Multiple sequence alignment - TraesCS7D01G151700

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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 TraesCS7D01G151700 chr7D 100.000 2867 0 0 1 2867 100752279 100749413 0.000000e+00 5295
1 TraesCS7D01G151700 chr7D 98.544 824 11 1 2044 2867 552297235 552296413 0.000000e+00 1454
2 TraesCS7D01G151700 chr7D 86.970 660 59 13 93 733 269041140 269040489 0.000000e+00 717
3 TraesCS7D01G151700 chr7D 89.151 212 21 2 1 210 195318024 195318235 2.190000e-66 263
4 TraesCS7D01G151700 chr7B 92.322 1107 57 13 953 2037 56924020 56925120 0.000000e+00 1548
5 TraesCS7D01G151700 chr7B 86.115 785 84 21 1 765 598418633 598419412 0.000000e+00 822
6 TraesCS7D01G151700 chr2D 97.983 843 17 0 2025 2867 28935980 28935138 0.000000e+00 1463
7 TraesCS7D01G151700 chr2D 98.313 830 12 1 2038 2867 313228971 313229798 0.000000e+00 1454
8 TraesCS7D01G151700 chr2D 97.967 836 15 1 2034 2867 44732598 44731763 0.000000e+00 1448
9 TraesCS7D01G151700 chr6D 98.434 830 12 1 2038 2867 2561898 2562726 0.000000e+00 1459
10 TraesCS7D01G151700 chr6D 98.665 824 8 1 2044 2867 1944105 1943285 0.000000e+00 1458
11 TraesCS7D01G151700 chr6D 98.199 833 13 1 2035 2867 20744955 20745785 0.000000e+00 1454
12 TraesCS7D01G151700 chr3D 98.665 824 10 1 2044 2867 475645971 475646793 0.000000e+00 1459
13 TraesCS7D01G151700 chrUn 98.665 824 8 1 2044 2867 114784210 114785030 0.000000e+00 1458
14 TraesCS7D01G151700 chr5D 86.829 782 74 16 2 766 50812662 50813431 0.000000e+00 846
15 TraesCS7D01G151700 chr5D 89.358 639 58 10 1 633 538976442 538975808 0.000000e+00 795
16 TraesCS7D01G151700 chr5D 88.247 485 35 14 151 629 538998455 538997987 6.940000e-156 560
17 TraesCS7D01G151700 chr5D 91.892 148 11 1 1 148 538999597 538999451 3.740000e-49 206
18 TraesCS7D01G151700 chr7A 87.651 745 68 12 8 735 296562801 296562064 0.000000e+00 845
19 TraesCS7D01G151700 chr7A 91.549 213 9 2 1699 1902 102749402 102749190 4.680000e-73 285
20 TraesCS7D01G151700 chr5B 85.476 778 67 21 2 762 53699995 53700743 0.000000e+00 769
21 TraesCS7D01G151700 chr5B 88.784 633 61 10 1 629 680494777 680494151 0.000000e+00 767
22 TraesCS7D01G151700 chr4A 87.536 690 55 20 1 677 629527287 629527958 0.000000e+00 769
23 TraesCS7D01G151700 chr5A 88.535 628 52 14 2 623 40136202 40136815 0.000000e+00 743


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 TraesCS7D01G151700 chr7D 100749413 100752279 2866 True 5295 5295 100.0000 1 2867 1 chr7D.!!$R1 2866
1 TraesCS7D01G151700 chr7D 552296413 552297235 822 True 1454 1454 98.5440 2044 2867 1 chr7D.!!$R3 823
2 TraesCS7D01G151700 chr7D 269040489 269041140 651 True 717 717 86.9700 93 733 1 chr7D.!!$R2 640
3 TraesCS7D01G151700 chr7B 56924020 56925120 1100 False 1548 1548 92.3220 953 2037 1 chr7B.!!$F1 1084
4 TraesCS7D01G151700 chr7B 598418633 598419412 779 False 822 822 86.1150 1 765 1 chr7B.!!$F2 764
5 TraesCS7D01G151700 chr2D 28935138 28935980 842 True 1463 1463 97.9830 2025 2867 1 chr2D.!!$R1 842
6 TraesCS7D01G151700 chr2D 313228971 313229798 827 False 1454 1454 98.3130 2038 2867 1 chr2D.!!$F1 829
7 TraesCS7D01G151700 chr2D 44731763 44732598 835 True 1448 1448 97.9670 2034 2867 1 chr2D.!!$R2 833
8 TraesCS7D01G151700 chr6D 2561898 2562726 828 False 1459 1459 98.4340 2038 2867 1 chr6D.!!$F1 829
9 TraesCS7D01G151700 chr6D 1943285 1944105 820 True 1458 1458 98.6650 2044 2867 1 chr6D.!!$R1 823
10 TraesCS7D01G151700 chr6D 20744955 20745785 830 False 1454 1454 98.1990 2035 2867 1 chr6D.!!$F2 832
11 TraesCS7D01G151700 chr3D 475645971 475646793 822 False 1459 1459 98.6650 2044 2867 1 chr3D.!!$F1 823
