Multiple sequence alignment - TraesCS4B01G185200

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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 TraesCS4B01G185200 chr4B 100.000 2588 0 0 1 2588 404566947 404569534 0.000000e+00 4780
1 TraesCS4B01G185200 chr4A 93.695 904 20 11 855 1724 147365148 147364248 0.000000e+00 1319
2 TraesCS4B01G185200 chr4A 88.662 441 20 11 418 831 147365581 147365144 6.390000e-141 510
3 TraesCS4B01G185200 chr4A 89.098 266 9 10 92 342 147365857 147365597 1.930000e-81 313
4 TraesCS4B01G185200 chr4D 94.407 733 32 5 864 1595 324214102 324214826 0.000000e+00 1118
5 TraesCS4B01G185200 chr4D 90.671 611 52 3 1983 2588 324215543 324216153 0.000000e+00 808
6 TraesCS4B01G185200 chr4D 93.556 419 12 6 425 831 324213686 324214101 6.120000e-171 610
7 TraesCS4B01G185200 chr4D 85.440 364 20 18 1627 1983 324214826 324215163 5.300000e-92 348
8 TraesCS4B01G185200 chr4D 88.235 289 11 8 23 310 324213339 324213605 8.930000e-85 324


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 TraesCS4B01G185200 chr4B 404566947 404569534 2587 False 4780.0 4780 100.0000 1 2588 1 chr4B.!!$F1 2587
1 TraesCS4B01G185200 chr4A 147364248 147365857 1609 True 714.0 1319 90.4850 92 1724 3 chr4A.!!$R1 1632
2 TraesCS4B01G185200 chr4D 324213339 324216153 2814 False 641.6 1118 90.4618 23 2588 5 chr4D.!!$F1 2565

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
78 79 0.034089 ACTAATGCTCTGCAACCCCC 60.034 55.0 0.0 0.0 43.62 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2520 0.171231 CTCACTGGATCGTTCGCAGA 59.829 55.0 14.85 0.03 0.0 4.26 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
18 19 3.483869 GGAGAGGCCCCGCTTCAT 61.484 66.667 0.00 0.00 37.11 2.57
19 20 2.110006 GAGAGGCCCCGCTTCATC 59.890 66.667 0.00 0.00 37.11 2.92
20 21 2.688666 AGAGGCCCCGCTTCATCA 60.689 61.111 0.00 0.00 37.11 3.07
21 22 2.203126 GAGGCCCCGCTTCATCAG 60.203 66.667 0.00 0.00 34.72 2.90
64 65 1.070289 GCTACTAGCCGGCCAACTAAT 59.930 52.381 26.15 4.77 34.48 1.73
68 69 0.179056 TAGCCGGCCAACTAATGCTC 60.179 55.000 26.15 0.00 0.00 4.26
70 71 1.718757 GCCGGCCAACTAATGCTCTG 61.719 60.000 18.11 0.00 0.00 3.35
71 72 1.718757 CCGGCCAACTAATGCTCTGC 61.719 60.000 2.24 0.00 0.00 4.26
72 73 1.026182 CGGCCAACTAATGCTCTGCA 61.026 55.000 2.24 0.00 44.86 4.41
74 75 1.135286 GGCCAACTAATGCTCTGCAAC 60.135 52.381 0.00 0.00 43.62 4.17
75 76 1.135286 GCCAACTAATGCTCTGCAACC 60.135 52.381 0.00 0.00 43.62 3.77
76 77 1.474077 CCAACTAATGCTCTGCAACCC 59.526 52.381 0.00 0.00 43.62 4.11
77 78 1.474077 CAACTAATGCTCTGCAACCCC 59.526 52.381 0.00 0.00 43.62 4.95
78 79 0.034089 ACTAATGCTCTGCAACCCCC 60.034 55.000 0.00 0.00 43.62 5.40
79 80 1.077787 TAATGCTCTGCAACCCCCG 60.078 57.895 0.00 0.00 43.62 5.73
83 84 2.597217 CTCTGCAACCCCCGCAAA 60.597 61.111 0.00 0.00 39.30 3.68
84 85 2.123683 TCTGCAACCCCCGCAAAA 60.124 55.556 0.00 0.00 39.30 2.44
85 86 1.743321 CTCTGCAACCCCCGCAAAAA 61.743 55.000 0.00 0.00 39.30 1.94
153 157 2.560542 CCAAGCTAGCTACCGATCTCAT 59.439 50.000 19.70 0.00 0.00 2.90
162 166 3.256879 GCTACCGATCTCATGAGGAATGA 59.743 47.826 22.42 3.35 43.24 2.57
217 221 2.369629 CGAAATGGTCGCACGTCGT 61.370 57.895 0.00 0.00 44.14 4.34
311 330 2.118404 CCACACCACACCACACCAC 61.118 63.158 0.00 0.00 0.00 4.16
313 332 1.377987 ACACCACACCACACCACAC 60.378 57.895 0.00 0.00 0.00 3.82
327 346 0.391661 CCACACCACCCATTCTCGAG 60.392 60.000 5.93 5.93 0.00 4.04
342 361 8.364142 CCCATTCTCGAGTCTATTTCTTTCTAT 58.636 37.037 13.13 0.00 0.00 1.98
