Multiple sequence alignment - TraesCS5B01G177200

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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 TraesCS5B01G177200 chr5B 100.000 2809 0 0 1 2809 322925046 322922238 0.000000e+00 5188
1 TraesCS5B01G177200 chr5D 95.629 1899 59 7 929 2809 285475516 285473624 0.000000e+00 3025
2 TraesCS5B01G177200 chr5D 86.320 519 61 10 1 512 285544362 285543847 8.790000e-155 556
3 TraesCS5B01G177200 chr5D 87.054 224 29 0 623 846 74150473 74150250 1.290000e-63 254
4 TraesCS5B01G177200 chr5A 94.729 1935 74 11 898 2809 377193268 377191339 0.000000e+00 2983
5 TraesCS5B01G177200 chr5A 89.000 600 46 13 1 587 377196073 377195481 0.000000e+00 725
6 TraesCS5B01G177200 chr5A 87.983 233 26 1 614 846 436638992 436638762 9.910000e-70 274
7 TraesCS5B01G177200 chr4B 89.316 234 25 0 614 847 81362337 81362570 7.610000e-76 294
8 TraesCS5B01G177200 chr4A 88.938 226 25 0 622 847 690425789 690425564 2.130000e-71 279
9 TraesCS5B01G177200 chr4A 87.660 235 27 1 613 847 703330196 703330428 3.570000e-69 272
10 TraesCS5B01G177200 chr3D 87.712 236 27 2 613 847 16320507 16320273 9.910000e-70 274
11 TraesCS5B01G177200 chrUn 87.607 234 28 1 614 847 404872074 404871842 1.280000e-68 270
12 TraesCS5B01G177200 chr1B 86.752 234 31 0 614 847 119134933 119135166 7.720000e-66 261
13 TraesCS5B01G177200 chr7A 87.500 224 27 1 624 847 425772067 425772289 9.980000e-65 257
14 TraesCS5B01G177200 chr2D 83.471 121 19 1 400 520 526118585 526118466 8.230000e-21 111


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 TraesCS5B01G177200 chr5B 322922238 322925046 2808 True 5188 5188 100.0000 1 2809 1 chr5B.!!$R1 2808
1 TraesCS5B01G177200 chr5D 285473624 285475516 1892 True 3025 3025 95.6290 929 2809 1 chr5D.!!$R2 1880
2 TraesCS5B01G177200 chr5D 285543847 285544362 515 True 556 556 86.3200 1 512 1 chr5D.!!$R3 511
3 TraesCS5B01G177200 chr5A 377191339 377196073 4734 True 1854 2983 91.8645 1 2809 2 chr5A.!!$R2 2808

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
764 2774 0.036952 CTCTGGCACCACCACAGTAG 60.037 60.0 0.0 0.0 46.36 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2662 4705 1.370051 GCAAGGAACGGAACAACGC 60.37 57.895 0.0 0.0 37.37 4.84 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
31 32 8.430801 TCTAGTATTAGAGTTACGGTTGAGAC 57.569 38.462 0.00 0.00 32.21 3.36
87 88 2.041485 TGGATCAGAAGCCATTTCACCA 59.959 45.455 0.00 0.00 35.57 4.17
158 159 5.670361 AGCTGGATCCTAAAATAGGGTTGTA 59.330 40.000 14.23 0.00 46.24 2.41
202 203 5.728637 AGATATGACGGCTGATGATGTTA 57.271 39.130 0.00 0.00 0.00 2.41
261 262 6.368516 TGAAACTTGAAAGAGCAAAAAGTTGG 59.631 34.615 0.00 0.00 39.49 3.77
280 281 2.224843 TGGAATGACTGAGGCAATGTGT 60.225 45.455 0.00 0.00 0.00 3.72
284 285 5.392380 GGAATGACTGAGGCAATGTGTAAAG 60.392 44.000 0.00 0.00 0.00 1.85
358 365 4.380233 GCAGCAACAGAGAAGCAACATAAT 60.380 41.667 0.00 0.00 0.00 1.28
362 369 7.809331 CAGCAACAGAGAAGCAACATAATAAAA 59.191 33.333 0.00 0.00 0.00 1.52
404 412 4.995487 ACTTTGACAACCGAGGAACTATTC 59.005 41.667 0.00 0.00 41.55 1.75
454 462 8.237267 ACTGCAATTTGTTAGTAGTTAGAATGC 58.763 33.333 6.65 0.00 0.00 3.56
456 464 7.094975 TGCAATTTGTTAGTAGTTAGAATGCGT 60.095 33.333 0.00 0.00 0.00 5.24
498 513 8.299570 AGTTAGGACTGAAACAATGCTTATTTG 58.700 33.333 0.00 0.00 33.99 2.32
499 514 6.899393 AGGACTGAAACAATGCTTATTTGA 57.101 33.333 0.00 0.00 0.00 2.69
582 597 3.244976 GCACAATCAAACACCACATAGC 58.755 45.455 0.00 0.00 0.00 2.97
587 602 5.414454 ACAATCAAACACCACATAGCGTATT 59.586 36.000 0.00 0.00 0.00 1.89
588 603 6.072175 ACAATCAAACACCACATAGCGTATTT 60.072 34.615 0.00 0.00 0.00 1.40
589 604 7.119992 ACAATCAAACACCACATAGCGTATTTA 59.880 33.333 0.00 0.00 0.00 1.40
590 605 7.801716 ATCAAACACCACATAGCGTATTTAT 57.198 32.000 0.00 0.00 0.00 1.40
591 606 8.896320 ATCAAACACCACATAGCGTATTTATA 57.104 30.769 0.00 0.00 0.00 0.98
592 607 8.719560 TCAAACACCACATAGCGTATTTATAA 57.280 30.769 0.00 0.00 0.00 0.98
593 608 9.163899 TCAAACACCACATAGCGTATTTATAAA 57.836 29.630 0.00 0.00 0.00 1.40
594 609 9.433317 CAAACACCACATAGCGTATTTATAAAG 57.567 33.333 3.94 0.00 0.00 1.85
595 610 8.951787 AACACCACATAGCGTATTTATAAAGA 57.048 30.769 3.94 0.00 0.00 2.52
596 611 9.555727 AACACCACATAGCGTATTTATAAAGAT 57.444 29.630 3.94 0.00 0.00 2.40
607 622 9.068008 GCGTATTTATAAAGATAGTCTCTCAGC 57.932 37.037 3.94 0.00 31.03 4.26
608 623 9.268255 CGTATTTATAAAGATAGTCTCTCAGCG 57.732 37.037 3.94 0.00 31.03 5.18
