Multiple sequence alignment - TraesCS5A01G069300

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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 TraesCS5A01G069300 chr5A 100.000 3648 0 0 1 3648 77798712 77795065 0.000000e+00 6737.0
1 TraesCS5A01G069300 chr5A 83.099 142 18 3 2500 2641 24796721 24796586 1.380000e-24 124.0
2 TraesCS5A01G069300 chr5A 79.870 154 29 2 2429 2580 35035904 35035751 1.070000e-20 111.0
3 TraesCS5A01G069300 chr5D 93.212 1871 92 9 1047 2917 82080029 82078194 0.000000e+00 2719.0
4 TraesCS5A01G069300 chr5D 85.771 759 105 3 2 759 303708284 303709040 0.000000e+00 800.0
5 TraesCS5A01G069300 chr5D 79.870 154 29 2 2429 2580 44609448 44609295 1.070000e-20 111.0
6 TraesCS5A01G069300 chr4A 98.765 729 9 0 2920 3648 537195328 537194600 0.000000e+00 1297.0
7 TraesCS5A01G069300 chr6B 98.628 729 10 0 2920 3648 58830306 58829578 0.000000e+00 1291.0
8 TraesCS5A01G069300 chr6B 95.728 749 30 2 1 747 610844923 610844175 0.000000e+00 1205.0
9 TraesCS5A01G069300 chr6A 98.628 729 10 0 2920 3648 84702677 84703405 0.000000e+00 1291.0
10 TraesCS5A01G069300 chr6A 89.005 764 84 0 1 764 393531256 393530493 0.000000e+00 946.0
11 TraesCS5A01G069300 chr6A 88.451 762 88 0 1 762 431591595 431592356 0.000000e+00 920.0
12 TraesCS5A01G069300 chr5B 98.628 729 10 0 2920 3648 4863581 4864309 0.000000e+00 1291.0
13 TraesCS5A01G069300 chr5B 98.628 729 10 0 2920 3648 48315464 48316192 0.000000e+00 1291.0
14 TraesCS5A01G069300 chr5B 93.665 663 42 0 1 663 580669467 580668805 0.000000e+00 992.0
15 TraesCS5A01G069300 chr5B 89.556 766 76 2 1 762 665689058 665689823 0.000000e+00 968.0
16 TraesCS5A01G069300 chr5B 72.145 578 120 26 2081 2641 26936489 26935936 1.770000e-28 137.0
17 TraesCS5A01G069300 chr3D 98.628 729 10 0 2920 3648 413766901 413766173 0.000000e+00 1291.0
18 TraesCS5A01G069300 chr1A 98.628 729 10 0 2920 3648 222362549 222361821 0.000000e+00 1291.0
19 TraesCS5A01G069300 chr1A 98.628 729 10 0 2920 3648 306638338 306639066 0.000000e+00 1291.0
20 TraesCS5A01G069300 chr1A 98.628 729 10 0 2920 3648 517045969 517045241 0.000000e+00 1291.0
21 TraesCS5A01G069300 chr4B 94.634 764 41 0 1 764 429677855 429677092 0.000000e+00 1184.0
22 TraesCS5A01G069300 chr2B 90.052 764 76 0 1 764 58891454 58890691 0.000000e+00 990.0
23 TraesCS5A01G069300 chr2B 91.304 46 2 2 1897 1941 198354481 198354437 1.090000e-05 62.1
24 TraesCS5A01G069300 chr7D 90.552 688 65 0 1 688 42179207 42178520 0.000000e+00 911.0
25 TraesCS5A01G069300 chr6D 100.000 29 0 0 1913 1941 193071732 193071760 2.000000e-03 54.7


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 TraesCS5A01G069300 chr5A 77795065 77798712 3647 True 6737 6737 100.000 1 3648 1 chr5A.!!$R3 3647
1 TraesCS5A01G069300 chr5D 82078194 82080029 1835 True 2719 2719 93.212 1047 2917 1 chr5D.!!$R2 1870
2 TraesCS5A01G069300 chr5D 303708284 303709040 756 False 800 800 85.771 2 759 1 chr5D.!!$F1 757
3 TraesCS5A01G069300 chr4A 537194600 537195328 728 True 1297 1297 98.765 2920 3648 1 chr4A.!!$R1 728
4 TraesCS5A01G069300 chr6B 58829578 58830306 728 True 1291 1291 98.628 2920 3648 1 chr6B.!!$R1 728
5 TraesCS5A01G069300 chr6B 610844175 610844923 748 True 1205 1205 95.728 1 747 1 chr6B.!!$R2 746
6 TraesCS5A01G069300 chr6A 84702677 84703405 728 False 1291 1291 98.628 2920 3648 1 chr6A.!!$F1 728
7 TraesCS5A01G069300 chr6A 393530493 393531256 763 True 946 946 89.005 1 764 1 chr6A.!!$R1 763
8 TraesCS5A01G069300 chr6A 431591595 431592356 761 False 920 920 88.451 1 762 1 chr6A.!!$F2 761
9 TraesCS5A01G069300 chr5B 4863581 4864309 728 False 1291 1291 98.628 2920 3648 1 chr5B.!!$F1 728
10 TraesCS5A01G069300 chr5B 48315464 48316192 728 False 1291 1291 98.628 2920 3648 1 chr5B.!!$F2 728
11 TraesCS5A01G069300 chr5B 580668805 580669467 662 True 992 992 93.665 1 663 1 chr5B.!!$R2 662
12 TraesCS5A01G069300 chr5B 665689058 665689823 765 False 968 968 89.556 1 762 1 chr5B.!!$F3 761
13 TraesCS5A01G069300 chr3D 413766173 413766901 728 True 1291 1291 98.628 2920 3648 1 chr3D.!!$R1 728
14 TraesCS5A01G069300 chr1A 222361821 222362549 728 True 1291 1291 98.628 2920 3648 1 chr1A.!!$R1 728
15 TraesCS5A01G069300 chr1A 306638338 306639066 728 False 1291 1291 98.628 2920 3648 1 chr1A.!!$F1 728
16 TraesCS5A01G069300 chr1A 517045241 517045969 728 True 1291 1291 98.628 2920 3648 1 chr1A.!!$R2 728
17 TraesCS5A01G069300 chr4B 429677092 429677855 763 True 1184 1184 94.634 1 764 1 chr4B.!!$R1 763
18 TraesCS5A01G069300 chr2B 58890691 58891454 763 True 990 990 90.052 1 764 1 chr2B.!!$R1 763
19 TraesCS5A01G069300 chr7D 42178520 42179207 687 True 911 911 90.552 1 688 1 chr7D.!!$R1 687

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
773 779 0.106708 AGACTTGCGTCAAGCTGGAA 59.893 50.0 16.24 0.0 44.43 3.53 F
1045 1051 0.025898 GAGGACGAAATTTACGGCGC 59.974 55.0 6.90 0.0 39.91 6.53 F
1587 1593 0.394565 AGCAGCTCGGACTTGAACTT 59.605 50.0 0.00 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1911 0.249868 TGGAGCCAAACACGAGTCTG 60.250 55.0 0.00 0.0 0.0 3.51 R
2477 2483 0.555769 TCATTGTAATCCCTGGCCCC 59.444 55.0 0.00 0.0 0.0 5.80 R
2986 2992 0.815095 ACCGCACATCATGTACTCGA 59.185 50.0 7.57 0.0 0.0 4.04 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
