Multiple sequence alignment - TraesCS5A01G373200

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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 TraesCS5A01G373200 chr5A 100.000 3071 0 0 1 3071 571325529 571328599 0.000000e+00 5672
1 TraesCS5A01G373200 chr5A 96.237 186 7 0 2886 3071 41348365 41348180 3.850000e-79 305
2 TraesCS5A01G373200 chr5D 95.000 2880 80 28 29 2887 452483780 452486616 0.000000e+00 4462
3 TraesCS5A01G373200 chr5B 93.985 2926 94 34 1 2887 552748271 552751153 0.000000e+00 4353
4 TraesCS5A01G373200 chr5B 95.767 189 8 0 2883 3071 288645873 288646061 3.850000e-79 305
5 TraesCS5A01G373200 chr2D 96.296 189 7 0 2883 3071 213696992 213697180 8.270000e-81 311
6 TraesCS5A01G373200 chr2D 96.216 185 7 0 2887 3071 565050482 565050298 1.380000e-78 303
7 TraesCS5A01G373200 chr7D 95.767 189 8 0 2883 3071 539381770 539381958 3.850000e-79 305
8 TraesCS5A01G373200 chr4D 96.237 186 6 1 2886 3071 76824686 76824502 1.380000e-78 303
9 TraesCS5A01G373200 chr4D 93.909 197 11 1 2876 3071 414346552 414346356 2.320000e-76 296
10 TraesCS5A01G373200 chr6A 95.722 187 8 0 2885 3071 265995649 265995463 4.980000e-78 302
11 TraesCS5A01G373200 chr2A 95.263 190 9 0 2882 3071 217354799 217354610 4.980000e-78 302


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 TraesCS5A01G373200 chr5A 571325529 571328599 3070 False 5672 5672 100.000 1 3071 1 chr5A.!!$F1 3070
1 TraesCS5A01G373200 chr5D 452483780 452486616 2836 False 4462 4462 95.000 29 2887 1 chr5D.!!$F1 2858
2 TraesCS5A01G373200 chr5B 552748271 552751153 2882 False 4353 4353 93.985 1 2887 1 chr5B.!!$F2 2886

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
109 110 0.109342 AACAGAAGCAGGTGGGAGTG 59.891 55.0 0.0 0.0 0.0 3.51 F
296 298 0.123266 TCCCCATCTTCCCTTCCCTT 59.877 55.0 0.0 0.0 0.0 3.95 F
893 934 0.464373 GCCAATCGCTCTCAATCCCA 60.464 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 1757 0.471191 TGATGGCATGCCTCCTAGTG 59.529 55.000 35.53 0.0 36.94 2.74 R
1774 1815 1.739562 GCTCGACCAGACAAGGCAG 60.740 63.158 0.00 0.0 0.00 4.85 R
2878 2919 0.991920 CCAAAGGAGGCCTAAGTCCA 59.008 55.000 4.42 0.0 35.02 4.02 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
27 28 5.070580 ACGAAGAAAAAGGAAGGAAGAGAGA 59.929 40.000 0.00 0.00 0.00 3.10
29 30 4.905429 AGAAAAAGGAAGGAAGAGAGAGC 58.095 43.478 0.00 0.00 0.00 4.09
31 32 2.223803 AAGGAAGGAAGAGAGAGCGA 57.776 50.000 0.00 0.00 0.00 4.93
35 36 2.365582 GAAGGAAGAGAGAGCGAGAGT 58.634 52.381 0.00 0.00 0.00 3.24
103 104 1.060713 CGACGTAACAGAAGCAGGTG 58.939 55.000 0.00 0.00 0.00 4.00
108 109 1.348036 GTAACAGAAGCAGGTGGGAGT 59.652 52.381 0.00 0.00 0.00 3.85
109 110 0.109342 AACAGAAGCAGGTGGGAGTG 59.891 55.000 0.00 0.00 0.00 3.51
136 137 0.395586 GGCATGCCATCCACCACTAA 60.396 55.000 32.08 0.00 35.81 2.24
137 138 0.740737 GCATGCCATCCACCACTAAC 59.259 55.000 6.36 0.00 0.00 2.34
138 139 1.392589 CATGCCATCCACCACTAACC 58.607 55.000 0.00 0.00 0.00 2.85
139 140 1.064463 CATGCCATCCACCACTAACCT 60.064 52.381 0.00 0.00 0.00 3.50
140 141 0.618458 TGCCATCCACCACTAACCTC 59.382 55.000 0.00 0.00 0.00 3.85
141 142 0.618458 GCCATCCACCACTAACCTCA 59.382 55.000 0.00 0.00 0.00 3.86
142 143 1.679032 GCCATCCACCACTAACCTCAC 60.679 57.143 0.00 0.00 0.00 3.51
143 144 1.065418 CCATCCACCACTAACCTCACC 60.065 57.143 0.00 0.00 0.00 4.02
144 145 1.909302 CATCCACCACTAACCTCACCT 59.091 52.381 0.00 0.00 0.00 4.00
