Multiple sequence alignment - TraesCS4D01G174300

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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 TraesCS4D01G174300 chr4D 100.000 4078 0 0 1 4078 301957017 301952940 0.000000e+00 7531.0
1 TraesCS4D01G174300 chr4D 91.224 809 60 7 1 804 19400631 19401433 0.000000e+00 1090.0
2 TraesCS4D01G174300 chr4D 90.652 813 64 5 1 808 105140584 105141389 0.000000e+00 1070.0
3 TraesCS4D01G174300 chr4A 91.827 3169 149 50 980 4078 178371444 178374572 0.000000e+00 4316.0
4 TraesCS4D01G174300 chr4A 89.855 207 12 2 1616 1822 527578572 527578375 1.450000e-64 257.0
5 TraesCS4D01G174300 chr4B 93.487 1305 48 7 2189 3487 376426422 376425149 0.000000e+00 1905.0
6 TraesCS4D01G174300 chr4B 92.827 1199 39 10 900 2060 376427610 376426421 0.000000e+00 1694.0
7 TraesCS4D01G174300 chr4B 82.875 327 28 14 1506 1827 369782624 369782321 6.720000e-68 268.0
8 TraesCS4D01G174300 chr4B 95.652 161 6 1 3919 4078 376424939 376424779 1.450000e-64 257.0
9 TraesCS4D01G174300 chr4B 89.773 176 8 2 3700 3865 376425110 376424935 2.470000e-52 217.0
10 TraesCS4D01G174300 chr7D 90.898 813 62 8 1 808 574071202 574072007 0.000000e+00 1081.0
11 TraesCS4D01G174300 chr7D 90.271 812 70 9 1 808 379844384 379845190 0.000000e+00 1053.0
12 TraesCS4D01G174300 chr7D 89.681 814 70 8 1 808 22846891 22847696 0.000000e+00 1026.0
13 TraesCS4D01G174300 chr7D 89.409 812 75 7 1 808 269698413 269699217 0.000000e+00 1013.0
14 TraesCS4D01G174300 chr7D 81.373 306 23 19 986 1260 179189154 179188852 6.860000e-53 219.0
15 TraesCS4D01G174300 chr5D 90.465 818 67 10 1 811 400268001 400267188 0.000000e+00 1068.0
16 TraesCS4D01G174300 chr5D 78.425 584 80 29 983 1553 339304276 339303726 5.050000e-89 339.0
17 TraesCS4D01G174300 chr3D 89.642 811 74 7 2 808 20754276 20755080 0.000000e+00 1024.0
18 TraesCS4D01G174300 chr3D 78.783 608 49 38 1262 1822 75769509 75768935 6.530000e-88 335.0
19 TraesCS4D01G174300 chr2D 89.442 824 69 8 1 811 323637978 323637160 0.000000e+00 1024.0
20 TraesCS4D01G174300 chr2D 78.678 605 60 34 1258 1822 348078686 348078111 5.050000e-89 339.0
21 TraesCS4D01G174300 chr7A 93.080 448 24 4 1160 1604 635648818 635648375 0.000000e+00 649.0
22 TraesCS4D01G174300 chr7A 91.351 185 15 1 983 1166 34969133 34969317 6.770000e-63 252.0
23 TraesCS4D01G174300 chr7A 90.000 190 11 7 983 1166 183718480 183718293 5.270000e-59 239.0
24 TraesCS4D01G174300 chr7A 88.557 201 10 6 1627 1827 219382255 219382068 8.820000e-57 231.0
25 TraesCS4D01G174300 chr1B 78.266 934 81 62 979 1822 188443018 188443919 4.740000e-134 488.0
26 TraesCS4D01G174300 chr1B 89.950 199 11 3 1628 1826 83210759 83210570 8.750000e-62 248.0
27 TraesCS4D01G174300 chrUn 82.124 565 70 24 977 1537 79708144 79708681 4.810000e-124 455.0
28 TraesCS4D01G174300 chr2B 80.360 611 42 33 1258 1822 182355124 182355702 3.820000e-105 392.0
29 TraesCS4D01G174300 chr2B 91.457 199 8 4 1624 1822 198532241 198532052 8.690000e-67 265.0
30 TraesCS4D01G174300 chr2B 91.620 179 13 1 1377 1553 688434728 688434906 3.150000e-61 246.0
31 TraesCS4D01G174300 chr2B 88.172 186 12 5 982 1166 688434390 688434566 3.190000e-51 213.0
32 TraesCS4D01G174300 chr2A 79.549 577 62 36 977 1546 71077164 71077691 1.080000e-95 361.0
