Multiple sequence alignment - TraesCS1D01G250800

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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 TraesCS1D01G250800 chr1D 100.000 2163 0 0 1779 3941 343174890 343177052 0.000000e+00 3995.0
1 TraesCS1D01G250800 chr1D 100.000 1227 0 0 1 1227 343173112 343174338 0.000000e+00 2266.0
2 TraesCS1D01G250800 chr1D 99.574 235 1 0 1779 2013 343174104 343174338 2.810000e-116 429.0
3 TraesCS1D01G250800 chr1D 99.574 235 1 0 993 1227 343174890 343175124 2.810000e-116 429.0
4 TraesCS1D01G250800 chr1A 96.737 2176 44 10 1779 3941 442797445 442799606 0.000000e+00 3600.0
5 TraesCS1D01G250800 chr1A 97.909 287 4 2 932 1216 442797382 442797668 2.740000e-136 496.0
6 TraesCS1D01G250800 chr1A 96.667 60 1 1 860 919 442797334 442797392 9.010000e-17 99.0
7 TraesCS1D01G250800 chr1B 97.875 800 17 0 1779 2578 460269812 460270611 0.000000e+00 1384.0
8 TraesCS1D01G250800 chr1B 88.272 810 79 10 1 796 95776850 95777657 0.000000e+00 955.0
9 TraesCS1D01G250800 chr1B 93.844 601 27 6 2570 3169 460271920 460272511 0.000000e+00 896.0
10 TraesCS1D01G250800 chr1B 97.279 294 8 0 934 1227 460269753 460270046 2.110000e-137 499.0
11 TraesCS1D01G250800 chr1B 85.870 92 6 1 3292 3383 26851514 26851598 1.510000e-14 91.6
12 TraesCS1D01G250800 chr4A 89.506 810 69 13 1 796 73256259 73255452 0.000000e+00 1011.0
13 TraesCS1D01G250800 chr2B 89.493 809 71 11 1 796 460858134 460857327 0.000000e+00 1011.0
14 TraesCS1D01G250800 chr7A 89.259 810 72 13 1 796 140099869 140100677 0.000000e+00 1000.0
15 TraesCS1D01G250800 chr7A 83.871 93 8 1 3291 3383 31103508 31103423 9.080000e-12 82.4
16 TraesCS1D01G250800 chr5D 89.383 810 64 11 1 796 230546999 230547800 0.000000e+00 1000.0
17 TraesCS1D01G250800 chr5D 84.198 810 113 9 1 796 272333792 272332984 0.000000e+00 773.0
18 TraesCS1D01G250800 chr7D 89.586 797 66 13 13 796 242768737 242769529 0.000000e+00 996.0
19 TraesCS1D01G250800 chr7D 88.462 806 80 11 1 796 149563001 149563803 0.000000e+00 961.0
20 TraesCS1D01G250800 chr7D 86.022 93 6 1 3291 3383 16713332 16713247 4.190000e-15 93.5
21 TraesCS1D01G250800 chr6D 88.519 810 78 12 1 796 307583915 307583107 0.000000e+00 966.0
22 TraesCS1D01G250800 chr6D 89.057 265 19 5 541 796 5271381 5271644 1.770000e-83 320.0
23 TraesCS1D01G250800 chr4D 88.533 811 75 15 1 796 492508116 492508923 0.000000e+00 966.0
24 TraesCS1D01G250800 chr6B 81.058 813 131 14 1 796 207191351 207190545 9.300000e-176 627.0
25 TraesCS1D01G250800 chr6B 88.034 234 19 1 572 796 485776001 485775768 6.490000e-68 268.0
26 TraesCS1D01G250800 chr3D 84.800 500 60 9 310 796 229654711 229654215 4.580000e-134 488.0
27 TraesCS1D01G250800 chr2A 81.453 523 74 16 291 796 503650808 503651324 1.320000e-109 407.0
28 TraesCS1D01G250800 chr2A 86.000 100 7 2 3284 3383 685967668 685967760 2.510000e-17 100.0
29 TraesCS1D01G250800 chr7B 89.407 236 16 4 570 796 36000313 36000078 4.980000e-74 289.0
30 TraesCS1D01G250800 chr5B 85.654 237 26 5 568 796 333554935 333555171 3.930000e-60 243.0
31 TraesCS1D01G250800 chr5B 88.043 92 4 1 3292 3383 629934766 629934850 6.970000e-18 102.0