12 TraesCS7D01G151700 chrUn 114784210 114785030 820 False 1458 1458 98.6650 2044 2867 1 chrUn.!!$F1 823
13 TraesCS7D01G151700 chr5D 50812662 50813431 769 False 846 846 86.8290 2 766 1 chr5D.!!$F1 764
14 TraesCS7D01G151700 chr5D 538975808 538976442 634 True 795 795 89.3580 1 633 1 chr5D.!!$R1 632
15 TraesCS7D01G151700 chr5D 538997987 538999597 1610 True 383 560 90.0695 1 629 2 chr5D.!!$R2 628
16 TraesCS7D01G151700 chr7A 296562064 296562801 737 True 845 845 87.6510 8 735 1 chr7A.!!$R2 727
17 TraesCS7D01G151700 chr5B 53699995 53700743 748 False 769 769 85.4760 2 762 1 chr5B.!!$F1 760
18 TraesCS7D01G151700 chr5B 680494151 680494777 626 True 767 767 88.7840 1 629 1 chr5B.!!$R1 628
19 TraesCS7D01G151700 chr4A 629527287 629527958 671 False 769 769 87.5360 1 677 1 chr4A.!!$F1 676
20 TraesCS7D01G151700 chr5A 40136202 40136815 613 False 743 743 88.5350 2 623 1 chr5A.!!$F1 621


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
868 1934 0.035056 ACTAGCAACACCAGATGGCC 60.035 55.0 0.00 0.00 39.32 5.36 F
869 1935 0.035152 CTAGCAACACCAGATGGCCA 60.035 55.0 8.56 8.56 39.32 5.36 F
870 1936 0.035152 TAGCAACACCAGATGGCCAG 60.035 55.0 13.05 0.00 39.32 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2910 0.107993 ACGATGATGGCACTCCTGTG 60.108 55.000 0.0 0.0 46.37 3.66 R
1848 2934 1.308069 ATCATGCGTCCACTGCAACC 61.308 55.000 0.0 0.0 46.87 3.77 R
1910 2996 1.596203 CGCAGGGACATGATCGCAT 60.596 57.895 0.0 0.0 42.75 4.73 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
46 47 5.189659 TGTTTTACACCAGTACAATTGCC 57.810 39.130 5.05 0.00 0.00 4.52
100 101 4.637534 GCATAAAAGAGCAGATCAAGTGGA 59.362 41.667 0.00 0.00 0.00 4.02
225 1221 7.613585 TCACCAATTGCTGATGAAAATGTTAT 58.386 30.769 0.00 0.00 0.00 1.89
258 1254 6.097356 TGTTGTAAGTCCACGATATGAAGTC 58.903 40.000 0.00 0.00 0.00 3.01
324 1321 2.369394 GCGACCCTGAAATGGAGAATT 58.631 47.619 0.00 0.00 0.00 2.17
370 1367 6.414732 TCGTCATCACCTAATCTCCAAAAAT 58.585 36.000 0.00 0.00 0.00 1.82
388 1385 0.893727 ATGTTTGGTGACGGAAGCCC 60.894 55.000 0.00 0.00 0.00 5.19
425 1431 7.997773 ACTAATCTTACTATGTGCGGAGATA 57.002 36.000 0.00 0.00 0.00 1.98
685 1732 0.394625 GGTAGAGAGAGTGCGGGAGT 60.395 60.000 0.00 0.00 0.00 3.85
693 1740 1.228583 AGTGCGGGAGTGAGAGACA 60.229 57.895 0.00 0.00 0.00 3.41
696 1743 2.888863 CGGGAGTGAGAGACAGGC 59.111 66.667 0.00 0.00 0.00 4.85
745 1811 4.450082 AATTAAAAGGTCCGTGGCAATC 57.550 40.909 0.00 0.00 0.00 2.67
746 1812 1.444836 TAAAAGGTCCGTGGCAATCG 58.555 50.000 0.00 0.00 0.00 3.34
747 1813 1.862602 AAAAGGTCCGTGGCAATCGC 61.863 55.000 0.00 0.00 37.44 4.58
748 1814 3.545124 AAGGTCCGTGGCAATCGCA 62.545 57.895 0.00 0.00 41.24 5.10
749 1815 3.799755 GGTCCGTGGCAATCGCAC 61.800 66.667 0.00 0.00 41.24 5.34
765 1831 1.268437 CGCACGGGCTTCTACTAGTAC 60.268 57.143 8.62 0.00 38.10 2.73
766 1832 2.022934 GCACGGGCTTCTACTAGTACT 58.977 52.381 0.00 0.00 36.96 2.73
767 1833 3.209410 GCACGGGCTTCTACTAGTACTA 58.791 50.000 0.00 1.89 36.96 1.82
768 1834 3.003171 GCACGGGCTTCTACTAGTACTAC 59.997 52.174 0.00 0.00 36.96 2.73
769 1835 4.450053 CACGGGCTTCTACTAGTACTACT 58.550 47.826 0.00 0.00 0.00 2.57
770 1836 5.605534 CACGGGCTTCTACTAGTACTACTA 58.394 45.833 0.00 0.00 0.00 1.82
771 1837 6.051717 CACGGGCTTCTACTAGTACTACTAA 58.948 44.000 0.00 0.00 29.00 2.24
772 1838 6.202570 CACGGGCTTCTACTAGTACTACTAAG 59.797 46.154 0.00 2.15 29.00 2.18
773 1839 6.126911 ACGGGCTTCTACTAGTACTACTAAGT 60.127 42.308 0.00 0.00 39.91 2.24
774 1840 6.765512 CGGGCTTCTACTAGTACTACTAAGTT 59.234 42.308 0.00 0.00 37.15 2.66