33 TraesCS4D01G174300 chr6A 79.664 536 72 23 2540 3047 67646416 67646942 6.490000e-93 351.0
34 TraesCS4D01G174300 chr3A 78.783 608 56 38 1257 1822 323383393 323383969 1.400000e-89 340.0
35 TraesCS4D01G174300 chr3A 84.814 349 30 7 977 1303 323383048 323383395 3.040000e-86 329.0
36 TraesCS4D01G174300 chr6B 84.098 327 24 14 1506 1827 101245485 101245182 1.430000e-74 291.0
37 TraesCS4D01G174300 chr6B 92.647 204 6 4 1624 1827 578014838 578015032 6.670000e-73 285.0
38 TraesCS4D01G174300 chr6B 87.671 146 15 2 2640 2783 123915526 123915670 2.520000e-37 167.0
39 TraesCS4D01G174300 chr6B 90.909 44 4 0 811 854 232759616 232759659 4.400000e-05 60.2
40 TraesCS4D01G174300 chr3B 83.851 322 24 14 1506 1822 52857744 52857446 8.630000e-72 281.0
41 TraesCS4D01G174300 chr1A 79.655 290 34 13 1257 1525 41410414 41410699 6.960000e-43 185.0


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 TraesCS4D01G174300 chr4D 301952940 301957017 4077 True 7531.00 7531 100.00000 1 4078 1 chr4D.!!$R1 4077
1 TraesCS4D01G174300 chr4D 19400631 19401433 802 False 1090.00 1090 91.22400 1 804 1 chr4D.!!$F1 803
2 TraesCS4D01G174300 chr4D 105140584 105141389 805 False 1070.00 1070 90.65200 1 808 1 chr4D.!!$F2 807
3 TraesCS4D01G174300 chr4A 178371444 178374572 3128 False 4316.00 4316 91.82700 980 4078 1 chr4A.!!$F1 3098
4 TraesCS4D01G174300 chr4B 376424779 376427610 2831 True 1018.25 1905 92.93475 900 4078 4 chr4B.!!$R2 3178
5 TraesCS4D01G174300 chr7D 574071202 574072007 805 False 1081.00 1081 90.89800 1 808 1 chr7D.!!$F4 807
6 TraesCS4D01G174300 chr7D 379844384 379845190 806 False 1053.00 1053 90.27100 1 808 1 chr7D.!!$F3 807
7 TraesCS4D01G174300 chr7D 22846891 22847696 805 False 1026.00 1026 89.68100 1 808 1 chr7D.!!$F1 807
8 TraesCS4D01G174300 chr7D 269698413 269699217 804 False 1013.00 1013 89.40900 1 808 1 chr7D.!!$F2 807
9 TraesCS4D01G174300 chr5D 400267188 400268001 813 True 1068.00 1068 90.46500 1 811 1 chr5D.!!$R2 810
10 TraesCS4D01G174300 chr5D 339303726 339304276 550 True 339.00 339 78.42500 983 1553 1 chr5D.!!$R1 570
11 TraesCS4D01G174300 chr3D 20754276 20755080 804 False 1024.00 1024 89.64200 2 808 1 chr3D.!!$F1 806
12 TraesCS4D01G174300 chr3D 75768935 75769509 574 True 335.00 335 78.78300 1262 1822 1 chr3D.!!$R1 560
13 TraesCS4D01G174300 chr2D 323637160 323637978 818 True 1024.00 1024 89.44200 1 811 1 chr2D.!!$R1 810
14 TraesCS4D01G174300 chr2D 348078111 348078686 575 True 339.00 339 78.67800 1258 1822 1 chr2D.!!$R2 564
15 TraesCS4D01G174300 chr1B 188443018 188443919 901 False 488.00 488 78.26600 979 1822 1 chr1B.!!$F1 843
16 TraesCS4D01G174300 chrUn 79708144 79708681 537 False 455.00 455 82.12400 977 1537 1 chrUn.!!$F1 560
17 TraesCS4D01G174300 chr2B 182355124 182355702 578 False 392.00 392 80.36000 1258 1822 1 chr2B.!!$F1 564
18 TraesCS4D01G174300 chr2B 688434390 688434906 516 False 229.50 246 89.89600 982 1553 2 chr2B.!!$F2 571
19 TraesCS4D01G174300 chr2A 71077164 71077691 527 False 361.00 361 79.54900 977 1546 1 chr2A.!!$F1 569
20 TraesCS4D01G174300 chr6A 67646416 67646942 526 False 351.00 351 79.66400 2540 3047 1 chr6A.!!$F1 507
21 TraesCS4D01G174300 chr3A 323383048 323383969 921 False 334.50 340 81.79850 977 1822 2 chr3A.!!$F1 845

