Multiple sequence alignment - TraesCS2A01G272300

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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 TraesCS2A01G272300 chr2A 100.000 2627 0 0 1 2627 445751630 445749004 0.000000e+00 4815
1 TraesCS2A01G272300 chr2A 98.428 1654 26 0 876 2529 628679971 628681624 0.000000e+00 2911
2 TraesCS2A01G272300 chr2A 97.585 828 20 0 1 828 628679146 628679973 0.000000e+00 1419
3 TraesCS2A01G272300 chr2A 98.864 88 1 0 2540 2627 445749406 445749319 9.730000e-35 158
4 TraesCS2A01G272300 chr2A 98.864 88 1 0 2540 2627 628681320 628681407 9.730000e-35 158
5 TraesCS2A01G272300 chr6A 97.462 2246 53 4 1 2246 105157339 105155098 0.000000e+00 3829
6 TraesCS2A01G272300 chr6A 97.959 441 7 2 2089 2529 105155349 105154911 0.000000e+00 763
7 TraesCS2A01G272300 chr5A 97.928 2172 44 1 1 2172 561198045 561195875 0.000000e+00 3760
8 TraesCS2A01G272300 chr5A 99.478 383 2 0 2147 2529 561194790 561194408 0.000000e+00 697
9 TraesCS2A01G272300 chr5A 98.864 88 1 0 2540 2627 561194712 561194625 9.730000e-35 158
10 TraesCS2A01G272300 chr3A 97.490 2191 55 0 1 2191 19597268 19599458 0.000000e+00 3742
11 TraesCS2A01G272300 chr7A 98.292 2108 36 0 1 2108 89128342 89130449 0.000000e+00 3694
12 TraesCS2A01G272300 chr7A 97.718 2103 48 0 1 2103 38244986 38247088 0.000000e+00 3618
13 TraesCS2A01G272300 chr7A 96.458 1835 42 2 1 1835 21449588 21451399 0.000000e+00 3007
14 TraesCS2A01G272300 chr7A 96.250 480 16 2 2050 2529 38264704 38265181 0.000000e+00 785
15 TraesCS2A01G272300 chr7A 100.000 385 0 0 2145 2529 89131008 89131392 0.000000e+00 712
16 TraesCS2A01G272300 chr7A 99.417 343 2 0 2187 2529 21452617 21452959 7.980000e-175 623
17 TraesCS2A01G272300 chr7A 99.115 339 3 0 2191 2529 89131403 89131741 6.220000e-171 610
18 TraesCS2A01G272300 chr7A 98.864 88 1 0 2540 2627 89131088 89131175 9.730000e-35 158
19 TraesCS2A01G272300 chr7A 97.727 88 2 0 2540 2627 21452655 21452742 4.530000e-33 152
20 TraesCS2A01G272300 chr7A 97.727 88 2 0 2540 2627 89131437 89131524 4.530000e-33 152
21 TraesCS2A01G272300 chr1A 97.883 2078 39 2 1 2078 381286509 381284437 0.000000e+00 3589
22 TraesCS2A01G272300 chr1A 100.000 385 0 0 2145 2529 381284118 381283734 0.000000e+00 712
23 TraesCS2A01G272300 chr1A 98.864 88 1 0 2540 2627 381284038 381283951 9.730000e-35 158
24 TraesCS2A01G272300 chr4A 96.732 1836 59 1 1 1835 618192698 618194533 0.000000e+00 3057
25 TraesCS2A01G272300 chr4A 85.944 498 52 7 1849 2342 692944177 692943694 1.390000e-142 516
26 TraesCS2A01G272300 chr7B 97.705 828 19 0 1 828 72337830 72338657 0.000000e+00 1424
27 TraesCS2A01G272300 chr7B 90.476 462 37 7 1839 2300 197006272 197006726 1.040000e-168 603
28 TraesCS2A01G272300 chrUn 97.052 441 12 1 2089 2529 238606062 238605623 0.000000e+00 741
29 TraesCS2A01G272300 chr3D 88.049 410 43 4 1922 2330 405845358 405845762 5.090000e-132 481
30 TraesCS2A01G272300 chr4B 98.864 88 1 0 2540 2627 147358924 147358837 9.730000e-35 158
31 TraesCS2A01G272300 chr2B 97.727 88 2 0 2540 2627 366914983 366914896 4.530000e-33 152
32 TraesCS2A01G272300 chr1D 97.727 88 2 0 2540 2627 348025309 348025222 4.530000e-33 152


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 TraesCS2A01G272300 chr2A 445749004 445751630 2626 True 2486.500000 4815 99.432000 1 2627 2 chr2A.!!$R1 2626
