Multiple sequence alignment - TraesCS1B01G431700

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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 TraesCS1B01G431700 chr1B 100.000 3325 0 0 1 3325 656181810 656185134 0.000000e+00 6141.0
1 TraesCS1B01G431700 chr1B 81.250 128 22 2 1683 1809 484691128 484691002 5.870000e-18 102.0
2 TraesCS1B01G431700 chr1B 80.800 125 22 2 1697 1820 484463743 484463620 2.730000e-16 97.1
3 TraesCS1B01G431700 chr4A 91.068 3370 214 35 1 3319 598297035 598293702 0.000000e+00 4475.0
4 TraesCS1B01G431700 chr4A 77.099 262 54 5 635 893 598247027 598246769 2.670000e-31 147.0
5 TraesCS1B01G431700 chr2D 80.534 262 49 2 632 892 6905154 6904894 2.020000e-47 200.0
6 TraesCS1B01G431700 chr1A 75.216 464 89 18 631 1084 573033383 573032936 2.620000e-46 196.0
7 TraesCS1B01G431700 chr1A 80.159 126 23 2 1685 1809 461642419 461642295 3.530000e-15 93.5
8 TraesCS1B01G431700 chr1D 78.462 260 54 2 635 893 472202618 472202360 5.700000e-38 169.0
9 TraesCS1B01G431700 chr1D 80.952 126 22 2 1685 1809 362131014 362130890 7.590000e-17 99.0
10 TraesCS1B01G431700 chr6A 100.000 28 0 0 2368 2395 115272502 115272475 6.000000e-03 52.8
11 TraesCS1B01G431700 chr5B 100.000 28 0 0 2368 2395 548044664 548044637 6.000000e-03 52.8


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 TraesCS1B01G431700 chr1B 656181810 656185134 3324 False 6141 6141 100.000 1 3325 1 chr1B.!!$F1 3324
1 TraesCS1B01G431700 chr4A 598293702 598297035 3333 True 4475 4475 91.068 1 3319 1 chr4A.!!$R2 3318

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
163 166 0.461548 TGCCTCGGATGATGTGTCTC 59.538 55.0 0.0 0.0 0.00 3.36 F
1823 1848 0.251634 TGGCTCACGGCATCAATGTA 59.748 50.0 0.0 0.0 44.01 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 1962 0.736325 CGTTCCTCACACTTAGGGCG 60.736 60.0 0.0 0.0 34.66 6.13 R
2652 2687 0.174845 TTGATCGGAACAGCCTACGG 59.825 55.0 0.0 0.0 0.00 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
21 22 4.948341 TGGTCGTGTATATGCTTACCAT 57.052 40.909 7.88 0.00 37.97 3.55
44 45 2.947652 TCACCGTCTCCGATAGTTTAGG 59.052 50.000 0.00 0.00 35.63 2.69
53 54 3.635373 TCCGATAGTTTAGGTTCTGCGAT 59.365 43.478 0.00 0.00 0.00 4.58
71 72 5.357257 TGCGATGACTCCTTTTTCCTATAC 58.643 41.667 0.00 0.00 0.00 1.47
90 91 8.517056 TCCTATACAGATAATTTTGCGACGATA 58.483 33.333 0.00 0.00 0.00 2.92
163 166 0.461548 TGCCTCGGATGATGTGTCTC 59.538 55.000 0.00 0.00 0.00 3.36
165 168 1.957177 GCCTCGGATGATGTGTCTCTA 59.043 52.381 0.00 0.00 0.00 2.43
186 189 6.513180 TCTATATAGTTGGTGTTGTGCTAGC 58.487 40.000 8.10 8.10 0.00 3.42
189 192 2.767505 AGTTGGTGTTGTGCTAGCTAC 58.232 47.619 17.23 12.72 0.00 3.58
202 206 4.081586 GTGCTAGCTACTGAACTAGGGTTT 60.082 45.833 17.23 0.00 37.05 3.27
216 220 3.806949 AGGGTTTGATTGGAGTTAGCA 57.193 42.857 0.00 0.00 0.00 3.49
219 223 3.763897 GGGTTTGATTGGAGTTAGCACAT 59.236 43.478 0.00 0.00 0.00 3.21
293 301 9.136323 TGAGCATAAGATGACAATAGAGAACTA 57.864 33.333 0.00 0.00 0.00 2.24
294 302 9.405587 GAGCATAAGATGACAATAGAGAACTAC 57.594 37.037 0.00 0.00 0.00 2.73
295 303 8.918116 AGCATAAGATGACAATAGAGAACTACA 58.082 33.333 0.00 0.00 0.00 2.74
296 304 9.190858 GCATAAGATGACAATAGAGAACTACAG 57.809 37.037 0.00 0.00 0.00 2.74
345 365 8.022550 CAGCTGATGACAATAGAGTATGAGTAG 58.977 40.741 8.42 0.00 0.00 2.57
347 367 7.522889 GCTGATGACAATAGAGTATGAGTAGCA 60.523 40.741 0.00 0.00 0.00 3.49
380 400 2.326550 CGGCGCACGTTTTTCACT 59.673 55.556 10.83 0.00 37.93 3.41
381 401 1.721133 CGGCGCACGTTTTTCACTC 60.721 57.895 10.83 0.00 37.93 3.51
