Multiple sequence alignment - TraesCS1A01G206300

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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 TraesCS1A01G206300 chr1A 100.000 3844 0 0 1 3844 368796608 368800451 0.000000e+00 7099
1 TraesCS1A01G206300 chr1A 95.218 711 30 2 1 707 368755881 368756591 0.000000e+00 1122
2 TraesCS1A01G206300 chr1A 94.796 711 33 2 1 707 398204575 398205285 0.000000e+00 1105
3 TraesCS1A01G206300 chr1B 91.371 3048 165 45 832 3844 397051903 397054887 0.000000e+00 4082
4 TraesCS1A01G206300 chr1B 83.410 868 78 29 1306 2143 48108606 48109437 0.000000e+00 745
5 TraesCS1A01G206300 chr1D 93.454 2551 133 18 844 3376 295535879 295538413 0.000000e+00 3755
6 TraesCS1A01G206300 chr1D 86.542 535 42 12 3317 3844 295538412 295538923 2.590000e-156 562
7 TraesCS1A01G206300 chr5A 94.818 714 33 2 1 710 573679096 573678383 0.000000e+00 1110
8 TraesCS1A01G206300 chr3A 94.937 711 32 2 1 707 421944007 421944717 0.000000e+00 1110
9 TraesCS1A01G206300 chr3A 94.374 711 36 2 1 707 601042963 601043673 0.000000e+00 1088
10 TraesCS1A01G206300 chr3A 93.535 727 42 3 1 723 443431407 443430682 0.000000e+00 1077
11 TraesCS1A01G206300 chr2A 94.818 714 33 2 1 710 676272863 676272150 0.000000e+00 1110
12 TraesCS1A01G206300 chr2A 86.408 721 67 18 1309 2005 19604514 19603801 0.000000e+00 760
13 TraesCS1A01G206300 chr7A 94.655 711 34 2 1 707 124113660 124112950 0.000000e+00 1099
14 TraesCS1A01G206300 chr7A 87.240 721 61 18 1309 2005 14509143 14508430 0.000000e+00 793
15 TraesCS1A01G206300 chr7A 86.685 721 60 20 1309 2005 64563735 64563027 0.000000e+00 767
16 TraesCS1A01G206300 chr4A 94.429 718 35 3 1 714 566869426 566870142 0.000000e+00 1099
17 TraesCS1A01G206300 chrUn 87.155 724 62 18 1306 2005 82063789 82064505 0.000000e+00 793
18 TraesCS1A01G206300 chrUn 87.155 724 62 18 1306 2005 377313350 377314066 0.000000e+00 793
19 TraesCS1A01G206300 chr5D 87.029 717 66 16 1309 2005 41587999 41587290 0.000000e+00 784
20 TraesCS1A01G206300 chr6B 83.986 868 80 27 1306 2143 244812858 244813696 0.000000e+00 778
21 TraesCS1A01G206300 chr7B 82.818 873 76 34 1309 2143 720575558 720574722 0.000000e+00 713


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 TraesCS1A01G206300 chr1A 368796608 368800451 3843 False 7099.0 7099 100.000 1 3844 1 chr1A.!!$F2 3843
1 TraesCS1A01G206300 chr1A 368755881 368756591 710 False 1122.0 1122 95.218 1 707 1 chr1A.!!$F1 706
2 TraesCS1A01G206300 chr1A 398204575 398205285 710 False 1105.0 1105 94.796 1 707 1 chr1A.!!$F3 706
3 TraesCS1A01G206300 chr1B 397051903 397054887 2984 False 4082.0 4082 91.371 832 3844 1 chr1B.!!$F2 3012
4 TraesCS1A01G206300 chr1B 48108606 48109437 831 False 745.0 745 83.410 1306 2143 1 chr1B.!!$F1 837
5 TraesCS1A01G206300 chr1D 295535879 295538923 3044 False 2158.5 3755 89.998 844 3844 2 chr1D.!!$F1 3000
6 TraesCS1A01G206300 chr5A 573678383 573679096 713 True 1110.0 1110 94.818 1 710 1 chr5A.!!$R1 709
7 TraesCS1A01G206300 chr3A 421944007 421944717 710 False 1110.0 1110 94.937 1 707 1 chr3A.!!$F1 706
8 TraesCS1A01G206300 chr3A 601042963 601043673 710 False 1088.0 1088 94.374 1 707 1 chr3A.!!$F2 706
9 TraesCS1A01G206300 chr3A 443430682 443431407 725 True 1077.0 1077 93.535 1 723 1 chr3A.!!$R1 722
10 TraesCS1A01G206300 chr2A 676272150 676272863 713 True 1110.0 1110 94.818 1 710 1 chr2A.!!$R2 709
11 TraesCS1A01G206300 chr2A 19603801 19604514 713 True 760.0 760 86.408 1309 2005 1 chr2A.!!$R1 696
12 TraesCS1A01G206300 chr7A 124112950 124113660 710 True 1099.0 1099 94.655 1 707 1 chr7A.!!$R3 706
13 TraesCS1A01G206300 chr7A 14508430 14509143 713 True 793.0 793 87.240 1309 2005 1 chr7A.!!$R1 696
14 TraesCS1A01G206300 chr7A 64563027 64563735 708 True 767.0 767 86.685 1309 2005 1 chr7A.!!$R2 696
15 TraesCS1A01G206300 chr4A 566869426 566870142 716 False 1099.0 1099 94.429 1 714 1 chr4A.!!$F1 713
16 TraesCS1A01G206300 chrUn 82063789 82064505 716 False 793.0 793 87.155 1306 2005 1 chrUn.!!$F1 699
17 TraesCS1A01G206300 chrUn 377313350 377314066 716 False 793.0 793 87.155 1306 2005 1 chrUn.!!$F2 699
18 TraesCS1A01G206300 chr5D 41587290 41587999 709 True 784.0 784 87.029 1309 2005 1 chr5D.!!$R1 696
19 TraesCS1A01G206300 chr6B 244812858 244813696 838 False 778.0 778 83.986 1306 2143 1 chr6B.!!$F1 837
20 TraesCS1A01G206300 chr7B 720574722 720575558 836 True 713.0 713 82.818 1309 2143 1 chr7B.!!$R1 834

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
776 781 0.039617 CGGCGAACAATGGAAGCAAA 60.040 50.0 0.0 0.0 0.0 3.68 F
805 810 0.394938 ACGAACATACCACCACTGCA 59.605 50.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2651 2731 0.038892 TTGTACAACCTCCGAGACGC 60.039 55.0 3.59 0.0 0.0 5.19 R
2883 2970 1.029681 AAACGGCCAGAAAACTGACC 58.970 50.0 2.24 0.0 0.0 4.02 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