609 624 9.562583 GTATTTATAAAGATAGTCTCTCAGCGG 57.437 37.037 3.94 0.00 31.03 5.52
610 625 7.584122 TTTATAAAGATAGTCTCTCAGCGGT 57.416 36.000 0.00 0.00 31.03 5.68
611 626 3.791973 AAAGATAGTCTCTCAGCGGTG 57.208 47.619 8.67 8.67 31.03 4.94
613 628 1.028905 GATAGTCTCTCAGCGGTGCT 58.971 55.000 10.38 3.21 40.77 4.40
614 629 1.407258 GATAGTCTCTCAGCGGTGCTT 59.593 52.381 10.38 0.00 36.40 3.91
615 630 1.257743 TAGTCTCTCAGCGGTGCTTT 58.742 50.000 10.38 0.00 36.40 3.51
616 631 0.394565 AGTCTCTCAGCGGTGCTTTT 59.605 50.000 10.38 0.00 36.40 2.27
635 650 4.343811 TTTTTCCGCATGGTAATACGTG 57.656 40.909 0.00 0.00 36.30 4.49
636 651 2.676632 TTCCGCATGGTAATACGTGT 57.323 45.000 0.00 0.00 36.30 4.49
639 654 2.124903 CCGCATGGTAATACGTGTCTC 58.875 52.381 0.00 0.00 0.00 3.36
640 655 2.480587 CCGCATGGTAATACGTGTCTCA 60.481 50.000 0.00 0.00 0.00 3.27
641 656 3.381045 CGCATGGTAATACGTGTCTCAT 58.619 45.455 0.00 0.00 0.00 2.90
642 657 3.802139 CGCATGGTAATACGTGTCTCATT 59.198 43.478 0.00 0.00 0.00 2.57
643 658 4.270084 CGCATGGTAATACGTGTCTCATTT 59.730 41.667 0.00 0.00 0.00 2.32
644 659 5.501715 GCATGGTAATACGTGTCTCATTTG 58.498 41.667 0.00 0.00 0.00 2.32
645 660 5.064707 GCATGGTAATACGTGTCTCATTTGT 59.935 40.000 0.00 0.00 0.00 2.83
646 661 6.256975 GCATGGTAATACGTGTCTCATTTGTA 59.743 38.462 0.00 0.00 0.00 2.41
648 663 7.997107 TGGTAATACGTGTCTCATTTGTATC 57.003 36.000 0.00 0.00 0.00 2.24
649 664 6.693978 TGGTAATACGTGTCTCATTTGTATCG 59.306 38.462 0.00 0.00 0.00 2.92
650 665 6.694411 GGTAATACGTGTCTCATTTGTATCGT 59.306 38.462 0.00 0.00 0.00 3.73
652 667 9.225201 GTAATACGTGTCTCATTTGTATCGTAA 57.775 33.333 0.00 0.00 36.44 3.18
653 668 7.909777 ATACGTGTCTCATTTGTATCGTAAG 57.090 36.000 0.00 0.00 36.44 2.34
655 670 5.106038 ACGTGTCTCATTTGTATCGTAAGGA 60.106 40.000 0.00 0.00 38.47 3.36
656 671 5.803461 CGTGTCTCATTTGTATCGTAAGGAA 59.197 40.000 0.00 0.00 38.47 3.36
657 672 6.237490 CGTGTCTCATTTGTATCGTAAGGAAC 60.237 42.308 0.00 0.00 38.47 3.62
658 673 6.588756 GTGTCTCATTTGTATCGTAAGGAACA 59.411 38.462 0.00 0.00 38.47 3.18
659 674 7.117236 GTGTCTCATTTGTATCGTAAGGAACAA 59.883 37.037 0.00 0.00 39.46 2.83
667 682 7.878477 TGTATCGTAAGGAACAAAGTACAAG 57.122 36.000 0.00 0.00 38.47 3.16
668 683 7.436118 TGTATCGTAAGGAACAAAGTACAAGT 58.564 34.615 0.00 0.00 38.47 3.16
669 684 7.596248 TGTATCGTAAGGAACAAAGTACAAGTC 59.404 37.037 0.00 0.00 38.47 3.01
673 2683 6.257193 CGTAAGGAACAAAGTACAAGTCAAGT 59.743 38.462 0.00 0.00 0.00 3.16
676 2686 7.787725 AGGAACAAAGTACAAGTCAAGTAAG 57.212 36.000 0.00 0.00 0.00 2.34
677 2687 6.766467 AGGAACAAAGTACAAGTCAAGTAAGG 59.234 38.462 0.00 0.00 0.00 2.69
680 2690 7.964604 ACAAAGTACAAGTCAAGTAAGGATC 57.035 36.000 0.00 0.00 0.00 3.36
685 2695 5.407407 ACAAGTCAAGTAAGGATCGACAT 57.593 39.130 0.00 0.00 0.00 3.06
689 2699 4.462834 AGTCAAGTAAGGATCGACATGACA 59.537 41.667 21.34 0.00 43.39 3.58
693 2703 6.147164 TCAAGTAAGGATCGACATGACAAAAC 59.853 38.462 0.00 0.00 0.00 2.43
695 2705 6.931838 AGTAAGGATCGACATGACAAAACTA 58.068 36.000 0.00 0.00 0.00 2.24
696 2706 7.383687 AGTAAGGATCGACATGACAAAACTAA 58.616 34.615 0.00 0.00 0.00 2.24
699 2709 7.504924 AGGATCGACATGACAAAACTAAAAA 57.495 32.000 0.00 0.00 0.00 1.94
701 2711 7.444183 AGGATCGACATGACAAAACTAAAAAGA 59.556 33.333 0.00 0.00 0.00 2.52
702 2712 8.237267 GGATCGACATGACAAAACTAAAAAGAT 58.763 33.333 0.00 0.00 0.00 2.40
705 2715 8.227791 TCGACATGACAAAACTAAAAAGATAGC 58.772 33.333 0.00 0.00 0.00 2.97
706 2716 8.015087 CGACATGACAAAACTAAAAAGATAGCA 58.985 33.333 0.00 0.00 0.00 3.49
707 2717 9.677567 GACATGACAAAACTAAAAAGATAGCAA 57.322 29.630 0.00 0.00 0.00 3.91
711 2721 9.862371 TGACAAAACTAAAAAGATAGCAAAACA 57.138 25.926 0.00 0.00 0.00 2.83
720 2730 7.880059 AAAAGATAGCAAAACATTTCTGAGC 57.120 32.000 0.00 0.00 0.00 4.26
721 2731 6.830873 AAGATAGCAAAACATTTCTGAGCT 57.169 33.333 0.00 0.00 34.84 4.09
723 2733 6.618811 AGATAGCAAAACATTTCTGAGCTTG 58.381 36.000 0.00 0.00 32.49 4.01
724 2734 4.924305 AGCAAAACATTTCTGAGCTTGA 57.076 36.364 0.00 0.00 0.00 3.02
725 2735 4.614946 AGCAAAACATTTCTGAGCTTGAC 58.385 39.130 0.00 0.00 0.00 3.18
727 2737 4.207841 GCAAAACATTTCTGAGCTTGACAC 59.792 41.667 0.00 0.00 0.00 3.67
728 2738 4.574599 AAACATTTCTGAGCTTGACACC 57.425 40.909 0.00 0.00 0.00 4.16
730 2740 3.554934 ACATTTCTGAGCTTGACACCAA 58.445 40.909 0.00 0.00 0.00 3.67
737 2747 2.113139 CTTGACACCAAGGCCCGT 59.887 61.111 0.00 0.00 44.58 5.28
