Multiple sequence alignment - TraesCS1A01G224600

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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 TraesCS1A01G224600 chr1A 100.000 2355 0 0 1 2355 394586930 394589284 0.000000e+00 4349
1 TraesCS1A01G224600 chr1A 81.667 600 63 32 822 1392 394481968 394482549 2.760000e-124 455
2 TraesCS1A01G224600 chr1A 85.301 449 42 15 965 1392 394566777 394567222 2.150000e-120 442
3 TraesCS1A01G224600 chr1A 81.984 383 51 15 994 1365 394444492 394444867 2.270000e-80 309
4 TraesCS1A01G224600 chr1A 81.984 383 51 15 994 1365 394532886 394533261 2.270000e-80 309
5 TraesCS1A01G224600 chr1D 87.034 1851 130 48 1 1777 314425341 314427155 0.000000e+00 1988
6 TraesCS1A01G224600 chr1D 85.445 371 15 17 2015 2355 314431033 314431394 1.340000e-92 350
7 TraesCS1A01G224600 chr1D 95.261 211 7 2 1185 1392 314419165 314419375 4.850000e-87 331
8 TraesCS1A01G224600 chr1D 92.857 196 10 3 1188 1379 314196484 314196679 4.960000e-72 281
9 TraesCS1A01G224600 chr1D 80.259 309 39 18 822 1125 314418776 314419067 1.830000e-51 213
10 TraesCS1A01G224600 chr1B 85.861 1266 72 35 484 1686 424534818 424536039 0.000000e+00 1247
11 TraesCS1A01G224600 chr1B 82.544 401 45 17 994 1379 424414309 424414699 1.740000e-86 329
12 TraesCS1A01G224600 chr1B 95.522 201 8 1 1185 1384 424531663 424531863 1.050000e-83 320
13 TraesCS1A01G224600 chr1B 84.054 370 17 18 2017 2354 424537907 424538266 3.780000e-83 318
14 TraesCS1A01G224600 chr1B 81.350 311 35 17 822 1125 424531272 424531566 5.060000e-57 231
15 TraesCS1A01G224600 chr1B 93.519 108 6 1 1804 1911 424537747 424537853 2.420000e-35 159
16 TraesCS1A01G224600 chr5B 95.833 72 1 1 1911 1980 493986335 493986406 5.320000e-22 115
17 TraesCS1A01G224600 chrUn 94.595 74 2 1 1911 1982 327661366 327661293 1.910000e-21 113
18 TraesCS1A01G224600 chr7D 95.775 71 1 1 1911 1979 231602874 231602944 1.910000e-21 113
19 TraesCS1A01G224600 chr7A 94.595 74 2 1 1911 1982 201367878 201367805 1.910000e-21 113
20 TraesCS1A01G224600 chr6B 94.595 74 2 1 1911 1982 10883191 10883118 1.910000e-21 113
21 TraesCS1A01G224600 chr6A 95.775 71 1 1 1911 1979 271183961 271184031 1.910000e-21 113
22 TraesCS1A01G224600 chr5D 95.775 71 1 1 1911 1979 560878980 560879050 1.910000e-21 113
23 TraesCS1A01G224600 chr2D 94.595 74 2 1 1911 1982 272799720 272799647 1.910000e-21 113
24 TraesCS1A01G224600 chr2D 94.595 74 2 1 1911 1982 563306333 563306260 1.910000e-21 113


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 TraesCS1A01G224600 chr1A 394586930 394589284 2354 False 4349 4349 100.0000 1 2355 1 chr1A.!!$F5 2354
1 TraesCS1A01G224600 chr1A 394481968 394482549 581 False 455 455 81.6670 822 1392 1 chr1A.!!$F2 570
2 TraesCS1A01G224600 chr1D 314425341 314431394 6053 False 1169 1988 86.2395 1 2355 2 chr1D.!!$F3 2354
3 TraesCS1A01G224600 chr1D 314418776 314419375 599 False 272 331 87.7600 822 1392 2 chr1D.!!$F2 570
4 TraesCS1A01G224600 chr1B 424531272 424538266 6994 False 455 1247 88.0612 484 2354 5 chr1B.!!$F2 1870

