Multiple sequence alignment - TraesCS5B01G149000

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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 TraesCS5B01G149000 chr5B 100.000 4067 0 0 1 4067 276961767 276957701 0.000000e+00 7511.0
1 TraesCS5B01G149000 chr5B 84.144 555 68 11 1 543 700042972 700042426 1.680000e-143 520.0
2 TraesCS5B01G149000 chr5B 81.688 628 98 12 1 622 681096015 681096631 1.300000e-139 507.0
3 TraesCS5B01G149000 chr5D 97.389 2911 72 2 894 3804 243834773 243831867 0.000000e+00 4951.0
4 TraesCS5B01G149000 chr5D 83.813 556 67 11 1 543 551758812 551758267 1.300000e-139 507.0
5 TraesCS5B01G149000 chr5D 100.000 28 0 0 3995 4022 74428098 74428071 7.000000e-03 52.8
6 TraesCS5B01G149000 chr5A 97.573 2184 53 0 911 3094 328009684 328007501 0.000000e+00 3740.0
7 TraesCS5B01G149000 chr5A 86.622 897 62 24 3129 3987 328007501 328006625 0.000000e+00 939.0
8 TraesCS5B01G149000 chr5A 100.000 28 0 0 3995 4022 69798456 69798429 7.000000e-03 52.8
9 TraesCS5B01G149000 chr6D 86.328 629 73 11 29 653 350126343 350125724 0.000000e+00 673.0
10 TraesCS5B01G149000 chr6D 100.000 29 0 0 3993 4021 147149346 147149374 2.000000e-03 54.7
11 TraesCS5B01G149000 chr6B 84.738 629 84 10 29 653 529865474 529866094 1.610000e-173 619.0
12 TraesCS5B01G149000 chr6B 84.565 609 77 9 29 636 529877669 529878261 4.530000e-164 588.0
13 TraesCS5B01G149000 chr6B 100.000 29 0 0 3993 4021 258013287 258013259 2.000000e-03 54.7
14 TraesCS5B01G149000 chr6A 83.046 637 76 16 29 653 493973840 493974456 2.140000e-152 549.0
15 TraesCS5B01G149000 chr6A 100.000 29 0 0 3993 4021 200254536 200254508 2.000000e-03 54.7
16 TraesCS5B01G149000 chr3D 89.252 428 41 4 1 424 116478283 116477857 7.740000e-147 531.0
17 TraesCS5B01G149000 chr3D 76.887 636 111 20 54 677 438063550 438062939 1.090000e-85 327.0
18 TraesCS5B01G149000 chr3D 79.096 177 20 7 535 695 116477799 116477624 5.560000e-19 106.0
19 TraesCS5B01G149000 chrUn 82.343 606 89 7 42 639 97298376 97298971 1.010000e-140 510.0
20 TraesCS5B01G149000 chrUn 79.433 141 20 7 648 782 97203990 97204127 1.560000e-14 91.6
21 TraesCS5B01G149000 chr1D 82.716 567 82 14 185 739 445649609 445650171 1.310000e-134 490.0
22 TraesCS5B01G149000 chr3B 77.273 594 88 27 52 625 11086065 11085499 5.110000e-79 305.0
23 TraesCS5B01G149000 chr2B 74.933 375 77 12 283 645 781282660 781282291 5.440000e-34 156.0
24 TraesCS5B01G149000 chr2B 94.737 38 2 0 3995 4032 350299954 350299991 4.390000e-05 60.2
25 TraesCS5B01G149000 chr2D 76.754 228 44 8 422 645 236666316 236666094 7.140000e-23 119.0
26 TraesCS5B01G149000 chr2D 95.122 41 2 0 3995 4035 270480431 270480391 9.440000e-07 65.8
27 TraesCS5B01G149000 chr4A 89.796 49 5 0 3994 4042 673086275 673086227 3.390000e-06 63.9
28 TraesCS5B01G149000 chr2A 97.297 37 1 0 3996 4032 346210511 346210475 3.390000e-06 63.9


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 TraesCS5B01G149000 chr5B 276957701 276961767 4066 True 7511.0 7511 100.0000 1 4067 1 chr5B.!!$R1 4066
1 TraesCS5B01G149000 chr5B 700042426 700042972 546 True 520.0 520 84.1440 1 543 1 chr5B.!!$R2 542
2 TraesCS5B01G149000 chr5B 681096015 681096631 616 False 507.0 507 81.6880 1 622 1 chr5B.!!$F1 621
3 TraesCS5B01G149000 chr5D 243831867 243834773 2906 True 4951.0 4951 97.3890 894 3804 1 chr5D.!!$R2 2910
4 TraesCS5B01G149000 chr5D 551758267 551758812 545 True 507.0 507 83.8130 1 543 1 chr5D.!!$R3 542
5 TraesCS5B01G149000 chr5A 328006625 328009684 3059 True 2339.5 3740 92.0975 911 3987 2 chr5A.!!$R2 3076
6 TraesCS5B01G149000 chr6D 350125724 350126343 619 True 673.0 673 86.3280 29 653 1 chr6D.!!$R1 624
7 TraesCS5B01G149000 chr6B 529865474 529866094 620 False 619.0 619 84.7380 29 653 1 chr6B.!!$F1 624
8 TraesCS5B01G149000 chr6B 529877669 529878261 592 False 588.0 588 84.5650 29 636 1 chr6B.!!$F2 607
9 TraesCS5B01G149000 chr6A 493973840 493974456 616 False 549.0 549 83.0460 29 653 1 chr6A.!!$F1 624
10 TraesCS5B01G149000 chr3D 438062939 438063550 611 True 327.0 327 76.8870 54 677 1 chr3D.!!$R1 623
11 TraesCS5B01G149000 chr3D 116477624 116478283 659 True 318.5 531 84.1740 1 695 2 chr3D.!!$R2 694
12 TraesCS5B01G149000 chrUn 97298376 97298971 595 False 510.0 510 82.3430 42 639 1 chrUn.!!$F2 597
13 TraesCS5B01G149000 chr1D 445649609 445650171 562 False 490.0 490 82.7160 185 739 1 chr1D.!!$F1 554
14 TraesCS5B01G149000 chr3B 11085499 11086065 566 True 305.0 305 77.2730 52 625 1 chr3B.!!$R1 573

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