739 2749 2.674563 CTTGACACCAAGGCCCGTCA 62.675 60.000 0.00 1.94 44.58 4.35
740 2750 2.668550 GACACCAAGGCCCGTCAC 60.669 66.667 0.00 0.00 0.00 3.67
742 2752 2.113139 CACCAAGGCCCGTCACTT 59.887 61.111 0.00 0.00 0.00 3.16
743 2753 2.113139 ACCAAGGCCCGTCACTTG 59.887 61.111 0.00 0.00 42.77 3.16
744 2754 2.113139 CCAAGGCCCGTCACTTGT 59.887 61.111 0.00 0.00 41.84 3.16
745 2755 1.966451 CCAAGGCCCGTCACTTGTC 60.966 63.158 0.00 0.00 41.84 3.18
746 2756 1.071471 CAAGGCCCGTCACTTGTCT 59.929 57.895 0.00 0.00 39.30 3.41
747 2757 0.951040 CAAGGCCCGTCACTTGTCTC 60.951 60.000 0.00 0.00 39.30 3.36
750 2760 1.374758 GCCCGTCACTTGTCTCTGG 60.375 63.158 0.00 0.00 0.00 3.86
751 2761 1.374758 CCCGTCACTTGTCTCTGGC 60.375 63.158 0.00 0.00 0.00 4.85
752 2762 1.367471 CCGTCACTTGTCTCTGGCA 59.633 57.895 0.00 0.00 0.00 4.92
753 2763 0.946221 CCGTCACTTGTCTCTGGCAC 60.946 60.000 0.00 0.00 0.00 5.01
754 2764 0.946221 CGTCACTTGTCTCTGGCACC 60.946 60.000 0.00 0.00 0.00 5.01
755 2765 0.106708 GTCACTTGTCTCTGGCACCA 59.893 55.000 0.00 0.00 0.00 4.17
756 2766 0.106708 TCACTTGTCTCTGGCACCAC 59.893 55.000 0.00 0.00 0.00 4.16
757 2767 0.886490 CACTTGTCTCTGGCACCACC 60.886 60.000 0.00 0.00 39.84 4.61
759 2769 0.886490 CTTGTCTCTGGCACCACCAC 60.886 60.000 0.00 0.00 46.36 4.16
760 2770 1.631071 TTGTCTCTGGCACCACCACA 61.631 55.000 0.00 0.00 46.36 4.17
761 2771 1.302033 GTCTCTGGCACCACCACAG 60.302 63.158 0.00 0.00 46.36 3.66
762 2772 1.766059 TCTCTGGCACCACCACAGT 60.766 57.895 0.00 0.00 46.36 3.55
764 2774 0.036952 CTCTGGCACCACCACAGTAG 60.037 60.000 0.00 0.00 46.36 2.57
767 2777 2.429930 GCACCACCACAGTAGCCA 59.570 61.111 0.00 0.00 0.00 4.75
768 2778 1.966451 GCACCACCACAGTAGCCAC 60.966 63.158 0.00 0.00 0.00 5.01
769 2779 1.302511 CACCACCACAGTAGCCACC 60.303 63.158 0.00 0.00 0.00 4.61
770 2780 2.047274 CCACCACAGTAGCCACCG 60.047 66.667 0.00 0.00 0.00 4.94
771 2781 2.579657 CCACCACAGTAGCCACCGA 61.580 63.158 0.00 0.00 0.00 4.69
772 2782 1.369692 CACCACAGTAGCCACCGAA 59.630 57.895 0.00 0.00 0.00 4.30
774 2784 0.830444 ACCACAGTAGCCACCGAAGA 60.830 55.000 0.00 0.00 0.00 2.87
775 2785 0.320374 CCACAGTAGCCACCGAAGAA 59.680 55.000 0.00 0.00 0.00 2.52
776 2786 1.270625 CCACAGTAGCCACCGAAGAAA 60.271 52.381 0.00 0.00 0.00 2.52
777 2787 2.489971 CACAGTAGCCACCGAAGAAAA 58.510 47.619 0.00 0.00 0.00 2.29
797 2807 2.990066 AAATGACGGATCACCTCCTC 57.010 50.000 0.00 0.00 42.47 3.71
798 2808 1.866015 AATGACGGATCACCTCCTCA 58.134 50.000 0.00 0.00 42.47 3.86
799 2809 1.115467 ATGACGGATCACCTCCTCAC 58.885 55.000 0.00 0.00 42.47 3.51
800 2810 0.039764 TGACGGATCACCTCCTCACT 59.960 55.000 0.00 0.00 42.47 3.41
802 2812 0.898320 ACGGATCACCTCCTCACTTG 59.102 55.000 0.00 0.00 42.47 3.16
803 2813 1.186200 CGGATCACCTCCTCACTTGA 58.814 55.000 0.00 0.00 42.47 3.02
804 2814 1.135915 CGGATCACCTCCTCACTTGAG 59.864 57.143 0.00 0.00 42.47 3.02
805 2815 1.134551 GGATCACCTCCTCACTTGAGC 60.135 57.143 0.26 0.00 41.29 4.26
806 2816 1.830477 GATCACCTCCTCACTTGAGCT 59.170 52.381 0.26 0.00 40.75 4.09
807 2817 1.722034 TCACCTCCTCACTTGAGCTT 58.278 50.000 0.26 0.00 40.75 3.74
808 2818 1.345741 TCACCTCCTCACTTGAGCTTG 59.654 52.381 0.26 0.00 40.75 4.01
809 2819 1.345741 CACCTCCTCACTTGAGCTTGA 59.654 52.381 0.26 0.00 40.75 3.02
810 2820 1.346068 ACCTCCTCACTTGAGCTTGAC 59.654 52.381 0.26 0.00 40.75 3.18
811 2821 1.671261 CCTCCTCACTTGAGCTTGACG 60.671 57.143 0.26 0.00 40.75 4.35
812 2822 0.319900 TCCTCACTTGAGCTTGACGC 60.320 55.000 0.26 0.00 40.75 5.19
813 2823 1.621301 CCTCACTTGAGCTTGACGCG 61.621 60.000 3.53 3.53 45.59 6.01
814 2824 1.621301 CTCACTTGAGCTTGACGCGG 61.621 60.000 12.47 0.00 45.59 6.46
815 2825 3.044305 ACTTGAGCTTGACGCGGC 61.044 61.111 12.47 8.67 45.59 6.53
816 2826 2.740055 CTTGAGCTTGACGCGGCT 60.740 61.111 15.80 11.04 45.59 5.52
819 2829 4.742201 GAGCTTGACGCGGCTCCA 62.742 66.667 15.80 0.34 46.32 3.86
820 2830 4.087892 AGCTTGACGCGGCTCCAT 62.088 61.111 15.80 0.00 45.59 3.41
821 2831 3.567797 GCTTGACGCGGCTCCATC 61.568 66.667 15.80 0.00 0.00 3.51
822 2832 2.125552 CTTGACGCGGCTCCATCA 60.126 61.111 15.80 1.17 0.00 3.07
823 2833 1.522355 CTTGACGCGGCTCCATCAT 60.522 57.895 15.80 0.00 0.00 2.45
824 2834 1.078497 TTGACGCGGCTCCATCATT 60.078 52.632 15.80 0.00 0.00 2.57
825 2835 1.368345 TTGACGCGGCTCCATCATTG 61.368 55.000 15.80 0.00 0.00 2.82
826 2836 1.521457 GACGCGGCTCCATCATTGA 60.521 57.895 12.47 0.00 0.00 2.57
827 2837 0.882042 GACGCGGCTCCATCATTGAT 60.882 55.000 12.47 0.00 0.00 2.57
