Multiple sequence alignment - TraesCS3A01G225300

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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 TraesCS3A01G225300 chr3A 100.000 3080 0 0 1 3080 422618265 422621344 0.000000e+00 5688
1 TraesCS3A01G225300 chr3D 92.191 2241 62 27 873 3080 309946240 309944080 0.000000e+00 3064
2 TraesCS3A01G225300 chr3B 90.756 2250 107 33 870 3080 411293316 411295503 0.000000e+00 2909
3 TraesCS3A01G225300 chr7A 93.777 707 24 7 1 698 195525912 195526607 0.000000e+00 1044
4 TraesCS3A01G225300 chr7A 85.575 409 52 6 147 550 554472399 554471993 3.670000e-114 422
5 TraesCS3A01G225300 chr7A 91.304 184 16 0 698 881 195546919 195547102 5.100000e-63 252
6 TraesCS3A01G225300 chr5D 84.518 394 53 7 163 550 553781200 553781591 1.730000e-102 383


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 TraesCS3A01G225300 chr3A 422618265 422621344 3079 False 5688 5688 100.000 1 3080 1 chr3A.!!$F1 3079
1 TraesCS3A01G225300 chr3D 309944080 309946240 2160 True 3064 3064 92.191 873 3080 1 chr3D.!!$R1 2207
2 TraesCS3A01G225300 chr3B 411293316 411295503 2187 False 2909 2909 90.756 870 3080 1 chr3B.!!$F1 2210
3 TraesCS3A01G225300 chr7A 195525912 195526607 695 False 1044 1044 93.777 1 698 1 chr7A.!!$F1 697

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
814 824 0.026933 CTCGTGACAGAGATCGGACG 59.973 60.0 0.0 0.0 40.57 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2750 2797 0.108615 ATCTTTGTCCTCGCCAGTCG 60.109 55.0 0.0 0.0 40.15 4.18 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
173 178 4.776308 AGACTAGTTTGGTTGGTAGGTAGG 59.224 45.833 0.00 0.00 0.00 3.18
222 227 1.199615 TCCATCCATCCGTACAAGCA 58.800 50.000 0.00 0.00 0.00 3.91
259 264 7.796838 TCTGAACTAAAAGAAACATCATCACG 58.203 34.615 0.00 0.00 0.00 4.35
269 274 0.458370 CATCATCACGTCCGACAGCA 60.458 55.000 0.00 0.00 0.00 4.41
306 311 1.434188 ATTAGGATCCCCGCATGTCA 58.566 50.000 8.55 0.00 37.58 3.58
335 340 5.335113 GCATGACAACTAGCTGAATTCAACA 60.335 40.000 9.88 0.00 0.00 3.33
344 349 4.553323 AGCTGAATTCAACAAGACAATGC 58.447 39.130 9.88 5.32 0.00 3.56
356 361 2.082231 AGACAATGCAGCTCACATGAC 58.918 47.619 0.00 0.00 0.00 3.06
374 379 3.381045 TGACAGACGAGATTCAACACAC 58.619 45.455 0.00 0.00 0.00 3.82
377 382 2.733552 CAGACGAGATTCAACACACCAG 59.266 50.000 0.00 0.00 0.00 4.00
396 401 1.073284 AGCGGGAAATTACCACACACT 59.927 47.619 0.00 0.00 0.00 3.55
441 446 3.181464 TGACCGTGAAATCCTACACACAA 60.181 43.478 0.00 0.00 36.91 3.33
498 503 4.680110 CAGGTCATAATCGACGAACATACC 59.320 45.833 0.00 6.64 36.73 2.73
499 504 4.340097 AGGTCATAATCGACGAACATACCA 59.660 41.667 16.85 0.00 36.73 3.25
500 505 5.045215 GGTCATAATCGACGAACATACCAA 58.955 41.667 0.00 0.00 36.73 3.67
511 516 3.374058 CGAACATACCAAATCACAGGACC 59.626 47.826 0.00 0.00 0.00 4.46
512 517 4.331968 GAACATACCAAATCACAGGACCA 58.668 43.478 0.00 0.00 0.00 4.02
513 518 4.591321 ACATACCAAATCACAGGACCAT 57.409 40.909 0.00 0.00 0.00 3.55
514 519 5.708736 ACATACCAAATCACAGGACCATA 57.291 39.130 0.00 0.00 0.00 2.74
515 520 6.073447 ACATACCAAATCACAGGACCATAA 57.927 37.500 0.00 0.00 0.00 1.90
516 521 6.489603 ACATACCAAATCACAGGACCATAAA 58.510 36.000 0.00 0.00 0.00 1.40
551 556 3.094498 GAGGCCGGGGTTGGGTAT 61.094 66.667 2.18 0.00 0.00 2.73
573 578 2.746359 GCCGAGATATGCTGCCCT 59.254 61.111 0.00 0.00 0.00 5.19
576 581 0.683973 CCGAGATATGCTGCCCTTCT 59.316 55.000 0.00 0.00 0.00 2.85
578 583 1.607509 CGAGATATGCTGCCCTTCTGG 60.608 57.143 0.00 0.00 37.09 3.86
597 602 1.215382 CACGGACATCGGAGAAGCA 59.785 57.895 0.00 0.00 43.58 3.91
605 610 3.474570 CGGAGAAGCAGGAGGGGG 61.475 72.222 0.00 0.00 0.00 5.40
693 703 3.982730 TCTCCATGGATCTCTCTCTCTCT 59.017 47.826 16.63 0.00 0.00 3.10
694 704 4.042062 TCTCCATGGATCTCTCTCTCTCTC 59.958 50.000 16.63 0.00 0.00 3.20
695 705 3.982730 TCCATGGATCTCTCTCTCTCTCT 59.017 47.826 11.44 0.00 0.00 3.10
696 706 4.042062 TCCATGGATCTCTCTCTCTCTCTC 59.958 50.000 11.44 0.00 0.00 3.20
697 707 4.042560 CCATGGATCTCTCTCTCTCTCTCT 59.957 50.000 5.56 0.00 0.00 3.10
698 708 4.963318 TGGATCTCTCTCTCTCTCTCTC 57.037 50.000 0.00 0.00 0.00 3.20
699 709 4.560739 TGGATCTCTCTCTCTCTCTCTCT 58.439 47.826 0.00 0.00 0.00 3.10
700 710 4.590647 TGGATCTCTCTCTCTCTCTCTCTC 59.409 50.000 0.00 0.00 0.00 3.20
701 711 4.837860 GGATCTCTCTCTCTCTCTCTCTCT 59.162 50.000 0.00 0.00 0.00 3.10
702 712 5.047377 GGATCTCTCTCTCTCTCTCTCTCTC 60.047 52.000 0.00 0.00 0.00 3.20
703 713 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
