Multiple sequence alignment - TraesCS2B01G062700

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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 TraesCS2B01G062700 chr2B 100.000 2342 0 0 1 2342 29992309 29989968 0.000000e+00 4325
1 TraesCS2B01G062700 chr2B 87.633 1698 168 20 1 1683 29045885 29047555 0.000000e+00 1934
2 TraesCS2B01G062700 chr2B 91.069 627 51 4 942 1564 28921248 28921873 0.000000e+00 843
3 TraesCS2B01G062700 chr2B 87.103 535 55 4 1701 2222 29047547 29048080 5.570000e-166 593
4 TraesCS2B01G062700 chr2B 86.570 484 51 4 1701 2170 28921953 28922436 2.670000e-144 521
5 TraesCS2B01G062700 chr2B 93.333 240 16 0 322 561 28921014 28921253 2.860000e-94 355
6 TraesCS2B01G062700 chr2B 85.542 332 45 3 1 329 28920500 28920831 6.200000e-91 344
7 TraesCS2B01G062700 chr2A 90.792 1705 131 13 1 1680 18635477 18637180 0.000000e+00 2255
8 TraesCS2B01G062700 chr2A 89.164 1698 149 22 1 1680 18585912 18587592 0.000000e+00 2084
9 TraesCS2B01G062700 chr2A 84.656 189 15 4 1715 1890 18587601 18587788 2.390000e-40 176
10 TraesCS2B01G062700 chr2D 89.461 1708 126 29 1 1680 17311836 17313517 0.000000e+00 2108
11 TraesCS2B01G062700 chr2D 90.056 885 71 5 812 1680 17169522 17170405 0.000000e+00 1131
12 TraesCS2B01G062700 chr2D 89.300 757 63 9 1 748 17168775 17169522 0.000000e+00 933
13 TraesCS2B01G062700 chr2D 89.600 250 24 2 1184 1433 17208272 17208519 1.350000e-82 316
14 TraesCS2B01G062700 chr2D 87.452 263 24 3 1429 1683 17208646 17208907 6.330000e-76 294


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 TraesCS2B01G062700 chr2B 29989968 29992309 2341 True 4325.00 4325 100.0000 1 2342 1 chr2B.!!$R1 2341
1 TraesCS2B01G062700 chr2B 29045885 29048080 2195 False 1263.50 1934 87.3680 1 2222 2 chr2B.!!$F2 2221
2 TraesCS2B01G062700 chr2B 28920500 28922436 1936 False 515.75 843 89.1285 1 2170 4 chr2B.!!$F1 2169
3 TraesCS2B01G062700 chr2A 18635477 18637180 1703 False 2255.00 2255 90.7920 1 1680 1 chr2A.!!$F1 1679
4 TraesCS2B01G062700 chr2A 18585912 18587788 1876 False 1130.00 2084 86.9100 1 1890 2 chr2A.!!$F2 1889
5 TraesCS2B01G062700 chr2D 17311836 17313517 1681 False 2108.00 2108 89.4610 1 1680 1 chr2D.!!$F1 1679
6 TraesCS2B01G062700 chr2D 17168775 17170405 1630 False 1032.00 1131 89.6780 1 1680 2 chr2D.!!$F2 1679
7 TraesCS2B01G062700 chr2D 17208272 17208907 635 False 305.00 316 88.5260 1184 1683 2 chr2D.!!$F3 499

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
922 1135 1.065551 AGCCTTCAAGAAACAACACGC 59.934 47.619 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 2682 0.037326 GGCCTCGTGTCATGTTGAGA 60.037 55.0 0.0 0.0 0.0 3.27 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
73 80 6.240894 GGGATGCTGGAATAATGAGATGTTA 58.759 40.000 0.00 0.00 0.00 2.41
93 100 9.573133 GATGTTATCCTTTGGTTCAGTATTTTG 57.427 33.333 0.00 0.00 0.00 2.44
116 123 6.973843 TGGCAAAATGCTAGCTATTATTCTG 58.026 36.000 17.23 5.43 44.28 3.02
172 180 8.918202 TGACAAAATTACTGAGATTTACCTGT 57.082 30.769 0.00 0.00 0.00 4.00
284 294 2.028658 AGAGAACTTTCATCTGCAGCGA 60.029 45.455 9.47 5.09 0.00 4.93
318 328 1.259609 CAGAGCAAAATGCCCAAGGA 58.740 50.000 0.00 0.00 46.52 3.36
325 525 1.463674 AAATGCCCAAGGATCACGAC 58.536 50.000 0.00 0.00 0.00 4.34
386 589 3.995199 TCCACTGTGTTTAAGAGCTCAG 58.005 45.455 17.77 4.81 34.86 3.35
487 690 4.528987 GGTTGGGTTAAAATTTAGGCAGGA 59.471 41.667 0.00 0.00 0.00 3.86
550 753 5.610409 GCGTCGTCGTAATAAAAGCATAAAG 59.390 40.000 3.66 0.00 39.49 1.85