225 230 6.806668 TCCATAACTGTATTGATCCACTGA 57.193 37.500 0.00 0.00 0.00 3.41
261 266 2.957402 TAGCCATAATGCCCTTCAGG 57.043 50.000 0.00 0.00 39.47 3.86
291 296 6.208204 GCCATTCCAGTCTATCATATGCTTTT 59.792 38.462 0.00 0.00 0.00 2.27
684 690 1.704628 TGAGCAGGAAAACCATCAGGA 59.295 47.619 0.00 0.00 38.69 3.86
734 740 4.748277 ATAGCGCTGTTTTTACCTCCTA 57.252 40.909 22.90 0.00 0.00 2.94
764 770 0.939577 TCAGCGTTCAGACTTGCGTC 60.940 55.000 0.00 0.00 40.54 5.19
765 771 1.067416 AGCGTTCAGACTTGCGTCA 59.933 52.632 0.00 0.00 42.73 4.35
766 772 0.529773 AGCGTTCAGACTTGCGTCAA 60.530 50.000 0.00 0.00 42.73 3.18
767 773 0.111089 GCGTTCAGACTTGCGTCAAG 60.111 55.000 15.16 15.16 45.85 3.02
768 774 0.111089 CGTTCAGACTTGCGTCAAGC 60.111 55.000 16.24 10.76 44.43 4.01
769 775 1.221414 GTTCAGACTTGCGTCAAGCT 58.779 50.000 16.24 12.32 44.43 3.74
770 776 1.070309 GTTCAGACTTGCGTCAAGCTG 60.070 52.381 22.24 22.24 44.43 4.24
771 777 0.601046 TCAGACTTGCGTCAAGCTGG 60.601 55.000 24.65 14.75 44.43 4.85
772 778 0.601046 CAGACTTGCGTCAAGCTGGA 60.601 55.000 21.44 0.00 44.43 3.86
773 779 0.106708 AGACTTGCGTCAAGCTGGAA 59.893 50.000 16.24 0.00 44.43 3.53
774 780 0.944386 GACTTGCGTCAAGCTGGAAA 59.056 50.000 16.24 0.00 44.43 3.13
775 781 0.663153 ACTTGCGTCAAGCTGGAAAC 59.337 50.000 16.24 0.00 44.43 2.78
776 782 2.682469 ACTTGCGTCAAGCTGGAAACC 61.682 52.381 16.24 0.00 44.43 3.27
777 783 4.065110 GCGTCAAGCTGGAAACCT 57.935 55.556 0.00 0.00 44.04 3.50
778 784 2.331265 GCGTCAAGCTGGAAACCTT 58.669 52.632 0.00 0.00 44.04 3.50
779 785 0.668535 GCGTCAAGCTGGAAACCTTT 59.331 50.000 0.00 0.00 44.04 3.11
780 786 1.877443 GCGTCAAGCTGGAAACCTTTA 59.123 47.619 0.00 0.00 44.04 1.85
781 787 2.350484 GCGTCAAGCTGGAAACCTTTAC 60.350 50.000 0.00 0.00 44.04 2.01
782 788 3.139077 CGTCAAGCTGGAAACCTTTACT 58.861 45.455 0.00 0.00 0.00 2.24
783 789 3.058914 CGTCAAGCTGGAAACCTTTACTG 60.059 47.826 0.00 0.00 0.00 2.74
784 790 3.253432 GTCAAGCTGGAAACCTTTACTGG 59.747 47.826 0.00 0.00 0.00 4.00
785 791 1.911057 AGCTGGAAACCTTTACTGGC 58.089 50.000 0.00 0.00 0.00 4.85
786 792 1.144913 AGCTGGAAACCTTTACTGGCA 59.855 47.619 0.00 0.00 0.00 4.92
787 793 1.541588 GCTGGAAACCTTTACTGGCAG 59.458 52.381 14.16 14.16 0.00 4.85
788 794 2.863809 CTGGAAACCTTTACTGGCAGT 58.136 47.619 25.34 25.34 0.00 4.40
789 795 3.809324 GCTGGAAACCTTTACTGGCAGTA 60.809 47.826 22.96 22.96 0.00 2.74
790 796 4.394729 CTGGAAACCTTTACTGGCAGTAA 58.605 43.478 30.85 30.85 38.79 2.24
791 797 4.794334 TGGAAACCTTTACTGGCAGTAAA 58.206 39.130 36.98 36.98 45.41 2.01
792 798 4.581409 TGGAAACCTTTACTGGCAGTAAAC 59.419 41.667 36.57 28.16 43.48 2.01
793 799 4.825634 GGAAACCTTTACTGGCAGTAAACT 59.174 41.667 36.57 25.52 43.48 2.66
794 800 5.301045 GGAAACCTTTACTGGCAGTAAACTT 59.699 40.000 36.57 29.45 43.48 2.66
795 801 6.183360 GGAAACCTTTACTGGCAGTAAACTTT 60.183 38.462 36.57 32.57 43.48 2.66
796 802 7.013559 GGAAACCTTTACTGGCAGTAAACTTTA 59.986 37.037 36.57 22.89 43.48 1.85
797 803 7.506328 AACCTTTACTGGCAGTAAACTTTAG 57.494 36.000 36.57 28.53 43.48 1.85
798 804 6.002082 ACCTTTACTGGCAGTAAACTTTAGG 58.998 40.000 36.57 34.80 43.48 2.69
799 805 5.414765 CCTTTACTGGCAGTAAACTTTAGGG 59.585 44.000 36.57 30.89 43.48 3.53
800 806 3.434940 ACTGGCAGTAAACTTTAGGGG 57.565 47.619 20.61 0.00 0.00 4.79
801 807 2.983898 ACTGGCAGTAAACTTTAGGGGA 59.016 45.455 20.61 0.00 0.00 4.81
802 808 3.009143 ACTGGCAGTAAACTTTAGGGGAG 59.991 47.826 20.61 0.00 0.00 4.30
803 809 2.290705 TGGCAGTAAACTTTAGGGGAGC 60.291 50.000 0.00 0.00 0.00 4.70
804 810 2.026169 GGCAGTAAACTTTAGGGGAGCT 60.026 50.000 0.00 0.00 0.00 4.09
805 811 3.199289 GGCAGTAAACTTTAGGGGAGCTA 59.801 47.826 0.00 0.00 0.00 3.32
806 812 4.141459 GGCAGTAAACTTTAGGGGAGCTAT 60.141 45.833 0.00 0.00 0.00 2.97
807 813 5.437946 GCAGTAAACTTTAGGGGAGCTATT 58.562 41.667 0.00 0.00 0.00 1.73
808 814 5.886474 GCAGTAAACTTTAGGGGAGCTATTT 59.114 40.000 0.00 0.00 0.00 1.40
809 815 6.183360 GCAGTAAACTTTAGGGGAGCTATTTG 60.183 42.308 0.00 0.00 0.00 2.32
810 816 7.110155 CAGTAAACTTTAGGGGAGCTATTTGA 58.890 38.462 0.00 0.00 0.00 2.69
811 817 7.610305 CAGTAAACTTTAGGGGAGCTATTTGAA 59.390 37.037 0.00 0.00 0.00 2.69
812 818 8.336987 AGTAAACTTTAGGGGAGCTATTTGAAT 58.663 33.333 0.00 0.00 0.00 2.57
813 819 8.967918 GTAAACTTTAGGGGAGCTATTTGAATT 58.032 33.333 0.00 0.00 0.00 2.17
815 821 8.753497 AACTTTAGGGGAGCTATTTGAATTAG 57.247 34.615 0.00 0.00 0.00 1.73
816 822 7.290813 ACTTTAGGGGAGCTATTTGAATTAGG 58.709 38.462 0.00 0.00 0.00 2.69
817 823 4.105754 AGGGGAGCTATTTGAATTAGGC 57.894 45.455 0.00 0.00 0.00 3.93
818 824 3.463329 AGGGGAGCTATTTGAATTAGGCA 59.537 43.478 0.00 0.00 0.00 4.75
819 825 4.079212 AGGGGAGCTATTTGAATTAGGCAA 60.079 41.667 0.00 0.00 0.00 4.52
820 826 4.835056 GGGGAGCTATTTGAATTAGGCAAT 59.165 41.667 0.00 0.00 0.00 3.56
821 827 5.047731 GGGGAGCTATTTGAATTAGGCAATC 60.048 44.000 0.00 0.00 0.00 2.67
822 828 5.772169 GGGAGCTATTTGAATTAGGCAATCT 59.228 40.000 0.00 0.00 0.00 2.40
823 829 6.266330 GGGAGCTATTTGAATTAGGCAATCTT 59.734 38.462 0.00 0.00 0.00 2.40
824 830 7.448469 GGGAGCTATTTGAATTAGGCAATCTTA 59.552 37.037 0.00 0.00 0.00 2.10
825 831 8.293157 GGAGCTATTTGAATTAGGCAATCTTAC 58.707 37.037 0.00 0.00 0.00 2.34
826 832 8.986929 AGCTATTTGAATTAGGCAATCTTACT 57.013 30.769 0.00 0.00 0.00 2.24
827 833 9.061435 AGCTATTTGAATTAGGCAATCTTACTC 57.939 33.333 0.00 0.00 0.00 2.59
