Multiple sequence alignment - TraesCS2B01G048100

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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 TraesCS2B01G048100 chr2B 100.000 3365 0 0 1 3365 23807681 23811045 0.000000e+00 6215
1 TraesCS2B01G048100 chr2D 92.692 2422 155 14 935 3346 13218763 13221172 0.000000e+00 3472
2 TraesCS2B01G048100 chr2D 77.882 642 103 23 126 751 450938990 450938372 2.470000e-96 363
3 TraesCS2B01G048100 chr2D 83.042 401 38 15 2924 3299 13428295 13427900 1.500000e-88 337
4 TraesCS2B01G048100 chr2D 77.753 445 84 11 1058 1499 13431404 13430972 3.330000e-65 259
5 TraesCS2B01G048100 chr2A 93.693 1522 83 8 928 2438 15235764 15237283 0.000000e+00 2266
6 TraesCS2B01G048100 chr2A 90.919 892 68 4 2440 3321 15237333 15238221 0.000000e+00 1186
7 TraesCS2B01G048100 chr7D 79.447 759 115 22 1 751 479031725 479031000 1.800000e-137 499
8 TraesCS2B01G048100 chr7D 81.848 303 46 7 452 751 500814486 500814190 2.590000e-61 246
9 TraesCS2B01G048100 chr5D 80.746 670 101 19 26 685 412212816 412212165 6.480000e-137 497
10 TraesCS2B01G048100 chr5A 77.025 753 127 30 18 751 682891543 682892268 1.130000e-104 390
11 TraesCS2B01G048100 chr5A 76.856 229 49 3 199 425 482442025 482441799 3.520000e-25 126
12 TraesCS2B01G048100 chr3B 79.181 562 85 19 194 751 782644474 782645007 8.880000e-96 361
13 TraesCS2B01G048100 chr3B 76.344 558 101 23 197 751 807725687 807726216 1.540000e-68 270
14 TraesCS2B01G048100 chr3B 83.607 122 13 5 128 242 807735476 807735355 1.280000e-19 108
15 TraesCS2B01G048100 chr1D 75.928 781 118 32 1 751 332686019 332686759 1.500000e-88 337
16 TraesCS2B01G048100 chrUn 82.331 266 44 3 487 751 90003669 90003406 9.390000e-56 228
17 TraesCS2B01G048100 chr7B 81.053 285 45 7 470 751 741804944 741804666 5.650000e-53 219


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 TraesCS2B01G048100 chr2B 23807681 23811045 3364 False 6215 6215 100.0000 1 3365 1 chr2B.!!$F1 3364
1 TraesCS2B01G048100 chr2D 13218763 13221172 2409 False 3472 3472 92.6920 935 3346 1 chr2D.!!$F1 2411
2 TraesCS2B01G048100 chr2D 450938372 450938990 618 True 363 363 77.8820 126 751 1 chr2D.!!$R1 625
3 TraesCS2B01G048100 chr2D 13427900 13431404 3504 True 298 337 80.3975 1058 3299 2 chr2D.!!$R2 2241
4 TraesCS2B01G048100 chr2A 15235764 15238221 2457 False 1726 2266 92.3060 928 3321 2 chr2A.!!$F1 2393
5 TraesCS2B01G048100 chr7D 479031000 479031725 725 True 499 499 79.4470 1 751 1 chr7D.!!$R1 750
6 TraesCS2B01G048100 chr5D 412212165 412212816 651 True 497 497 80.7460 26 685 1 chr5D.!!$R1 659
7 TraesCS2B01G048100 chr5A 682891543 682892268 725 False 390 390 77.0250 18 751 1 chr5A.!!$F1 733
8 TraesCS2B01G048100 chr3B 782644474 782645007 533 False 361 361 79.1810 194 751 1 chr3B.!!$F1 557
9 TraesCS2B01G048100 chr3B 807725687 807726216 529 False 270 270 76.3440 197 751 1 chr3B.!!$F2 554
10 TraesCS2B01G048100 chr1D 332686019 332686759 740 False 337 337 75.9280 1 751 1 chr1D.!!$F1 750

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
706 768 0.036858 TCCGTGGATGTGCGATCAAA 60.037 50.0 0.00 0.0 0.0 2.69 F
1140 1202 0.683504 ACAGCCTCTACGATTCGGGT 60.684 55.0 11.29 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 1811 0.396811 AACAGAACTTGGGGGAGTCG 59.603 55.0 0.0 0.0 0.00 4.18 R
2866 4728 0.400815 TTACCACCACCTGACCTGGT 60.401 55.0 0.0 0.0 43.22 4.00 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
46 47 2.273449 CTCCCGCCAGAGCCAAAT 59.727 61.111 0.00 0.00 34.57 2.32
71 72 0.810031 CGAAAGCCGATAGTGGTGGG 60.810 60.000 0.00 0.00 41.76 4.61
73 74 1.205460 AAAGCCGATAGTGGTGGGGT 61.205 55.000 0.00 0.00 0.00 4.95
74 75 1.623542 AAGCCGATAGTGGTGGGGTC 61.624 60.000 0.00 0.00 0.00 4.46
118 122 4.219264 AGAAGAAGATGAAGAAGGCCAG 57.781 45.455 5.01 0.00 0.00 4.85
122 126 3.328931 AGAAGATGAAGAAGGCCAGAACA 59.671 43.478 5.01 0.00 0.00 3.18
144 166 1.645704 GACTCGTGCAGCTACTCCGA 61.646 60.000 0.00 0.00 0.00 4.55
152 174 2.517875 GCTACTCCGACGCCCCTA 60.518 66.667 0.00 0.00 0.00 3.53
153 175 1.902432 GCTACTCCGACGCCCCTAT 60.902 63.158 0.00 0.00 0.00 2.57
154 176 1.957562 CTACTCCGACGCCCCTATG 59.042 63.158 0.00 0.00 0.00 2.23
156 178 0.820891 TACTCCGACGCCCCTATGAC 60.821 60.000 0.00 0.00 0.00 3.06
158 180 3.151710 CCGACGCCCCTATGACCA 61.152 66.667 0.00 0.00 0.00 4.02
232 261 5.107298 GCTCGATGAAATGCCTACAAGATAC 60.107 44.000 0.00 0.00 0.00 2.24
253 286 2.844122 AAAAACTCACGTCCTGTTGC 57.156 45.000 0.00 0.00 0.00 4.17
299 336 2.472816 GGTGGTGATGCACTTTGTTTG 58.527 47.619 0.00 0.00 34.40 2.93
304 341 5.578727 GTGGTGATGCACTTTGTTTGTTTTA 59.421 36.000 0.00 0.00 34.40 1.52
308 345 6.628461 GTGATGCACTTTGTTTGTTTTATTGC 59.372 34.615 0.00 0.00 0.00 3.56
320 357 1.157585 TTTATTGCCGTAGTGCGCAA 58.842 45.000 14.00 11.33 39.47 4.85
353 390 2.073816 GAATTCCTCGCGTCTTTGGAA 58.926 47.619 5.77 13.39 41.96 3.53
380 417 2.288666 GCCGCTATTGGACTTGATGAA 58.711 47.619 0.00 0.00 0.00 2.57
