Multiple sequence alignment - TraesCS6D01G329400

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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 TraesCS6D01G329400 chr6D 100.000 3116 0 0 1 3116 433546631 433549746 0.000000e+00 5755.0
1 TraesCS6D01G329400 chr6D 98.524 3116 44 2 1 3116 433561757 433564870 0.000000e+00 5498.0
2 TraesCS6D01G329400 chr6D 98.486 2840 41 2 1 2839 433567458 433570296 0.000000e+00 5005.0
3 TraesCS6D01G329400 chr6D 95.791 2162 88 2 1 2160 433538225 433540385 0.000000e+00 3485.0
4 TraesCS6D01G329400 chr6A 93.900 3131 162 14 3 3113 579753017 579756138 0.000000e+00 4697.0
5 TraesCS6D01G329400 chr6A 93.774 3116 166 8 3 3097 579516134 579519242 0.000000e+00 4654.0
6 TraesCS6D01G329400 chr6A 94.709 2854 122 8 3 2839 579758038 579760879 0.000000e+00 4407.0
7 TraesCS6D01G329400 chr6B 93.818 2831 142 11 3 2813 655052471 655055288 0.000000e+00 4228.0
8 TraesCS6D01G329400 chr6B 93.323 2621 152 5 3 2600 654853090 654855710 0.000000e+00 3849.0
9 TraesCS6D01G329400 chr6B 93.171 2621 156 5 3 2600 654877187 654879807 0.000000e+00 3827.0
10 TraesCS6D01G329400 chr6B 93.163 2618 159 4 3 2600 654887310 654889927 0.000000e+00 3825.0
11 TraesCS6D01G329400 chr6B 93.848 2227 119 3 548 2756 654917154 654919380 0.000000e+00 3338.0
12 TraesCS6D01G329400 chr6B 91.611 453 27 6 2599 3051 654886012 654886453 1.590000e-172 616.0
13 TraesCS6D01G329400 chr6B 91.611 453 27 5 2599 3051 654902676 654903117 1.590000e-172 616.0
14 TraesCS6D01G329400 chr6B 91.530 366 28 3 2750 3113 654949745 654950109 4.640000e-138 501.0
15 TraesCS6D01G329400 chr6B 93.651 63 4 0 2208 2270 653787437 653787375 9.200000e-16 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 TraesCS6D01G329400 chr6D 433546631 433549746 3115 False 5755.0 5755 100.0000 1 3116 1 chr6D.!!$F2 3115
1 TraesCS6D01G329400 chr6D 433561757 433570296 8539 False 5251.5 5498 98.5050 1 3116 2 chr6D.!!$F3 3115
2 TraesCS6D01G329400 chr6D 433538225 433540385 2160 False 3485.0 3485 95.7910 1 2160 1 chr6D.!!$F1 2159
3 TraesCS6D01G329400 chr6A 579516134 579519242 3108 False 4654.0 4654 93.7740 3 3097 1 chr6A.!!$F1 3094
4 TraesCS6D01G329400 chr6A 579753017 579760879 7862 False 4552.0 4697 94.3045 3 3113 2 chr6A.!!$F2 3110
5 TraesCS6D01G329400 chr6B 655052471 655055288 2817 False 4228.0 4228 93.8180 3 2813 1 chr6B.!!$F6 2810
6 TraesCS6D01G329400 chr6B 654853090 654855710 2620 False 3849.0 3849 93.3230 3 2600 1 chr6B.!!$F1 2597
7 TraesCS6D01G329400 chr6B 654877187 654879807 2620 False 3827.0 3827 93.1710 3 2600 1 chr6B.!!$F2 2597
8 TraesCS6D01G329400 chr6B 654917154 654919380 2226 False 3338.0 3338 93.8480 548 2756 1 chr6B.!!$F4 2208
9 TraesCS6D01G329400 chr6B 654886012 654889927 3915 False 2220.5 3825 92.3870 3 3051 2 chr6B.!!$F7 3048

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
254 1555 3.495434 ACCATTTACGTGTCTGGGAAA 57.505 42.857 14.23 0.0 32.89 3.13 F
1067 7386 1.819288 CTTCTGCAGTTCGGTCCTAGA 59.181 52.381 14.67 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1126 7445 0.039256 TTGTACACACGGCCGTACTC 60.039 55.0 33.7 19.13 39.0 2.59 R
2874 14942 0.312102 GTTTTGCAGGTGAGGTGAGC 59.688 55.0 0.0 0.00 0.0 4.26 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
254 1555 3.495434 ACCATTTACGTGTCTGGGAAA 57.505 42.857 14.23 0.00 32.89 3.13
260 1561 7.996644 ACCATTTACGTGTCTGGGAAATATATT 59.003 33.333 14.23 0.00 32.89 1.28
466 6783 3.694566 GCGGTCACATCTAATCCCTTTTT 59.305 43.478 0.00 0.00 0.00 1.94
470 6787 6.992715 CGGTCACATCTAATCCCTTTTTATCT 59.007 38.462 0.00 0.00 0.00 1.98