382 402 1.647084 GGCGCACGTTTTTCACTCT 59.353 52.632 10.83 0.00 0.00 3.24
466 486 7.781324 ACCATGGCTTTTGGATATAAATAGG 57.219 36.000 13.04 0.00 37.69 2.57
470 490 8.859090 CATGGCTTTTGGATATAAATAGGTCAA 58.141 33.333 0.00 0.00 0.00 3.18
544 564 4.321217 GCTATTGCTTGCGACTATACTACG 59.679 45.833 0.00 0.00 36.03 3.51
549 569 4.094739 TGCTTGCGACTATACTACGTACAA 59.905 41.667 0.00 0.00 0.00 2.41
886 907 2.580601 AAGTTCCTGTACGCGCCCT 61.581 57.895 5.73 0.00 0.00 5.19
991 1012 2.607750 GGCCACTGTGGAGGGAGA 60.608 66.667 30.23 0.00 40.96 3.71
1014 1035 0.918799 ACTGGATGGGGTATGTGGCA 60.919 55.000 0.00 0.00 0.00 4.92
1060 1081 4.467084 TGGGGAGGCGCGACATTC 62.467 66.667 17.71 2.85 0.00 2.67
1062 1083 2.586357 GGGAGGCGCGACATTCTC 60.586 66.667 17.71 0.00 0.00 2.87
1074 1095 4.373116 ATTCTCGTGGCGTGGCGT 62.373 61.111 0.00 0.00 0.00 5.68
1101 1122 3.122948 CCGTGACGAAACTGGAGTATTTG 59.877 47.826 6.54 0.00 0.00 2.32
1103 1124 4.446385 CGTGACGAAACTGGAGTATTTGAA 59.554 41.667 0.00 0.00 0.00 2.69
1110 1131 2.559668 ACTGGAGTATTTGAACGACGGA 59.440 45.455 0.00 0.00 0.00 4.69
1173 1194 4.547367 GCGGCCGCCTACAAGGAT 62.547 66.667 39.89 0.00 37.67 3.24
1176 1197 2.902343 GCCGCCTACAAGGATGCC 60.902 66.667 0.00 0.00 37.67 4.40
1188 1209 2.043652 GATGCCAGGGTGCACCAT 60.044 61.111 35.78 28.59 45.48 3.55
1245 1266 3.500448 TCCAAGCACAATAACACCAGA 57.500 42.857 0.00 0.00 0.00 3.86
1273 1294 9.042450 TCCAAGATCAGGTATTACTTCACTTTA 57.958 33.333 0.00 0.00 0.00 1.85
1288 1309 8.429493 ACTTCACTTTAAACTTACGCTTAACT 57.571 30.769 0.00 0.00 0.00 2.24
1306 1327 9.478019 CGCTTAACTAACTATTGAACTGAATTG 57.522 33.333 0.00 0.00 0.00 2.32
1315 1336 5.972107 ATTGAACTGAATTGAGAAGTGGG 57.028 39.130 0.00 0.00 0.00 4.61
1339 1360 8.251026 GGGAAATTATTTTGGAGGTACTTCTTG 58.749 37.037 4.85 0.00 41.55 3.02
1340 1361 9.020731 GGAAATTATTTTGGAGGTACTTCTTGA 57.979 33.333 4.85 0.00 41.55 3.02
1346 1367 7.797038 TTTTGGAGGTACTTCTTGAGTTTAC 57.203 36.000 4.85 0.00 41.55 2.01
1348 1369 6.742559 TGGAGGTACTTCTTGAGTTTACTT 57.257 37.500 4.85 0.00 41.55 2.24
1349 1370 7.133133 TGGAGGTACTTCTTGAGTTTACTTT 57.867 36.000 4.85 0.00 41.55 2.66
1350 1371 6.990349 TGGAGGTACTTCTTGAGTTTACTTTG 59.010 38.462 4.85 0.00 41.55 2.77
1351 1372 7.147620 TGGAGGTACTTCTTGAGTTTACTTTGA 60.148 37.037 4.85 0.00 41.55 2.69
1352 1373 7.171167 GGAGGTACTTCTTGAGTTTACTTTGAC 59.829 40.741 4.85 0.00 41.55 3.18
1366 1387 9.063615 AGTTTACTTTGACCATCGATTTAACTT 57.936 29.630 0.00 0.00 0.00 2.66
1370 1391 8.029642 ACTTTGACCATCGATTTAACTTACAG 57.970 34.615 0.00 0.00 0.00 2.74
1521 1544 7.462571 AGGTAGAAACAAAAATACCATGTCC 57.537 36.000 3.31 0.00 40.16 4.02
1526 1549 4.108699 ACAAAAATACCATGTCCATGCG 57.891 40.909 1.64 0.00 37.49 4.73
1533 1556 0.308684 CCATGTCCATGCGTGCATAC 59.691 55.000 7.07 3.98 37.49 2.39
1535 1558 1.401199 CATGTCCATGCGTGCATACAA 59.599 47.619 12.84 0.00 34.91 2.41
1539 1562 2.916716 GTCCATGCGTGCATACAAAAAG 59.083 45.455 7.07 0.00 34.91 2.27
1545 1568 2.973224 GCGTGCATACAAAAAGTGAGTG 59.027 45.455 0.00 0.00 0.00 3.51
1553 1576 8.668353 TGCATACAAAAAGTGAGTGAATATCTC 58.332 33.333 0.00 0.00 0.00 2.75
1556 1579 7.121974 ACAAAAAGTGAGTGAATATCTCGTG 57.878 36.000 0.00 0.00 34.99 4.35
1571 1594 1.200252 CTCGTGACGGAACAGAGACAT 59.800 52.381 4.70 0.00 0.00 3.06
1572 1595 1.199327 TCGTGACGGAACAGAGACATC 59.801 52.381 4.70 0.00 0.00 3.06
1606 1631 9.126151 TCATCAATAACAAAACCTTCACAAGTA 57.874 29.630 0.00 0.00 0.00 2.24
1634 1659 1.774110 TGGTCAAGCCACAATTGTGT 58.226 45.000 31.20 15.56 43.61 3.72
1677 1702 2.584791 CTTGCGTGTTGATTAAGCACC 58.415 47.619 0.00 0.00 37.57 5.01