392 429 5.047306 TGGACTTGATGAACTCAACTACGAT 60.047 40.000 0.00 0.00 38.97 3.73
405 442 4.096231 TCAACTACGATTCCATTTGGCATG 59.904 41.667 0.00 0.00 34.44 4.06
407 444 3.879295 ACTACGATTCCATTTGGCATGAG 59.121 43.478 0.00 0.00 34.44 2.90
425 480 1.840635 GAGTTGGAGGTGGCCTAAGAT 59.159 52.381 3.32 0.00 31.76 2.40
450 511 1.604378 CAAGAGGTGGCCGAGGAAT 59.396 57.895 0.00 0.00 0.00 3.01
460 521 0.178958 GCCGAGGAATAGGAGGAGGA 60.179 60.000 0.00 0.00 0.00 3.71
461 522 1.917872 CCGAGGAATAGGAGGAGGAG 58.082 60.000 0.00 0.00 0.00 3.69
462 523 1.253100 CGAGGAATAGGAGGAGGAGC 58.747 60.000 0.00 0.00 0.00 4.70
463 524 1.479573 CGAGGAATAGGAGGAGGAGCA 60.480 57.143 0.00 0.00 0.00 4.26
464 525 2.247358 GAGGAATAGGAGGAGGAGCAG 58.753 57.143 0.00 0.00 0.00 4.24
465 526 1.862911 AGGAATAGGAGGAGGAGCAGA 59.137 52.381 0.00 0.00 0.00 4.26
497 558 0.695462 TGGATGATGAGGAGGTGGGG 60.695 60.000 0.00 0.00 0.00 4.96
501 562 0.400525 TGATGAGGAGGTGGGGGATC 60.401 60.000 0.00 0.00 0.00 3.36
513 574 1.368203 TGGGGGATCAAGAGGAGGTTA 59.632 52.381 0.00 0.00 0.00 2.85
530 591 0.174845 TTATGGAGGTGACCGAAGCG 59.825 55.000 0.00 0.00 0.00 4.68
564 625 3.284449 GGTCACGCACCACCAACC 61.284 66.667 0.00 0.00 45.98 3.77
567 628 3.947841 CACGCACCACCAACCACG 61.948 66.667 0.00 0.00 0.00 4.94
646 707 5.221891 ACGATTGAAACGGATCAAATCAG 57.778 39.130 8.87 4.57 42.22 2.90
706 768 0.036858 TCCGTGGATGTGCGATCAAA 60.037 50.000 0.00 0.00 0.00 2.69
708 770 1.078709 CGTGGATGTGCGATCAAACT 58.921 50.000 0.00 0.00 0.00 2.66
712 774 3.623060 GTGGATGTGCGATCAAACTGTAT 59.377 43.478 0.00 0.00 0.00 2.29
746 808 1.718757 GGCATCGTTGGAGCACCATC 61.719 60.000 2.87 2.04 46.34 3.51
758 820 1.180029 GCACCATCCATGCTTGAAGT 58.820 50.000 0.22 0.00 40.08 3.01
759 821 1.547372 GCACCATCCATGCTTGAAGTT 59.453 47.619 0.22 0.00 40.08 2.66
760 822 2.673043 GCACCATCCATGCTTGAAGTTG 60.673 50.000 0.22 0.00 40.08 3.16
761 823 2.821378 CACCATCCATGCTTGAAGTTGA 59.179 45.455 0.22 0.00 0.00 3.18
762 824 3.446161 CACCATCCATGCTTGAAGTTGAT 59.554 43.478 0.22 0.00 0.00 2.57
763 825 4.641541 CACCATCCATGCTTGAAGTTGATA 59.358 41.667 0.22 0.00 0.00 2.15
764 826 4.641989 ACCATCCATGCTTGAAGTTGATAC 59.358 41.667 0.22 0.00 0.00 2.24
765 827 4.260907 CCATCCATGCTTGAAGTTGATACG 60.261 45.833 0.22 0.00 0.00 3.06
766 828 3.270027 TCCATGCTTGAAGTTGATACGG 58.730 45.455 0.22 0.00 0.00 4.02
767 829 2.223340 CCATGCTTGAAGTTGATACGGC 60.223 50.000 0.22 0.00 0.00 5.68
768 830 2.472695 TGCTTGAAGTTGATACGGCT 57.527 45.000 0.00 0.00 0.00 5.52
769 831 3.603158 TGCTTGAAGTTGATACGGCTA 57.397 42.857 0.00 0.00 0.00 3.93
770 832 3.932822 TGCTTGAAGTTGATACGGCTAA 58.067 40.909 0.00 0.00 0.00 3.09
771 833 3.932710 TGCTTGAAGTTGATACGGCTAAG 59.067 43.478 0.00 0.00 0.00 2.18
772 834 4.181578 GCTTGAAGTTGATACGGCTAAGA 58.818 43.478 0.00 0.00 0.00 2.10
773 835 4.033014 GCTTGAAGTTGATACGGCTAAGAC 59.967 45.833 0.00 0.00 0.00 3.01
774 836 4.794278 TGAAGTTGATACGGCTAAGACA 57.206 40.909 0.00 0.00 0.00 3.41
775 837 5.339008 TGAAGTTGATACGGCTAAGACAT 57.661 39.130 0.00 0.00 0.00 3.06
776 838 6.459670 TGAAGTTGATACGGCTAAGACATA 57.540 37.500 0.00 0.00 0.00 2.29
777 839 6.869695 TGAAGTTGATACGGCTAAGACATAA 58.130 36.000 0.00 0.00 0.00 1.90
778 840 7.324935 TGAAGTTGATACGGCTAAGACATAAA 58.675 34.615 0.00 0.00 0.00 1.40
779 841 7.820386 TGAAGTTGATACGGCTAAGACATAAAA 59.180 33.333 0.00 0.00 0.00 1.52
780 842 8.732746 AAGTTGATACGGCTAAGACATAAAAT 57.267 30.769 0.00 0.00 0.00 1.82
781 843 8.366671 AGTTGATACGGCTAAGACATAAAATC 57.633 34.615 0.00 0.00 0.00 2.17
782 844 8.204836 AGTTGATACGGCTAAGACATAAAATCT 58.795 33.333 0.00 0.00 0.00 2.40
783 845 9.472361 GTTGATACGGCTAAGACATAAAATCTA 57.528 33.333 0.00 0.00 0.00 1.98
784 846 9.472361 TTGATACGGCTAAGACATAAAATCTAC 57.528 33.333 0.00 0.00 0.00 2.59
785 847 8.635328 TGATACGGCTAAGACATAAAATCTACA 58.365 33.333 0.00 0.00 0.00 2.74
786 848 9.472361 GATACGGCTAAGACATAAAATCTACAA 57.528 33.333 0.00 0.00 0.00 2.41
787 849 9.826574 ATACGGCTAAGACATAAAATCTACAAA 57.173 29.630 0.00 0.00 0.00 2.83
788 850 8.197988 ACGGCTAAGACATAAAATCTACAAAG 57.802 34.615 0.00 0.00 0.00 2.77
789 851 7.822822 ACGGCTAAGACATAAAATCTACAAAGT 59.177 33.333 0.00 0.00 0.00 2.66
790 852 8.665685 CGGCTAAGACATAAAATCTACAAAGTT 58.334 33.333 0.00 0.00 0.00 2.66
810 872 9.413048 CAAAGTTTTGTTTTTACTCCACTAACA 57.587 29.630 0.00 0.00 33.59 2.41
811 873 9.984190 AAAGTTTTGTTTTTACTCCACTAACAA 57.016 25.926 0.00 0.00 37.04 2.83
817 879 8.398878 TGTTTTTACTCCACTAACAATAAGGG 57.601 34.615 0.00 0.00 0.00 3.95
818 880 8.219178 TGTTTTTACTCCACTAACAATAAGGGA 58.781 33.333 0.00 0.00 0.00 4.20
819 881 9.239551 GTTTTTACTCCACTAACAATAAGGGAT 57.760 33.333 0.00 0.00 0.00 3.85
820 882 9.457436 TTTTTACTCCACTAACAATAAGGGATC 57.543 33.333 0.00 0.00 0.00 3.36
821 883 5.277857 ACTCCACTAACAATAAGGGATCG 57.722 43.478 0.00 0.00 0.00 3.69
822 884 4.101119 ACTCCACTAACAATAAGGGATCGG 59.899 45.833 0.00 0.00 0.00 4.18
823 885 3.139077 CCACTAACAATAAGGGATCGGC 58.861 50.000 0.00 0.00 0.00 5.54
