Multiple sequence alignment - TraesCS5D01G118400

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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 TraesCS5D01G118400 chr5D 100.000 4061 0 0 1 4061 158173860 158169800 0.000000e+00 7500
1 TraesCS5D01G118400 chr5A 98.043 3168 53 6 899 4061 207662250 207659087 0.000000e+00 5498
2 TraesCS5D01G118400 chr7B 92.424 660 42 7 1 657 497925763 497925109 0.000000e+00 935
3 TraesCS5D01G118400 chr2B 90.455 660 56 6 3 657 486118672 486118015 0.000000e+00 863
4 TraesCS5D01G118400 chr2B 87.709 659 65 9 3 657 569521602 569522248 0.000000e+00 754
5 TraesCS5D01G118400 chr7D 90.744 659 42 7 1 657 545338957 545338316 0.000000e+00 861
6 TraesCS5D01G118400 chrUn 89.666 658 63 5 3 657 348808187 348808842 0.000000e+00 833
7 TraesCS5D01G118400 chrUn 89.379 612 60 5 3 611 424290140 424290749 0.000000e+00 765
8 TraesCS5D01G118400 chr3B 89.259 661 61 8 3 657 804347762 804348418 0.000000e+00 819
9 TraesCS5D01G118400 chr5B 100.000 121 0 0 3941 4061 159711444 159711564 1.470000e-54 224


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 TraesCS5D01G118400 chr5D 158169800 158173860 4060 True 7500 7500 100.000 1 4061 1 chr5D.!!$R1 4060
1 TraesCS5D01G118400 chr5A 207659087 207662250 3163 True 5498 5498 98.043 899 4061 1 chr5A.!!$R1 3162
2 TraesCS5D01G118400 chr7B 497925109 497925763 654 True 935 935 92.424 1 657 1 chr7B.!!$R1 656
3 TraesCS5D01G118400 chr2B 486118015 486118672 657 True 863 863 90.455 3 657 1 chr2B.!!$R1 654
4 TraesCS5D01G118400 chr2B 569521602 569522248 646 False 754 754 87.709 3 657 1 chr2B.!!$F1 654
5 TraesCS5D01G118400 chr7D 545338316 545338957 641 True 861 861 90.744 1 657 1 chr7D.!!$R1 656
6 TraesCS5D01G118400 chrUn 348808187 348808842 655 False 833 833 89.666 3 657 1 chrUn.!!$F1 654
7 TraesCS5D01G118400 chrUn 424290140 424290749 609 False 765 765 89.379 3 611 1 chrUn.!!$F2 608
8 TraesCS5D01G118400 chr3B 804347762 804348418 656 False 819 819 89.259 3 657 1 chr3B.!!$F1 654

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
670 681 0.037046 GGAAGCGTACCCTCGGAAAA 60.037 55.0 0.00 0.00 0.00 2.29 F
870 881 0.100861 CTCCCTAGTCGCGTCCTTTC 59.899 60.0 5.77 0.00 0.00 2.62 F
872 883 0.179134 CCCTAGTCGCGTCCTTTCTG 60.179 60.0 5.77 0.00 0.00 3.02 F
873 884 0.179134 CCTAGTCGCGTCCTTTCTGG 60.179 60.0 5.77 1.39 37.10 3.86 F
1689 1702 0.322816 ACGCCATGCTGGTCAAGAAT 60.323 50.0 4.45 0.00 40.46 2.40 F
2634 2647 0.037605 AACCTCTCCCGTTAGTTGCG 60.038 55.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1603 0.166814 AGCCGTACGTGTACTCGTTC 59.833 55.0 25.78 19.82 43.8 3.95 R
1846 1859 0.252881 TCCAGTGCCTCCCTCTTCAT 60.253 55.0 0.00 0.00 0.0 2.57 R
1890 1903 0.679505 CCGAGTTCACCTTGACTCCA 59.320 55.0 0.00 0.00 0.0 3.86 R
2574 2587 0.804989 GACCATGAACTTCCTTGCCG 59.195 55.0 0.00 0.00 0.0 5.69 R
2706 2719 1.265454 ACGTCAGGGATCCCTTGGAC 61.265 60.0 31.98 30.48 45.7 4.02 R
3919 3935 1.209621 TGGTGCCTACTCCCCATTAC 58.790 55.0 0.00 0.00 0.0 1.89 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
33 34 2.221169 GGCTGTGTGAAGTCAACATGA 58.779 47.619 0.00 0.00 0.00 3.07
118 119 9.914834 TCATAATAGTTGCCTAAAACTGGTAAT 57.085 29.630 0.00 0.00 40.58 1.89
344 350 3.393609 TGAGAAAGGGAGATGCAGCATAT 59.606 43.478 8.22 4.62 0.00 1.78
394 400 8.693542 AGTGAACAAAAGAGTCAAAAGAATTG 57.306 30.769 0.00 0.00 0.00 2.32
485 496 2.620585 GCTTCTGTTCTGAGTTTTGCCT 59.379 45.455 0.00 0.00 0.00 4.75
528 539 2.712944 CCTCATGCCGCCATTGCAA 61.713 57.895 0.00 0.00 42.92 4.08
541 552 2.444421 CATTGCAAGGAGAAGGAAGCT 58.556 47.619 4.81 0.00 0.00 3.74
580 591 2.496070 GGGAAAACCCTAACTTGATGGC 59.504 50.000 0.00 0.00 34.51 4.40
581 592 3.161866 GGAAAACCCTAACTTGATGGCA 58.838 45.455 0.00 0.00 0.00 4.92
595 606 4.524802 TGATGGCAAAGAAGATGGGTAT 57.475 40.909 0.00 0.00 0.00 2.73
596 607 4.209538 TGATGGCAAAGAAGATGGGTATG 58.790 43.478 0.00 0.00 0.00 2.39
