Multiple sequence alignment - TraesCS5A01G465100

Loading Multiple Alignment...

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 TraesCS5A01G465100 chr5A 100.000 2329 0 0 548 2876 644133586 644135914 0.000000e+00 4301.0
1 TraesCS5A01G465100 chr5A 100.000 240 0 0 1 240 644133039 644133278 7.310000e-121 444.0
2 TraesCS5A01G465100 chr5A 91.228 57 5 0 2452 2508 644135436 644135492 8.540000e-11 78.7
3 TraesCS5A01G465100 chr5A 91.228 57 5 0 2398 2454 644135490 644135546 8.540000e-11 78.7
4 TraesCS5A01G465100 chr5B 92.266 1849 121 14 1026 2854 649402161 649404007 0.000000e+00 2603.0
5 TraesCS5A01G465100 chr5B 95.062 81 4 0 27 107 649401309 649401389 8.360000e-26 128.0
6 TraesCS5A01G465100 chr5B 82.609 115 11 8 127 239 649401376 649401483 3.050000e-15 93.5
7 TraesCS5A01G465100 chr5B 94.915 59 3 0 2396 2454 649403600 649403658 3.050000e-15 93.5
8 TraesCS5A01G465100 chr5D 93.034 1450 86 10 1015 2457 516816834 516818275 0.000000e+00 2104.0
9 TraesCS5A01G465100 chr5D 91.898 432 28 3 2452 2876 516818215 516818646 5.300000e-167 597.0
10 TraesCS5A01G465100 chr5D 96.154 78 3 0 30 107 516815998 516816075 8.360000e-26 128.0
11 TraesCS5A01G465100 chr1B 88.871 1249 117 19 1310 2549 34730809 34729574 0.000000e+00 1517.0
12 TraesCS5A01G465100 chr1B 87.698 252 31 0 1067 1318 34731588 34731337 7.790000e-76 294.0
13 TraesCS5A01G465100 chr1B 84.906 265 33 2 2498 2762 34729574 34729317 7.900000e-66 261.0
14 TraesCS5A01G465100 chr1B 89.256 121 11 2 2757 2876 34727984 34727865 1.790000e-32 150.0
15 TraesCS5A01G465100 chr1B 85.294 102 9 3 1018 1116 97811670 97811572 1.820000e-17 100.0


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 TraesCS5A01G465100 chr5A 644133039 644135914 2875 False 1225.6 4301 95.614000 1 2876 4 chr5A.!!$F1 2875
1 TraesCS5A01G465100 chr5B 649401309 649404007 2698 False 729.5 2603 91.213000 27 2854 4 chr5B.!!$F1 2827
2 TraesCS5A01G465100 chr5D 516815998 516818646 2648 False 943.0 2104 93.695333 30 2876 3 chr5D.!!$F1 2846
3 TraesCS5A01G465100 chr1B 34727865 34731588 3723 True 555.5 1517 87.682750 1067 2876 4 chr1B.!!$R2 1809

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
742 820 0.034380 GAAGGCAGGGTTAAGGTCCC 60.034 60.0 0.00 0.0 44.9 4.46 F
946 1040 0.181114 GCCACATGTAGCTGGGATGA 59.819 55.0 9.16 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 2417 0.107703 CCGCCTCAGCAACATCCTTA 60.108 55.0 0.0 0.0 39.83 2.69 R
2807 4890 0.251354 GAGATCTGCTGCAACCTGGA 59.749 55.0 0.0 0.0 0.00 3.86 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
23 24 6.901699 CCACGTGTAGTAGCGTATATTAAC 57.098 41.667 15.65 0.00 39.48 2.01
24 25 6.662616 CCACGTGTAGTAGCGTATATTAACT 58.337 40.000 15.65 0.00 39.48 2.24
25 26 6.576313 CCACGTGTAGTAGCGTATATTAACTG 59.424 42.308 15.65 0.00 39.48 3.16
26 27 7.128331 CACGTGTAGTAGCGTATATTAACTGT 58.872 38.462 7.58 0.00 39.48 3.55
27 28 8.275632 CACGTGTAGTAGCGTATATTAACTGTA 58.724 37.037 7.58 0.00 39.48 2.74
28 29 8.491152 ACGTGTAGTAGCGTATATTAACTGTAG 58.509 37.037 0.00 0.00 39.72 2.74
54 55 3.009301 ACTCTTCCGTAGTCAACAACG 57.991 47.619 0.00 0.00 38.80 4.10
87 88 1.816679 GGCATCGCATCTCACAGCA 60.817 57.895 0.00 0.00 0.00 4.41
107 108 0.107456 CACACTCCACCAGCAAGAGT 59.893 55.000 0.00 0.00 41.49 3.24
