Multiple sequence alignment - TraesCS6A01G304400

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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 TraesCS6A01G304400 chr6A 100.000 2614 0 0 1 2614 537318471 537315858 0.000000e+00 4828.0
1 TraesCS6A01G304400 chr6A 94.643 168 9 0 1800 1967 297678790 297678623 7.180000e-66 261.0
2 TraesCS6A01G304400 chr6A 81.481 135 18 3 1 130 98893784 98893652 1.280000e-18 104.0
3 TraesCS6A01G304400 chr6D 91.847 1803 85 15 1 1799 390838850 390837106 0.000000e+00 2459.0
4 TraesCS6A01G304400 chr6D 87.330 663 52 14 1969 2614 390837102 390836455 0.000000e+00 730.0
5 TraesCS6A01G304400 chr6D 92.453 53 4 0 29 81 390838699 390838647 2.790000e-10 76.8
6 TraesCS6A01G304400 chr6B 91.540 1182 55 13 621 1801 583624063 583625200 0.000000e+00 1587.0
7 TraesCS6A01G304400 chr6B 93.393 333 9 3 2082 2413 583625602 583625922 5.060000e-132 481.0
8 TraesCS6A01G304400 chr6B 93.567 171 10 1 1796 1966 211161646 211161477 1.200000e-63 254.0
9 TraesCS6A01G304400 chr6B 93.789 161 10 0 2454 2614 583625992 583626152 2.600000e-60 243.0
10 TraesCS6A01G304400 chr6B 96.000 75 3 0 2011 2085 583625353 583625427 3.530000e-24 122.0
11 TraesCS6A01G304400 chr6B 94.366 71 4 0 525 595 583623992 583624062 2.750000e-20 110.0
12 TraesCS6A01G304400 chr6B 96.226 53 2 0 1961 2013 583625197 583625249 1.290000e-13 87.9
13 TraesCS6A01G304400 chr4B 92.265 181 14 0 1787 1967 80990826 80990646 9.280000e-65 257.0
14 TraesCS6A01G304400 chr7D 92.614 176 11 2 1793 1967 70053726 70053900 4.320000e-63 252.0
15 TraesCS6A01G304400 chr2D 92.571 175 13 0 1793 1967 554128202 554128376 4.320000e-63 252.0
16 TraesCS6A01G304400 chr2D 92.571 175 12 1 1796 1970 560959652 560959479 1.550000e-62 250.0
17 TraesCS6A01G304400 chr5B 92.571 175 12 1 1793 1967 577516044 577516217 1.550000e-62 250.0
18 TraesCS6A01G304400 chr2A 91.713 181 14 1 1789 1968 746756979 746757159 1.550000e-62 250.0
19 TraesCS6A01G304400 chr3D 90.860 186 16 1 1782 1967 165471215 165471399 5.590000e-62 248.0
20 TraesCS6A01G304400 chr4A 82.979 94 13 3 35 126 36405422 36405330 6.000000e-12 82.4


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 TraesCS6A01G304400 chr6A 537315858 537318471 2613 True 4828.000000 4828 100.000000 1 2614 1 chr6A.!!$R3 2613
1 TraesCS6A01G304400 chr6D 390836455 390838850 2395 True 1088.600000 2459 90.543333 1 2614 3 chr6D.!!$R1 2613
2 TraesCS6A01G304400 chr6B 583623992 583626152 2160 False 438.483333 1587 94.219000 525 2614 6 chr6B.!!$F1 2089

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
372 374 0.540830 CCGGGCTCTAGGCTCTGTAT 60.541 60.000 0.00 0.0 39.79 2.29 F
374 376 1.000283 CGGGCTCTAGGCTCTGTATTG 60.000 57.143 3.36 0.0 39.79 1.90 F
794 796 1.146485 CTCTCCGTCGCTCTCCCTA 59.854 63.158 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 1294 0.044855 AACCAGCCAGGACCCTCTAT 59.955 55.0 0.0 0.0 41.22 1.98 R
1532 1536 0.835941 AGCCATCTCGCCTTCTGAAT 59.164 50.0 0.0 0.0 0.00 2.57 R
1613 1617 1.028868 GCTCTCATGGGCAGTGTTCC 61.029 60.0 0.0 0.0 0.00 3.62 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
37 38 1.308998 GGTGACCCACAGTGTTTGAG 58.691 55.000 0.00 0.00 35.86 3.02
44 45 1.071471 ACAGTGTTTGAGAGCGGGG 59.929 57.895 0.00 0.00 0.00 5.73
51 52 0.889186 TTTGAGAGCGGGGAAAGTGC 60.889 55.000 0.00 0.00 0.00 4.40
57 58 2.672996 CGGGGAAAGTGCTGGGTG 60.673 66.667 0.00 0.00 0.00 4.61
