Multiple sequence alignment - TraesCS6A01G356600

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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 TraesCS6A01G356600 chr6A 100.000 3383 0 0 1 3383 587684110 587687492 0.000000e+00 6248
1 TraesCS6A01G356600 chr6A 93.454 718 41 6 1 713 603181000 603180284 0.000000e+00 1061
2 TraesCS6A01G356600 chr6B 89.973 2234 156 31 866 3056 663985162 663987370 0.000000e+00 2822
3 TraesCS6A01G356600 chr6D 90.986 1886 126 13 877 2736 438829815 438831682 0.000000e+00 2501
4 TraesCS6A01G356600 chr6D 93.586 608 28 7 2783 3383 438831691 438832294 0.000000e+00 896
5 TraesCS6A01G356600 chr3A 94.282 717 37 4 1 713 106491191 106490475 0.000000e+00 1094
6 TraesCS6A01G356600 chr3A 93.305 717 43 5 1 713 722732707 722731992 0.000000e+00 1053
7 TraesCS6A01G356600 chr1A 94.390 713 36 4 1 711 554638268 554637558 0.000000e+00 1092
8 TraesCS6A01G356600 chr3D 93.863 717 38 6 1 712 110279057 110278342 0.000000e+00 1075
9 TraesCS6A01G356600 chr5A 93.223 723 39 6 1 713 372929319 372930041 0.000000e+00 1055
10 TraesCS6A01G356600 chr7A 93.305 717 40 6 1 713 25424371 25423659 0.000000e+00 1051
11 TraesCS6A01G356600 chr7A 93.166 717 44 5 1 713 699464295 699463580 0.000000e+00 1048
12 TraesCS6A01G356600 chr7A 79.471 1398 192 52 1026 2368 103051824 103053181 0.000000e+00 904
13 TraesCS6A01G356600 chr1D 93.315 718 38 7 2 711 226831483 226832198 0.000000e+00 1051
14 TraesCS6A01G356600 chr7D 79.759 1329 178 51 1091 2368 100884992 100886280 0.000000e+00 880
15 TraesCS6A01G356600 chr7B 78.781 1395 204 52 1026 2368 56497751 56496397 0.000000e+00 852
16 TraesCS6A01G356600 chr4A 79.798 198 25 9 2919 3114 88019634 88019818 2.740000e-26 130
17 TraesCS6A01G356600 chr2B 80.667 150 25 4 3074 3221 697671327 697671180 2.760000e-21 113


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 TraesCS6A01G356600 chr6A 587684110 587687492 3382 False 6248.0 6248 100.000 1 3383 1 chr6A.!!$F1 3382
1 TraesCS6A01G356600 chr6A 603180284 603181000 716 True 1061.0 1061 93.454 1 713 1 chr6A.!!$R1 712
2 TraesCS6A01G356600 chr6B 663985162 663987370 2208 False 2822.0 2822 89.973 866 3056 1 chr6B.!!$F1 2190
3 TraesCS6A01G356600 chr6D 438829815 438832294 2479 False 1698.5 2501 92.286 877 3383 2 chr6D.!!$F1 2506
4 TraesCS6A01G356600 chr3A 106490475 106491191 716 True 1094.0 1094 94.282 1 713 1 chr3A.!!$R1 712
5 TraesCS6A01G356600 chr3A 722731992 722732707 715 True 1053.0 1053 93.305 1 713 1 chr3A.!!$R2 712
6 TraesCS6A01G356600 chr1A 554637558 554638268 710 True 1092.0 1092 94.390 1 711 1 chr1A.!!$R1 710
7 TraesCS6A01G356600 chr3D 110278342 110279057 715 True 1075.0 1075 93.863 1 712 1 chr3D.!!$R1 711
8 TraesCS6A01G356600 chr5A 372929319 372930041 722 False 1055.0 1055 93.223 1 713 1 chr5A.!!$F1 712
9 TraesCS6A01G356600 chr7A 25423659 25424371 712 True 1051.0 1051 93.305 1 713 1 chr7A.!!$R1 712
10 TraesCS6A01G356600 chr7A 699463580 699464295 715 True 1048.0 1048 93.166 1 713 1 chr7A.!!$R2 712
11 TraesCS6A01G356600 chr7A 103051824 103053181 1357 False 904.0 904 79.471 1026 2368 1 chr7A.!!$F1 1342
12 TraesCS6A01G356600 chr1D 226831483 226832198 715 False 1051.0 1051 93.315 2 711 1 chr1D.!!$F1 709
13 TraesCS6A01G356600 chr7D 100884992 100886280 1288 False 880.0 880 79.759 1091 2368 1 chr7D.!!$F1 1277