97 98 2.362077 CAAGTTGGACCACCTTTCTTGG 59.638 50.000 0.68 0.00 40.32 3.61
171 172 0.674895 GAGCCACTCTTCCGCACATT 60.675 55.000 0.00 0.00 0.00 2.71
212 213 2.095567 CACAATGGACGGAAAGCTTCAG 60.096 50.000 0.00 0.00 0.00 3.02
304 305 3.518590 GAAGACCATGGGTTAGTACACG 58.481 50.000 18.09 0.00 35.25 4.49
309 310 2.354303 CCATGGGTTAGTACACGAAGCA 60.354 50.000 2.85 0.00 31.97 3.91
317 318 6.349033 GGGTTAGTACACGAAGCAAAATTGAT 60.349 38.462 0.00 0.00 31.97 2.57
426 427 8.733458 TGACTTAATCTTGATCAACCTTGAATG 58.267 33.333 3.38 0.00 41.13 2.67
445 446 8.560576 TTGAATGTTTTCAATTCTCTTCGTTC 57.439 30.769 0.00 0.00 44.81 3.95
537 541 4.717877 ACACTCACATGACCAATCTTTGA 58.282 39.130 0.00 0.00 0.00 2.69
680 685 4.925054 AGATTGTCATCAATTGCCAAAACG 59.075 37.500 0.00 0.00 43.33 3.60
727 732 6.985188 TTTTAGATTGGAGTTTGGAGATCG 57.015 37.500 0.00 0.00 0.00 3.69
728 733 2.911484 AGATTGGAGTTTGGAGATCGC 58.089 47.619 0.00 0.00 0.00 4.58
729 734 2.503356 AGATTGGAGTTTGGAGATCGCT 59.497 45.455 0.00 0.00 0.00 4.93
730 735 3.706594 AGATTGGAGTTTGGAGATCGCTA 59.293 43.478 0.00 0.00 0.00 4.26
731 736 3.526931 TTGGAGTTTGGAGATCGCTAG 57.473 47.619 0.00 0.00 0.00 3.42
732 737 1.137086 TGGAGTTTGGAGATCGCTAGC 59.863 52.381 4.06 4.06 0.00 3.42
733 738 1.410882 GGAGTTTGGAGATCGCTAGCT 59.589 52.381 13.93 0.00 0.00 3.32
734 739 2.544903 GGAGTTTGGAGATCGCTAGCTC 60.545 54.545 13.93 4.36 37.42 4.09
735 740 2.360801 GAGTTTGGAGATCGCTAGCTCT 59.639 50.000 13.93 9.81 38.26 4.09
736 741 3.556999 AGTTTGGAGATCGCTAGCTCTA 58.443 45.455 13.93 0.00 38.26 2.43
737 742 3.954904 AGTTTGGAGATCGCTAGCTCTAA 59.045 43.478 13.93 4.79 36.90 2.10
738 743 3.992260 TTGGAGATCGCTAGCTCTAAC 57.008 47.619 13.93 7.10 38.26 2.34
739 744 1.874231 TGGAGATCGCTAGCTCTAACG 59.126 52.381 13.93 0.00 38.26 3.18
740 745 1.400500 GGAGATCGCTAGCTCTAACGC 60.400 57.143 13.93 1.81 38.26 4.84
741 746 1.264557 GAGATCGCTAGCTCTAACGCA 59.735 52.381 13.93 0.00 35.20 5.24
742 747 1.883275 AGATCGCTAGCTCTAACGCAT 59.117 47.619 13.93 0.00 0.00 4.73
743 748 1.982223 GATCGCTAGCTCTAACGCATG 59.018 52.381 13.93 0.00 0.00 4.06
744 749 1.021968 TCGCTAGCTCTAACGCATGA 58.978 50.000 13.93 0.00 0.00 3.07
745 750 1.404035 TCGCTAGCTCTAACGCATGAA 59.596 47.619 13.93 0.00 0.00 2.57
746 751 2.159296 TCGCTAGCTCTAACGCATGAAA 60.159 45.455 13.93 0.00 0.00 2.69
747 752 2.217393 CGCTAGCTCTAACGCATGAAAG 59.783 50.000 13.93 0.00 0.00 2.62
748 753 2.541762 GCTAGCTCTAACGCATGAAAGG 59.458 50.000 7.70 0.00 0.00 3.11
749 754 3.738281 GCTAGCTCTAACGCATGAAAGGA 60.738 47.826 7.70 0.00 0.00 3.36
750 755 3.550437 AGCTCTAACGCATGAAAGGAT 57.450 42.857 0.00 0.00 0.00 3.24
751 756 4.672587 AGCTCTAACGCATGAAAGGATA 57.327 40.909 0.00 0.00 0.00 2.59
752 757 4.626042 AGCTCTAACGCATGAAAGGATAG 58.374 43.478 0.00 0.00 0.00 2.08
753 758 4.342378 AGCTCTAACGCATGAAAGGATAGA 59.658 41.667 0.00 0.00 0.00 1.98
754 759 4.683781 GCTCTAACGCATGAAAGGATAGAG 59.316 45.833 0.00 9.61 38.46 2.43
755 760 5.201713 TCTAACGCATGAAAGGATAGAGG 57.798 43.478 0.00 0.00 0.00 3.69
756 761 4.893524 TCTAACGCATGAAAGGATAGAGGA 59.106 41.667 0.00 0.00 0.00 3.71
757 762 3.460857 ACGCATGAAAGGATAGAGGAC 57.539 47.619 0.00 0.00 0.00 3.85
758 763 2.223829 ACGCATGAAAGGATAGAGGACG 60.224 50.000 0.00 0.00 0.00 4.79
759 764 2.760374 GCATGAAAGGATAGAGGACGG 58.240 52.381 0.00 0.00 0.00 4.79
760 765 2.760374 CATGAAAGGATAGAGGACGGC 58.240 52.381 0.00 0.00 0.00 5.68
761 766 0.744874 TGAAAGGATAGAGGACGGCG 59.255 55.000 4.80 4.80 0.00 6.46
762 767 1.030457 GAAAGGATAGAGGACGGCGA 58.970 55.000 16.62 0.00 0.00 5.54
763 768 1.407979 GAAAGGATAGAGGACGGCGAA 59.592 52.381 16.62 0.00 0.00 4.70
764 769 0.745468 AAGGATAGAGGACGGCGAAC 59.255 55.000 16.62 5.56 0.00 3.95
765 770 0.395311 AGGATAGAGGACGGCGAACA 60.395 55.000 16.62 0.00 0.00 3.18
766 771 0.458669 GGATAGAGGACGGCGAACAA 59.541 55.000 16.62 0.00 0.00 2.83
767 772 1.068741 GGATAGAGGACGGCGAACAAT 59.931 52.381 16.62 0.00 0.00 2.71
768 773 2.128035 GATAGAGGACGGCGAACAATG 58.872 52.381 16.62 0.00 0.00 2.82
769 774 0.174845 TAGAGGACGGCGAACAATGG 59.825 55.000 16.62 0.00 0.00 3.16
770 775 1.079405 GAGGACGGCGAACAATGGA 60.079 57.895 16.62 0.00 0.00 3.41
771 776 0.672401 GAGGACGGCGAACAATGGAA 60.672 55.000 16.62 0.00 0.00 3.53
772 777 0.673644 AGGACGGCGAACAATGGAAG 60.674 55.000 16.62 0.00 0.00 3.46
773 778 1.134694 GACGGCGAACAATGGAAGC 59.865 57.895 16.62 0.00 0.00 3.86
774 779 1.573829 GACGGCGAACAATGGAAGCA 61.574 55.000 16.62 0.00 0.00 3.91
775 780 1.169661 ACGGCGAACAATGGAAGCAA 61.170 50.000 16.62 0.00 0.00 3.91
776 781 0.039617 CGGCGAACAATGGAAGCAAA 60.040 50.000 0.00 0.00 0.00 3.68
777 782 1.418373 GGCGAACAATGGAAGCAAAC 58.582 50.000 0.00 0.00 0.00 2.93
778 783 1.052287 GCGAACAATGGAAGCAAACG 58.948 50.000 0.00 0.00 0.00 3.60