651 855 5.049405 GGCCAAGTAATCACCATAATCTTCG 60.049 44.000 0.00 0.00 0.00 3.79
673 879 5.912396 TCGATTGGCGATATTTGCAAATAAC 59.088 36.000 30.12 26.23 45.59 1.89
720 926 1.664321 GGCTCTGATTTGGCTGCCAG 61.664 60.000 22.17 10.03 40.04 4.85
729 935 5.016173 TGATTTGGCTGCCAGTTTTACTAT 58.984 37.500 22.17 6.43 33.81 2.12
739 945 8.097662 GCTGCCAGTTTTACTATAGGATTCTAT 58.902 37.037 4.43 0.00 39.38 1.98
752 958 4.119155 AGGATTCTATTGGTCCCAAAGGA 58.881 43.478 2.32 2.01 41.08 3.36
899 1112 1.474320 CGTTCCTGACCTGACCAAACA 60.474 52.381 0.00 0.00 0.00 2.83
922 1135 1.065551 AGCCTTCAAGAAACAACACGC 59.934 47.619 0.00 0.00 0.00 5.34
983 1207 5.308825 CCAGGTATGACTCTTTGTTCAAGT 58.691 41.667 0.00 0.00 33.66 3.16
984 1208 5.409826 CCAGGTATGACTCTTTGTTCAAGTC 59.590 44.000 0.00 0.00 39.87 3.01
1019 1243 7.260558 TGCTCATGATCATCTTTCATTCTTC 57.739 36.000 4.86 0.00 31.50 2.87
1051 1275 7.698506 AACTTCATGATATTCCTATGCATGG 57.301 36.000 10.16 6.20 37.51 3.66
1057 1281 4.225942 TGATATTCCTATGCATGGGTCTCC 59.774 45.833 26.49 14.30 0.00 3.71
1072 1296 3.683340 GGGTCTCCGTCAAGTTAATTCAC 59.317 47.826 0.00 0.00 0.00 3.18
1090 1314 3.489355 TCACACACCATGAAAGAGCAAT 58.511 40.909 0.00 0.00 0.00 3.56
1105 1329 1.001633 AGCAATTGAAAGCAAGCAGGG 59.998 47.619 10.34 0.00 37.45 4.45
1135 1359 1.303155 GCTGCCTTGCTGGTCTTCT 60.303 57.895 0.00 0.00 38.35 2.85
1141 1365 1.093159 CTTGCTGGTCTTCTCCATGC 58.907 55.000 0.00 0.00 36.84 4.06
1153 1377 1.908619 TCTCCATGCTTACTCAAGGCA 59.091 47.619 0.00 0.00 40.32 4.75
1159 1383 1.718757 GCTTACTCAAGGCATGGCGG 61.719 60.000 14.30 10.52 31.96 6.13
1175 1399 4.324991 GGTTCGCGTCAAGGGGGT 62.325 66.667 5.77 0.00 0.00 4.95
1187 1411 1.509548 AAGGGGGTGGTGAGGAATGG 61.510 60.000 0.00 0.00 0.00 3.16
1358 1582 2.763448 ACTAGTGCCATTCTCTGAGACC 59.237 50.000 6.92 0.00 0.00 3.85
1367 1591 4.082190 CCATTCTCTGAGACCGTTCTGTTA 60.082 45.833 6.92 0.00 29.47 2.41
1370 1594 2.490115 CTCTGAGACCGTTCTGTTAGCT 59.510 50.000 0.00 0.00 29.47 3.32
1463 1819 4.158949 TGTCTACGTGGAAATAAGCTGCTA 59.841 41.667 2.06 0.00 0.00 3.49
1584 1948 8.891367 TGTAATAGATGTAATATTCTCGCGTC 57.109 34.615 5.77 0.00 0.00 5.19
1626 1990 1.089481 ATGTTACACGGCAGCCATCG 61.089 55.000 13.30 0.66 0.00 3.84
1643 2007 5.948162 AGCCATCGATAAAATTCATGCCTAT 59.052 36.000 0.00 0.00 0.00 2.57
1683 2047 5.064441 AGAACCAAATTAACTGCATGCTC 57.936 39.130 20.33 2.84 0.00 4.26
1684 2048 3.874392 ACCAAATTAACTGCATGCTCC 57.126 42.857 20.33 0.00 0.00 4.70
1686 2050 3.834231 ACCAAATTAACTGCATGCTCCTT 59.166 39.130 20.33 9.52 0.00 3.36
1688 2052 3.515330 AATTAACTGCATGCTCCTTGC 57.485 42.857 20.33 0.00 43.25 4.01
1721 2085 7.395190 AATCTGCATGCTTACAATTCAGTAA 57.605 32.000 20.33 0.00 33.28 2.24
1790 2154 1.064654 GTCCTACACGTACTAAGGGCG 59.935 57.143 0.00 0.00 0.00 6.13
1810 2188 2.797156 CGACTCTAATCGATGCCCAAAG 59.203 50.000 0.00 0.00 45.13 2.77
1812 2190 1.876156 CTCTAATCGATGCCCAAAGCC 59.124 52.381 0.00 0.00 42.71 4.35
1870 2248 2.879103 TTGGGAAGGTGGCTTCTAAG 57.121 50.000 0.00 0.00 34.06 2.18
1882 2260 3.772060 GCTTCTAAGTGATGCCCAAAG 57.228 47.619 0.00 0.00 39.19 2.77
1936 2316 2.751259 TCTCCAGCTTTGTGCATTCATC 59.249 45.455 0.00 0.00 45.94 2.92
1988 2368 8.766151 CACATGAACATCATTTGAACATTGAAA 58.234 29.630 0.00 0.00 36.85 2.69
2156 2546 6.544931 GGATGAGGAAATGATGATGAAGTTGA 59.455 38.462 0.00 0.00 0.00 3.18
2180 2570 0.109342 CTCCTCATTGGCCGCCTTAT 59.891 55.000 11.61 1.21 35.26 1.73