1754 1779 2.094659 GGTCAGCATCACCGTGACG 61.095 63.158 2.57 0.00 41.33 4.35
1811 1836 2.094659 CGTCGACATGGTGGCTCAC 61.095 63.158 17.16 0.00 0.00 3.51
1823 1848 0.251634 TGGCTCACGGCATCAATGTA 59.748 50.000 0.00 0.00 44.01 2.29
1847 1872 2.758648 TGCCTACTCCAAGCAGTCA 58.241 52.632 0.00 0.00 31.65 3.41
1934 1959 1.005630 CGCCTCATTCCCCGATCTC 60.006 63.158 0.00 0.00 0.00 2.75
1937 1962 1.005630 CTCATTCCCCGATCTCCGC 60.006 63.158 0.00 0.00 36.84 5.54
1976 2001 0.482446 AATTTGACCCTGTGCCCTCA 59.518 50.000 0.00 0.00 0.00 3.86
2121 2146 2.603473 AGGTCTACCTGCACGGCA 60.603 61.111 0.00 0.00 46.55 5.69
2171 2196 3.499737 CGCCTGGTGGTCAATCGC 61.500 66.667 0.00 0.00 35.27 4.58
2174 2199 2.100631 CCTGGTGGTCAATCGCGAC 61.101 63.158 12.93 0.00 35.03 5.19
2179 2204 1.515519 TGGTCAATCGCGACGTAGC 60.516 57.895 12.93 10.95 36.73 3.58
2180 2205 1.515519 GGTCAATCGCGACGTAGCA 60.516 57.895 20.68 8.21 36.73 3.49
2198 2223 1.972872 CACTTCTGAACAAGTGGGCT 58.027 50.000 5.57 0.00 46.57 5.19
2273 2298 1.973281 GTGCATGGTCAGGGGTGTG 60.973 63.158 0.00 0.00 0.00 3.82
2300 2325 4.130118 GCCACTGGAAATTCGATGACTAT 58.870 43.478 0.00 0.00 0.00 2.12
2306 2331 5.601662 TGGAAATTCGATGACTATGAGGAC 58.398 41.667 0.00 0.00 0.00 3.85
2333 2358 7.045126 CCAATTAAGTGGTTAGGTTTTCACA 57.955 36.000 13.84 0.00 33.63 3.58
2334 2359 6.921307 CCAATTAAGTGGTTAGGTTTTCACAC 59.079 38.462 13.84 0.00 33.63 3.82
2335 2360 7.416890 CCAATTAAGTGGTTAGGTTTTCACACA 60.417 37.037 13.84 0.00 33.63 3.72
2375 2400 0.541863 AAGGATAACCACGGCCTCTG 59.458 55.000 0.00 0.00 38.94 3.35
2380 2405 1.549243 TAACCACGGCCTCTGCATCA 61.549 55.000 0.00 0.00 40.13 3.07
2382 2407 1.452651 CCACGGCCTCTGCATCAAT 60.453 57.895 0.00 0.00 40.13 2.57
2383 2408 1.033746 CCACGGCCTCTGCATCAATT 61.034 55.000 0.00 0.00 40.13 2.32
2488 2523 6.839134 ACAATAAGAAAAGGGAAAACCAGAGT 59.161 34.615 0.00 0.00 43.89 3.24
2497 2532 6.636454 AGGGAAAACCAGAGTTCATACATA 57.364 37.500 0.00 0.00 43.89 2.29
2498 2533 7.213178 AGGGAAAACCAGAGTTCATACATAT 57.787 36.000 0.00 0.00 43.89 1.78
2499 2534 7.643123 AGGGAAAACCAGAGTTCATACATATT 58.357 34.615 0.00 0.00 43.89 1.28
2500 2535 8.116026 AGGGAAAACCAGAGTTCATACATATTT 58.884 33.333 0.00 0.00 43.89 1.40
2501 2536 8.190784 GGGAAAACCAGAGTTCATACATATTTG 58.809 37.037 0.00 0.00 39.85 2.32
2502 2537 8.956426 GGAAAACCAGAGTTCATACATATTTGA 58.044 33.333 0.00 0.00 34.19 2.69
2526 2561 2.683968 TGACCAGCTTCACGATTGTAC 58.316 47.619 0.00 0.00 0.00 2.90
2530 2565 2.271800 CAGCTTCACGATTGTACCTCC 58.728 52.381 0.00 0.00 0.00 4.30
2534 2569 3.125316 GCTTCACGATTGTACCTCCAAAG 59.875 47.826 0.00 0.00 0.00 2.77
2535 2570 4.315803 CTTCACGATTGTACCTCCAAAGT 58.684 43.478 0.00 0.00 0.00 2.66
2537 2572 4.710324 TCACGATTGTACCTCCAAAGTTT 58.290 39.130 0.00 0.00 0.00 2.66
2587 2622 4.166011 GCCGGTCGAGCAACATGC 62.166 66.667 15.89 4.99 45.46 4.06
2636 2671 9.312904 TCCATGAAAACATCTAAAGAAGGAATT 57.687 29.630 0.00 0.00 0.00 2.17
2638 2673 8.866956 CATGAAAACATCTAAAGAAGGAATTGC 58.133 33.333 0.00 0.00 0.00 3.56
2640 2675 5.567138 AACATCTAAAGAAGGAATTGCCG 57.433 39.130 0.00 0.00 43.43 5.69
2653 2688 4.830765 TGCCGTCCGCATGCTACC 62.831 66.667 17.13 1.61 44.64 3.18
2685 2720 2.230992 CCGATCAAAGGAAAACATGGCA 59.769 45.455 0.00 0.00 0.00 4.92
2687 2722 4.497300 CGATCAAAGGAAAACATGGCAAT 58.503 39.130 0.00 0.00 0.00 3.56
2688 2723 5.394005 CCGATCAAAGGAAAACATGGCAATA 60.394 40.000 0.00 0.00 0.00 1.90
2692 2727 6.397272 TCAAAGGAAAACATGGCAATATCAC 58.603 36.000 0.00 0.00 0.00 3.06
2695 2730 3.181466 GGAAAACATGGCAATATCACCCC 60.181 47.826 0.00 0.00 0.00 4.95
