Multiple sequence alignment - TraesCS2D01G238200

Loading Multiple Alignment...

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 TraesCS2D01G238200 chr2D 100.000 2360 0 0 1 2360 247440060 247437701 0.000000e+00 4359.0
1 TraesCS2D01G238200 chr2A 90.698 731 27 7 894 1585 280108811 280108083 0.000000e+00 935.0
2 TraesCS2D01G238200 chr2A 95.890 438 18 0 1580 2017 280102908 280102471 0.000000e+00 710.0
3 TraesCS2D01G238200 chr2A 95.665 346 10 2 2016 2360 280102173 280101832 3.430000e-153 551.0
4 TraesCS2D01G238200 chrUn 86.494 770 77 13 1 759 244163749 244164502 0.000000e+00 821.0
5 TraesCS2D01G238200 chrUn 86.494 770 77 13 1 759 244176384 244177137 0.000000e+00 821.0
6 TraesCS2D01G238200 chrUn 86.494 770 77 13 1 759 316237998 316237245 0.000000e+00 821.0
7 TraesCS2D01G238200 chrUn 83.071 254 38 4 1758 2008 391856911 391857162 2.360000e-55 226.0
8 TraesCS2D01G238200 chr3D 86.957 230 26 3 1781 2008 363269517 363269744 3.010000e-64 255.0
9 TraesCS2D01G238200 chr3B 85.375 253 26 6 1758 2008 377862307 377862064 3.890000e-63 252.0
10 TraesCS2D01G238200 chr6D 83.858 254 36 4 1758 2008 285775106 285775357 1.090000e-58 237.0
11 TraesCS2D01G238200 chr4A 83.529 255 35 6 1758 2008 591598968 591598717 5.070000e-57 231.0
12 TraesCS2D01G238200 chr4A 83.594 256 32 9 1758 2008 592444244 592444494 5.070000e-57 231.0
13 TraesCS2D01G238200 chr4A 83.594 256 32 9 1758 2008 592722752 592723002 5.070000e-57 231.0
14 TraesCS2D01G238200 chr4A 83.594 256 32 9 1758 2008 593011557 593011807 5.070000e-57 231.0
15 TraesCS2D01G238200 chr4A 86.154 65 7 2 775 838 153778778 153778841 4.210000e-08 69.4
16 TraesCS2D01G238200 chr1B 79.435 248 33 13 598 844 31567077 31566847 2.430000e-35 159.0
17 TraesCS2D01G238200 chr1B 79.435 248 32 14 598 844 31544106 31543877 8.730000e-35 158.0
18 TraesCS2D01G238200 chr1B 78.629 248 33 15 598 844 31570652 31570424 1.890000e-31 147.0
19 TraesCS2D01G238200 chr5A 92.157 51 2 2 775 824 659357244 659357293 1.170000e-08 71.3
20 TraesCS2D01G238200 chr6A 77.876 113 20 5 714 824 26754758 26754649 5.440000e-07 65.8


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 TraesCS2D01G238200 chr2D 247437701 247440060 2359 True 4359.0 4359 100.0000 1 2360 1 chr2D.!!$R1 2359
1 TraesCS2D01G238200 chr2A 280108083 280108811 728 True 935.0 935 90.6980 894 1585 1 chr2A.!!$R1 691
2 TraesCS2D01G238200 chr2A 280101832 280102908 1076 True 630.5 710 95.7775 1580 2360 2 chr2A.!!$R2 780
3 TraesCS2D01G238200 chrUn 244163749 244164502 753 False 821.0 821 86.4940 1 759 1 chrUn.!!$F1 758
4 TraesCS2D01G238200 chrUn 244176384 244177137 753 False 821.0 821 86.4940 1 759 1 chrUn.!!$F2 758
5 TraesCS2D01G238200 chrUn 316237245 316237998 753 True 821.0 821 86.4940 1 759 1 chrUn.!!$R1 758

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
503 512 0.026674 CACCGCTTCACATATGTGCG 59.973 55.0 27.71 25.89 45.25 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 2685 0.251634 CCAACTCAGGAAGGAGGCTC 59.748 60.0 5.78 5.78 39.27 4.7 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
21 22 2.923426 CTAGCAATTGGGCGAGCGGA 62.923 60.000 7.72 0.00 39.27 5.54
22 23 2.529454 TAGCAATTGGGCGAGCGGAA 62.529 55.000 7.72 0.00 39.27 4.30
23 24 2.988688 GCAATTGGGCGAGCGGAAA 61.989 57.895 7.72 0.00 0.00 3.13
57 58 0.459411 GGACGAGAAGAGCAAGGAGC 60.459 60.000 0.00 0.00 46.19 4.70
92 93 2.599578 AGCTTTGTGGGCTGGCTG 60.600 61.111 0.00 0.00 38.73 4.85
93 94 2.598394 GCTTTGTGGGCTGGCTGA 60.598 61.111 0.00 0.00 0.00 4.26
157 166 7.176690 ACCGGTCAAGACAGATAAAATTCAAAT 59.823 33.333 0.00 0.00 0.00 2.32
216 225 9.234384 CGATATAAAAGAGTTAATCACACGAGT 57.766 33.333 0.00 0.00 0.00 4.18
246 255 0.588980 GCGGCAAAGCGTATGTTAGC 60.589 55.000 0.00 0.00 0.00 3.09
248 257 1.379527 GGCAAAGCGTATGTTAGCCT 58.620 50.000 7.62 0.00 37.67 4.58
249 258 1.064060 GGCAAAGCGTATGTTAGCCTG 59.936 52.381 7.62 0.00 37.67 4.85
284 293 6.178239 ACCGAATAATCAACACTGTAAAGC 57.822 37.500 0.00 0.00 0.00 3.51
297 306 2.303022 CTGTAAAGCTTGGAGAGGGTCA 59.697 50.000 0.00 0.00 0.00 4.02
301 310 1.115467 AGCTTGGAGAGGGTCATACG 58.885 55.000 0.00 0.00 0.00 3.06
308 317 0.106819 AGAGGGTCATACGCGTAGGT 60.107 55.000 27.68 10.96 36.04 3.08
332 341 6.312918 GTGCCTTAGTTTAATCATCGTTCTGA 59.687 38.462 0.00 0.00 0.00 3.27
342 351 1.197721 CATCGTTCTGAACACAAGGCC 59.802 52.381 19.56 0.00 0.00 5.19
