1894 1935 2.364002 CTCTTTTCTTTTTGCGGGGGAA 59.636 45.455 0.00 0.00 0.00 3.97
1932 1974 4.035558 TCAGCTTCAACAGATCACAACAAC 59.964 41.667 0.00 0.00 0.00 3.32
1938 1980 4.816385 TCAACAGATCACAACAACTCCTTC 59.184 41.667 0.00 0.00 0.00 3.46
1939 1981 4.422073 ACAGATCACAACAACTCCTTCA 57.578 40.909 0.00 0.00 0.00 3.02
1956 1998 7.060421 ACTCCTTCATTTCCTTGACAAGTTAA 58.940 34.615 14.03 7.85 0.00 2.01
1965 2007 8.880878 TTTCCTTGACAAGTTAATTTTTAGCC 57.119 30.769 14.03 0.00 0.00 3.93
1966 2008 6.988522 TCCTTGACAAGTTAATTTTTAGCCC 58.011 36.000 14.03 0.00 0.00 5.19
1967 2009 6.780522 TCCTTGACAAGTTAATTTTTAGCCCT 59.219 34.615 14.03 0.00 0.00 5.19
1968 2010 7.289084 TCCTTGACAAGTTAATTTTTAGCCCTT 59.711 33.333 14.03 0.00 0.00 3.95
1969 2011 7.931407 CCTTGACAAGTTAATTTTTAGCCCTTT 59.069 33.333 14.03 0.00 0.00 3.11
1970 2012 9.325198 CTTGACAAGTTAATTTTTAGCCCTTTT 57.675 29.630 7.05 0.00 0.00 2.27
1971 2013 9.674068 TTGACAAGTTAATTTTTAGCCCTTTTT 57.326 25.926 0.00 0.00 0.00 1.94
2043 2087 7.330946 TCGTTTTATCAATGAAGTTCGAGACAT 59.669 33.333 0.00 0.00 0.00 3.06
2050 2094 6.531594 TCAATGAAGTTCGAGACATACACATC 59.468 38.462 0.00 0.00 0.00 3.06
2062 2106 9.034544 CGAGACATACACATCAATTCAAATCTA 57.965 33.333 0.00 0.00 0.00 1.98
2096 2181 9.921637 AAACAACAGTGAAAAATTTAGAGAACA 57.078 25.926 0.00 0.00 0.00 3.18
2105 2190 8.801299 TGAAAAATTTAGAGAACATGCATACCA 58.199 29.630 0.00 0.00 0.00 3.25
2129 2214 2.023181 CACCGGATGCGCGAATTG 59.977 61.111 12.10 0.90 0.00 2.32
2457 2548 9.703892 ACTGATCAAATGATACATAGAAGCTAC 57.296 33.333 0.00 0.00 34.37 3.58
2473 2565 4.970860 AGCTACCCTACTCGTACTGATA 57.029 45.455 0.00 0.00 0.00 2.15
2487 2579 7.040340 ACTCGTACTGATAATATTCCCTGTGAG 60.040 40.741 0.00 3.03 0.00 3.51
2495 2587 4.803329 ATATTCCCTGTGAGCAAAGGAT 57.197 40.909 8.31 0.00 35.40 3.24
2523 2617 2.354510 GTGTGAGTGCTGCACTTGTTTA 59.645 45.455 33.33 16.85 45.44 2.01
2524 2618 3.003689 GTGTGAGTGCTGCACTTGTTTAT 59.996 43.478 33.33 12.30 45.44 1.40
2525 2619 3.631686 TGTGAGTGCTGCACTTGTTTATT 59.368 39.130 33.33 11.54 45.44 1.40
2526 2620 4.097741 TGTGAGTGCTGCACTTGTTTATTT 59.902 37.500 33.33 10.79 45.44 1.40
2550 2644 5.126067 TGGACTTATTAATCTGCTTGGCTC 58.874 41.667 0.00 0.00 0.00 4.70
2551 2645 4.212214 GGACTTATTAATCTGCTTGGCTCG 59.788 45.833 0.00 0.00 0.00 5.03
2593 2688 2.781431 AATTTGGGAGGACCGTGGCC 62.781 60.000 0.00 0.00 44.64 5.36
2605 2700 2.556622 GACCGTGGCCATAATAATTGGG 59.443 50.000 9.72 2.00 34.66 4.12
2693 2788 9.014297 CCTCTAAATTATGTCAGACCAAACTTT 57.986 33.333 0.00 0.00 0.00 2.66
2703 2798 8.117813 TGTCAGACCAAACTTTAGTTTTTCTT 57.882 30.769 5.16 0.00 45.07 2.52
2706 2806 9.634163 TCAGACCAAACTTTAGTTTTTCTTTTC 57.366 29.630 5.16 0.00 45.07 2.29
2719 2819 8.981724 AGTTTTTCTTTTCTACCAAACTTCAC 57.018 30.769 0.00 0.00 31.88 3.18
