Multiple sequence alignment - TraesCS1D01G281100

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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 TraesCS1D01G281100 chr1D 100.000 2976 0 0 1 2976 379461178 379458203 0.000000e+00 5496.0
1 TraesCS1D01G281100 chr1D 96.462 537 19 0 2437 2973 289949356 289949892 0.000000e+00 887.0
2 TraesCS1D01G281100 chr1B 91.828 1187 64 10 919 2077 508546296 508545115 0.000000e+00 1624.0
3 TraesCS1D01G281100 chr1B 95.362 539 25 0 2437 2975 259786214 259785676 0.000000e+00 857.0
4 TraesCS1D01G281100 chr1B 95.522 335 13 2 2079 2413 31253153 31252821 4.370000e-148 534.0
5 TraesCS1D01G281100 chr1A 91.912 1088 67 15 1002 2077 480551646 480550568 0.000000e+00 1502.0
6 TraesCS1D01G281100 chr1A 93.662 284 17 1 2079 2362 495178212 495178494 9.860000e-115 424.0
7 TraesCS1D01G281100 chr7D 93.463 719 22 7 3 699 422347373 422346658 0.000000e+00 1044.0
8 TraesCS1D01G281100 chr7D 86.765 68 5 3 672 737 500220561 500220626 4.110000e-09 73.1
9 TraesCS1D01G281100 chr2A 93.220 708 34 5 5 699 93998326 93999032 0.000000e+00 1029.0
10 TraesCS1D01G281100 chr2A 97.059 544 16 0 2433 2976 689768129 689767586 0.000000e+00 917.0
11 TraesCS1D01G281100 chr2A 95.095 367 11 6 2079 2440 689768730 689768366 3.330000e-159 571.0
12 TraesCS1D01G281100 chr6D 93.099 710 35 6 3 699 448352636 448351928 0.000000e+00 1027.0
13 TraesCS1D01G281100 chr6D 88.267 750 55 15 3 739 91075267 91075996 0.000000e+00 867.0
14 TraesCS1D01G281100 chr3D 91.586 725 34 10 1 699 121648997 121648274 0.000000e+00 976.0
15 TraesCS1D01G281100 chr3B 90.039 763 47 13 3 739 487764071 487764830 0.000000e+00 961.0
16 TraesCS1D01G281100 chr5D 91.384 708 41 14 3 699 415245234 415244536 0.000000e+00 952.0
17 TraesCS1D01G281100 chr5D 85.915 71 6 3 672 740 499852656 499852588 4.110000e-09 73.1
18 TraesCS1D01G281100 chr2D 89.958 717 48 13 4 699 72687815 72687102 0.000000e+00 904.0
19 TraesCS1D01G281100 chr2D 89.466 712 50 17 4 699 12769497 12770199 0.000000e+00 876.0
20 TraesCS1D01G281100 chr4A 96.507 544 19 0 2433 2976 144631165 144631708 0.000000e+00 900.0
21 TraesCS1D01G281100 chr4A 96.289 539 20 0 2437 2975 733876882 733877420 0.000000e+00 885.0
22 TraesCS1D01G281100 chr4A 95.772 544 23 0 2433 2976 648135533 648136076 0.000000e+00 878.0
23 TraesCS1D01G281100 chr4A 95.547 539 24 0 2437 2975 699615796 699615258 0.000000e+00 863.0
24 TraesCS1D01G281100 chr4A 95.095 367 12 2 2079 2440 144630563 144630928 9.250000e-160 573.0
25 TraesCS1D01G281100 chr4A 94.809 366 13 2 2080 2440 648134932 648135296 1.550000e-157 566.0
26 TraesCS1D01G281100 chr4A 94.718 284 14 1 2079 2362 195388228 195388510 9.790000e-120 440.0
27 TraesCS1D01G281100 chr4A 89.308 159 8 5 2293 2444 733876520 733876676 1.090000e-44 191.0
28 TraesCS1D01G281100 chr7A 96.481 540 19 0 2437 2976 188887612 188887073 0.000000e+00 893.0
29 TraesCS1D01G281100 chr7A 95.918 539 22 0 2437 2975 173131756 173131218 0.000000e+00 874.0
30 TraesCS1D01G281100 chr7A 95.640 367 10 5 2079 2440 619193855 619193490 4.270000e-163 584.0
31 TraesCS1D01G281100 chr7A 95.368 367 11 2 2079 2440 188888218 188887853 1.990000e-161 579.0
32 TraesCS1D01G281100 chr7A 94.475 362 17 2 2079 2440 173132355 173131997 3.350000e-154 555.0
33 TraesCS1D01G281100 chr7A 86.667 225 20 10 482 699 188055393 188055614 1.070000e-59 241.0
34 TraesCS1D01G281100 chr4D 89.621 713 55 10 3 699 55060432 55059723 0.000000e+00 889.0
35 TraesCS1D01G281100 chr3A 88.172 744 73 9 3 737 444500589 444501326 0.000000e+00 872.0
36 TraesCS1D01G281100 chr6B 84.095 591 65 14 135 702 346712392 346711808 7.250000e-151 544.0