896 7215 5.244626 CCATCTCAATCCCCCATATTCAAAC 59.755 44.000 0.00 0.00 0.00 2.93
1067 7386 1.819288 CTTCTGCAGTTCGGTCCTAGA 59.181 52.381 14.67 0.00 0.00 2.43
1126 7445 1.153489 CACGAGAGCTGGATGGTGG 60.153 63.158 0.00 0.00 0.00 4.61
1790 8110 0.037419 GGTGCCGCAACCATCAAAAT 60.037 50.000 0.00 0.00 40.22 1.82
2427 14478 7.901029 TGGTGGAGTTGATTTGCAAATAAATA 58.099 30.769 24.15 8.90 38.44 1.40
2485 14552 0.999712 GATGGACTTTTCCCTCCCCA 59.000 55.000 0.00 0.00 42.01 4.96
2509 14576 1.141881 CCGTCTTCATGGTCCCTCG 59.858 63.158 0.00 0.00 0.00 4.63
2527 14594 1.853319 GACGCTCGACAACAACCTG 59.147 57.895 0.00 0.00 0.00 4.00
2784 14851 7.434897 TGTGACTATTGTTTCATTTTGCACTTC 59.565 33.333 0.00 0.00 0.00 3.01
2843 14911 6.755542 AAAAATGATTTGGTCCCAAGGTAA 57.244 33.333 0.00 0.00 37.24 2.85
2844 14912 6.950860 AAAATGATTTGGTCCCAAGGTAAT 57.049 33.333 0.00 0.00 37.24 1.89
2845 14913 6.544928 AAATGATTTGGTCCCAAGGTAATC 57.455 37.500 0.00 0.89 37.24 1.75
2846 14914 4.666412 TGATTTGGTCCCAAGGTAATCA 57.334 40.909 6.94 6.94 37.24 2.57
2847 14915 5.205517 TGATTTGGTCCCAAGGTAATCAT 57.794 39.130 6.94 0.00 37.24 2.45
2848 14916 5.200483 TGATTTGGTCCCAAGGTAATCATC 58.800 41.667 6.94 3.46 37.24 2.92
2849 14917 4.946160 TTTGGTCCCAAGGTAATCATCT 57.054 40.909 0.00 0.00 37.24 2.90
2850 14918 6.159575 TGATTTGGTCCCAAGGTAATCATCTA 59.840 38.462 6.94 0.00 37.24 1.98
2851 14919 5.367945 TTGGTCCCAAGGTAATCATCTAC 57.632 43.478 0.00 0.00 0.00 2.59
2852 14920 4.367166 TGGTCCCAAGGTAATCATCTACA 58.633 43.478 0.00 0.00 0.00 2.74
2853 14921 4.408921 TGGTCCCAAGGTAATCATCTACAG 59.591 45.833 0.00 0.00 0.00 2.74
2854 14922 4.654262 GGTCCCAAGGTAATCATCTACAGA 59.346 45.833 0.00 0.00 0.00 3.41
2855 14923 5.130477 GGTCCCAAGGTAATCATCTACAGAA 59.870 44.000 0.00 0.00 0.00 3.02
2856 14924 6.352737 GGTCCCAAGGTAATCATCTACAGAAA 60.353 42.308 0.00 0.00 0.00 2.52
2857 14925 6.763610 GTCCCAAGGTAATCATCTACAGAAAG 59.236 42.308 0.00 0.00 0.00 2.62
2858 14926 5.529060 CCCAAGGTAATCATCTACAGAAAGC 59.471 44.000 0.00 0.00 0.00 3.51
2859 14927 6.115446 CCAAGGTAATCATCTACAGAAAGCA 58.885 40.000 0.00 0.00 0.00 3.91
2860 14928 6.599244 CCAAGGTAATCATCTACAGAAAGCAA 59.401 38.462 0.00 0.00 0.00 3.91
2861 14929 7.414540 CCAAGGTAATCATCTACAGAAAGCAAC 60.415 40.741 0.00 0.00 0.00 4.17
2862 14930 6.951971 AGGTAATCATCTACAGAAAGCAACT 58.048 36.000 0.00 0.00 0.00 3.16
2863 14931 7.398024 AGGTAATCATCTACAGAAAGCAACTT 58.602 34.615 0.00 0.00 0.00 2.66
2864 14932 7.550906 AGGTAATCATCTACAGAAAGCAACTTC 59.449 37.037 0.00 0.00 0.00 3.01
2865 14933 7.334421 GGTAATCATCTACAGAAAGCAACTTCA 59.666 37.037 0.00 0.00 0.00 3.02
2866 14934 7.750229 AATCATCTACAGAAAGCAACTTCAA 57.250 32.000 0.00 0.00 0.00 2.69
2867 14935 7.934855 ATCATCTACAGAAAGCAACTTCAAT 57.065 32.000 0.00 0.00 0.00 2.57
2868 14936 7.369803 TCATCTACAGAAAGCAACTTCAATC 57.630 36.000 0.00 0.00 0.00 2.67
2869 14937 6.936335 TCATCTACAGAAAGCAACTTCAATCA 59.064 34.615 0.00 0.00 0.00 2.57
2870 14938 7.445096 TCATCTACAGAAAGCAACTTCAATCAA 59.555 33.333 0.00 0.00 0.00 2.57
2871 14939 7.566760 TCTACAGAAAGCAACTTCAATCAAA 57.433 32.000 0.00 0.00 0.00 2.69
2872 14940 7.642669 TCTACAGAAAGCAACTTCAATCAAAG 58.357 34.615 0.00 0.00 0.00 2.77
2873 14941 5.594926 ACAGAAAGCAACTTCAATCAAAGG 58.405 37.500 0.00 0.00 0.00 3.11
2874 14942 4.986659 CAGAAAGCAACTTCAATCAAAGGG 59.013 41.667 0.00 0.00 0.00 3.95
2875 14943 3.391506 AAGCAACTTCAATCAAAGGGC 57.608 42.857 0.00 0.00 33.46 5.19
2876 14944 2.601905 AGCAACTTCAATCAAAGGGCT 58.398 42.857 0.00 0.00 36.67 5.19