824 886 3.181454 CCACTAACAATAAGGGATCGGCT 60.181 47.826 0.00 0.00 0.00 5.52
825 887 4.039973 CCACTAACAATAAGGGATCGGCTA 59.960 45.833 0.00 0.00 0.00 3.93
826 888 5.230942 CACTAACAATAAGGGATCGGCTAG 58.769 45.833 0.00 0.00 0.00 3.42
827 889 5.010719 CACTAACAATAAGGGATCGGCTAGA 59.989 44.000 0.00 0.00 0.00 2.43
828 890 5.780793 ACTAACAATAAGGGATCGGCTAGAT 59.219 40.000 0.00 0.00 43.51 1.98
829 891 4.543590 ACAATAAGGGATCGGCTAGATG 57.456 45.455 0.00 0.00 40.26 2.90
830 892 3.261897 ACAATAAGGGATCGGCTAGATGG 59.738 47.826 0.00 0.00 40.26 3.51
831 893 1.267121 TAAGGGATCGGCTAGATGGC 58.733 55.000 0.00 0.00 40.26 4.40
841 903 2.134789 GCTAGATGGCCATATTGGGG 57.865 55.000 20.84 7.98 38.19 4.96
842 904 1.355720 GCTAGATGGCCATATTGGGGT 59.644 52.381 20.84 0.00 38.19 4.95
843 905 2.576191 GCTAGATGGCCATATTGGGGTA 59.424 50.000 20.84 0.00 38.19 3.69
844 906 3.010138 GCTAGATGGCCATATTGGGGTAA 59.990 47.826 20.84 0.00 38.19 2.85
845 907 4.508405 GCTAGATGGCCATATTGGGGTAAA 60.508 45.833 20.84 0.00 38.19 2.01
846 908 4.551215 AGATGGCCATATTGGGGTAAAA 57.449 40.909 20.84 0.00 38.19 1.52
847 909 4.482990 AGATGGCCATATTGGGGTAAAAG 58.517 43.478 20.84 0.00 38.19 2.27
848 910 3.767309 TGGCCATATTGGGGTAAAAGT 57.233 42.857 0.00 0.00 38.19 2.66
849 911 4.067944 TGGCCATATTGGGGTAAAAGTT 57.932 40.909 0.00 0.00 38.19 2.66
850 912 4.430441 TGGCCATATTGGGGTAAAAGTTT 58.570 39.130 0.00 0.00 38.19 2.66
851 913 5.590818 TGGCCATATTGGGGTAAAAGTTTA 58.409 37.500 0.00 0.00 38.19 2.01
852 914 5.422650 TGGCCATATTGGGGTAAAAGTTTAC 59.577 40.000 0.00 5.53 39.11 2.01
853 915 5.659525 GGCCATATTGGGGTAAAAGTTTACT 59.340 40.000 12.42 0.00 39.43 2.24
854 916 6.183360 GGCCATATTGGGGTAAAAGTTTACTC 60.183 42.308 12.42 9.12 42.14 2.59
855 917 6.605995 GCCATATTGGGGTAAAAGTTTACTCT 59.394 38.462 12.38 0.00 42.42 3.24
856 918 7.776500 GCCATATTGGGGTAAAAGTTTACTCTA 59.224 37.037 12.38 5.01 42.42 2.43
857 919 9.117183 CCATATTGGGGTAAAAGTTTACTCTAC 57.883 37.037 12.38 0.00 42.42 2.59
858 920 9.901172 CATATTGGGGTAAAAGTTTACTCTACT 57.099 33.333 12.38 4.95 42.42 2.57
877 939 9.138596 ACTCTACTAAATTTACTCTGGATCCTC 57.861 37.037 14.23 0.00 0.00 3.71
878 940 9.362151 CTCTACTAAATTTACTCTGGATCCTCT 57.638 37.037 14.23 0.00 0.00 3.69
879 941 9.357161 TCTACTAAATTTACTCTGGATCCTCTC 57.643 37.037 14.23 0.00 0.00 3.20
880 942 9.362151 CTACTAAATTTACTCTGGATCCTCTCT 57.638 37.037 14.23 0.00 0.00 3.10
881 943 8.616799 ACTAAATTTACTCTGGATCCTCTCTT 57.383 34.615 14.23 0.00 0.00 2.85
882 944 9.716556 ACTAAATTTACTCTGGATCCTCTCTTA 57.283 33.333 14.23 0.00 0.00 2.10
887 949 9.890915 ATTTACTCTGGATCCTCTCTTATAAGT 57.109 33.333 14.23 5.71 0.00 2.24
890 952 8.700439 ACTCTGGATCCTCTCTTATAAGTAAC 57.300 38.462 14.23 0.00 0.00 2.50
891 953 7.726738 ACTCTGGATCCTCTCTTATAAGTAACC 59.273 40.741 14.23 8.02 0.00 2.85
892 954 7.827787 TCTGGATCCTCTCTTATAAGTAACCT 58.172 38.462 14.23 0.00 0.00 3.50
893 955 8.290277 TCTGGATCCTCTCTTATAAGTAACCTT 58.710 37.037 14.23 0.00 34.56 3.50
894 956 8.855804 TGGATCCTCTCTTATAAGTAACCTTT 57.144 34.615 14.23 0.00 31.89 3.11
895 957 9.947189 TGGATCCTCTCTTATAAGTAACCTTTA 57.053 33.333 14.23 0.00 31.89 1.85
899 961 9.643735 TCCTCTCTTATAAGTAACCTTTAGGAG 57.356 37.037 12.19 0.00 38.94 3.69
900 962 9.643735 CCTCTCTTATAAGTAACCTTTAGGAGA 57.356 37.037 12.19 3.08 38.94 3.71
904 966 9.075678 TCTTATAAGTAACCTTTAGGAGATCGG 57.924 37.037 12.19 0.00 38.94 4.18
905 967 8.773033 TTATAAGTAACCTTTAGGAGATCGGT 57.227 34.615 2.06 0.00 38.94 4.69
906 968 7.672122 ATAAGTAACCTTTAGGAGATCGGTT 57.328 36.000 2.06 4.64 40.72 4.44
907 969 8.773033 ATAAGTAACCTTTAGGAGATCGGTTA 57.227 34.615 2.06 2.99 38.74 2.85
908 970 6.712179 AGTAACCTTTAGGAGATCGGTTAG 57.288 41.667 2.06 0.00 39.94 2.34
909 971 6.430007 AGTAACCTTTAGGAGATCGGTTAGA 58.570 40.000 2.06 0.00 39.94 2.10
910 972 6.894103 AGTAACCTTTAGGAGATCGGTTAGAA 59.106 38.462 2.06 0.00 39.94 2.10
911 973 6.616237 AACCTTTAGGAGATCGGTTAGAAA 57.384 37.500 2.06 0.00 36.28 2.52
912 974 6.809976 ACCTTTAGGAGATCGGTTAGAAAT 57.190 37.500 2.06 0.00 38.94 2.17
913 975 6.818233 ACCTTTAGGAGATCGGTTAGAAATC 58.182 40.000 2.06 0.00 38.94 2.17
914 976 6.183360 ACCTTTAGGAGATCGGTTAGAAATCC 60.183 42.308 2.06 0.00 37.64 3.01
915 977 5.803237 TTAGGAGATCGGTTAGAAATCCC 57.197 43.478 0.00 0.00 37.94 3.85
916 978 2.973406 AGGAGATCGGTTAGAAATCCCC 59.027 50.000 0.00 0.00 37.94 4.81
917 979 2.288886 GGAGATCGGTTAGAAATCCCCG 60.289 54.545 0.00 0.00 41.75 5.73
918 980 2.364647 GAGATCGGTTAGAAATCCCCGT 59.635 50.000 0.00 0.00 41.17 5.28
919 981 3.569491 AGATCGGTTAGAAATCCCCGTA 58.431 45.455 0.00 0.00 41.17 4.02
920 982 3.320256 AGATCGGTTAGAAATCCCCGTAC 59.680 47.826 0.00 0.00 41.17 3.67
921 983 2.455557 TCGGTTAGAAATCCCCGTACA 58.544 47.619 0.00 0.00 41.17 2.90
922 984 2.166254 TCGGTTAGAAATCCCCGTACAC 59.834 50.000 0.00 0.00 41.17 2.90
923 985 2.094078 CGGTTAGAAATCCCCGTACACA 60.094 50.000 0.00 0.00 35.78 3.72
924 986 3.264947 GGTTAGAAATCCCCGTACACAC 58.735 50.000 0.00 0.00 0.00 3.82
925 987 3.264947 GTTAGAAATCCCCGTACACACC 58.735 50.000 0.00 0.00 0.00 4.16