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
258 263 0.027455 TCAGCAACGTTGAACTTGCG 59.973 50.0 31.62 11.87 46.16 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 4740 0.179056 CCACAACCACACTTCCGACT 60.179 55.0 0.0 0.0 0.0 4.18 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
35 36 2.422231 AAGCCGCCAAGCAAACACA 61.422 52.632 0.00 0.00 34.23 3.72
40 41 0.656205 CGCCAAGCAAACACACGTAC 60.656 55.000 0.00 0.00 0.00 3.67
42 43 1.305201 CCAAGCAAACACACGTACCT 58.695 50.000 0.00 0.00 0.00 3.08
45 46 3.105203 CAAGCAAACACACGTACCTTTG 58.895 45.455 0.00 0.00 0.00 2.77
65 66 4.451150 GGACCTGATGGCGCGTCA 62.451 66.667 19.03 19.03 36.63 4.35
107 108 1.620822 ACCAACAGGCCAAAGATGAC 58.379 50.000 5.01 0.00 0.00 3.06
108 109 1.133513 ACCAACAGGCCAAAGATGACA 60.134 47.619 5.01 0.00 0.00 3.58
121 122 3.287312 AGATGACAACAAACAATGGCG 57.713 42.857 0.00 0.00 0.00 5.69
184 189 7.220683 CCGTCATCAAAATAATGATTGGAACAC 59.779 37.037 0.00 0.00 39.29 3.32
193 198 8.821686 AATAATGATTGGAACACCACTTCATA 57.178 30.769 11.59 4.87 39.29 2.15
209 214 6.884295 CCACTTCATATCCAAGGTGAAAACTA 59.116 38.462 0.00 0.00 32.08 2.24
216 221 9.838339 CATATCCAAGGTGAAAACTACTATTCT 57.162 33.333 0.00 0.00 0.00 2.40
220 225 4.844884 AGGTGAAAACTACTATTCTGGCC 58.155 43.478 0.00 0.00 0.00 5.36
221 226 4.536489 AGGTGAAAACTACTATTCTGGCCT 59.464 41.667 3.32 0.00 0.00 5.19
222 227 5.014228 AGGTGAAAACTACTATTCTGGCCTT 59.986 40.000 3.32 0.00 0.00 4.35
223 228 5.354513 GGTGAAAACTACTATTCTGGCCTTC 59.645 44.000 3.32 0.00 0.00 3.46
224 229 5.938125 GTGAAAACTACTATTCTGGCCTTCA 59.062 40.000 3.32 0.00 0.00 3.02
225 230 6.599638 GTGAAAACTACTATTCTGGCCTTCAT 59.400 38.462 3.32 0.00 0.00 2.57
226 231 7.121315 GTGAAAACTACTATTCTGGCCTTCATT 59.879 37.037 3.32 0.00 0.00 2.57
227 232 7.336931 TGAAAACTACTATTCTGGCCTTCATTC 59.663 37.037 3.32 0.00 0.00 2.67
248 253 0.107831 TTGGTTAGGCTCAGCAACGT 59.892 50.000 9.11 0.00 0.00 3.99
258 263 0.027455 TCAGCAACGTTGAACTTGCG 59.973 50.000 31.62 11.87 46.16 4.85
271 276 3.682858 TGAACTTGCGCTGTTACCTTATC 59.317 43.478 16.67 6.19 0.00 1.75
302 307 4.021102 ACCTTGTTGCTATTGTGCTAGT 57.979 40.909 0.00 0.00 0.00 2.57
307 312 4.893608 TGTTGCTATTGTGCTAGTCTTCA 58.106 39.130 0.00 0.00 0.00 3.02
308 313 5.304778 TGTTGCTATTGTGCTAGTCTTCAA 58.695 37.500 0.00 0.00 0.00 2.69
311 316 4.877823 TGCTATTGTGCTAGTCTTCAATGG 59.122 41.667 11.21 9.99 33.48 3.16
343 348 4.321230 GGCAACAAGAATGAAAATCCTCGT 60.321 41.667 0.00 0.00 0.00 4.18
348 353 5.765182 ACAAGAATGAAAATCCTCGTCTTGT 59.235 36.000 9.68 9.68 42.56 3.16
357 362 3.107642 TCCTCGTCTTGTTTGTCTTCC 57.892 47.619 0.00 0.00 0.00 3.46
373 378 3.918977 CCACCGGACGTGACCACA 61.919 66.667 9.46 0.00 46.20 4.17
382 387 1.372872 CGTGACCACAGCGATGTGA 60.373 57.895 33.74 12.62 42.02 3.58
402 407 5.106948 TGTGAGAGCGCTTATTTCTTGAAAG 60.107 40.000 13.26 0.00 0.00 2.62
406 411 5.703130 AGAGCGCTTATTTCTTGAAAGAAGT 59.297 36.000 22.90 9.65 45.01 3.01
408 413 5.470098 AGCGCTTATTTCTTGAAAGAAGTCA 59.530 36.000 22.90 0.02 45.01 3.41
430 435 9.593134 AGTCAGATTAGTCATAGATGTTTGTTC 57.407 33.333 0.00 0.00 0.00 3.18
