Multiple sequence alignment - TraesCS2D01G413600

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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 TraesCS2D01G413600 chr2D 100.000 4395 0 0 1 4395 528076104 528080498 0.000000e+00 8117
1 TraesCS2D01G413600 chr2B 97.143 2975 78 3 921 3890 625917013 625919985 0.000000e+00 5016
2 TraesCS2D01G413600 chr2B 93.411 516 16 3 3886 4395 625926662 625927165 0.000000e+00 749
3 TraesCS2D01G413600 chr2B 81.523 709 105 17 7 694 439421711 439422414 1.070000e-155 560
4 TraesCS2D01G413600 chr2A 92.345 3070 230 4 969 4037 672836676 672839741 0.000000e+00 4362
5 TraesCS2D01G413600 chr2A 91.034 290 19 4 4103 4386 672839746 672840034 6.900000e-103 385
6 TraesCS2D01G413600 chr1D 75.776 2803 613 57 1000 3769 44651977 44649208 0.000000e+00 1354
7 TraesCS2D01G413600 chr1D 81.694 803 107 30 4 781 424732930 424732143 2.230000e-177 632
8 TraesCS2D01G413600 chr5D 82.475 816 117 20 7 805 458557569 458558375 0.000000e+00 691
9 TraesCS2D01G413600 chr7D 85.565 672 81 12 7 665 536462041 536462709 0.000000e+00 689
10 TraesCS2D01G413600 chr3B 80.467 814 136 19 6 805 199549423 199550227 6.290000e-168 601
11 TraesCS2D01G413600 chr3B 80.025 816 136 21 6 805 199593753 199594557 2.950000e-161 579
12 TraesCS2D01G413600 chr6A 80.392 816 135 21 5 801 376921417 376922226 8.140000e-167 597
13 TraesCS2D01G413600 chr4D 80.294 817 132 25 6 803 319338125 319337319 1.360000e-164 590
14 TraesCS2D01G413600 chr3D 79.577 803 125 28 21 803 446755918 446756701 5.000000e-149 538


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 TraesCS2D01G413600 chr2D 528076104 528080498 4394 False 8117.0 8117 100.0000 1 4395 1 chr2D.!!$F1 4394
1 TraesCS2D01G413600 chr2B 625917013 625919985 2972 False 5016.0 5016 97.1430 921 3890 1 chr2B.!!$F2 2969
2 TraesCS2D01G413600 chr2B 625926662 625927165 503 False 749.0 749 93.4110 3886 4395 1 chr2B.!!$F3 509
3 TraesCS2D01G413600 chr2B 439421711 439422414 703 False 560.0 560 81.5230 7 694 1 chr2B.!!$F1 687
4 TraesCS2D01G413600 chr2A 672836676 672840034 3358 False 2373.5 4362 91.6895 969 4386 2 chr2A.!!$F1 3417
5 TraesCS2D01G413600 chr1D 44649208 44651977 2769 True 1354.0 1354 75.7760 1000 3769 1 chr1D.!!$R1 2769
6 TraesCS2D01G413600 chr1D 424732143 424732930 787 True 632.0 632 81.6940 4 781 1 chr1D.!!$R2 777
7 TraesCS2D01G413600 chr5D 458557569 458558375 806 False 691.0 691 82.4750 7 805 1 chr5D.!!$F1 798
8 TraesCS2D01G413600 chr7D 536462041 536462709 668 False 689.0 689 85.5650 7 665 1 chr7D.!!$F1 658
9 TraesCS2D01G413600 chr3B 199549423 199550227 804 False 601.0 601 80.4670 6 805 1 chr3B.!!$F1 799
10 TraesCS2D01G413600 chr3B 199593753 199594557 804 False 579.0 579 80.0250 6 805 1 chr3B.!!$F2 799
11 TraesCS2D01G413600 chr6A 376921417 376922226 809 False 597.0 597 80.3920 5 801 1 chr6A.!!$F1 796
12 TraesCS2D01G413600 chr4D 319337319 319338125 806 True 590.0 590 80.2940 6 803 1 chr4D.!!$R1 797
