Multiple sequence alignment - TraesCS2B01G413300

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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 TraesCS2B01G413300 chr2B 100.000 2182 0 0 1 2182 589035668 589037849 0.000000e+00 4030
1 TraesCS2B01G413300 chr2B 100.000 253 0 0 2759 3011 589038426 589038678 4.550000e-128 468
2 TraesCS2B01G413300 chr2A 91.438 2219 104 26 1 2165 646850845 646853031 0.000000e+00 2966
3 TraesCS2B01G413300 chr2D 95.979 1691 49 4 486 2176 501554833 501553162 0.000000e+00 2728


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 TraesCS2B01G413300 chr2B 589035668 589038678 3010 False 2249 4030 100.000 1 3011 2 chr2B.!!$F1 3010
1 TraesCS2B01G413300 chr2A 646850845 646853031 2186 False 2966 2966 91.438 1 2165 1 chr2A.!!$F1 2164
2 TraesCS2B01G413300 chr2D 501553162 501554833 1671 True 2728 2728 95.979 486 2176 1 chr2D.!!$R1 1690

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
935 989 0.034059 ACAGCTCCCACAAGAGAACG 59.966 55.0 0.0 0.0 35.82 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2842 2911 0.308684 CACACATTGCGCAGAGTTGT 59.691 50.0 11.31 10.72 0.0 3.32 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
39 40 1.864711 TCGGAAGCACAAAAGAACTCG 59.135 47.619 0.00 0.00 0.00 4.18
40 41 1.864711 CGGAAGCACAAAAGAACTCGA 59.135 47.619 0.00 0.00 0.00 4.04
45 46 2.225019 AGCACAAAAGAACTCGATGCTG 59.775 45.455 3.73 0.00 40.29 4.41
76 81 4.124943 TCCTCCCTCCTCCGGACG 62.125 72.222 0.00 0.00 0.00 4.79
108 113 3.221771 AGCTGTCAACAAAACCTGCATA 58.778 40.909 0.00 0.00 0.00 3.14
114 119 5.767665 TGTCAACAAAACCTGCATATACTGT 59.232 36.000 0.00 0.00 0.00 3.55
120 125 6.884295 ACAAAACCTGCATATACTGTATGTGT 59.116 34.615 20.84 3.75 30.90 3.72
148 153 7.391554 CAGTAGATTTTCCAGATCAGAACCAAA 59.608 37.037 0.00 0.00 0.00 3.28
172 177 3.879892 GGGTTCTGAATATCACAAGAGGC 59.120 47.826 0.00 0.00 0.00 4.70
245 256 4.007644 CCTCAGGTGTGCCGCAGA 62.008 66.667 0.00 0.00 40.50 4.26
258 272 1.752683 CCGCAGAGGACAGTAGTAGT 58.247 55.000 0.00 0.00 45.00 2.73
305 319 5.981315 GCATCCGACAATCAATTCAATCAAT 59.019 36.000 0.00 0.00 0.00 2.57
340 354 9.639601 CGTGGTATATCTAGAGCAAAAATCATA 57.360 33.333 0.00 0.00 0.00 2.15
364 378 4.082026 AGCAATGCCTTAGAAATGACCAAC 60.082 41.667 0.00 0.00 0.00 3.77
366 380 3.517296 TGCCTTAGAAATGACCAACCA 57.483 42.857 0.00 0.00 0.00 3.67
367 381 3.838565 TGCCTTAGAAATGACCAACCAA 58.161 40.909 0.00 0.00 0.00 3.67
368 382 4.415596 TGCCTTAGAAATGACCAACCAAT 58.584 39.130 0.00 0.00 0.00 3.16
369 383 4.462483 TGCCTTAGAAATGACCAACCAATC 59.538 41.667 0.00 0.00 0.00 2.67
380 416 0.529378 CAACCAATCTCTGCTTGGCC 59.471 55.000 0.00 0.00 45.83 5.36
382 418 2.117156 CCAATCTCTGCTTGGCCCG 61.117 63.158 0.00 0.00 36.98 6.13
416 452 6.758416 CCAGACGATATTCTGAATGAAGAACA 59.242 38.462 13.01 0.00 45.19 3.18
418 454 9.468532 CAGACGATATTCTGAATGAAGAACATA 57.531 33.333 13.01 0.00 45.19 2.29
443 479 1.795286 CTGTTCTTTCGGCTGTCACTC 59.205 52.381 0.00 0.00 0.00 3.51
454 490 0.037512 CTGTCACTCCTGTCAGGCAG 60.038 60.000 14.64 14.06 44.63 4.85
477 513 3.249687 CCTGTGGCAGGTTACTTCC 57.750 57.895 6.99 0.00 45.82 3.46
534 570 3.052745 CACACATAGGTACATAGCGCAG 58.947 50.000 11.47 0.64 0.00 5.18