108 109 0.839946 ACACTCCACCAGCAAGAGTT 59.160 50.000 0.00 0.00 38.80 3.01
109 110 1.212935 ACACTCCACCAGCAAGAGTTT 59.787 47.619 0.00 0.00 38.80 2.66
110 111 2.301346 CACTCCACCAGCAAGAGTTTT 58.699 47.619 0.00 0.00 38.80 2.43
111 112 2.689983 CACTCCACCAGCAAGAGTTTTT 59.310 45.455 0.00 0.00 38.80 1.94
135 136 2.877097 TTTGAAGCTATCCACCAGCA 57.123 45.000 0.00 0.00 41.66 4.41
136 137 2.877097 TTGAAGCTATCCACCAGCAA 57.123 45.000 0.00 0.00 41.66 3.91
137 138 2.408271 TGAAGCTATCCACCAGCAAG 57.592 50.000 0.00 0.00 41.66 4.01
138 139 1.908619 TGAAGCTATCCACCAGCAAGA 59.091 47.619 0.00 0.00 41.66 3.02
139 140 2.093288 TGAAGCTATCCACCAGCAAGAG 60.093 50.000 0.00 0.00 41.66 2.85
140 141 1.577736 AGCTATCCACCAGCAAGAGT 58.422 50.000 0.00 0.00 41.66 3.24
145 146 4.991687 GCTATCCACCAGCAAGAGTATTAC 59.008 45.833 0.00 0.00 38.93 1.89
189 200 3.062466 CTCTCTCCCCACGACGCA 61.062 66.667 0.00 0.00 0.00 5.24
615 626 2.544685 AGTAGCGCTGCTTTAGATGTG 58.455 47.619 23.18 0.00 40.44 3.21
618 629 2.544685 AGCGCTGCTTTAGATGTGTAG 58.455 47.619 10.39 0.00 33.89 2.74
619 630 1.004504 GCGCTGCTTTAGATGTGTAGC 60.005 52.381 0.00 0.00 36.37 3.58
620 631 2.270923 CGCTGCTTTAGATGTGTAGCA 58.729 47.619 0.00 0.00 41.01 3.49
621 632 2.029728 CGCTGCTTTAGATGTGTAGCAC 59.970 50.000 0.00 0.00 38.61 4.40
623 634 3.866651 CTGCTTTAGATGTGTAGCACCT 58.133 45.455 0.00 0.00 38.61 4.00
626 637 4.116238 GCTTTAGATGTGTAGCACCTCTC 58.884 47.826 9.64 0.00 39.38 3.20
636 647 2.825836 CACCTCTCCAATGGCGCC 60.826 66.667 22.73 22.73 0.00 6.53
675 686 2.599578 CCTGCAGTTTGGCTGGCT 60.600 61.111 13.81 0.00 44.30 4.75
676 687 2.205152 CCTGCAGTTTGGCTGGCTT 61.205 57.895 13.81 0.00 44.30 4.35
678 689 0.105408 CTGCAGTTTGGCTGGCTTTT 59.895 50.000 5.25 0.00 45.14 2.27
679 690 1.340889 CTGCAGTTTGGCTGGCTTTTA 59.659 47.619 5.25 0.00 45.14 1.52
691 769 2.808543 CTGGCTTTTACTGTCTGTGTCC 59.191 50.000 0.00 0.00 0.00 4.02
700 778 3.458189 ACTGTCTGTGTCCTTTTCTTCG 58.542 45.455 0.00 0.00 0.00 3.79
714 792 0.685097 TCTTCGGGAGTTCAGGTTGG 59.315 55.000 0.00 0.00 0.00 3.77
715 793 0.321653 CTTCGGGAGTTCAGGTTGGG 60.322 60.000 0.00 0.00 0.00 4.12
726 804 3.071874 TCAGGTTGGGTATTGCAGAAG 57.928 47.619 0.00 0.00 0.00 2.85
727 805 2.094675 CAGGTTGGGTATTGCAGAAGG 58.905 52.381 0.00 0.00 0.00 3.46
728 806 0.817654 GGTTGGGTATTGCAGAAGGC 59.182 55.000 0.00 0.00 45.13 4.35
739 817 0.038310 GCAGAAGGCAGGGTTAAGGT 59.962 55.000 0.00 0.00 43.97 3.50
740 818 1.950954 GCAGAAGGCAGGGTTAAGGTC 60.951 57.143 0.00 0.00 43.97 3.85
741 819 0.992695 AGAAGGCAGGGTTAAGGTCC 59.007 55.000 0.00 0.00 0.00 4.46
742 820 0.034380 GAAGGCAGGGTTAAGGTCCC 60.034 60.000 0.00 0.00 44.90 4.46
755 839 5.583854 GGTTAAGGTCCCTAGATTCGAAAAC 59.416 44.000 0.00 0.00 0.00 2.43
756 840 4.903045 AAGGTCCCTAGATTCGAAAACA 57.097 40.909 0.00 0.00 0.00 2.83
758 842 5.024785 AGGTCCCTAGATTCGAAAACATC 57.975 43.478 0.00 0.00 0.00 3.06
773 857 1.182667 ACATCATGCTGCATGTTGCT 58.817 45.000 35.74 25.65 45.31 3.91
774 858 2.371306 ACATCATGCTGCATGTTGCTA 58.629 42.857 35.74 22.50 45.31 3.49
775 859 2.098607 ACATCATGCTGCATGTTGCTAC 59.901 45.455 35.74 0.00 45.31 3.58
776 860 2.118313 TCATGCTGCATGTTGCTACT 57.882 45.000 34.14 1.57 45.31 2.57
778 862 1.741145 CATGCTGCATGTTGCTACTGA 59.259 47.619 29.59 0.00 45.31 3.41
779 863 1.894881 TGCTGCATGTTGCTACTGAA 58.105 45.000 0.00 0.00 45.31 3.02