828 834 8.012241 GCTATTTGAATTAGGCAATCTTACTCG 58.988 37.037 0.00 0.00 0.00 4.18
829 835 7.865706 ATTTGAATTAGGCAATCTTACTCGT 57.134 32.000 0.00 0.00 0.00 4.18
830 836 6.903883 TTGAATTAGGCAATCTTACTCGTC 57.096 37.500 0.00 0.00 0.00 4.20
831 837 5.972935 TGAATTAGGCAATCTTACTCGTCA 58.027 37.500 0.00 0.00 0.00 4.35
832 838 6.403049 TGAATTAGGCAATCTTACTCGTCAA 58.597 36.000 0.00 0.00 0.00 3.18
833 839 6.535150 TGAATTAGGCAATCTTACTCGTCAAG 59.465 38.462 0.00 0.00 0.00 3.02
834 840 2.622436 AGGCAATCTTACTCGTCAAGC 58.378 47.619 0.00 0.00 0.00 4.01
835 841 2.234908 AGGCAATCTTACTCGTCAAGCT 59.765 45.455 0.00 0.00 0.00 3.74
836 842 2.349886 GGCAATCTTACTCGTCAAGCTG 59.650 50.000 0.00 0.00 0.00 4.24
837 843 2.349886 GCAATCTTACTCGTCAAGCTGG 59.650 50.000 0.00 0.00 0.00 4.85
838 844 3.849911 CAATCTTACTCGTCAAGCTGGA 58.150 45.455 0.00 0.00 0.00 3.86
839 845 4.245660 CAATCTTACTCGTCAAGCTGGAA 58.754 43.478 0.00 0.00 0.00 3.53
840 846 4.537135 ATCTTACTCGTCAAGCTGGAAA 57.463 40.909 0.00 0.00 0.00 3.13
841 847 3.650139 TCTTACTCGTCAAGCTGGAAAC 58.350 45.455 0.00 0.00 0.00 2.78
842 848 2.450609 TACTCGTCAAGCTGGAAACC 57.549 50.000 0.00 0.00 0.00 3.27
843 849 0.759346 ACTCGTCAAGCTGGAAACCT 59.241 50.000 0.00 0.00 0.00 3.50
844 850 1.270358 ACTCGTCAAGCTGGAAACCTC 60.270 52.381 0.00 0.00 0.00 3.85
845 851 0.756294 TCGTCAAGCTGGAAACCTCA 59.244 50.000 0.00 0.00 0.00 3.86
846 852 1.151668 CGTCAAGCTGGAAACCTCAG 58.848 55.000 0.00 0.00 35.49 3.35
850 856 2.669569 GCTGGAAACCTCAGCGCA 60.670 61.111 11.47 0.00 46.33 6.09
851 857 2.260869 GCTGGAAACCTCAGCGCAA 61.261 57.895 11.47 0.00 46.33 4.85
852 858 1.871772 CTGGAAACCTCAGCGCAAG 59.128 57.895 11.47 6.49 43.44 4.01
868 874 4.277257 CGCAAGCAACATAATAAGCAGA 57.723 40.909 0.00 0.00 0.00 4.26
869 875 4.661125 CGCAAGCAACATAATAAGCAGAA 58.339 39.130 0.00 0.00 0.00 3.02
870 876 5.094812 CGCAAGCAACATAATAAGCAGAAA 58.905 37.500 0.00 0.00 0.00 2.52
871 877 5.228635 CGCAAGCAACATAATAAGCAGAAAG 59.771 40.000 0.00 0.00 0.00 2.62
872 878 5.517770 GCAAGCAACATAATAAGCAGAAAGG 59.482 40.000 0.00 0.00 0.00 3.11
873 879 5.254339 AGCAACATAATAAGCAGAAAGGC 57.746 39.130 0.00 0.00 0.00 4.35
874 880 4.098501 AGCAACATAATAAGCAGAAAGGCC 59.901 41.667 0.00 0.00 0.00 5.19
875 881 4.737649 GCAACATAATAAGCAGAAAGGCCC 60.738 45.833 0.00 0.00 0.00 5.80
876 882 3.214328 ACATAATAAGCAGAAAGGCCCG 58.786 45.455 0.00 0.00 0.00 6.13
877 883 2.341846 TAATAAGCAGAAAGGCCCGG 57.658 50.000 0.00 0.00 0.00 5.73
878 884 1.037579 AATAAGCAGAAAGGCCCGGC 61.038 55.000 0.00 0.00 0.00 6.13
895 901 4.729918 CCCACTGCACTGCCCTCC 62.730 72.222 0.00 0.00 0.00 4.30
896 902 3.644606 CCACTGCACTGCCCTCCT 61.645 66.667 0.00 0.00 0.00 3.69
897 903 2.433446 CACTGCACTGCCCTCCTT 59.567 61.111 0.00 0.00 0.00 3.36
898 904 1.673665 CACTGCACTGCCCTCCTTC 60.674 63.158 0.00 0.00 0.00 3.46
899 905 2.045536 CTGCACTGCCCTCCTTCC 60.046 66.667 0.00 0.00 0.00 3.46
900 906 2.530151 TGCACTGCCCTCCTTCCT 60.530 61.111 0.00 0.00 0.00 3.36
901 907 2.270527 GCACTGCCCTCCTTCCTC 59.729 66.667 0.00 0.00 0.00 3.71
902 908 2.993853 CACTGCCCTCCTTCCTCC 59.006 66.667 0.00 0.00 0.00 4.30
903 909 2.685380 ACTGCCCTCCTTCCTCCG 60.685 66.667 0.00 0.00 0.00 4.63
904 910 2.364317 CTGCCCTCCTTCCTCCGA 60.364 66.667 0.00 0.00 0.00 4.55
905 911 2.683933 TGCCCTCCTTCCTCCGAC 60.684 66.667 0.00 0.00 0.00 4.79
906 912 2.683933 GCCCTCCTTCCTCCGACA 60.684 66.667 0.00 0.00 0.00 4.35
907 913 2.726351 GCCCTCCTTCCTCCGACAG 61.726 68.421 0.00 0.00 0.00 3.51
908 914 2.060980 CCCTCCTTCCTCCGACAGG 61.061 68.421 0.00 0.00 45.15 4.00
909 915 1.305381 CCTCCTTCCTCCGACAGGT 60.305 63.158 0.77 0.00 43.95 4.00
910 916 1.608717 CCTCCTTCCTCCGACAGGTG 61.609 65.000 0.77 0.00 43.95 4.00
911 917 0.612174 CTCCTTCCTCCGACAGGTGA 60.612 60.000 0.77 0.00 43.95 4.02
912 918 0.178944 TCCTTCCTCCGACAGGTGAA 60.179 55.000 0.77 0.00 43.95 3.18
913 919 0.685097 CCTTCCTCCGACAGGTGAAA 59.315 55.000 0.77 0.00 43.95 2.69
914 920 1.338200 CCTTCCTCCGACAGGTGAAAG 60.338 57.143 0.77 0.00 43.95 2.62
915 921 0.685097 TTCCTCCGACAGGTGAAAGG 59.315 55.000 0.77 0.00 43.95 3.11
916 922 0.178944 TCCTCCGACAGGTGAAAGGA 60.179 55.000 0.77 0.00 43.95 3.36
917 923 0.685097 CCTCCGACAGGTGAAAGGAA 59.315 55.000 0.00 0.00 37.53 3.36
918 924 1.071699 CCTCCGACAGGTGAAAGGAAA 59.928 52.381 0.00 0.00 37.53 3.13
919 925 2.486548 CCTCCGACAGGTGAAAGGAAAA 60.487 50.000 0.00 0.00 37.53 2.29
920 926 3.211045 CTCCGACAGGTGAAAGGAAAAA 58.789 45.455 0.00 0.00 39.05 1.94
954 960 2.502080 GTCGAGACCACGAGTGCG 60.502 66.667 0.00 0.00 42.88 5.34
955 961 3.733960 TCGAGACCACGAGTGCGG 61.734 66.667 0.00 0.00 43.17 5.69
978 984 4.351054 CTCCACCCACCTGTGCCC 62.351 72.222 0.00 0.00 34.85 5.36
979 985 4.918360 TCCACCCACCTGTGCCCT 62.918 66.667 0.00 0.00 34.85 5.19
980 986 2.933287 CCACCCACCTGTGCCCTA 60.933 66.667 0.00 0.00 34.85 3.53
981 987 2.671070 CACCCACCTGTGCCCTAG 59.329 66.667 0.00 0.00 0.00 3.02
982 988 2.207189 ACCCACCTGTGCCCTAGT 59.793 61.111 0.00 0.00 0.00 2.57
983 989 1.918800 ACCCACCTGTGCCCTAGTC 60.919 63.158 0.00 0.00 0.00 2.59
984 990 2.670148 CCCACCTGTGCCCTAGTCC 61.670 68.421 0.00 0.00 0.00 3.85
985 991 2.579201 CACCTGTGCCCTAGTCCG 59.421 66.667 0.00 0.00 0.00 4.79
986 992 2.683933 ACCTGTGCCCTAGTCCGG 60.684 66.667 0.00 0.00 0.00 5.14
