Multiple sequence alignment - TraesCS6A01G340900

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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 TraesCS6A01G340900 chr6A 100.000 2330 0 0 1 2330 573847408 573849737 0.000000e+00 4303.0
1 TraesCS6A01G340900 chr1B 96.712 1095 32 2 260 1354 570887695 570888785 0.000000e+00 1820.0
2 TraesCS6A01G340900 chr1B 88.435 294 6 1 1 266 570855749 570856042 1.730000e-86 329.0
3 TraesCS6A01G340900 chr3D 98.384 928 13 1 427 1354 43673607 43674532 0.000000e+00 1629.0
4 TraesCS6A01G340900 chr3D 91.605 405 6 1 1 377 43673202 43673606 3.410000e-148 534.0
5 TraesCS6A01G340900 chr7A 82.886 1268 202 7 99 1354 223529159 223530423 0.000000e+00 1125.0
6 TraesCS6A01G340900 chr7A 91.753 97 8 0 1 97 223529033 223529129 4.040000e-28 135.0
7 TraesCS6A01G340900 chr7A 90.000 60 5 1 1821 1880 33452922 33452864 2.480000e-10 76.8
8 TraesCS6A01G340900 chr7D 82.780 1266 205 9 99 1354 211639355 211640617 0.000000e+00 1118.0
9 TraesCS6A01G340900 chr7D 90.722 97 9 0 1 97 211639229 211639325 1.880000e-26 130.0
10 TraesCS6A01G340900 chr7D 93.548 62 2 2 1824 1883 573908726 573908665 8.870000e-15 91.6
11 TraesCS6A01G340900 chr7D 90.476 63 3 1 1820 1879 101475463 101475401 1.920000e-11 80.5
12 TraesCS6A01G340900 chr7D 90.000 60 2 1 1824 1879 25821401 25821460 8.930000e-10 75.0
13 TraesCS6A01G340900 chr2D 94.918 610 31 0 745 1354 523312480 523313089 0.000000e+00 955.0
14 TraesCS6A01G340900 chr2D 94.737 57 2 1 1824 1879 629605559 629605503 1.150000e-13 87.9
15 TraesCS6A01G340900 chr6B 80.079 1260 240 8 101 1354 62115206 62113952 0.000000e+00 926.0
16 TraesCS6A01G340900 chr6B 96.009 426 15 1 1404 1827 645812458 645812883 0.000000e+00 691.0
17 TraesCS6A01G340900 chr6B 96.246 293 9 2 1878 2169 645812880 645813171 1.620000e-131 479.0
18 TraesCS6A01G340900 chr6B 97.516 161 4 0 2170 2330 645813204 645813364 2.280000e-70 276.0
19 TraesCS6A01G340900 chr7B 82.188 960 171 0 271 1230 189897599 189896640 0.000000e+00 826.0
20 TraesCS6A01G340900 chr7B 95.280 339 13 1 1009 1344 733462522 733462860 3.410000e-148 534.0
21 TraesCS6A01G340900 chr7B 91.781 146 12 0 99 244 189898566 189898421 1.090000e-48 204.0
22 TraesCS6A01G340900 chr7B 90.722 97 9 0 1 97 189898692 189898596 1.880000e-26 130.0
23 TraesCS6A01G340900 chr7B 88.889 63 7 0 1821 1883 670286289 670286351 6.900000e-11 78.7
24 TraesCS6A01G340900 chr1A 78.493 1274 240 30 99 1354 457823241 457821984 0.000000e+00 804.0
25 TraesCS6A01G340900 chr3A 98.333 300 4 1 1055 1354 34530916 34530618 2.050000e-145 525.0
26 TraesCS6A01G340900 chr4A 76.856 687 126 18 237 893 695909049 695908366 7.920000e-95 357.0
27 TraesCS6A01G340900 chr4A 76.509 464 78 10 889 1339 624021938 624022383 8.380000e-55 224.0
28 TraesCS6A01G340900 chr4A 92.857 42 3 0 1358 1399 343484880 343484839 6.950000e-06 62.1