145 146 1.640917 TCCACCACTAACCTCACCTC 58.359 55.000 0.00 0.00 0.00 3.85
200 202 5.944007 CCCTAACCAATCCTATTTAATCCCG 59.056 44.000 0.00 0.00 0.00 5.14
245 247 0.251564 CACATAAACAGGCCACCCCA 60.252 55.000 5.01 0.00 35.39 4.96
246 248 0.251608 ACATAAACAGGCCACCCCAC 60.252 55.000 5.01 0.00 35.39 4.61
247 249 0.970427 CATAAACAGGCCACCCCACC 60.970 60.000 5.01 0.00 35.39 4.61
248 250 2.163021 ATAAACAGGCCACCCCACCC 62.163 60.000 5.01 0.00 35.39 4.61
292 294 1.135960 CTCCTCCCCATCTTCCCTTC 58.864 60.000 0.00 0.00 0.00 3.46
293 295 0.327576 TCCTCCCCATCTTCCCTTCC 60.328 60.000 0.00 0.00 0.00 3.46
294 296 1.356494 CCTCCCCATCTTCCCTTCCC 61.356 65.000 0.00 0.00 0.00 3.97
295 297 0.327964 CTCCCCATCTTCCCTTCCCT 60.328 60.000 0.00 0.00 0.00 4.20
296 298 0.123266 TCCCCATCTTCCCTTCCCTT 59.877 55.000 0.00 0.00 0.00 3.95
297 299 0.553333 CCCCATCTTCCCTTCCCTTC 59.447 60.000 0.00 0.00 0.00 3.46
332 334 1.000955 TCTTCTTCTCGGCCTCACAAC 59.999 52.381 0.00 0.00 0.00 3.32
360 362 2.172717 TCTCCCCAAAATCTCCCGATTC 59.827 50.000 0.00 0.00 38.89 2.52
361 363 1.214424 TCCCCAAAATCTCCCGATTCC 59.786 52.381 0.00 0.00 38.89 3.01
362 364 1.692411 CCCAAAATCTCCCGATTCCC 58.308 55.000 0.00 0.00 38.89 3.97
363 365 1.692411 CCAAAATCTCCCGATTCCCC 58.308 55.000 0.00 0.00 38.89 4.81
510 526 1.003233 GCTCCGTTCCTGGCTCTTT 60.003 57.895 0.00 0.00 0.00 2.52
515 531 0.519077 CGTTCCTGGCTCTTTCTTGC 59.481 55.000 0.00 0.00 0.00 4.01
522 538 1.303970 GCTCTTTCTTGCCTGCCCT 60.304 57.895 0.00 0.00 0.00 5.19
557 576 3.319198 TGCCGTTCCTGGTCTCCC 61.319 66.667 0.00 0.00 0.00 4.30
603 623 1.901085 GGATCTCGTGGTGAAGCCT 59.099 57.895 0.00 0.00 38.35 4.58
688 728 1.328680 CTCGCCATTTGGTCTGATTCG 59.671 52.381 0.00 0.00 37.57 3.34
695 735 0.537188 TTGGTCTGATTCGGAGGAGC 59.463 55.000 0.00 0.00 0.00 4.70
718 758 4.809496 CATGCCCGGCTGCTCCTT 62.809 66.667 11.61 0.00 0.00 3.36
792 832 4.704833 TGTCCTGCTTCAGCCCGC 62.705 66.667 0.00 0.00 41.18 6.13
832 872 0.805711 CCAATTCGCGGGGCATTTTC 60.806 55.000 6.13 0.00 0.00 2.29
849 890 3.400054 CCCGTCCTCCTCCCCAAC 61.400 72.222 0.00 0.00 0.00 3.77
893 934 0.464373 GCCAATCGCTCTCAATCCCA 60.464 55.000 0.00 0.00 0.00 4.37
909 950 7.561356 TCTCAATCCCATCCTCTTTAAAAATCC 59.439 37.037 0.00 0.00 0.00 3.01
1083 1124 2.416432 CCCGGTCGTCTTCCTCCTC 61.416 68.421 0.00 0.00 0.00 3.71
1335 1376 2.484264 GCTGTTCAACCTGTATGTCCAC 59.516 50.000 0.00 0.00 0.00 4.02
1341 1382 1.518572 CCTGTATGTCCACGCCGAC 60.519 63.158 0.00 0.00 0.00 4.79
1368 1409 4.228567 GTCCTAGAGCTGCCGCCC 62.229 72.222 0.00 0.00 36.60 6.13
1506 1547 1.081840 GTTCTTTGCGCTGCTGTCC 60.082 57.895 9.73 0.00 0.00 4.02
1654 1695 0.944311 GTACTATGCCCGCGGTGATG 60.944 60.000 26.12 9.88 0.00 3.07
1655 1696 2.709125 TACTATGCCCGCGGTGATGC 62.709 60.000 26.12 20.58 0.00 3.91
1716 1757 1.129437 GGATCGCAGTTCTTTGTGCTC 59.871 52.381 0.00 0.00 37.55 4.26
1719 1760 0.940126 CGCAGTTCTTTGTGCTCACT 59.060 50.000 1.47 0.00 37.55 3.41
1774 1815 2.416893 CGGCTCTGGAAGAAGTTTAAGC 59.583 50.000 0.00 0.00 46.34 3.09
2124 2165 6.459923 GGATAAACTGAGATGATGAGGTACC 58.540 44.000 2.73 2.73 0.00 3.34
2194 2235 7.231925 TGTGTAGGTGTTGTATTGAGAGAGTTA 59.768 37.037 0.00 0.00 0.00 2.24
2225 2266 8.414003 TGAGTGGAGTGTACATAGTATGAAATC 58.586 37.037 17.13 9.82 0.00 2.17
2289 2330 7.537306 CACTTACATAATAAAGTTGCACGCTTT 59.463 33.333 16.55 16.55 39.26 3.51