792 885 4.582869 TGCTACTGAAATGTTGATGCTCT 58.417 39.130 0.00 0.00 0.00 4.09
796 889 4.392047 ACTGAAATGTTGATGCTCTGTCA 58.608 39.130 0.00 0.00 0.00 3.58
799 892 4.694037 TGAAATGTTGATGCTCTGTCAGAG 59.306 41.667 23.34 23.34 45.04 3.35
801 894 4.548451 ATGTTGATGCTCTGTCAGAGAA 57.452 40.909 30.22 22.49 45.07 2.87
803 896 3.323115 TGTTGATGCTCTGTCAGAGAACT 59.677 43.478 30.22 14.86 45.07 3.01
804 897 4.524328 TGTTGATGCTCTGTCAGAGAACTA 59.476 41.667 30.22 12.11 45.07 2.24
805 898 4.979943 TGATGCTCTGTCAGAGAACTAG 57.020 45.455 30.22 7.07 45.07 2.57
810 903 5.561679 TGCTCTGTCAGAGAACTAGTAGAA 58.438 41.667 30.22 0.00 45.07 2.10
814 907 7.362574 GCTCTGTCAGAGAACTAGTAGAACAAT 60.363 40.741 30.22 0.00 45.07 2.71
833 926 8.511321 AGAACAATAAATGAAACGTTGATGCTA 58.489 29.630 0.00 0.00 0.00 3.49
834 927 9.123709 GAACAATAAATGAAACGTTGATGCTAA 57.876 29.630 0.00 0.00 0.00 3.09
835 928 9.469807 AACAATAAATGAAACGTTGATGCTAAA 57.530 25.926 0.00 0.00 0.00 1.85
836 929 8.911662 ACAATAAATGAAACGTTGATGCTAAAC 58.088 29.630 0.00 0.00 0.00 2.01
837 930 8.910666 CAATAAATGAAACGTTGATGCTAAACA 58.089 29.630 0.00 0.00 0.00 2.83
838 931 6.991485 AAATGAAACGTTGATGCTAAACAG 57.009 33.333 0.00 0.00 0.00 3.16
839 932 5.940192 ATGAAACGTTGATGCTAAACAGA 57.060 34.783 0.00 0.00 0.00 3.41
840 933 5.743026 TGAAACGTTGATGCTAAACAGAA 57.257 34.783 0.00 0.00 0.00 3.02
841 934 6.125327 TGAAACGTTGATGCTAAACAGAAA 57.875 33.333 0.00 0.00 0.00 2.52
842 935 5.968848 TGAAACGTTGATGCTAAACAGAAAC 59.031 36.000 0.00 0.00 0.00 2.78
843 936 5.493133 AACGTTGATGCTAAACAGAAACA 57.507 34.783 0.00 0.00 31.16 2.83
844 937 5.095691 ACGTTGATGCTAAACAGAAACAG 57.904 39.130 0.00 0.00 31.16 3.16
845 938 4.814234 ACGTTGATGCTAAACAGAAACAGA 59.186 37.500 0.00 0.00 31.16 3.41
846 939 5.295787 ACGTTGATGCTAAACAGAAACAGAA 59.704 36.000 0.00 0.00 31.16 3.02
847 940 5.848036 CGTTGATGCTAAACAGAAACAGAAG 59.152 40.000 0.00 0.00 31.16 2.85
848 941 5.362556 TGATGCTAAACAGAAACAGAAGC 57.637 39.130 0.00 0.00 0.00 3.86
849 942 4.821260 TGATGCTAAACAGAAACAGAAGCA 59.179 37.500 0.00 0.00 42.14 3.91
850 943 5.972107 ATGCTAAACAGAAACAGAAGCAT 57.028 34.783 1.27 1.27 42.65 3.79
851 944 6.654582 TGATGCTAAACAGAAACAGAAGCATA 59.345 34.615 6.87 0.00 46.19 3.14
852 945 7.337689 TGATGCTAAACAGAAACAGAAGCATAT 59.662 33.333 6.87 0.00 46.19 1.78
853 946 7.452880 TGCTAAACAGAAACAGAAGCATATT 57.547 32.000 0.00 0.00 33.84 1.28
854 947 7.885297 TGCTAAACAGAAACAGAAGCATATTT 58.115 30.769 0.00 0.00 33.84 1.40
855 948 8.359642 TGCTAAACAGAAACAGAAGCATATTTT 58.640 29.630 0.00 0.00 33.84 1.82
896 990 2.202479 GCGGGCGCAGAAACATTC 60.202 61.111 10.83 0.00 41.49 2.67
902 996 0.446222 GCGCAGAAACATTCGGCTTA 59.554 50.000 0.30 0.00 46.57 3.09
903 997 1.135803 GCGCAGAAACATTCGGCTTAA 60.136 47.619 0.30 0.00 46.57 1.85
915 1009 7.266922 ACATTCGGCTTAAAAGTTTGTTAGA 57.733 32.000 0.00 0.00 0.00 2.10
917 1011 7.860872 ACATTCGGCTTAAAAGTTTGTTAGAAG 59.139 33.333 0.00 0.00 0.00 2.85
928 1022 7.674471 AAGTTTGTTAGAAGAAGTGATAGGC 57.326 36.000 0.00 0.00 0.00 3.93
929 1023 6.174049 AGTTTGTTAGAAGAAGTGATAGGCC 58.826 40.000 0.00 0.00 0.00 5.19
930 1024 5.755409 TTGTTAGAAGAAGTGATAGGCCA 57.245 39.130 5.01 0.00 0.00 5.36
931 1025 5.086104 TGTTAGAAGAAGTGATAGGCCAC 57.914 43.478 5.01 0.00 37.32 5.01