14 TraesCS6A01G356600 chr7B 56496397 56497751 1354 True 852.0 852 78.781 1026 2368 1 chr7B.!!$R1 1342

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
765 782 0.174617 CAACCAAACACGCCCTTTGT 59.825 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2649 2751 0.093535 CATTGTGTGCGACTAGTGCG 59.906 55.0 0.0 5.2 34.24 5.34 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
70 71 3.623060 GCTCCAATCTCGATTTGCTGTTA 59.377 43.478 3.36 0.00 0.00 2.41
543 549 1.317613 GCCAATTGTCGCCCATATGA 58.682 50.000 3.65 0.00 0.00 2.15
556 562 4.142038 GCCCATATGAACCCTTTATTCGT 58.858 43.478 3.65 0.00 0.00 3.85
586 593 2.760092 GCTGAAAAGTGGGCCAATATCA 59.240 45.455 8.40 14.76 0.00 2.15
590 597 2.507407 AAGTGGGCCAATATCAACGT 57.493 45.000 8.40 0.00 0.00 3.99
596 603 2.639065 GGCCAATATCAACGTCTGGAA 58.361 47.619 0.00 0.00 0.00 3.53
625 633 4.072088 CGACGACTGGGCGCAAAC 62.072 66.667 10.83 0.00 33.86 2.93
683 694 1.668751 GGAGGCGATTTTTATGCGTCA 59.331 47.619 8.17 0.00 43.29 4.35
686 703 2.942376 AGGCGATTTTTATGCGTCATGA 59.058 40.909 0.00 0.00 31.06 3.07
687 704 3.376859 AGGCGATTTTTATGCGTCATGAA 59.623 39.130 0.00 0.00 31.06 2.57
713 730 1.418334 ACGGCTGGAGATGCTCTTAT 58.582 50.000 0.00 0.00 0.00 1.73
714 731 1.765314 ACGGCTGGAGATGCTCTTATT 59.235 47.619 0.00 0.00 0.00 1.40
715 732 2.224161 ACGGCTGGAGATGCTCTTATTC 60.224 50.000 0.00 0.00 0.00 1.75
716 733 2.777094 GGCTGGAGATGCTCTTATTCC 58.223 52.381 0.00 0.00 0.00 3.01
717 734 2.551938 GGCTGGAGATGCTCTTATTCCC 60.552 54.545 0.00 0.00 0.00 3.97
718 735 2.869636 GCTGGAGATGCTCTTATTCCCG 60.870 54.545 0.00 0.00 0.00 5.14
719 736 1.070758 TGGAGATGCTCTTATTCCCGC 59.929 52.381 0.00 0.00 0.00 6.13
720 737 1.423395 GAGATGCTCTTATTCCCGCG 58.577 55.000 0.00 0.00 0.00 6.46
721 738 0.601311 AGATGCTCTTATTCCCGCGC 60.601 55.000 0.00 0.00 0.00 6.86
722 739 1.891060 GATGCTCTTATTCCCGCGCG 61.891 60.000 25.67 25.67 0.00 6.86
723 740 2.279252 GCTCTTATTCCCGCGCGA 60.279 61.111 34.63 12.79 0.00 5.87
724 741 2.303676 GCTCTTATTCCCGCGCGAG 61.304 63.158 34.63 20.97 0.00 5.03
742 759 4.567318 CCAGACTGGGCCTAATGC 57.433 61.111 14.26 0.00 40.16 3.56
743 760 1.524621 CCAGACTGGGCCTAATGCG 60.525 63.158 14.26 0.00 42.61 4.73
749 766 4.552745 GGGCCTAATGCGCGCAAC 62.553 66.667 39.68 23.27 43.53 4.17
750 767 4.552745 GGCCTAATGCGCGCAACC 62.553 66.667 39.68 27.76 42.61 3.77
751 768 3.809775 GCCTAATGCGCGCAACCA 61.810 61.111 39.68 23.75 0.00 3.67
752 769 2.874019 CCTAATGCGCGCAACCAA 59.126 55.556 39.68 21.47 0.00 3.67
753 770 1.211449 CCTAATGCGCGCAACCAAA 59.789 52.632 39.68 19.63 0.00 3.28
754 771 1.070471 CCTAATGCGCGCAACCAAAC 61.070 55.000 39.68 2.95 0.00 2.93
755 772 0.386605 CTAATGCGCGCAACCAAACA 60.387 50.000 39.68 12.72 0.00 2.83
756 773 0.661780 TAATGCGCGCAACCAAACAC 60.662 50.000 39.68 1.18 0.00 3.32
757 774 4.896028 TGCGCGCAACCAAACACG 62.896 61.111 34.66 0.00 0.00 4.49
761 778 3.591835 CGCAACCAAACACGCCCT 61.592 61.111 0.00 0.00 0.00 5.19
762 779 2.811799 GCAACCAAACACGCCCTT 59.188 55.556 0.00 0.00 0.00 3.95
763 780 1.142965 GCAACCAAACACGCCCTTT 59.857 52.632 0.00 0.00 0.00 3.11
764 781 1.151172 GCAACCAAACACGCCCTTTG 61.151 55.000 0.00 0.00 0.00 2.77
765 782 0.174617 CAACCAAACACGCCCTTTGT 59.825 50.000 0.00 0.00 0.00 2.83