2364 2405 3.243873 TGTCAGCTTCTTGTAGGACAGTG 60.244 47.826 0.00 0.00 32.13 3.66
2394 2435 7.174253 GTGAAATGTATTTCCTCACTTGGTACA 59.826 37.037 13.19 0.00 44.16 2.90
2435 2476 5.036737 AGTGCTTTTTCAATGAAGTGAACG 58.963 37.500 0.00 0.00 37.24 3.95
2477 2518 9.884636 TTCTAGCAGTTTGTATATGTACATTGT 57.115 29.630 14.77 6.19 40.35 2.71
2519 2560 5.596361 TCTCTCTGGATTATTGTCAGACTCC 59.404 44.000 1.31 0.40 34.33 3.85
2693 2734 4.196193 CGAGCTAGTCCATCTATCCCTAG 58.804 52.174 0.00 0.00 0.00 3.02
2732 2773 1.925255 TCCCATCCTTGCTCTTCCATT 59.075 47.619 0.00 0.00 0.00 3.16
2770 2811 1.255667 AATAGACGGTGCTGGTCGGT 61.256 55.000 0.00 0.00 39.38 4.69
2789 2830 3.069016 CGGTGAGTATGGTATGGCAACTA 59.931 47.826 0.00 0.00 37.61 2.24
2804 2845 7.701539 ATGGCAACTAATTGTTCTATGTGAA 57.298 32.000 0.00 0.00 38.17 3.18
2852 2893 6.049149 TCTTGGCAAGTAACATATCAGTAGC 58.951 40.000 25.39 0.00 0.00 3.58
2887 2928 9.035890 TCATCCTATGTATTACATGGACTTAGG 57.964 37.037 18.64 15.15 39.12 2.69
2888 2929 7.241042 TCCTATGTATTACATGGACTTAGGC 57.759 40.000 18.64 0.00 39.12 3.93
2889 2930 6.212791 TCCTATGTATTACATGGACTTAGGCC 59.787 42.308 18.64 0.00 39.12 5.19
2890 2931 6.213600 CCTATGTATTACATGGACTTAGGCCT 59.786 42.308 18.64 11.78 39.12 5.19
2891 2932 5.546621 TGTATTACATGGACTTAGGCCTC 57.453 43.478 9.68 0.00 0.00 4.70
2892 2933 4.347000 TGTATTACATGGACTTAGGCCTCC 59.653 45.833 9.68 4.82 0.00 4.30
2893 2934 2.868964 TACATGGACTTAGGCCTCCT 57.131 50.000 9.68 0.00 37.71 3.69
2894 2935 1.972588 ACATGGACTTAGGCCTCCTT 58.027 50.000 9.68 0.00 34.61 3.36
2895 2936 2.279173 ACATGGACTTAGGCCTCCTTT 58.721 47.619 9.68 0.00 34.61 3.11
2896 2937 2.025887 ACATGGACTTAGGCCTCCTTTG 60.026 50.000 9.68 9.45 34.61 2.77
2897 2938 0.991920 TGGACTTAGGCCTCCTTTGG 59.008 55.000 9.68 0.00 34.61 3.28
2898 2939 0.992695 GGACTTAGGCCTCCTTTGGT 59.007 55.000 9.68 0.00 34.61 3.67
2899 2940 1.354705 GGACTTAGGCCTCCTTTGGTT 59.645 52.381 9.68 0.00 34.61 3.67
2900 2941 2.618302 GGACTTAGGCCTCCTTTGGTTC 60.618 54.545 9.68 0.00 34.61 3.62
2901 2942 2.039879 GACTTAGGCCTCCTTTGGTTCA 59.960 50.000 9.68 0.00 34.61 3.18
2902 2943 2.649816 ACTTAGGCCTCCTTTGGTTCAT 59.350 45.455 9.68 0.00 34.61 2.57
2903 2944 3.850173 ACTTAGGCCTCCTTTGGTTCATA 59.150 43.478 9.68 0.00 34.61 2.15
2904 2945 4.080299 ACTTAGGCCTCCTTTGGTTCATAG 60.080 45.833 9.68 0.00 34.61 2.23
2905 2946 1.566231 AGGCCTCCTTTGGTTCATAGG 59.434 52.381 0.00 0.00 34.61 2.57
2906 2947 1.410224 GGCCTCCTTTGGTTCATAGGG 60.410 57.143 0.00 0.00 34.20 3.53
2907 2948 1.285078 GCCTCCTTTGGTTCATAGGGT 59.715 52.381 4.94 0.00 34.20 4.34
2908 2949 2.508300 GCCTCCTTTGGTTCATAGGGTA 59.492 50.000 4.94 0.00 34.20 3.69
2909 2950 3.433740 GCCTCCTTTGGTTCATAGGGTAG 60.434 52.174 4.94 0.00 34.20 3.18
2910 2951 3.136626 CCTCCTTTGGTTCATAGGGTAGG 59.863 52.174 4.94 2.50 34.20 3.18
2911 2952 4.037927 CTCCTTTGGTTCATAGGGTAGGA 58.962 47.826 4.94 0.00 34.20 2.94
2912 2953 4.440808 TCCTTTGGTTCATAGGGTAGGAA 58.559 43.478 4.94 0.00 34.20 3.36
2913 2954 4.853276 TCCTTTGGTTCATAGGGTAGGAAA 59.147 41.667 4.94 0.00 34.20 3.13
2914 2955 5.313772 TCCTTTGGTTCATAGGGTAGGAAAA 59.686 40.000 4.94 0.00 34.20 2.29
2915 2956 6.011096 TCCTTTGGTTCATAGGGTAGGAAAAT 60.011 38.462 4.94 0.00 34.20 1.82
2916 2957 6.321435 CCTTTGGTTCATAGGGTAGGAAAATC 59.679 42.308 0.00 0.00 30.68 2.17
2917 2958 5.031066 TGGTTCATAGGGTAGGAAAATCG 57.969 43.478 0.00 0.00 29.56 3.34
2918 2959 4.472108 TGGTTCATAGGGTAGGAAAATCGT 59.528 41.667 0.00 0.00 29.56 3.73
