Multiple sequence alignment - TraesCS3B01G225400

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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 TraesCS3B01G225400 chr3B 100.000 3722 0 0 1 3722 309422423 309418702 0.000000e+00 6874
1 TraesCS3B01G225400 chr3B 94.286 840 43 5 1 837 311517787 311516950 0.000000e+00 1280
2 TraesCS3B01G225400 chr3B 94.160 839 45 3 1 837 325700250 325701086 0.000000e+00 1275
3 TraesCS3B01G225400 chr3B 94.041 839 46 4 1 837 382610878 382610042 0.000000e+00 1269
4 TraesCS3B01G225400 chr3A 96.312 2061 69 2 937 2990 336598389 336600449 0.000000e+00 3378
5 TraesCS3B01G225400 chr3A 94.930 355 15 2 3370 3722 336600967 336601320 1.510000e-153 553
6 TraesCS3B01G225400 chr3A 91.858 393 14 6 2990 3370 336600539 336600925 1.970000e-147 532
7 TraesCS3B01G225400 chr3D 97.060 2007 54 1 937 2938 253520031 253522037 0.000000e+00 3374
8 TraesCS3B01G225400 chr3D 94.405 840 40 7 1 837 237920955 237921790 0.000000e+00 1284
9 TraesCS3B01G225400 chr3D 94.174 841 41 7 1 837 237942837 237943673 0.000000e+00 1275
10 TraesCS3B01G225400 chr3D 96.034 353 14 0 3370 3722 253522197 253522549 3.220000e-160 575
11 TraesCS3B01G225400 chr3D 97.479 119 3 0 3251 3369 253522036 253522154 1.750000e-48 204
12 TraesCS3B01G225400 chr2B 94.293 841 40 8 1 837 115464279 115465115 0.000000e+00 1280
13 TraesCS3B01G225400 chr1B 94.279 839 41 6 2 837 216736809 216735975 0.000000e+00 1277
14 TraesCS3B01G225400 chr7B 94.033 838 44 6 2 836 553319708 553320542 0.000000e+00 1266
15 TraesCS3B01G225400 chr4B 94.041 839 43 7 1 837 643723675 643722842 0.000000e+00 1266


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 TraesCS3B01G225400 chr3B 309418702 309422423 3721 True 6874.000000 6874 100.000000 1 3722 1 chr3B.!!$R1 3721
1 TraesCS3B01G225400 chr3B 311516950 311517787 837 True 1280.000000 1280 94.286000 1 837 1 chr3B.!!$R2 836
2 TraesCS3B01G225400 chr3B 325700250 325701086 836 False 1275.000000 1275 94.160000 1 837 1 chr3B.!!$F1 836
3 TraesCS3B01G225400 chr3B 382610042 382610878 836 True 1269.000000 1269 94.041000 1 837 1 chr3B.!!$R3 836
4 TraesCS3B01G225400 chr3A 336598389 336601320 2931 False 1487.666667 3378 94.366667 937 3722 3 chr3A.!!$F1 2785
5 TraesCS3B01G225400 chr3D 253520031 253522549 2518 False 1384.333333 3374 96.857667 937 3722 3 chr3D.!!$F3 2785
6 TraesCS3B01G225400 chr3D 237920955 237921790 835 False 1284.000000 1284 94.405000 1 837 1 chr3D.!!$F1 836
7 TraesCS3B01G225400 chr3D 237942837 237943673 836 False 1275.000000 1275 94.174000 1 837 1 chr3D.!!$F2 836
8 TraesCS3B01G225400 chr2B 115464279 115465115 836 False 1280.000000 1280 94.293000 1 837 1 chr2B.!!$F1 836
9 TraesCS3B01G225400 chr1B 216735975 216736809 834 True 1277.000000 1277 94.279000 2 837 1 chr1B.!!$R1 835
10 TraesCS3B01G225400 chr7B 553319708 553320542 834 False 1266.000000 1266 94.033000 2 836 1 chr7B.!!$F1 834
11 TraesCS3B01G225400 chr4B 643722842 643723675 833 True 1266.000000 1266 94.041000 1 837 1 chr4B.!!$R1 836

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
933 943 0.173708 TTCCCACCAAACAAACACGC 59.826 50.0 0.0 0.0 0.00 5.34 F
1920 1941 0.036732 TTGACAGGATGGTCCACAGC 59.963 55.0 0.0 0.0 43.62 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 2419 0.619832 TTGCCATCTGAGCTCCTCCT 60.620 55.0 12.15 0.00 0.00 3.69 R