766 783 0.174617 AACCAAACACGCCCTTTGTG 59.825 50.000 0.00 0.00 42.99 3.33
774 791 2.928694 CACGCCCTTTGTGTTTGTATC 58.071 47.619 0.00 0.00 34.84 2.24
775 792 2.552315 CACGCCCTTTGTGTTTGTATCT 59.448 45.455 0.00 0.00 34.84 1.98
776 793 2.812011 ACGCCCTTTGTGTTTGTATCTC 59.188 45.455 0.00 0.00 32.53 2.75
777 794 3.074412 CGCCCTTTGTGTTTGTATCTCT 58.926 45.455 0.00 0.00 0.00 3.10
778 795 3.125316 CGCCCTTTGTGTTTGTATCTCTC 59.875 47.826 0.00 0.00 0.00 3.20
779 796 4.327680 GCCCTTTGTGTTTGTATCTCTCT 58.672 43.478 0.00 0.00 0.00 3.10
780 797 5.488341 GCCCTTTGTGTTTGTATCTCTCTA 58.512 41.667 0.00 0.00 0.00 2.43
781 798 5.351740 GCCCTTTGTGTTTGTATCTCTCTAC 59.648 44.000 0.00 0.00 0.00 2.59
782 799 6.464222 CCCTTTGTGTTTGTATCTCTCTACA 58.536 40.000 0.00 0.00 0.00 2.74
783 800 7.106239 CCCTTTGTGTTTGTATCTCTCTACAT 58.894 38.462 0.00 0.00 31.94 2.29
784 801 7.607991 CCCTTTGTGTTTGTATCTCTCTACATT 59.392 37.037 0.00 0.00 31.94 2.71
785 802 9.003658 CCTTTGTGTTTGTATCTCTCTACATTT 57.996 33.333 0.00 0.00 31.94 2.32
788 805 9.778741 TTGTGTTTGTATCTCTCTACATTTTCT 57.221 29.630 0.00 0.00 31.94 2.52
810 827 9.999009 TTTCTAGAAATCATATATACGCTACCG 57.001 33.333 13.99 0.00 41.14 4.02
811 828 8.953368 TCTAGAAATCATATATACGCTACCGA 57.047 34.615 0.00 0.00 38.29 4.69
812 829 8.824781 TCTAGAAATCATATATACGCTACCGAC 58.175 37.037 0.00 0.00 38.29 4.79
813 830 7.387119 AGAAATCATATATACGCTACCGACA 57.613 36.000 0.00 0.00 38.29 4.35
814 831 7.823665 AGAAATCATATATACGCTACCGACAA 58.176 34.615 0.00 0.00 38.29 3.18
815 832 7.968956 AGAAATCATATATACGCTACCGACAAG 59.031 37.037 0.00 0.00 38.29 3.16
816 833 4.978186 TCATATATACGCTACCGACAAGC 58.022 43.478 0.00 0.00 38.29 4.01
817 834 4.698780 TCATATATACGCTACCGACAAGCT 59.301 41.667 0.00 0.00 37.85 3.74
818 835 2.768833 TATACGCTACCGACAAGCTG 57.231 50.000 0.00 0.00 37.85 4.24
819 836 0.527817 ATACGCTACCGACAAGCTGC 60.528 55.000 0.00 0.00 37.85 5.25
820 837 1.868987 TACGCTACCGACAAGCTGCA 61.869 55.000 1.02 0.00 37.85 4.41
821 838 2.730672 CGCTACCGACAAGCTGCAC 61.731 63.158 1.02 0.00 37.85 4.57
822 839 1.374758 GCTACCGACAAGCTGCACT 60.375 57.895 1.02 0.00 37.01 4.40
823 840 0.951040 GCTACCGACAAGCTGCACTT 60.951 55.000 1.02 0.00 40.05 3.16
824 841 1.512926 CTACCGACAAGCTGCACTTT 58.487 50.000 1.02 0.00 36.04 2.66
825 842 1.195448 CTACCGACAAGCTGCACTTTG 59.805 52.381 1.02 0.00 36.04 2.77
826 843 0.748005 ACCGACAAGCTGCACTTTGT 60.748 50.000 10.07 10.07 36.04 2.83
827 844 0.317269 CCGACAAGCTGCACTTTGTG 60.317 55.000 14.05 7.86 36.04 3.33
836 853 4.597032 CACTTTGTGCCCCTCCAA 57.403 55.556 0.00 0.00 0.00 3.53
837 854 2.819477 CACTTTGTGCCCCTCCAAA 58.181 52.632 0.00 0.00 0.00 3.28
838 855 1.118838 CACTTTGTGCCCCTCCAAAA 58.881 50.000 0.00 0.00 30.75 2.44
839 856 1.484240 CACTTTGTGCCCCTCCAAAAA 59.516 47.619 0.00 0.00 30.75 1.94
840 857 1.484653 ACTTTGTGCCCCTCCAAAAAC 59.515 47.619 0.00 0.00 30.75 2.43
841 858 1.484240 CTTTGTGCCCCTCCAAAAACA 59.516 47.619 0.00 0.00 30.75 2.83
842 859 1.799933 TTGTGCCCCTCCAAAAACAT 58.200 45.000 0.00 0.00 0.00 2.71
843 860 2.685106 TGTGCCCCTCCAAAAACATA 57.315 45.000 0.00 0.00 0.00 2.29
844 861 2.964209 TGTGCCCCTCCAAAAACATAA 58.036 42.857 0.00 0.00 0.00 1.90
845 862 2.630580 TGTGCCCCTCCAAAAACATAAC 59.369 45.455 0.00 0.00 0.00 1.89
846 863 2.630580 GTGCCCCTCCAAAAACATAACA 59.369 45.455 0.00 0.00 0.00 2.41