1 TraesCS2A01G272300 chr2A 628679146 628681624 2478 False 1496.000000 2911 98.292333 1 2627 3 chr2A.!!$F1 2626
2 TraesCS2A01G272300 chr6A 105154911 105157339 2428 True 2296.000000 3829 97.710500 1 2529 2 chr6A.!!$R1 2528
3 TraesCS2A01G272300 chr5A 561194408 561198045 3637 True 1538.333333 3760 98.756667 1 2627 3 chr5A.!!$R1 2626
4 TraesCS2A01G272300 chr3A 19597268 19599458 2190 False 3742.000000 3742 97.490000 1 2191 1 chr3A.!!$F1 2190
5 TraesCS2A01G272300 chr7A 38244986 38247088 2102 False 3618.000000 3618 97.718000 1 2103 1 chr7A.!!$F1 2102
6 TraesCS2A01G272300 chr7A 21449588 21452959 3371 False 1260.666667 3007 97.867333 1 2627 3 chr7A.!!$F3 2626
7 TraesCS2A01G272300 chr7A 89128342 89131741 3399 False 1065.200000 3694 98.799600 1 2627 5 chr7A.!!$F4 2626
8 TraesCS2A01G272300 chr1A 381283734 381286509 2775 True 1486.333333 3589 98.915667 1 2627 3 chr1A.!!$R1 2626
9 TraesCS2A01G272300 chr4A 618192698 618194533 1835 False 3057.000000 3057 96.732000 1 1835 1 chr4A.!!$F1 1834
10 TraesCS2A01G272300 chr7B 72337830 72338657 827 False 1424.000000 1424 97.705000 1 828 1 chr7B.!!$F1 827

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
161 162 1.372087 CGAGAAGCATGGGAAGCCAC 61.372 60.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 2917 0.035739 GACGGAACCACCTAAAGCCA 59.964 55.0 0.0 0.0 36.31 4.75 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
161 162 1.372087 CGAGAAGCATGGGAAGCCAC 61.372 60.000 0.00 0.00 0.00 5.01
257 258 6.964807 TCTTGCCTTATTGATTATGCACAT 57.035 33.333 0.00 0.00 0.00 3.21
388 389 5.047566 TGGTGAATATTATGGTCAGTGGG 57.952 43.478 0.00 0.00 0.00 4.61
518 541 3.136626 ACTCACATTAGCCCCTCCATTAC 59.863 47.826 0.00 0.00 0.00 1.89
656 679 6.703319 TGGTTTGATAACTCTTCATTCGGTA 58.297 36.000 0.00 0.00 34.59 4.02
936 959 9.469807 TGTATTGTACTAAATTTTGCCTTGTTG 57.530 29.630 0.00 0.00 0.00 3.33
945 968 6.581171 AATTTTGCCTTGTTGTTTTTCCAA 57.419 29.167 0.00 0.00 0.00 3.53
985 1008 3.576078 TTGTTCAGTGGGTTGATGAGT 57.424 42.857 0.00 0.00 0.00 3.41
1124 1147 5.472820 CAGAAGAAAAGAAGAAGCTGGATGT 59.527 40.000 0.00 0.00 0.00 3.06
1186 1209 3.454812 GGACTTTCAGCAGGATAGGGTTA 59.545 47.826 0.00 0.00 0.00 2.85
1318 1341 7.663081 AGAAGCTTCAACAGAAGTATGAAATCA 59.337 33.333 27.57 0.00 40.66 2.57
1459 1482 3.059325 CACAAAGTTTGAGGAGAAGCTCG 60.059 47.826 22.23 0.00 0.00 5.03
1536 1559 6.721208 AGGAAAACCATAATGAAGAGAAGCAA 59.279 34.615 0.00 0.00 0.00 3.91
1703 1727 7.097192 TGTGCAATGACCTAGTAACTTAGAAG 58.903 38.462 0.00 0.00 0.00 2.85
2096 2873 3.041946 CCTAGACCCTAGTTGATGGCTT 58.958 50.000 0.00 0.00 0.00 4.35
2097 2874 3.456277 CCTAGACCCTAGTTGATGGCTTT 59.544 47.826 0.00 0.00 0.00 3.51
2098 2875 4.654262 CCTAGACCCTAGTTGATGGCTTTA 59.346 45.833 0.00 0.00 0.00 1.85
2099 2876 4.762289 AGACCCTAGTTGATGGCTTTAG 57.238 45.455 0.00 0.00 0.00 1.85
2100 2877 3.456277 AGACCCTAGTTGATGGCTTTAGG 59.544 47.826 0.00 0.00 0.00 2.69
2101 2878 3.190439 ACCCTAGTTGATGGCTTTAGGT 58.810 45.455 0.00 0.00 31.06 3.08
2102 2879 3.054361 ACCCTAGTTGATGGCTTTAGGTG 60.054 47.826 0.00 0.00 31.06 4.00
2103 2880 3.545703 CCTAGTTGATGGCTTTAGGTGG 58.454 50.000 0.00 0.00 0.00 4.61
2104 2881 3.054361 CCTAGTTGATGGCTTTAGGTGGT 60.054 47.826 0.00 0.00 0.00 4.16
2105 2882 3.525800 AGTTGATGGCTTTAGGTGGTT 57.474 42.857 0.00 0.00 0.00 3.67
2106 2883 3.844640 AGTTGATGGCTTTAGGTGGTTT 58.155 40.909 0.00 0.00 0.00 3.27