988 994 4.162690 CTGTGCCCTAGTCCGGCC 62.163 72.222 0.00 0.00 46.48 6.13
1030 1036 2.822215 GGTCCTATGCCGAAGAGGA 58.178 57.895 0.00 0.00 45.00 3.71
1032 1038 2.415825 TCCTATGCCGAAGAGGACG 58.584 57.895 0.00 0.00 45.00 4.79
1033 1039 0.106868 TCCTATGCCGAAGAGGACGA 60.107 55.000 0.00 0.00 45.00 4.20
1034 1040 0.744874 CCTATGCCGAAGAGGACGAA 59.255 55.000 0.00 0.00 45.00 3.85
1035 1041 1.136305 CCTATGCCGAAGAGGACGAAA 59.864 52.381 0.00 0.00 45.00 3.46
1036 1042 2.224066 CCTATGCCGAAGAGGACGAAAT 60.224 50.000 0.00 0.00 45.00 2.17
1037 1043 2.403252 ATGCCGAAGAGGACGAAATT 57.597 45.000 0.00 0.00 45.00 1.82
1038 1044 2.178912 TGCCGAAGAGGACGAAATTT 57.821 45.000 0.00 0.00 45.00 1.82
1039 1045 3.322211 TGCCGAAGAGGACGAAATTTA 57.678 42.857 0.00 0.00 45.00 1.40
1040 1046 2.997986 TGCCGAAGAGGACGAAATTTAC 59.002 45.455 0.00 0.00 45.00 2.01
1041 1047 2.028883 GCCGAAGAGGACGAAATTTACG 59.971 50.000 0.00 0.00 45.00 3.18
1042 1048 2.601763 CCGAAGAGGACGAAATTTACGG 59.398 50.000 12.45 0.00 45.00 4.02
1043 1049 2.028883 CGAAGAGGACGAAATTTACGGC 59.971 50.000 12.45 9.97 38.12 5.68
1044 1050 1.636988 AGAGGACGAAATTTACGGCG 58.363 50.000 4.80 4.80 39.91 6.46
1045 1051 0.025898 GAGGACGAAATTTACGGCGC 59.974 55.000 6.90 0.00 39.91 6.53
1097 1103 2.759973 AGCGGGCGAGGATGAAGA 60.760 61.111 0.00 0.00 0.00 2.87
1129 1135 3.019003 ATCAGCAACCTCCCCGACG 62.019 63.158 0.00 0.00 0.00 5.12
1196 1202 4.147449 CACCCAGATCCTCGCGCA 62.147 66.667 8.75 0.00 0.00 6.09
1232 1238 2.026879 GAGCTCCGCGCCTCTTAG 59.973 66.667 0.87 0.00 40.39 2.18
1387 1393 1.313091 GGACAAATGGCTCCGAACCC 61.313 60.000 0.00 0.00 0.00 4.11
1428 1434 2.487265 GGAGCTGGAGTTCTGGTTCAAA 60.487 50.000 0.00 0.00 0.00 2.69
1587 1593 0.394565 AGCAGCTCGGACTTGAACTT 59.605 50.000 0.00 0.00 0.00 2.66
1639 1645 1.534717 ATTGCCAGTTGCCCTGCTT 60.535 52.632 0.00 0.00 40.06 3.91
1654 1660 1.288127 GCTTTGGAGTGCTTGCTGG 59.712 57.895 0.00 0.00 0.00 4.85
1758 1764 4.082733 GGCAATGACCAGTTAAAGGAACTC 60.083 45.833 2.40 0.00 45.81 3.01
1759 1765 4.518970 GCAATGACCAGTTAAAGGAACTCA 59.481 41.667 2.40 0.00 45.81 3.41
1773 1779 3.002791 GGAACTCATTGTCGAGAATGCA 58.997 45.455 25.97 15.67 36.47 3.96
1788 1794 2.611224 GAATGCACCTTGCCTTCAAAGG 60.611 50.000 10.25 4.33 44.08 3.11
1816 1822 6.441093 TGCATCTTGATTTTGACTATGGTC 57.559 37.500 1.56 1.56 42.42 4.02
1827 1833 7.889589 TTTTGACTATGGTCTGCATATATCG 57.110 36.000 10.82 0.00 42.54 2.92
1830 1836 6.184789 TGACTATGGTCTGCATATATCGGTA 58.815 40.000 10.82 0.00 42.54 4.02
1833 1839 4.783764 TGGTCTGCATATATCGGTAGTG 57.216 45.455 0.00 0.00 0.00 2.74
1853 1859 1.519455 CCGCGCCTAAACTGGAGAG 60.519 63.158 0.00 0.00 0.00 3.20
1855 1861 1.079127 GCGCCTAAACTGGAGAGCA 60.079 57.895 0.00 0.00 0.00 4.26
1884 1890 4.837860 TGCCTTTCTGATGGGTTTTACATT 59.162 37.500 0.53 0.00 0.00 2.71
1891 1897 6.991938 TCTGATGGGTTTTACATTTCCAAAG 58.008 36.000 0.00 0.00 0.00 2.77
1892 1898 6.780031 TCTGATGGGTTTTACATTTCCAAAGA 59.220 34.615 0.00 0.00 0.00 2.52
1893 1899 6.991938 TGATGGGTTTTACATTTCCAAAGAG 58.008 36.000 0.00 0.00 0.00 2.85
1909 1915 4.202243 CCAAAGAGGATGATCTCTCCAGAC 60.202 50.000 14.80 7.66 42.75 3.51
1940 1946 2.167900 GCTCCACGGTTATTCAGGTACT 59.832 50.000 0.00 0.00 43.88 2.73
1941 1947 3.737355 GCTCCACGGTTATTCAGGTACTC 60.737 52.174 0.00 0.00 34.60 2.59
1942 1948 2.424601 TCCACGGTTATTCAGGTACTCG 59.575 50.000 0.00 0.00 34.60 4.18
1943 1949 2.165030 CCACGGTTATTCAGGTACTCGT 59.835 50.000 0.00 0.00 34.60 4.18
1944 1950 3.176708 CACGGTTATTCAGGTACTCGTG 58.823 50.000 0.00 0.00 40.14 4.35
1964 1970 2.890311 TGTTTGGCCATCCTACTTGTTG 59.110 45.455 6.09 0.00 0.00 3.33
1971 1977 3.624777 CCATCCTACTTGTTGCCTTCAT 58.375 45.455 0.00 0.00 0.00 2.57
1973 1979 4.264253 CATCCTACTTGTTGCCTTCATGA 58.736 43.478 0.00 0.00 0.00 3.07
1996 2002 5.729510 AGGCTTCTCAGTTTTATCTCTGTC 58.270 41.667 0.00 0.00 33.89 3.51
2011 2017 6.749923 ATCTCTGTCTGCAGGAAAAATAAC 57.250 37.500 15.13 2.16 42.78 1.89
2098 2104 1.817520 CTGACAACGGTGGTGCACA 60.818 57.895 20.43 1.62 35.86 4.57
2128 2134 8.400947 TGAAGAATTTAGCTGTCAATATGAAGC 58.599 33.333 0.00 6.48 33.66 3.86
2172 2178 0.729116 AGTTGATGCGATGCTTTCCG 59.271 50.000 0.00 0.00 0.00 4.30
2187 2193 2.099141 TTCCGTGCTTGGAGAAGATG 57.901 50.000 0.00 0.00 39.72 2.90
2190 2196 2.094182 TCCGTGCTTGGAGAAGATGTAC 60.094 50.000 0.00 0.00 33.05 2.90
2203 2209 6.314896 GGAGAAGATGTACATTGAGGTGAAAG 59.685 42.308 10.30 0.00 0.00 2.62
2258 2264 5.448360 GCTCATTTGATCTACTTGCTGAACC 60.448 44.000 0.00 0.00 0.00 3.62
2305 2311 5.333645 CCATGTTCTTTTTCAGTCAGAGTCG 60.334 44.000 0.00 0.00 0.00 4.18
2416 2422 8.768397 TGTTATGAGGGTATTAAGTCTGACATT 58.232 33.333 10.88 4.40 0.00 2.71
2455 2461 2.035449 TGTACTGAACGCTACAGTGCTT 59.965 45.455 19.16 0.86 45.93 3.91
2466 2472 4.201628 CGCTACAGTGCTTGAGTTAATGAC 60.202 45.833 0.00 0.00 0.00 3.06
2477 2483 6.454848 GCTTGAGTTAATGACACTTCAGATCG 60.455 42.308 0.00 0.00 34.35 3.69
2479 2485 4.759782 AGTTAATGACACTTCAGATCGGG 58.240 43.478 0.00 0.00 34.35 5.14
2491 2497 1.128188 AGATCGGGGCCAGGGATTAC 61.128 60.000 4.39 0.00 0.00 1.89
2498 2504 2.625617 GGGGCCAGGGATTACAATGAAA 60.626 50.000 4.39 0.00 0.00 2.69
2549 2555 4.460263 TCAGCTAGAAAACAAGGCTTCAA 58.540 39.130 0.00 0.00 0.00 2.69
2580 2586 6.961554 GCTCGGTTTCATTTTACAACTGATAG 59.038 38.462 0.00 0.00 35.69 2.08