2720 2820 8.803235 AGTTTTTCTTTTCTACCAAACTTCACT 58.197 29.630 0.00 0.00 31.88 3.41
2721 2821 9.419297 GTTTTTCTTTTCTACCAAACTTCACTT 57.581 29.630 0.00 0.00 0.00 3.16
2722 2822 8.980143 TTTTCTTTTCTACCAAACTTCACTTG 57.020 30.769 0.00 0.00 0.00 3.16
2723 2823 7.696992 TTCTTTTCTACCAAACTTCACTTGT 57.303 32.000 0.00 0.00 0.00 3.16
2724 2824 7.083875 TCTTTTCTACCAAACTTCACTTGTG 57.916 36.000 0.00 0.00 0.00 3.33
2739 2839 3.870419 CACTTGTGATTGTTGGGGTTTTG 59.130 43.478 0.00 0.00 0.00 2.44
2743 2843 3.118956 TGTGATTGTTGGGGTTTTGTCAC 60.119 43.478 0.00 0.00 36.26 3.67
2751 2851 1.745890 GGTTTTGTCACCCAAGCCC 59.254 57.895 0.00 0.00 33.75 5.19
2765 2865 3.056322 CCCAAGCCCAGAAATGAGAAAAG 60.056 47.826 0.00 0.00 0.00 2.27
2766 2866 3.056322 CCAAGCCCAGAAATGAGAAAAGG 60.056 47.826 0.00 0.00 0.00 3.11
2767 2867 3.814504 AGCCCAGAAATGAGAAAAGGA 57.185 42.857 0.00 0.00 0.00 3.36
2768 2868 4.118168 AGCCCAGAAATGAGAAAAGGAA 57.882 40.909 0.00 0.00 0.00 3.36
2769 2869 4.085009 AGCCCAGAAATGAGAAAAGGAAG 58.915 43.478 0.00 0.00 0.00 3.46
2770 2870 4.082125 GCCCAGAAATGAGAAAAGGAAGA 58.918 43.478 0.00 0.00 0.00 2.87
2771 2871 4.157472 GCCCAGAAATGAGAAAAGGAAGAG 59.843 45.833 0.00 0.00 0.00 2.85
2772 2872 4.704057 CCCAGAAATGAGAAAAGGAAGAGG 59.296 45.833 0.00 0.00 0.00 3.69
2773 2873 5.515534 CCCAGAAATGAGAAAAGGAAGAGGA 60.516 44.000 0.00 0.00 0.00 3.71
2774 2874 5.647225 CCAGAAATGAGAAAAGGAAGAGGAG 59.353 44.000 0.00 0.00 0.00 3.69
2775 2875 5.647225 CAGAAATGAGAAAAGGAAGAGGAGG 59.353 44.000 0.00 0.00 0.00 4.30
2776 2876 5.311913 AGAAATGAGAAAAGGAAGAGGAGGT 59.688 40.000 0.00 0.00 0.00 3.85
2777 2877 5.590976 AATGAGAAAAGGAAGAGGAGGTT 57.409 39.130 0.00 0.00 0.00 3.50
2778 2878 6.704056 AATGAGAAAAGGAAGAGGAGGTTA 57.296 37.500 0.00 0.00 0.00 2.85
2779 2879 5.485209 TGAGAAAAGGAAGAGGAGGTTAC 57.515 43.478 0.00 0.00 0.00 2.50
2780 2880 4.286291 TGAGAAAAGGAAGAGGAGGTTACC 59.714 45.833 0.00 0.00 0.00 2.85
2781 2881 3.261137 AGAAAAGGAAGAGGAGGTTACCG 59.739 47.826 0.00 0.00 34.73 4.02
2782 2882 0.903236 AAGGAAGAGGAGGTTACCGC 59.097 55.000 0.00 0.00 34.73 5.68
2783 2883 0.252103 AGGAAGAGGAGGTTACCGCA 60.252 55.000 7.54 0.00 34.73 5.69
2784 2884 0.831307 GGAAGAGGAGGTTACCGCAT 59.169 55.000 7.54 0.00 34.73 4.73
2785 2885 1.202545 GGAAGAGGAGGTTACCGCATC 60.203 57.143 11.63 11.63 34.54 3.91
2786 2886 1.480954 GAAGAGGAGGTTACCGCATCA 59.519 52.381 20.47 0.00 36.64 3.07
2787 2887 1.568504 AGAGGAGGTTACCGCATCAA 58.431 50.000 20.47 0.00 36.64 2.57
2788 2888 1.482593 AGAGGAGGTTACCGCATCAAG 59.517 52.381 20.47 0.00 36.64 3.02
2789 2889 1.207329 GAGGAGGTTACCGCATCAAGT 59.793 52.381 14.40 0.00 34.48 3.16
2790 2890 2.429610 GAGGAGGTTACCGCATCAAGTA 59.570 50.000 14.40 0.00 34.48 2.24
2791 2891 2.167900 AGGAGGTTACCGCATCAAGTAC 59.832 50.000 7.54 0.00 34.73 2.73