2920 2942 0.800631 AACAGCATGCTCACATCACG 59.199 50.0 19.68 6.54 42.53 4.35 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
45 48 5.641155 TGGGCTCTAGCATAGTTGAGTATA 58.359 41.667 4.07 0.00 44.36 1.47
107 110 4.900054 GGGATGTAGGTTGGTACTGTCTAT 59.100 45.833 0.00 0.00 0.00 1.98
263 266 8.640651 TGTATAAACTAATCATGGTTAGCCGTA 58.359 33.333 23.00 13.76 35.55 4.02
315 318 9.822727 TCTAGTACCTGGATTATCATGTGAATA 57.177 33.333 0.00 0.00 0.00 1.75
533 542 9.905713 TGATAGCCTTATTTCTGTTCATTACTT 57.094 29.630 0.00 0.00 0.00 2.24
553 562 8.574251 TTACTTTCTATGTGTTACATTGCCAT 57.426 30.769 0.00 0.00 39.88 4.40
619 628 2.124903 GCAGACTTTTCAGACGACGAA 58.875 47.619 0.00 0.00 0.00 3.85
620 629 2.097347 GCAGACTTTTCAGACGACGAAC 60.097 50.000 0.00 0.00 0.00 3.95
678 687 1.336887 CGTTGGAGTTGATGGACTCGT 60.337 52.381 0.00 0.00 45.53 4.18
685 694 4.571176 GGAGTTGATGGACTCGTTTATTCC 59.429 45.833 0.00 0.00 45.53 3.01
727 736 5.284861 TCGTTATTAGATGGCCTTAAGCA 57.715 39.130 3.32 0.00 46.50 3.91
837 847 2.107366 TGTCAGCATTACCGATCCAGA 58.893 47.619 0.00 0.00 0.00 3.86
838 848 2.700371 TGTCAGCATTACCGATCCAGAT 59.300 45.455 0.00 0.00 0.00 2.90
839 849 3.134623 TGTCAGCATTACCGATCCAGATT 59.865 43.478 0.00 0.00 0.00 2.40
840 850 4.130118 GTCAGCATTACCGATCCAGATTT 58.870 43.478 0.00 0.00 0.00 2.17
841 851 5.163353 TGTCAGCATTACCGATCCAGATTTA 60.163 40.000 0.00 0.00 0.00 1.40
842 852 5.758296 GTCAGCATTACCGATCCAGATTTAA 59.242 40.000 0.00 0.00 0.00 1.52
843 853 6.260050 GTCAGCATTACCGATCCAGATTTAAA 59.740 38.462 0.00 0.00 0.00 1.52
844 854 6.260050 TCAGCATTACCGATCCAGATTTAAAC 59.740 38.462 0.00 0.00 0.00 2.01
845 855 6.260936 CAGCATTACCGATCCAGATTTAAACT 59.739 38.462 0.00 0.00 0.00 2.66
846 856 6.483640 AGCATTACCGATCCAGATTTAAACTC 59.516 38.462 0.00 0.00 0.00 3.01
847 857 6.483640 GCATTACCGATCCAGATTTAAACTCT 59.516 38.462 0.00 0.00 0.00 3.24
848 858 7.307455 GCATTACCGATCCAGATTTAAACTCTC 60.307 40.741 0.00 0.00 0.00 3.20
849 859 5.677319 ACCGATCCAGATTTAAACTCTCA 57.323 39.130 0.00 0.00 0.00 3.27
850 860 6.240549 ACCGATCCAGATTTAAACTCTCAT 57.759 37.500 0.00 0.00 0.00 2.90
851 861 6.653989 ACCGATCCAGATTTAAACTCTCATT 58.346 36.000 0.00 0.00 0.00 2.57
852 862 6.763610 ACCGATCCAGATTTAAACTCTCATTC 59.236 38.462 0.00 0.00 0.00 2.67
853 863 6.203723 CCGATCCAGATTTAAACTCTCATTCC 59.796 42.308 0.00 0.00 0.00 3.01
854 864 6.203723 CGATCCAGATTTAAACTCTCATTCCC 59.796 42.308 0.00 0.00 0.00 3.97
855 865 6.642733 TCCAGATTTAAACTCTCATTCCCT 57.357 37.500 0.00 0.00 0.00 4.20
856 866 6.653989 TCCAGATTTAAACTCTCATTCCCTC 58.346 40.000 0.00 0.00 0.00 4.30
857 867 6.445139 TCCAGATTTAAACTCTCATTCCCTCT 59.555 38.462 0.00 0.00 0.00 3.69
858 868 7.623677 TCCAGATTTAAACTCTCATTCCCTCTA 59.376 37.037 0.00 0.00 0.00 2.43
859 869 8.267894 CCAGATTTAAACTCTCATTCCCTCTAA 58.732 37.037 0.00 0.00 0.00 2.10
860 870 9.672673 CAGATTTAAACTCTCATTCCCTCTAAA 57.327 33.333 0.00 0.00 0.00 1.85
861 871 9.674068 AGATTTAAACTCTCATTCCCTCTAAAC 57.326 33.333 0.00 0.00 0.00 2.01
862 872 9.449719 GATTTAAACTCTCATTCCCTCTAAACA 57.550 33.333 0.00 0.00 0.00 2.83
863 873 9.807921 ATTTAAACTCTCATTCCCTCTAAACAA 57.192 29.630 0.00 0.00 0.00 2.83