469 474 4.916870 ACTAAGCCGTGTTTGTCTTTTTC 58.083 39.130 0.00 0.00 0.00 2.29
470 475 4.638865 ACTAAGCCGTGTTTGTCTTTTTCT 59.361 37.500 0.00 0.00 0.00 2.52
472 477 5.570234 AAGCCGTGTTTGTCTTTTTCTAA 57.430 34.783 0.00 0.00 0.00 2.10
473 478 4.916870 AGCCGTGTTTGTCTTTTTCTAAC 58.083 39.130 0.00 0.00 0.00 2.34
474 479 4.638865 AGCCGTGTTTGTCTTTTTCTAACT 59.361 37.500 0.00 0.00 0.00 2.24
475 480 4.968181 GCCGTGTTTGTCTTTTTCTAACTC 59.032 41.667 0.00 0.00 0.00 3.01
476 481 5.220796 GCCGTGTTTGTCTTTTTCTAACTCT 60.221 40.000 0.00 0.00 0.00 3.24
477 482 6.192360 CCGTGTTTGTCTTTTTCTAACTCTG 58.808 40.000 0.00 0.00 0.00 3.35
478 483 5.677178 CGTGTTTGTCTTTTTCTAACTCTGC 59.323 40.000 0.00 0.00 0.00 4.26
579 3647 1.335182 CAGTAGACGCTCGATCCATGT 59.665 52.381 0.00 0.00 0.00 3.21
587 3656 1.667724 GCTCGATCCATGTCTGGTTTG 59.332 52.381 0.00 0.00 43.61 2.93
597 3666 1.005867 TCTGGTTTGTACGACCGGC 60.006 57.895 17.87 0.00 42.21 6.13
619 3688 1.369209 CGACGAACACACGTACGGT 60.369 57.895 21.06 11.73 46.52 4.83
640 3709 1.891150 AGTGACAAGTACGGTAGTGGG 59.109 52.381 2.57 0.00 0.00 4.61
683 3752 1.153168 ACAGTGCCAAGACAACGCT 60.153 52.632 0.00 0.00 0.00 5.07
684 3753 0.105964 ACAGTGCCAAGACAACGCTA 59.894 50.000 0.00 0.00 0.00 4.26
686 3755 0.320771 AGTGCCAAGACAACGCTAGG 60.321 55.000 0.00 0.00 0.00 3.02
687 3756 1.671054 TGCCAAGACAACGCTAGGC 60.671 57.895 0.00 0.00 42.32 3.93
689 3758 1.362406 GCCAAGACAACGCTAGGCTC 61.362 60.000 0.00 0.00 39.02 4.70
690 3759 0.741221 CCAAGACAACGCTAGGCTCC 60.741 60.000 0.00 0.00 0.00 4.70
720 3802 3.197790 CTCATTCCGGTGGCTGCG 61.198 66.667 0.00 0.00 0.00 5.18
723 3805 4.015406 ATTCCGGTGGCTGCGTCA 62.015 61.111 0.00 0.00 0.00 4.35
873 3956 1.002087 CCTCCTCGCCGGCTATAAAAT 59.998 52.381 26.68 0.00 0.00 1.82
957 4049 3.479269 GCGGTAGAGCACACACGC 61.479 66.667 0.00 0.00 40.19 5.34
990 4091 1.262151 GAGGTCGAAGTAGCTAGCGAG 59.738 57.143 9.55 0.00 33.00 5.03
994 4095 1.134461 TCGAAGTAGCTAGCGAGGAGT 60.134 52.381 9.55 0.00 0.00 3.85
1149 4257 1.269883 TGCACGTCGACCTTATGTGTT 60.270 47.619 17.86 0.00 36.45 3.32
1410 4589 2.741145 AGTTGGTTGGTTTACCTTGCA 58.259 42.857 0.00 0.00 39.04 4.08
1432 4611 5.555017 CAGGATGAATAATGTAGGTCAGGG 58.445 45.833 0.00 0.00 39.69 4.45
1466 4645 3.259123 TGCACGCATGTAGGAGATCATAT 59.741 43.478 0.00 0.00 0.00 1.78
1490 4676 3.603532 ACTAGATCATGTGTGCTTGGTG 58.396 45.455 0.00 0.00 0.00 4.17
1493 4679 1.888512 GATCATGTGTGCTTGGTGGTT 59.111 47.619 0.00 0.00 0.00 3.67
1494 4680 2.647683 TCATGTGTGCTTGGTGGTTA 57.352 45.000 0.00 0.00 0.00 2.85
1497 4683 4.657013 TCATGTGTGCTTGGTGGTTAATA 58.343 39.130 0.00 0.00 0.00 0.98
1498 4684 4.699735 TCATGTGTGCTTGGTGGTTAATAG 59.300 41.667 0.00 0.00 0.00 1.73
1541 4727 2.558265 CTGATGGTCAGTCAGAGTCG 57.442 55.000 0.00 0.00 44.57 4.18
1554 4740 1.099295 AGAGTCGTGTGTCCGTGTCA 61.099 55.000 0.00 0.00 0.00 3.58
1580 4766 4.947147 TGTGGTTGTGGCTCCGGC 62.947 66.667 0.00 0.00 37.82 6.13
1604 4790 2.683933 TCCGGCCTCTCTTCCCAC 60.684 66.667 0.00 0.00 0.00 4.61