779 784 1.334599 GCGAACAATGGAAGCAAACGA 60.335 47.619 0.00 0.00 0.00 3.85
780 785 2.307049 CGAACAATGGAAGCAAACGAC 58.693 47.619 0.00 0.00 0.00 4.34
781 786 2.307049 GAACAATGGAAGCAAACGACG 58.693 47.619 0.00 0.00 0.00 5.12
782 787 1.588674 ACAATGGAAGCAAACGACGA 58.411 45.000 0.00 0.00 0.00 4.20
783 788 1.263217 ACAATGGAAGCAAACGACGAC 59.737 47.619 0.00 0.00 0.00 4.34
784 789 1.531149 CAATGGAAGCAAACGACGACT 59.469 47.619 0.00 0.00 0.00 4.18
785 790 1.878953 ATGGAAGCAAACGACGACTT 58.121 45.000 0.00 0.00 0.00 3.01
786 791 2.512485 TGGAAGCAAACGACGACTTA 57.488 45.000 0.00 0.00 0.00 2.24
787 792 2.129607 TGGAAGCAAACGACGACTTAC 58.870 47.619 0.00 1.00 0.00 2.34
789 794 2.046313 GAAGCAAACGACGACTTACGA 58.954 47.619 0.00 0.00 45.77 3.43
790 795 2.124011 AGCAAACGACGACTTACGAA 57.876 45.000 0.00 0.00 45.77 3.85
791 796 1.783140 AGCAAACGACGACTTACGAAC 59.217 47.619 0.00 0.00 45.77 3.95
792 797 1.518102 GCAAACGACGACTTACGAACA 59.482 47.619 0.00 0.00 45.77 3.18
793 798 2.154389 GCAAACGACGACTTACGAACAT 59.846 45.455 0.00 0.00 45.77 2.71
794 799 3.361644 GCAAACGACGACTTACGAACATA 59.638 43.478 0.00 0.00 45.77 2.29
795 800 4.716514 GCAAACGACGACTTACGAACATAC 60.717 45.833 0.00 0.00 45.77 2.39
796 801 3.122937 ACGACGACTTACGAACATACC 57.877 47.619 0.00 0.00 45.77 2.73
797 802 2.483877 ACGACGACTTACGAACATACCA 59.516 45.455 0.00 0.00 45.77 3.25
798 803 2.842485 CGACGACTTACGAACATACCAC 59.158 50.000 0.00 0.00 45.77 4.16
799 804 3.174375 GACGACTTACGAACATACCACC 58.826 50.000 0.00 0.00 45.77 4.61
800 805 2.557924 ACGACTTACGAACATACCACCA 59.442 45.455 0.00 0.00 45.77 4.17
801 806 2.919229 CGACTTACGAACATACCACCAC 59.081 50.000 0.00 0.00 45.77 4.16
802 807 3.366679 CGACTTACGAACATACCACCACT 60.367 47.826 0.00 0.00 45.77 4.00
803 808 3.921677 ACTTACGAACATACCACCACTG 58.078 45.455 0.00 0.00 0.00 3.66
804 809 2.373540 TACGAACATACCACCACTGC 57.626 50.000 0.00 0.00 0.00 4.40
805 810 0.394938 ACGAACATACCACCACTGCA 59.605 50.000 0.00 0.00 0.00 4.41
806 811 1.202710 ACGAACATACCACCACTGCAA 60.203 47.619 0.00 0.00 0.00 4.08
807 812 2.083774 CGAACATACCACCACTGCAAT 58.916 47.619 0.00 0.00 0.00 3.56
808 813 3.266636 CGAACATACCACCACTGCAATA 58.733 45.455 0.00 0.00 0.00 1.90
809 814 3.309682 CGAACATACCACCACTGCAATAG 59.690 47.826 0.00 0.00 0.00 1.73
810 815 4.513442 GAACATACCACCACTGCAATAGA 58.487 43.478 0.00 0.00 0.00 1.98
811 816 3.873910 ACATACCACCACTGCAATAGAC 58.126 45.455 0.00 0.00 0.00 2.59
812 817 3.519510 ACATACCACCACTGCAATAGACT 59.480 43.478 0.00 0.00 0.00 3.24
813 818 2.479566 ACCACCACTGCAATAGACTG 57.520 50.000 0.00 0.00 0.00 3.51
814 819 1.699634 ACCACCACTGCAATAGACTGT 59.300 47.619 0.00 0.00 0.00 3.55
815 820 2.289694 ACCACCACTGCAATAGACTGTC 60.290 50.000 0.00 0.00 0.00 3.51
816 821 2.350522 CACCACTGCAATAGACTGTCC 58.649 52.381 3.76 0.00 0.00 4.02
817 822 1.279271 ACCACTGCAATAGACTGTCCC 59.721 52.381 3.76 0.00 0.00 4.46
818 823 1.556911 CCACTGCAATAGACTGTCCCT 59.443 52.381 3.76 0.00 0.00 4.20
819 824 2.026822 CCACTGCAATAGACTGTCCCTT 60.027 50.000 3.76 0.00 0.00 3.95
820 825 3.560025 CCACTGCAATAGACTGTCCCTTT 60.560 47.826 3.76 0.00 0.00 3.11
821 826 4.323485 CCACTGCAATAGACTGTCCCTTTA 60.323 45.833 3.76 0.00 0.00 1.85
822 827 4.872691 CACTGCAATAGACTGTCCCTTTAG 59.127 45.833 3.76 0.00 0.00 1.85
823 828 4.080863 ACTGCAATAGACTGTCCCTTTAGG 60.081 45.833 3.76 0.00 0.00 2.69
824 829 4.101114 TGCAATAGACTGTCCCTTTAGGA 58.899 43.478 3.76 0.00 44.91 2.94
837 842 5.281314 TCCCTTTAGGAGTAGAGATGCTTT 58.719 41.667 0.00 0.00 40.93 3.51
842 847 8.424918 CCTTTAGGAGTAGAGATGCTTTCAATA 58.575 37.037 0.00 0.00 37.39 1.90
846 851 6.609212 AGGAGTAGAGATGCTTTCAATACAGA 59.391 38.462 0.00 0.00 0.00 3.41
856 861 9.422196 GATGCTTTCAATACAGAATACGTAAAC 57.578 33.333 0.00 0.00 0.00 2.01
857 862 8.542497 TGCTTTCAATACAGAATACGTAAACT 57.458 30.769 0.00 0.00 0.00 2.66
859 864 9.897349 GCTTTCAATACAGAATACGTAAACTAC 57.103 33.333 0.00 0.00 0.00 2.73
869 875 3.182341 ACGTAAACTACTGTTGGCACA 57.818 42.857 0.00 0.00 36.39 4.57
878 884 3.757745 ACTGTTGGCACATAATTACGC 57.242 42.857 0.00 0.00 39.30 4.42
883 889 4.457603 TGTTGGCACATAATTACGCTTTCT 59.542 37.500 0.00 0.00 39.30 2.52
884 890 5.644206 TGTTGGCACATAATTACGCTTTCTA 59.356 36.000 0.00 0.00 39.30 2.10
893 899 2.689766 CGCTTTCTAGTGCGCGTC 59.310 61.111 8.43 0.00 45.50 5.19
902 908 4.135570 GTGCGCGTCACGTAACTA 57.864 55.556 15.77 0.00 46.11 2.24
934 942 0.966920 GTCAAACCCAGAGGACGAGA 59.033 55.000 0.00 0.00 36.73 4.04
942 950 1.748493 CCAGAGGACGAGAGGAAAGAG 59.252 57.143 0.00 0.00 0.00 2.85
1247 1261 1.614317 GCACCTACCTGCATCCAACTT 60.614 52.381 0.00 0.00 37.11 2.66
1399 1413 2.616330 CGCAAGTCAACCGGCATGT 61.616 57.895 0.00 0.00 0.00 3.21
1442 1457 6.983906 AATTCCCCAAATATTCATCTCACC 57.016 37.500 0.00 0.00 0.00 4.02
1466 1481 6.435430 TGTGGCAAACATTACATGATAGAC 57.565 37.500 0.00 0.00 32.36 2.59