351 360 1.474077 GAACACAAGGCCATCATGGTC 59.526 52.381 5.01 0.00 44.07 4.02
375 384 1.303236 CAAGACCGGCCAACCATCA 60.303 57.895 0.00 0.00 34.57 3.07
395 404 7.094634 ACCATCATGTAATTAATCAATCGGAGC 60.095 37.037 0.00 0.00 0.00 4.70
411 420 1.531149 GGAGCACGCGTAATATGCATT 59.469 47.619 13.44 0.00 41.97 3.56
430 439 4.927425 GCATTTGCAGATCAATGAACAGTT 59.073 37.500 12.05 0.00 41.59 3.16
491 500 3.389741 CGTACTACGTTCACCGCTT 57.610 52.632 0.00 0.00 41.42 4.68
492 501 1.253999 CGTACTACGTTCACCGCTTC 58.746 55.000 0.00 0.00 41.42 3.86
493 502 1.400113 CGTACTACGTTCACCGCTTCA 60.400 52.381 0.00 0.00 41.42 3.02
494 503 1.981533 GTACTACGTTCACCGCTTCAC 59.018 52.381 0.00 0.00 41.42 3.18
495 504 0.386476 ACTACGTTCACCGCTTCACA 59.614 50.000 0.00 0.00 41.42 3.58
498 507 2.380084 ACGTTCACCGCTTCACATAT 57.620 45.000 0.00 0.00 41.42 1.78
503 512 0.026674 CACCGCTTCACATATGTGCG 59.973 55.000 27.71 25.89 45.25 5.34
525 534 4.661461 CGCTCTCTGTGCAAGACA 57.339 55.556 0.00 0.00 0.00 3.41
542 551 2.432628 ACACTACCAAGCGAGCGC 60.433 61.111 6.78 6.78 42.33 5.92
582 591 4.189580 ACCCAAGCACAGCACGGT 62.190 61.111 0.00 0.00 0.00 4.83
613 622 5.238214 GCACTCTGGATTCAGGTGATATTTC 59.762 44.000 20.64 4.31 40.96 2.17
614 623 5.762218 CACTCTGGATTCAGGTGATATTTCC 59.238 44.000 14.31 0.00 40.96 3.13
615 624 5.669447 ACTCTGGATTCAGGTGATATTTCCT 59.331 40.000 0.00 0.00 41.23 3.36
620 629 5.532779 GGATTCAGGTGATATTTCCTTCCAC 59.467 44.000 9.54 0.00 31.90 4.02
626 635 1.947456 GATATTTCCTTCCACGGCCAC 59.053 52.381 2.24 0.00 0.00 5.01
637 646 3.066190 CGGCCACGAGGTGTCCTA 61.066 66.667 2.24 0.00 44.60 2.94
641 650 1.676635 CCACGAGGTGTCCTACGGA 60.677 63.158 0.00 0.00 31.76 4.69
649 658 4.514401 GAGGTGTCCTACGGATTGATTTT 58.486 43.478 0.00 0.00 31.76 1.82
656 665 6.084277 GTCCTACGGATTGATTTTGACAAAC 58.916 40.000 0.00 0.00 32.73 2.93
657 666 5.765677 TCCTACGGATTGATTTTGACAAACA 59.234 36.000 0.00 0.00 0.00 2.83
661 670 4.383649 CGGATTGATTTTGACAAACAGCAG 59.616 41.667 0.00 0.00 0.00 4.24
680 689 3.558958 GCAGGGGGTTATTTGCAAAACAT 60.559 43.478 17.19 2.12 36.59 2.71
692 701 0.311790 CAAAACATGCAGCACCGACT 59.688 50.000 0.00 0.00 0.00 4.18
695 704 1.230635 AACATGCAGCACCGACTGTC 61.231 55.000 0.00 0.00 39.96 3.51
697 706 1.375140 ATGCAGCACCGACTGTCTG 60.375 57.895 0.00 1.64 39.96 3.51
708 717 0.759346 GACTGTCTGGTCCAGTTGGT 59.241 55.000 18.65 14.27 43.00 3.67
709 718 0.469917 ACTGTCTGGTCCAGTTGGTG 59.530 55.000 18.65 8.30 40.14 4.17
719 728 2.787473 CCAGTTGGTGGCTTCTGATA 57.213 50.000 0.00 0.00 40.39 2.15
723 732 2.237392 AGTTGGTGGCTTCTGATAGGTC 59.763 50.000 0.00 0.00 0.00 3.85
729 738 2.334023 GGCTTCTGATAGGTCCAGGAT 58.666 52.381 0.00 0.00 32.73 3.24
740 749 4.046286 AGGTCCAGGATTAAATGTGCAA 57.954 40.909 0.00 0.00 0.00 4.08
741 750 4.415596 AGGTCCAGGATTAAATGTGCAAA 58.584 39.130 0.00 0.00 0.00 3.68
759 768 4.418392 GCAAATCTGATGCAAGTGTTAGG 58.582 43.478 0.00 0.00 43.29 2.69
760 769 4.156556 GCAAATCTGATGCAAGTGTTAGGA 59.843 41.667 0.00 0.00 43.29 2.94
761 770 5.634896 CAAATCTGATGCAAGTGTTAGGAC 58.365 41.667 0.00 0.00 0.00 3.85
762 771 3.334583 TCTGATGCAAGTGTTAGGACC 57.665 47.619 0.00 0.00 0.00 4.46
763 772 2.637382 TCTGATGCAAGTGTTAGGACCA 59.363 45.455 0.00 0.00 0.00 4.02
764 773 3.072330 TCTGATGCAAGTGTTAGGACCAA 59.928 43.478 0.00 0.00 0.00 3.67
765 774 3.820467 CTGATGCAAGTGTTAGGACCAAA 59.180 43.478 0.00 0.00 0.00 3.28
766 775 4.406456 TGATGCAAGTGTTAGGACCAAAT 58.594 39.130 0.00 0.00 0.00 2.32
767 776 5.565509 TGATGCAAGTGTTAGGACCAAATA 58.434 37.500 0.00 0.00 0.00 1.40
768 777 5.647658 TGATGCAAGTGTTAGGACCAAATAG 59.352 40.000 0.00 0.00 0.00 1.73
769 778 4.980573 TGCAAGTGTTAGGACCAAATAGT 58.019 39.130 0.00 0.00 0.00 2.12
770 779 5.381757 TGCAAGTGTTAGGACCAAATAGTT 58.618 37.500 0.00 0.00 0.00 2.24
771 780 5.240623 TGCAAGTGTTAGGACCAAATAGTTG 59.759 40.000 0.00 0.00 33.78 3.16
772 781 5.699839 CAAGTGTTAGGACCAAATAGTTGC 58.300 41.667 0.00 0.00 33.01 4.17
773 782 4.332828 AGTGTTAGGACCAAATAGTTGCC 58.667 43.478 0.00 0.00 33.01 4.52
774 783 4.042934 AGTGTTAGGACCAAATAGTTGCCT 59.957 41.667 7.17 7.17 33.34 4.75
775 784 4.765339 GTGTTAGGACCAAATAGTTGCCTT 59.235 41.667 7.28 0.00 31.74 4.35
776 785 5.243060 GTGTTAGGACCAAATAGTTGCCTTT 59.757 40.000 7.28 0.00 31.74 3.11
777 786 5.836358 TGTTAGGACCAAATAGTTGCCTTTT 59.164 36.000 7.28 0.00 31.74 2.27
778 787 4.871933 AGGACCAAATAGTTGCCTTTTG 57.128 40.909 0.00 0.00 33.01 2.44