864 874 9.807921 TTTAAACTCTCATTCCCTCTAAACAAT 57.192 29.630 0.00 0.00 0.00 2.71
865 875 7.929941 AAACTCTCATTCCCTCTAAACAATC 57.070 36.000 0.00 0.00 0.00 2.67
866 876 6.627087 ACTCTCATTCCCTCTAAACAATCA 57.373 37.500 0.00 0.00 0.00 2.57
867 877 7.020827 ACTCTCATTCCCTCTAAACAATCAA 57.979 36.000 0.00 0.00 0.00 2.57
868 878 7.637511 ACTCTCATTCCCTCTAAACAATCAAT 58.362 34.615 0.00 0.00 0.00 2.57
869 879 7.555554 ACTCTCATTCCCTCTAAACAATCAATG 59.444 37.037 0.00 0.00 0.00 2.82
870 880 7.632861 TCTCATTCCCTCTAAACAATCAATGA 58.367 34.615 0.00 0.00 0.00 2.57
871 881 8.108999 TCTCATTCCCTCTAAACAATCAATGAA 58.891 33.333 0.00 0.00 30.65 2.57
872 882 8.055279 TCATTCCCTCTAAACAATCAATGAAC 57.945 34.615 0.00 0.00 0.00 3.18
873 883 7.890127 TCATTCCCTCTAAACAATCAATGAACT 59.110 33.333 0.00 0.00 0.00 3.01
874 884 8.526147 CATTCCCTCTAAACAATCAATGAACTT 58.474 33.333 0.00 0.00 0.00 2.66
875 885 8.477419 TTCCCTCTAAACAATCAATGAACTTT 57.523 30.769 0.00 0.00 0.00 2.66
876 886 8.477419 TCCCTCTAAACAATCAATGAACTTTT 57.523 30.769 0.00 0.00 0.00 2.27
877 887 9.581289 TCCCTCTAAACAATCAATGAACTTTTA 57.419 29.630 0.00 0.00 0.00 1.52
886 896 9.918630 ACAATCAATGAACTTTTATTCTCCTTG 57.081 29.630 0.00 0.00 0.00 3.61
887 897 8.866956 CAATCAATGAACTTTTATTCTCCTTGC 58.133 33.333 0.00 0.00 0.00 4.01
888 898 6.924111 TCAATGAACTTTTATTCTCCTTGCC 58.076 36.000 0.00 0.00 0.00 4.52
889 899 5.567138 ATGAACTTTTATTCTCCTTGCCG 57.433 39.130 0.00 0.00 0.00 5.69
890 900 3.190535 TGAACTTTTATTCTCCTTGCCGC 59.809 43.478 0.00 0.00 0.00 6.53
891 901 3.073274 ACTTTTATTCTCCTTGCCGCT 57.927 42.857 0.00 0.00 0.00 5.52
892 902 3.010420 ACTTTTATTCTCCTTGCCGCTC 58.990 45.455 0.00 0.00 0.00 5.03
893 903 2.779755 TTTATTCTCCTTGCCGCTCA 57.220 45.000 0.00 0.00 0.00 4.26
894 904 2.779755 TTATTCTCCTTGCCGCTCAA 57.220 45.000 0.00 0.00 0.00 3.02
895 905 2.024176 TATTCTCCTTGCCGCTCAAC 57.976 50.000 0.00 0.00 0.00 3.18
896 906 0.326264 ATTCTCCTTGCCGCTCAACT 59.674 50.000 0.00 0.00 0.00 3.16
897 907 0.320771 TTCTCCTTGCCGCTCAACTC 60.321 55.000 0.00 0.00 0.00 3.01
898 908 1.743252 CTCCTTGCCGCTCAACTCC 60.743 63.158 0.00 0.00 0.00 3.85
899 909 2.747855 CCTTGCCGCTCAACTCCC 60.748 66.667 0.00 0.00 0.00 4.30
900 910 2.032528 CTTGCCGCTCAACTCCCA 59.967 61.111 0.00 0.00 0.00 4.37
901 911 1.377725 CTTGCCGCTCAACTCCCAT 60.378 57.895 0.00 0.00 0.00 4.00
902 912 0.962356 CTTGCCGCTCAACTCCCATT 60.962 55.000 0.00 0.00 0.00 3.16
903 913 0.960364 TTGCCGCTCAACTCCCATTC 60.960 55.000 0.00 0.00 0.00 2.67
904 914 2.115291 GCCGCTCAACTCCCATTCC 61.115 63.158 0.00 0.00 0.00 3.01
905 915 1.452108 CCGCTCAACTCCCATTCCC 60.452 63.158 0.00 0.00 0.00 3.97
906 916 1.452108 CGCTCAACTCCCATTCCCC 60.452 63.158 0.00 0.00 0.00 4.81
907 917 1.691219 GCTCAACTCCCATTCCCCA 59.309 57.895 0.00 0.00 0.00 4.96
908 918 0.259938 GCTCAACTCCCATTCCCCAT 59.740 55.000 0.00 0.00 0.00 4.00
909 919 1.342374 GCTCAACTCCCATTCCCCATT 60.342 52.381 0.00 0.00 0.00 3.16
910 920 2.889756 GCTCAACTCCCATTCCCCATTT 60.890 50.000 0.00 0.00 0.00 2.32
911 921 3.444029 CTCAACTCCCATTCCCCATTTT 58.556 45.455 0.00 0.00 0.00 1.82
912 922 4.609301 CTCAACTCCCATTCCCCATTTTA 58.391 43.478 0.00 0.00 0.00 1.52
913 923 4.609301 TCAACTCCCATTCCCCATTTTAG 58.391 43.478 0.00 0.00 0.00 1.85
914 924 4.045334 TCAACTCCCATTCCCCATTTTAGT 59.955 41.667 0.00 0.00 0.00 2.24