775 1841 7.281999 CGGGCTTCTACTAGTACTACTAAGTTT 59.718 40.741 0.00 0.00 37.15 2.66
776 1842 8.965819 GGGCTTCTACTAGTACTACTAAGTTTT 58.034 37.037 0.00 0.00 37.15 2.43
808 1874 7.527084 AAAAGAATCAGTCGATGTACTAAGC 57.473 36.000 0.00 0.00 30.13 3.09
809 1875 5.836821 AGAATCAGTCGATGTACTAAGCA 57.163 39.130 0.00 0.00 30.13 3.91
810 1876 6.208988 AGAATCAGTCGATGTACTAAGCAA 57.791 37.500 0.00 0.00 30.13 3.91
811 1877 6.631016 AGAATCAGTCGATGTACTAAGCAAA 58.369 36.000 0.00 0.00 30.13 3.68
812 1878 6.754209 AGAATCAGTCGATGTACTAAGCAAAG 59.246 38.462 0.00 0.00 30.13 2.77
813 1879 4.744570 TCAGTCGATGTACTAAGCAAAGG 58.255 43.478 0.00 0.00 0.00 3.11
814 1880 4.461431 TCAGTCGATGTACTAAGCAAAGGA 59.539 41.667 0.00 0.00 0.00 3.36
815 1881 5.047590 TCAGTCGATGTACTAAGCAAAGGAA 60.048 40.000 0.00 0.00 0.00 3.36
816 1882 5.637810 CAGTCGATGTACTAAGCAAAGGAAA 59.362 40.000 0.00 0.00 0.00 3.13
817 1883 5.638234 AGTCGATGTACTAAGCAAAGGAAAC 59.362 40.000 0.00 0.00 0.00 2.78
819 1885 5.867716 TCGATGTACTAAGCAAAGGAAACTC 59.132 40.000 0.00 0.00 42.68 3.01
820 1886 5.220228 CGATGTACTAAGCAAAGGAAACTCG 60.220 44.000 0.00 0.00 42.68 4.18
821 1887 3.744426 TGTACTAAGCAAAGGAAACTCGC 59.256 43.478 0.00 0.00 42.68 5.03
822 1888 2.846193 ACTAAGCAAAGGAAACTCGCA 58.154 42.857 0.00 0.00 42.68 5.10
823 1889 3.211045 ACTAAGCAAAGGAAACTCGCAA 58.789 40.909 0.00 0.00 42.68 4.85
824 1890 3.630312 ACTAAGCAAAGGAAACTCGCAAA 59.370 39.130 0.00 0.00 42.68 3.68
825 1891 3.518634 AAGCAAAGGAAACTCGCAAAA 57.481 38.095 0.00 0.00 42.68 2.44
826 1892 3.733443 AGCAAAGGAAACTCGCAAAAT 57.267 38.095 0.00 0.00 42.68 1.82
827 1893 4.058721 AGCAAAGGAAACTCGCAAAATT 57.941 36.364 0.00 0.00 42.68 1.82
828 1894 3.803778 AGCAAAGGAAACTCGCAAAATTG 59.196 39.130 0.00 0.00 42.68 2.32
829 1895 3.604543 GCAAAGGAAACTCGCAAAATTGC 60.605 43.478 8.06 8.06 46.17 3.56
845 1911 7.109006 CAAAATTGCTTGAATGTGTTAGTCC 57.891 36.000 0.00 0.00 0.00 3.85
846 1912 6.403866 AAATTGCTTGAATGTGTTAGTCCA 57.596 33.333 0.00 0.00 0.00 4.02
847 1913 5.633830 ATTGCTTGAATGTGTTAGTCCAG 57.366 39.130 0.00 0.00 0.00 3.86
848 1914 2.813754 TGCTTGAATGTGTTAGTCCAGC 59.186 45.455 0.00 0.00 41.10 4.85
849 1915 2.813754 GCTTGAATGTGTTAGTCCAGCA 59.186 45.455 0.00 0.00 40.61 4.41
850 1916 3.365364 GCTTGAATGTGTTAGTCCAGCAC 60.365 47.826 0.00 0.00 40.61 4.40
851 1917 3.769739 TGAATGTGTTAGTCCAGCACT 57.230 42.857 0.00 0.00 39.02 4.40
852 1918 4.882842 TGAATGTGTTAGTCCAGCACTA 57.117 40.909 0.00 0.00 39.02 2.74
853 1919 4.820897 TGAATGTGTTAGTCCAGCACTAG 58.179 43.478 0.00 0.00 38.90 2.57
854 1920 2.743636 TGTGTTAGTCCAGCACTAGC 57.256 50.000 0.00 0.00 38.90 3.42
855 1921 1.967779 TGTGTTAGTCCAGCACTAGCA 59.032 47.619 0.00 0.00 44.21 3.49
856 1922 2.367241 TGTGTTAGTCCAGCACTAGCAA 59.633 45.455 1.61 0.00 46.83 3.91
857 1923 2.737252 GTGTTAGTCCAGCACTAGCAAC 59.263 50.000 1.61 0.00 46.83 4.17
858 1924 2.367241 TGTTAGTCCAGCACTAGCAACA 59.633 45.455 0.00 0.00 43.66 3.33
859 1925 2.737252 GTTAGTCCAGCACTAGCAACAC 59.263 50.000 0.00 0.00 45.49 3.32
860 1926 0.035458 AGTCCAGCACTAGCAACACC 59.965 55.000 0.00 0.00 45.49 4.16
861 1927 0.250295 GTCCAGCACTAGCAACACCA 60.250 55.000 0.00 0.00 45.49 4.17
862 1928 0.035317 TCCAGCACTAGCAACACCAG 59.965 55.000 0.00 0.00 45.49 4.00
863 1929 0.035317 CCAGCACTAGCAACACCAGA 59.965 55.000 0.00 0.00 45.49 3.86
864 1930 1.339438 CCAGCACTAGCAACACCAGAT 60.339 52.381 0.00 0.00 45.49 2.90
865 1931 1.736126 CAGCACTAGCAACACCAGATG 59.264 52.381 0.00 0.00 45.49 2.90
866 1932 1.089920 GCACTAGCAACACCAGATGG 58.910 55.000 0.00 0.00 41.58 3.51
867 1933 1.089920 CACTAGCAACACCAGATGGC 58.910 55.000 0.00 0.00 39.32 4.40