779 788 3.006859 AGGACCAAATAGTTGCCTTTTGC 59.993 43.478 0.00 0.00 41.77 3.68
792 801 4.371855 GCCTTTTGCAAGTTATAGGACC 57.628 45.455 14.12 0.00 40.77 4.46
793 802 3.761752 GCCTTTTGCAAGTTATAGGACCA 59.238 43.478 14.12 0.00 40.77 4.02
794 803 4.219725 GCCTTTTGCAAGTTATAGGACCAA 59.780 41.667 14.12 0.00 40.77 3.67
795 804 5.279256 GCCTTTTGCAAGTTATAGGACCAAA 60.279 40.000 14.12 0.00 40.77 3.28
796 805 6.156519 CCTTTTGCAAGTTATAGGACCAAAC 58.843 40.000 0.00 0.00 0.00 2.93
797 806 5.715434 TTTGCAAGTTATAGGACCAAACC 57.285 39.130 0.00 0.00 0.00 3.27
798 807 4.374689 TGCAAGTTATAGGACCAAACCA 57.625 40.909 0.00 0.00 0.00 3.67
799 808 4.929479 TGCAAGTTATAGGACCAAACCAT 58.071 39.130 0.00 0.00 0.00 3.55
800 809 4.947388 TGCAAGTTATAGGACCAAACCATC 59.053 41.667 0.00 0.00 0.00 3.51
801 810 4.947388 GCAAGTTATAGGACCAAACCATCA 59.053 41.667 0.00 0.00 0.00 3.07
802 811 5.163652 GCAAGTTATAGGACCAAACCATCAC 60.164 44.000 0.00 0.00 0.00 3.06
803 812 5.772393 AGTTATAGGACCAAACCATCACA 57.228 39.130 0.00 0.00 0.00 3.58
804 813 6.327386 AGTTATAGGACCAAACCATCACAT 57.673 37.500 0.00 0.00 0.00 3.21
805 814 6.731467 AGTTATAGGACCAAACCATCACATT 58.269 36.000 0.00 0.00 0.00 2.71
806 815 6.603201 AGTTATAGGACCAAACCATCACATTG 59.397 38.462 0.00 0.00 0.00 2.82
807 816 3.524095 AGGACCAAACCATCACATTGA 57.476 42.857 0.00 0.00 0.00 2.57
808 817 3.843422 AGGACCAAACCATCACATTGAA 58.157 40.909 0.00 0.00 0.00 2.69
809 818 3.828451 AGGACCAAACCATCACATTGAAG 59.172 43.478 0.00 0.00 0.00 3.02
810 819 3.826157 GGACCAAACCATCACATTGAAGA 59.174 43.478 0.00 0.00 0.00 2.87
811 820 4.321230 GGACCAAACCATCACATTGAAGAC 60.321 45.833 0.00 0.00 0.00 3.01
812 821 4.214310 ACCAAACCATCACATTGAAGACA 58.786 39.130 0.00 0.00 0.00 3.41
813 822 4.648762 ACCAAACCATCACATTGAAGACAA 59.351 37.500 0.00 0.00 40.42 3.18
814 823 5.221303 ACCAAACCATCACATTGAAGACAAG 60.221 40.000 0.00 0.00 39.46 3.16
815 824 5.221303 CCAAACCATCACATTGAAGACAAGT 60.221 40.000 0.00 0.00 39.46 3.16
816 825 6.275335 CAAACCATCACATTGAAGACAAGTT 58.725 36.000 0.00 0.00 39.46 2.66
817 826 5.443185 ACCATCACATTGAAGACAAGTTG 57.557 39.130 0.00 0.00 39.46 3.16
818 827 4.889409 ACCATCACATTGAAGACAAGTTGT 59.111 37.500 8.61 8.61 39.46 3.32
819 828 6.061441 ACCATCACATTGAAGACAAGTTGTA 58.939 36.000 8.88 0.00 39.46 2.41
820 829 6.205464 ACCATCACATTGAAGACAAGTTGTAG 59.795 38.462 8.88 0.00 39.46 2.74
821 830 6.348786 CCATCACATTGAAGACAAGTTGTAGG 60.349 42.308 8.88 0.00 39.46 3.18
822 831 5.924356 TCACATTGAAGACAAGTTGTAGGA 58.076 37.500 8.88 0.00 39.46 2.94
823 832 5.758296 TCACATTGAAGACAAGTTGTAGGAC 59.242 40.000 8.88 0.00 39.46 3.85
824 833 5.049405 CACATTGAAGACAAGTTGTAGGACC 60.049 44.000 8.88 0.00 39.46 4.46
825 834 5.163195 ACATTGAAGACAAGTTGTAGGACCT 60.163 40.000 8.88 0.00 39.46 3.85
826 835 4.336889 TGAAGACAAGTTGTAGGACCTG 57.663 45.455 8.88 0.00 0.00 4.00
827 836 2.841442 AGACAAGTTGTAGGACCTGC 57.159 50.000 8.88 2.72 0.00 4.85
828 837 1.000955 AGACAAGTTGTAGGACCTGCG 59.999 52.381 8.88 0.00 0.00 5.18
829 838 1.000506 GACAAGTTGTAGGACCTGCGA 59.999 52.381 8.88 0.00 0.00 5.10
830 839 1.623811 ACAAGTTGTAGGACCTGCGAT 59.376 47.619 6.75 0.00 0.00 4.58
831 840 2.002586 CAAGTTGTAGGACCTGCGATG 58.997 52.381 3.53 0.00 0.00 3.84
832 841 0.108138 AGTTGTAGGACCTGCGATGC 60.108 55.000 3.53 0.00 0.00 3.91
833 842 0.108138 GTTGTAGGACCTGCGATGCT 60.108 55.000 3.53 0.00 0.00 3.79
834 843 1.136305 GTTGTAGGACCTGCGATGCTA 59.864 52.381 3.53 0.00 0.00 3.49
835 844 1.704641 TGTAGGACCTGCGATGCTAT 58.295 50.000 3.53 0.00 0.00 2.97
836 845 2.039418 TGTAGGACCTGCGATGCTATT 58.961 47.619 3.53 0.00 0.00 1.73
837 846 3.227614 TGTAGGACCTGCGATGCTATTA 58.772 45.455 3.53 0.00 0.00 0.98
838 847 2.821991 AGGACCTGCGATGCTATTAC 57.178 50.000 0.00 0.00 0.00 1.89
839 848 1.344763 AGGACCTGCGATGCTATTACC 59.655 52.381 0.00 0.00 0.00 2.85
840 849 1.344763 GGACCTGCGATGCTATTACCT 59.655 52.381 0.00 0.00 0.00 3.08
841 850 2.224305 GGACCTGCGATGCTATTACCTT 60.224 50.000 0.00 0.00 0.00 3.50
842 851 3.467803 GACCTGCGATGCTATTACCTTT 58.532 45.455 0.00 0.00 0.00 3.11
843 852 4.502604 GGACCTGCGATGCTATTACCTTTA 60.503 45.833 0.00 0.00 0.00 1.85
844 853 5.031066 ACCTGCGATGCTATTACCTTTAA 57.969 39.130 0.00 0.00 0.00 1.52
845 854 5.433526 ACCTGCGATGCTATTACCTTTAAA 58.566 37.500 0.00 0.00 0.00 1.52
846 855 5.883673 ACCTGCGATGCTATTACCTTTAAAA 59.116 36.000 0.00 0.00 0.00 1.52
847 856 6.038271 ACCTGCGATGCTATTACCTTTAAAAG 59.962 38.462 0.00 0.00 0.00 2.27