372 391 8.817876 ACTCCTTCTATACAGAAATATAAGGGC 58.182 37.037 0.00 0.00 40.28 5.19
373 392 7.837863 TCCTTCTATACAGAAATATAAGGGCG 58.162 38.462 0.00 0.00 40.28 6.13
375 394 8.095169 CCTTCTATACAGAAATATAAGGGCGTT 58.905 37.037 0.00 0.00 40.28 4.84
376 395 9.490379 CTTCTATACAGAAATATAAGGGCGTTT 57.510 33.333 0.00 0.00 40.28 3.60
382 401 8.514330 ACAGAAATATAAGGGCGTTTAAATCA 57.486 30.769 0.00 0.00 0.00 2.57
383 402 8.403236 ACAGAAATATAAGGGCGTTTAAATCAC 58.597 33.333 0.00 0.00 0.00 3.06
384 403 8.621286 CAGAAATATAAGGGCGTTTAAATCACT 58.379 33.333 0.00 0.00 0.00 3.41
385 404 9.841295 AGAAATATAAGGGCGTTTAAATCACTA 57.159 29.630 0.00 0.00 0.00 2.74
393 412 9.797556 AAGGGCGTTTAAATCACTATTTATTTC 57.202 29.630 0.00 0.00 37.40 2.17
394 413 9.185680 AGGGCGTTTAAATCACTATTTATTTCT 57.814 29.630 0.00 0.00 37.40 2.52
395 414 9.797556 GGGCGTTTAAATCACTATTTATTTCTT 57.202 29.630 0.00 0.00 37.40 2.52
581 609 7.088272 ACGTTCCAAAGAATTTATTGTTAGGC 58.912 34.615 0.00 0.00 35.03 3.93
588 616 9.341899 CAAAGAATTTATTGTTAGGCTGTGTAC 57.658 33.333 0.00 0.00 35.03 2.90
590 618 8.494016 AGAATTTATTGTTAGGCTGTGTACTC 57.506 34.615 0.00 0.00 0.00 2.59
592 620 2.736144 TTGTTAGGCTGTGTACTCCG 57.264 50.000 0.00 0.00 0.00 4.63
593 621 1.624336 TGTTAGGCTGTGTACTCCGT 58.376 50.000 0.00 0.00 0.00 4.69
596 624 0.036105 TAGGCTGTGTACTCCGTCGA 60.036 55.000 0.00 0.00 0.00 4.20
598 626 1.577922 GCTGTGTACTCCGTCGACA 59.422 57.895 17.16 0.00 0.00 4.35
600 628 1.402456 GCTGTGTACTCCGTCGACAAT 60.402 52.381 17.16 0.00 0.00 2.71
601 629 2.925306 GCTGTGTACTCCGTCGACAATT 60.925 50.000 17.16 0.00 0.00 2.32
602 630 3.314553 CTGTGTACTCCGTCGACAATTT 58.685 45.455 17.16 0.00 0.00 1.82
676 704 1.332552 GCGAAAAACAAGTCGAAGCGA 60.333 47.619 0.00 0.00 39.64 4.93
822 869 3.074836 CCTAAACCCCCTCCACACTTTTA 59.925 47.826 0.00 0.00 0.00 1.52
825 872 5.342361 AAACCCCCTCCACACTTTTATAA 57.658 39.130 0.00 0.00 0.00 0.98
826 873 4.311520 ACCCCCTCCACACTTTTATAAC 57.688 45.455 0.00 0.00 0.00 1.89
827 874 3.010920 ACCCCCTCCACACTTTTATAACC 59.989 47.826 0.00 0.00 0.00 2.85
828 875 3.268595 CCCCCTCCACACTTTTATAACCT 59.731 47.826 0.00 0.00 0.00 3.50
829 876 4.475747 CCCCCTCCACACTTTTATAACCTA 59.524 45.833 0.00 0.00 0.00 3.08
831 878 6.296803 CCCCTCCACACTTTTATAACCTATC 58.703 44.000 0.00 0.00 0.00 2.08
832 879 5.989777 CCCTCCACACTTTTATAACCTATCG 59.010 44.000 0.00 0.00 0.00 2.92
833 880 6.407752 CCCTCCACACTTTTATAACCTATCGT 60.408 42.308 0.00 0.00 0.00 3.73
834 881 6.700520 CCTCCACACTTTTATAACCTATCGTC 59.299 42.308 0.00 0.00 0.00 4.20
835 882 6.576185 TCCACACTTTTATAACCTATCGTCC 58.424 40.000 0.00 0.00 0.00 4.79
836 883 5.461078 CCACACTTTTATAACCTATCGTCCG 59.539 44.000 0.00 0.00 0.00 4.79
837 884 6.038356 CACACTTTTATAACCTATCGTCCGT 58.962 40.000 0.00 0.00 0.00 4.69
838 885 6.020121 CACACTTTTATAACCTATCGTCCGTG 60.020 42.308 0.00 0.00 0.00 4.94
839 886 5.461078 CACTTTTATAACCTATCGTCCGTGG 59.539 44.000 0.00 0.00 0.00 4.94
840 887 5.127682 ACTTTTATAACCTATCGTCCGTGGT 59.872 40.000 0.00 0.00 0.00 4.16
841 888 4.572985 TTATAACCTATCGTCCGTGGTG 57.427 45.455 0.00 0.00 32.53 4.17
842 889 0.457035 TAACCTATCGTCCGTGGTGC 59.543 55.000 0.00 0.00 32.53 5.01
843 890 1.255667 AACCTATCGTCCGTGGTGCT 61.256 55.000 0.00 0.00 32.53 4.40
844 891 1.255667 ACCTATCGTCCGTGGTGCTT 61.256 55.000 0.00 0.00 0.00 3.91
845 892 0.527817 CCTATCGTCCGTGGTGCTTC 60.528 60.000 0.00 0.00 0.00 3.86
846 893 0.527817 CTATCGTCCGTGGTGCTTCC 60.528 60.000 0.00 0.00 0.00 3.46
847 894 1.252215 TATCGTCCGTGGTGCTTCCA 61.252 55.000 0.00 0.00 45.01 3.53