704 714 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
705 715 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
706 716 4.078922 TCTCTCTCTCTCTCTCTCTCTCCT 60.079 50.000 0.00 0.00 0.00 3.69
707 717 4.219115 TCTCTCTCTCTCTCTCTCTCCTC 58.781 52.174 0.00 0.00 0.00 3.71
708 718 4.078922 TCTCTCTCTCTCTCTCTCTCCTCT 60.079 50.000 0.00 0.00 0.00 3.69
709 719 5.134509 TCTCTCTCTCTCTCTCTCTCCTCTA 59.865 48.000 0.00 0.00 0.00 2.43
710 720 5.970289 TCTCTCTCTCTCTCTCTCCTCTAT 58.030 45.833 0.00 0.00 0.00 1.98
711 721 6.385443 TCTCTCTCTCTCTCTCTCCTCTATT 58.615 44.000 0.00 0.00 0.00 1.73
712 722 6.495181 TCTCTCTCTCTCTCTCTCCTCTATTC 59.505 46.154 0.00 0.00 0.00 1.75
713 723 6.385443 TCTCTCTCTCTCTCTCCTCTATTCT 58.615 44.000 0.00 0.00 0.00 2.40
714 724 6.268617 TCTCTCTCTCTCTCTCCTCTATTCTG 59.731 46.154 0.00 0.00 0.00 3.02
715 725 5.307976 TCTCTCTCTCTCTCCTCTATTCTGG 59.692 48.000 0.00 0.00 0.00 3.86
716 726 4.975147 TCTCTCTCTCTCCTCTATTCTGGT 59.025 45.833 0.00 0.00 0.00 4.00
717 727 5.431731 TCTCTCTCTCTCCTCTATTCTGGTT 59.568 44.000 0.00 0.00 0.00 3.67
718 728 5.445069 TCTCTCTCTCCTCTATTCTGGTTG 58.555 45.833 0.00 0.00 0.00 3.77
719 729 3.957497 TCTCTCTCCTCTATTCTGGTTGC 59.043 47.826 0.00 0.00 0.00 4.17
720 730 2.690497 TCTCTCCTCTATTCTGGTTGCG 59.310 50.000 0.00 0.00 0.00 4.85
721 731 2.690497 CTCTCCTCTATTCTGGTTGCGA 59.310 50.000 0.00 0.00 0.00 5.10
722 732 2.690497 TCTCCTCTATTCTGGTTGCGAG 59.310 50.000 0.00 0.00 0.00 5.03
723 733 1.757118 TCCTCTATTCTGGTTGCGAGG 59.243 52.381 0.00 0.00 39.44 4.63
724 734 1.757118 CCTCTATTCTGGTTGCGAGGA 59.243 52.381 0.00 0.00 40.27 3.71
725 735 2.223923 CCTCTATTCTGGTTGCGAGGAG 60.224 54.545 0.00 0.00 40.27 3.69
726 736 2.690497 CTCTATTCTGGTTGCGAGGAGA 59.310 50.000 0.00 0.00 0.00 3.71
727 737 3.096852 TCTATTCTGGTTGCGAGGAGAA 58.903 45.455 0.00 0.00 0.00 2.87
728 738 2.393271 ATTCTGGTTGCGAGGAGAAG 57.607 50.000 0.00 0.00 0.00 2.85
729 739 0.321671 TTCTGGTTGCGAGGAGAAGG 59.678 55.000 0.00 0.00 0.00 3.46
730 740 1.078848 CTGGTTGCGAGGAGAAGGG 60.079 63.158 0.00 0.00 0.00 3.95
731 741 1.535444 TGGTTGCGAGGAGAAGGGA 60.535 57.895 0.00 0.00 0.00 4.20
732 742 1.125093 TGGTTGCGAGGAGAAGGGAA 61.125 55.000 0.00 0.00 0.00 3.97
733 743 0.673956 GGTTGCGAGGAGAAGGGAAC 60.674 60.000 0.00 0.00 0.00 3.62
734 744 0.034896 GTTGCGAGGAGAAGGGAACA 59.965 55.000 0.00 0.00 33.00 3.18
735 745 0.034896 TTGCGAGGAGAAGGGAACAC 59.965 55.000 0.00 0.00 0.00 3.32
736 746 1.446272 GCGAGGAGAAGGGAACACG 60.446 63.158 0.00 0.00 0.00 4.49
737 747 1.965219 CGAGGAGAAGGGAACACGT 59.035 57.895 0.00 0.00 0.00 4.49
738 748 0.388649 CGAGGAGAAGGGAACACGTG 60.389 60.000 15.48 15.48 0.00 4.49
739 749 0.680061 GAGGAGAAGGGAACACGTGT 59.320 55.000 17.22 17.22 0.00 4.49
740 750 1.070289 GAGGAGAAGGGAACACGTGTT 59.930 52.381 32.77 32.77 41.64 3.32
741 751 1.489230 AGGAGAAGGGAACACGTGTTT 59.511 47.619 32.71 18.55 38.56 2.83
742 752 1.871676 GGAGAAGGGAACACGTGTTTC 59.128 52.381 32.71 30.47 38.56 2.78
743 753 2.484947 GGAGAAGGGAACACGTGTTTCT 60.485 50.000 32.85 29.10 38.56 2.52
744 754 2.544267 GAGAAGGGAACACGTGTTTCTG 59.456 50.000 32.85 3.19 38.56 3.02
745 755 1.002792 GAAGGGAACACGTGTTTCTGC 60.003 52.381 32.85 26.10 38.56 4.26
746 756 1.157870 AGGGAACACGTGTTTCTGCG 61.158 55.000 32.85 1.56 38.56 5.18
747 757 1.278637 GGAACACGTGTTTCTGCGG 59.721 57.895 32.71 0.00 38.56 5.69
748 758 1.278637 GAACACGTGTTTCTGCGGG 59.721 57.895 32.71 0.00 38.56 6.13
749 759 1.153329 AACACGTGTTTCTGCGGGA 60.153 52.632 27.70 0.00 33.93 5.14
750 760 0.745128 AACACGTGTTTCTGCGGGAA 60.745 50.000 27.70 0.00 33.93 3.97
751 761 1.157870 ACACGTGTTTCTGCGGGAAG 61.158 55.000 17.22 0.00 35.16 3.46
752 762 1.597027 ACGTGTTTCTGCGGGAAGG 60.597 57.895 0.00 0.00 35.16 3.46
753 763 1.301401 CGTGTTTCTGCGGGAAGGA 60.301 57.895 0.00 0.00 35.16 3.36
754 764 1.566018 CGTGTTTCTGCGGGAAGGAC 61.566 60.000 0.00 0.00 35.16 3.85
755 765 0.534203 GTGTTTCTGCGGGAAGGACA 60.534 55.000 0.00 0.00 35.16 4.02
756 766 0.534203 TGTTTCTGCGGGAAGGACAC 60.534 55.000 0.00 0.00 35.16 3.67
757 767 0.534203 GTTTCTGCGGGAAGGACACA 60.534 55.000 0.00 0.00 35.16 3.72
758 768 0.534203 TTTCTGCGGGAAGGACACAC 60.534 55.000 0.00 0.00 35.16 3.82
759 769 2.358737 CTGCGGGAAGGACACACC 60.359 66.667 0.00 0.00 39.35 4.16
763 773 3.948719 GGGAAGGACACACCGGCA 61.949 66.667 0.00 0.00 44.74 5.69
764 774 2.668550 GGAAGGACACACCGGCAC 60.669 66.667 0.00 0.00 44.74 5.01
777 787 2.112297 GGCACGGGTCAAAGTGGA 59.888 61.111 0.00 0.00 38.68 4.02