2919 2960 5.662208 TGGTTCATAGGGTAGGAAAATCGTA 59.338 40.000 0.00 0.00 29.56 3.43
2920 2961 6.183360 TGGTTCATAGGGTAGGAAAATCGTAG 60.183 42.308 0.00 0.00 29.56 3.51
2921 2962 6.221659 GTTCATAGGGTAGGAAAATCGTAGG 58.778 44.000 0.00 0.00 29.56 3.18
2922 2963 5.708544 TCATAGGGTAGGAAAATCGTAGGA 58.291 41.667 0.00 0.00 0.00 2.94
2923 2964 6.138263 TCATAGGGTAGGAAAATCGTAGGAA 58.862 40.000 0.00 0.00 0.00 3.36
2924 2965 6.785963 TCATAGGGTAGGAAAATCGTAGGAAT 59.214 38.462 0.00 0.00 0.00 3.01
2925 2966 7.951806 TCATAGGGTAGGAAAATCGTAGGAATA 59.048 37.037 0.00 0.00 0.00 1.75
2926 2967 6.667558 AGGGTAGGAAAATCGTAGGAATAG 57.332 41.667 0.00 0.00 0.00 1.73
2927 2968 5.543020 AGGGTAGGAAAATCGTAGGAATAGG 59.457 44.000 0.00 0.00 0.00 2.57
2928 2969 5.279859 GGGTAGGAAAATCGTAGGAATAGGG 60.280 48.000 0.00 0.00 0.00 3.53
2929 2970 5.541484 GGTAGGAAAATCGTAGGAATAGGGA 59.459 44.000 0.00 0.00 0.00 4.20
2930 2971 6.042437 GGTAGGAAAATCGTAGGAATAGGGAA 59.958 42.308 0.00 0.00 0.00 3.97
2931 2972 6.176014 AGGAAAATCGTAGGAATAGGGAAG 57.824 41.667 0.00 0.00 0.00 3.46
2932 2973 5.666265 AGGAAAATCGTAGGAATAGGGAAGT 59.334 40.000 0.00 0.00 0.00 3.01
2933 2974 5.990386 GGAAAATCGTAGGAATAGGGAAGTC 59.010 44.000 0.00 0.00 0.00 3.01
2934 2975 6.407752 GGAAAATCGTAGGAATAGGGAAGTCA 60.408 42.308 0.00 0.00 0.00 3.41
2935 2976 6.749036 AAATCGTAGGAATAGGGAAGTCAT 57.251 37.500 0.00 0.00 0.00 3.06
2936 2977 7.850935 AAATCGTAGGAATAGGGAAGTCATA 57.149 36.000 0.00 0.00 0.00 2.15
2937 2978 7.469537 AATCGTAGGAATAGGGAAGTCATAG 57.530 40.000 0.00 0.00 0.00 2.23
2938 2979 6.196918 TCGTAGGAATAGGGAAGTCATAGA 57.803 41.667 0.00 0.00 0.00 1.98
2939 2980 6.607970 TCGTAGGAATAGGGAAGTCATAGAA 58.392 40.000 0.00 0.00 0.00 2.10
2940 2981 7.064866 TCGTAGGAATAGGGAAGTCATAGAAA 58.935 38.462 0.00 0.00 0.00 2.52
2941 2982 7.562454 TCGTAGGAATAGGGAAGTCATAGAAAA 59.438 37.037 0.00 0.00 0.00 2.29
2942 2983 8.368668 CGTAGGAATAGGGAAGTCATAGAAAAT 58.631 37.037 0.00 0.00 0.00 1.82
2943 2984 9.495572 GTAGGAATAGGGAAGTCATAGAAAATG 57.504 37.037 0.00 0.00 0.00 2.32
2944 2985 8.337118 AGGAATAGGGAAGTCATAGAAAATGA 57.663 34.615 0.00 0.00 0.00 2.57
2945 2986 8.435982 AGGAATAGGGAAGTCATAGAAAATGAG 58.564 37.037 0.00 0.00 0.00 2.90
2946 2987 8.432805 GGAATAGGGAAGTCATAGAAAATGAGA 58.567 37.037 0.00 0.00 0.00 3.27
2948 2989 9.790344 AATAGGGAAGTCATAGAAAATGAGATG 57.210 33.333 0.00 0.00 0.00 2.90
2949 2990 7.443302 AGGGAAGTCATAGAAAATGAGATGA 57.557 36.000 0.00 0.00 0.00 2.92
2950 2991 7.278875 AGGGAAGTCATAGAAAATGAGATGAC 58.721 38.462 5.86 5.86 45.57 3.06
2951 2992 7.050377 GGGAAGTCATAGAAAATGAGATGACA 58.950 38.462 14.37 0.00 46.94 3.58
2952 2993 7.718753 GGGAAGTCATAGAAAATGAGATGACAT 59.281 37.037 14.37 4.35 46.94 3.06
2953 2994 8.557864 GGAAGTCATAGAAAATGAGATGACATG 58.442 37.037 14.37 0.00 46.94 3.21
2954 2995 9.107177 GAAGTCATAGAAAATGAGATGACATGT 57.893 33.333 14.37 0.00 46.94 3.21
2966 3007 6.343716 GAGATGACATGTATCTCACATCCT 57.656 41.667 24.95 13.10 44.99 3.24
2967 3008 7.459795 GAGATGACATGTATCTCACATCCTA 57.540 40.000 24.95 0.00 44.99 2.94
2968 3009 8.065473 GAGATGACATGTATCTCACATCCTAT 57.935 38.462 24.95 9.87 44.99 2.57
2969 3010 7.838884 AGATGACATGTATCTCACATCCTATG 58.161 38.462 15.57 0.00 44.99 2.23
2970 3011 7.673082 AGATGACATGTATCTCACATCCTATGA 59.327 37.037 15.57 0.00 44.99 2.15
2971 3012 7.224522 TGACATGTATCTCACATCCTATGAG 57.775 40.000 0.00 0.00 44.99 2.90