548 584 0.318191 GCGCAGAGATGATCACGCTA 60.318 55.000 16.22 0.00 46.37 4.26
686 722 0.034896 GTCACCAACCCATGTCTCGT 59.965 55.000 0.00 0.00 0.00 4.18
770 806 1.475280 TCGACTGTCCCACCGAATTAG 59.525 52.381 1.55 0.00 0.00 1.73
793 829 1.567504 CGCTCCCCTACGTACATTTG 58.432 55.000 0.00 0.00 0.00 2.32
824 874 3.188492 CACGTAATAATACACCGCACCA 58.812 45.455 0.00 0.00 32.02 4.17
825 875 3.805422 CACGTAATAATACACCGCACCAT 59.195 43.478 0.00 0.00 32.02 3.55
826 876 4.271533 CACGTAATAATACACCGCACCATT 59.728 41.667 0.00 0.00 32.02 3.16
827 877 4.508861 ACGTAATAATACACCGCACCATTC 59.491 41.667 0.00 0.00 32.02 2.67
828 878 4.748102 CGTAATAATACACCGCACCATTCT 59.252 41.667 0.00 0.00 32.02 2.40
829 879 5.921976 CGTAATAATACACCGCACCATTCTA 59.078 40.000 0.00 0.00 32.02 2.10
830 880 6.129009 CGTAATAATACACCGCACCATTCTAC 60.129 42.308 0.00 0.00 32.02 2.59
831 881 2.614829 ATACACCGCACCATTCTACC 57.385 50.000 0.00 0.00 0.00 3.18
832 882 1.268066 TACACCGCACCATTCTACCA 58.732 50.000 0.00 0.00 0.00 3.25
833 883 0.321298 ACACCGCACCATTCTACCAC 60.321 55.000 0.00 0.00 0.00 4.16
834 884 0.036388 CACCGCACCATTCTACCACT 60.036 55.000 0.00 0.00 0.00 4.00
835 885 1.206132 CACCGCACCATTCTACCACTA 59.794 52.381 0.00 0.00 0.00 2.74
836 886 1.206371 ACCGCACCATTCTACCACTAC 59.794 52.381 0.00 0.00 0.00 2.73
837 887 1.472728 CCGCACCATTCTACCACTACC 60.473 57.143 0.00 0.00 0.00 3.18
847 897 5.453567 TTCTACCACTACCATCATCATCG 57.546 43.478 0.00 0.00 0.00 3.84
935 989 0.034059 ACAGCTCCCACAAGAGAACG 59.966 55.000 0.00 0.00 35.82 3.95
947 1001 1.375523 GAGAACGATGCCAACGGGT 60.376 57.895 0.00 0.00 36.17 5.28
954 1008 3.628646 ATGCCAACGGGTCTGCTCC 62.629 63.158 0.00 0.00 36.17 4.70
1200 1263 2.592861 GTCATCATGGAGGCCGCC 60.593 66.667 20.28 20.28 0.00 6.13
2031 2097 4.082300 TGACAGAAACAAGTGCACATTTGT 60.082 37.500 21.04 18.35 41.99 2.83
2170 2239 5.186603 TGATCCAGAGATGCATGATACTACC 59.813 44.000 2.46 0.00 30.90 3.18
2176 2245 5.182190 AGAGATGCATGATACTACCTACGTG 59.818 44.000 2.46 0.00 0.00 4.49
2177 2246 3.364889 TGCATGATACTACCTACGTGC 57.635 47.619 0.00 0.00 43.01 5.34
2178 2247 2.287368 TGCATGATACTACCTACGTGCG 60.287 50.000 0.00 0.00 44.80 5.34
2179 2248 2.031420 GCATGATACTACCTACGTGCGA 60.031 50.000 0.00 0.00 35.98 5.10
2180 2249 3.366070 GCATGATACTACCTACGTGCGAT 60.366 47.826 0.00 0.00 35.98 4.58
2181 2250 4.404324 CATGATACTACCTACGTGCGATC 58.596 47.826 0.00 0.00 0.00 3.69
2780 2849 5.043189 GTAACCTGCTTTTGGTGTATCAC 57.957 43.478 0.00 0.00 37.93 3.06
2781 2850 3.508845 ACCTGCTTTTGGTGTATCACT 57.491 42.857 0.06 0.00 36.30 3.41
2782 2851 3.412386 ACCTGCTTTTGGTGTATCACTC 58.588 45.455 0.06 0.00 36.30 3.51
2783 2852 3.073062 ACCTGCTTTTGGTGTATCACTCT 59.927 43.478 0.06 0.00 36.30 3.24
2784 2853 4.286032 ACCTGCTTTTGGTGTATCACTCTA 59.714 41.667 0.06 0.00 36.30 2.43
2785 2854 4.872691 CCTGCTTTTGGTGTATCACTCTAG 59.127 45.833 0.06 0.00 34.40 2.43
2786 2855 4.253685 TGCTTTTGGTGTATCACTCTAGC 58.746 43.478 0.06 0.00 34.40 3.42
2787 2856 4.020218 TGCTTTTGGTGTATCACTCTAGCT 60.020 41.667 0.00 0.00 34.40 3.32
2788 2857 5.186992 TGCTTTTGGTGTATCACTCTAGCTA 59.813 40.000 0.00 0.00 34.40 3.32
2789 2858 6.127054 TGCTTTTGGTGTATCACTCTAGCTAT 60.127 38.462 0.00 0.00 34.40 2.97