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 TraesCS1D01G281100 chr1D 379458203 379461178 2975 True 5496.0 5496 100.0000 1 2976 1 chr1D.!!$R1 2975
1 TraesCS1D01G281100 chr1D 289949356 289949892 536 False 887.0 887 96.4620 2437 2973 1 chr1D.!!$F1 536
2 TraesCS1D01G281100 chr1B 508545115 508546296 1181 True 1624.0 1624 91.8280 919 2077 1 chr1B.!!$R3 1158
3 TraesCS1D01G281100 chr1B 259785676 259786214 538 True 857.0 857 95.3620 2437 2975 1 chr1B.!!$R2 538
4 TraesCS1D01G281100 chr1A 480550568 480551646 1078 True 1502.0 1502 91.9120 1002 2077 1 chr1A.!!$R1 1075
5 TraesCS1D01G281100 chr7D 422346658 422347373 715 True 1044.0 1044 93.4630 3 699 1 chr7D.!!$R1 696
6 TraesCS1D01G281100 chr2A 93998326 93999032 706 False 1029.0 1029 93.2200 5 699 1 chr2A.!!$F1 694
7 TraesCS1D01G281100 chr2A 689767586 689768730 1144 True 744.0 917 96.0770 2079 2976 2 chr2A.!!$R1 897
8 TraesCS1D01G281100 chr6D 448351928 448352636 708 True 1027.0 1027 93.0990 3 699 1 chr6D.!!$R1 696
9 TraesCS1D01G281100 chr6D 91075267 91075996 729 False 867.0 867 88.2670 3 739 1 chr6D.!!$F1 736
10 TraesCS1D01G281100 chr3D 121648274 121648997 723 True 976.0 976 91.5860 1 699 1 chr3D.!!$R1 698
11 TraesCS1D01G281100 chr3B 487764071 487764830 759 False 961.0 961 90.0390 3 739 1 chr3B.!!$F1 736
12 TraesCS1D01G281100 chr5D 415244536 415245234 698 True 952.0 952 91.3840 3 699 1 chr5D.!!$R1 696
13 TraesCS1D01G281100 chr2D 72687102 72687815 713 True 904.0 904 89.9580 4 699 1 chr2D.!!$R1 695
14 TraesCS1D01G281100 chr2D 12769497 12770199 702 False 876.0 876 89.4660 4 699 1 chr2D.!!$F1 695
15 TraesCS1D01G281100 chr4A 699615258 699615796 538 True 863.0 863 95.5470 2437 2975 1 chr4A.!!$R1 538
16 TraesCS1D01G281100 chr4A 144630563 144631708 1145 False 736.5 900 95.8010 2079 2976 2 chr4A.!!$F2 897
17 TraesCS1D01G281100 chr4A 648134932 648136076 1144 False 722.0 878 95.2905 2080 2976 2 chr4A.!!$F3 896
18 TraesCS1D01G281100 chr4A 733876520 733877420 900 False 538.0 885 92.7985 2293 2975 2 chr4A.!!$F4 682
19 TraesCS1D01G281100 chr7A 188887073 188888218 1145 True 736.0 893 95.9245 2079 2976 2 chr7A.!!$R3 897
20 TraesCS1D01G281100 chr7A 173131218 173132355 1137 True 714.5 874 95.1965 2079 2975 2 chr7A.!!$R2 896
21 TraesCS1D01G281100 chr4D 55059723 55060432 709 True 889.0 889 89.6210 3 699 1 chr4D.!!$R1 696
22 TraesCS1D01G281100 chr3A 444500589 444501326 737 False 872.0 872 88.1720 3 737 1 chr3A.!!$F1 734
23 TraesCS1D01G281100 chr6B 346711808 346712392 584 True 544.0 544 84.0950 135 702 1 chr6B.!!$R1 567

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
720 779 0.034896 ATGAGTTCGTTTGGGTCGCT 59.965 50.0 0.0 0.0 0.0 4.93 F
813 872 0.039035 GCAGTATCCCCAAACCACCA 59.961 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1663 0.390340 TGCGAATCCTCACAGTGAGC 60.390 55.0 23.46 13.26 42.98 4.26 R
2007 2109 0.608308 GCCCAAACTACCACCCAGAC 60.608 60.0 0.00 0.00 0.00 3.51 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
701 760 1.440938 CGACCCAAACGGACAAAGCA 61.441 55.000 0.00 0.00 34.64 3.91
702 761 0.958822 GACCCAAACGGACAAAGCAT 59.041 50.000 0.00 0.00 34.64 3.79
704 763 0.958091 CCCAAACGGACAAAGCATGA 59.042 50.000 0.00 0.00 0.00 3.07
707 766 2.034558 CCAAACGGACAAAGCATGAGTT 59.965 45.455 0.00 0.00 0.00 3.01
720 779 0.034896 ATGAGTTCGTTTGGGTCGCT 59.965 50.000 0.00 0.00 0.00 4.93
721 780 0.878523 TGAGTTCGTTTGGGTCGCTG 60.879 55.000 0.00 0.00 0.00 5.18
739 798 2.143122 CTGCGTTGGAGTTGCTCTAAA 58.857 47.619 0.00 0.00 33.06 1.85
740 799 2.548057 CTGCGTTGGAGTTGCTCTAAAA 59.452 45.455 0.00 0.00 33.06 1.52