848 857 5.816919 TGCGATGCTATTACCTTTAAAAGC 58.183 37.500 1.20 1.20 0.00 3.51
849 858 5.355630 TGCGATGCTATTACCTTTAAAAGCA 59.644 36.000 11.32 11.32 43.43 3.91
850 859 5.681543 GCGATGCTATTACCTTTAAAAGCAC 59.318 40.000 11.19 6.17 42.23 4.40
851 860 5.901884 CGATGCTATTACCTTTAAAAGCACG 59.098 40.000 11.19 12.24 42.23 5.34
852 861 5.554822 TGCTATTACCTTTAAAAGCACGG 57.445 39.130 6.01 0.00 35.20 4.94
853 862 4.142556 TGCTATTACCTTTAAAAGCACGGC 60.143 41.667 6.01 0.00 35.20 5.68
854 863 4.095932 GCTATTACCTTTAAAAGCACGGCT 59.904 41.667 3.06 0.00 42.56 5.52
855 864 5.295045 GCTATTACCTTTAAAAGCACGGCTA 59.705 40.000 3.06 0.00 38.25 3.93
856 865 6.183360 GCTATTACCTTTAAAAGCACGGCTAA 60.183 38.462 3.06 0.00 38.25 3.09
857 866 5.616488 TTACCTTTAAAAGCACGGCTAAG 57.384 39.130 0.00 0.27 38.25 2.18
858 867 3.483421 ACCTTTAAAAGCACGGCTAAGT 58.517 40.909 0.00 0.00 38.25 2.24
859 868 3.501062 ACCTTTAAAAGCACGGCTAAGTC 59.499 43.478 0.00 0.00 38.25 3.01
860 869 3.119955 CCTTTAAAAGCACGGCTAAGTCC 60.120 47.826 0.00 0.00 38.25 3.85
861 870 2.843401 TAAAAGCACGGCTAAGTCCA 57.157 45.000 0.00 0.00 38.25 4.02
862 871 1.235724 AAAAGCACGGCTAAGTCCAC 58.764 50.000 0.00 0.00 38.25 4.02
863 872 0.107831 AAAGCACGGCTAAGTCCACA 59.892 50.000 0.00 0.00 38.25 4.17
864 873 0.324943 AAGCACGGCTAAGTCCACAT 59.675 50.000 0.00 0.00 38.25 3.21
865 874 1.191535 AGCACGGCTAAGTCCACATA 58.808 50.000 0.00 0.00 36.99 2.29
866 875 1.137086 AGCACGGCTAAGTCCACATAG 59.863 52.381 0.00 0.00 36.99 2.23
867 876 1.136305 GCACGGCTAAGTCCACATAGA 59.864 52.381 0.00 0.00 0.00 1.98
868 877 2.418197 GCACGGCTAAGTCCACATAGAA 60.418 50.000 0.00 0.00 0.00 2.10
869 878 3.741388 GCACGGCTAAGTCCACATAGAAT 60.741 47.826 0.00 0.00 0.00 2.40
870 879 4.051922 CACGGCTAAGTCCACATAGAATC 58.948 47.826 0.00 0.00 0.00 2.52
871 880 3.243434 ACGGCTAAGTCCACATAGAATCG 60.243 47.826 0.00 0.00 0.00 3.34
872 881 3.060602 GGCTAAGTCCACATAGAATCGC 58.939 50.000 0.00 0.00 0.00 4.58
873 882 3.492656 GGCTAAGTCCACATAGAATCGCA 60.493 47.826 0.00 0.00 0.00 5.10
874 883 4.310769 GCTAAGTCCACATAGAATCGCAT 58.689 43.478 0.00 0.00 0.00 4.73
875 884 4.151335 GCTAAGTCCACATAGAATCGCATG 59.849 45.833 0.00 0.00 0.00 4.06
876 885 2.487934 AGTCCACATAGAATCGCATGC 58.512 47.619 7.91 7.91 0.00 4.06
877 886 1.193203 GTCCACATAGAATCGCATGCG 59.807 52.381 33.61 33.61 41.35 4.73
887 896 2.070049 TCGCATGCGAAGAAAGACG 58.930 52.632 38.48 7.97 46.01 4.18
888 897 0.388006 TCGCATGCGAAGAAAGACGA 60.388 50.000 38.48 13.59 46.01 4.20
889 898 0.246912 CGCATGCGAAGAAAGACGAC 60.247 55.000 35.82 0.00 42.83 4.34
890 899 1.071605 GCATGCGAAGAAAGACGACT 58.928 50.000 0.00 0.00 0.00 4.18
891 900 2.259618 GCATGCGAAGAAAGACGACTA 58.740 47.619 0.00 0.00 0.00 2.59
892 901 2.860735 GCATGCGAAGAAAGACGACTAT 59.139 45.455 0.00 0.00 0.00 2.12
926 936 7.256190 CCATTTCATCTAGTTCCCGTTATCCTA 60.256 40.741 0.00 0.00 0.00 2.94
939 955 3.190118 CGTTATCCTATGGTCTACCGTCC 59.810 52.174 0.00 0.00 39.43 4.79
976 992 2.816411 CCTGTCAGGGGTAGTAGAACA 58.184 52.381 11.46 0.00 0.00 3.18
980 996 3.830755 TGTCAGGGGTAGTAGAACAACTC 59.169 47.826 0.00 0.00 0.00 3.01
1128 1159 2.740826 GCAGCGCGGTTCCTACAA 60.741 61.111 8.73 0.00 0.00 2.41
1238 1269 1.889530 GCCTACTCCAAGCCTGTCGT 61.890 60.000 0.00 0.00 0.00 4.34
1337 1368 2.348998 CGGCCCACTCTGCTTCTT 59.651 61.111 0.00 0.00 0.00 2.52
1372 1403 2.297597 GTGCTGTAGTGTCTCCTTCACT 59.702 50.000 4.11 4.11 46.10 3.41
1377 1408 5.455056 TGTAGTGTCTCCTTCACTTTCTC 57.545 43.478 3.98 0.00 42.50 2.87
1400 1431 2.276493 CGTCGTCGAGTACAGGCG 60.276 66.667 8.73 8.73 39.71 5.52
1450 1481 0.954449 GCAGGATGATGCGGGAGATG 60.954 60.000 0.00 0.00 39.69 2.90
1452 1483 1.002868 GGATGATGCGGGAGATGGG 60.003 63.158 0.00 0.00 0.00 4.00
1483 1514 1.939934 TCAGGTTCGTGTTTTGCTCTG 59.060 47.619 0.00 0.00 0.00 3.35
1503 1534 6.092807 GCTCTGTTCCTTCCAAATACTAAGTG 59.907 42.308 0.00 0.00 0.00 3.16
1575 1623 6.543831 ACATCAACTATCACCAGCTTTATTCC 59.456 38.462 0.00 0.00 0.00 3.01
1621 1669 3.827008 TTGTTCTGTCTGCTCTCAGTT 57.173 42.857 0.00 0.00 41.10 3.16
1638 1686 5.248477 TCTCAGTTCTTTATGTGGCCTAGTT 59.752 40.000 3.32 0.00 0.00 2.24
1740 1788 5.857268 ACATCAAGCAAAGCCTATTTTTGT 58.143 33.333 0.00 0.00 37.73 2.83
1811 1859 0.179234 TTGCACAAGGGAGTTCGTCA 59.821 50.000 0.00 0.00 0.00 4.35
1833 1881 3.584294 AGGTATTAGGCGTGGGAAGTAT 58.416 45.455 0.00 0.00 0.00 2.12