32 TraesCS1D01G250800 chr2D 89.247 93 3 1 3291 3383 615394354 615394269 4.160000e-20 110.0
33 TraesCS1D01G250800 chr2D 88.172 93 3 2 3292 3383 95418728 95418643 1.940000e-18 104.0
34 TraesCS1D01G250800 chr2D 84.848 99 5 2 3293 3388 49386153 49386244 1.510000e-14 91.6


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 TraesCS1D01G250800 chr1D 343173112 343177052 3940 False 1779.750000 3995 99.787000 1 3941 4 chr1D.!!$F1 3940
1 TraesCS1D01G250800 chr1A 442797334 442799606 2272 False 1398.333333 3600 97.104333 860 3941 3 chr1A.!!$F1 3081
2 TraesCS1D01G250800 chr1B 95776850 95777657 807 False 955.000000 955 88.272000 1 796 1 chr1B.!!$F2 795
3 TraesCS1D01G250800 chr1B 460269753 460272511 2758 False 926.333333 1384 96.332667 934 3169 3 chr1B.!!$F3 2235
4 TraesCS1D01G250800 chr4A 73255452 73256259 807 True 1011.000000 1011 89.506000 1 796 1 chr4A.!!$R1 795
5 TraesCS1D01G250800 chr2B 460857327 460858134 807 True 1011.000000 1011 89.493000 1 796 1 chr2B.!!$R1 795
6 TraesCS1D01G250800 chr7A 140099869 140100677 808 False 1000.000000 1000 89.259000 1 796 1 chr7A.!!$F1 795
7 TraesCS1D01G250800 chr5D 230546999 230547800 801 False 1000.000000 1000 89.383000 1 796 1 chr5D.!!$F1 795
8 TraesCS1D01G250800 chr5D 272332984 272333792 808 True 773.000000 773 84.198000 1 796 1 chr5D.!!$R1 795
9 TraesCS1D01G250800 chr7D 242768737 242769529 792 False 996.000000 996 89.586000 13 796 1 chr7D.!!$F2 783
10 TraesCS1D01G250800 chr7D 149563001 149563803 802 False 961.000000 961 88.462000 1 796 1 chr7D.!!$F1 795
11 TraesCS1D01G250800 chr6D 307583107 307583915 808 True 966.000000 966 88.519000 1 796 1 chr6D.!!$R1 795
12 TraesCS1D01G250800 chr4D 492508116 492508923 807 False 966.000000 966 88.533000 1 796 1 chr4D.!!$F1 795
13 TraesCS1D01G250800 chr6B 207190545 207191351 806 True 627.000000 627 81.058000 1 796 1 chr6B.!!$R1 795
14 TraesCS1D01G250800 chr2A 503650808 503651324 516 False 407.000000 407 81.453000 291 796 1 chr2A.!!$F1 505

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
211 216 0.038744 ACCTCTCAACAAGGGCATGG 59.961 55.0 0.0 0.0 38.29 3.66 F
848 871 0.106868 GGGGGTATGAGGGGTTTTCG 60.107 60.0 0.0 0.0 0.00 3.46 F
850 873 0.255033 GGGTATGAGGGGTTTTCGCT 59.745 55.0 0.0 0.0 41.69 4.93 F
857 880 0.771755 AGGGGTTTTCGCTCTTCCTT 59.228 50.0 0.0 0.0 32.84 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 1932 1.073199 GAGTGGGGTGGTGGAAGTG 59.927 63.158 0.0 0.0 0.00 3.16 R
2808 4155 0.397254 ACGAGTAGTGCCCATAGCCT 60.397 55.000 0.0 0.0 42.71 4.58 R
2927 4274 2.965783 TCTGTCAGTCAGAGCCGC 59.034 61.111 0.0 0.0 46.77 6.53 R
3178 4526 2.949644 ACACCCAAGCTTCAGTAAACAC 59.050 45.455 0.0 0.0 0.00 3.32 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
71 72 5.572896 GGAAAACTTTGTCAACTGTTGTCTG 59.427 40.000 19.12 10.92 30.01 3.51
72 73 5.705609 AAACTTTGTCAACTGTTGTCTGT 57.294 34.783 19.12 11.44 0.00 3.41
118 121 0.613260 AGCGATTGTAGCACCCAGAA 59.387 50.000 0.00 0.00 37.01 3.02
211 216 0.038744 ACCTCTCAACAAGGGCATGG 59.961 55.000 0.00 0.00 38.29 3.66
252 258 6.647229 TCAGCTCTTGAAACATCTCATATGT 58.353 36.000 1.90 0.00 31.34 2.29