598 609 2.291475 TGGCAAAGAAGATGGGTATGCA 60.291 45.455 0.00 0.00 34.14 3.96
619 630 1.078159 GGGGAAAGGGGTTTGGTATGT 59.922 52.381 0.00 0.00 0.00 2.29
657 668 1.553690 TTTGGGAGGGAGAGGAAGCG 61.554 60.000 0.00 0.00 0.00 4.68
658 669 2.364448 GGGAGGGAGAGGAAGCGT 60.364 66.667 0.00 0.00 0.00 5.07
659 670 1.076192 GGGAGGGAGAGGAAGCGTA 60.076 63.158 0.00 0.00 0.00 4.42
660 671 1.393487 GGGAGGGAGAGGAAGCGTAC 61.393 65.000 0.00 0.00 0.00 3.67
661 672 1.393487 GGAGGGAGAGGAAGCGTACC 61.393 65.000 0.00 0.00 0.00 3.34
662 673 1.381463 AGGGAGAGGAAGCGTACCC 60.381 63.158 0.00 0.00 37.79 3.69
663 674 1.381463 GGGAGAGGAAGCGTACCCT 60.381 63.158 0.00 0.00 35.03 4.34
664 675 3.765079 AGGGAGAGGAAGCGTACCCTC 62.765 61.905 7.60 7.60 43.37 4.30
666 677 2.806237 GAGGAAGCGTACCCTCGG 59.194 66.667 0.79 0.00 39.49 4.63
667 678 1.751927 GAGGAAGCGTACCCTCGGA 60.752 63.158 0.79 0.00 39.49 4.55
668 679 1.304713 AGGAAGCGTACCCTCGGAA 60.305 57.895 0.00 0.00 0.00 4.30
669 680 0.901580 AGGAAGCGTACCCTCGGAAA 60.902 55.000 0.00 0.00 0.00 3.13
670 681 0.037046 GGAAGCGTACCCTCGGAAAA 60.037 55.000 0.00 0.00 0.00 2.29
671 682 1.608801 GGAAGCGTACCCTCGGAAAAA 60.609 52.381 0.00 0.00 0.00 1.94
689 700 3.527507 AAAAAGGAAGGGAGAGGAACC 57.472 47.619 0.00 0.00 0.00 3.62
690 701 0.984995 AAAGGAAGGGAGAGGAACCG 59.015 55.000 0.00 0.00 0.00 4.44
691 702 0.178900 AAGGAAGGGAGAGGAACCGT 60.179 55.000 0.00 0.00 0.00 4.83
692 703 0.708802 AGGAAGGGAGAGGAACCGTA 59.291 55.000 0.00 0.00 0.00 4.02
693 704 0.822811 GGAAGGGAGAGGAACCGTAC 59.177 60.000 0.00 0.00 0.00 3.67
694 705 0.822811 GAAGGGAGAGGAACCGTACC 59.177 60.000 0.00 0.00 0.00 3.34
695 706 0.616964 AAGGGAGAGGAACCGTACCC 60.617 60.000 11.73 11.73 37.79 3.69
696 707 1.001376 GGGAGAGGAACCGTACCCT 59.999 63.158 12.16 0.00 35.03 4.34
697 708 3.433336 AGGGAGAGGAACCGTACCCTC 62.433 61.905 14.77 7.60 43.37 4.30
720 731 2.889170 AAAAAGGAGGGAGAGGAAGC 57.111 50.000 0.00 0.00 0.00 3.86
721 732 1.747444 AAAAGGAGGGAGAGGAAGCA 58.253 50.000 0.00 0.00 0.00 3.91
722 733 0.988063 AAAGGAGGGAGAGGAAGCAC 59.012 55.000 0.00 0.00 0.00 4.40
723 734 1.261238 AAGGAGGGAGAGGAAGCACG 61.261 60.000 0.00 0.00 0.00 5.34
724 735 1.985116 GGAGGGAGAGGAAGCACGT 60.985 63.158 0.00 0.00 0.00 4.49
725 736 1.216710 GAGGGAGAGGAAGCACGTG 59.783 63.158 12.28 12.28 0.00 4.49
726 737 1.534235 AGGGAGAGGAAGCACGTGT 60.534 57.895 18.38 0.00 0.00 4.49
727 738 1.374758 GGGAGAGGAAGCACGTGTG 60.375 63.158 18.38 0.00 0.00 3.82
728 739 1.374758 GGAGAGGAAGCACGTGTGG 60.375 63.158 18.38 0.00 0.00 4.17
729 740 1.374758 GAGAGGAAGCACGTGTGGG 60.375 63.158 18.38 0.00 0.00 4.61
730 741 2.358737 GAGGAAGCACGTGTGGGG 60.359 66.667 18.38 0.00 0.00 4.96
731 742 2.847234 AGGAAGCACGTGTGGGGA 60.847 61.111 18.38 0.00 0.00 4.81
732 743 2.358737 GGAAGCACGTGTGGGGAG 60.359 66.667 18.38 0.00 0.00 4.30
733 744 2.358737 GAAGCACGTGTGGGGAGG 60.359 66.667 18.38 0.00 0.00 4.30
734 745 3.901797 GAAGCACGTGTGGGGAGGG 62.902 68.421 18.38 0.00 0.00 4.30
740 751 4.035102 GTGTGGGGAGGGGCAGAC 62.035 72.222 0.00 0.00 0.00 3.51
744 755 4.741239 GGGGAGGGGCAGACCAGA 62.741 72.222 0.00 0.00 42.91 3.86
745 756 2.367512 GGGAGGGGCAGACCAGAT 60.368 66.667 0.00 0.00 42.91 2.90
746 757 2.750657 GGGAGGGGCAGACCAGATG 61.751 68.421 0.00 0.00 42.91 2.90
747 758 2.750657 GGAGGGGCAGACCAGATGG 61.751 68.421 0.00 0.00 42.91 3.51
748 759 2.693864 AGGGGCAGACCAGATGGG 60.694 66.667 3.48 0.00 42.91 4.00
749 760 3.813724 GGGGCAGACCAGATGGGG 61.814 72.222 3.48 0.00 42.91 4.96
750 761 2.692368 GGGCAGACCAGATGGGGA 60.692 66.667 3.48 0.00 42.91 4.81
751 762 2.308722 GGGCAGACCAGATGGGGAA 61.309 63.158 3.48 0.00 42.91 3.97
752 763 1.691219 GGCAGACCAGATGGGGAAA 59.309 57.895 3.48 0.00 42.91 3.13
753 764 0.394899 GGCAGACCAGATGGGGAAAG 60.395 60.000 3.48 0.00 42.91 2.62
754 765 1.034292 GCAGACCAGATGGGGAAAGC 61.034 60.000 3.48 0.00 42.91 3.51
755 766 0.745845 CAGACCAGATGGGGAAAGCG 60.746 60.000 3.48 0.00 42.91 4.68