2877 14945 2.560105 AGCAACTTCAATCAAAGGGCTC 59.440 45.455 0.00 0.00 36.75 4.70
2878 14946 2.297033 GCAACTTCAATCAAAGGGCTCA 59.703 45.455 0.00 0.00 31.73 4.26
2879 14947 3.858503 GCAACTTCAATCAAAGGGCTCAC 60.859 47.826 0.00 0.00 31.73 3.51
2880 14948 2.519013 ACTTCAATCAAAGGGCTCACC 58.481 47.619 0.00 0.00 40.67 4.02
2889 14957 3.640407 GGGCTCACCTCACCTGCA 61.640 66.667 0.00 0.00 35.85 4.41
2890 14958 2.431683 GGCTCACCTCACCTGCAA 59.568 61.111 0.00 0.00 0.00 4.08
2891 14959 1.228245 GGCTCACCTCACCTGCAAA 60.228 57.895 0.00 0.00 0.00 3.68
2892 14960 0.823356 GGCTCACCTCACCTGCAAAA 60.823 55.000 0.00 0.00 0.00 2.44
2893 14961 0.312102 GCTCACCTCACCTGCAAAAC 59.688 55.000 0.00 0.00 0.00 2.43
2894 14962 0.588252 CTCACCTCACCTGCAAAACG 59.412 55.000 0.00 0.00 0.00 3.60
2895 14963 0.817634 TCACCTCACCTGCAAAACGG 60.818 55.000 0.00 0.00 0.00 4.44
2896 14964 2.193536 ACCTCACCTGCAAAACGGC 61.194 57.895 0.00 0.00 0.00 5.68
2897 14965 2.644992 CTCACCTGCAAAACGGCC 59.355 61.111 0.00 0.00 0.00 6.13
2898 14966 3.254014 CTCACCTGCAAAACGGCCG 62.254 63.158 26.86 26.86 0.00 6.13
2899 14967 4.341502 CACCTGCAAAACGGCCGG 62.342 66.667 31.76 12.94 43.06 6.13
2900 14968 4.572571 ACCTGCAAAACGGCCGGA 62.573 61.111 31.76 4.55 40.22 5.14
2901 14969 3.291383 CCTGCAAAACGGCCGGAA 61.291 61.111 31.76 4.58 40.22 4.30
2902 14970 2.050442 CTGCAAAACGGCCGGAAC 60.050 61.111 31.76 14.32 0.00 3.62
2920 14988 5.160699 GGAACGGGTTCGATTAATTAACC 57.839 43.478 18.66 18.66 41.62 2.85
2921 14989 4.635324 GGAACGGGTTCGATTAATTAACCA 59.365 41.667 24.14 0.00 43.68 3.67
2922 14990 5.447683 GGAACGGGTTCGATTAATTAACCAC 60.448 44.000 24.14 16.55 43.68 4.16
2923 14991 3.618150 ACGGGTTCGATTAATTAACCACG 59.382 43.478 24.14 23.99 43.68 4.94
2924 14992 3.864583 CGGGTTCGATTAATTAACCACGA 59.135 43.478 24.14 15.15 43.68 4.35
2925 14993 4.259930 CGGGTTCGATTAATTAACCACGAC 60.260 45.833 24.14 12.75 43.68 4.34
2926 14994 4.630940 GGGTTCGATTAATTAACCACGACA 59.369 41.667 24.14 10.20 43.68 4.35
2927 14995 5.220529 GGGTTCGATTAATTAACCACGACAG 60.221 44.000 24.14 0.30 43.68 3.51
2928 14996 5.349543 GGTTCGATTAATTAACCACGACAGT 59.650 40.000 20.61 0.00 41.89 3.55
2929 14997 6.531240 GGTTCGATTAATTAACCACGACAGTA 59.469 38.462 20.61 6.46 41.89 2.74
2930 14998 7.223387 GGTTCGATTAATTAACCACGACAGTAT 59.777 37.037 20.61 0.00 41.89 2.12
2931 14999 9.236691 GTTCGATTAATTAACCACGACAGTATA 57.763 33.333 17.36 5.73 0.00 1.47
2932 15000 9.454585 TTCGATTAATTAACCACGACAGTATAG 57.545 33.333 17.36 0.00 0.00 1.31
2933 15001 8.623903 TCGATTAATTAACCACGACAGTATAGT 58.376 33.333 15.15 0.00 0.00 2.12
2934 15002 8.688184 CGATTAATTAACCACGACAGTATAGTG 58.312 37.037 6.00 6.00 35.79 2.74
2935 15003 7.760131 TTAATTAACCACGACAGTATAGTGC 57.240 36.000 7.51 0.34 34.79 4.40
2936 15004 5.593679 ATTAACCACGACAGTATAGTGCT 57.406 39.130 7.51 0.00 34.79 4.40
2937 15005 2.941453 ACCACGACAGTATAGTGCTG 57.059 50.000 7.51 3.08 39.67 4.41
2938 15006 2.443416 ACCACGACAGTATAGTGCTGA 58.557 47.619 7.51 0.00 37.40 4.26
2939 15007 2.823747 ACCACGACAGTATAGTGCTGAA 59.176 45.455 7.51 0.00 37.40 3.02
2940 15008 3.119459 ACCACGACAGTATAGTGCTGAAG 60.119 47.826 7.51 0.00 37.40 3.02
2941 15009 3.439293 CACGACAGTATAGTGCTGAAGG 58.561 50.000 7.51 0.00 37.40 3.46
2942 15010 3.128764 CACGACAGTATAGTGCTGAAGGA 59.871 47.826 7.51 0.00 37.40 3.36
2943 15011 3.378742 ACGACAGTATAGTGCTGAAGGAG 59.621 47.826 7.51 0.00 37.40 3.69
2944 15012 3.628032 CGACAGTATAGTGCTGAAGGAGA 59.372 47.826 7.51 0.00 37.40 3.71
2945 15013 4.096532 CGACAGTATAGTGCTGAAGGAGAA 59.903 45.833 7.51 0.00 37.40 2.87