2790 2859 6.422400 GCTTTTGGTGTATCACTCTAGCTATC 59.578 42.308 0.00 0.00 34.40 2.08
2791 2860 7.418337 TTTTGGTGTATCACTCTAGCTATCA 57.582 36.000 0.00 0.00 34.40 2.15
2792 2861 6.641169 TTGGTGTATCACTCTAGCTATCAG 57.359 41.667 0.00 0.00 34.40 2.90
2793 2862 4.520874 TGGTGTATCACTCTAGCTATCAGC 59.479 45.833 0.00 0.00 36.62 4.26
2794 2863 4.764823 GGTGTATCACTCTAGCTATCAGCT 59.235 45.833 5.90 5.90 43.57 4.24
2795 2864 5.242838 GGTGTATCACTCTAGCTATCAGCTT 59.757 44.000 5.92 0.00 40.68 3.74
2796 2865 6.431543 GGTGTATCACTCTAGCTATCAGCTTA 59.568 42.308 5.92 0.00 40.68 3.09
2797 2866 7.574217 GGTGTATCACTCTAGCTATCAGCTTAC 60.574 44.444 5.92 2.06 40.68 2.34
2808 2877 6.428385 GCTATCAGCTTACAAATGTTCAGT 57.572 37.500 0.00 0.00 38.45 3.41
2809 2878 6.846350 GCTATCAGCTTACAAATGTTCAGTT 58.154 36.000 0.00 0.00 38.45 3.16
2810 2879 7.308435 GCTATCAGCTTACAAATGTTCAGTTT 58.692 34.615 0.00 0.00 38.45 2.66
2811 2880 8.450964 GCTATCAGCTTACAAATGTTCAGTTTA 58.549 33.333 0.00 0.00 38.45 2.01
2815 2884 9.677567 TCAGCTTACAAATGTTCAGTTTAATTC 57.322 29.630 0.00 0.00 0.00 2.17
2816 2885 9.683069 CAGCTTACAAATGTTCAGTTTAATTCT 57.317 29.630 0.00 0.00 0.00 2.40
2817 2886 9.683069 AGCTTACAAATGTTCAGTTTAATTCTG 57.317 29.630 0.00 2.87 0.00 3.02
2818 2887 8.915654 GCTTACAAATGTTCAGTTTAATTCTGG 58.084 33.333 7.87 0.00 34.15 3.86
2822 2891 8.859090 ACAAATGTTCAGTTTAATTCTGGATGA 58.141 29.630 7.87 0.00 34.15 2.92
2823 2892 9.350357 CAAATGTTCAGTTTAATTCTGGATGAG 57.650 33.333 7.87 0.00 34.15 2.90
2824 2893 8.868522 AATGTTCAGTTTAATTCTGGATGAGA 57.131 30.769 7.87 0.00 34.15 3.27
2825 2894 9.471702 AATGTTCAGTTTAATTCTGGATGAGAT 57.528 29.630 7.87 0.00 34.15 2.75
2826 2895 8.498054 TGTTCAGTTTAATTCTGGATGAGATC 57.502 34.615 7.87 0.00 34.15 2.75
2846 2915 3.038788 CCCATGTTAGGGCAAAACAAC 57.961 47.619 7.79 0.00 43.10 3.32
2847 2916 2.632512 CCCATGTTAGGGCAAAACAACT 59.367 45.455 7.79 0.00 43.10 3.16
2848 2917 3.306019 CCCATGTTAGGGCAAAACAACTC 60.306 47.826 7.79 0.00 43.10 3.01
2849 2918 3.573967 CCATGTTAGGGCAAAACAACTCT 59.426 43.478 7.79 0.00 40.05 3.24
2850 2919 4.549458 CATGTTAGGGCAAAACAACTCTG 58.451 43.478 7.79 0.00 40.05 3.35
2851 2920 2.360801 TGTTAGGGCAAAACAACTCTGC 59.639 45.455 1.85 0.00 34.04 4.26
2852 2921 1.234821 TAGGGCAAAACAACTCTGCG 58.765 50.000 0.00 0.00 36.93 5.18
2853 2922 1.661509 GGGCAAAACAACTCTGCGC 60.662 57.895 0.00 0.00 41.04 6.09
2854 2923 1.065600 GGCAAAACAACTCTGCGCA 59.934 52.632 10.98 10.98 36.93 6.09
2855 2924 0.527385 GGCAAAACAACTCTGCGCAA 60.527 50.000 13.05 1.37 36.93 4.85
2856 2925 1.490621 GCAAAACAACTCTGCGCAAT 58.509 45.000 13.05 0.00 0.00 3.56
2857 2926 1.190763 GCAAAACAACTCTGCGCAATG 59.809 47.619 13.05 9.81 0.00 2.82
2858 2927 2.462889 CAAAACAACTCTGCGCAATGT 58.537 42.857 13.05 10.55 0.00 2.71
2859 2928 2.124011 AAACAACTCTGCGCAATGTG 57.876 45.000 13.05 9.97 0.00 3.21
2860 2929 1.024271 AACAACTCTGCGCAATGTGT 58.976 45.000 13.05 10.66 0.00 3.72
2861 2930 0.308684 ACAACTCTGCGCAATGTGTG 59.691 50.000 13.05 14.86 0.00 3.82
2862 2931 0.587768 CAACTCTGCGCAATGTGTGA 59.412 50.000 13.05 2.59 0.00 3.58
2863 2932 1.198408 CAACTCTGCGCAATGTGTGAT 59.802 47.619 13.05 0.00 0.00 3.06
2864 2933 0.800631 ACTCTGCGCAATGTGTGATG 59.199 50.000 13.05 0.00 0.00 3.07