1605 4791 3.787001 CCGGCCTCTCTTCCCACC 61.787 72.222 0.00 0.00 0.00 4.61
1606 4792 3.003173 CGGCCTCTCTTCCCACCA 61.003 66.667 0.00 0.00 0.00 4.17
1607 4793 2.993853 GGCCTCTCTTCCCACCAG 59.006 66.667 0.00 0.00 0.00 4.00
1608 4794 2.270527 GCCTCTCTTCCCACCAGC 59.729 66.667 0.00 0.00 0.00 4.85
1609 4795 2.297129 GCCTCTCTTCCCACCAGCT 61.297 63.158 0.00 0.00 0.00 4.24
1627 4814 1.398390 GCTTTCCGCTGTATCCTTGTG 59.602 52.381 0.00 0.00 35.14 3.33
1675 4862 5.049198 TGCTGAAATCTGAAGCTTTGTAGTG 60.049 40.000 0.00 0.00 37.82 2.74
1714 6327 1.783071 ATTGTTGGTGTTCCCGGTTT 58.217 45.000 0.00 0.00 35.15 3.27
1741 6354 4.961438 TGTTTACCGTAAAACCTCTCCT 57.039 40.909 5.28 0.00 38.35 3.69
1754 6375 2.224917 ACCTCTCCTGAACGAGAACTCT 60.225 50.000 0.00 0.00 38.41 3.24
1766 6387 0.179134 AGAACTCTACGTGCCGCATC 60.179 55.000 0.00 0.00 0.00 3.91
1769 6390 1.878522 CTCTACGTGCCGCATCACC 60.879 63.158 0.00 0.00 33.57 4.02
1777 6437 4.720902 CCGCATCACCAGCCACCA 62.721 66.667 0.00 0.00 0.00 4.17
1778 6438 2.672651 CGCATCACCAGCCACCAA 60.673 61.111 0.00 0.00 0.00 3.67
1779 6439 2.267351 CGCATCACCAGCCACCAAA 61.267 57.895 0.00 0.00 0.00 3.28
1780 6440 1.290009 GCATCACCAGCCACCAAAC 59.710 57.895 0.00 0.00 0.00 2.93
1783 6443 2.086869 CATCACCAGCCACCAAACTAG 58.913 52.381 0.00 0.00 0.00 2.57
1784 6444 0.250727 TCACCAGCCACCAAACTAGC 60.251 55.000 0.00 0.00 0.00 3.42
1785 6445 1.074951 ACCAGCCACCAAACTAGCC 59.925 57.895 0.00 0.00 0.00 3.93
1786 6446 1.074775 CCAGCCACCAAACTAGCCA 59.925 57.895 0.00 0.00 0.00 4.75
1788 6448 1.549203 CAGCCACCAAACTAGCCAAT 58.451 50.000 0.00 0.00 0.00 3.16
1789 6449 1.203052 CAGCCACCAAACTAGCCAATG 59.797 52.381 0.00 0.00 0.00 2.82
1790 6450 0.108662 GCCACCAAACTAGCCAATGC 60.109 55.000 0.00 0.00 37.95 3.56
1791 6451 0.532115 CCACCAAACTAGCCAATGCC 59.468 55.000 0.00 0.00 38.69 4.40
1794 6454 0.532115 CCAAACTAGCCAATGCCACC 59.468 55.000 0.00 0.00 38.69 4.61
1795 6455 1.255882 CAAACTAGCCAATGCCACCA 58.744 50.000 0.00 0.00 38.69 4.17
1796 6456 1.203052 CAAACTAGCCAATGCCACCAG 59.797 52.381 0.00 0.00 38.69 4.00
1798 6458 0.405585 ACTAGCCAATGCCACCAGTT 59.594 50.000 0.00 0.00 38.69 3.16
1800 6460 2.292267 CTAGCCAATGCCACCAGTTAG 58.708 52.381 0.00 0.00 38.69 2.34
1801 6461 0.698238 AGCCAATGCCACCAGTTAGA 59.302 50.000 0.00 0.00 38.69 2.10
1804 7329 2.159198 GCCAATGCCACCAGTTAGAATG 60.159 50.000 0.00 0.00 0.00 2.67
1820 7345 0.330604 AATGTGAGCATGCAGGAGGT 59.669 50.000 21.98 0.00 35.15 3.85
1829 7354 2.625737 CATGCAGGAGGTAGTGTTCTG 58.374 52.381 0.00 0.00 0.00 3.02
1835 7360 2.176889 GGAGGTAGTGTTCTGGCAGTA 58.823 52.381 15.27 1.01 0.00 2.74
1861 8447 2.741878 CGGATAAGGACGGCACTTGAAT 60.742 50.000 0.00 0.00 0.00 2.57
1889 10245 2.484770 GCCTAGACATTCATAACGGGCA 60.485 50.000 0.00 0.00 37.30 5.36
1911 10267 6.187125 CAATATTGCTGCAAGTACAAGACT 57.813 37.500 20.72 3.01 41.56 3.24
1912 10268 7.307493 CAATATTGCTGCAAGTACAAGACTA 57.693 36.000 20.72 5.22 37.44 2.59
1914 10270 8.400947 CAATATTGCTGCAAGTACAAGACTAAT 58.599 33.333 20.72 1.56 37.44 1.73
1915 10271 5.862924 TTGCTGCAAGTACAAGACTAATC 57.137 39.130 11.69 0.00 37.44 1.75