778 788 2.258726 GGCACGGGTCAAAGTGGAC 61.259 63.158 0.00 0.00 38.68 4.02
779 789 2.604174 GCACGGGTCAAAGTGGACG 61.604 63.158 0.00 0.00 38.70 4.79
780 790 1.959226 CACGGGTCAAAGTGGACGG 60.959 63.158 0.00 0.00 38.70 4.79
781 791 2.135581 ACGGGTCAAAGTGGACGGA 61.136 57.895 0.00 0.00 38.70 4.69
782 792 1.070105 CGGGTCAAAGTGGACGGAA 59.930 57.895 0.00 0.00 38.70 4.30
783 793 0.533308 CGGGTCAAAGTGGACGGAAA 60.533 55.000 0.00 0.00 38.70 3.13
784 794 1.682740 GGGTCAAAGTGGACGGAAAA 58.317 50.000 0.00 0.00 38.70 2.29
785 795 2.025898 GGGTCAAAGTGGACGGAAAAA 58.974 47.619 0.00 0.00 38.70 1.94
812 822 3.855159 TCTCGTGACAGAGATCGGA 57.145 52.632 3.65 0.00 41.86 4.55
813 823 1.370609 TCTCGTGACAGAGATCGGAC 58.629 55.000 3.65 0.00 41.86 4.79
814 824 0.026933 CTCGTGACAGAGATCGGACG 59.973 60.000 0.00 0.00 40.57 4.79
815 825 1.583967 CGTGACAGAGATCGGACGC 60.584 63.158 0.00 0.00 0.00 5.19
816 826 1.803943 GTGACAGAGATCGGACGCT 59.196 57.895 0.00 0.00 0.00 5.07
817 827 0.248296 GTGACAGAGATCGGACGCTC 60.248 60.000 2.41 2.41 0.00 5.03
818 828 1.010574 GACAGAGATCGGACGCTCG 60.011 63.158 4.62 0.00 36.29 5.03
819 829 2.329690 CAGAGATCGGACGCTCGG 59.670 66.667 4.62 1.19 36.29 4.63
820 830 2.180862 CAGAGATCGGACGCTCGGA 61.181 63.158 4.57 0.00 36.29 4.55
821 831 1.451567 AGAGATCGGACGCTCGGAA 60.452 57.895 4.62 0.00 36.29 4.30
822 832 1.030488 AGAGATCGGACGCTCGGAAA 61.030 55.000 4.62 0.00 36.29 3.13
823 833 0.179145 GAGATCGGACGCTCGGAAAA 60.179 55.000 0.00 0.00 29.49 2.29
824 834 0.245539 AGATCGGACGCTCGGAAAAA 59.754 50.000 0.00 0.00 29.49 1.94
825 835 0.369248 GATCGGACGCTCGGAAAAAC 59.631 55.000 0.00 0.00 29.49 2.43
826 836 1.349259 ATCGGACGCTCGGAAAAACG 61.349 55.000 0.00 0.00 29.49 3.60
827 837 2.858158 GGACGCTCGGAAAAACGG 59.142 61.111 0.00 0.00 0.00 4.44
828 838 1.665599 GGACGCTCGGAAAAACGGA 60.666 57.895 0.00 0.00 0.00 4.69
829 839 1.017701 GGACGCTCGGAAAAACGGAT 61.018 55.000 0.00 0.00 0.00 4.18
830 840 0.094730 GACGCTCGGAAAAACGGATG 59.905 55.000 0.00 0.00 0.00 3.51
831 841 0.320073 ACGCTCGGAAAAACGGATGA 60.320 50.000 0.00 0.00 0.00 2.92
832 842 0.793861 CGCTCGGAAAAACGGATGAA 59.206 50.000 0.00 0.00 0.00 2.57
833 843 1.201921 CGCTCGGAAAAACGGATGAAG 60.202 52.381 0.00 0.00 0.00 3.02
834 844 1.804748 GCTCGGAAAAACGGATGAAGT 59.195 47.619 0.00 0.00 0.00 3.01
835 845 2.159693 GCTCGGAAAAACGGATGAAGTC 60.160 50.000 0.00 0.00 0.00 3.01
836 846 2.415512 CTCGGAAAAACGGATGAAGTCC 59.584 50.000 0.00 0.00 44.10 3.85
852 862 6.449635 TGAAGTCCAATTAATTTCATCCGG 57.550 37.500 0.00 0.00 0.00 5.14
853 863 6.184068 TGAAGTCCAATTAATTTCATCCGGA 58.816 36.000 6.61 6.61 0.00 5.14
854 864 6.833416 TGAAGTCCAATTAATTTCATCCGGAT 59.167 34.615 12.38 12.38 0.00 4.18
855 865 6.639632 AGTCCAATTAATTTCATCCGGATG 57.360 37.500 34.42 34.42 40.09 3.51
856 866 6.364701 AGTCCAATTAATTTCATCCGGATGA 58.635 36.000 37.61 37.61 45.30 2.92
857 867 7.006509 AGTCCAATTAATTTCATCCGGATGAT 58.993 34.615 40.23 29.77 46.12 2.45
858 868 8.163408 AGTCCAATTAATTTCATCCGGATGATA 58.837 33.333 40.23 35.60 46.12 2.15
859 869 8.792633 GTCCAATTAATTTCATCCGGATGATAA 58.207 33.333 40.23 33.60 46.12 1.75
860 870 9.360901 TCCAATTAATTTCATCCGGATGATAAA 57.639 29.630 40.23 32.74 46.12 1.40
865 875 9.513906 TTAATTTCATCCGGATGATAAATAGCA 57.486 29.630 40.23 24.04 46.12 3.49
866 876 8.408043 AATTTCATCCGGATGATAAATAGCAA 57.592 30.769 40.23 29.60 46.12 3.91
867 877 8.585471 ATTTCATCCGGATGATAAATAGCAAT 57.415 30.769 40.23 30.29 46.12 3.56
868 878 8.408043 TTTCATCCGGATGATAAATAGCAATT 57.592 30.769 40.23 2.29 46.12 2.32
869 879 7.615582 TCATCCGGATGATAAATAGCAATTC 57.384 36.000 37.61 0.00 42.42 2.17
870 880 6.599244 TCATCCGGATGATAAATAGCAATTCC 59.401 38.462 37.61 0.00 42.42 3.01
871 881 4.935205 TCCGGATGATAAATAGCAATTCCG 59.065 41.667 0.00 11.74 41.39 4.30
922 932 0.109919 GCTCCCGTTTAAAAGCCACG 60.110 55.000 0.00 0.00 0.00 4.94
923 933 1.515081 CTCCCGTTTAAAAGCCACGA 58.485 50.000 0.00 0.00 35.93 4.35
924 934 1.463444 CTCCCGTTTAAAAGCCACGAG 59.537 52.381 0.00 0.00 35.93 4.18
951 961 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
952 962 3.018193 ACCACCACCACCACCACA 61.018 61.111 0.00 0.00 0.00 4.17
959 969 2.203337 CCACCACCACACCACCAG 60.203 66.667 0.00 0.00 0.00 4.00
960 970 2.595095 CACCACCACACCACCAGT 59.405 61.111 0.00 0.00 0.00 4.00
961 971 1.525995 CACCACCACACCACCAGTC 60.526 63.158 0.00 0.00 0.00 3.51
962 972 2.113139 CCACCACACCACCAGTCC 59.887 66.667 0.00 0.00 0.00 3.85
963 973 2.751731 CCACCACACCACCAGTCCA 61.752 63.158 0.00 0.00 0.00 4.02