756 767 1.452108 GACCAGATGGGGAAAGCGG 60.452 63.158 3.48 0.00 42.91 5.52
757 768 2.124151 CCAGATGGGGAAAGCGGG 60.124 66.667 0.00 0.00 0.00 6.13
758 769 2.677228 CAGATGGGGAAAGCGGGT 59.323 61.111 0.00 0.00 0.00 5.28
759 770 1.000896 CAGATGGGGAAAGCGGGTT 60.001 57.895 0.00 0.00 0.00 4.11
760 771 0.254747 CAGATGGGGAAAGCGGGTTA 59.745 55.000 0.00 0.00 0.00 2.85
761 772 1.133792 CAGATGGGGAAAGCGGGTTAT 60.134 52.381 0.00 0.00 0.00 1.89
762 773 2.105821 CAGATGGGGAAAGCGGGTTATA 59.894 50.000 0.00 0.00 0.00 0.98
763 774 2.372172 AGATGGGGAAAGCGGGTTATAG 59.628 50.000 0.00 0.00 0.00 1.31
764 775 0.181824 TGGGGAAAGCGGGTTATAGC 59.818 55.000 0.00 0.00 0.00 2.97
765 776 0.883370 GGGGAAAGCGGGTTATAGCG 60.883 60.000 0.00 0.00 38.61 4.26
766 777 0.179065 GGGAAAGCGGGTTATAGCGT 60.179 55.000 0.00 0.00 38.61 5.07
767 778 0.935196 GGAAAGCGGGTTATAGCGTG 59.065 55.000 0.00 0.00 38.61 5.34
768 779 0.935196 GAAAGCGGGTTATAGCGTGG 59.065 55.000 0.00 0.00 38.61 4.94
769 780 0.463116 AAAGCGGGTTATAGCGTGGG 60.463 55.000 0.00 0.00 38.61 4.61
770 781 2.935627 AAGCGGGTTATAGCGTGGGC 62.936 60.000 0.00 0.00 38.61 5.36
771 782 2.280592 CGGGTTATAGCGTGGGCC 60.281 66.667 0.00 0.00 41.24 5.80
772 783 2.280592 GGGTTATAGCGTGGGCCG 60.281 66.667 0.00 0.00 41.24 6.13
773 784 2.280592 GGTTATAGCGTGGGCCGG 60.281 66.667 0.00 0.00 41.24 6.13
774 785 2.970868 GTTATAGCGTGGGCCGGC 60.971 66.667 21.18 21.18 41.24 6.13
775 786 3.471806 TTATAGCGTGGGCCGGCA 61.472 61.111 30.85 5.28 41.24 5.69
776 787 3.032667 TTATAGCGTGGGCCGGCAA 62.033 57.895 30.85 13.68 41.24 4.52
777 788 2.933878 TTATAGCGTGGGCCGGCAAG 62.934 60.000 30.85 16.69 41.24 4.01
781 792 3.601685 CGTGGGCCGGCAAGTTTT 61.602 61.111 30.85 0.00 0.00 2.43
782 793 2.338620 GTGGGCCGGCAAGTTTTC 59.661 61.111 30.85 8.62 0.00 2.29
783 794 2.915137 TGGGCCGGCAAGTTTTCC 60.915 61.111 30.85 18.77 0.00 3.13
784 795 2.600470 GGGCCGGCAAGTTTTCCT 60.600 61.111 30.85 0.00 0.00 3.36
785 796 2.207229 GGGCCGGCAAGTTTTCCTT 61.207 57.895 30.85 0.00 0.00 3.36
786 797 1.745890 GGCCGGCAAGTTTTCCTTT 59.254 52.632 30.85 0.00 0.00 3.11
787 798 0.105964 GGCCGGCAAGTTTTCCTTTT 59.894 50.000 30.85 0.00 0.00 2.27
788 799 1.474320 GGCCGGCAAGTTTTCCTTTTT 60.474 47.619 30.85 0.00 0.00 1.94
789 800 2.224090 GGCCGGCAAGTTTTCCTTTTTA 60.224 45.455 30.85 0.00 0.00 1.52
790 801 3.556213 GGCCGGCAAGTTTTCCTTTTTAT 60.556 43.478 30.85 0.00 0.00 1.40
791 802 3.678072 GCCGGCAAGTTTTCCTTTTTATC 59.322 43.478 24.80 0.00 0.00 1.75
792 803 4.797933 GCCGGCAAGTTTTCCTTTTTATCA 60.798 41.667 24.80 0.00 0.00 2.15
793 804 4.923281 CCGGCAAGTTTTCCTTTTTATCAG 59.077 41.667 0.00 0.00 0.00 2.90
794 805 4.923281 CGGCAAGTTTTCCTTTTTATCAGG 59.077 41.667 0.00 0.00 0.00 3.86
795 806 5.237815 GGCAAGTTTTCCTTTTTATCAGGG 58.762 41.667 0.00 0.00 31.50 4.45
796 807 5.237815 GCAAGTTTTCCTTTTTATCAGGGG 58.762 41.667 0.00 0.00 31.50 4.79
797 808 5.011635 GCAAGTTTTCCTTTTTATCAGGGGA 59.988 40.000 0.00 0.00 31.50 4.81
798 809 6.455647 CAAGTTTTCCTTTTTATCAGGGGAC 58.544 40.000 0.00 0.00 31.50 4.46
832 843 3.224324 GCAGGCTGCCATGGGATG 61.224 66.667 28.87 10.25 37.42 3.51
833 844 3.224324 CAGGCTGCCATGGGATGC 61.224 66.667 22.65 15.62 0.00 3.91
834 845 3.426836 AGGCTGCCATGGGATGCT 61.427 61.111 22.65 9.40 0.00 3.79
835 846 2.080536 AGGCTGCCATGGGATGCTA 61.081 57.895 22.65 0.00 0.00 3.49
836 847 1.602888 GGCTGCCATGGGATGCTAG 60.603 63.158 15.17 6.40 0.00 3.42
837 848 1.602888 GCTGCCATGGGATGCTAGG 60.603 63.158 15.13 0.00 0.00 3.02
838 849 1.074423 CTGCCATGGGATGCTAGGG 59.926 63.158 15.13 0.00 0.00 3.53
839 850 1.385773 TGCCATGGGATGCTAGGGA 60.386 57.895 15.13 0.00 0.00 4.20
840 851 1.377994 GCCATGGGATGCTAGGGAG 59.622 63.158 15.13 0.00 0.00 4.30
841 852 2.073232 CCATGGGATGCTAGGGAGG 58.927 63.158 2.85 0.00 0.00 4.30
842 853 0.474466 CCATGGGATGCTAGGGAGGA 60.474 60.000 2.85 0.00 0.00 3.71
843 854 0.982704 CATGGGATGCTAGGGAGGAG 59.017 60.000 0.00 0.00 0.00 3.69