828 2838 0.392706 ACGCGGCTCCATCATTGATA 59.607 50.000 12.47 0.00 0.00 2.15
829 2839 1.002430 ACGCGGCTCCATCATTGATAT 59.998 47.619 12.47 0.00 0.00 1.63
830 2840 1.395954 CGCGGCTCCATCATTGATATG 59.604 52.381 0.00 0.00 0.00 1.78
831 2841 1.131883 GCGGCTCCATCATTGATATGC 59.868 52.381 0.00 4.33 0.00 3.14
832 2842 2.429478 CGGCTCCATCATTGATATGCA 58.571 47.619 14.98 0.00 0.00 3.96
833 2843 2.418976 CGGCTCCATCATTGATATGCAG 59.581 50.000 14.98 9.91 0.00 4.41
834 2844 2.163815 GGCTCCATCATTGATATGCAGC 59.836 50.000 14.98 11.89 0.00 5.25
835 2845 3.082548 GCTCCATCATTGATATGCAGCT 58.917 45.455 0.00 0.00 0.00 4.24
836 2846 3.506455 GCTCCATCATTGATATGCAGCTT 59.494 43.478 0.00 0.00 0.00 3.74
837 2847 4.022242 GCTCCATCATTGATATGCAGCTTT 60.022 41.667 0.00 0.00 0.00 3.51
838 2848 5.447624 TCCATCATTGATATGCAGCTTTG 57.552 39.130 0.00 0.00 0.00 2.77
839 2849 3.987868 CCATCATTGATATGCAGCTTTGC 59.012 43.478 0.00 0.00 0.00 3.68
840 2850 3.343380 TCATTGATATGCAGCTTTGCG 57.657 42.857 0.00 0.00 37.69 4.85
841 2851 2.033675 TCATTGATATGCAGCTTTGCGG 59.966 45.455 0.00 0.00 37.69 5.69
842 2852 1.748950 TTGATATGCAGCTTTGCGGA 58.251 45.000 0.00 0.00 37.69 5.54
843 2853 1.016627 TGATATGCAGCTTTGCGGAC 58.983 50.000 0.00 0.00 37.69 4.79
844 2854 0.308993 GATATGCAGCTTTGCGGACC 59.691 55.000 0.00 0.00 37.69 4.46
845 2855 0.107017 ATATGCAGCTTTGCGGACCT 60.107 50.000 0.00 0.00 37.69 3.85
846 2856 0.744414 TATGCAGCTTTGCGGACCTC 60.744 55.000 0.00 0.00 37.69 3.85
847 2857 2.359230 GCAGCTTTGCGGACCTCT 60.359 61.111 0.00 0.00 0.00 3.69
848 2858 2.394563 GCAGCTTTGCGGACCTCTC 61.395 63.158 0.00 0.00 0.00 3.20
849 2859 1.294780 CAGCTTTGCGGACCTCTCT 59.705 57.895 0.00 0.00 0.00 3.10
850 2860 0.739112 CAGCTTTGCGGACCTCTCTC 60.739 60.000 0.00 0.00 0.00 3.20
851 2861 1.807573 GCTTTGCGGACCTCTCTCG 60.808 63.158 0.00 0.00 0.00 4.04
852 2862 1.153745 CTTTGCGGACCTCTCTCGG 60.154 63.158 0.00 0.00 0.00 4.63
853 2863 1.595993 CTTTGCGGACCTCTCTCGGA 61.596 60.000 0.00 0.00 0.00 4.55
854 2864 1.595993 TTTGCGGACCTCTCTCGGAG 61.596 60.000 0.00 0.00 41.51 4.63
862 2872 3.790691 CTCTCTCGGAGGTGCTAGA 57.209 57.895 4.96 0.00 38.35 2.43
863 2873 1.593196 CTCTCTCGGAGGTGCTAGAG 58.407 60.000 4.96 5.79 38.35 2.43
864 2874 1.140052 CTCTCTCGGAGGTGCTAGAGA 59.860 57.143 12.84 3.27 41.58 3.10
865 2875 1.593196 CTCTCGGAGGTGCTAGAGAG 58.407 60.000 4.96 6.89 46.91 3.20
866 2876 2.413862 CTCTCGGAGGTGCTAGAGAGC 61.414 61.905 4.96 0.00 46.53 4.09
874 2884 4.823276 GCTAGAGAGCGTGCATGT 57.177 55.556 7.93 0.00 39.39 3.21
875 2885 2.295692 GCTAGAGAGCGTGCATGTG 58.704 57.895 7.93 0.00 39.39 3.21
876 2886 0.459237 GCTAGAGAGCGTGCATGTGT 60.459 55.000 7.93 0.00 39.39 3.72
877 2887 2.001812 CTAGAGAGCGTGCATGTGTT 57.998 50.000 7.93 0.00 0.00 3.32
878 2888 2.341257 CTAGAGAGCGTGCATGTGTTT 58.659 47.619 7.93 0.00 0.00 2.83
879 2889 2.455674 AGAGAGCGTGCATGTGTTTA 57.544 45.000 7.93 0.00 0.00 2.01
880 2890 2.977914 AGAGAGCGTGCATGTGTTTAT 58.022 42.857 7.93 0.00 0.00 1.40
881 2891 4.123497 AGAGAGCGTGCATGTGTTTATA 57.877 40.909 7.93 0.00 0.00 0.98
882 2892 4.503910 AGAGAGCGTGCATGTGTTTATAA 58.496 39.130 7.93 0.00 0.00 0.98
883 2893 4.935205 AGAGAGCGTGCATGTGTTTATAAA 59.065 37.500 7.93 0.00 0.00 1.40
884 2894 5.063944 AGAGAGCGTGCATGTGTTTATAAAG 59.936 40.000 7.93 0.00 0.00 1.85
885 2895 4.935205 AGAGCGTGCATGTGTTTATAAAGA 59.065 37.500 7.93 0.00 0.00 2.52
886 2896 5.586243 AGAGCGTGCATGTGTTTATAAAGAT 59.414 36.000 7.93 0.00 0.00 2.40
887 2897 5.572211 AGCGTGCATGTGTTTATAAAGATG 58.428 37.500 7.93 3.28 0.00 2.90
888 2898 5.353956 AGCGTGCATGTGTTTATAAAGATGA 59.646 36.000 7.93 0.00 0.00 2.92
889 2899 5.452302 GCGTGCATGTGTTTATAAAGATGAC 59.548 40.000 7.93 8.62 0.00 3.06
890 2900 5.672426 CGTGCATGTGTTTATAAAGATGACG 59.328 40.000 12.73 13.51 0.00 4.35
891 2901 6.542852 GTGCATGTGTTTATAAAGATGACGT 58.457 36.000 12.73 0.00 0.00 4.34
892 2902 7.463515 CGTGCATGTGTTTATAAAGATGACGTA 60.464 37.037 12.73 0.00 0.00 3.57
893 2903 8.335356 GTGCATGTGTTTATAAAGATGACGTAT 58.665 33.333 12.73 0.00 0.00 3.06
894 2904 8.334632 TGCATGTGTTTATAAAGATGACGTATG 58.665 33.333 12.73 6.26 0.00 2.39
895 2905 7.321271 GCATGTGTTTATAAAGATGACGTATGC 59.679 37.037 12.73 10.51 0.00 3.14
896 2906 7.835634 TGTGTTTATAAAGATGACGTATGCA 57.164 32.000 0.00 0.00 0.00 3.96
904 2914 2.995939 AGATGACGTATGCACTTGTGTG 59.004 45.455 0.00 0.00 46.37 3.82
908 2918 3.054166 GACGTATGCACTTGTGTGTGTA 58.946 45.455 0.00 0.00 45.44 2.90