2946 15014 5.587289 GACAGTATAGTGCTGAAGGAGAAG 58.413 45.833 7.51 0.00 37.40 2.85
2947 15015 5.265191 ACAGTATAGTGCTGAAGGAGAAGA 58.735 41.667 7.51 0.00 37.40 2.87
2948 15016 5.896678 ACAGTATAGTGCTGAAGGAGAAGAT 59.103 40.000 7.51 0.00 37.40 2.40
2949 15017 6.183360 ACAGTATAGTGCTGAAGGAGAAGATG 60.183 42.308 7.51 0.00 37.40 2.90
2950 15018 6.040278 CAGTATAGTGCTGAAGGAGAAGATGA 59.960 42.308 0.00 0.00 36.12 2.92
2951 15019 3.608316 AGTGCTGAAGGAGAAGATGAC 57.392 47.619 0.00 0.00 0.00 3.06
2952 15020 2.902486 AGTGCTGAAGGAGAAGATGACA 59.098 45.455 0.00 0.00 0.00 3.58
2953 15021 3.518705 AGTGCTGAAGGAGAAGATGACAT 59.481 43.478 0.00 0.00 0.00 3.06
2954 15022 3.622163 GTGCTGAAGGAGAAGATGACATG 59.378 47.826 0.00 0.00 0.00 3.21
2955 15023 3.262660 TGCTGAAGGAGAAGATGACATGT 59.737 43.478 0.00 0.00 0.00 3.21
2956 15024 4.467438 TGCTGAAGGAGAAGATGACATGTA 59.533 41.667 0.00 0.00 0.00 2.29
2957 15025 5.049167 GCTGAAGGAGAAGATGACATGTAG 58.951 45.833 0.00 0.00 0.00 2.74
2958 15026 5.163468 GCTGAAGGAGAAGATGACATGTAGA 60.163 44.000 0.00 0.00 0.00 2.59
2959 15027 6.462552 TGAAGGAGAAGATGACATGTAGAG 57.537 41.667 0.00 0.00 0.00 2.43
2960 15028 6.190587 TGAAGGAGAAGATGACATGTAGAGA 58.809 40.000 0.00 0.00 0.00 3.10
2961 15029 6.320926 TGAAGGAGAAGATGACATGTAGAGAG 59.679 42.308 0.00 0.00 0.00 3.20
2962 15030 6.012337 AGGAGAAGATGACATGTAGAGAGA 57.988 41.667 0.00 0.00 0.00 3.10
2963 15031 6.064060 AGGAGAAGATGACATGTAGAGAGAG 58.936 44.000 0.00 0.00 0.00 3.20
2964 15032 6.061441 GGAGAAGATGACATGTAGAGAGAGA 58.939 44.000 0.00 0.00 0.00 3.10
2965 15033 6.716628 GGAGAAGATGACATGTAGAGAGAGAT 59.283 42.308 0.00 0.00 0.00 2.75
2966 15034 7.308770 GGAGAAGATGACATGTAGAGAGAGATG 60.309 44.444 0.00 0.00 0.00 2.90
2967 15035 7.289310 AGAAGATGACATGTAGAGAGAGATGA 58.711 38.462 0.00 0.00 0.00 2.92
2968 15036 7.446319 AGAAGATGACATGTAGAGAGAGATGAG 59.554 40.741 0.00 0.00 0.00 2.90
2969 15037 6.840527 AGATGACATGTAGAGAGAGATGAGA 58.159 40.000 0.00 0.00 0.00 3.27
2970 15038 7.464273 AGATGACATGTAGAGAGAGATGAGAT 58.536 38.462 0.00 0.00 0.00 2.75
2971 15039 6.880942 TGACATGTAGAGAGAGATGAGATG 57.119 41.667 0.00 0.00 0.00 2.90
2972 15040 5.769162 TGACATGTAGAGAGAGATGAGATGG 59.231 44.000 0.00 0.00 0.00 3.51
2973 15041 5.704354 ACATGTAGAGAGAGATGAGATGGT 58.296 41.667 0.00 0.00 0.00 3.55
2974 15042 5.769662 ACATGTAGAGAGAGATGAGATGGTC 59.230 44.000 0.00 0.00 0.00 4.02
2975 15043 5.379706 TGTAGAGAGAGATGAGATGGTCA 57.620 43.478 0.00 0.00 40.38 4.02
2976 15044 5.375773 TGTAGAGAGAGATGAGATGGTCAG 58.624 45.833 0.00 0.00 39.07 3.51
2977 15045 4.524802 AGAGAGAGATGAGATGGTCAGT 57.475 45.455 0.00 0.00 39.07 3.41
2978 15046 4.209538 AGAGAGAGATGAGATGGTCAGTG 58.790 47.826 0.00 0.00 39.07 3.66
2979 15047 4.079844 AGAGAGAGATGAGATGGTCAGTGA 60.080 45.833 0.00 0.00 39.07 3.41
2980 15048 4.209538 AGAGAGATGAGATGGTCAGTGAG 58.790 47.826 0.00 0.00 39.07 3.51
2981 15049 2.694628 AGAGATGAGATGGTCAGTGAGC 59.305 50.000 15.47 15.47 39.07 4.26
2982 15050 2.694628 GAGATGAGATGGTCAGTGAGCT 59.305 50.000 22.08 8.69 39.07 4.09
2983 15051 3.106054 AGATGAGATGGTCAGTGAGCTT 58.894 45.455 22.08 16.31 39.07 3.74
2984 15052 3.518705 AGATGAGATGGTCAGTGAGCTTT 59.481 43.478 22.08 10.50 39.07 3.51
2985 15053 4.713814 AGATGAGATGGTCAGTGAGCTTTA 59.286 41.667 22.08 3.63 39.07 1.85
2986 15054 4.890158 TGAGATGGTCAGTGAGCTTTAA 57.110 40.909 22.08 3.26 0.00 1.52
2987 15055 5.426689 TGAGATGGTCAGTGAGCTTTAAT 57.573 39.130 22.08 8.12 0.00 1.40
2988 15056 5.809001 TGAGATGGTCAGTGAGCTTTAATT 58.191 37.500 22.08 4.93 0.00 1.40
2989 15057 6.240894 TGAGATGGTCAGTGAGCTTTAATTT 58.759 36.000 22.08 3.78 0.00 1.82
