Multiple sequence alignment - TraesCS1A01G141000

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 TraesCS1A01G141000 chr1A 100.000 2659 0 0 1 2659 238871506 238868848 0.000000e+00 4911.0
1 TraesCS1A01G141000 chr1D 95.596 1317 35 10 856 2151 192663226 192661912 0.000000e+00 2089.0
2 TraesCS1A01G141000 chr1D 89.938 646 64 1 1 645 306667245 306667890 0.000000e+00 832.0
3 TraesCS1A01G141000 chr1D 94.841 504 14 4 2165 2659 192661929 192661429 0.000000e+00 776.0
4 TraesCS1A01G141000 chr4A 92.284 648 48 2 1 646 11732244 11732891 0.000000e+00 918.0
5 TraesCS1A01G141000 chr3D 92.154 650 47 2 1 646 461316794 461317443 0.000000e+00 915.0
6 TraesCS1A01G141000 chr3D 89.692 650 64 3 1 649 342666951 342666304 0.000000e+00 826.0
7 TraesCS1A01G141000 chr5D 91.757 643 52 1 1 642 562055786 562055144 0.000000e+00 893.0
8 TraesCS1A01G141000 chr5B 91.038 636 53 4 1 632 286882479 286881844 0.000000e+00 856.0
9 TraesCS1A01G141000 chr5B 94.595 37 1 1 2185 2221 185514063 185514028 3.700000e-04 56.5
10 TraesCS1A01G141000 chr2D 90.308 650 58 4 1 649 381225695 381225050 0.000000e+00 846.0
11 TraesCS1A01G141000 chrUn 89.862 651 63 3 1 649 342612606 342611957 0.000000e+00 833.0
12 TraesCS1A01G141000 chr5A 90.047 643 61 3 1 642 708179163 708179803 0.000000e+00 830.0
13 TraesCS1A01G141000 chr5A 95.238 42 2 0 2180 2221 359344150 359344191 1.710000e-07 67.6
14 TraesCS1A01G141000 chr2B 89.583 48 5 0 2176 2223 773173762 773173809 7.950000e-06 62.1
15 TraesCS1A01G141000 chr2B 92.500 40 2 1 2184 2223 748082374 748082336 3.700000e-04 56.5
16 TraesCS1A01G141000 chr2B 92.500 40 2 1 2184 2223 748341681 748341643 3.700000e-04 56.5
17 TraesCS1A01G141000 chr7B 89.362 47 4 1 2180 2225 163503940 163503986 1.030000e-04 58.4


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 TraesCS1A01G141000 chr1A 238868848 238871506 2658 True 4911.0 4911 100.0000 1 2659 1 chr1A.!!$R1 2658
1 TraesCS1A01G141000 chr1D 192661429 192663226 1797 True 1432.5 2089 95.2185 856 2659 2 chr1D.!!$R1 1803
2 TraesCS1A01G141000 chr1D 306667245 306667890 645 False 832.0 832 89.9380 1 645 1 chr1D.!!$F1 644
3 TraesCS1A01G141000 chr4A 11732244 11732891 647 False 918.0 918 92.2840 1 646 1 chr4A.!!$F1 645
4 TraesCS1A01G141000 chr3D 461316794 461317443 649 False 915.0 915 92.1540 1 646 1 chr3D.!!$F1 645
5 TraesCS1A01G141000 chr3D 342666304 342666951 647 True 826.0 826 89.6920 1 649 1 chr3D.!!$R1 648
6 TraesCS1A01G141000 chr5D 562055144 562055786 642 True 893.0 893 91.7570 1 642 1 chr5D.!!$R1 641