2792 2892 2.547826 GAGGTTACCGCATCAAGTACC 58.452 52.381 0.00 0.00 0.00 3.34
2793 2893 1.134907 AGGTTACCGCATCAAGTACCG 60.135 52.381 0.00 0.00 0.00 4.02
2794 2894 1.404583 GGTTACCGCATCAAGTACCGT 60.405 52.381 0.00 0.00 0.00 4.83
2795 2895 1.922545 GTTACCGCATCAAGTACCGTC 59.077 52.381 0.00 0.00 0.00 4.79
2796 2896 0.099259 TACCGCATCAAGTACCGTCG 59.901 55.000 0.00 0.00 0.00 5.12
2797 2897 1.876714 CCGCATCAAGTACCGTCGG 60.877 63.158 10.48 10.48 0.00 4.79
2798 2898 1.876714 CGCATCAAGTACCGTCGGG 60.877 63.158 17.28 0.00 40.11 5.14
2799 2899 2.171725 GCATCAAGTACCGTCGGGC 61.172 63.158 17.28 8.13 36.48 6.13
2803 2903 1.736645 CAAGTACCGTCGGGCACAG 60.737 63.158 17.28 6.33 36.48 3.66
2857 2969 2.428187 CACACGGCCCAGGTTACA 59.572 61.111 0.00 0.00 0.00 2.41
2886 3001 5.181245 GCTACAGCATTAGAGACTAGAGGAG 59.819 48.000 0.00 0.00 41.59 3.69
2887 3002 3.888930 ACAGCATTAGAGACTAGAGGAGC 59.111 47.826 0.00 0.00 0.00 4.70
2888 3003 3.888323 CAGCATTAGAGACTAGAGGAGCA 59.112 47.826 0.00 0.00 0.00 4.26
2889 3004 4.022935 CAGCATTAGAGACTAGAGGAGCAG 60.023 50.000 0.00 0.00 0.00 4.24
2890 3005 3.255642 GCATTAGAGACTAGAGGAGCAGG 59.744 52.174 0.00 0.00 0.00 4.85
2891 3006 4.724399 CATTAGAGACTAGAGGAGCAGGA 58.276 47.826 0.00 0.00 0.00 3.86
2892 3007 2.729028 AGAGACTAGAGGAGCAGGAC 57.271 55.000 0.00 0.00 0.00 3.85
2896 3011 0.328592 ACTAGAGGAGCAGGACGACA 59.671 55.000 0.00 0.00 0.00 4.35
2913 3028 2.485426 CGACAACATGGCATCAGAAGTT 59.515 45.455 0.00 0.00 0.00 2.66
2951 3078 1.154150 GGCTGCACATTCGCACTTC 60.154 57.895 0.50 0.00 36.86 3.01
2957 3084 2.279741 GCACATTCGCACTTCCATAGA 58.720 47.619 0.00 0.00 0.00 1.98
3020 3171 8.780249 CGGTTTTTCCTATTTTACTTTGAGAGA 58.220 33.333 0.00 0.00 0.00 3.10
3109 3319 0.240945 GCTAACCACACACCATGCAC 59.759 55.000 0.00 0.00 0.00 4.57
3118 3328 4.260743 CCACACACCATGCACGATTAATAG 60.261 45.833 0.00 0.00 0.00 1.73
3122 3332 4.743151 ACACCATGCACGATTAATAGTACG 59.257 41.667 0.54 0.00 0.00 3.67
3123 3333 4.743151 CACCATGCACGATTAATAGTACGT 59.257 41.667 0.54 0.00 39.53 3.57
3186 3396 5.105473 GCCACATTCTTATATAGTCGGCCTA 60.105 44.000 0.00 0.00 0.00 3.93
3204 3414 6.039270 TCGGCCTAAAGGTTATTTTGATGATG 59.961 38.462 0.00 0.00 37.57 3.07
3205 3415 6.039270 CGGCCTAAAGGTTATTTTGATGATGA 59.961 38.462 0.00 0.00 37.57 2.92
3206 3416 7.255590 CGGCCTAAAGGTTATTTTGATGATGAT 60.256 37.037 0.00 0.00 37.57 2.45
3261 3480 3.093814 TCACATAAGCCGAGGACAAGTA 58.906 45.455 0.00 0.00 0.00 2.24
3262 3481 3.512329 TCACATAAGCCGAGGACAAGTAA 59.488 43.478 0.00 0.00 0.00 2.24
3263 3482 3.617263 CACATAAGCCGAGGACAAGTAAC 59.383 47.826 0.00 0.00 0.00 2.50
3322 3541 1.369625 CGCTGTACCCTTGGATCAAC 58.630 55.000 0.00 0.00 0.00 3.18
3388 3607 0.443869 CTTCCTTCATCGTTGTGCCG 59.556 55.000 0.00 0.00 0.00 5.69
3469 3688 2.499981 CGATCCGCAATGAGACTCG 58.500 57.895 0.00 0.00 0.00 4.18