1514 1529 0.675633 GATGGTGCAAAGCTTGTGGT 59.324 50.000 0.00 0.00 0.00 4.16
1614 1638 0.658897 AGTTCTCGCTAGCGCTCTAC 59.341 55.000 31.82 23.38 39.59 2.59
1907 1969 2.068519 TGCTGCTTGACGAATACAGTG 58.931 47.619 0.00 0.00 0.00 3.66
1930 1992 4.158394 GGTGCAAATGGTATCATGAGTGTT 59.842 41.667 0.09 0.00 33.18 3.32
2052 2132 1.417145 ACCTGGCATGTTTTTGCACAT 59.583 42.857 0.00 0.00 44.59 3.21
2070 2150 5.476254 TGCACATTAAAACATGATCTGTGGA 59.524 36.000 0.00 2.99 38.39 4.02
2154 2234 3.515602 AGCTCAAACATCCTGGTTTCT 57.484 42.857 0.00 0.00 38.86 2.52
2162 2242 4.286297 ACATCCTGGTTTCTCGATTGAA 57.714 40.909 0.00 0.00 0.00 2.69
2201 2281 5.696724 CACTCCATATATCGTTTGAGGTTCC 59.303 44.000 0.00 0.00 0.00 3.62
2214 2294 5.497464 TTGAGGTTCCTTGTGATATGTCA 57.503 39.130 0.00 0.00 0.00 3.58
2265 2345 6.399639 TGAGCATGTATTCTGTATAACGGA 57.600 37.500 0.00 0.00 0.00 4.69
2274 2354 7.652105 TGTATTCTGTATAACGGAGAAGCAATC 59.348 37.037 0.00 0.00 34.53 2.67
2307 2387 6.756542 AGTTTTGTTTTGCTCAATAGTTGGAC 59.243 34.615 0.00 0.00 0.00 4.02
2308 2388 6.463995 TTTGTTTTGCTCAATAGTTGGACT 57.536 33.333 0.00 0.00 0.00 3.85
2584 2664 7.653713 ACATAGTACTGTATCAGCTAATGCAAC 59.346 37.037 5.39 0.00 42.74 4.17
2883 2970 1.750778 ACAAAGAGTGGCTTGTGGTTG 59.249 47.619 0.00 0.00 36.80 3.77
2911 2998 0.878523 TCTGGCCGTTTTGACTCGTG 60.879 55.000 0.00 0.00 0.00 4.35
3051 3145 4.003648 GTGCCTTTGCTACTGAACATAGT 58.996 43.478 0.00 0.00 38.71 2.12
3053 3147 4.455533 TGCCTTTGCTACTGAACATAGTTG 59.544 41.667 0.00 0.00 38.71 3.16
3056 3150 5.882557 CCTTTGCTACTGAACATAGTTGGAT 59.117 40.000 0.00 0.00 32.19 3.41
3093 3187 1.468395 GCTGCTCCTCTGAAGACGTAC 60.468 57.143 0.00 0.00 0.00 3.67
3094 3188 2.088423 CTGCTCCTCTGAAGACGTACT 58.912 52.381 0.00 0.00 0.00 2.73
3095 3189 2.085320 TGCTCCTCTGAAGACGTACTC 58.915 52.381 0.00 0.00 0.00 2.59
3096 3190 1.062880 GCTCCTCTGAAGACGTACTCG 59.937 57.143 0.00 0.00 43.34 4.18
3138 3232 1.056660 GGGAGGAACTGAGTGGTCAA 58.943 55.000 0.00 0.00 41.55 3.18
3144 3238 2.630580 GGAACTGAGTGGTCAAGAGAGT 59.369 50.000 0.00 0.00 33.02 3.24
3156 3250 0.892063 AAGAGAGTTCGACTCCTGGC 59.108 55.000 10.24 0.00 46.18 4.85
3159 3253 0.605589 AGAGTTCGACTCCTGGCTTG 59.394 55.000 10.24 0.00 46.18 4.01
3164 3258 0.318441 TCGACTCCTGGCTTGTTCTG 59.682 55.000 0.00 0.00 0.00 3.02
3175 3269 3.625764 TGGCTTGTTCTGTTCTGTGTTAC 59.374 43.478 0.00 0.00 0.00 2.50
3176 3270 3.877508 GGCTTGTTCTGTTCTGTGTTACT 59.122 43.478 0.00 0.00 0.00 2.24
3177 3271 5.054477 GGCTTGTTCTGTTCTGTGTTACTA 58.946 41.667 0.00 0.00 0.00 1.82
3201 3295 9.241317 CTATTTTATTTCAGTTATGGCTTGCAG 57.759 33.333 0.00 0.00 0.00 4.41
3218 3312 3.540617 TGCAGACACTTGCTCTTGTTTA 58.459 40.909 0.00 0.00 44.38 2.01
3230 3324 4.093408 TGCTCTTGTTTATCTGCATCGTTC 59.907 41.667 0.00 0.00 0.00 3.95
3238 3332 6.017523 TGTTTATCTGCATCGTTCAGTTTCAA 60.018 34.615 0.00 0.00 33.48 2.69
3254 3348 3.699411 TTCAATTTGATTTGGGGCCTG 57.301 42.857 0.84 0.00 0.00 4.85
3268 3362 1.087771 GGCCTGGTCGACGTAATTGG 61.088 60.000 9.92 6.16 0.00 3.16
3290 3384 4.202020 GGGAACAAGTTGTGAAAGAGGAAC 60.202 45.833 9.79 0.00 0.00 3.62
3292 3386 2.943033 ACAAGTTGTGAAAGAGGAACGG 59.057 45.455 7.96 0.00 0.00 4.44
3415 3567 4.570772 TGCTCAAAGTGAACACTACTTGAC 59.429 41.667 14.23 12.32 41.58 3.18
3417 3569 5.001237 TCAAAGTGAACACTACTTGACGA 57.999 39.130 14.23 0.00 41.58 4.20
3426 3578 6.314152 TGAACACTACTTGACGAACAAATTCA 59.686 34.615 0.00 0.00 38.08 2.57
3440 3592 6.017440 CGAACAAATTCAACTACCAGAAAGGA 60.017 38.462 0.00 0.00 36.23 3.36
3443 3595 8.073467 ACAAATTCAACTACCAGAAAGGAAAA 57.927 30.769 0.00 0.00 41.22 2.29
3449 3601 8.561738 TCAACTACCAGAAAGGAAAATATGTC 57.438 34.615 0.00 0.00 41.22 3.06
3452 3604 9.533831 AACTACCAGAAAGGAAAATATGTCAAT 57.466 29.630 0.00 0.00 41.22 2.57
3469 3623 4.072131 GTCAATTAAACAGTGAGCTCCCA 58.928 43.478 12.15 0.00 27.51 4.37
3476 3630 2.047061 ACAGTGAGCTCCCAAACACTA 58.953 47.619 12.15 0.00 40.84 2.74
3477 3631 2.037772 ACAGTGAGCTCCCAAACACTAG 59.962 50.000 12.15 5.32 40.84 2.57
3501 3655 2.869233 TTTCAGAAGCAACTTGCCAC 57.131 45.000 10.25 5.08 46.52 5.01
3502 3656 1.032014 TTCAGAAGCAACTTGCCACC 58.968 50.000 10.25 0.35 46.52 4.61
3504 3658 0.313043 CAGAAGCAACTTGCCACCAG 59.687 55.000 10.25 0.00 46.52 4.00
3505 3659 1.006922 GAAGCAACTTGCCACCAGC 60.007 57.895 10.25 0.00 46.52 4.85
3507 3661 2.914097 GCAACTTGCCACCAGCCT 60.914 61.111 1.95 0.00 42.71 4.58
3508 3662 2.924105 GCAACTTGCCACCAGCCTC 61.924 63.158 1.95 0.00 42.71 4.70
3509 3663 1.529010 CAACTTGCCACCAGCCTCA 60.529 57.895 0.00 0.00 42.71 3.86
3510 3664 1.228367 AACTTGCCACCAGCCTCAG 60.228 57.895 0.00 0.00 42.71 3.35
3511 3665 3.060615 CTTGCCACCAGCCTCAGC 61.061 66.667 0.00 0.00 42.71 4.26
3512 3666 4.666253 TTGCCACCAGCCTCAGCC 62.666 66.667 0.00 0.00 42.71 4.85