964 974 1.525995 CACCACACCACCAGTCCAC 60.526 63.158 0.00 0.00 0.00 4.02
965 975 2.113139 CCACACCACCAGTCCACC 59.887 66.667 0.00 0.00 0.00 4.61
966 976 2.751731 CCACACCACCAGTCCACCA 61.752 63.158 0.00 0.00 0.00 4.17
1008 1018 3.261951 GCACACTCACACGCACGT 61.262 61.111 0.00 0.00 0.00 4.49
1009 1019 2.920869 CACACTCACACGCACGTC 59.079 61.111 0.00 0.00 0.00 4.34
1010 1020 2.279252 ACACTCACACGCACGTCC 60.279 61.111 0.00 0.00 0.00 4.79
1011 1021 2.279186 CACTCACACGCACGTCCA 60.279 61.111 0.00 0.00 0.00 4.02
1012 1022 2.027605 ACTCACACGCACGTCCAG 59.972 61.111 0.00 0.00 0.00 3.86
1013 1023 2.335011 CTCACACGCACGTCCAGA 59.665 61.111 0.00 0.00 0.00 3.86
1014 1024 2.016704 CTCACACGCACGTCCAGAC 61.017 63.158 0.00 0.00 0.00 3.51
1019 1029 2.126307 CGCACGTCCAGACTCCAG 60.126 66.667 0.00 0.00 0.00 3.86
1380 1402 3.044305 GCCAAGTTCTGCGCGTCT 61.044 61.111 8.43 0.00 0.00 4.18
1528 1550 4.882396 GCTCGGCGAGGCTCTTCC 62.882 72.222 35.03 15.12 0.00 3.46
1536 1558 2.444140 AGGCTCTTCCCCGCGTAT 60.444 61.111 4.92 0.00 34.51 3.06
1633 1655 0.173481 CAAGATCTCGAGGCGGTTGA 59.827 55.000 13.56 0.00 0.00 3.18
1857 1879 1.148310 ACTCGTTGGTTGATGAAGCG 58.852 50.000 0.00 0.00 31.82 4.68
1861 1883 1.662876 CGTTGGTTGATGAAGCGGTTG 60.663 52.381 3.70 0.00 31.82 3.77
1862 1884 1.336755 GTTGGTTGATGAAGCGGTTGT 59.663 47.619 3.70 0.00 31.82 3.32
1863 1885 1.234821 TGGTTGATGAAGCGGTTGTC 58.765 50.000 3.70 3.35 31.82 3.18
1886 1908 1.259507 GACGTGCGTTTCACTTTGCTA 59.740 47.619 0.00 0.00 43.46 3.49
1913 1935 3.527427 TCCATGTCGGAGCGCGAT 61.527 61.111 12.10 1.23 39.64 4.58
1975 1998 6.396829 ACTTGCACTCTCAAAGCTATTTTT 57.603 33.333 0.00 0.00 0.00 1.94
1997 2020 0.109597 CAGTGGGTTCGCATGCTTTC 60.110 55.000 17.13 5.27 0.00 2.62
1998 2021 1.212751 GTGGGTTCGCATGCTTTCC 59.787 57.895 17.13 13.86 0.00 3.13
1999 2022 1.976474 TGGGTTCGCATGCTTTCCC 60.976 57.895 24.42 24.42 35.85 3.97
2000 2023 1.976474 GGGTTCGCATGCTTTCCCA 60.976 57.895 25.48 0.92 35.43 4.37
2001 2024 1.212751 GGTTCGCATGCTTTCCCAC 59.787 57.895 17.13 2.93 0.00 4.61
2057 2091 1.887320 CGCTGAATTTCGCAAAGGAG 58.113 50.000 11.71 0.00 0.00 3.69
2067 2101 1.959985 TCGCAAAGGAGGCAATGAAAA 59.040 42.857 0.00 0.00 0.00 2.29
2125 2159 1.094785 CATGCGGTGGTTTAGGAAGG 58.905 55.000 0.00 0.00 0.00 3.46
2126 2160 0.034477 ATGCGGTGGTTTAGGAAGGG 60.034 55.000 0.00 0.00 0.00 3.95
2127 2161 1.128809 TGCGGTGGTTTAGGAAGGGA 61.129 55.000 0.00 0.00 0.00 4.20
2128 2162 0.037160 GCGGTGGTTTAGGAAGGGAA 59.963 55.000 0.00 0.00 0.00 3.97
2129 2163 1.949079 GCGGTGGTTTAGGAAGGGAAG 60.949 57.143 0.00 0.00 0.00 3.46
2168 2202 4.944962 TGTGTGTGAGTGAGTTCTTTTG 57.055 40.909 0.00 0.00 0.00 2.44
2250 2284 0.179250 CACATGTACAAGCGTCGTGC 60.179 55.000 0.00 0.00 46.98 5.34
2325 2359 5.591643 TCTTTTCGCATTGTACAAGAGAC 57.408 39.130 14.65 2.54 0.00 3.36
2332 2366 5.633601 TCGCATTGTACAAGAGACTTGTAAG 59.366 40.000 20.74 13.94 36.74 2.34
2333 2367 5.622378 GCATTGTACAAGAGACTTGTAAGC 58.378 41.667 20.74 17.93 36.74 3.09
2334 2368 5.409826 GCATTGTACAAGAGACTTGTAAGCT 59.590 40.000 20.74 9.36 36.74 3.74
2335 2369 6.619446 GCATTGTACAAGAGACTTGTAAGCTG 60.619 42.308 20.74 17.85 36.74 4.24
2336 2370 5.531122 TGTACAAGAGACTTGTAAGCTGT 57.469 39.130 20.74 1.74 36.74 4.40
2337 2371 6.644248 TGTACAAGAGACTTGTAAGCTGTA 57.356 37.500 20.74 2.46 36.74 2.74
2338 2372 7.046292 TGTACAAGAGACTTGTAAGCTGTAA 57.954 36.000 20.74 1.85 36.74 2.41
2380 2414 3.764972 AGTTAGGCACTTCACTCCTAGTC 59.235 47.826 0.00 0.00 41.75 2.59
2400 2434 3.068873 GTCCACTCCTAGCCTATTGACAG 59.931 52.174 0.00 0.00 0.00 3.51
2447 2481 3.539791 CCATTTCCATGGCCCCGC 61.540 66.667 6.96 0.00 43.95 6.13
2513 2550 3.153919 TGCTAAAATTCGGCCTCTTGTT 58.846 40.909 0.00 0.00 0.00 2.83
2543 2580 2.340337 ACTTGGCGTACGTAATGGTTC 58.660 47.619 17.90 0.00 0.00 3.62
2554 2592 2.420022 CGTAATGGTTCCTTCTTGGCTG 59.580 50.000 0.00 0.00 35.26 4.85
2566 2604 0.508641 CTTGGCTGTTTCGTCTCGTG 59.491 55.000 0.00 0.00 0.00 4.35
2701 2745 4.742201 CCGGTGCTGGTGGAGACG 62.742 72.222 0.00 0.00 0.00 4.18
2747 2794 1.068333 GTGTGTACGTACGATGTGGGT 60.068 52.381 24.41 0.00 0.00 4.51
2748 2795 1.068402 TGTGTACGTACGATGTGGGTG 60.068 52.381 24.41 0.00 0.00 4.61
2749 2796 0.527113 TGTACGTACGATGTGGGTGG 59.473 55.000 24.41 0.00 0.00 4.61
2750 2797 0.803380 GTACGTACGATGTGGGTGGC 60.803 60.000 24.41 0.00 0.00 5.01
2751 2798 2.268988 TACGTACGATGTGGGTGGCG 62.269 60.000 24.41 0.00 0.00 5.69
2752 2799 2.574929 GTACGATGTGGGTGGCGA 59.425 61.111 0.00 0.00 0.00 5.54