991 3003 0.665670 CTCTGGCAGTCACACACTCG 60.666 60.000 15.27 0.00 30.26 4.18
1117 3139 2.434359 GGTCGCGTTCCCAGAAGG 60.434 66.667 5.77 0.00 0.00 3.46
1345 3367 2.110967 CAGGAAGGTGATGCGCCAG 61.111 63.158 4.18 0.00 36.32 4.85
1368 3390 1.134521 TGATTCCCCTTCGGTTCATCG 60.135 52.381 0.00 0.00 0.00 3.84
1415 3437 3.245284 AGCTATTGTGCGCTACATTTACG 59.755 43.478 9.73 0.99 39.48 3.18
1443 3465 3.372660 TTGCAACCACGATTTTTACCC 57.627 42.857 0.00 0.00 0.00 3.69
1567 3595 8.633075 AATGATAAAGCGTGTAATCATTTTGG 57.367 30.769 10.33 0.00 43.21 3.28
1760 3788 5.828328 GCTTACTGCCCTTGGAGTTATAAAT 59.172 40.000 0.00 0.00 35.15 1.40
1794 3822 1.644509 TCCCGGTCTGGATATGGATG 58.355 55.000 0.00 0.00 42.00 3.51
1888 3916 8.498054 AAACCAGTGATAGATATTGTTCACAG 57.502 34.615 12.53 6.84 40.69 3.66
1889 3917 6.051717 ACCAGTGATAGATATTGTTCACAGC 58.948 40.000 12.53 0.00 40.69 4.40
1890 3918 6.051074 CCAGTGATAGATATTGTTCACAGCA 58.949 40.000 12.53 0.00 40.69 4.41
1936 3964 8.975439 CGTAAGGTATGAATAAACTGTATGACC 58.025 37.037 0.00 0.00 0.00 4.02
1958 3986 8.522830 TGACCTTTTCTATTCTTTGCCTTATTG 58.477 33.333 0.00 0.00 0.00 1.90
2274 4317 6.222038 TCCGTGAATATTGTAGCTCTTTCT 57.778 37.500 0.00 0.00 0.00 2.52
2509 4552 4.799428 GCACGTTGTTCTATCTCTTAGTCC 59.201 45.833 0.00 0.00 0.00 3.85
2662 4705 4.637534 AGCAGTGCACATAAGTAAATCCTG 59.362 41.667 21.04 4.53 0.00 3.86
2666 4709 4.006989 TGCACATAAGTAAATCCTGCGTT 58.993 39.130 0.00 0.00 0.00 4.84
2769 4812 6.006449 ACAAACCAGAGAGCATTAATGAACT 58.994 36.000 19.73 15.48 0.00 3.01
2786 4829 0.109412 ACTCGCTACACCGTTAGCAC 60.109 55.000 8.23 0.00 39.15 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.243873 TGTCTTTAGAGCTCCATATGCCG 60.244 47.826 10.93 0.00 0.00 5.69
73 74 3.006752 TGGTGAAATGGTGAAATGGCTTC 59.993 43.478 0.00 0.00 34.31 3.86
158 159 1.831736 CCTCCCCGACATAAGTTCACT 59.168 52.381 0.00 0.00 0.00 3.41
170 171 1.617322 CGTCATATCTTCCTCCCCGA 58.383 55.000 0.00 0.00 0.00 5.14
261 262 5.412594 TCTTTACACATTGCCTCAGTCATTC 59.587 40.000 0.00 0.00 0.00 2.67
292 293 6.947464 TCTTCTTTTTCGGATCCTTGTCTAT 58.053 36.000 10.75 0.00 0.00 1.98
404 412 9.042008 AGTACAAATTAACACTTATATGGCTCG 57.958 33.333 0.00 0.00 0.00 5.03
454 462 9.017669 GTCCTAACTAGTAAACATATCACAACG 57.982 37.037 0.00 0.00 0.00 4.10
532 547 9.209048 TGTCTATATTATGTTACTGGTGACCTT 57.791 33.333 2.11 0.00 0.00 3.50
535 550 9.464714 CACTGTCTATATTATGTTACTGGTGAC 57.535 37.037 0.00 0.00 0.00 3.67
536 551 8.141909 GCACTGTCTATATTATGTTACTGGTGA 58.858 37.037 0.00 0.00 0.00 4.02
537 552 7.926018 TGCACTGTCTATATTATGTTACTGGTG 59.074 37.037 0.00 0.00 0.00 4.17
539 554 7.926018 TGTGCACTGTCTATATTATGTTACTGG 59.074 37.037 19.41 0.00 0.00 4.00
540 555 8.871686 TGTGCACTGTCTATATTATGTTACTG 57.128 34.615 19.41 0.00 0.00 2.74
544 559 8.962884 TGATTGTGCACTGTCTATATTATGTT 57.037 30.769 19.41 0.00 0.00 2.71
545 560 8.962884 TTGATTGTGCACTGTCTATATTATGT 57.037 30.769 19.41 0.00 0.00 2.29
556 571 2.098614 TGGTGTTTGATTGTGCACTGT 58.901 42.857 19.41 6.31 32.90 3.55
582 597 9.268255 CGCTGAGAGACTATCTTTATAAATACG 57.732 37.037 0.00 0.00 38.84 3.06
587 602 6.515200 GCACCGCTGAGAGACTATCTTTATAA 60.515 42.308 0.00 0.00 38.84 0.98
588 603 5.048643 GCACCGCTGAGAGACTATCTTTATA 60.049 44.000 0.00 0.00 38.84 0.98
589 604 4.261825 GCACCGCTGAGAGACTATCTTTAT 60.262 45.833 0.00 0.00 38.84 1.40
590 605 3.066900 GCACCGCTGAGAGACTATCTTTA 59.933 47.826 0.00 0.00 38.84 1.85
591 606 2.159170 GCACCGCTGAGAGACTATCTTT 60.159 50.000 0.00 0.00 38.84 2.52
592 607 1.407258 GCACCGCTGAGAGACTATCTT 59.593 52.381 0.00 0.00 38.84 2.40
593 608 1.028905 GCACCGCTGAGAGACTATCT 58.971 55.000 0.00 0.00 42.61 1.98
594 609 1.028905 AGCACCGCTGAGAGACTATC 58.971 55.000 0.00 0.00 37.57 2.08
595 610 1.479709 AAGCACCGCTGAGAGACTAT 58.520 50.000 0.00 0.00 39.62 2.12
596 611 1.257743 AAAGCACCGCTGAGAGACTA 58.742 50.000 0.00 0.00 39.62 2.59
597 612 0.394565 AAAAGCACCGCTGAGAGACT 59.605 50.000 0.00 0.00 39.62 3.24
599 614 3.706055 AAAAAGCACCGCTGAGAGA 57.294 47.368 0.00 0.00 39.62 3.10
614 629 3.752222 ACACGTATTACCATGCGGAAAAA 59.248 39.130 0.00 0.00 42.36 1.94
615 630 3.336468 ACACGTATTACCATGCGGAAAA 58.664 40.909 0.00 0.00 42.36 2.29
616 631 2.931325 GACACGTATTACCATGCGGAAA 59.069 45.455 0.00 0.00 42.36 3.13
618 633 1.752498 AGACACGTATTACCATGCGGA 59.248 47.619 0.00 0.00 42.36 5.54
619 634 2.124903 GAGACACGTATTACCATGCGG 58.875 52.381 0.00 0.00 42.36 5.69
620 635 2.804647 TGAGACACGTATTACCATGCG 58.195 47.619 0.00 0.00 43.57 4.73