844 855 0.839853 ATGGGATGCTAGGGAGGAGC 60.840 60.000 0.00 0.00 40.53 4.70
845 856 3.477582 GGATGCTAGGGAGGAGCC 58.522 66.667 0.00 0.00 42.81 4.70
846 857 2.578714 GGATGCTAGGGAGGAGCCG 61.579 68.421 0.00 0.00 40.01 5.52
847 858 2.525381 ATGCTAGGGAGGAGCCGG 60.525 66.667 0.00 0.00 39.30 6.13
865 876 4.253257 CCGCTCCCTAGTCGCGTC 62.253 72.222 5.77 0.00 44.92 5.19
866 877 4.253257 CGCTCCCTAGTCGCGTCC 62.253 72.222 5.77 0.00 41.78 4.79
867 878 2.829458 GCTCCCTAGTCGCGTCCT 60.829 66.667 5.77 6.12 0.00 3.85
868 879 2.416432 GCTCCCTAGTCGCGTCCTT 61.416 63.158 5.77 0.00 0.00 3.36
869 880 1.946475 GCTCCCTAGTCGCGTCCTTT 61.946 60.000 5.77 0.00 0.00 3.11
870 881 0.100861 CTCCCTAGTCGCGTCCTTTC 59.899 60.000 5.77 0.00 0.00 2.62
871 882 0.323178 TCCCTAGTCGCGTCCTTTCT 60.323 55.000 5.77 0.00 0.00 2.52
872 883 0.179134 CCCTAGTCGCGTCCTTTCTG 60.179 60.000 5.77 0.00 0.00 3.02
873 884 0.179134 CCTAGTCGCGTCCTTTCTGG 60.179 60.000 5.77 1.39 37.10 3.86
874 885 0.526662 CTAGTCGCGTCCTTTCTGGT 59.473 55.000 5.77 0.00 37.07 4.00
875 886 1.741706 CTAGTCGCGTCCTTTCTGGTA 59.258 52.381 5.77 0.00 37.07 3.25
876 887 0.963962 AGTCGCGTCCTTTCTGGTAA 59.036 50.000 5.77 0.00 37.07 2.85
877 888 1.549170 AGTCGCGTCCTTTCTGGTAAT 59.451 47.619 5.77 0.00 37.07 1.89
878 889 2.756760 AGTCGCGTCCTTTCTGGTAATA 59.243 45.455 5.77 0.00 37.07 0.98
879 890 2.856557 GTCGCGTCCTTTCTGGTAATAC 59.143 50.000 5.77 0.00 37.07 1.89
880 891 2.756760 TCGCGTCCTTTCTGGTAATACT 59.243 45.455 5.77 0.00 37.07 2.12
881 892 3.947196 TCGCGTCCTTTCTGGTAATACTA 59.053 43.478 5.77 0.00 37.07 1.82
882 893 4.398988 TCGCGTCCTTTCTGGTAATACTAA 59.601 41.667 5.77 0.00 37.07 2.24
883 894 5.068198 TCGCGTCCTTTCTGGTAATACTAAT 59.932 40.000 5.77 0.00 37.07 1.73
884 895 5.175126 CGCGTCCTTTCTGGTAATACTAATG 59.825 44.000 0.00 0.00 37.07 1.90
885 896 6.278363 GCGTCCTTTCTGGTAATACTAATGA 58.722 40.000 0.00 0.00 37.07 2.57
886 897 6.759827 GCGTCCTTTCTGGTAATACTAATGAA 59.240 38.462 0.00 0.00 37.07 2.57
887 898 7.042658 GCGTCCTTTCTGGTAATACTAATGAAG 60.043 40.741 0.00 0.00 37.07 3.02
888 899 7.042658 CGTCCTTTCTGGTAATACTAATGAAGC 60.043 40.741 0.00 0.00 37.07 3.86
889 900 7.988028 GTCCTTTCTGGTAATACTAATGAAGCT 59.012 37.037 0.00 0.00 37.07 3.74
890 901 8.548877 TCCTTTCTGGTAATACTAATGAAGCTT 58.451 33.333 0.00 0.00 37.07 3.74
891 902 8.831550 CCTTTCTGGTAATACTAATGAAGCTTC 58.168 37.037 19.89 19.89 0.00 3.86
892 903 9.383519 CTTTCTGGTAATACTAATGAAGCTTCA 57.616 33.333 30.23 30.23 42.14 3.02
893 904 9.733556 TTTCTGGTAATACTAATGAAGCTTCAA 57.266 29.630 31.55 16.23 41.13 2.69
894 905 8.718102 TCTGGTAATACTAATGAAGCTTCAAC 57.282 34.615 31.55 21.22 41.13 3.18
895 906 8.540388 TCTGGTAATACTAATGAAGCTTCAACT 58.460 33.333 31.55 22.92 41.13 3.16
896 907 9.817809 CTGGTAATACTAATGAAGCTTCAACTA 57.182 33.333 31.55 22.82 41.13 2.24
897 908 9.817809 TGGTAATACTAATGAAGCTTCAACTAG 57.182 33.333 31.55 30.38 41.13 2.57
1009 1022 2.591429 CGCTCGCCATGGCCATTA 60.591 61.111 30.79 12.87 37.98 1.90
1035 1048 1.755008 CTCGACCTCCTCCCCTGTC 60.755 68.421 0.00 0.00 0.00 3.51
1072 1085 3.282885 CCCCATTTTCTAGACTCCAAGC 58.717 50.000 0.00 0.00 0.00 4.01
1077 1090 1.867363 TTCTAGACTCCAAGCCCCTC 58.133 55.000 0.00 0.00 0.00 4.30
1081 1094 1.377856 GACTCCAAGCCCCTCAAGC 60.378 63.158 0.00 0.00 0.00 4.01
1089 1102 1.136329 AGCCCCTCAAGCCTCTCAAA 61.136 55.000 0.00 0.00 0.00 2.69
1401 1414 4.751767 CTCCAATGAGTTTCTCCTAGCT 57.248 45.455 0.00 0.00 33.70 3.32
1590 1603 3.589881 GCTGCTGGGGCTAATGCG 61.590 66.667 0.00 0.00 40.82 4.73
1689 1702 0.322816 ACGCCATGCTGGTCAAGAAT 60.323 50.000 4.45 0.00 40.46 2.40
1846 1859 2.112297 GGTTCGCACACAAGGGGA 59.888 61.111 0.00 0.00 0.00 4.81
1890 1903 0.701731 TCCGGTGGATGGTGGAAAAT 59.298 50.000 0.00 0.00 0.00 1.82
1979 1992 4.014273 ACTTAGGGAGGGAGATTCATGT 57.986 45.455 0.00 0.00 0.00 3.21
2217 2230 3.379452 AGAAGGAATCCGACCAGATCTT 58.621 45.455 0.00 0.00 0.00 2.40