29 TraesCS6A01G340900 chr5D 77.963 481 78 18 887 1364 545277394 545276939 2.280000e-70 276.0
30 TraesCS6A01G340900 chr5D 81.935 155 28 0 1590 1744 505462549 505462395 5.220000e-27 132.0
31 TraesCS6A01G340900 chr5D 90.625 96 9 0 1590 1685 505348579 505348484 6.760000e-26 128.0
32 TraesCS6A01G340900 chr5D 86.869 99 9 4 1445 1542 505360722 505360627 8.800000e-20 108.0
33 TraesCS6A01G340900 chr5D 85.870 92 13 0 1590 1681 505369042 505368951 5.300000e-17 99.0
34 TraesCS6A01G340900 chr5D 89.231 65 2 5 1822 1884 476013600 476013539 2.480000e-10 76.8
35 TraesCS6A01G340900 chr5D 79.000 100 9 7 2170 2258 505403245 505403147 8.990000e-05 58.4
36 TraesCS6A01G340900 chrUn 76.293 464 79 11 889 1339 1669617 1670062 3.900000e-53 219.0
37 TraesCS6A01G340900 chr5B 89.051 137 15 0 1608 1744 635508351 635508215 1.110000e-38 171.0
38 TraesCS6A01G340900 chr5B 82.119 151 27 0 1594 1744 635574302 635574152 1.880000e-26 130.0
39 TraesCS6A01G340900 chr5B 88.542 96 11 0 1590 1685 635347261 635347166 1.460000e-22 117.0
40 TraesCS6A01G340900 chr5B 80.986 142 22 5 1446 1586 635561162 635561025 8.800000e-20 108.0
41 TraesCS6A01G340900 chr5B 84.848 99 11 4 1445 1542 635358453 635358358 1.910000e-16 97.1
42 TraesCS6A01G340900 chr5B 83.838 99 15 1 1590 1688 635377772 635377675 2.470000e-15 93.5
43 TraesCS6A01G340900 chr5B 94.444 36 2 0 2170 2205 635464845 635464810 3.230000e-04 56.5
44 TraesCS6A01G340900 chr5A 85.859 99 10 4 1445 1542 632853410 632853315 4.100000e-18 102.0
45 TraesCS6A01G340900 chr5A 84.783 92 14 0 1590 1681 632874848 632874757 2.470000e-15 93.5
46 TraesCS6A01G340900 chr3B 83.505 97 16 0 1 97 235889778 235889682 8.870000e-15 91.6
47 TraesCS6A01G340900 chr6D 96.226 53 0 2 1829 1879 363382374 363382426 4.130000e-13 86.1
48 TraesCS6A01G340900 chr2A 91.379 58 3 2 1810 1865 107387167 107387224 6.900000e-11 78.7


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 TraesCS6A01G340900 chr6A 573847408 573849737 2329 False 4303.000000 4303 100.000000 1 2330 1 chr6A.!!$F1 2329
1 TraesCS6A01G340900 chr1B 570887695 570888785 1090 False 1820.000000 1820 96.712000 260 1354 1 chr1B.!!$F2 1094
2 TraesCS6A01G340900 chr3D 43673202 43674532 1330 False 1081.500000 1629 94.994500 1 1354 2 chr3D.!!$F1 1353
3 TraesCS6A01G340900 chr7A 223529033 223530423 1390 False 630.000000 1125 87.319500 1 1354 2 chr7A.!!$F1 1353
4 TraesCS6A01G340900 chr7D 211639229 211640617 1388 False 624.000000 1118 86.751000 1 1354 2 chr7D.!!$F2 1353
5 TraesCS6A01G340900 chr2D 523312480 523313089 609 False 955.000000 955 94.918000 745 1354 1 chr2D.!!$F1 609
6 TraesCS6A01G340900 chr6B 62113952 62115206 1254 True 926.000000 926 80.079000 101 1354 1 chr6B.!!$R1 1253
7 TraesCS6A01G340900 chr6B 645812458 645813364 906 False 482.000000 691 96.590333 1404 2330 3 chr6B.!!$F1 926