621 636 5.064707 ACAAATGAGACACGTATTACCATGC 59.935 40.000 0.00 0.00 0.00 4.06
622 637 6.662414 ACAAATGAGACACGTATTACCATG 57.338 37.500 0.00 0.00 0.00 3.66
624 639 6.693978 CGATACAAATGAGACACGTATTACCA 59.306 38.462 0.00 0.00 0.00 3.25
625 640 6.694411 ACGATACAAATGAGACACGTATTACC 59.306 38.462 0.00 0.00 0.00 2.85
626 641 7.675270 ACGATACAAATGAGACACGTATTAC 57.325 36.000 0.00 0.00 0.00 1.89
627 642 9.442033 CTTACGATACAAATGAGACACGTATTA 57.558 33.333 0.00 0.00 35.54 0.98
628 643 7.434307 CCTTACGATACAAATGAGACACGTATT 59.566 37.037 0.00 0.00 35.54 1.89
629 644 6.916387 CCTTACGATACAAATGAGACACGTAT 59.084 38.462 0.00 0.00 35.54 3.06
630 645 6.093909 TCCTTACGATACAAATGAGACACGTA 59.906 38.462 0.00 0.00 34.70 3.57
631 646 5.100259 CCTTACGATACAAATGAGACACGT 58.900 41.667 0.00 0.00 36.71 4.49
632 647 5.337554 TCCTTACGATACAAATGAGACACG 58.662 41.667 0.00 0.00 0.00 4.49
634 649 6.693466 TGTTCCTTACGATACAAATGAGACA 58.307 36.000 0.00 0.00 0.00 3.41
635 650 7.591006 TTGTTCCTTACGATACAAATGAGAC 57.409 36.000 0.00 0.00 0.00 3.36
636 651 7.876068 ACTTTGTTCCTTACGATACAAATGAGA 59.124 33.333 0.00 0.00 39.10 3.27
639 654 8.714179 TGTACTTTGTTCCTTACGATACAAATG 58.286 33.333 0.00 0.00 39.10 2.32
640 655 8.836268 TGTACTTTGTTCCTTACGATACAAAT 57.164 30.769 0.00 0.00 39.10 2.32
641 656 8.659925 TTGTACTTTGTTCCTTACGATACAAA 57.340 30.769 0.00 0.00 37.95 2.83
642 657 7.927629 ACTTGTACTTTGTTCCTTACGATACAA 59.072 33.333 0.00 0.00 0.00 2.41
643 658 7.436118 ACTTGTACTTTGTTCCTTACGATACA 58.564 34.615 0.00 0.00 0.00 2.29
644 659 7.596248 TGACTTGTACTTTGTTCCTTACGATAC 59.404 37.037 0.00 0.00 0.00 2.24
645 660 7.660112 TGACTTGTACTTTGTTCCTTACGATA 58.340 34.615 0.00 0.00 0.00 2.92
646 661 6.518493 TGACTTGTACTTTGTTCCTTACGAT 58.482 36.000 0.00 0.00 0.00 3.73
648 663 6.257193 ACTTGACTTGTACTTTGTTCCTTACG 59.743 38.462 0.00 0.00 0.00 3.18
649 664 7.549615 ACTTGACTTGTACTTTGTTCCTTAC 57.450 36.000 0.00 0.00 0.00 2.34
650 665 9.321562 CTTACTTGACTTGTACTTTGTTCCTTA 57.678 33.333 0.00 0.00 0.00 2.69
652 667 6.766467 CCTTACTTGACTTGTACTTTGTTCCT 59.234 38.462 0.00 0.00 0.00 3.36
653 668 6.764560 TCCTTACTTGACTTGTACTTTGTTCC 59.235 38.462 0.00 0.00 0.00 3.62
655 670 7.170998 CGATCCTTACTTGACTTGTACTTTGTT 59.829 37.037 0.00 0.00 0.00 2.83
656 671 6.645415 CGATCCTTACTTGACTTGTACTTTGT 59.355 38.462 0.00 0.00 0.00 2.83
657 672 6.866770 TCGATCCTTACTTGACTTGTACTTTG 59.133 38.462 0.00 0.00 0.00 2.77
658 673 6.867293 GTCGATCCTTACTTGACTTGTACTTT 59.133 38.462 0.00 0.00 0.00 2.66
659 674 6.015688 TGTCGATCCTTACTTGACTTGTACTT 60.016 38.462 0.00 0.00 0.00 2.24
660 675 5.475909 TGTCGATCCTTACTTGACTTGTACT 59.524 40.000 0.00 0.00 0.00 2.73
661 676 5.706916 TGTCGATCCTTACTTGACTTGTAC 58.293 41.667 0.00 0.00 0.00 2.90
662 677 5.970317 TGTCGATCCTTACTTGACTTGTA 57.030 39.130 0.00 0.00 0.00 2.41
663 678 4.866508 TGTCGATCCTTACTTGACTTGT 57.133 40.909 0.00 0.00 0.00 3.16
664 679 5.289675 GTCATGTCGATCCTTACTTGACTTG 59.710 44.000 19.08 12.76 42.77 3.16
665 680 5.047306 TGTCATGTCGATCCTTACTTGACTT 60.047 40.000 22.88 7.29 44.68 3.01
667 682 4.744570 TGTCATGTCGATCCTTACTTGAC 58.255 43.478 19.32 19.32 44.66 3.18
668 683 5.400066 TTGTCATGTCGATCCTTACTTGA 57.600 39.130 0.00 0.00 0.00 3.02
669 684 6.147821 AGTTTTGTCATGTCGATCCTTACTTG 59.852 38.462 0.00 0.00 0.00 3.16
673 2683 8.610248 TTTTAGTTTTGTCATGTCGATCCTTA 57.390 30.769 0.00 0.00 0.00 2.69
676 2686 7.581476 TCTTTTTAGTTTTGTCATGTCGATCC 58.419 34.615 0.00 0.00 0.00 3.36
680 2690 8.015087 TGCTATCTTTTTAGTTTTGTCATGTCG 58.985 33.333 0.00 0.00 0.00 4.35
685 2695 9.862371 TGTTTTGCTATCTTTTTAGTTTTGTCA 57.138 25.926 0.00 0.00 0.00 3.58
695 2705 8.146412 AGCTCAGAAATGTTTTGCTATCTTTTT 58.854 29.630 0.00 0.00 0.00 1.94
696 2706 7.664758 AGCTCAGAAATGTTTTGCTATCTTTT 58.335 30.769 0.00 0.00 0.00 2.27
699 2709 6.432162 TCAAGCTCAGAAATGTTTTGCTATCT 59.568 34.615 0.00 0.00 0.00 1.98
701 2711 6.016024 TGTCAAGCTCAGAAATGTTTTGCTAT 60.016 34.615 0.00 0.00 0.00 2.97
702 2712 5.299028 TGTCAAGCTCAGAAATGTTTTGCTA 59.701 36.000 0.00 0.00 0.00 3.49
703 2713 4.098349 TGTCAAGCTCAGAAATGTTTTGCT 59.902 37.500 0.00 0.00 0.00 3.91
704 2714 4.207841 GTGTCAAGCTCAGAAATGTTTTGC 59.792 41.667 0.00 0.00 0.00 3.68
705 2715 4.741676 GGTGTCAAGCTCAGAAATGTTTTG 59.258 41.667 0.00 0.00 0.00 2.44
706 2716 4.402155 TGGTGTCAAGCTCAGAAATGTTTT 59.598 37.500 0.00 0.00 0.00 2.43
707 2717 3.953612 TGGTGTCAAGCTCAGAAATGTTT 59.046 39.130 0.00 0.00 0.00 2.83