2648 2654 9.123902 TGGATTTAACTGATCCATTTGTATGAG 57.876 33.333 3.63 0.00 46.11 2.90
2649 2655 9.125026 GGATTTAACTGATCCATTTGTATGAGT 57.875 33.333 0.54 0.00 42.17 3.41
2655 2661 8.498054 ACTGATCCATTTGTATGAGTAAAGTG 57.502 34.615 0.00 0.00 33.37 3.16
2658 2664 5.815581 TCCATTTGTATGAGTAAAGTGGCT 58.184 37.500 0.00 0.00 33.37 4.75
2671 2677 4.326504 AAAGTGGCTCTTGTCCATTTTG 57.673 40.909 2.09 0.00 40.51 2.44
2700 2706 9.739276 ATTGTTCTTCAATGTTAACCTATCTCA 57.261 29.630 2.48 0.00 44.06 3.27
2745 2751 0.649993 GCTTTTGGTGTTTGCCGTTG 59.350 50.000 0.00 0.00 0.00 4.10
2751 2757 2.025155 TGGTGTTTGCCGTTGTTGTAT 58.975 42.857 0.00 0.00 0.00 2.29
2761 2767 9.557338 GTTTGCCGTTGTTGTATGTTTATATTA 57.443 29.630 0.00 0.00 0.00 0.98
2763 2769 9.938670 TTGCCGTTGTTGTATGTTTATATTATC 57.061 29.630 0.00 0.00 0.00 1.75
2764 2770 9.332502 TGCCGTTGTTGTATGTTTATATTATCT 57.667 29.630 0.00 0.00 0.00 1.98
2765 2771 9.594038 GCCGTTGTTGTATGTTTATATTATCTG 57.406 33.333 0.00 0.00 0.00 2.90
2812 2818 9.618890 AGCTGTTTGTGTCTTATGATATAACAT 57.381 29.630 0.81 0.81 0.00 2.71
2813 2819 9.655769 GCTGTTTGTGTCTTATGATATAACATG 57.344 33.333 5.78 0.00 0.00 3.21
2816 2822 9.935682 GTTTGTGTCTTATGATATAACATGTGG 57.064 33.333 0.00 0.00 0.00 4.17
2839 2845 3.615496 CAGCCTTGCAATTTATGAAGCAC 59.385 43.478 0.00 0.00 36.62 4.40
2856 2862 5.045942 TGAAGCACAGGGTAATCTGATTGTA 60.046 40.000 13.01 0.00 38.11 2.41
2867 2873 9.220767 GGGTAATCTGATTGTAATATTGAGGAC 57.779 37.037 13.01 0.00 0.00 3.85
2894 2900 7.685849 ATTAAGAATGGTAGGGTAGCTACAA 57.314 36.000 24.75 7.42 0.00 2.41
2895 2901 5.354842 AAGAATGGTAGGGTAGCTACAAC 57.645 43.478 24.75 17.82 0.00 3.32
2896 2902 4.621769 AGAATGGTAGGGTAGCTACAACT 58.378 43.478 24.75 22.01 0.00 3.16
2897 2903 5.030820 AGAATGGTAGGGTAGCTACAACTT 58.969 41.667 24.75 7.98 0.00 2.66
2898 2904 6.200114 AGAATGGTAGGGTAGCTACAACTTA 58.800 40.000 24.75 7.01 0.00 2.24
2899 2905 6.844917 AGAATGGTAGGGTAGCTACAACTTAT 59.155 38.462 24.75 13.88 0.00 1.73
2917 2923 9.533253 ACAACTTATTTTGATTTCTGGTGAAAG 57.467 29.630 0.00 0.00 44.25 2.62
2918 2924 8.981647 CAACTTATTTTGATTTCTGGTGAAAGG 58.018 33.333 0.00 0.00 44.25 3.11
2986 2992 8.833734 AGGGTTTAGGCTTAGTAGAACTAAAAT 58.166 33.333 0.00 0.00 39.89 1.82
3300 3306 6.861065 AAAGACGACATGTTCAACAGTTAT 57.139 33.333 0.00 0.00 0.00 1.89
3461 3467 2.721971 ATATTCAGCGCAGGCCTCCG 62.722 60.000 13.10 13.10 41.24 4.63
3585 3591 5.800296 TGAAGGATTGGAGTATCGACAAAA 58.200 37.500 0.00 0.00 34.37 2.44
3636 3642 1.206878 TGCTATCCATGTGCCAGAGT 58.793 50.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 0.099968 CGACGAGAGGTATTCGGCAA 59.900 55.000 1.22 0.00 46.23 4.52
203 208 6.994496 ACATCAGTGGATCAATACAGTTATGG 59.006 38.462 8.42 0.00 32.43 2.74
225 230 2.158696 GGCTAAGCTGGGATTCTCACAT 60.159 50.000 0.00 0.00 0.00 3.21
385 391 6.016276 GCTTTTGTTCCTGGAAGACTTATCAA 60.016 38.462 9.92 5.87 34.07 2.57
419 425 4.194640 GCTGCCTCACATAATTTCTGAGA 58.805 43.478 7.82 0.00 34.46 3.27
498 504 5.423015 TCACAGCTTCATCCAATAAGTCTC 58.577 41.667 0.00 0.00 0.00 3.36
684 690 2.754375 CCTACAAAGGCACCGGGT 59.246 61.111 6.32 0.00 35.64 5.28
734 740 2.099921 CTGAACGCTGAGTATACTGCCT 59.900 50.000 10.90 0.00 0.00 4.75
764 770 2.029918 GCCAGTAAAGGTTTCCAGCTTG 60.030 50.000 0.00 0.00 39.96 4.01
765 771 2.239400 GCCAGTAAAGGTTTCCAGCTT 58.761 47.619 0.00 0.00 42.81 3.74
766 772 1.144913 TGCCAGTAAAGGTTTCCAGCT 59.855 47.619 0.00 0.00 0.00 4.24
767 773 1.541588 CTGCCAGTAAAGGTTTCCAGC 59.458 52.381 0.00 0.00 0.00 4.85
768 774 2.863809 ACTGCCAGTAAAGGTTTCCAG 58.136 47.619 0.00 0.00 0.00 3.86
769 775 4.440826 TTACTGCCAGTAAAGGTTTCCA 57.559 40.909 14.73 0.00 37.71 3.53
777 783 5.073417 TCCCCTAAAGTTTACTGCCAGTAAA 59.927 40.000 22.76 22.76 45.41 2.01
778 784 4.598373 TCCCCTAAAGTTTACTGCCAGTAA 59.402 41.667 13.19 13.19 38.79 2.24
779 785 4.169666 TCCCCTAAAGTTTACTGCCAGTA 58.830 43.478 0.00 0.00 0.00 2.74
780 786 2.983898 TCCCCTAAAGTTTACTGCCAGT 59.016 45.455 1.54 1.54 0.00 4.00
781 787 3.610911 CTCCCCTAAAGTTTACTGCCAG 58.389 50.000 0.00 0.00 0.00 4.85
782 788 2.290705 GCTCCCCTAAAGTTTACTGCCA 60.291 50.000 0.00 0.00 0.00 4.92
783 789 2.026169 AGCTCCCCTAAAGTTTACTGCC 60.026 50.000 0.00 0.00 0.00 4.85
784 790 3.351794 AGCTCCCCTAAAGTTTACTGC 57.648 47.619 0.00 0.00 0.00 4.40
785 791 7.110155 TCAAATAGCTCCCCTAAAGTTTACTG 58.890 38.462 0.00 0.00 0.00 2.74
786 792 7.266905 TCAAATAGCTCCCCTAAAGTTTACT 57.733 36.000 0.00 0.00 0.00 2.24
787 793 7.933215 TTCAAATAGCTCCCCTAAAGTTTAC 57.067 36.000 0.00 0.00 0.00 2.01
789 795 9.190317 CTAATTCAAATAGCTCCCCTAAAGTTT 57.810 33.333 0.00 0.00 0.00 2.66
790 796 7.780271 CCTAATTCAAATAGCTCCCCTAAAGTT 59.220 37.037 0.00 0.00 0.00 2.66
791 797 7.290813 CCTAATTCAAATAGCTCCCCTAAAGT 58.709 38.462 0.00 0.00 0.00 2.66
792 798 6.207614 GCCTAATTCAAATAGCTCCCCTAAAG 59.792 42.308 0.00 0.00 0.00 1.85
793 799 6.068670 GCCTAATTCAAATAGCTCCCCTAAA 58.931 40.000 0.00 0.00 0.00 1.85
794 800 5.133660 TGCCTAATTCAAATAGCTCCCCTAA 59.866 40.000 0.00 0.00 0.00 2.69
795 801 4.663120 TGCCTAATTCAAATAGCTCCCCTA 59.337 41.667 0.00 0.00 0.00 3.53
796 802 3.463329 TGCCTAATTCAAATAGCTCCCCT 59.537 43.478 0.00 0.00 0.00 4.79
797 803 3.832527 TGCCTAATTCAAATAGCTCCCC 58.167 45.455 0.00 0.00 0.00 4.81
798 804 5.772169 AGATTGCCTAATTCAAATAGCTCCC 59.228 40.000 0.00 0.00 0.00 4.30