2753 2800 1.808390 GTACGATGTGGGTGGCGAC 60.808 63.158 0.00 0.00 0.00 5.19
2848 2903 0.041135 TTTCGGCTTTGTTTACGGCG 60.041 50.000 4.80 4.80 46.34 6.46
2871 2926 3.941483 CCTTTGTTTATCTCCATGCTCGT 59.059 43.478 0.00 0.00 0.00 4.18
2912 2967 2.096069 GCCTTTCGTTCGTTTACTTCCC 60.096 50.000 0.00 0.00 0.00 3.97
2936 2991 0.327673 TTTATCCCCGACCCCATCCA 60.328 55.000 0.00 0.00 0.00 3.41
2937 2992 1.057851 TTATCCCCGACCCCATCCAC 61.058 60.000 0.00 0.00 0.00 4.02
2938 2993 2.258928 TATCCCCGACCCCATCCACA 62.259 60.000 0.00 0.00 0.00 4.17
2966 3021 3.857854 GCCTGTGTGCGATGCGAG 61.858 66.667 0.00 0.00 0.00 5.03
3038 3093 2.037367 GGAGGAAAAGGGGGTGGC 59.963 66.667 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 87 8.429641 CACCACCCTGACAACTAAAGTATATAT 58.570 37.037 0.00 0.00 0.00 0.86
142 147 4.565652 CCAACCAAACTAGTCTACTGCCAT 60.566 45.833 0.00 0.00 0.00 4.40
173 178 1.200020 CATTTGTTTCCTCGCCCTCAC 59.800 52.381 0.00 0.00 0.00 3.51
222 227 6.379988 TCTTTTAGTTCAGAACCCTTGCTTTT 59.620 34.615 9.85 0.00 0.00 2.27
259 264 0.602638 TGTCCATGTTGCTGTCGGAC 60.603 55.000 0.00 0.00 45.24 4.79
269 274 6.434302 TCCTAATTTCATCCATGTCCATGTT 58.566 36.000 6.53 0.00 37.11 2.71
306 311 0.036010 AGCTAGTTGTCATGCGCCTT 60.036 50.000 4.18 0.00 0.00 4.35
335 340 2.486982 GTCATGTGAGCTGCATTGTCTT 59.513 45.455 1.02 0.00 0.00 3.01
344 349 1.200948 TCTCGTCTGTCATGTGAGCTG 59.799 52.381 0.00 0.00 0.00 4.24
356 361 2.733552 CTGGTGTGTTGAATCTCGTCTG 59.266 50.000 0.00 0.00 0.00 3.51
374 379 0.808755 GTGTGGTAATTTCCCGCTGG 59.191 55.000 0.00 0.00 33.54 4.85
377 382 1.530323 AGTGTGTGGTAATTTCCCGC 58.470 50.000 0.00 0.00 0.00 6.13
396 401 3.017048 TCTATTCCCCTTTCGTCCGTA 57.983 47.619 0.00 0.00 0.00 4.02
441 446 1.972795 TCGCTAGGGGTTGTTGTTAGT 59.027 47.619 6.99 0.00 0.00 2.24
498 503 4.685924 GGCATTTATGGTCCTGTGATTTG 58.314 43.478 0.00 0.00 0.00 2.32
499 504 3.381272 CGGCATTTATGGTCCTGTGATTT 59.619 43.478 0.00 0.00 0.00 2.17
500 505 2.951642 CGGCATTTATGGTCCTGTGATT 59.048 45.455 0.00 0.00 0.00 2.57
511 516 3.294493 CCCCCGCCGGCATTTATG 61.294 66.667 28.98 8.71 0.00 1.90
512 517 2.575455 TTTCCCCCGCCGGCATTTAT 62.575 55.000 28.98 0.00 0.00 1.40
513 518 2.575455 ATTTCCCCCGCCGGCATTTA 62.575 55.000 28.98 4.06 0.00 1.40
514 519 3.974573 ATTTCCCCCGCCGGCATTT 62.975 57.895 28.98 0.00 0.00 2.32
515 520 4.457181 ATTTCCCCCGCCGGCATT 62.457 61.111 28.98 0.00 0.00 3.56
551 556 3.233980 AGCATATCTCGGCCGCCA 61.234 61.111 23.51 9.70 0.00 5.69
554 559 2.740055 GGCAGCATATCTCGGCCG 60.740 66.667 22.12 22.12 35.28 6.13
573 578 2.225791 CTCCGATGTCCGTGCCAGAA 62.226 60.000 0.00 0.00 36.31 3.02
576 581 2.225791 CTTCTCCGATGTCCGTGCCA 62.226 60.000 0.00 0.00 36.31 4.92
578 583 2.167861 GCTTCTCCGATGTCCGTGC 61.168 63.158 0.00 0.00 36.31 5.34
580 585 1.513158 CTGCTTCTCCGATGTCCGT 59.487 57.895 0.00 0.00 36.31 4.69
589 594 1.925972 AACCCCCTCCTGCTTCTCC 60.926 63.158 0.00 0.00 0.00 3.71
693 703 4.975147 ACCAGAATAGAGGAGAGAGAGAGA 59.025 45.833 0.00 0.00 0.00 3.10
694 704 5.310409 ACCAGAATAGAGGAGAGAGAGAG 57.690 47.826 0.00 0.00 0.00 3.20
695 705 5.445069 CAACCAGAATAGAGGAGAGAGAGA 58.555 45.833 0.00 0.00 0.00 3.10
696 706 4.037923 GCAACCAGAATAGAGGAGAGAGAG 59.962 50.000 0.00 0.00 0.00 3.20
697 707 3.957497 GCAACCAGAATAGAGGAGAGAGA 59.043 47.826 0.00 0.00 0.00 3.10
698 708 3.243367 CGCAACCAGAATAGAGGAGAGAG 60.243 52.174 0.00 0.00 0.00 3.20
699 709 2.690497 CGCAACCAGAATAGAGGAGAGA 59.310 50.000 0.00 0.00 0.00 3.10
700 710 2.690497 TCGCAACCAGAATAGAGGAGAG 59.310 50.000 0.00 0.00 0.00 3.20
701 711 2.690497 CTCGCAACCAGAATAGAGGAGA 59.310 50.000 0.00 0.00 0.00 3.71
702 712 2.223923 CCTCGCAACCAGAATAGAGGAG 60.224 54.545 3.40 0.00 45.88 3.69
703 713 1.757118 CCTCGCAACCAGAATAGAGGA 59.243 52.381 3.40 0.00 45.88 3.71
704 714 1.757118 TCCTCGCAACCAGAATAGAGG 59.243 52.381 3.11 3.11 44.75 3.69
705 715 2.690497 TCTCCTCGCAACCAGAATAGAG 59.310 50.000 0.00 0.00 0.00 2.43
706 716 2.735151 TCTCCTCGCAACCAGAATAGA 58.265 47.619 0.00 0.00 0.00 1.98
707 717 3.452474 CTTCTCCTCGCAACCAGAATAG 58.548 50.000 0.00 0.00 0.00 1.73
708 718 2.168521 CCTTCTCCTCGCAACCAGAATA 59.831 50.000 0.00 0.00 0.00 1.75
709 719 1.065854 CCTTCTCCTCGCAACCAGAAT 60.066 52.381 0.00 0.00 0.00 2.40
710 720 0.321671 CCTTCTCCTCGCAACCAGAA 59.678 55.000 0.00 0.00 0.00 3.02
711 721 1.544825 CCCTTCTCCTCGCAACCAGA 61.545 60.000 0.00 0.00 0.00 3.86
712 722 1.078848 CCCTTCTCCTCGCAACCAG 60.079 63.158 0.00 0.00 0.00 4.00
713 723 1.125093 TTCCCTTCTCCTCGCAACCA 61.125 55.000 0.00 0.00 0.00 3.67