510 566 0.039074 CTCTTGTGCGGTCTCGAACT 60.039 55.0 0.00 0.0 44.96 3.01 F
864 945 0.099613 TTGTTCTTTTTGCAGCGCGA 59.900 45.0 12.10 0.0 0.00 5.87 F
880 961 0.106819 GCGAGTACTCTACCTCCCCA 60.107 60.0 20.34 0.0 0.00 4.96 F
1777 1858 0.759959 TTCCCGTGGACAGCTAAACA 59.240 50.0 0.00 0.0 0.00 2.83 F
2884 2965 0.182061 GGGCAATGAGGCTCTGATCA 59.818 55.0 16.72 0.0 43.56 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2154 0.179089 CTCGACAAGCATCCTCCCAG 60.179 60.000 0.00 0.00 0.00 4.45 R
2609 2690 0.178533 TGTCCGTTCGGTTGGTCTTT 59.821 50.000 11.04 0.00 0.00 2.52 R
2858 2939 1.823041 GCCTCATTGCCCTGAGCTC 60.823 63.158 6.82 6.82 44.23 4.09 R
2997 3078 2.172505 ACGCATCATACCCCTCATTTCA 59.827 45.455 0.00 0.00 0.00 2.69 R
3945 4066 0.323178 AGCAGGAGCACCAGATTTGG 60.323 55.000 2.07 0.00 45.49 3.28 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
39 41 9.781834 TGCAAATAAAACTAGATAAAACGATGG 57.218 29.630 0.00 0.00 0.00 3.51
237 264 2.050351 ACGTGTGACTCGCTTCGG 60.050 61.111 6.99 0.00 0.00 4.30
248 275 4.087892 GCTTCGGCCTCCTCTGCA 62.088 66.667 0.00 0.00 34.32 4.41
287 314 1.670087 CGACGACATCTTGCTGGAAGT 60.670 52.381 8.80 0.00 35.30 3.01
437 483 1.265568 GCGCGTTCGAGAAGTTCATA 58.734 50.000 8.43 0.00 38.10 2.15
510 566 0.039074 CTCTTGTGCGGTCTCGAACT 60.039 55.000 0.00 0.00 44.96 3.01
523 579 1.153628 CGAACTTTCCGAGCCCGAT 60.154 57.895 0.00 0.00 38.22 4.18
531 587 1.956170 CCGAGCCCGATGCATGTAC 60.956 63.158 2.46 0.00 44.83 2.90
597 654 4.880537 CGCAGCGGTAGCCTGAGG 62.881 72.222 7.00 0.00 46.67 3.86
679 754 1.215647 GAAGCGAGGAAGAAGGCGA 59.784 57.895 0.00 0.00 0.00 5.54
690 771 1.040339 AGAAGGCGAGGCGAGAAGAT 61.040 55.000 0.00 0.00 0.00 2.40
694 775 2.656651 CGAGGCGAGAAGATGGCG 60.657 66.667 0.00 0.00 32.50 5.69
698 779 1.745489 GGCGAGAAGATGGCGGTTT 60.745 57.895 0.00 0.00 32.50 3.27
725 806 4.217111 CGCGCGCGGCTTTTATCA 62.217 61.111 43.28 0.00 40.44 2.15
729 810 1.136565 GCGCGGCTTTTATCAAGCA 59.863 52.632 8.83 0.00 44.71 3.91
732 813 0.168128 GCGGCTTTTATCAAGCACGT 59.832 50.000 8.74 0.00 44.71 4.49
739 820 2.442212 TTATCAAGCACGTTGGACGA 57.558 45.000 7.54 0.00 46.05 4.20
740 821 1.705256 TATCAAGCACGTTGGACGAC 58.295 50.000 7.54 0.00 46.05 4.34
741 822 0.249699 ATCAAGCACGTTGGACGACA 60.250 50.000 7.54 0.00 46.05 4.35
742 823 1.149361 TCAAGCACGTTGGACGACAC 61.149 55.000 7.54 0.00 46.05 3.67
743 824 2.235016 AAGCACGTTGGACGACACG 61.235 57.895 7.54 0.00 46.05 4.49
744 825 2.894240 AAGCACGTTGGACGACACGT 62.894 55.000 7.54 0.00 46.05 4.49
745 826 2.917901 CACGTTGGACGACACGTG 59.082 61.111 15.48 15.48 46.05 4.49
746 827 2.958016 ACGTTGGACGACACGTGC 60.958 61.111 17.22 7.72 46.05 5.34
751 832 3.412061 GGACGACACGTGCCAAAA 58.588 55.556 17.22 0.00 42.09 2.44
752 833 1.010462 GGACGACACGTGCCAAAAC 60.010 57.895 17.22 2.53 42.09 2.43
753 834 1.433837 GGACGACACGTGCCAAAACT 61.434 55.000 17.22 0.00 42.09 2.66
754 835 0.315869 GACGACACGTGCCAAAACTG 60.316 55.000 17.22 0.00 41.37 3.16
755 836 1.654137 CGACACGTGCCAAAACTGC 60.654 57.895 17.22 0.00 0.00 4.40
756 837 1.299089 GACACGTGCCAAAACTGCC 60.299 57.895 17.22 0.00 0.00 4.85
757 838 2.353376 CACGTGCCAAAACTGCCG 60.353 61.111 0.82 0.00 0.00 5.69
758 839 3.591835 ACGTGCCAAAACTGCCGG 61.592 61.111 0.00 0.00 0.00 6.13
759 840 4.341502 CGTGCCAAAACTGCCGGG 62.342 66.667 2.18 0.00 0.00 5.73
760 841 4.662961 GTGCCAAAACTGCCGGGC 62.663 66.667 13.32 13.32 46.58 6.13
779 860 4.536687 CGATGCCGCTTTTCCGCC 62.537 66.667 0.00 0.00 0.00 6.13
780 861 4.193334 GATGCCGCTTTTCCGCCC 62.193 66.667 0.00 0.00 0.00 6.13
786 867 4.753877 GCTTTTCCGCCCGCGTTC 62.754 66.667 4.92 0.00 37.81 3.95
787 868 3.047877 CTTTTCCGCCCGCGTTCT 61.048 61.111 4.92 0.00 37.81 3.01
788 869 2.592287 TTTTCCGCCCGCGTTCTT 60.592 55.556 4.92 0.00 37.81 2.52
789 870 1.293267 CTTTTCCGCCCGCGTTCTTA 61.293 55.000 4.92 0.00 37.81 2.10
790 871 0.674269 TTTTCCGCCCGCGTTCTTAT 60.674 50.000 4.92 0.00 37.81 1.73
791 872 0.674269 TTTCCGCCCGCGTTCTTATT 60.674 50.000 4.92 0.00 37.81 1.40
792 873 0.674269 TTCCGCCCGCGTTCTTATTT 60.674 50.000 4.92 0.00 37.81 1.40
793 874 0.674269 TCCGCCCGCGTTCTTATTTT 60.674 50.000 4.92 0.00 37.81 1.82
794 875 0.169451 CCGCCCGCGTTCTTATTTTT 59.831 50.000 4.92 0.00 37.81 1.94
815 896 2.953466 TTTACGCGTCTATTGGAGCT 57.047 45.000 18.63 0.00 0.00 4.09
816 897 2.486951 TTACGCGTCTATTGGAGCTC 57.513 50.000 18.63 4.71 0.00 4.09
817 898 0.306840 TACGCGTCTATTGGAGCTCG 59.693 55.000 18.63 0.00 0.00 5.03
818 899 2.296480 CGCGTCTATTGGAGCTCGC 61.296 63.158 7.83 4.79 41.43 5.03