8 TraesCS6A01G340900 chr7B 189896640 189898692 2052 True 386.666667 826 88.230333 1 1230 3 chr7B.!!$R1 1229
9 TraesCS6A01G340900 chr1A 457821984 457823241 1257 True 804.000000 804 78.493000 99 1354 1 chr1A.!!$R1 1255
10 TraesCS6A01G340900 chr4A 695908366 695909049 683 True 357.000000 357 76.856000 237 893 1 chr4A.!!$R2 656

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
569 1419 0.250467 GTGTGGAGGAAAGCTCAGCA 60.25 55.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 2736 0.033306 GAAGTACTCCCTCCGTCCCT 60.033 60.0 0.0 0.0 0.0 4.2 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
34 35 4.878968 TCATATGGAGAGTTGGTAGTGGA 58.121 43.478 2.13 0.00 0.00 4.02
150 179 5.700402 ACTGGGATGCAGACTTAATAAGT 57.300 39.130 5.20 5.20 46.38 2.24
569 1419 0.250467 GTGTGGAGGAAAGCTCAGCA 60.250 55.000 0.00 0.00 0.00 4.41
997 1868 1.048601 ACTTCACTCGGAGGCTTTGA 58.951 50.000 10.23 0.90 0.00 2.69
1009 1880 2.742053 GAGGCTTTGACGATGCTTTACA 59.258 45.455 0.00 0.00 0.00 2.41
1354 2225 4.448732 GGAATGCATTGTGTTCCTTCAAAC 59.551 41.667 18.59 0.00 38.65 2.93
1355 2226 3.077229 TGCATTGTGTTCCTTCAAACG 57.923 42.857 0.00 0.00 31.58 3.60
1356 2227 2.685388 TGCATTGTGTTCCTTCAAACGA 59.315 40.909 0.00 0.00 31.58 3.85
1357 2228 3.129462 TGCATTGTGTTCCTTCAAACGAA 59.871 39.130 0.00 0.00 31.58 3.85
1358 2229 4.109050 GCATTGTGTTCCTTCAAACGAAA 58.891 39.130 0.00 0.00 31.58 3.46
1359 2230 4.207019 GCATTGTGTTCCTTCAAACGAAAG 59.793 41.667 0.00 0.00 31.58 2.62
1360 2231 4.364415 TTGTGTTCCTTCAAACGAAAGG 57.636 40.909 0.00 0.00 43.94 3.11
1365 2236 2.681152 CCTTCAAACGAAAGGAACGG 57.319 50.000 0.00 0.00 45.15 4.44
1366 2237 1.265905 CCTTCAAACGAAAGGAACGGG 59.734 52.381 0.00 0.00 45.15 5.28
1367 2238 0.664224 TTCAAACGAAAGGAACGGGC 59.336 50.000 0.00 0.00 34.93 6.13
1368 2239 1.082366 CAAACGAAAGGAACGGGCG 60.082 57.895 0.00 0.00 34.93 6.13
1369 2240 2.900167 AAACGAAAGGAACGGGCGC 61.900 57.895 0.00 0.00 34.93 6.53
1370 2241 4.612412 ACGAAAGGAACGGGCGCA 62.612 61.111 10.83 0.00 34.93 6.09
1371 2242 3.788766 CGAAAGGAACGGGCGCAG 61.789 66.667 10.83 4.90 0.00 5.18
1372 2243 2.358247 GAAAGGAACGGGCGCAGA 60.358 61.111 10.83 0.00 0.00 4.26
1373 2244 2.358737 AAAGGAACGGGCGCAGAG 60.359 61.111 10.83 1.38 0.00 3.35
1374 2245 2.781595 GAAAGGAACGGGCGCAGAGA 62.782 60.000 10.83 0.00 0.00 3.10
1375 2246 2.788191 AAAGGAACGGGCGCAGAGAG 62.788 60.000 10.83 0.00 0.00 3.20
1385 2256 3.389206 GCAGAGAGCGCCGTTTAG 58.611 61.111 2.29 0.00 0.00 1.85
1386 2257 2.167861 GCAGAGAGCGCCGTTTAGG 61.168 63.158 2.29 0.00 44.97 2.69
1387 2258 1.511305 CAGAGAGCGCCGTTTAGGA 59.489 57.895 2.29 0.00 45.00 2.94
1388 2259 0.103208 CAGAGAGCGCCGTTTAGGAT 59.897 55.000 2.29 0.00 45.00 3.24
1389 2260 0.824759 AGAGAGCGCCGTTTAGGATT 59.175 50.000 2.29 0.00 45.00 3.01