714 724 0.673956 GTTCCCTTCTCCTCGCAACC 60.674 60.000 0.00 0.00 0.00 3.77
715 725 0.034896 TGTTCCCTTCTCCTCGCAAC 59.965 55.000 0.00 0.00 0.00 4.17
716 726 0.034896 GTGTTCCCTTCTCCTCGCAA 59.965 55.000 0.00 0.00 0.00 4.85
717 727 1.671742 GTGTTCCCTTCTCCTCGCA 59.328 57.895 0.00 0.00 0.00 5.10
718 728 1.446272 CGTGTTCCCTTCTCCTCGC 60.446 63.158 0.00 0.00 0.00 5.03
719 729 0.388649 CACGTGTTCCCTTCTCCTCG 60.389 60.000 7.58 0.00 0.00 4.63
720 730 0.680061 ACACGTGTTCCCTTCTCCTC 59.320 55.000 17.22 0.00 0.00 3.71
721 731 1.129058 AACACGTGTTCCCTTCTCCT 58.871 50.000 27.70 1.89 31.64 3.69
722 732 1.871676 GAAACACGTGTTCCCTTCTCC 59.128 52.381 32.36 11.53 37.25 3.71
723 733 2.544267 CAGAAACACGTGTTCCCTTCTC 59.456 50.000 32.36 23.81 37.25 2.87
724 734 2.561569 CAGAAACACGTGTTCCCTTCT 58.438 47.619 32.36 26.48 37.25 2.85
725 735 1.002792 GCAGAAACACGTGTTCCCTTC 60.003 52.381 32.36 24.82 37.25 3.46
726 736 1.021968 GCAGAAACACGTGTTCCCTT 58.978 50.000 32.36 18.21 37.25 3.95
727 737 1.157870 CGCAGAAACACGTGTTCCCT 61.158 55.000 32.36 26.79 37.25 4.20
728 738 1.278637 CGCAGAAACACGTGTTCCC 59.721 57.895 32.36 25.21 37.25 3.97
729 739 1.278637 CCGCAGAAACACGTGTTCC 59.721 57.895 32.36 22.32 37.25 3.62
730 740 1.155424 TCCCGCAGAAACACGTGTTC 61.155 55.000 32.36 23.88 37.25 3.18
731 741 0.745128 TTCCCGCAGAAACACGTGTT 60.745 50.000 27.70 27.70 40.50 3.32
732 742 1.153329 TTCCCGCAGAAACACGTGT 60.153 52.632 17.22 17.22 0.00 4.49
733 743 1.569493 CTTCCCGCAGAAACACGTG 59.431 57.895 15.48 15.48 32.88 4.49
734 744 1.597027 CCTTCCCGCAGAAACACGT 60.597 57.895 0.00 0.00 32.88 4.49
735 745 1.301401 TCCTTCCCGCAGAAACACG 60.301 57.895 0.00 0.00 32.88 4.49
736 746 0.534203 TGTCCTTCCCGCAGAAACAC 60.534 55.000 0.00 0.00 32.88 3.32
737 747 0.534203 GTGTCCTTCCCGCAGAAACA 60.534 55.000 0.00 0.00 32.88 2.83
738 748 0.534203 TGTGTCCTTCCCGCAGAAAC 60.534 55.000 0.00 0.00 32.88 2.78
739 749 0.534203 GTGTGTCCTTCCCGCAGAAA 60.534 55.000 0.00 0.00 32.88 2.52
740 750 1.070786 GTGTGTCCTTCCCGCAGAA 59.929 57.895 0.00 0.00 0.00 3.02
741 751 2.741092 GTGTGTCCTTCCCGCAGA 59.259 61.111 0.00 0.00 0.00 4.26
742 752 2.358737 GGTGTGTCCTTCCCGCAG 60.359 66.667 0.00 0.00 0.00 5.18
743 753 4.308458 CGGTGTGTCCTTCCCGCA 62.308 66.667 0.00 0.00 33.20 5.69
746 756 3.948719 TGCCGGTGTGTCCTTCCC 61.949 66.667 1.90 0.00 0.00 3.97
747 757 2.668550 GTGCCGGTGTGTCCTTCC 60.669 66.667 1.90 0.00 0.00 3.46
748 758 3.041940 CGTGCCGGTGTGTCCTTC 61.042 66.667 1.90 0.00 0.00 3.46
749 759 4.619227 CCGTGCCGGTGTGTCCTT 62.619 66.667 1.90 0.00 42.73 3.36
754 764 4.920112 TTGACCCGTGCCGGTGTG 62.920 66.667 1.90 0.00 46.80 3.82
755 765 4.178169 TTTGACCCGTGCCGGTGT 62.178 61.111 1.90 9.34 46.80 4.16
756 766 3.353836 CTTTGACCCGTGCCGGTG 61.354 66.667 1.90 6.69 46.80 4.94
757 767 3.868985 ACTTTGACCCGTGCCGGT 61.869 61.111 1.90 0.02 46.80 5.28
759 769 3.353836 CCACTTTGACCCGTGCCG 61.354 66.667 0.00 0.00 0.00 5.69
760 770 2.112297 TCCACTTTGACCCGTGCC 59.888 61.111 0.00 0.00 0.00 5.01
761 771 2.604174 CGTCCACTTTGACCCGTGC 61.604 63.158 0.00 0.00 31.35 5.34
762 772 1.959226 CCGTCCACTTTGACCCGTG 60.959 63.158 0.00 0.00 31.35 4.94
763 773 1.688269 TTCCGTCCACTTTGACCCGT 61.688 55.000 0.00 0.00 31.35 5.28
764 774 0.533308 TTTCCGTCCACTTTGACCCG 60.533 55.000 0.00 0.00 31.35 5.28
765 775 1.682740 TTTTCCGTCCACTTTGACCC 58.317 50.000 0.00 0.00 31.35 4.46
794 804 1.370609 GTCCGATCTCTGTCACGAGA 58.629 55.000 2.47 2.47 43.61 4.04
795 805 0.026933 CGTCCGATCTCTGTCACGAG 59.973 60.000 0.00 0.00 0.00 4.18
796 806 1.978712 GCGTCCGATCTCTGTCACGA 61.979 60.000 0.00 0.00 0.00 4.35
797 807 1.583967 GCGTCCGATCTCTGTCACG 60.584 63.158 0.00 0.00 0.00 4.35
798 808 0.248296 GAGCGTCCGATCTCTGTCAC 60.248 60.000 0.00 0.00 0.00 3.67
799 809 1.706287 CGAGCGTCCGATCTCTGTCA 61.706 60.000 3.34 0.00 0.00 3.58
800 810 1.010574 CGAGCGTCCGATCTCTGTC 60.011 63.158 3.34 0.00 0.00 3.51
801 811 2.473760 CCGAGCGTCCGATCTCTGT 61.474 63.158 3.34 0.00 0.00 3.41
802 812 1.715862 TTCCGAGCGTCCGATCTCTG 61.716 60.000 3.34 0.00 0.00 3.35
803 813 1.030488 TTTCCGAGCGTCCGATCTCT 61.030 55.000 3.34 0.00 0.00 3.10
804 814 0.179145 TTTTCCGAGCGTCCGATCTC 60.179 55.000 3.34 0.00 0.00 2.75
805 815 0.245539 TTTTTCCGAGCGTCCGATCT 59.754 50.000 3.34 0.00 0.00 2.75
806 816 0.369248 GTTTTTCCGAGCGTCCGATC 59.631 55.000 0.00 0.00 0.00 3.69
807 817 1.349259 CGTTTTTCCGAGCGTCCGAT 61.349 55.000 0.34 0.00 0.00 4.18
808 818 2.017783 CGTTTTTCCGAGCGTCCGA 61.018 57.895 0.34 0.00 0.00 4.55