932 1026 4.530553 TGTTAGAAGAAGTGATAGGCCACA 59.469 41.667 5.01 0.00 39.42 4.17
933 1027 5.189736 TGTTAGAAGAAGTGATAGGCCACAT 59.810 40.000 5.01 0.00 39.42 3.21
934 1028 4.148128 AGAAGAAGTGATAGGCCACATG 57.852 45.455 5.01 0.00 39.42 3.21
937 1031 4.679373 AGAAGTGATAGGCCACATGTAG 57.321 45.455 5.01 0.00 39.42 2.74
938 1032 2.918712 AGTGATAGGCCACATGTAGC 57.081 50.000 7.83 7.83 39.42 3.58
940 1034 2.103771 AGTGATAGGCCACATGTAGCTG 59.896 50.000 15.89 0.00 39.42 4.24
941 1035 1.417517 TGATAGGCCACATGTAGCTGG 59.582 52.381 15.89 5.97 0.00 4.85
942 1036 0.767375 ATAGGCCACATGTAGCTGGG 59.233 55.000 15.89 5.52 0.00 4.45
943 1037 0.326143 TAGGCCACATGTAGCTGGGA 60.326 55.000 15.89 0.00 0.00 4.37
944 1038 0.990282 AGGCCACATGTAGCTGGGAT 60.990 55.000 15.89 0.00 0.00 3.85
945 1039 0.820891 GGCCACATGTAGCTGGGATG 60.821 60.000 15.89 0.00 0.00 3.51
946 1040 0.181114 GCCACATGTAGCTGGGATGA 59.819 55.000 9.16 0.00 0.00 2.92
947 1041 1.813092 GCCACATGTAGCTGGGATGAG 60.813 57.143 9.16 0.00 0.00 2.90
950 1044 1.134280 ACATGTAGCTGGGATGAGCAC 60.134 52.381 0.00 0.00 41.83 4.40
969 1063 1.766625 CTGGGGGCTCAGCTGGATAG 61.767 65.000 15.13 5.10 0.00 2.08
1002 1096 3.864243 AGCCATGGTTGTTTAATGCATG 58.136 40.909 14.67 0.00 0.00 4.06
1004 1098 3.864243 CCATGGTTGTTTAATGCATGCT 58.136 40.909 20.33 1.26 0.00 3.79
1009 1103 4.398988 TGGTTGTTTAATGCATGCTAGGAG 59.601 41.667 20.33 0.00 0.00 3.69
1017 1111 9.273016 GTTTAATGCATGCTAGGAGTAAGATTA 57.727 33.333 20.33 7.40 0.00 1.75
1043 1175 5.356882 TCAGTATGTTTGCTTGCTGTAAC 57.643 39.130 0.00 0.00 37.40 2.50
1049 1181 5.261209 TGTTTGCTTGCTGTAACTTTGAT 57.739 34.783 0.00 0.00 0.00 2.57
1062 1194 7.608308 TGTAACTTTGATTGCTTTGCTTTTT 57.392 28.000 0.00 0.00 0.00 1.94
1098 1230 1.172812 AAGGAAAGGTTGCGCTGGTC 61.173 55.000 9.73 0.00 0.00 4.02
1113 1245 4.980805 GTCACCGGTGGCGCTTCA 62.981 66.667 33.40 10.46 0.00 3.02
1257 1389 2.335369 GTCCACTGCGACGTCACT 59.665 61.111 17.16 0.00 0.00 3.41
1473 2141 0.909610 TGATCCCGAGCAAGAAGGGT 60.910 55.000 0.00 0.00 45.27 4.34
1500 2168 2.358615 TCATTGGCGAGCGTTGCT 60.359 55.556 0.00 0.00 43.88 3.91
1506 2174 4.196826 GCGAGCGTTGCTAGCGTG 62.197 66.667 10.77 3.15 45.84 5.34
1527 2195 2.451294 GGAGGGATGGGGCCTCAT 60.451 66.667 21.08 21.08 32.77 2.90
1530 2198 3.505773 GGGATGGGGCCTCATGCT 61.506 66.667 33.14 7.06 40.92 3.79
1596 2264 2.988839 ATTGGAGCTGGGGAGGCAC 61.989 63.158 0.00 0.00 0.00 5.01
1710 2378 1.515521 GGGACTTCCTGGCGTTTGTG 61.516 60.000 0.00 0.00 35.95 3.33
1749 2417 0.403271 AAGGTGTTGATCTGCTGCCT 59.597 50.000 0.00 0.00 0.00 4.75
1758 2434 2.507058 TGATCTGCTGCCTAAGGATGTT 59.493 45.455 0.00 0.00 0.00 2.71
1761 2437 0.329261 TGCTGCCTAAGGATGTTGCT 59.671 50.000 0.00 0.00 0.00 3.91
1882 2558 3.321111 AGCGTTTGAGGACTAGTTGAAGA 59.679 43.478 0.00 0.00 0.00 2.87
1929 2605 6.543831 GGTATCTGAAAGCATTTGAGTACCAT 59.456 38.462 11.60 0.00 41.10 3.55
1946 2622 4.961438 ACCATTTTCTGATTTGCCTGTT 57.039 36.364 0.00 0.00 0.00 3.16
1985 2661 5.779771 AGGTGGGTGATCATGTGTAAAATTT 59.220 36.000 0.00 0.00 0.00 1.82
1986 2662 6.269769 AGGTGGGTGATCATGTGTAAAATTTT 59.730 34.615 8.75 8.75 0.00 1.82
2077 2753 5.068329 TGAGATGTGACAGGAGCTTGTATAG 59.932 44.000 0.00 0.00 0.00 1.31
2110 2787 6.793492 AGAGTTTCATAAAGACTTCTGTGC 57.207 37.500 0.00 0.00 0.00 4.57