3515 3669 4.729918 CCACCAGCCTCAGCCACC 62.730 72.222 0.00 0.00 41.25 4.61
3516 3670 3.957586 CACCAGCCTCAGCCACCA 61.958 66.667 0.00 0.00 41.25 4.17
3517 3671 3.177884 ACCAGCCTCAGCCACCAA 61.178 61.111 0.00 0.00 41.25 3.67
3531 3685 2.092914 GCCACCAACTCCTGCTACTATT 60.093 50.000 0.00 0.00 0.00 1.73
3566 3720 3.343788 CTCGCCAGACACCTCGTCC 62.344 68.421 0.00 0.00 46.69 4.79
3592 3746 6.239148 GCAGGAAAATCTTTTCTCAGGAAACT 60.239 38.462 13.46 0.00 44.49 2.66
3626 3780 4.452733 CTGGCGACGGGGACTTCC 62.453 72.222 0.00 0.00 0.00 3.46
3634 3788 2.108970 GACGGGGACTTCCATCTTACT 58.891 52.381 0.00 0.00 37.91 2.24
3643 3797 7.879957 GGACTTCCATCTTACTGAAGCCCAG 62.880 52.000 0.00 2.49 38.21 4.45
3654 3811 0.034670 GAAGCCCAGGTCAAGCTCAT 60.035 55.000 0.00 0.00 35.30 2.90
3656 3813 1.817099 GCCCAGGTCAAGCTCATCG 60.817 63.158 0.00 0.00 0.00 3.84
3703 3864 0.759346 AAGAACACCTTCCTGCGACT 59.241 50.000 0.00 0.00 0.00 4.18
3760 3921 0.944386 GCTGCTCGGAACTTTCAACA 59.056 50.000 0.00 0.00 0.00 3.33
3819 3981 1.528129 GCAACAAGACTTCCTCCTGG 58.472 55.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 3.746492 AGTCTTTATCGAGCCAACACAAC 59.254 43.478 0.00 0.00 0.00 3.32
171 172 3.317711 GTGGTGACAATGGACATGTGAAA 59.682 43.478 1.15 0.00 46.06 2.69
212 213 6.293516 GGAGCATCATGAAGAGATCAAATGTC 60.294 42.308 0.00 0.00 42.54 3.06
317 318 7.037370 AGTGATCCCATGGTATGATAAGCATTA 60.037 37.037 11.73 0.00 38.44 1.90
352 353 0.530744 AGCGCAGAAGATGTACCGAA 59.469 50.000 11.47 0.00 0.00 4.30
426 427 5.338614 TCCGAACGAAGAGAATTGAAAAC 57.661 39.130 0.00 0.00 0.00 2.43
442 443 2.159226 ACCTTCGAGACATCATCCGAAC 60.159 50.000 0.00 0.00 36.03 3.95
445 446 2.879026 TCTACCTTCGAGACATCATCCG 59.121 50.000 0.00 0.00 0.00 4.18
506 510 1.067142 TCATGTGAGTGTCGGGCTTAC 60.067 52.381 0.00 0.00 0.00 2.34
512 516 2.002586 GATTGGTCATGTGAGTGTCGG 58.997 52.381 0.00 0.00 0.00 4.79
537 541 6.443527 ACCAAGGTGCCATTTAAGGAATTATT 59.556 34.615 0.00 0.00 0.00 1.40
548 552 0.179004 TGTCGACCAAGGTGCCATTT 60.179 50.000 14.12 0.00 0.00 2.32
633 638 3.517296 TGGACTAATGGTTGCCTTGAA 57.483 42.857 0.00 0.00 0.00 2.69
680 685 1.203052 CATGTGGTGCCCTCATGTTTC 59.797 52.381 19.74 0.00 45.14 2.78
703 708 6.128007 GCGATCTCCAAACTCCAATCTAAAAA 60.128 38.462 0.00 0.00 0.00 1.94
707 712 3.706594 AGCGATCTCCAAACTCCAATCTA 59.293 43.478 0.00 0.00 0.00 1.98
710 715 3.742640 GCTAGCGATCTCCAAACTCCAAT 60.743 47.826 0.00 0.00 0.00 3.16
713 718 1.410882 AGCTAGCGATCTCCAAACTCC 59.589 52.381 9.55 0.00 0.00 3.85
719 724 1.874231 CGTTAGAGCTAGCGATCTCCA 59.126 52.381 9.55 0.00 41.31 3.86
721 726 1.264557 TGCGTTAGAGCTAGCGATCTC 59.735 52.381 16.19 0.81 41.31 2.75
722 727 1.309950 TGCGTTAGAGCTAGCGATCT 58.690 50.000 16.19 10.36 41.31 2.75
723 728 1.982223 CATGCGTTAGAGCTAGCGATC 59.018 52.381 16.19 2.04 41.31 3.69
724 729 1.609072 TCATGCGTTAGAGCTAGCGAT 59.391 47.619 16.19 4.41 41.31 4.58
725 730 1.021968 TCATGCGTTAGAGCTAGCGA 58.978 50.000 16.19 0.00 41.31 4.93
726 731 1.840181 TTCATGCGTTAGAGCTAGCG 58.160 50.000 9.55 9.04 41.63 4.26
727 732 2.541762 CCTTTCATGCGTTAGAGCTAGC 59.458 50.000 6.62 6.62 38.13 3.42
728 733 4.046938 TCCTTTCATGCGTTAGAGCTAG 57.953 45.455 0.00 0.00 38.13 3.42
729 734 4.672587 ATCCTTTCATGCGTTAGAGCTA 57.327 40.909 0.00 0.00 38.13 3.32
730 735 3.550437 ATCCTTTCATGCGTTAGAGCT 57.450 42.857 0.00 0.00 38.13 4.09
731 736 4.621991 TCTATCCTTTCATGCGTTAGAGC 58.378 43.478 0.00 0.00 37.71 4.09
732 737 5.010112 TCCTCTATCCTTTCATGCGTTAGAG 59.990 44.000 2.75 2.75 33.92 2.43
733 738 4.893524 TCCTCTATCCTTTCATGCGTTAGA 59.106 41.667 0.00 0.00 0.00 2.10
734 739 4.985409 GTCCTCTATCCTTTCATGCGTTAG 59.015 45.833 0.00 0.00 0.00 2.34
735 740 4.499188 CGTCCTCTATCCTTTCATGCGTTA 60.499 45.833 0.00 0.00 0.00 3.18
736 741 3.738281 CGTCCTCTATCCTTTCATGCGTT 60.738 47.826 0.00 0.00 0.00 4.84
737 742 2.223829 CGTCCTCTATCCTTTCATGCGT 60.224 50.000 0.00 0.00 0.00 5.24
738 743 2.398498 CGTCCTCTATCCTTTCATGCG 58.602 52.381 0.00 0.00 0.00 4.73
739 744 2.760374 CCGTCCTCTATCCTTTCATGC 58.240 52.381 0.00 0.00 0.00 4.06
740 745 2.760374 GCCGTCCTCTATCCTTTCATG 58.240 52.381 0.00 0.00 0.00 3.07
741 746 1.341531 CGCCGTCCTCTATCCTTTCAT 59.658 52.381 0.00 0.00 0.00 2.57
742 747 0.744874 CGCCGTCCTCTATCCTTTCA 59.255 55.000 0.00 0.00 0.00 2.69
743 748 1.030457 TCGCCGTCCTCTATCCTTTC 58.970 55.000 0.00 0.00 0.00 2.62
744 749 1.136500 GTTCGCCGTCCTCTATCCTTT 59.864 52.381 0.00 0.00 0.00 3.11
745 750 0.745468 GTTCGCCGTCCTCTATCCTT 59.255 55.000 0.00 0.00 0.00 3.36
746 751 0.395311 TGTTCGCCGTCCTCTATCCT 60.395 55.000 0.00 0.00 0.00 3.24
747 752 0.458669 TTGTTCGCCGTCCTCTATCC 59.541 55.000 0.00 0.00 0.00 2.59
748 753 2.128035 CATTGTTCGCCGTCCTCTATC 58.872 52.381 0.00 0.00 0.00 2.08
749 754 1.202533 CCATTGTTCGCCGTCCTCTAT 60.203 52.381 0.00 0.00 0.00 1.98