1917 10273 5.551233 TGCTGCAAGTACAAGACTAATCTT 58.449 37.500 0.00 0.00 40.60 2.40
1918 10274 5.997746 TGCTGCAAGTACAAGACTAATCTTT 59.002 36.000 0.00 0.00 38.78 2.52
1919 10275 6.486657 TGCTGCAAGTACAAGACTAATCTTTT 59.513 34.615 0.00 0.00 38.78 2.27
1920 10276 6.798959 GCTGCAAGTACAAGACTAATCTTTTG 59.201 38.462 0.00 0.00 38.78 2.44
1921 10277 7.202016 TGCAAGTACAAGACTAATCTTTTGG 57.798 36.000 0.00 0.00 42.91 3.28
1922 10278 6.995686 TGCAAGTACAAGACTAATCTTTTGGA 59.004 34.615 0.00 0.00 42.91 3.53
1923 10279 7.500892 TGCAAGTACAAGACTAATCTTTTGGAA 59.499 33.333 0.00 0.00 42.91 3.53
1924 10280 8.349983 GCAAGTACAAGACTAATCTTTTGGAAA 58.650 33.333 0.00 0.00 42.91 3.13
1954 10310 8.768501 AAGTCCCTTCTTGAATTTTAGAACTT 57.231 30.769 0.53 1.52 0.00 2.66
1955 10311 9.862149 AAGTCCCTTCTTGAATTTTAGAACTTA 57.138 29.630 0.53 0.00 0.00 2.24
1956 10312 9.508642 AGTCCCTTCTTGAATTTTAGAACTTAG 57.491 33.333 0.53 0.00 0.00 2.18
1957 10313 9.503399 GTCCCTTCTTGAATTTTAGAACTTAGA 57.497 33.333 0.00 0.00 0.00 2.10
2012 10368 1.002468 CTGTTTTCCAGCACAAGACGG 60.002 52.381 0.00 0.00 33.59 4.79
2013 10369 1.305201 GTTTTCCAGCACAAGACGGA 58.695 50.000 0.00 0.00 0.00 4.69
2015 10371 0.534203 TTTCCAGCACAAGACGGACC 60.534 55.000 0.00 0.00 0.00 4.46
2071 10444 2.619147 GAACGGAAGGAGAGGCTTTAC 58.381 52.381 0.00 0.00 0.00 2.01
2112 10516 7.337689 CAGGAGAAACAATCTGATCATAAACCA 59.662 37.037 0.00 0.00 38.96 3.67
2114 10518 8.689972 GGAGAAACAATCTGATCATAAACCATT 58.310 33.333 0.00 0.00 38.96 3.16
2115 10519 9.512435 GAGAAACAATCTGATCATAAACCATTG 57.488 33.333 0.00 1.63 38.96 2.82
2117 10521 9.294030 GAAACAATCTGATCATAAACCATTGTC 57.706 33.333 0.00 0.00 33.03 3.18
2130 10536 2.114056 CCATTGTCACGTACCGTATCG 58.886 52.381 0.00 0.00 38.32 2.92
2131 10537 2.478370 CCATTGTCACGTACCGTATCGT 60.478 50.000 0.00 1.80 38.32 3.73
2147 10553 7.199766 ACCGTATCGTATCCAAAATTACGTTA 58.800 34.615 0.00 0.00 41.38 3.18
2188 10594 1.066502 ACAAACAAACAACCTGGCACC 60.067 47.619 0.00 0.00 0.00 5.01
2215 10621 3.978373 CGGTCTACGCGCACTAAG 58.022 61.111 5.73 0.00 34.82 2.18
2216 10622 1.585521 CGGTCTACGCGCACTAAGG 60.586 63.158 5.73 0.00 34.82 2.69
2217 10623 1.877165 GGTCTACGCGCACTAAGGC 60.877 63.158 5.73 0.00 0.00 4.35
2218 10624 1.153901 GTCTACGCGCACTAAGGCA 60.154 57.895 5.73 0.00 0.00 4.75
2219 10625 1.153901 TCTACGCGCACTAAGGCAC 60.154 57.895 5.73 0.00 0.00 5.01
2326 10737 7.467811 GCAGATTTATTCCACTATCTGTGTTGG 60.468 40.741 11.30 0.00 43.64 3.77
2327 10738 7.554118 CAGATTTATTCCACTATCTGTGTTGGT 59.446 37.037 0.00 0.00 44.81 3.67
2328 10739 7.554118 AGATTTATTCCACTATCTGTGTTGGTG 59.446 37.037 0.00 0.00 44.81 4.17
2329 10740 4.640771 ATTCCACTATCTGTGTTGGTGT 57.359 40.909 0.00 0.00 44.81 4.16
2330 10741 3.401033 TCCACTATCTGTGTTGGTGTG 57.599 47.619 0.00 0.00 44.81 3.82
2342 10753 3.027412 TGTTGGTGTGTACAAAATGCCT 58.973 40.909 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.124060 TTTGCTTGGCGGCTTGTCA 61.124 52.632 11.43 0.00 0.00 3.58
35 36 1.151965 AGGTCCCCCAAAGGTACGT 60.152 57.895 0.00 0.00 0.00 3.57