386 394 2.187946 CGCTAGAGGGGTTGGCAG 59.812 66.667 0.00 0.00 0.00 4.85
389 397 1.268283 GCTAGAGGGGTTGGCAGACT 61.268 60.000 0.00 0.00 0.00 3.24
406 414 0.250467 ACTGAGCGGTGCATCAAGTT 60.250 50.000 0.00 0.00 0.00 2.66
528 541 9.162764 GAATGTATTAAAACAGGAAGCTACAGA 57.837 33.333 0.00 0.00 31.70 3.41
707 730 1.281867 TGAGATGGGGTGGTCATCAAC 59.718 52.381 6.80 2.05 42.38 3.18
723 746 6.160576 TCATCAACGATGAACATCTCCATA 57.839 37.500 12.05 0.00 44.70 2.74
751 774 8.272173 TGATCATATCTACTATATGACCCGTGA 58.728 37.037 9.29 0.00 41.94 4.35
781 804 1.752833 GTCCTCCGTGTTCCAAGGT 59.247 57.895 0.00 0.00 34.70 3.50
802 825 2.561733 ATGTCTGTACATGTCGACCG 57.438 50.000 14.12 6.83 44.79 4.79
803 826 1.525941 TGTCTGTACATGTCGACCGA 58.474 50.000 14.12 0.00 0.00 4.69
804 827 1.881324 TGTCTGTACATGTCGACCGAA 59.119 47.619 14.12 0.00 0.00 4.30
805 828 2.095415 TGTCTGTACATGTCGACCGAAG 60.095 50.000 14.12 2.59 0.00 3.79
806 829 1.135489 TCTGTACATGTCGACCGAAGC 60.135 52.381 14.12 1.36 0.00 3.86
807 830 0.108992 TGTACATGTCGACCGAAGCC 60.109 55.000 14.12 0.00 0.00 4.35
808 831 0.172803 GTACATGTCGACCGAAGCCT 59.827 55.000 14.12 0.00 0.00 4.58
809 832 1.402968 GTACATGTCGACCGAAGCCTA 59.597 52.381 14.12 0.00 0.00 3.93
810 833 0.456221 ACATGTCGACCGAAGCCTAG 59.544 55.000 14.12 0.00 0.00 3.02
811 834 0.872021 CATGTCGACCGAAGCCTAGC 60.872 60.000 14.12 0.00 0.00 3.42
812 835 1.320344 ATGTCGACCGAAGCCTAGCA 61.320 55.000 14.12 0.00 0.00 3.49
813 836 1.516603 GTCGACCGAAGCCTAGCAC 60.517 63.158 3.51 0.00 0.00 4.40
814 837 2.202756 CGACCGAAGCCTAGCACC 60.203 66.667 0.00 0.00 0.00 5.01
815 838 2.187163 GACCGAAGCCTAGCACCC 59.813 66.667 0.00 0.00 0.00 4.61
816 839 3.387225 GACCGAAGCCTAGCACCCC 62.387 68.421 0.00 0.00 0.00 4.95
817 840 4.176752 CCGAAGCCTAGCACCCCC 62.177 72.222 0.00 0.00 0.00 5.40
837 860 2.851195 CCTTTCGAATGAGGGGGTATG 58.149 52.381 12.31 0.00 0.00 2.39
838 861 2.438021 CCTTTCGAATGAGGGGGTATGA 59.562 50.000 12.31 0.00 0.00 2.15
839 862 3.495100 CCTTTCGAATGAGGGGGTATGAG 60.495 52.174 12.31 0.00 0.00 2.90
840 863 1.717032 TCGAATGAGGGGGTATGAGG 58.283 55.000 0.00 0.00 0.00 3.86
841 864 0.687354 CGAATGAGGGGGTATGAGGG 59.313 60.000 0.00 0.00 0.00 4.30
842 865 1.068121 GAATGAGGGGGTATGAGGGG 58.932 60.000 0.00 0.00 0.00 4.79
843 866 0.350541 AATGAGGGGGTATGAGGGGT 59.649 55.000 0.00 0.00 0.00 4.95
844 867 0.350541 ATGAGGGGGTATGAGGGGTT 59.649 55.000 0.00 0.00 0.00 4.11
845 868 0.122435 TGAGGGGGTATGAGGGGTTT 59.878 55.000 0.00 0.00 0.00 3.27
846 869 1.305886 GAGGGGGTATGAGGGGTTTT 58.694 55.000 0.00 0.00 0.00 2.43
847 870 1.214673 GAGGGGGTATGAGGGGTTTTC 59.785 57.143 0.00 0.00 0.00 2.29
848 871 0.106868 GGGGGTATGAGGGGTTTTCG 60.107 60.000 0.00 0.00 0.00 3.46
849 872 0.750546 GGGGTATGAGGGGTTTTCGC 60.751 60.000 0.00 0.00 0.00 4.70
850 873 0.255033 GGGTATGAGGGGTTTTCGCT 59.745 55.000 0.00 0.00 41.69 4.93
856 879 2.464582 AGGGGTTTTCGCTCTTCCT 58.535 52.632 0.00 0.00 32.84 3.36
857 880 0.771755 AGGGGTTTTCGCTCTTCCTT 59.228 50.000 0.00 0.00 32.84 3.36
858 881 1.145119 AGGGGTTTTCGCTCTTCCTTT 59.855 47.619 0.00 0.00 32.84 3.11
859 882 1.961394 GGGGTTTTCGCTCTTCCTTTT 59.039 47.619 0.00 0.00 0.00 2.27