13 TraesCS2D01G413600 chr3D 446755918 446756701 783 False 538.0 538 79.5770 21 803 1 chr3D.!!$F1 782

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
917 973 0.313672 AGAGAGAATCGGATCGCTGC 59.686 55.000 0.0 0.0 42.67 5.25 F
918 974 0.665972 GAGAGAATCGGATCGCTGCC 60.666 60.000 0.0 0.0 42.67 4.85 F
927 983 1.446099 GATCGCTGCCGTCAGTCAA 60.446 57.895 0.0 0.0 42.29 3.18 F
1630 1700 1.874345 CGTGTACAAGGAGGTCGCCT 61.874 60.000 0.0 0.0 40.93 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2017 1.371467 ACATGATGGTCCTGGTGGAA 58.629 50.0 0.00 0.0 45.18 3.53 R
2445 2518 1.710013 TCGCTCGTCCAAACTCATTC 58.290 50.0 0.00 0.0 0.00 2.67 R
2952 3025 1.263356 CTGTACCAGGGAACGGAGAA 58.737 55.0 0.00 0.0 0.00 2.87 R
3567 3640 0.391661 TGAGGTTCTCGATGCCTTGC 60.392 55.0 4.42 0.0 32.35 4.01 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
43 45 3.699894 CACCTGGCTCAGCTCCGT 61.700 66.667 0.00 0.00 0.00 4.69
44 46 2.925170 ACCTGGCTCAGCTCCGTT 60.925 61.111 0.00 0.00 0.00 4.44
90 92 1.466025 TTGCGGGTAGACGTGGAAGT 61.466 55.000 0.00 0.00 35.98 3.01
146 148 2.187946 GACAGCACCATCCGAGGG 59.812 66.667 0.00 0.00 0.00 4.30
215 217 2.553466 CCCGTGATGACCAGGGTTTAAA 60.553 50.000 0.00 0.00 46.62 1.52
327 352 1.377202 GCTTCGTCCCTTGCATCCA 60.377 57.895 0.00 0.00 0.00 3.41
353 378 2.586792 CTCCGGCCCTTCCTCTTG 59.413 66.667 0.00 0.00 0.00 3.02
361 386 1.078848 CCTTCCTCTTGGCCGACTG 60.079 63.158 0.00 0.00 0.00 3.51
363 388 2.454832 CTTCCTCTTGGCCGACTGCA 62.455 60.000 0.00 0.00 43.89 4.41
377 402 1.817099 CTGCATGACCCGCTCCTTC 60.817 63.158 0.00 0.00 0.00 3.46
403 431 2.694760 GCTGCTTCTTCTTGGGCGG 61.695 63.158 0.00 0.00 0.00 6.13
405 433 2.672996 GCTTCTTCTTGGGCGGCA 60.673 61.111 12.47 0.00 0.00 5.69
408 436 0.677731 CTTCTTCTTGGGCGGCATGA 60.678 55.000 12.47 2.18 0.00 3.07
716 768 3.732892 CGGGCACGCGTCCATTTT 61.733 61.111 23.07 0.00 36.30 1.82
718 770 2.622011 GGGCACGCGTCCATTTTGA 61.622 57.895 23.07 0.00 36.65 2.69
722 774 0.718904 CACGCGTCCATTTTGATCGA 59.281 50.000 9.86 0.00 0.00 3.59
738 790 2.652530 GACGTGTTGGGCCGACTA 59.347 61.111 24.11 8.55 0.00 2.59
778 833 2.126385 ACGCGCGTGGACGAAATA 60.126 55.556 37.37 0.00 43.02 1.40
781 836 1.343821 GCGCGTGGACGAAATAGTG 59.656 57.895 8.43 0.00 43.02 2.74
782 837 1.995991 CGCGTGGACGAAATAGTGG 59.004 57.895 2.73 0.00 43.02 4.00
783 838 0.734942 CGCGTGGACGAAATAGTGGT 60.735 55.000 2.73 0.00 43.02 4.16
805 861 3.057456 TCTCGTTGGAGTTGCTCTTAGAC 60.057 47.826 0.00 0.00 41.26 2.59
806 862 2.626266 TCGTTGGAGTTGCTCTTAGACA 59.374 45.455 0.00 0.00 0.00 3.41
807 863 2.731976 CGTTGGAGTTGCTCTTAGACAC 59.268 50.000 0.00 0.00 0.00 3.67
808 864 3.553096 CGTTGGAGTTGCTCTTAGACACT 60.553 47.826 0.00 0.00 0.00 3.55
809 865 3.667497 TGGAGTTGCTCTTAGACACTG 57.333 47.619 0.00 0.00 0.00 3.66
810 866 2.965831 TGGAGTTGCTCTTAGACACTGT 59.034 45.455 0.00 0.00 0.00 3.55
811 867 3.005897 TGGAGTTGCTCTTAGACACTGTC 59.994 47.826 0.38 0.38 0.00 3.51
812 868 3.257127 GGAGTTGCTCTTAGACACTGTCT 59.743 47.826 16.00 16.00 45.54 3.41