2865 2934 0.800631 CTCTGCGCAATGTGTGATGT 59.199 50.000 13.05 0.00 0.00 3.06
2866 2935 0.798159 TCTGCGCAATGTGTGATGTC 59.202 50.000 13.05 0.00 0.00 3.06
2867 2936 0.800631 CTGCGCAATGTGTGATGTCT 59.199 50.000 13.05 0.00 0.00 3.41
2868 2937 0.798159 TGCGCAATGTGTGATGTCTC 59.202 50.000 8.16 0.00 0.00 3.36
2869 2938 0.798159 GCGCAATGTGTGATGTCTCA 59.202 50.000 0.30 0.00 0.00 3.27
2870 2939 1.399440 GCGCAATGTGTGATGTCTCAT 59.601 47.619 0.30 0.00 32.98 2.90
2871 2940 2.790123 GCGCAATGTGTGATGTCTCATG 60.790 50.000 0.30 0.00 32.98 3.07
2872 2941 2.223180 CGCAATGTGTGATGTCTCATGG 60.223 50.000 0.00 0.00 32.98 3.66
2873 2942 3.011818 GCAATGTGTGATGTCTCATGGA 58.988 45.455 0.00 0.00 32.98 3.41
2874 2943 3.181503 GCAATGTGTGATGTCTCATGGAC 60.182 47.826 7.22 7.22 44.70 4.02
2888 2957 7.454260 GTCTCATGGACAAGGTAATTCTTTT 57.546 36.000 8.84 0.00 43.94 2.27
2889 2958 7.886338 GTCTCATGGACAAGGTAATTCTTTTT 58.114 34.615 8.84 0.00 43.94 1.94
2927 2996 8.942338 GGAATCACCCTTTAATTTCCATAAAC 57.058 34.615 0.00 0.00 0.00 2.01
2928 2997 8.536175 GGAATCACCCTTTAATTTCCATAAACA 58.464 33.333 0.00 0.00 0.00 2.83
2930 2999 9.889128 AATCACCCTTTAATTTCCATAAACATG 57.111 29.630 0.00 0.00 0.00 3.21
2931 3000 8.657387 TCACCCTTTAATTTCCATAAACATGA 57.343 30.769 0.00 0.00 0.00 3.07
2932 3001 9.094578 TCACCCTTTAATTTCCATAAACATGAA 57.905 29.630 0.00 0.00 0.00 2.57
2933 3002 9.369904 CACCCTTTAATTTCCATAAACATGAAG 57.630 33.333 0.00 0.00 0.00 3.02
2934 3003 9.100197 ACCCTTTAATTTCCATAAACATGAAGT 57.900 29.630 0.00 0.00 0.00 3.01
2935 3004 9.586435 CCCTTTAATTTCCATAAACATGAAGTC 57.414 33.333 0.00 0.00 0.00 3.01
2950 3019 4.933505 TGAAGTCATGGTTCAATGCAAA 57.066 36.364 8.47 0.00 30.89 3.68
2951 3020 5.471556 TGAAGTCATGGTTCAATGCAAAT 57.528 34.783 8.47 0.00 30.89 2.32
2952 3021 5.856156 TGAAGTCATGGTTCAATGCAAATT 58.144 33.333 8.47 0.00 30.89 1.82
2953 3022 5.927689 TGAAGTCATGGTTCAATGCAAATTC 59.072 36.000 8.47 0.00 30.89 2.17
2954 3023 5.471556 AGTCATGGTTCAATGCAAATTCA 57.528 34.783 0.00 0.00 0.00 2.57
2955 3024 5.856156 AGTCATGGTTCAATGCAAATTCAA 58.144 33.333 0.00 0.00 0.00 2.69
2956 3025 6.289834 AGTCATGGTTCAATGCAAATTCAAA 58.710 32.000 0.00 0.00 0.00 2.69
2957 3026 6.766944 AGTCATGGTTCAATGCAAATTCAAAA 59.233 30.769 0.00 0.00 0.00 2.44
2958 3027 7.282675 AGTCATGGTTCAATGCAAATTCAAAAA 59.717 29.630 0.00 0.00 0.00 1.94
2959 3028 8.077386 GTCATGGTTCAATGCAAATTCAAAAAT 58.923 29.630 0.00 0.00 0.00 1.82
2960 3029 8.630917 TCATGGTTCAATGCAAATTCAAAAATT 58.369 25.926 0.00 0.00 36.64 1.82
2961 3030 9.250624 CATGGTTCAATGCAAATTCAAAAATTT 57.749 25.926 0.00 0.00 44.12 1.82
2974 3043 9.833182 AAATTCAAAAATTTGTTAACTGCGTTT 57.167 22.222 7.22 0.28 42.21 3.60
2975 3044 8.819152 ATTCAAAAATTTGTTAACTGCGTTTG 57.181 26.923 7.22 10.48 39.18 2.93
2976 3045 6.766084 TCAAAAATTTGTTAACTGCGTTTGG 58.234 32.000 7.22 1.18 39.18 3.28
2977 3046 6.369065 TCAAAAATTTGTTAACTGCGTTTGGT 59.631 30.769 7.22 0.00 39.18 3.67
2978 3047 5.959652 AAATTTGTTAACTGCGTTTGGTC 57.040 34.783 7.22 0.00 0.00 4.02
2979 3048 4.911514 ATTTGTTAACTGCGTTTGGTCT 57.088 36.364 7.22 0.00 0.00 3.85
2980 3049 3.955771 TTGTTAACTGCGTTTGGTCTC 57.044 42.857 7.22 0.00 0.00 3.36
2981 3050 3.188159 TGTTAACTGCGTTTGGTCTCT 57.812 42.857 7.22 0.00 0.00 3.10