926 988 1.354101 AGAAATCCCCGTACACACCA 58.646 50.000 0.00 0.00 0.00 4.17
939 1001 4.321750 CGTACACACCAGTTATCCAAGTCT 60.322 45.833 0.00 0.00 0.00 3.24
942 1004 2.371841 ACACCAGTTATCCAAGTCTGCA 59.628 45.455 0.00 0.00 0.00 4.41
952 1014 1.228367 AAGTCTGCAGGCCACAAGG 60.228 57.895 16.31 0.00 38.23 3.61
1134 1196 2.005960 GCGTCCACAGCCTCTACGAT 62.006 60.000 0.00 0.00 35.66 3.73
1140 1202 0.683504 ACAGCCTCTACGATTCGGGT 60.684 55.000 11.29 0.00 0.00 5.28
1523 1585 5.123027 GTGGTTTCCTTCTCTGCTGAAATAG 59.877 44.000 0.00 0.00 0.00 1.73
1552 1627 7.748241 GCAGACACATTATTTCTGAAGTCTTTC 59.252 37.037 2.02 0.00 39.36 2.62
1553 1628 8.997323 CAGACACATTATTTCTGAAGTCTTTCT 58.003 33.333 4.15 0.00 39.36 2.52
1577 1652 7.647715 TCTTCTTTTTGATCCGAAAATCACAAC 59.352 33.333 5.01 0.00 35.44 3.32
1596 1671 8.417780 TCACAACAAATTTTGTATTCAACTGG 57.582 30.769 14.81 3.60 44.59 4.00
1616 1691 6.648192 ACTGGAAATCACAACAAATTTTGGA 58.352 32.000 13.42 1.78 34.12 3.53
1618 1693 6.648192 TGGAAATCACAACAAATTTTGGACT 58.352 32.000 13.42 0.00 34.12 3.85
1647 1722 5.886960 ACCAGAGTATTTGATTGAACTGC 57.113 39.130 0.00 0.00 0.00 4.40
1659 1734 5.531634 TGATTGAACTGCCAAGATTTGAAC 58.468 37.500 0.00 0.00 0.00 3.18
1675 1750 3.448093 TGAACCCACATCTTGCCATTA 57.552 42.857 0.00 0.00 0.00 1.90
1699 1774 3.921119 TTGCAAATTGCTCAACGAGAT 57.079 38.095 19.34 0.00 45.31 2.75
1702 1777 3.120095 TGCAAATTGCTCAACGAGATCAG 60.120 43.478 19.34 0.00 45.31 2.90
1709 1784 2.797792 GCTCAACGAGATCAGCAGTAGG 60.798 54.545 0.00 0.00 0.00 3.18
1736 1811 7.650104 GTGCTAGAATTCAGAGTACCTTACATC 59.350 40.741 8.44 0.00 0.00 3.06
1739 1814 6.797454 AGAATTCAGAGTACCTTACATCGAC 58.203 40.000 8.44 0.00 0.00 4.20
1770 1848 8.892723 CCAAGTTCTGTTCTTTGCATACATATA 58.107 33.333 0.00 0.00 0.00 0.86
1814 1897 9.651718 GAAACTGATGTCAATATTTATTCCGAC 57.348 33.333 0.00 0.00 0.00 4.79
1815 1898 8.964476 AACTGATGTCAATATTTATTCCGACT 57.036 30.769 3.80 0.00 0.00 4.18
1874 2843 0.107214 TTGGGGAGCATCGGTTCATC 60.107 55.000 0.00 0.00 34.37 2.92
1932 2901 0.390860 CCTATCACTCCAGAAGGGCG 59.609 60.000 0.00 0.00 36.21 6.13
1959 2928 5.755861 GGATTCAGCTACCATCTCTTACAAC 59.244 44.000 0.00 0.00 0.00 3.32
1995 2964 1.464734 TCAACCTCGCTCTCGAATCT 58.535 50.000 0.00 0.00 44.98 2.40
2010 2979 1.585668 GAATCTGACGTGCTCATCGTG 59.414 52.381 0.00 0.00 41.64 4.35
2051 3020 4.624882 TCAAACAAAGCACATTGTCAACAC 59.375 37.500 3.48 0.00 42.49 3.32
2067 3036 2.203788 ACGGAAGTCCTGGAGGCA 60.204 61.111 0.00 0.00 44.19 4.75
2124 3093 0.036388 GAGGGAACGTTGATGAGGCA 60.036 55.000 5.00 0.00 0.00 4.75
2130 3099 2.806856 CGTTGATGAGGCAGCGCTC 61.807 63.158 7.13 2.01 35.82 5.03
2134 3103 2.905681 ATGAGGCAGCGCTCATCA 59.094 55.556 20.57 20.57 35.64 3.07
2408 3377 3.370978 CCACGTCAGGTTTCATATGACAC 59.629 47.826 12.69 12.69 42.76 3.67
2613 4475 3.013276 TGTGAAGTACTTGACTGCTCG 57.987 47.619 23.03 0.00 38.87 5.03
2649 4511 3.107601 ACTACCAGTCTACCATGCATGT 58.892 45.455 24.58 15.01 0.00 3.21
2662 4524 4.584325 ACCATGCATGTAAATCCCATGTAC 59.416 41.667 24.58 0.00 41.38 2.90
2690 4552 0.038526 GACCATCACGTCTGGTTCGT 60.039 55.000 17.96 0.00 46.95 3.85
2693 4555 0.708370 CATCACGTCTGGTTCGTTCG 59.292 55.000 0.00 0.00 39.55 3.95
2694 4556 0.388134 ATCACGTCTGGTTCGTTCGG 60.388 55.000 0.00 0.00 39.55 4.30
2728 4590 2.103094 TCTCTGAAGAACCAGGTGTGTG 59.897 50.000 0.00 0.00 34.99 3.82
2747 4609 1.154205 GCATGTACGTAGCAGCCCAG 61.154 60.000 0.00 0.00 0.00 4.45
2777 4639 3.281158 TGATTGTGGAGCCATGTACATG 58.719 45.455 26.02 26.02 38.51 3.21
2823 4685 8.825745 GGCAGAAACTTGTGATGAAATTTAAAA 58.174 29.630 0.00 0.00 0.00 1.52
2844 4706 0.392863 TGAACTCCATCCATGTGGCG 60.393 55.000 0.00 0.00 39.19 5.69
2853 4715 2.516227 TCCATGTGGCGGGATAAAAA 57.484 45.000 0.00 0.00 34.44 1.94
2866 4728 5.005094 CGGGATAAAAACAAGGAACACCTA 58.995 41.667 0.00 0.00 33.17 3.08
2869 4731 5.771165 GGATAAAAACAAGGAACACCTACCA 59.229 40.000 0.00 0.00 33.17 3.25
2896 4758 2.568509 GGTGGTGGTAACTGGCTAACTA 59.431 50.000 0.00 0.00 37.61 2.24
2897 4759 3.199289 GGTGGTGGTAACTGGCTAACTAT 59.801 47.826 0.00 0.00 37.61 2.12
2910 4772 3.330267 GCTAACTATCCAGGTATGCAGC 58.670 50.000 0.00 0.00 0.00 5.25
2918 4780 2.239402 TCCAGGTATGCAGCAAATGAGA 59.761 45.455 0.00 0.00 0.00 3.27
2922 4784 2.874701 GGTATGCAGCAAATGAGATCGT 59.125 45.455 0.00 0.00 0.00 3.73
2951 4815 1.353022 TGGGTCCCATGTTCCTGTAAC 59.647 52.381 6.47 0.00 38.67 2.50
2969 4833 5.498393 TGTAACCTGGTACAAAACTCAACA 58.502 37.500 0.00 0.00 38.70 3.33
2996 4860 4.194720 GCGCCGTGACTCTCCGAT 62.195 66.667 0.00 0.00 0.00 4.18
3042 4906 1.209621 GTACAGGCCAGTTGGGGATA 58.790 55.000 5.94 0.00 37.04 2.59
3055 4919 4.542525 AGTTGGGGATAAATGGTGGACTTA 59.457 41.667 0.00 0.00 0.00 2.24
3056 4920 5.195756 AGTTGGGGATAAATGGTGGACTTAT 59.804 40.000 0.00 0.00 0.00 1.73
3057 4921 5.060427 TGGGGATAAATGGTGGACTTATG 57.940 43.478 0.00 0.00 0.00 1.90
3065 4929 9.288576 GATAAATGGTGGACTTATGATGATCAA 57.711 33.333 0.00 0.00 0.00 2.57
