Multiple sequence alignment - TraesCS6B01G249000

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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 TraesCS6B01G249000 chr6B 100.000 3292 0 0 1 3292 446835280 446838571 0.000000e+00 6080
1 TraesCS6B01G249000 chr6D 93.867 2772 114 34 33 2770 285868765 285871514 0.000000e+00 4126
2 TraesCS6B01G249000 chr6D 87.615 218 13 6 3086 3289 285871901 285872118 1.180000e-59 241
3 TraesCS6B01G249000 chr6D 91.216 148 9 2 2833 2978 285871514 285871659 7.210000e-47 198
4 TraesCS6B01G249000 chr6A 94.108 2563 130 14 1 2551 407084609 407087162 0.000000e+00 3877
5 TraesCS6B01G249000 chr6A 88.532 218 11 6 3086 3289 407087369 407087586 5.450000e-63 252
6 TraesCS6B01G249000 chr2B 80.827 991 188 2 1009 1998 531466730 531467719 0.000000e+00 776
7 TraesCS6B01G249000 chr2B 82.877 146 18 4 604 748 531466328 531466467 1.240000e-24 124
8 TraesCS6B01G249000 chr2A 80.422 996 189 6 1009 2001 598162350 598161358 0.000000e+00 754
9 TraesCS6B01G249000 chr7D 85.864 191 24 2 2664 2852 541861794 541861605 2.000000e-47 200
10 TraesCS6B01G249000 chr5D 81.868 182 29 3 2668 2846 401400757 401400577 2.050000e-32 150
11 TraesCS6B01G249000 chr2D 82.877 146 18 4 604 748 451287397 451287536 1.240000e-24 124


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 TraesCS6B01G249000 chr6B 446835280 446838571 3291 False 6080.000000 6080 100.000000 1 3292 1 chr6B.!!$F1 3291
1 TraesCS6B01G249000 chr6D 285868765 285872118 3353 False 1521.666667 4126 90.899333 33 3289 3 chr6D.!!$F1 3256
2 TraesCS6B01G249000 chr6A 407084609 407087586 2977 False 2064.500000 3877 91.320000 1 3289 2 chr6A.!!$F1 3288
3 TraesCS6B01G249000 chr2B 531466328 531467719 1391 False 450.000000 776 81.852000 604 1998 2 chr2B.!!$F1 1394
4 TraesCS6B01G249000 chr2A 598161358 598162350 992 True 754.000000 754 80.422000 1009 2001 1 chr2A.!!$R1 992

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
409 416 0.734889 CCCTTTCTGTTATGCTGCGG 59.265 55.0 0.0 0.0 0.0 5.69 F
1007 1024 0.527565 CCTTCTGAAACAATGGCCGG 59.472 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1827 1.224592 CCAGGTCACCATAGGCCAC 59.775 63.158 5.01 0.0 0.0 5.01 R
2773 2849 0.033504 TCGCTTCCGCCATATTCCTC 59.966 55.000 0.00 0.0 0.0 3.71 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
34 35 1.248486 TCAAGGTCTGTGACGAGGAG 58.752 55.000 0.00 0.00 32.65 3.69
46 50 1.361993 CGAGGAGGAGCAGATTCGG 59.638 63.158 0.00 0.00 0.00 4.30
216 223 9.027202 GGGTTGGATAGGAAAAGTAAATAAACA 57.973 33.333 0.00 0.00 0.00 2.83
268 275 7.243487 ACAGACTTTGTGAAATATATGCAACG 58.757 34.615 0.00 0.00 38.99 4.10
269 276 6.688385 CAGACTTTGTGAAATATATGCAACGG 59.312 38.462 0.00 0.00 0.00 4.44
274 281 4.506288 TGTGAAATATATGCAACGGAGTCG 59.494 41.667 0.00 0.00 45.00 4.18
323 330 5.643379 ATGCTGTTCGGTACATCAATTTT 57.357 34.783 0.00 0.00 36.55 1.82
339 346 7.938490 ACATCAATTTTTGGTAGATTTTGGCTT 59.062 29.630 0.00 0.00 0.00 4.35
380 387 8.183536 TGATGTCAATTCGTTTCTATTTCATGG 58.816 33.333 0.00 0.00 0.00 3.66
405 412 4.593956 CTTTCCTCCCTTTCTGTTATGCT 58.406 43.478 0.00 0.00 0.00 3.79
406 413 3.634397 TCCTCCCTTTCTGTTATGCTG 57.366 47.619 0.00 0.00 0.00 4.41