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
838 864 0.034863 GGACAAAATGGGTCGCCCTA 60.035 55.000 14.76 0.0 45.7 3.53 F
1158 1185 0.906066 GTTGAACTCTCCTCCTCCCC 59.094 60.000 0.00 0.0 0.0 4.81 F
1183 1234 1.074727 TCTCGGATCCCTCTCATCTCC 59.925 57.143 6.06 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 2145 0.607489 CCTGAGCCCCTGACAAACTG 60.607 60.000 0.0 0.0 0.00 3.16 R
2386 2608 1.098050 GTCACAGGAATGCCCATGTC 58.902 55.000 0.0 0.0 37.41 3.06 R
3135 3394 1.555075 ACATGGTGATCAAGGTAGCGT 59.445 47.619 0.0 0.0 0.00 5.07 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
107 109 3.698382 GCTCTCTCGGTTGCGATG 58.302 61.111 0.00 0.00 0.00 3.84
136 138 4.506255 GGTGGCCCGGAATGGAGG 62.506 72.222 0.73 0.00 42.00 4.30
214 216 2.045242 CCTCCTCCTCGTCGGACA 60.045 66.667 9.10 0.00 36.69 4.02
276 280 2.038269 TCGGCGGAGTCCATTTTGC 61.038 57.895 10.49 3.56 0.00 3.68
368 373 3.402681 GGACCAGCTAGCTGCCCA 61.403 66.667 34.82 0.00 44.23 5.36
650 673 0.321564 CGAGGGTTGCTGTTGGATGA 60.322 55.000 0.00 0.00 0.00 2.92
679 702 1.884075 AATGTGCCACCGACTAGCGA 61.884 55.000 7.94 0.00 44.57 4.93
726 752 4.634133 GTCCGTCACGTGTCCGCA 62.634 66.667 16.51 2.46 37.70 5.69
741 767 2.699212 GCACCGACGTAAATCCGC 59.301 61.111 0.00 0.00 0.00 5.54
769 795 1.326951 TGGATCGGGAATGAGTCGCA 61.327 55.000 0.00 0.00 39.14 5.10
784 810 4.007940 GCACGCGGACGAAAAGCA 62.008 61.111 12.47 0.00 43.93 3.91
808 834 2.359354 CGTCCATTTGGGTCGGCA 60.359 61.111 0.00 0.00 43.28 5.69
827 853 3.428282 GACGGCGGCGGACAAAAT 61.428 61.111 35.05 12.66 0.00 1.82
828 854 3.661025 GACGGCGGCGGACAAAATG 62.661 63.158 35.05 4.63 0.00 2.32
829 855 4.474846 CGGCGGCGGACAAAATGG 62.475 66.667 25.36 0.00 0.00 3.16
830 856 4.128388 GGCGGCGGACAAAATGGG 62.128 66.667 9.78 0.00 0.00 4.00
831 857 3.370231 GCGGCGGACAAAATGGGT 61.370 61.111 9.78 0.00 0.00 4.51
832 858 2.874751 CGGCGGACAAAATGGGTC 59.125 61.111 0.00 0.00 34.52 4.46
833 859 2.874751 GGCGGACAAAATGGGTCG 59.125 61.111 0.00 0.00 36.12 4.79
834 860 2.178273 GCGGACAAAATGGGTCGC 59.822 61.111 0.00 0.00 36.12 5.19
835 861 2.874751 CGGACAAAATGGGTCGCC 59.125 61.111 0.00 0.00 36.12 5.54
836 862 2.696759 CGGACAAAATGGGTCGCCC 61.697 63.158 7.87 7.87 45.71 6.13
837 863 1.304134 GGACAAAATGGGTCGCCCT 60.304 57.895 14.76 0.10 45.70 5.19
838 864 0.034863 GGACAAAATGGGTCGCCCTA 60.035 55.000 14.76 0.00 45.70 3.53
839 865 1.409661 GGACAAAATGGGTCGCCCTAT 60.410 52.381 14.76 0.00 45.70 2.57
840 866 2.375146 GACAAAATGGGTCGCCCTATT 58.625 47.619 14.76 2.20 45.70 1.73
841 867 3.547746 GACAAAATGGGTCGCCCTATTA 58.452 45.455 14.76 0.00 45.70 0.98
842 868 3.949113 GACAAAATGGGTCGCCCTATTAA 59.051 43.478 14.76 0.00 45.70 1.40
843 869 4.345854 ACAAAATGGGTCGCCCTATTAAA 58.654 39.130 14.76 0.00 45.70 1.52
844 870 4.401202 ACAAAATGGGTCGCCCTATTAAAG 59.599 41.667 14.76 2.25 45.70 1.85
845 871 3.945640 AATGGGTCGCCCTATTAAAGT 57.054 42.857 14.76 0.00 45.70 2.66
846 872 3.945640 ATGGGTCGCCCTATTAAAGTT 57.054 42.857 14.76 0.00 45.70 2.66
847 873 2.993937 TGGGTCGCCCTATTAAAGTTG 58.006 47.619 14.76 0.00 45.70 3.16
848 874 2.294979 GGGTCGCCCTATTAAAGTTGG 58.705 52.381 7.58 0.00 41.34 3.77
849 875 2.356432 GGGTCGCCCTATTAAAGTTGGT 60.356 50.000 7.58 0.00 41.34 3.67
850 876 2.941064 GGTCGCCCTATTAAAGTTGGTC 59.059 50.000 0.00 0.00 0.00 4.02