2185 2575 0.588252 CATTGGCCGCCTTATTCTCG 59.412 55.000 11.61 0.00 0.00 4.04
2195 2586 2.742204 GCCTTATTCTCGTCCCTTCCAC 60.742 54.545 0.00 0.00 0.00 4.02
2202 2593 2.214216 CGTCCCTTCCACCTCCACA 61.214 63.158 0.00 0.00 0.00 4.17
2203 2594 1.764571 CGTCCCTTCCACCTCCACAA 61.765 60.000 0.00 0.00 0.00 3.33
2205 2596 0.696143 TCCCTTCCACCTCCACAACA 60.696 55.000 0.00 0.00 0.00 3.33
2208 2599 1.442769 CTTCCACCTCCACAACATCG 58.557 55.000 0.00 0.00 0.00 3.84
2213 2604 2.002586 CACCTCCACAACATCGATGTC 58.997 52.381 30.06 0.00 40.80 3.06
2222 2613 4.327357 CACAACATCGATGTCTTCCTGTAC 59.673 45.833 30.06 0.00 40.80 2.90
2223 2614 3.802948 ACATCGATGTCTTCCTGTACC 57.197 47.619 25.18 0.00 35.87 3.34
2224 2615 3.366396 ACATCGATGTCTTCCTGTACCT 58.634 45.455 25.18 0.00 35.87 3.08
2225 2616 3.381908 ACATCGATGTCTTCCTGTACCTC 59.618 47.826 25.18 0.00 35.87 3.85
2226 2617 3.367646 TCGATGTCTTCCTGTACCTCT 57.632 47.619 0.00 0.00 0.00 3.69
2227 2618 4.498894 TCGATGTCTTCCTGTACCTCTA 57.501 45.455 0.00 0.00 0.00 2.43
2228 2619 5.050126 TCGATGTCTTCCTGTACCTCTAT 57.950 43.478 0.00 0.00 0.00 1.98
2229 2620 4.822350 TCGATGTCTTCCTGTACCTCTATG 59.178 45.833 0.00 0.00 0.00 2.23
2230 2621 4.822350 CGATGTCTTCCTGTACCTCTATGA 59.178 45.833 0.00 0.00 0.00 2.15
2231 2622 5.299531 CGATGTCTTCCTGTACCTCTATGAA 59.700 44.000 0.00 0.00 0.00 2.57
2232 2623 6.514212 CGATGTCTTCCTGTACCTCTATGAAG 60.514 46.154 0.00 0.00 0.00 3.02
2233 2624 4.956700 TGTCTTCCTGTACCTCTATGAAGG 59.043 45.833 0.00 0.00 42.55 3.46
2234 2625 3.961408 TCTTCCTGTACCTCTATGAAGGC 59.039 47.826 0.00 0.00 40.34 4.35
2235 2626 2.679082 TCCTGTACCTCTATGAAGGCC 58.321 52.381 0.00 0.00 40.34 5.19
2236 2627 2.023404 TCCTGTACCTCTATGAAGGCCA 60.023 50.000 5.01 0.00 40.34 5.36
2237 2628 2.103263 CCTGTACCTCTATGAAGGCCAC 59.897 54.545 5.01 0.00 40.34 5.01
2238 2629 2.103263 CTGTACCTCTATGAAGGCCACC 59.897 54.545 5.01 0.00 40.34 4.61
2239 2630 2.292918 TGTACCTCTATGAAGGCCACCT 60.293 50.000 5.01 0.00 40.34 4.00
2241 2632 1.561542 ACCTCTATGAAGGCCACCTTG 59.438 52.381 5.01 0.00 44.82 3.61
2242 2633 1.561542 CCTCTATGAAGGCCACCTTGT 59.438 52.381 5.01 0.00 44.82 3.16
2243 2634 2.636830 CTCTATGAAGGCCACCTTGTG 58.363 52.381 5.01 0.00 44.82 3.33
2254 2645 2.292828 CACCTTGTGGGACCTTCATT 57.707 50.000 0.00 0.00 38.76 2.57
2255 2646 1.888512 CACCTTGTGGGACCTTCATTG 59.111 52.381 0.00 0.00 38.76 2.82
2256 2647 1.499007 ACCTTGTGGGACCTTCATTGT 59.501 47.619 0.00 0.00 38.76 2.71
2257 2648 1.888512 CCTTGTGGGACCTTCATTGTG 59.111 52.381 0.00 0.00 37.23 3.33
2258 2649 1.270550 CTTGTGGGACCTTCATTGTGC 59.729 52.381 0.00 0.00 0.00 4.57
2259 2650 0.478072 TGTGGGACCTTCATTGTGCT 59.522 50.000 0.00 0.00 0.00 4.40
2260 2651 1.133513 TGTGGGACCTTCATTGTGCTT 60.134 47.619 0.00 0.00 0.00 3.91
2261 2652 1.963515 GTGGGACCTTCATTGTGCTTT 59.036 47.619 0.00 0.00 0.00 3.51
2262 2653 3.153919 GTGGGACCTTCATTGTGCTTTA 58.846 45.455 0.00 0.00 0.00 1.85
2263 2654 3.763897 GTGGGACCTTCATTGTGCTTTAT 59.236 43.478 0.00 0.00 0.00 1.40
2264 2655 4.947388 GTGGGACCTTCATTGTGCTTTATA 59.053 41.667 0.00 0.00 0.00 0.98
2265 2656 5.066505 GTGGGACCTTCATTGTGCTTTATAG 59.933 44.000 0.00 0.00 0.00 1.31
2266 2657 4.580580 GGGACCTTCATTGTGCTTTATAGG 59.419 45.833 0.00 0.00 0.00 2.57
2267 2658 4.036852 GGACCTTCATTGTGCTTTATAGGC 59.963 45.833 0.00 0.00 0.00 3.93
2268 2659 3.627577 ACCTTCATTGTGCTTTATAGGCG 59.372 43.478 0.00 0.00 0.00 5.52
2269 2660 3.876914 CCTTCATTGTGCTTTATAGGCGA 59.123 43.478 0.00 0.00 0.00 5.54