2107 2884 3.826729 AGTTGATGGCTTTAGGTGGTTTC 59.173 43.478 0.00 0.00 0.00 2.78
2108 2885 3.517296 TGATGGCTTTAGGTGGTTTCA 57.483 42.857 0.00 0.00 0.00 2.69
2109 2886 4.046286 TGATGGCTTTAGGTGGTTTCAT 57.954 40.909 0.00 0.00 0.00 2.57
2110 2887 4.016444 TGATGGCTTTAGGTGGTTTCATC 58.984 43.478 0.00 0.00 0.00 2.92
2111 2888 2.432444 TGGCTTTAGGTGGTTTCATCG 58.568 47.619 0.00 0.00 0.00 3.84
2112 2889 2.039216 TGGCTTTAGGTGGTTTCATCGA 59.961 45.455 0.00 0.00 0.00 3.59
2113 2890 2.418976 GGCTTTAGGTGGTTTCATCGAC 59.581 50.000 0.00 0.00 0.00 4.20
2114 2891 2.418976 GCTTTAGGTGGTTTCATCGACC 59.581 50.000 0.00 0.00 36.64 4.79
2115 2892 2.773993 TTAGGTGGTTTCATCGACCC 57.226 50.000 0.00 0.00 36.99 4.46
2116 2893 0.906775 TAGGTGGTTTCATCGACCCC 59.093 55.000 0.00 0.00 36.99 4.95
2117 2894 1.743995 GGTGGTTTCATCGACCCCG 60.744 63.158 0.00 0.00 36.30 5.73
2128 2905 3.155167 GACCCCGAGCCACCCTAG 61.155 72.222 0.00 0.00 0.00 3.02
2129 2906 3.674050 GACCCCGAGCCACCCTAGA 62.674 68.421 0.00 0.00 0.00 2.43
2130 2907 3.155167 CCCCGAGCCACCCTAGAC 61.155 72.222 0.00 0.00 0.00 2.59
2131 2908 3.155167 CCCGAGCCACCCTAGACC 61.155 72.222 0.00 0.00 0.00 3.85
2132 2909 3.155167 CCGAGCCACCCTAGACCC 61.155 72.222 0.00 0.00 0.00 4.46
2133 2910 2.042843 CGAGCCACCCTAGACCCT 60.043 66.667 0.00 0.00 0.00 4.34
2134 2911 1.229359 CGAGCCACCCTAGACCCTA 59.771 63.158 0.00 0.00 0.00 3.53
2135 2912 0.824182 CGAGCCACCCTAGACCCTAG 60.824 65.000 0.00 0.00 0.00 3.02
2136 2913 0.262285 GAGCCACCCTAGACCCTAGT 59.738 60.000 0.00 0.00 0.00 2.57
2137 2914 0.717196 AGCCACCCTAGACCCTAGTT 59.283 55.000 0.00 0.00 0.00 2.24
2138 2915 0.831307 GCCACCCTAGACCCTAGTTG 59.169 60.000 0.00 0.00 0.00 3.16
2139 2916 1.621622 GCCACCCTAGACCCTAGTTGA 60.622 57.143 0.00 0.00 0.00 3.18
2140 2917 2.960104 GCCACCCTAGACCCTAGTTGAT 60.960 54.545 0.00 0.00 0.00 2.57
2141 2918 2.700897 CCACCCTAGACCCTAGTTGATG 59.299 54.545 0.00 0.00 0.00 3.07
2142 2919 2.700897 CACCCTAGACCCTAGTTGATGG 59.299 54.545 0.00 0.00 0.00 3.51
2143 2920 1.694696 CCCTAGACCCTAGTTGATGGC 59.305 57.143 0.00 0.00 0.00 4.40
2144 2921 2.683768 CCTAGACCCTAGTTGATGGCT 58.316 52.381 0.00 0.00 0.00 4.75
2145 2922 3.041946 CCTAGACCCTAGTTGATGGCTT 58.958 50.000 0.00 0.00 0.00 4.35
2146 2923 3.456277 CCTAGACCCTAGTTGATGGCTTT 59.544 47.826 0.00 0.00 0.00 3.51
2147 2924 4.654262 CCTAGACCCTAGTTGATGGCTTTA 59.346 45.833 0.00 0.00 0.00 1.85
2148 2925 4.762289 AGACCCTAGTTGATGGCTTTAG 57.238 45.455 0.00 0.00 0.00 1.85
2149 2926 3.456277 AGACCCTAGTTGATGGCTTTAGG 59.544 47.826 0.00 0.00 0.00 2.69
2150 2927 3.190439 ACCCTAGTTGATGGCTTTAGGT 58.810 45.455 0.00 0.00 31.06 3.08
2151 2928 3.054361 ACCCTAGTTGATGGCTTTAGGTG 60.054 47.826 0.00 0.00 31.06 4.00
2152 2929 3.545703 CCTAGTTGATGGCTTTAGGTGG 58.454 50.000 0.00 0.00 0.00 4.61
2153 2930 3.054361 CCTAGTTGATGGCTTTAGGTGGT 60.054 47.826 0.00 0.00 0.00 4.16
2154 2931 3.525800 AGTTGATGGCTTTAGGTGGTT 57.474 42.857 0.00 0.00 0.00 3.67
2155 2932 3.421844 AGTTGATGGCTTTAGGTGGTTC 58.578 45.455 0.00 0.00 0.00 3.62
2156 2933 2.492088 GTTGATGGCTTTAGGTGGTTCC 59.508 50.000 0.00 0.00 0.00 3.62
2157 2934 1.339631 TGATGGCTTTAGGTGGTTCCG 60.340 52.381 0.00 0.00 41.99 4.30
2158 2935 0.696501 ATGGCTTTAGGTGGTTCCGT 59.303 50.000 0.00 0.00 41.99 4.69
2159 2936 0.035739 TGGCTTTAGGTGGTTCCGTC 59.964 55.000 0.00 0.00 41.99 4.79