799 805 6.890979 AGATTGCCTAATTCAAATAGCTCC 57.109 37.500 0.00 0.00 0.00 4.70
800 806 9.061435 AGTAAGATTGCCTAATTCAAATAGCTC 57.939 33.333 0.00 0.00 0.00 4.09
801 807 8.986929 AGTAAGATTGCCTAATTCAAATAGCT 57.013 30.769 0.00 0.00 0.00 3.32
802 808 8.012241 CGAGTAAGATTGCCTAATTCAAATAGC 58.988 37.037 0.00 0.00 0.00 2.97
803 809 9.046296 ACGAGTAAGATTGCCTAATTCAAATAG 57.954 33.333 0.00 0.00 0.00 1.73
804 810 8.958119 ACGAGTAAGATTGCCTAATTCAAATA 57.042 30.769 0.00 0.00 0.00 1.40
805 811 7.552687 TGACGAGTAAGATTGCCTAATTCAAAT 59.447 33.333 0.00 0.00 0.00 2.32
806 812 6.876789 TGACGAGTAAGATTGCCTAATTCAAA 59.123 34.615 0.00 0.00 0.00 2.69
807 813 6.403049 TGACGAGTAAGATTGCCTAATTCAA 58.597 36.000 0.00 0.00 0.00 2.69
808 814 5.972935 TGACGAGTAAGATTGCCTAATTCA 58.027 37.500 0.00 0.00 0.00 2.57
809 815 6.510317 GCTTGACGAGTAAGATTGCCTAATTC 60.510 42.308 0.00 0.00 0.00 2.17
810 816 5.294552 GCTTGACGAGTAAGATTGCCTAATT 59.705 40.000 0.00 0.00 0.00 1.40
811 817 4.811557 GCTTGACGAGTAAGATTGCCTAAT 59.188 41.667 0.00 0.00 0.00 1.73
812 818 4.081642 AGCTTGACGAGTAAGATTGCCTAA 60.082 41.667 0.00 0.00 0.00 2.69
813 819 3.447586 AGCTTGACGAGTAAGATTGCCTA 59.552 43.478 0.00 0.00 0.00 3.93
814 820 2.234908 AGCTTGACGAGTAAGATTGCCT 59.765 45.455 0.00 0.00 0.00 4.75
815 821 2.349886 CAGCTTGACGAGTAAGATTGCC 59.650 50.000 0.00 0.00 0.00 4.52
816 822 2.349886 CCAGCTTGACGAGTAAGATTGC 59.650 50.000 0.00 0.00 0.00 3.56
817 823 3.849911 TCCAGCTTGACGAGTAAGATTG 58.150 45.455 0.00 0.00 0.00 2.67
818 824 4.537135 TTCCAGCTTGACGAGTAAGATT 57.463 40.909 0.00 0.00 0.00 2.40
819 825 4.246458 GTTTCCAGCTTGACGAGTAAGAT 58.754 43.478 0.00 0.00 0.00 2.40
820 826 3.554337 GGTTTCCAGCTTGACGAGTAAGA 60.554 47.826 0.00 0.00 0.00 2.10
821 827 2.737252 GGTTTCCAGCTTGACGAGTAAG 59.263 50.000 0.00 0.00 0.00 2.34
822 828 2.367567 AGGTTTCCAGCTTGACGAGTAA 59.632 45.455 0.00 0.00 0.00 2.24
823 829 1.968493 AGGTTTCCAGCTTGACGAGTA 59.032 47.619 0.00 0.00 0.00 2.59
824 830 0.759346 AGGTTTCCAGCTTGACGAGT 59.241 50.000 0.00 0.00 0.00 4.18
825 831 1.270305 TGAGGTTTCCAGCTTGACGAG 60.270 52.381 0.00 0.00 0.00 4.18
826 832 0.756294 TGAGGTTTCCAGCTTGACGA 59.244 50.000 0.00 0.00 0.00 4.20
827 833 1.151668 CTGAGGTTTCCAGCTTGACG 58.848 55.000 0.00 0.00 0.00 4.35
834 840 1.871772 CTTGCGCTGAGGTTTCCAG 59.128 57.895 9.73 0.00 34.88 3.86
835 841 2.260869 GCTTGCGCTGAGGTTTCCA 61.261 57.895 9.73 0.00 0.00 3.53
836 842 1.795170 TTGCTTGCGCTGAGGTTTCC 61.795 55.000 9.73 0.00 36.97 3.13
837 843 0.661483 GTTGCTTGCGCTGAGGTTTC 60.661 55.000 9.73 0.00 36.97 2.78
838 844 1.360192 GTTGCTTGCGCTGAGGTTT 59.640 52.632 9.73 0.00 36.97 3.27
839 845 1.174712 ATGTTGCTTGCGCTGAGGTT 61.175 50.000 9.73 0.00 36.97 3.50
840 846 0.321564 TATGTTGCTTGCGCTGAGGT 60.322 50.000 9.73 0.00 36.97 3.85
841 847 0.804364 TTATGTTGCTTGCGCTGAGG 59.196 50.000 9.73 0.00 36.97 3.86
842 848 2.838386 ATTATGTTGCTTGCGCTGAG 57.162 45.000 9.73 8.06 36.97 3.35
843 849 3.487376 GCTTATTATGTTGCTTGCGCTGA 60.487 43.478 9.73 0.00 36.97 4.26
844 850 2.785477 GCTTATTATGTTGCTTGCGCTG 59.215 45.455 9.73 2.28 36.97 5.18
845 851 2.423185 TGCTTATTATGTTGCTTGCGCT 59.577 40.909 9.73 0.00 36.97 5.92
846 852 2.785477 CTGCTTATTATGTTGCTTGCGC 59.215 45.455 0.00 0.00 0.00 6.09
847 853 4.277257 TCTGCTTATTATGTTGCTTGCG 57.723 40.909 0.00 0.00 0.00 4.85
848 854 5.517770 CCTTTCTGCTTATTATGTTGCTTGC 59.482 40.000 0.00 0.00 0.00 4.01
849 855 5.517770 GCCTTTCTGCTTATTATGTTGCTTG 59.482 40.000 0.00 0.00 0.00 4.01
850 856 5.394553 GGCCTTTCTGCTTATTATGTTGCTT 60.395 40.000 0.00 0.00 0.00 3.91
851 857 4.098501 GGCCTTTCTGCTTATTATGTTGCT 59.901 41.667 0.00 0.00 0.00 3.91
852 858 4.363138 GGCCTTTCTGCTTATTATGTTGC 58.637 43.478 0.00 0.00 0.00 4.17
853 859 4.498009 CGGGCCTTTCTGCTTATTATGTTG 60.498 45.833 0.84 0.00 0.00 3.33
854 860 3.632145 CGGGCCTTTCTGCTTATTATGTT 59.368 43.478 0.84 0.00 0.00 2.71
855 861 3.214328 CGGGCCTTTCTGCTTATTATGT 58.786 45.455 0.84 0.00 0.00 2.29
856 862 2.554032 CCGGGCCTTTCTGCTTATTATG 59.446 50.000 0.84 0.00 0.00 1.90
857 863 2.863809 CCGGGCCTTTCTGCTTATTAT 58.136 47.619 0.84 0.00 0.00 1.28
858 864 1.749286 GCCGGGCCTTTCTGCTTATTA 60.749 52.381 8.12 0.00 0.00 0.98
859 865 1.037579 GCCGGGCCTTTCTGCTTATT 61.038 55.000 8.12 0.00 0.00 1.40
860 866 1.453928 GCCGGGCCTTTCTGCTTAT 60.454 57.895 8.12 0.00 0.00 1.73
861 867 2.045340 GCCGGGCCTTTCTGCTTA 60.045 61.111 8.12 0.00 0.00 3.09
878 884 4.729918 GGAGGGCAGTGCAGTGGG 62.730 72.222 22.71 0.00 0.00 4.61
879 885 3.201707 AAGGAGGGCAGTGCAGTGG 62.202 63.158 22.71 5.23 0.00 4.00
880 886 1.673665 GAAGGAGGGCAGTGCAGTG 60.674 63.158 18.61 17.56 0.00 3.66
881 887 2.753029 GAAGGAGGGCAGTGCAGT 59.247 61.111 18.61 2.21 0.00 4.40
882 888 2.045536 GGAAGGAGGGCAGTGCAG 60.046 66.667 18.61 0.00 0.00 4.41
883 889 2.530151 AGGAAGGAGGGCAGTGCA 60.530 61.111 18.61 0.00 0.00 4.57
884 890 2.270527 GAGGAAGGAGGGCAGTGC 59.729 66.667 6.55 6.55 0.00 4.40
885 891 2.993853 GGAGGAAGGAGGGCAGTG 59.006 66.667 0.00 0.00 0.00 3.66
886 892 2.685380 CGGAGGAAGGAGGGCAGT 60.685 66.667 0.00 0.00 0.00 4.40
887 893 2.364317 TCGGAGGAAGGAGGGCAG 60.364 66.667 0.00 0.00 0.00 4.85
888 894 2.683933 GTCGGAGGAAGGAGGGCA 60.684 66.667 0.00 0.00 0.00 5.36
889 895 2.683933 TGTCGGAGGAAGGAGGGC 60.684 66.667 0.00 0.00 0.00 5.19