868 1934 0.035056 ACTAGCAACACCAGATGGCC 60.035 55.000 0.00 0.00 39.32 5.36
869 1935 0.035152 CTAGCAACACCAGATGGCCA 60.035 55.000 8.56 8.56 39.32 5.36
870 1936 0.035152 TAGCAACACCAGATGGCCAG 60.035 55.000 13.05 0.00 39.32 4.85
871 1937 1.604593 GCAACACCAGATGGCCAGT 60.605 57.895 13.05 0.00 39.32 4.00
872 1938 1.181098 GCAACACCAGATGGCCAGTT 61.181 55.000 13.05 5.69 39.32 3.16
873 1939 1.331214 CAACACCAGATGGCCAGTTT 58.669 50.000 13.05 0.00 39.32 2.66
874 1940 1.688197 CAACACCAGATGGCCAGTTTT 59.312 47.619 13.05 0.00 39.32 2.43
875 1941 2.890311 CAACACCAGATGGCCAGTTTTA 59.110 45.455 13.05 0.00 39.32 1.52
876 1942 3.456380 ACACCAGATGGCCAGTTTTAT 57.544 42.857 13.05 0.00 39.32 1.40
877 1943 3.778265 ACACCAGATGGCCAGTTTTATT 58.222 40.909 13.05 0.00 39.32 1.40
878 1944 4.159557 ACACCAGATGGCCAGTTTTATTT 58.840 39.130 13.05 0.00 39.32 1.40
879 1945 5.329399 ACACCAGATGGCCAGTTTTATTTA 58.671 37.500 13.05 0.00 39.32 1.40
880 1946 5.957774 ACACCAGATGGCCAGTTTTATTTAT 59.042 36.000 13.05 0.00 39.32 1.40
881 1947 7.122715 ACACCAGATGGCCAGTTTTATTTATA 58.877 34.615 13.05 0.00 39.32 0.98
882 1948 7.784550 ACACCAGATGGCCAGTTTTATTTATAT 59.215 33.333 13.05 0.00 39.32 0.86
883 1949 8.299570 CACCAGATGGCCAGTTTTATTTATATC 58.700 37.037 13.05 0.00 39.32 1.63
884 1950 8.227507 ACCAGATGGCCAGTTTTATTTATATCT 58.772 33.333 13.05 0.47 39.32 1.98
885 1951 8.517878 CCAGATGGCCAGTTTTATTTATATCTG 58.482 37.037 13.05 13.93 38.19 2.90
886 1952 9.288576 CAGATGGCCAGTTTTATTTATATCTGA 57.711 33.333 13.05 0.00 39.86 3.27
887 1953 9.866655 AGATGGCCAGTTTTATTTATATCTGAA 57.133 29.630 13.05 0.00 0.00 3.02
890 1956 9.420118 TGGCCAGTTTTATTTATATCTGAATGT 57.580 29.630 0.00 0.00 0.00 2.71
926 1992 7.810766 TTGAAAAGTGTCAACAAATTCTCAC 57.189 32.000 0.00 0.00 32.56 3.51
927 1993 6.918626 TGAAAAGTGTCAACAAATTCTCACA 58.081 32.000 0.00 0.00 0.00 3.58
928 1994 7.546358 TGAAAAGTGTCAACAAATTCTCACAT 58.454 30.769 0.00 0.00 0.00 3.21
929 1995 8.034215 TGAAAAGTGTCAACAAATTCTCACATT 58.966 29.630 0.00 0.00 0.00 2.71
930 1996 7.760131 AAAGTGTCAACAAATTCTCACATTG 57.240 32.000 0.00 0.00 0.00 2.82
931 1997 6.698008 AGTGTCAACAAATTCTCACATTGA 57.302 33.333 0.00 0.00 0.00 2.57
932 1998 7.281040 AGTGTCAACAAATTCTCACATTGAT 57.719 32.000 0.00 0.00 0.00 2.57
933 1999 7.143340 AGTGTCAACAAATTCTCACATTGATG 58.857 34.615 0.00 0.00 0.00 3.07
934 2000 7.013559 AGTGTCAACAAATTCTCACATTGATGA 59.986 33.333 0.00 0.00 34.71 2.92
935 2001 7.325338 GTGTCAACAAATTCTCACATTGATGAG 59.675 37.037 0.00 8.90 46.40 2.90
945 2011 5.051409 TCACATTGATGAGAATATGCCCA 57.949 39.130 0.00 0.00 0.00 5.36
946 2012 5.447757 TCACATTGATGAGAATATGCCCAA 58.552 37.500 0.00 0.00 0.00 4.12
947 2013 5.300034 TCACATTGATGAGAATATGCCCAAC 59.700 40.000 0.00 0.00 0.00 3.77
948 2014 5.301045 CACATTGATGAGAATATGCCCAACT 59.699 40.000 0.00 0.00 0.00 3.16
949 2015 6.487668 CACATTGATGAGAATATGCCCAACTA 59.512 38.462 0.00 0.00 0.00 2.24
950 2016 6.488006 ACATTGATGAGAATATGCCCAACTAC 59.512 38.462 0.00 0.00 0.00 2.73
951 2017 5.628797 TGATGAGAATATGCCCAACTACA 57.371 39.130 0.00 0.00 0.00 2.74
966 2032 6.438763 CCCAACTACAAGAAATGTGAAAGAC 58.561 40.000 0.00 0.00 43.77 3.01
980 2046 6.808008 TGTGAAAGACATTTGAGAAGATCC 57.192 37.500 0.00 0.00 0.00 3.36
991 2057 2.026822 TGAGAAGATCCTCAACCAAGCC 60.027 50.000 0.00 0.00 39.96 4.35
992 2058 1.988107 AGAAGATCCTCAACCAAGCCA 59.012 47.619 0.00 0.00 0.00 4.75
993 2059 2.579860 AGAAGATCCTCAACCAAGCCAT 59.420 45.455 0.00 0.00 0.00 4.40
1002 2068 2.897207 CCAAGCCATGGGTGCATG 59.103 61.111 19.09 12.21 46.27 4.06
1012 2078 3.264104 CATGGGTGCATGCCTTTTAAAG 58.736 45.455 16.68 0.00 0.00 1.85