847 864 3.260632 GTGCCCCTCCAAAAACATAACAT 59.739 43.478 0.00 0.00 0.00 2.71
848 865 3.513515 TGCCCCTCCAAAAACATAACATC 59.486 43.478 0.00 0.00 0.00 3.06
849 866 3.513515 GCCCCTCCAAAAACATAACATCA 59.486 43.478 0.00 0.00 0.00 3.07
850 867 4.020662 GCCCCTCCAAAAACATAACATCAA 60.021 41.667 0.00 0.00 0.00 2.57
851 868 5.338300 GCCCCTCCAAAAACATAACATCAAT 60.338 40.000 0.00 0.00 0.00 2.57
852 869 6.710278 CCCCTCCAAAAACATAACATCAATT 58.290 36.000 0.00 0.00 0.00 2.32
853 870 7.167535 CCCCTCCAAAAACATAACATCAATTT 58.832 34.615 0.00 0.00 0.00 1.82
854 871 7.334171 CCCCTCCAAAAACATAACATCAATTTC 59.666 37.037 0.00 0.00 0.00 2.17
855 872 7.063308 CCCTCCAAAAACATAACATCAATTTCG 59.937 37.037 0.00 0.00 0.00 3.46
856 873 7.598493 CCTCCAAAAACATAACATCAATTTCGT 59.402 33.333 0.00 0.00 0.00 3.85
857 874 9.619316 CTCCAAAAACATAACATCAATTTCGTA 57.381 29.630 0.00 0.00 0.00 3.43
858 875 9.619316 TCCAAAAACATAACATCAATTTCGTAG 57.381 29.630 0.00 0.00 0.00 3.51
859 876 9.405587 CCAAAAACATAACATCAATTTCGTAGT 57.594 29.630 0.00 0.00 0.00 2.73
862 879 9.749490 AAAACATAACATCAATTTCGTAGTACG 57.251 29.630 16.65 16.65 44.19 3.67
876 893 2.363795 TACGAGGGAGCTGGTGGG 60.364 66.667 0.00 0.00 0.00 4.61
877 894 3.233919 TACGAGGGAGCTGGTGGGT 62.234 63.158 0.00 0.00 0.00 4.51
884 901 3.170672 AGCTGGTGGGTCTGTGCA 61.171 61.111 0.00 0.00 0.00 4.57
891 908 2.347490 GGGTCTGTGCATCCACGT 59.653 61.111 0.00 0.00 45.04 4.49
920 937 1.004440 GCTGGCCTTCTCGTGAACT 60.004 57.895 3.32 0.00 0.00 3.01
925 942 1.061485 GCCTTCTCGTGAACTTCGTC 58.939 55.000 0.00 0.00 0.00 4.20
966 984 4.752879 CCACGCCACCCCAGTACG 62.753 72.222 0.00 0.00 0.00 3.67
967 985 3.687102 CACGCCACCCCAGTACGA 61.687 66.667 0.00 0.00 0.00 3.43
968 986 2.682494 ACGCCACCCCAGTACGAT 60.682 61.111 0.00 0.00 0.00 3.73
969 987 2.288025 ACGCCACCCCAGTACGATT 61.288 57.895 0.00 0.00 0.00 3.34
970 988 1.520787 CGCCACCCCAGTACGATTC 60.521 63.158 0.00 0.00 0.00 2.52
987 1005 3.365465 CGATTCGATTCGAGGTAGCAGAT 60.365 47.826 21.74 0.00 41.62 2.90
1491 1548 1.038681 TGTTCCCTCGCGCAGGTATA 61.039 55.000 19.93 5.34 41.51 1.47
2032 2111 2.362503 AGGAGGATCACGACGGCA 60.363 61.111 0.00 0.00 36.25 5.69
2034 2113 2.105128 GAGGATCACGACGGCAGG 59.895 66.667 0.00 0.00 33.17 4.85
2294 2376 3.334054 GGCCCTGGCAGAGAACCT 61.334 66.667 17.94 0.00 44.11 3.50
2393 2487 2.202570 CCGGTGAAGCGTACGAGG 60.203 66.667 21.65 5.84 0.00 4.63
2606 2704 1.080772 TGCAGAGCGTACGAACTGG 60.081 57.895 28.95 17.91 0.00 4.00
2624 2722 4.245660 ACTGGTGTGTCGATTGTGAATAG 58.754 43.478 0.00 0.00 0.00 1.73
2625 2723 4.021456 ACTGGTGTGTCGATTGTGAATAGA 60.021 41.667 0.00 0.00 0.00 1.98
2626 2724 4.494484 TGGTGTGTCGATTGTGAATAGAG 58.506 43.478 0.00 0.00 0.00 2.43
2627 2725 4.021456 TGGTGTGTCGATTGTGAATAGAGT 60.021 41.667 0.00 0.00 0.00 3.24
2628 2726 5.184287 TGGTGTGTCGATTGTGAATAGAGTA 59.816 40.000 0.00 0.00 0.00 2.59
2629 2727 6.127451 TGGTGTGTCGATTGTGAATAGAGTAT 60.127 38.462 0.00 0.00 0.00 2.12
2630 2728 6.418226 GGTGTGTCGATTGTGAATAGAGTATC 59.582 42.308 0.00 0.00 0.00 2.24
2631 2729 6.972901 GTGTGTCGATTGTGAATAGAGTATCA 59.027 38.462 0.00 0.00 37.82 2.15
2632 2730 7.488150 GTGTGTCGATTGTGAATAGAGTATCAA 59.512 37.037 0.00 0.00 37.82 2.57
2633 2731 8.197439 TGTGTCGATTGTGAATAGAGTATCAAT 58.803 33.333 0.00 0.00 37.82 2.57