3078 4942 6.785337 ATGATGATCAAGCAAAGGATGAAA 57.215 33.333 0.00 0.00 0.00 2.69
3084 4948 6.716628 TGATCAAGCAAAGGATGAAAGTTAGT 59.283 34.615 0.00 0.00 0.00 2.24
3116 4982 2.156917 CAAGCAGCAGATTCTGAACCA 58.843 47.619 17.87 0.00 36.19 3.67
3119 4985 2.089980 GCAGCAGATTCTGAACCATGT 58.910 47.619 17.87 0.00 36.19 3.21
3120 4986 2.159421 GCAGCAGATTCTGAACCATGTG 60.159 50.000 17.87 3.78 36.19 3.21
3121 4987 2.422479 CAGCAGATTCTGAACCATGTGG 59.578 50.000 17.87 0.00 37.46 4.17
3140 5006 2.347490 GTTCTGGCCCTTCGCAGA 59.653 61.111 0.00 0.00 40.31 4.26
3171 5037 8.121305 TGTGCCATTTCAGAAATAATTGTAGT 57.879 30.769 8.12 0.00 0.00 2.73
3209 5075 2.816087 GCTTCTGGTTCATTGCTCAAGA 59.184 45.455 0.00 0.00 0.00 3.02
3285 5173 0.328258 GCTCCTAAGTCCTGGCCAAA 59.672 55.000 7.01 0.00 0.00 3.28
3300 5188 2.843730 GGCCAAATTTCCCCCTTGTTAT 59.156 45.455 0.00 0.00 0.00 1.89
3321 5209 1.927487 TGGTTACCAGTCGAAGGCTA 58.073 50.000 0.00 0.00 46.86 3.93
3322 5210 2.463752 TGGTTACCAGTCGAAGGCTAT 58.536 47.619 0.00 0.00 46.86 2.97
3323 5211 2.167693 TGGTTACCAGTCGAAGGCTATG 59.832 50.000 0.00 0.00 46.86 2.23
3326 5214 0.176680 ACCAGTCGAAGGCTATGCTG 59.823 55.000 5.13 0.00 46.86 4.41
3341 5229 2.046285 GCTGGGCGCAATGGTAAGT 61.046 57.895 10.83 0.00 38.92 2.24
3346 5234 1.102978 GGCGCAATGGTAAGTTGGAT 58.897 50.000 10.83 0.00 0.00 3.41
3347 5235 2.294074 GGCGCAATGGTAAGTTGGATA 58.706 47.619 10.83 0.00 0.00 2.59
3348 5236 2.685897 GGCGCAATGGTAAGTTGGATAA 59.314 45.455 10.83 0.00 0.00 1.75
3349 5237 3.243068 GGCGCAATGGTAAGTTGGATAAG 60.243 47.826 10.83 0.00 0.00 1.73
3350 5238 3.243068 GCGCAATGGTAAGTTGGATAAGG 60.243 47.826 0.30 0.00 0.00 2.69
3351 5239 3.945285 CGCAATGGTAAGTTGGATAAGGT 59.055 43.478 0.00 0.00 0.00 3.50
3352 5240 4.201910 CGCAATGGTAAGTTGGATAAGGTG 60.202 45.833 0.00 0.00 0.00 4.00
3353 5241 4.097892 GCAATGGTAAGTTGGATAAGGTGG 59.902 45.833 0.00 0.00 0.00 4.61
3354 5242 5.505780 CAATGGTAAGTTGGATAAGGTGGA 58.494 41.667 0.00 0.00 0.00 4.02
3355 5243 5.994416 ATGGTAAGTTGGATAAGGTGGAT 57.006 39.130 0.00 0.00 0.00 3.41
3356 5244 5.789574 TGGTAAGTTGGATAAGGTGGATT 57.210 39.130 0.00 0.00 0.00 3.01
3357 5245 5.505780 TGGTAAGTTGGATAAGGTGGATTG 58.494 41.667 0.00 0.00 0.00 2.67
3358 5246 5.251932 TGGTAAGTTGGATAAGGTGGATTGA 59.748 40.000 0.00 0.00 0.00 2.57
3359 5247 5.823045 GGTAAGTTGGATAAGGTGGATTGAG 59.177 44.000 0.00 0.00 0.00 3.02
3360 5248 5.779241 AAGTTGGATAAGGTGGATTGAGA 57.221 39.130 0.00 0.00 0.00 3.27
3361 5249 5.983333 AGTTGGATAAGGTGGATTGAGAT 57.017 39.130 0.00 0.00 0.00 2.75
3362 5250 5.688807 AGTTGGATAAGGTGGATTGAGATG 58.311 41.667 0.00 0.00 0.00 2.90
3363 5251 5.429762 AGTTGGATAAGGTGGATTGAGATGA 59.570 40.000 0.00 0.00 0.00 2.92
3364 5252 5.557576 TGGATAAGGTGGATTGAGATGAG 57.442 43.478 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 87 4.129737 TTCTTCGAGGCCGCTCGG 62.130 66.667 13.82 3.56 45.82 4.63
85 89 0.804156 CTTCTTCTTCGAGGCCGCTC 60.804 60.000 4.53 0.00 35.37 5.03
86 90 1.216710 CTTCTTCTTCGAGGCCGCT 59.783 57.895 4.53 0.00 35.37 5.52
93 97 4.499183 GCCTTCTTCATCTTCTTCTTCGA 58.501 43.478 0.00 0.00 0.00 3.71
118 122 0.598680 AGCTGCACGAGTCACTGTTC 60.599 55.000 1.02 0.00 0.00 3.18
122 126 0.523966 GAGTAGCTGCACGAGTCACT 59.476 55.000 4.12 0.00 0.00 3.41
144 166 2.064581 GGAGTGGTCATAGGGGCGT 61.065 63.158 0.00 0.00 0.00 5.68
246 279 1.091771 CACTATCGGCCAGCAACAGG 61.092 60.000 2.24 0.00 0.00 4.00
247 280 0.108186 TCACTATCGGCCAGCAACAG 60.108 55.000 2.24 0.00 0.00 3.16
253 286 1.942657 CCAACAATCACTATCGGCCAG 59.057 52.381 2.24 0.00 0.00 4.85
289 322 5.710613 ACGGCAATAAAACAAACAAAGTG 57.289 34.783 0.00 0.00 0.00 3.16
299 336 1.135916 TGCGCACTACGGCAATAAAAC 60.136 47.619 5.66 0.00 43.93 2.43
304 341 0.179166 CATTTGCGCACTACGGCAAT 60.179 50.000 11.12 1.69 43.93 3.56
308 345 0.515127 TGTTCATTTGCGCACTACGG 59.485 50.000 11.12 0.00 43.93 4.02
320 357 3.000727 GAGGAATTCGGTCGTGTTCATT 58.999 45.455 0.00 0.00 0.00 2.57
353 390 1.837051 TCCAATAGCGGCCGAGGAT 60.837 57.895 33.48 15.56 0.00 3.24
380 417 3.689649 GCCAAATGGAATCGTAGTTGAGT 59.310 43.478 2.98 0.00 37.39 3.41
392 429 2.827322 CTCCAACTCATGCCAAATGGAA 59.173 45.455 2.98 0.00 36.59 3.53
405 442 1.276622 TCTTAGGCCACCTCCAACTC 58.723 55.000 5.01 0.00 34.61 3.01
407 444 3.496870 CCATATCTTAGGCCACCTCCAAC 60.497 52.174 5.01 0.00 34.61 3.77
425 480 1.915228 GGCCACCTCTTGCTCCATA 59.085 57.895 0.00 0.00 0.00 2.74
450 511 1.227664 CGGTCTGCTCCTCCTCCTA 59.772 63.158 0.00 0.00 0.00 2.94
460 521 2.681778 CCACCTCCTCGGTCTGCT 60.682 66.667 0.00 0.00 44.93 4.24
461 522 2.997897 ACCACCTCCTCGGTCTGC 60.998 66.667 0.00 0.00 44.93 4.26
462 523 2.650116 CCACCACCTCCTCGGTCTG 61.650 68.421 0.00 0.00 44.93 3.51
463 524 2.169590 ATCCACCACCTCCTCGGTCT 62.170 60.000 0.00 0.00 44.93 3.85
464 525 1.686110 ATCCACCACCTCCTCGGTC 60.686 63.158 0.00 0.00 44.93 4.79
481 542 0.273161 ATCCCCCACCTCCTCATCAT 59.727 55.000 0.00 0.00 0.00 2.45
482 543 0.400525 GATCCCCCACCTCCTCATCA 60.401 60.000 0.00 0.00 0.00 3.07