890 896 2.060980 CCTGTCGGAGGAAGGAGGG 61.061 68.421 0.00 0.00 46.33 4.30
891 897 1.305381 ACCTGTCGGAGGAAGGAGG 60.305 63.158 8.26 0.00 46.33 4.30
892 898 0.612174 TCACCTGTCGGAGGAAGGAG 60.612 60.000 8.26 1.60 46.33 3.69
893 899 0.178944 TTCACCTGTCGGAGGAAGGA 60.179 55.000 8.26 1.18 46.33 3.36
894 900 0.685097 TTTCACCTGTCGGAGGAAGG 59.315 55.000 8.26 0.88 46.33 3.46
895 901 1.338200 CCTTTCACCTGTCGGAGGAAG 60.338 57.143 8.26 2.46 46.33 3.46
896 902 0.685097 CCTTTCACCTGTCGGAGGAA 59.315 55.000 8.26 0.00 46.33 3.36
897 903 0.178944 TCCTTTCACCTGTCGGAGGA 60.179 55.000 8.26 0.00 46.33 3.71
899 905 2.543777 TTTCCTTTCACCTGTCGGAG 57.456 50.000 0.00 0.00 0.00 4.63
900 906 3.284793 TTTTTCCTTTCACCTGTCGGA 57.715 42.857 0.00 0.00 0.00 4.55
919 925 3.690628 TCGACCTTTCGGTTTGAGTTTTT 59.309 39.130 0.00 0.00 45.73 1.94
920 926 3.272581 TCGACCTTTCGGTTTGAGTTTT 58.727 40.909 0.00 0.00 45.73 2.43
921 927 2.870411 CTCGACCTTTCGGTTTGAGTTT 59.130 45.455 0.00 0.00 45.73 2.66
922 928 2.101917 TCTCGACCTTTCGGTTTGAGTT 59.898 45.455 11.77 0.00 45.73 3.01
923 929 1.684983 TCTCGACCTTTCGGTTTGAGT 59.315 47.619 11.77 0.00 45.73 3.41
924 930 2.059541 GTCTCGACCTTTCGGTTTGAG 58.940 52.381 7.83 7.83 45.73 3.02
925 931 1.269936 GGTCTCGACCTTTCGGTTTGA 60.270 52.381 8.82 0.00 45.73 2.69
926 932 1.145803 GGTCTCGACCTTTCGGTTTG 58.854 55.000 8.82 0.00 45.73 2.93
927 933 3.601277 GGTCTCGACCTTTCGGTTT 57.399 52.632 8.82 0.00 45.73 3.27
937 943 2.502080 CGCACTCGTGGTCTCGAC 60.502 66.667 0.00 0.00 35.91 4.20
938 944 3.733960 CCGCACTCGTGGTCTCGA 61.734 66.667 0.00 0.00 38.06 4.04
961 967 4.351054 GGGCACAGGTGGGTGGAG 62.351 72.222 1.10 0.00 39.19 3.86
962 968 3.492457 TAGGGCACAGGTGGGTGGA 62.492 63.158 1.10 0.00 39.19 4.02
963 969 2.933287 TAGGGCACAGGTGGGTGG 60.933 66.667 1.10 0.00 39.19 4.61
964 970 2.185310 GACTAGGGCACAGGTGGGTG 62.185 65.000 1.10 0.00 41.72 4.61
965 971 1.918800 GACTAGGGCACAGGTGGGT 60.919 63.158 1.10 0.00 0.00 4.51
966 972 2.670148 GGACTAGGGCACAGGTGGG 61.670 68.421 1.10 0.00 0.00 4.61
967 973 2.990479 GGACTAGGGCACAGGTGG 59.010 66.667 1.10 0.00 0.00 4.61
968 974 2.579201 CGGACTAGGGCACAGGTG 59.421 66.667 0.00 0.00 0.00 4.00
969 975 2.683933 CCGGACTAGGGCACAGGT 60.684 66.667 0.00 0.00 0.00 4.00
989 995 4.864334 CCTCCATGTCTGGCCGGC 62.864 72.222 21.18 21.18 42.80 6.13
990 996 4.864334 GCCTCCATGTCTGGCCGG 62.864 72.222 4.71 4.71 42.80 6.13
1012 1018 2.822215 TCCTCTTCGGCATAGGACC 58.178 57.895 0.00 0.00 34.46 4.46
1014 1020 0.106868 TCGTCCTCTTCGGCATAGGA 60.107 55.000 0.00 0.00 37.07 2.94
1015 1021 0.744874 TTCGTCCTCTTCGGCATAGG 59.255 55.000 0.00 0.00 0.00 2.57
1016 1022 2.579207 TTTCGTCCTCTTCGGCATAG 57.421 50.000 0.00 0.00 0.00 2.23
1017 1023 3.536956 AATTTCGTCCTCTTCGGCATA 57.463 42.857 0.00 0.00 0.00 3.14
1018 1024 2.403252 AATTTCGTCCTCTTCGGCAT 57.597 45.000 0.00 0.00 0.00 4.40
1019 1025 2.178912 AAATTTCGTCCTCTTCGGCA 57.821 45.000 0.00 0.00 0.00 5.69
1020 1026 2.028883 CGTAAATTTCGTCCTCTTCGGC 59.971 50.000 0.00 0.00 0.00 5.54
1021 1027 2.601763 CCGTAAATTTCGTCCTCTTCGG 59.398 50.000 0.00 0.00 0.00 4.30
1022 1028 2.028883 GCCGTAAATTTCGTCCTCTTCG 59.971 50.000 0.00 0.00 0.00 3.79
1023 1029 2.028883 CGCCGTAAATTTCGTCCTCTTC 59.971 50.000 0.00 0.00 0.00 2.87
1024 1030 1.997606 CGCCGTAAATTTCGTCCTCTT 59.002 47.619 0.00 0.00 0.00 2.85
1025 1031 1.636988 CGCCGTAAATTTCGTCCTCT 58.363 50.000 0.00 0.00 0.00 3.69
1026 1032 0.025898 GCGCCGTAAATTTCGTCCTC 59.974 55.000 0.00 0.00 0.00 3.71
1027 1033 1.363885 GGCGCCGTAAATTTCGTCCT 61.364 55.000 12.58 0.00 0.00 3.85
1028 1034 1.061411 GGCGCCGTAAATTTCGTCC 59.939 57.895 12.58 0.00 0.00 4.79
1029 1035 1.061411 GGGCGCCGTAAATTTCGTC 59.939 57.895 22.54 0.00 0.00 4.20
1030 1036 2.400962 GGGGCGCCGTAAATTTCGT 61.401 57.895 22.54 0.00 0.00 3.85
1031 1037 2.405997 GGGGCGCCGTAAATTTCG 59.594 61.111 22.54 0.00 0.00 3.46
1032 1038 2.802792 GGGGGCGCCGTAAATTTC 59.197 61.111 22.54 2.98 0.00 2.17
1176 1182 4.899239 GCGAGGATCTGGGTGCGG 62.899 72.222 0.00 0.00 0.00 5.69
1290 1296 1.154488 CGGATGCGTTGAAACCGTG 60.154 57.895 0.00 0.00 38.97 4.94
1362 1368 1.586154 GGAGCCATTTGTCCACCGTG 61.586 60.000 0.00 0.00 32.55 4.94
1365 1371 0.608035 TTCGGAGCCATTTGTCCACC 60.608 55.000 0.00 0.00 32.55 4.61
1387 1393 4.410400 GAGGTTGTCCAGGGCGGG 62.410 72.222 0.00 0.00 35.89 6.13
1428 1434 2.020131 CTGCGGTCGATAGTACGGT 58.980 57.895 0.00 0.00 36.95 4.83
1431 1437 1.370172 CGGCTGCGGTCGATAGTAC 60.370 63.158 16.09 0.00 44.06 2.73
1458 1464 4.856801 ATGGACGATGGTGGCGGC 62.857 66.667 0.00 0.00 35.64 6.53
1587 1593 1.216444 GCACTCCGAGATGCTGACA 59.784 57.895 1.33 0.00 38.84 3.58
1639 1645 1.896220 CTAACCAGCAAGCACTCCAA 58.104 50.000 0.00 0.00 0.00 3.53
1675 1681 0.809241 GAGTTGATCCTGAGGCAGCG 60.809 60.000 0.00 0.00 0.00 5.18
1758 1764 2.730090 GCAAGGTGCATTCTCGACAATG 60.730 50.000 8.86 8.86 44.26 2.82
1759 1765 1.470098 GCAAGGTGCATTCTCGACAAT 59.530 47.619 0.00 0.00 44.26 2.71
1788 1794 4.553323 AGTCAAAATCAAGATGCAGCAAC 58.447 39.130 4.07 0.00 0.00 4.17
1794 1800 6.493116 CAGACCATAGTCAAAATCAAGATGC 58.507 40.000 0.00 0.00 46.15 3.91
1827 1833 1.080435 GTTTAGGCGCGGACACTACC 61.080 60.000 8.83 0.00 0.00 3.18
1830 1836 1.374252 CAGTTTAGGCGCGGACACT 60.374 57.895 8.83 0.00 0.00 3.55
1833 1839 1.810030 CTCCAGTTTAGGCGCGGAC 60.810 63.158 8.83 0.00 0.00 4.79