1844 1892 5.237996 GGCGTGGGAAGTATAATTTTACTCC 59.762 44.000 8.75 10.77 31.19 3.85
1867 1915 3.696051 CACTCCCTTGTTTGGTATGATGG 59.304 47.826 0.00 0.00 0.00 3.51
1905 1953 0.034863 GGCCTCCCCACGAATTAACA 60.035 55.000 0.00 0.00 0.00 2.41
1959 2007 0.681243 GCACCCTCAACTCCCATTCC 60.681 60.000 0.00 0.00 0.00 3.01
1968 2016 1.214992 ACTCCCATTCCCCTTCCCAC 61.215 60.000 0.00 0.00 0.00 4.61
1995 2043 1.633945 TCCCCTTCCCTCTAAACAAGC 59.366 52.381 0.00 0.00 0.00 4.01
2051 2398 7.338710 TCTTGAGGGTCATTTATGGTAGAAAG 58.661 38.462 0.00 0.00 0.00 2.62
2056 2403 5.339695 GGGTCATTTATGGTAGAAAGGGTGA 60.340 44.000 0.00 0.00 0.00 4.02
2099 2447 9.000486 AGAAAATGGCTTACTAGTGTAGTTTTC 58.000 33.333 5.39 13.22 40.14 2.29
2151 2499 4.718774 TCACTTCTCTGCCAATCCTTATCT 59.281 41.667 0.00 0.00 0.00 1.98
2162 2510 5.654209 GCCAATCCTTATCTTTTTCAGGACT 59.346 40.000 0.00 0.00 38.28 3.85
2168 2516 6.044404 TCCTTATCTTTTTCAGGACTGGTTCT 59.956 38.462 0.00 0.00 29.97 3.01
2169 2517 6.150140 CCTTATCTTTTTCAGGACTGGTTCTG 59.850 42.308 2.77 2.77 0.00 3.02
2170 2518 4.503714 TCTTTTTCAGGACTGGTTCTGT 57.496 40.909 8.65 0.00 33.13 3.41
2171 2519 4.855340 TCTTTTTCAGGACTGGTTCTGTT 58.145 39.130 8.65 0.00 33.13 3.16
2280 2628 9.582431 CTTGATTGCAATCTGATCACTAAAAAT 57.418 29.630 33.23 0.00 36.39 1.82
2337 2685 8.984891 TTGCACAAATGTAGATAGGATTTTTG 57.015 30.769 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.802136 GCTCTCGCTCACTCATCTTGG 60.802 57.143 0.00 0.00 0.00 3.61
119 120 5.533154 TGTCTTGACCGGTGTTTTAATGATT 59.467 36.000 14.63 0.00 0.00 2.57
122 131 4.513692 TCTGTCTTGACCGGTGTTTTAATG 59.486 41.667 14.63 0.00 0.00 1.90
190 199 9.234384 ACTCGTGTGATTAACTCTTTTATATCG 57.766 33.333 0.00 0.00 0.00 2.92
211 220 2.431601 GCGCTGCTCTTCACTCGT 60.432 61.111 0.00 0.00 0.00 4.18
216 225 4.986645 TTGCCGCGCTGCTCTTCA 62.987 61.111 24.31 0.58 0.00 3.02
232 241 4.467198 AGTACAGGCTAACATACGCTTT 57.533 40.909 0.00 0.00 0.00 3.51
238 247 9.605275 CGGTATATACTAGTACAGGCTAACATA 57.395 37.037 12.54 0.00 0.00 2.29
239 248 8.324306 TCGGTATATACTAGTACAGGCTAACAT 58.676 37.037 12.54 0.00 0.00 2.71
240 249 7.679783 TCGGTATATACTAGTACAGGCTAACA 58.320 38.462 12.54 0.00 0.00 2.41
241 250 8.553459 TTCGGTATATACTAGTACAGGCTAAC 57.447 38.462 12.54 0.00 0.00 2.34
276 285 2.303022 TGACCCTCTCCAAGCTTTACAG 59.697 50.000 0.00 0.00 0.00 2.74
284 293 0.249073 CGCGTATGACCCTCTCCAAG 60.249 60.000 0.00 0.00 0.00 3.61
297 306 1.396653 ACTAAGGCACCTACGCGTAT 58.603 50.000 20.91 2.37 0.00 3.06
301 310 4.186159 TGATTAAACTAAGGCACCTACGC 58.814 43.478 0.00 0.00 0.00 4.42
308 317 6.403049 TCAGAACGATGATTAAACTAAGGCA 58.597 36.000 0.00 0.00 0.00 4.75
332 341 1.076024 AGACCATGATGGCCTTGTGTT 59.924 47.619 12.25 0.00 42.67 3.32
351 360 0.310854 GTTGGCCGGTCTTGTTTCAG 59.689 55.000 7.97 0.00 0.00 3.02
375 384 5.334105 GCGTGCTCCGATTGATTAATTACAT 60.334 40.000 0.43 0.00 39.56 2.29
411 420 5.234757 GCAAAAACTGTTCATTGATCTGCAA 59.765 36.000 17.87 0.00 41.53 4.08
448 457 1.378911 TCACCATCACCATGCCTGC 60.379 57.895 0.00 0.00 0.00 4.85
474 483 1.981533 GTGAAGCGGTGAACGTAGTAC 59.018 52.381 0.00 0.00 45.00 2.73
503 512 4.724602 TGCACAGAGAGCGCGACC 62.725 66.667 12.10 0.00 33.85 4.79
521 530 0.038159 GCTCGCTTGGTAGTGTGTCT 60.038 55.000 0.00 0.00 33.54 3.41
523 532 1.372997 CGCTCGCTTGGTAGTGTGT 60.373 57.895 0.00 0.00 33.54 3.72
524 533 2.730672 GCGCTCGCTTGGTAGTGTG 61.731 63.158 0.00 0.00 38.26 3.82
525 534 2.432628 GCGCTCGCTTGGTAGTGT 60.433 61.111 0.00 0.00 38.26 3.55
542 551 3.450115 GGACGGGAGGGACGACAG 61.450 72.222 0.00 0.00 34.93 3.51
561 570 4.641645 TGCTGTGCTTGGGTCCGG 62.642 66.667 0.00 0.00 0.00 5.14
564 573 3.357079 CCGTGCTGTGCTTGGGTC 61.357 66.667 0.00 0.00 0.00 4.46
565 574 4.189580 ACCGTGCTGTGCTTGGGT 62.190 61.111 0.00 0.00 0.00 4.51
582 591 2.835701 GAATCCAGAGTGCGGCGTGA 62.836 60.000 9.37 0.00 0.00 4.35
593 602 6.409695 GGAAGGAAATATCACCTGAATCCAGA 60.410 42.308 10.19 0.00 43.02 3.86
594 603 5.767168 GGAAGGAAATATCACCTGAATCCAG 59.233 44.000 10.19 0.00 40.09 3.86
597 606 5.237344 CGTGGAAGGAAATATCACCTGAATC 59.763 44.000 2.10 0.00 36.56 2.52
637 646 4.202101 TGCTGTTTGTCAAAATCAATCCGT 60.202 37.500 0.00 0.00 0.00 4.69
641 650 4.503643 CCCCTGCTGTTTGTCAAAATCAAT 60.504 41.667 0.00 0.00 0.00 2.57
649 658 0.847373 TAACCCCCTGCTGTTTGTCA 59.153 50.000 0.00 0.00 0.00 3.58
656 665 1.265236 TTGCAAATAACCCCCTGCTG 58.735 50.000 0.00 0.00 35.78 4.41