708 2718 3.554934 TGGTGTCAAGCTCAGAAATGTT 58.445 40.909 0.00 0.00 0.00 2.71
709 2719 3.213206 TGGTGTCAAGCTCAGAAATGT 57.787 42.857 0.00 0.00 0.00 2.71
710 2720 3.057736 CCTTGGTGTCAAGCTCAGAAATG 60.058 47.826 0.00 0.00 46.69 2.32
711 2721 3.152341 CCTTGGTGTCAAGCTCAGAAAT 58.848 45.455 0.00 0.00 46.69 2.17
712 2722 2.575532 CCTTGGTGTCAAGCTCAGAAA 58.424 47.619 0.00 0.00 46.69 2.52
716 2726 1.228245 GGCCTTGGTGTCAAGCTCA 60.228 57.895 0.00 0.00 46.69 4.26
717 2727 1.973812 GGGCCTTGGTGTCAAGCTC 60.974 63.158 0.84 0.00 46.69 4.09
718 2728 2.116125 GGGCCTTGGTGTCAAGCT 59.884 61.111 0.84 0.00 46.69 3.74
719 2729 3.365265 CGGGCCTTGGTGTCAAGC 61.365 66.667 0.84 0.00 46.69 4.01
721 2731 2.112297 GACGGGCCTTGGTGTCAA 59.888 61.111 0.84 0.00 0.00 3.18
723 2733 2.668550 GTGACGGGCCTTGGTGTC 60.669 66.667 0.84 1.25 0.00 3.67
724 2734 2.752807 AAGTGACGGGCCTTGGTGT 61.753 57.895 0.84 0.00 0.00 4.16
725 2735 2.113139 AAGTGACGGGCCTTGGTG 59.887 61.111 0.84 0.00 0.00 4.17
727 2737 1.966451 GACAAGTGACGGGCCTTGG 60.966 63.158 0.84 0.00 41.84 3.61
728 2738 0.951040 GAGACAAGTGACGGGCCTTG 60.951 60.000 0.84 9.62 42.91 3.61
730 2740 1.534235 AGAGACAAGTGACGGGCCT 60.534 57.895 0.84 0.00 0.00 5.19
732 2742 1.374758 CCAGAGACAAGTGACGGGC 60.375 63.158 0.00 0.00 0.00 6.13
733 2743 1.374758 GCCAGAGACAAGTGACGGG 60.375 63.158 0.00 0.00 0.00 5.28
734 2744 0.946221 GTGCCAGAGACAAGTGACGG 60.946 60.000 0.00 0.00 0.00 4.79
736 2746 0.106708 TGGTGCCAGAGACAAGTGAC 59.893 55.000 0.00 0.00 0.00 3.67
737 2747 0.106708 GTGGTGCCAGAGACAAGTGA 59.893 55.000 0.00 0.00 0.00 3.41
739 2749 1.344953 TGGTGGTGCCAGAGACAAGT 61.345 55.000 0.00 0.00 43.61 3.16
740 2750 1.451504 TGGTGGTGCCAGAGACAAG 59.548 57.895 0.00 0.00 43.61 3.16
750 2760 1.966451 GTGGCTACTGTGGTGGTGC 60.966 63.158 0.00 0.00 0.00 5.01
751 2761 1.302511 GGTGGCTACTGTGGTGGTG 60.303 63.158 0.00 0.00 0.00 4.17
752 2762 2.879233 CGGTGGCTACTGTGGTGGT 61.879 63.158 0.00 0.00 0.00 4.16
753 2763 2.047274 CGGTGGCTACTGTGGTGG 60.047 66.667 0.00 0.00 0.00 4.61
754 2764 0.670546 CTTCGGTGGCTACTGTGGTG 60.671 60.000 9.07 0.00 34.68 4.17
755 2765 0.830444 TCTTCGGTGGCTACTGTGGT 60.830 55.000 9.07 0.00 34.68 4.16
756 2766 0.320374 TTCTTCGGTGGCTACTGTGG 59.680 55.000 9.07 3.62 34.68 4.17
757 2767 2.163818 TTTCTTCGGTGGCTACTGTG 57.836 50.000 9.07 3.96 34.68 3.66
786 2796 1.830477 AGCTCAAGTGAGGAGGTGATC 59.170 52.381 10.25 0.00 41.23 2.92
787 2797 1.949799 AGCTCAAGTGAGGAGGTGAT 58.050 50.000 10.25 0.00 41.23 3.06
789 2799 1.345741 TCAAGCTCAAGTGAGGAGGTG 59.654 52.381 10.25 0.00 41.88 4.00
790 2800 1.346068 GTCAAGCTCAAGTGAGGAGGT 59.654 52.381 10.25 0.00 44.38 3.85
791 2801 1.671261 CGTCAAGCTCAAGTGAGGAGG 60.671 57.143 10.25 1.85 42.29 4.30
793 2803 0.319900 GCGTCAAGCTCAAGTGAGGA 60.320 55.000 10.25 0.00 44.04 3.71
794 2804 1.621301 CGCGTCAAGCTCAAGTGAGG 61.621 60.000 10.25 2.21 45.59 3.86
795 2805 1.621301 CCGCGTCAAGCTCAAGTGAG 61.621 60.000 4.92 3.84 45.59 3.51
797 2807 2.856032 CCGCGTCAAGCTCAAGTG 59.144 61.111 4.92 0.00 45.59 3.16
798 2808 3.044305 GCCGCGTCAAGCTCAAGT 61.044 61.111 4.92 0.00 45.59 3.16
799 2809 2.740055 AGCCGCGTCAAGCTCAAG 60.740 61.111 4.92 0.00 45.59 3.02
803 2813 4.087892 ATGGAGCCGCGTCAAGCT 62.088 61.111 7.32 7.32 45.59 3.74
804 2814 3.567797 GATGGAGCCGCGTCAAGC 61.568 66.667 4.92 0.00 43.95 4.01
805 2815 1.091771 AATGATGGAGCCGCGTCAAG 61.092 55.000 4.92 0.00 0.00 3.02
806 2816 1.078497 AATGATGGAGCCGCGTCAA 60.078 52.632 4.92 0.00 0.00 3.18
807 2817 1.815003 CAATGATGGAGCCGCGTCA 60.815 57.895 4.92 0.39 0.00 4.35
808 2818 0.882042 ATCAATGATGGAGCCGCGTC 60.882 55.000 4.92 0.00 0.00 5.19
809 2819 0.392706 TATCAATGATGGAGCCGCGT 59.607 50.000 4.92 0.00 0.00 6.01
810 2820 1.395954 CATATCAATGATGGAGCCGCG 59.604 52.381 5.91 0.00 34.84 6.46
811 2821 1.131883 GCATATCAATGATGGAGCCGC 59.868 52.381 5.91 0.00 34.84 6.53
812 2822 2.418976 CTGCATATCAATGATGGAGCCG 59.581 50.000 5.91 0.40 36.19 5.52
815 2825 5.461526 CAAAGCTGCATATCAATGATGGAG 58.538 41.667 5.91 3.52 43.49 3.86
816 2826 5.447624 CAAAGCTGCATATCAATGATGGA 57.552 39.130 5.91 0.00 34.84 3.41
830 2840 2.359230 AGAGGTCCGCAAAGCTGC 60.359 61.111 0.00 0.00 45.75 5.25
831 2841 0.739112 GAGAGAGGTCCGCAAAGCTG 60.739 60.000 0.00 0.00 0.00 4.24
832 2842 1.594310 GAGAGAGGTCCGCAAAGCT 59.406 57.895 0.00 0.00 0.00 3.74
833 2843 1.807573 CGAGAGAGGTCCGCAAAGC 60.808 63.158 0.00 0.00 0.00 3.51
834 2844 1.153745 CCGAGAGAGGTCCGCAAAG 60.154 63.158 0.00 0.00 0.00 2.77