61 62 1.973812 GGAAAGTGCTGGGTGCTCC 60.974 63.158 0.00 0.00 43.37 4.70
136 137 4.215613 AGAAAAGACCTCAAATACGTTGGC 59.784 41.667 0.00 0.00 37.85 4.52
142 143 1.127951 CTCAAATACGTTGGCGGTGAC 59.872 52.381 0.00 0.00 43.45 3.67
159 160 2.876550 GTGACCCACCTGTAAGTGTTTC 59.123 50.000 0.00 0.00 35.93 2.78
165 166 2.808543 CACCTGTAAGTGTTTCAGAGCC 59.191 50.000 0.00 0.00 32.89 4.70
186 187 0.690762 GGAAAGTGCTGGGTACTCCA 59.309 55.000 0.00 0.00 44.79 3.86
194 195 0.895530 CTGGGTACTCCACGTGTGAT 59.104 55.000 15.65 1.17 41.46 3.06
246 248 0.685097 GCACCTCCTGGTCAACTACA 59.315 55.000 0.00 0.00 46.60 2.74
268 270 2.710902 CGATCTGTCCACTCGGCCA 61.711 63.158 2.24 0.00 0.00 5.36
314 316 9.820229 CTCTTAGATAGAAAAGCTATGTAGACG 57.180 37.037 0.00 0.00 39.90 4.18
322 324 1.007271 CTATGTAGACGCAGGCCCG 60.007 63.158 0.00 0.00 0.00 6.13
372 374 0.540830 CCGGGCTCTAGGCTCTGTAT 60.541 60.000 0.00 0.00 39.79 2.29
373 375 1.333177 CGGGCTCTAGGCTCTGTATT 58.667 55.000 3.36 0.00 39.79 1.89
374 376 1.000283 CGGGCTCTAGGCTCTGTATTG 60.000 57.143 3.36 0.00 39.79 1.90
375 377 1.346068 GGGCTCTAGGCTCTGTATTGG 59.654 57.143 3.36 0.00 38.65 3.16
376 378 1.346068 GGCTCTAGGCTCTGTATTGGG 59.654 57.143 0.00 0.00 41.46 4.12
377 379 2.320781 GCTCTAGGCTCTGTATTGGGA 58.679 52.381 0.00 0.00 38.06 4.37
378 380 2.903135 GCTCTAGGCTCTGTATTGGGAT 59.097 50.000 0.00 0.00 38.06 3.85
379 381 3.326297 GCTCTAGGCTCTGTATTGGGATT 59.674 47.826 0.00 0.00 38.06 3.01
409 411 3.758300 CCCAAAATAGCAGTAGCAAACG 58.242 45.455 0.00 0.00 45.49 3.60
432 434 2.297895 ACAACGCAGGCCCTATCCA 61.298 57.895 0.00 0.00 0.00 3.41
446 448 2.695666 CCTATCCACACGACCTCAGAAT 59.304 50.000 0.00 0.00 0.00 2.40
447 449 3.889538 CCTATCCACACGACCTCAGAATA 59.110 47.826 0.00 0.00 0.00 1.75
484 486 7.792508 GGTTTGTTTCGTTATCGCTAATGATAG 59.207 37.037 2.01 0.00 33.83 2.08
610 612 2.304751 CCTCAAAAGGCCATTCATGC 57.695 50.000 5.01 0.00 35.37 4.06
611 613 1.551430 CCTCAAAAGGCCATTCATGCA 59.449 47.619 5.01 0.00 35.37 3.96
612 614 2.027929 CCTCAAAAGGCCATTCATGCAA 60.028 45.455 5.01 0.00 35.37 4.08
613 615 3.557475 CCTCAAAAGGCCATTCATGCAAA 60.557 43.478 5.01 0.00 35.37 3.68
614 616 4.066490 CTCAAAAGGCCATTCATGCAAAA 58.934 39.130 5.01 0.00 0.00 2.44
615 617 3.814283 TCAAAAGGCCATTCATGCAAAAC 59.186 39.130 5.01 0.00 0.00 2.43
616 618 3.488778 AAAGGCCATTCATGCAAAACA 57.511 38.095 5.01 0.00 0.00 2.83
617 619 3.488778 AAGGCCATTCATGCAAAACAA 57.511 38.095 5.01 0.00 0.00 2.83
618 620 3.488778 AGGCCATTCATGCAAAACAAA 57.511 38.095 5.01 0.00 0.00 2.83
619 621 3.818180 AGGCCATTCATGCAAAACAAAA 58.182 36.364 5.01 0.00 0.00 2.44
627 629 7.427214 CATTCATGCAAAACAAAAGGGAAATT 58.573 30.769 0.00 0.00 0.00 1.82
652 654 3.179048 GCGAACTTCCATAATGGTTTGC 58.821 45.455 0.00 0.00 40.36 3.68
658 660 3.182887 TCCATAATGGTTTGCAAGGGT 57.817 42.857 0.00 0.00 39.03 4.34
678 680 7.881775 AGGGTATTAGGAAATGCTGTAAAAG 57.118 36.000 0.00 0.00 0.00 2.27
680 682 7.775561 AGGGTATTAGGAAATGCTGTAAAAGAG 59.224 37.037 0.00 0.00 0.00 2.85
761 763 7.626446 CCACATGCATAAAAATGATTGATGTG 58.374 34.615 0.00 0.00 35.60 3.21
762 764 7.254624 CCACATGCATAAAAATGATTGATGTGG 60.255 37.037 0.00 0.00 45.05 4.17
781 783 1.202867 GGGGCCAATCATTCTCTCTCC 60.203 57.143 4.39 0.00 0.00 3.71
794 796 1.146485 CTCTCCGTCGCTCTCCCTA 59.854 63.158 0.00 0.00 0.00 3.53
816 818 4.411927 AGTCTCACCAAGCTCTAGAGAAA 58.588 43.478 24.24 0.00 37.13 2.52
970 972 1.464997 GGCACGCAAAGAAAGAGTAGG 59.535 52.381 0.00 0.00 0.00 3.18