860 883 3.151554 GGGGTTTTCGCTCTTCCTTTTA 58.848 45.455 0.00 0.00 0.00 1.52
861 884 3.057736 GGGGTTTTCGCTCTTCCTTTTAC 60.058 47.826 0.00 0.00 0.00 2.01
895 918 7.747155 TTGAAGGGTAACATCGACATTTAAA 57.253 32.000 0.00 0.00 39.74 1.52
916 939 6.827586 AAAGTCCAACTCTACAAACAAACA 57.172 33.333 0.00 0.00 0.00 2.83
917 940 6.827586 AAGTCCAACTCTACAAACAAACAA 57.172 33.333 0.00 0.00 0.00 2.83
918 941 6.827586 AGTCCAACTCTACAAACAAACAAA 57.172 33.333 0.00 0.00 0.00 2.83
919 942 7.404671 AGTCCAACTCTACAAACAAACAAAT 57.595 32.000 0.00 0.00 0.00 2.32
920 943 8.514330 AGTCCAACTCTACAAACAAACAAATA 57.486 30.769 0.00 0.00 0.00 1.40
921 944 8.403236 AGTCCAACTCTACAAACAAACAAATAC 58.597 33.333 0.00 0.00 0.00 1.89
922 945 7.646526 GTCCAACTCTACAAACAAACAAATACC 59.353 37.037 0.00 0.00 0.00 2.73
923 946 6.921307 CCAACTCTACAAACAAACAAATACCC 59.079 38.462 0.00 0.00 0.00 3.69
924 947 7.416890 CCAACTCTACAAACAAACAAATACCCA 60.417 37.037 0.00 0.00 0.00 4.51
925 948 7.833285 ACTCTACAAACAAACAAATACCCAT 57.167 32.000 0.00 0.00 0.00 4.00
926 949 8.245195 ACTCTACAAACAAACAAATACCCATT 57.755 30.769 0.00 0.00 0.00 3.16
927 950 8.357402 ACTCTACAAACAAACAAATACCCATTC 58.643 33.333 0.00 0.00 0.00 2.67
928 951 7.662897 TCTACAAACAAACAAATACCCATTCC 58.337 34.615 0.00 0.00 0.00 3.01
929 952 5.616270 ACAAACAAACAAATACCCATTCCC 58.384 37.500 0.00 0.00 0.00 3.97
930 953 5.368230 ACAAACAAACAAATACCCATTCCCT 59.632 36.000 0.00 0.00 0.00 4.20
931 954 6.555360 ACAAACAAACAAATACCCATTCCCTA 59.445 34.615 0.00 0.00 0.00 3.53
932 955 7.071321 ACAAACAAACAAATACCCATTCCCTAA 59.929 33.333 0.00 0.00 0.00 2.69
1128 1151 1.671901 CTCCTCTCCTCGGCCACTTC 61.672 65.000 2.24 0.00 0.00 3.01
1818 1841 2.772189 GCGATGACGGCGATATGC 59.228 61.111 16.62 7.04 45.38 3.14
1880 1903 4.214327 CCGCCTCTTCTCCCGCTC 62.214 72.222 0.00 0.00 0.00 5.03
1881 1904 4.214327 CGCCTCTTCTCCCGCTCC 62.214 72.222 0.00 0.00 0.00 4.70
1882 1905 3.855853 GCCTCTTCTCCCGCTCCC 61.856 72.222 0.00 0.00 0.00 4.30
1883 1906 3.157949 CCTCTTCTCCCGCTCCCC 61.158 72.222 0.00 0.00 0.00 4.81
1884 1907 3.157949 CTCTTCTCCCGCTCCCCC 61.158 72.222 0.00 0.00 0.00 5.40
1905 1928 4.219999 GCCTGCGCTCCTCTCCTC 62.220 72.222 9.73 0.00 0.00 3.71
1906 1929 3.898509 CCTGCGCTCCTCTCCTCG 61.899 72.222 9.73 0.00 0.00 4.63
1907 1930 3.898509 CTGCGCTCCTCTCCTCGG 61.899 72.222 9.73 0.00 0.00 4.63
1911 1934 3.844090 GCTCCTCTCCTCGGCCAC 61.844 72.222 2.24 0.00 0.00 5.01
1912 1935 2.043450 CTCCTCTCCTCGGCCACT 60.043 66.667 2.24 0.00 0.00 4.00
1913 1936 1.684049 CTCCTCTCCTCGGCCACTT 60.684 63.158 2.24 0.00 0.00 3.16
1914 1937 1.671901 CTCCTCTCCTCGGCCACTTC 61.672 65.000 2.24 0.00 0.00 3.01
1915 1938 2.726351 CCTCTCCTCGGCCACTTCC 61.726 68.421 2.24 0.00 0.00 3.46
1916 1939 1.984570 CTCTCCTCGGCCACTTCCA 60.985 63.158 2.24 0.00 0.00 3.53
1917 1940 2.232298 CTCTCCTCGGCCACTTCCAC 62.232 65.000 2.24 0.00 0.00 4.02
1918 1941 3.316573 CTCCTCGGCCACTTCCACC 62.317 68.421 2.24 0.00 0.00 4.61
1919 1942 3.636231 CCTCGGCCACTTCCACCA 61.636 66.667 2.24 0.00 0.00 4.17
1920 1943 2.358737 CTCGGCCACTTCCACCAC 60.359 66.667 2.24 0.00 0.00 4.16
1921 1944 3.901797 CTCGGCCACTTCCACCACC 62.902 68.421 2.24 0.00 0.00 4.61