657 666 2.022718 TTTGCAAATAACCCCCTGCT 57.977 45.000 8.05 0.00 35.78 4.24
680 689 2.029518 CAGACAGTCGGTGCTGCA 59.970 61.111 0.00 0.00 39.96 4.41
683 692 2.574955 GGACCAGACAGTCGGTGCT 61.575 63.158 20.89 2.25 40.25 4.40
684 693 2.048127 GGACCAGACAGTCGGTGC 60.048 66.667 18.25 17.19 37.66 5.01
685 694 1.290324 CTGGACCAGACAGTCGGTG 59.710 63.158 17.22 2.78 37.66 4.94
686 695 1.152525 ACTGGACCAGACAGTCGGT 60.153 57.895 28.56 14.59 45.50 4.69
687 696 3.778955 ACTGGACCAGACAGTCGG 58.221 61.111 28.56 9.20 45.50 4.79
692 701 1.836391 CCACCAACTGGACCAGACA 59.164 57.895 28.56 0.00 43.95 3.41
695 704 0.890996 GAAGCCACCAACTGGACCAG 60.891 60.000 20.45 20.45 43.95 4.00
697 706 0.890996 CAGAAGCCACCAACTGGACC 60.891 60.000 1.86 0.00 43.95 4.46
708 717 1.008327 TCCTGGACCTATCAGAAGCCA 59.992 52.381 0.00 0.00 34.36 4.75
709 718 1.794714 TCCTGGACCTATCAGAAGCC 58.205 55.000 0.00 0.00 34.36 4.35
719 728 3.737559 TGCACATTTAATCCTGGACCT 57.262 42.857 0.00 0.00 0.00 3.85
723 732 6.211587 TCAGATTTGCACATTTAATCCTGG 57.788 37.500 4.76 0.00 0.00 4.45
740 749 4.263462 TGGTCCTAACACTTGCATCAGATT 60.263 41.667 0.00 0.00 0.00 2.40
741 750 3.264193 TGGTCCTAACACTTGCATCAGAT 59.736 43.478 0.00 0.00 0.00 2.90
752 761 4.696899 GGCAACTATTTGGTCCTAACAC 57.303 45.455 0.00 0.00 32.81 3.32
771 780 3.761752 TGGTCCTATAACTTGCAAAAGGC 59.238 43.478 0.00 0.31 45.13 4.35
772 781 5.975693 TTGGTCCTATAACTTGCAAAAGG 57.024 39.130 0.00 3.05 0.00 3.11
773 782 6.156519 GGTTTGGTCCTATAACTTGCAAAAG 58.843 40.000 0.00 0.00 0.00 2.27
774 783 5.598830 TGGTTTGGTCCTATAACTTGCAAAA 59.401 36.000 0.00 0.00 0.00 2.44
775 784 5.141182 TGGTTTGGTCCTATAACTTGCAAA 58.859 37.500 0.00 0.00 0.00 3.68
776 785 4.730966 TGGTTTGGTCCTATAACTTGCAA 58.269 39.130 0.00 0.00 0.00 4.08
777 786 4.374689 TGGTTTGGTCCTATAACTTGCA 57.625 40.909 0.00 0.00 0.00 4.08
778 787 4.947388 TGATGGTTTGGTCCTATAACTTGC 59.053 41.667 0.00 0.00 0.00 4.01
779 788 5.943416 TGTGATGGTTTGGTCCTATAACTTG 59.057 40.000 0.00 0.00 0.00 3.16
780 789 6.134535 TGTGATGGTTTGGTCCTATAACTT 57.865 37.500 0.00 0.00 0.00 2.66
781 790 5.772393 TGTGATGGTTTGGTCCTATAACT 57.228 39.130 0.00 0.00 0.00 2.24
782 791 6.601613 TCAATGTGATGGTTTGGTCCTATAAC 59.398 38.462 0.00 0.00 0.00 1.89
783 792 6.726379 TCAATGTGATGGTTTGGTCCTATAA 58.274 36.000 0.00 0.00 0.00 0.98
784 793 6.320434 TCAATGTGATGGTTTGGTCCTATA 57.680 37.500 0.00 0.00 0.00 1.31
785 794 5.191727 TCAATGTGATGGTTTGGTCCTAT 57.808 39.130 0.00 0.00 0.00 2.57
786 795 4.649267 TCAATGTGATGGTTTGGTCCTA 57.351 40.909 0.00 0.00 0.00 2.94
787 796 3.524095 TCAATGTGATGGTTTGGTCCT 57.476 42.857 0.00 0.00 0.00 3.85
788 797 3.826157 TCTTCAATGTGATGGTTTGGTCC 59.174 43.478 0.00 0.00 0.00 4.46
789 798 4.278170 TGTCTTCAATGTGATGGTTTGGTC 59.722 41.667 0.00 0.00 0.00 4.02
790 799 4.214310 TGTCTTCAATGTGATGGTTTGGT 58.786 39.130 0.00 0.00 0.00 3.67
791 800 4.852134 TGTCTTCAATGTGATGGTTTGG 57.148 40.909 0.00 0.00 0.00 3.28
792 801 5.835257 ACTTGTCTTCAATGTGATGGTTTG 58.165 37.500 0.00 0.00 32.82 2.93
793 802 6.127366 ACAACTTGTCTTCAATGTGATGGTTT 60.127 34.615 0.00 0.00 32.82 3.27
794 803 5.360714 ACAACTTGTCTTCAATGTGATGGTT 59.639 36.000 0.00 0.00 32.82 3.67
795 804 4.889409 ACAACTTGTCTTCAATGTGATGGT 59.111 37.500 0.00 0.00 32.82 3.55
796 805 5.443185 ACAACTTGTCTTCAATGTGATGG 57.557 39.130 0.00 0.00 32.82 3.51
797 806 6.427853 TCCTACAACTTGTCTTCAATGTGATG 59.572 38.462 0.00 0.00 31.78 3.07
798 807 6.428159 GTCCTACAACTTGTCTTCAATGTGAT 59.572 38.462 0.00 0.00 31.78 3.06
799 808 5.758296 GTCCTACAACTTGTCTTCAATGTGA 59.242 40.000 0.00 0.00 31.78 3.58
800 809 5.049405 GGTCCTACAACTTGTCTTCAATGTG 60.049 44.000 0.00 0.00 31.78 3.21
801 810 5.063880 GGTCCTACAACTTGTCTTCAATGT 58.936 41.667 0.00 0.00 33.29 2.71
802 811 5.180117 CAGGTCCTACAACTTGTCTTCAATG 59.820 44.000 0.00 0.00 32.82 2.82
803 812 5.308825 CAGGTCCTACAACTTGTCTTCAAT 58.691 41.667 0.00 0.00 32.82 2.57
804 813 4.703897 CAGGTCCTACAACTTGTCTTCAA 58.296 43.478 0.00 0.00 0.00 2.69
805 814 3.494398 GCAGGTCCTACAACTTGTCTTCA 60.494 47.826 0.00 0.00 0.00 3.02
806 815 3.067833 GCAGGTCCTACAACTTGTCTTC 58.932 50.000 0.00 0.00 0.00 2.87
807 816 2.548067 CGCAGGTCCTACAACTTGTCTT 60.548 50.000 0.00 0.00 0.00 3.01
808 817 1.000955 CGCAGGTCCTACAACTTGTCT 59.999 52.381 0.00 0.00 0.00 3.41
809 818 1.000506 TCGCAGGTCCTACAACTTGTC 59.999 52.381 0.00 0.00 0.00 3.18
810 819 1.045407 TCGCAGGTCCTACAACTTGT 58.955 50.000 0.00 0.00 0.00 3.16