881 928 1.804748 CCGACCTCAAAGTTTACCAGC 59.195 52.381 0.00 0.00 0.00 4.85
902 949 2.919971 GCATTCGCTCCTATCCCAC 58.080 57.895 0.00 0.00 34.30 4.61
903 950 0.603975 GCATTCGCTCCTATCCCACC 60.604 60.000 0.00 0.00 34.30 4.61
904 951 0.035458 CATTCGCTCCTATCCCACCC 59.965 60.000 0.00 0.00 0.00 4.61
905 952 0.399949 ATTCGCTCCTATCCCACCCA 60.400 55.000 0.00 0.00 0.00 4.51
906 953 1.335132 TTCGCTCCTATCCCACCCAC 61.335 60.000 0.00 0.00 0.00 4.61
907 954 2.808206 CGCTCCTATCCCACCCACC 61.808 68.421 0.00 0.00 0.00 4.61
908 955 2.808206 GCTCCTATCCCACCCACCG 61.808 68.421 0.00 0.00 0.00 4.94
909 956 1.382695 CTCCTATCCCACCCACCGT 60.383 63.158 0.00 0.00 0.00 4.83
910 957 0.981277 CTCCTATCCCACCCACCGTT 60.981 60.000 0.00 0.00 0.00 4.44
911 958 0.548197 TCCTATCCCACCCACCGTTT 60.548 55.000 0.00 0.00 0.00 3.60
912 959 0.330267 CCTATCCCACCCACCGTTTT 59.670 55.000 0.00 0.00 0.00 2.43
913 960 1.560611 CCTATCCCACCCACCGTTTTA 59.439 52.381 0.00 0.00 0.00 1.52
914 961 2.026075 CCTATCCCACCCACCGTTTTAA 60.026 50.000 0.00 0.00 0.00 1.52
915 962 2.911552 ATCCCACCCACCGTTTTAAT 57.088 45.000 0.00 0.00 0.00 1.40
945 1026 1.137404 CAACCACGCCATTAGCAGC 59.863 57.895 0.00 0.00 44.04 5.25
991 1075 1.721389 GATATCGTGTGTGCATAGCGG 59.279 52.381 7.33 0.00 0.00 5.52
993 1077 3.864686 CGTGTGTGCATAGCGGGC 61.865 66.667 0.00 0.00 0.00 6.13
1452 1551 4.467107 AGGAGGGAGGAGACGGCC 62.467 72.222 0.00 0.00 0.00 6.13
1608 1707 4.332543 TGAATTTCTTTCCGATGGATGACG 59.667 41.667 0.00 0.00 33.04 4.35
1670 1772 6.498538 TCAGGATCTAGTCTCTTCTTCCTTT 58.501 40.000 0.00 0.00 29.81 3.11
1671 1773 6.957020 TCAGGATCTAGTCTCTTCTTCCTTTT 59.043 38.462 0.00 0.00 29.81 2.27
1672 1774 7.123547 TCAGGATCTAGTCTCTTCTTCCTTTTC 59.876 40.741 0.00 0.00 29.81 2.29
1704 1806 7.449934 TTCTTTTTCTTCGTTCAAATGCTTC 57.550 32.000 0.00 0.00 0.00 3.86
1732 1834 4.670621 GTCAACTGCATGTGTAACGAAAAG 59.329 41.667 0.00 0.00 42.39 2.27
1735 1837 1.950216 TGCATGTGTAACGAAAAGGCA 59.050 42.857 0.00 0.00 42.39 4.75
1736 1838 2.556189 TGCATGTGTAACGAAAAGGCAT 59.444 40.909 0.00 0.00 42.39 4.40
1737 1839 2.916716 GCATGTGTAACGAAAAGGCATG 59.083 45.455 0.00 0.00 42.39 4.06
1739 1841 4.378978 GCATGTGTAACGAAAAGGCATGTA 60.379 41.667 0.00 0.00 42.39 2.29
1740 1842 4.735662 TGTGTAACGAAAAGGCATGTAC 57.264 40.909 0.00 0.00 42.39 2.90
1741 1843 4.382291 TGTGTAACGAAAAGGCATGTACT 58.618 39.130 0.00 0.00 42.39 2.73
1742 1844 4.212425 TGTGTAACGAAAAGGCATGTACTG 59.788 41.667 0.00 0.00 42.39 2.74
1745 1847 5.990386 TGTAACGAAAAGGCATGTACTGTAA 59.010 36.000 0.00 0.00 0.00 2.41
1746 1848 5.352643 AACGAAAAGGCATGTACTGTAAC 57.647 39.130 0.00 0.00 0.00 2.50
1747 1849 3.430895 ACGAAAAGGCATGTACTGTAACG 59.569 43.478 0.00 1.98 0.00 3.18
1748 1850 3.676172 CGAAAAGGCATGTACTGTAACGA 59.324 43.478 0.00 0.00 0.00 3.85
1752 1860 5.607119 AAGGCATGTACTGTAACGAAAAG 57.393 39.130 0.00 0.00 0.00 2.27
1767 1875 3.376234 ACGAAAAGGCATGTGATGAGATG 59.624 43.478 0.00 0.00 0.00 2.90
1787 1895 2.961741 TGGTGCAAGTGAAATTAAGCCA 59.038 40.909 0.00 0.00 0.00 4.75
1790 1898 2.030363 TGCAAGTGAAATTAAGCCACCG 60.030 45.455 0.00 0.00 0.00 4.94
1828 1936 3.055458 TGATTAGTTGGATGGTTGAGCGA 60.055 43.478 0.00 0.00 0.00 4.93
1834 1942 1.097547 GGATGGTTGAGCGATGTGGG 61.098 60.000 0.00 0.00 0.00 4.61
1841 1951 1.775385 TGAGCGATGTGGGTCTATGA 58.225 50.000 0.00 0.00 35.52 2.15
1857 1967 8.134895 TGGGTCTATGAAAATTAATCGAATTGC 58.865 33.333 0.00 0.00 37.82 3.56
1858 1968 8.134895 GGGTCTATGAAAATTAATCGAATTGCA 58.865 33.333 0.00 0.00 37.82 4.08
1859 1969 9.515020 GGTCTATGAAAATTAATCGAATTGCAA 57.485 29.630 0.00 0.00 37.82 4.08