1024 2090 0.472161 TTTTAAAGGCCACCACCCCC 60.472 55.000 5.01 0.00 0.00 5.40
1039 2105 1.602237 CCCCGTGCACCTGATAACT 59.398 57.895 12.15 0.00 0.00 2.24
1042 2128 1.421410 CCGTGCACCTGATAACTCGC 61.421 60.000 12.15 0.00 0.00 5.03
1048 2134 1.944676 CCTGATAACTCGCGACGGC 60.945 63.158 3.71 0.00 0.00 5.68
1366 2452 0.241213 CTGCGACTTCCTCTTCGTCA 59.759 55.000 0.00 0.00 37.56 4.35
1368 2454 1.066114 GCGACTTCCTCTTCGTCACG 61.066 60.000 0.00 0.00 37.56 4.35
1507 2593 1.457346 CAAGAACTGGTCCTCCATGC 58.543 55.000 0.00 0.00 43.43 4.06
1541 2627 4.636435 CCACCCCAAGAACCGCGT 62.636 66.667 4.92 0.00 0.00 6.01
1542 2628 3.047877 CACCCCAAGAACCGCGTC 61.048 66.667 4.92 0.00 0.00 5.19
1543 2629 4.675029 ACCCCAAGAACCGCGTCG 62.675 66.667 4.92 0.00 0.00 5.12
1665 2751 4.308458 CTCGTGGGGCACAACCGA 62.308 66.667 2.36 2.36 40.62 4.69
1800 2886 2.476051 GACGCGTACGAGTCCGAA 59.524 61.111 33.39 0.00 43.93 4.30
1814 2900 3.147629 AGTCCGAAGAGAAAGAAGACGA 58.852 45.455 0.00 0.00 0.00 4.20
1824 2910 0.321996 AAGAAGACGAGGTGGAAGGC 59.678 55.000 0.00 0.00 0.00 4.35
1848 2934 1.485838 GAGTGCCATCATCGTCTGCG 61.486 60.000 0.00 0.00 39.92 5.18
1879 2965 1.580942 GCATGATGCACCACGTGTT 59.419 52.632 13.36 0.00 44.26 3.32
1886 2972 1.275657 GCACCACGTGTTCTGTTCG 59.724 57.895 15.65 0.00 35.75 3.95
1904 2990 6.316640 TCTGTTCGTCTTTGTTGTTTTCCATA 59.683 34.615 0.00 0.00 0.00 2.74
1906 2992 7.484975 TGTTCGTCTTTGTTGTTTTCCATATT 58.515 30.769 0.00 0.00 0.00 1.28
1910 2996 6.915300 CGTCTTTGTTGTTTTCCATATTGACA 59.085 34.615 0.00 0.00 0.00 3.58
1943 3031 2.169327 GCGTACGCCGTTGTCAAC 59.831 61.111 29.51 5.58 39.32 3.18
1960 3048 7.272948 CGTTGTCAACTTAGTTCCTACTATGAC 59.727 40.741 13.67 0.00 41.00 3.06
1968 3056 4.586884 AGTTCCTACTATGACTGTGACGA 58.413 43.478 0.00 0.00 31.21 4.20
1969 3057 4.395542 AGTTCCTACTATGACTGTGACGAC 59.604 45.833 0.00 0.00 31.21 4.34
1994 3082 8.499406 ACACTATCATGTAAAAATAAGGCCCTA 58.501 33.333 0.00 0.00 0.00 3.53
2126 3214 5.589192 ACTAAATATGCGCGACTAAAGACT 58.411 37.500 12.10 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 5.319453 TCAATCCACTTGATCTGCTCTTTT 58.681 37.500 0.00 0.00 38.97 2.27
148 149 6.552008 TCCTTTAAGGTCACTCCATTCATTT 58.448 36.000 11.13 0.00 36.53 2.32
149 150 6.012508 TCTCCTTTAAGGTCACTCCATTCATT 60.013 38.462 11.13 0.00 36.53 2.57
258 1254 7.489435 CACCAATAGTACTTGACTCATACACAG 59.511 40.741 0.00 0.00 39.81 3.66
324 1321 1.899814 AGTAAACCGAGACATGCCTGA 59.100 47.619 0.00 0.00 0.00 3.86
370 1367 1.527380 GGGCTTCCGTCACCAAACA 60.527 57.895 0.00 0.00 0.00 2.83
380 1377 3.317603 ACAAAATTTGATGGGCTTCCG 57.682 42.857 13.19 0.00 0.00 4.30
412 1418 7.045416 AGTAACAACAATTATCTCCGCACATA 58.955 34.615 0.00 0.00 0.00 2.29
520 1533 4.142425 GCCGGCTACAGTATATCCTAGAAC 60.142 50.000 22.15 0.00 0.00 3.01
576 1590 8.840321 CCTCTCAAGACTCAAAGTTTAATTTGA 58.160 33.333 5.40 5.40 44.72 2.69
685 1732 3.370209 CCTCAATTGATGCCTGTCTCTCA 60.370 47.826 8.96 0.00 0.00 3.27
693 1740 1.927487 TTGCACCTCAATTGATGCCT 58.073 45.000 24.31 0.75 37.26 4.75
696 1743 5.840243 TTCCTATTGCACCTCAATTGATG 57.160 39.130 8.96 8.96 42.48 3.07
745 1811 1.019673 TACTAGTAGAAGCCCGTGCG 58.980 55.000 3.59 0.00 44.33 5.34
746 1812 2.022934 AGTACTAGTAGAAGCCCGTGC 58.977 52.381 1.87 0.00 37.95 5.34
747 1813 4.450053 AGTAGTACTAGTAGAAGCCCGTG 58.550 47.826 8.55 0.00 0.00 4.94
748 1814 4.769345 AGTAGTACTAGTAGAAGCCCGT 57.231 45.455 8.55 0.00 0.00 5.28
749 1815 6.287525 ACTTAGTAGTACTAGTAGAAGCCCG 58.712 44.000 15.40 4.98 31.47 6.13
782 1848 9.084164 GCTTAGTACATCGACTGATTCTTTTTA 57.916 33.333 0.00 0.00 30.49 1.52