7 TraesCS1A01G141000 chr5B 286881844 286882479 635 True 856.0 856 91.0380 1 632 1 chr5B.!!$R2 631
8 TraesCS1A01G141000 chr2D 381225050 381225695 645 True 846.0 846 90.3080 1 649 1 chr2D.!!$R1 648
9 TraesCS1A01G141000 chrUn 342611957 342612606 649 True 833.0 833 89.8620 1 649 1 chrUn.!!$R1 648
10 TraesCS1A01G141000 chr5A 708179163 708179803 640 False 830.0 830 90.0470 1 642 1 chr5A.!!$F2 641

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
812 820 0.044092 TGGTGGCTATCTGGAAGGGA 59.956 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 2476 0.031994 AAACCTTGCAACATCCACGC 59.968 50.0 0.0 0.0 0.0 5.34 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
44 46 1.179152 TGAACTTCTCCACGGCGATA 58.821 50.000 16.62 0.00 0.00 2.92
99 102 4.101448 CCGGCCTTGGCAGCTAGT 62.101 66.667 14.04 0.00 0.00 2.57
199 203 2.131023 GGGACTGGATGAAAGGGATCT 58.869 52.381 0.00 0.00 0.00 2.75
257 261 4.430765 CCTACAGCCGACGCCGTT 62.431 66.667 0.00 0.00 34.57 4.44
344 348 1.330655 ACCAGATTGGCGATCTCGGT 61.331 55.000 22.74 22.74 43.32 4.69
539 547 1.689233 ATAGGCCAGGCTTCACCGA 60.689 57.895 12.43 0.00 46.52 4.69
554 562 2.121538 CCGATGAGACCTCAGGCGA 61.122 63.158 19.60 0.00 43.61 5.54
557 565 1.377366 GATGAGACCTCAGGCGACGA 61.377 60.000 0.00 0.00 43.61 4.20
650 658 4.143333 CGCAGGGGTGGGTACGAG 62.143 72.222 0.00 0.00 0.00 4.18
651 659 3.782443 GCAGGGGTGGGTACGAGG 61.782 72.222 0.00 0.00 0.00 4.63
652 660 2.038329 CAGGGGTGGGTACGAGGA 59.962 66.667 0.00 0.00 0.00 3.71
653 661 1.382695 CAGGGGTGGGTACGAGGAT 60.383 63.158 0.00 0.00 0.00 3.24
654 662 0.981277 CAGGGGTGGGTACGAGGATT 60.981 60.000 0.00 0.00 0.00 3.01
655 663 0.253020 AGGGGTGGGTACGAGGATTT 60.253 55.000 0.00 0.00 0.00 2.17
656 664 0.622136 GGGGTGGGTACGAGGATTTT 59.378 55.000 0.00 0.00 0.00 1.82
657 665 1.407851 GGGGTGGGTACGAGGATTTTC 60.408 57.143 0.00 0.00 0.00 2.29
658 666 1.558294 GGGTGGGTACGAGGATTTTCT 59.442 52.381 0.00 0.00 0.00 2.52
659 667 2.767960 GGGTGGGTACGAGGATTTTCTA 59.232 50.000 0.00 0.00 0.00 2.10
660 668 3.181468 GGGTGGGTACGAGGATTTTCTAG 60.181 52.174 0.00 0.00 0.00 2.43
661 669 3.703052 GGTGGGTACGAGGATTTTCTAGA 59.297 47.826 0.00 0.00 0.00 2.43
662 670 4.202131 GGTGGGTACGAGGATTTTCTAGAG 60.202 50.000 0.00 0.00 0.00 2.43
663 671 3.958798 TGGGTACGAGGATTTTCTAGAGG 59.041 47.826 0.00 0.00 0.00 3.69
664 672 3.321396 GGGTACGAGGATTTTCTAGAGGG 59.679 52.174 0.00 0.00 0.00 4.30
665 673 4.213513 GGTACGAGGATTTTCTAGAGGGA 58.786 47.826 0.00 0.00 0.00 4.20
666 674 4.278919 GGTACGAGGATTTTCTAGAGGGAG 59.721 50.000 0.00 0.00 0.00 4.30