2270 2661 4.260784 CCTTCATTGTGCTTTATAGGCGAC 60.261 45.833 0.00 0.00 0.00 5.19
2271 2662 3.867857 TCATTGTGCTTTATAGGCGACA 58.132 40.909 0.00 0.00 0.00 4.35
2272 2663 3.621268 TCATTGTGCTTTATAGGCGACAC 59.379 43.478 0.00 0.00 0.00 3.67
2273 2664 1.635844 TGTGCTTTATAGGCGACACG 58.364 50.000 0.00 0.00 0.00 4.49
2274 2665 0.928229 GTGCTTTATAGGCGACACGG 59.072 55.000 0.00 0.00 0.00 4.94
2275 2666 0.533491 TGCTTTATAGGCGACACGGT 59.467 50.000 0.00 0.00 0.00 4.83
2276 2667 0.928229 GCTTTATAGGCGACACGGTG 59.072 55.000 6.58 6.58 0.00 4.94
2277 2668 0.928229 CTTTATAGGCGACACGGTGC 59.072 55.000 8.30 0.19 0.00 5.01
2278 2669 0.533491 TTTATAGGCGACACGGTGCT 59.467 50.000 8.30 0.00 0.00 4.40
2279 2670 0.101759 TTATAGGCGACACGGTGCTC 59.898 55.000 8.30 4.51 0.00 4.26
2280 2671 1.033202 TATAGGCGACACGGTGCTCA 61.033 55.000 8.30 0.00 0.00 4.26
2281 2672 1.676678 ATAGGCGACACGGTGCTCAT 61.677 55.000 8.30 0.00 0.00 2.90
2282 2673 2.557059 TAGGCGACACGGTGCTCATG 62.557 60.000 8.30 0.00 0.00 3.07
2283 2674 3.490759 GCGACACGGTGCTCATGG 61.491 66.667 8.30 0.00 0.00 3.66
2284 2675 2.048222 CGACACGGTGCTCATGGT 60.048 61.111 8.30 0.00 0.00 3.55
2285 2676 2.382746 CGACACGGTGCTCATGGTG 61.383 63.158 8.30 0.00 36.50 4.17
2286 2677 1.301716 GACACGGTGCTCATGGTGT 60.302 57.895 8.30 3.24 45.53 4.16
2287 2678 1.568612 GACACGGTGCTCATGGTGTG 61.569 60.000 8.30 3.85 43.14 3.82
2288 2679 1.597854 CACGGTGCTCATGGTGTGT 60.598 57.895 0.00 0.00 0.00 3.72
2289 2680 1.597854 ACGGTGCTCATGGTGTGTG 60.598 57.895 0.00 0.00 0.00 3.82
2290 2681 1.301637 CGGTGCTCATGGTGTGTGA 60.302 57.895 0.00 0.00 0.00 3.58
2291 2682 0.674581 CGGTGCTCATGGTGTGTGAT 60.675 55.000 0.00 0.00 0.00 3.06
2292 2683 1.089920 GGTGCTCATGGTGTGTGATC 58.910 55.000 0.00 0.00 0.00 2.92
2293 2684 1.339438 GGTGCTCATGGTGTGTGATCT 60.339 52.381 0.00 0.00 0.00 2.75
2294 2685 2.005451 GTGCTCATGGTGTGTGATCTC 58.995 52.381 0.00 0.00 0.00 2.75
2295 2686 1.624813 TGCTCATGGTGTGTGATCTCA 59.375 47.619 0.00 0.00 0.00 3.27
2296 2687 2.038820 TGCTCATGGTGTGTGATCTCAA 59.961 45.455 0.00 0.00 0.00 3.02
2297 2688 2.417933 GCTCATGGTGTGTGATCTCAAC 59.582 50.000 0.00 1.14 0.00 3.18
2298 2689 3.667360 CTCATGGTGTGTGATCTCAACA 58.333 45.455 0.00 2.96 38.76 3.33
2299 2690 4.259356 CTCATGGTGTGTGATCTCAACAT 58.741 43.478 0.00 5.13 43.40 2.71
2301 2692 3.767902 TGGTGTGTGATCTCAACATGA 57.232 42.857 0.00 0.00 31.15 3.07
2302 2693 3.402110 TGGTGTGTGATCTCAACATGAC 58.598 45.455 0.00 0.00 31.15 3.06
2303 2694 3.181456 TGGTGTGTGATCTCAACATGACA 60.181 43.478 0.00 0.00 31.15 3.58
2304 2695 3.187227 GGTGTGTGATCTCAACATGACAC 59.813 47.826 0.00 1.03 40.27 3.67
2305 2696 3.059166 TGTGTGATCTCAACATGACACG 58.941 45.455 0.00 0.00 42.09 4.49
2306 2697 3.243704 TGTGTGATCTCAACATGACACGA 60.244 43.478 0.00 0.00 42.09 4.35
2307 2698 3.366121 GTGTGATCTCAACATGACACGAG 59.634 47.826 0.00 0.00 32.29 4.18
2308 2699 2.926200 GTGATCTCAACATGACACGAGG 59.074 50.000 0.00 0.00 0.00 4.63
2309 2700 1.929836 GATCTCAACATGACACGAGGC 59.070 52.381 0.00 0.00 0.00 4.70
2310 2701 0.037326 TCTCAACATGACACGAGGCC 60.037 55.000 0.00 0.00 0.00 5.19
2311 2702 0.320683 CTCAACATGACACGAGGCCA 60.321 55.000 5.01 0.00 0.00 5.36
2312 2703 0.107643 TCAACATGACACGAGGCCAA 59.892 50.000 5.01 0.00 0.00 4.52
2313 2704 0.518636 CAACATGACACGAGGCCAAG 59.481 55.000 5.01 0.00 0.00 3.61
2314 2705 0.606401 AACATGACACGAGGCCAAGG 60.606 55.000 5.01 0.00 0.00 3.61
2315 2706 1.296392 CATGACACGAGGCCAAGGA 59.704 57.895 5.01 0.00 0.00 3.36