2337 2350 5.393352 GCCAAATGTCTCATTATGCACTTCA 60.393 40.000 0.00 0.00 0.00 3.02
2574 2587 7.418840 CTCTGATATTGGAGCATTACAACTC 57.581 40.000 0.00 0.00 0.00 3.01
2634 2647 0.037605 AACCTCTCCCGTTAGTTGCG 60.038 55.000 0.00 0.00 0.00 4.85
2719 2732 1.210722 GAACAGAGTCCAAGGGATCCC 59.789 57.143 24.59 24.59 32.73 3.85
2892 2905 5.220815 GCATGATGAAGCTCTCGAGATTTTT 60.221 40.000 17.03 10.50 37.15 1.94
3194 3207 4.770795 ACTAACCAGTAATGCCATCAGTC 58.229 43.478 0.00 0.00 31.45 3.51
3272 3285 3.153919 TGCCTTTATTCCCTCACAACAC 58.846 45.455 0.00 0.00 0.00 3.32
3273 3286 2.161609 GCCTTTATTCCCTCACAACACG 59.838 50.000 0.00 0.00 0.00 4.49
3316 3329 3.778075 GGGGTTTGGGTTTATGGCTTATT 59.222 43.478 0.00 0.00 0.00 1.40
3334 3347 6.016111 GCTTATTTGTTCGCTTCAGTTAGAC 58.984 40.000 0.00 0.00 0.00 2.59
3426 3439 8.157476 ACTGAGCCATAATAAATAGGGTTAGTG 58.843 37.037 6.20 0.00 43.79 2.74
3496 3509 9.809395 ATGTATAGCTAGTAGTCTAATTGTCCA 57.191 33.333 0.00 0.00 0.00 4.02
3743 3759 0.949105 ACTTCTAGTGGTTTGCGGCG 60.949 55.000 0.51 0.51 0.00 6.46
3755 3771 0.671251 TTGCGGCGTTTCCTTTTGAT 59.329 45.000 9.37 0.00 0.00 2.57
3757 3773 2.088423 TGCGGCGTTTCCTTTTGATAT 58.912 42.857 9.37 0.00 0.00 1.63
3919 3935 1.761784 CTCCTCTCCATCCAAGGACTG 59.238 57.143 0.00 0.00 35.38 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.430042 AATCAGGCAAGTGATGAGTGT 57.570 42.857 0.00 0.00 37.24 3.55
118 119 9.613428 ACTAATAGCAGTATTGTAAGCAATTCA 57.387 29.630 0.00 0.00 42.19 2.57
147 150 4.403432 CCATATGATCTGGGCAAAACACTT 59.597 41.667 3.65 0.00 0.00 3.16
294 298 7.715249 GTGGGTTACTGAAAAGCATCTGATATA 59.285 37.037 0.00 0.00 0.00 0.86
296 300 5.880332 GTGGGTTACTGAAAAGCATCTGATA 59.120 40.000 0.00 0.00 0.00 2.15
375 381 7.042797 TCCCTCAATTCTTTTGACTCTTTTG 57.957 36.000 0.00 0.00 0.00 2.44
394 400 7.569639 AAAAACTGTAGAAAACTCTTCCCTC 57.430 36.000 0.00 0.00 0.00 4.30
425 431 1.000938 GCCAGGTTTGCTCAACTCTTG 60.001 52.381 0.00 0.00 35.46 3.02
485 496 3.084039 GGTCAGCAGATCCAAATTGACA 58.916 45.455 12.49 0.00 37.31 3.58
513 524 2.202824 CCTTGCAATGGCGGCATG 60.203 61.111 26.50 19.20 45.35 4.06
528 539 2.982488 TCCAGAAAAGCTTCCTTCTCCT 59.018 45.455 9.92 0.00 29.29 3.69
541 552 2.993146 TCCCTTCCCAAGATCCAGAAAA 59.007 45.455 0.00 0.00 0.00 2.29
580 591 2.954318 CCCTGCATACCCATCTTCTTTG 59.046 50.000 0.00 0.00 0.00 2.77
581 592 2.091665 CCCCTGCATACCCATCTTCTTT 60.092 50.000 0.00 0.00 0.00 2.52
595 606 1.152355 CAAACCCCTTTCCCCTGCA 60.152 57.895 0.00 0.00 0.00 4.41
596 607 1.913262 CCAAACCCCTTTCCCCTGC 60.913 63.158 0.00 0.00 0.00 4.85
598 609 1.361197 CATACCAAACCCCTTTCCCCT 59.639 52.381 0.00 0.00 0.00 4.79
619 630 3.009115 CCGCCCCCTTCTCCTGAA 61.009 66.667 0.00 0.00 0.00 3.02
669 680 2.224793 CGGTTCCTCTCCCTTCCTTTTT 60.225 50.000 0.00 0.00 0.00 1.94
670 681 1.351350 CGGTTCCTCTCCCTTCCTTTT 59.649 52.381 0.00 0.00 0.00 2.27
671 682 0.984995 CGGTTCCTCTCCCTTCCTTT 59.015 55.000 0.00 0.00 0.00 3.11
672 683 0.178900 ACGGTTCCTCTCCCTTCCTT 60.179 55.000 0.00 0.00 0.00 3.36
673 684 0.708802 TACGGTTCCTCTCCCTTCCT 59.291 55.000 0.00 0.00 0.00 3.36
674 685 0.822811 GTACGGTTCCTCTCCCTTCC 59.177 60.000 0.00 0.00 0.00 3.46
675 686 0.822811 GGTACGGTTCCTCTCCCTTC 59.177 60.000 0.00 0.00 0.00 3.46
676 687 0.616964 GGGTACGGTTCCTCTCCCTT 60.617 60.000 3.72 0.00 32.89 3.95
677 688 1.001376 GGGTACGGTTCCTCTCCCT 59.999 63.158 3.72 0.00 32.89 4.20
678 689 1.001376 AGGGTACGGTTCCTCTCCC 59.999 63.158 3.72 0.00 35.56 4.30
679 690 1.382692 CGAGGGTACGGTTCCTCTCC 61.383 65.000 20.42 0.75 45.46 3.71
680 691 1.382692 CCGAGGGTACGGTTCCTCTC 61.383 65.000 20.42 15.45 45.46 3.20
681 692 1.379576 CCGAGGGTACGGTTCCTCT 60.380 63.158 20.42 10.17 45.46 3.69
682 693 3.204418 CCGAGGGTACGGTTCCTC 58.796 66.667 15.83 15.83 46.70 3.71
701 712 2.065799 TGCTTCCTCTCCCTCCTTTTT 58.934 47.619 0.00 0.00 0.00 1.94
702 713 1.352687 GTGCTTCCTCTCCCTCCTTTT 59.647 52.381 0.00 0.00 0.00 2.27