40 41 1.307647 CCATCAGGTCCCCCAAAGG 59.692 63.158 0.00 0.00 0.00 3.11
42 43 2.770130 GCCATCAGGTCCCCCAAA 59.230 61.111 0.00 0.00 37.19 3.28
53 54 2.046411 ATGGTTGACGCGCCATCA 60.046 55.556 5.73 2.77 41.24 3.07
80 81 0.178950 TGGCCTGTTGGTTATTGCCA 60.179 50.000 3.32 0.00 45.96 4.92
107 108 1.769733 CTCCACGCCATTGTTTGTTG 58.230 50.000 0.00 0.00 0.00 3.33
108 109 0.031994 GCTCCACGCCATTGTTTGTT 59.968 50.000 0.00 0.00 0.00 2.83
121 122 1.740025 GCCAGTTTATCTGTGCTCCAC 59.260 52.381 0.00 0.00 42.19 4.02
133 134 2.449464 TCTAGTAGCCACGCCAGTTTA 58.551 47.619 0.00 0.00 0.00 2.01
136 137 0.747255 CATCTAGTAGCCACGCCAGT 59.253 55.000 0.00 0.00 0.00 4.00
137 138 0.032678 CCATCTAGTAGCCACGCCAG 59.967 60.000 0.00 0.00 0.00 4.85
141 142 0.311165 CGGACCATCTAGTAGCCACG 59.689 60.000 0.00 0.00 0.00 4.94
184 189 5.711976 AGTTTTCACCTTGGATATGAAGTGG 59.288 40.000 0.00 0.00 34.04 4.00
193 198 7.112779 CCAGAATAGTAGTTTTCACCTTGGAT 58.887 38.462 3.94 0.00 0.00 3.41
209 214 4.891756 CCAATGAATGAAGGCCAGAATAGT 59.108 41.667 5.01 0.00 0.00 2.12
216 221 3.364549 CCTAACCAATGAATGAAGGCCA 58.635 45.455 5.01 0.00 0.00 5.36
220 225 4.201990 GCTGAGCCTAACCAATGAATGAAG 60.202 45.833 0.00 0.00 0.00 3.02
221 226 3.696051 GCTGAGCCTAACCAATGAATGAA 59.304 43.478 0.00 0.00 0.00 2.57
222 227 3.282021 GCTGAGCCTAACCAATGAATGA 58.718 45.455 0.00 0.00 0.00 2.57
223 228 3.018856 TGCTGAGCCTAACCAATGAATG 58.981 45.455 0.23 0.00 0.00 2.67
224 229 3.370840 TGCTGAGCCTAACCAATGAAT 57.629 42.857 0.23 0.00 0.00 2.57
225 230 2.819608 GTTGCTGAGCCTAACCAATGAA 59.180 45.455 0.23 0.00 0.00 2.57
226 231 2.436417 GTTGCTGAGCCTAACCAATGA 58.564 47.619 0.23 0.00 0.00 2.57
227 232 1.131126 CGTTGCTGAGCCTAACCAATG 59.869 52.381 0.23 0.00 0.00 2.82
248 253 1.961793 AGGTAACAGCGCAAGTTCAA 58.038 45.000 19.42 3.25 38.84 2.69
291 296 7.620880 ACTAACCATTGAAGACTAGCACAATA 58.379 34.615 0.00 0.00 32.75 1.90
302 307 5.127845 TGTTGCCAAAACTAACCATTGAAGA 59.872 36.000 0.00 0.00 0.00 2.87
307 312 5.606348 TCTTGTTGCCAAAACTAACCATT 57.394 34.783 0.00 0.00 0.00 3.16
308 313 5.606348 TTCTTGTTGCCAAAACTAACCAT 57.394 34.783 0.00 0.00 0.00 3.55
311 316 7.532682 TTTCATTCTTGTTGCCAAAACTAAC 57.467 32.000 0.00 0.00 0.00 2.34
326 331 6.884280 AACAAGACGAGGATTTTCATTCTT 57.116 33.333 0.00 0.00 0.00 2.52
343 348 1.487142 TCCGGTGGAAGACAAACAAGA 59.513 47.619 0.00 0.00 0.00 3.02
348 353 0.531090 CACGTCCGGTGGAAGACAAA 60.531 55.000 0.00 0.00 43.16 2.83
382 387 5.703130 ACTTCTTTCAAGAAATAAGCGCTCT 59.297 36.000 12.06 0.00 43.84 4.09
402 407 9.593134 ACAAACATCTATGACTAATCTGACTTC 57.407 33.333 0.00 0.00 0.00 3.01
430 435 9.424319 ACGGCTTAGTCATTATGAAATGTATAG 57.576 33.333 0.00 0.00 42.66 1.31
505 3569 4.094830 TGCCTCTGCATCATCATAATGT 57.905 40.909 0.00 0.00 44.23 2.71
579 3647 1.005867 GCCGGTCGTACAAACCAGA 60.006 57.895 1.90 0.00 36.53 3.86
587 3656 4.818835 GTCGTCGGCCGGTCGTAC 62.819 72.222 29.96 22.60 37.11 3.67
597 3666 1.082821 TACGTGTGTTCGTCGTCGG 60.083 57.895 0.00 0.00 43.12 4.79
609 3678 1.949525 ACTTGTCACTACCGTACGTGT 59.050 47.619 15.21 13.81 33.07 4.49