741 800 2.548057 TGCGTTGGAGTTGCTCTAAAAG 59.452 45.455 0.00 0.00 33.06 2.27
742 801 2.095718 GCGTTGGAGTTGCTCTAAAAGG 60.096 50.000 0.00 0.00 33.06 3.11
743 802 2.484264 CGTTGGAGTTGCTCTAAAAGGG 59.516 50.000 0.00 0.00 33.06 3.95
744 803 2.200373 TGGAGTTGCTCTAAAAGGGC 57.800 50.000 0.00 0.00 0.00 5.19
745 804 1.271926 TGGAGTTGCTCTAAAAGGGCC 60.272 52.381 0.00 0.00 0.00 5.80
746 805 1.271926 GGAGTTGCTCTAAAAGGGCCA 60.272 52.381 6.18 0.00 0.00 5.36
747 806 2.514803 GAGTTGCTCTAAAAGGGCCAA 58.485 47.619 6.18 0.00 0.00 4.52
748 807 2.229062 GAGTTGCTCTAAAAGGGCCAAC 59.771 50.000 6.18 0.00 0.00 3.77
749 808 1.272490 GTTGCTCTAAAAGGGCCAACC 59.728 52.381 6.18 0.00 40.67 3.77
765 824 6.112734 GGGCCAACCTCTAAAATTTTAATGG 58.887 40.000 19.29 19.29 35.85 3.16
766 825 6.070481 GGGCCAACCTCTAAAATTTTAATGGA 60.070 38.462 24.17 13.62 35.85 3.41
767 826 7.390823 GGCCAACCTCTAAAATTTTAATGGAA 58.609 34.615 24.17 3.20 0.00 3.53
768 827 7.333423 GGCCAACCTCTAAAATTTTAATGGAAC 59.667 37.037 24.17 14.45 0.00 3.62
769 828 8.094548 GCCAACCTCTAAAATTTTAATGGAACT 58.905 33.333 24.17 12.34 0.00 3.01
770 829 9.996554 CCAACCTCTAAAATTTTAATGGAACTT 57.003 29.630 24.17 12.65 0.00 2.66
773 832 9.981114 ACCTCTAAAATTTTAATGGAACTTGTG 57.019 29.630 24.17 7.22 0.00 3.33
774 833 9.423061 CCTCTAAAATTTTAATGGAACTTGTGG 57.577 33.333 17.40 8.13 0.00 4.17
775 834 9.981114 CTCTAAAATTTTAATGGAACTTGTGGT 57.019 29.630 11.62 0.00 0.00 4.16
778 837 7.800155 AAATTTTAATGGAACTTGTGGTTGG 57.200 32.000 0.00 0.00 38.41 3.77
779 838 5.941555 TTTTAATGGAACTTGTGGTTGGT 57.058 34.783 0.00 0.00 38.41 3.67
780 839 5.941555 TTTAATGGAACTTGTGGTTGGTT 57.058 34.783 0.00 0.00 38.41 3.67
781 840 3.817709 AATGGAACTTGTGGTTGGTTG 57.182 42.857 0.00 0.00 38.41 3.77
782 841 1.479709 TGGAACTTGTGGTTGGTTGG 58.520 50.000 0.00 0.00 38.41 3.77
783 842 1.272760 TGGAACTTGTGGTTGGTTGGT 60.273 47.619 0.00 0.00 38.41 3.67
784 843 1.828595 GGAACTTGTGGTTGGTTGGTT 59.171 47.619 0.00 0.00 38.41 3.67
785 844 2.418060 GGAACTTGTGGTTGGTTGGTTG 60.418 50.000 0.00 0.00 38.41 3.77
786 845 2.223803 ACTTGTGGTTGGTTGGTTGA 57.776 45.000 0.00 0.00 0.00 3.18
787 846 2.099405 ACTTGTGGTTGGTTGGTTGAG 58.901 47.619 0.00 0.00 0.00 3.02
788 847 2.291282 ACTTGTGGTTGGTTGGTTGAGA 60.291 45.455 0.00 0.00 0.00 3.27
789 848 2.516227 TGTGGTTGGTTGGTTGAGAA 57.484 45.000 0.00 0.00 0.00 2.87
790 849 2.808919 TGTGGTTGGTTGGTTGAGAAA 58.191 42.857 0.00 0.00 0.00 2.52
791 850 3.165875 TGTGGTTGGTTGGTTGAGAAAA 58.834 40.909 0.00 0.00 0.00 2.29
792 851 3.056465 TGTGGTTGGTTGGTTGAGAAAAC 60.056 43.478 0.00 0.00 0.00 2.43
793 852 3.056465 GTGGTTGGTTGGTTGAGAAAACA 60.056 43.478 0.00 0.00 0.00 2.83
794 853 3.194542 TGGTTGGTTGGTTGAGAAAACAG 59.805 43.478 0.00 0.00 0.00 3.16
795 854 3.186909 GTTGGTTGGTTGAGAAAACAGC 58.813 45.455 0.00 0.00 0.00 4.40
796 855 2.451490 TGGTTGGTTGAGAAAACAGCA 58.549 42.857 0.00 0.00 0.00 4.41
797 856 2.426738 TGGTTGGTTGAGAAAACAGCAG 59.573 45.455 0.00 0.00 0.00 4.24
798 857 2.427095 GGTTGGTTGAGAAAACAGCAGT 59.573 45.455 0.00 0.00 0.00 4.40
799 858 3.630312 GGTTGGTTGAGAAAACAGCAGTA 59.370 43.478 0.00 0.00 0.00 2.74
800 859 4.278419 GGTTGGTTGAGAAAACAGCAGTAT 59.722 41.667 0.00 0.00 0.00 2.12
801 860 5.452777 GTTGGTTGAGAAAACAGCAGTATC 58.547 41.667 0.00 0.00 0.00 2.24
802 861 4.072131 TGGTTGAGAAAACAGCAGTATCC 58.928 43.478 0.00 0.00 0.00 2.59
803 862 3.440522 GGTTGAGAAAACAGCAGTATCCC 59.559 47.826 0.00 0.00 0.00 3.85
804 863 3.350219 TGAGAAAACAGCAGTATCCCC 57.650 47.619 0.00 0.00 0.00 4.81
805 864 2.642311 TGAGAAAACAGCAGTATCCCCA 59.358 45.455 0.00 0.00 0.00 4.96