819 900 1.951631 GCGTCTATTGGAGCTCGCC 60.952 63.158 7.83 0.00 40.09 5.54
820 901 1.437573 CGTCTATTGGAGCTCGCCA 59.562 57.895 7.83 0.00 35.78 5.69
825 906 4.001248 TTGGAGCTCGCCAAATGG 57.999 55.556 7.83 0.00 44.55 3.16
835 916 2.502093 CCAAATGGCCATGCGCAT 59.498 55.556 21.63 19.28 40.31 4.73
836 917 1.740905 CCAAATGGCCATGCGCATA 59.259 52.632 24.84 7.98 40.31 3.14
837 918 0.598158 CCAAATGGCCATGCGCATAC 60.598 55.000 24.84 17.94 40.31 2.39
838 919 0.386476 CAAATGGCCATGCGCATACT 59.614 50.000 24.84 0.00 40.31 2.12
839 920 1.608109 CAAATGGCCATGCGCATACTA 59.392 47.619 24.84 16.51 40.31 1.82
840 921 1.979855 AATGGCCATGCGCATACTAA 58.020 45.000 24.84 10.02 40.31 2.24
841 922 1.979855 ATGGCCATGCGCATACTAAA 58.020 45.000 24.84 8.48 40.31 1.85
842 923 1.756430 TGGCCATGCGCATACTAAAA 58.244 45.000 24.84 4.01 40.31 1.52
843 924 2.305928 TGGCCATGCGCATACTAAAAT 58.694 42.857 24.84 0.00 40.31 1.82
844 925 2.034432 TGGCCATGCGCATACTAAAATG 59.966 45.455 24.84 9.66 40.31 2.32
845 926 2.034558 GGCCATGCGCATACTAAAATGT 59.965 45.455 24.84 0.00 40.31 2.71
846 927 3.490761 GGCCATGCGCATACTAAAATGTT 60.491 43.478 24.84 0.00 40.31 2.71
847 928 3.486841 GCCATGCGCATACTAAAATGTTG 59.513 43.478 24.84 7.45 37.47 3.33
848 929 4.671377 CCATGCGCATACTAAAATGTTGT 58.329 39.130 24.84 0.00 0.00 3.32
849 930 5.101628 CCATGCGCATACTAAAATGTTGTT 58.898 37.500 24.84 0.00 0.00 2.83
850 931 5.229887 CCATGCGCATACTAAAATGTTGTTC 59.770 40.000 24.84 0.00 0.00 3.18
851 932 5.621197 TGCGCATACTAAAATGTTGTTCT 57.379 34.783 5.66 0.00 0.00 3.01
852 933 6.007936 TGCGCATACTAAAATGTTGTTCTT 57.992 33.333 5.66 0.00 0.00 2.52
853 934 6.442952 TGCGCATACTAAAATGTTGTTCTTT 58.557 32.000 5.66 0.00 0.00 2.52
854 935 6.920758 TGCGCATACTAAAATGTTGTTCTTTT 59.079 30.769 5.66 0.00 0.00 2.27
855 936 7.436673 TGCGCATACTAAAATGTTGTTCTTTTT 59.563 29.630 5.66 0.00 37.26 1.94
856 937 7.735586 GCGCATACTAAAATGTTGTTCTTTTTG 59.264 33.333 0.30 0.00 35.79 2.44
857 938 7.735586 CGCATACTAAAATGTTGTTCTTTTTGC 59.264 33.333 0.00 0.00 35.79 3.68
858 939 8.547069 GCATACTAAAATGTTGTTCTTTTTGCA 58.453 29.630 0.00 0.00 35.79 4.08
860 941 7.003939 ACTAAAATGTTGTTCTTTTTGCAGC 57.996 32.000 0.00 0.00 35.79 5.25
861 942 4.519191 AAATGTTGTTCTTTTTGCAGCG 57.481 36.364 0.00 0.00 0.00 5.18
862 943 1.276415 TGTTGTTCTTTTTGCAGCGC 58.724 45.000 0.00 0.00 0.00 5.92
863 944 0.226984 GTTGTTCTTTTTGCAGCGCG 59.773 50.000 0.00 0.00 0.00 6.86
864 945 0.099613 TTGTTCTTTTTGCAGCGCGA 59.900 45.000 12.10 0.00 0.00 5.87
865 946 0.316937 TGTTCTTTTTGCAGCGCGAG 60.317 50.000 12.10 1.41 0.00 5.03
866 947 0.317020 GTTCTTTTTGCAGCGCGAGT 60.317 50.000 12.10 0.00 0.00 4.18
867 948 1.070175 GTTCTTTTTGCAGCGCGAGTA 60.070 47.619 12.10 0.00 0.00 2.59
868 949 0.511221 TCTTTTTGCAGCGCGAGTAC 59.489 50.000 12.10 0.00 0.00 2.73
869 950 0.512952 CTTTTTGCAGCGCGAGTACT 59.487 50.000 12.10 0.00 0.00 2.73
870 951 0.511221 TTTTTGCAGCGCGAGTACTC 59.489 50.000 12.10 13.18 0.00 2.59
871 952 0.319555 TTTTGCAGCGCGAGTACTCT 60.320 50.000 20.34 0.00 0.00 3.24
872 953 0.524414 TTTGCAGCGCGAGTACTCTA 59.476 50.000 20.34 0.00 0.00 2.43
873 954 0.179171 TTGCAGCGCGAGTACTCTAC 60.179 55.000 20.34 11.37 0.00 2.59
874 955 1.298488 GCAGCGCGAGTACTCTACC 60.298 63.158 20.34 8.13 0.00 3.18
875 956 1.716826 GCAGCGCGAGTACTCTACCT 61.717 60.000 20.34 10.16 0.00 3.08
876 957 0.305313 CAGCGCGAGTACTCTACCTC 59.695 60.000 20.34 4.46 0.00 3.85
877 958 0.814812 AGCGCGAGTACTCTACCTCC 60.815 60.000 20.34 3.54 0.00 4.30
878 959 1.784036 GCGCGAGTACTCTACCTCCC 61.784 65.000 20.34 0.00 0.00 4.30
879 960 1.165284 CGCGAGTACTCTACCTCCCC 61.165 65.000 20.34 0.00 0.00 4.81
880 961 0.106819 GCGAGTACTCTACCTCCCCA 60.107 60.000 20.34 0.00 0.00 4.96
881 962 1.479021 GCGAGTACTCTACCTCCCCAT 60.479 57.143 20.34 0.00 0.00 4.00
882 963 2.946785 CGAGTACTCTACCTCCCCATT 58.053 52.381 20.34 0.00 0.00 3.16
883 964 2.623889 CGAGTACTCTACCTCCCCATTG 59.376 54.545 20.34 0.00 0.00 2.82
884 965 2.966516 GAGTACTCTACCTCCCCATTGG 59.033 54.545 15.91 0.00 0.00 3.16
885 966 2.590611 AGTACTCTACCTCCCCATTGGA 59.409 50.000 3.62 0.00 42.41 3.53
893 974 3.347158 TCCCCATTGGAGATGCTCT 57.653 52.632 3.62 0.00 38.61 4.09
894 975 1.135094 TCCCCATTGGAGATGCTCTC 58.865 55.000 3.62 5.01 42.66 3.20
895 976 0.841961 CCCCATTGGAGATGCTCTCA 59.158 55.000 3.62 0.00 45.12 3.27
896 977 1.202782 CCCCATTGGAGATGCTCTCAG 60.203 57.143 3.62 3.04 45.12 3.35
897 978 1.489649 CCCATTGGAGATGCTCTCAGT 59.510 52.381 3.62 0.00 45.12 3.41