2972 3013 6.779539 TGACATGTATCTCACATCCTATGAGT 59.220 38.462 0.00 0.00 44.99 3.41
2973 3014 7.944554 TGACATGTATCTCACATCCTATGAGTA 59.055 37.037 0.00 0.00 44.99 2.59
2974 3015 8.347004 ACATGTATCTCACATCCTATGAGTAG 57.653 38.462 0.00 0.00 44.99 2.57
2975 3016 7.395772 ACATGTATCTCACATCCTATGAGTAGG 59.604 40.741 0.00 0.00 44.99 3.18
2990 3031 8.893563 CTATGAGTAGGAATAGGAAAGGAGAT 57.106 38.462 0.00 0.00 0.00 2.75
2991 3032 6.985653 TGAGTAGGAATAGGAAAGGAGATG 57.014 41.667 0.00 0.00 0.00 2.90
2992 3033 6.683537 TGAGTAGGAATAGGAAAGGAGATGA 58.316 40.000 0.00 0.00 0.00 2.92
2993 3034 6.551601 TGAGTAGGAATAGGAAAGGAGATGAC 59.448 42.308 0.00 0.00 0.00 3.06
2994 3035 5.841783 AGTAGGAATAGGAAAGGAGATGACC 59.158 44.000 0.00 0.00 0.00 4.02
2995 3036 4.901927 AGGAATAGGAAAGGAGATGACCT 58.098 43.478 0.00 0.00 42.69 3.85
3005 3046 4.916041 AGGAGATGACCTTTGATTCACA 57.084 40.909 0.00 0.00 36.86 3.58
3006 3047 5.447778 AGGAGATGACCTTTGATTCACAT 57.552 39.130 0.00 0.00 36.86 3.21
3007 3048 5.435291 AGGAGATGACCTTTGATTCACATC 58.565 41.667 0.00 0.00 36.86 3.06
3008 3049 5.045359 AGGAGATGACCTTTGATTCACATCA 60.045 40.000 13.54 4.62 36.86 3.07
3009 3050 5.826737 GGAGATGACCTTTGATTCACATCAT 59.173 40.000 13.54 8.21 39.28 2.45
3010 3051 6.994496 GGAGATGACCTTTGATTCACATCATA 59.006 38.462 13.54 0.00 39.28 2.15
3011 3052 7.172875 GGAGATGACCTTTGATTCACATCATAG 59.827 40.741 13.54 1.71 39.28 2.23
3035 3076 3.764237 TTTTTCCGTTGAGTCTAGGCT 57.236 42.857 0.00 0.00 0.00 4.58
3036 3077 4.877378 TTTTTCCGTTGAGTCTAGGCTA 57.123 40.909 0.00 0.00 0.00 3.93
3037 3078 4.877378 TTTTCCGTTGAGTCTAGGCTAA 57.123 40.909 0.00 0.00 0.00 3.09
3038 3079 5.416271 TTTTCCGTTGAGTCTAGGCTAAT 57.584 39.130 0.00 0.00 0.00 1.73
3039 3080 4.386867 TTCCGTTGAGTCTAGGCTAATG 57.613 45.455 0.00 0.00 0.00 1.90
3040 3081 3.362706 TCCGTTGAGTCTAGGCTAATGT 58.637 45.455 0.00 0.00 0.00 2.71
3041 3082 3.767673 TCCGTTGAGTCTAGGCTAATGTT 59.232 43.478 0.00 0.00 0.00 2.71
3042 3083 4.222145 TCCGTTGAGTCTAGGCTAATGTTT 59.778 41.667 0.00 0.00 0.00 2.83
3043 3084 5.419788 TCCGTTGAGTCTAGGCTAATGTTTA 59.580 40.000 0.00 0.00 0.00 2.01
3044 3085 6.097839 TCCGTTGAGTCTAGGCTAATGTTTAT 59.902 38.462 0.00 0.00 0.00 1.40
3045 3086 6.761714 CCGTTGAGTCTAGGCTAATGTTTATT 59.238 38.462 0.00 0.00 0.00 1.40
3046 3087 7.280205 CCGTTGAGTCTAGGCTAATGTTTATTT 59.720 37.037 0.00 0.00 0.00 1.40
3047 3088 8.665685 CGTTGAGTCTAGGCTAATGTTTATTTT 58.334 33.333 0.00 0.00 0.00 1.82
3048 3089 9.989869 GTTGAGTCTAGGCTAATGTTTATTTTC 57.010 33.333 0.00 0.00 0.00 2.29
3049 3090 8.732746 TGAGTCTAGGCTAATGTTTATTTTCC 57.267 34.615 0.00 0.00 0.00 3.13
3050 3091 8.548877 TGAGTCTAGGCTAATGTTTATTTTCCT 58.451 33.333 0.00 0.00 33.86 3.36
3064 3105 8.748412 TGTTTATTTTCCTATGAATTGTGGAGG 58.252 33.333 0.00 0.00 0.00 4.30
3065 3106 8.966868 GTTTATTTTCCTATGAATTGTGGAGGA 58.033 33.333 0.00 0.00 34.46 3.71
3066 3107 9.713684 TTTATTTTCCTATGAATTGTGGAGGAT 57.286 29.630 0.00 0.00 36.22 3.24
3068 3109 8.930846 ATTTTCCTATGAATTGTGGAGGATAG 57.069 34.615 0.00 0.00 36.22 2.08
3069 3110 6.439636 TTCCTATGAATTGTGGAGGATAGG 57.560 41.667 0.00 0.00 36.22 2.57
3070 3111 5.726560 TCCTATGAATTGTGGAGGATAGGA 58.273 41.667 0.00 0.00 39.29 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.542779 TCTCTCTTCCTTCCTTTTTCTTCG 58.457 41.667 0.00 0.00 0.00 3.79
16 17 2.026262 AGACTCTCGCTCTCTCTTCCTT 60.026 50.000 0.00 0.00 0.00 3.36