1865 1975 9.421806 TGAAAATTAATCGAATTGCAATGAACT 57.578 25.926 13.82 0.00 37.82 3.01
1866 1976 9.891535 GAAAATTAATCGAATTGCAATGAACTC 57.108 29.630 13.82 5.72 37.82 3.01
1867 1977 7.669438 AATTAATCGAATTGCAATGAACTCG 57.331 32.000 20.14 20.14 36.35 4.18
1868 1978 4.685169 AATCGAATTGCAATGAACTCGT 57.315 36.364 23.37 12.82 0.00 4.18
1869 1979 5.794687 AATCGAATTGCAATGAACTCGTA 57.205 34.783 23.37 14.45 0.00 3.43
1870 1980 5.794687 ATCGAATTGCAATGAACTCGTAA 57.205 34.783 23.37 11.33 0.00 3.18
1871 1981 5.794687 TCGAATTGCAATGAACTCGTAAT 57.205 34.783 23.37 2.46 0.00 1.89
1872 1982 5.795766 TCGAATTGCAATGAACTCGTAATC 58.204 37.500 23.37 9.77 0.00 1.75
1873 1983 5.580691 TCGAATTGCAATGAACTCGTAATCT 59.419 36.000 23.37 1.81 0.00 2.40
1874 1984 5.898606 CGAATTGCAATGAACTCGTAATCTC 59.101 40.000 13.82 0.78 0.00 2.75
1875 1985 4.840401 TTGCAATGAACTCGTAATCTCG 57.160 40.909 0.00 0.00 0.00 4.04
1876 1986 3.186909 TGCAATGAACTCGTAATCTCGG 58.813 45.455 0.00 0.00 0.00 4.63
1917 2027 4.097286 GTGATGCTCCGGGCTTATTTTTAA 59.903 41.667 14.76 0.00 42.39 1.52
1929 2039 6.978080 GGGCTTATTTTTAATTCGCTGATGAA 59.022 34.615 0.00 0.00 0.00 2.57
1943 2053 5.641636 TCGCTGATGAAAACAAATAGCTACA 59.358 36.000 0.00 0.00 0.00 2.74
1961 2071 7.807977 AGCTACAGATTGAAACAGAAAAAGA 57.192 32.000 0.00 0.00 0.00 2.52
1962 2072 8.401490 AGCTACAGATTGAAACAGAAAAAGAT 57.599 30.769 0.00 0.00 0.00 2.40
1963 2073 8.510505 AGCTACAGATTGAAACAGAAAAAGATC 58.489 33.333 0.00 0.00 0.00 2.75
1988 2478 8.141909 TCAGCTACGCATACACTAAATTAGATT 58.858 33.333 7.06 0.00 0.00 2.40
2014 2504 3.446161 TGACACTAATAGGGGAGTCAACG 59.554 47.826 0.00 0.00 33.55 4.10
2017 2507 2.167900 ACTAATAGGGGAGTCAACGTGC 59.832 50.000 0.00 0.00 0.00 5.34
2022 2512 1.586154 GGGGAGTCAACGTGCCATTG 61.586 60.000 0.00 0.00 0.00 2.82
2030 2520 3.367743 CGTGCCATTGCTGGTGCT 61.368 61.111 0.00 0.00 45.10 4.40
2045 2535 1.153765 TGCTCTGCGAACGATCCAG 60.154 57.895 0.00 0.00 0.00 3.86
2046 2536 1.153745 GCTCTGCGAACGATCCAGT 60.154 57.895 9.72 0.00 0.00 4.00
2061 2551 6.698380 ACGATCCAGTGAGTAACAAAAGTAT 58.302 36.000 0.00 0.00 0.00 2.12
2070 2560 7.661847 AGTGAGTAACAAAAGTATTTCTCCTGG 59.338 37.037 0.00 0.00 37.28 4.45
2080 2570 1.367346 TTTCTCCTGGCCCACATGTA 58.633 50.000 0.00 0.00 0.00 2.29
2114 2604 2.311841 AGGGAGGGGTAAAAATGTCCAG 59.688 50.000 0.00 0.00 0.00 3.86
2120 2610 6.353602 GGAGGGGTAAAAATGTCCAGAGAATA 60.354 42.308 0.00 0.00 0.00 1.75
2138 2628 7.445402 CAGAGAATACTTTGGAGAAGGTCAAAA 59.555 37.037 0.00 0.00 33.24 2.44
2152 2642 1.970640 GTCAAAACCCTTTGGCTGGAT 59.029 47.619 0.00 0.00 42.71 3.41
2153 2643 1.969923 TCAAAACCCTTTGGCTGGATG 59.030 47.619 0.00 0.00 41.98 3.51
2173 2663 3.376636 TGGAAACATCACGGAGGGTATA 58.623 45.455 0.00 0.00 33.40 1.47
2174 2664 3.971305 TGGAAACATCACGGAGGGTATAT 59.029 43.478 0.00 0.00 33.40 0.86
2189 2679 3.067106 GGTATATCCATCAACGCACCAG 58.933 50.000 0.00 0.00 35.97 4.00
2206 2696 0.391263 CAGACGGTAGAGGGGCAAAC 60.391 60.000 0.00 0.00 0.00 2.93
2246 2738 7.776618 TTTGGAGTAAAGATGAGAGTAGACA 57.223 36.000 0.00 0.00 0.00 3.41
2265 2757 9.778741 AGTAGACACAAATAAGTGAAAGAATGA 57.221 29.630 0.57 0.00 42.05 2.57
2327 2819 4.468095 AATGTTGTTAGTGCGTTGTCTC 57.532 40.909 0.00 0.00 0.00 3.36
2418 2912 1.853250 AAAGGGAAAGGGGCGGAGAG 61.853 60.000 0.00 0.00 0.00 3.20
2441 2935 4.636249 ACACAAGATGGAGTTCTCACTTC 58.364 43.478 2.24 0.84 31.22 3.01
2446 2940 5.146010 AGATGGAGTTCTCACTTCAAGTC 57.854 43.478 0.00 0.00 42.26 3.01
2449 2943 5.097742 TGGAGTTCTCACTTCAAGTCAAA 57.902 39.130 0.00 0.00 35.34 2.69