813 869 4.262249 GGAGTTGCTCTTAGACACTGTCTT 60.262 45.833 16.89 2.18 40.28 3.01
814 870 5.283457 AGTTGCTCTTAGACACTGTCTTT 57.717 39.130 16.89 0.00 40.28 2.52
815 871 5.675538 AGTTGCTCTTAGACACTGTCTTTT 58.324 37.500 16.89 0.00 40.28 2.27
816 872 6.116126 AGTTGCTCTTAGACACTGTCTTTTT 58.884 36.000 16.89 0.00 40.28 1.94
817 873 6.258947 AGTTGCTCTTAGACACTGTCTTTTTC 59.741 38.462 16.89 4.57 40.28 2.29
818 874 5.670485 TGCTCTTAGACACTGTCTTTTTCA 58.330 37.500 16.89 6.82 40.28 2.69
819 875 6.112734 TGCTCTTAGACACTGTCTTTTTCAA 58.887 36.000 16.89 4.34 40.28 2.69
820 876 6.037172 TGCTCTTAGACACTGTCTTTTTCAAC 59.963 38.462 16.89 2.95 40.28 3.18
821 877 6.511929 GCTCTTAGACACTGTCTTTTTCAACC 60.512 42.308 16.89 0.00 40.28 3.77
822 878 5.820947 TCTTAGACACTGTCTTTTTCAACCC 59.179 40.000 16.89 0.00 40.28 4.11
823 879 3.963129 AGACACTGTCTTTTTCAACCCA 58.037 40.909 5.82 0.00 40.28 4.51
824 880 4.340617 AGACACTGTCTTTTTCAACCCAA 58.659 39.130 5.82 0.00 40.28 4.12
825 881 4.770010 AGACACTGTCTTTTTCAACCCAAA 59.230 37.500 5.82 0.00 40.28 3.28
826 882 5.245075 AGACACTGTCTTTTTCAACCCAAAA 59.755 36.000 5.82 0.00 40.28 2.44
827 883 5.859495 ACACTGTCTTTTTCAACCCAAAAA 58.141 33.333 0.00 0.00 34.72 1.94
829 885 5.931724 CACTGTCTTTTTCAACCCAAAAAGT 59.068 36.000 14.82 0.00 46.68 2.66
830 886 6.426633 CACTGTCTTTTTCAACCCAAAAAGTT 59.573 34.615 14.82 0.00 46.68 2.66
831 887 6.426633 ACTGTCTTTTTCAACCCAAAAAGTTG 59.573 34.615 14.82 0.00 46.68 3.16
832 888 6.292150 TGTCTTTTTCAACCCAAAAAGTTGT 58.708 32.000 14.82 0.00 46.68 3.32
833 889 6.768381 TGTCTTTTTCAACCCAAAAAGTTGTT 59.232 30.769 14.82 0.00 46.68 2.83
834 890 7.041712 TGTCTTTTTCAACCCAAAAAGTTGTTC 60.042 33.333 14.82 6.14 46.68 3.18
835 891 6.428465 TCTTTTTCAACCCAAAAAGTTGTTCC 59.572 34.615 14.82 0.00 46.68 3.62
836 892 4.891992 TTCAACCCAAAAAGTTGTTCCA 57.108 36.364 3.80 0.00 44.02 3.53
837 893 4.891992 TCAACCCAAAAAGTTGTTCCAA 57.108 36.364 3.80 0.00 44.02 3.53
838 894 4.826556 TCAACCCAAAAAGTTGTTCCAAG 58.173 39.130 3.80 0.00 44.02 3.61
839 895 4.528596 TCAACCCAAAAAGTTGTTCCAAGA 59.471 37.500 3.80 0.00 44.02 3.02
840 896 4.465632 ACCCAAAAAGTTGTTCCAAGAC 57.534 40.909 0.00 0.00 32.40 3.01
841 897 3.119280 ACCCAAAAAGTTGTTCCAAGACG 60.119 43.478 0.00 0.00 32.40 4.18
842 898 3.129638 CCCAAAAAGTTGTTCCAAGACGA 59.870 43.478 0.00 0.00 32.40 4.20
843 899 4.202111 CCCAAAAAGTTGTTCCAAGACGAT 60.202 41.667 0.00 0.00 32.40 3.73
844 900 4.976116 CCAAAAAGTTGTTCCAAGACGATC 59.024 41.667 0.00 0.00 32.40 3.69
845 901 5.449862 CCAAAAAGTTGTTCCAAGACGATCA 60.450 40.000 0.00 0.00 32.40 2.92
846 902 5.828299 AAAAGTTGTTCCAAGACGATCAA 57.172 34.783 0.00 0.00 0.00 2.57
847 903 5.424121 AAAGTTGTTCCAAGACGATCAAG 57.576 39.130 0.00 0.00 0.00 3.02
848 904 2.808543 AGTTGTTCCAAGACGATCAAGC 59.191 45.455 0.00 0.00 0.00 4.01
849 905 2.542020 TGTTCCAAGACGATCAAGCA 57.458 45.000 0.00 0.00 0.00 3.91
850 906 2.844946 TGTTCCAAGACGATCAAGCAA 58.155 42.857 0.00 0.00 0.00 3.91
851 907 3.210227 TGTTCCAAGACGATCAAGCAAA 58.790 40.909 0.00 0.00 0.00 3.68