1923 1946 4.678743 GGCCACTTCCACCACCCC 62.679 72.222 0.00 0.00 0.00 4.95
1924 1947 3.897122 GCCACTTCCACCACCCCA 61.897 66.667 0.00 0.00 0.00 4.96
1925 1948 2.115266 CCACTTCCACCACCCCAC 59.885 66.667 0.00 0.00 0.00 4.61
1926 1949 2.460853 CCACTTCCACCACCCCACT 61.461 63.158 0.00 0.00 0.00 4.00
1927 1950 1.073199 CACTTCCACCACCCCACTC 59.927 63.158 0.00 0.00 0.00 3.51
1928 1951 2.154074 ACTTCCACCACCCCACTCC 61.154 63.158 0.00 0.00 0.00 3.85
1929 1952 3.246112 TTCCACCACCCCACTCCG 61.246 66.667 0.00 0.00 0.00 4.63
1930 1953 3.777818 TTCCACCACCCCACTCCGA 62.778 63.158 0.00 0.00 0.00 4.55
1931 1954 4.016706 CCACCACCCCACTCCGAC 62.017 72.222 0.00 0.00 0.00 4.79
1932 1955 4.373116 CACCACCCCACTCCGACG 62.373 72.222 0.00 0.00 0.00 5.12
1953 1976 3.904617 CCCCGTCCCAAAACCCCA 61.905 66.667 0.00 0.00 0.00 4.96
1954 1977 2.282887 CCCGTCCCAAAACCCCAG 60.283 66.667 0.00 0.00 0.00 4.45
1955 1978 2.989253 CCGTCCCAAAACCCCAGC 60.989 66.667 0.00 0.00 0.00 4.85
1956 1979 2.115266 CGTCCCAAAACCCCAGCT 59.885 61.111 0.00 0.00 0.00 4.24
1957 1980 1.971695 CGTCCCAAAACCCCAGCTC 60.972 63.158 0.00 0.00 0.00 4.09
1958 1981 1.606601 GTCCCAAAACCCCAGCTCC 60.607 63.158 0.00 0.00 0.00 4.70
1959 1982 2.676471 CCCAAAACCCCAGCTCCG 60.676 66.667 0.00 0.00 0.00 4.63
1960 1983 2.115266 CCAAAACCCCAGCTCCGT 59.885 61.111 0.00 0.00 0.00 4.69
1961 1984 1.530655 CCAAAACCCCAGCTCCGTT 60.531 57.895 0.00 0.00 0.00 4.44
1962 1985 1.524008 CCAAAACCCCAGCTCCGTTC 61.524 60.000 0.00 0.00 0.00 3.95
1963 1986 1.228459 AAAACCCCAGCTCCGTTCC 60.228 57.895 0.00 0.00 0.00 3.62
1964 1987 2.708593 AAAACCCCAGCTCCGTTCCC 62.709 60.000 0.00 0.00 0.00 3.97
2379 2402 1.444553 GGAGTGTCTGCTTCGGTCG 60.445 63.158 0.00 0.00 0.00 4.79
2603 3943 1.391485 CTGCTTCGGTTCGATGTCAAG 59.609 52.381 0.00 0.00 35.23 3.02
2864 4211 4.521062 GCTCGAGCGCCTGGTGAT 62.521 66.667 23.61 3.96 0.00 3.06
2878 4225 4.492160 TGATGGACGACGGCGAGC 62.492 66.667 22.49 9.09 41.64 5.03
3054 4402 1.698506 TGTTGCCTTGGGTACTTTGG 58.301 50.000 0.00 0.00 0.00 3.28
3178 4526 3.485013 CGTGTTCTCTGATGATCATGTCG 59.515 47.826 14.30 1.00 0.00 4.35
3205 4553 2.037772 ACTGAAGCTTGGGTGTCTACTG 59.962 50.000 2.10 0.00 0.00 2.74
3244 4592 9.031360 GTTCTGTAGATAGCATATGTTTTCGAA 57.969 33.333 4.29 0.00 0.00 3.71
3285 4633 9.117183 GGAGAAATATAGCATGCATCATTGATA 57.883 33.333 21.98 0.43 0.00 2.15
3296 4644 9.447040 GCATGCATCATTGATATACAATATCAC 57.553 33.333 14.21 0.00 46.01 3.06
3337 4685 1.676014 CGCTGGGGGAGTTCAGTTTAG 60.676 57.143 0.00 0.00 33.81 1.85
3338 4686 1.628846 GCTGGGGGAGTTCAGTTTAGA 59.371 52.381 0.00 0.00 33.81 2.10
3339 4687 2.355209 GCTGGGGGAGTTCAGTTTAGAG 60.355 54.545 0.00 0.00 33.81 2.43
3340 4688 2.907042 CTGGGGGAGTTCAGTTTAGAGT 59.093 50.000 0.00 0.00 0.00 3.24
3341 4689 3.323775 TGGGGGAGTTCAGTTTAGAGTT 58.676 45.455 0.00 0.00 0.00 3.01
3342 4690 3.720002 TGGGGGAGTTCAGTTTAGAGTTT 59.280 43.478 0.00 0.00 0.00 2.66
3343 4691 4.909088 TGGGGGAGTTCAGTTTAGAGTTTA 59.091 41.667 0.00 0.00 0.00 2.01
3373 4721 6.018507 CCCCCAACGACTTATATTTAAGAACG 60.019 42.308 9.58 14.29 40.56 3.95
3603 4951 3.374988 TCATCGAGGTTGATCAACAATGC 59.625 43.478 33.42 19.45 42.85 3.56