783 1849 7.602644 TGCTTAGTACATCGACTGATTCTTTTT 59.397 33.333 0.00 0.00 30.49 1.94
784 1850 7.097192 TGCTTAGTACATCGACTGATTCTTTT 58.903 34.615 0.00 0.00 30.49 2.27
785 1851 6.631016 TGCTTAGTACATCGACTGATTCTTT 58.369 36.000 0.00 0.00 30.49 2.52
786 1852 6.208988 TGCTTAGTACATCGACTGATTCTT 57.791 37.500 0.00 0.00 30.49 2.52
787 1853 5.836821 TGCTTAGTACATCGACTGATTCT 57.163 39.130 0.00 0.00 30.49 2.40
788 1854 6.019479 CCTTTGCTTAGTACATCGACTGATTC 60.019 42.308 0.00 0.00 30.49 2.52
789 1855 5.812642 CCTTTGCTTAGTACATCGACTGATT 59.187 40.000 0.00 0.00 30.49 2.57
790 1856 5.127194 TCCTTTGCTTAGTACATCGACTGAT 59.873 40.000 0.00 0.00 34.28 2.90
791 1857 4.461431 TCCTTTGCTTAGTACATCGACTGA 59.539 41.667 0.00 0.00 0.00 3.41
792 1858 4.744570 TCCTTTGCTTAGTACATCGACTG 58.255 43.478 0.00 0.00 0.00 3.51
793 1859 5.401531 TTCCTTTGCTTAGTACATCGACT 57.598 39.130 0.00 0.00 0.00 4.18
794 1860 5.638234 AGTTTCCTTTGCTTAGTACATCGAC 59.362 40.000 0.00 0.00 0.00 4.20
795 1861 5.790593 AGTTTCCTTTGCTTAGTACATCGA 58.209 37.500 0.00 0.00 0.00 3.59
796 1862 5.220228 CGAGTTTCCTTTGCTTAGTACATCG 60.220 44.000 0.00 0.00 0.00 3.84
797 1863 5.446073 GCGAGTTTCCTTTGCTTAGTACATC 60.446 44.000 0.00 0.00 0.00 3.06
798 1864 4.392138 GCGAGTTTCCTTTGCTTAGTACAT 59.608 41.667 0.00 0.00 0.00 2.29
799 1865 3.744426 GCGAGTTTCCTTTGCTTAGTACA 59.256 43.478 0.00 0.00 0.00 2.90
800 1866 3.744426 TGCGAGTTTCCTTTGCTTAGTAC 59.256 43.478 0.00 0.00 0.00 2.73
801 1867 3.997762 TGCGAGTTTCCTTTGCTTAGTA 58.002 40.909 0.00 0.00 0.00 1.82
802 1868 2.846193 TGCGAGTTTCCTTTGCTTAGT 58.154 42.857 0.00 0.00 0.00 2.24
803 1869 3.896648 TTGCGAGTTTCCTTTGCTTAG 57.103 42.857 0.00 0.00 0.00 2.18
804 1870 4.640789 TTTTGCGAGTTTCCTTTGCTTA 57.359 36.364 0.00 0.00 0.00 3.09
805 1871 3.518634 TTTTGCGAGTTTCCTTTGCTT 57.481 38.095 0.00 0.00 0.00 3.91
806 1872 3.733443 ATTTTGCGAGTTTCCTTTGCT 57.267 38.095 0.00 0.00 0.00 3.91
807 1873 3.604543 GCAATTTTGCGAGTTTCCTTTGC 60.605 43.478 0.00 0.00 45.11 3.68
808 1874 4.119334 GCAATTTTGCGAGTTTCCTTTG 57.881 40.909 0.00 0.00 45.11 2.77
821 1887 6.700960 TGGACTAACACATTCAAGCAATTTTG 59.299 34.615 0.00 0.00 0.00 2.44
822 1888 6.815089 TGGACTAACACATTCAAGCAATTTT 58.185 32.000 0.00 0.00 0.00 1.82
823 1889 6.403866 TGGACTAACACATTCAAGCAATTT 57.596 33.333 0.00 0.00 0.00 1.82
824 1890 5.565439 GCTGGACTAACACATTCAAGCAATT 60.565 40.000 0.00 0.00 0.00 2.32
825 1891 4.082571 GCTGGACTAACACATTCAAGCAAT 60.083 41.667 0.00 0.00 0.00 3.56
826 1892 3.253188 GCTGGACTAACACATTCAAGCAA 59.747 43.478 0.00 0.00 0.00 3.91
827 1893 2.813754 GCTGGACTAACACATTCAAGCA 59.186 45.455 0.00 0.00 0.00 3.91
828 1894 2.813754 TGCTGGACTAACACATTCAAGC 59.186 45.455 0.00 0.00 0.00 4.01
829 1895 4.067896 AGTGCTGGACTAACACATTCAAG 58.932 43.478 0.00 0.00 36.76 3.02
830 1896 4.085357 AGTGCTGGACTAACACATTCAA 57.915 40.909 0.00 0.00 36.76 2.69
831 1897 3.769739 AGTGCTGGACTAACACATTCA 57.230 42.857 0.00 0.00 36.76 2.57
832 1898 3.619038 GCTAGTGCTGGACTAACACATTC 59.381 47.826 10.31 0.00 36.69 2.67
833 1899 3.007940 TGCTAGTGCTGGACTAACACATT 59.992 43.478 10.31 0.00 36.69 2.71
834 1900 2.567169 TGCTAGTGCTGGACTAACACAT 59.433 45.455 10.31 0.00 36.69 3.21
835 1901 1.967779 TGCTAGTGCTGGACTAACACA 59.032 47.619 10.31 6.42 36.69 3.72
836 1902 2.737252 GTTGCTAGTGCTGGACTAACAC 59.263 50.000 11.27 4.67 36.69 3.32
837 1903 2.367241 TGTTGCTAGTGCTGGACTAACA 59.633 45.455 10.31 10.57 36.69 2.41
838 1904 2.737252 GTGTTGCTAGTGCTGGACTAAC 59.263 50.000 10.31 8.23 36.69 2.34
839 1905 2.289444 GGTGTTGCTAGTGCTGGACTAA 60.289 50.000 10.31 0.00 36.69 2.24