915 925 4.692523 ACTCCCATTCCCCATTTTAGTT 57.307 40.909 0.00 0.00 0.00 2.24
916 926 4.610333 ACTCCCATTCCCCATTTTAGTTC 58.390 43.478 0.00 0.00 0.00 3.01
917 927 3.960755 CTCCCATTCCCCATTTTAGTTCC 59.039 47.826 0.00 0.00 0.00 3.62
918 928 3.038280 CCCATTCCCCATTTTAGTTCCC 58.962 50.000 0.00 0.00 0.00 3.97
919 929 3.567663 CCCATTCCCCATTTTAGTTCCCA 60.568 47.826 0.00 0.00 0.00 4.37
920 930 3.450817 CCATTCCCCATTTTAGTTCCCAC 59.549 47.826 0.00 0.00 0.00 4.61
921 931 2.911552 TCCCCATTTTAGTTCCCACC 57.088 50.000 0.00 0.00 0.00 4.61
922 932 2.074579 TCCCCATTTTAGTTCCCACCA 58.925 47.619 0.00 0.00 0.00 4.17
923 933 2.451273 TCCCCATTTTAGTTCCCACCAA 59.549 45.455 0.00 0.00 0.00 3.67
924 934 3.116707 TCCCCATTTTAGTTCCCACCAAA 60.117 43.478 0.00 0.00 0.00 3.28
925 935 3.007506 CCCCATTTTAGTTCCCACCAAAC 59.992 47.826 0.00 0.00 0.00 2.93
926 936 3.643792 CCCATTTTAGTTCCCACCAAACA 59.356 43.478 0.00 0.00 0.00 2.83
927 937 4.101741 CCCATTTTAGTTCCCACCAAACAA 59.898 41.667 0.00 0.00 0.00 2.83
928 938 5.396884 CCCATTTTAGTTCCCACCAAACAAA 60.397 40.000 0.00 0.00 0.00 2.83
929 939 5.525745 CCATTTTAGTTCCCACCAAACAAAC 59.474 40.000 0.00 0.00 0.00 2.93
930 940 5.740290 TTTTAGTTCCCACCAAACAAACA 57.260 34.783 0.00 0.00 0.00 2.83
931 941 4.722361 TTAGTTCCCACCAAACAAACAC 57.278 40.909 0.00 0.00 0.00 3.32
932 942 1.474879 AGTTCCCACCAAACAAACACG 59.525 47.619 0.00 0.00 0.00 4.49
933 943 0.173708 TTCCCACCAAACAAACACGC 59.826 50.000 0.00 0.00 0.00 5.34
934 944 1.587613 CCCACCAAACAAACACGCG 60.588 57.895 3.53 3.53 0.00 6.01
935 945 1.429825 CCACCAAACAAACACGCGA 59.570 52.632 15.93 0.00 0.00 5.87
959 969 0.250166 AGTCGGAGGGTTTCGGTTTG 60.250 55.000 0.00 0.00 0.00 2.93
1541 1562 2.430921 CTTCAACGCGCTCCTCGT 60.431 61.111 5.73 0.00 42.54 4.18
1572 1593 1.369091 GCACGGAGCGTTTCCATGAT 61.369 55.000 8.09 0.00 41.76 2.45
1584 1605 2.664185 CATGATCTCTGGGCCGCG 60.664 66.667 0.00 0.00 0.00 6.46
1788 1809 3.308014 GAGGCTGCAGGACGCTCTT 62.308 63.158 17.12 0.00 43.06 2.85
1914 1935 1.131126 CGCATGTTTGACAGGATGGTC 59.869 52.381 0.00 0.00 43.62 4.02
1920 1941 0.036732 TTGACAGGATGGTCCACAGC 59.963 55.000 0.00 0.00 43.62 4.40
1941 1962 2.731571 GGTGAGCCCCGATGCTGTA 61.732 63.158 3.26 0.00 42.95 2.74
1995 2016 1.739562 GTGCAGAGTGAAGGAGGCG 60.740 63.158 0.00 0.00 0.00 5.52
2019 2040 3.433598 GGTTGCTGCTAATGGAGATGGTA 60.434 47.826 0.00 0.00 33.10 3.25
2022 2043 2.634940 GCTGCTAATGGAGATGGTAGGA 59.365 50.000 0.00 0.00 33.10 2.94
2028 2049 5.163195 GCTAATGGAGATGGTAGGAAAAGGA 60.163 44.000 0.00 0.00 0.00 3.36
2045 2066 2.650322 AGGACTCTCGTCTGAAGGATC 58.350 52.381 0.00 0.00 40.10 3.36
2048 2069 1.340211 ACTCTCGTCTGAAGGATCCGT 60.340 52.381 5.98 1.90 0.00 4.69
2145 2166 4.017591 AGGAAATATGGTGTTGTCATCCCA 60.018 41.667 0.00 0.00 0.00 4.37
2209 2230 2.673523 GTCCTCATGCTGCCAGGT 59.326 61.111 0.00 0.00 0.00 4.00
2379 2400 4.801147 TGATACTTACCGTACGCTAGTG 57.199 45.455 10.49 0.59 0.00 2.74
2469 2490 2.887783 TCTCCAGCCGAATGAGACTATC 59.112 50.000 0.00 0.00 30.48 2.08
2559 2580 4.571984 GCTTTTGTTCTTGATTTGCAGGTT 59.428 37.500 0.00 0.00 0.00 3.50
2676 2697 1.963515 GGTTTTGTCCCAAGCAGTGAT 59.036 47.619 0.00 0.00 0.00 3.06
2943 2965 4.348656 GTGATGTGAGCATGCTGTTAATG 58.651 43.478 28.27 0.00 35.07 1.90