979 981 4.984146 AAGAAAGAGTAGGTCAGCCTTT 57.016 40.909 0.00 0.00 44.18 3.11
989 991 1.163554 GTCAGCCTTTTGAGAGCCTG 58.836 55.000 0.00 0.00 0.00 4.85
1042 1044 1.890041 CCCCTTGTGTTTGCGTCGA 60.890 57.895 0.00 0.00 0.00 4.20
1279 1282 2.202650 GCGCGAAAGGCATGCAAT 60.203 55.556 21.36 4.13 43.84 3.56
1312 1315 2.121963 AGGGTCCTGGCTGGTTCA 60.122 61.111 10.44 0.00 37.07 3.18
1349 1352 2.821378 TGTTCGAAGATCCAAGGTACGA 59.179 45.455 0.00 0.00 35.04 3.43
1350 1353 3.446161 TGTTCGAAGATCCAAGGTACGAT 59.554 43.478 0.00 0.00 35.04 3.73
1351 1354 3.984508 TCGAAGATCCAAGGTACGATC 57.015 47.619 0.00 1.45 36.03 3.69
1352 1355 3.284617 TCGAAGATCCAAGGTACGATCA 58.715 45.455 10.05 0.00 37.87 2.92
1353 1356 3.889538 TCGAAGATCCAAGGTACGATCAT 59.110 43.478 10.05 0.08 37.87 2.45
1441 1444 9.154632 TGATAAAGATAGTCTATGTTTAGGGCA 57.845 33.333 20.67 16.53 37.34 5.36
1442 1445 9.998106 GATAAAGATAGTCTATGTTTAGGGCAA 57.002 33.333 20.67 5.88 37.34 4.52
1475 1479 9.715121 ACATAACATTTCTCGTTACTCCTAAAA 57.285 29.630 0.00 0.00 31.94 1.52
1478 1482 8.617290 AACATTTCTCGTTACTCCTAAAATGT 57.383 30.769 0.00 0.00 43.73 2.71
1479 1483 9.715121 AACATTTCTCGTTACTCCTAAAATGTA 57.285 29.630 10.03 0.00 42.07 2.29
1480 1484 9.886132 ACATTTCTCGTTACTCCTAAAATGTAT 57.114 29.630 8.36 0.00 41.48 2.29
1527 1531 4.226384 TGCAGTGATGGGTCAGTATCTAT 58.774 43.478 0.00 0.00 35.84 1.98
1528 1532 4.281941 TGCAGTGATGGGTCAGTATCTATC 59.718 45.833 0.00 0.00 35.84 2.08
1529 1533 4.281941 GCAGTGATGGGTCAGTATCTATCA 59.718 45.833 0.00 0.00 35.84 2.15
1530 1534 5.566429 GCAGTGATGGGTCAGTATCTATCAG 60.566 48.000 0.00 0.00 35.84 2.90
1531 1535 5.772169 CAGTGATGGGTCAGTATCTATCAGA 59.228 44.000 0.00 0.00 35.84 3.27
1532 1536 6.266330 CAGTGATGGGTCAGTATCTATCAGAA 59.734 42.308 0.00 0.00 35.84 3.02
1533 1537 7.015680 AGTGATGGGTCAGTATCTATCAGAAT 58.984 38.462 0.00 0.00 36.26 2.40
1583 1587 1.153289 CAGGAGAGTTCGCCATGGG 60.153 63.158 15.13 3.69 38.37 4.00
1611 1615 3.248602 GCGTCATCAAGTTCAGAACAGTT 59.751 43.478 15.85 0.00 0.00 3.16
1613 1617 5.388890 GCGTCATCAAGTTCAGAACAGTTAG 60.389 44.000 15.85 2.84 0.00 2.34
1646 1650 4.083110 CCATGAGAGCTACAAACAACTTGG 60.083 45.833 0.00 0.00 39.56 3.61
1685 1689 3.872771 GTCCCAACTCGTGTAAGTGAAAA 59.127 43.478 0.00 0.00 0.00 2.29
1686 1690 4.514066 GTCCCAACTCGTGTAAGTGAAAAT 59.486 41.667 0.00 0.00 0.00 1.82
1687 1691 5.008316 GTCCCAACTCGTGTAAGTGAAAATT 59.992 40.000 0.00 0.00 0.00 1.82
1727 1731 2.307098 ACTCCCTCCCTTTCAGAATGTG 59.693 50.000 0.00 0.00 37.40 3.21
1767 1774 7.501892 TGAGAATTGCCATAATGTATTAGTGCA 59.498 33.333 6.71 6.71 33.61 4.57
1810 1817 9.969001 GATATTCTTAGATAGTACTCCCTCTGT 57.031 37.037 0.00 0.00 0.00 3.41
1813 1820 8.522542 TTCTTAGATAGTACTCCCTCTGTTTC 57.477 38.462 0.00 0.00 0.00 2.78
1814 1821 7.874252 TCTTAGATAGTACTCCCTCTGTTTCT 58.126 38.462 0.00 0.00 0.00 2.52
1815 1822 9.000978 TCTTAGATAGTACTCCCTCTGTTTCTA 57.999 37.037 0.00 0.00 0.00 2.10
1816 1823 9.629878 CTTAGATAGTACTCCCTCTGTTTCTAA 57.370 37.037 0.00 0.14 0.00 2.10
1817 1824 9.986157 TTAGATAGTACTCCCTCTGTTTCTAAA 57.014 33.333 0.00 0.00 0.00 1.85
1823 1830 9.892130 AGTACTCCCTCTGTTTCTAAATATTTG 57.108 33.333 11.05 1.65 0.00 2.32
1824 1831 9.668497 GTACTCCCTCTGTTTCTAAATATTTGT 57.332 33.333 11.05 0.00 0.00 2.83
1825 1832 8.794335 ACTCCCTCTGTTTCTAAATATTTGTC 57.206 34.615 11.05 0.00 0.00 3.18
1826 1833 8.606830 ACTCCCTCTGTTTCTAAATATTTGTCT 58.393 33.333 11.05 0.00 0.00 3.41