497 558 3.326297 CCTCCATAACCTCCTCTTGATCC 59.674 52.174 0.00 0.00 0.00 3.36
501 562 3.107601 TCACCTCCATAACCTCCTCTTG 58.892 50.000 0.00 0.00 0.00 3.02
513 574 1.949847 CTCGCTTCGGTCACCTCCAT 61.950 60.000 0.00 0.00 0.00 3.41
530 591 2.811317 CTTGACTCCCGCGTGCTC 60.811 66.667 4.92 0.00 0.00 4.26
541 602 1.227556 GTGGTGCGTGACCTTGACT 60.228 57.895 7.21 0.00 46.32 3.41
564 625 4.396166 AGCAATATCCTCTTTTTGGTCGTG 59.604 41.667 0.00 0.00 0.00 4.35
567 628 6.765915 AAGAGCAATATCCTCTTTTTGGTC 57.234 37.500 11.03 5.77 44.88 4.02
646 707 6.258068 CGTAATTCTCTCCCAAAACATAGTCC 59.742 42.308 0.00 0.00 0.00 3.85
746 808 2.223340 GCCGTATCAACTTCAAGCATGG 60.223 50.000 0.00 0.00 0.00 3.66
751 813 5.168569 TGTCTTAGCCGTATCAACTTCAAG 58.831 41.667 0.00 0.00 0.00 3.02
752 814 5.142061 TGTCTTAGCCGTATCAACTTCAA 57.858 39.130 0.00 0.00 0.00 2.69
753 815 4.794278 TGTCTTAGCCGTATCAACTTCA 57.206 40.909 0.00 0.00 0.00 3.02
754 816 7.766219 TTTATGTCTTAGCCGTATCAACTTC 57.234 36.000 0.00 0.00 0.00 3.01
755 817 8.732746 ATTTTATGTCTTAGCCGTATCAACTT 57.267 30.769 0.00 0.00 0.00 2.66
756 818 8.204836 AGATTTTATGTCTTAGCCGTATCAACT 58.795 33.333 0.00 0.00 0.00 3.16
757 819 8.366671 AGATTTTATGTCTTAGCCGTATCAAC 57.633 34.615 0.00 0.00 0.00 3.18
758 820 9.472361 GTAGATTTTATGTCTTAGCCGTATCAA 57.528 33.333 0.00 0.00 0.00 2.57
759 821 8.635328 TGTAGATTTTATGTCTTAGCCGTATCA 58.365 33.333 0.00 0.00 0.00 2.15
760 822 9.472361 TTGTAGATTTTATGTCTTAGCCGTATC 57.528 33.333 0.00 0.00 0.00 2.24
761 823 9.826574 TTTGTAGATTTTATGTCTTAGCCGTAT 57.173 29.630 0.00 0.00 0.00 3.06
762 824 9.309516 CTTTGTAGATTTTATGTCTTAGCCGTA 57.690 33.333 0.00 0.00 0.00 4.02
763 825 7.822822 ACTTTGTAGATTTTATGTCTTAGCCGT 59.177 33.333 0.00 0.00 0.00 5.68
764 826 8.197988 ACTTTGTAGATTTTATGTCTTAGCCG 57.802 34.615 0.00 0.00 0.00 5.52
784 846 9.413048 TGTTAGTGGAGTAAAAACAAAACTTTG 57.587 29.630 0.60 0.60 43.62 2.77
785 847 9.984190 TTGTTAGTGGAGTAAAAACAAAACTTT 57.016 25.926 0.00 0.00 37.17 2.66
791 853 8.852135 CCCTTATTGTTAGTGGAGTAAAAACAA 58.148 33.333 0.00 0.00 42.35 2.83
792 854 8.219178 TCCCTTATTGTTAGTGGAGTAAAAACA 58.781 33.333 0.00 0.00 0.00 2.83
793 855 8.625786 TCCCTTATTGTTAGTGGAGTAAAAAC 57.374 34.615 0.00 0.00 0.00 2.43
794 856 9.457436 GATCCCTTATTGTTAGTGGAGTAAAAA 57.543 33.333 0.00 0.00 0.00 1.94
795 857 7.767198 CGATCCCTTATTGTTAGTGGAGTAAAA 59.233 37.037 0.00 0.00 0.00 1.52
796 858 7.270047 CGATCCCTTATTGTTAGTGGAGTAAA 58.730 38.462 0.00 0.00 0.00 2.01
797 859 6.183360 CCGATCCCTTATTGTTAGTGGAGTAA 60.183 42.308 0.00 0.00 0.00 2.24
798 860 5.303589 CCGATCCCTTATTGTTAGTGGAGTA 59.696 44.000 0.00 0.00 0.00 2.59
799 861 4.101119 CCGATCCCTTATTGTTAGTGGAGT 59.899 45.833 0.00 0.00 0.00 3.85
800 862 4.632153 CCGATCCCTTATTGTTAGTGGAG 58.368 47.826 0.00 0.00 0.00 3.86
801 863 3.181458 GCCGATCCCTTATTGTTAGTGGA 60.181 47.826 0.00 0.00 0.00 4.02
802 864 3.139077 GCCGATCCCTTATTGTTAGTGG 58.861 50.000 0.00 0.00 0.00 4.00
803 865 4.073293 AGCCGATCCCTTATTGTTAGTG 57.927 45.455 0.00 0.00 0.00 2.74
804 866 5.145564 TCTAGCCGATCCCTTATTGTTAGT 58.854 41.667 0.00 0.00 0.00 2.24
805 867 5.723672 TCTAGCCGATCCCTTATTGTTAG 57.276 43.478 0.00 0.00 0.00 2.34
806 868 5.046591 CCATCTAGCCGATCCCTTATTGTTA 60.047 44.000 0.00 0.00 0.00 2.41
807 869 4.263068 CCATCTAGCCGATCCCTTATTGTT 60.263 45.833 0.00 0.00 0.00 2.83
808 870 3.261897 CCATCTAGCCGATCCCTTATTGT 59.738 47.826 0.00 0.00 0.00 2.71
809 871 3.866651 CCATCTAGCCGATCCCTTATTG 58.133 50.000 0.00 0.00 0.00 1.90
810 872 2.237392 GCCATCTAGCCGATCCCTTATT 59.763 50.000 0.00 0.00 0.00 1.40
811 873 1.834263 GCCATCTAGCCGATCCCTTAT 59.166 52.381 0.00 0.00 0.00 1.73
812 874 1.267121 GCCATCTAGCCGATCCCTTA 58.733 55.000 0.00 0.00 0.00 2.69
813 875 1.484444 GGCCATCTAGCCGATCCCTT 61.484 60.000 0.00 0.00 44.57 3.95
814 876 1.915769 GGCCATCTAGCCGATCCCT 60.916 63.158 0.00 0.00 44.57 4.20
815 877 2.665603 GGCCATCTAGCCGATCCC 59.334 66.667 0.00 0.00 44.57 3.85
822 884 1.355720 ACCCCAATATGGCCATCTAGC 59.644 52.381 24.80 0.00 35.79 3.42
823 885 4.927267 TTACCCCAATATGGCCATCTAG 57.073 45.455 24.80 12.78 35.79 2.43
824 886 5.135362 ACTTTTACCCCAATATGGCCATCTA 59.865 40.000 24.80 5.96 35.79 1.98
825 887 4.078630 ACTTTTACCCCAATATGGCCATCT 60.079 41.667 24.80 10.30 35.79 2.90
826 888 4.223144 ACTTTTACCCCAATATGGCCATC 58.777 43.478 24.80 0.00 35.79 3.51
827 889 4.279288 ACTTTTACCCCAATATGGCCAT 57.721 40.909 24.45 24.45 35.79 4.40
828 890 3.767309 ACTTTTACCCCAATATGGCCA 57.233 42.857 8.56 8.56 35.79 5.36
829 891 5.659525 AGTAAACTTTTACCCCAATATGGCC 59.340 40.000 0.00 0.00 43.03 5.36
830 892 6.605995 AGAGTAAACTTTTACCCCAATATGGC 59.394 38.462 8.02 0.00 43.03 4.40
831 893 9.117183 GTAGAGTAAACTTTTACCCCAATATGG 57.883 37.037 8.02 0.00 43.03 2.74
832 894 9.901172 AGTAGAGTAAACTTTTACCCCAATATG 57.099 33.333 8.02 0.00 43.03 1.78
851 913 9.138596 GAGGATCCAGAGTAAATTTAGTAGAGT 57.861 37.037 15.82 0.00 0.00 3.24
852 914 9.362151 AGAGGATCCAGAGTAAATTTAGTAGAG 57.638 37.037 15.82 0.00 33.66 2.43