840 1906 1.275291 GGTGTTGCTAGTGCTGGACTA 59.725 52.381 8.78 8.78 40.48 2.59
841 1907 0.035458 GGTGTTGCTAGTGCTGGACT 59.965 55.000 7.10 7.10 40.48 3.85
842 1908 0.250295 TGGTGTTGCTAGTGCTGGAC 60.250 55.000 0.00 0.00 40.48 4.02
843 1909 0.035317 CTGGTGTTGCTAGTGCTGGA 59.965 55.000 0.00 0.00 40.48 3.86
844 1910 0.035317 TCTGGTGTTGCTAGTGCTGG 59.965 55.000 0.00 0.00 40.48 4.85
845 1911 1.736126 CATCTGGTGTTGCTAGTGCTG 59.264 52.381 0.00 0.00 40.48 4.41
846 1912 1.339438 CCATCTGGTGTTGCTAGTGCT 60.339 52.381 0.00 0.00 40.48 4.40
847 1913 1.089920 CCATCTGGTGTTGCTAGTGC 58.910 55.000 0.00 0.00 40.20 4.40
848 1914 1.089920 GCCATCTGGTGTTGCTAGTG 58.910 55.000 0.00 0.00 37.57 2.74
849 1915 0.035056 GGCCATCTGGTGTTGCTAGT 60.035 55.000 0.00 0.00 37.57 2.57
850 1916 0.035152 TGGCCATCTGGTGTTGCTAG 60.035 55.000 0.00 0.00 37.57 3.42
851 1917 0.035152 CTGGCCATCTGGTGTTGCTA 60.035 55.000 5.51 0.00 37.57 3.49
852 1918 1.303888 CTGGCCATCTGGTGTTGCT 60.304 57.895 5.51 0.00 37.57 3.91
853 1919 1.181098 AACTGGCCATCTGGTGTTGC 61.181 55.000 5.51 0.00 37.57 4.17
854 1920 1.331214 AAACTGGCCATCTGGTGTTG 58.669 50.000 5.51 0.00 37.57 3.33
855 1921 2.086610 AAAACTGGCCATCTGGTGTT 57.913 45.000 5.51 2.24 37.57 3.32
856 1922 2.969821 TAAAACTGGCCATCTGGTGT 57.030 45.000 5.51 0.00 37.57 4.16
857 1923 4.806640 AAATAAAACTGGCCATCTGGTG 57.193 40.909 5.51 0.00 37.57 4.17
858 1924 8.227507 AGATATAAATAAAACTGGCCATCTGGT 58.772 33.333 5.51 0.00 37.57 4.00
859 1925 8.517878 CAGATATAAATAAAACTGGCCATCTGG 58.482 37.037 5.51 0.00 34.62 3.86
860 1926 9.288576 TCAGATATAAATAAAACTGGCCATCTG 57.711 33.333 5.51 11.89 37.87 2.90
861 1927 9.866655 TTCAGATATAAATAAAACTGGCCATCT 57.133 29.630 5.51 0.00 0.00 2.90
864 1930 9.420118 ACATTCAGATATAAATAAAACTGGCCA 57.580 29.630 4.71 4.71 0.00 5.36
900 1966 8.872845 GTGAGAATTTGTTGACACTTTTCAAAT 58.127 29.630 0.00 0.00 37.24 2.32
901 1967 7.869937 TGTGAGAATTTGTTGACACTTTTCAAA 59.130 29.630 0.00 0.00 37.24 2.69
902 1968 7.374272 TGTGAGAATTTGTTGACACTTTTCAA 58.626 30.769 0.00 0.00 32.94 2.69
903 1969 6.918626 TGTGAGAATTTGTTGACACTTTTCA 58.081 32.000 0.00 0.00 0.00 2.69
904 1970 7.992180 ATGTGAGAATTTGTTGACACTTTTC 57.008 32.000 0.00 0.00 0.00 2.29
905 1971 8.034215 TCAATGTGAGAATTTGTTGACACTTTT 58.966 29.630 0.00 0.00 0.00 2.27
906 1972 7.546358 TCAATGTGAGAATTTGTTGACACTTT 58.454 30.769 0.00 0.00 0.00 2.66
907 1973 7.099266 TCAATGTGAGAATTTGTTGACACTT 57.901 32.000 0.00 0.00 0.00 3.16
908 1974 6.698008 TCAATGTGAGAATTTGTTGACACT 57.302 33.333 0.00 0.00 0.00 3.55
909 1975 7.140705 TCATCAATGTGAGAATTTGTTGACAC 58.859 34.615 0.00 0.00 29.00 3.67
910 1976 7.274603 TCATCAATGTGAGAATTTGTTGACA 57.725 32.000 0.00 0.00 29.00 3.58
911 1977 7.792383 CTCATCAATGTGAGAATTTGTTGAC 57.208 36.000 6.91 0.00 46.77 3.18
922 1988 5.067954 TGGGCATATTCTCATCAATGTGAG 58.932 41.667 6.53 6.53 45.51 3.51
923 1989 5.051409 TGGGCATATTCTCATCAATGTGA 57.949 39.130 0.00 0.00 28.77 3.58
924 1990 5.301045 AGTTGGGCATATTCTCATCAATGTG 59.699 40.000 0.00 0.00 0.00 3.21
925 1991 5.452255 AGTTGGGCATATTCTCATCAATGT 58.548 37.500 0.00 0.00 0.00 2.71
926 1992 6.487668 TGTAGTTGGGCATATTCTCATCAATG 59.512 38.462 0.00 0.00 0.00 2.82
927 1993 6.604171 TGTAGTTGGGCATATTCTCATCAAT 58.396 36.000 0.00 0.00 0.00 2.57
928 1994 6.000246 TGTAGTTGGGCATATTCTCATCAA 58.000 37.500 0.00 0.00 0.00 2.57
929 1995 5.628797 TGTAGTTGGGCATATTCTCATCA 57.371 39.130 0.00 0.00 0.00 3.07
930 1996 6.291377 TCTTGTAGTTGGGCATATTCTCATC 58.709 40.000 0.00 0.00 0.00 2.92
931 1997 6.252599 TCTTGTAGTTGGGCATATTCTCAT 57.747 37.500 0.00 0.00 0.00 2.90
932 1998 5.692115 TCTTGTAGTTGGGCATATTCTCA 57.308 39.130 0.00 0.00 0.00 3.27