750 755 0.174845 CCATTGTTCGCCGTCCTCTA 59.825 55.000 0.00 0.00 0.00 2.43
751 756 1.079127 CCATTGTTCGCCGTCCTCT 60.079 57.895 0.00 0.00 0.00 3.69
752 757 0.672401 TTCCATTGTTCGCCGTCCTC 60.672 55.000 0.00 0.00 0.00 3.71
753 758 0.673644 CTTCCATTGTTCGCCGTCCT 60.674 55.000 0.00 0.00 0.00 3.85
754 759 1.794222 CTTCCATTGTTCGCCGTCC 59.206 57.895 0.00 0.00 0.00 4.79
755 760 1.134694 GCTTCCATTGTTCGCCGTC 59.865 57.895 0.00 0.00 0.00 4.79
756 761 1.169661 TTGCTTCCATTGTTCGCCGT 61.170 50.000 0.00 0.00 0.00 5.68
757 762 0.039617 TTTGCTTCCATTGTTCGCCG 60.040 50.000 0.00 0.00 0.00 6.46
758 763 1.418373 GTTTGCTTCCATTGTTCGCC 58.582 50.000 0.00 0.00 0.00 5.54
759 764 1.052287 CGTTTGCTTCCATTGTTCGC 58.948 50.000 0.00 0.00 0.00 4.70
760 765 2.307049 GTCGTTTGCTTCCATTGTTCG 58.693 47.619 0.00 0.00 0.00 3.95
761 766 2.032377 TCGTCGTTTGCTTCCATTGTTC 60.032 45.455 0.00 0.00 0.00 3.18
762 767 1.944024 TCGTCGTTTGCTTCCATTGTT 59.056 42.857 0.00 0.00 0.00 2.83
763 768 1.263217 GTCGTCGTTTGCTTCCATTGT 59.737 47.619 0.00 0.00 0.00 2.71
764 769 1.531149 AGTCGTCGTTTGCTTCCATTG 59.469 47.619 0.00 0.00 0.00 2.82
765 770 1.878953 AGTCGTCGTTTGCTTCCATT 58.121 45.000 0.00 0.00 0.00 3.16
766 771 1.878953 AAGTCGTCGTTTGCTTCCAT 58.121 45.000 0.00 0.00 0.00 3.41
767 772 2.129607 GTAAGTCGTCGTTTGCTTCCA 58.870 47.619 0.00 0.00 0.00 3.53
768 773 1.123756 CGTAAGTCGTCGTTTGCTTCC 59.876 52.381 0.00 0.00 34.52 3.46
769 774 2.046313 TCGTAAGTCGTCGTTTGCTTC 58.954 47.619 0.00 0.00 40.80 3.86
770 775 2.124011 TCGTAAGTCGTCGTTTGCTT 57.876 45.000 0.00 0.00 40.80 3.91
771 776 1.783140 GTTCGTAAGTCGTCGTTTGCT 59.217 47.619 0.00 0.00 40.80 3.91
772 777 1.518102 TGTTCGTAAGTCGTCGTTTGC 59.482 47.619 0.00 0.00 40.80 3.68
773 778 4.201428 GGTATGTTCGTAAGTCGTCGTTTG 60.201 45.833 0.00 0.00 40.80 2.93
774 779 3.914364 GGTATGTTCGTAAGTCGTCGTTT 59.086 43.478 0.00 0.00 40.80 3.60
775 780 3.058293 TGGTATGTTCGTAAGTCGTCGTT 60.058 43.478 0.00 0.00 40.80 3.85
776 781 2.483877 TGGTATGTTCGTAAGTCGTCGT 59.516 45.455 0.00 0.00 40.80 4.34
777 782 2.842485 GTGGTATGTTCGTAAGTCGTCG 59.158 50.000 0.00 0.00 40.80 5.12
778 783 3.174375 GGTGGTATGTTCGTAAGTCGTC 58.826 50.000 0.00 0.00 40.80 4.20
779 784 2.557924 TGGTGGTATGTTCGTAAGTCGT 59.442 45.455 0.00 0.00 40.80 4.34
780 785 2.919229 GTGGTGGTATGTTCGTAAGTCG 59.081 50.000 0.00 0.00 41.41 4.18
781 786 3.924686 CAGTGGTGGTATGTTCGTAAGTC 59.075 47.826 0.00 0.00 39.48 3.01
782 787 3.863400 GCAGTGGTGGTATGTTCGTAAGT 60.863 47.826 0.00 0.00 39.48 2.24
783 788 2.671396 GCAGTGGTGGTATGTTCGTAAG 59.329 50.000 0.00 0.00 0.00 2.34
784 789 2.037381 TGCAGTGGTGGTATGTTCGTAA 59.963 45.455 0.00 0.00 0.00 3.18
785 790 1.619332 TGCAGTGGTGGTATGTTCGTA 59.381 47.619 0.00 0.00 0.00 3.43
786 791 0.394938 TGCAGTGGTGGTATGTTCGT 59.605 50.000 0.00 0.00 0.00 3.85
787 792 1.518325 TTGCAGTGGTGGTATGTTCG 58.482 50.000 0.00 0.00 0.00 3.95
788 793 4.332819 GTCTATTGCAGTGGTGGTATGTTC 59.667 45.833 0.00 0.00 0.00 3.18
789 794 4.019321 AGTCTATTGCAGTGGTGGTATGTT 60.019 41.667 0.00 0.00 0.00 2.71
790 795 3.519510 AGTCTATTGCAGTGGTGGTATGT 59.480 43.478 0.00 0.00 0.00 2.29
791 796 3.873361 CAGTCTATTGCAGTGGTGGTATG 59.127 47.826 0.00 0.00 0.00 2.39
792 797 3.519510 ACAGTCTATTGCAGTGGTGGTAT 59.480 43.478 0.00 0.00 0.00 2.73
793 798 2.903784 ACAGTCTATTGCAGTGGTGGTA 59.096 45.455 0.00 0.00 0.00 3.25
794 799 1.699634 ACAGTCTATTGCAGTGGTGGT 59.300 47.619 0.00 0.00 0.00 4.16
795 800 2.350522 GACAGTCTATTGCAGTGGTGG 58.649 52.381 0.00 0.00 0.00 4.61
796 801 2.350522 GGACAGTCTATTGCAGTGGTG 58.649 52.381 0.00 0.00 0.00 4.17
797 802 1.279271 GGGACAGTCTATTGCAGTGGT 59.721 52.381 0.00 0.00 0.00 4.16
798 803 1.556911 AGGGACAGTCTATTGCAGTGG 59.443 52.381 0.00 0.00 0.00 4.00
799 804 3.340814 AAGGGACAGTCTATTGCAGTG 57.659 47.619 0.00 0.00 0.00 3.66
800 805 4.080863 CCTAAAGGGACAGTCTATTGCAGT 60.081 45.833 0.00 0.00 37.23 4.40
801 806 4.162320 TCCTAAAGGGACAGTCTATTGCAG 59.838 45.833 0.00 0.00 39.58 4.41
802 807 4.101114 TCCTAAAGGGACAGTCTATTGCA 58.899 43.478 0.00 0.00 39.58 4.08
803 808 4.162509 ACTCCTAAAGGGACAGTCTATTGC 59.837 45.833 0.00 0.00 39.58 3.56
804 809 5.941555 ACTCCTAAAGGGACAGTCTATTG 57.058 43.478 0.00 0.00 39.58 1.90
805 810 6.982899 TCTACTCCTAAAGGGACAGTCTATT 58.017 40.000 0.00 0.00 39.58 1.73
806 811 6.390461 TCTCTACTCCTAAAGGGACAGTCTAT 59.610 42.308 0.00 0.00 39.58 1.98
807 812 5.730207 TCTCTACTCCTAAAGGGACAGTCTA 59.270 44.000 0.00 0.00 39.58 2.59
808 813 4.540906 TCTCTACTCCTAAAGGGACAGTCT 59.459 45.833 0.00 0.00 39.58 3.24
809 814 4.857679 TCTCTACTCCTAAAGGGACAGTC 58.142 47.826 0.00 0.00 39.58 3.51
810 815 4.949966 TCTCTACTCCTAAAGGGACAGT 57.050 45.455 0.00 0.00 39.58 3.55
811 816 4.038642 GCATCTCTACTCCTAAAGGGACAG 59.961 50.000 0.00 0.00 39.58 3.51
812 817 3.961408 GCATCTCTACTCCTAAAGGGACA 59.039 47.826 0.00 0.00 39.58 4.02