851 877 3.370209 GGTCGCCCTATTAAAGTTGGTCT 60.370 47.826 0.00 0.00 0.00 3.85
852 878 4.259356 GTCGCCCTATTAAAGTTGGTCTT 58.741 43.478 0.00 0.00 38.10 3.01
853 879 5.422145 GTCGCCCTATTAAAGTTGGTCTTA 58.578 41.667 0.00 0.00 35.02 2.10
854 880 5.876460 GTCGCCCTATTAAAGTTGGTCTTAA 59.124 40.000 0.00 0.00 35.02 1.85
855 881 6.036844 GTCGCCCTATTAAAGTTGGTCTTAAG 59.963 42.308 0.00 0.00 35.02 1.85
856 882 6.070653 TCGCCCTATTAAAGTTGGTCTTAAGA 60.071 38.462 0.00 0.00 35.02 2.10
857 883 6.596497 CGCCCTATTAAAGTTGGTCTTAAGAA 59.404 38.462 6.78 0.00 35.02 2.52
858 884 7.282450 CGCCCTATTAAAGTTGGTCTTAAGAAT 59.718 37.037 6.78 0.00 35.02 2.40
859 885 9.623000 GCCCTATTAAAGTTGGTCTTAAGAATA 57.377 33.333 6.78 0.00 35.02 1.75
873 899 9.952188 GGTCTTAAGAATATCAAATGTAAAGGC 57.048 33.333 6.78 0.00 0.00 4.35
878 904 8.579850 AAGAATATCAAATGTAAAGGCTCACA 57.420 30.769 4.58 4.58 0.00 3.58
879 905 7.989826 AGAATATCAAATGTAAAGGCTCACAC 58.010 34.615 4.23 0.00 0.00 3.82
880 906 7.831193 AGAATATCAAATGTAAAGGCTCACACT 59.169 33.333 4.23 0.00 0.00 3.55
881 907 5.886960 ATCAAATGTAAAGGCTCACACTC 57.113 39.130 4.23 0.00 0.00 3.51
882 908 4.973168 TCAAATGTAAAGGCTCACACTCT 58.027 39.130 4.23 0.00 0.00 3.24
883 909 4.997395 TCAAATGTAAAGGCTCACACTCTC 59.003 41.667 4.23 0.00 0.00 3.20
884 910 4.623932 AATGTAAAGGCTCACACTCTCA 57.376 40.909 4.23 0.00 0.00 3.27
885 911 4.833478 ATGTAAAGGCTCACACTCTCAT 57.167 40.909 4.23 0.00 0.00 2.90
886 912 5.939764 ATGTAAAGGCTCACACTCTCATA 57.060 39.130 4.23 0.00 0.00 2.15
887 913 5.330455 TGTAAAGGCTCACACTCTCATAG 57.670 43.478 0.00 0.00 0.00 2.23
888 914 5.016831 TGTAAAGGCTCACACTCTCATAGA 58.983 41.667 0.00 0.00 0.00 1.98
890 916 2.031120 AGGCTCACACTCTCATAGAGC 58.969 52.381 3.85 0.00 46.12 4.09
892 918 3.731652 GCTCACACTCTCATAGAGCAT 57.268 47.619 7.76 0.00 46.12 3.79
893 919 3.382855 GCTCACACTCTCATAGAGCATG 58.617 50.000 7.76 3.33 46.12 4.06
894 920 3.799574 GCTCACACTCTCATAGAGCATGG 60.800 52.174 7.76 0.11 46.12 3.66
895 921 3.369175 TCACACTCTCATAGAGCATGGT 58.631 45.455 0.00 0.00 46.12 3.55
896 922 3.382865 TCACACTCTCATAGAGCATGGTC 59.617 47.826 17.19 17.19 46.12 4.02
897 923 3.384146 CACACTCTCATAGAGCATGGTCT 59.616 47.826 28.82 28.82 46.12 3.85
898 924 3.636300 ACACTCTCATAGAGCATGGTCTC 59.364 47.826 29.62 11.33 46.12 3.36
928 954 4.797933 GCCATTAGGATCTTCTCTTCGTCC 60.798 50.000 0.00 0.00 36.89 4.79
934 960 5.017490 AGGATCTTCTCTTCGTCCTGTAAA 58.983 41.667 0.00 0.00 37.88 2.01
970 996 8.688151 ACTTAATAAAGTTTGCAAGGTTGTGTA 58.312 29.630 0.00 0.00 43.60 2.90
972 998 9.871238 TTAATAAAGTTTGCAAGGTTGTGTAAA 57.129 25.926 0.00 0.00 31.71 2.01
1158 1185 0.906066 GTTGAACTCTCCTCCTCCCC 59.094 60.000 0.00 0.00 0.00 4.81
1183 1234 1.074727 TCTCGGATCCCTCTCATCTCC 59.925 57.143 6.06 0.00 0.00 3.71
1295 1428 3.806667 GAGCTCCCTGCCATGGCT 61.807 66.667 35.53 15.41 44.23 4.75
1546 1727 2.303022 TCTGTCCCCAAGAGTTTGCTAG 59.697 50.000 0.00 0.00 32.79 3.42
1711 1919 8.982723 TGCCCATGCCTTTATTAGTTTATAAAA 58.017 29.630 0.00 0.00 36.33 1.52
1809 2025 3.070748 GGTTTGGTTGCTGTTTTGTGTT 58.929 40.909 0.00 0.00 0.00 3.32
1822 2038 5.268387 TGTTTTGTGTTCCTATATGGCCAT 58.732 37.500 24.45 24.45 35.26 4.40
1903 2119 9.160496 CTCAAGACTGATAGTAAGCTTGAATTT 57.840 33.333 9.86 0.00 37.36 1.82