1390 2261 1.207329 AGAGAGCGCCGTTTAGGATTT 59.793 47.619 2.29 0.00 45.00 2.17
1391 2262 1.327764 GAGAGCGCCGTTTAGGATTTG 59.672 52.381 2.29 0.00 45.00 2.32
1392 2263 0.248094 GAGCGCCGTTTAGGATTTGC 60.248 55.000 2.29 0.00 45.00 3.68
1393 2264 1.226575 GCGCCGTTTAGGATTTGCC 60.227 57.895 0.00 0.00 45.00 4.52
1395 2266 0.377203 CGCCGTTTAGGATTTGCCTC 59.623 55.000 0.00 0.00 46.97 4.70
1396 2267 1.459450 GCCGTTTAGGATTTGCCTCA 58.541 50.000 0.00 0.00 46.97 3.86
1397 2268 1.816224 GCCGTTTAGGATTTGCCTCAA 59.184 47.619 0.00 0.00 46.97 3.02
1398 2269 2.230266 GCCGTTTAGGATTTGCCTCAAA 59.770 45.455 0.00 0.00 46.97 2.69
1399 2270 3.305744 GCCGTTTAGGATTTGCCTCAAAA 60.306 43.478 0.00 0.00 46.97 2.44
1400 2271 4.797933 GCCGTTTAGGATTTGCCTCAAAAA 60.798 41.667 0.00 0.00 46.97 1.94
1424 2295 0.955919 GCACCAGCAACTACCACCTC 60.956 60.000 0.00 0.00 41.58 3.85
1432 2303 1.498176 AACTACCACCTCCCCCTTGC 61.498 60.000 0.00 0.00 0.00 4.01
1474 2345 1.299541 ACACTTGAAACACCAGCTCG 58.700 50.000 0.00 0.00 0.00 5.03
1605 2476 1.674057 CAACCTTCCTGACTCGCCT 59.326 57.895 0.00 0.00 0.00 5.52
1609 2480 0.390472 CCTTCCTGACTCGCCTTGAC 60.390 60.000 0.00 0.00 0.00 3.18
1723 2596 0.636647 TCTAGAGGGCCATGTCAGGA 59.363 55.000 6.18 0.00 0.00 3.86
1740 2613 3.449018 TCAGGAAGCAGTGTCCTAAGATC 59.551 47.826 2.10 0.00 44.00 2.75
1744 2617 4.295051 GAAGCAGTGTCCTAAGATCGATC 58.705 47.826 17.91 17.91 0.00 3.69
1745 2618 2.292016 AGCAGTGTCCTAAGATCGATCG 59.708 50.000 19.33 9.36 0.00 3.69
1801 2674 2.295253 ACTGCTACCTTGTGTATCGC 57.705 50.000 0.00 0.00 0.00 4.58
1802 2675 1.825474 ACTGCTACCTTGTGTATCGCT 59.175 47.619 0.00 0.00 0.00 4.93
1827 2700 4.788617 ACCCCACATTACCTTCATCTACTT 59.211 41.667 0.00 0.00 0.00 2.24
1828 2701 5.104485 ACCCCACATTACCTTCATCTACTTC 60.104 44.000 0.00 0.00 0.00 3.01
1829 2702 5.368989 CCCACATTACCTTCATCTACTTCC 58.631 45.833 0.00 0.00 0.00 3.46
1830 2703 5.131142 CCCACATTACCTTCATCTACTTCCT 59.869 44.000 0.00 0.00 0.00 3.36
1831 2704 6.284459 CCACATTACCTTCATCTACTTCCTC 58.716 44.000 0.00 0.00 0.00 3.71
1832 2705 6.284459 CACATTACCTTCATCTACTTCCTCC 58.716 44.000 0.00 0.00 0.00 4.30
1833 2706 5.069251 ACATTACCTTCATCTACTTCCTCCG 59.931 44.000 0.00 0.00 0.00 4.63
1834 2707 3.103080 ACCTTCATCTACTTCCTCCGT 57.897 47.619 0.00 0.00 0.00 4.69
1835 2708 3.025262 ACCTTCATCTACTTCCTCCGTC 58.975 50.000 0.00 0.00 0.00 4.79
1836 2709 3.292460 CCTTCATCTACTTCCTCCGTCT 58.708 50.000 0.00 0.00 0.00 4.18
1837 2710 3.316868 CCTTCATCTACTTCCTCCGTCTC 59.683 52.174 0.00 0.00 0.00 3.36
1838 2711 3.646736 TCATCTACTTCCTCCGTCTCA 57.353 47.619 0.00 0.00 0.00 3.27
1839 2712 4.171878 TCATCTACTTCCTCCGTCTCAT 57.828 45.455 0.00 0.00 0.00 2.90
1840 2713 5.306114 TCATCTACTTCCTCCGTCTCATA 57.694 43.478 0.00 0.00 0.00 2.15
1841 2714 5.691896 TCATCTACTTCCTCCGTCTCATAA 58.308 41.667 0.00 0.00 0.00 1.90