2982 3051 3.128349 TGTTAACTGCGTTTGGTCTCTC 58.872 45.455 7.22 0.00 0.00 3.20
2983 3052 3.128349 GTTAACTGCGTTTGGTCTCTCA 58.872 45.455 0.00 0.00 0.00 3.27
2984 3053 2.325583 AACTGCGTTTGGTCTCTCAA 57.674 45.000 0.00 0.00 0.00 3.02
2985 3054 1.583054 ACTGCGTTTGGTCTCTCAAC 58.417 50.000 0.00 0.00 0.00 3.18
2986 3055 1.139058 ACTGCGTTTGGTCTCTCAACT 59.861 47.619 0.00 0.00 0.00 3.16
2987 3056 2.213499 CTGCGTTTGGTCTCTCAACTT 58.787 47.619 0.00 0.00 0.00 2.66
2988 3057 3.181469 ACTGCGTTTGGTCTCTCAACTTA 60.181 43.478 0.00 0.00 0.00 2.24
2989 3058 3.128349 TGCGTTTGGTCTCTCAACTTAC 58.872 45.455 0.00 0.00 0.00 2.34
2990 3059 3.128349 GCGTTTGGTCTCTCAACTTACA 58.872 45.455 0.00 0.00 0.00 2.41
2991 3060 3.558418 GCGTTTGGTCTCTCAACTTACAA 59.442 43.478 0.00 0.00 0.00 2.41
2992 3061 4.034742 GCGTTTGGTCTCTCAACTTACAAA 59.965 41.667 0.00 0.00 0.00 2.83
2993 3062 5.499047 CGTTTGGTCTCTCAACTTACAAAC 58.501 41.667 0.00 0.00 41.40 2.93
2994 3063 5.499047 GTTTGGTCTCTCAACTTACAAACG 58.501 41.667 0.00 0.00 37.52 3.60
2995 3064 4.659111 TGGTCTCTCAACTTACAAACGA 57.341 40.909 0.00 0.00 0.00 3.85
2996 3065 5.209818 TGGTCTCTCAACTTACAAACGAT 57.790 39.130 0.00 0.00 0.00 3.73
2997 3066 5.607477 TGGTCTCTCAACTTACAAACGATT 58.393 37.500 0.00 0.00 0.00 3.34
2998 3067 5.694910 TGGTCTCTCAACTTACAAACGATTC 59.305 40.000 0.00 0.00 0.00 2.52
2999 3068 5.694910 GGTCTCTCAACTTACAAACGATTCA 59.305 40.000 0.00 0.00 0.00 2.57
3000 3069 6.369065 GGTCTCTCAACTTACAAACGATTCAT 59.631 38.462 0.00 0.00 0.00 2.57
3001 3070 7.412020 GGTCTCTCAACTTACAAACGATTCATC 60.412 40.741 0.00 0.00 0.00 2.92
3002 3071 7.116376 GTCTCTCAACTTACAAACGATTCATCA 59.884 37.037 0.00 0.00 0.00 3.07
3003 3072 7.819415 TCTCTCAACTTACAAACGATTCATCAT 59.181 33.333 0.00 0.00 0.00 2.45
3004 3073 8.996024 TCTCAACTTACAAACGATTCATCATA 57.004 30.769 0.00 0.00 0.00 2.15
3005 3074 9.430623 TCTCAACTTACAAACGATTCATCATAA 57.569 29.630 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.578495 CAGCATCGAGTTCTTTTGTGC 58.422 47.619 0.00 0.00 0.00 4.57
76 81 3.198068 TGTTGACAGCTTCAGTGACTTC 58.802 45.455 0.00 0.00 34.94 3.01
92 97 7.609918 ACATACAGTATATGCAGGTTTTGTTGA 59.390 33.333 0.00 0.00 0.00 3.18
108 113 7.495934 GGAAAATCTACTGCACACATACAGTAT 59.504 37.037 3.55 0.00 45.63 2.12
114 119 6.048732 TCTGGAAAATCTACTGCACACATA 57.951 37.500 0.00 0.00 0.00 2.29
120 125 5.682234 TCTGATCTGGAAAATCTACTGCA 57.318 39.130 0.00 0.00 0.00 4.41
148 153 5.749462 CCTCTTGTGATATTCAGAACCCTT 58.251 41.667 0.00 0.00 0.00 3.95
156 161 3.785486 CACTCGCCTCTTGTGATATTCA 58.215 45.455 0.00 0.00 33.95 2.57
172 177 1.205655 TCCCAAGAGATTCAGCACTCG 59.794 52.381 0.00 0.00 38.08 4.18
210 220 3.135994 GAGGTACAAAGGTCGCTGAAAA 58.864 45.455 0.00 0.00 0.00 2.29
258 272 6.823182 TGCAGTTATCCTTACAGTACGTAGTA 59.177 38.462 1.81 0.00 45.11 1.82
268 282 3.449377 TGTCGGATGCAGTTATCCTTACA 59.551 43.478 2.71 4.30 43.64 2.41
271 285 3.627395 TTGTCGGATGCAGTTATCCTT 57.373 42.857 2.71 0.00 43.64 3.36
305 319 4.891168 TCTAGATATACCACGTCCTTGCAA 59.109 41.667 0.00 0.00 0.00 4.08
340 354 4.088634 TGGTCATTTCTAAGGCATTGCTT 58.911 39.130 8.82 0.00 0.00 3.91
366 380 2.273449 CCGGGCCAAGCAGAGATT 59.727 61.111 4.39 0.00 0.00 2.40