898 979 2.562635 CCATTGGAGATGCTCTCAGTG 58.437 52.381 13.06 8.86 45.12 3.66
899 980 2.093075 CCATTGGAGATGCTCTCAGTGT 60.093 50.000 13.06 0.00 45.12 3.55
900 981 3.133542 CCATTGGAGATGCTCTCAGTGTA 59.866 47.826 13.06 0.00 45.12 2.90
901 982 4.202336 CCATTGGAGATGCTCTCAGTGTAT 60.202 45.833 13.06 0.00 45.12 2.29
902 983 4.397481 TTGGAGATGCTCTCAGTGTATG 57.603 45.455 13.06 0.00 45.12 2.39
903 984 3.369175 TGGAGATGCTCTCAGTGTATGT 58.631 45.455 13.06 0.00 45.12 2.29
904 985 3.131755 TGGAGATGCTCTCAGTGTATGTG 59.868 47.826 13.06 0.00 45.12 3.21
905 986 3.131933 GGAGATGCTCTCAGTGTATGTGT 59.868 47.826 13.06 0.00 45.12 3.72
906 987 4.111198 GAGATGCTCTCAGTGTATGTGTG 58.889 47.826 7.93 0.00 42.90 3.82
907 988 2.749280 TGCTCTCAGTGTATGTGTGG 57.251 50.000 0.00 0.00 0.00 4.17
908 989 1.970640 TGCTCTCAGTGTATGTGTGGT 59.029 47.619 0.00 0.00 0.00 4.16
909 990 2.029020 TGCTCTCAGTGTATGTGTGGTC 60.029 50.000 0.00 0.00 0.00 4.02
936 1017 2.357517 GCACACCCGTGAGTCCAG 60.358 66.667 0.96 0.00 46.80 3.86
948 1029 2.887152 GTGAGTCCAGCAGTCCAAAAAT 59.113 45.455 0.00 0.00 0.00 1.82
951 1032 4.405358 TGAGTCCAGCAGTCCAAAAATTTT 59.595 37.500 0.00 0.00 0.00 1.82
1101 1182 2.266055 CTCCTCAAGTCCGGCCAC 59.734 66.667 2.24 0.00 0.00 5.01
1158 1239 0.892755 TCATGTACGCCCGTTTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
1367 1448 3.131478 GGATTTGGACACCGCCCG 61.131 66.667 0.00 0.00 0.00 6.13
1419 1500 1.439353 CTGTGGCTGTCAACGCTGTT 61.439 55.000 0.00 0.00 0.00 3.16
1489 1570 1.066858 TCAGAGAGATTGGTTCGGCAC 60.067 52.381 0.00 0.00 0.00 5.01
1576 1657 1.067142 GTGCTGACCGGATGAAGTACA 60.067 52.381 9.46 0.00 0.00 2.90
1597 1678 4.832266 ACAATTTTGGGAGACAAGTGCATA 59.168 37.500 0.00 0.00 40.82 3.14
1761 1842 2.289945 CCTGGTCTATGGCTATGCTTCC 60.290 54.545 0.00 0.00 0.00 3.46
1777 1858 0.759959 TTCCCGTGGACAGCTAAACA 59.240 50.000 0.00 0.00 0.00 2.83
1797 1878 9.567848 CTAAACAAGGCGTTACATATTTTTGAT 57.432 29.630 0.00 0.00 36.59 2.57
2069 2150 6.902341 TCATTGACTTCTACTCAAAATGCAC 58.098 36.000 0.00 0.00 31.48 4.57
2073 2154 4.327680 ACTTCTACTCAAAATGCACCCTC 58.672 43.478 0.00 0.00 0.00 4.30
2115 2196 4.319839 GCTTTCAGTGAGCTTAGGTTTCAC 60.320 45.833 0.00 4.27 41.10 3.18
2304 2385 1.065273 CAAGATGCATCGCCTTGGC 59.935 57.895 20.67 0.75 35.05 4.52
2487 2568 0.835941 ACTTGGCCAATGGTTGCAAA 59.164 45.000 20.85 0.00 0.00 3.68
2503 2584 7.102346 TGGTTGCAAAATTTTCGATGGAATAT 58.898 30.769 0.00 0.00 30.88 1.28
2609 2690 1.135139 GCTGATGAGAGTTAGCGGTGA 59.865 52.381 0.00 0.00 0.00 4.02
2658 2739 4.389576 CTTTCCGCGTGCTGCCAC 62.390 66.667 4.92 0.00 42.08 5.01
2695 2776 5.825593 AGAAGGACTGACATGGTTTAAGA 57.174 39.130 0.00 0.00 0.00 2.10
2858 2939 0.817013 ACAGTTGTTGGTGGTTGCAG 59.183 50.000 0.00 0.00 0.00 4.41
2884 2965 0.182061 GGGCAATGAGGCTCTGATCA 59.818 55.000 16.72 0.00 43.56 2.92
2925 3006 2.187239 AGCAGATGGAGGAATCAGGA 57.813 50.000 0.00 0.00 0.00 3.86
2997 3078 0.688749 GGGATTGGGCCAAATCAGCT 60.689 55.000 30.07 5.06 38.14 4.24
3218 3301 4.688413 TGCTGGAAAAACACAAACAAAGAC 59.312 37.500 0.00 0.00 0.00 3.01
3219 3302 4.688413 GCTGGAAAAACACAAACAAAGACA 59.312 37.500 0.00 0.00 0.00 3.41
3230 3313 6.027749 CACAAACAAAGACACACCTAGAAAC 58.972 40.000 0.00 0.00 0.00 2.78
3746 3865 2.358737 CTGAAGCCACCCACGGTC 60.359 66.667 0.00 0.00 31.02 4.79
3815 3935 6.515272 TTCAGATTGCAAGAAAAGTATCCC 57.485 37.500 4.94 0.00 0.00 3.85
3816 3936 4.635765 TCAGATTGCAAGAAAAGTATCCCG 59.364 41.667 4.94 0.00 0.00 5.14
3817 3937 3.947834 AGATTGCAAGAAAAGTATCCCGG 59.052 43.478 4.94 0.00 0.00 5.73
3818 3938 2.122783 TGCAAGAAAAGTATCCCGGG 57.877 50.000 16.85 16.85 0.00 5.73
3819 3939 1.631388 TGCAAGAAAAGTATCCCGGGA 59.369 47.619 29.18 29.18 0.00 5.14
3820 3940 2.014857 GCAAGAAAAGTATCCCGGGAC 58.985 52.381 29.69 15.88 0.00 4.46
3821 3941 2.640184 CAAGAAAAGTATCCCGGGACC 58.360 52.381 29.69 20.06 0.00 4.46
3856 3976 7.012515 TCTCTCTATTGAGATGAACCTACGAAC 59.987 40.741 7.34 0.00 46.93 3.95
3925 4045 6.539826 AGATGCATTTGAATATTGAGACACGA 59.460 34.615 0.00 0.00 0.00 4.35
3936 4056 3.637998 TGAGACACGACTAACTTCACC 57.362 47.619 0.00 0.00 0.00 4.02
3945 4066 4.142138 ACGACTAACTTCACCCTCATGATC 60.142 45.833 0.00 0.00 0.00 2.92
3951 4072 4.530875 ACTTCACCCTCATGATCCAAATC 58.469 43.478 0.00 0.00 0.00 2.17
3962 4083 2.295885 GATCCAAATCTGGTGCTCCTG 58.704 52.381 6.34 5.84 43.97 3.86
3970 4091 2.466846 TCTGGTGCTCCTGCTTACATA 58.533 47.619 6.34 0.00 40.48 2.29
3983 4104 8.492673 TCCTGCTTACATAAATACACTCTTTG 57.507 34.615 0.00 0.00 0.00 2.77
3988 4109 9.556030 GCTTACATAAATACACTCTTTGTTTCC 57.444 33.333 0.00 0.00 39.91 3.13