19 20 3.270877 AGAAGACTCTCGCTCTCTCTTC 58.729 50.000 0.00 0.00 37.98 2.87
20 21 3.350219 AGAAGACTCTCGCTCTCTCTT 57.650 47.619 0.00 0.00 0.00 2.85
21 22 3.704566 TCTAGAAGACTCTCGCTCTCTCT 59.295 47.826 0.00 0.00 32.70 3.10
27 28 1.011333 GCGTCTAGAAGACTCTCGCT 58.989 55.000 10.08 0.00 42.92 4.93
29 30 0.315544 GCGCGTCTAGAAGACTCTCG 60.316 60.000 8.43 4.27 42.92 4.04
31 32 1.020333 ACGCGCGTCTAGAAGACTCT 61.020 55.000 32.73 1.29 42.92 3.24
103 104 2.606587 ATGCCACTGTCCCACTCCC 61.607 63.158 0.00 0.00 0.00 4.30
108 109 3.578286 TGGCATGCCACTGTCCCA 61.578 61.111 35.59 10.49 41.89 4.37
131 132 2.028930 GTGAGGTGAGGTGAGGTTAGTG 60.029 54.545 0.00 0.00 0.00 2.74
136 137 0.543174 GAGGTGAGGTGAGGTGAGGT 60.543 60.000 0.00 0.00 0.00 3.85
137 138 0.542938 TGAGGTGAGGTGAGGTGAGG 60.543 60.000 0.00 0.00 0.00 3.86
138 139 0.894141 CTGAGGTGAGGTGAGGTGAG 59.106 60.000 0.00 0.00 0.00 3.51
139 140 0.188587 ACTGAGGTGAGGTGAGGTGA 59.811 55.000 0.00 0.00 0.00 4.02
140 141 1.051812 AACTGAGGTGAGGTGAGGTG 58.948 55.000 0.00 0.00 0.00 4.00
141 142 1.051812 CAACTGAGGTGAGGTGAGGT 58.948 55.000 0.00 0.00 31.73 3.85
142 143 0.321122 GCAACTGAGGTGAGGTGAGG 60.321 60.000 0.00 0.00 31.73 3.86
143 144 0.321122 GGCAACTGAGGTGAGGTGAG 60.321 60.000 0.00 0.00 31.73 3.51
144 145 1.754745 GGCAACTGAGGTGAGGTGA 59.245 57.895 0.00 0.00 31.73 4.02
145 146 1.302832 GGGCAACTGAGGTGAGGTG 60.303 63.158 0.00 0.00 33.41 4.00
307 309 1.406180 GAGGCCGAGAAGAAGAGGTAC 59.594 57.143 0.00 0.00 0.00 3.34
332 334 3.956848 GGAGATTTTGGGGAGATCTTTGG 59.043 47.826 0.00 0.00 30.64 3.28
421 423 4.883354 GAGGGGGAATGGCGGCTG 62.883 72.222 11.43 0.00 0.00 4.85
466 468 2.551912 CGACTGCCCCAACAACCAC 61.552 63.158 0.00 0.00 0.00 4.16
760 800 0.174617 GGACAAGAAGGCGAGGAGAG 59.825 60.000 0.00 0.00 0.00 3.20
832 872 3.400054 GTTGGGGAGGAGGACGGG 61.400 72.222 0.00 0.00 0.00 5.28
893 934 6.887002 AGAAAGAGCGGATTTTTAAAGAGGAT 59.113 34.615 0.00 0.00 0.00 3.24
909 950 0.686112 AGGGGGAGAGAGAAAGAGCG 60.686 60.000 0.00 0.00 0.00 5.03
1312 1353 3.181445 TGGACATACAGGTTGAACAGCTT 60.181 43.478 0.00 0.00 0.00 3.74
1716 1757 0.471191 TGATGGCATGCCTCCTAGTG 59.529 55.000 35.53 0.00 36.94 2.74
1774 1815 1.739562 GCTCGACCAGACAAGGCAG 60.740 63.158 0.00 0.00 0.00 4.85
1947 1988 2.630158 CTCAGCTCCCTGATCAAGTTG 58.370 52.381 0.00 0.00 46.44 3.16
2094 2135 4.386867 TCATCTCAGTTTATCCGACACC 57.613 45.455 0.00 0.00 0.00 4.16
2124 2165 2.430942 GCAGCAAGTGCGCATTTCG 61.431 57.895 15.91 11.73 43.99 3.46
2194 2235 5.761205 ACTATGTACACTCCACTCAGAGAT 58.239 41.667 3.79 0.00 37.33 2.75
2225 2266 4.204012 TGCATAATTCCTAAAACTCCCGG 58.796 43.478 0.00 0.00 0.00 5.73
2289 2330 8.994170 TCAAATTGATGACATAACGACTTAACA 58.006 29.630 0.00 0.00 0.00 2.41
2340 2381 2.288213 TGTCCTACAAGAAGCTGACACG 60.288 50.000 0.00 0.00 0.00 4.49
2364 2405 7.253422 CAAGTGAGGAAATACATTTCACATCC 58.747 38.462 14.80 0.37 46.03 3.51
2424 2465 2.095567 GCAACAGATGCGTTCACTTCAT 60.096 45.455 0.00 0.00 46.87 2.57
2477 2518 8.470805 CCAGAGAGACAGTAAAGCTTTCTATAA 58.529 37.037 16.57 0.00 34.62 0.98
2480 2521 6.010850 TCCAGAGAGACAGTAAAGCTTTCTA 58.989 40.000 16.57 0.00 34.62 2.10
2519 2560 6.154445 AGCAAATCAAATTACTTCAGTGCTG 58.846 36.000 0.00 0.00 37.24 4.41
2693 2734 5.749462 TGGGAATTCCTCAAGAAAGATCTC 58.251 41.667 23.63 2.79 38.21 2.75
2770 2811 6.658849 ACAATTAGTTGCCATACCATACTCA 58.341 36.000 0.00 0.00 38.96 3.41