2124 2801 1.341209 TCTGTGCCAGTATATCTGCGG 59.659 52.381 2.68 0.00 42.38 5.69
2125 2802 0.392706 TGTGCCAGTATATCTGCGGG 59.607 55.000 0.00 0.00 42.38 6.13
2136 2816 5.721960 AGTATATCTGCGGGATAGAAACCAT 59.278 40.000 0.00 0.00 39.89 3.55
2156 2837 6.218746 ACCATTGAGCTTCAAAATTTGAGTC 58.781 36.000 8.51 7.89 40.12 3.36
2157 2838 6.183360 ACCATTGAGCTTCAAAATTTGAGTCA 60.183 34.615 8.51 10.10 40.12 3.41
2168 2849 6.375455 TCAAAATTTGAGTCAGAAGCCCTATC 59.625 38.462 4.03 0.00 34.08 2.08
2264 2952 7.667043 TCCAGAGTTGTTATAATGTGTGTTC 57.333 36.000 0.00 0.00 0.00 3.18
2307 2998 0.309612 GGCCTGTGGTACAACAAACG 59.690 55.000 4.26 0.00 44.16 3.60
2351 3042 4.861102 CCAAGAAAGGCTTCTGTCAAAT 57.139 40.909 0.00 0.00 41.23 2.32
2352 3043 5.964958 CCAAGAAAGGCTTCTGTCAAATA 57.035 39.130 0.00 0.00 41.23 1.40
2438 3129 9.979578 CTCTCTAAATAGACACTGCAATTATCT 57.020 33.333 0.00 0.00 0.00 1.98
2533 3279 9.237846 GCTGCAATAAACCACTAAGAATTATTC 57.762 33.333 0.00 0.00 0.00 1.75
2549 3295 9.593134 AAGAATTATTCAATATCTAGCCTAGCG 57.407 33.333 7.74 0.00 0.00 4.26
2550 3296 7.708752 AGAATTATTCAATATCTAGCCTAGCGC 59.291 37.037 7.74 0.00 37.98 5.92
2561 3307 0.249322 GCCTAGCGCCTTCGTTATCA 60.249 55.000 2.29 0.00 38.14 2.15
2567 3313 1.003866 GCGCCTTCGTTATCATCAACC 60.004 52.381 0.00 0.00 38.14 3.77
2619 3365 2.445145 TGAGAAACCAAGGGATTGTCCA 59.555 45.455 0.00 0.00 38.64 4.02
2732 3478 1.304962 TAAGGAGCTCTCGGCCACA 60.305 57.895 14.64 0.00 43.05 4.17
2807 4890 0.037734 GAATCCCGTTGGTGGTCCTT 59.962 55.000 0.00 0.00 34.23 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.576313 CAGTTAATATACGCTACTACACGTGG 59.424 42.308 21.57 5.28 43.44 4.94
1 2 7.128331 ACAGTTAATATACGCTACTACACGTG 58.872 38.462 15.48 15.48 43.44 4.49
2 3 7.251704 ACAGTTAATATACGCTACTACACGT 57.748 36.000 0.00 0.00 45.85 4.49
3 4 8.491152 ACTACAGTTAATATACGCTACTACACG 58.509 37.037 0.00 0.00 0.00 4.49
20 21 9.672673 ACTACGGAAGAGTAATTACTACAGTTA 57.327 33.333 18.03 5.42 36.50 2.24
21 22 8.572855 ACTACGGAAGAGTAATTACTACAGTT 57.427 34.615 18.03 9.38 36.50 3.16
22 23 7.826252 TGACTACGGAAGAGTAATTACTACAGT 59.174 37.037 18.03 18.23 36.50 3.55
23 24 8.206325 TGACTACGGAAGAGTAATTACTACAG 57.794 38.462 18.03 14.27 36.50 2.74
24 25 8.454106 GTTGACTACGGAAGAGTAATTACTACA 58.546 37.037 18.03 4.06 36.50 2.74
25 26 8.454106 TGTTGACTACGGAAGAGTAATTACTAC 58.546 37.037 18.03 11.51 36.50 2.73
26 27 8.565896 TGTTGACTACGGAAGAGTAATTACTA 57.434 34.615 18.03 0.20 36.50 1.82
27 28 7.458409 TGTTGACTACGGAAGAGTAATTACT 57.542 36.000 18.05 18.05 39.71 2.24
28 29 7.201299 CGTTGTTGACTACGGAAGAGTAATTAC 60.201 40.741 7.57 7.57 40.41 1.89
42 43 6.642683 AATACAGTATGCGTTGTTGACTAC 57.357 37.500 0.00 0.00 42.53 2.73
54 55 3.125316 GCGATGCCCTAAATACAGTATGC 59.875 47.826 0.00 0.00 42.53 3.14
87 88 0.107456 CTCTTGCTGGTGGAGTGTGT 59.893 55.000 0.00 0.00 0.00 3.72
114 115 3.495331 TGCTGGTGGATAGCTTCAAAAA 58.505 40.909 0.00 0.00 41.66 1.94
115 116 3.153369 TGCTGGTGGATAGCTTCAAAA 57.847 42.857 0.00 0.00 41.66 2.44
116 117 2.877097 TGCTGGTGGATAGCTTCAAA 57.123 45.000 0.00 0.00 41.66 2.69
117 118 2.305635 TCTTGCTGGTGGATAGCTTCAA 59.694 45.455 0.00 0.00 41.66 2.69
118 119 1.908619 TCTTGCTGGTGGATAGCTTCA 59.091 47.619 0.00 0.00 41.66 3.02
119 120 2.093235 ACTCTTGCTGGTGGATAGCTTC 60.093 50.000 0.00 0.00 41.66 3.86