853 915 9.357161 GAGAGGATCCAGAGTAAATTTAGTAGA 57.643 37.037 15.82 4.39 33.66 2.59
854 916 9.362151 AGAGAGGATCCAGAGTAAATTTAGTAG 57.638 37.037 15.82 2.45 33.66 2.57
855 917 9.716556 AAGAGAGGATCCAGAGTAAATTTAGTA 57.283 33.333 15.82 0.00 33.66 1.82
856 918 8.616799 AAGAGAGGATCCAGAGTAAATTTAGT 57.383 34.615 15.82 5.20 33.66 2.24
861 923 9.890915 ACTTATAAGAGAGGATCCAGAGTAAAT 57.109 33.333 19.38 1.79 33.66 1.40
864 926 9.796180 GTTACTTATAAGAGAGGATCCAGAGTA 57.204 37.037 19.38 5.50 33.66 2.59
865 927 7.726738 GGTTACTTATAAGAGAGGATCCAGAGT 59.273 40.741 19.38 6.39 33.66 3.24
866 928 7.947890 AGGTTACTTATAAGAGAGGATCCAGAG 59.052 40.741 19.38 0.71 33.66 3.35
867 929 7.827787 AGGTTACTTATAAGAGAGGATCCAGA 58.172 38.462 19.38 0.00 33.66 3.86
868 930 8.485578 AAGGTTACTTATAAGAGAGGATCCAG 57.514 38.462 19.38 1.14 34.49 3.86
869 931 8.855804 AAAGGTTACTTATAAGAGAGGATCCA 57.144 34.615 19.38 0.00 35.41 3.41
873 935 9.643735 CTCCTAAAGGTTACTTATAAGAGAGGA 57.356 37.037 19.38 14.49 35.41 3.71
874 936 9.643735 TCTCCTAAAGGTTACTTATAAGAGAGG 57.356 37.037 19.38 11.66 35.41 3.69
878 940 9.075678 CCGATCTCCTAAAGGTTACTTATAAGA 57.924 37.037 19.38 0.27 35.41 2.10
879 941 8.858094 ACCGATCTCCTAAAGGTTACTTATAAG 58.142 37.037 11.05 11.05 35.41 1.73
880 942 8.773033 ACCGATCTCCTAAAGGTTACTTATAA 57.227 34.615 0.00 0.00 35.41 0.98
881 943 8.773033 AACCGATCTCCTAAAGGTTACTTATA 57.227 34.615 0.00 0.00 42.68 0.98
882 944 7.672122 AACCGATCTCCTAAAGGTTACTTAT 57.328 36.000 0.00 0.00 42.68 1.73
883 945 8.055181 TCTAACCGATCTCCTAAAGGTTACTTA 58.945 37.037 1.71 0.00 43.92 2.24
884 946 6.894103 TCTAACCGATCTCCTAAAGGTTACTT 59.106 38.462 1.71 0.00 43.92 2.24
885 947 6.430007 TCTAACCGATCTCCTAAAGGTTACT 58.570 40.000 1.71 0.00 43.92 2.24
886 948 6.705863 TCTAACCGATCTCCTAAAGGTTAC 57.294 41.667 1.71 0.00 43.92 2.50
887 949 7.722949 TTTCTAACCGATCTCCTAAAGGTTA 57.277 36.000 5.44 5.44 43.92 2.85
888 950 6.616237 TTTCTAACCGATCTCCTAAAGGTT 57.384 37.500 3.61 3.61 45.84 3.50
889 951 6.183360 GGATTTCTAACCGATCTCCTAAAGGT 60.183 42.308 0.00 0.00 36.66 3.50
890 952 6.224584 GGATTTCTAACCGATCTCCTAAAGG 58.775 44.000 0.00 0.00 0.00 3.11
891 953 6.224584 GGGATTTCTAACCGATCTCCTAAAG 58.775 44.000 0.00 0.00 0.00 1.85
892 954 5.071384 GGGGATTTCTAACCGATCTCCTAAA 59.929 44.000 0.00 0.00 37.44 1.85
893 955 4.591924 GGGGATTTCTAACCGATCTCCTAA 59.408 45.833 0.00 0.00 37.44 2.69
894 956 4.158015 GGGGATTTCTAACCGATCTCCTA 58.842 47.826 0.00 0.00 37.44 2.94
895 957 2.973406 GGGGATTTCTAACCGATCTCCT 59.027 50.000 0.00 0.00 37.44 3.69
896 958 3.404224 GGGGATTTCTAACCGATCTCC 57.596 52.381 0.00 0.00 33.57 3.71
903 965 3.264947 GTGTGTACGGGGATTTCTAACC 58.735 50.000 0.00 0.00 0.00 2.85
904 966 3.264947 GGTGTGTACGGGGATTTCTAAC 58.735 50.000 0.00 0.00 0.00 2.34
905 967 2.905085 TGGTGTGTACGGGGATTTCTAA 59.095 45.455 0.00 0.00 0.00 2.10
906 968 2.498481 CTGGTGTGTACGGGGATTTCTA 59.502 50.000 0.00 0.00 0.00 2.10
907 969 1.278127 CTGGTGTGTACGGGGATTTCT 59.722 52.381 0.00 0.00 0.00 2.52
908 970 1.002773 ACTGGTGTGTACGGGGATTTC 59.997 52.381 0.00 0.00 0.00 2.17
909 971 1.061546 ACTGGTGTGTACGGGGATTT 58.938 50.000 0.00 0.00 0.00 2.17
910 972 1.061546 AACTGGTGTGTACGGGGATT 58.938 50.000 0.00 0.00 0.00 3.01
911 973 1.941377 TAACTGGTGTGTACGGGGAT 58.059 50.000 0.00 0.00 0.00 3.85
912 974 1.826720 GATAACTGGTGTGTACGGGGA 59.173 52.381 0.00 0.00 0.00 4.81
913 975 1.134610 GGATAACTGGTGTGTACGGGG 60.135 57.143 0.00 0.00 0.00 5.73
914 976 1.551430 TGGATAACTGGTGTGTACGGG 59.449 52.381 0.00 0.00 0.00 5.28
915 977 3.259064 CTTGGATAACTGGTGTGTACGG 58.741 50.000 0.00 0.00 0.00 4.02
916 978 3.921677 ACTTGGATAACTGGTGTGTACG 58.078 45.455 0.00 0.00 0.00 3.67
917 979 4.929808 CAGACTTGGATAACTGGTGTGTAC 59.070 45.833 0.00 0.00 0.00 2.90
918 980 4.562757 GCAGACTTGGATAACTGGTGTGTA 60.563 45.833 0.00 0.00 0.00 2.90
919 981 3.807209 GCAGACTTGGATAACTGGTGTGT 60.807 47.826 0.00 0.00 0.00 3.72
920 982 2.744202 GCAGACTTGGATAACTGGTGTG 59.256 50.000 0.00 0.00 0.00 3.82
921 983 2.371841 TGCAGACTTGGATAACTGGTGT 59.628 45.455 0.00 0.00 0.00 4.16
922 984 3.005554 CTGCAGACTTGGATAACTGGTG 58.994 50.000 8.42 0.00 0.00 4.17
923 985 2.026822 CCTGCAGACTTGGATAACTGGT 60.027 50.000 17.39 0.00 0.00 4.00
924 986 2.636830 CCTGCAGACTTGGATAACTGG 58.363 52.381 17.39 0.00 0.00 4.00
925 987 2.012673 GCCTGCAGACTTGGATAACTG 58.987 52.381 17.39 0.00 0.00 3.16
926 988 1.065126 GGCCTGCAGACTTGGATAACT 60.065 52.381 17.39 0.00 0.00 2.24
939 1001 1.001764 CTGATCCTTGTGGCCTGCA 60.002 57.895 3.32 0.00 0.00 4.41
942 1004 1.004044 CTGAACTGATCCTTGTGGCCT 59.996 52.381 3.32 0.00 0.00 5.19
952 1014 3.719924 CTGATCCAGAGCTGAACTGATC 58.280 50.000 0.00 3.75 37.54 2.92
1358 1420 2.230025 ACGTCAGTGGAGAATGTCTCAG 59.770 50.000 7.52 0.00 45.12 3.35
1488 1550 0.179012 GGAAACCACGGACCTTGGAA 60.179 55.000 23.29 0.00 37.58 3.53
1523 1585 7.547370 AGACTTCAGAAATAATGTGTCTGCTAC 59.453 37.037 0.00 0.00 38.92 3.58
1552 1627 7.434897 TGTTGTGATTTTCGGATCAAAAAGAAG 59.565 33.333 10.02 0.00 35.58 2.85