2990 15058 6.716628 TGAGATGGTCAGTGAGCTTTAATTTT 59.283 34.615 22.08 1.93 0.00 1.82
2991 15059 7.094634 TGAGATGGTCAGTGAGCTTTAATTTTC 60.095 37.037 22.08 10.05 0.00 2.29
2992 15060 6.944862 AGATGGTCAGTGAGCTTTAATTTTCT 59.055 34.615 22.08 5.85 0.00 2.52
2993 15061 8.103305 AGATGGTCAGTGAGCTTTAATTTTCTA 58.897 33.333 22.08 0.00 0.00 2.10
2994 15062 7.672983 TGGTCAGTGAGCTTTAATTTTCTAG 57.327 36.000 22.08 0.00 0.00 2.43
2995 15063 7.224297 TGGTCAGTGAGCTTTAATTTTCTAGT 58.776 34.615 22.08 0.00 0.00 2.57
2996 15064 7.719633 TGGTCAGTGAGCTTTAATTTTCTAGTT 59.280 33.333 22.08 0.00 0.00 2.24
2997 15065 9.216117 GGTCAGTGAGCTTTAATTTTCTAGTTA 57.784 33.333 15.08 0.00 0.00 2.24
2999 15067 9.998106 TCAGTGAGCTTTAATTTTCTAGTTAGT 57.002 29.630 0.00 0.00 0.00 2.24
3034 15102 9.586435 AGGTTTCATTTTCTTTACTTTTGTCAG 57.414 29.630 0.00 0.00 0.00 3.51
3035 15103 9.366216 GGTTTCATTTTCTTTACTTTTGTCAGT 57.634 29.630 0.00 0.00 0.00 3.41
3045 15113 9.607988 TCTTTACTTTTGTCAGTACTTTGATGA 57.392 29.630 0.00 0.00 0.00 2.92
3049 15117 8.225603 ACTTTTGTCAGTACTTTGATGATTGT 57.774 30.769 0.00 0.00 0.00 2.71
3050 15118 8.686334 ACTTTTGTCAGTACTTTGATGATTGTT 58.314 29.630 0.00 0.00 0.00 2.83
3054 15122 9.500785 TTGTCAGTACTTTGATGATTGTTATGA 57.499 29.630 0.00 0.00 0.00 2.15
3055 15123 9.500785 TGTCAGTACTTTGATGATTGTTATGAA 57.499 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 1377 6.398095 TGAGTGATGGTATGTAACACTTCAG 58.602 40.000 0.00 0.00 41.01 3.02
166 1466 1.698506 TTTCTGGCGGACATGGTTTT 58.301 45.000 0.00 0.00 0.00 2.43
260 1561 8.041919 TCCATGAATTAATATTAATACCGCCGA 58.958 33.333 18.75 9.35 33.25 5.54
470 6787 8.826710 CATCGATAAAAATTCTTGTAGCCTACA 58.173 33.333 0.00 0.00 36.79 2.74
530 6847 4.554200 CGTAACACGAAGTCTAAGCTTCTC 59.446 45.833 0.00 0.00 46.05 2.87
538 6855 7.642071 AATTTTAAGCGTAACACGAAGTCTA 57.358 32.000 2.35 0.00 46.05 2.59
833 7152 1.964223 AGTACATCTGGTAGGCGGATG 59.036 52.381 0.00 0.00 41.56 3.51
896 7215 9.657419 TCTTATATAGTTGCATGGATGTATGTG 57.343 33.333 0.00 0.00 0.00 3.21
1126 7445 0.039256 TTGTACACACGGCCGTACTC 60.039 55.000 33.70 19.13 39.00 2.59
1722 8042 1.270465 GCCGCGGTATATGGGTAGTTT 60.270 52.381 28.70 0.00 0.00 2.66
1790 8110 2.763039 TGGCTGGAACATCCTCATAGA 58.237 47.619 0.00 0.00 46.24 1.98
2345 14396 9.690434 CGTGAAAATAAATACTACTCAAAGAGC 57.310 33.333 0.00 0.00 32.04 4.09
2427 14478 3.053095 AGGTTCCATTCTCAGGATGCAAT 60.053 43.478 0.00 0.00 34.56 3.56
2433 14484 2.103373 CTCGAGGTTCCATTCTCAGGA 58.897 52.381 3.91 0.00 0.00 3.86
2485 14552 2.620627 GGGACCATGAAGACGGGAATTT 60.621 50.000 0.00 0.00 0.00 1.82
2509 14576 1.853319 CAGGTTGTTGTCGAGCGTC 59.147 57.895 0.00 0.00 0.00 5.19
2527 14594 1.610886 GGTGTTGTAGTTGGGGAGAGC 60.611 57.143 0.00 0.00 0.00 4.09
2612 14679 7.092623 ACCCCCACGATGCTAATCATAATATTA 60.093 37.037 0.00 0.00 35.05 0.98
2773 14840 9.905713 TGTTCTATAGATTAGGAAGTGCAAAAT 57.094 29.630 2.58 0.00 0.00 1.82
2784 14851 8.258007 TGTGGTGAAGTTGTTCTATAGATTAGG 58.742 37.037 2.58 0.00 33.38 2.69
2795 14862 7.681939 TCCTTATTATGTGGTGAAGTTGTTC 57.318 36.000 0.00 0.00 0.00 3.18
2839 14907 7.334421 TGAAGTTGCTTTCTGTAGATGATTACC 59.666 37.037 0.00 0.00 0.00 2.85
2840 14908 8.256611 TGAAGTTGCTTTCTGTAGATGATTAC 57.743 34.615 0.00 0.00 0.00 1.89
2841 14909 8.846943 TTGAAGTTGCTTTCTGTAGATGATTA 57.153 30.769 0.00 0.00 0.00 1.75
2842 14910 7.750229 TTGAAGTTGCTTTCTGTAGATGATT 57.250 32.000 0.00 0.00 0.00 2.57
2843 14911 7.609146 TGATTGAAGTTGCTTTCTGTAGATGAT 59.391 33.333 0.00 0.00 0.00 2.45
2844 14912 6.936335 TGATTGAAGTTGCTTTCTGTAGATGA 59.064 34.615 0.00 0.00 0.00 2.92