852 908 3.629855 TGTTCCAAGACGATCAAGCAAAA 59.370 39.130 0.00 0.00 0.00 2.44
853 909 4.222114 GTTCCAAGACGATCAAGCAAAAG 58.778 43.478 0.00 0.00 0.00 2.27
854 910 2.813754 TCCAAGACGATCAAGCAAAAGG 59.186 45.455 0.00 0.00 0.00 3.11
855 911 2.813754 CCAAGACGATCAAGCAAAAGGA 59.186 45.455 0.00 0.00 0.00 3.36
856 912 3.253188 CCAAGACGATCAAGCAAAAGGAA 59.747 43.478 0.00 0.00 0.00 3.36
857 913 4.261572 CCAAGACGATCAAGCAAAAGGAAA 60.262 41.667 0.00 0.00 0.00 3.13
858 914 5.280945 CAAGACGATCAAGCAAAAGGAAAA 58.719 37.500 0.00 0.00 0.00 2.29
859 915 5.113502 AGACGATCAAGCAAAAGGAAAAG 57.886 39.130 0.00 0.00 0.00 2.27
860 916 4.821805 AGACGATCAAGCAAAAGGAAAAGA 59.178 37.500 0.00 0.00 0.00 2.52
861 917 5.299279 AGACGATCAAGCAAAAGGAAAAGAA 59.701 36.000 0.00 0.00 0.00 2.52
862 918 5.901552 ACGATCAAGCAAAAGGAAAAGAAA 58.098 33.333 0.00 0.00 0.00 2.52
863 919 6.337356 ACGATCAAGCAAAAGGAAAAGAAAA 58.663 32.000 0.00 0.00 0.00 2.29
864 920 6.476706 ACGATCAAGCAAAAGGAAAAGAAAAG 59.523 34.615 0.00 0.00 0.00 2.27
865 921 6.697019 CGATCAAGCAAAAGGAAAAGAAAAGA 59.303 34.615 0.00 0.00 0.00 2.52
866 922 7.222611 CGATCAAGCAAAAGGAAAAGAAAAGAA 59.777 33.333 0.00 0.00 0.00 2.52
867 923 8.791327 ATCAAGCAAAAGGAAAAGAAAAGAAA 57.209 26.923 0.00 0.00 0.00 2.52
868 924 8.614469 TCAAGCAAAAGGAAAAGAAAAGAAAA 57.386 26.923 0.00 0.00 0.00 2.29
869 925 8.720562 TCAAGCAAAAGGAAAAGAAAAGAAAAG 58.279 29.630 0.00 0.00 0.00 2.27
870 926 8.720562 CAAGCAAAAGGAAAAGAAAAGAAAAGA 58.279 29.630 0.00 0.00 0.00 2.52
871 927 8.846943 AGCAAAAGGAAAAGAAAAGAAAAGAA 57.153 26.923 0.00 0.00 0.00 2.52
872 928 9.283768 AGCAAAAGGAAAAGAAAAGAAAAGAAA 57.716 25.926 0.00 0.00 0.00 2.52
873 929 9.891828 GCAAAAGGAAAAGAAAAGAAAAGAAAA 57.108 25.926 0.00 0.00 0.00 2.29
896 952 2.702592 AAACTGTTCCCAACGAGACA 57.297 45.000 0.00 0.00 0.00 3.41
897 953 2.240493 AACTGTTCCCAACGAGACAG 57.760 50.000 0.00 0.00 43.81 3.51
898 954 1.410004 ACTGTTCCCAACGAGACAGA 58.590 50.000 9.10 0.00 41.46 3.41
899 955 1.341531 ACTGTTCCCAACGAGACAGAG 59.658 52.381 9.10 0.00 41.46 3.35
900 956 1.613925 CTGTTCCCAACGAGACAGAGA 59.386 52.381 0.00 0.00 41.46 3.10
901 957 1.613925 TGTTCCCAACGAGACAGAGAG 59.386 52.381 0.00 0.00 0.00 3.20
902 958 1.887198 GTTCCCAACGAGACAGAGAGA 59.113 52.381 0.00 0.00 0.00 3.10
903 959 1.827681 TCCCAACGAGACAGAGAGAG 58.172 55.000 0.00 0.00 0.00 3.20
904 960 1.351350 TCCCAACGAGACAGAGAGAGA 59.649 52.381 0.00 0.00 0.00 3.10
905 961 2.163509 CCCAACGAGACAGAGAGAGAA 58.836 52.381 0.00 0.00 0.00 2.87
906 962 2.757868 CCCAACGAGACAGAGAGAGAAT 59.242 50.000 0.00 0.00 0.00 2.40
907 963 3.181491 CCCAACGAGACAGAGAGAGAATC 60.181 52.174 0.00 0.00 0.00 2.52
908 964 3.486708 CCAACGAGACAGAGAGAGAATCG 60.487 52.174 0.00 0.00 42.67 3.34
909 965 2.285083 ACGAGACAGAGAGAGAATCGG 58.715 52.381 0.00 0.00 42.67 4.18
910 966 2.093394 ACGAGACAGAGAGAGAATCGGA 60.093 50.000 0.00 0.00 42.67 4.55
911 967 3.138304 CGAGACAGAGAGAGAATCGGAT 58.862 50.000 0.00 0.00 42.67 4.18