407 414 2.019984 CCTCCCTTTCTGTTATGCTGC 58.980 52.381 0.00 0.00 0.00 5.25
408 415 1.667724 CTCCCTTTCTGTTATGCTGCG 59.332 52.381 0.00 0.00 0.00 5.18
409 416 0.734889 CCCTTTCTGTTATGCTGCGG 59.265 55.000 0.00 0.00 0.00 5.69
410 417 1.678728 CCCTTTCTGTTATGCTGCGGA 60.679 52.381 0.00 0.00 0.00 5.54
754 763 4.603985 TGCCTACTCAAACGTATGTATCG 58.396 43.478 0.00 0.00 0.00 2.92
786 795 3.139077 GCTCCTCCTTTCTTTTCGTTGA 58.861 45.455 0.00 0.00 0.00 3.18
881 891 0.962489 CCTGATAATCCCTCTCGCGT 59.038 55.000 5.77 0.00 0.00 6.01
1007 1024 0.527565 CCTTCTGAAACAATGGCCGG 59.472 55.000 0.00 0.00 0.00 6.13
1221 1244 5.809001 TCTGAATCAAGCCTCTTTGTGTAT 58.191 37.500 0.00 0.00 0.00 2.29
1527 1550 2.433446 CCTGAGCAGCCTGTGGTT 59.567 61.111 0.00 0.00 36.87 3.67
1656 1679 3.047857 TGGCATCTCTGACATAATCCCA 58.952 45.455 0.00 0.00 34.67 4.37
1804 1827 4.410400 GGTTGGACCCTGCCTCCG 62.410 72.222 0.00 0.00 30.04 4.63
1825 1848 1.144057 GCCTATGGTGACCTGGTCG 59.856 63.158 21.15 6.80 34.95 4.79
2010 2033 1.005630 GAGCTTCACTGCTGTCGGT 60.006 57.895 0.00 0.00 44.17 4.69
2022 2045 0.962489 CTGTCGGTGAAGACTCCACT 59.038 55.000 0.00 0.00 41.47 4.00
2028 2051 0.038159 GTGAAGACTCCACTGGGTCG 60.038 60.000 9.70 0.00 37.52 4.79
2050 2073 3.618351 CCAAGATCTGTCCTGAATTGCT 58.382 45.455 0.00 0.00 0.00 3.91
2052 2075 5.374921 CCAAGATCTGTCCTGAATTGCTAT 58.625 41.667 0.00 0.00 0.00 2.97
2163 2186 4.141959 GCTGGTAAGAAGATGAAGAGCTCT 60.142 45.833 11.45 11.45 0.00 4.09
2184 2207 1.561076 TGATGGTGATGCTAGCTGGTT 59.439 47.619 17.23 0.00 0.00 3.67
2287 2320 0.521735 GGTTAGCGTTTTCTGCCAGG 59.478 55.000 0.00 0.00 0.00 4.45
2428 2465 4.647611 TGTTTGTCGTGGACCTATTGAAT 58.352 39.130 0.00 0.00 0.00 2.57
2431 2468 4.819105 TGTCGTGGACCTATTGAATTCT 57.181 40.909 7.05 0.00 0.00 2.40
2432 2469 4.503910 TGTCGTGGACCTATTGAATTCTG 58.496 43.478 7.05 0.00 0.00 3.02
2460 2497 6.459298 GCGAATCTGATTCAATTCTGATGGTT 60.459 38.462 25.32 0.00 39.22 3.67
2501 2538 1.330521 CCGCTTGTGGTGATTATTCGG 59.669 52.381 0.00 0.00 0.00 4.30
2522 2559 6.366340 TCGGTAAGAATCTATCTCTTGGAGT 58.634 40.000 0.00 0.00 37.42 3.85
2549 2586 5.802451 TCGATGCTCGATAAGAAAGATATGC 59.198 40.000 4.47 0.00 44.82 3.14
2599 2636 2.704065 CCCCTCGAACCACACCTTATAT 59.296 50.000 0.00 0.00 0.00 0.86
2609 2646 2.172505 CACACCTTATATGTGGAGGCCA 59.827 50.000 5.01 0.00 43.11 5.36
2627 2664 0.800012 CACCGAATACACCCGTTTGG 59.200 55.000 0.00 0.00 41.37 3.28
2636 2673 4.492604 CCCGTTTGGTGGTGACAT 57.507 55.556 0.00 0.00 46.14 3.06
2637 2674 2.727103 CCCGTTTGGTGGTGACATT 58.273 52.632 0.00 0.00 46.14 2.71
2638 2675 0.313672 CCCGTTTGGTGGTGACATTG 59.686 55.000 0.00 0.00 46.14 2.82
2639 2676 0.318614 CCGTTTGGTGGTGACATTGC 60.319 55.000 0.00 0.00 46.14 3.56
2640 2677 0.383590 CGTTTGGTGGTGACATTGCA 59.616 50.000 0.00 0.00 46.14 4.08
2641 2678 1.202348 CGTTTGGTGGTGACATTGCAA 60.202 47.619 0.00 0.00 46.14 4.08
2642 2679 2.472816 GTTTGGTGGTGACATTGCAAG 58.527 47.619 4.94 0.00 46.14 4.01
2643 2680 1.774110 TTGGTGGTGACATTGCAAGT 58.226 45.000 4.94 3.11 46.14 3.16
2644 2681 2.647683 TGGTGGTGACATTGCAAGTA 57.352 45.000 4.94 0.00 46.14 2.24
2645 2682 2.937519 TGGTGGTGACATTGCAAGTAA 58.062 42.857 4.94 0.00 46.14 2.24