367 381 4.496336 GCCGGGCCAAGCAGAGAT 62.496 66.667 8.12 0.00 0.00 2.75
416 452 5.127194 TGACAGCCGAAAGAACAGAGTATAT 59.873 40.000 0.00 0.00 0.00 0.86
418 454 3.258372 TGACAGCCGAAAGAACAGAGTAT 59.742 43.478 0.00 0.00 0.00 2.12
419 455 2.626266 TGACAGCCGAAAGAACAGAGTA 59.374 45.455 0.00 0.00 0.00 2.59
420 456 1.412710 TGACAGCCGAAAGAACAGAGT 59.587 47.619 0.00 0.00 0.00 3.24
431 467 1.527433 CTGACAGGAGTGACAGCCGA 61.527 60.000 0.00 0.00 39.16 5.54
434 470 1.375268 GCCTGACAGGAGTGACAGC 60.375 63.158 26.25 2.88 42.89 4.40
534 570 2.154580 CGTGCAATAGCGTGATCATCTC 59.845 50.000 0.00 0.00 46.23 2.75
686 722 1.613437 GCAGGAAAGCTTTGCCACTTA 59.387 47.619 25.04 0.00 31.79 2.24
736 772 1.373748 GTCGACAGGCGCCTTGTAA 60.374 57.895 30.60 16.27 40.61 2.41
770 806 3.142838 TACGTAGGGGAGCGGTGC 61.143 66.667 0.00 0.00 0.00 5.01
824 874 5.540337 ACGATGATGATGGTAGTGGTAGAAT 59.460 40.000 0.00 0.00 0.00 2.40
825 875 4.893524 ACGATGATGATGGTAGTGGTAGAA 59.106 41.667 0.00 0.00 0.00 2.10
826 876 4.470602 ACGATGATGATGGTAGTGGTAGA 58.529 43.478 0.00 0.00 0.00 2.59
827 877 4.321304 GGACGATGATGATGGTAGTGGTAG 60.321 50.000 0.00 0.00 0.00 3.18
828 878 3.572682 GGACGATGATGATGGTAGTGGTA 59.427 47.826 0.00 0.00 0.00 3.25
829 879 2.365617 GGACGATGATGATGGTAGTGGT 59.634 50.000 0.00 0.00 0.00 4.16
830 880 2.289072 GGGACGATGATGATGGTAGTGG 60.289 54.545 0.00 0.00 0.00 4.00
831 881 2.289072 GGGGACGATGATGATGGTAGTG 60.289 54.545 0.00 0.00 0.00 2.74
832 882 1.971357 GGGGACGATGATGATGGTAGT 59.029 52.381 0.00 0.00 0.00 2.73
833 883 1.970640 TGGGGACGATGATGATGGTAG 59.029 52.381 0.00 0.00 0.00 3.18
834 884 2.095604 TGGGGACGATGATGATGGTA 57.904 50.000 0.00 0.00 0.00 3.25
835 885 1.349026 GATGGGGACGATGATGATGGT 59.651 52.381 0.00 0.00 0.00 3.55
836 886 1.673923 CGATGGGGACGATGATGATGG 60.674 57.143 0.00 0.00 0.00 3.51
837 887 1.273327 TCGATGGGGACGATGATGATG 59.727 52.381 0.00 0.00 34.85 3.07
847 897 1.571919 CGATCAAAGTCGATGGGGAC 58.428 55.000 0.00 0.00 44.06 4.46
935 989 2.045926 AGCAGACCCGTTGGCATC 60.046 61.111 0.00 0.00 33.59 3.91
947 1001 4.147449 CATGGCGTCGGGAGCAGA 62.147 66.667 0.00 0.00 36.08 4.26
954 1008 2.815825 TTTGCAATGCATGGCGTCGG 62.816 55.000 21.00 0.00 38.76 4.79
1004 1058 1.172180 TGTTGGAGGAGCAAAAGCGG 61.172 55.000 0.00 0.00 0.00 5.52
1200 1263 1.153823 CCCGTTGTAGCACTCCTCG 60.154 63.158 0.00 0.00 0.00 4.63
1404 1470 2.281139 TTGCCCATGTTGACGCGA 60.281 55.556 15.93 0.00 0.00 5.87
1464 1530 3.252484 GGCGACACGATGCGGTAC 61.252 66.667 0.00 0.00 0.00 3.34
2004 2070 3.171277 GTGCACTTGTTTCTGTCACAAC 58.829 45.455 10.32 0.00 30.83 3.32
2135 2204 6.070824 TGCATCTCTGGATCAAGTTACAACTA 60.071 38.462 0.00 0.00 38.57 2.24
2136 2205 5.181748 GCATCTCTGGATCAAGTTACAACT 58.818 41.667 0.00 0.00 42.04 3.16
2758 2827 4.760204 AGTGATACACCAAAAGCAGGTTAC 59.240 41.667 0.00 0.00 37.23 2.50
2759 2828 4.980573 AGTGATACACCAAAAGCAGGTTA 58.019 39.130 0.00 0.00 37.23 2.85
2760 2829 3.821033 GAGTGATACACCAAAAGCAGGTT 59.179 43.478 0.00 0.00 37.23 3.50
2761 2830 3.073062 AGAGTGATACACCAAAAGCAGGT 59.927 43.478 0.00 0.00 40.85 4.00
2762 2831 3.679389 AGAGTGATACACCAAAAGCAGG 58.321 45.455 0.00 0.00 34.49 4.85
2763 2832 4.331168 GCTAGAGTGATACACCAAAAGCAG 59.669 45.833 0.00 0.00 34.49 4.24