2789 2830 9.577110 CAAACAGCATATTCACATAGAACAATT 57.423 29.630 0.00 0.00 39.49 2.32
2804 2845 2.415168 CGGTCGTGTTCAAACAGCATAT 59.585 45.455 0.00 0.00 40.05 1.78
2878 2919 0.991920 CCAAAGGAGGCCTAAGTCCA 59.008 55.000 4.42 0.00 35.02 4.02
2887 2928 1.285078 ACCCTATGAACCAAAGGAGGC 59.715 52.381 0.00 0.00 31.64 4.70
2888 2929 3.136626 CCTACCCTATGAACCAAAGGAGG 59.863 52.174 0.00 0.00 31.64 4.30
2889 2930 4.037927 TCCTACCCTATGAACCAAAGGAG 58.962 47.826 0.00 0.00 31.64 3.69
2890 2931 4.083080 TCCTACCCTATGAACCAAAGGA 57.917 45.455 0.00 0.00 31.64 3.36
2891 2932 4.855298 TTCCTACCCTATGAACCAAAGG 57.145 45.455 0.00 0.00 0.00 3.11
2892 2933 6.038271 CGATTTTCCTACCCTATGAACCAAAG 59.962 42.308 0.00 0.00 0.00 2.77
2893 2934 5.883673 CGATTTTCCTACCCTATGAACCAAA 59.116 40.000 0.00 0.00 0.00 3.28
2894 2935 5.045432 ACGATTTTCCTACCCTATGAACCAA 60.045 40.000 0.00 0.00 0.00 3.67
2895 2936 4.472108 ACGATTTTCCTACCCTATGAACCA 59.528 41.667 0.00 0.00 0.00 3.67
2896 2937 5.032327 ACGATTTTCCTACCCTATGAACC 57.968 43.478 0.00 0.00 0.00 3.62
2897 2938 6.041296 TCCTACGATTTTCCTACCCTATGAAC 59.959 42.308 0.00 0.00 0.00 3.18
2898 2939 6.138263 TCCTACGATTTTCCTACCCTATGAA 58.862 40.000 0.00 0.00 0.00 2.57
2899 2940 5.708544 TCCTACGATTTTCCTACCCTATGA 58.291 41.667 0.00 0.00 0.00 2.15
2900 2941 6.415206 TTCCTACGATTTTCCTACCCTATG 57.585 41.667 0.00 0.00 0.00 2.23
2901 2942 7.399478 CCTATTCCTACGATTTTCCTACCCTAT 59.601 40.741 0.00 0.00 0.00 2.57
2902 2943 6.723052 CCTATTCCTACGATTTTCCTACCCTA 59.277 42.308 0.00 0.00 0.00 3.53
2903 2944 5.543020 CCTATTCCTACGATTTTCCTACCCT 59.457 44.000 0.00 0.00 0.00 4.34
2904 2945 5.279859 CCCTATTCCTACGATTTTCCTACCC 60.280 48.000 0.00 0.00 0.00 3.69
2905 2946 5.541484 TCCCTATTCCTACGATTTTCCTACC 59.459 44.000 0.00 0.00 0.00 3.18
2906 2947 6.661304 TCCCTATTCCTACGATTTTCCTAC 57.339 41.667 0.00 0.00 0.00 3.18
2907 2948 6.842807 ACTTCCCTATTCCTACGATTTTCCTA 59.157 38.462 0.00 0.00 0.00 2.94
2908 2949 5.666265 ACTTCCCTATTCCTACGATTTTCCT 59.334 40.000 0.00 0.00 0.00 3.36
2909 2950 5.926663 ACTTCCCTATTCCTACGATTTTCC 58.073 41.667 0.00 0.00 0.00 3.13
2910 2951 6.579865 TGACTTCCCTATTCCTACGATTTTC 58.420 40.000 0.00 0.00 0.00 2.29
2911 2952 6.555463 TGACTTCCCTATTCCTACGATTTT 57.445 37.500 0.00 0.00 0.00 1.82
2912 2953 6.749036 ATGACTTCCCTATTCCTACGATTT 57.251 37.500 0.00 0.00 0.00 2.17
2913 2954 7.239438 TCTATGACTTCCCTATTCCTACGATT 58.761 38.462 0.00 0.00 0.00 3.34
2914 2955 6.791371 TCTATGACTTCCCTATTCCTACGAT 58.209 40.000 0.00 0.00 0.00 3.73
2915 2956 6.196918 TCTATGACTTCCCTATTCCTACGA 57.803 41.667 0.00 0.00 0.00 3.43
2916 2957 6.896021 TTCTATGACTTCCCTATTCCTACG 57.104 41.667 0.00 0.00 0.00 3.51
2917 2958 9.495572 CATTTTCTATGACTTCCCTATTCCTAC 57.504 37.037 0.00 0.00 0.00 3.18
2918 2959 9.447279 TCATTTTCTATGACTTCCCTATTCCTA 57.553 33.333 0.00 0.00 0.00 2.94
2919 2960 8.337118 TCATTTTCTATGACTTCCCTATTCCT 57.663 34.615 0.00 0.00 0.00 3.36
2920 2961 8.432805 TCTCATTTTCTATGACTTCCCTATTCC 58.567 37.037 0.00 0.00 0.00 3.01
2922 2963 9.790344 CATCTCATTTTCTATGACTTCCCTATT 57.210 33.333 0.00 0.00 0.00 1.73
2923 2964 9.163894 TCATCTCATTTTCTATGACTTCCCTAT 57.836 33.333 0.00 0.00 0.00 2.57
2924 2965 8.424918 GTCATCTCATTTTCTATGACTTCCCTA 58.575 37.037 0.00 0.00 43.07 3.53
2925 2966 7.092712 TGTCATCTCATTTTCTATGACTTCCCT 60.093 37.037 13.59 0.00 45.40 4.20
2926 2967 7.050377 TGTCATCTCATTTTCTATGACTTCCC 58.950 38.462 13.59 0.00 45.40 3.97