806 865 3.073798 TGAGAAAACAGCAGTATCCCCAA 59.926 43.478 0.00 0.00 0.00 4.12
807 866 4.079253 GAGAAAACAGCAGTATCCCCAAA 58.921 43.478 0.00 0.00 0.00 3.28
808 867 3.826729 AGAAAACAGCAGTATCCCCAAAC 59.173 43.478 0.00 0.00 0.00 2.93
809 868 2.215942 AACAGCAGTATCCCCAAACC 57.784 50.000 0.00 0.00 0.00 3.27
810 869 1.072266 ACAGCAGTATCCCCAAACCA 58.928 50.000 0.00 0.00 0.00 3.67
811 870 1.271926 ACAGCAGTATCCCCAAACCAC 60.272 52.381 0.00 0.00 0.00 4.16
812 871 0.331616 AGCAGTATCCCCAAACCACC 59.668 55.000 0.00 0.00 0.00 4.61
813 872 0.039035 GCAGTATCCCCAAACCACCA 59.961 55.000 0.00 0.00 0.00 4.17
814 873 1.955208 GCAGTATCCCCAAACCACCAG 60.955 57.143 0.00 0.00 0.00 4.00
815 874 1.633432 CAGTATCCCCAAACCACCAGA 59.367 52.381 0.00 0.00 0.00 3.86
816 875 1.916181 AGTATCCCCAAACCACCAGAG 59.084 52.381 0.00 0.00 0.00 3.35
817 876 1.633945 GTATCCCCAAACCACCAGAGT 59.366 52.381 0.00 0.00 0.00 3.24
818 877 1.158007 ATCCCCAAACCACCAGAGTT 58.842 50.000 0.00 0.00 0.00 3.01
819 878 0.476771 TCCCCAAACCACCAGAGTTC 59.523 55.000 0.00 0.00 0.00 3.01
820 879 0.184933 CCCCAAACCACCAGAGTTCA 59.815 55.000 0.00 0.00 0.00 3.18
821 880 1.410932 CCCCAAACCACCAGAGTTCAA 60.411 52.381 0.00 0.00 0.00 2.69
822 881 1.956477 CCCAAACCACCAGAGTTCAAG 59.044 52.381 0.00 0.00 0.00 3.02
823 882 2.654863 CCAAACCACCAGAGTTCAAGT 58.345 47.619 0.00 0.00 0.00 3.16
824 883 3.023832 CCAAACCACCAGAGTTCAAGTT 58.976 45.455 0.00 0.00 0.00 2.66
825 884 3.066760 CCAAACCACCAGAGTTCAAGTTC 59.933 47.826 0.00 0.00 0.00 3.01
826 885 3.933861 AACCACCAGAGTTCAAGTTCT 57.066 42.857 0.00 0.00 0.00 3.01
827 886 5.123227 CAAACCACCAGAGTTCAAGTTCTA 58.877 41.667 0.00 0.00 0.00 2.10
828 887 5.367945 AACCACCAGAGTTCAAGTTCTAA 57.632 39.130 0.00 0.00 0.00 2.10
829 888 5.367945 ACCACCAGAGTTCAAGTTCTAAA 57.632 39.130 0.00 0.00 0.00 1.85
830 889 5.123936 ACCACCAGAGTTCAAGTTCTAAAC 58.876 41.667 0.00 0.00 0.00 2.01
831 890 5.123227 CCACCAGAGTTCAAGTTCTAAACA 58.877 41.667 0.00 0.00 0.00 2.83
832 891 5.765182 CCACCAGAGTTCAAGTTCTAAACAT 59.235 40.000 0.00 0.00 0.00 2.71
833 892 6.934645 CCACCAGAGTTCAAGTTCTAAACATA 59.065 38.462 0.00 0.00 0.00 2.29
834 893 7.444183 CCACCAGAGTTCAAGTTCTAAACATAA 59.556 37.037 0.00 0.00 0.00 1.90
835 894 8.283291 CACCAGAGTTCAAGTTCTAAACATAAC 58.717 37.037 0.00 0.00 0.00 1.89
836 895 7.990886 ACCAGAGTTCAAGTTCTAAACATAACA 59.009 33.333 0.00 0.00 0.00 2.41
837 896 9.003658 CCAGAGTTCAAGTTCTAAACATAACAT 57.996 33.333 0.00 0.00 0.00 2.71
847 906 8.338259 AGTTCTAAACATAACATTGATGATCGC 58.662 33.333 0.00 0.00 0.00 4.58
848 907 7.784633 TCTAAACATAACATTGATGATCGCA 57.215 32.000 0.00 0.00 0.00 5.10
849 908 8.382030 TCTAAACATAACATTGATGATCGCAT 57.618 30.769 0.00 0.00 37.47 4.73
850 909 8.839343 TCTAAACATAACATTGATGATCGCATT 58.161 29.630 0.00 0.00 34.11 3.56
851 910 9.454585 CTAAACATAACATTGATGATCGCATTT 57.545 29.630 0.00 0.00 34.11 2.32
852 911 8.706492 AAACATAACATTGATGATCGCATTTT 57.294 26.923 0.00 0.00 34.11 1.82
853 912 8.706492 AACATAACATTGATGATCGCATTTTT 57.294 26.923 0.00 0.00 34.11 1.94
876 935 6.799926 TTTGAATTTATTTCAGGCCTTTGC 57.200 33.333 0.00 0.00 44.90 3.68
877 936 4.493547 TGAATTTATTTCAGGCCTTTGCG 58.506 39.130 0.00 0.00 39.44 4.85
878 937 4.021544 TGAATTTATTTCAGGCCTTTGCGT 60.022 37.500 0.00 0.00 39.44 5.24
879 938 4.535526 ATTTATTTCAGGCCTTTGCGTT 57.464 36.364 0.00 0.00 38.85 4.84
880 939 5.652994 ATTTATTTCAGGCCTTTGCGTTA 57.347 34.783 0.00 0.00 38.85 3.18
881 940 5.455056 TTTATTTCAGGCCTTTGCGTTAA 57.545 34.783 0.00 0.00 38.85 2.01
882 941 5.455056 TTATTTCAGGCCTTTGCGTTAAA 57.545 34.783 0.00 0.00 38.85 1.52
883 942 3.363341 TTTCAGGCCTTTGCGTTAAAG 57.637 42.857 0.00 7.16 44.35 1.85