619 3688 3.084039 CCCACTACCGTACTTGTCACTA 58.916 50.000 0.00 0.00 0.00 2.74
640 3709 3.945434 TCGGCGCGTAGGATCGTC 61.945 66.667 8.43 0.00 0.00 4.20
720 3802 1.883084 CCGGGCGTGCTTATCTGAC 60.883 63.158 0.00 0.00 0.00 3.51
723 3805 2.499685 GTCCGGGCGTGCTTATCT 59.500 61.111 0.00 0.00 0.00 1.98
776 3858 0.957395 CTTGCTGTCCCTGACGCATT 60.957 55.000 12.11 0.00 39.87 3.56
957 4049 0.247736 CGACCTCAACTGGAAGGGAG 59.752 60.000 0.00 0.00 39.30 4.30
990 4091 2.107953 GAGGCCATCGCTCACTCC 59.892 66.667 5.01 0.00 34.44 3.85
1125 4233 1.006832 ATAAGGTCGACGTGCATTGC 58.993 50.000 12.13 0.46 0.00 3.56
1129 4237 0.315886 ACACATAAGGTCGACGTGCA 59.684 50.000 12.13 3.40 0.00 4.57
1149 4257 1.264749 ATGAGTAGCCGAAGCCACCA 61.265 55.000 0.00 0.00 41.25 4.17
1410 4589 5.476983 TCCCTGACCTACATTATTCATCCT 58.523 41.667 0.00 0.00 0.00 3.24
1466 4645 4.222810 ACCAAGCACACATGATCTAGTACA 59.777 41.667 0.00 0.00 0.00 2.90
1490 4676 4.511617 GGACTACCGGCTACTATTAACC 57.488 50.000 0.00 0.00 0.00 2.85
1535 4721 1.099295 TGACACGGACACACGACTCT 61.099 55.000 0.00 0.00 37.61 3.24
1541 4727 3.917870 CGACTGACACGGACACAC 58.082 61.111 0.00 0.00 0.00 3.82
1554 4740 0.179056 CCACAACCACACTTCCGACT 60.179 55.000 0.00 0.00 0.00 4.18
1608 4794 2.699954 ACACAAGGATACAGCGGAAAG 58.300 47.619 0.00 0.00 41.41 2.62
1609 4795 2.851263 ACACAAGGATACAGCGGAAA 57.149 45.000 0.00 0.00 41.41 3.13
1627 4814 4.919754 ACGACGACTTACATTACTGGAAAC 59.080 41.667 0.00 0.00 0.00 2.78
1675 4862 4.954092 ATTAGCAAAGCAGAAGTAGCAC 57.046 40.909 0.00 0.00 0.00 4.40
1714 6327 8.567104 GGAGAGGTTTTACGGTAAACAATAAAA 58.433 33.333 12.62 0.00 39.27 1.52
1717 6330 6.875195 CAGGAGAGGTTTTACGGTAAACAATA 59.125 38.462 12.62 0.00 39.27 1.90
1723 6336 4.559300 CGTTCAGGAGAGGTTTTACGGTAA 60.559 45.833 0.00 0.00 0.00 2.85
1724 6337 3.057315 CGTTCAGGAGAGGTTTTACGGTA 60.057 47.826 0.00 0.00 0.00 4.02
1725 6338 2.288640 CGTTCAGGAGAGGTTTTACGGT 60.289 50.000 0.00 0.00 0.00 4.83
1726 6339 2.029649 TCGTTCAGGAGAGGTTTTACGG 60.030 50.000 0.00 0.00 0.00 4.02
1727 6340 3.057736 TCTCGTTCAGGAGAGGTTTTACG 60.058 47.826 0.00 0.00 38.12 3.18
1728 6341 4.516365 TCTCGTTCAGGAGAGGTTTTAC 57.484 45.455 0.00 0.00 38.12 2.01
1729 6342 4.587684 AGTTCTCGTTCAGGAGAGGTTTTA 59.412 41.667 0.00 0.00 43.49 1.52
1732 6345 2.559231 GAGTTCTCGTTCAGGAGAGGTT 59.441 50.000 0.00 0.00 43.49 3.50
1733 6346 2.164338 GAGTTCTCGTTCAGGAGAGGT 58.836 52.381 0.00 0.00 43.49 3.85
1734 6347 2.442413 AGAGTTCTCGTTCAGGAGAGG 58.558 52.381 0.00 0.00 43.49 3.69
1736 6349 3.001414 CGTAGAGTTCTCGTTCAGGAGA 58.999 50.000 0.00 0.00 41.16 3.71
1737 6350 2.743126 ACGTAGAGTTCTCGTTCAGGAG 59.257 50.000 0.00 0.00 34.07 3.69
1738 6351 2.483106 CACGTAGAGTTCTCGTTCAGGA 59.517 50.000 0.00 0.00 35.62 3.86
1741 6354 1.068748 GGCACGTAGAGTTCTCGTTCA 60.069 52.381 0.00 0.00 35.62 3.18
1766 6387 1.244019 GGCTAGTTTGGTGGCTGGTG 61.244 60.000 0.00 0.00 0.00 4.17
1769 6390 1.203052 CATTGGCTAGTTTGGTGGCTG 59.797 52.381 0.00 0.00 0.00 4.85
1777 6437 1.203050 ACTGGTGGCATTGGCTAGTTT 60.203 47.619 11.84 0.00 40.87 2.66