912 968 3.186409 CGAGACAGAGAGAGAATCGGATC 59.814 52.174 0.00 0.00 42.67 3.36
913 969 3.138304 AGACAGAGAGAGAATCGGATCG 58.862 50.000 0.00 0.00 42.67 3.69
914 970 1.606668 ACAGAGAGAGAATCGGATCGC 59.393 52.381 0.00 0.00 42.67 4.58
915 971 1.879380 CAGAGAGAGAATCGGATCGCT 59.121 52.381 0.00 0.00 42.67 4.93
916 972 1.879380 AGAGAGAGAATCGGATCGCTG 59.121 52.381 0.00 0.00 42.67 5.18
917 973 0.313672 AGAGAGAATCGGATCGCTGC 59.686 55.000 0.00 0.00 42.67 5.25
918 974 0.665972 GAGAGAATCGGATCGCTGCC 60.666 60.000 0.00 0.00 42.67 4.85
926 982 2.181777 GATCGCTGCCGTCAGTCA 59.818 61.111 0.00 0.00 42.29 3.41
927 983 1.446099 GATCGCTGCCGTCAGTCAA 60.446 57.895 0.00 0.00 42.29 3.18
947 1003 4.687948 TCAAAGAGAATCGCTGACTTTCTG 59.312 41.667 0.00 0.00 42.67 3.02
948 1004 3.244033 AGAGAATCGCTGACTTTCTGG 57.756 47.619 0.00 0.00 42.67 3.86
949 1005 2.828520 AGAGAATCGCTGACTTTCTGGA 59.171 45.455 0.00 0.00 42.67 3.86
966 1027 2.435805 CTGGATAGGGCAGCACTTTCTA 59.564 50.000 14.08 7.91 0.00 2.10
987 1048 3.705638 CACACCACGCAGCTCACG 61.706 66.667 4.17 4.17 0.00 4.35
991 1052 2.049526 CCACGCAGCTCACGTACA 60.050 61.111 10.73 0.00 42.96 2.90
1368 1438 2.342279 CTGTCGGACGCCAAGGAA 59.658 61.111 3.34 0.00 0.00 3.36
1416 1486 2.202676 GAGTCAAGCTCCGCTCCG 60.203 66.667 0.00 0.00 38.25 4.63
1566 1636 4.749310 CGGCGCTCTCTGGTTGCT 62.749 66.667 7.64 0.00 0.00 3.91
1630 1700 1.874345 CGTGTACAAGGAGGTCGCCT 61.874 60.000 0.00 0.00 40.93 5.52
1944 2017 1.897225 ATGTTGCCTCTCTCGCAGCT 61.897 55.000 0.00 0.00 38.19 4.24
2382 2455 2.283821 GGCCAGGGCACAATGGAA 60.284 61.111 13.10 0.00 44.11 3.53
2445 2518 2.032030 CCTGTTGCAGGTCACGTTAAAG 60.032 50.000 6.99 0.00 45.82 1.85
2552 2625 6.233434 TCACTGTATTCTCAAAATGTCAGCT 58.767 36.000 0.00 0.00 0.00 4.24
2952 3025 0.108424 GCCGATCTGCAGACTTCAGT 60.108 55.000 20.97 0.66 33.48 3.41
2988 3061 5.048083 TGGTACAGCAATTGAATTTCCAGAC 60.048 40.000 10.34 0.00 0.00 3.51
3255 3328 4.963318 ACAGAGACTTTCATTGACAGGA 57.037 40.909 4.92 0.00 0.00 3.86
3567 3640 5.109210 TGTGATGAGCTAACTGAAATACCG 58.891 41.667 0.00 0.00 0.00 4.02
3829 3902 0.403655 TACTGGATTTGCTGGGCACA 59.596 50.000 0.00 0.00 38.71 4.57
3856 3929 1.317613 TGGATGCGCATCATTAACCC 58.682 50.000 41.80 28.15 39.54 4.11
3882 3955 4.653868 TGGAGGCGTTATTTTGAGGTTTA 58.346 39.130 0.00 0.00 0.00 2.01
3967 4040 2.416162 GCGTTCTCTCAGAGTTTCGGAT 60.416 50.000 0.36 0.00 0.00 4.18
4099 4172 3.472652 TCGGCTTTTCTGTTCTTAAGCA 58.527 40.909 0.00 0.00 43.58 3.91
4139 4212 0.035152 ATCCTCAATGCTTCGCCACA 60.035 50.000 0.00 0.00 0.00 4.17
4181 4258 9.494271 GTTCATCTATTTGTATCAGCCTGATTA 57.506 33.333 13.32 0.00 38.26 1.75
4228 4305 3.719699 AAAAAGCGAATCATGCCCG 57.280 47.368 0.00 0.00 0.00 6.13
4293 4370 4.687901 TGAAGTTGATCCTGAACTGTGA 57.312 40.909 0.00 0.00 33.85 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 32 2.659016 CTCAACGGAGCTGAGCCA 59.341 61.111 0.00 0.00 44.00 4.75
43 45 0.909610 ACTCTCCGGGGAATGCTCAA 60.910 55.000 5.02 0.00 0.00 3.02
44 46 1.306141 ACTCTCCGGGGAATGCTCA 60.306 57.895 5.02 0.00 0.00 4.26