893 952 2.631418 TGCGTTAAAGAGAGGAGACG 57.369 50.000 0.00 0.00 0.00 4.18
894 953 1.884579 TGCGTTAAAGAGAGGAGACGT 59.115 47.619 0.00 0.00 33.46 4.34
895 954 2.295349 TGCGTTAAAGAGAGGAGACGTT 59.705 45.455 0.00 0.00 33.46 3.99
896 955 2.662156 GCGTTAAAGAGAGGAGACGTTG 59.338 50.000 0.00 0.00 33.46 4.10
897 956 3.856267 GCGTTAAAGAGAGGAGACGTTGT 60.856 47.826 0.00 0.00 33.46 3.32
898 957 3.913163 CGTTAAAGAGAGGAGACGTTGTC 59.087 47.826 0.00 0.00 0.00 3.18
899 958 2.708386 AAAGAGAGGAGACGTTGTCG 57.292 50.000 0.00 0.00 37.67 4.35
930 991 5.479716 AAATTAAACGAAGTGATAGGGCG 57.520 39.130 0.00 0.00 45.00 6.13
974 1037 5.396324 GCCAAGGGGAGAAAAGAAAAGAAAA 60.396 40.000 0.00 0.00 35.59 2.29
977 1040 4.341235 AGGGGAGAAAAGAAAAGAAAACCG 59.659 41.667 0.00 0.00 0.00 4.44
994 1057 0.989602 CCGAACCCCCTAGAACCTTT 59.010 55.000 0.00 0.00 0.00 3.11
999 1062 0.991920 CCCCCTAGAACCTTTCTGCA 59.008 55.000 0.00 0.00 40.94 4.41
1011 1080 1.249469 TTTCTGCAATGGCCATCGCA 61.249 50.000 28.95 28.95 40.13 5.10
1344 1413 7.307870 GCTGATCTGAAGATGTAACAATGGATC 60.308 40.741 3.42 0.00 34.37 3.36
1449 1518 2.359169 GGACCCATCAGGACGAGCA 61.359 63.158 0.00 0.00 39.89 4.26
1464 1533 1.000993 AGCAGATCGAGGTGGAGGT 59.999 57.895 0.00 0.00 0.00 3.85
1578 1650 1.308998 GGTGGCGATGTCCCAAATAG 58.691 55.000 0.00 0.00 33.39 1.73
1591 1663 2.494059 CCAAATAGGTACTGCATCCCG 58.506 52.381 0.00 0.00 41.52 5.14
1615 1687 1.089920 CTGTGAGGATTCGCAAAGGG 58.910 55.000 0.00 0.00 42.84 3.95
1617 1689 1.378514 TGAGGATTCGCAAAGGGGC 60.379 57.895 0.00 0.00 0.00 5.80
1640 1715 1.744798 CGGCTTCATGCTTGGAGATCA 60.745 52.381 12.02 0.00 42.39 2.92
1836 1938 0.106967 GACATTCCTGGGGAGCTTCC 60.107 60.000 0.70 0.70 35.23 3.46
1879 1981 1.112113 GAAGTAGGGGCATCTCGACA 58.888 55.000 0.00 0.00 0.00 4.35
1889 1991 3.270877 GGCATCTCGACACATTTTACCT 58.729 45.455 0.00 0.00 0.00 3.08
1903 2005 4.614555 TTTTACCTACTTCATGCATGCG 57.385 40.909 22.25 16.64 0.00 4.73
1966 2068 4.199310 TGAGAAAACTCAAAGGTCTGGTG 58.801 43.478 0.00 0.00 0.00 4.17
1997 2099 3.208747 TGGAGTGGAAGTTCAGGTTTC 57.791 47.619 5.01 0.00 0.00 2.78
2007 2109 6.095440 TGGAAGTTCAGGTTTCTTTCTTTCAG 59.905 38.462 5.01 0.00 0.00 3.02
2025 2127 1.064825 AGTCTGGGTGGTAGTTTGGG 58.935 55.000 0.00 0.00 0.00 4.12
2032 2134 2.243810 GGTGGTAGTTTGGGCAAATGA 58.756 47.619 0.00 0.00 32.36 2.57
2040 2147 4.536765 AGTTTGGGCAAATGATACTAGGG 58.463 43.478 0.00 0.00 32.36 3.53
2077 2184 7.829725 TGGAACATGAATCCTACAAAAATGAG 58.170 34.615 18.63 0.00 37.85 2.90
2580 2944 4.722700 GTGGCCACATGCTCCGGT 62.723 66.667 31.23 0.00 40.92 5.28
2699 3063 1.616725 GGATGATTGGTGGGCTTGTCA 60.617 52.381 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
241 255 1.097547 GCATGGCCTCGTAGTGCATT 61.098 55.000 3.32 0.00 35.93 3.56
246 260 1.264749 TTGGAGCATGGCCTCGTAGT 61.265 55.000 3.32 0.00 32.57 2.73
463 495 4.435436 CGCACGCTGCCCTAGACA 62.435 66.667 0.00 0.00 41.12 3.41
701 760 0.034896 AGCGACCCAAACGAACTCAT 59.965 50.000 0.00 0.00 0.00 2.90
702 761 0.878523 CAGCGACCCAAACGAACTCA 60.879 55.000 0.00 0.00 0.00 3.41
704 763 2.251642 GCAGCGACCCAAACGAACT 61.252 57.895 0.00 0.00 0.00 3.01
707 766 4.595538 ACGCAGCGACCCAAACGA 62.596 61.111 24.65 0.00 0.00 3.85
720 779 2.248280 TTTAGAGCAACTCCAACGCA 57.752 45.000 0.00 0.00 0.00 5.24
721 780 2.095718 CCTTTTAGAGCAACTCCAACGC 60.096 50.000 0.00 0.00 0.00 4.84
739 798 7.394016 CATTAAAATTTTAGAGGTTGGCCCTT 58.606 34.615 10.40 0.00 46.51 3.95
741 800 6.070481 TCCATTAAAATTTTAGAGGTTGGCCC 60.070 38.462 20.91 0.00 34.57 5.80
742 801 6.941857 TCCATTAAAATTTTAGAGGTTGGCC 58.058 36.000 20.91 0.00 0.00 5.36