1842 2715 6.307776 TCATCTACTTCCTCCGTCTCATAAT 58.692 40.000 0.00 0.00 0.00 1.28
1843 2716 7.459234 TCATCTACTTCCTCCGTCTCATAATA 58.541 38.462 0.00 0.00 0.00 0.98
1844 2717 8.110271 TCATCTACTTCCTCCGTCTCATAATAT 58.890 37.037 0.00 0.00 0.00 1.28
1845 2718 9.397280 CATCTACTTCCTCCGTCTCATAATATA 57.603 37.037 0.00 0.00 0.00 0.86
1846 2719 9.976776 ATCTACTTCCTCCGTCTCATAATATAA 57.023 33.333 0.00 0.00 0.00 0.98
1847 2720 9.451002 TCTACTTCCTCCGTCTCATAATATAAG 57.549 37.037 0.00 0.00 0.00 1.73
1848 2721 9.451002 CTACTTCCTCCGTCTCATAATATAAGA 57.549 37.037 0.00 0.00 0.00 2.10
1849 2722 8.343168 ACTTCCTCCGTCTCATAATATAAGAG 57.657 38.462 0.00 0.00 0.00 2.85
1850 2723 6.761099 TCCTCCGTCTCATAATATAAGAGC 57.239 41.667 0.00 0.00 0.00 4.09
1851 2724 5.354513 TCCTCCGTCTCATAATATAAGAGCG 59.645 44.000 0.00 0.00 0.00 5.03
1852 2725 5.124138 CCTCCGTCTCATAATATAAGAGCGT 59.876 44.000 0.00 0.00 31.69 5.07
1853 2726 6.349445 CCTCCGTCTCATAATATAAGAGCGTT 60.349 42.308 0.00 0.00 31.69 4.84
1854 2727 6.978338 TCCGTCTCATAATATAAGAGCGTTT 58.022 36.000 0.00 0.00 31.69 3.60
1855 2728 7.431249 TCCGTCTCATAATATAAGAGCGTTTT 58.569 34.615 0.00 0.00 31.69 2.43
1856 2729 7.924412 TCCGTCTCATAATATAAGAGCGTTTTT 59.076 33.333 0.00 0.00 31.69 1.94
1857 2730 8.004344 CCGTCTCATAATATAAGAGCGTTTTTG 58.996 37.037 0.00 0.00 31.69 2.44
1858 2731 8.752254 CGTCTCATAATATAAGAGCGTTTTTGA 58.248 33.333 0.00 0.00 0.00 2.69
1859 2732 9.851043 GTCTCATAATATAAGAGCGTTTTTGAC 57.149 33.333 0.00 0.00 0.00 3.18
1860 2733 9.594478 TCTCATAATATAAGAGCGTTTTTGACA 57.406 29.630 0.00 0.00 0.00 3.58
1861 2734 9.638300 CTCATAATATAAGAGCGTTTTTGACAC 57.362 33.333 0.00 0.00 0.00 3.67
1862 2735 9.378551 TCATAATATAAGAGCGTTTTTGACACT 57.621 29.630 0.00 0.00 0.00 3.55
1865 2738 7.772332 ATATAAGAGCGTTTTTGACACTAGG 57.228 36.000 0.00 0.00 0.00 3.02
1866 2739 2.767505 AGAGCGTTTTTGACACTAGGG 58.232 47.619 0.00 0.00 0.00 3.53
1867 2740 2.367567 AGAGCGTTTTTGACACTAGGGA 59.632 45.455 0.00 0.00 0.00 4.20
1868 2741 2.479275 GAGCGTTTTTGACACTAGGGAC 59.521 50.000 0.00 0.00 0.00 4.46
1869 2742 1.193874 GCGTTTTTGACACTAGGGACG 59.806 52.381 0.00 0.00 0.00 4.79
1870 2743 1.796459 CGTTTTTGACACTAGGGACGG 59.204 52.381 0.00 0.00 0.00 4.79
1871 2744 2.546373 CGTTTTTGACACTAGGGACGGA 60.546 50.000 0.00 0.00 0.00 4.69
1872 2745 3.064931 GTTTTTGACACTAGGGACGGAG 58.935 50.000 0.00 0.00 0.00 4.63
1873 2746 1.263356 TTTGACACTAGGGACGGAGG 58.737 55.000 0.00 0.00 0.00 4.30
1874 2747 0.613853 TTGACACTAGGGACGGAGGG 60.614 60.000 0.00 0.00 0.00 4.30
1875 2748 1.305623 GACACTAGGGACGGAGGGA 59.694 63.158 0.00 0.00 0.00 4.20
1876 2749 0.752376 GACACTAGGGACGGAGGGAG 60.752 65.000 0.00 0.00 0.00 4.30
1877 2750 1.306970 CACTAGGGACGGAGGGAGT 59.693 63.158 0.00 0.00 0.00 3.85
1878 2751 0.549950 CACTAGGGACGGAGGGAGTA 59.450 60.000 0.00 0.00 0.00 2.59