1827 1834 9.454859 CTCCCTCTGTTTCTAAATATTTGTCTT 57.545 33.333 11.05 0.00 0.00 3.01
1828 1835 9.807921 TCCCTCTGTTTCTAAATATTTGTCTTT 57.192 29.630 11.05 0.00 0.00 2.52
1847 1854 9.787532 TTGTCTTTCTAAAGATTTCAACAAGTG 57.212 29.630 8.31 0.00 45.83 3.16
1848 1855 9.173021 TGTCTTTCTAAAGATTTCAACAAGTGA 57.827 29.630 8.31 0.00 45.83 3.41
1849 1856 9.439537 GTCTTTCTAAAGATTTCAACAAGTGAC 57.560 33.333 8.31 0.00 45.83 3.67
1850 1857 9.396022 TCTTTCTAAAGATTTCAACAAGTGACT 57.604 29.630 1.00 0.00 39.95 3.41
1853 1860 9.607988 TTCTAAAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
1854 1861 9.778741 TCTAAAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
1858 1865 8.498054 AGATTTCAACAAGTGACTACATATGG 57.502 34.615 7.80 0.00 35.39 2.74
1859 1866 8.321353 AGATTTCAACAAGTGACTACATATGGA 58.679 33.333 7.80 0.00 35.39 3.41
1860 1867 7.905604 TTTCAACAAGTGACTACATATGGAG 57.094 36.000 13.77 13.77 35.39 3.86
1861 1868 5.419542 TCAACAAGTGACTACATATGGAGC 58.580 41.667 15.30 8.47 0.00 4.70
1862 1869 5.046663 TCAACAAGTGACTACATATGGAGCA 60.047 40.000 15.30 10.95 0.00 4.26
1863 1870 5.420725 ACAAGTGACTACATATGGAGCAA 57.579 39.130 15.30 0.16 0.00 3.91
1864 1871 5.804639 ACAAGTGACTACATATGGAGCAAA 58.195 37.500 15.30 0.00 0.00 3.68
1865 1872 5.877012 ACAAGTGACTACATATGGAGCAAAG 59.123 40.000 15.30 9.25 0.00 2.77
1866 1873 5.683876 AGTGACTACATATGGAGCAAAGT 57.316 39.130 15.30 1.00 0.00 2.66
1867 1874 5.423015 AGTGACTACATATGGAGCAAAGTG 58.577 41.667 15.30 0.00 0.00 3.16
1868 1875 5.187772 AGTGACTACATATGGAGCAAAGTGA 59.812 40.000 15.30 0.00 0.00 3.41
1869 1876 5.521735 GTGACTACATATGGAGCAAAGTGAG 59.478 44.000 15.30 0.00 0.00 3.51
1870 1877 5.187772 TGACTACATATGGAGCAAAGTGAGT 59.812 40.000 15.30 0.00 0.00 3.41
1871 1878 5.423015 ACTACATATGGAGCAAAGTGAGTG 58.577 41.667 15.30 0.00 0.00 3.51
1872 1879 4.558226 ACATATGGAGCAAAGTGAGTGA 57.442 40.909 7.80 0.00 0.00 3.41
1873 1880 4.910195 ACATATGGAGCAAAGTGAGTGAA 58.090 39.130 7.80 0.00 0.00 3.18
1874 1881 5.503927 ACATATGGAGCAAAGTGAGTGAAT 58.496 37.500 7.80 0.00 0.00 2.57
1875 1882 5.948162 ACATATGGAGCAAAGTGAGTGAATT 59.052 36.000 7.80 0.00 0.00 2.17
1876 1883 6.435277 ACATATGGAGCAAAGTGAGTGAATTT 59.565 34.615 7.80 0.00 0.00 1.82
1877 1884 7.611467 ACATATGGAGCAAAGTGAGTGAATTTA 59.389 33.333 7.80 0.00 0.00 1.40
1878 1885 5.689383 TGGAGCAAAGTGAGTGAATTTAC 57.311 39.130 0.00 0.00 0.00 2.01
1879 1886 5.129634 TGGAGCAAAGTGAGTGAATTTACA 58.870 37.500 2.93 0.00 0.00 2.41
1880 1887 5.008613 TGGAGCAAAGTGAGTGAATTTACAC 59.991 40.000 2.93 0.00 40.60 2.90
1913 1920 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
1915 1922 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
1916 1923 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
1917 1924 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
1918 1925 8.546322 TCTATATACATCCGTATGTGGTAGTCT 58.454 37.037 3.56 0.00 45.99 3.24
1919 1926 9.828039 CTATATACATCCGTATGTGGTAGTCTA 57.172 37.037 3.56 0.00 45.99 2.59
1921 1928 9.696572 ATATACATCCGTATGTGGTAGTCTATT 57.303 33.333 3.56 0.00 45.99 1.73
1922 1929 6.726490 ACATCCGTATGTGGTAGTCTATTT 57.274 37.500 0.00 0.00 44.79 1.40
1923 1930 6.513180 ACATCCGTATGTGGTAGTCTATTTG 58.487 40.000 0.00 0.00 44.79 2.32
1924 1931 6.322969 ACATCCGTATGTGGTAGTCTATTTGA 59.677 38.462 0.00 0.00 44.79 2.69
1925 1932 6.778834 TCCGTATGTGGTAGTCTATTTGAA 57.221 37.500 0.00 0.00 0.00 2.69