2316 2707 0.742281 CATGACACGAGGCCAAGGAG 60.742 60.000 5.01 0.00 0.00 3.69
2317 2708 1.903877 ATGACACGAGGCCAAGGAGG 61.904 60.000 5.01 0.00 41.84 4.30
2327 2718 3.086733 CCAAGGAGGCCTCGATTTC 57.913 57.895 26.36 12.17 30.89 2.17
2328 2719 0.543749 CCAAGGAGGCCTCGATTTCT 59.456 55.000 26.36 14.38 30.89 2.52
2329 2720 1.065126 CCAAGGAGGCCTCGATTTCTT 60.065 52.381 26.36 19.34 30.89 2.52
2330 2721 2.012673 CAAGGAGGCCTCGATTTCTTG 58.987 52.381 26.36 25.55 30.89 3.02
2331 2722 0.543749 AGGAGGCCTCGATTTCTTGG 59.456 55.000 26.36 0.00 0.00 3.61
2332 2723 0.253327 GGAGGCCTCGATTTCTTGGT 59.747 55.000 26.36 0.00 0.00 3.67
2333 2724 1.340114 GGAGGCCTCGATTTCTTGGTT 60.340 52.381 26.36 0.00 0.00 3.67
2334 2725 2.010497 GAGGCCTCGATTTCTTGGTTC 58.990 52.381 19.06 0.00 0.00 3.62
2335 2726 1.630878 AGGCCTCGATTTCTTGGTTCT 59.369 47.619 0.00 0.00 0.00 3.01
2336 2727 2.010497 GGCCTCGATTTCTTGGTTCTC 58.990 52.381 0.00 0.00 0.00 2.87
2337 2728 1.661112 GCCTCGATTTCTTGGTTCTCG 59.339 52.381 0.00 0.00 0.00 4.04
2338 2729 2.931320 GCCTCGATTTCTTGGTTCTCGT 60.931 50.000 0.00 0.00 0.00 4.18
2339 2730 2.924290 CCTCGATTTCTTGGTTCTCGTC 59.076 50.000 0.00 0.00 0.00 4.20
2340 2731 3.575630 CTCGATTTCTTGGTTCTCGTCA 58.424 45.455 0.00 0.00 0.00 4.35
2341 2732 3.985008 TCGATTTCTTGGTTCTCGTCAA 58.015 40.909 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 18 7.414098 GGGCACATGTACACTAATGACTAAAAG 60.414 40.741 0.00 0.00 0.00 2.27
20 22 4.141801 GGGGCACATGTACACTAATGACTA 60.142 45.833 0.00 0.00 0.00 2.59
48 55 3.795688 TCTCATTATTCCAGCATCCCC 57.204 47.619 0.00 0.00 0.00 4.81
54 61 7.992754 AAGGATAACATCTCATTATTCCAGC 57.007 36.000 0.00 0.00 0.00 4.85
73 80 4.837860 TGCCAAAATACTGAACCAAAGGAT 59.162 37.500 0.00 0.00 0.00 3.24
93 100 6.015940 ACCAGAATAATAGCTAGCATTTTGCC 60.016 38.462 18.83 1.00 46.52 4.52
145 152 9.612620 CAGGTAAATCTCAGTAATTTTGTCAAC 57.387 33.333 0.00 0.00 0.00 3.18
172 180 3.330126 AGCATAGGGACCTTGTAGCTA 57.670 47.619 0.00 0.00 0.00 3.32
236 245 6.241645 CAGACTAGAGGGTCCAGAAATTTTT 58.758 40.000 0.00 0.00 36.95 1.94
238 247 4.323868 GCAGACTAGAGGGTCCAGAAATTT 60.324 45.833 0.00 0.00 36.95 1.82
239 248 3.198853 GCAGACTAGAGGGTCCAGAAATT 59.801 47.826 0.00 0.00 36.95 1.82
240 249 2.769095 GCAGACTAGAGGGTCCAGAAAT 59.231 50.000 0.00 0.00 36.95 2.17
241 250 2.180276 GCAGACTAGAGGGTCCAGAAA 58.820 52.381 0.00 0.00 36.95 2.52
284 294 1.779221 CTCTGGGCTCTCATCTCAGT 58.221 55.000 0.00 0.00 0.00 3.41
305 315 1.818674 GTCGTGATCCTTGGGCATTTT 59.181 47.619 0.00 0.00 0.00 1.82
386 589 6.322712 AGAAGGACAGATATTAGTGGAGTCAC 59.677 42.308 0.00 0.00 43.93 3.67
522 725 2.525750 TTTATTACGACGACGCGACT 57.474 45.000 15.93 0.00 43.96 4.18
607 811 5.104151 TGGCCCAATCATTGTCAGTCTAATA 60.104 40.000 0.00 0.00 0.00 0.98
614 818 2.173519 ACTTGGCCCAATCATTGTCAG 58.826 47.619 0.00 0.00 0.00 3.51
620 824 3.299503 GGTGATTACTTGGCCCAATCAT 58.700 45.455 17.16 0.00 39.95 2.45
651 855 7.698836 AAGTTATTTGCAAATATCGCCAATC 57.301 32.000 27.83 9.90 31.47 2.67
673 879 5.702670 CCATTACTATGGCCAGTGACATAAG 59.297 44.000 13.05 0.76 44.64 1.73
720 926 9.722184 GGGACCAATAGAATCCTATAGTAAAAC 57.278 37.037 0.00 0.00 34.63 2.43
729 935 5.293643 TCCTTTGGGACCAATAGAATCCTA 58.706 41.667 4.36 0.00 36.57 2.94
739 945 0.189574 TGCCATTCCTTTGGGACCAA 59.810 50.000 0.00 0.00 42.05 3.67
752 958 5.594317 GGATGTAAAAGGTACTCATGCCATT 59.406 40.000 0.00 0.00 38.49 3.16
831 1039 7.037438 AGTGCACAATTCATATAGGCAAAAAG 58.963 34.615 21.04 0.00 0.00 2.27