3506 3734 2.079925 GAAGCCGCTCAAGAGTCAAAT 58.920 47.619 0.00 0.00 0.00 2.32
3510 3738 2.031437 GCCGCTCAAGAGTCAAATCATC 59.969 50.000 0.00 0.00 0.00 2.92
3512 3740 3.875727 CCGCTCAAGAGTCAAATCATCAT 59.124 43.478 0.00 0.00 0.00 2.45
3513 3741 4.025061 CCGCTCAAGAGTCAAATCATCATC 60.025 45.833 0.00 0.00 0.00 2.92
3515 3743 5.064325 CGCTCAAGAGTCAAATCATCATCAA 59.936 40.000 0.00 0.00 0.00 2.57
3516 3744 6.256686 GCTCAAGAGTCAAATCATCATCAAC 58.743 40.000 0.00 0.00 0.00 3.18
3517 3745 6.128090 GCTCAAGAGTCAAATCATCATCAACA 60.128 38.462 0.00 0.00 0.00 3.33
3518 3746 7.415318 GCTCAAGAGTCAAATCATCATCAACAT 60.415 37.037 0.00 0.00 0.00 2.71
3519 3747 8.344446 TCAAGAGTCAAATCATCATCAACATT 57.656 30.769 0.00 0.00 0.00 2.71
3520 3748 9.452287 TCAAGAGTCAAATCATCATCAACATTA 57.548 29.630 0.00 0.00 0.00 1.90
3687 3915 7.069826 CCAAATAGGAGCTTCCCAATAAAATCA 59.930 37.037 0.00 0.00 41.22 2.57
3798 4026 4.892934 AGCTCATACTGAAACCAAACCAAA 59.107 37.500 0.00 0.00 0.00 3.28
3800 4028 6.041979 AGCTCATACTGAAACCAAACCAAAAT 59.958 34.615 0.00 0.00 0.00 1.82
3821 4049 3.268023 ACCTTCAGCTAACATAGGCAC 57.732 47.619 0.00 0.00 0.00 5.01
3822 4050 2.571653 ACCTTCAGCTAACATAGGCACA 59.428 45.455 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 117 2.677979 GGCCGTGCCTCTCGAAAAC 61.678 63.158 7.58 0.00 46.69 2.43
214 227 4.557296 CGATTTTGCTTTCAAGAGAGGCAA 60.557 41.667 0.00 0.00 40.15 4.52
224 237 2.226437 GAGAGGCACGATTTTGCTTTCA 59.774 45.455 0.00 0.00 42.56 2.69
225 238 2.726066 CGAGAGGCACGATTTTGCTTTC 60.726 50.000 0.00 0.00 42.56 2.62
351 368 3.391955 TCCACCGGTCTCCTTTAGAAAAA 59.608 43.478 2.59 0.00 35.47 1.94
356 373 2.614734 GGTTTCCACCGGTCTCCTTTAG 60.615 54.545 2.59 0.00 31.60 1.85
360 387 2.222013 GGGTTTCCACCGGTCTCCT 61.222 63.158 2.59 0.00 45.39 3.69
372 399 2.853594 GGTTTTCGACGTTTTGGGTTTC 59.146 45.455 0.00 0.00 0.00 2.78
376 403 0.031043 GGGGTTTTCGACGTTTTGGG 59.969 55.000 0.00 0.00 0.00 4.12
405 432 3.966218 CGTGTTTTCGGCTTTCTAAACAG 59.034 43.478 0.00 0.00 40.10 3.16
407 434 3.722289 CACGTGTTTTCGGCTTTCTAAAC 59.278 43.478 7.58 0.00 34.94 2.01
437 464 2.296190 GCTCCCTCCGAATTTTGTTTGT 59.704 45.455 0.00 0.00 0.00 2.83
448 475 3.354472 TTCTAGGCGCTCCCTCCGA 62.354 63.158 7.64 0.00 44.96 4.55
451 478 2.413765 CGTTCTAGGCGCTCCCTC 59.586 66.667 7.64 0.00 44.96 4.30
490 517 4.077188 GCGTCACTTGGCGTGCTC 62.077 66.667 4.98 0.00 46.15 4.26
494 521 1.738099 GATCAGCGTCACTTGGCGT 60.738 57.895 4.98 0.00 46.15 5.68
530 557 2.285660 GCAACTAATTAACGAGCGCTCC 60.286 50.000 30.66 13.79 0.00 4.70
531 558 2.603560 AGCAACTAATTAACGAGCGCTC 59.396 45.455 27.64 27.64 0.00 5.03
580 607 0.872388 CGTTTGCACCTACCAACTCC 59.128 55.000 0.00 0.00 0.00 3.85
588 615 1.508808 GGCCGAAACGTTTGCACCTA 61.509 55.000 20.10 0.00 0.00 3.08