667 675 3.983821 ACGAGGATTTTCTAGAGGGAGT 58.016 45.455 0.00 0.00 0.00 3.85
668 676 5.126699 ACGAGGATTTTCTAGAGGGAGTA 57.873 43.478 0.00 0.00 0.00 2.59
669 677 5.134661 ACGAGGATTTTCTAGAGGGAGTAG 58.865 45.833 0.00 0.00 0.00 2.57
670 678 4.521256 CGAGGATTTTCTAGAGGGAGTAGG 59.479 50.000 0.00 0.00 0.00 3.18
671 679 4.228010 AGGATTTTCTAGAGGGAGTAGGC 58.772 47.826 0.00 0.00 0.00 3.93
672 680 3.325425 GGATTTTCTAGAGGGAGTAGGCC 59.675 52.174 0.00 0.00 0.00 5.19
673 681 2.068834 TTTCTAGAGGGAGTAGGCCG 57.931 55.000 0.00 0.00 0.00 6.13
674 682 0.924823 TTCTAGAGGGAGTAGGCCGT 59.075 55.000 0.00 0.00 0.00 5.68
675 683 0.924823 TCTAGAGGGAGTAGGCCGTT 59.075 55.000 0.00 0.00 0.00 4.44
676 684 1.133853 TCTAGAGGGAGTAGGCCGTTC 60.134 57.143 0.00 0.00 0.00 3.95
677 685 0.924823 TAGAGGGAGTAGGCCGTTCT 59.075 55.000 0.00 0.00 0.00 3.01
678 686 0.684805 AGAGGGAGTAGGCCGTTCTG 60.685 60.000 0.00 0.00 0.00 3.02
679 687 2.187163 GGGAGTAGGCCGTTCTGC 59.813 66.667 0.00 2.27 0.00 4.26
680 688 2.202756 GGAGTAGGCCGTTCTGCG 60.203 66.667 0.00 0.00 40.95 5.18
692 700 2.270923 CGTTCTGCGGATCTGAAATCA 58.729 47.619 5.48 0.00 34.97 2.57
693 701 2.672874 CGTTCTGCGGATCTGAAATCAA 59.327 45.455 5.48 0.00 34.97 2.57
694 702 3.484229 CGTTCTGCGGATCTGAAATCAAC 60.484 47.826 5.48 0.00 34.97 3.18
695 703 3.333029 TCTGCGGATCTGAAATCAACA 57.667 42.857 5.48 0.00 0.00 3.33
696 704 3.877559 TCTGCGGATCTGAAATCAACAT 58.122 40.909 5.48 0.00 0.00 2.71
697 705 4.264253 TCTGCGGATCTGAAATCAACATT 58.736 39.130 5.48 0.00 0.00 2.71
698 706 4.701651 TCTGCGGATCTGAAATCAACATTT 59.298 37.500 5.48 0.00 34.70 2.32
699 707 5.183713 TCTGCGGATCTGAAATCAACATTTT 59.816 36.000 5.48 0.00 31.94 1.82
700 708 5.782047 TGCGGATCTGAAATCAACATTTTT 58.218 33.333 5.48 0.00 31.94 1.94
722 730 4.513198 TTTCCAAAACCATAAAGCGAGG 57.487 40.909 0.00 0.00 0.00 4.63
723 731 2.442413 TCCAAAACCATAAAGCGAGGG 58.558 47.619 0.00 0.00 0.00 4.30
724 732 2.167662 CCAAAACCATAAAGCGAGGGT 58.832 47.619 0.00 0.00 34.15 4.34
725 733 2.560981 CCAAAACCATAAAGCGAGGGTT 59.439 45.455 0.34 0.34 45.14 4.11
726 734 3.759618 CCAAAACCATAAAGCGAGGGTTA 59.240 43.478 5.93 0.00 42.50 2.85
727 735 4.401202 CCAAAACCATAAAGCGAGGGTTAT 59.599 41.667 5.93 0.00 42.50 1.89
728 736 5.105513 CCAAAACCATAAAGCGAGGGTTATT 60.106 40.000 5.93 1.99 42.50 1.40
729 737 6.394809 CAAAACCATAAAGCGAGGGTTATTT 58.605 36.000 5.93 0.00 42.50 1.40
730 738 5.830000 AACCATAAAGCGAGGGTTATTTC 57.170 39.130 3.95 0.00 41.55 2.17
731 739 5.112129 ACCATAAAGCGAGGGTTATTTCT 57.888 39.130 0.00 0.00 25.71 2.52
732 740 6.243216 ACCATAAAGCGAGGGTTATTTCTA 57.757 37.500 0.00 0.00 25.71 2.10