703 714 0.988063 GTGCTTCCTCTCCCTCCTTT 59.012 55.000 0.00 0.00 0.00 3.11
704 715 1.261238 CGTGCTTCCTCTCCCTCCTT 61.261 60.000 0.00 0.00 0.00 3.36
705 716 1.684049 CGTGCTTCCTCTCCCTCCT 60.684 63.158 0.00 0.00 0.00 3.69
706 717 1.985116 ACGTGCTTCCTCTCCCTCC 60.985 63.158 0.00 0.00 0.00 4.30
707 718 1.216710 CACGTGCTTCCTCTCCCTC 59.783 63.158 0.82 0.00 0.00 4.30
708 719 1.534235 ACACGTGCTTCCTCTCCCT 60.534 57.895 17.22 0.00 0.00 4.20
709 720 1.374758 CACACGTGCTTCCTCTCCC 60.375 63.158 17.22 0.00 0.00 4.30
710 721 1.374758 CCACACGTGCTTCCTCTCC 60.375 63.158 17.22 0.00 0.00 3.71
711 722 1.374758 CCCACACGTGCTTCCTCTC 60.375 63.158 17.22 0.00 0.00 3.20
712 723 2.743718 CCCACACGTGCTTCCTCT 59.256 61.111 17.22 0.00 0.00 3.69
713 724 2.358737 CCCCACACGTGCTTCCTC 60.359 66.667 17.22 0.00 0.00 3.71
714 725 2.847234 TCCCCACACGTGCTTCCT 60.847 61.111 17.22 0.00 0.00 3.36
715 726 2.358737 CTCCCCACACGTGCTTCC 60.359 66.667 17.22 0.00 0.00 3.46
716 727 2.358737 CCTCCCCACACGTGCTTC 60.359 66.667 17.22 0.00 0.00 3.86
717 728 3.953775 CCCTCCCCACACGTGCTT 61.954 66.667 17.22 0.00 0.00 3.91
723 734 4.035102 GTCTGCCCCTCCCCACAC 62.035 72.222 0.00 0.00 0.00 3.82
727 738 4.741239 TCTGGTCTGCCCCTCCCC 62.741 72.222 0.00 0.00 0.00 4.81
728 739 2.367512 ATCTGGTCTGCCCCTCCC 60.368 66.667 0.00 0.00 0.00 4.30
729 740 2.750657 CCATCTGGTCTGCCCCTCC 61.751 68.421 0.00 0.00 0.00 4.30
730 741 2.750657 CCCATCTGGTCTGCCCCTC 61.751 68.421 0.00 0.00 0.00 4.30
731 742 2.693864 CCCATCTGGTCTGCCCCT 60.694 66.667 0.00 0.00 0.00 4.79
732 743 3.813724 CCCCATCTGGTCTGCCCC 61.814 72.222 0.00 0.00 0.00 5.80
733 744 1.863155 TTTCCCCATCTGGTCTGCCC 61.863 60.000 0.00 0.00 0.00 5.36
734 745 0.394899 CTTTCCCCATCTGGTCTGCC 60.395 60.000 0.00 0.00 0.00 4.85
735 746 1.034292 GCTTTCCCCATCTGGTCTGC 61.034 60.000 0.00 0.00 0.00 4.26
736 747 0.745845 CGCTTTCCCCATCTGGTCTG 60.746 60.000 0.00 0.00 0.00 3.51
737 748 1.604378 CGCTTTCCCCATCTGGTCT 59.396 57.895 0.00 0.00 0.00 3.85
738 749 1.452108 CCGCTTTCCCCATCTGGTC 60.452 63.158 0.00 0.00 0.00 4.02
739 750 2.677228 CCGCTTTCCCCATCTGGT 59.323 61.111 0.00 0.00 0.00 4.00
740 751 2.124151 CCCGCTTTCCCCATCTGG 60.124 66.667 0.00 0.00 0.00 3.86
741 752 0.254747 TAACCCGCTTTCCCCATCTG 59.745 55.000 0.00 0.00 0.00 2.90
742 753 1.222567 ATAACCCGCTTTCCCCATCT 58.777 50.000 0.00 0.00 0.00 2.90
743 754 2.779506 CTATAACCCGCTTTCCCCATC 58.220 52.381 0.00 0.00 0.00 3.51
744 755 1.202891 GCTATAACCCGCTTTCCCCAT 60.203 52.381 0.00 0.00 0.00 4.00
745 756 0.181824 GCTATAACCCGCTTTCCCCA 59.818 55.000 0.00 0.00 0.00 4.96
746 757 0.883370 CGCTATAACCCGCTTTCCCC 60.883 60.000 0.00 0.00 0.00 4.81
747 758 0.179065 ACGCTATAACCCGCTTTCCC 60.179 55.000 0.00 0.00 0.00 3.97
748 759 0.935196 CACGCTATAACCCGCTTTCC 59.065 55.000 0.00 0.00 0.00 3.13
749 760 0.935196 CCACGCTATAACCCGCTTTC 59.065 55.000 0.00 0.00 0.00 2.62
750 761 0.463116 CCCACGCTATAACCCGCTTT 60.463 55.000 0.00 0.00 0.00 3.51
751 762 1.145377 CCCACGCTATAACCCGCTT 59.855 57.895 0.00 0.00 0.00 4.68
752 763 2.819550 CCCACGCTATAACCCGCT 59.180 61.111 0.00 0.00 0.00 5.52
753 764 2.970868 GCCCACGCTATAACCCGC 60.971 66.667 0.00 0.00 0.00 6.13
754 765 2.280592 GGCCCACGCTATAACCCG 60.281 66.667 0.00 0.00 34.44 5.28
755 766 2.280592 CGGCCCACGCTATAACCC 60.281 66.667 0.00 0.00 34.82 4.11
756 767 2.280592 CCGGCCCACGCTATAACC 60.281 66.667 0.00 0.00 42.52 2.85
757 768 2.970868 GCCGGCCCACGCTATAAC 60.971 66.667 18.11 0.00 42.52 1.89
758 769 2.933878 CTTGCCGGCCCACGCTATAA 62.934 60.000 26.77 6.96 42.52 0.98
759 770 3.454587 CTTGCCGGCCCACGCTATA 62.455 63.158 26.77 0.00 42.52 1.31
760 771 4.856801 CTTGCCGGCCCACGCTAT 62.857 66.667 26.77 0.00 42.52 2.97
764 775 3.551887 GAAAACTTGCCGGCCCACG 62.552 63.158 26.77 11.93 43.80 4.94
765 776 2.338620 GAAAACTTGCCGGCCCAC 59.661 61.111 26.77 4.51 0.00 4.61
766 777 2.915137 GGAAAACTTGCCGGCCCA 60.915 61.111 26.77 9.99 0.00 5.36