2160 2937 1.017701 GGCTTTAGGTGGTTCCGTCG 61.018 60.000 0.00 0.00 41.99 5.12
2161 2938 0.037975 GCTTTAGGTGGTTCCGTCGA 60.038 55.000 0.00 0.00 41.99 4.20
2162 2939 1.706443 CTTTAGGTGGTTCCGTCGAC 58.294 55.000 5.18 5.18 41.99 4.20
2163 2940 0.318120 TTTAGGTGGTTCCGTCGACC 59.682 55.000 10.58 0.00 41.99 4.79
2164 2941 1.535204 TTAGGTGGTTCCGTCGACCC 61.535 60.000 10.58 5.77 41.99 4.46
2165 2942 4.383861 GGTGGTTCCGTCGACCCC 62.384 72.222 10.58 5.66 36.30 4.95
2166 2943 4.729856 GTGGTTCCGTCGACCCCG 62.730 72.222 10.58 0.00 36.30 5.73
2167 2944 4.972733 TGGTTCCGTCGACCCCGA 62.973 66.667 10.58 0.00 43.35 5.14
2168 2945 4.125695 GGTTCCGTCGACCCCGAG 62.126 72.222 10.58 0.00 46.52 4.63
2169 2946 4.790861 GTTCCGTCGACCCCGAGC 62.791 72.222 10.58 1.60 46.52 5.03
2177 2954 3.541713 GACCCCGAGCCAGCCTAG 61.542 72.222 0.00 0.00 0.00 3.02
2178 2955 4.075793 ACCCCGAGCCAGCCTAGA 62.076 66.667 0.00 0.00 0.00 2.43
2179 2956 3.541713 CCCCGAGCCAGCCTAGAC 61.542 72.222 0.00 0.00 0.00 2.59
2180 2957 3.541713 CCCGAGCCAGCCTAGACC 61.542 72.222 0.00 0.00 0.00 3.85
2181 2958 3.541713 CCGAGCCAGCCTAGACCC 61.542 72.222 0.00 0.00 0.00 4.46
2182 2959 2.443016 CGAGCCAGCCTAGACCCT 60.443 66.667 0.00 0.00 0.00 4.34
2183 2960 1.152735 CGAGCCAGCCTAGACCCTA 60.153 63.158 0.00 0.00 0.00 3.53
2184 2961 1.175983 CGAGCCAGCCTAGACCCTAG 61.176 65.000 0.00 0.00 0.00 3.02
2185 2962 0.105913 GAGCCAGCCTAGACCCTAGT 60.106 60.000 0.00 0.00 0.00 2.57
2186 2963 0.340208 AGCCAGCCTAGACCCTAGTT 59.660 55.000 0.00 0.00 0.00 2.24
2187 2964 0.466124 GCCAGCCTAGACCCTAGTTG 59.534 60.000 0.00 0.00 0.00 3.16
2188 2965 1.965318 GCCAGCCTAGACCCTAGTTGA 60.965 57.143 0.00 0.00 0.00 3.18
2189 2966 2.683768 CCAGCCTAGACCCTAGTTGAT 58.316 52.381 0.00 0.00 0.00 2.57
2190 2967 2.366916 CCAGCCTAGACCCTAGTTGATG 59.633 54.545 0.00 0.00 0.00 3.07
2191 2968 2.366916 CAGCCTAGACCCTAGTTGATGG 59.633 54.545 0.00 0.00 0.00 3.51
2192 2969 1.070914 GCCTAGACCCTAGTTGATGGC 59.929 57.143 0.00 0.00 0.00 4.40
2193 2970 2.683768 CCTAGACCCTAGTTGATGGCT 58.316 52.381 0.00 0.00 0.00 4.75
2561 5680 4.762289 AGACCCTAGTTGATGGCTTTAG 57.238 45.455 0.00 0.00 0.00 1.85
2562 5681 3.456277 AGACCCTAGTTGATGGCTTTAGG 59.544 47.826 0.00 0.00 0.00 2.69
2563 5682 3.190439 ACCCTAGTTGATGGCTTTAGGT 58.810 45.455 0.00 0.00 31.06 3.08
2564 5683 3.054361 ACCCTAGTTGATGGCTTTAGGTG 60.054 47.826 0.00 0.00 31.06 4.00
2565 5684 3.545703 CCTAGTTGATGGCTTTAGGTGG 58.454 50.000 0.00 0.00 0.00 4.61
2566 5685 3.054361 CCTAGTTGATGGCTTTAGGTGGT 60.054 47.826 0.00 0.00 0.00 4.16
2567 5686 3.525800 AGTTGATGGCTTTAGGTGGTT 57.474 42.857 0.00 0.00 0.00 3.67
2568 5687 3.421844 AGTTGATGGCTTTAGGTGGTTC 58.578 45.455 0.00 0.00 0.00 3.62
2569 5688 2.492088 GTTGATGGCTTTAGGTGGTTCC 59.508 50.000 0.00 0.00 0.00 3.62
2570 5689 1.339631 TGATGGCTTTAGGTGGTTCCG 60.340 52.381 0.00 0.00 41.99 4.30
2571 5690 0.696501 ATGGCTTTAGGTGGTTCCGT 59.303 50.000 0.00 0.00 41.99 4.69
2572 5691 0.035739 TGGCTTTAGGTGGTTCCGTC 59.964 55.000 0.00 0.00 41.99 4.79
2573 5692 1.017701 GGCTTTAGGTGGTTCCGTCG 61.018 60.000 0.00 0.00 41.99 5.12
2574 5693 1.632948 GCTTTAGGTGGTTCCGTCGC 61.633 60.000 0.00 0.00 41.99 5.19
2575 5694 1.004679 TTTAGGTGGTTCCGTCGCC 60.005 57.895 0.00 0.00 41.99 5.54
2576 5695 2.453379 TTTAGGTGGTTCCGTCGCCC 62.453 60.000 0.00 0.00 41.99 6.13
2589 5708 4.794648 CGCCCCCGAGCCATCAAA 62.795 66.667 0.00 0.00 36.29 2.69