2725 2760 3.565307 ACTTCAAGCCAACATCCTCAAA 58.435 40.909 0.00 0.00 0.00 2.69
2732 2767 5.612725 AGCCAACATCCTCAAAAAGAAAA 57.387 34.783 0.00 0.00 0.00 2.29
2734 2769 4.751600 GCCAACATCCTCAAAAAGAAAAGG 59.248 41.667 0.00 0.00 0.00 3.11
2735 2770 5.453198 GCCAACATCCTCAAAAAGAAAAGGA 60.453 40.000 0.00 0.00 41.93 3.36
2736 2771 5.985530 CCAACATCCTCAAAAAGAAAAGGAC 59.014 40.000 0.00 0.00 40.59 3.85
2737 2772 5.438761 ACATCCTCAAAAAGAAAAGGACG 57.561 39.130 0.00 0.00 40.59 4.79
2754 2789 2.233355 GACGTGCAAATGTCGATGTTG 58.767 47.619 0.00 0.00 0.00 3.33
2786 2821 2.351738 CCAAAAAGGCGAAGTCATGGTC 60.352 50.000 0.00 0.00 0.00 4.02
2802 2837 2.042831 GTCATGCCACCAGCCAGTC 61.043 63.158 0.00 0.00 42.71 3.51
2803 2838 2.034532 CATGCCACCAGCCAGTCA 59.965 61.111 0.00 0.00 42.71 3.41
2822 2866 3.993081 GTCAGTGTCTCTTCCTTGATGTG 59.007 47.826 0.00 0.00 0.00 3.21
2827 2871 6.875726 CAGTGTCTCTTCCTTGATGTGAAATA 59.124 38.462 0.00 0.00 0.00 1.40
2866 2910 6.806739 GGTCACATTTAGTAGATTGTTTTGGC 59.193 38.462 0.00 0.00 0.00 4.52
2887 2931 4.697352 GGCGAATATAAAGATGCAGTGGAT 59.303 41.667 0.00 0.00 0.00 3.41
2921 2965 0.550914 AGTGACCAGGCCAAGAACAA 59.449 50.000 5.01 0.00 0.00 2.83
2922 2966 0.954452 GTGACCAGGCCAAGAACAAG 59.046 55.000 5.01 0.00 0.00 3.16
2923 2967 0.823356 TGACCAGGCCAAGAACAAGC 60.823 55.000 5.01 0.00 0.00 4.01
2924 2968 0.538287 GACCAGGCCAAGAACAAGCT 60.538 55.000 5.01 0.00 0.00 3.74
2925 2969 0.825010 ACCAGGCCAAGAACAAGCTG 60.825 55.000 5.01 0.00 0.00 4.24
2926 2970 0.538057 CCAGGCCAAGAACAAGCTGA 60.538 55.000 5.01 0.00 0.00 4.26
2927 2971 1.542492 CAGGCCAAGAACAAGCTGAT 58.458 50.000 5.01 0.00 0.00 2.90
2928 2972 1.891150 CAGGCCAAGAACAAGCTGATT 59.109 47.619 5.01 0.00 0.00 2.57
2950 2994 9.072375 TGATTCACAGTTATTTTGTTCATGGTA 57.928 29.630 0.00 0.00 0.00 3.25
2977 3039 2.557924 AGCAAGGCATCGAATCAACAAA 59.442 40.909 0.00 0.00 0.00 2.83
2994 3056 5.580297 TCAACAAAAACAAATCCTTGTCAGC 59.420 36.000 0.00 0.00 45.25 4.26
3041 3104 6.503616 CTATGCTAGCTTTTCTGTTCTACG 57.496 41.667 17.23 0.00 0.00 3.51
3046 3109 5.405873 GCTAGCTTTTCTGTTCTACGAGTTT 59.594 40.000 7.70 0.00 0.00 2.66
3050 3113 7.208080 AGCTTTTCTGTTCTACGAGTTTTCTA 58.792 34.615 0.00 0.00 0.00 2.10
3078 3141 3.773667 AGCAAGAGATGAGAGATCAACCA 59.226 43.478 0.00 0.00 0.00 3.67
3088 3151 9.775854 AGATGAGAGATCAACCAAACTATATTG 57.224 33.333 0.00 0.00 0.00 1.90
3100 3163 8.904099 ACCAAACTATATTGTTCCTATGTAGC 57.096 34.615 2.97 0.00 0.00 3.58
3101 3164 7.656137 ACCAAACTATATTGTTCCTATGTAGCG 59.344 37.037 2.97 0.00 0.00 4.26
3122 3185 6.656902 AGCGTCCATTCATATATGATCCAAT 58.343 36.000 16.06 4.19 36.56 3.16
3143 3206 4.796038 TTTGTTACTCCCTCCGTAAGAG 57.204 45.455 0.00 0.00 42.83 2.85
3164 3227 6.744112 AGAGATGAGTAATTTCGATCAGGAC 58.256 40.000 0.00 0.00 0.00 3.85
3165 3228 6.322456 AGAGATGAGTAATTTCGATCAGGACA 59.678 38.462 0.00 0.00 0.00 4.02
3181 3244 1.674519 GGACATGTGCCACGTGATACA 60.675 52.381 23.23 20.62 37.29 2.29
3185 3248 2.177394 TGTGCCACGTGATACACAAT 57.823 45.000 26.20 0.00 39.91 2.71
3234 3301 1.886222 GCTGTCTTGCCATGTTACCCA 60.886 52.381 0.00 0.00 0.00 4.51
3255 3322 3.353836 GCGGTTGCACGTGGATGT 61.354 61.111 18.88 0.00 42.15 3.06
3289 3356 2.125512 GCAGCTGACCGACCGATT 60.126 61.111 20.43 0.00 0.00 3.34
3290 3357 1.741770 GCAGCTGACCGACCGATTT 60.742 57.895 20.43 0.00 0.00 2.17
3303 3370 1.485066 ACCGATTTAGGTCCATCGCTT 59.515 47.619 4.86 0.00 41.46 4.68
3313 3380 2.362077 GGTCCATCGCTTTAATTGGCAT 59.638 45.455 0.00 0.00 0.00 4.40
3319 3386 5.446709 CATCGCTTTAATTGGCATACTGAG 58.553 41.667 0.00 0.00 0.00 3.35