2948 2970 6.513806 TGTGAGCATGCTGTTAATGTAATT 57.486 33.333 28.27 0.00 41.28 1.40
2973 2995 7.287061 TCTCCTCATAAAGACTTGGTTTTTCA 58.713 34.615 0.00 0.00 0.00 2.69
2975 2997 8.477419 TCCTCATAAAGACTTGGTTTTTCAAT 57.523 30.769 0.00 0.00 0.00 2.57
2980 3002 6.790232 AAAGACTTGGTTTTTCAATCCAGA 57.210 33.333 0.00 0.00 32.63 3.86
3077 3191 3.053693 TGATGGCTTAGTGGGCTAACAAT 60.054 43.478 0.00 0.00 33.92 2.71
3087 3201 1.887707 GCTAACAATCCGAGGCCCG 60.888 63.158 0.00 2.20 38.18 6.13
3088 3202 1.820581 CTAACAATCCGAGGCCCGA 59.179 57.895 14.30 1.19 41.76 5.14
3089 3203 0.249489 CTAACAATCCGAGGCCCGAG 60.249 60.000 14.30 5.70 41.76 4.63
3090 3204 0.974010 TAACAATCCGAGGCCCGAGT 60.974 55.000 14.30 0.00 41.76 4.18
3091 3205 1.838073 AACAATCCGAGGCCCGAGTT 61.838 55.000 14.30 10.17 41.76 3.01
3092 3206 1.521681 CAATCCGAGGCCCGAGTTC 60.522 63.158 14.30 0.00 41.76 3.01
3123 3237 3.319972 GCTGAATGATGGCCATGTACATT 59.680 43.478 26.56 24.96 35.24 2.71
3133 3247 2.061773 CCATGTACATTCCTCGCGATC 58.938 52.381 10.36 0.00 0.00 3.69
3146 3260 1.299976 GCGATCCTGGGTTCCTTGT 59.700 57.895 0.00 0.00 0.00 3.16
3159 3273 5.303333 TGGGTTCCTTGTATTTTTGGAGAAC 59.697 40.000 0.00 0.00 33.34 3.01
3171 3285 2.275134 TGGAGAACAGATGCAAAGCA 57.725 45.000 0.00 0.00 44.86 3.91
3304 3428 2.702261 GGTGATGCATGTTTGGCAAAT 58.298 42.857 16.74 0.00 45.60 2.32
3426 3592 0.816825 AGTGCTGCATCCAATAGCCG 60.817 55.000 5.27 0.00 36.64 5.52
3445 3613 3.119990 GCCGCAATTGTATTACACAGTGT 60.120 43.478 11.87 11.87 38.72 3.55
3468 3636 3.119849 ACTGTTTGGTAAATCTCATGCGC 60.120 43.478 0.00 0.00 0.00 6.09
3499 3667 1.814394 TCCAAGAGTTCACATGCATGC 59.186 47.619 26.53 11.82 0.00 4.06
3518 3686 4.177165 TGCTGAACAATAGCATTTGTGG 57.823 40.909 5.21 1.80 45.52 4.17
3583 3751 5.388111 CACTGAGCACAAATGTTGATGTAG 58.612 41.667 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 48 3.480470 CCACTGAAAGAGGTCACACAAT 58.520 45.455 0.00 0.00 40.12 2.71
107 110 8.758829 TCAGAAGCATTAACTATTTACTCTGGA 58.241 33.333 0.00 0.00 0.00 3.86
140 143 3.452264 TGAGAAATGGATGACCGAGACAT 59.548 43.478 0.00 0.00 39.42 3.06
263 266 0.913924 AAACGTCCATAACCGGGGAT 59.086 50.000 6.32 0.00 35.25 3.85
353 356 7.270047 CAACTCAATCCCAATTAAGCATCATT 58.730 34.615 0.00 0.00 0.00 2.57
433 438 4.268359 AGCCAATTTTTCCTGCAACAAAA 58.732 34.783 0.00 0.00 0.00 2.44
441 446 6.557291 TTTGCATAAAGCCAATTTTTCCTG 57.443 33.333 0.00 0.00 44.83 3.86
520 529 9.990360 TGTAACACATAGAAAGTAATGAACAGA 57.010 29.630 0.00 0.00 0.00 3.41
533 542 8.922931 ATATGATGGCAATGTAACACATAGAA 57.077 30.769 0.00 0.00 37.97 2.10
553 562 3.205338 CGGGTCAGCACATGAAATATGA 58.795 45.455 0.00 0.00 40.43 2.15
619 628 1.004745 CCATGACCTAAGGCACCTTGT 59.995 52.381 12.29 2.15 37.47 3.16
620 629 1.004745 ACCATGACCTAAGGCACCTTG 59.995 52.381 12.29 0.00 37.47 3.61
678 687 2.944094 GCGGAAGGCTTGGAGGAATAAA 60.944 50.000 3.46 0.00 39.11 1.40
766 776 8.260818 ACAGAGTAGCAATCACACACTTATTAT 58.739 33.333 0.00 0.00 0.00 1.28
837 847 9.807921 TTGTTTAGAGGGAATGAGAGTTTAAAT 57.192 29.630 0.00 0.00 0.00 1.40
838 848 9.807921 ATTGTTTAGAGGGAATGAGAGTTTAAA 57.192 29.630 0.00 0.00 0.00 1.52
839 849 9.449719 GATTGTTTAGAGGGAATGAGAGTTTAA 57.550 33.333 0.00 0.00 0.00 1.52
840 850 8.602424 TGATTGTTTAGAGGGAATGAGAGTTTA 58.398 33.333 0.00 0.00 0.00 2.01