2590 5709 2.362375 GCCCCCGAGCCATCAAAA 60.362 61.111 0.00 0.00 0.00 2.44
2591 5710 2.710902 GCCCCCGAGCCATCAAAAC 61.711 63.158 0.00 0.00 0.00 2.43
2592 5711 2.052104 CCCCCGAGCCATCAAAACC 61.052 63.158 0.00 0.00 0.00 3.27
2593 5712 2.052104 CCCCGAGCCATCAAAACCC 61.052 63.158 0.00 0.00 0.00 4.11
2594 5713 1.304052 CCCGAGCCATCAAAACCCA 60.304 57.895 0.00 0.00 0.00 4.51
2595 5714 0.897863 CCCGAGCCATCAAAACCCAA 60.898 55.000 0.00 0.00 0.00 4.12
2596 5715 0.965439 CCGAGCCATCAAAACCCAAA 59.035 50.000 0.00 0.00 0.00 3.28
2597 5716 1.342819 CCGAGCCATCAAAACCCAAAA 59.657 47.619 0.00 0.00 0.00 2.44
2598 5717 2.028203 CCGAGCCATCAAAACCCAAAAT 60.028 45.455 0.00 0.00 0.00 1.82
2599 5718 2.995258 CGAGCCATCAAAACCCAAAATG 59.005 45.455 0.00 0.00 0.00 2.32
2600 5719 3.305950 CGAGCCATCAAAACCCAAAATGA 60.306 43.478 0.00 0.00 0.00 2.57
2601 5720 4.621274 CGAGCCATCAAAACCCAAAATGAT 60.621 41.667 0.00 0.00 32.94 2.45
2602 5721 4.581868 AGCCATCAAAACCCAAAATGATG 58.418 39.130 7.45 7.45 45.47 3.07
2604 5723 4.950434 CATCAAAACCCAAAATGATGGC 57.050 40.909 6.69 0.00 43.33 4.40
2605 5724 4.581868 CATCAAAACCCAAAATGATGGCT 58.418 39.130 6.69 0.00 43.33 4.75
2606 5725 4.703379 TCAAAACCCAAAATGATGGCTT 57.297 36.364 0.00 0.00 39.26 4.35
2607 5726 5.046288 TCAAAACCCAAAATGATGGCTTT 57.954 34.783 0.00 0.00 39.26 3.51
2608 5727 6.179906 TCAAAACCCAAAATGATGGCTTTA 57.820 33.333 0.00 0.00 39.26 1.85
2609 5728 6.229733 TCAAAACCCAAAATGATGGCTTTAG 58.770 36.000 0.00 0.00 39.26 1.85
2610 5729 4.824479 AACCCAAAATGATGGCTTTAGG 57.176 40.909 0.00 0.00 39.26 2.69
2611 5730 3.790126 ACCCAAAATGATGGCTTTAGGT 58.210 40.909 0.00 0.00 39.26 3.08
2612 5731 3.515104 ACCCAAAATGATGGCTTTAGGTG 59.485 43.478 0.00 0.00 39.26 4.00
2613 5732 3.118665 CCCAAAATGATGGCTTTAGGTGG 60.119 47.826 0.00 0.00 39.26 4.61
2614 5733 3.515104 CCAAAATGATGGCTTTAGGTGGT 59.485 43.478 0.00 0.00 32.78 4.16
2615 5734 4.020307 CCAAAATGATGGCTTTAGGTGGTT 60.020 41.667 0.00 0.00 32.78 3.67
2616 5735 5.512921 CCAAAATGATGGCTTTAGGTGGTTT 60.513 40.000 0.00 0.00 32.78 3.27
2617 5736 5.405935 AAATGATGGCTTTAGGTGGTTTC 57.594 39.130 0.00 0.00 0.00 2.78
2618 5737 2.432444 TGATGGCTTTAGGTGGTTTCG 58.568 47.619 0.00 0.00 0.00 3.46
2619 5738 2.224670 TGATGGCTTTAGGTGGTTTCGT 60.225 45.455 0.00 0.00 0.00 3.85
2620 5739 1.886886 TGGCTTTAGGTGGTTTCGTC 58.113 50.000 0.00 0.00 0.00 4.20
2621 5740 0.794473 GGCTTTAGGTGGTTTCGTCG 59.206 55.000 0.00 0.00 0.00 5.12
2622 5741 1.606224 GGCTTTAGGTGGTTTCGTCGA 60.606 52.381 0.00 0.00 0.00 4.20
2623 5742 1.458445 GCTTTAGGTGGTTTCGTCGAC 59.542 52.381 5.18 5.18 0.00 4.20
2624 5743 2.064014 CTTTAGGTGGTTTCGTCGACC 58.936 52.381 10.58 0.00 36.64 4.79
2625 5744 0.318120 TTAGGTGGTTTCGTCGACCC 59.682 55.000 10.58 5.77 36.99 4.46
2626 5745 1.535204 TAGGTGGTTTCGTCGACCCC 61.535 60.000 10.58 5.66 36.99 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 1.542492 AATGCAACAAGCCTCTCTGG 58.458 50.000 0.00 0.00 44.83 3.86
257 258 6.710278 TCTGTCACTTCCAATGAACATATCA 58.290 36.000 0.00 0.00 43.67 2.15
340 341 5.891551 TCCTACAATGAGCACTACAGTATGA 59.108 40.000 0.00 0.00 39.69 2.15
388 389 5.946377 AGCCTATATTTAGCCTAAATGCACC 59.054 40.000 17.91 4.84 38.70 5.01
518 541 9.088512 GTTACTTATTAAGAGTCACACATCAGG 57.911 37.037 10.39 0.00 0.00 3.86
936 959 6.476706 CACAATTCTGACCTTCTTGGAAAAAC 59.523 38.462 0.00 0.00 39.71 2.43