811 820 2.002586 CATCGCAGGTCCTACAACTTG 58.997 52.381 0.00 0.00 0.00 3.16
812 821 1.676014 GCATCGCAGGTCCTACAACTT 60.676 52.381 0.00 0.00 0.00 2.66
813 822 0.108138 GCATCGCAGGTCCTACAACT 60.108 55.000 0.00 0.00 0.00 3.16
814 823 0.108138 AGCATCGCAGGTCCTACAAC 60.108 55.000 0.00 0.00 0.00 3.32
815 824 1.480789 TAGCATCGCAGGTCCTACAA 58.519 50.000 0.00 0.00 0.00 2.41
816 825 1.704641 ATAGCATCGCAGGTCCTACA 58.295 50.000 0.00 0.00 0.00 2.74
817 826 2.821991 AATAGCATCGCAGGTCCTAC 57.178 50.000 0.00 0.00 0.00 3.18
818 827 2.561419 GGTAATAGCATCGCAGGTCCTA 59.439 50.000 0.00 0.00 0.00 2.94
819 828 1.344763 GGTAATAGCATCGCAGGTCCT 59.655 52.381 0.00 0.00 0.00 3.85
820 829 1.344763 AGGTAATAGCATCGCAGGTCC 59.655 52.381 0.00 0.00 0.00 4.46
821 830 2.821991 AGGTAATAGCATCGCAGGTC 57.178 50.000 0.00 0.00 0.00 3.85
822 831 3.560636 AAAGGTAATAGCATCGCAGGT 57.439 42.857 0.00 0.00 0.00 4.00
823 832 6.371809 TTTTAAAGGTAATAGCATCGCAGG 57.628 37.500 0.00 0.00 0.00 4.85
824 833 5.909610 GCTTTTAAAGGTAATAGCATCGCAG 59.090 40.000 6.84 0.00 41.39 5.18
825 834 5.355630 TGCTTTTAAAGGTAATAGCATCGCA 59.644 36.000 6.84 0.00 44.39 5.10
826 835 5.816919 TGCTTTTAAAGGTAATAGCATCGC 58.183 37.500 6.84 0.00 44.39 4.58
830 839 4.142556 GCCGTGCTTTTAAAGGTAATAGCA 60.143 41.667 6.84 6.01 45.95 3.49
831 840 4.095932 AGCCGTGCTTTTAAAGGTAATAGC 59.904 41.667 6.84 0.13 41.83 2.97
832 841 5.813080 AGCCGTGCTTTTAAAGGTAATAG 57.187 39.130 6.84 0.00 33.89 1.73
833 842 6.880529 ACTTAGCCGTGCTTTTAAAGGTAATA 59.119 34.615 6.84 0.00 40.44 0.98
834 843 5.708697 ACTTAGCCGTGCTTTTAAAGGTAAT 59.291 36.000 6.84 0.00 40.44 1.89
835 844 5.065235 ACTTAGCCGTGCTTTTAAAGGTAA 58.935 37.500 6.84 0.00 40.44 2.85
836 845 4.644498 ACTTAGCCGTGCTTTTAAAGGTA 58.356 39.130 6.84 0.00 40.44 3.08
837 846 3.483421 ACTTAGCCGTGCTTTTAAAGGT 58.517 40.909 6.84 0.00 40.44 3.50
838 847 3.119955 GGACTTAGCCGTGCTTTTAAAGG 60.120 47.826 6.84 0.00 40.44 3.11
839 848 3.500680 TGGACTTAGCCGTGCTTTTAAAG 59.499 43.478 0.00 0.00 40.44 1.85
840 849 3.251487 GTGGACTTAGCCGTGCTTTTAAA 59.749 43.478 3.71 0.00 40.44 1.52
841 850 2.809696 GTGGACTTAGCCGTGCTTTTAA 59.190 45.455 3.71 0.00 40.44 1.52
842 851 2.224329 TGTGGACTTAGCCGTGCTTTTA 60.224 45.455 3.71 0.00 40.44 1.52
843 852 1.235724 GTGGACTTAGCCGTGCTTTT 58.764 50.000 3.71 0.00 40.44 2.27
844 853 0.107831 TGTGGACTTAGCCGTGCTTT 59.892 50.000 3.71 0.00 40.44 3.51
845 854 0.324943 ATGTGGACTTAGCCGTGCTT 59.675 50.000 3.71 0.00 40.44 3.91
846 855 1.137086 CTATGTGGACTTAGCCGTGCT 59.863 52.381 3.87 3.87 43.41 4.40
847 856 1.136305 TCTATGTGGACTTAGCCGTGC 59.864 52.381 0.00 0.00 0.00 5.34
848 857 3.520290 TTCTATGTGGACTTAGCCGTG 57.480 47.619 0.00 0.00 0.00 4.94
849 858 3.243434 CGATTCTATGTGGACTTAGCCGT 60.243 47.826 0.00 0.00 0.00 5.68
850 859 3.309388 CGATTCTATGTGGACTTAGCCG 58.691 50.000 0.00 0.00 0.00 5.52
851 860 3.060602 GCGATTCTATGTGGACTTAGCC 58.939 50.000 0.00 0.00 0.00 3.93
852 861 3.717707 TGCGATTCTATGTGGACTTAGC 58.282 45.455 0.00 0.00 0.00 3.09
853 862 4.151335 GCATGCGATTCTATGTGGACTTAG 59.849 45.833 0.00 0.00 0.00 2.18
854 863 4.058124 GCATGCGATTCTATGTGGACTTA 58.942 43.478 0.00 0.00 0.00 2.24
855 864 2.874701 GCATGCGATTCTATGTGGACTT 59.125 45.455 0.00 0.00 0.00 3.01
856 865 2.487934 GCATGCGATTCTATGTGGACT 58.512 47.619 0.00 0.00 0.00 3.85
857 866 1.193203 CGCATGCGATTCTATGTGGAC 59.807 52.381 35.82 0.00 42.83 4.02
858 867 1.068434 TCGCATGCGATTCTATGTGGA 59.932 47.619 37.21 12.23 44.01 4.02
859 868 1.501169 TCGCATGCGATTCTATGTGG 58.499 50.000 37.21 6.58 44.01 4.17
870 879 0.246912 GTCGTCTTTCTTCGCATGCG 60.247 55.000 33.61 33.61 41.35 4.73
871 880 1.071605 AGTCGTCTTTCTTCGCATGC 58.928 50.000 7.91 7.91 0.00 4.06
872 881 4.105486 TCATAGTCGTCTTTCTTCGCATG 58.895 43.478 0.00 0.00 0.00 4.06
873 882 4.355437 CTCATAGTCGTCTTTCTTCGCAT 58.645 43.478 0.00 0.00 0.00 4.73
874 883 3.759418 CTCATAGTCGTCTTTCTTCGCA 58.241 45.455 0.00 0.00 0.00 5.10
875 884 2.532317 GCTCATAGTCGTCTTTCTTCGC 59.468 50.000 0.00 0.00 0.00 4.70
876 885 2.778928 CGCTCATAGTCGTCTTTCTTCG 59.221 50.000 0.00 0.00 0.00 3.79
877 886 2.532317 GCGCTCATAGTCGTCTTTCTTC 59.468 50.000 0.00 0.00 0.00 2.87
878 887 2.531206 GCGCTCATAGTCGTCTTTCTT 58.469 47.619 0.00 0.00 0.00 2.52
879 888 1.532090 CGCGCTCATAGTCGTCTTTCT 60.532 52.381 5.56 0.00 0.00 2.52
880 889 0.840729 CGCGCTCATAGTCGTCTTTC 59.159 55.000 5.56 0.00 0.00 2.62