813 818 4.219919 AGCATCTCTACTCCTAAAGGGAC 58.780 47.826 0.00 0.00 39.58 4.46
814 819 4.544564 AGCATCTCTACTCCTAAAGGGA 57.455 45.455 0.00 0.00 42.77 4.20
815 820 5.129485 TGAAAGCATCTCTACTCCTAAAGGG 59.871 44.000 0.00 0.00 35.41 3.95
816 821 6.227298 TGAAAGCATCTCTACTCCTAAAGG 57.773 41.667 0.00 0.00 0.00 3.11
817 822 9.255304 GTATTGAAAGCATCTCTACTCCTAAAG 57.745 37.037 0.00 0.00 0.00 1.85
818 823 8.758829 TGTATTGAAAGCATCTCTACTCCTAAA 58.241 33.333 0.00 0.00 0.00 1.85
819 824 8.306313 TGTATTGAAAGCATCTCTACTCCTAA 57.694 34.615 0.00 0.00 0.00 2.69
820 825 7.780271 TCTGTATTGAAAGCATCTCTACTCCTA 59.220 37.037 0.00 0.00 0.00 2.94
821 826 6.609212 TCTGTATTGAAAGCATCTCTACTCCT 59.391 38.462 0.00 0.00 0.00 3.69
822 827 6.810911 TCTGTATTGAAAGCATCTCTACTCC 58.189 40.000 0.00 0.00 0.00 3.85
823 828 8.885494 ATTCTGTATTGAAAGCATCTCTACTC 57.115 34.615 0.00 0.00 0.00 2.59
824 829 9.757227 GTATTCTGTATTGAAAGCATCTCTACT 57.243 33.333 0.00 0.00 0.00 2.57
825 830 8.695284 CGTATTCTGTATTGAAAGCATCTCTAC 58.305 37.037 0.00 0.00 0.00 2.59
826 831 8.414003 ACGTATTCTGTATTGAAAGCATCTCTA 58.586 33.333 0.00 0.00 0.00 2.43
827 832 7.268586 ACGTATTCTGTATTGAAAGCATCTCT 58.731 34.615 0.00 0.00 0.00 3.10
828 833 7.470289 ACGTATTCTGTATTGAAAGCATCTC 57.530 36.000 0.00 0.00 0.00 2.75
829 834 8.942338 TTACGTATTCTGTATTGAAAGCATCT 57.058 30.769 0.00 0.00 0.00 2.90
830 835 9.422196 GTTTACGTATTCTGTATTGAAAGCATC 57.578 33.333 0.00 0.00 0.00 3.91
842 847 5.636543 GCCAACAGTAGTTTACGTATTCTGT 59.363 40.000 0.00 0.00 35.28 3.41
846 851 5.299148 TGTGCCAACAGTAGTTTACGTATT 58.701 37.500 0.00 0.00 35.28 1.89
856 861 4.570772 AGCGTAATTATGTGCCAACAGTAG 59.429 41.667 6.55 0.00 40.39 2.57
857 862 4.509616 AGCGTAATTATGTGCCAACAGTA 58.490 39.130 6.55 0.00 40.39 2.74
859 864 4.355543 AAGCGTAATTATGTGCCAACAG 57.644 40.909 6.55 0.00 40.39 3.16
860 865 4.457603 AGAAAGCGTAATTATGTGCCAACA 59.542 37.500 6.55 0.00 41.58 3.33
861 866 4.981794 AGAAAGCGTAATTATGTGCCAAC 58.018 39.130 6.55 0.00 0.00 3.77
862 867 5.878116 ACTAGAAAGCGTAATTATGTGCCAA 59.122 36.000 6.55 0.00 0.00 4.52
878 884 1.002250 ACGTGACGCGCACTAGAAAG 61.002 55.000 24.04 13.86 45.49 2.62
883 889 0.795698 TAGTTACGTGACGCGCACTA 59.204 50.000 24.04 11.99 45.49 2.74
884 890 0.169672 ATAGTTACGTGACGCGCACT 59.830 50.000 24.04 15.71 45.49 4.40
889 895 2.091588 CCACAACATAGTTACGTGACGC 59.908 50.000 4.25 0.00 0.00 5.19
893 899 3.567530 TCGACCACAACATAGTTACGTG 58.432 45.455 0.00 0.00 0.00 4.49
902 908 2.218603 GGTTTGACTCGACCACAACAT 58.781 47.619 0.00 0.00 35.95 2.71
934 942 4.083862 GGGCGCCGTCTCTTTCCT 62.084 66.667 22.54 0.00 0.00 3.36
954 968 4.824515 AGCGGAGGAGTCGGAGGG 62.825 72.222 0.00 0.00 0.00 4.30
961 975 3.126225 GACGACGAGCGGAGGAGT 61.126 66.667 0.00 0.00 46.49 3.85
1247 1261 4.713553 TGGAGAATCTTTGTGTTAGCACA 58.286 39.130 8.48 8.48 44.28 4.57
1399 1413 2.776526 AAGTGGGCAGGTGGGTGA 60.777 61.111 0.00 0.00 0.00 4.02
1442 1457 6.093909 TGTCTATCATGTAATGTTTGCCACAG 59.906 38.462 0.00 0.00 46.80 3.66
1466 1481 2.671396 GAGCAAAGCAAAGATGGCATTG 59.329 45.455 0.00 0.00 41.44 2.82
1614 1638 1.600663 CGTGCAGTCCTATAAGCTCCG 60.601 57.143 0.00 0.00 0.00 4.63
1764 1808 6.917477 TGACATTTGTTCTTGTTCTGCATAAC 59.083 34.615 7.96 7.96 0.00 1.89
1876 1933 1.471287 TCAAGCAGCAGCAATAGCAAG 59.529 47.619 3.17 0.00 45.49 4.01
1907 1969 3.696051 ACACTCATGATACCATTTGCACC 59.304 43.478 0.00 0.00 0.00 5.01
1930 1992 6.233434 AGAAAATACACAGATTCAGTGAGCA 58.767 36.000 15.22 1.79 40.16 4.26
1944 2006 9.659830 ATTCGACAGTTTAACAAGAAAATACAC 57.340 29.630 0.00 0.00 0.00 2.90
1994 2063 3.915437 AACCTTGTACAATGGAAAGCG 57.085 42.857 22.90 5.86 0.00 4.68
2052 2132 8.859090 AGTGAATTTCCACAGATCATGTTTTAA 58.141 29.630 0.00 0.00 41.41 1.52
2070 2150 8.487313 TGTAAGCATTCGTATACAGTGAATTT 57.513 30.769 3.32 0.37 30.23 1.82
2103 2183 5.956068 AGCTTTTGAGAGAAAGAATGGAC 57.044 39.130 1.82 0.00 38.60 4.02
2154 2234 5.471797 TGCTTATCAAAACTGGTTCAATCGA 59.528 36.000 0.00 0.00 0.00 3.59
2162 2242 4.098914 TGGAGTGCTTATCAAAACTGGT 57.901 40.909 0.00 0.00 0.00 4.00
2201 2281 6.557110 TCACATGCAAATGACATATCACAAG 58.443 36.000 0.00 0.00 37.79 3.16
2214 2294 6.015688 ACTCTGAAGAAACATCACATGCAAAT 60.016 34.615 0.00 0.00 0.00 2.32
2265 2345 4.373156 AAACTACACAGGGATTGCTTCT 57.627 40.909 0.00 0.00 0.00 2.85
2274 2354 4.142271 TGAGCAAAACAAAACTACACAGGG 60.142 41.667 0.00 0.00 0.00 4.45
2307 2387 5.139727 TCCCAGCAATTTACATTCCCATAG 58.860 41.667 0.00 0.00 0.00 2.23
2308 2388 5.136068 TCCCAGCAATTTACATTCCCATA 57.864 39.130 0.00 0.00 0.00 2.74
2439 2519 2.975489 AGACACACTTGGAACCTGATCT 59.025 45.455 0.00 0.00 0.00 2.75
2651 2731 0.038892 TTGTACAACCTCCGAGACGC 60.039 55.000 3.59 0.00 0.00 5.19
2883 2970 1.029681 AAACGGCCAGAAAACTGACC 58.970 50.000 2.24 0.00 0.00 4.02
2898 2985 0.381428 GTGCGACACGAGTCAAAACG 60.381 55.000 13.46 0.41 45.23 3.60