945 968 3.884037 AACCCACAATTCTGACCTTCT 57.116 42.857 0.00 0.00 0.00 2.85
985 1008 1.143329 TCCATTGTTGGGGGCCACTA 61.143 55.000 7.61 0.00 43.81 2.74
1147 1170 4.019792 AGTCCACAAGTTGATGCACATA 57.980 40.909 10.54 0.00 0.00 2.29
1186 1209 6.261826 GCTGACTGCAGATAACTAAAATCCAT 59.738 38.462 23.35 0.00 45.17 3.41
1318 1341 0.670162 GCACTTGTCAGGTTGCACAT 59.330 50.000 0.00 0.00 0.00 3.21
1459 1482 2.234908 TCAACTCTAGCTTCTCTTGGGC 59.765 50.000 0.00 0.00 0.00 5.36
1536 1559 7.609532 AGCTCAGTTATCTTAAACTCTTGCATT 59.390 33.333 0.00 0.00 37.61 3.56
1703 1727 7.859325 AGAACCATACATTACACAACCATAC 57.141 36.000 0.00 0.00 0.00 2.39
1970 2026 8.458843 GCATCACTGTACCATAACAAACTATTT 58.541 33.333 0.00 0.00 0.00 1.40
2096 2873 1.279846 GGGGTCGATGAAACCACCTAA 59.720 52.381 0.00 0.00 38.62 2.69
2097 2874 0.906775 GGGGTCGATGAAACCACCTA 59.093 55.000 0.00 0.00 38.62 3.08
2098 2875 1.683441 GGGGTCGATGAAACCACCT 59.317 57.895 0.00 0.00 38.62 4.00
2099 2876 1.743995 CGGGGTCGATGAAACCACC 60.744 63.158 0.00 0.00 36.83 4.61
2100 2877 0.739813 CTCGGGGTCGATGAAACCAC 60.740 60.000 0.00 0.00 45.04 4.16
2101 2878 1.594833 CTCGGGGTCGATGAAACCA 59.405 57.895 0.00 0.00 45.04 3.67
2102 2879 1.814169 GCTCGGGGTCGATGAAACC 60.814 63.158 0.00 0.00 45.04 3.27
2103 2880 1.814169 GGCTCGGGGTCGATGAAAC 60.814 63.158 0.00 0.00 45.04 2.78
2104 2881 2.287274 TGGCTCGGGGTCGATGAAA 61.287 57.895 0.00 0.00 45.04 2.69
2105 2882 2.682136 TGGCTCGGGGTCGATGAA 60.682 61.111 0.00 0.00 45.04 2.57
2106 2883 3.458163 GTGGCTCGGGGTCGATGA 61.458 66.667 0.00 0.00 45.04 2.92
2107 2884 4.530857 GGTGGCTCGGGGTCGATG 62.531 72.222 0.00 0.00 45.04 3.84
2111 2888 3.155167 CTAGGGTGGCTCGGGGTC 61.155 72.222 0.00 0.00 0.00 4.46
2112 2889 3.680196 TCTAGGGTGGCTCGGGGT 61.680 66.667 0.00 0.00 0.00 4.95
2113 2890 3.155167 GTCTAGGGTGGCTCGGGG 61.155 72.222 0.00 0.00 0.00 5.73
2114 2891 3.155167 GGTCTAGGGTGGCTCGGG 61.155 72.222 0.00 0.00 0.00 5.14
2115 2892 2.294170 TAGGGTCTAGGGTGGCTCGG 62.294 65.000 0.00 0.00 0.00 4.63
2116 2893 0.824182 CTAGGGTCTAGGGTGGCTCG 60.824 65.000 0.00 0.00 0.00 5.03
2117 2894 0.262285 ACTAGGGTCTAGGGTGGCTC 59.738 60.000 6.86 0.00 0.00 4.70
2118 2895 0.717196 AACTAGGGTCTAGGGTGGCT 59.283 55.000 6.86 0.00 0.00 4.75
2119 2896 0.831307 CAACTAGGGTCTAGGGTGGC 59.169 60.000 6.86 0.00 0.00 5.01
2120 2897 2.544844 TCAACTAGGGTCTAGGGTGG 57.455 55.000 6.86 0.00 0.00 4.61
2121 2898 2.700897 CCATCAACTAGGGTCTAGGGTG 59.299 54.545 6.86 4.80 0.00 4.61
2122 2899 2.960104 GCCATCAACTAGGGTCTAGGGT 60.960 54.545 6.86 0.00 0.00 4.34
2123 2900 1.694696 GCCATCAACTAGGGTCTAGGG 59.305 57.143 6.86 0.00 0.00 3.53
2124 2901 2.683768 AGCCATCAACTAGGGTCTAGG 58.316 52.381 6.86 0.00 0.00 3.02
2125 2902 4.762289 AAAGCCATCAACTAGGGTCTAG 57.238 45.455 0.00 0.83 33.84 2.43
2126 2903 4.654262 CCTAAAGCCATCAACTAGGGTCTA 59.346 45.833 0.00 0.00 33.84 2.59
2127 2904 3.456277 CCTAAAGCCATCAACTAGGGTCT 59.544 47.826 0.00 0.00 33.84 3.85
2128 2905 3.200165 ACCTAAAGCCATCAACTAGGGTC 59.800 47.826 0.00 0.00 34.58 4.46
2129 2906 3.054361 CACCTAAAGCCATCAACTAGGGT 60.054 47.826 0.00 0.00 34.58 4.34
2130 2907 3.545703 CACCTAAAGCCATCAACTAGGG 58.454 50.000 0.00 0.00 34.58 3.53
2131 2908 3.054361 ACCACCTAAAGCCATCAACTAGG 60.054 47.826 0.00 0.00 36.09 3.02
2132 2909 4.222124 ACCACCTAAAGCCATCAACTAG 57.778 45.455 0.00 0.00 0.00 2.57
2133 2910 4.566907 GGAACCACCTAAAGCCATCAACTA 60.567 45.833 0.00 0.00 35.41 2.24