1926 1933 7.172868 TCCGTATGTGGTAGTCTATTTGAAA 57.827 36.000 0.00 0.00 0.00 2.69
1927 1934 7.788026 TCCGTATGTGGTAGTCTATTTGAAAT 58.212 34.615 0.00 0.00 0.00 2.17
1928 1935 8.916062 TCCGTATGTGGTAGTCTATTTGAAATA 58.084 33.333 0.00 0.00 0.00 1.40
1929 1936 9.706691 CCGTATGTGGTAGTCTATTTGAAATAT 57.293 33.333 0.00 0.00 0.00 1.28
1961 1968 9.892130 AAGACAAATATTTAGTAACTGAGGGAG 57.108 33.333 0.00 0.00 0.00 4.30
1962 1969 9.047947 AGACAAATATTTAGTAACTGAGGGAGT 57.952 33.333 0.00 0.00 35.94 3.85
2015 2128 9.531942 GATGATGATGGCAATTTTACATACAAA 57.468 29.630 0.00 0.00 0.00 2.83
2085 2198 4.085884 CACGTTAACATTTGATGCGTACC 58.914 43.478 6.39 0.00 0.00 3.34
2110 2401 7.386299 CCTCTGATCTTCCGTTAAAATGGATAG 59.614 40.741 4.52 5.88 43.32 2.08
2245 2537 5.452776 CCCATTACCGTCATCTAGTAAAGCA 60.453 44.000 0.00 0.00 30.33 3.91
2247 2539 3.166489 ACCGTCATCTAGTAAAGCAGC 57.834 47.619 0.00 0.00 0.00 5.25
2259 2551 5.644977 AGTAAAGCAGCCTAAATTTGTCC 57.355 39.130 0.00 0.00 0.00 4.02
2323 2615 5.569413 AGCTTGTCGTTGTTTTACTTTCAG 58.431 37.500 0.00 0.00 0.00 3.02
2410 2750 9.973450 TGCTTGTTATTGTTTGTATAACATGTT 57.027 25.926 16.68 16.68 43.89 2.71
2526 2866 3.122297 TGAAATGCTTTGTTCAAAGGCG 58.878 40.909 21.56 3.79 30.93 5.52
2527 2867 2.888834 AATGCTTTGTTCAAAGGCGT 57.111 40.000 21.56 14.19 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.747855 CCAGCACTTTCCCCGCTC 60.748 66.667 0.00 0.00 32.48 5.03
142 143 3.403038 CTCTGAAACACTTACAGGTGGG 58.597 50.000 0.00 0.00 41.09 4.61
159 160 2.037136 CAGCACTTTCCCGGCTCTG 61.037 63.158 0.00 0.00 35.27 3.35
165 166 0.391263 GAGTACCCAGCACTTTCCCG 60.391 60.000 0.00 0.00 0.00 5.14
246 248 1.380403 CCGAGTGGACAGATCGAGCT 61.380 60.000 0.00 0.00 38.72 4.09
268 270 1.135517 GGTGAACGCGTGGCATATTTT 60.136 47.619 14.98 0.00 0.00 1.82
372 374 4.885709 GGCCTTCCCAAATCCCAA 57.114 55.556 0.00 0.00 0.00 4.12
412 414 1.078426 GATAGGGCCTGCGTTGTGT 60.078 57.895 18.53 0.00 0.00 3.72
432 434 4.281182 AGTTCAAGTATTCTGAGGTCGTGT 59.719 41.667 0.00 0.00 0.00 4.49
446 448 5.108517 ACGAAACAAACCGTAGTTCAAGTA 58.891 37.500 0.00 0.00 37.23 2.24
447 449 3.934579 ACGAAACAAACCGTAGTTCAAGT 59.065 39.130 0.00 0.00 37.23 3.16
484 486 1.032114 AAAGCCTAGCCGGATTGCAC 61.032 55.000 5.05 0.00 41.47 4.57
609 611 4.319190 GCCGTAATTTCCCTTTTGTTTTGC 60.319 41.667 0.00 0.00 0.00 3.68
610 612 4.084797 CGCCGTAATTTCCCTTTTGTTTTG 60.085 41.667 0.00 0.00 0.00 2.44
611 613 4.052608 CGCCGTAATTTCCCTTTTGTTTT 58.947 39.130 0.00 0.00 0.00 2.43
612 614 3.318557 TCGCCGTAATTTCCCTTTTGTTT 59.681 39.130 0.00 0.00 0.00 2.83
613 615 2.885894 TCGCCGTAATTTCCCTTTTGTT 59.114 40.909 0.00 0.00 0.00 2.83
614 616 2.506444 TCGCCGTAATTTCCCTTTTGT 58.494 42.857 0.00 0.00 0.00 2.83
615 617 3.057806 AGTTCGCCGTAATTTCCCTTTTG 60.058 43.478 0.00 0.00 0.00 2.44
616 618 3.151554 AGTTCGCCGTAATTTCCCTTTT 58.848 40.909 0.00 0.00 0.00 2.27
617 619 2.786777 AGTTCGCCGTAATTTCCCTTT 58.213 42.857 0.00 0.00 0.00 3.11
618 620 2.484742 AGTTCGCCGTAATTTCCCTT 57.515 45.000 0.00 0.00 0.00 3.95
619 621 2.353323 GAAGTTCGCCGTAATTTCCCT 58.647 47.619 0.00 0.00 0.00 4.20
627 629 2.168936 ACCATTATGGAAGTTCGCCGTA 59.831 45.455 19.23 0.00 40.96 4.02
652 654 7.639113 TTTACAGCATTTCCTAATACCCTTG 57.361 36.000 0.00 0.00 0.00 3.61
658 660 6.546034 GCCCTCTTTTACAGCATTTCCTAATA 59.454 38.462 0.00 0.00 0.00 0.98
678 680 1.515521 CTTGGTTCGTTGGTGCCCTC 61.516 60.000 0.00 0.00 0.00 4.30