841 851 7.461749 TGATTGTTTAGAGGGAATGAGAGTTT 58.538 34.615 0.00 0.00 0.00 2.66
842 852 7.020827 TGATTGTTTAGAGGGAATGAGAGTT 57.979 36.000 0.00 0.00 0.00 3.01
843 853 6.627087 TGATTGTTTAGAGGGAATGAGAGT 57.373 37.500 0.00 0.00 0.00 3.24
844 854 7.772292 TCATTGATTGTTTAGAGGGAATGAGAG 59.228 37.037 0.00 0.00 0.00 3.20
845 855 7.632861 TCATTGATTGTTTAGAGGGAATGAGA 58.367 34.615 0.00 0.00 0.00 3.27
846 856 7.870509 TCATTGATTGTTTAGAGGGAATGAG 57.129 36.000 0.00 0.00 0.00 2.90
847 857 7.890127 AGTTCATTGATTGTTTAGAGGGAATGA 59.110 33.333 0.00 0.00 0.00 2.57
848 858 8.059798 AGTTCATTGATTGTTTAGAGGGAATG 57.940 34.615 0.00 0.00 0.00 2.67
849 859 8.655935 AAGTTCATTGATTGTTTAGAGGGAAT 57.344 30.769 0.00 0.00 0.00 3.01
850 860 8.477419 AAAGTTCATTGATTGTTTAGAGGGAA 57.523 30.769 0.00 0.00 0.00 3.97
851 861 8.477419 AAAAGTTCATTGATTGTTTAGAGGGA 57.523 30.769 0.00 0.00 0.00 4.20
860 870 9.918630 CAAGGAGAATAAAAGTTCATTGATTGT 57.081 29.630 0.00 0.00 0.00 2.71
861 871 8.866956 GCAAGGAGAATAAAAGTTCATTGATTG 58.133 33.333 2.40 0.00 0.00 2.67
862 872 8.037166 GGCAAGGAGAATAAAAGTTCATTGATT 58.963 33.333 2.40 0.00 0.00 2.57
863 873 7.550712 GGCAAGGAGAATAAAAGTTCATTGAT 58.449 34.615 2.40 0.00 0.00 2.57
864 874 6.349280 CGGCAAGGAGAATAAAAGTTCATTGA 60.349 38.462 2.40 0.00 0.00 2.57
865 875 5.801947 CGGCAAGGAGAATAAAAGTTCATTG 59.198 40.000 0.00 0.00 0.00 2.82
866 876 5.622233 GCGGCAAGGAGAATAAAAGTTCATT 60.622 40.000 0.00 0.00 0.00 2.57
867 877 4.142381 GCGGCAAGGAGAATAAAAGTTCAT 60.142 41.667 0.00 0.00 0.00 2.57
868 878 3.190535 GCGGCAAGGAGAATAAAAGTTCA 59.809 43.478 0.00 0.00 0.00 3.18
869 879 3.440522 AGCGGCAAGGAGAATAAAAGTTC 59.559 43.478 1.45 0.00 0.00 3.01
870 880 3.421844 AGCGGCAAGGAGAATAAAAGTT 58.578 40.909 1.45 0.00 0.00 2.66
871 881 3.010420 GAGCGGCAAGGAGAATAAAAGT 58.990 45.455 1.45 0.00 0.00 2.66
872 882 3.009723 TGAGCGGCAAGGAGAATAAAAG 58.990 45.455 1.45 0.00 0.00 2.27
873 883 3.066291 TGAGCGGCAAGGAGAATAAAA 57.934 42.857 1.45 0.00 0.00 1.52
874 884 2.747446 GTTGAGCGGCAAGGAGAATAAA 59.253 45.455 1.45 0.00 37.12 1.40
875 885 2.027192 AGTTGAGCGGCAAGGAGAATAA 60.027 45.455 1.45 0.00 37.12 1.40
876 886 1.555075 AGTTGAGCGGCAAGGAGAATA 59.445 47.619 1.45 0.00 37.12 1.75
877 887 0.326264 AGTTGAGCGGCAAGGAGAAT 59.674 50.000 1.45 0.00 37.12 2.40
878 888 0.320771 GAGTTGAGCGGCAAGGAGAA 60.321 55.000 1.45 0.00 37.12 2.87
879 889 1.293498 GAGTTGAGCGGCAAGGAGA 59.707 57.895 1.45 0.00 37.12 3.71
880 890 1.743252 GGAGTTGAGCGGCAAGGAG 60.743 63.158 1.45 0.00 37.12 3.69
881 891 2.347490 GGAGTTGAGCGGCAAGGA 59.653 61.111 1.45 0.00 37.12 3.36
882 892 2.747855 GGGAGTTGAGCGGCAAGG 60.748 66.667 1.45 0.00 37.12 3.61
883 893 0.962356 AATGGGAGTTGAGCGGCAAG 60.962 55.000 1.45 0.00 37.12 4.01
884 894 0.960364 GAATGGGAGTTGAGCGGCAA 60.960 55.000 1.45 0.00 0.00 4.52
885 895 1.377202 GAATGGGAGTTGAGCGGCA 60.377 57.895 1.45 0.00 0.00 5.69
886 896 2.115291 GGAATGGGAGTTGAGCGGC 61.115 63.158 0.00 0.00 0.00 6.53
887 897 1.452108 GGGAATGGGAGTTGAGCGG 60.452 63.158 0.00 0.00 0.00 5.52
888 898 1.452108 GGGGAATGGGAGTTGAGCG 60.452 63.158 0.00 0.00 0.00 5.03
889 899 0.259938 ATGGGGAATGGGAGTTGAGC 59.740 55.000 0.00 0.00 0.00 4.26
890 900 2.834638 AATGGGGAATGGGAGTTGAG 57.165 50.000 0.00 0.00 0.00 3.02