3320 3387 4.765273 TCGCTTTAATTGGCATACTGAGA 58.235 39.130 0.00 0.00 0.00 3.27
3321 3388 4.811024 TCGCTTTAATTGGCATACTGAGAG 59.189 41.667 0.00 0.00 0.00 3.20
3322 3389 4.024556 CGCTTTAATTGGCATACTGAGAGG 60.025 45.833 0.00 0.00 0.00 3.69
3323 3390 4.276926 GCTTTAATTGGCATACTGAGAGGG 59.723 45.833 0.00 0.00 0.00 4.30
3324 3391 5.440610 CTTTAATTGGCATACTGAGAGGGT 58.559 41.667 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.923871 GGTGAGATGGTAAGCATATACACG 59.076 45.833 0.00 0.00 0.00 4.49
8 9 5.077564 AGACGGTGAGATGGTAAGCATATA 58.922 41.667 0.00 0.00 0.00 0.86
44 45 3.120165 GGAAAAAGGAGTCATCGCAGAAC 60.120 47.826 0.00 0.00 43.58 3.01
71 72 6.510746 TGACTATCGTCGCAAAATTATCTG 57.489 37.500 0.00 0.00 43.21 2.90
90 91 0.110486 AAGGTGATGCGGGTTTGACT 59.890 50.000 0.00 0.00 0.00 3.41
97 98 0.886490 GCTATCCAAGGTGATGCGGG 60.886 60.000 0.00 0.00 0.00 6.13
99 100 0.107456 AGGCTATCCAAGGTGATGCG 59.893 55.000 0.00 0.00 33.74 4.73
100 101 1.141657 TGAGGCTATCCAAGGTGATGC 59.858 52.381 0.00 0.00 33.74 3.91
101 102 3.565764 TTGAGGCTATCCAAGGTGATG 57.434 47.619 0.00 0.00 33.74 3.07
163 166 6.516718 AGCTAGCACAACACCAACTATATAG 58.483 40.000 18.83 8.27 0.00 1.31
165 168 5.359194 AGCTAGCACAACACCAACTATAT 57.641 39.130 18.83 0.00 0.00 0.86
186 189 6.049955 TCCAATCAAACCCTAGTTCAGTAG 57.950 41.667 0.00 0.00 34.19 2.57
189 192 4.911390 ACTCCAATCAAACCCTAGTTCAG 58.089 43.478 0.00 0.00 34.19 3.02
202 206 8.486210 AGAACTATAATGTGCTAACTCCAATCA 58.514 33.333 0.00 0.00 0.00 2.57
216 220 5.542635 TGGATAAGGCCGAGAACTATAATGT 59.457 40.000 0.00 0.00 0.00 2.71
219 223 5.187186 GGATGGATAAGGCCGAGAACTATAA 59.813 44.000 0.00 0.00 0.00 0.98
293 301 5.186021 CCAAGACCTCAACATACTCTACTGT 59.814 44.000 0.00 0.00 0.00 3.55
294 302 5.186021 ACCAAGACCTCAACATACTCTACTG 59.814 44.000 0.00 0.00 0.00 2.74
295 303 5.334421 ACCAAGACCTCAACATACTCTACT 58.666 41.667 0.00 0.00 0.00 2.57
296 304 5.185249 TGACCAAGACCTCAACATACTCTAC 59.815 44.000 0.00 0.00 0.00 2.59
345 365 4.992511 TGGCCGGGTTACACGTGC 62.993 66.667 17.22 9.03 0.00 5.34
379 399 3.951037 TGGTCTAGCTTAGCTTGAGAGAG 59.049 47.826 17.75 5.89 40.54 3.20
380 400 3.951037 CTGGTCTAGCTTAGCTTGAGAGA 59.049 47.826 17.75 9.28 40.54 3.10
381 401 4.305989 CTGGTCTAGCTTAGCTTGAGAG 57.694 50.000 17.75 12.81 40.54 3.20
405 425 2.158957 TCCGAGCAACTTAATGGCCTAG 60.159 50.000 3.32 0.00 0.00 3.02
406 426 1.834896 TCCGAGCAACTTAATGGCCTA 59.165 47.619 3.32 0.00 0.00 3.93
466 486 2.743938 TCTCTCTGCTTCGTTGTTGAC 58.256 47.619 0.00 0.00 0.00 3.18
470 490 3.179443 TGTTTCTCTCTGCTTCGTTGT 57.821 42.857 0.00 0.00 0.00 3.32
505 525 5.715070 GCAATAGCTCTAGGTATGGTACTG 58.285 45.833 2.62 0.00 38.57 2.74
542 562 2.654877 CCGAGGCCACTTGTACGT 59.345 61.111 5.01 0.00 0.00 3.57
544 564 2.267961 CCCCGAGGCCACTTGTAC 59.732 66.667 5.01 0.00 0.00 2.90
792 813 1.374947 GCTGTACAGGCAGGAACCA 59.625 57.895 23.95 0.00 37.00 3.67
859 880 0.034337 TACAGGAACTTGGTGACGGC 59.966 55.000 0.00 0.00 34.60 5.68
861 882 1.415374 CGTACAGGAACTTGGTGACG 58.585 55.000 0.00 0.00 34.60 4.35
904 925 2.583593 GGACGCCGATGTGCTCTC 60.584 66.667 0.00 0.00 0.00 3.20
978 999 0.104934 AGTTGGTCTCCCTCCACAGT 60.105 55.000 0.00 0.00 34.45 3.55
991 1012 1.284785 CACATACCCCATCCAGTTGGT 59.715 52.381 0.00 0.00 34.77 3.67
1014 1035 3.461773 CCCTCATCCGTCGCCACT 61.462 66.667 0.00 0.00 0.00 4.00
1074 1095 1.885388 CAGTTTCGTCACGGTGCCA 60.885 57.895 2.51 0.00 0.00 4.92
1085 1106 4.432503 CGTCGTTCAAATACTCCAGTTTCG 60.433 45.833 0.00 0.00 0.00 3.46
1101 1122 1.444553 CAGCCAGTCTCCGTCGTTC 60.445 63.158 0.00 0.00 0.00 3.95