2649 2751 8.187480 AGAGTATCAATATCATGTAGCGTCATC 58.813 37.037 0.00 0.00 37.82 2.92
2660 2762 3.589982 CGTCATCGCACTAGTCGC 58.410 61.111 0.00 0.00 0.00 5.19
2692 2794 1.587613 GCAACGGCGTTTTGCTTGA 60.588 52.632 24.49 0.00 44.96 3.02
2701 2807 1.971962 CGTTTTGCTTGAGTTGATCGC 59.028 47.619 0.00 0.00 0.00 4.58
2711 2817 3.329386 TGAGTTGATCGCTTCTCCTTTG 58.671 45.455 0.00 0.00 0.00 2.77
2714 2820 2.814336 GTTGATCGCTTCTCCTTTGGTT 59.186 45.455 0.00 0.00 0.00 3.67
2724 2831 4.893424 TCTCCTTTGGTTTCGAACTTTG 57.107 40.909 0.00 0.00 0.00 2.77
2730 2837 4.377839 TTGGTTTCGAACTTTGCATGAA 57.622 36.364 0.00 0.00 0.00 2.57
2731 2838 4.582701 TGGTTTCGAACTTTGCATGAAT 57.417 36.364 0.00 0.00 0.00 2.57
2732 2839 4.297510 TGGTTTCGAACTTTGCATGAATG 58.702 39.130 0.00 0.00 0.00 2.67
2770 2877 1.243902 GCCGGAAATGGACAACAGAA 58.756 50.000 5.05 0.00 0.00 3.02
2786 2896 4.332428 ACAGAAATACCATAGCCGTACC 57.668 45.455 0.00 0.00 0.00 3.34
2816 2926 3.748568 AGCACTTCGAAACTCCAAGATTC 59.251 43.478 0.00 0.00 0.00 2.52
2882 2992 0.806492 GCCTTCGAATCGGACTCACC 60.806 60.000 7.59 0.00 0.00 4.02
2883 2993 0.818296 CCTTCGAATCGGACTCACCT 59.182 55.000 1.76 0.00 36.31 4.00
2884 2994 2.022195 CCTTCGAATCGGACTCACCTA 58.978 52.381 1.76 0.00 36.31 3.08
2885 2995 2.623889 CCTTCGAATCGGACTCACCTAT 59.376 50.000 1.76 0.00 36.31 2.57
2888 2998 1.000163 CGAATCGGACTCACCTATGGG 60.000 57.143 0.00 0.00 36.31 4.00
2918 3033 1.614903 ACGAAAGTCGGACATGTACCA 59.385 47.619 11.27 0.00 45.59 3.25
2975 3090 4.561735 TTTTTCTTTAAGTCCACGGCAG 57.438 40.909 0.00 0.00 0.00 4.85
3137 3252 6.183347 AGTTCTTCCCTTTAATCATCCACAG 58.817 40.000 0.00 0.00 0.00 3.66
3149 3264 3.443099 CATCCACAGATGCTCGTCTAA 57.557 47.619 0.00 0.00 43.35 2.10
3182 3298 1.994467 CTCATGAGTTGCTCGACGC 59.006 57.895 14.95 0.58 39.77 5.19
3240 3356 7.876896 AACGTTAACTGCAAAAAGAAAAAGA 57.123 28.000 0.00 0.00 0.00 2.52
3283 3399 5.863935 GGACTTTGAATTGCAAGTTGGATAC 59.136 40.000 4.94 0.00 37.87 2.24
3314 3430 4.154195 CGTGTTCTTAAATTCCAGACCAGG 59.846 45.833 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
250 251 3.149981 CCTGACGCATACTGAGATAGGA 58.850 50.000 0.00 0.00 30.56 2.94
527 533 2.091885 AGGGTTCATATGGGCGACAATT 60.092 45.455 2.13 0.00 0.00 2.32
543 549 3.767131 CCCCATTTGACGAATAAAGGGTT 59.233 43.478 8.02 0.00 37.29 4.11
556 562 1.969923 CCACTTTTCAGCCCCATTTGA 59.030 47.619 0.00 0.00 0.00 2.69
590 597 3.003173 CCCCCAGCTCGTTCCAGA 61.003 66.667 0.00 0.00 0.00 3.86
665 675 2.942376 TCATGACGCATAAAAATCGCCT 59.058 40.909 0.00 0.00 0.00 5.52
683 694 2.436646 CAGCCGTTCGCCCTTCAT 60.437 61.111 0.00 0.00 38.78 2.57
686 703 4.394712 CTCCAGCCGTTCGCCCTT 62.395 66.667 0.00 0.00 38.78 3.95
725 742 1.524621 CGCATTAGGCCCAGTCTGG 60.525 63.158 12.40 12.40 40.31 3.86
726 743 2.182842 GCGCATTAGGCCCAGTCTG 61.183 63.158 0.30 0.00 40.31 3.51
727 744 2.190578 GCGCATTAGGCCCAGTCT 59.809 61.111 0.30 0.00 40.31 3.24
728 745 3.272334 CGCGCATTAGGCCCAGTC 61.272 66.667 8.75 0.00 40.31 3.51
732 749 4.552745 GTTGCGCGCATTAGGCCC 62.553 66.667 36.83 12.72 40.31 5.80
733 750 4.552745 GGTTGCGCGCATTAGGCC 62.553 66.667 36.83 25.42 40.31 5.19
734 751 2.810903 TTTGGTTGCGCGCATTAGGC 62.811 55.000 36.83 20.95 39.90 3.93
735 752 1.070471 GTTTGGTTGCGCGCATTAGG 61.070 55.000 36.83 0.00 0.00 2.69