2666 2740 7.717568 AGTAATAGCATCAGTCAAGTTCGTAT 58.282 34.615 0.00 0.00 0.00 3.06
2669 2743 7.932120 ATAGCATCAGTCAAGTTCGTATAAC 57.068 36.000 0.00 0.00 0.00 1.89
2672 2746 5.500931 GCATCAGTCAAGTTCGTATAACTGC 60.501 44.000 0.00 0.00 35.30 4.40
2679 2753 6.924060 GTCAAGTTCGTATAACTGCTGGATAT 59.076 38.462 0.00 0.00 0.00 1.63
2683 2757 5.801531 TCGTATAACTGCTGGATATTGGT 57.198 39.130 0.00 0.00 0.00 3.67
2692 2766 2.555757 GCTGGATATTGGTTGATGGAGC 59.444 50.000 0.00 0.00 0.00 4.70
2693 2767 3.152341 CTGGATATTGGTTGATGGAGCC 58.848 50.000 0.00 0.00 0.00 4.70
2694 2768 2.158475 TGGATATTGGTTGATGGAGCCC 60.158 50.000 0.00 0.00 0.00 5.19
2733 2809 1.607801 GCAATCCAAGCAAGGTCCCC 61.608 60.000 0.00 0.00 0.00 4.81
2752 2828 1.738099 GAGAGCATCACGCACCGTT 60.738 57.895 0.00 0.00 46.13 4.44
2770 2846 5.687285 CACCGTTGAATTCTTCCTTTTTGAG 59.313 40.000 7.05 0.00 0.00 3.02
2771 2847 5.592688 ACCGTTGAATTCTTCCTTTTTGAGA 59.407 36.000 7.05 0.00 0.00 3.27
2772 2848 6.265422 ACCGTTGAATTCTTCCTTTTTGAGAT 59.735 34.615 7.05 0.00 0.00 2.75
2773 2849 6.583806 CCGTTGAATTCTTCCTTTTTGAGATG 59.416 38.462 7.05 0.00 0.00 2.90
2774 2850 7.362662 CGTTGAATTCTTCCTTTTTGAGATGA 58.637 34.615 7.05 0.00 0.00 2.92
2775 2851 7.536622 CGTTGAATTCTTCCTTTTTGAGATGAG 59.463 37.037 7.05 0.00 0.00 2.90
2776 2852 7.458409 TGAATTCTTCCTTTTTGAGATGAGG 57.542 36.000 7.05 0.00 0.00 3.86
2777 2853 7.233632 TGAATTCTTCCTTTTTGAGATGAGGA 58.766 34.615 7.05 0.00 36.55 3.71
2778 2854 7.725397 TGAATTCTTCCTTTTTGAGATGAGGAA 59.275 33.333 7.05 3.89 43.91 3.36
2779 2855 8.661752 AATTCTTCCTTTTTGAGATGAGGAAT 57.338 30.769 4.33 0.00 44.73 3.01
2780 2856 9.759473 AATTCTTCCTTTTTGAGATGAGGAATA 57.241 29.630 4.33 0.00 44.73 1.75
2781 2857 9.933240 ATTCTTCCTTTTTGAGATGAGGAATAT 57.067 29.630 4.33 0.20 44.73 1.28
2782 2858 8.743085 TCTTCCTTTTTGAGATGAGGAATATG 57.257 34.615 4.33 0.00 44.73 1.78
2783 2859 7.776969 TCTTCCTTTTTGAGATGAGGAATATGG 59.223 37.037 4.33 0.00 44.73 2.74
2784 2860 5.829924 TCCTTTTTGAGATGAGGAATATGGC 59.170 40.000 0.00 0.00 35.45 4.40
2785 2861 5.278169 CCTTTTTGAGATGAGGAATATGGCG 60.278 44.000 0.00 0.00 0.00 5.69
2786 2862 3.407424 TTGAGATGAGGAATATGGCGG 57.593 47.619 0.00 0.00 0.00 6.13
2787 2863 2.608623 TGAGATGAGGAATATGGCGGA 58.391 47.619 0.00 0.00 0.00 5.54
2788 2864 2.972021 TGAGATGAGGAATATGGCGGAA 59.028 45.455 0.00 0.00 0.00 4.30
2789 2865 3.007290 TGAGATGAGGAATATGGCGGAAG 59.993 47.826 0.00 0.00 0.00 3.46
2802 2878 3.108521 CGGAAGCGATATCCTTCGG 57.891 57.895 19.28 18.75 39.61 4.30
2803 2879 1.009389 CGGAAGCGATATCCTTCGGC 61.009 60.000 19.28 8.85 39.61 5.54
2804 2880 0.318762 GGAAGCGATATCCTTCGGCT 59.681 55.000 19.28 10.56 39.61 5.52
2805 2881 1.270358 GGAAGCGATATCCTTCGGCTT 60.270 52.381 19.28 16.45 39.61 4.35
2806 2882 2.062519 GAAGCGATATCCTTCGGCTTC 58.937 52.381 19.70 19.70 40.91 3.86
2807 2883 0.318762 AGCGATATCCTTCGGCTTCC 59.681 55.000 0.00 0.00 39.49 3.46
2808 2884 0.033504 GCGATATCCTTCGGCTTCCA 59.966 55.000 0.00 0.00 39.49 3.53
2809 2885 1.784525 CGATATCCTTCGGCTTCCAC 58.215 55.000 0.00 0.00 35.50 4.02
2810 2886 1.605712 CGATATCCTTCGGCTTCCACC 60.606 57.143 0.00 0.00 35.50 4.61
2811 2887 0.765510 ATATCCTTCGGCTTCCACCC 59.234 55.000 0.00 0.00 0.00 4.61