743 802 8.094548 AGTTCCATTAAAATTTTAGAGGTTGGC 58.905 33.333 20.91 13.61 0.00 4.52
744 803 9.996554 AAGTTCCATTAAAATTTTAGAGGTTGG 57.003 29.630 20.91 17.29 0.00 3.77
747 806 9.981114 CACAAGTTCCATTAAAATTTTAGAGGT 57.019 29.630 20.91 7.87 0.00 3.85
748 807 9.423061 CCACAAGTTCCATTAAAATTTTAGAGG 57.577 33.333 17.95 17.95 0.00 3.69
749 808 9.981114 ACCACAAGTTCCATTAAAATTTTAGAG 57.019 29.630 10.40 7.51 0.00 2.43
752 811 9.331282 CCAACCACAAGTTCCATTAAAATTTTA 57.669 29.630 6.54 6.54 36.18 1.52
753 812 7.831690 ACCAACCACAAGTTCCATTAAAATTTT 59.168 29.630 8.75 8.75 36.18 1.82
754 813 7.342581 ACCAACCACAAGTTCCATTAAAATTT 58.657 30.769 0.00 0.00 36.18 1.82
755 814 6.894682 ACCAACCACAAGTTCCATTAAAATT 58.105 32.000 0.00 0.00 36.18 1.82
756 815 6.493189 ACCAACCACAAGTTCCATTAAAAT 57.507 33.333 0.00 0.00 36.18 1.82
757 816 5.941555 ACCAACCACAAGTTCCATTAAAA 57.058 34.783 0.00 0.00 36.18 1.52
758 817 5.395768 CCAACCAACCACAAGTTCCATTAAA 60.396 40.000 0.00 0.00 36.18 1.52
759 818 4.100189 CCAACCAACCACAAGTTCCATTAA 59.900 41.667 0.00 0.00 36.18 1.40
760 819 3.639094 CCAACCAACCACAAGTTCCATTA 59.361 43.478 0.00 0.00 36.18 1.90
761 820 2.433970 CCAACCAACCACAAGTTCCATT 59.566 45.455 0.00 0.00 36.18 3.16
762 821 2.038659 CCAACCAACCACAAGTTCCAT 58.961 47.619 0.00 0.00 36.18 3.41
763 822 1.272760 ACCAACCAACCACAAGTTCCA 60.273 47.619 0.00 0.00 36.18 3.53
764 823 1.480789 ACCAACCAACCACAAGTTCC 58.519 50.000 0.00 0.00 36.18 3.62
765 824 2.494073 TCAACCAACCAACCACAAGTTC 59.506 45.455 0.00 0.00 36.18 3.01
766 825 2.495669 CTCAACCAACCAACCACAAGTT 59.504 45.455 0.00 0.00 40.16 2.66
767 826 2.099405 CTCAACCAACCAACCACAAGT 58.901 47.619 0.00 0.00 0.00 3.16
768 827 2.374184 TCTCAACCAACCAACCACAAG 58.626 47.619 0.00 0.00 0.00 3.16
769 828 2.516227 TCTCAACCAACCAACCACAA 57.484 45.000 0.00 0.00 0.00 3.33
770 829 2.516227 TTCTCAACCAACCAACCACA 57.484 45.000 0.00 0.00 0.00 4.17
771 830 3.056465 TGTTTTCTCAACCAACCAACCAC 60.056 43.478 0.00 0.00 0.00 4.16
772 831 3.165875 TGTTTTCTCAACCAACCAACCA 58.834 40.909 0.00 0.00 0.00 3.67
773 832 3.780902 CTGTTTTCTCAACCAACCAACC 58.219 45.455 0.00 0.00 0.00 3.77
774 833 3.186909 GCTGTTTTCTCAACCAACCAAC 58.813 45.455 0.00 0.00 0.00 3.77
775 834 2.828520 TGCTGTTTTCTCAACCAACCAA 59.171 40.909 0.00 0.00 0.00 3.67
776 835 2.426738 CTGCTGTTTTCTCAACCAACCA 59.573 45.455 0.00 0.00 0.00 3.67
777 836 2.427095 ACTGCTGTTTTCTCAACCAACC 59.573 45.455 0.00 0.00 0.00 3.77
778 837 3.782889 ACTGCTGTTTTCTCAACCAAC 57.217 42.857 0.00 0.00 0.00 3.77
779 838 4.518970 GGATACTGCTGTTTTCTCAACCAA 59.481 41.667 0.09 0.00 0.00 3.67
780 839 4.072131 GGATACTGCTGTTTTCTCAACCA 58.928 43.478 0.09 0.00 0.00 3.67
781 840 3.440522 GGGATACTGCTGTTTTCTCAACC 59.559 47.826 0.09 0.00 0.00 3.77
782 841 3.440522 GGGGATACTGCTGTTTTCTCAAC 59.559 47.826 0.09 0.00 0.00 3.18
783 842 3.073798 TGGGGATACTGCTGTTTTCTCAA 59.926 43.478 0.09 0.00 0.00 3.02
784 843 2.642311 TGGGGATACTGCTGTTTTCTCA 59.358 45.455 0.09 0.00 0.00 3.27
785 844 3.350219 TGGGGATACTGCTGTTTTCTC 57.650 47.619 0.09 0.00 0.00 2.87
786 845 3.806949 TTGGGGATACTGCTGTTTTCT 57.193 42.857 0.09 0.00 0.00 2.52
787 846 3.056821 GGTTTGGGGATACTGCTGTTTTC 60.057 47.826 0.09 0.00 0.00 2.29
788 847 2.897326 GGTTTGGGGATACTGCTGTTTT 59.103 45.455 0.09 0.00 0.00 2.43
789 848 2.158385 TGGTTTGGGGATACTGCTGTTT 60.158 45.455 0.09 0.00 0.00 2.83
790 849 1.427368 TGGTTTGGGGATACTGCTGTT 59.573 47.619 0.09 0.00 0.00 3.16
791 850 1.072266 TGGTTTGGGGATACTGCTGT 58.928 50.000 0.66 0.66 0.00 4.40
792 851 1.463674 GTGGTTTGGGGATACTGCTG 58.536 55.000 0.00 0.00 0.00 4.41