767 778 1.754380 AAAGGAAAACTTGCCGGCCC 61.754 55.000 26.77 16.19 39.96 5.80
768 779 0.105964 AAAAGGAAAACTTGCCGGCC 59.894 50.000 26.77 5.93 39.96 6.13
769 780 1.948104 AAAAAGGAAAACTTGCCGGC 58.052 45.000 22.73 22.73 39.96 6.13
770 781 4.877282 TGATAAAAAGGAAAACTTGCCGG 58.123 39.130 0.00 0.00 39.96 6.13
771 782 4.923281 CCTGATAAAAAGGAAAACTTGCCG 59.077 41.667 0.00 0.00 39.96 5.69
772 783 5.237815 CCCTGATAAAAAGGAAAACTTGCC 58.762 41.667 0.00 0.00 39.96 4.52
773 784 5.011635 TCCCCTGATAAAAAGGAAAACTTGC 59.988 40.000 0.00 0.00 39.96 4.01
774 785 6.455647 GTCCCCTGATAAAAAGGAAAACTTG 58.544 40.000 0.00 0.00 39.96 3.16
775 786 5.542635 GGTCCCCTGATAAAAAGGAAAACTT 59.457 40.000 0.00 0.00 42.52 2.66
776 787 5.084519 GGTCCCCTGATAAAAAGGAAAACT 58.915 41.667 0.00 0.00 36.91 2.66
777 788 4.082408 CGGTCCCCTGATAAAAAGGAAAAC 60.082 45.833 0.00 0.00 36.91 2.43
778 789 4.083565 CGGTCCCCTGATAAAAAGGAAAA 58.916 43.478 0.00 0.00 36.91 2.29
779 790 3.331294 TCGGTCCCCTGATAAAAAGGAAA 59.669 43.478 0.00 0.00 36.91 3.13
780 791 2.914278 TCGGTCCCCTGATAAAAAGGAA 59.086 45.455 0.00 0.00 36.91 3.36
781 792 2.553464 TCGGTCCCCTGATAAAAAGGA 58.447 47.619 0.00 0.00 36.91 3.36
782 793 3.359695 TTCGGTCCCCTGATAAAAAGG 57.640 47.619 0.00 0.00 34.31 3.11
783 794 4.332828 ACTTTCGGTCCCCTGATAAAAAG 58.667 43.478 0.00 0.00 0.00 2.27
784 795 4.376225 ACTTTCGGTCCCCTGATAAAAA 57.624 40.909 0.00 0.00 0.00 1.94
785 796 4.376225 AACTTTCGGTCCCCTGATAAAA 57.624 40.909 0.00 0.00 0.00 1.52
786 797 4.376225 AAACTTTCGGTCCCCTGATAAA 57.624 40.909 0.00 0.00 0.00 1.40
787 798 4.376225 AAAACTTTCGGTCCCCTGATAA 57.624 40.909 0.00 0.00 0.00 1.75
788 799 4.376225 AAAAACTTTCGGTCCCCTGATA 57.624 40.909 0.00 0.00 0.00 2.15
789 800 2.971901 AAAACTTTCGGTCCCCTGAT 57.028 45.000 0.00 0.00 0.00 2.90
790 801 2.740506 AAAAACTTTCGGTCCCCTGA 57.259 45.000 0.00 0.00 0.00 3.86
815 826 3.224324 CATCCCATGGCAGCCTGC 61.224 66.667 14.15 8.55 44.08 4.85
816 827 2.347691 TAGCATCCCATGGCAGCCTG 62.348 60.000 14.15 8.41 0.00 4.85
817 828 2.065470 CTAGCATCCCATGGCAGCCT 62.065 60.000 14.15 2.33 0.00 4.58
818 829 1.602888 CTAGCATCCCATGGCAGCC 60.603 63.158 6.09 3.66 0.00 4.85
819 830 1.602888 CCTAGCATCCCATGGCAGC 60.603 63.158 6.09 9.73 0.00 5.25
820 831 1.074423 CCCTAGCATCCCATGGCAG 59.926 63.158 6.09 0.00 0.00 4.85
821 832 1.385773 TCCCTAGCATCCCATGGCA 60.386 57.895 6.09 0.00 0.00 4.92
822 833 1.377994 CTCCCTAGCATCCCATGGC 59.622 63.158 6.09 0.00 0.00 4.40
823 834 0.474466 TCCTCCCTAGCATCCCATGG 60.474 60.000 4.14 4.14 0.00 3.66
824 835 0.982704 CTCCTCCCTAGCATCCCATG 59.017 60.000 0.00 0.00 0.00 3.66
825 836 0.839853 GCTCCTCCCTAGCATCCCAT 60.840 60.000 0.00 0.00 39.83 4.00
826 837 1.460305 GCTCCTCCCTAGCATCCCA 60.460 63.158 0.00 0.00 39.83 4.37
827 838 2.220586 GGCTCCTCCCTAGCATCCC 61.221 68.421 0.00 0.00 41.93 3.85
828 839 2.578714 CGGCTCCTCCCTAGCATCC 61.579 68.421 0.00 0.00 41.93 3.51
829 840 2.578714 CCGGCTCCTCCCTAGCATC 61.579 68.421 0.00 0.00 41.93 3.91
830 841 2.525381 CCGGCTCCTCCCTAGCAT 60.525 66.667 0.00 0.00 41.93 3.79
850 861 1.946475 AAAGGACGCGACTAGGGAGC 61.946 60.000 15.93 0.00 36.53 4.70
851 862 0.100861 GAAAGGACGCGACTAGGGAG 59.899 60.000 15.93 0.00 36.53 4.30
852 863 0.323178 AGAAAGGACGCGACTAGGGA 60.323 55.000 15.93 0.00 36.53 4.20
853 864 0.179134 CAGAAAGGACGCGACTAGGG 60.179 60.000 15.93 0.00 38.93 3.53
854 865 0.179134 CCAGAAAGGACGCGACTAGG 60.179 60.000 15.93 7.40 41.22 3.02
855 866 0.526662 ACCAGAAAGGACGCGACTAG 59.473 55.000 15.93 2.10 41.22 2.57
856 867 1.825090 TACCAGAAAGGACGCGACTA 58.175 50.000 15.93 0.00 41.22 2.59
857 868 0.963962 TTACCAGAAAGGACGCGACT 59.036 50.000 15.93 7.85 41.22 4.18
858 869 2.005971 ATTACCAGAAAGGACGCGAC 57.994 50.000 15.93 6.56 41.22 5.19
859 870 2.756760 AGTATTACCAGAAAGGACGCGA 59.243 45.455 15.93 0.00 41.22 5.87
860 871 3.160777 AGTATTACCAGAAAGGACGCG 57.839 47.619 3.53 3.53 41.22 6.01
861 872 6.278363 TCATTAGTATTACCAGAAAGGACGC 58.722 40.000 0.00 0.00 41.22 5.19