116 118 3.432588 CTGTCGGAGTCGCCTCGT 61.433 66.667 0.00 0.00 38.70 4.18
119 121 4.057428 GTGCTGTCGGAGTCGCCT 62.057 66.667 0.00 0.00 36.13 5.52
128 130 2.202797 CCTCGGATGGTGCTGTCG 60.203 66.667 0.00 0.00 0.00 4.35
215 217 1.148236 GAGGCCCTGATCTACCTAGGT 59.852 57.143 20.57 20.57 30.95 3.08
361 386 2.892425 CGAAGGAGCGGGTCATGC 60.892 66.667 9.66 0.00 0.00 4.06
377 402 2.734673 GAAGAAGCAGCTGACGCCG 61.735 63.158 20.43 0.00 36.60 6.46
403 431 1.817099 CCTCGCAAGACCCTCATGC 60.817 63.158 0.00 0.00 45.01 4.06
405 433 2.370445 CCCCTCGCAAGACCCTCAT 61.370 63.158 0.00 0.00 45.01 2.90
431 460 2.643232 CCCTCTGGCAAAGGCAAGC 61.643 63.158 0.00 0.00 41.16 4.01
457 488 2.745100 TCACCTCGTCCGACCTCG 60.745 66.667 0.00 0.00 39.44 4.63
460 491 3.450115 CCCTCACCTCGTCCGACC 61.450 72.222 0.00 0.00 0.00 4.79
496 527 2.423898 ATGGACGACGCCCTCGATT 61.424 57.895 0.79 0.00 46.14 3.34
545 578 3.628832 TCCCTCCACTTTCCCAAAAAT 57.371 42.857 0.00 0.00 0.00 1.82
546 579 3.406512 TTCCCTCCACTTTCCCAAAAA 57.593 42.857 0.00 0.00 0.00 1.94
665 715 0.685458 GCCAAGCCATTCATGACCCT 60.685 55.000 0.00 0.00 0.00 4.34
679 729 1.791103 TTTTTCGTCCGCCTGCCAAG 61.791 55.000 0.00 0.00 0.00 3.61
714 766 1.231958 GGCCCAACACGTCGATCAAA 61.232 55.000 0.00 0.00 0.00 2.69
716 768 2.047655 GGCCCAACACGTCGATCA 60.048 61.111 0.00 0.00 0.00 2.92
718 770 3.687102 TCGGCCCAACACGTCGAT 61.687 61.111 0.00 0.00 0.00 3.59
722 774 2.205152 AGTAGTCGGCCCAACACGT 61.205 57.895 0.00 0.00 0.00 4.49
725 777 1.669440 GACAGTAGTCGGCCCAACA 59.331 57.895 0.00 0.00 34.60 3.33
738 790 1.466025 TTTAGGTCACGGCGGACAGT 61.466 55.000 23.27 15.13 39.59 3.55
778 833 0.249911 GCAACTCCAACGAGACCACT 60.250 55.000 0.00 0.00 38.52 4.00
781 836 0.318762 AGAGCAACTCCAACGAGACC 59.681 55.000 0.00 0.00 38.52 3.85
782 837 2.156343 AAGAGCAACTCCAACGAGAC 57.844 50.000 0.00 0.00 38.52 3.36
783 838 3.057456 GTCTAAGAGCAACTCCAACGAGA 60.057 47.826 0.00 0.00 38.52 4.04
812 868 6.062095 TGGAACAACTTTTTGGGTTGAAAAA 58.938 32.000 12.53 0.00 44.58 1.94
813 869 5.621193 TGGAACAACTTTTTGGGTTGAAAA 58.379 33.333 12.53 0.00 44.58 2.29
814 870 5.228945 TGGAACAACTTTTTGGGTTGAAA 57.771 34.783 12.53 0.00 44.58 2.69
815 871 4.891992 TGGAACAACTTTTTGGGTTGAA 57.108 36.364 12.53 0.00 44.58 2.69
830 886 2.542020 TGCTTGATCGTCTTGGAACA 57.458 45.000 0.00 0.00 0.00 3.18
831 887 3.896648 TTTGCTTGATCGTCTTGGAAC 57.103 42.857 0.00 0.00 0.00 3.62
832 888 3.253188 CCTTTTGCTTGATCGTCTTGGAA 59.747 43.478 0.00 0.00 0.00 3.53
833 889 2.813754 CCTTTTGCTTGATCGTCTTGGA 59.186 45.455 0.00 0.00 0.00 3.53
834 890 2.813754 TCCTTTTGCTTGATCGTCTTGG 59.186 45.455 0.00 0.00 0.00 3.61
835 891 4.488126 TTCCTTTTGCTTGATCGTCTTG 57.512 40.909 0.00 0.00 0.00 3.02
836 892 5.299279 TCTTTTCCTTTTGCTTGATCGTCTT 59.701 36.000 0.00 0.00 0.00 3.01
837 893 4.821805 TCTTTTCCTTTTGCTTGATCGTCT 59.178 37.500 0.00 0.00 0.00 4.18
838 894 5.108385 TCTTTTCCTTTTGCTTGATCGTC 57.892 39.130 0.00 0.00 0.00 4.20
839 895 5.514274 TTCTTTTCCTTTTGCTTGATCGT 57.486 34.783 0.00 0.00 0.00 3.73