2134 2911 3.421844 GAACCACCTAAAGCCATCAACT 58.578 45.455 0.00 0.00 0.00 3.16
2135 2912 2.492088 GGAACCACCTAAAGCCATCAAC 59.508 50.000 0.00 0.00 35.41 3.18
2136 2913 2.802719 GGAACCACCTAAAGCCATCAA 58.197 47.619 0.00 0.00 35.41 2.57
2137 2914 1.339631 CGGAACCACCTAAAGCCATCA 60.340 52.381 0.00 0.00 36.31 3.07
2138 2915 1.339727 ACGGAACCACCTAAAGCCATC 60.340 52.381 0.00 0.00 36.31 3.51
2139 2916 0.696501 ACGGAACCACCTAAAGCCAT 59.303 50.000 0.00 0.00 36.31 4.40
2140 2917 0.035739 GACGGAACCACCTAAAGCCA 59.964 55.000 0.00 0.00 36.31 4.75
2141 2918 1.017701 CGACGGAACCACCTAAAGCC 61.018 60.000 0.00 0.00 36.31 4.35
2142 2919 0.037975 TCGACGGAACCACCTAAAGC 60.038 55.000 0.00 0.00 36.31 3.51
2143 2920 1.670967 GGTCGACGGAACCACCTAAAG 60.671 57.143 9.92 0.00 36.31 1.85
2144 2921 0.318120 GGTCGACGGAACCACCTAAA 59.682 55.000 9.92 0.00 36.31 1.85
2145 2922 1.966762 GGTCGACGGAACCACCTAA 59.033 57.895 9.92 0.00 36.31 2.69
2146 2923 3.685435 GGTCGACGGAACCACCTA 58.315 61.111 9.92 0.00 36.31 3.08
2152 2929 4.790861 GCTCGGGGTCGACGGAAC 62.791 72.222 9.92 0.00 40.88 3.62
2160 2937 3.541713 CTAGGCTGGCTCGGGGTC 61.542 72.222 7.13 0.00 0.00 4.46
2161 2938 4.075793 TCTAGGCTGGCTCGGGGT 62.076 66.667 7.13 0.00 0.00 4.95
2162 2939 3.541713 GTCTAGGCTGGCTCGGGG 61.542 72.222 7.13 0.00 0.00 5.73
2163 2940 3.541713 GGTCTAGGCTGGCTCGGG 61.542 72.222 7.13 0.00 0.00 5.14
2164 2941 2.642183 TAGGGTCTAGGCTGGCTCGG 62.642 65.000 7.13 2.25 0.00 4.63
2165 2942 1.152735 TAGGGTCTAGGCTGGCTCG 60.153 63.158 7.13 0.74 0.00 5.03
2166 2943 0.105913 ACTAGGGTCTAGGCTGGCTC 60.106 60.000 7.13 0.00 0.00 4.70
2167 2944 0.340208 AACTAGGGTCTAGGCTGGCT 59.660 55.000 9.28 9.28 0.00 4.75
2168 2945 0.466124 CAACTAGGGTCTAGGCTGGC 59.534 60.000 0.00 0.00 0.00 4.85
2169 2946 2.160721 TCAACTAGGGTCTAGGCTGG 57.839 55.000 0.00 0.00 0.00 4.85
2170 2947 2.366916 CCATCAACTAGGGTCTAGGCTG 59.633 54.545 0.00 4.19 0.00 4.85
2171 2948 2.683768 CCATCAACTAGGGTCTAGGCT 58.316 52.381 0.00 0.00 0.00 4.58
2172 2949 1.070914 GCCATCAACTAGGGTCTAGGC 59.929 57.143 6.86 0.00 0.00 3.93
2173 2950 2.683768 AGCCATCAACTAGGGTCTAGG 58.316 52.381 6.86 0.00 0.00 3.02
2174 2951 4.762289 AAAGCCATCAACTAGGGTCTAG 57.238 45.455 0.00 0.83 33.84 2.43
2175 2952 4.654262 CCTAAAGCCATCAACTAGGGTCTA 59.346 45.833 0.00 0.00 33.84 2.59
2176 2953 3.456277 CCTAAAGCCATCAACTAGGGTCT 59.544 47.826 0.00 0.00 33.84 3.85
2177 2954 3.200165 ACCTAAAGCCATCAACTAGGGTC 59.800 47.826 0.00 0.00 34.58 4.46
2178 2955 3.054361 CACCTAAAGCCATCAACTAGGGT 60.054 47.826 0.00 0.00 34.58 4.34
2179 2956 3.545703 CACCTAAAGCCATCAACTAGGG 58.454 50.000 0.00 0.00 34.58 3.53
2180 2957 3.054361 ACCACCTAAAGCCATCAACTAGG 60.054 47.826 0.00 0.00 36.09 3.02
2181 2958 4.222124 ACCACCTAAAGCCATCAACTAG 57.778 45.455 0.00 0.00 0.00 2.57
2182 2959 4.650972 AACCACCTAAAGCCATCAACTA 57.349 40.909 0.00 0.00 0.00 2.24
2183 2960 3.525800 AACCACCTAAAGCCATCAACT 57.474 42.857 0.00 0.00 0.00 3.16
2184 2961 3.365969 CGAAACCACCTAAAGCCATCAAC 60.366 47.826 0.00 0.00 0.00 3.18
2185 2962 2.817258 CGAAACCACCTAAAGCCATCAA 59.183 45.455 0.00 0.00 0.00 2.57
2186 2963 2.224670 ACGAAACCACCTAAAGCCATCA 60.225 45.455 0.00 0.00 0.00 3.07
2187 2964 2.418976 GACGAAACCACCTAAAGCCATC 59.581 50.000 0.00 0.00 0.00 3.51
2188 2965 2.433436 GACGAAACCACCTAAAGCCAT 58.567 47.619 0.00 0.00 0.00 4.40