891 901 3.558608 AAAATGGGGAATGGGAGTTGA 57.441 42.857 0.00 0.00 0.00 3.18
892 902 4.352893 ACTAAAATGGGGAATGGGAGTTG 58.647 43.478 0.00 0.00 0.00 3.16
893 903 4.692523 ACTAAAATGGGGAATGGGAGTT 57.307 40.909 0.00 0.00 0.00 3.01
894 904 4.572007 GGAACTAAAATGGGGAATGGGAGT 60.572 45.833 0.00 0.00 0.00 3.85
895 905 3.960755 GGAACTAAAATGGGGAATGGGAG 59.039 47.826 0.00 0.00 0.00 4.30
896 906 3.310288 GGGAACTAAAATGGGGAATGGGA 60.310 47.826 0.00 0.00 0.00 4.37
897 907 3.038280 GGGAACTAAAATGGGGAATGGG 58.962 50.000 0.00 0.00 0.00 4.00
898 908 3.450817 GTGGGAACTAAAATGGGGAATGG 59.549 47.826 0.00 0.00 0.00 3.16
899 909 3.450817 GGTGGGAACTAAAATGGGGAATG 59.549 47.826 0.00 0.00 0.00 2.67
900 910 3.078305 TGGTGGGAACTAAAATGGGGAAT 59.922 43.478 0.00 0.00 0.00 3.01
901 911 2.451273 TGGTGGGAACTAAAATGGGGAA 59.549 45.455 0.00 0.00 0.00 3.97
902 912 2.074579 TGGTGGGAACTAAAATGGGGA 58.925 47.619 0.00 0.00 0.00 4.81
903 913 2.614134 TGGTGGGAACTAAAATGGGG 57.386 50.000 0.00 0.00 0.00 4.96
904 914 3.643792 TGTTTGGTGGGAACTAAAATGGG 59.356 43.478 0.00 0.00 0.00 4.00
905 915 4.946478 TGTTTGGTGGGAACTAAAATGG 57.054 40.909 0.00 0.00 0.00 3.16
906 916 6.036626 GTGTTTGTTTGGTGGGAACTAAAATG 59.963 38.462 0.00 0.00 0.00 2.32
907 917 6.110033 GTGTTTGTTTGGTGGGAACTAAAAT 58.890 36.000 0.00 0.00 0.00 1.82
908 918 5.480205 GTGTTTGTTTGGTGGGAACTAAAA 58.520 37.500 0.00 0.00 0.00 1.52
909 919 4.380655 CGTGTTTGTTTGGTGGGAACTAAA 60.381 41.667 0.00 0.00 0.00 1.85
910 920 3.128938 CGTGTTTGTTTGGTGGGAACTAA 59.871 43.478 0.00 0.00 0.00 2.24
911 921 2.683867 CGTGTTTGTTTGGTGGGAACTA 59.316 45.455 0.00 0.00 0.00 2.24
912 922 1.474879 CGTGTTTGTTTGGTGGGAACT 59.525 47.619 0.00 0.00 0.00 3.01
913 923 1.915952 CGTGTTTGTTTGGTGGGAAC 58.084 50.000 0.00 0.00 0.00 3.62
914 924 0.173708 GCGTGTTTGTTTGGTGGGAA 59.826 50.000 0.00 0.00 0.00 3.97
915 925 1.810532 GCGTGTTTGTTTGGTGGGA 59.189 52.632 0.00 0.00 0.00 4.37
916 926 1.587613 CGCGTGTTTGTTTGGTGGG 60.588 57.895 0.00 0.00 0.00 4.61
917 927 0.030101 ATCGCGTGTTTGTTTGGTGG 59.970 50.000 5.77 0.00 0.00 4.61
918 928 1.394697 GATCGCGTGTTTGTTTGGTG 58.605 50.000 5.77 0.00 0.00 4.17
919 929 0.041663 CGATCGCGTGTTTGTTTGGT 60.042 50.000 5.77 0.00 0.00 3.67
920 930 0.724453 CCGATCGCGTGTTTGTTTGG 60.724 55.000 10.32 0.00 35.23 3.28
921 931 0.233590 TCCGATCGCGTGTTTGTTTG 59.766 50.000 10.32 0.00 35.23 2.93
922 932 0.511221 CTCCGATCGCGTGTTTGTTT 59.489 50.000 10.32 0.00 35.23 2.83
923 933 0.599204 ACTCCGATCGCGTGTTTGTT 60.599 50.000 10.32 0.00 35.23 2.83
924 934 1.006571 ACTCCGATCGCGTGTTTGT 60.007 52.632 10.32 0.00 35.23 2.83
925 935 1.702299 GACTCCGATCGCGTGTTTG 59.298 57.895 10.32 0.00 35.23 2.93
926 936 1.800315 CGACTCCGATCGCGTGTTT 60.800 57.895 10.32 0.00 38.22 2.83
927 937 2.202440 CGACTCCGATCGCGTGTT 60.202 61.111 10.32 0.00 38.22 3.32
928 938 4.175489 CCGACTCCGATCGCGTGT 62.175 66.667 10.32 10.05 40.87 4.49
929 939 3.791928 CTCCGACTCCGATCGCGTG 62.792 68.421 10.32 6.84 40.87 5.34
930 940 3.574445 CTCCGACTCCGATCGCGT 61.574 66.667 10.32 8.87 40.87 6.01
931 941 4.315122 CCTCCGACTCCGATCGCG 62.315 72.222 10.32 7.77 40.87 5.87
932 942 3.967335 CCCTCCGACTCCGATCGC 61.967 72.222 10.32 0.00 40.87 4.58
933 943 1.664321 AAACCCTCCGACTCCGATCG 61.664 60.000 8.51 8.51 41.89 3.69