731 759 7.985589 TCTTTTCTTAACATTTACTCCTCCCT 58.014 34.615 0.00 0.00 0.00 4.20
1173 1201 1.295423 GTTGCTCTGGAAGGCGGTA 59.705 57.895 0.00 0.00 33.58 4.02
1196 1224 3.765257 ATGGAGGCGAGGAGGGAGG 62.765 68.421 0.00 0.00 0.00 4.30
1491 1519 3.576004 CTGCTGGAGCTGCACTTC 58.424 61.111 2.72 0.00 42.66 3.01
1814 1845 2.843401 TAGTTGGCATTGTACCACGT 57.157 45.000 0.00 0.00 36.76 4.49
1815 1846 3.006940 ACATAGTTGGCATTGTACCACG 58.993 45.455 0.00 0.00 36.76 4.94
1816 1847 6.150474 ACTTAACATAGTTGGCATTGTACCAC 59.850 38.462 0.00 0.00 36.76 4.16
1817 1848 6.242396 ACTTAACATAGTTGGCATTGTACCA 58.758 36.000 0.00 0.00 34.65 3.25
1841 1877 5.597182 AGATGGTTTTACTCCTACAGCGATA 59.403 40.000 0.00 0.00 0.00 2.92
1894 1935 5.869579 TGAAGCTGAAGATGGTTTTACTCT 58.130 37.500 0.00 0.00 0.00 3.24
1932 1974 7.510549 TTAACTTGTCAAGGAAATGAAGGAG 57.489 36.000 16.85 0.00 0.00 3.69
1939 1981 9.489084 GGCTAAAAATTAACTTGTCAAGGAAAT 57.511 29.630 16.85 11.96 0.00 2.17
2016 2059 7.170151 TGTCTCGAACTTCATTGATAAAACGAA 59.830 33.333 0.00 0.00 0.00 3.85
2018 2061 6.817396 TGTCTCGAACTTCATTGATAAAACG 58.183 36.000 0.00 0.00 0.00 3.60
2043 2087 9.599866 AATCTCGTAGATTTGAATTGATGTGTA 57.400 29.630 4.81 0.00 41.90 2.90
2062 2106 9.581099 AAATTTTTCACTGTTGTTTAATCTCGT 57.419 25.926 0.00 0.00 0.00 4.18
2096 2181 1.152483 GTGGGGCCATGGTATGCAT 60.152 57.895 14.67 3.79 0.00 3.96
2129 2214 0.037326 TCCAGTTGCATCTGACGACC 60.037 55.000 23.46 0.00 37.61 4.79
2138 2223 4.290093 TCTATAGTGGTCTCCAGTTGCAT 58.710 43.478 0.00 0.00 38.30 3.96
2252 2341 7.530863 GCTTGTCCTCCTCTTTATAAACTTTG 58.469 38.462 0.00 0.00 0.00 2.77
2259 2348 3.638860 TCCGCTTGTCCTCCTCTTTATA 58.361 45.455 0.00 0.00 0.00 0.98
2296 2385 4.988540 CCTCACTCACATCTAACAAAACGA 59.011 41.667 0.00 0.00 0.00 3.85
2379 2470 2.487934 AGCGCCATGATATGAAGTCAC 58.512 47.619 2.29 0.00 0.00 3.67
2380 2471 2.916702 AGCGCCATGATATGAAGTCA 57.083 45.000 2.29 0.00 0.00 3.41
2382 2473 4.273480 GTGTAAAGCGCCATGATATGAAGT 59.727 41.667 2.29 0.00 0.00 3.01
2383 2474 4.273235 TGTGTAAAGCGCCATGATATGAAG 59.727 41.667 2.29 0.00 0.00 3.02
2439 2530 7.121463 CGAGTAGGGTAGCTTCTATGTATCATT 59.879 40.741 0.00 0.00 0.00 2.57
2446 2537 5.179742 CAGTACGAGTAGGGTAGCTTCTATG 59.820 48.000 0.00 0.00 0.00 2.23
2448 2539 4.406972 TCAGTACGAGTAGGGTAGCTTCTA 59.593 45.833 0.00 0.00 0.00 2.10
2449 2540 3.199508 TCAGTACGAGTAGGGTAGCTTCT 59.800 47.826 0.00 0.00 0.00 2.85
2450 2541 3.539604 TCAGTACGAGTAGGGTAGCTTC 58.460 50.000 0.00 0.00 0.00 3.86
2452 2543 3.860968 ATCAGTACGAGTAGGGTAGCT 57.139 47.619 0.00 0.00 0.00 3.32
2453 2544 7.862512 ATATTATCAGTACGAGTAGGGTAGC 57.137 40.000 0.00 0.00 0.00 3.58
2455 2546 7.831193 GGGAATATTATCAGTACGAGTAGGGTA 59.169 40.741 0.00 0.00 0.00 3.69
2456 2547 6.662663 GGGAATATTATCAGTACGAGTAGGGT 59.337 42.308 0.00 0.00 0.00 4.34