1103 1124 4.057428 GCAGCCAGTCTCCGTCGT 62.057 66.667 0.00 0.00 0.00 4.34
1159 1180 2.902343 GGCATCCTTGTAGGCGGC 60.902 66.667 0.00 0.00 34.61 6.53
1173 1194 4.682334 CCATGGTGCACCCTGGCA 62.682 66.667 37.39 19.86 43.27 4.92
1176 1197 0.819582 GAAATCCATGGTGCACCCTG 59.180 55.000 32.62 30.43 34.29 4.45
1188 1209 3.034721 GTGTACACGGACAGAAATCCA 57.965 47.619 10.84 0.00 38.87 3.41
1245 1266 6.670027 AGTGAAGTAATACCTGATCTTGGACT 59.330 38.462 11.38 3.00 0.00 3.85
1279 1300 8.773404 ATTCAGTTCAATAGTTAGTTAAGCGT 57.227 30.769 0.00 0.00 0.00 5.07
1280 1301 9.478019 CAATTCAGTTCAATAGTTAGTTAAGCG 57.522 33.333 0.00 0.00 0.00 4.68
1288 1309 9.219603 CCACTTCTCAATTCAGTTCAATAGTTA 57.780 33.333 0.00 0.00 0.00 2.24
1306 1327 6.437477 ACCTCCAAAATAATTTCCCACTTCTC 59.563 38.462 0.00 0.00 0.00 2.87
1339 1360 8.718734 AGTTAAATCGATGGTCAAAGTAAACTC 58.281 33.333 0.00 0.00 0.00 3.01
1340 1361 8.617290 AGTTAAATCGATGGTCAAAGTAAACT 57.383 30.769 0.00 0.00 0.00 2.66
1346 1367 8.251750 TCTGTAAGTTAAATCGATGGTCAAAG 57.748 34.615 0.00 0.00 33.76 2.77
1348 1369 7.876068 ACTTCTGTAAGTTAAATCGATGGTCAA 59.124 33.333 0.00 0.00 43.60 3.18
1349 1370 7.383687 ACTTCTGTAAGTTAAATCGATGGTCA 58.616 34.615 0.00 0.00 43.60 4.02
1350 1371 7.829378 ACTTCTGTAAGTTAAATCGATGGTC 57.171 36.000 0.00 0.00 43.60 4.02
1351 1372 9.314321 CATACTTCTGTAAGTTAAATCGATGGT 57.686 33.333 0.00 0.00 43.60 3.55
1352 1373 9.529325 TCATACTTCTGTAAGTTAAATCGATGG 57.471 33.333 0.00 0.00 43.60 3.51
1366 1387 9.131791 TCAGTGCATATAACTCATACTTCTGTA 57.868 33.333 0.00 0.00 0.00 2.74
1521 1544 3.563508 TCACTTTTTGTATGCACGCATG 58.436 40.909 14.70 0.00 37.82 4.06
1526 1549 8.454106 AGATATTCACTCACTTTTTGTATGCAC 58.546 33.333 0.00 0.00 0.00 4.57
1533 1556 7.230222 GTCACGAGATATTCACTCACTTTTTG 58.770 38.462 0.00 0.00 34.47 2.44
1535 1558 5.573282 CGTCACGAGATATTCACTCACTTTT 59.427 40.000 0.00 0.00 34.47 2.27
1539 1562 3.064958 TCCGTCACGAGATATTCACTCAC 59.935 47.826 0.00 0.00 34.47 3.51
1545 1568 4.035324 TCTCTGTTCCGTCACGAGATATTC 59.965 45.833 0.00 0.00 0.00 1.75
1553 1576 1.068541 TGATGTCTCTGTTCCGTCACG 60.069 52.381 0.00 0.00 0.00 4.35
1556 1579 3.305398 AAGTGATGTCTCTGTTCCGTC 57.695 47.619 0.00 0.00 0.00 4.79
1571 1594 9.295825 AGGTTTTGTTATTGATGACATAAGTGA 57.704 29.630 0.00 0.00 0.00 3.41
1572 1595 9.912634 AAGGTTTTGTTATTGATGACATAAGTG 57.087 29.630 0.00 0.00 0.00 3.16
1596 1621 5.580691 TGACCAAGCGATAATACTTGTGAAG 59.419 40.000 0.00 0.00 41.36 3.02
1657 1682 2.668279 GGGTGCTTAATCAACACGCAAG 60.668 50.000 0.00 0.00 44.14 4.01
1659 1684 0.878416 GGGTGCTTAATCAACACGCA 59.122 50.000 0.00 0.00 44.14 5.24
1660 1685 0.878416 TGGGTGCTTAATCAACACGC 59.122 50.000 0.00 0.00 44.74 5.34
1677 1702 3.434319 GCGGACCTGCATGTGTGG 61.434 66.667 0.00 0.00 34.15 4.17
1730 1755 1.142748 GGTGATGCTGACCTCCTCG 59.857 63.158 0.00 0.00 0.00 4.63
1754 1779 4.840005 GCGCCTAGGCTGTGACCC 62.840 72.222 30.55 8.05 39.32 4.46
1811 1836 1.586422 CAGGAGGTACATTGATGCCG 58.414 55.000 0.00 0.00 0.00 5.69
1823 1848 1.268283 GCTTGGAGTAGGCAGGAGGT 61.268 60.000 0.00 0.00 0.00 3.85
1919 1944 1.005630 GCGGAGATCGGGGAATGAG 60.006 63.158 0.00 0.00 39.69 2.90
1934 1959 2.509336 CTCACACTTAGGGCGCGG 60.509 66.667 8.83 0.00 0.00 6.46
1937 1962 0.736325 CGTTCCTCACACTTAGGGCG 60.736 60.000 0.00 0.00 34.66 6.13
2063 2088 2.286184 CCAAAACCTGAACAAGTCGACG 60.286 50.000 10.46 0.00 0.00 5.12
2066 2091 3.243068 CCTTCCAAAACCTGAACAAGTCG 60.243 47.826 0.00 0.00 0.00 4.18
2121 2146 0.751643 GCACCTTGATACCCGGCAAT 60.752 55.000 0.00 0.00 0.00 3.56
2171 2196 2.046283 TGTTCAGAAGTGCTACGTCG 57.954 50.000 0.00 0.00 31.81 5.12