2479 2973 2.152016 GAGGAAGGTGTTTGGTGCTAC 58.848 52.381 0.00 0.00 0.00 3.58
2480 2974 1.493022 AGGAAGGTGTTTGGTGCTACA 59.507 47.619 0.00 0.00 0.00 2.74
2498 2992 3.764885 ACAATTGCATTTCTACGGAGC 57.235 42.857 5.05 0.00 0.00 4.70
2533 3027 4.572389 GCATTCAGTCACACCGATATTCTT 59.428 41.667 0.00 0.00 0.00 2.52
2534 3028 5.503031 GCATTCAGTCACACCGATATTCTTG 60.503 44.000 0.00 0.00 0.00 3.02
2545 3039 5.994054 CACCGATATTCTTGTGGAGATGAAT 59.006 40.000 0.00 0.00 33.49 2.57
2552 3046 0.327924 TGTGGAGATGAATTGGGCGT 59.672 50.000 0.00 0.00 0.00 5.68
2556 3050 2.503765 TGGAGATGAATTGGGCGTCTTA 59.496 45.455 0.00 0.00 32.04 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.468326 GATGAAGCGGGGCCTCTCC 62.468 68.421 0.00 0.00 0.00 3.71
2 3 2.110006 GATGAAGCGGGGCCTCTC 59.890 66.667 0.00 0.00 0.00 3.20
3 4 2.688666 TGATGAAGCGGGGCCTCT 60.689 61.111 0.00 0.00 0.00 3.69
4 5 2.203126 CTGATGAAGCGGGGCCTC 60.203 66.667 0.84 0.00 0.00 4.70
5 6 2.688666 TCTGATGAAGCGGGGCCT 60.689 61.111 0.84 0.00 0.00 5.19
6 7 2.514824 GTCTGATGAAGCGGGGCC 60.515 66.667 0.00 0.00 0.00 5.80
7 8 2.892425 CGTCTGATGAAGCGGGGC 60.892 66.667 0.00 0.00 0.00 5.80
8 9 2.892425 GCGTCTGATGAAGCGGGG 60.892 66.667 0.00 0.00 37.87 5.73
12 13 1.059994 CAAGCGCGTCTGATGAAGC 59.940 57.895 8.43 5.44 42.76 3.86
13 14 1.699656 CCCAAGCGCGTCTGATGAAG 61.700 60.000 8.43 0.00 0.00 3.02
14 15 1.741401 CCCAAGCGCGTCTGATGAA 60.741 57.895 8.43 0.00 0.00 2.57
15 16 1.960040 ATCCCAAGCGCGTCTGATGA 61.960 55.000 8.43 6.15 0.00 2.92
16 17 1.091771 AATCCCAAGCGCGTCTGATG 61.092 55.000 8.43 1.73 0.00 3.07
17 18 0.464036 TAATCCCAAGCGCGTCTGAT 59.536 50.000 8.43 0.00 0.00 2.90
18 19 0.464036 ATAATCCCAAGCGCGTCTGA 59.536 50.000 8.43 0.00 0.00 3.27
19 20 1.261619 GAATAATCCCAAGCGCGTCTG 59.738 52.381 8.43 5.17 0.00 3.51
20 21 1.139058 AGAATAATCCCAAGCGCGTCT 59.861 47.619 8.43 1.94 0.00 4.18
21 22 1.583054 AGAATAATCCCAAGCGCGTC 58.417 50.000 8.43 0.00 0.00 5.19
68 69 2.818132 TTTTTGCGGGGGTTGCAG 59.182 55.556 0.00 0.00 44.28 4.41
86 87 5.009854 AGCACTACTGTTGTTGCATTTTT 57.990 34.783 14.71 0.00 0.00 1.94
87 88 4.654091 AGCACTACTGTTGTTGCATTTT 57.346 36.364 14.71 0.00 0.00 1.82
88 89 5.964958 ATAGCACTACTGTTGTTGCATTT 57.035 34.783 14.71 2.97 0.00 2.32
89 90 6.402118 CGTTATAGCACTACTGTTGTTGCATT 60.402 38.462 14.71 7.54 0.00 3.56
90 91 5.063438 CGTTATAGCACTACTGTTGTTGCAT 59.937 40.000 14.71 10.34 0.00 3.96
153 157 1.014044 GCGTGCTCGTTCATTCCTCA 61.014 55.000 10.18 0.00 39.49 3.86
217 221 1.022735 GTCTCAGCTCCGACCGAATA 58.977 55.000 1.30 0.00 0.00 1.75
311 330 0.898320 AGACTCGAGAATGGGTGGTG 59.102 55.000 21.68 0.00 0.00 4.17
313 332 4.100189 AGAAATAGACTCGAGAATGGGTGG 59.900 45.833 21.68 0.00 0.00 4.61
347 366 7.976734 CGCCCTTATATTTCTGTATAGAAGGAG 59.023 40.741 18.60 13.11 45.77 3.69
349 368 7.612677 ACGCCCTTATATTTCTGTATAGAAGG 58.387 38.462 13.84 13.84 43.95 3.46
350 369 9.490379 AAACGCCCTTATATTTCTGTATAGAAG 57.510 33.333 1.97 0.00 43.41 2.85
356 375 9.616156 TGATTTAAACGCCCTTATATTTCTGTA 57.384 29.630 0.00 0.00 0.00 2.74
357 376 8.403236 GTGATTTAAACGCCCTTATATTTCTGT 58.597 33.333 0.00 0.00 0.00 3.41
358 377 8.621286 AGTGATTTAAACGCCCTTATATTTCTG 58.379 33.333 0.00 0.00 0.00 3.02
367 386 9.797556 GAAATAAATAGTGATTTAAACGCCCTT 57.202 29.630 0.00 0.00 40.17 3.95
368 387 9.185680 AGAAATAAATAGTGATTTAAACGCCCT 57.814 29.630 0.00 0.00 40.17 5.19
369 388 9.797556 AAGAAATAAATAGTGATTTAAACGCCC 57.202 29.630 0.00 0.00 40.17 6.13
412 431 6.509523 TGGTAGGAGAAAAGAGAGGAAAAA 57.490 37.500 0.00 0.00 0.00 1.94