3738 5086 5.831103 ACCATCCATGTATTTTCCAGAAGT 58.169 37.500 0.00 0.00 0.00 3.01
3907 5255 5.678132 TGTGTTGTCTGATCAAGTGATTG 57.322 39.130 0.00 0.00 34.37 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 131 7.042389 GGAGAATAACTTAGTTAGTGAGCATGC 60.042 40.741 10.51 10.51 37.12 4.06
143 146 5.435291 CTGCAAGATGGAGGAGAATAACTT 58.565 41.667 0.00 0.00 34.07 2.66
272 278 0.897621 CTGAAATCAGGGCCCCAAAC 59.102 55.000 21.43 6.24 40.20 2.93
386 394 0.671781 ACTTGATGCACCGCTCAGTC 60.672 55.000 0.00 0.00 0.00 3.51
389 397 0.250252 TGAACTTGATGCACCGCTCA 60.250 50.000 0.00 0.00 0.00 4.26
406 414 1.003464 TGCTGCACAGAAGGCTTATGA 59.997 47.619 27.10 5.27 0.00 2.15
618 632 7.918076 ACTTGAGGGATGTTGATTTAAGTAGA 58.082 34.615 0.00 0.00 0.00 2.59
620 634 7.942341 ACAACTTGAGGGATGTTGATTTAAGTA 59.058 33.333 11.30 0.00 40.55 2.24
707 730 7.845066 ATGATCAATATGGAGATGTTCATCG 57.155 36.000 0.00 0.00 31.28 3.84
723 746 9.647918 ACGGGTCATATAGTAGATATGATCAAT 57.352 33.333 16.00 0.00 41.54 2.57
796 819 2.707849 GGTGCTAGGCTTCGGTCGA 61.708 63.158 0.00 0.00 0.00 4.20
797 820 2.202756 GGTGCTAGGCTTCGGTCG 60.203 66.667 0.00 0.00 0.00 4.79
798 821 2.187163 GGGTGCTAGGCTTCGGTC 59.813 66.667 0.00 0.00 0.00 4.79
799 822 3.400054 GGGGTGCTAGGCTTCGGT 61.400 66.667 0.00 0.00 0.00 4.69
800 823 4.176752 GGGGGTGCTAGGCTTCGG 62.177 72.222 0.00 0.00 0.00 4.30
817 840 2.438021 TCATACCCCCTCATTCGAAAGG 59.562 50.000 0.00 5.31 0.00 3.11
818 841 3.495100 CCTCATACCCCCTCATTCGAAAG 60.495 52.174 0.00 0.00 0.00 2.62
819 842 2.438021 CCTCATACCCCCTCATTCGAAA 59.562 50.000 0.00 0.00 0.00 3.46
820 843 2.047061 CCTCATACCCCCTCATTCGAA 58.953 52.381 0.00 0.00 0.00 3.71
821 844 1.717032 CCTCATACCCCCTCATTCGA 58.283 55.000 0.00 0.00 0.00 3.71
822 845 0.687354 CCCTCATACCCCCTCATTCG 59.313 60.000 0.00 0.00 0.00 3.34
823 846 1.068121 CCCCTCATACCCCCTCATTC 58.932 60.000 0.00 0.00 0.00 2.67
824 847 0.350541 ACCCCTCATACCCCCTCATT 59.649 55.000 0.00 0.00 0.00 2.57
825 848 0.350541 AACCCCTCATACCCCCTCAT 59.649 55.000 0.00 0.00 0.00 2.90
826 849 0.122435 AAACCCCTCATACCCCCTCA 59.878 55.000 0.00 0.00 0.00 3.86
827 850 1.214673 GAAAACCCCTCATACCCCCTC 59.785 57.143 0.00 0.00 0.00 4.30
828 851 1.305886 GAAAACCCCTCATACCCCCT 58.694 55.000 0.00 0.00 0.00 4.79
829 852 0.106868 CGAAAACCCCTCATACCCCC 60.107 60.000 0.00 0.00 0.00 5.40
830 853 0.750546 GCGAAAACCCCTCATACCCC 60.751 60.000 0.00 0.00 0.00 4.95
831 854 0.255033 AGCGAAAACCCCTCATACCC 59.745 55.000 0.00 0.00 0.00 3.69
832 855 1.209747 AGAGCGAAAACCCCTCATACC 59.790 52.381 0.00 0.00 0.00 2.73
833 856 2.693267 AGAGCGAAAACCCCTCATAC 57.307 50.000 0.00 0.00 0.00 2.39
834 857 2.093128 GGAAGAGCGAAAACCCCTCATA 60.093 50.000 0.00 0.00 0.00 2.15
835 858 1.340114 GGAAGAGCGAAAACCCCTCAT 60.340 52.381 0.00 0.00 0.00 2.90
836 859 0.036306 GGAAGAGCGAAAACCCCTCA 59.964 55.000 0.00 0.00 0.00 3.86
837 860 0.325272 AGGAAGAGCGAAAACCCCTC 59.675 55.000 0.00 0.00 0.00 4.30
838 861 0.771755 AAGGAAGAGCGAAAACCCCT 59.228 50.000 0.00 0.00 0.00 4.79
839 862 1.617322 AAAGGAAGAGCGAAAACCCC 58.383 50.000 0.00 0.00 0.00 4.95
840 863 3.819337 AGTAAAAGGAAGAGCGAAAACCC 59.181 43.478 0.00 0.00 0.00 4.11