120 121 1.912043 ACTCTTGCTGGTGGATAGCTT 59.088 47.619 0.00 0.00 41.66 3.74
121 122 1.577736 ACTCTTGCTGGTGGATAGCT 58.422 50.000 0.00 0.00 41.66 3.32
122 123 3.760580 ATACTCTTGCTGGTGGATAGC 57.239 47.619 0.00 0.00 41.49 2.97
123 124 6.040955 TGAGTAATACTCTTGCTGGTGGATAG 59.959 42.308 19.76 0.00 45.27 2.08
124 125 5.897250 TGAGTAATACTCTTGCTGGTGGATA 59.103 40.000 19.76 0.00 45.27 2.59
125 126 4.716784 TGAGTAATACTCTTGCTGGTGGAT 59.283 41.667 19.76 0.00 45.27 3.41
126 127 4.093743 TGAGTAATACTCTTGCTGGTGGA 58.906 43.478 19.76 0.00 45.27 4.02
127 128 4.081420 ACTGAGTAATACTCTTGCTGGTGG 60.081 45.833 19.76 3.75 45.27 4.61
128 129 4.867047 CACTGAGTAATACTCTTGCTGGTG 59.133 45.833 19.76 13.90 45.27 4.17
129 130 4.081420 CCACTGAGTAATACTCTTGCTGGT 60.081 45.833 19.76 7.60 45.27 4.00
130 131 4.160439 TCCACTGAGTAATACTCTTGCTGG 59.840 45.833 19.76 16.68 45.27 4.85
131 132 5.330455 TCCACTGAGTAATACTCTTGCTG 57.670 43.478 19.76 9.95 45.27 4.41
132 133 5.625656 GCTTCCACTGAGTAATACTCTTGCT 60.626 44.000 19.76 0.00 45.27 3.91
133 134 4.568760 GCTTCCACTGAGTAATACTCTTGC 59.431 45.833 19.76 10.15 45.27 4.01
134 135 5.971763 AGCTTCCACTGAGTAATACTCTTG 58.028 41.667 19.76 15.79 45.27 3.02
135 136 5.955355 AGAGCTTCCACTGAGTAATACTCTT 59.045 40.000 19.76 5.76 45.27 2.85
136 137 5.515106 AGAGCTTCCACTGAGTAATACTCT 58.485 41.667 19.76 0.00 45.27 3.24
137 138 5.358442 TGAGAGCTTCCACTGAGTAATACTC 59.642 44.000 13.20 13.20 45.26 2.59
138 139 5.126384 GTGAGAGCTTCCACTGAGTAATACT 59.874 44.000 10.92 0.00 0.00 2.12
139 140 5.344884 GTGAGAGCTTCCACTGAGTAATAC 58.655 45.833 10.92 0.00 0.00 1.89
140 141 4.096532 CGTGAGAGCTTCCACTGAGTAATA 59.903 45.833 14.69 0.00 0.00 0.98
145 146 0.735632 GCGTGAGAGCTTCCACTGAG 60.736 60.000 14.69 4.11 0.00 3.35
580 591 2.701163 CTACTTGGCCTCGATCCGGC 62.701 65.000 3.32 11.32 46.83 6.13
590 601 1.024579 TAAAGCAGCGCTACTTGGCC 61.025 55.000 23.17 0.00 38.25 5.36
615 626 0.811616 CGCCATTGGAGAGGTGCTAC 60.812 60.000 6.95 0.00 0.00 3.58
619 630 2.825836 GGCGCCATTGGAGAGGTG 60.826 66.667 24.80 0.00 38.43 4.00
620 631 4.473520 CGGCGCCATTGGAGAGGT 62.474 66.667 28.98 0.00 0.00 3.85
623 634 4.467084 GACCGGCGCCATTGGAGA 62.467 66.667 28.98 0.00 0.00 3.71
645 656 2.107953 GCAGGGACCTCTCGCATC 59.892 66.667 0.00 0.00 0.00 3.91
673 684 5.297029 AGAAAAGGACACAGACAGTAAAAGC 59.703 40.000 0.00 0.00 0.00 3.51
675 686 6.036735 CGAAGAAAAGGACACAGACAGTAAAA 59.963 38.462 0.00 0.00 0.00 1.52
676 687 5.522460 CGAAGAAAAGGACACAGACAGTAAA 59.478 40.000 0.00 0.00 0.00 2.01
678 689 4.500887 CCGAAGAAAAGGACACAGACAGTA 60.501 45.833 0.00 0.00 0.00 2.74
679 690 3.458189 CGAAGAAAAGGACACAGACAGT 58.542 45.455 0.00 0.00 0.00 3.55
691 769 3.127425 ACCTGAACTCCCGAAGAAAAG 57.873 47.619 0.00 0.00 0.00 2.27
700 778 2.723273 CAATACCCAACCTGAACTCCC 58.277 52.381 0.00 0.00 0.00 4.30
731 809 5.349061 TTTCGAATCTAGGGACCTTAACC 57.651 43.478 0.00 0.00 0.00 2.85
733 811 6.363167 TGTTTTCGAATCTAGGGACCTTAA 57.637 37.500 0.00 0.00 0.00 1.85
734 812 6.155565 TGATGTTTTCGAATCTAGGGACCTTA 59.844 38.462 0.00 0.00 0.00 2.69
735 813 4.903045 TGTTTTCGAATCTAGGGACCTT 57.097 40.909 0.00 0.00 0.00 3.50
737 815 4.766375 TGATGTTTTCGAATCTAGGGACC 58.234 43.478 0.00 0.00 0.00 4.46
739 817 4.816385 GCATGATGTTTTCGAATCTAGGGA 59.184 41.667 0.00 0.00 0.00 4.20