680 682 2.561037 CCTTGGTTCGTTGGTGCCC 61.561 63.158 0.00 0.00 0.00 5.36
761 763 1.202867 GGAGAGAGAATGATTGGCCCC 60.203 57.143 0.00 0.00 0.00 5.80
762 764 1.542108 CGGAGAGAGAATGATTGGCCC 60.542 57.143 0.00 0.00 0.00 5.80
781 783 0.462225 TGAGACTAGGGAGAGCGACG 60.462 60.000 0.00 0.00 0.00 5.12
794 796 3.730215 TCTCTAGAGCTTGGTGAGACT 57.270 47.619 15.35 0.00 0.00 3.24
979 981 2.069776 CTGGGGTTCAGGCTCTCAA 58.930 57.895 0.00 0.00 39.76 3.02
1042 1044 1.353694 GGCCATGGCTAGGATGAAGAT 59.646 52.381 34.70 0.00 41.60 2.40
1279 1282 1.522092 CCTCTATGTCCGCCTGCAA 59.478 57.895 0.00 0.00 0.00 4.08
1291 1294 0.044855 AACCAGCCAGGACCCTCTAT 59.955 55.000 0.00 0.00 41.22 1.98
1353 1356 9.355916 AGTGCTGAATCACTAGTAGTATGATTA 57.644 33.333 13.30 0.18 44.77 1.75
1437 1440 5.594317 AGAAATGTTATGTATCACCTTGCCC 59.406 40.000 0.00 0.00 0.00 5.36
1438 1441 6.511767 CGAGAAATGTTATGTATCACCTTGCC 60.512 42.308 0.00 0.00 0.00 4.52
1439 1442 6.037172 ACGAGAAATGTTATGTATCACCTTGC 59.963 38.462 0.00 0.00 0.00 4.01
1440 1443 7.539712 ACGAGAAATGTTATGTATCACCTTG 57.460 36.000 0.00 0.00 0.00 3.61
1441 1444 9.095065 GTAACGAGAAATGTTATGTATCACCTT 57.905 33.333 0.00 0.00 34.59 3.50
1442 1445 8.475639 AGTAACGAGAAATGTTATGTATCACCT 58.524 33.333 0.00 0.00 34.59 4.00
1475 1479 5.010719 CGACCCACTGAACCTGTATATACAT 59.989 44.000 15.81 1.55 35.36 2.29
1476 1480 4.340097 CGACCCACTGAACCTGTATATACA 59.660 45.833 14.75 14.75 34.56 2.29
1477 1481 4.581824 TCGACCCACTGAACCTGTATATAC 59.418 45.833 5.89 5.89 0.00 1.47
1478 1482 4.581824 GTCGACCCACTGAACCTGTATATA 59.418 45.833 3.51 0.00 0.00 0.86
1479 1483 3.383825 GTCGACCCACTGAACCTGTATAT 59.616 47.826 3.51 0.00 0.00 0.86
1480 1484 2.756760 GTCGACCCACTGAACCTGTATA 59.243 50.000 3.51 0.00 0.00 1.47
1481 1485 1.549170 GTCGACCCACTGAACCTGTAT 59.451 52.381 3.51 0.00 0.00 2.29
1482 1486 0.963962 GTCGACCCACTGAACCTGTA 59.036 55.000 3.51 0.00 0.00 2.74
1483 1487 1.746517 GTCGACCCACTGAACCTGT 59.253 57.895 3.51 0.00 0.00 4.00
1484 1488 1.372997 CGTCGACCCACTGAACCTG 60.373 63.158 10.58 0.00 0.00 4.00
1491 1495 3.865929 CTGCAAGCGTCGACCCACT 62.866 63.158 10.58 2.01 0.00 4.00
1527 1531 3.431346 CCATCTCGCCTTCTGAATTCTGA 60.431 47.826 10.68 10.68 0.00 3.27
1528 1532 2.871022 CCATCTCGCCTTCTGAATTCTG 59.129 50.000 7.05 6.50 0.00 3.02
1529 1533 2.744494 GCCATCTCGCCTTCTGAATTCT 60.744 50.000 7.05 0.00 0.00 2.40
1530 1534 1.601430 GCCATCTCGCCTTCTGAATTC 59.399 52.381 0.00 0.00 0.00 2.17
1531 1535 1.211457 AGCCATCTCGCCTTCTGAATT 59.789 47.619 0.00 0.00 0.00 2.17
1532 1536 0.835941 AGCCATCTCGCCTTCTGAAT 59.164 50.000 0.00 0.00 0.00 2.57
1533 1537 1.485124 TAGCCATCTCGCCTTCTGAA 58.515 50.000 0.00 0.00 0.00 3.02
1583 1587 2.240612 GAACTTGATGACGCCACGCC 62.241 60.000 0.00 0.00 0.00 5.68
1611 1615 1.833630 CTCTCATGGGCAGTGTTCCTA 59.166 52.381 0.00 0.00 0.00 2.94
1613 1617 1.028868 GCTCTCATGGGCAGTGTTCC 61.029 60.000 0.00 0.00 0.00 3.62
1646 1650 5.290493 TGGGACATAGAATGTGTGGATAC 57.710 43.478 0.00 0.00 45.03 2.24
1685 1689 9.301897 GGGAGTATGGATTAAGCATTAGAAAAT 57.698 33.333 0.00 0.00 0.00 1.82
1686 1690 8.502738 AGGGAGTATGGATTAAGCATTAGAAAA 58.497 33.333 0.00 0.00 0.00 2.29
1687 1691 8.045720 AGGGAGTATGGATTAAGCATTAGAAA 57.954 34.615 0.00 0.00 0.00 2.52
1727 1731 4.624452 GCAATTCTCAAAGAAGAATGCACC 59.376 41.667 14.71 0.00 43.53 5.01
1801 1808 9.454859 AAGACAAATATTTAGAAACAGAGGGAG 57.545 33.333 0.00 0.00 0.00 4.30