733 741 6.053650 ACCATAAAGCGAGGGTTATTTCTAC 58.946 40.000 0.00 0.00 25.71 2.59
734 742 6.053005 CCATAAAGCGAGGGTTATTTCTACA 58.947 40.000 0.00 0.00 0.00 2.74
735 743 6.202954 CCATAAAGCGAGGGTTATTTCTACAG 59.797 42.308 0.00 0.00 0.00 2.74
736 744 5.416271 AAAGCGAGGGTTATTTCTACAGA 57.584 39.130 0.00 0.00 0.00 3.41
737 745 5.615925 AAGCGAGGGTTATTTCTACAGAT 57.384 39.130 0.00 0.00 0.00 2.90
738 746 6.726490 AAGCGAGGGTTATTTCTACAGATA 57.274 37.500 0.00 0.00 0.00 1.98
739 747 6.334102 AGCGAGGGTTATTTCTACAGATAG 57.666 41.667 0.00 0.00 0.00 2.08
740 748 5.244178 AGCGAGGGTTATTTCTACAGATAGG 59.756 44.000 0.00 0.00 0.00 2.57
741 749 5.243283 GCGAGGGTTATTTCTACAGATAGGA 59.757 44.000 0.00 0.00 0.00 2.94
742 750 6.570764 GCGAGGGTTATTTCTACAGATAGGAG 60.571 46.154 0.00 0.00 0.00 3.69
743 751 6.570764 CGAGGGTTATTTCTACAGATAGGAGC 60.571 46.154 0.00 0.00 0.00 4.70
744 752 5.544562 AGGGTTATTTCTACAGATAGGAGCC 59.455 44.000 0.00 0.00 0.00 4.70
745 753 5.544562 GGGTTATTTCTACAGATAGGAGCCT 59.455 44.000 0.00 0.00 0.00 4.58
746 754 6.043358 GGGTTATTTCTACAGATAGGAGCCTT 59.957 42.308 0.00 0.00 0.00 4.35
747 755 7.420330 GGGTTATTTCTACAGATAGGAGCCTTT 60.420 40.741 0.00 0.00 0.00 3.11
748 756 7.993758 GGTTATTTCTACAGATAGGAGCCTTTT 59.006 37.037 0.00 0.00 0.00 2.27
751 759 5.769484 TCTACAGATAGGAGCCTTTTACG 57.231 43.478 0.00 0.00 0.00 3.18
752 760 5.443283 TCTACAGATAGGAGCCTTTTACGA 58.557 41.667 0.00 0.00 0.00 3.43
753 761 4.657436 ACAGATAGGAGCCTTTTACGAG 57.343 45.455 0.00 0.00 0.00 4.18
754 762 3.385111 ACAGATAGGAGCCTTTTACGAGG 59.615 47.826 0.00 0.00 39.93 4.63
755 763 2.966516 AGATAGGAGCCTTTTACGAGGG 59.033 50.000 0.00 0.00 37.29 4.30
756 764 2.537633 TAGGAGCCTTTTACGAGGGA 57.462 50.000 0.00 0.00 37.29 4.20
757 765 1.880941 AGGAGCCTTTTACGAGGGAT 58.119 50.000 0.00 0.00 37.29 3.85
758 766 1.763545 AGGAGCCTTTTACGAGGGATC 59.236 52.381 0.00 0.00 37.29 3.36
759 767 1.202663 GGAGCCTTTTACGAGGGATCC 60.203 57.143 1.92 1.92 46.26 3.36
760 768 0.464452 AGCCTTTTACGAGGGATCCG 59.536 55.000 5.45 0.00 37.29 4.18
761 769 0.532196 GCCTTTTACGAGGGATCCGG 60.532 60.000 5.45 0.00 37.29 5.14
762 770 0.532196 CCTTTTACGAGGGATCCGGC 60.532 60.000 5.45 0.00 32.94 6.13
763 771 0.532196 CTTTTACGAGGGATCCGGCC 60.532 60.000 5.45 0.00 0.00 6.13
764 772 2.300850 TTTTACGAGGGATCCGGCCG 62.301 60.000 21.04 21.04 0.00 6.13
772 780 4.256180 GATCCGGCCGGGCAAGAT 62.256 66.667 42.36 28.64 34.94 2.40
773 781 3.774599 GATCCGGCCGGGCAAGATT 62.775 63.158 42.36 18.89 34.94 2.40
774 782 3.358932 ATCCGGCCGGGCAAGATTT 62.359 57.895 42.36 15.09 34.94 2.17