3990 4111 9.575868 TTACATAAATACACTCTTTGTTTCCCA 57.424 29.630 0.00 0.00 39.91 4.37
3991 4112 8.472007 ACATAAATACACTCTTTGTTTCCCAA 57.528 30.769 0.00 0.00 39.91 4.12
3992 4113 8.919145 ACATAAATACACTCTTTGTTTCCCAAA 58.081 29.630 0.00 0.00 40.71 3.28
3993 4114 9.927668 CATAAATACACTCTTTGTTTCCCAAAT 57.072 29.630 0.00 0.00 42.02 2.32
4004 4125 9.267084 TCTTTGTTTCCCAAATATTTAAACTGC 57.733 29.630 18.83 5.03 42.02 4.40
4005 4126 7.971183 TTGTTTCCCAAATATTTAAACTGCC 57.029 32.000 18.83 2.15 32.57 4.85
4006 4127 7.067496 TGTTTCCCAAATATTTAAACTGCCA 57.933 32.000 18.83 4.03 32.57 4.92
4007 4128 7.509546 TGTTTCCCAAATATTTAAACTGCCAA 58.490 30.769 18.83 3.73 32.57 4.52
4008 4129 7.993183 TGTTTCCCAAATATTTAAACTGCCAAA 59.007 29.630 18.83 3.23 32.57 3.28
4009 4130 8.841300 GTTTCCCAAATATTTAAACTGCCAAAA 58.159 29.630 13.98 0.48 0.00 2.44
4010 4131 7.971183 TCCCAAATATTTAAACTGCCAAAAC 57.029 32.000 0.00 0.00 0.00 2.43
4011 4132 6.647067 TCCCAAATATTTAAACTGCCAAAACG 59.353 34.615 0.00 0.00 0.00 3.60
4012 4133 6.425417 CCCAAATATTTAAACTGCCAAAACGT 59.575 34.615 0.00 0.00 0.00 3.99
4013 4134 7.359681 CCCAAATATTTAAACTGCCAAAACGTC 60.360 37.037 0.00 0.00 0.00 4.34
4014 4135 7.383843 CCAAATATTTAAACTGCCAAAACGTCT 59.616 33.333 0.00 0.00 0.00 4.18
4015 4136 8.760569 CAAATATTTAAACTGCCAAAACGTCTT 58.239 29.630 0.00 0.00 0.00 3.01
4016 4137 9.968870 AAATATTTAAACTGCCAAAACGTCTTA 57.031 25.926 0.00 0.00 0.00 2.10
4017 4138 8.959734 ATATTTAAACTGCCAAAACGTCTTAC 57.040 30.769 0.00 0.00 0.00 2.34
4018 4139 5.814764 TTAAACTGCCAAAACGTCTTACA 57.185 34.783 0.00 0.00 0.00 2.41
4019 4140 4.911514 AAACTGCCAAAACGTCTTACAT 57.088 36.364 0.00 0.00 0.00 2.29
4020 4141 4.911514 AACTGCCAAAACGTCTTACATT 57.088 36.364 0.00 0.00 0.00 2.71
4021 4142 4.483476 ACTGCCAAAACGTCTTACATTC 57.517 40.909 0.00 0.00 0.00 2.67
4022 4143 3.880490 ACTGCCAAAACGTCTTACATTCA 59.120 39.130 0.00 0.00 0.00 2.57
4023 4144 4.336993 ACTGCCAAAACGTCTTACATTCAA 59.663 37.500 0.00 0.00 0.00 2.69
4024 4145 5.163602 ACTGCCAAAACGTCTTACATTCAAA 60.164 36.000 0.00 0.00 0.00 2.69
4025 4146 5.651530 TGCCAAAACGTCTTACATTCAAAA 58.348 33.333 0.00 0.00 0.00 2.44
4026 4147 6.100004 TGCCAAAACGTCTTACATTCAAAAA 58.900 32.000 0.00 0.00 0.00 1.94
4027 4148 6.035112 TGCCAAAACGTCTTACATTCAAAAAC 59.965 34.615 0.00 0.00 0.00 2.43
4028 4149 6.035112 GCCAAAACGTCTTACATTCAAAAACA 59.965 34.615 0.00 0.00 0.00 2.83
4029 4150 7.608755 CCAAAACGTCTTACATTCAAAAACAG 58.391 34.615 0.00 0.00 0.00 3.16
4030 4151 7.486551 CCAAAACGTCTTACATTCAAAAACAGA 59.513 33.333 0.00 0.00 0.00 3.41
4031 4152 8.523464 CAAAACGTCTTACATTCAAAAACAGAG 58.477 33.333 0.00 0.00 0.00 3.35
4032 4153 6.300354 ACGTCTTACATTCAAAAACAGAGG 57.700 37.500 0.00 0.00 0.00 3.69
4033 4154 5.820947 ACGTCTTACATTCAAAAACAGAGGT 59.179 36.000 0.00 0.00 0.00 3.85
4034 4155 6.987992 ACGTCTTACATTCAAAAACAGAGGTA 59.012 34.615 0.00 0.00 0.00 3.08
4035 4156 7.042254 ACGTCTTACATTCAAAAACAGAGGTAC 60.042 37.037 0.00 0.00 0.00 3.34
4037 4158 8.837389 GTCTTACATTCAAAAACAGAGGTACTT 58.163 33.333 0.00 0.00 41.55 2.24
4038 4159 9.052759 TCTTACATTCAAAAACAGAGGTACTTC 57.947 33.333 0.00 0.00 41.55 3.01
4039 4160 6.635030 ACATTCAAAAACAGAGGTACTTCC 57.365 37.500 0.61 0.00 41.55 3.46
4057 4178 9.847224 GGTACTTCCTTGGATCTAAATTAATCA 57.153 33.333 0.00 0.00 0.00 2.57
4060 4181 9.277783 ACTTCCTTGGATCTAAATTAATCATCG 57.722 33.333 0.00 0.00 0.00 3.84
4061 4182 9.277783 CTTCCTTGGATCTAAATTAATCATCGT 57.722 33.333 0.00 0.00 0.00 3.73
4062 4183 9.627123 TTCCTTGGATCTAAATTAATCATCGTT 57.373 29.630 0.00 0.00 0.00 3.85
4063 4184 9.056005 TCCTTGGATCTAAATTAATCATCGTTG 57.944 33.333 0.00 0.00 0.00 4.10
4064 4185 9.056005 CCTTGGATCTAAATTAATCATCGTTGA 57.944 33.333 0.00 0.00 36.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 264 2.596851 TTCTGGGTGCAGAGGAGGC 61.597 63.158 0.00 0.00 32.21 4.70
424 462 1.409064 AGGCGCATATGAACTTCTCGA 59.591 47.619 10.83 0.00 0.00 4.04
494 550 1.214367 GAAAGTTCGAGACCGCACAA 58.786 50.000 0.00 0.00 34.44 3.33
497 553 1.372499 CGGAAAGTTCGAGACCGCA 60.372 57.895 0.00 0.00 37.32 5.69
510 566 1.819208 CATGCATCGGGCTCGGAAA 60.819 57.895 5.94 0.00 45.15 3.13
523 579 2.267642 GCTCCGGTGGTACATGCA 59.732 61.111 0.00 0.00 44.52 3.96
583 640 3.775654 GCACCTCAGGCTACCGCT 61.776 66.667 0.00 0.00 36.09 5.52
663 738 2.716017 CCTCGCCTTCTTCCTCGCT 61.716 63.158 0.00 0.00 0.00 4.93
679 754 2.185310 AAACCGCCATCTTCTCGCCT 62.185 55.000 0.00 0.00 0.00 5.52
709 790 1.934476 CTTGATAAAAGCCGCGCGC 60.934 57.895 27.36 23.91 37.98 6.86