1553 1628 7.261325 TGTTGTGATTTTCGGATCAAAAAGAA 58.739 30.769 10.02 0.00 35.58 2.52
1555 1630 7.462109 TTGTTGTGATTTTCGGATCAAAAAG 57.538 32.000 10.02 0.00 35.58 2.27
1558 1633 8.430801 AAATTTGTTGTGATTTTCGGATCAAA 57.569 26.923 0.00 0.00 37.75 2.69
1596 1671 8.450180 ACAAAGTCCAAAATTTGTTGTGATTTC 58.550 29.630 10.34 0.00 44.96 2.17
1616 1691 7.502226 TCAATCAAATACTCTGGTTGACAAAGT 59.498 33.333 0.00 0.00 38.65 2.66
1618 1693 7.815840 TCAATCAAATACTCTGGTTGACAAA 57.184 32.000 0.00 0.00 38.65 2.83
1659 1734 4.497300 CAAAACTAATGGCAAGATGTGGG 58.503 43.478 0.00 0.00 0.00 4.61
1702 1777 3.133003 TCTGAATTCTAGCACCCTACTGC 59.867 47.826 7.05 0.00 37.44 4.40
1709 1784 5.346181 AAGGTACTCTGAATTCTAGCACC 57.654 43.478 16.91 16.91 38.49 5.01
1736 1811 0.396811 AACAGAACTTGGGGGAGTCG 59.603 55.000 0.00 0.00 0.00 4.18
1739 1814 2.887152 CAAAGAACAGAACTTGGGGGAG 59.113 50.000 0.00 0.00 0.00 4.30
1814 1897 1.094073 GCCACTGAGCTGGTGCATAG 61.094 60.000 10.04 0.00 42.74 2.23
1815 1898 1.078214 GCCACTGAGCTGGTGCATA 60.078 57.895 10.04 0.00 42.74 3.14
1932 2901 4.953940 AGAGATGGTAGCTGAATCCTTC 57.046 45.455 0.00 2.05 0.00 3.46
1959 2928 3.947834 GGTTGATGACACTGGGGAAATAG 59.052 47.826 0.00 0.00 0.00 1.73
1995 2964 2.432456 GCCACGATGAGCACGTCA 60.432 61.111 4.21 0.00 42.07 4.35
2010 2979 2.098842 GATCATTGAGAGCGCACGCC 62.099 60.000 11.47 3.39 43.17 5.68
2051 3020 0.970937 TAGTGCCTCCAGGACTTCCG 60.971 60.000 0.00 0.00 42.08 4.30
2067 3036 1.568504 TGACGCCATCTTTCCCTAGT 58.431 50.000 0.00 0.00 0.00 2.57
2115 3084 2.905681 ATGAGCGCTGCCTCATCA 59.094 55.556 18.48 4.86 46.75 3.07
2130 3099 1.078918 TCCCTTGAGTGCGCTGATG 60.079 57.895 3.44 0.00 0.00 3.07
2134 3103 3.710722 CCCTCCCTTGAGTGCGCT 61.711 66.667 9.73 0.00 36.86 5.92
2166 3135 1.561643 TCTCAAAGACATCGAGGCCT 58.438 50.000 3.86 3.86 0.00 5.19
2408 3377 5.023920 GTCGCATGTAACATCAATCACAAG 58.976 41.667 0.00 0.00 0.00 3.16
2662 4524 2.002586 GACGTGATGGTCATGTTCAGG 58.997 52.381 0.00 1.40 45.80 3.86
2673 4535 1.068474 GAACGAACCAGACGTGATGG 58.932 55.000 13.58 13.58 43.16 3.51
2674 4536 0.708370 CGAACGAACCAGACGTGATG 59.292 55.000 0.00 0.00 43.16 3.07
2690 4552 1.153369 GATGCAGCAGCTACCCGAA 60.153 57.895 2.53 0.00 42.74 4.30
2693 4555 0.532417 CAGAGATGCAGCAGCTACCC 60.532 60.000 14.54 0.82 42.74 3.69
2694 4556 0.463204 TCAGAGATGCAGCAGCTACC 59.537 55.000 14.54 1.65 42.74 3.18
2728 4590 1.153449 TGGGCTGCTACGTACATGC 60.153 57.895 0.00 0.00 0.00 4.06
2747 4609 3.696051 TGGCTCCACAATCAAAATAGCTC 59.304 43.478 0.00 0.00 0.00 4.09
2777 4639 1.928503 CAAATTTCACGGGCATGCATC 59.071 47.619 21.36 10.11 0.00 3.91
2823 4685 2.381911 GCCACATGGATGGAGTTCAAT 58.618 47.619 6.54 0.00 43.02 2.57
2844 4706 5.184479 GGTAGGTGTTCCTTGTTTTTATCCC 59.816 44.000 0.00 0.00 42.12 3.85
2866 4728 0.400815 TTACCACCACCTGACCTGGT 60.401 55.000 0.00 0.00 43.22 4.00
2869 4731 1.056660 CAGTTACCACCACCTGACCT 58.943 55.000 0.00 0.00 0.00 3.85
2896 4758 3.117776 TCTCATTTGCTGCATACCTGGAT 60.118 43.478 1.84 0.00 0.00 3.41
2897 4759 2.239402 TCTCATTTGCTGCATACCTGGA 59.761 45.455 1.84 0.00 0.00 3.86
2910 4772 4.261322 CCATAAGGGCAACGATCTCATTTG 60.261 45.833 0.00 0.00 37.60 2.32
2951 4815 4.196193 TGTCTGTTGAGTTTTGTACCAGG 58.804 43.478 0.00 0.00 0.00 4.45
2969 4833 1.069090 TCACGGCGCTCTTTTGTCT 59.931 52.632 6.90 0.00 0.00 3.41
3014 4878 4.576463 CCAACTGGCCTGTACATATTTCTC 59.424 45.833 16.48 0.00 0.00 2.87
3028 4892 1.342975 ACCATTTATCCCCAACTGGCC 60.343 52.381 0.00 0.00 32.83 5.36
3042 4906 6.040166 GCTTGATCATCATAAGTCCACCATTT 59.960 38.462 0.00 0.00 0.00 2.32
3055 4919 6.380274 ACTTTCATCCTTTGCTTGATCATCAT 59.620 34.615 0.00 0.00 0.00 2.45
3056 4920 5.713389 ACTTTCATCCTTTGCTTGATCATCA 59.287 36.000 0.00 0.00 0.00 3.07
3057 4921 6.205101 ACTTTCATCCTTTGCTTGATCATC 57.795 37.500 0.00 0.00 0.00 2.92
3065 4929 5.140454 ACCAACTAACTTTCATCCTTTGCT 58.860 37.500 0.00 0.00 0.00 3.91
3078 4942 2.638480 TGAGCAGCAACCAACTAACT 57.362 45.000 0.00 0.00 0.00 2.24
3129 4995 3.479255 CAGTTTTTCTGCGAAGGGC 57.521 52.632 0.00 0.00 43.96 5.19
3171 5037 7.725251 ACCAGAAGCAATTTGAAAAAGTCATA 58.275 30.769 0.00 0.00 35.70 2.15
3174 5040 6.534793 TGAACCAGAAGCAATTTGAAAAAGTC 59.465 34.615 0.00 0.00 0.00 3.01
3176 5042 6.907206 TGAACCAGAAGCAATTTGAAAAAG 57.093 33.333 0.00 0.00 0.00 2.27
3181 5047 4.039488 AGCAATGAACCAGAAGCAATTTGA 59.961 37.500 0.00 0.00 0.00 2.69
3209 5075 5.197451 CCAGACTACAGATCACTCTACCTT 58.803 45.833 0.00 0.00 0.00 3.50
3285 5173 6.068140 TGGTAACCATATAACAAGGGGGAAAT 60.068 38.462 0.00 0.00 0.00 2.17
3300 5188 2.463752 AGCCTTCGACTGGTAACCATA 58.536 47.619 5.65 0.00 30.82 2.74
3326 5214 0.963355 TCCAACTTACCATTGCGCCC 60.963 55.000 4.18 0.00 0.00 6.13
3334 5222 5.251932 TCAATCCACCTTATCCAACTTACCA 59.748 40.000 0.00 0.00 0.00 3.25
3336 5224 6.650120 TCTCAATCCACCTTATCCAACTTAC 58.350 40.000 0.00 0.00 0.00 2.34
3341 5229 5.933617 CTCATCTCAATCCACCTTATCCAA 58.066 41.667 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.