775 783 3.825611 CCGGCCGGGCAAGATTTG 61.826 66.667 37.42 6.27 0.00 2.32
776 784 3.061848 CGGCCGGGCAAGATTTGT 61.062 61.111 29.19 0.00 0.00 2.83
777 785 2.635443 CGGCCGGGCAAGATTTGTT 61.635 57.895 29.19 0.00 0.00 2.83
778 786 1.309499 CGGCCGGGCAAGATTTGTTA 61.309 55.000 29.19 0.00 0.00 2.41
779 787 0.172578 GGCCGGGCAAGATTTGTTAC 59.827 55.000 25.33 0.00 0.00 2.50
780 788 0.885196 GCCGGGCAAGATTTGTTACA 59.115 50.000 15.62 0.00 0.00 2.41
781 789 1.135402 GCCGGGCAAGATTTGTTACAG 60.135 52.381 15.62 0.00 0.00 2.74
782 790 2.432444 CCGGGCAAGATTTGTTACAGA 58.568 47.619 0.00 0.00 0.00 3.41
783 791 2.161609 CCGGGCAAGATTTGTTACAGAC 59.838 50.000 0.00 0.00 0.00 3.51
784 792 2.159707 CGGGCAAGATTTGTTACAGACG 60.160 50.000 0.00 0.00 0.00 4.18
785 793 3.071479 GGGCAAGATTTGTTACAGACGA 58.929 45.455 0.00 0.00 0.00 4.20
786 794 3.120304 GGGCAAGATTTGTTACAGACGAC 60.120 47.826 0.00 0.00 0.00 4.34
787 795 3.746492 GGCAAGATTTGTTACAGACGACT 59.254 43.478 0.00 0.00 0.00 4.18
788 796 4.143094 GGCAAGATTTGTTACAGACGACTC 60.143 45.833 0.00 0.00 0.00 3.36
789 797 4.686554 GCAAGATTTGTTACAGACGACTCT 59.313 41.667 0.00 0.00 34.16 3.24
790 798 5.164041 GCAAGATTTGTTACAGACGACTCTC 60.164 44.000 0.00 0.00 32.18 3.20
791 799 5.707242 AGATTTGTTACAGACGACTCTCA 57.293 39.130 0.00 0.00 28.28 3.27
792 800 5.704888 AGATTTGTTACAGACGACTCTCAG 58.295 41.667 0.00 0.00 28.28 3.35
793 801 4.913335 TTTGTTACAGACGACTCTCAGT 57.087 40.909 0.00 0.00 0.00 3.41
794 802 3.898517 TGTTACAGACGACTCTCAGTG 57.101 47.619 0.00 0.00 0.00 3.66
795 803 2.552743 TGTTACAGACGACTCTCAGTGG 59.447 50.000 0.00 0.00 0.00 4.00
796 804 2.553172 GTTACAGACGACTCTCAGTGGT 59.447 50.000 0.00 0.00 39.92 4.16
797 805 0.955178 ACAGACGACTCTCAGTGGTG 59.045 55.000 0.00 0.00 37.29 4.17
798 806 0.242286 CAGACGACTCTCAGTGGTGG 59.758 60.000 0.00 0.00 37.29 4.61
799 807 1.080434 GACGACTCTCAGTGGTGGC 60.080 63.158 0.00 0.00 37.29 5.01
800 808 1.528292 GACGACTCTCAGTGGTGGCT 61.528 60.000 0.00 0.00 37.29 4.75
801 809 0.251209 ACGACTCTCAGTGGTGGCTA 60.251 55.000 0.00 0.00 35.80 3.93
802 810 1.107114 CGACTCTCAGTGGTGGCTAT 58.893 55.000 0.00 0.00 0.00 2.97
803 811 1.066303 CGACTCTCAGTGGTGGCTATC 59.934 57.143 0.00 0.00 0.00 2.08
804 812 2.383855 GACTCTCAGTGGTGGCTATCT 58.616 52.381 0.00 0.00 0.00 1.98
805 813 2.100584 GACTCTCAGTGGTGGCTATCTG 59.899 54.545 0.00 0.00 0.00 2.90
806 814 1.411977 CTCTCAGTGGTGGCTATCTGG 59.588 57.143 0.00 0.00 0.00 3.86
807 815 1.007118 TCTCAGTGGTGGCTATCTGGA 59.993 52.381 0.00 0.00 0.00 3.86
808 816 1.833630 CTCAGTGGTGGCTATCTGGAA 59.166 52.381 0.00 0.00 0.00 3.53