1879 2752 0.550432 ACTAGGGACGGAGGGAGTAC 59.450 60.000 0.00 0.00 0.00 2.73
1880 2753 0.845337 CTAGGGACGGAGGGAGTACT 59.155 60.000 0.00 0.00 0.00 2.73
1881 2754 1.214923 CTAGGGACGGAGGGAGTACTT 59.785 57.143 0.00 0.00 0.00 2.24
1895 2768 3.063588 GGAGTACTTCGCAAAATGCCTAC 59.936 47.826 0.00 0.00 41.12 3.18
1896 2769 2.671396 AGTACTTCGCAAAATGCCTACG 59.329 45.455 0.00 0.00 41.12 3.51
1973 2846 6.074516 CGAAGAAACGATTCAGACTAACACAA 60.075 38.462 8.22 0.00 38.06 3.33
1978 2851 6.080648 ACGATTCAGACTAACACAACACTA 57.919 37.500 0.00 0.00 0.00 2.74
2062 2936 4.752879 GCGACTGGTGGCGGCTAA 62.753 66.667 11.43 0.00 0.00 3.09
2065 2939 4.410400 ACTGGTGGCGGCTAAGGC 62.410 66.667 11.43 0.00 37.82 4.35
2135 3009 5.133999 ACTCTACTCTATAGCCCAGGTTACA 59.866 44.000 0.00 0.00 0.00 2.41
2250 3156 4.407496 TCAAAATAGCGGGTGTTTAACG 57.593 40.909 2.36 0.00 0.00 3.18
2270 3176 2.935201 CGGAAGAAAGGATCAGAGCAAG 59.065 50.000 0.00 0.00 0.00 4.01
2316 3222 5.652452 TGACTATGTAACTGCTTAGAGCTCA 59.348 40.000 17.77 0.00 42.97 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.820947 GTCGGTCCAGATATTAATGTTGGTT 59.179 40.000 0.00 0.00 0.00 3.67
150 179 2.701551 TCTTCAGGGAGGAAGGTTTGA 58.298 47.619 3.37 0.00 43.52 2.69
569 1419 1.217511 CGCAGTCTCACATGCTCCT 59.782 57.895 0.00 0.00 40.34 3.69
624 1475 6.999272 CCTCCTCATTGAGATTCATGATTTCT 59.001 38.462 15.36 8.09 34.11 2.52
997 1868 4.189231 GTCCTTATGGTGTAAAGCATCGT 58.811 43.478 0.00 0.00 34.23 3.73
1009 1880 1.556911 CTGAGTGGCTGTCCTTATGGT 59.443 52.381 0.00 0.00 34.23 3.55
1354 2225 3.788766 CTGCGCCCGTTCCTTTCG 61.789 66.667 4.18 0.00 0.00 3.46
1355 2226 2.358247 TCTGCGCCCGTTCCTTTC 60.358 61.111 4.18 0.00 0.00 2.62
1356 2227 2.358737 CTCTGCGCCCGTTCCTTT 60.359 61.111 4.18 0.00 0.00 3.11
1357 2228 3.302347 CTCTCTGCGCCCGTTCCTT 62.302 63.158 4.18 0.00 0.00 3.36
1358 2229 3.764466 CTCTCTGCGCCCGTTCCT 61.764 66.667 4.18 0.00 0.00 3.36
1368 2239 2.167861 CCTAAACGGCGCTCTCTGC 61.168 63.158 6.90 0.00 38.57 4.26
1369 2240 0.103208 ATCCTAAACGGCGCTCTCTG 59.897 55.000 6.90 0.00 0.00 3.35
1370 2241 0.824759 AATCCTAAACGGCGCTCTCT 59.175 50.000 6.90 0.00 0.00 3.10
1371 2242 1.327764 CAAATCCTAAACGGCGCTCTC 59.672 52.381 6.90 0.00 0.00 3.20
1372 2243 1.369625 CAAATCCTAAACGGCGCTCT 58.630 50.000 6.90 0.00 0.00 4.09
1373 2244 0.248094 GCAAATCCTAAACGGCGCTC 60.248 55.000 6.90 0.00 0.00 5.03
1374 2245 1.654023 GGCAAATCCTAAACGGCGCT 61.654 55.000 6.90 0.00 0.00 5.92
1375 2246 1.226575 GGCAAATCCTAAACGGCGC 60.227 57.895 6.90 0.00 0.00 6.53
1376 2247 2.477880 AGGCAAATCCTAAACGGCG 58.522 52.632 4.80 4.80 45.41 6.46
1400 2271 2.100749 GTGGTAGTTGCTGGTGCTTTTT 59.899 45.455 0.00 0.00 40.48 1.94
1401 2272 1.681264 GTGGTAGTTGCTGGTGCTTTT 59.319 47.619 0.00 0.00 40.48 2.27
1402 2273 1.318576 GTGGTAGTTGCTGGTGCTTT 58.681 50.000 0.00 0.00 40.48 3.51