793 852 0.331616 GGTGGTTTGGGGATACTGCT 59.668 55.000 0.00 0.00 0.00 4.24
794 853 0.039035 TGGTGGTTTGGGGATACTGC 59.961 55.000 0.00 0.00 0.00 4.40
795 854 1.633432 TCTGGTGGTTTGGGGATACTG 59.367 52.381 0.00 0.00 0.00 2.74
796 855 1.916181 CTCTGGTGGTTTGGGGATACT 59.084 52.381 0.00 0.00 0.00 2.12
797 856 1.633945 ACTCTGGTGGTTTGGGGATAC 59.366 52.381 0.00 0.00 0.00 2.24
798 857 2.053747 ACTCTGGTGGTTTGGGGATA 57.946 50.000 0.00 0.00 0.00 2.59
799 858 1.075536 GAACTCTGGTGGTTTGGGGAT 59.924 52.381 0.00 0.00 0.00 3.85
800 859 0.476771 GAACTCTGGTGGTTTGGGGA 59.523 55.000 0.00 0.00 0.00 4.81
801 860 0.184933 TGAACTCTGGTGGTTTGGGG 59.815 55.000 0.00 0.00 0.00 4.96
802 861 1.956477 CTTGAACTCTGGTGGTTTGGG 59.044 52.381 0.00 0.00 0.00 4.12
803 862 2.654863 ACTTGAACTCTGGTGGTTTGG 58.345 47.619 0.00 0.00 0.00 3.28
804 863 3.947834 AGAACTTGAACTCTGGTGGTTTG 59.052 43.478 0.00 0.00 0.00 2.93
805 864 4.236527 AGAACTTGAACTCTGGTGGTTT 57.763 40.909 0.00 0.00 0.00 3.27
806 865 3.933861 AGAACTTGAACTCTGGTGGTT 57.066 42.857 0.00 0.00 0.00 3.67
807 866 5.123936 GTTTAGAACTTGAACTCTGGTGGT 58.876 41.667 0.00 0.00 0.00 4.16
808 867 5.123227 TGTTTAGAACTTGAACTCTGGTGG 58.877 41.667 0.00 0.00 0.00 4.61
809 868 6.867662 ATGTTTAGAACTTGAACTCTGGTG 57.132 37.500 0.00 0.00 0.00 4.17
810 869 7.990886 TGTTATGTTTAGAACTTGAACTCTGGT 59.009 33.333 0.00 0.00 0.00 4.00
811 870 8.378172 TGTTATGTTTAGAACTTGAACTCTGG 57.622 34.615 0.00 0.00 0.00 3.86
821 880 8.338259 GCGATCATCAATGTTATGTTTAGAACT 58.662 33.333 0.00 0.00 0.00 3.01
822 881 8.122330 TGCGATCATCAATGTTATGTTTAGAAC 58.878 33.333 0.00 0.00 0.00 3.01
823 882 8.207521 TGCGATCATCAATGTTATGTTTAGAA 57.792 30.769 0.00 0.00 0.00 2.10
824 883 7.784633 TGCGATCATCAATGTTATGTTTAGA 57.215 32.000 0.00 0.00 0.00 2.10
825 884 9.454585 AAATGCGATCATCAATGTTATGTTTAG 57.545 29.630 0.00 0.00 31.27 1.85
826 885 9.800433 AAAATGCGATCATCAATGTTATGTTTA 57.200 25.926 0.00 0.00 31.27 2.01
827 886 8.706492 AAAATGCGATCATCAATGTTATGTTT 57.294 26.923 0.00 0.00 31.27 2.83
828 887 8.706492 AAAAATGCGATCATCAATGTTATGTT 57.294 26.923 0.00 0.00 31.27 2.71
855 914 4.021544 ACGCAAAGGCCTGAAATAAATTCA 60.022 37.500 5.69 0.00 45.23 2.57
856 915 4.494484 ACGCAAAGGCCTGAAATAAATTC 58.506 39.130 5.69 0.00 36.11 2.17
857 916 4.535526 ACGCAAAGGCCTGAAATAAATT 57.464 36.364 5.69 0.00 36.38 1.82
858 917 4.535526 AACGCAAAGGCCTGAAATAAAT 57.464 36.364 5.69 0.00 36.38 1.40
859 918 5.455056 TTAACGCAAAGGCCTGAAATAAA 57.545 34.783 5.69 0.00 36.38 1.40
860 919 5.241949 TCTTTAACGCAAAGGCCTGAAATAA 59.758 36.000 5.69 0.00 43.37 1.40
861 920 4.762765 TCTTTAACGCAAAGGCCTGAAATA 59.237 37.500 5.69 0.00 43.37 1.40
862 921 3.572255 TCTTTAACGCAAAGGCCTGAAAT 59.428 39.130 5.69 0.00 43.37 2.17
863 922 2.952978 TCTTTAACGCAAAGGCCTGAAA 59.047 40.909 5.69 0.00 43.37 2.69
864 923 2.552315 CTCTTTAACGCAAAGGCCTGAA 59.448 45.455 5.69 0.00 43.37 3.02
865 924 2.151202 CTCTTTAACGCAAAGGCCTGA 58.849 47.619 5.69 0.00 43.37 3.86
866 925 2.151202 TCTCTTTAACGCAAAGGCCTG 58.849 47.619 5.69 0.00 43.37 4.85
867 926 2.427506 CTCTCTTTAACGCAAAGGCCT 58.572 47.619 0.00 0.00 43.37 5.19
868 927 1.468914 CCTCTCTTTAACGCAAAGGCC 59.531 52.381 0.00 0.00 43.37 5.19
869 928 2.416893 CTCCTCTCTTTAACGCAAAGGC 59.583 50.000 9.50 0.00 43.37 4.35
870 929 3.680458 GTCTCCTCTCTTTAACGCAAAGG 59.320 47.826 9.50 2.67 43.37 3.11
871 930 3.365220 CGTCTCCTCTCTTTAACGCAAAG 59.635 47.826 4.18 4.18 44.36 2.77
872 931 3.243636 ACGTCTCCTCTCTTTAACGCAAA 60.244 43.478 0.00 0.00 33.68 3.68
873 932 2.295349 ACGTCTCCTCTCTTTAACGCAA 59.705 45.455 0.00 0.00 33.68 4.85
874 933 1.884579 ACGTCTCCTCTCTTTAACGCA 59.115 47.619 0.00 0.00 33.68 5.24