717 798 3.185594 TCGTCCAACGTGCTTGATAAAAG 59.814 43.478 0.00 0.00 43.14 2.27
724 805 1.275657 GTGTCGTCCAACGTGCTTG 59.724 57.895 0.00 0.00 43.14 4.01
725 806 2.235016 CGTGTCGTCCAACGTGCTT 61.235 57.895 0.00 0.00 43.14 3.91
729 810 2.958016 GCACGTGTCGTCCAACGT 60.958 61.111 18.38 0.00 43.14 3.99
732 813 1.025113 TTTTGGCACGTGTCGTCCAA 61.025 50.000 16.50 17.36 41.37 3.53
762 843 4.536687 GGCGGAAAAGCGGCATCG 62.537 66.667 1.45 0.00 43.94 3.84
763 844 4.193334 GGGCGGAAAAGCGGCATC 62.193 66.667 1.45 0.00 43.94 3.91
769 850 4.753877 GAACGCGGGCGGAAAAGC 62.754 66.667 18.03 0.00 44.69 3.51
770 851 1.293267 TAAGAACGCGGGCGGAAAAG 61.293 55.000 18.03 0.00 44.69 2.27
771 852 0.674269 ATAAGAACGCGGGCGGAAAA 60.674 50.000 18.03 0.00 44.69 2.29
772 853 0.674269 AATAAGAACGCGGGCGGAAA 60.674 50.000 18.03 0.00 44.69 3.13
773 854 0.674269 AAATAAGAACGCGGGCGGAA 60.674 50.000 18.03 0.00 44.69 4.30
774 855 0.674269 AAAATAAGAACGCGGGCGGA 60.674 50.000 18.03 0.00 44.69 5.54
775 856 0.169451 AAAAATAAGAACGCGGGCGG 59.831 50.000 18.03 0.00 44.69 6.13
776 857 3.687340 AAAAATAAGAACGCGGGCG 57.313 47.368 12.47 12.04 46.03 6.13
794 875 3.592059 AGCTCCAATAGACGCGTAAAAA 58.408 40.909 13.97 0.00 0.00 1.94
795 876 3.184541 GAGCTCCAATAGACGCGTAAAA 58.815 45.455 13.97 0.00 0.00 1.52
796 877 2.793585 CGAGCTCCAATAGACGCGTAAA 60.794 50.000 13.97 2.88 0.00 2.01
797 878 1.268386 CGAGCTCCAATAGACGCGTAA 60.268 52.381 13.97 3.35 0.00 3.18
798 879 0.306840 CGAGCTCCAATAGACGCGTA 59.693 55.000 13.97 0.00 0.00 4.42
799 880 1.064296 CGAGCTCCAATAGACGCGT 59.936 57.895 13.85 13.85 0.00 6.01
800 881 2.296480 GCGAGCTCCAATAGACGCG 61.296 63.158 8.47 3.53 40.54 6.01
801 882 1.951631 GGCGAGCTCCAATAGACGC 60.952 63.158 8.47 5.84 45.22 5.19
802 883 0.179111 TTGGCGAGCTCCAATAGACG 60.179 55.000 8.47 0.00 40.92 4.18
803 884 2.024176 TTTGGCGAGCTCCAATAGAC 57.976 50.000 8.47 0.00 44.78 2.59
804 885 2.564771 CATTTGGCGAGCTCCAATAGA 58.435 47.619 8.47 0.00 44.78 1.98
805 886 1.605710 CCATTTGGCGAGCTCCAATAG 59.394 52.381 8.47 4.08 44.78 1.73
806 887 1.679139 CCATTTGGCGAGCTCCAATA 58.321 50.000 8.47 0.43 44.78 1.90
807 888 2.496942 CCATTTGGCGAGCTCCAAT 58.503 52.632 8.47 0.00 44.78 3.16
808 889 4.001248 CCATTTGGCGAGCTCCAA 57.999 55.556 8.47 5.35 43.84 3.53
818 899 0.598158 GTATGCGCATGGCCATTTGG 60.598 55.000 32.48 9.35 42.61 3.28
819 900 0.386476 AGTATGCGCATGGCCATTTG 59.614 50.000 32.48 12.77 42.61 2.32
820 901 1.979855 TAGTATGCGCATGGCCATTT 58.020 45.000 32.48 7.17 42.61 2.32
821 902 1.979855 TTAGTATGCGCATGGCCATT 58.020 45.000 32.48 11.96 42.61 3.16
822 903 1.979855 TTTAGTATGCGCATGGCCAT 58.020 45.000 32.48 14.09 42.61 4.40
823 904 1.756430 TTTTAGTATGCGCATGGCCA 58.244 45.000 32.48 8.56 42.61 5.36
824 905 2.034558 ACATTTTAGTATGCGCATGGCC 59.965 45.455 32.48 19.10 42.61 5.36
825 906 3.354089 ACATTTTAGTATGCGCATGGC 57.646 42.857 32.48 23.24 43.96 4.40
826 907 4.671377 ACAACATTTTAGTATGCGCATGG 58.329 39.130 32.48 13.02 0.00 3.66
827 908 6.029607 AGAACAACATTTTAGTATGCGCATG 58.970 36.000 32.48 17.12 0.00 4.06
828 909 6.194796 AGAACAACATTTTAGTATGCGCAT 57.805 33.333 28.23 28.23 0.00 4.73
829 910 5.621197 AGAACAACATTTTAGTATGCGCA 57.379 34.783 14.96 14.96 0.00 6.09
830 911 6.927933 AAAGAACAACATTTTAGTATGCGC 57.072 33.333 0.00 0.00 0.00 6.09
831 912 7.735586 GCAAAAAGAACAACATTTTAGTATGCG 59.264 33.333 0.00 0.00 30.02 4.73
832 913 8.547069 TGCAAAAAGAACAACATTTTAGTATGC 58.453 29.630 0.00 0.00 32.77 3.14
834 915 8.764287 GCTGCAAAAAGAACAACATTTTAGTAT 58.236 29.630 0.00 0.00 30.02 2.12
835 916 7.043722 CGCTGCAAAAAGAACAACATTTTAGTA 60.044 33.333 0.00 0.00 30.02 1.82
836 917 6.237808 CGCTGCAAAAAGAACAACATTTTAGT 60.238 34.615 0.00 0.00 30.02 2.24
837 918 6.122125 CGCTGCAAAAAGAACAACATTTTAG 58.878 36.000 0.00 0.00 30.02 1.85
838 919 5.501574 GCGCTGCAAAAAGAACAACATTTTA 60.502 36.000 0.00 0.00 30.02 1.52
839 920 4.727448 GCGCTGCAAAAAGAACAACATTTT 60.727 37.500 0.00 0.00 30.99 1.82
840 921 3.242381 GCGCTGCAAAAAGAACAACATTT 60.242 39.130 0.00 0.00 0.00 2.32
841 922 2.284952 GCGCTGCAAAAAGAACAACATT 59.715 40.909 0.00 0.00 0.00 2.71
842 923 1.860326 GCGCTGCAAAAAGAACAACAT 59.140 42.857 0.00 0.00 0.00 2.71
843 924 1.276415 GCGCTGCAAAAAGAACAACA 58.724 45.000 0.00 0.00 0.00 3.33
844 925 0.226984 CGCGCTGCAAAAAGAACAAC 59.773 50.000 5.56 0.00 0.00 3.32
845 926 0.099613 TCGCGCTGCAAAAAGAACAA 59.900 45.000 5.56 0.00 0.00 2.83
846 927 0.316937 CTCGCGCTGCAAAAAGAACA 60.317 50.000 5.56 0.00 0.00 3.18