2812 2888 0.619255 TATCCTTCGGCTTCCACCCA 60.619 55.000 0.00 0.00 0.00 4.51
2813 2889 1.281925 ATCCTTCGGCTTCCACCCAT 61.282 55.000 0.00 0.00 0.00 4.00
2814 2890 1.000896 CCTTCGGCTTCCACCCATT 60.001 57.895 0.00 0.00 0.00 3.16
2815 2891 1.315257 CCTTCGGCTTCCACCCATTG 61.315 60.000 0.00 0.00 0.00 2.82
2816 2892 0.322456 CTTCGGCTTCCACCCATTGA 60.322 55.000 0.00 0.00 0.00 2.57
2817 2893 0.322456 TTCGGCTTCCACCCATTGAG 60.322 55.000 0.00 0.00 0.00 3.02
2818 2894 2.409870 CGGCTTCCACCCATTGAGC 61.410 63.158 0.00 0.00 0.00 4.26
2819 2895 2.054453 GGCTTCCACCCATTGAGCC 61.054 63.158 0.00 0.00 45.21 4.70
2820 2896 1.304381 GCTTCCACCCATTGAGCCA 60.304 57.895 0.00 0.00 0.00 4.75
2821 2897 0.899717 GCTTCCACCCATTGAGCCAA 60.900 55.000 0.00 0.00 0.00 4.52
2822 2898 1.180029 CTTCCACCCATTGAGCCAAG 58.820 55.000 0.00 0.00 0.00 3.61
2823 2899 0.251742 TTCCACCCATTGAGCCAAGG 60.252 55.000 0.00 0.00 0.00 3.61
2824 2900 1.077265 CCACCCATTGAGCCAAGGT 59.923 57.895 0.00 0.00 0.00 3.50
2825 2901 1.252904 CCACCCATTGAGCCAAGGTG 61.253 60.000 14.30 14.30 46.14 4.00
2826 2902 2.163454 ACCCATTGAGCCAAGGTGA 58.837 52.632 0.00 0.00 0.00 4.02
2827 2903 0.038744 ACCCATTGAGCCAAGGTGAG 59.961 55.000 0.00 0.00 0.00 3.51
2828 2904 0.038744 CCCATTGAGCCAAGGTGAGT 59.961 55.000 0.00 0.00 0.00 3.41
2829 2905 1.171308 CCATTGAGCCAAGGTGAGTG 58.829 55.000 0.00 0.00 0.00 3.51
2830 2906 0.524862 CATTGAGCCAAGGTGAGTGC 59.475 55.000 0.00 0.00 0.00 4.40
2831 2907 0.610232 ATTGAGCCAAGGTGAGTGCC 60.610 55.000 0.00 0.00 0.00 5.01
2832 2908 1.993701 TTGAGCCAAGGTGAGTGCCA 61.994 55.000 0.00 0.00 0.00 4.92
2856 2932 2.836360 GGCCATGCAGGTGATGGG 60.836 66.667 0.00 0.00 40.80 4.00
2871 2947 1.285962 GATGGGGGTGGCTGCATATAT 59.714 52.381 0.50 0.00 0.00 0.86
2874 2950 1.075374 GGGGGTGGCTGCATATATGAA 59.925 52.381 17.10 4.90 0.00 2.57
2883 2959 4.348656 GCTGCATATATGAAATCCATGCG 58.651 43.478 17.10 0.00 43.03 4.73
2934 3010 4.088634 ACCAAAGCTCTGGCATATTTTGA 58.911 39.130 5.81 0.00 40.45 2.69
2938 3014 4.450305 AGCTCTGGCATATTTTGAGGAT 57.550 40.909 0.00 0.00 41.70 3.24
2961 3087 0.039618 GAGAACCCCCAAGCCATCAA 59.960 55.000 0.00 0.00 0.00 2.57
2962 3088 0.040204 AGAACCCCCAAGCCATCAAG 59.960 55.000 0.00 0.00 0.00 3.02
2963 3089 0.251787 GAACCCCCAAGCCATCAAGT 60.252 55.000 0.00 0.00 0.00 3.16
2964 3090 0.251787 AACCCCCAAGCCATCAAGTC 60.252 55.000 0.00 0.00 0.00 3.01
2966 3092 0.040204 CCCCCAAGCCATCAAGTCTT 59.960 55.000 0.00 0.00 0.00 3.01
2969 3095 2.634453 CCCCAAGCCATCAAGTCTTTTT 59.366 45.455 0.00 0.00 0.00 1.94
2970 3096 3.555586 CCCCAAGCCATCAAGTCTTTTTG 60.556 47.826 0.00 0.00 0.00 2.44
2971 3097 3.555586 CCCAAGCCATCAAGTCTTTTTGG 60.556 47.826 6.29 6.29 34.92 3.28
2973 3099 4.301628 CAAGCCATCAAGTCTTTTTGGTC 58.698 43.478 10.76 5.29 0.00 4.02
2974 3100 3.837355 AGCCATCAAGTCTTTTTGGTCT 58.163 40.909 10.76 6.90 0.00 3.85
2975 3101 3.571401 AGCCATCAAGTCTTTTTGGTCTG 59.429 43.478 10.76 0.00 0.00 3.51
3010 3138 2.933260 GCCCTCTCGATCTTCTCAAAAC 59.067 50.000 0.00 0.00 0.00 2.43
3031 3159 1.109609 GGGTACTAGGGTCGTCCTTG 58.890 60.000 5.49 6.46 45.47 3.61
3034 3162 2.426381 GGTACTAGGGTCGTCCTTGAAG 59.574 54.545 13.34 5.56 45.47 3.02