840 896 6.697019 TCTTTTCTTTTCCTTTTGCTTGATCG 59.303 34.615 0.00 0.00 0.00 3.69
841 897 8.424274 TTCTTTTCTTTTCCTTTTGCTTGATC 57.576 30.769 0.00 0.00 0.00 2.92
842 898 8.791327 TTTCTTTTCTTTTCCTTTTGCTTGAT 57.209 26.923 0.00 0.00 0.00 2.57
843 899 8.614469 TTTTCTTTTCTTTTCCTTTTGCTTGA 57.386 26.923 0.00 0.00 0.00 3.02
844 900 8.720562 TCTTTTCTTTTCTTTTCCTTTTGCTTG 58.279 29.630 0.00 0.00 0.00 4.01
845 901 8.846943 TCTTTTCTTTTCTTTTCCTTTTGCTT 57.153 26.923 0.00 0.00 0.00 3.91
846 902 8.846943 TTCTTTTCTTTTCTTTTCCTTTTGCT 57.153 26.923 0.00 0.00 0.00 3.91
847 903 9.891828 TTTTCTTTTCTTTTCTTTTCCTTTTGC 57.108 25.926 0.00 0.00 0.00 3.68
875 931 3.349022 TGTCTCGTTGGGAACAGTTTTT 58.651 40.909 0.00 0.00 44.54 1.94
876 932 2.943033 CTGTCTCGTTGGGAACAGTTTT 59.057 45.455 0.00 0.00 44.54 2.43
877 933 2.169769 TCTGTCTCGTTGGGAACAGTTT 59.830 45.455 0.00 0.00 44.54 2.66
878 934 1.760613 TCTGTCTCGTTGGGAACAGTT 59.239 47.619 0.00 0.00 44.54 3.16
879 935 1.341531 CTCTGTCTCGTTGGGAACAGT 59.658 52.381 0.00 0.00 44.54 3.55
880 936 1.613925 TCTCTGTCTCGTTGGGAACAG 59.386 52.381 0.00 0.00 44.54 3.16
881 937 1.613925 CTCTCTGTCTCGTTGGGAACA 59.386 52.381 0.00 0.00 39.83 3.18
882 938 1.887198 TCTCTCTGTCTCGTTGGGAAC 59.113 52.381 0.00 0.00 0.00 3.62
883 939 2.163509 CTCTCTCTGTCTCGTTGGGAA 58.836 52.381 0.00 0.00 0.00 3.97
884 940 1.351350 TCTCTCTCTGTCTCGTTGGGA 59.649 52.381 0.00 0.00 0.00 4.37
885 941 1.827681 TCTCTCTCTGTCTCGTTGGG 58.172 55.000 0.00 0.00 0.00 4.12
886 942 3.486708 CGATTCTCTCTCTGTCTCGTTGG 60.487 52.174 0.00 0.00 0.00 3.77
887 943 3.486708 CCGATTCTCTCTCTGTCTCGTTG 60.487 52.174 0.00 0.00 0.00 4.10
888 944 2.680841 CCGATTCTCTCTCTGTCTCGTT 59.319 50.000 0.00 0.00 0.00 3.85
889 945 2.093394 TCCGATTCTCTCTCTGTCTCGT 60.093 50.000 0.00 0.00 0.00 4.18
890 946 2.556257 TCCGATTCTCTCTCTGTCTCG 58.444 52.381 0.00 0.00 0.00 4.04
891 947 3.186409 CGATCCGATTCTCTCTCTGTCTC 59.814 52.174 0.00 0.00 0.00 3.36
892 948 3.138304 CGATCCGATTCTCTCTCTGTCT 58.862 50.000 0.00 0.00 0.00 3.41
893 949 2.350388 GCGATCCGATTCTCTCTCTGTC 60.350 54.545 0.00 0.00 0.00 3.51
894 950 1.606668 GCGATCCGATTCTCTCTCTGT 59.393 52.381 0.00 0.00 0.00 3.41
895 951 1.879380 AGCGATCCGATTCTCTCTCTG 59.121 52.381 0.00 0.00 0.00 3.35
896 952 1.879380 CAGCGATCCGATTCTCTCTCT 59.121 52.381 0.00 0.00 0.00 3.10
897 953 1.665735 GCAGCGATCCGATTCTCTCTC 60.666 57.143 0.00 0.00 0.00 3.20
898 954 0.313672 GCAGCGATCCGATTCTCTCT 59.686 55.000 0.00 0.00 0.00 3.10
899 955 0.665972 GGCAGCGATCCGATTCTCTC 60.666 60.000 0.00 0.00 0.00 3.20
900 956 1.365633 GGCAGCGATCCGATTCTCT 59.634 57.895 0.00 0.00 0.00 3.10
901 957 3.943967 GGCAGCGATCCGATTCTC 58.056 61.111 0.00 0.00 0.00 2.87
908 964 2.583593 GACTGACGGCAGCGATCC 60.584 66.667 20.90 0.00 46.26 3.36
909 965 1.014044 TTTGACTGACGGCAGCGATC 61.014 55.000 20.90 9.57 46.26 3.69
910 966 1.005037 TTTGACTGACGGCAGCGAT 60.005 52.632 20.90 0.00 46.26 4.58
911 967 1.664649 CTTTGACTGACGGCAGCGA 60.665 57.895 20.90 8.47 46.26 4.93