841 864 5.008316 TGAAGTAAAAGGAAGAGCGAAAACC 59.992 40.000 0.00 0.00 0.00 3.27
842 865 6.056428 TGAAGTAAAAGGAAGAGCGAAAAC 57.944 37.500 0.00 0.00 0.00 2.43
843 866 6.687081 TTGAAGTAAAAGGAAGAGCGAAAA 57.313 33.333 0.00 0.00 0.00 2.29
844 867 6.687081 TTTGAAGTAAAAGGAAGAGCGAAA 57.313 33.333 0.00 0.00 0.00 3.46
845 868 6.485313 TCATTTGAAGTAAAAGGAAGAGCGAA 59.515 34.615 0.00 0.00 27.71 4.70
846 869 5.995282 TCATTTGAAGTAAAAGGAAGAGCGA 59.005 36.000 0.00 0.00 27.71 4.93
847 870 6.241207 TCATTTGAAGTAAAAGGAAGAGCG 57.759 37.500 0.00 0.00 27.71 5.03
848 871 8.299570 TCAATCATTTGAAGTAAAAGGAAGAGC 58.700 33.333 0.00 0.00 38.90 4.09
895 918 6.827586 TTTGTTTGTTTGTAGAGTTGGACT 57.172 33.333 0.00 0.00 0.00 3.85
1128 1151 4.016706 GTCGGAGTGGGGTGGTGG 62.017 72.222 0.00 0.00 0.00 4.61
1797 1820 3.841379 TATCGCCGTCATCGCCAGC 62.841 63.158 0.00 0.00 35.54 4.85
1798 1821 1.080501 ATATCGCCGTCATCGCCAG 60.081 57.895 0.00 0.00 35.54 4.85
1799 1822 1.372872 CATATCGCCGTCATCGCCA 60.373 57.895 0.00 0.00 35.54 5.69
1800 1823 2.730672 GCATATCGCCGTCATCGCC 61.731 63.158 0.00 0.00 35.54 5.54
1801 1824 2.772189 GCATATCGCCGTCATCGC 59.228 61.111 0.00 0.00 35.54 4.58
1863 1886 4.214327 GAGCGGGAGAAGAGGCGG 62.214 72.222 0.00 0.00 0.00 6.13
1864 1887 4.214327 GGAGCGGGAGAAGAGGCG 62.214 72.222 0.00 0.00 0.00 5.52
1865 1888 3.855853 GGGAGCGGGAGAAGAGGC 61.856 72.222 0.00 0.00 0.00 4.70
1866 1889 3.157949 GGGGAGCGGGAGAAGAGG 61.158 72.222 0.00 0.00 0.00 3.69
1867 1890 3.157949 GGGGGAGCGGGAGAAGAG 61.158 72.222 0.00 0.00 0.00 2.85
1888 1911 4.219999 GAGGAGAGGAGCGCAGGC 62.220 72.222 11.47 0.00 40.37 4.85
1889 1912 3.898509 CGAGGAGAGGAGCGCAGG 61.899 72.222 11.47 0.00 0.00 4.85
1890 1913 3.898509 CCGAGGAGAGGAGCGCAG 61.899 72.222 11.47 0.00 0.00 5.18
1894 1917 3.844090 GTGGCCGAGGAGAGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
1895 1918 1.671901 GAAGTGGCCGAGGAGAGGAG 61.672 65.000 0.00 0.00 0.00 3.69
1896 1919 1.682684 GAAGTGGCCGAGGAGAGGA 60.683 63.158 0.00 0.00 0.00 3.71
1897 1920 2.726351 GGAAGTGGCCGAGGAGAGG 61.726 68.421 0.00 0.00 0.00 3.69
1898 1921 1.984570 TGGAAGTGGCCGAGGAGAG 60.985 63.158 0.00 0.00 0.00 3.20
1899 1922 2.119611 TGGAAGTGGCCGAGGAGA 59.880 61.111 0.00 0.00 0.00 3.71
1900 1923 2.266055 GTGGAAGTGGCCGAGGAG 59.734 66.667 0.00 0.00 0.00 3.69
1901 1924 3.319198 GGTGGAAGTGGCCGAGGA 61.319 66.667 0.00 0.00 0.00 3.71
1902 1925 3.636231 TGGTGGAAGTGGCCGAGG 61.636 66.667 0.00 0.00 0.00 4.63
1903 1926 2.358737 GTGGTGGAAGTGGCCGAG 60.359 66.667 0.00 0.00 0.00 4.63
1904 1927 3.948719 GGTGGTGGAAGTGGCCGA 61.949 66.667 0.00 0.00 0.00 5.54
1906 1929 4.678743 GGGGTGGTGGAAGTGGCC 62.679 72.222 0.00 0.00 0.00 5.36
1907 1930 3.897122 TGGGGTGGTGGAAGTGGC 61.897 66.667 0.00 0.00 0.00 5.01
1908 1931 2.115266 GTGGGGTGGTGGAAGTGG 59.885 66.667 0.00 0.00 0.00 4.00
1909 1932 1.073199 GAGTGGGGTGGTGGAAGTG 59.927 63.158 0.00 0.00 0.00 3.16
1910 1933 2.154074 GGAGTGGGGTGGTGGAAGT 61.154 63.158 0.00 0.00 0.00 3.01
1911 1934 2.757077 GGAGTGGGGTGGTGGAAG 59.243 66.667 0.00 0.00 0.00 3.46
1912 1935 3.246112 CGGAGTGGGGTGGTGGAA 61.246 66.667 0.00 0.00 0.00 3.53
1913 1936 4.242586 TCGGAGTGGGGTGGTGGA 62.243 66.667 0.00 0.00 0.00 4.02