881 890 1.140407 GCGCGCTCATAGTCGTCTTT 61.140 55.000 26.67 0.00 0.00 2.52
882 891 1.586564 GCGCGCTCATAGTCGTCTT 60.587 57.895 26.67 0.00 0.00 3.01
883 892 2.024871 GCGCGCTCATAGTCGTCT 59.975 61.111 26.67 0.00 0.00 4.18
884 893 3.025176 GGCGCGCTCATAGTCGTC 61.025 66.667 32.29 5.91 0.00 4.20
885 894 2.629050 AATGGCGCGCTCATAGTCGT 62.629 55.000 32.29 13.54 0.00 4.34
886 895 1.490693 AAATGGCGCGCTCATAGTCG 61.491 55.000 32.29 0.00 0.00 4.18
887 896 0.233332 GAAATGGCGCGCTCATAGTC 59.767 55.000 32.29 24.29 0.00 2.59
888 897 0.461870 TGAAATGGCGCGCTCATAGT 60.462 50.000 32.29 21.15 0.00 2.12
889 898 0.870393 ATGAAATGGCGCGCTCATAG 59.130 50.000 32.29 0.00 0.00 2.23
890 899 0.867746 GATGAAATGGCGCGCTCATA 59.132 50.000 32.29 16.86 0.00 2.15
891 900 0.816825 AGATGAAATGGCGCGCTCAT 60.817 50.000 32.29 29.38 0.00 2.90
892 901 0.179086 TAGATGAAATGGCGCGCTCA 60.179 50.000 32.29 26.01 0.00 4.26
926 936 0.338814 AGAAGGGGACGGTAGACCAT 59.661 55.000 0.00 0.00 33.80 3.55
939 955 0.469892 AGGGTGTTTGGCAAGAAGGG 60.470 55.000 0.00 0.00 0.00 3.95
966 982 6.602410 AACCCTAAGGAGTTGTTCTACTAC 57.398 41.667 0.00 0.00 36.08 2.73
969 985 4.492611 CGAACCCTAAGGAGTTGTTCTAC 58.507 47.826 0.00 0.00 33.51 2.59
976 992 1.209747 GGATGCGAACCCTAAGGAGTT 59.790 52.381 0.00 0.00 36.73 3.01
980 996 1.887707 GCGGATGCGAACCCTAAGG 60.888 63.158 12.10 0.00 40.04 2.69
1062 1093 3.515286 TTAGCCGTCGCGAGGGAG 61.515 66.667 42.80 23.16 41.18 4.30
1112 1143 2.726691 CGTTGTAGGAACCGCGCTG 61.727 63.158 5.56 0.00 0.00 5.18
1114 1145 4.143363 GCGTTGTAGGAACCGCGC 62.143 66.667 0.00 0.00 39.36 6.86
1322 1353 3.272031 GCAAGAAGCAGAGTGGGC 58.728 61.111 0.00 0.00 44.79 5.36
1337 1368 3.350612 GCACGTAACCGGCAAGCA 61.351 61.111 0.00 0.00 38.78 3.91
1372 1403 1.439858 CGACGACGACGCAGAGAAA 60.440 57.895 7.30 0.00 43.96 2.52
1377 1408 1.577117 GTACTCGACGACGACGCAG 60.577 63.158 14.67 14.13 43.81 5.18
1425 1456 1.818363 CGCATCATCCTGCTGCACT 60.818 57.895 0.00 0.00 39.27 4.40
1450 1481 2.095461 GAACCTGAGCTTGAAATCCCC 58.905 52.381 0.00 0.00 0.00 4.81
1452 1483 2.160417 CACGAACCTGAGCTTGAAATCC 59.840 50.000 0.00 0.00 0.00 3.01
1483 1514 9.626045 CAAATTCACTTAGTATTTGGAAGGAAC 57.374 33.333 10.97 0.00 39.75 3.62
1542 1590 5.693961 TGGTGATAGTTGATGTGGCAATAT 58.306 37.500 0.00 0.00 0.00 1.28
1590 1638 4.692625 GCAGACAGAACAATCTAAAGCTGA 59.307 41.667 0.00 0.00 33.50 4.26
1638 1686 8.217111 TCCAAGAATATTACATAGAATGTGCCA 58.783 33.333 2.83 0.00 44.60 4.92
1700 1748 3.127721 TGATGTTGACTAGTCTGCTCTCG 59.872 47.826 23.01 0.00 0.00 4.04
1740 1788 6.464749 CCAAACAGGGTCACTACTAAAACCTA 60.465 42.308 0.00 0.00 32.22 3.08
1756 1804 1.967779 CCCAAAGGTTACCAAACAGGG 59.032 52.381 3.51 3.64 43.89 4.45
1811 1859 2.193993 ACTTCCCACGCCTAATACCTT 58.806 47.619 0.00 0.00 0.00 3.50
1833 1881 5.853572 ACAAGGGAGTGGGAGTAAAATTA 57.146 39.130 0.00 0.00 0.00 1.40
1844 1892 3.433306 TCATACCAAACAAGGGAGTGG 57.567 47.619 0.00 0.00 37.17 4.00
1847 1895 3.053693 TCCCATCATACCAAACAAGGGAG 60.054 47.826 0.00 0.00 39.06 4.30
1867 1915 3.885901 GGCCTTCATCCTGAACTAATTCC 59.114 47.826 0.00 0.00 32.21 3.01
1887 1935 1.379527 CTGTTAATTCGTGGGGAGGC 58.620 55.000 0.00 0.00 0.00 4.70
1959 2007 1.005569 GGGGAGTTTAAGTGGGAAGGG 59.994 57.143 0.00 0.00 0.00 3.95
1968 2016 5.013808 TGTTTAGAGGGAAGGGGAGTTTAAG 59.986 44.000 0.00 0.00 0.00 1.85
1995 2043 2.503895 AGAGGGCAAAAGATCCACTG 57.496 50.000 0.00 0.00 0.00 3.66
2051 2398 2.227149 GGTTCCGTTTTACATGTCACCC 59.773 50.000 0.00 0.00 0.00 4.61
2056 2403 5.838531 TTTTCTGGTTCCGTTTTACATGT 57.161 34.783 2.69 2.69 0.00 3.21
2134 2482 6.183360 CCTGAAAAAGATAAGGATTGGCAGAG 60.183 42.308 0.00 0.00 30.92 3.35
2151 2499 4.594970 TCAACAGAACCAGTCCTGAAAAA 58.405 39.130 0.00 0.00 34.65 1.94
2162 2510 2.489971 GGATCACGTTCAACAGAACCA 58.510 47.619 0.00 0.00 38.71 3.67
2168 2516 3.973206 ACATAGGGATCACGTTCAACA 57.027 42.857 0.00 0.00 0.00 3.33
2169 2517 5.657474 TCTAACATAGGGATCACGTTCAAC 58.343 41.667 0.00 0.00 0.00 3.18
2170 2518 5.925506 TCTAACATAGGGATCACGTTCAA 57.074 39.130 0.00 0.00 0.00 2.69
2171 2519 5.596772 TCATCTAACATAGGGATCACGTTCA 59.403 40.000 0.00 0.00 0.00 3.18
2280 2628 9.374838 CATGGATGATACTTCGATCAATAATCA 57.625 33.333 0.00 0.00 39.25 2.57
2337 2685 0.251634 CCAACTCAGGAAGGAGGCTC 59.748 60.000 5.78 5.78 39.27 4.70


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

AutoCloner maintained by Alex Coulton.