847 928 0.317020 ACTCGCGCTGCAAAAAGAAC 60.317 50.000 5.56 0.00 0.00 3.01
848 929 1.070175 GTACTCGCGCTGCAAAAAGAA 60.070 47.619 5.56 0.00 0.00 2.52
849 930 0.511221 GTACTCGCGCTGCAAAAAGA 59.489 50.000 5.56 0.00 0.00 2.52
850 931 0.512952 AGTACTCGCGCTGCAAAAAG 59.487 50.000 5.56 0.00 0.00 2.27
851 932 0.511221 GAGTACTCGCGCTGCAAAAA 59.489 50.000 7.22 0.00 0.00 1.94
852 933 0.319555 AGAGTACTCGCGCTGCAAAA 60.320 50.000 17.07 0.00 34.09 2.44
853 934 0.524414 TAGAGTACTCGCGCTGCAAA 59.476 50.000 17.07 0.00 34.09 3.68
854 935 0.179171 GTAGAGTACTCGCGCTGCAA 60.179 55.000 17.07 0.00 34.09 4.08
855 936 1.428219 GTAGAGTACTCGCGCTGCA 59.572 57.895 17.07 0.00 34.09 4.41
856 937 1.298488 GGTAGAGTACTCGCGCTGC 60.298 63.158 17.07 3.49 34.09 5.25
857 938 0.305313 GAGGTAGAGTACTCGCGCTG 59.695 60.000 17.07 0.00 34.09 5.18
858 939 0.814812 GGAGGTAGAGTACTCGCGCT 60.815 60.000 17.07 12.35 34.58 5.92
859 940 1.648174 GGAGGTAGAGTACTCGCGC 59.352 63.158 17.07 10.81 34.58 6.86
860 941 1.165284 GGGGAGGTAGAGTACTCGCG 61.165 65.000 17.07 0.00 44.70 5.87
861 942 0.106819 TGGGGAGGTAGAGTACTCGC 60.107 60.000 17.07 13.49 43.51 5.03
862 943 2.623889 CAATGGGGAGGTAGAGTACTCG 59.376 54.545 17.07 0.00 34.58 4.18
863 944 2.966516 CCAATGGGGAGGTAGAGTACTC 59.033 54.545 15.41 15.41 40.01 2.59
864 945 2.590611 TCCAATGGGGAGGTAGAGTACT 59.409 50.000 0.00 0.00 42.15 2.73
865 946 3.042059 TCCAATGGGGAGGTAGAGTAC 57.958 52.381 0.00 0.00 42.15 2.73
886 967 3.193263 CCACACATACACTGAGAGCATC 58.807 50.000 0.00 0.00 0.00 3.91
887 968 2.568956 ACCACACATACACTGAGAGCAT 59.431 45.455 0.00 0.00 0.00 3.79
888 969 1.970640 ACCACACATACACTGAGAGCA 59.029 47.619 0.00 0.00 0.00 4.26
889 970 2.029020 TGACCACACATACACTGAGAGC 60.029 50.000 0.00 0.00 0.00 4.09
890 971 3.942130 TGACCACACATACACTGAGAG 57.058 47.619 0.00 0.00 0.00 3.20
891 972 4.890158 AATGACCACACATACACTGAGA 57.110 40.909 0.00 0.00 0.00 3.27
892 973 4.756642 ACAAATGACCACACATACACTGAG 59.243 41.667 0.00 0.00 0.00 3.35
893 974 4.713553 ACAAATGACCACACATACACTGA 58.286 39.130 0.00 0.00 0.00 3.41
894 975 5.468409 TGTACAAATGACCACACATACACTG 59.532 40.000 0.00 0.00 0.00 3.66
895 976 5.616270 TGTACAAATGACCACACATACACT 58.384 37.500 0.00 0.00 0.00 3.55
896 977 5.616866 GCTGTACAAATGACCACACATACAC 60.617 44.000 0.00 0.00 0.00 2.90
897 978 4.454161 GCTGTACAAATGACCACACATACA 59.546 41.667 0.00 0.00 0.00 2.29
898 979 4.454161 TGCTGTACAAATGACCACACATAC 59.546 41.667 0.00 0.00 0.00 2.39
899 980 4.454161 GTGCTGTACAAATGACCACACATA 59.546 41.667 0.00 0.00 0.00 2.29
900 981 3.253188 GTGCTGTACAAATGACCACACAT 59.747 43.478 0.00 0.00 0.00 3.21
901 982 2.616376 GTGCTGTACAAATGACCACACA 59.384 45.455 0.00 0.00 0.00 3.72
902 983 2.616376 TGTGCTGTACAAATGACCACAC 59.384 45.455 0.00 0.00 36.06 3.82
903 984 2.616376 GTGTGCTGTACAAATGACCACA 59.384 45.455 0.00 1.57 41.89 4.17
904 985 2.031157 GGTGTGCTGTACAAATGACCAC 60.031 50.000 0.00 0.00 41.89 4.16
905 986 2.226330 GGTGTGCTGTACAAATGACCA 58.774 47.619 0.00 0.00 41.89 4.02
906 987 1.539827 GGGTGTGCTGTACAAATGACC 59.460 52.381 0.00 1.25 41.89 4.02
907 988 1.196808 CGGGTGTGCTGTACAAATGAC 59.803 52.381 0.00 0.00 41.89 3.06
908 989 1.202710 ACGGGTGTGCTGTACAAATGA 60.203 47.619 0.00 0.00 41.89 2.57
909 990 1.069296 CACGGGTGTGCTGTACAAATG 60.069 52.381 0.00 0.00 41.89 2.32
948 1029 4.468153 AGTTAAACCCCAGAAAGTGCAAAA 59.532 37.500 0.00 0.00 0.00 2.44
951 1032 2.955660 CAGTTAAACCCCAGAAAGTGCA 59.044 45.455 0.00 0.00 0.00 4.57
1276 1357 1.519719 GCATGGAGCGGAAGAGACT 59.480 57.895 0.00 0.00 0.00 3.24
1314 1395 0.792640 CTGTGATCACTGCGTTCCAC 59.207 55.000 25.55 0.00 0.00 4.02
1367 1448 0.805322 CATCTCGTCCAGCAGACTGC 60.805 60.000 20.12 20.12 43.91 4.40
1419 1500 2.028476 GCACCGGACATACCTATGCATA 60.028 50.000 9.46 6.20 42.74 3.14
1576 1657 5.079643 ACTATGCACTTGTCTCCCAAAATT 58.920 37.500 0.00 0.00 31.20 1.82
1597 1678 0.396435 TTGGCAGTCACCATTCGACT 59.604 50.000 0.00 0.00 44.55 4.18
1761 1842 1.156736 CCTTGTTTAGCTGTCCACGG 58.843 55.000 0.00 0.00 0.00 4.94
1777 1858 6.831868 ACCCTATCAAAAATATGTAACGCCTT 59.168 34.615 0.00 0.00 0.00 4.35
2073 2154 0.179089 CTCGACAAGCATCCTCCCAG 60.179 60.000 0.00 0.00 0.00 4.45
2115 2196 3.261580 TGAATTGAGCACCACAGTATCG 58.738 45.455 0.00 0.00 0.00 2.92
2487 2568 6.293955 CGGGCTTGTATATTCCATCGAAAATT 60.294 38.462 0.00 0.00 0.00 1.82
2503 2584 0.892755 ATGACTTCGTCGGGCTTGTA 59.107 50.000 0.00 0.00 34.95 2.41
2609 2690 0.178533 TGTCCGTTCGGTTGGTCTTT 59.821 50.000 11.04 0.00 0.00 2.52
2658 2739 2.634940 TCCTTCTTCCACAAGTCCAGAG 59.365 50.000 0.00 0.00 0.00 3.35