1905 2121 8.394121 CAAGACTGATAGTAAGCTTGAATTTCC 58.606 37.037 9.86 0.00 33.96 3.13
1922 2138 7.493367 TGAATTTCCTAAGCCGAAAAGAAAAA 58.507 30.769 0.00 0.00 33.19 1.94
1988 2210 8.217131 AGTTTATTTCCACCGTAATCCATAAC 57.783 34.615 0.00 0.00 0.00 1.89
2015 2237 5.131809 TGTTTTTGGAACTTCAAATCCCCAT 59.868 36.000 0.00 0.00 36.63 4.00
2093 2315 3.358111 TTGCCTGGATTGTAATTCGGA 57.642 42.857 0.00 0.00 0.00 4.55
2109 2331 1.623811 TCGGACTGCTCTAGCCTTTTT 59.376 47.619 0.00 0.00 41.18 1.94
2142 2364 7.047891 TGTGAACAATTGAGTCCTACCATATC 58.952 38.462 13.59 0.00 0.00 1.63
2150 2372 6.392625 TGAGTCCTACCATATCTTTCTTCG 57.607 41.667 0.00 0.00 0.00 3.79
2151 2373 5.203060 AGTCCTACCATATCTTTCTTCGC 57.797 43.478 0.00 0.00 0.00 4.70
2160 2382 5.760253 CCATATCTTTCTTCGCTGTTACCAT 59.240 40.000 0.00 0.00 0.00 3.55
2161 2383 6.073548 CCATATCTTTCTTCGCTGTTACCATC 60.074 42.308 0.00 0.00 0.00 3.51
2170 2392 3.704566 TCGCTGTTACCATCCTCAGTTAT 59.295 43.478 0.00 0.00 0.00 1.89
2370 2592 3.824414 GTGTTGGTCACCTTATTTCCG 57.176 47.619 0.00 0.00 40.84 4.30
2386 2608 2.093306 TCCGTAGTGATGGTTTGCTG 57.907 50.000 0.00 0.00 32.93 4.41
2924 3176 1.004440 GGCTGAGGCTCTTTGTCGT 60.004 57.895 16.72 0.00 38.73 4.34
2938 3190 0.744281 TGTCGTGTCTCTGCTGTTGA 59.256 50.000 0.00 0.00 0.00 3.18
3052 3311 3.367395 GCTTTGTTGCTGTAAATCCCTCC 60.367 47.826 0.00 0.00 0.00 4.30
3088 3347 6.763610 GGTAATCTTTCCTCCTGTATGACTTG 59.236 42.308 0.00 0.00 0.00 3.16
3135 3394 0.621609 GGTGTGGGGGTATGCACTTA 59.378 55.000 0.00 0.00 32.90 2.24
3392 3664 9.076596 GGCACTGCTTTTATATTTAAACTCTTG 57.923 33.333 0.00 0.00 0.00 3.02
3429 3701 9.053840 CAACTTTAGATGATGATCAAGCTATGT 57.946 33.333 0.00 4.64 0.00 2.29
3455 3727 3.624777 AGGATGATTGACCCATTCACAC 58.375 45.455 0.00 0.00 32.26 3.82
3478 3750 3.667497 TTTGTGTTGCAAGTTGGACAA 57.333 38.095 0.00 1.69 38.47 3.18
3480 3752 3.667497 TGTGTTGCAAGTTGGACAAAA 57.333 38.095 0.00 0.00 0.00 2.44
3483 3755 4.218635 TGTGTTGCAAGTTGGACAAAAGTA 59.781 37.500 0.00 0.00 0.00 2.24
3487 3759 3.636300 TGCAAGTTGGACAAAAGTATGCT 59.364 39.130 4.75 0.00 32.74 3.79
3488 3760 3.983344 GCAAGTTGGACAAAAGTATGCTG 59.017 43.478 4.75 0.00 0.00 4.41
3489 3761 3.923017 AGTTGGACAAAAGTATGCTGC 57.077 42.857 0.00 0.00 0.00 5.25
3490 3762 3.221771 AGTTGGACAAAAGTATGCTGCA 58.778 40.909 4.13 4.13 0.00 4.41
3491 3763 3.004734 AGTTGGACAAAAGTATGCTGCAC 59.995 43.478 3.57 0.00 0.00 4.57
3493 3765 1.606606 GACAAAAGTATGCTGCACGC 58.393 50.000 3.57 0.11 39.77 5.34
3496 3768 2.811431 ACAAAAGTATGCTGCACGCTTA 59.189 40.909 17.09 0.00 40.11 3.09
3497 3769 3.120199 ACAAAAGTATGCTGCACGCTTAG 60.120 43.478 17.09 15.09 40.11 2.18
3498 3770 2.386661 AAGTATGCTGCACGCTTAGT 57.613 45.000 15.78 1.44 40.11 2.24
3539 3826 8.810652 TTGTTTTCCTTTATTCACATGCTTAC 57.189 30.769 0.00 0.00 0.00 2.34
3560 3850 9.291664 GCTTACTACACTCTAGTCTTGTAATTG 57.708 37.037 0.00 0.00 0.00 2.32
3575 3865 8.964150 GTCTTGTAATTGGTGTTGTATTTTGAC 58.036 33.333 0.00 0.00 0.00 3.18
3583 3873 4.216902 GGTGTTGTATTTTGACCTGGGTAC 59.783 45.833 0.00 0.00 0.00 3.34
3588 3880 5.496556 TGTATTTTGACCTGGGTACTCATG 58.503 41.667 0.00 0.00 0.00 3.07
3617 3909 3.303990 GCTGCGACTGTTTTCTTGAATGA 60.304 43.478 0.00 0.00 0.00 2.57