934 944 0.102663 GAAACCCTCCGACTCCGATC 59.897 60.000 0.00 0.00 38.22 3.69
935 945 1.664321 CGAAACCCTCCGACTCCGAT 61.664 60.000 0.00 0.00 38.22 4.18
959 969 1.527433 GGCCTTGGCTTGGACACTTC 61.527 60.000 11.71 0.00 31.53 3.01
1533 1554 4.897856 GAGAGCGCGACGAGGAGC 62.898 72.222 12.10 0.00 0.00 4.70
1557 1578 2.208431 CAGAGATCATGGAAACGCTCC 58.792 52.381 0.00 0.00 45.64 4.70
1567 1588 2.664185 CGCGGCCCAGAGATCATG 60.664 66.667 0.00 0.00 0.00 3.07
1690 1711 3.455737 GCTCCTCCAGCTCCTCTAT 57.544 57.895 0.00 0.00 45.83 1.98
1788 1809 2.746904 CGGCATAACATCAAACAGGTGA 59.253 45.455 0.00 0.00 0.00 4.02
1941 1962 5.509840 CCCTGCGATAAGAACACTATAAGCT 60.510 44.000 0.00 0.00 0.00 3.74
1995 2016 2.698855 TCTCCATTAGCAGCAACCTC 57.301 50.000 0.00 0.00 0.00 3.85
2045 2066 3.653344 TCAATCACACTCTTGAGAACGG 58.347 45.455 4.49 0.00 0.00 4.44
2145 2166 7.318141 CAATCAAGCAATTGTAACTCTCCAAT 58.682 34.615 7.40 0.00 32.97 3.16
2209 2230 5.491070 CTCTATCATCCACTGGAACAAACA 58.509 41.667 0.66 0.00 38.70 2.83
2398 2419 0.619832 TTGCCATCTGAGCTCCTCCT 60.620 55.000 12.15 0.00 0.00 3.69
2469 2490 1.563111 CACAAACCAAAGCAGCACAG 58.437 50.000 0.00 0.00 0.00 3.66
2559 2580 8.370940 AGAGTATTATAGCTCTTATTGCAGCAA 58.629 33.333 11.07 11.07 38.81 3.91
2676 2697 6.280643 CCCATAAACAAGAGATCGACATGTA 58.719 40.000 0.00 0.00 0.00 2.29
2920 2942 0.800631 AACAGCATGCTCACATCACG 59.199 50.000 19.68 6.54 42.53 4.35
2943 2965 8.794335 AACCAAGTCTTTATGAGGAGAATTAC 57.206 34.615 0.00 0.00 30.03 1.89
2948 2970 7.287061 TGAAAAACCAAGTCTTTATGAGGAGA 58.713 34.615 0.00 0.00 0.00 3.71
2980 3002 5.308014 TGCATCACACAGACTAGAATTTGT 58.692 37.500 0.00 0.00 0.00 2.83
3077 3191 3.976490 ATGGAACTCGGGCCTCGGA 62.976 63.158 0.84 0.00 39.77 4.55
3087 3201 4.005650 TCATTCAGCAAGTCATGGAACTC 58.994 43.478 0.00 0.00 0.00 3.01
3088 3202 4.025040 TCATTCAGCAAGTCATGGAACT 57.975 40.909 0.00 0.00 0.00 3.01
3089 3203 4.439700 CCATCATTCAGCAAGTCATGGAAC 60.440 45.833 0.00 0.00 32.51 3.62
3090 3204 3.697542 CCATCATTCAGCAAGTCATGGAA 59.302 43.478 0.00 0.00 32.51 3.53
3091 3205 3.284617 CCATCATTCAGCAAGTCATGGA 58.715 45.455 0.00 0.00 32.51 3.41
3092 3206 2.223735 GCCATCATTCAGCAAGTCATGG 60.224 50.000 0.00 0.00 33.72 3.66
3123 3237 2.363795 AACCCAGGATCGCGAGGA 60.364 61.111 16.66 0.00 0.00 3.71
3133 3247 4.156477 TCCAAAAATACAAGGAACCCAGG 58.844 43.478 0.00 0.00 0.00 4.45
3146 3260 6.158598 GCTTTGCATCTGTTCTCCAAAAATA 58.841 36.000 0.00 0.00 0.00 1.40
3159 3273 4.393990 TCATGAACTAGTGCTTTGCATCTG 59.606 41.667 1.64 0.00 41.91 2.90
3171 3285 5.658634 TCAGCATTAGTCCTCATGAACTAGT 59.341 40.000 7.22 2.90 0.00 2.57
3304 3428 0.836606 TGTGGTCAGGACAAGAGCAA 59.163 50.000 1.41 0.00 44.08 3.91
3411 3577 0.956633 ATTGCGGCTATTGGATGCAG 59.043 50.000 0.00 0.00 36.83 4.41
3422 3588 3.126858 CACTGTGTAATACAATTGCGGCT 59.873 43.478 5.05 0.00 39.20 5.52
3445 3613 4.094294 GCGCATGAGATTTACCAAACAGTA 59.906 41.667 0.30 0.00 0.00 2.74
3499 3667 5.404946 CCTTCCACAAATGCTATTGTTCAG 58.595 41.667 5.15 2.90 41.44 3.02
3518 3686 4.423625 ACCATACTGCATTCTACCCTTC 57.576 45.455 0.00 0.00 0.00 3.46
3583 3751 1.064654 GCAAATCCGCATGAGGAAGAC 59.935 52.381 22.69 8.64 44.50 3.01


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

AutoCloner maintained by Alex Coulton.