3035 3163 1.558233 ACTAGGGTCGTCCTTGAAGG 58.442 55.000 4.45 4.45 45.47 3.46
3036 3164 1.203149 ACTAGGGTCGTCCTTGAAGGT 60.203 52.381 11.60 0.00 45.47 3.50
3037 3165 1.477295 CTAGGGTCGTCCTTGAAGGTC 59.523 57.143 11.60 4.62 45.47 3.85
3038 3166 0.178929 AGGGTCGTCCTTGAAGGTCT 60.179 55.000 11.60 0.00 45.47 3.85
3039 3167 0.246910 GGGTCGTCCTTGAAGGTCTC 59.753 60.000 11.60 2.80 36.53 3.36
3042 3170 2.610727 GGTCGTCCTTGAAGGTCTCTTG 60.611 54.545 11.60 0.00 36.53 3.02
3043 3171 2.296471 GTCGTCCTTGAAGGTCTCTTGA 59.704 50.000 11.60 0.00 36.53 3.02
3045 3173 4.158025 GTCGTCCTTGAAGGTCTCTTGATA 59.842 45.833 11.60 0.00 36.53 2.15
3048 3176 5.336849 CGTCCTTGAAGGTCTCTTGATACTT 60.337 44.000 11.60 0.00 36.53 2.24
3049 3177 6.103330 GTCCTTGAAGGTCTCTTGATACTTC 58.897 44.000 11.60 0.00 38.44 3.01
3050 3178 5.187967 TCCTTGAAGGTCTCTTGATACTTCC 59.812 44.000 11.60 0.00 37.81 3.46
3058 3241 8.485578 AGGTCTCTTGATACTTCCCTAATTAG 57.514 38.462 5.43 5.43 0.00 1.73
3068 3251 6.936968 ACTTCCCTAATTAGAGTGTGAACT 57.063 37.500 14.28 0.00 0.00 3.01
3076 3259 8.185505 CCTAATTAGAGTGTGAACTAGAGTGTC 58.814 40.741 14.28 0.00 0.00 3.67
3080 3263 1.000607 GTGTGAACTAGAGTGTCGGCA 60.001 52.381 0.00 0.00 0.00 5.69
3135 3359 8.814931 CATGTATATCAAATCCTCTTCTCTCCT 58.185 37.037 0.00 0.00 0.00 3.69
3136 3360 8.187913 TGTATATCAAATCCTCTTCTCTCCTG 57.812 38.462 0.00 0.00 0.00 3.86
3149 3373 2.027745 TCTCTCCTGGCTGAATTGTCAC 60.028 50.000 0.00 0.00 0.00 3.67
3221 3447 6.782082 AGAATTTTAGGCCTCCTTTGATTC 57.218 37.500 9.68 11.75 34.61 2.52
3250 3476 7.883833 AGGAGTTTTGTAGGAATTCTAAAGGAC 59.116 37.037 5.23 0.00 0.00 3.85
3254 3480 8.793592 GTTTTGTAGGAATTCTAAAGGACATGT 58.206 33.333 0.00 0.00 0.00 3.21
3265 3491 7.825331 TCTAAAGGACATGTATCTGTAGGAG 57.175 40.000 18.47 4.46 0.00 3.69
3282 3508 4.817318 AGGAGAGAATTCTTCGAAGCTT 57.183 40.909 20.56 15.26 33.82 3.74
3289 3515 5.763088 AGAATTCTTCGAAGCTTTTTGACC 58.237 37.500 20.56 4.36 34.02 4.02
3290 3516 5.532779 AGAATTCTTCGAAGCTTTTTGACCT 59.467 36.000 20.56 6.33 34.02 3.85
3291 3517 4.552166 TTCTTCGAAGCTTTTTGACCTG 57.448 40.909 20.56 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.112606 TCCTCCTCGTCACAGACCTT 59.887 55.000 0.00 0.00 0.00 3.50
22 23 0.962855 TCTGCTCCTCCTCGTCACAG 60.963 60.000 0.00 0.00 0.00 3.66
51 55 3.388841 GGAAGAACCTCGGAGGCA 58.611 61.111 23.84 0.00 39.63 4.75
216 223 9.828852 GAAATTACAGATAATCTAGACGACGAT 57.171 33.333 0.00 0.00 30.27 3.73
274 281 4.741676 CGTACAGTTACACGGATAATTCCC 59.258 45.833 0.00 0.00 39.01 3.97
289 296 3.863424 CCGAACAGCATATTCGTACAGTT 59.137 43.478 13.65 0.00 45.88 3.16
323 330 5.249780 TCAGGTAAGCCAAAATCTACCAA 57.750 39.130 0.00 0.00 37.19 3.67
339 346 8.523915 AATTGACATCAAGCAATATTCAGGTA 57.476 30.769 0.23 0.00 39.47 3.08
380 387 2.278332 ACAGAAAGGGAGGAAAGCAC 57.722 50.000 0.00 0.00 0.00 4.40
410 417 6.037786 TGATTTGAAGACGACTATTCCAGT 57.962 37.500 0.00 0.00 41.47 4.00
422 429 7.225538 ACATGATATTCGACCTGATTTGAAGAC 59.774 37.037 0.00 0.00 0.00 3.01
467 474 7.584122 AAGTAGAGGAATAGTTCGCTAATCA 57.416 36.000 0.00 0.00 32.58 2.57
474 481 8.848182 AGGTACATAAAGTAGAGGAATAGTTCG 58.152 37.037 0.00 0.00 32.19 3.95
478 485 8.361139 CACCAGGTACATAAAGTAGAGGAATAG 58.639 40.741 0.00 0.00 32.19 1.73