413 432 6.704056 ATGGTAGGAGAAAAGAGAGGAAAA 57.296 37.500 0.00 0.00 0.00 2.29
414 433 7.808279 TTATGGTAGGAGAAAAGAGAGGAAA 57.192 36.000 0.00 0.00 0.00 3.13
415 434 7.311109 GGTTTATGGTAGGAGAAAAGAGAGGAA 60.311 40.741 0.00 0.00 0.00 3.36
416 435 6.156429 GGTTTATGGTAGGAGAAAAGAGAGGA 59.844 42.308 0.00 0.00 0.00 3.71
699 727 1.080366 TTGGCGCGTTGACTCGTAT 60.080 52.632 8.43 0.00 0.00 3.06
822 869 1.068127 GCACCACGGACGATAGGTTAT 59.932 52.381 0.00 0.00 43.77 1.89
825 872 1.255667 AAGCACCACGGACGATAGGT 61.256 55.000 0.00 0.62 43.77 3.08
826 873 0.527817 GAAGCACCACGGACGATAGG 60.528 60.000 0.00 0.00 43.77 2.57
827 874 0.527817 GGAAGCACCACGGACGATAG 60.528 60.000 0.00 0.00 38.79 2.08
828 875 1.252215 TGGAAGCACCACGGACGATA 61.252 55.000 0.00 0.00 44.64 2.92
829 876 2.264794 GGAAGCACCACGGACGAT 59.735 61.111 0.00 0.00 38.79 3.73
838 885 0.178068 TAGGCGAGAATGGAAGCACC 59.822 55.000 0.00 0.00 39.54 5.01
839 886 1.869767 CATAGGCGAGAATGGAAGCAC 59.130 52.381 0.00 0.00 0.00 4.40
840 887 1.762370 TCATAGGCGAGAATGGAAGCA 59.238 47.619 0.00 0.00 0.00 3.91
841 888 2.139118 GTCATAGGCGAGAATGGAAGC 58.861 52.381 0.00 0.00 0.00 3.86
842 889 2.760374 GGTCATAGGCGAGAATGGAAG 58.240 52.381 0.00 0.00 0.00 3.46
843 890 1.068588 CGGTCATAGGCGAGAATGGAA 59.931 52.381 0.00 0.00 0.00 3.53
844 891 0.673985 CGGTCATAGGCGAGAATGGA 59.326 55.000 0.00 0.00 0.00 3.41
845 892 0.673985 TCGGTCATAGGCGAGAATGG 59.326 55.000 0.00 0.00 0.00 3.16
846 893 1.603172 GGTCGGTCATAGGCGAGAATG 60.603 57.143 0.00 0.00 0.00 2.67
847 894 0.674534 GGTCGGTCATAGGCGAGAAT 59.325 55.000 0.00 0.00 0.00 2.40
848 895 0.395311 AGGTCGGTCATAGGCGAGAA 60.395 55.000 0.00 0.00 0.00 2.87
849 896 0.818445 GAGGTCGGTCATAGGCGAGA 60.818 60.000 0.00 0.00 0.00 4.04
850 897 1.101635 TGAGGTCGGTCATAGGCGAG 61.102 60.000 0.00 0.00 0.00 5.03
851 898 0.681887 TTGAGGTCGGTCATAGGCGA 60.682 55.000 0.00 0.00 0.00 5.54
852 899 0.174845 TTTGAGGTCGGTCATAGGCG 59.825 55.000 0.00 0.00 0.00 5.52
853 900 1.207329 ACTTTGAGGTCGGTCATAGGC 59.793 52.381 0.00 0.00 31.74 3.93
895 942 4.385088 GGTATTAAAACGGTGGGTGGGATA 60.385 45.833 0.00 0.00 0.00 2.59
901 948 2.025981 GGAGGGTATTAAAACGGTGGGT 60.026 50.000 0.00 0.00 0.00 4.51
902 949 2.646930 GGAGGGTATTAAAACGGTGGG 58.353 52.381 0.00 0.00 0.00 4.61
903 950 2.282407 CGGAGGGTATTAAAACGGTGG 58.718 52.381 0.00 0.00 0.00 4.61
904 951 2.931969 GACGGAGGGTATTAAAACGGTG 59.068 50.000 0.00 0.00 0.00 4.94
905 952 2.093500 GGACGGAGGGTATTAAAACGGT 60.093 50.000 0.00 0.00 0.00 4.83
906 953 2.554142 GGACGGAGGGTATTAAAACGG 58.446 52.381 0.00 0.00 0.00 4.44
907 954 2.093553 TGGGACGGAGGGTATTAAAACG 60.094 50.000 0.00 0.00 0.00 3.60
908 955 3.632643 TGGGACGGAGGGTATTAAAAC 57.367 47.619 0.00 0.00 0.00 2.43
909 956 3.308331 GGTTGGGACGGAGGGTATTAAAA 60.308 47.826 0.00 0.00 0.00 1.52
910 957 2.239402 GGTTGGGACGGAGGGTATTAAA 59.761 50.000 0.00 0.00 0.00 1.52
911 958 1.839354 GGTTGGGACGGAGGGTATTAA 59.161 52.381 0.00 0.00 0.00 1.40
912 959 1.273724 TGGTTGGGACGGAGGGTATTA 60.274 52.381 0.00 0.00 0.00 0.98
913 960 0.548197 TGGTTGGGACGGAGGGTATT 60.548 55.000 0.00 0.00 0.00 1.89
914 961 1.081462 TGGTTGGGACGGAGGGTAT 59.919 57.895 0.00 0.00 0.00 2.73
915 962 1.914764 GTGGTTGGGACGGAGGGTA 60.915 63.158 0.00 0.00 0.00 3.69
945 1026 1.779025 CTCGATCGGCAATGGGCTTG 61.779 60.000 16.41 0.00 44.01 4.01
1317 1407 2.351276 GGCATTGACCTGGACCGT 59.649 61.111 0.00 0.00 0.00 4.83
1320 1410 2.438434 CCCGGCATTGACCTGGAC 60.438 66.667 0.00 0.00 36.21 4.02
1418 1517 2.125147 TCTCCATTTCTGCCGCCG 60.125 61.111 0.00 0.00 0.00 6.46