736 753 0.386605 TGTTTGGTTGCGCGCATTAG 60.387 50.000 36.83 0.00 0.00 1.73
737 754 0.661780 GTGTTTGGTTGCGCGCATTA 60.662 50.000 36.83 19.50 0.00 1.90
738 755 1.948635 GTGTTTGGTTGCGCGCATT 60.949 52.632 36.83 0.00 0.00 3.56
739 756 2.354539 GTGTTTGGTTGCGCGCAT 60.355 55.556 36.83 0.00 0.00 4.73
740 757 4.896028 CGTGTTTGGTTGCGCGCA 62.896 61.111 33.09 33.09 0.00 6.09
744 761 2.621371 AAAGGGCGTGTTTGGTTGCG 62.621 55.000 0.00 0.00 0.00 4.85
745 762 1.142965 AAAGGGCGTGTTTGGTTGC 59.857 52.632 0.00 0.00 0.00 4.17
746 763 0.174617 ACAAAGGGCGTGTTTGGTTG 59.825 50.000 9.51 0.00 38.90 3.77
747 764 0.174617 CACAAAGGGCGTGTTTGGTT 59.825 50.000 9.51 0.00 38.90 3.67
748 765 0.968393 ACACAAAGGGCGTGTTTGGT 60.968 50.000 9.51 3.58 45.12 3.67
749 766 1.813192 ACACAAAGGGCGTGTTTGG 59.187 52.632 9.51 3.12 45.12 3.28
754 771 2.552315 AGATACAAACACAAAGGGCGTG 59.448 45.455 0.00 0.00 40.32 5.34
755 772 2.812011 GAGATACAAACACAAAGGGCGT 59.188 45.455 0.00 0.00 0.00 5.68
756 773 3.074412 AGAGATACAAACACAAAGGGCG 58.926 45.455 0.00 0.00 0.00 6.13
757 774 4.327680 AGAGAGATACAAACACAAAGGGC 58.672 43.478 0.00 0.00 0.00 5.19
758 775 6.464222 TGTAGAGAGATACAAACACAAAGGG 58.536 40.000 0.00 0.00 32.80 3.95
759 776 8.553459 AATGTAGAGAGATACAAACACAAAGG 57.447 34.615 0.00 0.00 39.04 3.11
762 779 9.778741 AGAAAATGTAGAGAGATACAAACACAA 57.221 29.630 0.00 0.00 39.04 3.33
784 801 9.999009 CGGTAGCGTATATATGATTTCTAGAAA 57.001 33.333 19.83 19.83 34.46 2.52
785 802 9.387257 TCGGTAGCGTATATATGATTTCTAGAA 57.613 33.333 14.79 0.00 0.00 2.10
786 803 8.824781 GTCGGTAGCGTATATATGATTTCTAGA 58.175 37.037 14.79 0.00 0.00 2.43
787 804 8.610035 TGTCGGTAGCGTATATATGATTTCTAG 58.390 37.037 14.79 0.00 0.00 2.43
788 805 8.496707 TGTCGGTAGCGTATATATGATTTCTA 57.503 34.615 14.79 0.00 0.00 2.10
789 806 7.387119 TGTCGGTAGCGTATATATGATTTCT 57.613 36.000 14.79 0.00 0.00 2.52
790 807 7.253684 GCTTGTCGGTAGCGTATATATGATTTC 60.254 40.741 14.79 0.00 0.00 2.17
791 808 6.530534 GCTTGTCGGTAGCGTATATATGATTT 59.469 38.462 14.79 0.00 0.00 2.17
792 809 6.034591 GCTTGTCGGTAGCGTATATATGATT 58.965 40.000 14.79 0.00 0.00 2.57
793 810 5.357314 AGCTTGTCGGTAGCGTATATATGAT 59.643 40.000 14.79 1.84 43.37 2.45
794 811 4.698780 AGCTTGTCGGTAGCGTATATATGA 59.301 41.667 14.79 0.00 43.37 2.15
795 812 4.793731 CAGCTTGTCGGTAGCGTATATATG 59.206 45.833 14.79 4.77 43.37 1.78
796 813 4.674623 GCAGCTTGTCGGTAGCGTATATAT 60.675 45.833 14.79 0.00 43.37 0.86
797 814 3.365666 GCAGCTTGTCGGTAGCGTATATA 60.366 47.826 14.79 0.00 43.37 0.86
798 815 2.607282 GCAGCTTGTCGGTAGCGTATAT 60.607 50.000 14.79 0.00 43.37 0.86
799 816 1.268896 GCAGCTTGTCGGTAGCGTATA 60.269 52.381 14.79 0.00 43.37 1.47
800 817 0.527817 GCAGCTTGTCGGTAGCGTAT 60.528 55.000 14.79 0.00 43.37 3.06
801 818 1.153901 GCAGCTTGTCGGTAGCGTA 60.154 57.895 14.79 2.00 43.37 4.42
802 819 2.432628 GCAGCTTGTCGGTAGCGT 60.433 61.111 14.79 0.00 43.37 5.07
803 820 2.432456 TGCAGCTTGTCGGTAGCG 60.432 61.111 8.29 8.29 43.37 4.26
804 821 0.951040 AAGTGCAGCTTGTCGGTAGC 60.951 55.000 0.00 0.00 35.80 3.58
805 822 1.195448 CAAAGTGCAGCTTGTCGGTAG 59.805 52.381 0.00 0.00 37.52 3.18
806 823 1.225855 CAAAGTGCAGCTTGTCGGTA 58.774 50.000 0.00 0.00 37.52 4.02
807 824 0.748005 ACAAAGTGCAGCTTGTCGGT 60.748 50.000 7.39 0.90 37.52 4.69
808 825 0.317269 CACAAAGTGCAGCTTGTCGG 60.317 55.000 9.80 0.00 37.52 4.79