740 818 4.818546 AGCATGATGTTTTCGAATCTAGGG 59.181 41.667 0.00 0.00 0.00 3.53
741 819 5.745514 CAGCATGATGTTTTCGAATCTAGG 58.254 41.667 1.88 0.00 39.69 3.02
742 820 5.203370 GCAGCATGATGTTTTCGAATCTAG 58.797 41.667 13.32 0.00 39.69 2.43
773 857 5.550290 TGACAGAGCATCAACATTTCAGTA 58.450 37.500 0.00 0.00 37.82 2.74
774 858 4.392047 TGACAGAGCATCAACATTTCAGT 58.608 39.130 0.00 0.00 37.82 3.41
775 859 4.694037 TCTGACAGAGCATCAACATTTCAG 59.306 41.667 0.00 0.00 37.82 3.02
776 860 4.644498 TCTGACAGAGCATCAACATTTCA 58.356 39.130 0.00 0.00 37.82 2.69
778 862 4.903054 TCTCTGACAGAGCATCAACATTT 58.097 39.130 25.08 0.00 42.04 2.32
779 863 4.548451 TCTCTGACAGAGCATCAACATT 57.452 40.909 25.08 0.00 42.04 2.71
804 897 9.825972 CATCAACGTTTCATTTATTGTTCTACT 57.174 29.630 0.00 0.00 0.00 2.57
805 898 8.575454 GCATCAACGTTTCATTTATTGTTCTAC 58.425 33.333 0.00 0.00 0.00 2.59
810 903 8.911662 GTTTAGCATCAACGTTTCATTTATTGT 58.088 29.630 0.00 0.00 0.00 2.71
814 907 7.866729 TCTGTTTAGCATCAACGTTTCATTTA 58.133 30.769 0.00 0.00 0.00 1.40
823 916 5.342806 TCTGTTTCTGTTTAGCATCAACG 57.657 39.130 0.00 0.00 0.00 4.10
825 918 5.299028 TGCTTCTGTTTCTGTTTAGCATCAA 59.701 36.000 0.00 0.00 32.73 2.57
826 919 4.821260 TGCTTCTGTTTCTGTTTAGCATCA 59.179 37.500 0.00 0.00 32.73 3.07
880 973 2.098298 CGAATGTTTCTGCGCCCG 59.902 61.111 4.18 0.00 0.00 6.13
884 978 2.892373 TTAAGCCGAATGTTTCTGCG 57.108 45.000 0.00 0.00 43.53 5.18
896 990 7.376072 CACTTCTTCTAACAAACTTTTAAGCCG 59.624 37.037 0.00 0.00 0.00 5.52
902 996 8.568794 GCCTATCACTTCTTCTAACAAACTTTT 58.431 33.333 0.00 0.00 0.00 2.27
903 997 7.175119 GGCCTATCACTTCTTCTAACAAACTTT 59.825 37.037 0.00 0.00 0.00 2.66
915 1009 4.684485 GCTACATGTGGCCTATCACTTCTT 60.684 45.833 22.56 0.00 38.40 2.52
917 1011 3.134458 GCTACATGTGGCCTATCACTTC 58.866 50.000 22.56 0.00 38.40 3.01
925 1019 0.990282 ATCCCAGCTACATGTGGCCT 60.990 55.000 28.24 14.29 37.85 5.19
927 1021 0.181114 TCATCCCAGCTACATGTGGC 59.819 55.000 25.24 25.24 37.33 5.01
928 1022 1.813092 GCTCATCCCAGCTACATGTGG 60.813 57.143 9.11 6.75 36.38 4.17
929 1023 1.134310 TGCTCATCCCAGCTACATGTG 60.134 52.381 9.11 0.00 40.39 3.21
930 1024 1.134280 GTGCTCATCCCAGCTACATGT 60.134 52.381 2.69 2.69 40.39 3.21
931 1025 1.140452 AGTGCTCATCCCAGCTACATG 59.860 52.381 0.00 0.00 40.39 3.21
932 1026 1.140452 CAGTGCTCATCCCAGCTACAT 59.860 52.381 0.00 0.00 40.39 2.29
933 1027 0.538584 CAGTGCTCATCCCAGCTACA 59.461 55.000 0.00 0.00 40.39 2.74
934 1028 0.179062 CCAGTGCTCATCCCAGCTAC 60.179 60.000 0.00 0.00 40.39 3.58
937 1031 2.124403 CCCAGTGCTCATCCCAGC 60.124 66.667 0.00 0.00 40.13 4.85
938 1032 2.593978 CCCCAGTGCTCATCCCAG 59.406 66.667 0.00 0.00 0.00 4.45
940 1034 4.512914 GCCCCCAGTGCTCATCCC 62.513 72.222 0.00 0.00 0.00 3.85
941 1035 3.415087 AGCCCCCAGTGCTCATCC 61.415 66.667 0.00 0.00 32.41 3.51
950 1044 1.766625 CTATCCAGCTGAGCCCCCAG 61.767 65.000 17.39 0.00 37.23 4.45
962 1056 3.254657 GGCTCTACTACTGTGCTATCCAG 59.745 52.174 0.00 0.00 36.01 3.86
969 1063 1.482593 ACCATGGCTCTACTACTGTGC 59.517 52.381 13.04 0.00 0.00 4.57
970 1064 3.055819 ACAACCATGGCTCTACTACTGTG 60.056 47.826 13.04 0.00 0.00 3.66
971 1065 3.173965 ACAACCATGGCTCTACTACTGT 58.826 45.455 13.04 0.00 0.00 3.55
972 1066 3.895232 ACAACCATGGCTCTACTACTG 57.105 47.619 13.04 0.00 0.00 2.74
973 1067 4.910458 AAACAACCATGGCTCTACTACT 57.090 40.909 13.04 0.00 0.00 2.57