2845 14913 7.137490 TGATTGAAGTTGCTTTCTGTAGATG 57.863 36.000 0.00 0.00 0.00 2.90
2846 14914 7.750229 TTGATTGAAGTTGCTTTCTGTAGAT 57.250 32.000 0.00 0.00 0.00 1.98
2847 14915 7.255242 CCTTTGATTGAAGTTGCTTTCTGTAGA 60.255 37.037 0.00 0.00 0.00 2.59
2848 14916 6.860023 CCTTTGATTGAAGTTGCTTTCTGTAG 59.140 38.462 0.00 0.00 0.00 2.74
2849 14917 6.239008 CCCTTTGATTGAAGTTGCTTTCTGTA 60.239 38.462 0.00 0.00 0.00 2.74
2850 14918 5.452356 CCCTTTGATTGAAGTTGCTTTCTGT 60.452 40.000 0.00 0.00 0.00 3.41
2851 14919 4.986659 CCCTTTGATTGAAGTTGCTTTCTG 59.013 41.667 0.00 0.00 0.00 3.02
2852 14920 4.502087 GCCCTTTGATTGAAGTTGCTTTCT 60.502 41.667 0.00 0.00 0.00 2.52
2853 14921 3.742882 GCCCTTTGATTGAAGTTGCTTTC 59.257 43.478 0.00 0.00 0.00 2.62
2854 14922 3.389002 AGCCCTTTGATTGAAGTTGCTTT 59.611 39.130 0.00 0.00 32.33 3.51
2855 14923 2.967887 AGCCCTTTGATTGAAGTTGCTT 59.032 40.909 0.00 0.00 32.33 3.91
2856 14924 2.560105 GAGCCCTTTGATTGAAGTTGCT 59.440 45.455 0.00 0.00 36.29 3.91
2857 14925 2.297033 TGAGCCCTTTGATTGAAGTTGC 59.703 45.455 0.00 0.00 0.00 4.17
2858 14926 3.305608 GGTGAGCCCTTTGATTGAAGTTG 60.306 47.826 0.00 0.00 0.00 3.16
2859 14927 2.893489 GGTGAGCCCTTTGATTGAAGTT 59.107 45.455 0.00 0.00 0.00 2.66
2860 14928 2.108952 AGGTGAGCCCTTTGATTGAAGT 59.891 45.455 0.00 0.00 42.73 3.01
2861 14929 2.751806 GAGGTGAGCCCTTTGATTGAAG 59.248 50.000 0.00 0.00 46.51 3.02
2862 14930 2.108075 TGAGGTGAGCCCTTTGATTGAA 59.892 45.455 0.00 0.00 46.51 2.69
2863 14931 1.704628 TGAGGTGAGCCCTTTGATTGA 59.295 47.619 0.00 0.00 46.51 2.57
2864 14932 1.815003 GTGAGGTGAGCCCTTTGATTG 59.185 52.381 0.00 0.00 46.51 2.67
2865 14933 1.272147 GGTGAGGTGAGCCCTTTGATT 60.272 52.381 0.00 0.00 46.51 2.57
2866 14934 0.329596 GGTGAGGTGAGCCCTTTGAT 59.670 55.000 0.00 0.00 46.51 2.57
2867 14935 0.768221 AGGTGAGGTGAGCCCTTTGA 60.768 55.000 0.00 0.00 46.51 2.69
2868 14936 0.607489 CAGGTGAGGTGAGCCCTTTG 60.607 60.000 0.00 0.00 46.51 2.77
2869 14937 1.763770 CAGGTGAGGTGAGCCCTTT 59.236 57.895 0.00 0.00 46.51 3.11
2870 14938 2.900106 GCAGGTGAGGTGAGCCCTT 61.900 63.158 0.00 0.00 46.51 3.95
2872 14940 2.697147 TTTGCAGGTGAGGTGAGCCC 62.697 60.000 0.00 0.00 34.57 5.19
2873 14941 0.823356 TTTTGCAGGTGAGGTGAGCC 60.823 55.000 0.00 0.00 0.00 4.70
2874 14942 0.312102 GTTTTGCAGGTGAGGTGAGC 59.688 55.000 0.00 0.00 0.00 4.26
2875 14943 0.588252 CGTTTTGCAGGTGAGGTGAG 59.412 55.000 0.00 0.00 0.00 3.51
2876 14944 0.817634 CCGTTTTGCAGGTGAGGTGA 60.818 55.000 0.00 0.00 0.00 4.02
2877 14945 1.654220 CCGTTTTGCAGGTGAGGTG 59.346 57.895 0.00 0.00 0.00 4.00
2878 14946 2.193536 GCCGTTTTGCAGGTGAGGT 61.194 57.895 0.00 0.00 0.00 3.85
2879 14947 2.644992 GCCGTTTTGCAGGTGAGG 59.355 61.111 0.00 0.00 0.00 3.86
2880 14948 2.644992 GGCCGTTTTGCAGGTGAG 59.355 61.111 0.00 0.00 0.00 3.51
2881 14949 3.283684 CGGCCGTTTTGCAGGTGA 61.284 61.111 19.50 0.00 0.00 4.02
2882 14950 4.341502 CCGGCCGTTTTGCAGGTG 62.342 66.667 26.12 0.00 41.09 4.00
2883 14951 4.572571 TCCGGCCGTTTTGCAGGT 62.573 61.111 26.12 0.00 45.47 4.00
2884 14952 3.291383 TTCCGGCCGTTTTGCAGG 61.291 61.111 26.12 5.84 46.48 4.85
2885 14953 2.050442 GTTCCGGCCGTTTTGCAG 60.050 61.111 26.12 6.69 0.00 4.41
2886 14954 3.955101 CGTTCCGGCCGTTTTGCA 61.955 61.111 26.12 0.00 0.00 4.08
2887 14955 4.693525 CCGTTCCGGCCGTTTTGC 62.694 66.667 26.12 8.33 41.17 3.68
2888 14956 4.032987 CCCGTTCCGGCCGTTTTG 62.033 66.667 26.12 8.83 46.86 2.44
2889 14957 4.567488 ACCCGTTCCGGCCGTTTT 62.567 61.111 26.12 0.00 46.86 2.43
2890 14958 4.567488 AACCCGTTCCGGCCGTTT 62.567 61.111 26.12 2.08 46.86 3.60