2457 2548 6.890814 AGGGAATATTATCAGTACGAGTAGGG 59.109 42.308 0.00 0.00 0.00 3.53
2473 2565 4.591321 TCCTTTGCTCACAGGGAATATT 57.409 40.909 2.57 0.00 30.08 1.28
2523 2617 7.124750 AGCCAAGCAGATTAATAAGTCCAAAAT 59.875 33.333 0.00 0.00 0.00 1.82
2524 2618 6.437162 AGCCAAGCAGATTAATAAGTCCAAAA 59.563 34.615 0.00 0.00 0.00 2.44
2525 2619 5.951747 AGCCAAGCAGATTAATAAGTCCAAA 59.048 36.000 0.00 0.00 0.00 3.28
2526 2620 5.509498 AGCCAAGCAGATTAATAAGTCCAA 58.491 37.500 0.00 0.00 0.00 3.53
2550 2644 1.299165 CCCGAATAGTCTGTCGCCG 60.299 63.158 2.97 0.00 35.93 6.46
2551 2645 0.030908 CTCCCGAATAGTCTGTCGCC 59.969 60.000 2.97 0.00 35.93 5.54
2593 2688 4.158394 CCGGCCAAGATCCCAATTATTATG 59.842 45.833 2.24 0.00 0.00 1.90
2605 2700 2.281139 GCTAGCCCGGCCAAGATC 60.281 66.667 5.55 0.00 0.00 2.75
2684 2779 9.865321 GGTAGAAAAGAAAAACTAAAGTTTGGT 57.135 29.630 8.78 0.00 46.47 3.67
2699 2794 7.392113 TCACAAGTGAAGTTTGGTAGAAAAGAA 59.608 33.333 0.00 0.00 36.53 2.52
2701 2796 7.083875 TCACAAGTGAAGTTTGGTAGAAAAG 57.916 36.000 0.00 0.00 36.53 2.27
2703 2798 7.122055 ACAATCACAAGTGAAGTTTGGTAGAAA 59.878 33.333 15.45 0.00 43.58 2.52
2706 2806 6.377327 ACAATCACAAGTGAAGTTTGGTAG 57.623 37.500 15.45 0.00 43.58 3.18
2717 2817 3.817709 AAACCCCAACAATCACAAGTG 57.182 42.857 0.00 0.00 0.00 3.16
2718 2818 3.517500 ACAAAACCCCAACAATCACAAGT 59.482 39.130 0.00 0.00 0.00 3.16
2719 2819 4.119136 GACAAAACCCCAACAATCACAAG 58.881 43.478 0.00 0.00 0.00 3.16
2720 2820 3.515502 TGACAAAACCCCAACAATCACAA 59.484 39.130 0.00 0.00 0.00 3.33
2721 2821 3.099905 TGACAAAACCCCAACAATCACA 58.900 40.909 0.00 0.00 0.00 3.58
2722 2822 3.453424 GTGACAAAACCCCAACAATCAC 58.547 45.455 0.00 0.00 0.00 3.06
2723 2823 2.432510 GGTGACAAAACCCCAACAATCA 59.567 45.455 0.00 0.00 33.79 2.57
2724 2824 3.106242 GGTGACAAAACCCCAACAATC 57.894 47.619 0.00 0.00 33.79 2.67
2739 2839 0.890683 CATTTCTGGGCTTGGGTGAC 59.109 55.000 0.00 0.00 0.00 3.67
2743 2843 2.220653 TTCTCATTTCTGGGCTTGGG 57.779 50.000 0.00 0.00 0.00 4.12
2751 2851 5.647225 CCTCCTCTTCCTTTTCTCATTTCTG 59.353 44.000 0.00 0.00 0.00 3.02
2765 2865 0.831307 ATGCGGTAACCTCCTCTTCC 59.169 55.000 0.00 0.00 0.00 3.46
2766 2866 1.480954 TGATGCGGTAACCTCCTCTTC 59.519 52.381 0.00 0.00 0.00 2.87
2767 2867 1.568504 TGATGCGGTAACCTCCTCTT 58.431 50.000 0.00 0.00 0.00 2.85
2768 2868 1.482593 CTTGATGCGGTAACCTCCTCT 59.517 52.381 0.00 0.00 0.00 3.69
2769 2869 1.207329 ACTTGATGCGGTAACCTCCTC 59.793 52.381 0.00 0.00 0.00 3.71
2770 2870 1.276622 ACTTGATGCGGTAACCTCCT 58.723 50.000 0.00 0.00 0.00 3.69
2771 2871 2.547826 GTACTTGATGCGGTAACCTCC 58.452 52.381 0.00 0.00 0.00 4.30
2772 2872 2.547826 GGTACTTGATGCGGTAACCTC 58.452 52.381 0.00 0.00 0.00 3.85
2773 2873 1.134907 CGGTACTTGATGCGGTAACCT 60.135 52.381 0.00 0.00 0.00 3.50
2774 2874 1.283736 CGGTACTTGATGCGGTAACC 58.716 55.000 0.00 0.00 0.00 2.85