2189 2966 1.874739 CGACGAAACCACCTAAAGCCA 60.875 52.381 0.00 0.00 0.00 4.75
2190 2967 0.794473 CGACGAAACCACCTAAAGCC 59.206 55.000 0.00 0.00 0.00 4.35
2191 2968 1.458445 GTCGACGAAACCACCTAAAGC 59.542 52.381 0.00 0.00 0.00 3.51
2192 2969 2.064014 GGTCGACGAAACCACCTAAAG 58.936 52.381 9.92 0.00 36.75 1.85
2193 2970 1.270252 GGGTCGACGAAACCACCTAAA 60.270 52.381 9.92 0.00 38.62 1.85
2543 5662 3.545703 CACCTAAAGCCATCAACTAGGG 58.454 50.000 0.00 0.00 34.58 3.53
2555 5674 1.632948 GCGACGGAACCACCTAAAGC 61.633 60.000 0.00 0.00 36.31 3.51
2556 5675 1.017701 GGCGACGGAACCACCTAAAG 61.018 60.000 0.00 0.00 36.31 1.85
2557 5676 1.004679 GGCGACGGAACCACCTAAA 60.005 57.895 0.00 0.00 36.31 1.85
2558 5677 2.658422 GGCGACGGAACCACCTAA 59.342 61.111 0.00 0.00 36.31 2.69
2559 5678 3.384532 GGGCGACGGAACCACCTA 61.385 66.667 0.00 0.00 36.31 3.08
2572 5691 4.794648 TTTGATGGCTCGGGGGCG 62.795 66.667 0.00 0.00 44.11 6.13
2573 5692 2.362375 TTTTGATGGCTCGGGGGC 60.362 61.111 0.00 0.00 41.27 5.80
2574 5693 2.052104 GGTTTTGATGGCTCGGGGG 61.052 63.158 0.00 0.00 0.00 5.40
2575 5694 2.052104 GGGTTTTGATGGCTCGGGG 61.052 63.158 0.00 0.00 0.00 5.73
2576 5695 0.897863 TTGGGTTTTGATGGCTCGGG 60.898 55.000 0.00 0.00 0.00 5.14
2577 5696 0.965439 TTTGGGTTTTGATGGCTCGG 59.035 50.000 0.00 0.00 0.00 4.63
2578 5697 2.810439 TTTTGGGTTTTGATGGCTCG 57.190 45.000 0.00 0.00 0.00 5.03
2579 5698 4.270245 TCATTTTGGGTTTTGATGGCTC 57.730 40.909 0.00 0.00 0.00 4.70
2580 5699 4.581868 CATCATTTTGGGTTTTGATGGCT 58.418 39.130 4.28 0.00 40.99 4.75
2581 5700 4.950434 CATCATTTTGGGTTTTGATGGC 57.050 40.909 4.28 0.00 40.99 4.40
2583 5702 4.581868 AGCCATCATTTTGGGTTTTGATG 58.418 39.130 5.07 5.07 44.96 3.07
2584 5703 4.914177 AGCCATCATTTTGGGTTTTGAT 57.086 36.364 0.00 0.00 44.96 2.57
2591 5710 3.118665 CCACCTAAAGCCATCATTTTGGG 60.119 47.826 4.42 0.00 39.84 4.12
2592 5711 3.515104 ACCACCTAAAGCCATCATTTTGG 59.485 43.478 0.00 0.00 38.16 3.28
2593 5712 4.806640 ACCACCTAAAGCCATCATTTTG 57.193 40.909 0.00 0.00 0.00 2.44
2594 5713 5.566627 CGAAACCACCTAAAGCCATCATTTT 60.567 40.000 0.00 0.00 0.00 1.82
2595 5714 4.082245 CGAAACCACCTAAAGCCATCATTT 60.082 41.667 0.00 0.00 0.00 2.32
2596 5715 3.443681 CGAAACCACCTAAAGCCATCATT 59.556 43.478 0.00 0.00 0.00 2.57
2597 5716 3.016736 CGAAACCACCTAAAGCCATCAT 58.983 45.455 0.00 0.00 0.00 2.45
2598 5717 2.224670 ACGAAACCACCTAAAGCCATCA 60.225 45.455 0.00 0.00 0.00 3.07
2599 5718 2.418976 GACGAAACCACCTAAAGCCATC 59.581 50.000 0.00 0.00 0.00 3.51
2600 5719 2.433436 GACGAAACCACCTAAAGCCAT 58.567 47.619 0.00 0.00 0.00 4.40
2601 5720 1.874739 CGACGAAACCACCTAAAGCCA 60.875 52.381 0.00 0.00 0.00 4.75
2602 5721 0.794473 CGACGAAACCACCTAAAGCC 59.206 55.000 0.00 0.00 0.00 4.35
2603 5722 1.458445 GTCGACGAAACCACCTAAAGC 59.542 52.381 0.00 0.00 0.00 3.51
2604 5723 2.064014 GGTCGACGAAACCACCTAAAG 58.936 52.381 9.92 0.00 36.75 1.85
2605 5724 1.270252 GGGTCGACGAAACCACCTAAA 60.270 52.381 9.92 0.00 38.62 1.85
2606 5725 0.318120 GGGTCGACGAAACCACCTAA 59.682 55.000 9.92 0.00 38.62 2.69
2607 5726 1.535204 GGGGTCGACGAAACCACCTA 61.535 60.000 18.27 0.00 38.62 3.08
2608 5727 2.739132 GGGTCGACGAAACCACCT 59.261 61.111 9.92 0.00 38.62 4.00
2609 5728 2.357881 GGGGTCGACGAAACCACC 60.358 66.667 18.27 5.91 38.62 4.61


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

AutoCloner maintained by Alex Coulton.