912 968 1.621301 CTCTTTGACTGACGGCAGCG 61.621 60.000 20.90 0.00 46.26 5.18
913 969 0.319900 TCTCTTTGACTGACGGCAGC 60.320 55.000 20.90 12.21 46.26 5.25
915 971 2.688507 GATTCTCTTTGACTGACGGCA 58.311 47.619 0.00 0.00 0.00 5.69
916 972 1.656095 CGATTCTCTTTGACTGACGGC 59.344 52.381 0.00 0.00 0.00 5.68
917 973 1.656095 GCGATTCTCTTTGACTGACGG 59.344 52.381 0.00 0.00 0.00 4.79
918 974 2.343843 CAGCGATTCTCTTTGACTGACG 59.656 50.000 0.00 0.00 0.00 4.35
919 975 3.366422 GTCAGCGATTCTCTTTGACTGAC 59.634 47.826 0.00 0.00 43.80 3.51
926 982 3.999663 CCAGAAAGTCAGCGATTCTCTTT 59.000 43.478 0.00 0.00 31.26 2.52
927 983 3.259374 TCCAGAAAGTCAGCGATTCTCTT 59.741 43.478 0.00 0.00 31.26 2.85
947 1003 2.224402 CCTAGAAAGTGCTGCCCTATCC 60.224 54.545 0.00 0.00 0.00 2.59
948 1004 2.808567 GCCTAGAAAGTGCTGCCCTATC 60.809 54.545 0.00 0.00 0.00 2.08
949 1005 1.141858 GCCTAGAAAGTGCTGCCCTAT 59.858 52.381 0.00 0.00 0.00 2.57
985 1046 1.511305 CCATGACCTCGCTGTACGT 59.489 57.895 0.00 0.00 44.19 3.57
987 1048 1.878522 CGCCATGACCTCGCTGTAC 60.879 63.158 0.00 0.00 0.00 2.90
991 1052 3.842923 CTCCGCCATGACCTCGCT 61.843 66.667 0.00 0.00 0.00 4.93
1455 1525 1.400990 GCAAGAAATGCGCTGCTTCG 61.401 55.000 9.73 3.72 46.87 3.79
1554 1624 1.563435 CGCACACAGCAACCAGAGAG 61.563 60.000 0.00 0.00 46.13 3.20
1557 1627 2.591429 CCGCACACAGCAACCAGA 60.591 61.111 0.00 0.00 46.13 3.86
1563 1633 4.720902 CCCATCCCGCACACAGCA 62.721 66.667 0.00 0.00 46.13 4.41
1630 1700 2.357034 GTCGAAGTGGCGGCTTGA 60.357 61.111 11.43 0.00 32.23 3.02
1851 1924 3.648339 GCATTGCGGATTTCATACCAT 57.352 42.857 0.00 0.00 0.00 3.55
1944 2017 1.371467 ACATGATGGTCCTGGTGGAA 58.629 50.000 0.00 0.00 45.18 3.53
2382 2455 3.805108 GCAGGTAATCATCCGCAATCTCT 60.805 47.826 0.00 0.00 0.00 3.10
2445 2518 1.710013 TCGCTCGTCCAAACTCATTC 58.290 50.000 0.00 0.00 0.00 2.67
2952 3025 1.263356 CTGTACCAGGGAACGGAGAA 58.737 55.000 0.00 0.00 0.00 2.87
2988 3061 2.867429 CAAGTAAGATTTTGCAGCCCG 58.133 47.619 0.00 0.00 0.00 6.13
3255 3328 4.021456 GGCAACTTACCTTTGGCTAACATT 60.021 41.667 1.69 0.00 44.13 2.71
3567 3640 0.391661 TGAGGTTCTCGATGCCTTGC 60.392 55.000 4.42 0.00 32.35 4.01
3856 3929 3.375299 CCTCAAAATAACGCCTCCAAGAG 59.625 47.826 0.00 0.00 0.00 2.85
3869 3942 4.069304 AGCAGTGCGTAAACCTCAAAATA 58.931 39.130 10.00 0.00 0.00 1.40
3882 3955 0.748005 ACAAAGTGGAAGCAGTGCGT 60.748 50.000 10.00 6.30 0.00 5.24
3967 4040 3.143010 ACCGACAAAGAGGTGAGGA 57.857 52.632 0.00 0.00 39.66 3.71
4006 4079 1.558233 TCATGGCAATGCACATTCCA 58.442 45.000 7.79 13.35 34.73 3.53
4047 4120 4.305539 ACACATCATCTTCAATCCACCA 57.694 40.909 0.00 0.00 0.00 4.17
4099 4172 1.013596 CACACACACACCAACACGAT 58.986 50.000 0.00 0.00 0.00 3.73
4139 4212 0.252197 GAACCCGGCCTCTACAACAT 59.748 55.000 0.00 0.00 0.00 2.71
4181 4258 7.765819 GCTTGGAAACCAGCTATTTTATTGAAT 59.234 33.333 0.00 0.00 33.81 2.57
4260 4337 8.102676 TCAGGATCAACTTCATTCACTAATTGA 58.897 33.333 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.