809 826 3.153364 CACAAAGTGCAGCTTGTCG 57.847 52.632 9.80 4.04 37.52 4.35
819 836 1.118838 TTTTGGAGGGGCACAAAGTG 58.881 50.000 0.00 0.00 37.80 3.16
820 837 1.484653 GTTTTTGGAGGGGCACAAAGT 59.515 47.619 0.00 0.00 37.80 2.66
821 838 1.484240 TGTTTTTGGAGGGGCACAAAG 59.516 47.619 0.00 0.00 37.80 2.77
822 839 1.573108 TGTTTTTGGAGGGGCACAAA 58.427 45.000 0.00 0.00 35.01 2.83
823 840 1.799933 ATGTTTTTGGAGGGGCACAA 58.200 45.000 0.00 0.00 0.00 3.33
824 841 2.630580 GTTATGTTTTTGGAGGGGCACA 59.369 45.455 0.00 0.00 0.00 4.57
825 842 2.630580 TGTTATGTTTTTGGAGGGGCAC 59.369 45.455 0.00 0.00 0.00 5.01
826 843 2.964209 TGTTATGTTTTTGGAGGGGCA 58.036 42.857 0.00 0.00 0.00 5.36
827 844 3.513515 TGATGTTATGTTTTTGGAGGGGC 59.486 43.478 0.00 0.00 0.00 5.80
828 845 5.736951 TTGATGTTATGTTTTTGGAGGGG 57.263 39.130 0.00 0.00 0.00 4.79
829 846 7.063308 CGAAATTGATGTTATGTTTTTGGAGGG 59.937 37.037 0.00 0.00 0.00 4.30
830 847 7.598493 ACGAAATTGATGTTATGTTTTTGGAGG 59.402 33.333 0.00 0.00 0.00 4.30
831 848 8.519492 ACGAAATTGATGTTATGTTTTTGGAG 57.481 30.769 0.00 0.00 0.00 3.86
832 849 9.619316 CTACGAAATTGATGTTATGTTTTTGGA 57.381 29.630 0.00 0.00 0.00 3.53
833 850 9.405587 ACTACGAAATTGATGTTATGTTTTTGG 57.594 29.630 0.00 0.00 0.00 3.28
836 853 9.749490 CGTACTACGAAATTGATGTTATGTTTT 57.251 29.630 2.17 0.00 46.05 2.43
854 871 0.747283 ACCAGCTCCCTCGTACTACG 60.747 60.000 1.93 1.93 44.19 3.51
855 872 0.739561 CACCAGCTCCCTCGTACTAC 59.260 60.000 0.00 0.00 0.00 2.73
856 873 0.395311 CCACCAGCTCCCTCGTACTA 60.395 60.000 0.00 0.00 0.00 1.82
857 874 1.682684 CCACCAGCTCCCTCGTACT 60.683 63.158 0.00 0.00 0.00 2.73
858 875 2.722201 CCCACCAGCTCCCTCGTAC 61.722 68.421 0.00 0.00 0.00 3.67
859 876 2.363795 CCCACCAGCTCCCTCGTA 60.364 66.667 0.00 0.00 0.00 3.43
860 877 4.640690 ACCCACCAGCTCCCTCGT 62.641 66.667 0.00 0.00 0.00 4.18
861 878 3.775654 GACCCACCAGCTCCCTCG 61.776 72.222 0.00 0.00 0.00 4.63
862 879 2.284995 AGACCCACCAGCTCCCTC 60.285 66.667 0.00 0.00 0.00 4.30
863 880 2.608988 CAGACCCACCAGCTCCCT 60.609 66.667 0.00 0.00 0.00 4.20
864 881 2.930562 ACAGACCCACCAGCTCCC 60.931 66.667 0.00 0.00 0.00 4.30
876 893 0.737715 GGAGACGTGGATGCACAGAC 60.738 60.000 18.05 10.18 0.00 3.51
877 894 0.900182 AGGAGACGTGGATGCACAGA 60.900 55.000 18.05 0.00 0.00 3.41
884 901 1.954362 GCAGAGCAGGAGACGTGGAT 61.954 60.000 0.00 0.00 0.00 3.41
891 908 3.397439 GGCCAGCAGAGCAGGAGA 61.397 66.667 0.00 0.00 37.40 3.71
966 984 3.627732 TCTGCTACCTCGAATCGAATC 57.372 47.619 6.84 0.00 34.74 2.52
967 985 3.570125 TGATCTGCTACCTCGAATCGAAT 59.430 43.478 6.84 0.30 34.74 3.34
968 986 2.949644 TGATCTGCTACCTCGAATCGAA 59.050 45.455 6.84 0.00 34.74 3.71
969 987 2.290916 GTGATCTGCTACCTCGAATCGA 59.709 50.000 4.91 4.91 0.00 3.59
970 988 2.292016 AGTGATCTGCTACCTCGAATCG 59.708 50.000 0.00 0.00 0.00 3.34
987 1005 1.078497 CGCCATTGGTGCCTAGTGA 60.078 57.895 2.75 0.00 0.00 3.41
1149 1179 3.982372 CTCCGCGCTGCCGTAGAAA 62.982 63.158 5.56 0.00 36.67 2.52
1215 1245 1.755783 GGCCAGGGATGCCTTGAAG 60.756 63.158 8.69 0.00 45.70 3.02
1777 1849 2.280660 CATCCGGCCTAGCAGCTG 60.281 66.667 10.11 10.11 38.96 4.24
1792 1864 4.514577 CTCGACGCGCTTCCCCAT 62.515 66.667 5.73 0.00 0.00 4.00
1914 1986 1.079405 GAACCCGAACTGATGCCGA 60.079 57.895 0.00 0.00 0.00 5.54