2174 2199 3.777807 CACTTGTTCAGAAGTGCTACG 57.222 47.619 4.07 0.00 44.70 3.51
2180 2205 1.490490 TCAGCCCACTTGTTCAGAAGT 59.510 47.619 0.00 0.00 36.58 3.01
2198 2223 1.348696 TGCTCATCCTTCAGCAAGTCA 59.651 47.619 0.00 0.00 42.74 3.41
2273 2298 0.740737 CGAATTTCCAGTGGCCATCC 59.259 55.000 9.72 0.00 0.00 3.51
2300 2325 3.328382 CCACTTAATTGGTCGTCCTCA 57.672 47.619 3.70 0.00 34.23 3.86
2352 2377 2.433239 GAGGCCGTGGTTATCCTTTAGA 59.567 50.000 0.00 0.00 34.23 2.10
2353 2378 2.434702 AGAGGCCGTGGTTATCCTTTAG 59.565 50.000 0.00 0.00 34.23 1.85
2356 2381 0.541863 CAGAGGCCGTGGTTATCCTT 59.458 55.000 0.00 0.00 34.23 3.36
2406 2441 9.364989 GCATTTGCTTGGTGTTTCTAAATATAA 57.635 29.630 0.00 0.00 38.21 0.98
2407 2442 7.978975 GGCATTTGCTTGGTGTTTCTAAATATA 59.021 33.333 2.12 0.00 41.70 0.86
2408 2443 6.818142 GGCATTTGCTTGGTGTTTCTAAATAT 59.182 34.615 2.12 0.00 41.70 1.28
2409 2444 6.014669 AGGCATTTGCTTGGTGTTTCTAAATA 60.015 34.615 2.12 0.00 41.70 1.40
2410 2445 4.996758 GGCATTTGCTTGGTGTTTCTAAAT 59.003 37.500 2.12 0.00 41.70 1.40
2411 2446 4.100808 AGGCATTTGCTTGGTGTTTCTAAA 59.899 37.500 2.12 0.00 41.70 1.85
2412 2447 3.640967 AGGCATTTGCTTGGTGTTTCTAA 59.359 39.130 2.12 0.00 41.70 2.10
2413 2448 3.230134 AGGCATTTGCTTGGTGTTTCTA 58.770 40.909 2.12 0.00 41.70 2.10
2414 2449 2.041701 AGGCATTTGCTTGGTGTTTCT 58.958 42.857 2.12 0.00 41.70 2.52
2415 2450 2.531522 AGGCATTTGCTTGGTGTTTC 57.468 45.000 2.12 0.00 41.70 2.78
2416 2451 2.289010 GCTAGGCATTTGCTTGGTGTTT 60.289 45.455 2.12 0.00 41.70 2.83
2417 2452 1.273327 GCTAGGCATTTGCTTGGTGTT 59.727 47.619 2.12 0.00 41.70 3.32
2418 2453 0.890683 GCTAGGCATTTGCTTGGTGT 59.109 50.000 2.12 0.00 41.70 4.16
2419 2454 0.889994 TGCTAGGCATTTGCTTGGTG 59.110 50.000 2.12 0.00 41.70 4.17
2420 2455 3.362040 TGCTAGGCATTTGCTTGGT 57.638 47.368 2.12 0.00 41.70 3.67
2467 2502 6.428295 TGAACTCTGGTTTTCCCTTTTCTTA 58.572 36.000 0.00 0.00 39.73 2.10
2475 2510 7.881775 AATATGTATGAACTCTGGTTTTCCC 57.118 36.000 0.00 0.00 39.73 3.97
2488 2523 8.970020 AGCTGGTCAAATTCAAATATGTATGAA 58.030 29.630 0.00 2.46 39.66 2.57
2497 2532 4.278170 TCGTGAAGCTGGTCAAATTCAAAT 59.722 37.500 0.00 0.00 33.74 2.32
2498 2533 3.629855 TCGTGAAGCTGGTCAAATTCAAA 59.370 39.130 0.00 0.00 33.74 2.69
2499 2534 3.210227 TCGTGAAGCTGGTCAAATTCAA 58.790 40.909 0.00 0.00 33.74 2.69
2500 2535 2.844946 TCGTGAAGCTGGTCAAATTCA 58.155 42.857 0.00 0.00 0.00 2.57
2501 2536 4.161333 CAATCGTGAAGCTGGTCAAATTC 58.839 43.478 0.00 0.00 0.00 2.17
2502 2537 3.569701 ACAATCGTGAAGCTGGTCAAATT 59.430 39.130 0.00 0.00 0.00 1.82
2526 2561 3.069016 GGTTGGTGGTAAAACTTTGGAGG 59.931 47.826 0.00 0.00 0.00 4.30
2530 2565 5.536916 TCATAGGGTTGGTGGTAAAACTTTG 59.463 40.000 0.00 0.00 0.00 2.77
2534 2569 5.479027 ACAATCATAGGGTTGGTGGTAAAAC 59.521 40.000 5.24 0.00 0.00 2.43
2535 2570 5.646215 ACAATCATAGGGTTGGTGGTAAAA 58.354 37.500 5.24 0.00 0.00 1.52
2537 2572 4.938575 ACAATCATAGGGTTGGTGGTAA 57.061 40.909 5.24 0.00 0.00 2.85
2572 2607 3.853330 CCGCATGTTGCTCGACCG 61.853 66.667 0.00 0.00 42.25 4.79
2594 2629 2.280592 GAGTCCCGTGCCGTTTGT 60.281 61.111 0.00 0.00 0.00 2.83
2595 2630 3.047877 GGAGTCCCGTGCCGTTTG 61.048 66.667 0.00 0.00 0.00 2.93
2606 2641 7.148171 CCTTCTTTAGATGTTTTCATGGAGTCC 60.148 40.741 0.73 0.73 41.05 3.85
2613 2648 8.037166 GGCAATTCCTTCTTTAGATGTTTTCAT 58.963 33.333 0.00 0.00 43.99 2.57
2638 2673 3.128632 TACGGTAGCATGCGGACGG 62.129 63.158 26.05 24.41 0.00 4.79
2640 2675 1.299926 CCTACGGTAGCATGCGGAC 60.300 63.158 13.01 14.31 0.00 4.79