1419 1518 1.821332 CCTCTCCATTTCTGCCGCC 60.821 63.158 0.00 0.00 0.00 6.13
1420 1519 0.813210 CTCCTCTCCATTTCTGCCGC 60.813 60.000 0.00 0.00 0.00 6.53
1421 1520 0.179062 CCTCCTCTCCATTTCTGCCG 60.179 60.000 0.00 0.00 0.00 5.69
1608 1707 1.133407 CTACTCGGCTCACCTTGTCTC 59.867 57.143 0.00 0.00 0.00 3.36
1670 1772 6.769134 ACGAAGAAAAAGAAAAGGAAGGAA 57.231 33.333 0.00 0.00 0.00 3.36
1671 1773 6.376018 TGAACGAAGAAAAAGAAAAGGAAGGA 59.624 34.615 0.00 0.00 0.00 3.36
1672 1774 6.560711 TGAACGAAGAAAAAGAAAAGGAAGG 58.439 36.000 0.00 0.00 0.00 3.46
1704 1806 4.609113 CGTTACACATGCAGTTGACAGAAG 60.609 45.833 4.40 0.00 0.00 2.85
1732 1834 3.425758 GCCTTTTCGTTACAGTACATGCC 60.426 47.826 0.00 0.00 0.00 4.40
1735 1837 5.001232 ACATGCCTTTTCGTTACAGTACAT 58.999 37.500 0.00 0.00 0.00 2.29
1736 1838 4.212425 CACATGCCTTTTCGTTACAGTACA 59.788 41.667 0.00 0.00 0.00 2.90
1737 1839 4.449743 TCACATGCCTTTTCGTTACAGTAC 59.550 41.667 0.00 0.00 0.00 2.73
1739 1841 3.472652 TCACATGCCTTTTCGTTACAGT 58.527 40.909 0.00 0.00 0.00 3.55
1740 1842 4.154015 TCATCACATGCCTTTTCGTTACAG 59.846 41.667 0.00 0.00 0.00 2.74
1741 1843 4.068599 TCATCACATGCCTTTTCGTTACA 58.931 39.130 0.00 0.00 0.00 2.41
1742 1844 4.391830 TCTCATCACATGCCTTTTCGTTAC 59.608 41.667 0.00 0.00 0.00 2.50
1745 1847 3.057969 TCTCATCACATGCCTTTTCGT 57.942 42.857 0.00 0.00 0.00 3.85
1746 1848 3.242969 CCATCTCATCACATGCCTTTTCG 60.243 47.826 0.00 0.00 0.00 3.46
1747 1849 3.698040 ACCATCTCATCACATGCCTTTTC 59.302 43.478 0.00 0.00 0.00 2.29
1748 1850 3.446161 CACCATCTCATCACATGCCTTTT 59.554 43.478 0.00 0.00 0.00 2.27
1752 1860 0.666913 GCACCATCTCATCACATGCC 59.333 55.000 0.00 0.00 0.00 4.40
1767 1875 3.317150 GTGGCTTAATTTCACTTGCACC 58.683 45.455 0.00 0.00 0.00 5.01
1787 1895 8.877195 ACTAATCAATCCTATAATTACACCGGT 58.123 33.333 0.00 0.00 0.00 5.28
1828 1936 8.746052 TTCGATTAATTTTCATAGACCCACAT 57.254 30.769 0.00 0.00 0.00 3.21
1841 1951 8.586273 CGAGTTCATTGCAATTCGATTAATTTT 58.414 29.630 21.15 0.00 37.62 1.82
1857 1967 5.281727 TGATCCGAGATTACGAGTTCATTG 58.718 41.667 0.00 0.00 35.09 2.82
1858 1968 5.515797 TGATCCGAGATTACGAGTTCATT 57.484 39.130 0.00 0.00 35.09 2.57
1859 1969 5.465051 CATGATCCGAGATTACGAGTTCAT 58.535 41.667 0.00 0.00 35.09 2.57
1860 1970 4.261614 CCATGATCCGAGATTACGAGTTCA 60.262 45.833 0.00 0.00 35.09 3.18
1861 1971 4.230657 CCATGATCCGAGATTACGAGTTC 58.769 47.826 0.00 0.00 35.09 3.01
1862 1972 3.637229 ACCATGATCCGAGATTACGAGTT 59.363 43.478 0.00 0.00 35.09 3.01
1863 1973 3.223435 ACCATGATCCGAGATTACGAGT 58.777 45.455 0.00 0.00 35.09 4.18
1864 1974 3.924918 ACCATGATCCGAGATTACGAG 57.075 47.619 0.00 0.00 35.09 4.18
1865 1975 3.005472 GGAACCATGATCCGAGATTACGA 59.995 47.826 0.00 0.00 35.09 3.43
1866 1976 3.005897 AGGAACCATGATCCGAGATTACG 59.994 47.826 10.68 0.00 42.03 3.18
1867 1977 4.039245 TCAGGAACCATGATCCGAGATTAC 59.961 45.833 10.68 0.00 42.03 1.89
1868 1978 4.223144 TCAGGAACCATGATCCGAGATTA 58.777 43.478 10.68 0.00 42.03 1.75
1869 1979 3.041211 TCAGGAACCATGATCCGAGATT 58.959 45.455 10.68 0.00 42.03 2.40
1870 1980 2.682594 TCAGGAACCATGATCCGAGAT 58.317 47.619 10.68 0.00 42.03 2.75
1871 1981 2.159179 TCAGGAACCATGATCCGAGA 57.841 50.000 10.68 10.18 42.03 4.04
1872 1982 2.988010 TTCAGGAACCATGATCCGAG 57.012 50.000 10.68 8.49 42.03 4.63
1873 1983 3.054434 ACAATTCAGGAACCATGATCCGA 60.054 43.478 10.68 8.89 42.03 4.55
1874 1984 3.065786 CACAATTCAGGAACCATGATCCG 59.934 47.826 10.68 7.19 42.03 4.18
1875 1985 4.272489 TCACAATTCAGGAACCATGATCC 58.728 43.478 8.93 8.93 37.22 3.36