835 1043 6.356556 ACTAGTGCACAATTCATATAGGCAA 58.643 36.000 21.04 0.00 0.00 4.52
899 1112 4.556699 GCGTGTTGTTTCTTGAAGGCTATT 60.557 41.667 0.00 0.00 0.00 1.73
922 1135 5.291858 TGAGATTCGATCGAAGTTTGGATTG 59.708 40.000 31.66 0.00 37.56 2.67
983 1207 5.554070 TGATCATGAGCAAGAAGAAACTGA 58.446 37.500 12.06 0.00 0.00 3.41
984 1208 5.874895 TGATCATGAGCAAGAAGAAACTG 57.125 39.130 12.06 0.00 0.00 3.16
1019 1243 7.969536 AGGAATATCATGAAGTTAATGGTCG 57.030 36.000 0.00 0.00 0.00 4.79
1051 1275 4.151867 GTGTGAATTAACTTGACGGAGACC 59.848 45.833 0.00 0.00 0.00 3.85
1057 1281 4.804608 TGGTGTGTGAATTAACTTGACG 57.195 40.909 0.00 0.00 0.00 4.35
1072 1296 4.508461 TCAATTGCTCTTTCATGGTGTG 57.492 40.909 0.00 0.00 0.00 3.82
1090 1314 3.561143 TCTTAACCCTGCTTGCTTTCAA 58.439 40.909 0.00 0.00 0.00 2.69
1105 1329 2.159324 GCAAGGCAGCCAAGATCTTAAC 60.159 50.000 15.80 3.16 0.00 2.01
1135 1359 2.646930 CATGCCTTGAGTAAGCATGGA 58.353 47.619 14.74 0.00 40.61 3.41
1141 1365 0.392998 ACCGCCATGCCTTGAGTAAG 60.393 55.000 0.00 0.00 0.00 2.34
1159 1383 3.047877 CACCCCCTTGACGCGAAC 61.048 66.667 15.93 7.16 0.00 3.95
1164 1388 2.347490 CTCACCACCCCCTTGACG 59.653 66.667 0.00 0.00 0.00 4.35
1175 1399 3.575506 GTGATGCCATTCCTCACCA 57.424 52.632 0.00 0.00 34.55 4.17
1187 1411 1.153289 ACAGCCTCATCGGTGATGC 60.153 57.895 17.11 17.11 43.68 3.91
1243 1467 1.285641 CATGGTGGTTGTTGACGGC 59.714 57.895 0.00 0.00 0.00 5.68
1248 1472 1.338011 GGGATTGCATGGTGGTTGTTG 60.338 52.381 0.00 0.00 0.00 3.33
1249 1473 0.975887 GGGATTGCATGGTGGTTGTT 59.024 50.000 0.00 0.00 0.00 2.83
1397 1623 5.866092 CGCTGCTGACATCTATACAATATGT 59.134 40.000 0.00 0.00 36.57 2.29
1447 1803 4.270008 TCCCTTTAGCAGCTTATTTCCAC 58.730 43.478 0.00 0.00 0.00 4.02
1450 1806 5.883115 ACTCTTCCCTTTAGCAGCTTATTTC 59.117 40.000 0.00 0.00 0.00 2.17
1463 1819 5.740290 TCTTCGACATTACTCTTCCCTTT 57.260 39.130 0.00 0.00 0.00 3.11
1584 1948 6.618287 TCATGAAAGTTTCCTTACACACAG 57.382 37.500 13.01 0.00 0.00 3.66
1694 2058 7.156673 ACTGAATTGTAAGCATGCAGATTTTT 58.843 30.769 21.98 6.65 0.00 1.94
1695 2059 6.694447 ACTGAATTGTAAGCATGCAGATTTT 58.306 32.000 21.98 7.44 0.00 1.82
1696 2060 6.276832 ACTGAATTGTAAGCATGCAGATTT 57.723 33.333 21.98 7.85 0.00 2.17
1697 2061 5.909621 ACTGAATTGTAAGCATGCAGATT 57.090 34.783 21.98 8.25 0.00 2.40
1698 2062 7.283807 TCATTACTGAATTGTAAGCATGCAGAT 59.716 33.333 21.98 8.21 36.10 2.90
1699 2063 6.598850 TCATTACTGAATTGTAAGCATGCAGA 59.401 34.615 21.98 3.59 36.10 4.26
1700 2064 6.788243 TCATTACTGAATTGTAAGCATGCAG 58.212 36.000 21.98 7.42 36.10 4.41
1701 2065 6.756299 TCATTACTGAATTGTAAGCATGCA 57.244 33.333 21.98 0.00 36.10 3.96
1702 2066 9.734620 TTAATCATTACTGAATTGTAAGCATGC 57.265 29.630 10.51 10.51 36.10 4.06
1790 2154 2.545946 GCTTTGGGCATCGATTAGAGTC 59.454 50.000 0.00 0.00 41.35 3.36
1810 2188 0.544120 TTCAGTTTTGGGGATGGGGC 60.544 55.000 0.00 0.00 0.00 5.80
1812 2190 3.444029 AGATTTCAGTTTTGGGGATGGG 58.556 45.455 0.00 0.00 0.00 4.00
1857 2235 2.409948 GCATCACTTAGAAGCCACCT 57.590 50.000 0.00 0.00 34.98 4.00
1870 2248 2.101415 GGGATTAAGCTTTGGGCATCAC 59.899 50.000 3.20 0.00 44.79 3.06
2110 2500 5.091552 TCCTCCTCCTAGAAGCACTAAAAA 58.908 41.667 0.00 0.00 0.00 1.94
2118 2508 2.158385 TCCTCATCCTCCTCCTAGAAGC 60.158 54.545 0.00 0.00 0.00 3.86
2122 2512 4.487804 TCATTTCCTCATCCTCCTCCTAG 58.512 47.826 0.00 0.00 0.00 3.02
2124 2514 3.428063 TCATTTCCTCATCCTCCTCCT 57.572 47.619 0.00 0.00 0.00 3.69
2180 2570 0.903454 GGAGGTGGAAGGGACGAGAA 60.903 60.000 0.00 0.00 0.00 2.87