3620 3912 5.273170 TGCGACTGTTTTCTTGAATGAAAG 58.727 37.500 0.00 0.00 37.27 2.62
3657 3949 2.327325 TCTGGCACCTTCCTCTAGTT 57.673 50.000 0.00 0.00 0.00 2.24
3658 3950 2.180276 TCTGGCACCTTCCTCTAGTTC 58.820 52.381 0.00 0.00 0.00 3.01
3682 3974 3.618019 GCTGAACCTTAACATACCCACGA 60.618 47.826 0.00 0.00 0.00 4.35
3819 4121 7.921214 AGGACGGATGCTAACATTATTATATCG 59.079 37.037 0.00 0.00 36.35 2.92
3864 4166 8.665643 AGTATGTAGTAGTAGTAGAAGCAGTG 57.334 38.462 0.00 0.00 0.00 3.66
3933 4235 2.342650 TTTCAGCGCTGGGGAATGC 61.343 57.895 35.36 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 117 2.677228 CATTCCGGGCCACCTTCT 59.323 61.111 4.39 0.00 33.28 2.85
136 138 4.683334 GCGGCCGTTGTTCTGTGC 62.683 66.667 28.70 0.77 0.00 4.57
214 216 1.513586 GCGACTCCGACGATTCGTT 60.514 57.895 13.72 0.00 44.28 3.85
276 280 1.021202 TTCGACAGTTTGCCAAGGTG 58.979 50.000 0.00 0.00 0.00 4.00
481 495 4.760047 CGACTGCTTCCCACCCCG 62.760 72.222 0.00 0.00 0.00 5.73
510 524 4.745751 CCGCCACCGCCGTCTTAA 62.746 66.667 0.00 0.00 0.00 1.85
726 752 0.817013 TTAGGCGGATTTACGTCGGT 59.183 50.000 0.00 0.00 44.42 4.69
753 779 1.226974 CGTGCGACTCATTCCCGAT 60.227 57.895 0.00 0.00 0.00 4.18
763 789 4.634133 TTTCGTCCGCGTGCGACT 62.634 61.111 16.91 0.00 42.83 4.18
769 795 2.028484 TCTGCTTTTCGTCCGCGT 59.972 55.556 4.92 0.00 39.49 6.01
811 837 3.732892 CATTTTGTCCGCCGCCGT 61.733 61.111 0.00 0.00 0.00 5.68
812 838 4.474846 CCATTTTGTCCGCCGCCG 62.475 66.667 0.00 0.00 0.00 6.46
813 839 4.128388 CCCATTTTGTCCGCCGCC 62.128 66.667 0.00 0.00 0.00 6.13
814 840 3.336715 GACCCATTTTGTCCGCCGC 62.337 63.158 0.00 0.00 0.00 6.53
815 841 2.874751 GACCCATTTTGTCCGCCG 59.125 61.111 0.00 0.00 0.00 6.46
816 842 2.874751 CGACCCATTTTGTCCGCC 59.125 61.111 0.00 0.00 0.00 6.13
817 843 2.178273 GCGACCCATTTTGTCCGC 59.822 61.111 0.00 0.00 0.00 5.54
818 844 2.874751 GGCGACCCATTTTGTCCG 59.125 61.111 0.00 0.00 0.00 4.79
828 854 7.838272 AAGACCAACTTTAATAGGGCGACCC 62.838 48.000 1.76 4.96 44.22 4.46
829 855 4.865698 AAGACCAACTTTAATAGGGCGACC 60.866 45.833 0.00 0.00 43.70 4.79
830 856 3.870274 AGACCAACTTTAATAGGGCGAC 58.130 45.455 0.00 0.00 33.20 5.19
831 857 4.563140 AAGACCAACTTTAATAGGGCGA 57.437 40.909 0.00 0.00 34.94 5.54
832 858 6.110707 TCTTAAGACCAACTTTAATAGGGCG 58.889 40.000 0.00 0.00 39.72 6.13
833 859 7.933215 TTCTTAAGACCAACTTTAATAGGGC 57.067 36.000 4.18 0.00 39.72 5.19
847 873 9.952188 GCCTTTACATTTGATATTCTTAAGACC 57.048 33.333 4.18 0.00 0.00 3.85
852 878 9.679661 TGTGAGCCTTTACATTTGATATTCTTA 57.320 29.630 0.00 0.00 0.00 2.10
853 879 8.462016 GTGTGAGCCTTTACATTTGATATTCTT 58.538 33.333 0.00 0.00 0.00 2.52
854 880 7.831193 AGTGTGAGCCTTTACATTTGATATTCT 59.169 33.333 0.00 0.00 0.00 2.40
855 881 7.989826 AGTGTGAGCCTTTACATTTGATATTC 58.010 34.615 0.00 0.00 0.00 1.75
856 882 7.831193 AGAGTGTGAGCCTTTACATTTGATATT 59.169 33.333 0.00 0.00 0.00 1.28
857 883 7.341805 AGAGTGTGAGCCTTTACATTTGATAT 58.658 34.615 0.00 0.00 0.00 1.63
858 884 6.711277 AGAGTGTGAGCCTTTACATTTGATA 58.289 36.000 0.00 0.00 0.00 2.15
859 885 5.564550 AGAGTGTGAGCCTTTACATTTGAT 58.435 37.500 0.00 0.00 0.00 2.57
860 886 4.973168 AGAGTGTGAGCCTTTACATTTGA 58.027 39.130 0.00 0.00 0.00 2.69
861 887 4.756642 TGAGAGTGTGAGCCTTTACATTTG 59.243 41.667 0.00 0.00 0.00 2.32
862 888 4.973168 TGAGAGTGTGAGCCTTTACATTT 58.027 39.130 0.00 0.00 0.00 2.32