1876 1986 5.735354 GCATCACAATTCAGGAACCATGATC 60.735 44.000 0.00 0.00 0.00 2.92
1917 2027 6.199937 AGCTATTTGTTTTCATCAGCGAAT 57.800 33.333 0.00 0.00 35.13 3.34
1929 2039 9.066892 TCTGTTTCAATCTGTAGCTATTTGTTT 57.933 29.630 0.00 0.00 0.00 2.83
1943 2053 7.521871 AGCTGATCTTTTTCTGTTTCAATCT 57.478 32.000 0.00 0.00 0.00 2.40
1988 2478 7.562135 GTTGACTCCCCTATTAGTGTCATTTA 58.438 38.462 0.00 0.00 36.65 1.40
2005 2495 1.210155 GCAATGGCACGTTGACTCC 59.790 57.895 5.05 0.00 40.72 3.85
2014 2504 1.975407 AGAGCACCAGCAATGGCAC 60.975 57.895 0.00 0.00 45.49 5.01
2017 2507 2.882876 GCAGAGCACCAGCAATGG 59.117 61.111 0.00 0.00 45.49 3.16
2022 2512 3.782244 CGTTCGCAGAGCACCAGC 61.782 66.667 0.00 0.00 37.72 4.85
2030 2520 0.171231 CTCACTGGATCGTTCGCAGA 59.829 55.000 14.85 0.03 0.00 4.26
2045 2535 7.573283 GCCAGGAGAAATACTTTTGTTACTCAC 60.573 40.741 0.00 0.00 0.00 3.51
2046 2536 6.430000 GCCAGGAGAAATACTTTTGTTACTCA 59.570 38.462 0.00 0.00 0.00 3.41
2061 2551 1.367346 TACATGTGGGCCAGGAGAAA 58.633 50.000 6.40 0.00 0.00 2.52
2080 2570 1.207791 CCTCCCTGCCTATGTCACTT 58.792 55.000 0.00 0.00 0.00 3.16
2094 2584 2.310647 TCTGGACATTTTTACCCCTCCC 59.689 50.000 0.00 0.00 0.00 4.30
2095 2585 3.265995 TCTCTGGACATTTTTACCCCTCC 59.734 47.826 0.00 0.00 0.00 4.30
2114 2604 7.308649 GGTTTTGACCTTCTCCAAAGTATTCTC 60.309 40.741 0.00 0.00 34.29 2.87
2120 2610 3.052869 AGGGTTTTGACCTTCTCCAAAGT 60.053 43.478 0.00 0.00 33.64 2.66
2138 2628 0.486879 TTTCCATCCAGCCAAAGGGT 59.513 50.000 0.00 0.00 36.17 4.34
2146 2636 0.734889 CCGTGATGTTTCCATCCAGC 59.265 55.000 0.60 0.00 45.78 4.85
2152 2642 1.646912 TACCCTCCGTGATGTTTCCA 58.353 50.000 0.00 0.00 0.00 3.53
2153 2643 4.562963 GGATATACCCTCCGTGATGTTTCC 60.563 50.000 0.00 0.00 0.00 3.13
2163 2653 2.674177 GCGTTGATGGATATACCCTCCG 60.674 54.545 0.00 0.00 38.00 4.63
2165 2655 3.326747 GTGCGTTGATGGATATACCCTC 58.673 50.000 0.00 0.00 38.00 4.30
2173 2663 0.740868 CGTCTGGTGCGTTGATGGAT 60.741 55.000 0.00 0.00 0.00 3.41
2174 2664 1.374125 CGTCTGGTGCGTTGATGGA 60.374 57.895 0.00 0.00 0.00 3.41
2189 2679 0.323957 AAGTTTGCCCCTCTACCGTC 59.676 55.000 0.00 0.00 0.00 4.79
2194 2684 2.173782 TGTGTTCAAGTTTGCCCCTCTA 59.826 45.455 0.00 0.00 0.00 2.43
2252 2744 6.983906 AGGGACAATTTCATTCTTTCACTT 57.016 33.333 0.00 0.00 0.00 3.16
2265 2757 9.603921 CATGCTGAAAATATTTAGGGACAATTT 57.396 29.630 0.01 0.00 0.00 1.82
2299 2791 6.205076 ACAACGCACTAACAACATTTATGGTA 59.795 34.615 0.00 0.00 0.00 3.25
2327 2819 9.903682 ATTTTCTAACAACTCATCATTCTGTTG 57.096 29.630 0.00 0.00 43.55 3.33
2345 2837 8.089597 TGCAATTTCAGCATCTTGATTTTCTAA 58.910 29.630 0.00 0.00 37.02 2.10
2376 2868 1.608590 CAAGCTCACCCAATTCAACGT 59.391 47.619 0.00 0.00 0.00 3.99
2418 2912 4.264460 AGTGAGAACTCCATCTTGTGTC 57.736 45.455 0.00 0.00 0.00 3.67
2441 2935 7.337942 ACCTTCCTCAAGCTATTATTTGACTTG 59.662 37.037 0.00 0.00 39.22 3.16
2446 2940 7.396540 AACACCTTCCTCAAGCTATTATTTG 57.603 36.000 0.00 0.00 0.00 2.32
2449 2943 5.888161 CCAAACACCTTCCTCAAGCTATTAT 59.112 40.000 0.00 0.00 0.00 1.28
2479 2973 3.763097 TGCTCCGTAGAAATGCAATTG 57.237 42.857 0.00 0.00 36.10 2.32
2480 2974 4.023707 GCTATGCTCCGTAGAAATGCAATT 60.024 41.667 0.00 0.00 38.98 2.32
2498 2992 5.163693 TGTGACTGAATGCTCATTTGCTATG 60.164 40.000 0.00 0.00 0.00 2.23
2533 3027 0.327924 ACGCCCAATTCATCTCCACA 59.672 50.000 0.00 0.00 0.00 4.17
2534 3028 1.017387 GACGCCCAATTCATCTCCAC 58.983 55.000 0.00 0.00 0.00 4.02
2545 3039 6.119536 AGATAATCATGTTTAAGACGCCCAA 58.880 36.000 0.49 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.