1855 1861 1.144503 CCCATCAGAAAGGCAGCCTAT 59.855 52.381 16.56 0.00 31.13 2.57
1891 1897 2.813754 CGAGTCTGGAGAGATCATCCTC 59.186 54.545 15.69 9.16 37.74 3.71
1892 1898 2.174639 ACGAGTCTGGAGAGATCATCCT 59.825 50.000 15.69 0.95 37.74 3.24
1893 1899 2.293122 CACGAGTCTGGAGAGATCATCC 59.707 54.545 9.50 9.50 37.35 3.51
1905 1911 0.249868 TGGAGCCAAACACGAGTCTG 60.250 55.000 0.00 0.00 0.00 3.51
1926 1932 4.390909 CCAAACACGAGTACCTGAATAACC 59.609 45.833 0.00 0.00 0.00 2.85
1940 1946 0.981183 AGTAGGATGGCCAAACACGA 59.019 50.000 10.96 0.00 36.29 4.35
1941 1947 1.468520 CAAGTAGGATGGCCAAACACG 59.531 52.381 10.96 0.00 36.29 4.49
1942 1948 2.514803 ACAAGTAGGATGGCCAAACAC 58.485 47.619 10.96 5.72 36.29 3.32
1943 1949 2.890311 CAACAAGTAGGATGGCCAAACA 59.110 45.455 10.96 0.00 36.29 2.83
1944 1950 2.352715 GCAACAAGTAGGATGGCCAAAC 60.353 50.000 10.96 5.56 36.29 2.93
1971 1977 5.247110 ACAGAGATAAAACTGAGAAGCCTCA 59.753 40.000 0.00 0.00 46.48 3.86
1973 1979 5.483583 AGACAGAGATAAAACTGAGAAGCCT 59.516 40.000 0.00 0.00 37.54 4.58
1996 2002 4.925054 CACATGGTGTTATTTTTCCTGCAG 59.075 41.667 6.78 6.78 0.00 4.41
2011 2017 0.662619 AACGACAAGTGCACATGGTG 59.337 50.000 24.49 18.00 36.51 4.17
2098 2104 8.671921 CATATTGACAGCTAAATTCTTCACTGT 58.328 33.333 0.00 0.00 40.85 3.55
2172 2178 4.937620 TCAATGTACATCTTCTCCAAGCAC 59.062 41.667 9.23 0.00 0.00 4.40
2187 2193 6.861065 TGAAGAACTTTCACCTCAATGTAC 57.139 37.500 0.00 0.00 0.00 2.90
2258 2264 3.181480 ACAAATGGAAACCAACCACTTCG 60.181 43.478 0.00 0.00 40.36 3.79
2334 2340 4.007659 ACATTTGGTAAGATTCCGGTGTC 58.992 43.478 0.00 0.37 0.00 3.67
2455 2461 5.410924 CCGATCTGAAGTGTCATTAACTCA 58.589 41.667 0.00 0.00 31.85 3.41
2466 2472 1.153289 CTGGCCCCGATCTGAAGTG 60.153 63.158 0.00 0.00 0.00 3.16
2477 2483 0.555769 TCATTGTAATCCCTGGCCCC 59.444 55.000 0.00 0.00 0.00 5.80
2479 2485 4.817318 TTTTTCATTGTAATCCCTGGCC 57.183 40.909 0.00 0.00 0.00 5.36
2491 2497 6.847956 TGTTCTGCCAAGAATTTTTCATTG 57.152 33.333 0.00 0.00 44.18 2.82
2498 2504 4.023193 CCTACGTTGTTCTGCCAAGAATTT 60.023 41.667 0.00 0.00 44.18 1.82
2535 2541 2.101415 GCACCTCTTGAAGCCTTGTTTT 59.899 45.455 0.00 0.00 0.00 2.43
2549 2555 2.568623 AAATGAAACCGAGCACCTCT 57.431 45.000 0.00 0.00 0.00 3.69
2580 2586 1.285641 CAAACACCACGGGCACATC 59.714 57.895 0.00 0.00 0.00 3.06
2647 2653 4.373156 AATGGACAAGAGCCACTTTACT 57.627 40.909 0.00 0.00 38.44 2.24
2648 2654 5.222631 CAAAATGGACAAGAGCCACTTTAC 58.777 41.667 0.00 0.00 33.04 2.01
2649 2655 4.280677 CCAAAATGGACAAGAGCCACTTTA 59.719 41.667 0.00 0.00 40.96 1.85
2653 2659 2.238521 TCCAAAATGGACAAGAGCCAC 58.761 47.619 0.00 0.00 42.67 5.01
2671 2677 9.788960 GATAGGTTAACATTGAAGAACAATTCC 57.211 33.333 8.10 0.00 45.60 3.01
2677 2683 8.779354 ACTGAGATAGGTTAACATTGAAGAAC 57.221 34.615 8.10 0.00 0.00 3.01
2691 2697 7.618019 TGCCAGAATAATAACTGAGATAGGT 57.382 36.000 0.00 0.00 36.38 3.08
2700 2706 9.643693 CAATCAAGTTTTGCCAGAATAATAACT 57.356 29.630 0.00 0.00 0.00 2.24
2704 2710 6.973229 GCAATCAAGTTTTGCCAGAATAAT 57.027 33.333 1.47 0.00 42.84 1.28
2762 2768 8.349983 GCTAGTTTAAATGTTTGAGGTTTCAGA 58.650 33.333 0.00 0.00 34.15 3.27
2763 2769 8.352942 AGCTAGTTTAAATGTTTGAGGTTTCAG 58.647 33.333 0.00 0.00 34.15 3.02
2764 2770 8.134895 CAGCTAGTTTAAATGTTTGAGGTTTCA 58.865 33.333 0.00 0.00 0.00 2.69
2765 2771 8.135529 ACAGCTAGTTTAAATGTTTGAGGTTTC 58.864 33.333 0.00 0.00 0.00 2.78
2766 2772 8.007405 ACAGCTAGTTTAAATGTTTGAGGTTT 57.993 30.769 0.00 0.00 0.00 3.27
2767 2773 7.582667 ACAGCTAGTTTAAATGTTTGAGGTT 57.417 32.000 0.00 0.00 0.00 3.50
2768 2774 7.582667 AACAGCTAGTTTAAATGTTTGAGGT 57.417 32.000 0.00 0.00 37.03 3.85
2799 2805 5.879763 AGGCTGCCACATGTTATATCATAA 58.120 37.500 22.65 0.00 0.00 1.90
2802 2808 3.862877 AGGCTGCCACATGTTATATCA 57.137 42.857 22.65 0.00 0.00 2.15
2803 2809 3.304928 GCAAGGCTGCCACATGTTATATC 60.305 47.826 22.65 0.00 43.26 1.63
2806 2812 0.819582 GCAAGGCTGCCACATGTTAT 59.180 50.000 22.65 0.00 43.26 1.89
2839 2845 9.224267 CCTCAATATTACAATCAGATTACCCTG 57.776 37.037 0.00 0.00 35.55 4.45
2867 2873 8.867097 TGTAGCTACCCTACCATTCTTAATTAG 58.133 37.037 21.01 0.00 44.77 1.73
2875 2881 5.354842 AAGTTGTAGCTACCCTACCATTC 57.645 43.478 21.01 1.80 44.77 2.67
2879 2885 7.333323 TCAAAATAAGTTGTAGCTACCCTACC 58.667 38.462 21.01 4.59 44.77 3.18
2883 2889 8.957466 AGAAATCAAAATAAGTTGTAGCTACCC 58.043 33.333 21.01 11.50 0.00 3.69
2894 2900 8.477419 TCCTTTCACCAGAAATCAAAATAAGT 57.523 30.769 0.00 0.00 42.49 2.24
2895 2901 9.933723 ATTCCTTTCACCAGAAATCAAAATAAG 57.066 29.630 0.00 0.00 42.49 1.73
2898 2904 8.534496 CCTATTCCTTTCACCAGAAATCAAAAT 58.466 33.333 0.00 0.00 42.49 1.82
2899 2905 7.728083 TCCTATTCCTTTCACCAGAAATCAAAA 59.272 33.333 0.00 0.00 42.49 2.44
2917 2923 8.361889 GTCTCCATAACTCTAACTTCCTATTCC 58.638 40.741 0.00 0.00 0.00 3.01
2918 2924 8.915036 TGTCTCCATAACTCTAACTTCCTATTC 58.085 37.037 0.00 0.00 0.00 1.75
2986 2992 0.815095 ACCGCACATCATGTACTCGA 59.185 50.000 7.57 0.00 0.00 4.04
3300 3306 1.955495 ATACGCATCTCCGCCACACA 61.955 55.000 0.00 0.00 0.00 3.72
3461 3467 1.156645 CGCTATGCACTGGAGCTTCC 61.157 60.000 9.31 0.00 36.96 3.46
3585 3591 2.171448 CACCCCTGTTCATAGCTAGCTT 59.829 50.000 24.88 8.10 0.00 3.74


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

AutoCloner maintained by Alex Coulton.