863 889 4.623932 TGAGAGTGTGAGCCTTTACATT 57.376 40.909 0.00 0.00 0.00 2.71
864 890 4.833478 ATGAGAGTGTGAGCCTTTACAT 57.167 40.909 0.00 0.00 0.00 2.29
865 891 5.016831 TCTATGAGAGTGTGAGCCTTTACA 58.983 41.667 0.00 0.00 0.00 2.41
866 892 5.584253 TCTATGAGAGTGTGAGCCTTTAC 57.416 43.478 0.00 0.00 0.00 2.01
867 893 4.098654 GCTCTATGAGAGTGTGAGCCTTTA 59.901 45.833 5.44 0.00 44.12 1.85
868 894 3.118811 GCTCTATGAGAGTGTGAGCCTTT 60.119 47.826 5.44 0.00 44.12 3.11
869 895 2.430332 GCTCTATGAGAGTGTGAGCCTT 59.570 50.000 5.44 0.00 44.12 4.35
870 896 2.031120 GCTCTATGAGAGTGTGAGCCT 58.969 52.381 5.44 0.00 44.12 4.58
871 897 1.753649 TGCTCTATGAGAGTGTGAGCC 59.246 52.381 10.19 0.00 46.56 4.70
872 898 3.382855 CATGCTCTATGAGAGTGTGAGC 58.617 50.000 5.44 0.00 44.12 4.26
873 899 3.384146 ACCATGCTCTATGAGAGTGTGAG 59.616 47.826 5.44 0.00 44.12 3.51
874 900 3.369175 ACCATGCTCTATGAGAGTGTGA 58.631 45.455 5.44 0.00 44.12 3.58
875 901 3.384146 AGACCATGCTCTATGAGAGTGTG 59.616 47.826 5.44 4.80 44.12 3.82
876 902 3.636300 GAGACCATGCTCTATGAGAGTGT 59.364 47.826 5.44 0.00 44.12 3.55
877 903 3.005684 GGAGACCATGCTCTATGAGAGTG 59.994 52.174 5.44 0.00 44.12 3.51
878 904 3.117169 AGGAGACCATGCTCTATGAGAGT 60.117 47.826 5.44 0.00 44.12 3.24
879 905 3.256383 CAGGAGACCATGCTCTATGAGAG 59.744 52.174 0.00 0.00 45.04 3.20
880 906 3.229293 CAGGAGACCATGCTCTATGAGA 58.771 50.000 0.00 0.00 39.21 3.27
881 907 2.964464 ACAGGAGACCATGCTCTATGAG 59.036 50.000 8.87 0.00 39.21 2.90
882 908 3.037851 ACAGGAGACCATGCTCTATGA 57.962 47.619 8.87 0.00 39.21 2.15
883 909 3.726607 GAACAGGAGACCATGCTCTATG 58.273 50.000 0.00 0.00 35.26 2.23
884 910 2.363680 CGAACAGGAGACCATGCTCTAT 59.636 50.000 0.00 0.00 35.26 1.98
885 911 1.751351 CGAACAGGAGACCATGCTCTA 59.249 52.381 0.00 0.00 35.26 2.43
886 912 0.534412 CGAACAGGAGACCATGCTCT 59.466 55.000 0.00 0.00 35.26 4.09
887 913 1.086634 GCGAACAGGAGACCATGCTC 61.087 60.000 0.00 0.00 0.00 4.26
888 914 1.078848 GCGAACAGGAGACCATGCT 60.079 57.895 0.00 0.00 0.00 3.79
889 915 2.109126 GGCGAACAGGAGACCATGC 61.109 63.158 0.00 0.00 0.00 4.06
890 916 0.107508 ATGGCGAACAGGAGACCATG 60.108 55.000 0.00 0.00 39.62 3.66
891 917 0.620556 AATGGCGAACAGGAGACCAT 59.379 50.000 0.00 0.00 42.89 3.55
892 918 1.207089 CTAATGGCGAACAGGAGACCA 59.793 52.381 0.00 0.00 34.28 4.02
893 919 1.473434 CCTAATGGCGAACAGGAGACC 60.473 57.143 0.00 0.00 0.00 3.85
894 920 1.480954 TCCTAATGGCGAACAGGAGAC 59.519 52.381 0.00 0.00 32.20 3.36
895 921 1.860641 TCCTAATGGCGAACAGGAGA 58.139 50.000 0.00 0.00 32.20 3.71
896 922 2.366916 AGATCCTAATGGCGAACAGGAG 59.633 50.000 7.55 0.00 40.43 3.69
897 923 2.398588 AGATCCTAATGGCGAACAGGA 58.601 47.619 4.48 4.48 41.31 3.86
898 924 2.918712 AGATCCTAATGGCGAACAGG 57.081 50.000 0.00 0.00 0.00 4.00
928 954 9.793245 CTTTATTAAGTCGTCACAAGTTTACAG 57.207 33.333 0.00 0.00 0.00 2.74
934 960 7.130269 GCAAACTTTATTAAGTCGTCACAAGT 58.870 34.615 0.00 0.00 43.74 3.16
972 998 2.811799 GTGGGTGCAGGCGTTTTT 59.188 55.556 0.00 0.00 0.00 1.94
1183 1234 2.437359 CAGCGCAAGGGGAAGAGG 60.437 66.667 11.47 0.00 38.28 3.69
1417 1595 0.107508 ATTCGGGACAGAGCATGTGG 60.108 55.000 0.00 0.00 44.17 4.17
1546 1727 6.151817 ACTGATTCCTTCTAATTTCCACAAGC 59.848 38.462 0.00 0.00 0.00 4.01