875 934 2.633199 ACGTCTCCTCTCTTTAACGC 57.367 50.000 0.00 0.00 33.68 4.84
876 935 3.898529 ACAACGTCTCCTCTCTTTAACG 58.101 45.455 0.00 0.00 36.29 3.18
877 936 3.913163 CGACAACGTCTCCTCTCTTTAAC 59.087 47.826 0.00 0.00 34.56 2.01
878 937 4.156664 CGACAACGTCTCCTCTCTTTAA 57.843 45.455 0.00 0.00 34.56 1.52
879 938 3.826236 CGACAACGTCTCCTCTCTTTA 57.174 47.619 0.00 0.00 34.56 1.85
880 939 2.708386 CGACAACGTCTCCTCTCTTT 57.292 50.000 0.00 0.00 34.56 2.52
906 965 6.072342 ACGCCCTATCACTTCGTTTAATTTTT 60.072 34.615 0.00 0.00 0.00 1.94
907 966 5.413523 ACGCCCTATCACTTCGTTTAATTTT 59.586 36.000 0.00 0.00 0.00 1.82
908 967 4.939439 ACGCCCTATCACTTCGTTTAATTT 59.061 37.500 0.00 0.00 0.00 1.82
909 968 4.510571 ACGCCCTATCACTTCGTTTAATT 58.489 39.130 0.00 0.00 0.00 1.40
910 969 4.117685 GACGCCCTATCACTTCGTTTAAT 58.882 43.478 0.00 0.00 33.21 1.40
911 970 3.056678 TGACGCCCTATCACTTCGTTTAA 60.057 43.478 0.00 0.00 33.21 1.52
912 971 2.492881 TGACGCCCTATCACTTCGTTTA 59.507 45.455 0.00 0.00 33.21 2.01
913 972 1.274167 TGACGCCCTATCACTTCGTTT 59.726 47.619 0.00 0.00 33.21 3.60
914 973 0.892755 TGACGCCCTATCACTTCGTT 59.107 50.000 0.00 0.00 33.21 3.85
915 974 1.112113 ATGACGCCCTATCACTTCGT 58.888 50.000 0.00 0.00 35.98 3.85
916 975 1.067060 TCATGACGCCCTATCACTTCG 59.933 52.381 0.00 0.00 0.00 3.79
917 976 2.362397 TCTCATGACGCCCTATCACTTC 59.638 50.000 0.00 0.00 0.00 3.01
928 987 1.587613 GAGACGCCTCTCATGACGC 60.588 63.158 7.73 0.00 42.50 5.19
930 991 0.028770 CTCGAGACGCCTCTCATGAC 59.971 60.000 6.58 0.00 43.03 3.06
942 1003 2.683933 TCCCCTTGGCCTCGAGAC 60.684 66.667 15.71 0.57 0.00 3.36
947 1008 0.698818 TCTTTTCTCCCCTTGGCCTC 59.301 55.000 3.32 0.00 0.00 4.70
948 1009 1.158007 TTCTTTTCTCCCCTTGGCCT 58.842 50.000 3.32 0.00 0.00 5.19
949 1010 2.009681 TTTCTTTTCTCCCCTTGGCC 57.990 50.000 0.00 0.00 0.00 5.36
951 1012 5.869649 TTTCTTTTCTTTTCTCCCCTTGG 57.130 39.130 0.00 0.00 0.00 3.61
953 1014 5.163447 CGGTTTTCTTTTCTTTTCTCCCCTT 60.163 40.000 0.00 0.00 0.00 3.95
974 1037 0.178882 AAGGTTCTAGGGGGTTCGGT 60.179 55.000 0.00 0.00 0.00 4.69
977 1040 2.618302 GCAGAAAGGTTCTAGGGGGTTC 60.618 54.545 0.00 0.00 38.11 3.62
999 1062 3.289834 GCGGATGCGATGGCCATT 61.290 61.111 21.84 2.81 38.85 3.16
1131 1200 1.456705 GGCGGAGAGGGATGAGAGT 60.457 63.158 0.00 0.00 0.00 3.24
1449 1518 1.000993 AGCACCTCCACCTCGATCT 59.999 57.895 0.00 0.00 0.00 2.75
1512 1581 0.915364 AGCTTGGTCATCCTCTTCCC 59.085 55.000 0.00 0.00 34.23 3.97
1591 1663 0.390340 TGCGAATCCTCACAGTGAGC 60.390 55.000 23.46 13.26 42.98 4.26
1836 1938 2.898705 AGTAGAGATGCAAAGCCTTCG 58.101 47.619 0.00 0.00 0.00 3.79
1879 1981 5.449041 CGCATGCATGAAGTAGGTAAAATGT 60.449 40.000 30.64 0.00 0.00 2.71
1903 2005 3.877508 GGCACTCCTTGGTTATCATGTAC 59.122 47.826 0.00 0.00 0.00 2.90
1966 2068 2.879103 TCCACTCCATTCAACCCTTC 57.121 50.000 0.00 0.00 0.00 3.46
1997 2099 3.214696 ACCACCCAGACTGAAAGAAAG 57.785 47.619 3.32 0.00 37.43 2.62
2007 2109 0.608308 GCCCAAACTACCACCCAGAC 60.608 60.000 0.00 0.00 0.00 3.51
2025 2127 5.105997 GGAATGCATCCCTAGTATCATTTGC 60.106 44.000 0.00 0.00 43.00 3.68
2040 2147 6.349944 GGATTCATGTTCCATAGGAATGCATC 60.350 42.308 0.00 3.27 44.04 3.91
2127 2234 2.329399 GGGAGAGGAGGAGGAGGGT 61.329 68.421 0.00 0.00 0.00 4.34
2406 2526 4.735132 GCACGCACTAGACGCCCA 62.735 66.667 0.00 0.00 0.00 5.36
2571 2935 2.927856 TCCACCACACCGGAGCAT 60.928 61.111 9.46 0.00 38.63 3.79
2790 3154 3.851128 TCACGACGGCCACAACCA 61.851 61.111 2.24 0.00 0.00 3.67
2793 3157 2.981977 GAAGGTCACGACGGCCACAA 62.982 60.000 2.24 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.