533 541 7.903431 CAGAACATATTGCGAGGTAAAAAGTAC 59.097 37.037 0.00 0.00 0.00 2.73
754 763 5.192176 AGAAAGGAGGAGCTCAATTGATTC 58.808 41.667 17.19 11.82 31.08 2.52
786 795 9.788889 TGAGCATCTAATCATCAACAAGATATT 57.211 29.630 0.00 0.00 32.67 1.28
881 891 6.306987 GGAATTCTAAGCAATTAGGATGGGA 58.693 40.000 5.23 0.00 0.00 4.37
1007 1024 1.424493 CTCGAACCCAATCGCAGAGC 61.424 60.000 0.00 0.00 43.63 4.09
1221 1244 3.322541 TCTTGATCACAACCTTGTACGGA 59.677 43.478 0.00 0.00 39.91 4.69
1527 1550 4.256110 CAGTCATGCACATCTCAAGGTTA 58.744 43.478 0.00 0.00 0.00 2.85
1656 1679 2.363306 AGTCGCAGATCTCCATCTCT 57.637 50.000 0.00 0.00 37.25 3.10
1804 1827 1.224592 CCAGGTCACCATAGGCCAC 59.775 63.158 5.01 0.00 0.00 5.01
1825 1848 1.494960 AAGGATCTCAGCACCCTCTC 58.505 55.000 0.00 0.00 0.00 3.20
2010 2033 1.816863 GCGACCCAGTGGAGTCTTCA 61.817 60.000 21.35 0.00 34.81 3.02
2022 2045 1.596934 GACAGATCTTGGCGACCCA 59.403 57.895 0.00 0.00 40.06 4.51
2028 2051 2.098770 GCAATTCAGGACAGATCTTGGC 59.901 50.000 0.00 0.00 32.82 4.52
2050 2073 5.237127 CGCTCTCTAAATTGCCATCAACATA 59.763 40.000 0.00 0.00 34.60 2.29
2052 2075 3.374988 CGCTCTCTAAATTGCCATCAACA 59.625 43.478 0.00 0.00 34.60 3.33
2163 2186 1.561076 ACCAGCTAGCATCACCATCAA 59.439 47.619 18.83 0.00 0.00 2.57
2184 2207 1.675483 ACGCAACACAAGCTCATTCAA 59.325 42.857 0.00 0.00 0.00 2.69
2287 2320 3.548818 GCATTTCCATACATTCGCTCACC 60.549 47.826 0.00 0.00 0.00 4.02
2345 2380 1.269206 ACATTTGCTCAACACAAGGCG 60.269 47.619 0.00 0.00 0.00 5.52
2409 2444 4.935205 CAGAATTCAATAGGTCCACGACAA 59.065 41.667 8.44 0.00 33.68 3.18
2428 2465 3.333029 TGAATCAGATTCGCCACAGAA 57.667 42.857 16.82 0.00 42.15 3.02
2431 2468 4.095334 CAGAATTGAATCAGATTCGCCACA 59.905 41.667 16.82 0.00 42.15 4.17
2432 2469 4.333649 TCAGAATTGAATCAGATTCGCCAC 59.666 41.667 16.82 9.46 42.15 5.01
2501 2538 7.646130 CGACAACTCCAAGAGATAGATTCTTAC 59.354 40.741 0.00 0.00 33.74 2.34
2580 2617 4.119862 CACATATAAGGTGTGGTTCGAGG 58.880 47.826 0.00 0.00 42.43 4.63
2588 2625 2.172505 TGGCCTCCACATATAAGGTGTG 59.827 50.000 3.32 3.29 44.99 3.82
2609 2646 3.236604 CCAAACGGGTGTATTCGGT 57.763 52.632 0.00 0.00 0.00 4.69
2627 2664 4.155826 TGCTATTACTTGCAATGTCACCAC 59.844 41.667 0.00 0.00 36.15 4.16
2628 2665 4.331108 TGCTATTACTTGCAATGTCACCA 58.669 39.130 0.00 0.00 36.15 4.17
2629 2666 4.963276 TGCTATTACTTGCAATGTCACC 57.037 40.909 0.00 0.00 36.15 4.02
2630 2667 6.122850 TGATGCTATTACTTGCAATGTCAC 57.877 37.500 0.00 0.00 42.74 3.67
2631 2668 5.882000 ACTGATGCTATTACTTGCAATGTCA 59.118 36.000 0.00 0.00 42.74 3.58
2632 2669 6.037500 TGACTGATGCTATTACTTGCAATGTC 59.962 38.462 0.00 0.00 42.74 3.06
2633 2670 5.882000 TGACTGATGCTATTACTTGCAATGT 59.118 36.000 0.00 3.09 42.74 2.71
2634 2671 6.367686 TGACTGATGCTATTACTTGCAATG 57.632 37.500 0.00 0.00 42.74 2.82
2635 2672 6.600822 ACTTGACTGATGCTATTACTTGCAAT 59.399 34.615 0.00 0.00 42.74 3.56
2636 2673 5.939883 ACTTGACTGATGCTATTACTTGCAA 59.060 36.000 0.00 0.00 42.74 4.08
2637 2674 5.491070 ACTTGACTGATGCTATTACTTGCA 58.509 37.500 0.00 0.00 43.67 4.08
2638 2675 6.428385 AACTTGACTGATGCTATTACTTGC 57.572 37.500 0.00 0.00 0.00 4.01
2639 2676 6.311445 ACGAACTTGACTGATGCTATTACTTG 59.689 38.462 0.00 0.00 0.00 3.16