2891 14959 4.994471 GAACCCGTTCCGGCCGTT 62.994 66.667 26.12 9.82 46.86 4.44
2894 14962 2.576643 TAATCGAACCCGTTCCGGCC 62.577 60.000 0.00 0.00 46.86 6.13
2895 14963 0.740516 TTAATCGAACCCGTTCCGGC 60.741 55.000 0.00 0.00 46.86 6.13
2897 14965 4.260334 GGTTAATTAATCGAACCCGTTCCG 60.260 45.833 16.38 0.00 37.28 4.30
2898 14966 4.635324 TGGTTAATTAATCGAACCCGTTCC 59.365 41.667 21.21 4.83 41.69 3.62
2899 14967 5.562917 GTGGTTAATTAATCGAACCCGTTC 58.437 41.667 21.21 10.93 41.69 3.95
2900 14968 4.093261 CGTGGTTAATTAATCGAACCCGTT 59.907 41.667 21.21 0.00 41.69 4.44
2901 14969 3.618150 CGTGGTTAATTAATCGAACCCGT 59.382 43.478 21.21 0.00 41.69 5.28
2902 14970 3.864583 TCGTGGTTAATTAATCGAACCCG 59.135 43.478 21.21 21.40 41.69 5.28
2903 14971 4.630940 TGTCGTGGTTAATTAATCGAACCC 59.369 41.667 21.21 14.66 41.69 4.11
2904 14972 5.349543 ACTGTCGTGGTTAATTAATCGAACC 59.650 40.000 18.87 18.87 42.54 3.62
2905 14973 6.399204 ACTGTCGTGGTTAATTAATCGAAC 57.601 37.500 17.70 10.64 0.00 3.95
2906 14974 9.454585 CTATACTGTCGTGGTTAATTAATCGAA 57.545 33.333 17.70 8.58 0.00 3.71
2907 14975 8.623903 ACTATACTGTCGTGGTTAATTAATCGA 58.376 33.333 14.40 14.40 0.00 3.59
2908 14976 8.688184 CACTATACTGTCGTGGTTAATTAATCG 58.312 37.037 0.31 7.45 0.00 3.34
2909 14977 8.485591 GCACTATACTGTCGTGGTTAATTAATC 58.514 37.037 0.31 0.79 0.00 1.75
2910 14978 8.202137 AGCACTATACTGTCGTGGTTAATTAAT 58.798 33.333 0.31 0.00 36.09 1.40
2911 14979 7.490079 CAGCACTATACTGTCGTGGTTAATTAA 59.510 37.037 0.00 0.00 37.28 1.40
2912 14980 6.976349 CAGCACTATACTGTCGTGGTTAATTA 59.024 38.462 6.73 0.00 37.28 1.40
2913 14981 5.810587 CAGCACTATACTGTCGTGGTTAATT 59.189 40.000 6.73 0.00 37.28 1.40
2914 14982 5.126545 TCAGCACTATACTGTCGTGGTTAAT 59.873 40.000 6.73 0.00 37.28 1.40
2915 14983 4.460034 TCAGCACTATACTGTCGTGGTTAA 59.540 41.667 6.73 0.00 37.28 2.01
2916 14984 4.011698 TCAGCACTATACTGTCGTGGTTA 58.988 43.478 6.73 0.00 37.28 2.85
2917 14985 2.823747 TCAGCACTATACTGTCGTGGTT 59.176 45.455 6.73 0.00 37.28 3.67
2918 14986 2.443416 TCAGCACTATACTGTCGTGGT 58.557 47.619 4.40 4.40 39.67 4.16
2919 14987 3.439293 CTTCAGCACTATACTGTCGTGG 58.561 50.000 6.84 0.00 36.50 4.94
2920 14988 3.128764 TCCTTCAGCACTATACTGTCGTG 59.871 47.826 0.00 0.00 36.50 4.35
2921 14989 3.353557 TCCTTCAGCACTATACTGTCGT 58.646 45.455 0.00 0.00 36.50 4.34
2922 14990 3.628032 TCTCCTTCAGCACTATACTGTCG 59.372 47.826 0.00 0.00 36.50 4.35
2923 14991 5.358442 TCTTCTCCTTCAGCACTATACTGTC 59.642 44.000 0.00 0.00 36.50 3.51
2924 14992 5.265191 TCTTCTCCTTCAGCACTATACTGT 58.735 41.667 0.00 0.00 36.50 3.55
2925 14993 5.843673 TCTTCTCCTTCAGCACTATACTG 57.156 43.478 0.00 0.00 36.44 2.74
2926 14994 6.040391 GTCATCTTCTCCTTCAGCACTATACT 59.960 42.308 0.00 0.00 0.00 2.12
2927 14995 6.183360 TGTCATCTTCTCCTTCAGCACTATAC 60.183 42.308 0.00 0.00 0.00 1.47
2928 14996 5.893824 TGTCATCTTCTCCTTCAGCACTATA 59.106 40.000 0.00 0.00 0.00 1.31
2929 14997 4.713814 TGTCATCTTCTCCTTCAGCACTAT 59.286 41.667 0.00 0.00 0.00 2.12
2930 14998 4.089361 TGTCATCTTCTCCTTCAGCACTA 58.911 43.478 0.00 0.00 0.00 2.74
2931 14999 2.902486 TGTCATCTTCTCCTTCAGCACT 59.098 45.455 0.00 0.00 0.00 4.40
2932 15000 3.325293 TGTCATCTTCTCCTTCAGCAC 57.675 47.619 0.00 0.00 0.00 4.40
2933 15001 3.262660 ACATGTCATCTTCTCCTTCAGCA 59.737 43.478 0.00 0.00 0.00 4.41
2934 15002 3.871485 ACATGTCATCTTCTCCTTCAGC 58.129 45.455 0.00 0.00 0.00 4.26
2935 15003 6.320926 TCTCTACATGTCATCTTCTCCTTCAG 59.679 42.308 0.00 0.00 0.00 3.02
2936 15004 6.190587 TCTCTACATGTCATCTTCTCCTTCA 58.809 40.000 0.00 0.00 0.00 3.02