862 873 7.042658 GCTTCATTAGTATTACCAGAAAGGACG 60.043 40.741 0.00 0.00 41.22 4.79
863 874 7.988028 AGCTTCATTAGTATTACCAGAAAGGAC 59.012 37.037 0.00 0.00 41.22 3.85
864 875 8.090788 AGCTTCATTAGTATTACCAGAAAGGA 57.909 34.615 0.00 0.00 41.22 3.36
865 876 8.738645 AAGCTTCATTAGTATTACCAGAAAGG 57.261 34.615 0.00 0.00 45.67 3.11
866 877 9.383519 TGAAGCTTCATTAGTATTACCAGAAAG 57.616 33.333 25.16 0.00 31.01 2.62
867 878 9.733556 TTGAAGCTTCATTAGTATTACCAGAAA 57.266 29.630 28.89 5.73 37.00 2.52
868 879 9.162764 GTTGAAGCTTCATTAGTATTACCAGAA 57.837 33.333 28.89 6.12 37.00 3.02
869 880 8.540388 AGTTGAAGCTTCATTAGTATTACCAGA 58.460 33.333 28.89 6.79 37.00 3.86
870 881 8.723942 AGTTGAAGCTTCATTAGTATTACCAG 57.276 34.615 28.89 0.00 37.00 4.00
871 882 9.817809 CTAGTTGAAGCTTCATTAGTATTACCA 57.182 33.333 28.89 10.27 37.00 3.25
872 883 9.819267 ACTAGTTGAAGCTTCATTAGTATTACC 57.181 33.333 32.09 14.07 36.77 2.85
896 907 9.431887 ACACATCGTTCACATTAATTAAGTACT 57.568 29.630 3.94 0.00 0.00 2.73
919 932 3.388350 AGCTAGATTTAGGCCACCTACAC 59.612 47.826 5.01 0.00 35.63 2.90
1009 1022 3.083997 GGAGGTCGAGGCCATGGT 61.084 66.667 14.67 0.00 0.00 3.55
1044 1057 3.017442 GTCTAGAAAATGGGGGTGCTTC 58.983 50.000 0.00 0.00 0.00 3.86
1072 1085 0.674895 CGTTTGAGAGGCTTGAGGGG 60.675 60.000 0.00 0.00 0.00 4.79
1077 1090 2.174349 GCGCGTTTGAGAGGCTTG 59.826 61.111 8.43 0.00 37.01 4.01
1081 1094 1.733041 TTCTCGCGCGTTTGAGAGG 60.733 57.895 30.98 10.46 41.87 3.69
1401 1414 2.928334 AGATAAACCTCGACGAGCCTA 58.072 47.619 19.55 9.82 0.00 3.93
1590 1603 0.166814 AGCCGTACGTGTACTCGTTC 59.833 55.000 25.78 19.82 43.80 3.95
1846 1859 0.252881 TCCAGTGCCTCCCTCTTCAT 60.253 55.000 0.00 0.00 0.00 2.57
1890 1903 0.679505 CCGAGTTCACCTTGACTCCA 59.320 55.000 0.00 0.00 0.00 3.86
1945 1958 1.337074 CCCTAAGTTCCGTGCACGTAA 60.337 52.381 34.81 25.23 37.74 3.18
1979 1992 2.687935 GGAAACTTCTTCAGCACCAACA 59.312 45.455 0.00 0.00 0.00 3.33
2217 2230 1.134340 AGAACAGTACCAACCGCAACA 60.134 47.619 0.00 0.00 0.00 3.33
2337 2350 3.376082 ACCGTACAGGGTGATGAGT 57.624 52.632 8.31 0.00 46.96 3.41
2356 2369 6.346439 CGAGAGTATTCTAAATGACAGCATGC 60.346 42.308 10.51 10.51 34.06 4.06
2484 2497 3.190079 GTTCGACAGCAGCATTGATCTA 58.810 45.455 0.00 0.00 0.00 1.98
2574 2587 0.804989 GACCATGAACTTCCTTGCCG 59.195 55.000 0.00 0.00 0.00 5.69
2634 2647 5.640732 CCATACATGTTAACAAGTTCTGCC 58.359 41.667 20.38 0.00 0.00 4.85
2706 2719 1.265454 ACGTCAGGGATCCCTTGGAC 61.265 60.000 31.98 30.48 45.70 4.02
2719 2732 3.865164 TCTATTATTGCAGTGCACGTCAG 59.135 43.478 19.58 11.50 38.71 3.51
2892 2905 2.038863 ACCCTTGTACCATGGAGTCA 57.961 50.000 21.47 11.26 31.33 3.41
2992 3005 3.556775 GCAGCTTTCAAATCAGCAAAACA 59.443 39.130 0.00 0.00 38.61 2.83
3178 3191 1.945387 AGCGACTGATGGCATTACTG 58.055 50.000 0.00 0.00 30.59 2.74
3194 3207 7.797123 GGTTAATATTGAATTTTCGACCTAGCG 59.203 37.037 0.00 0.00 0.00 4.26
3272 3285 6.807230 CCCCTAACTTTCTGATACGATAATCG 59.193 42.308 0.00 0.00 46.93 3.34
3273 3286 7.668492 ACCCCTAACTTTCTGATACGATAATC 58.332 38.462 0.00 0.00 0.00 1.75
3316 3329 6.431198 AAAAAGTCTAACTGAAGCGAACAA 57.569 33.333 0.00 0.00 0.00 2.83
3334 3347 2.749076 TCATGCATGAGTCCGGAAAAAG 59.251 45.455 25.42 0.00 32.11 2.27
3426 3439 9.744468 TTGCTGGAAAAAGAACTTAAGTAAATC 57.256 29.630 8.92 2.99 0.00 2.17
3433 3446 7.286775 ACACCTATTGCTGGAAAAAGAACTTAA 59.713 33.333 0.00 0.00 0.00 1.85
3505 3521 6.723298 AAAGGTCAATGTTCCACATAACAA 57.277 33.333 0.00 0.00 42.33 2.83
3619 3635 7.335422 AGTTATCAGCTATGTTCTGTTCCAAAG 59.665 37.037 0.00 0.00 33.48 2.77
3815 3831 4.909696 TTTCGCAGAAATGAAGTTCCAA 57.090 36.364 0.00 0.00 45.90 3.53
3816 3832 4.761739 AGATTTCGCAGAAATGAAGTTCCA 59.238 37.500 17.26 0.00 45.90 3.53
3832 3848 6.568869 ACCAGAACAGAAGATAGAGATTTCG 58.431 40.000 0.00 0.00 0.00 3.46
3919 3935 1.209621 TGGTGCCTACTCCCCATTAC 58.790 55.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.