2695 2776 4.461781 CAGACAGAAATCCTCCTGCATTTT 59.538 41.667 0.00 0.00 33.90 1.82
2858 2939 1.823041 GCCTCATTGCCCTGAGCTC 60.823 63.158 6.82 6.82 44.23 4.09
2925 3006 4.225942 ACATACAGACTGGAATGTGGTGAT 59.774 41.667 19.31 0.85 30.34 3.06
2997 3078 2.172505 ACGCATCATACCCCTCATTTCA 59.827 45.455 0.00 0.00 0.00 2.69
3655 3749 6.822170 TCATTGACTCAAGGATTTCTGATCTG 59.178 38.462 1.95 0.00 29.10 2.90
3746 3865 7.769272 TTTTGGAACAGCAATAAAAGAACTG 57.231 32.000 0.00 0.00 42.39 3.16
3815 3935 3.406595 GAGATTGCCCCAGGTCCCG 62.407 68.421 0.00 0.00 0.00 5.14
3816 3936 1.988982 GAGAGATTGCCCCAGGTCCC 61.989 65.000 0.00 0.00 0.00 4.46
3817 3937 0.985490 AGAGAGATTGCCCCAGGTCC 60.985 60.000 0.00 0.00 0.00 4.46
3818 3938 1.794714 TAGAGAGATTGCCCCAGGTC 58.205 55.000 0.00 0.00 0.00 3.85
3819 3939 2.441001 CAATAGAGAGATTGCCCCAGGT 59.559 50.000 0.00 0.00 30.43 4.00
3820 3940 2.707791 TCAATAGAGAGATTGCCCCAGG 59.292 50.000 0.00 0.00 36.85 4.45
3821 3941 3.645212 TCTCAATAGAGAGATTGCCCCAG 59.355 47.826 0.00 0.00 45.73 4.45
3849 3969 0.452987 TGTCCGGATTCCGTTCGTAG 59.547 55.000 22.83 7.34 46.80 3.51
3925 4045 4.104086 TGGATCATGAGGGTGAAGTTAGT 58.896 43.478 0.09 0.00 0.00 2.24
3945 4066 0.323178 AGCAGGAGCACCAGATTTGG 60.323 55.000 2.07 0.00 45.49 3.28
3951 4072 2.988010 TATGTAAGCAGGAGCACCAG 57.012 50.000 2.07 0.00 45.49 4.00
3962 4083 9.556030 GGAAACAAAGAGTGTATTTATGTAAGC 57.444 33.333 0.00 0.00 40.60 3.09
3983 4104 7.971183 TTGGCAGTTTAAATATTTGGGAAAC 57.029 32.000 11.05 12.59 0.00 2.78
3987 4108 6.425417 ACGTTTTGGCAGTTTAAATATTTGGG 59.575 34.615 11.05 0.00 0.00 4.12
3988 4109 7.383843 AGACGTTTTGGCAGTTTAAATATTTGG 59.616 33.333 11.05 0.00 0.00 3.28
3989 4110 8.293114 AGACGTTTTGGCAGTTTAAATATTTG 57.707 30.769 11.05 0.00 0.00 2.32
3990 4111 8.880878 AAGACGTTTTGGCAGTTTAAATATTT 57.119 26.923 5.89 5.89 0.00 1.40
3991 4112 9.401873 GTAAGACGTTTTGGCAGTTTAAATATT 57.598 29.630 0.83 0.00 0.00 1.28
3992 4113 8.569641 TGTAAGACGTTTTGGCAGTTTAAATAT 58.430 29.630 0.83 0.00 0.00 1.28
3993 4114 7.928103 TGTAAGACGTTTTGGCAGTTTAAATA 58.072 30.769 0.83 0.00 0.00 1.40
3994 4115 6.797454 TGTAAGACGTTTTGGCAGTTTAAAT 58.203 32.000 0.83 0.00 0.00 1.40
3995 4116 6.192234 TGTAAGACGTTTTGGCAGTTTAAA 57.808 33.333 0.83 0.00 0.00 1.52
3996 4117 5.814764 TGTAAGACGTTTTGGCAGTTTAA 57.185 34.783 0.83 0.00 0.00 1.52
3997 4118 6.038382 TGAATGTAAGACGTTTTGGCAGTTTA 59.962 34.615 0.83 0.00 0.00 2.01
3998 4119 4.911514 ATGTAAGACGTTTTGGCAGTTT 57.088 36.364 0.83 0.00 0.00 2.66
3999 4120 4.336993 TGAATGTAAGACGTTTTGGCAGTT 59.663 37.500 0.83 0.00 0.00 3.16
4000 4121 3.880490 TGAATGTAAGACGTTTTGGCAGT 59.120 39.130 0.83 0.13 0.00 4.40
4001 4122 4.481930 TGAATGTAAGACGTTTTGGCAG 57.518 40.909 0.83 0.00 0.00 4.85
4002 4123 4.902443 TTGAATGTAAGACGTTTTGGCA 57.098 36.364 0.83 1.32 0.00 4.92
4003 4124 6.035112 TGTTTTTGAATGTAAGACGTTTTGGC 59.965 34.615 0.83 0.00 0.00 4.52
4004 4125 7.486551 TCTGTTTTTGAATGTAAGACGTTTTGG 59.513 33.333 0.83 0.00 0.00 3.28
4005 4126 8.388319 TCTGTTTTTGAATGTAAGACGTTTTG 57.612 30.769 0.83 0.00 0.00 2.44
4006 4127 7.700656 CCTCTGTTTTTGAATGTAAGACGTTTT 59.299 33.333 0.00 0.00 0.00 2.43
4007 4128 7.148137 ACCTCTGTTTTTGAATGTAAGACGTTT 60.148 33.333 0.00 0.00 0.00 3.60
4008 4129 6.317893 ACCTCTGTTTTTGAATGTAAGACGTT 59.682 34.615 0.00 0.00 0.00 3.99
4009 4130 5.820947 ACCTCTGTTTTTGAATGTAAGACGT 59.179 36.000 0.00 0.00 0.00 4.34
4010 4131 6.300354 ACCTCTGTTTTTGAATGTAAGACG 57.700 37.500 0.00 0.00 0.00 4.18
4011 4132 8.379457 AGTACCTCTGTTTTTGAATGTAAGAC 57.621 34.615 0.00 0.00 0.00 3.01
4012 4133 8.974060 AAGTACCTCTGTTTTTGAATGTAAGA 57.026 30.769 0.00 0.00 0.00 2.10
4013 4134 8.290325 GGAAGTACCTCTGTTTTTGAATGTAAG 58.710 37.037 0.00 0.00 35.41 2.34
4014 4135 8.161699 GGAAGTACCTCTGTTTTTGAATGTAA 57.838 34.615 0.00 0.00 35.41 2.41
4015 4136 7.739498 GGAAGTACCTCTGTTTTTGAATGTA 57.261 36.000 0.00 0.00 35.41 2.29
4016 4137 6.635030 GGAAGTACCTCTGTTTTTGAATGT 57.365 37.500 0.00 0.00 35.41 2.71
4031 4152 9.847224 TGATTAATTTAGATCCAAGGAAGTACC 57.153 33.333 0.00 0.00 39.35 3.34
4034 4155 9.277783 CGATGATTAATTTAGATCCAAGGAAGT 57.722 33.333 0.00 0.00 0.00 3.01
4035 4156 9.277783 ACGATGATTAATTTAGATCCAAGGAAG 57.722 33.333 0.00 0.00 0.00 3.46
4036 4157 9.627123 AACGATGATTAATTTAGATCCAAGGAA 57.373 29.630 0.00 0.00 0.00 3.36
4037 4158 9.056005 CAACGATGATTAATTTAGATCCAAGGA 57.944 33.333 0.00 0.00 0.00 3.36
4038 4159 9.056005 TCAACGATGATTAATTTAGATCCAAGG 57.944 33.333 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.