2775 2875 1.922545 GACGGTACTTGATGCGGTAAC 59.077 52.381 0.00 0.00 0.00 2.50
2776 2876 1.467883 CGACGGTACTTGATGCGGTAA 60.468 52.381 0.00 0.00 0.00 2.85
2777 2877 0.099259 CGACGGTACTTGATGCGGTA 59.901 55.000 0.00 0.00 0.00 4.02
2778 2878 1.153901 CGACGGTACTTGATGCGGT 60.154 57.895 0.00 0.00 0.00 5.68
2779 2879 1.876714 CCGACGGTACTTGATGCGG 60.877 63.158 5.48 0.00 0.00 5.69
2780 2880 1.876714 CCCGACGGTACTTGATGCG 60.877 63.158 13.94 0.00 0.00 4.73
2781 2881 2.171725 GCCCGACGGTACTTGATGC 61.172 63.158 13.94 2.20 0.00 3.91
2782 2882 1.082117 GTGCCCGACGGTACTTGATG 61.082 60.000 13.94 0.00 41.31 3.07
2783 2883 1.217244 GTGCCCGACGGTACTTGAT 59.783 57.895 13.94 0.00 41.31 2.57
2784 2884 2.149803 CTGTGCCCGACGGTACTTGA 62.150 60.000 13.94 0.00 44.62 3.02
2785 2885 1.736645 CTGTGCCCGACGGTACTTG 60.737 63.158 13.94 0.00 44.62 3.16
2786 2886 1.751349 AACTGTGCCCGACGGTACTT 61.751 55.000 13.94 0.69 43.96 2.24
2787 2887 0.895100 TAACTGTGCCCGACGGTACT 60.895 55.000 13.94 0.00 43.96 2.73
2788 2888 0.038343 TTAACTGTGCCCGACGGTAC 60.038 55.000 13.94 12.00 43.96 3.34
2789 2889 0.038343 GTTAACTGTGCCCGACGGTA 60.038 55.000 13.94 0.00 43.96 4.02
2790 2890 1.301165 GTTAACTGTGCCCGACGGT 60.301 57.895 13.94 0.00 46.98 4.83
2791 2891 2.030958 GGTTAACTGTGCCCGACGG 61.031 63.158 6.99 6.99 36.94 4.79
2792 2892 0.672401 ATGGTTAACTGTGCCCGACG 60.672 55.000 5.42 0.00 0.00 5.12
2793 2893 1.530323 AATGGTTAACTGTGCCCGAC 58.470 50.000 5.42 0.00 0.00 4.79
2794 2894 2.279935 AAATGGTTAACTGTGCCCGA 57.720 45.000 5.42 0.00 0.00 5.14
2795 2895 3.313690 GAAAAATGGTTAACTGTGCCCG 58.686 45.455 5.42 0.00 0.00 6.13
2796 2896 3.070302 TGGAAAAATGGTTAACTGTGCCC 59.930 43.478 5.42 0.17 0.00 5.36
2797 2897 4.329462 TGGAAAAATGGTTAACTGTGCC 57.671 40.909 5.42 0.00 0.00 5.01
2798 2898 5.334028 GCATTGGAAAAATGGTTAACTGTGC 60.334 40.000 5.42 0.00 0.00 4.57
2799 2899 5.757320 TGCATTGGAAAAATGGTTAACTGTG 59.243 36.000 5.42 0.00 0.00 3.66
2803 2903 6.085573 GCATTGCATTGGAAAAATGGTTAAC 58.914 36.000 10.41 0.00 31.97 2.01
2857 2969 4.222336 AGTCTCTAATGCTGTAGCTGGAT 58.778 43.478 5.38 0.00 42.66 3.41
2886 3001 1.308069 ATGCCATGTTGTCGTCCTGC 61.308 55.000 0.00 0.00 0.00 4.85
2887 3002 0.729116 GATGCCATGTTGTCGTCCTG 59.271 55.000 0.00 0.00 0.00 3.86
2888 3003 0.324614 TGATGCCATGTTGTCGTCCT 59.675 50.000 0.00 0.00 0.00 3.85
2889 3004 0.729116 CTGATGCCATGTTGTCGTCC 59.271 55.000 0.00 0.00 0.00 4.79
2890 3005 1.725641 TCTGATGCCATGTTGTCGTC 58.274 50.000 0.00 0.00 0.00 4.20
2891 3006 2.079158 CTTCTGATGCCATGTTGTCGT 58.921 47.619 0.00 0.00 0.00 4.34
2892 3007 2.079158 ACTTCTGATGCCATGTTGTCG 58.921 47.619 0.00 0.00 0.00 4.35
2896 3011 3.508793 CCTTGAACTTCTGATGCCATGTT 59.491 43.478 0.00 0.00 0.00 2.71
2913 3028 2.433970 CCTTTGCTGGGTTTTTCCTTGA 59.566 45.455 0.00 0.00 36.25 3.02