2185 2575 0.250770 GTTGTGGAGGTGGAAGGGAC 60.251 60.000 0.00 0.00 0.00 4.46
2195 2586 2.680312 AGACATCGATGTTGTGGAGG 57.320 50.000 30.46 2.18 41.95 4.30
2202 2593 3.769844 AGGTACAGGAAGACATCGATGTT 59.230 43.478 30.46 17.10 41.95 2.71
2203 2594 3.366396 AGGTACAGGAAGACATCGATGT 58.634 45.455 30.37 30.37 45.16 3.06
2205 2596 3.904717 AGAGGTACAGGAAGACATCGAT 58.095 45.455 0.00 0.00 31.81 3.59
2208 2599 6.239176 CCTTCATAGAGGTACAGGAAGACATC 60.239 46.154 6.84 0.00 35.04 3.06
2213 2604 3.070302 GGCCTTCATAGAGGTACAGGAAG 59.930 52.174 0.00 0.00 39.11 3.46
2222 2613 1.561542 ACAAGGTGGCCTTCATAGAGG 59.438 52.381 3.32 0.00 42.67 3.69
2223 2614 2.636830 CACAAGGTGGCCTTCATAGAG 58.363 52.381 3.32 0.00 42.67 2.43
2224 2615 2.787473 CACAAGGTGGCCTTCATAGA 57.213 50.000 3.32 0.00 42.67 1.98
2235 2626 1.888512 CAATGAAGGTCCCACAAGGTG 59.111 52.381 0.00 0.00 36.75 4.00
2236 2627 1.499007 ACAATGAAGGTCCCACAAGGT 59.501 47.619 0.00 0.00 36.75 3.50
2237 2628 1.888512 CACAATGAAGGTCCCACAAGG 59.111 52.381 0.00 0.00 0.00 3.61
2238 2629 1.270550 GCACAATGAAGGTCCCACAAG 59.729 52.381 0.00 0.00 0.00 3.16
2239 2630 1.133513 AGCACAATGAAGGTCCCACAA 60.134 47.619 0.00 0.00 0.00 3.33
2240 2631 0.478072 AGCACAATGAAGGTCCCACA 59.522 50.000 0.00 0.00 0.00 4.17
2241 2632 1.620822 AAGCACAATGAAGGTCCCAC 58.379 50.000 0.00 0.00 0.00 4.61
2242 2633 2.380064 AAAGCACAATGAAGGTCCCA 57.620 45.000 0.00 0.00 0.00 4.37
2243 2634 4.580580 CCTATAAAGCACAATGAAGGTCCC 59.419 45.833 0.00 0.00 0.00 4.46
2244 2635 4.036852 GCCTATAAAGCACAATGAAGGTCC 59.963 45.833 0.00 0.00 0.00 4.46
2245 2636 4.260784 CGCCTATAAAGCACAATGAAGGTC 60.261 45.833 0.00 0.00 0.00 3.85
2246 2637 3.627577 CGCCTATAAAGCACAATGAAGGT 59.372 43.478 0.00 0.00 0.00 3.50
2247 2638 3.876914 TCGCCTATAAAGCACAATGAAGG 59.123 43.478 0.00 0.00 0.00 3.46
2248 2639 4.332543 TGTCGCCTATAAAGCACAATGAAG 59.667 41.667 0.00 0.00 0.00 3.02
2249 2640 4.094294 GTGTCGCCTATAAAGCACAATGAA 59.906 41.667 0.00 0.00 0.00 2.57
2250 2641 3.621268 GTGTCGCCTATAAAGCACAATGA 59.379 43.478 0.00 0.00 0.00 2.57
2251 2642 3.544048 CGTGTCGCCTATAAAGCACAATG 60.544 47.826 0.00 0.00 0.00 2.82
2252 2643 2.607635 CGTGTCGCCTATAAAGCACAAT 59.392 45.455 0.00 0.00 0.00 2.71
2253 2644 1.996898 CGTGTCGCCTATAAAGCACAA 59.003 47.619 0.00 0.00 0.00 3.33
2254 2645 1.635844 CGTGTCGCCTATAAAGCACA 58.364 50.000 0.00 0.00 0.00 4.57
2255 2646 0.928229 CCGTGTCGCCTATAAAGCAC 59.072 55.000 0.00 0.00 0.00 4.40
2256 2647 0.533491 ACCGTGTCGCCTATAAAGCA 59.467 50.000 0.00 0.00 0.00 3.91
2257 2648 0.928229 CACCGTGTCGCCTATAAAGC 59.072 55.000 0.00 0.00 0.00 3.51
2258 2649 0.928229 GCACCGTGTCGCCTATAAAG 59.072 55.000 0.00 0.00 0.00 1.85
2259 2650 0.533491 AGCACCGTGTCGCCTATAAA 59.467 50.000 0.00 0.00 0.00 1.40
2260 2651 0.101759 GAGCACCGTGTCGCCTATAA 59.898 55.000 0.00 0.00 0.00 0.98
2261 2652 1.033202 TGAGCACCGTGTCGCCTATA 61.033 55.000 0.00 0.00 0.00 1.31
2262 2653 1.676678 ATGAGCACCGTGTCGCCTAT 61.677 55.000 0.00 0.00 0.00 2.57
2263 2654 2.348104 ATGAGCACCGTGTCGCCTA 61.348 57.895 0.00 0.00 0.00 3.93
2264 2655 3.695606 ATGAGCACCGTGTCGCCT 61.696 61.111 0.00 0.00 0.00 5.52
2265 2656 3.490759 CATGAGCACCGTGTCGCC 61.491 66.667 0.00 0.00 0.00 5.54
2266 2657 3.490759 CCATGAGCACCGTGTCGC 61.491 66.667 0.00 0.00 0.00 5.19
2267 2658 2.048222 ACCATGAGCACCGTGTCG 60.048 61.111 0.00 0.00 0.00 4.35
2268 2659 1.301716 ACACCATGAGCACCGTGTC 60.302 57.895 0.00 0.00 34.42 3.67
2269 2660 1.597854 CACACCATGAGCACCGTGT 60.598 57.895 0.00 0.00 39.98 4.49