2286 2365 3.441290 CGGCCGTCGAGGTTCTCT 61.441 66.667 19.50 0.00 43.70 3.10
2467 2564 2.356553 CCCGCGTCGAAAAGGTGA 60.357 61.111 4.92 0.00 0.00 4.02
2606 2704 6.972901 TGATACTCTATTCACAATCGACACAC 59.027 38.462 0.00 0.00 0.00 3.82
2624 2722 7.164990 CGATGACGCTACATGATATTGATACTC 59.835 40.741 0.00 0.00 0.00 2.59
2625 2723 6.969473 CGATGACGCTACATGATATTGATACT 59.031 38.462 0.00 0.00 0.00 2.12
2626 2724 7.142828 CGATGACGCTACATGATATTGATAC 57.857 40.000 0.00 0.00 0.00 2.24
2643 2741 1.226295 TGCGACTAGTGCGATGACG 60.226 57.895 15.79 6.28 42.93 4.35
2645 2747 0.456142 GTGTGCGACTAGTGCGATGA 60.456 55.000 15.79 0.00 34.24 2.92
2649 2751 0.093535 CATTGTGTGCGACTAGTGCG 59.906 55.000 0.00 5.20 34.24 5.34
2692 2794 2.039084 ACCAAAGGAGAAGCGATCAACT 59.961 45.455 0.00 0.00 0.00 3.16
2701 2807 5.273944 CAAAGTTCGAAACCAAAGGAGAAG 58.726 41.667 0.00 0.00 0.00 2.85
2711 2817 4.891277 CATTCATGCAAAGTTCGAAACC 57.109 40.909 0.00 0.00 0.00 3.27
2733 2840 2.125147 ATCCGGTCGTGCATGGTG 60.125 61.111 5.98 0.00 0.00 4.17
2734 2841 2.125147 CATCCGGTCGTGCATGGT 60.125 61.111 5.98 0.00 0.00 3.55
2735 2842 3.576356 GCATCCGGTCGTGCATGG 61.576 66.667 19.29 0.00 40.94 3.66
2736 2843 3.576356 GGCATCCGGTCGTGCATG 61.576 66.667 23.34 11.63 43.00 4.06
2754 2861 5.975693 TGGTATTTCTGTTGTCCATTTCC 57.024 39.130 0.00 0.00 0.00 3.13
2756 2863 6.096846 GGCTATGGTATTTCTGTTGTCCATTT 59.903 38.462 0.00 0.00 37.03 2.32
2816 2926 5.458041 AGATGTTTGAACCATTTGACAGG 57.542 39.130 0.00 0.00 0.00 4.00
2882 2992 5.585390 ACTTTCGTATTCGTGTACCCATAG 58.415 41.667 0.00 0.00 38.33 2.23
2883 2993 5.581126 ACTTTCGTATTCGTGTACCCATA 57.419 39.130 0.00 0.00 38.33 2.74
2884 2994 4.427312 GACTTTCGTATTCGTGTACCCAT 58.573 43.478 0.00 0.00 38.33 4.00
2885 2995 3.670359 CGACTTTCGTATTCGTGTACCCA 60.670 47.826 0.00 0.00 38.33 4.51
2888 2998 3.539954 GTCCGACTTTCGTATTCGTGTAC 59.460 47.826 0.00 0.00 38.40 2.90
2918 3033 3.897239 TGGGCGAAAGTTTGATGGATAT 58.103 40.909 0.00 0.00 0.00 1.63
2959 3074 2.489971 TGAACTGCCGTGGACTTAAAG 58.510 47.619 0.00 0.00 0.00 1.85
2960 3075 2.623878 TGAACTGCCGTGGACTTAAA 57.376 45.000 0.00 0.00 0.00 1.52
2969 3084 7.551262 TCATGTATAGTTATTTTGAACTGCCGT 59.449 33.333 0.00 0.00 39.96 5.68
3099 3214 7.554959 AGGGAAGAACTAGAACATAACTTGA 57.445 36.000 0.00 0.00 0.00 3.02
3117 3232 8.861275 GAGCATCTGTGGATGATTAAAGGGAAG 61.861 44.444 9.78 0.00 46.83 3.46
3119 3234 5.688500 GAGCATCTGTGGATGATTAAAGGGA 60.689 44.000 9.78 0.00 46.83 4.20
3130 3245 3.638627 TGATTAGACGAGCATCTGTGGAT 59.361 43.478 0.00 0.00 0.00 3.41
3137 3252 8.272176 CAGTTTAAGAATGATTAGACGAGCATC 58.728 37.037 0.00 0.00 0.00 3.91
3144 3259 9.102757 TCATGAGCAGTTTAAGAATGATTAGAC 57.897 33.333 0.00 0.00 0.00 2.59
3149 3264 7.627939 GCAACTCATGAGCAGTTTAAGAATGAT 60.628 37.037 22.83 0.00 31.40 2.45
3182 3298 7.395190 TGTCCAGATAAATCAACAGATTTGG 57.605 36.000 12.35 6.92 40.97 3.28
3240 3356 1.613437 CCGGCAATGTTTGAGGAGTTT 59.387 47.619 0.00 0.00 33.60 2.66
3283 3399 5.347635 TGGAATTTAAGAACACGAGTGATCG 59.652 40.000 10.50 0.00 37.44 3.69
3299 3415 4.370776 TGAGATCCCTGGTCTGGAATTTA 58.629 43.478 0.00 0.00 35.03 1.40
3314 3430 5.109500 AGGAGGTCTGAAATTTGAGATCC 57.891 43.478 13.53 14.69 0.00 3.36


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

AutoCloner maintained by Alex Coulton.