835 2845 1.595993 CTCCGAGAGAGGTCCGCAAA 61.596 60.000 0.00 0.00 39.13 3.68
836 2846 2.035155 TCCGAGAGAGGTCCGCAA 59.965 61.111 0.00 0.00 0.00 4.85
837 2847 2.438614 CTCCGAGAGAGGTCCGCA 60.439 66.667 0.00 0.00 39.13 5.69
844 2854 1.140052 TCTCTAGCACCTCCGAGAGAG 59.860 57.143 0.00 1.04 39.56 3.20
845 2855 1.205055 TCTCTAGCACCTCCGAGAGA 58.795 55.000 0.00 0.00 41.62 3.10
846 2856 1.593196 CTCTCTAGCACCTCCGAGAG 58.407 60.000 0.00 0.00 42.24 3.20
847 2857 3.790691 CTCTCTAGCACCTCCGAGA 57.209 57.895 0.00 0.00 0.00 4.04
857 2867 0.459237 ACACATGCACGCTCTCTAGC 60.459 55.000 0.00 0.00 45.86 3.42
858 2868 2.001812 AACACATGCACGCTCTCTAG 57.998 50.000 0.00 0.00 0.00 2.43
859 2869 2.455674 AAACACATGCACGCTCTCTA 57.544 45.000 0.00 0.00 0.00 2.43
860 2870 2.455674 TAAACACATGCACGCTCTCT 57.544 45.000 0.00 0.00 0.00 3.10
861 2871 4.857871 TTATAAACACATGCACGCTCTC 57.142 40.909 0.00 0.00 0.00 3.20
862 2872 4.935205 TCTTTATAAACACATGCACGCTCT 59.065 37.500 0.00 0.00 0.00 4.09
863 2873 5.216566 TCTTTATAAACACATGCACGCTC 57.783 39.130 0.00 0.00 0.00 5.03
864 2874 5.353956 TCATCTTTATAAACACATGCACGCT 59.646 36.000 0.00 0.00 0.00 5.07
865 2875 5.452302 GTCATCTTTATAAACACATGCACGC 59.548 40.000 0.00 0.00 0.00 5.34
866 2876 5.672426 CGTCATCTTTATAAACACATGCACG 59.328 40.000 0.00 5.99 0.00 5.34
867 2877 6.542852 ACGTCATCTTTATAAACACATGCAC 58.457 36.000 0.00 0.00 0.00 4.57
868 2878 6.735678 ACGTCATCTTTATAAACACATGCA 57.264 33.333 0.00 0.00 0.00 3.96
869 2879 7.321271 GCATACGTCATCTTTATAAACACATGC 59.679 37.037 0.00 0.00 0.00 4.06
870 2880 8.334632 TGCATACGTCATCTTTATAAACACATG 58.665 33.333 0.00 0.00 0.00 3.21
871 2881 8.335356 GTGCATACGTCATCTTTATAAACACAT 58.665 33.333 0.00 0.00 0.00 3.21
872 2882 7.547722 AGTGCATACGTCATCTTTATAAACACA 59.452 33.333 0.00 0.00 0.00 3.72
873 2883 7.906160 AGTGCATACGTCATCTTTATAAACAC 58.094 34.615 0.00 0.00 0.00 3.32
874 2884 8.387354 CAAGTGCATACGTCATCTTTATAAACA 58.613 33.333 0.00 0.00 0.00 2.83
875 2885 8.388103 ACAAGTGCATACGTCATCTTTATAAAC 58.612 33.333 0.00 0.00 0.00 2.01
876 2886 8.387354 CACAAGTGCATACGTCATCTTTATAAA 58.613 33.333 0.00 0.00 0.00 1.40
877 2887 7.547722 ACACAAGTGCATACGTCATCTTTATAA 59.452 33.333 0.00 0.00 0.00 0.98
878 2888 7.010091 CACACAAGTGCATACGTCATCTTTATA 59.990 37.037 0.00 0.00 39.21 0.98
879 2889 5.874810 ACACAAGTGCATACGTCATCTTTAT 59.125 36.000 0.00 0.00 0.00 1.40
880 2890 5.120053 CACACAAGTGCATACGTCATCTTTA 59.880 40.000 0.00 0.00 39.21 1.85
881 2891 4.065088 ACACAAGTGCATACGTCATCTTT 58.935 39.130 0.00 0.00 0.00 2.52
882 2892 3.433274 CACACAAGTGCATACGTCATCTT 59.567 43.478 0.00 0.00 39.21 2.40
883 2893 2.995939 CACACAAGTGCATACGTCATCT 59.004 45.455 0.00 0.00 39.21 2.90
884 2894 3.374389 CACACAAGTGCATACGTCATC 57.626 47.619 0.00 0.00 39.21 2.92
904 2914 9.471084 AGCTTGTGTTGGTTTTATTTAATACAC 57.529 29.630 0.00 0.00 36.19 2.90
991 3003 3.758931 GCACGCCATGGGGTTTCC 61.759 66.667 30.40 17.85 39.30 3.13
1269 3291 3.417275 CTCACGGATTCGGCGCTCT 62.417 63.158 7.64 0.00 41.39 4.09
1400 3422 1.136197 TGCAACGTAAATGTAGCGCAC 60.136 47.619 11.47 6.60 0.00 5.34
1567 3595 2.352960 GAGGGATGACGCAAATCTTGTC 59.647 50.000 0.00 0.00 0.00 3.18
1642 3670 1.882623 GTGGAGAACTTCAGCCCAAAG 59.117 52.381 0.00 0.00 0.00 2.77
1760 3788 5.825679 CAGACCGGGAATATCAAATGGTAAA 59.174 40.000 6.32 0.00 0.00 2.01
1867 3895 6.760298 AGTGCTGTGAACAATATCTATCACTG 59.240 38.462 12.92 12.93 42.03 3.66
1888 3916 4.379793 CGAAACAAGCAACTTCAATAGTGC 59.620 41.667 0.00 0.00 37.12 4.40
1889 3917 5.510671 ACGAAACAAGCAACTTCAATAGTG 58.489 37.500 0.00 0.00 37.12 2.74
1890 3918 5.751243 ACGAAACAAGCAACTTCAATAGT 57.249 34.783 0.00 0.00 39.32 2.12
1949 3977 4.888326 AGTTTCCAATTGCAATAAGGCA 57.112 36.364 20.56 11.23 43.19 4.75
1958 3986 5.195001 TGTTACTCCAAGTTTCCAATTGC 57.805 39.130 0.00 0.00 0.00 3.56
2233 4268 8.624367 TTCACGGAAAATTATTCCAGAAGTAA 57.376 30.769 15.30 3.42 38.49 2.24
2246 4281 7.865706 AGAGCTACAATATTCACGGAAAATT 57.134 32.000 0.00 0.00 0.00 1.82
2274 4317 6.071051 GGCAACCCAAAAGTTTATCCTGAATA 60.071 38.462 0.00 0.00 0.00 1.75
2509 4552 4.870426 AGACATTATTTACGTCAGTGCAGG 59.130 41.667 0.00 0.00 31.92 4.85
2662 4705 1.370051 GCAAGGAACGGAACAACGC 60.370 57.895 0.00 0.00 37.37 4.84
2666 4709 2.714259 CTTGGCAAGGAACGGAACA 58.286 52.632 19.55 0.00 0.00 3.18
2786 4829 4.944962 TCAAAAGCTATGTGAATGACGG 57.055 40.909 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.