2270 2661 1.597854 ACACACCATGAGCACCGTG 60.598 57.895 0.00 0.00 0.00 4.94
2271 2662 1.597854 CACACACCATGAGCACCGT 60.598 57.895 0.00 0.00 0.00 4.83
2272 2663 0.674581 ATCACACACCATGAGCACCG 60.675 55.000 0.00 0.00 0.00 4.94
2273 2664 1.089920 GATCACACACCATGAGCACC 58.910 55.000 0.00 0.00 32.67 5.01
2274 2665 2.005451 GAGATCACACACCATGAGCAC 58.995 52.381 0.00 0.00 34.89 4.40
2275 2666 1.624813 TGAGATCACACACCATGAGCA 59.375 47.619 0.00 0.00 34.89 4.26
2276 2667 2.391616 TGAGATCACACACCATGAGC 57.608 50.000 0.00 0.00 32.56 4.26
2277 2668 3.667360 TGTTGAGATCACACACCATGAG 58.333 45.455 0.00 0.00 0.00 2.90
2278 2669 3.767902 TGTTGAGATCACACACCATGA 57.232 42.857 0.00 0.00 0.00 3.07
2279 2670 4.004982 TCATGTTGAGATCACACACCATG 58.995 43.478 14.90 14.90 38.23 3.66
2280 2671 4.005650 GTCATGTTGAGATCACACACCAT 58.994 43.478 0.00 0.00 0.00 3.55
2281 2672 3.181456 TGTCATGTTGAGATCACACACCA 60.181 43.478 0.00 0.00 0.00 4.17
2282 2673 3.187227 GTGTCATGTTGAGATCACACACC 59.813 47.826 0.00 0.00 31.36 4.16
2283 2674 3.120889 CGTGTCATGTTGAGATCACACAC 60.121 47.826 9.76 4.49 32.85 3.82
2284 2675 3.059166 CGTGTCATGTTGAGATCACACA 58.941 45.455 9.76 2.64 0.00 3.72
2285 2676 3.317150 TCGTGTCATGTTGAGATCACAC 58.683 45.455 0.00 0.00 0.00 3.82
2286 2677 3.578688 CTCGTGTCATGTTGAGATCACA 58.421 45.455 0.00 0.00 0.00 3.58
2287 2678 2.926200 CCTCGTGTCATGTTGAGATCAC 59.074 50.000 0.00 0.00 0.00 3.06
2288 2679 2.675032 GCCTCGTGTCATGTTGAGATCA 60.675 50.000 0.00 0.00 0.00 2.92
2289 2680 1.929836 GCCTCGTGTCATGTTGAGATC 59.070 52.381 0.00 0.00 0.00 2.75
2290 2681 1.406069 GGCCTCGTGTCATGTTGAGAT 60.406 52.381 0.00 0.00 0.00 2.75
2291 2682 0.037326 GGCCTCGTGTCATGTTGAGA 60.037 55.000 0.00 0.00 0.00 3.27
2292 2683 0.320683 TGGCCTCGTGTCATGTTGAG 60.321 55.000 3.32 0.00 0.00 3.02
2293 2684 0.107643 TTGGCCTCGTGTCATGTTGA 59.892 50.000 3.32 0.00 0.00 3.18
2294 2685 0.518636 CTTGGCCTCGTGTCATGTTG 59.481 55.000 3.32 0.00 0.00 3.33
2295 2686 0.606401 CCTTGGCCTCGTGTCATGTT 60.606 55.000 3.32 0.00 0.00 2.71
2296 2687 1.003355 CCTTGGCCTCGTGTCATGT 60.003 57.895 3.32 0.00 0.00 3.21
2297 2688 0.742281 CTCCTTGGCCTCGTGTCATG 60.742 60.000 3.32 0.00 0.00 3.07
2298 2689 1.599047 CTCCTTGGCCTCGTGTCAT 59.401 57.895 3.32 0.00 0.00 3.06
2299 2690 2.583441 CCTCCTTGGCCTCGTGTCA 61.583 63.158 3.32 0.00 0.00 3.58
2300 2691 2.266055 CCTCCTTGGCCTCGTGTC 59.734 66.667 3.32 0.00 0.00 3.67
2309 2700 0.543749 AGAAATCGAGGCCTCCTTGG 59.456 55.000 27.20 13.05 35.77 3.61
2310 2701 2.012673 CAAGAAATCGAGGCCTCCTTG 58.987 52.381 27.20 25.88 36.39 3.61
2311 2702 1.065126 CCAAGAAATCGAGGCCTCCTT 60.065 52.381 27.20 19.66 31.76 3.36
2312 2703 0.543749 CCAAGAAATCGAGGCCTCCT 59.456 55.000 27.20 14.69 36.03 3.69
2313 2704 0.253327 ACCAAGAAATCGAGGCCTCC 59.747 55.000 27.20 12.47 0.00 4.30
2314 2705 2.010497 GAACCAAGAAATCGAGGCCTC 58.990 52.381 23.79 23.79 0.00 4.70
2315 2706 1.630878 AGAACCAAGAAATCGAGGCCT 59.369 47.619 3.86 3.86 0.00 5.19
2316 2707 2.010497 GAGAACCAAGAAATCGAGGCC 58.990 52.381 0.00 0.00 0.00 5.19
2317 2708 1.661112 CGAGAACCAAGAAATCGAGGC 59.339 52.381 0.00 0.00 35.47 4.70
2318 2709 2.924290 GACGAGAACCAAGAAATCGAGG 59.076 50.000 0.00 0.00 37.16 4.63
2319 2710 3.575630 TGACGAGAACCAAGAAATCGAG 58.424 45.455 0.00 0.00 37.16 4.04
2320 2711 3.653539 TGACGAGAACCAAGAAATCGA 57.346 42.857 0.00 0.00 37.16 3.59


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

AutoCloner maintained by Alex Coulton.