2938 3065 3.496130 GGATCTATGGAAGTGCGAATGTG 59.504 47.826 0.00 0.00 0.00 3.21
2942 3069 2.766263 AGTGGATCTATGGAAGTGCGAA 59.234 45.455 0.00 0.00 0.00 4.70
2957 3084 5.012458 TGAGACAACTTGAAGATCAGTGGAT 59.988 40.000 0.00 0.00 36.13 3.41
3020 3171 8.951243 GTCTTAATTATTCAAGAGCAGTTTCCT 58.049 33.333 0.00 0.00 31.62 3.36
3055 3212 0.880278 TGCGTTCACAAGCAGACCTC 60.880 55.000 0.00 0.00 38.59 3.85
3118 3328 9.338291 CTGTGTGATGTATATTATACCACGTAC 57.662 37.037 10.59 8.23 0.00 3.67
3122 3332 9.923143 TTAGCTGTGTGATGTATATTATACCAC 57.077 33.333 10.59 11.75 0.00 4.16
3128 3338 8.826710 GTTGCTTTAGCTGTGTGATGTATATTA 58.173 33.333 0.00 0.00 42.66 0.98
3204 3414 7.713734 TGTATGGGGCTATTAGTAGTGTATC 57.286 40.000 0.00 0.00 0.00 2.24
3205 3415 8.680820 ATTGTATGGGGCTATTAGTAGTGTAT 57.319 34.615 0.00 0.00 0.00 2.29
3206 3416 9.028284 GTATTGTATGGGGCTATTAGTAGTGTA 57.972 37.037 0.00 0.00 0.00 2.90
3261 3480 3.941483 GAGGTGCATGCTAGTATGTTGTT 59.059 43.478 20.33 6.28 0.00 2.83
3262 3481 3.055167 TGAGGTGCATGCTAGTATGTTGT 60.055 43.478 20.33 5.05 0.00 3.32
3263 3482 3.534554 TGAGGTGCATGCTAGTATGTTG 58.465 45.455 20.33 0.00 0.00 3.33
3322 3541 4.193334 TCCGCGAGATGGAGCACG 62.193 66.667 8.23 0.00 0.00 5.34
3388 3607 7.465781 GCAAATATATGCAACAATGGTGTTTCC 60.466 37.037 0.00 0.00 46.47 3.13
3469 3688 2.275318 CTTCTTCAGGTGCGGATCTTC 58.725 52.381 0.00 0.00 0.00 2.87
3506 3734 8.186163 GCTCAGTCAATTTAATGTTGATGATGA 58.814 33.333 6.97 9.75 37.84 2.92
3510 3738 7.532571 TCAGCTCAGTCAATTTAATGTTGATG 58.467 34.615 6.97 6.94 37.84 3.07
3512 3740 7.509141 TTCAGCTCAGTCAATTTAATGTTGA 57.491 32.000 0.00 0.98 33.46 3.18
3513 3741 7.864379 AGTTTCAGCTCAGTCAATTTAATGTTG 59.136 33.333 0.00 0.00 0.00 3.33
3515 3743 7.516198 AGTTTCAGCTCAGTCAATTTAATGT 57.484 32.000 0.00 0.00 0.00 2.71
3516 3744 9.499585 CATAGTTTCAGCTCAGTCAATTTAATG 57.500 33.333 0.00 0.00 0.00 1.90
3517 3745 8.186821 GCATAGTTTCAGCTCAGTCAATTTAAT 58.813 33.333 0.00 0.00 0.00 1.40
3518 3746 7.174772 TGCATAGTTTCAGCTCAGTCAATTTAA 59.825 33.333 0.00 0.00 0.00 1.52
3519 3747 6.654582 TGCATAGTTTCAGCTCAGTCAATTTA 59.345 34.615 0.00 0.00 0.00 1.40
3520 3748 5.474532 TGCATAGTTTCAGCTCAGTCAATTT 59.525 36.000 0.00 0.00 0.00 1.82
3521 3749 5.005740 TGCATAGTTTCAGCTCAGTCAATT 58.994 37.500 0.00 0.00 0.00 2.32
3522 3750 4.582869 TGCATAGTTTCAGCTCAGTCAAT 58.417 39.130 0.00 0.00 0.00 2.57
3523 3751 3.999001 CTGCATAGTTTCAGCTCAGTCAA 59.001 43.478 0.00 0.00 0.00 3.18
3524 3752 3.593096 CTGCATAGTTTCAGCTCAGTCA 58.407 45.455 0.00 0.00 0.00 3.41
3687 3915 3.057033 GGAAGCATCTTGACAACAGCATT 60.057 43.478 5.02 0.00 0.00 3.56
3798 4026 5.104527 TGTGCCTATGTTAGCTGAAGGTATT 60.105 40.000 0.00 0.00 0.00 1.89
3800 4028 3.772572 TGTGCCTATGTTAGCTGAAGGTA 59.227 43.478 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.