1424 2295 1.000396 CCTTTCTGGAGCAAGGGGG 60.000 63.158 0.00 0.00 35.27 5.40
1474 2345 2.029307 CTCTACGGGCTAGGGGCAAC 62.029 65.000 0.00 0.00 44.01 4.17
1605 2476 3.961480 ACATGGTCGATCTCAAGTCAA 57.039 42.857 0.00 0.00 0.00 3.18
1609 2480 4.363999 GTTCCTACATGGTCGATCTCAAG 58.636 47.826 0.00 0.00 37.07 3.02
1679 2550 4.202441 CCAACACCTGAAGATGGGATTAG 58.798 47.826 0.00 0.00 0.00 1.73
1723 2596 3.243234 CGATCGATCTTAGGACACTGCTT 60.243 47.826 22.43 0.00 0.00 3.91
1740 2613 0.819259 ATTGTGGGGATTGGCGATCG 60.819 55.000 11.69 11.69 35.49 3.69
1744 2617 1.337703 CACATATTGTGGGGATTGGCG 59.662 52.381 0.00 0.00 44.27 5.69
1801 2674 3.200825 AGATGAAGGTAATGTGGGGTCAG 59.799 47.826 0.00 0.00 0.00 3.51
1802 2675 3.189606 AGATGAAGGTAATGTGGGGTCA 58.810 45.455 0.00 0.00 0.00 4.02
1827 2700 5.354513 CGCTCTTATATTATGAGACGGAGGA 59.645 44.000 0.00 0.00 33.20 3.71
1828 2701 5.124138 ACGCTCTTATATTATGAGACGGAGG 59.876 44.000 16.71 3.20 35.72 4.30
1829 2702 6.184580 ACGCTCTTATATTATGAGACGGAG 57.815 41.667 16.71 6.33 35.72 4.63
1830 2703 6.570672 AACGCTCTTATATTATGAGACGGA 57.429 37.500 16.71 0.00 35.72 4.69
1831 2704 7.639162 AAAACGCTCTTATATTATGAGACGG 57.361 36.000 16.71 7.11 35.72 4.79
1832 2705 8.752254 TCAAAAACGCTCTTATATTATGAGACG 58.248 33.333 13.57 13.57 36.53 4.18
1833 2706 9.851043 GTCAAAAACGCTCTTATATTATGAGAC 57.149 33.333 0.00 0.00 33.20 3.36
1834 2707 9.594478 TGTCAAAAACGCTCTTATATTATGAGA 57.406 29.630 0.00 0.00 33.20 3.27
1835 2708 9.638300 GTGTCAAAAACGCTCTTATATTATGAG 57.362 33.333 0.00 0.00 35.42 2.90
1836 2709 9.378551 AGTGTCAAAAACGCTCTTATATTATGA 57.621 29.630 0.00 0.00 45.69 2.15
1839 2712 9.309516 CCTAGTGTCAAAAACGCTCTTATATTA 57.690 33.333 0.00 0.00 45.69 0.98
1840 2713 7.280205 CCCTAGTGTCAAAAACGCTCTTATATT 59.720 37.037 0.00 0.00 45.69 1.28
1841 2714 6.761714 CCCTAGTGTCAAAAACGCTCTTATAT 59.238 38.462 0.00 0.00 45.69 0.86
1842 2715 6.071221 TCCCTAGTGTCAAAAACGCTCTTATA 60.071 38.462 0.00 0.00 45.69 0.98
1843 2716 4.935808 CCCTAGTGTCAAAAACGCTCTTAT 59.064 41.667 0.00 0.00 45.69 1.73
1844 2717 4.039488 TCCCTAGTGTCAAAAACGCTCTTA 59.961 41.667 0.00 0.00 45.69 2.10
1845 2718 3.139077 CCCTAGTGTCAAAAACGCTCTT 58.861 45.455 0.00 0.00 45.69 2.85
1846 2719 2.367567 TCCCTAGTGTCAAAAACGCTCT 59.632 45.455 0.00 0.00 45.69 4.09
1847 2720 2.479275 GTCCCTAGTGTCAAAAACGCTC 59.521 50.000 0.00 0.00 45.69 5.03
1849 2722 1.193874 CGTCCCTAGTGTCAAAAACGC 59.806 52.381 0.00 0.00 38.74 4.84
1850 2723 1.796459 CCGTCCCTAGTGTCAAAAACG 59.204 52.381 0.00 0.00 0.00 3.60
1851 2724 3.064931 CTCCGTCCCTAGTGTCAAAAAC 58.935 50.000 0.00 0.00 0.00 2.43
1852 2725 2.038033 CCTCCGTCCCTAGTGTCAAAAA 59.962 50.000 0.00 0.00 0.00 1.94
1853 2726 1.621814 CCTCCGTCCCTAGTGTCAAAA 59.378 52.381 0.00 0.00 0.00 2.44
1854 2727 1.263356 CCTCCGTCCCTAGTGTCAAA 58.737 55.000 0.00 0.00 0.00 2.69