2927 2968 8.557864 CATGTCATCTCATTTTCTATGACTTCC 58.442 37.037 13.59 0.00 45.40 3.46
2928 2969 9.107177 ACATGTCATCTCATTTTCTATGACTTC 57.893 33.333 13.59 0.00 45.40 3.01
2965 3006 8.748412 CATCTCCTTTCCTATTCCTACTCATAG 58.252 40.741 0.00 0.00 0.00 2.23
2966 3007 8.456940 TCATCTCCTTTCCTATTCCTACTCATA 58.543 37.037 0.00 0.00 0.00 2.15
2967 3008 7.234577 GTCATCTCCTTTCCTATTCCTACTCAT 59.765 40.741 0.00 0.00 0.00 2.90
2968 3009 6.551601 GTCATCTCCTTTCCTATTCCTACTCA 59.448 42.308 0.00 0.00 0.00 3.41
2969 3010 6.014925 GGTCATCTCCTTTCCTATTCCTACTC 60.015 46.154 0.00 0.00 0.00 2.59
2970 3011 5.841783 GGTCATCTCCTTTCCTATTCCTACT 59.158 44.000 0.00 0.00 0.00 2.57
2971 3012 5.841783 AGGTCATCTCCTTTCCTATTCCTAC 59.158 44.000 0.00 0.00 33.52 3.18
2972 3013 6.044411 AGGTCATCTCCTTTCCTATTCCTA 57.956 41.667 0.00 0.00 33.52 2.94
2973 3014 4.901927 AGGTCATCTCCTTTCCTATTCCT 58.098 43.478 0.00 0.00 33.52 3.36
2974 3015 5.638530 AAGGTCATCTCCTTTCCTATTCC 57.361 43.478 0.00 0.00 44.36 3.01
2984 3025 4.916041 TGTGAATCAAAGGTCATCTCCT 57.084 40.909 0.00 0.00 39.84 3.69
2985 3026 5.188434 TGATGTGAATCAAAGGTCATCTCC 58.812 41.667 10.68 0.00 34.63 3.71
2986 3027 6.939132 ATGATGTGAATCAAAGGTCATCTC 57.061 37.500 10.68 0.00 34.63 2.75
2987 3028 6.996879 CCTATGATGTGAATCAAAGGTCATCT 59.003 38.462 10.68 2.28 34.63 2.90
2988 3029 6.994496 TCCTATGATGTGAATCAAAGGTCATC 59.006 38.462 4.45 4.45 33.83 2.92
2989 3030 6.903516 TCCTATGATGTGAATCAAAGGTCAT 58.096 36.000 0.00 0.00 33.83 3.06
2990 3031 6.312141 TCCTATGATGTGAATCAAAGGTCA 57.688 37.500 0.00 0.00 33.83 4.02
2991 3032 7.814264 AATCCTATGATGTGAATCAAAGGTC 57.186 36.000 0.00 0.00 33.83 3.85
2992 3033 8.599624 AAAATCCTATGATGTGAATCAAAGGT 57.400 30.769 0.00 0.00 33.83 3.50
3015 3056 3.764237 AGCCTAGACTCAACGGAAAAA 57.236 42.857 0.00 0.00 0.00 1.94
3016 3057 4.877378 TTAGCCTAGACTCAACGGAAAA 57.123 40.909 0.00 0.00 0.00 2.29
3017 3058 4.222145 ACATTAGCCTAGACTCAACGGAAA 59.778 41.667 0.00 0.00 0.00 3.13
3018 3059 3.767673 ACATTAGCCTAGACTCAACGGAA 59.232 43.478 0.00 0.00 0.00 4.30
3019 3060 3.362706 ACATTAGCCTAGACTCAACGGA 58.637 45.455 0.00 0.00 0.00 4.69
3020 3061 3.802948 ACATTAGCCTAGACTCAACGG 57.197 47.619 0.00 0.00 0.00 4.44
3021 3062 7.772332 AATAAACATTAGCCTAGACTCAACG 57.228 36.000 0.00 0.00 0.00 4.10
3022 3063 9.989869 GAAAATAAACATTAGCCTAGACTCAAC 57.010 33.333 0.00 0.00 0.00 3.18
3023 3064 9.174166 GGAAAATAAACATTAGCCTAGACTCAA 57.826 33.333 0.00 0.00 0.00 3.02
3024 3065 8.548877 AGGAAAATAAACATTAGCCTAGACTCA 58.451 33.333 0.00 0.00 0.00 3.41
3025 3066 8.966069 AGGAAAATAAACATTAGCCTAGACTC 57.034 34.615 0.00 0.00 0.00 3.36
3038 3079 8.748412 CCTCCACAATTCATAGGAAAATAAACA 58.252 33.333 0.00 0.00 36.43 2.83
3039 3080 8.966868 TCCTCCACAATTCATAGGAAAATAAAC 58.033 33.333 0.00 0.00 36.43 2.01
3040 3081 9.713684 ATCCTCCACAATTCATAGGAAAATAAA 57.286 29.630 0.00 0.00 39.68 1.40
3043 3084 7.946776 CCTATCCTCCACAATTCATAGGAAAAT 59.053 37.037 0.00 0.00 39.68 1.82
3044 3085 7.128728 TCCTATCCTCCACAATTCATAGGAAAA 59.871 37.037 0.00 0.00 39.17 2.29
3045 3086 6.619437 TCCTATCCTCCACAATTCATAGGAAA 59.381 38.462 0.00 0.00 39.17 3.13
3046 3087 6.150332 TCCTATCCTCCACAATTCATAGGAA 58.850 40.000 3.47 0.00 39.17 3.36
3047 3088 5.726560 TCCTATCCTCCACAATTCATAGGA 58.273 41.667 2.01 2.01 39.61 2.94


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

AutoCloner maintained by Alex Coulton.