2640 2677 6.398918 ACGAACTTGACTGATGCTATTACTT 58.601 36.000 0.00 0.00 0.00 2.24
2641 2678 5.967088 ACGAACTTGACTGATGCTATTACT 58.033 37.500 0.00 0.00 0.00 2.24
2642 2679 7.932120 ATACGAACTTGACTGATGCTATTAC 57.068 36.000 0.00 0.00 0.00 1.89
2643 2680 9.459640 GTTATACGAACTTGACTGATGCTATTA 57.540 33.333 0.00 0.00 0.00 0.98
2644 2681 8.198109 AGTTATACGAACTTGACTGATGCTATT 58.802 33.333 0.00 0.00 0.00 1.73
2645 2682 7.649705 CAGTTATACGAACTTGACTGATGCTAT 59.350 37.037 0.00 0.00 37.32 2.97
2666 2740 5.104151 TCCATCAACCAATATCCAGCAGTTA 60.104 40.000 0.00 0.00 0.00 2.24
2669 2743 3.819337 CTCCATCAACCAATATCCAGCAG 59.181 47.826 0.00 0.00 0.00 4.24
2672 2746 3.152341 GGCTCCATCAACCAATATCCAG 58.848 50.000 0.00 0.00 0.00 3.86
2679 2753 0.608035 GAACGGGCTCCATCAACCAA 60.608 55.000 0.00 0.00 0.00 3.67
2683 2757 1.079405 GTCGAACGGGCTCCATCAA 60.079 57.895 0.00 0.00 0.00 2.57
2733 2809 3.250323 CGGTGCGTGATGCTCTCG 61.250 66.667 0.00 0.00 46.63 4.04
2770 2846 2.079925 GCTTCCGCCATATTCCTCATC 58.920 52.381 0.00 0.00 0.00 2.92
2771 2847 1.609061 CGCTTCCGCCATATTCCTCAT 60.609 52.381 0.00 0.00 0.00 2.90
2772 2848 0.249868 CGCTTCCGCCATATTCCTCA 60.250 55.000 0.00 0.00 0.00 3.86
2773 2849 0.033504 TCGCTTCCGCCATATTCCTC 59.966 55.000 0.00 0.00 0.00 3.71
2774 2850 0.687354 ATCGCTTCCGCCATATTCCT 59.313 50.000 0.00 0.00 0.00 3.36
2775 2851 2.380084 TATCGCTTCCGCCATATTCC 57.620 50.000 0.00 0.00 0.00 3.01
2776 2852 2.866762 GGATATCGCTTCCGCCATATTC 59.133 50.000 0.00 0.00 31.35 1.75
2777 2853 2.501723 AGGATATCGCTTCCGCCATATT 59.498 45.455 0.00 0.00 38.36 1.28
2778 2854 2.111384 AGGATATCGCTTCCGCCATAT 58.889 47.619 0.00 0.00 38.36 1.78
2779 2855 1.557099 AGGATATCGCTTCCGCCATA 58.443 50.000 0.00 0.00 38.36 2.74
2780 2856 0.687354 AAGGATATCGCTTCCGCCAT 59.313 50.000 0.00 0.00 38.36 4.40
2781 2857 0.033504 GAAGGATATCGCTTCCGCCA 59.966 55.000 16.91 0.00 38.36 5.69
2782 2858 1.009389 CGAAGGATATCGCTTCCGCC 61.009 60.000 19.71 5.14 38.36 6.13
2783 2859 2.435741 CGAAGGATATCGCTTCCGC 58.564 57.895 19.71 5.38 38.36 5.54
2802 2878 0.899717 TTGGCTCAATGGGTGGAAGC 60.900 55.000 0.00 0.00 0.00 3.86
2803 2879 1.180029 CTTGGCTCAATGGGTGGAAG 58.820 55.000 0.00 0.00 0.00 3.46
2804 2880 0.251742 CCTTGGCTCAATGGGTGGAA 60.252 55.000 0.00 0.00 0.00 3.53
2805 2881 1.383799 CCTTGGCTCAATGGGTGGA 59.616 57.895 0.00 0.00 0.00 4.02
2806 2882 1.077265 ACCTTGGCTCAATGGGTGG 59.923 57.895 0.00 0.00 0.00 4.61
2807 2883 0.251297 TCACCTTGGCTCAATGGGTG 60.251 55.000 14.75 14.75 46.03 4.61
2808 2884 0.038744 CTCACCTTGGCTCAATGGGT 59.961 55.000 0.00 0.00 0.00 4.51
2809 2885 0.038744 ACTCACCTTGGCTCAATGGG 59.961 55.000 0.00 0.00 0.00 4.00
2810 2886 1.171308 CACTCACCTTGGCTCAATGG 58.829 55.000 0.00 0.00 0.00 3.16
2811 2887 0.524862 GCACTCACCTTGGCTCAATG 59.475 55.000 0.00 0.00 0.00 2.82
2812 2888 0.610232 GGCACTCACCTTGGCTCAAT 60.610 55.000 0.00 0.00 36.62 2.57
2813 2889 1.228245 GGCACTCACCTTGGCTCAA 60.228 57.895 0.00 0.00 36.62 3.02
2814 2890 1.993701 TTGGCACTCACCTTGGCTCA 61.994 55.000 0.00 0.00 40.16 4.26
2815 2891 0.823356 TTTGGCACTCACCTTGGCTC 60.823 55.000 0.00 0.00 40.16 4.70
2816 2892 0.396974 TTTTGGCACTCACCTTGGCT 60.397 50.000 0.00 0.00 40.16 4.75