809 819 2.468532 CGTTTTTCCGAGCGTCCG 59.531 61.111 0.00 0.00 0.00 4.79
810 820 1.017701 ATCCGTTTTTCCGAGCGTCC 61.018 55.000 0.00 0.00 0.00 4.79
811 821 0.094730 CATCCGTTTTTCCGAGCGTC 59.905 55.000 0.00 0.00 0.00 5.19
812 822 0.320073 TCATCCGTTTTTCCGAGCGT 60.320 50.000 0.00 0.00 0.00 5.07
813 823 0.793861 TTCATCCGTTTTTCCGAGCG 59.206 50.000 0.00 0.00 0.00 5.03
814 824 1.804748 ACTTCATCCGTTTTTCCGAGC 59.195 47.619 0.00 0.00 0.00 5.03
815 825 2.415512 GGACTTCATCCGTTTTTCCGAG 59.584 50.000 0.00 0.00 37.88 4.63
816 826 2.419667 GGACTTCATCCGTTTTTCCGA 58.580 47.619 0.00 0.00 37.88 4.55
817 827 2.894307 GGACTTCATCCGTTTTTCCG 57.106 50.000 0.00 0.00 37.88 4.30
827 837 7.013274 TCCGGATGAAATTAATTGGACTTCATC 59.987 37.037 21.36 21.36 46.03 2.92
828 838 6.833416 TCCGGATGAAATTAATTGGACTTCAT 59.167 34.615 0.00 10.64 38.97 2.57
829 839 6.184068 TCCGGATGAAATTAATTGGACTTCA 58.816 36.000 0.00 1.81 0.00 3.02
830 840 6.693315 TCCGGATGAAATTAATTGGACTTC 57.307 37.500 0.00 4.99 0.00 3.01
831 841 6.833416 TCATCCGGATGAAATTAATTGGACTT 59.167 34.615 38.74 0.00 44.14 3.01
832 842 6.364701 TCATCCGGATGAAATTAATTGGACT 58.635 36.000 38.74 0.00 44.14 3.85
833 843 6.633500 TCATCCGGATGAAATTAATTGGAC 57.367 37.500 38.74 0.00 44.14 4.02
846 856 6.457392 CGGAATTGCTATTTATCATCCGGATG 60.457 42.308 34.42 34.42 43.52 3.51
847 857 5.586243 CGGAATTGCTATTTATCATCCGGAT 59.414 40.000 12.38 12.38 43.52 4.18
848 858 4.935205 CGGAATTGCTATTTATCATCCGGA 59.065 41.667 6.61 6.61 43.52 5.14
849 859 5.221891 CGGAATTGCTATTTATCATCCGG 57.778 43.478 8.30 0.00 43.52 5.14
851 861 7.440523 AGAACGGAATTGCTATTTATCATCC 57.559 36.000 0.00 0.00 0.00 3.51
852 862 8.559536 TGAAGAACGGAATTGCTATTTATCATC 58.440 33.333 0.00 0.00 0.00 2.92
853 863 8.450578 TGAAGAACGGAATTGCTATTTATCAT 57.549 30.769 0.00 0.00 0.00 2.45
854 864 7.857734 TGAAGAACGGAATTGCTATTTATCA 57.142 32.000 0.00 0.00 0.00 2.15
855 865 9.226345 CTTTGAAGAACGGAATTGCTATTTATC 57.774 33.333 0.00 0.00 0.00 1.75
856 866 8.739972 ACTTTGAAGAACGGAATTGCTATTTAT 58.260 29.630 0.00 0.00 0.00 1.40
857 867 8.106247 ACTTTGAAGAACGGAATTGCTATTTA 57.894 30.769 0.00 0.00 0.00 1.40
858 868 6.981722 ACTTTGAAGAACGGAATTGCTATTT 58.018 32.000 0.00 0.00 0.00 1.40
859 869 6.575162 ACTTTGAAGAACGGAATTGCTATT 57.425 33.333 0.00 0.00 0.00 1.73
860 870 6.575162 AACTTTGAAGAACGGAATTGCTAT 57.425 33.333 0.00 0.00 0.00 2.97
861 871 6.483974 TGTAACTTTGAAGAACGGAATTGCTA 59.516 34.615 0.00 0.00 0.00 3.49
862 872 4.918810 AACTTTGAAGAACGGAATTGCT 57.081 36.364 0.00 0.00 0.00 3.91
863 873 5.398416 GTGTAACTTTGAAGAACGGAATTGC 59.602 40.000 0.00 0.00 0.00 3.56
864 874 6.413818 GTGTGTAACTTTGAAGAACGGAATTG 59.586 38.462 0.00 0.00 38.04 2.32
865 875 6.094325 TGTGTGTAACTTTGAAGAACGGAATT 59.906 34.615 0.00 0.00 38.04 2.17
866 876 5.587043 TGTGTGTAACTTTGAAGAACGGAAT 59.413 36.000 0.00 0.00 38.04 3.01
867 877 4.936411 TGTGTGTAACTTTGAAGAACGGAA 59.064 37.500 0.00 0.00 38.04 4.30
868 878 4.505808 TGTGTGTAACTTTGAAGAACGGA 58.494 39.130 0.00 0.00 38.04 4.69
869 879 4.868450 TGTGTGTAACTTTGAAGAACGG 57.132 40.909 0.00 0.00 38.04 4.44
870 880 6.129393 CAGATGTGTGTAACTTTGAAGAACG 58.871 40.000 0.00 0.00 38.04 3.95
871 881 5.909610 GCAGATGTGTGTAACTTTGAAGAAC 59.090 40.000 0.00 0.00 38.04 3.01
922 932 2.594592 GTGGTGGTGGTGGTGCTC 60.595 66.667 0.00 0.00 0.00 4.26
923 933 4.204028 GGTGGTGGTGGTGGTGCT 62.204 66.667 0.00 0.00 0.00 4.40
924 934 4.514585 TGGTGGTGGTGGTGGTGC 62.515 66.667 0.00 0.00 0.00 5.01
951 961 2.113139 GGTGGTGGACTGGTGGTG 59.887 66.667 0.00 0.00 0.00 4.17
952 962 3.175710 GGGTGGTGGACTGGTGGT 61.176 66.667 0.00 0.00 0.00 4.16
959 969 2.517402 TTTGCGTGGGTGGTGGAC 60.517 61.111 0.00 0.00 0.00 4.02
960 970 2.517402 GTTTGCGTGGGTGGTGGA 60.517 61.111 0.00 0.00 0.00 4.02
961 971 3.959975 CGTTTGCGTGGGTGGTGG 61.960 66.667 0.00 0.00 0.00 4.61
962 972 4.622456 GCGTTTGCGTGGGTGGTG 62.622 66.667 0.00 0.00 40.81 4.17
965 975 3.417275 TTTGGCGTTTGCGTGGGTG 62.417 57.895 0.00 0.00 44.10 4.61
966 976 3.132481 CTTTGGCGTTTGCGTGGGT 62.132 57.895 0.00 0.00 44.10 4.51
1008 1018 1.379176 CCTCGCTCTGGAGTCTGGA 60.379 63.158 0.00 0.00 31.98 3.86
1009 1019 3.074999 GCCTCGCTCTGGAGTCTGG 62.075 68.421 0.00 1.24 31.98 3.86
1010 1020 2.346541 TGCCTCGCTCTGGAGTCTG 61.347 63.158 0.00 0.00 31.98 3.51
1011 1021 2.036414 TGCCTCGCTCTGGAGTCT 59.964 61.111 0.00 0.00 31.98 3.24
1012 1022 2.183046 GTGCCTCGCTCTGGAGTC 59.817 66.667 0.00 0.00 31.98 3.36
1013 1023 3.753434 CGTGCCTCGCTCTGGAGT 61.753 66.667 0.00 0.00 31.98 3.85