1821 1828 9.787532 CACTTGTTGAAATCTTTAGAAAGACAA 57.212 29.630 6.85 4.98 46.80 3.18
1822 1829 9.173021 TCACTTGTTGAAATCTTTAGAAAGACA 57.827 29.630 6.85 0.00 46.80 3.41
1823 1830 9.439537 GTCACTTGTTGAAATCTTTAGAAAGAC 57.560 33.333 6.85 0.00 40.95 3.01
1824 1831 9.396022 AGTCACTTGTTGAAATCTTTAGAAAGA 57.604 29.630 7.15 7.15 41.72 2.52
1827 1834 9.607988 TGTAGTCACTTGTTGAAATCTTTAGAA 57.392 29.630 0.00 0.00 35.39 2.10
1828 1835 9.778741 ATGTAGTCACTTGTTGAAATCTTTAGA 57.221 29.630 0.00 0.00 35.39 2.10
1832 1839 8.950210 CCATATGTAGTCACTTGTTGAAATCTT 58.050 33.333 1.24 0.00 35.39 2.40
1833 1840 8.321353 TCCATATGTAGTCACTTGTTGAAATCT 58.679 33.333 1.24 0.00 35.39 2.40
1834 1841 8.492673 TCCATATGTAGTCACTTGTTGAAATC 57.507 34.615 1.24 0.00 35.39 2.17
1835 1842 7.066284 GCTCCATATGTAGTCACTTGTTGAAAT 59.934 37.037 1.24 0.00 35.39 2.17
1836 1843 6.371548 GCTCCATATGTAGTCACTTGTTGAAA 59.628 38.462 1.24 0.00 35.39 2.69
1837 1844 5.874810 GCTCCATATGTAGTCACTTGTTGAA 59.125 40.000 1.24 0.00 35.39 2.69
1838 1845 5.046663 TGCTCCATATGTAGTCACTTGTTGA 60.047 40.000 1.24 0.00 0.00 3.18
1839 1846 5.178061 TGCTCCATATGTAGTCACTTGTTG 58.822 41.667 1.24 0.00 0.00 3.33
1840 1847 5.420725 TGCTCCATATGTAGTCACTTGTT 57.579 39.130 1.24 0.00 0.00 2.83
1841 1848 5.420725 TTGCTCCATATGTAGTCACTTGT 57.579 39.130 1.24 0.00 0.00 3.16
1842 1849 5.877012 ACTTTGCTCCATATGTAGTCACTTG 59.123 40.000 1.24 0.00 0.00 3.16
1843 1850 5.877012 CACTTTGCTCCATATGTAGTCACTT 59.123 40.000 1.24 0.00 0.00 3.16
1844 1851 5.187772 TCACTTTGCTCCATATGTAGTCACT 59.812 40.000 1.24 0.00 0.00 3.41
1845 1852 5.419542 TCACTTTGCTCCATATGTAGTCAC 58.580 41.667 1.24 0.00 0.00 3.67
1846 1853 5.187772 ACTCACTTTGCTCCATATGTAGTCA 59.812 40.000 1.24 0.00 0.00 3.41
1847 1854 5.521735 CACTCACTTTGCTCCATATGTAGTC 59.478 44.000 1.24 0.00 0.00 2.59
1848 1855 5.187772 TCACTCACTTTGCTCCATATGTAGT 59.812 40.000 1.24 0.00 0.00 2.73
1849 1856 5.664457 TCACTCACTTTGCTCCATATGTAG 58.336 41.667 1.24 0.00 0.00 2.74
1850 1857 5.675684 TCACTCACTTTGCTCCATATGTA 57.324 39.130 1.24 0.00 0.00 2.29
1851 1858 4.558226 TCACTCACTTTGCTCCATATGT 57.442 40.909 1.24 0.00 0.00 2.29
1852 1859 6.446781 AATTCACTCACTTTGCTCCATATG 57.553 37.500 0.00 0.00 0.00 1.78
1853 1860 7.611467 TGTAAATTCACTCACTTTGCTCCATAT 59.389 33.333 0.00 0.00 0.00 1.78
1854 1861 6.939730 TGTAAATTCACTCACTTTGCTCCATA 59.060 34.615 0.00 0.00 0.00 2.74
1855 1862 5.769662 TGTAAATTCACTCACTTTGCTCCAT 59.230 36.000 0.00 0.00 0.00 3.41
1856 1863 5.008613 GTGTAAATTCACTCACTTTGCTCCA 59.991 40.000 0.00 0.00 35.68 3.86
1857 1864 5.239525 AGTGTAAATTCACTCACTTTGCTCC 59.760 40.000 0.00 0.00 44.07 4.70
1858 1865 6.305693 AGTGTAAATTCACTCACTTTGCTC 57.694 37.500 0.00 0.00 44.07 4.26
1887 1894 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
1889 1896 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
1890 1897 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
1891 1898 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
1892 1899 8.546322 AGACTACCACATACGGATGTATATAGA 58.454 37.037 22.62 5.04 44.82 1.98
1893 1900 8.734218 AGACTACCACATACGGATGTATATAG 57.266 38.462 14.23 16.35 44.82 1.31
1895 1902 9.696572 AATAGACTACCACATACGGATGTATAT 57.303 33.333 14.23 4.37 44.82 0.86
1896 1903 9.524496 AAATAGACTACCACATACGGATGTATA 57.476 33.333 14.23 8.27 44.82 1.47
1897 1904 8.304596 CAAATAGACTACCACATACGGATGTAT 58.695 37.037 14.23 7.46 44.82 2.29
1898 1905 7.503230 TCAAATAGACTACCACATACGGATGTA 59.497 37.037 14.23 0.00 44.82 2.29