2817 2893 0.249447 GTTTTGGCACTCACCTTGGC 60.249 55.000 0.00 0.00 39.92 4.52
2818 2894 1.110442 TGTTTTGGCACTCACCTTGG 58.890 50.000 0.00 0.00 0.00 3.61
2819 2895 2.546373 CCATGTTTTGGCACTCACCTTG 60.546 50.000 0.00 0.00 39.09 3.61
2820 2896 1.688197 CCATGTTTTGGCACTCACCTT 59.312 47.619 0.00 0.00 39.09 3.50
2821 2897 1.331214 CCATGTTTTGGCACTCACCT 58.669 50.000 0.00 0.00 39.09 4.00
2822 2898 3.892200 CCATGTTTTGGCACTCACC 57.108 52.632 0.00 0.00 39.09 4.02
2831 2907 0.322322 ACCTGCATGGCCATGTTTTG 59.678 50.000 39.08 27.99 40.80 2.44
2832 2908 0.322322 CACCTGCATGGCCATGTTTT 59.678 50.000 39.08 22.37 40.80 2.43
2856 2932 3.445096 GGATTTCATATATGCAGCCACCC 59.555 47.826 7.92 0.00 0.00 4.61
2871 2947 4.438608 GCAATAACACTCGCATGGATTTCA 60.439 41.667 0.00 0.00 0.00 2.69
2874 2950 3.016031 TGCAATAACACTCGCATGGATT 58.984 40.909 0.00 0.00 0.00 3.01
2934 3010 1.355720 CTTGGGGGTTCTCAACATCCT 59.644 52.381 0.00 0.00 0.00 3.24
2938 3014 1.152830 GGCTTGGGGGTTCTCAACA 59.847 57.895 0.00 0.00 0.00 3.33
2961 3087 2.331265 GGCGCAGACCAAAAAGACT 58.669 52.632 10.83 0.00 0.00 3.24
2962 3088 4.944249 GGCGCAGACCAAAAAGAC 57.056 55.556 10.83 0.00 0.00 3.01
2971 3097 1.581447 CCTTTCTTTGGGCGCAGAC 59.419 57.895 10.83 0.00 0.00 3.51
2973 3099 2.259511 GCCTTTCTTTGGGCGCAG 59.740 61.111 10.83 0.00 38.91 5.18
3010 3138 0.258194 AGGACGACCCTAGTACCCTG 59.742 60.000 0.00 0.00 45.48 4.45
3029 3157 5.094387 AGGGAAGTATCAAGAGACCTTCAA 58.906 41.667 0.00 0.00 37.06 2.69
3031 3159 6.793505 TTAGGGAAGTATCAAGAGACCTTC 57.206 41.667 0.00 0.00 35.71 3.46
3034 3162 8.480133 TCTAATTAGGGAAGTATCAAGAGACC 57.520 38.462 12.54 0.00 0.00 3.85
3035 3163 9.138596 ACTCTAATTAGGGAAGTATCAAGAGAC 57.861 37.037 19.45 0.00 0.00 3.36
3036 3164 9.137459 CACTCTAATTAGGGAAGTATCAAGAGA 57.863 37.037 19.45 0.00 0.00 3.10
3037 3165 8.919145 ACACTCTAATTAGGGAAGTATCAAGAG 58.081 37.037 19.45 5.52 0.00 2.85
3038 3166 8.696374 CACACTCTAATTAGGGAAGTATCAAGA 58.304 37.037 19.45 0.00 0.00 3.02
3039 3167 8.696374 TCACACTCTAATTAGGGAAGTATCAAG 58.304 37.037 19.45 4.40 0.00 3.02
3042 3170 8.697292 AGTTCACACTCTAATTAGGGAAGTATC 58.303 37.037 19.45 9.79 0.00 2.24
3043 3171 8.611051 AGTTCACACTCTAATTAGGGAAGTAT 57.389 34.615 19.45 0.00 0.00 2.12
3045 3173 6.936968 AGTTCACACTCTAATTAGGGAAGT 57.063 37.500 19.45 13.28 0.00 3.01
3048 3176 7.339721 CACTCTAGTTCACACTCTAATTAGGGA 59.660 40.741 19.45 3.93 34.06 4.20
3049 3177 7.122948 ACACTCTAGTTCACACTCTAATTAGGG 59.877 40.741 10.98 10.98 34.06 3.53
3050 3178 8.057536 ACACTCTAGTTCACACTCTAATTAGG 57.942 38.462 12.54 6.10 34.06 2.69
3058 3241 2.668834 GCCGACACTCTAGTTCACACTC 60.669 54.545 0.00 0.00 34.06 3.51
3149 3373 3.605634 TGATATGGTCGTTGAGGTTTGG 58.394 45.455 0.00 0.00 0.00 3.28
3221 3447 7.979444 TTAGAATTCCTACAAAACTCCTGTG 57.021 36.000 0.65 0.00 0.00 3.66
3250 3476 7.807433 CGAAGAATTCTCTCCTACAGATACATG 59.193 40.741 8.78 0.00 44.75 3.21
3254 3480 7.255312 GCTTCGAAGAATTCTCTCCTACAGATA 60.255 40.741 28.95 0.00 44.75 1.98
3265 3491 5.853810 GGTCAAAAAGCTTCGAAGAATTCTC 59.146 40.000 28.95 9.62 44.75 2.87


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

AutoCloner maintained by Alex Coulton.