933 1999 7.067494 ACATTTCTTGTAGTTGGGCATATTCTC 59.933 37.037 0.00 0.00 36.57 2.87
934 2000 6.891908 ACATTTCTTGTAGTTGGGCATATTCT 59.108 34.615 0.00 0.00 36.57 2.40
935 2001 6.974622 CACATTTCTTGTAGTTGGGCATATTC 59.025 38.462 0.00 0.00 36.57 1.75
936 2002 6.663093 TCACATTTCTTGTAGTTGGGCATATT 59.337 34.615 0.00 0.00 36.57 1.28
937 2003 6.186957 TCACATTTCTTGTAGTTGGGCATAT 58.813 36.000 0.00 0.00 36.57 1.78
938 2004 5.565509 TCACATTTCTTGTAGTTGGGCATA 58.434 37.500 0.00 0.00 36.57 3.14
939 2005 4.406456 TCACATTTCTTGTAGTTGGGCAT 58.594 39.130 0.00 0.00 36.57 4.40
940 2006 3.826524 TCACATTTCTTGTAGTTGGGCA 58.173 40.909 0.00 0.00 36.57 5.36
941 2007 4.846779 TTCACATTTCTTGTAGTTGGGC 57.153 40.909 0.00 0.00 36.57 5.36
942 2008 6.039270 TGTCTTTCACATTTCTTGTAGTTGGG 59.961 38.462 0.00 0.00 36.57 4.12
943 2009 7.026631 TGTCTTTCACATTTCTTGTAGTTGG 57.973 36.000 0.00 0.00 36.57 3.77
979 2045 1.077265 ACCCATGGCTTGGTTGAGG 59.923 57.895 17.23 5.09 44.83 3.86
980 2046 1.880819 GCACCCATGGCTTGGTTGAG 61.881 60.000 19.17 6.51 40.25 3.02
992 2058 2.236893 CCTTTAAAAGGCATGCACCCAT 59.763 45.455 21.36 3.74 42.78 4.00
993 2059 1.622811 CCTTTAAAAGGCATGCACCCA 59.377 47.619 21.36 0.00 42.78 4.51
1024 2090 1.742900 CGCGAGTTATCAGGTGCACG 61.743 60.000 11.45 0.00 0.00 5.34
1062 2148 3.650950 TGGGAAGGTGCTGGAGGC 61.651 66.667 0.00 0.00 42.22 4.70
1063 2149 2.352805 GTGGGAAGGTGCTGGAGG 59.647 66.667 0.00 0.00 0.00 4.30
1064 2150 2.190488 GAGGTGGGAAGGTGCTGGAG 62.190 65.000 0.00 0.00 0.00 3.86
1107 2193 1.429148 CCACGTAGAAGCGGAATGGC 61.429 60.000 0.00 0.00 35.98 4.40
1263 2349 1.115930 ACTCTGTGCTCTCCGTTGGT 61.116 55.000 0.00 0.00 0.00 3.67
1266 2352 1.271102 GAGAACTCTGTGCTCTCCGTT 59.729 52.381 0.00 0.00 35.44 4.44
1329 2415 4.373116 TCCACGAAGAGCGCCCAC 62.373 66.667 2.29 0.00 46.04 4.61
1478 2564 1.289109 CCAGTTCTTGCGGTGGTACG 61.289 60.000 0.00 0.00 0.00 3.67
1484 2570 1.371558 GAGGACCAGTTCTTGCGGT 59.628 57.895 0.00 0.00 35.12 5.68
1507 2593 2.684843 GGCCGCAGTTGAAGAGCAG 61.685 63.158 0.00 0.00 0.00 4.24
1593 2679 4.116328 TCGTCGAGCCAGGCGAAG 62.116 66.667 5.55 0.51 45.75 3.79
1734 2820 1.448013 GCAGTCCTTGTACCGCTCC 60.448 63.158 0.00 0.00 0.00 4.70
1800 2886 2.877866 TCCACCTCGTCTTCTTTCTCT 58.122 47.619 0.00 0.00 0.00 3.10
1814 2900 1.462238 ACTCCTGTGCCTTCCACCT 60.462 57.895 0.00 0.00 44.01 4.00
1824 2910 0.107993 ACGATGATGGCACTCCTGTG 60.108 55.000 0.00 0.00 46.37 3.66
1837 2923 2.341911 TGCAACCGCAGACGATGA 59.658 55.556 0.00 0.00 45.36 2.92
1848 2934 1.308069 ATCATGCGTCCACTGCAACC 61.308 55.000 0.00 0.00 46.87 3.77
1879 2965 4.456222 TGGAAAACAACAAAGACGAACAGA 59.544 37.500 0.00 0.00 0.00 3.41
1886 2972 8.702438 CATGTCAATATGGAAAACAACAAAGAC 58.298 33.333 0.00 0.00 0.00 3.01
1910 2996 1.596203 CGCAGGGACATGATCGCAT 60.596 57.895 0.00 0.00 42.75 4.73
1943 3031 6.315642 TCGTCACAGTCATAGTAGGAACTAAG 59.684 42.308 0.00 0.00 45.48 2.18
1960 3048 6.944557 TTTTACATGATAGTGTCGTCACAG 57.055 37.500 15.05 0.84 46.01 3.66
1968 3056 7.354312 AGGGCCTTATTTTTACATGATAGTGT 58.646 34.615 0.00 0.00 36.13 3.55
1969 3057 7.823745 AGGGCCTTATTTTTACATGATAGTG 57.176 36.000 0.00 0.00 0.00 2.74
2041 3129 5.208890 GGGACTAAAGGCCCATTTTCTATT 58.791 41.667 16.61 0.00 44.07 1.73
2042 3130 4.688874 CGGGACTAAAGGCCCATTTTCTAT 60.689 45.833 21.10 0.00 44.94 1.98
2102 3190 6.040878 AGTCTTTAGTCGCGCATATTTAGTT 58.959 36.000 8.75 0.00 0.00 2.24
2508 3600 7.721842 TCCTAATTGTGTATGGAAACTTGTTCA 59.278 33.333 0.00 0.00 0.00 3.18



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

AutoCloner maintained by Alex Coulton.