2764 2833 4.020218 AGCTAGAGTGATACACCAAAAGCA 60.020 41.667 0.00 0.00 34.49 3.91
2765 2834 4.508662 AGCTAGAGTGATACACCAAAAGC 58.491 43.478 0.00 0.00 34.49 3.51
2766 2835 7.492524 TGATAGCTAGAGTGATACACCAAAAG 58.507 38.462 0.00 0.00 34.49 2.27
2767 2836 7.418337 TGATAGCTAGAGTGATACACCAAAA 57.582 36.000 0.00 0.00 34.49 2.44
2768 2837 6.461648 GCTGATAGCTAGAGTGATACACCAAA 60.462 42.308 0.00 0.00 38.45 3.28
2769 2838 5.010112 GCTGATAGCTAGAGTGATACACCAA 59.990 44.000 0.00 0.00 38.45 3.67
2770 2839 4.520874 GCTGATAGCTAGAGTGATACACCA 59.479 45.833 0.00 0.00 38.45 4.17
2771 2840 5.054390 GCTGATAGCTAGAGTGATACACC 57.946 47.826 0.00 0.00 38.45 4.16
2785 2854 6.428385 ACTGAACATTTGTAAGCTGATAGC 57.572 37.500 0.00 0.00 42.84 2.97
2789 2858 9.677567 GAATTAAACTGAACATTTGTAAGCTGA 57.322 29.630 0.00 0.00 0.00 4.26
2790 2859 9.683069 AGAATTAAACTGAACATTTGTAAGCTG 57.317 29.630 0.00 0.00 0.00 4.24
2791 2860 9.683069 CAGAATTAAACTGAACATTTGTAAGCT 57.317 29.630 7.08 0.00 37.54 3.74
2792 2861 8.915654 CCAGAATTAAACTGAACATTTGTAAGC 58.084 33.333 12.56 0.00 37.54 3.09
2796 2865 8.859090 TCATCCAGAATTAAACTGAACATTTGT 58.141 29.630 12.56 0.00 37.54 2.83
2797 2866 9.350357 CTCATCCAGAATTAAACTGAACATTTG 57.650 33.333 12.56 4.05 37.54 2.32
2798 2867 9.300681 TCTCATCCAGAATTAAACTGAACATTT 57.699 29.630 12.56 0.00 37.54 2.32
2799 2868 8.868522 TCTCATCCAGAATTAAACTGAACATT 57.131 30.769 12.56 0.00 37.54 2.71
2800 2869 9.118300 GATCTCATCCAGAATTAAACTGAACAT 57.882 33.333 12.56 2.37 37.54 2.71
2801 2870 8.498054 GATCTCATCCAGAATTAAACTGAACA 57.502 34.615 12.56 0.00 37.54 3.18
2827 2896 3.573967 AGAGTTGTTTTGCCCTAACATGG 59.426 43.478 0.00 0.00 35.60 3.66
2828 2897 4.549458 CAGAGTTGTTTTGCCCTAACATG 58.451 43.478 0.00 0.00 35.60 3.21
2829 2898 3.005791 GCAGAGTTGTTTTGCCCTAACAT 59.994 43.478 0.00 0.00 35.60 2.71
2830 2899 2.360801 GCAGAGTTGTTTTGCCCTAACA 59.639 45.455 0.00 0.00 33.92 2.41
2831 2900 2.604614 CGCAGAGTTGTTTTGCCCTAAC 60.605 50.000 0.00 0.00 34.42 2.34
2832 2901 1.606668 CGCAGAGTTGTTTTGCCCTAA 59.393 47.619 0.00 0.00 34.42 2.69
2833 2902 1.234821 CGCAGAGTTGTTTTGCCCTA 58.765 50.000 0.00 0.00 34.42 3.53
2834 2903 2.032981 CGCAGAGTTGTTTTGCCCT 58.967 52.632 0.00 0.00 34.42 5.19
2835 2904 1.661509 GCGCAGAGTTGTTTTGCCC 60.662 57.895 0.30 0.00 34.42 5.36
2836 2905 0.527385 TTGCGCAGAGTTGTTTTGCC 60.527 50.000 11.31 0.00 34.42 4.52
2837 2906 1.190763 CATTGCGCAGAGTTGTTTTGC 59.809 47.619 11.31 0.00 34.58 3.68
2838 2907 2.216940 CACATTGCGCAGAGTTGTTTTG 59.783 45.455 11.31 1.39 0.00 2.44
2839 2908 2.159254 ACACATTGCGCAGAGTTGTTTT 60.159 40.909 11.31 0.64 0.00 2.43
2840 2909 1.405105 ACACATTGCGCAGAGTTGTTT 59.595 42.857 11.31 4.03 0.00 2.83
2841 2910 1.024271 ACACATTGCGCAGAGTTGTT 58.976 45.000 11.31 2.69 0.00 2.83
2842 2911 0.308684 CACACATTGCGCAGAGTTGT 59.691 50.000 11.31 10.72 0.00 3.32
2843 2912 0.587768 TCACACATTGCGCAGAGTTG 59.412 50.000 11.31 10.05 0.00 3.16
2844 2913 1.198408 CATCACACATTGCGCAGAGTT 59.802 47.619 11.31 2.08 0.00 3.01
2845 2914 0.800631 CATCACACATTGCGCAGAGT 59.199 50.000 11.31 10.86 0.00 3.24
2846 2915 0.800631 ACATCACACATTGCGCAGAG 59.199 50.000 11.31 10.11 0.00 3.35
2847 2916 0.798159 GACATCACACATTGCGCAGA 59.202 50.000 11.31 3.22 0.00 4.26