2911 2998 3.243068 ACTTTCATTTCCACAAGTGCGAC 60.243 43.478 0.00 0.00 0.00 5.19
3035 3129 6.048732 TCATCCAACTATGTTCAGTAGCAA 57.951 37.500 0.00 0.00 0.00 3.91
3051 3145 1.642112 TTGGCCTTTGCATCATCCAA 58.358 45.000 3.32 6.84 40.13 3.53
3053 3147 2.557317 CATTTGGCCTTTGCATCATCC 58.443 47.619 3.32 0.00 40.13 3.51
3056 3150 0.978151 AGCATTTGGCCTTTGCATCA 59.022 45.000 21.67 0.00 46.50 3.07
3093 3187 5.730296 ACATGGATTCTATTCCCTACGAG 57.270 43.478 0.00 0.00 34.67 4.18
3094 3188 7.611770 CAATACATGGATTCTATTCCCTACGA 58.388 38.462 0.00 0.00 34.67 3.43
3095 3189 7.834068 CAATACATGGATTCTATTCCCTACG 57.166 40.000 0.00 0.00 34.67 3.51
3138 3232 0.039035 AGCCAGGAGTCGAACTCTCT 59.961 55.000 12.62 7.26 44.46 3.10
3144 3238 1.048601 AGAACAAGCCAGGAGTCGAA 58.951 50.000 0.00 0.00 0.00 3.71
3175 3269 9.241317 CTGCAAGCCATAACTGAAATAAAATAG 57.759 33.333 0.00 0.00 0.00 1.73
3176 3270 8.965819 TCTGCAAGCCATAACTGAAATAAAATA 58.034 29.630 0.00 0.00 0.00 1.40
3177 3271 7.761249 GTCTGCAAGCCATAACTGAAATAAAAT 59.239 33.333 0.00 0.00 0.00 1.82
3201 3295 4.214119 TGCAGATAAACAAGAGCAAGTGTC 59.786 41.667 0.00 0.00 0.00 3.67
3218 3312 5.633830 AATTGAAACTGAACGATGCAGAT 57.366 34.783 10.04 0.00 36.86 2.90
3230 3324 3.752747 GGCCCCAAATCAAATTGAAACTG 59.247 43.478 0.00 0.00 31.84 3.16
3238 3332 1.571955 GACCAGGCCCCAAATCAAAT 58.428 50.000 0.00 0.00 0.00 2.32
3254 3348 2.083167 TGTTCCCAATTACGTCGACC 57.917 50.000 10.58 0.00 0.00 4.79
3268 3362 4.495844 CGTTCCTCTTTCACAACTTGTTCC 60.496 45.833 0.00 0.00 0.00 3.62
3290 3384 3.304257 TCGAAATTGATGCACAAAACCG 58.696 40.909 5.94 8.79 42.03 4.44
3292 3386 5.610975 CCAATCGAAATTGATGCACAAAAC 58.389 37.500 0.26 1.69 44.25 2.43
3325 3419 5.509972 CGAACTGAAAACGACACAAATTCAA 59.490 36.000 0.00 0.00 30.37 2.69
3405 3557 6.715464 AGTTGAATTTGTTCGTCAAGTAGTG 58.285 36.000 0.00 0.00 37.35 2.74
3406 3558 6.920569 AGTTGAATTTGTTCGTCAAGTAGT 57.079 33.333 0.00 0.00 37.35 2.73
3408 3560 6.762187 TGGTAGTTGAATTTGTTCGTCAAGTA 59.238 34.615 0.00 0.00 37.35 2.24
3415 3567 6.017440 TCCTTTCTGGTAGTTGAATTTGTTCG 60.017 38.462 0.00 0.00 37.07 3.95
3417 3569 7.654022 TTCCTTTCTGGTAGTTGAATTTGTT 57.346 32.000 0.00 0.00 37.07 2.83
3426 3578 8.934023 TTGACATATTTTCCTTTCTGGTAGTT 57.066 30.769 0.00 0.00 37.07 2.24
3440 3592 9.846248 GAGCTCACTGTTTAATTGACATATTTT 57.154 29.630 9.40 0.00 0.00 1.82
3443 3595 6.543831 GGGAGCTCACTGTTTAATTGACATAT 59.456 38.462 17.19 0.00 0.00 1.78
3449 3601 5.221224 TGTTTGGGAGCTCACTGTTTAATTG 60.221 40.000 18.70 0.00 0.00 2.32
3452 3604 3.630312 GTGTTTGGGAGCTCACTGTTTAA 59.370 43.478 18.70 0.00 0.00 1.52
3469 3623 3.507622 GCTTCTGAAATGGCCTAGTGTTT 59.492 43.478 3.32 0.00 0.00 2.83
3476 3630 2.298163 CAAGTTGCTTCTGAAATGGCCT 59.702 45.455 3.32 0.00 0.00 5.19
3477 3631 2.680577 CAAGTTGCTTCTGAAATGGCC 58.319 47.619 0.00 0.00 0.00 5.36
3501 3655 2.674380 GTTGGTGGCTGAGGCTGG 60.674 66.667 7.74 0.00 38.73 4.85
3502 3656 1.673665 GAGTTGGTGGCTGAGGCTG 60.674 63.158 7.74 0.00 38.73 4.85
3504 3658 2.360475 GGAGTTGGTGGCTGAGGC 60.360 66.667 0.00 0.00 37.82 4.70
3505 3659 1.002868 CAGGAGTTGGTGGCTGAGG 60.003 63.158 0.00 0.00 0.00 3.86
3507 3661 0.835971 TAGCAGGAGTTGGTGGCTGA 60.836 55.000 0.00 0.00 38.18 4.26
3508 3662 0.674895 GTAGCAGGAGTTGGTGGCTG 60.675 60.000 0.00 0.00 38.18 4.85
3509 3663 0.838122 AGTAGCAGGAGTTGGTGGCT 60.838 55.000 0.00 0.00 38.18 4.75
3510 3664 0.902531 TAGTAGCAGGAGTTGGTGGC 59.097 55.000 0.00 0.00 38.18 5.01
3511 3665 3.197766 TGAATAGTAGCAGGAGTTGGTGG 59.802 47.826 0.00 0.00 38.18 4.61
3512 3666 4.081420 ACTGAATAGTAGCAGGAGTTGGTG 60.081 45.833 7.49 0.00 38.18 4.17
3513 3667 4.081420 CACTGAATAGTAGCAGGAGTTGGT 60.081 45.833 7.49 0.00 41.25 3.67
3514 3668 4.437239 CACTGAATAGTAGCAGGAGTTGG 58.563 47.826 7.49 0.00 34.74 3.77
3515 3669 3.868077 GCACTGAATAGTAGCAGGAGTTG 59.132 47.826 7.49 0.00 34.74 3.16
3516 3670 3.772025 AGCACTGAATAGTAGCAGGAGTT 59.228 43.478 7.49 0.00 34.74 3.01
3517 3671 3.131933 CAGCACTGAATAGTAGCAGGAGT 59.868 47.826 7.49 0.00 34.74 3.85
3556 3710 2.035237 TTTTCCTGCGGACGAGGTGT 62.035 55.000 0.00 0.00 31.85 4.16
3566 3720 3.753272 TCCTGAGAAAAGATTTTCCTGCG 59.247 43.478 13.12 1.83 45.84 5.18
3592 3746 0.395862 CAGGTCGCTCTTCCTCCCTA 60.396 60.000 0.00 0.00 30.91 3.53
3619 3773 3.536570 GGCTTCAGTAAGATGGAAGTCC 58.463 50.000 0.00 0.00 40.06 3.85
3626 3780 2.237143 TGACCTGGGCTTCAGTAAGATG 59.763 50.000 0.00 0.00 41.83 2.90
3634 3788 1.376466 GAGCTTGACCTGGGCTTCA 59.624 57.895 0.00 0.00 36.37 3.02
3654 3811 2.898840 CGCCGGTAGGAGCTACGA 60.899 66.667 1.90 0.00 41.02 3.43
3656 3813 2.720605 GACGCCGGTAGGAGCTAC 59.279 66.667 1.90 0.00 41.37 3.58
3760 3921 1.956170 CTCACGCCGTGCTGTTTCT 60.956 57.895 13.39 0.00 32.98 2.52


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

AutoCloner maintained by Alex Coulton.