1014 1024 4.504916 CCGTGCCTCGCTCTGGAG 62.505 72.222 0.00 0.00 38.35 3.86
1224 1246 2.438614 TCCTCGGACTCGGAGCTG 60.439 66.667 4.58 3.59 36.95 4.24
1368 1390 3.482783 GGCTCAGACGCGCAGAAC 61.483 66.667 5.73 0.00 0.00 3.01
1440 1462 1.884926 CTTGGCGGATCCGAAGCTC 60.885 63.158 37.64 18.76 42.83 4.09
1857 1879 1.433837 AAACGCACGTCAGGACAACC 61.434 55.000 0.00 0.00 0.00 3.77
1861 1883 1.563173 GTGAAACGCACGTCAGGAC 59.437 57.895 0.00 0.00 37.83 3.85
1862 1884 4.021650 GTGAAACGCACGTCAGGA 57.978 55.556 0.00 0.00 37.83 3.86
1886 1908 2.102438 CGACATGGACGCTGCACAT 61.102 57.895 0.00 0.00 0.00 3.21
1997 2020 1.595093 GAAGCGAAATGGTGGGTGGG 61.595 60.000 0.00 0.00 0.00 4.61
1998 2021 1.883021 GAAGCGAAATGGTGGGTGG 59.117 57.895 0.00 0.00 0.00 4.61
1999 2022 1.501741 CGAAGCGAAATGGTGGGTG 59.498 57.895 0.00 0.00 0.00 4.61
2000 2023 1.674322 CCGAAGCGAAATGGTGGGT 60.674 57.895 0.00 0.00 0.00 4.51
2001 2024 0.958382 TTCCGAAGCGAAATGGTGGG 60.958 55.000 0.00 0.00 0.00 4.61
2057 2091 5.992729 TGTACTACTTCGTTTTTCATTGCC 58.007 37.500 0.00 0.00 0.00 4.52
2097 2131 0.957395 ACCACCGCATGCTCTTCAAG 60.957 55.000 17.13 0.00 0.00 3.02
2125 2159 3.726291 AAGAAGATCTCGCTAGCTTCC 57.274 47.619 13.93 0.00 37.94 3.46
2126 2160 4.867608 ACAAAAGAAGATCTCGCTAGCTTC 59.132 41.667 13.93 8.52 37.58 3.86
2127 2161 4.629200 CACAAAAGAAGATCTCGCTAGCTT 59.371 41.667 13.93 0.00 0.00 3.74
2128 2162 4.180057 CACAAAAGAAGATCTCGCTAGCT 58.820 43.478 13.93 0.00 0.00 3.32
2129 2163 3.929610 ACACAAAAGAAGATCTCGCTAGC 59.070 43.478 4.06 4.06 0.00 3.42
2168 2202 2.497273 TCCCCACGCCTAAACTACTTAC 59.503 50.000 0.00 0.00 0.00 2.34
2221 2255 1.440618 TGTACATGTGGGAGGTGGTT 58.559 50.000 9.11 0.00 0.00 3.67
2222 2256 1.351017 CTTGTACATGTGGGAGGTGGT 59.649 52.381 9.11 0.00 0.00 4.16
2250 2284 2.699954 AGGATTAAACTGGCACGACTG 58.300 47.619 0.00 0.00 0.00 3.51
2254 2288 4.201685 CGAAAGTAGGATTAAACTGGCACG 60.202 45.833 0.00 0.00 0.00 5.34
2311 2345 6.425114 ACAGCTTACAAGTCTCTTGTACAATG 59.575 38.462 18.05 17.17 34.93 2.82
2312 2346 6.525629 ACAGCTTACAAGTCTCTTGTACAAT 58.474 36.000 18.05 7.49 34.93 2.71
2325 2359 3.650139 AGGTCGTGTTACAGCTTACAAG 58.350 45.455 0.00 0.00 0.00 3.16
2380 2414 3.300388 TCTGTCAATAGGCTAGGAGTGG 58.700 50.000 0.00 0.00 0.00 4.00
2400 2434 7.918536 ATTATACACCATGATTCATGCTCTC 57.081 36.000 19.26 0.00 40.20 3.20
2422 2456 2.092807 GGCCATGGAAATGGAAGCAATT 60.093 45.455 18.40 0.00 44.39 2.32
2447 2481 3.009723 ACATATTCAAGCGACAGTTGGG 58.990 45.455 0.00 0.00 0.00 4.12
2481 2515 5.050023 GCCGAATTTTAGCATCTCCTTCTAC 60.050 44.000 0.00 0.00 0.00 2.59
2484 2518 3.003793 GGCCGAATTTTAGCATCTCCTTC 59.996 47.826 0.00 0.00 0.00 3.46
2486 2520 2.173569 AGGCCGAATTTTAGCATCTCCT 59.826 45.455 0.00 0.00 0.00 3.69
2513 2550 0.249531 TACGCCAAGTTCTTGCACGA 60.250 50.000 22.74 0.00 0.00 4.35
2543 2580 1.801178 GAGACGAAACAGCCAAGAAGG 59.199 52.381 0.00 0.00 41.84 3.46
2554 2592 4.607778 GCTTCCTTTTACACGAGACGAAAC 60.608 45.833 0.00 0.00 0.00 2.78
2566 2604 6.663565 CAAGAAGAGAACAGCTTCCTTTTAC 58.336 40.000 0.00 0.00 42.04 2.01
2701 2745 2.505635 CTTGTGCAATTTCCGGCCCC 62.506 60.000 0.00 0.00 0.00 5.80
2748 2795 3.876589 TTTGTCCTCGCCAGTCGCC 62.877 63.158 0.00 0.00 38.27 5.54
2749 2796 2.357034 TTTGTCCTCGCCAGTCGC 60.357 61.111 0.00 0.00 38.27 5.19
2750 2797 0.108615 ATCTTTGTCCTCGCCAGTCG 60.109 55.000 0.00 0.00 40.15 4.18
2751 2798 1.205893 AGATCTTTGTCCTCGCCAGTC 59.794 52.381 0.00 0.00 0.00 3.51
2752 2799 1.066573 CAGATCTTTGTCCTCGCCAGT 60.067 52.381 0.00 0.00 0.00 4.00
2753 2800 1.649664 CAGATCTTTGTCCTCGCCAG 58.350 55.000 0.00 0.00 0.00 4.85
2848 2903 3.242870 CGAGCATGGAGATAAACAAAGGC 60.243 47.826 0.00 0.00 0.00 4.35
2871 2926 3.425492 GGCGCAACAAAAGAAAGCAAAAA 60.425 39.130 10.83 0.00 0.00 1.94
2912 2967 1.530283 GGGTCGGGGATAAACAGGG 59.470 63.158 0.00 0.00 0.00 4.45
2938 2993 4.935495 CACAGGCGCACAGGTGGT 62.935 66.667 10.83 0.00 0.00 4.16
2950 3005 3.190849 CCTCGCATCGCACACAGG 61.191 66.667 0.00 0.00 0.00 4.00
2966 3021 4.404098 TTTTCCCCTCGCCTCGCC 62.404 66.667 0.00 0.00 0.00 5.54
2973 3028 2.723464 TTTGGGCCCTTTTCCCCTCG 62.723 60.000 25.70 0.00 43.24 4.63
2974 3029 0.904865 CTTTGGGCCCTTTTCCCCTC 60.905 60.000 25.70 0.00 43.24 4.30
2975 3030 1.158466 CTTTGGGCCCTTTTCCCCT 59.842 57.895 25.70 0.00 43.24 4.79
3038 3093 5.695851 AGGTCAGACTAAACAATGCTTTG 57.304 39.130 10.58 10.58 38.86 2.77


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

AutoCloner maintained by Alex Coulton.