2848 2917 0.800631 AGACATCACACATTGCGCAG 59.199 50.000 11.31 1.78 0.00 5.18
2849 2918 0.798159 GAGACATCACACATTGCGCA 59.202 50.000 5.66 5.66 0.00 6.09
2850 2919 0.798159 TGAGACATCACACATTGCGC 59.202 50.000 0.00 0.00 0.00 6.09
2851 2920 2.223180 CCATGAGACATCACACATTGCG 60.223 50.000 0.00 0.00 38.57 4.85
2852 2921 3.011818 TCCATGAGACATCACACATTGC 58.988 45.455 0.00 0.00 38.57 3.56
2853 2922 4.611310 GTCCATGAGACATCACACATTG 57.389 45.455 0.00 0.00 45.55 2.82
2864 2933 7.454260 AAAAGAATTACCTTGTCCATGAGAC 57.546 36.000 0.00 0.39 46.51 3.36
2902 2971 8.536175 TGTTTATGGAAATTAAAGGGTGATTCC 58.464 33.333 0.00 0.00 37.44 3.01
2904 2973 9.889128 CATGTTTATGGAAATTAAAGGGTGATT 57.111 29.630 0.00 0.00 0.00 2.57
2905 2974 9.265862 TCATGTTTATGGAAATTAAAGGGTGAT 57.734 29.630 0.00 0.00 34.97 3.06
2906 2975 8.657387 TCATGTTTATGGAAATTAAAGGGTGA 57.343 30.769 0.00 0.00 34.97 4.02
2907 2976 9.369904 CTTCATGTTTATGGAAATTAAAGGGTG 57.630 33.333 0.00 0.00 34.97 4.61
2908 2977 9.100197 ACTTCATGTTTATGGAAATTAAAGGGT 57.900 29.630 0.00 0.00 34.97 4.34
2909 2978 9.586435 GACTTCATGTTTATGGAAATTAAAGGG 57.414 33.333 0.00 0.00 34.97 3.95
2928 2997 5.471556 TTTGCATTGAACCATGACTTCAT 57.528 34.783 0.00 0.00 36.96 2.57
2929 2998 4.933505 TTTGCATTGAACCATGACTTCA 57.066 36.364 0.00 0.00 0.00 3.02
2930 2999 5.927689 TGAATTTGCATTGAACCATGACTTC 59.072 36.000 0.00 0.00 0.00 3.01
2931 3000 5.856156 TGAATTTGCATTGAACCATGACTT 58.144 33.333 0.00 0.00 0.00 3.01
2932 3001 5.471556 TGAATTTGCATTGAACCATGACT 57.528 34.783 0.00 0.00 0.00 3.41
2933 3002 6.542574 TTTGAATTTGCATTGAACCATGAC 57.457 33.333 0.00 0.00 0.00 3.06
2934 3003 7.563888 TTTTTGAATTTGCATTGAACCATGA 57.436 28.000 0.00 0.00 0.00 3.07
2935 3004 8.804688 AATTTTTGAATTTGCATTGAACCATG 57.195 26.923 0.00 0.00 0.00 3.66
2936 3005 9.250624 CAAATTTTTGAATTTGCATTGAACCAT 57.749 25.926 10.54 0.00 41.46 3.55
2937 3006 8.630278 CAAATTTTTGAATTTGCATTGAACCA 57.370 26.923 10.54 0.00 41.46 3.67
2946 3015 7.427895 ACGCAGTTAACAAATTTTTGAATTTGC 59.572 29.630 19.11 11.39 45.18 3.68
2947 3016 8.819152 ACGCAGTTAACAAATTTTTGAATTTG 57.181 26.923 18.10 18.10 46.03 2.32
2967 3036 1.871080 AGTTGAGAGACCAAACGCAG 58.129 50.000 0.00 0.00 0.00 5.18
2968 3037 2.325583 AAGTTGAGAGACCAAACGCA 57.674 45.000 0.00 0.00 0.00 5.24
2969 3038 3.128349 TGTAAGTTGAGAGACCAAACGC 58.872 45.455 0.00 0.00 0.00 4.84
2970 3039 5.499047 GTTTGTAAGTTGAGAGACCAAACG 58.501 41.667 0.00 0.00 33.39 3.60
2971 3040 5.292589 TCGTTTGTAAGTTGAGAGACCAAAC 59.707 40.000 0.00 0.00 37.74 2.93
2972 3041 5.421277 TCGTTTGTAAGTTGAGAGACCAAA 58.579 37.500 0.00 0.00 0.00 3.28
2973 3042 5.013568 TCGTTTGTAAGTTGAGAGACCAA 57.986 39.130 0.00 0.00 0.00 3.67
2974 3043 4.659111 TCGTTTGTAAGTTGAGAGACCA 57.341 40.909 0.00 0.00 0.00 4.02
2975 3044 5.694910 TGAATCGTTTGTAAGTTGAGAGACC 59.305 40.000 0.00 0.00 0.00 3.85
2976 3045 6.764877 TGAATCGTTTGTAAGTTGAGAGAC 57.235 37.500 0.00 0.00 0.00 3.36
2977 3046 7.151976 TGATGAATCGTTTGTAAGTTGAGAGA 58.848 34.615 0.00 0.00 0.00 3.10
2978 3047 7.351414 TGATGAATCGTTTGTAAGTTGAGAG 57.649 36.000 0.00 0.00 0.00 3.20
2979 3048 7.905604 ATGATGAATCGTTTGTAAGTTGAGA 57.094 32.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.