2647 2682 1.895238 GGAACAGCCTACGGTAGCA 59.105 57.895 9.70 0.00 0.00 3.49
2652 2687 0.174845 TTGATCGGAACAGCCTACGG 59.825 55.000 0.00 0.00 0.00 4.02
2653 2688 1.927174 CTTTGATCGGAACAGCCTACG 59.073 52.381 0.00 0.00 0.00 3.51
2665 2700 3.574284 TGCCATGTTTTCCTTTGATCG 57.426 42.857 0.00 0.00 0.00 3.69
2685 2720 2.505819 AGTTCTGCTTCGGGGTGATATT 59.494 45.455 0.00 0.00 0.00 1.28
2687 2722 1.568504 AGTTCTGCTTCGGGGTGATA 58.431 50.000 0.00 0.00 0.00 2.15
2688 2723 0.693049 AAGTTCTGCTTCGGGGTGAT 59.307 50.000 0.00 0.00 30.06 3.06
2725 2760 4.359706 GACATTTGCACGTCCTTTTCTTT 58.640 39.130 0.00 0.00 0.00 2.52
2732 2767 1.078709 CATCGACATTTGCACGTCCT 58.921 50.000 0.00 0.00 0.00 3.85
2734 2769 2.233355 CAACATCGACATTTGCACGTC 58.767 47.619 0.00 0.00 0.00 4.34
2735 2770 1.601903 ACAACATCGACATTTGCACGT 59.398 42.857 0.00 0.00 0.00 4.49
2736 2771 2.233355 GACAACATCGACATTTGCACG 58.767 47.619 0.00 0.00 0.00 5.34
2737 2772 3.266541 TGACAACATCGACATTTGCAC 57.733 42.857 0.00 0.00 0.00 4.57
2795 2830 0.972883 GGAAGAGACACTGACTGGCT 59.027 55.000 0.00 0.00 43.26 4.75
2802 2837 4.263018 TCACATCAAGGAAGAGACACTG 57.737 45.455 0.00 0.00 0.00 3.66
2803 2838 4.963318 TTCACATCAAGGAAGAGACACT 57.037 40.909 0.00 0.00 0.00 3.55
2838 2882 9.612620 CAAAACAATCTACTAAATGTGACCTTC 57.387 33.333 0.00 0.00 0.00 3.46
2851 2895 9.391006 TCTTTATATTCGCCAAAACAATCTACT 57.609 29.630 0.00 0.00 0.00 2.57
2904 2948 0.823356 GCTTGTTCTTGGCCTGGTCA 60.823 55.000 3.32 0.00 0.00 4.02
2924 2968 7.950512 ACCATGAACAAAATAACTGTGAATCA 58.049 30.769 0.00 0.00 0.00 2.57
2926 2970 9.859427 CATACCATGAACAAAATAACTGTGAAT 57.141 29.630 0.00 0.00 0.00 2.57
2927 2971 7.812191 GCATACCATGAACAAAATAACTGTGAA 59.188 33.333 0.00 0.00 0.00 3.18
2928 2972 7.040132 TGCATACCATGAACAAAATAACTGTGA 60.040 33.333 0.00 0.00 0.00 3.58
2941 2985 2.357009 CCTTGCTCTGCATACCATGAAC 59.643 50.000 0.00 0.00 38.76 3.18
2942 2986 2.646930 CCTTGCTCTGCATACCATGAA 58.353 47.619 0.00 0.00 38.76 2.57
2947 2991 3.106738 ATGCCTTGCTCTGCATACC 57.893 52.632 5.75 0.00 45.89 2.73
2977 3039 6.543371 GCCAAGGCTGACAAGGATTTGTTT 62.543 45.833 3.29 0.00 41.75 2.83
2994 3056 4.370364 AGTATTTTATGTTGCGCCAAGG 57.630 40.909 4.18 0.00 0.00 3.61
3058 3121 6.171921 AGTTTGGTTGATCTCTCATCTCTTG 58.828 40.000 0.00 0.00 0.00 3.02
3071 3134 9.920946 ACATAGGAACAATATAGTTTGGTTGAT 57.079 29.630 0.00 0.00 0.00 2.57
3074 3137 9.338622 GCTACATAGGAACAATATAGTTTGGTT 57.661 33.333 0.00 0.00 0.00 3.67
3076 3139 7.656137 ACGCTACATAGGAACAATATAGTTTGG 59.344 37.037 0.00 0.00 0.00 3.28
3078 3141 7.871463 GGACGCTACATAGGAACAATATAGTTT 59.129 37.037 0.00 0.00 0.00 2.66
3088 3151 4.054780 TGAATGGACGCTACATAGGAAC 57.945 45.455 0.00 0.00 0.00 3.62
3100 3163 8.733458 ACAAATTGGATCATATATGAATGGACG 58.267 33.333 19.03 7.06 40.69 4.79
3122 3185 4.410099 TCTCTTACGGAGGGAGTAACAAA 58.590 43.478 0.00 0.00 42.10 2.83
3143 3206 6.703607 ACATGTCCTGATCGAAATTACTCATC 59.296 38.462 0.00 0.00 0.00 2.92
3165 3228 2.177394 TTGTGTATCACGTGGCACAT 57.823 45.000 28.03 14.75 40.82 3.21
3181 3244 0.392998 CAAGCGTAGGAGCCCATTGT 60.393 55.000 0.00 0.00 38.01 2.71
3185 3248 1.676678 CTAGCAAGCGTAGGAGCCCA 61.677 60.000 0.00 0.00 38.01 5.36
3253 3320 1.336517 GCTCTGCTGTTGGTACGTACA 60.337 52.381 26.02 8.37 0.00 2.90
3255 3322 0.963225 TGCTCTGCTGTTGGTACGTA 59.037 50.000 0.00 0.00 0.00 3.57
3289 3356 3.630312 GCCAATTAAAGCGATGGACCTAA 59.370 43.478 0.00 0.00 34.82 2.69
3290 3357 3.211045 GCCAATTAAAGCGATGGACCTA 58.789 45.455 0.00 0.00 34.82 3.08


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

AutoCloner maintained by Alex Coulton.