1754 1970 6.244999 CACTATCAGCGTATCTCGTTATCTC 58.755 44.000 0.00 0.00 42.13 2.75
1760 1976 1.947456 TGCACTATCAGCGTATCTCGT 59.053 47.619 0.00 0.00 42.13 4.18
1928 2145 0.607489 CCTGAGCCCCTGACAAACTG 60.607 60.000 0.00 0.00 0.00 3.16
1930 2147 1.303643 CCCTGAGCCCCTGACAAAC 60.304 63.158 0.00 0.00 0.00 2.93
1931 2148 3.170362 CCCTGAGCCCCTGACAAA 58.830 61.111 0.00 0.00 0.00 2.83
1932 2149 3.650950 GCCCTGAGCCCCTGACAA 61.651 66.667 0.00 0.00 34.35 3.18
1933 2150 4.664267 AGCCCTGAGCCCCTGACA 62.664 66.667 0.00 0.00 45.47 3.58
1934 2151 3.334054 AAGCCCTGAGCCCCTGAC 61.334 66.667 0.00 0.00 45.47 3.51
1935 2152 3.011517 GAAGCCCTGAGCCCCTGA 61.012 66.667 0.00 0.00 45.47 3.86
1936 2153 3.013932 AGAAGCCCTGAGCCCCTG 61.014 66.667 0.00 0.00 45.47 4.45
1937 2154 2.690510 GAGAAGCCCTGAGCCCCT 60.691 66.667 0.00 0.00 45.47 4.79
1988 2210 5.056480 GGATTTGAAGTTCCAAAAACAGGG 58.944 41.667 0.00 0.00 39.20 4.45
2015 2237 3.327464 TCAGATGGATGTTTGACTGGTGA 59.673 43.478 0.00 0.00 0.00 4.02
2109 2331 3.947196 ACTCAATTGTTCACAGCAGACAA 59.053 39.130 5.13 0.00 0.00 3.18
2113 2335 3.144506 AGGACTCAATTGTTCACAGCAG 58.855 45.455 5.13 0.00 0.00 4.24
2170 2392 7.124298 ACTGCTATTTGTAGTATCACTTCAGGA 59.876 37.037 0.00 0.00 39.83 3.86
2370 2592 3.127548 CCATGTCAGCAAACCATCACTAC 59.872 47.826 0.00 0.00 0.00 2.73
2386 2608 1.098050 GTCACAGGAATGCCCATGTC 58.902 55.000 0.00 0.00 37.41 3.06
2924 3176 3.118629 AGTTCAACTCAACAGCAGAGACA 60.119 43.478 0.00 0.00 36.91 3.41
3052 3311 4.080638 AGGAAAGATTACCCTCAGAGCAAG 60.081 45.833 0.00 0.00 0.00 4.01
3088 3347 3.710326 ACAGATGCATGCATGATTCAC 57.290 42.857 36.73 20.74 36.70 3.18
3135 3394 1.555075 ACATGGTGATCAAGGTAGCGT 59.445 47.619 0.00 0.00 0.00 5.07
3392 3664 5.174395 TCATCTAAAGTTGAGAAGCTCAGC 58.826 41.667 0.00 3.48 41.75 4.26
3429 3701 4.227982 TGAATGGGTCAATCATCCTTCTCA 59.772 41.667 0.00 0.00 31.51 3.27
3455 3727 3.931468 TGTCCAACTTGCAACACAAAATG 59.069 39.130 0.00 0.00 37.96 2.32
3518 3805 8.726988 GTGTAGTAAGCATGTGAATAAAGGAAA 58.273 33.333 0.00 0.00 0.00 3.13
3539 3826 7.603651 ACACCAATTACAAGACTAGAGTGTAG 58.396 38.462 0.00 0.00 33.29 2.74
3560 3850 3.227614 ACCCAGGTCAAAATACAACACC 58.772 45.455 0.00 0.00 0.00 4.16
3575 3865 3.389329 AGCTGTTATCATGAGTACCCAGG 59.611 47.826 0.09 0.00 0.00 4.45
3583 3873 2.538861 CAGTCGCAGCTGTTATCATGAG 59.461 50.000 16.64 0.00 0.00 2.90
3617 3909 7.500559 GCCAGATGAGTAAATGTCCTAATCTTT 59.499 37.037 0.00 0.00 0.00 2.52
3620 3912 6.203723 GTGCCAGATGAGTAAATGTCCTAATC 59.796 42.308 0.00 0.00 0.00 1.75
3657 3949 3.585289 TGGGTATGTTAAGGTTCAGCTGA 59.415 43.478 13.74 13.74 0.00 4.26
3658 3950 3.689649 GTGGGTATGTTAAGGTTCAGCTG 59.310 47.826 7.63 7.63 0.00 4.24
3682 3974 7.706607 TCGAATTTGTTCAGATATGATCGTTCT 59.293 33.333 8.19 0.00 0.00 3.01
3773 4069 3.682858 CCTGGCTCATGCAAAGAAATTTG 59.317 43.478 0.00 0.00 41.91 2.32
3837 4139 9.985730 ACTGCTTCTACTACTACTACATACTAG 57.014 37.037 0.00 0.00 0.00 2.57
3864 4166 2.293399 CCTCACCTTAACCAAAGTGCAC 59.707 50.000 9.40 9.40 32.89 4.57
3900 4202 2.544685 CTGAAACTCATAGTGGAGCCG 58.455 52.381 0.00 0.00 38.50 5.52
3933 4235 1.081509 GCTCTCGCCGCTCTATCAG 60.082 63.158 0.00 0.00 0.00 2.90
3963 4265 7.230849 ACTCATATCTCTCATCATCTCCAAC 57.769 40.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.