1900 1907 6.745116 TCAAATAGACTACCACATACGGATG 58.255 40.000 5.94 5.94 39.16 3.51
1901 1908 6.971726 TCAAATAGACTACCACATACGGAT 57.028 37.500 0.00 0.00 0.00 4.18
1902 1909 6.778834 TTCAAATAGACTACCACATACGGA 57.221 37.500 0.00 0.00 0.00 4.69
1903 1910 9.706691 ATATTTCAAATAGACTACCACATACGG 57.293 33.333 0.00 0.00 0.00 4.02
1935 1942 9.892130 CTCCCTCAGTTACTAAATATTTGTCTT 57.108 33.333 11.05 0.00 0.00 3.01
1936 1943 9.047947 ACTCCCTCAGTTACTAAATATTTGTCT 57.952 33.333 11.05 0.00 26.56 3.41
1942 1949 9.810870 CCTACTACTCCCTCAGTTACTAAATAT 57.189 37.037 0.00 0.00 36.43 1.28
1943 1950 8.223330 CCCTACTACTCCCTCAGTTACTAAATA 58.777 40.741 0.00 0.00 36.43 1.40
1944 1951 7.068061 CCCTACTACTCCCTCAGTTACTAAAT 58.932 42.308 0.00 0.00 36.43 1.40
1945 1952 6.011274 ACCCTACTACTCCCTCAGTTACTAAA 60.011 42.308 0.00 0.00 36.43 1.85
1946 1953 5.493977 ACCCTACTACTCCCTCAGTTACTAA 59.506 44.000 0.00 0.00 36.43 2.24
1947 1954 5.042387 ACCCTACTACTCCCTCAGTTACTA 58.958 45.833 0.00 0.00 36.43 1.82
1948 1955 3.857420 ACCCTACTACTCCCTCAGTTACT 59.143 47.826 0.00 0.00 36.43 2.24
1949 1956 3.952967 CACCCTACTACTCCCTCAGTTAC 59.047 52.174 0.00 0.00 36.43 2.50
1950 1957 3.854389 TCACCCTACTACTCCCTCAGTTA 59.146 47.826 0.00 0.00 36.43 2.24
1951 1958 2.653366 TCACCCTACTACTCCCTCAGTT 59.347 50.000 0.00 0.00 36.43 3.16
1952 1959 2.242708 CTCACCCTACTACTCCCTCAGT 59.757 54.545 0.00 0.00 39.41 3.41
1953 1960 2.510382 TCTCACCCTACTACTCCCTCAG 59.490 54.545 0.00 0.00 0.00 3.35
1954 1961 2.570098 TCTCACCCTACTACTCCCTCA 58.430 52.381 0.00 0.00 0.00 3.86
1955 1962 3.666345 TTCTCACCCTACTACTCCCTC 57.334 52.381 0.00 0.00 0.00 4.30
1956 1963 4.415224 TTTTCTCACCCTACTACTCCCT 57.585 45.455 0.00 0.00 0.00 4.20
1957 1964 5.695424 AATTTTCTCACCCTACTACTCCC 57.305 43.478 0.00 0.00 0.00 4.30
1958 1965 8.706521 AGATAAATTTTCTCACCCTACTACTCC 58.293 37.037 0.00 0.00 0.00 3.85
1959 1966 9.535878 CAGATAAATTTTCTCACCCTACTACTC 57.464 37.037 0.00 0.00 0.00 2.59
1960 1967 9.268282 TCAGATAAATTTTCTCACCCTACTACT 57.732 33.333 0.00 0.00 0.00 2.57
1961 1968 9.886132 TTCAGATAAATTTTCTCACCCTACTAC 57.114 33.333 0.00 0.00 0.00 2.73
1963 1970 9.401058 CATTCAGATAAATTTTCTCACCCTACT 57.599 33.333 0.00 0.00 0.00 2.57
1964 1971 9.396022 TCATTCAGATAAATTTTCTCACCCTAC 57.604 33.333 0.00 0.00 0.00 3.18
1966 1973 8.910944 CATCATTCAGATAAATTTTCTCACCCT 58.089 33.333 0.00 0.00 34.43 4.34
1967 1974 8.906867 TCATCATTCAGATAAATTTTCTCACCC 58.093 33.333 0.00 0.00 34.43 4.61
2085 2198 7.095439 GCTATCCATTTTAACGGAAGATCAGAG 60.095 40.741 0.00 0.00 34.22 3.35
2128 2419 8.280497 CGATAAACCATGCACTAATTAAGGTAC 58.720 37.037 0.00 0.00 0.00 3.34
2138 2429 2.799978 CGCATCGATAAACCATGCACTA 59.200 45.455 0.00 0.00 42.65 2.74
2184 2476 2.109774 CCCTGCATGCAAAATAAGGGA 58.890 47.619 28.15 0.98 46.20 4.20
2245 2537 3.262405 TGTAGTCCGGACAAATTTAGGCT 59.738 43.478 35.00 13.71 0.00 4.58
2247 2539 4.081309 TCCTGTAGTCCGGACAAATTTAGG 60.081 45.833 35.00 27.86 0.00 2.69
2259 2551 4.119862 CCATATGTGTTTCCTGTAGTCCG 58.880 47.826 1.24 0.00 0.00 4.79
2323 2615 7.556275 TCCAACACTCAAAATCCAGGTATTATC 59.444 37.037 0.00 0.00 0.00 1.75
2473 2813 7.168135 GCAACCAAGTTATTCAAAGAGAAACTG 59.832 37.037 0.00 0.00 40.22 3.16
2526 2866 5.469084 ACCAAAACTTCGAGAAATACAGGAC 59.531 40.000 0.00 0.00 0.00 3.85
2527 2867 5.617252 ACCAAAACTTCGAGAAATACAGGA 58.383 37.500 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.