1914 1937 4.016706 GTCGGAGTGGGGTGGTGG 62.017 72.222 0.00 0.00 0.00 4.61
1915 1938 4.373116 CGTCGGAGTGGGGTGGTG 62.373 72.222 0.00 0.00 0.00 4.17
1936 1959 3.879180 CTGGGGTTTTGGGACGGGG 62.879 68.421 0.00 0.00 0.00 5.73
1937 1960 2.282887 CTGGGGTTTTGGGACGGG 60.283 66.667 0.00 0.00 0.00 5.28
1938 1961 2.989253 GCTGGGGTTTTGGGACGG 60.989 66.667 0.00 0.00 0.00 4.79
1939 1962 1.971695 GAGCTGGGGTTTTGGGACG 60.972 63.158 0.00 0.00 0.00 4.79
1940 1963 1.606601 GGAGCTGGGGTTTTGGGAC 60.607 63.158 0.00 0.00 0.00 4.46
1941 1964 2.851045 GGAGCTGGGGTTTTGGGA 59.149 61.111 0.00 0.00 0.00 4.37
1942 1965 2.676471 CGGAGCTGGGGTTTTGGG 60.676 66.667 0.00 0.00 0.00 4.12
1943 1966 1.524008 GAACGGAGCTGGGGTTTTGG 61.524 60.000 0.00 0.00 0.00 3.28
1944 1967 1.524008 GGAACGGAGCTGGGGTTTTG 61.524 60.000 0.00 0.00 0.00 2.44
1945 1968 1.228459 GGAACGGAGCTGGGGTTTT 60.228 57.895 0.00 0.00 0.00 2.43
1946 1969 2.434774 GGAACGGAGCTGGGGTTT 59.565 61.111 0.00 0.00 0.00 3.27
1947 1970 3.647771 GGGAACGGAGCTGGGGTT 61.648 66.667 0.00 0.00 0.00 4.11
2379 2402 3.088500 GACGTTGCATCTCGCCTGC 62.089 63.158 0.00 0.00 41.33 4.85
2537 2560 1.719780 CGCGGTACTTGAGAAAGTGAC 59.280 52.381 0.00 0.00 34.37 3.67
2603 3943 0.461961 CTCCAGGTTCTCGTGATCCC 59.538 60.000 10.27 3.80 33.59 3.85
2656 3996 0.963962 TCCAGTACCCACACGTTCTC 59.036 55.000 0.00 0.00 0.00 2.87
2754 4101 0.745486 CATCCATGTCGCTCAGCCAA 60.745 55.000 0.00 0.00 0.00 4.52
2808 4155 0.397254 ACGAGTAGTGCCCATAGCCT 60.397 55.000 0.00 0.00 42.71 4.58
2927 4274 2.965783 TCTGTCAGTCAGAGCCGC 59.034 61.111 0.00 0.00 46.77 6.53
3178 4526 2.949644 ACACCCAAGCTTCAGTAAACAC 59.050 45.455 0.00 0.00 0.00 3.32
3219 4567 9.594478 TTTCGAAAACATATGCTATCTACAGAA 57.406 29.630 8.44 0.00 0.00 3.02
3220 4568 9.764363 ATTTCGAAAACATATGCTATCTACAGA 57.236 29.630 15.66 0.00 0.00 3.41
3222 4570 9.541143 TGATTTCGAAAACATATGCTATCTACA 57.459 29.630 15.66 0.00 0.00 2.74
3285 4633 4.152647 TCGGAGCAGAGGTGATATTGTAT 58.847 43.478 0.00 0.00 0.00 2.29
3294 4642 4.950050 ACTTATATTTCGGAGCAGAGGTG 58.050 43.478 0.00 0.00 0.00 4.00
3296 4644 4.230657 CGACTTATATTTCGGAGCAGAGG 58.769 47.826 0.00 0.00 0.00 3.69
3337 4685 1.345415 TCGTTGGGGGAGTGTAAACTC 59.655 52.381 4.27 4.27 36.08 3.01
3338 4686 1.071228 GTCGTTGGGGGAGTGTAAACT 59.929 52.381 0.00 0.00 0.00 2.66
3339 4687 1.071228 AGTCGTTGGGGGAGTGTAAAC 59.929 52.381 0.00 0.00 0.00 2.01
3340 4688 1.426751 AGTCGTTGGGGGAGTGTAAA 58.573 50.000 0.00 0.00 0.00 2.01
3341 4689 1.426751 AAGTCGTTGGGGGAGTGTAA 58.573 50.000 0.00 0.00 0.00 2.41
3342 4690 2.307496 TAAGTCGTTGGGGGAGTGTA 57.693 50.000 0.00 0.00 0.00 2.90
3343 4691 1.652947 ATAAGTCGTTGGGGGAGTGT 58.347 50.000 0.00 0.00 0.00 3.55
3373 4721 4.530161 ACATGCATATCTTCTACTCCCTCC 59.470 45.833 0.00 0.00 0.00 4.30
3636 4984 9.579768 TGCACATTATGTTAATGGATAAAACAC 57.420 29.630 10.94 0.00 36.06 3.32
3701 5049 0.876342 GATGGTCGACGCTTCATCCC 60.876 60.000 17.00 0.00 32.27 3.85
3738 5086 7.493971 GTGATAGCTTCTCTTCTTTAAGATGCA 59.506 37.037 11.32 0.00 42.21 3.96
3907 5255 4.265073 AGTCAAACTCAGATGTAATGCCC 58.735 43.478 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.