2937 15005 6.545666 TCTCTCTACATGTCATCTTCTCCTTC 59.454 42.308 0.00 0.00 0.00 3.46
2938 15006 6.430864 TCTCTCTACATGTCATCTTCTCCTT 58.569 40.000 0.00 0.00 0.00 3.36
2939 15007 6.012337 TCTCTCTACATGTCATCTTCTCCT 57.988 41.667 0.00 0.00 0.00 3.69
2940 15008 6.061441 TCTCTCTCTACATGTCATCTTCTCC 58.939 44.000 0.00 0.00 0.00 3.71
2941 15009 7.445096 TCATCTCTCTCTACATGTCATCTTCTC 59.555 40.741 0.00 0.00 0.00 2.87
2942 15010 7.289310 TCATCTCTCTCTACATGTCATCTTCT 58.711 38.462 0.00 0.00 0.00 2.85
2943 15011 7.445096 TCTCATCTCTCTCTACATGTCATCTTC 59.555 40.741 0.00 0.00 0.00 2.87
2944 15012 7.289310 TCTCATCTCTCTCTACATGTCATCTT 58.711 38.462 0.00 0.00 0.00 2.40
2945 15013 6.840527 TCTCATCTCTCTCTACATGTCATCT 58.159 40.000 0.00 0.00 0.00 2.90
2946 15014 7.362315 CCATCTCATCTCTCTCTACATGTCATC 60.362 44.444 0.00 0.00 0.00 2.92
2947 15015 6.434965 CCATCTCATCTCTCTCTACATGTCAT 59.565 42.308 0.00 0.00 0.00 3.06
2948 15016 5.769162 CCATCTCATCTCTCTCTACATGTCA 59.231 44.000 0.00 0.00 0.00 3.58
2949 15017 5.769662 ACCATCTCATCTCTCTCTACATGTC 59.230 44.000 0.00 0.00 0.00 3.06
2950 15018 5.704354 ACCATCTCATCTCTCTCTACATGT 58.296 41.667 2.69 2.69 0.00 3.21
2951 15019 5.769162 TGACCATCTCATCTCTCTCTACATG 59.231 44.000 0.00 0.00 0.00 3.21
2952 15020 5.951204 TGACCATCTCATCTCTCTCTACAT 58.049 41.667 0.00 0.00 0.00 2.29
2953 15021 5.104151 ACTGACCATCTCATCTCTCTCTACA 60.104 44.000 0.00 0.00 0.00 2.74
2954 15022 5.239306 CACTGACCATCTCATCTCTCTCTAC 59.761 48.000 0.00 0.00 0.00 2.59
2955 15023 5.131809 TCACTGACCATCTCATCTCTCTCTA 59.868 44.000 0.00 0.00 0.00 2.43
2956 15024 4.079844 TCACTGACCATCTCATCTCTCTCT 60.080 45.833 0.00 0.00 0.00 3.10
2957 15025 4.206375 TCACTGACCATCTCATCTCTCTC 58.794 47.826 0.00 0.00 0.00 3.20
2958 15026 4.209538 CTCACTGACCATCTCATCTCTCT 58.790 47.826 0.00 0.00 0.00 3.10
2959 15027 3.243501 GCTCACTGACCATCTCATCTCTC 60.244 52.174 0.00 0.00 0.00 3.20
2960 15028 2.694628 GCTCACTGACCATCTCATCTCT 59.305 50.000 0.00 0.00 0.00 3.10
2961 15029 2.694628 AGCTCACTGACCATCTCATCTC 59.305 50.000 0.00 0.00 0.00 2.75
2962 15030 2.749600 AGCTCACTGACCATCTCATCT 58.250 47.619 0.00 0.00 0.00 2.90
2963 15031 3.540314 AAGCTCACTGACCATCTCATC 57.460 47.619 0.00 0.00 0.00 2.92
2964 15032 3.996921 AAAGCTCACTGACCATCTCAT 57.003 42.857 0.00 0.00 0.00 2.90
2965 15033 4.890158 TTAAAGCTCACTGACCATCTCA 57.110 40.909 0.00 0.00 0.00 3.27
2966 15034 6.749923 AAATTAAAGCTCACTGACCATCTC 57.250 37.500 0.00 0.00 0.00 2.75
2967 15035 6.944862 AGAAAATTAAAGCTCACTGACCATCT 59.055 34.615 0.00 0.00 0.00 2.90
2968 15036 7.150783 AGAAAATTAAAGCTCACTGACCATC 57.849 36.000 0.00 0.00 0.00 3.51
2969 15037 7.885399 ACTAGAAAATTAAAGCTCACTGACCAT 59.115 33.333 0.00 0.00 0.00 3.55
2970 15038 7.224297 ACTAGAAAATTAAAGCTCACTGACCA 58.776 34.615 0.00 0.00 0.00 4.02
2971 15039 7.674471 ACTAGAAAATTAAAGCTCACTGACC 57.326 36.000 0.00 0.00 0.00 4.02
2973 15041 9.998106 ACTAACTAGAAAATTAAAGCTCACTGA 57.002 29.630 0.00 0.00 0.00 3.41
3008 15076 9.586435 CTGACAAAAGTAAAGAAAATGAAACCT 57.414 29.630 0.00 0.00 0.00 3.50
3009 15077 9.366216 ACTGACAAAAGTAAAGAAAATGAAACC 57.634 29.630 0.00 0.00 0.00 3.27
3019 15087 9.607988 TCATCAAAGTACTGACAAAAGTAAAGA 57.392 29.630 0.00 0.00 34.50 2.52
3023 15091 9.337396 ACAATCATCAAAGTACTGACAAAAGTA 57.663 29.630 0.00 0.00 0.00 2.24
3024 15092 8.225603 ACAATCATCAAAGTACTGACAAAAGT 57.774 30.769 0.00 0.00 0.00 2.66
3028 15096 9.500785 TCATAACAATCATCAAAGTACTGACAA 57.499 29.630 0.00 0.00 0.00 3.18
3029 15097 9.500785 TTCATAACAATCATCAAAGTACTGACA 57.499 29.630 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.