1778 6438 0.405585 ACTGGTGGCATTGGCTAGTT 59.594 50.000 11.84 0.00 40.87 2.24
1779 6439 0.405585 AACTGGTGGCATTGGCTAGT 59.594 50.000 11.84 9.97 40.87 2.57
1780 6440 2.092968 TCTAACTGGTGGCATTGGCTAG 60.093 50.000 11.84 9.40 40.87 3.42
1783 6443 1.544724 TTCTAACTGGTGGCATTGGC 58.455 50.000 2.73 2.73 40.13 4.52
1784 6444 3.091545 ACATTCTAACTGGTGGCATTGG 58.908 45.455 0.00 0.00 0.00 3.16
1785 6445 3.758023 TCACATTCTAACTGGTGGCATTG 59.242 43.478 0.00 0.00 32.29 2.82
1786 6446 4.012374 CTCACATTCTAACTGGTGGCATT 58.988 43.478 0.00 0.00 32.29 3.56
1788 6448 2.875672 GCTCACATTCTAACTGGTGGCA 60.876 50.000 0.00 0.00 31.89 4.92
1789 6449 1.740025 GCTCACATTCTAACTGGTGGC 59.260 52.381 0.00 0.00 32.29 5.01
1790 6450 3.057969 TGCTCACATTCTAACTGGTGG 57.942 47.619 0.00 0.00 32.29 4.61
1791 6451 3.181503 GCATGCTCACATTCTAACTGGTG 60.182 47.826 11.37 0.00 32.87 4.17
1794 6454 3.064958 CCTGCATGCTCACATTCTAACTG 59.935 47.826 20.33 0.00 32.87 3.16
1795 6455 3.054875 TCCTGCATGCTCACATTCTAACT 60.055 43.478 20.33 0.00 32.87 2.24
1796 6456 3.273434 TCCTGCATGCTCACATTCTAAC 58.727 45.455 20.33 0.00 32.87 2.34
1798 6458 2.158856 CCTCCTGCATGCTCACATTCTA 60.159 50.000 20.33 0.00 32.87 2.10
1800 6460 1.022735 CCTCCTGCATGCTCACATTC 58.977 55.000 20.33 0.00 32.87 2.67
1801 6461 0.330604 ACCTCCTGCATGCTCACATT 59.669 50.000 20.33 0.00 32.87 2.71
1804 7329 0.539051 ACTACCTCCTGCATGCTCAC 59.461 55.000 20.33 0.00 0.00 3.51
1820 7345 1.066858 GCTGCTACTGCCAGAACACTA 60.067 52.381 0.00 0.00 38.71 2.74
1829 7354 0.601311 CCTTATCCGCTGCTACTGCC 60.601 60.000 0.00 0.00 38.71 4.85
1835 7360 2.815308 CCGTCCTTATCCGCTGCT 59.185 61.111 0.00 0.00 0.00 4.24
1889 10245 7.921786 TTAGTCTTGTACTTGCAGCAATATT 57.078 32.000 8.67 0.00 39.80 1.28
1931 10287 9.503399 TCTAAGTTCTAAAATTCAAGAAGGGAC 57.497 33.333 3.36 0.00 32.56 4.46
1974 10330 5.473066 AACAGTGCTGCATAATCCTTTTT 57.527 34.783 5.27 0.00 0.00 1.94
1975 10331 5.473066 AAACAGTGCTGCATAATCCTTTT 57.527 34.783 5.27 0.00 0.00 2.27
1976 10332 5.473039 GAAAACAGTGCTGCATAATCCTTT 58.527 37.500 5.27 1.56 0.00 3.11
1977 10333 4.082026 GGAAAACAGTGCTGCATAATCCTT 60.082 41.667 5.27 0.00 0.00 3.36
1978 10334 3.445096 GGAAAACAGTGCTGCATAATCCT 59.555 43.478 5.27 0.00 0.00 3.24
1979 10335 3.193267 TGGAAAACAGTGCTGCATAATCC 59.807 43.478 5.27 8.95 0.00 3.01
1980 10336 4.418392 CTGGAAAACAGTGCTGCATAATC 58.582 43.478 5.27 0.00 42.42 1.75
2130 10536 8.145316 TGGCTGTATAACGTAATTTTGGATAC 57.855 34.615 0.00 0.00 0.00 2.24
2131 10537 8.614346 GTTGGCTGTATAACGTAATTTTGGATA 58.386 33.333 0.00 0.00 0.00 2.59
2147 10553 5.744171 TGTGATGTTATCAGTTGGCTGTAT 58.256 37.500 0.00 0.00 43.05 2.29
2326 10737 3.146066 TGAGGAGGCATTTTGTACACAC 58.854 45.455 0.00 0.00 0.00 3.82
2327 10738 3.500448 TGAGGAGGCATTTTGTACACA 57.500 42.857 0.00 0.00 0.00 3.72
2328 10739 3.378427 GGATGAGGAGGCATTTTGTACAC 59.622 47.826 0.00 0.00 0.00 2.90
2329 10740 3.010027 TGGATGAGGAGGCATTTTGTACA 59.990 43.478 0.00 0.00 0.00 2.90
2330 10741 3.620488 TGGATGAGGAGGCATTTTGTAC 58.380 45.455 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.