1855 2728 0.613853 CCCTCCGTCCCTAGTGTCAA 60.614 60.000 0.00 0.00 0.00 3.18
1856 2729 1.000019 CCCTCCGTCCCTAGTGTCA 60.000 63.158 0.00 0.00 0.00 3.58
1857 2730 0.752376 CTCCCTCCGTCCCTAGTGTC 60.752 65.000 0.00 0.00 0.00 3.67
1858 2731 1.306970 CTCCCTCCGTCCCTAGTGT 59.693 63.158 0.00 0.00 0.00 3.55
1859 2732 0.549950 TACTCCCTCCGTCCCTAGTG 59.450 60.000 0.00 0.00 0.00 2.74
1860 2733 0.550432 GTACTCCCTCCGTCCCTAGT 59.450 60.000 0.00 0.00 0.00 2.57
1861 2734 0.845337 AGTACTCCCTCCGTCCCTAG 59.155 60.000 0.00 0.00 0.00 3.02
1862 2735 1.213926 GAAGTACTCCCTCCGTCCCTA 59.786 57.143 0.00 0.00 0.00 3.53
1863 2736 0.033306 GAAGTACTCCCTCCGTCCCT 60.033 60.000 0.00 0.00 0.00 4.20
1864 2737 1.382692 CGAAGTACTCCCTCCGTCCC 61.383 65.000 0.00 0.00 0.00 4.46
1865 2738 2.002509 GCGAAGTACTCCCTCCGTCC 62.003 65.000 0.00 0.00 0.00 4.79
1866 2739 1.310933 TGCGAAGTACTCCCTCCGTC 61.311 60.000 0.00 0.00 0.00 4.79
1867 2740 0.896940 TTGCGAAGTACTCCCTCCGT 60.897 55.000 0.00 0.00 0.00 4.69
1868 2741 0.245539 TTTGCGAAGTACTCCCTCCG 59.754 55.000 0.00 0.00 0.00 4.63
1869 2742 2.467566 TTTTGCGAAGTACTCCCTCC 57.532 50.000 0.00 0.00 0.00 4.30
1870 2743 2.096013 GCATTTTGCGAAGTACTCCCTC 59.904 50.000 0.00 0.00 31.71 4.30
1871 2744 2.084546 GCATTTTGCGAAGTACTCCCT 58.915 47.619 0.00 0.00 31.71 4.20
1872 2745 1.132453 GGCATTTTGCGAAGTACTCCC 59.868 52.381 0.00 0.00 46.21 4.30
1873 2746 2.084546 AGGCATTTTGCGAAGTACTCC 58.915 47.619 0.00 0.00 46.21 3.85
1874 2747 3.241995 CGTAGGCATTTTGCGAAGTACTC 60.242 47.826 0.00 0.00 46.21 2.59
1875 2748 2.671396 CGTAGGCATTTTGCGAAGTACT 59.329 45.455 0.00 0.00 46.21 2.73
1876 2749 2.786700 GCGTAGGCATTTTGCGAAGTAC 60.787 50.000 1.75 0.00 46.21 2.73
1877 2750 1.395608 GCGTAGGCATTTTGCGAAGTA 59.604 47.619 1.75 0.00 46.21 2.24
1878 2751 0.168128 GCGTAGGCATTTTGCGAAGT 59.832 50.000 1.75 0.00 46.21 3.01
1879 2752 0.167908 TGCGTAGGCATTTTGCGAAG 59.832 50.000 5.89 0.00 46.21 3.79
1880 2753 2.248741 TGCGTAGGCATTTTGCGAA 58.751 47.368 5.89 0.00 46.21 4.70
1881 2754 3.973735 TGCGTAGGCATTTTGCGA 58.026 50.000 5.89 0.00 46.21 5.10
1919 2792 2.809446 TGATCCTGTCAACGCTTATCG 58.191 47.619 0.00 0.00 45.38 2.92
1925 2798 4.201822 GGTTTCTTATGATCCTGTCAACGC 60.202 45.833 0.00 0.00 40.97 4.84
1973 2846 2.041216 CCCAAAGTAGCCCCTTTAGTGT 59.959 50.000 0.00 0.00 33.00 3.55
1978 2851 1.163408 TTCCCCAAAGTAGCCCCTTT 58.837 50.000 0.00 0.00 35.06 3.11
2062 2936 0.838987 TGGTCCCGAAACTAAGGCCT 60.839 55.000 0.00 0.00 0.00 5.19
2065 2939 4.076394 TGATTTTGGTCCCGAAACTAAGG 58.924 43.478 0.77 0.00 32.76 2.69
2135 3009 9.163899 GCTTTAGCTGGTAGAAGTATTTTTACT 57.836 33.333 0.00 0.00 38.21 2.24
2205 3111 4.686972 TCAGACAACAGAGTGAAGTGAAG 58.313 43.478 0.00 0.00 0.00 3.02
2250 3156 3.688673 CACTTGCTCTGATCCTTTCTTCC 59.311 47.826 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.