974 1068 6.458342 GCATTAAACAACCATGGCTCTACTAC 60.458 42.308 13.04 0.00 0.00 2.73
1017 1111 6.764308 ACAGCAAGCAAACATACTGATAAT 57.236 33.333 0.00 0.00 0.00 1.28
1019 1113 6.878923 AGTTACAGCAAGCAAACATACTGATA 59.121 34.615 0.00 0.00 0.00 2.15
1021 1115 5.063204 AGTTACAGCAAGCAAACATACTGA 58.937 37.500 0.00 0.00 0.00 3.41
1104 1236 2.499205 CCGATACCTGAAGCGCCA 59.501 61.111 2.29 0.00 0.00 5.69
1133 1265 2.125350 GCTGTCTGAAGAGGCGGG 60.125 66.667 0.00 0.00 29.98 6.13
1257 1389 1.204146 GGCTTATGTCCTCCTCCACA 58.796 55.000 0.00 0.00 0.00 4.17
1473 2141 2.358957 CTCGCCAATGAGACAATGGAA 58.641 47.619 9.64 0.00 36.60 3.53
1500 2168 1.179174 CCATCCCTCCGATCACGCTA 61.179 60.000 0.00 0.00 38.29 4.26
1506 2174 3.641454 GGCCCCATCCCTCCGATC 61.641 72.222 0.00 0.00 0.00 3.69
1527 2195 1.731613 CTTCGACGCGGTGTAAGCA 60.732 57.895 12.47 0.00 34.19 3.91
1530 2198 2.017783 GTGCTTCGACGCGGTGTAA 61.018 57.895 12.47 0.00 0.00 2.41
1596 2264 2.461110 GCAGTTCACCCGTATGCCG 61.461 63.158 0.00 0.00 0.00 5.69
1704 2372 1.391157 TTGCCTCACTGCCCACAAAC 61.391 55.000 0.00 0.00 0.00 2.93
1710 2378 2.116125 AGGTTTGCCTCACTGCCC 59.884 61.111 0.00 0.00 42.67 5.36
1749 2417 0.107703 CCGCCTCAGCAACATCCTTA 60.108 55.000 0.00 0.00 39.83 2.69
1758 2434 2.679996 TAGAGCACCGCCTCAGCA 60.680 61.111 0.00 0.00 39.83 4.41
1793 2469 2.962253 GCGCGCTGATGTACCTCC 60.962 66.667 26.67 0.00 0.00 4.30
1882 2558 6.758254 ACCAAGTAACAAATGCAGCTAAAAT 58.242 32.000 0.00 0.00 0.00 1.82
1929 2605 5.911752 TGCTAAAACAGGCAAATCAGAAAA 58.088 33.333 0.00 0.00 35.40 2.29
1946 2622 4.704540 CACCCACCTTATTGACATGCTAAA 59.295 41.667 0.00 0.00 0.00 1.85
2000 2676 5.054477 TCAACACTGTCCTTAAGCACTAAC 58.946 41.667 0.00 0.00 0.00 2.34
2077 2753 7.116519 AGTCTTTATGAAACTCTAACTGAACGC 59.883 37.037 0.00 0.00 0.00 4.84
2110 2787 5.411781 GTTTCTATCCCGCAGATATACTGG 58.588 45.833 0.00 0.00 45.82 4.00
2124 2801 6.515272 TTTGAAGCTCAATGGTTTCTATCC 57.485 37.500 0.00 0.00 36.11 2.59
2125 2802 8.992835 AATTTTGAAGCTCAATGGTTTCTATC 57.007 30.769 0.00 0.00 36.11 2.08
2136 2816 6.698008 TCTGACTCAAATTTTGAAGCTCAA 57.302 33.333 12.62 0.00 39.58 3.02
2156 2837 7.845037 TCATATATGAACTGATAGGGCTTCTG 58.155 38.462 13.12 0.00 33.08 3.02
2157 2838 8.621126 ATCATATATGAACTGATAGGGCTTCT 57.379 34.615 19.03 0.00 40.69 2.85
2438 3129 8.785329 TTGCTGACAACAGTAATGATGTATAA 57.215 30.769 6.04 0.00 42.08 0.98
2450 3145 2.149578 GAGAGCATTGCTGACAACAGT 58.850 47.619 17.51 0.00 45.04 3.55
2454 3149 6.536582 GTCTATTTAGAGAGCATTGCTGACAA 59.463 38.462 17.51 1.83 39.88 3.18
2549 3295 2.540101 CTCGGTTGATGATAACGAAGGC 59.460 50.000 0.00 0.00 0.00 4.35
2550 3296 3.123804 CCTCGGTTGATGATAACGAAGG 58.876 50.000 0.00 0.00 31.18 3.46
2567 3313 1.601419 TAACTCCGCCTCAACCCTCG 61.601 60.000 0.00 0.00 0.00 4.63
2619 3365 5.482908 AGATAACAAAGATGTCGCTGACTT 58.517 37.500 9.49 4.11 39.40 3.01
2732 3478 2.238353 GCATAACGGCGATGCTGAT 58.762 52.632 21.85 0.00 45.14 2.90
2807 4890 0.251354 GAGATCTGCTGCAACCTGGA 59.749 55.000 0.00 0.00 0.00 3.86
2846 4929 5.297776 AGAGTCATGCAACAATAGCAATACC 59.702 40.000 0.00 0.00 46.27 2.73
2849 4932 4.703575 ACAGAGTCATGCAACAATAGCAAT 59.296 37.500 0.00 0.00 46.27 3.56


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

AutoCloner maintained by Alex Coulton.