809 817 1.833630 TCAGTGGTGGCTATCTGGAAG 59.166 52.381 0.00 0.00 0.00 3.46
810 818 1.134280 CAGTGGTGGCTATCTGGAAGG 60.134 57.143 0.00 0.00 0.00 3.46
811 819 0.181350 GTGGTGGCTATCTGGAAGGG 59.819 60.000 0.00 0.00 0.00 3.95
812 820 0.044092 TGGTGGCTATCTGGAAGGGA 59.956 55.000 0.00 0.00 0.00 4.20
813 821 0.470341 GGTGGCTATCTGGAAGGGAC 59.530 60.000 0.00 0.00 0.00 4.46
815 823 1.414550 GTGGCTATCTGGAAGGGACTC 59.585 57.143 0.00 0.00 38.49 3.36
816 824 0.676736 GGCTATCTGGAAGGGACTCG 59.323 60.000 0.00 0.00 38.49 4.18
817 825 1.693627 GCTATCTGGAAGGGACTCGA 58.306 55.000 0.00 0.00 38.49 4.04
818 826 2.032620 GCTATCTGGAAGGGACTCGAA 58.967 52.381 0.00 0.00 38.49 3.71
819 827 2.431057 GCTATCTGGAAGGGACTCGAAA 59.569 50.000 0.00 0.00 38.49 3.46
820 828 3.491792 GCTATCTGGAAGGGACTCGAAAG 60.492 52.174 0.00 0.00 38.49 2.62
821 829 2.304221 TCTGGAAGGGACTCGAAAGA 57.696 50.000 0.00 0.00 38.49 2.52
822 830 2.605257 TCTGGAAGGGACTCGAAAGAA 58.395 47.619 0.00 0.00 38.49 2.52
823 831 2.563179 TCTGGAAGGGACTCGAAAGAAG 59.437 50.000 0.00 0.00 38.49 2.85
824 832 2.300437 CTGGAAGGGACTCGAAAGAAGT 59.700 50.000 0.00 0.00 38.49 3.01
825 833 2.299297 TGGAAGGGACTCGAAAGAAGTC 59.701 50.000 0.00 0.00 38.49 3.01
826 834 2.299297 GGAAGGGACTCGAAAGAAGTCA 59.701 50.000 5.71 0.00 38.49 3.41
827 835 3.244112 GGAAGGGACTCGAAAGAAGTCAA 60.244 47.826 5.71 0.00 38.49 3.18
828 836 3.388345 AGGGACTCGAAAGAAGTCAAC 57.612 47.619 5.71 0.00 41.32 3.18
829 837 2.698797 AGGGACTCGAAAGAAGTCAACA 59.301 45.455 5.71 0.00 41.32 3.33
830 838 3.134081 AGGGACTCGAAAGAAGTCAACAA 59.866 43.478 5.71 0.00 41.32 2.83
831 839 3.875134 GGGACTCGAAAGAAGTCAACAAA 59.125 43.478 5.71 0.00 41.32 2.83
832 840 4.334481 GGGACTCGAAAGAAGTCAACAAAA 59.666 41.667 5.71 0.00 41.32 2.44
833 841 5.008712 GGGACTCGAAAGAAGTCAACAAAAT 59.991 40.000 5.71 0.00 41.32 1.82
834 842 6.459710 GGGACTCGAAAGAAGTCAACAAAATT 60.460 38.462 5.71 0.00 41.32 1.82
835 843 6.972901 GGACTCGAAAGAAGTCAACAAAATTT 59.027 34.615 5.71 0.00 41.32 1.82
836 844 8.126700 GGACTCGAAAGAAGTCAACAAAATTTA 58.873 33.333 5.71 0.00 41.32 1.40
837 845 9.665264 GACTCGAAAGAAGTCAACAAAATTTAT 57.335 29.630 0.00 0.00 41.32 1.40
882 890 8.499403 AGTATTAAAGAGTTGAATCTGGAAGC 57.501 34.615 0.00 0.00 0.00 3.86
899 907 2.978156 AGCTTGAAATGTTGGAGGGA 57.022 45.000 0.00 0.00 0.00 4.20
917 925 5.221783 GGAGGGAGTAAACTGAAAAGTACCA 60.222 44.000 0.00 0.00 0.00 3.25
1252 1274 1.000521 TTCTTCCCGCTCGGTCCTA 60.001 57.895 7.59 0.00 0.00 2.94
1257 1279 4.208686 CCGCTCGGTCCTACTGCC 62.209 72.222 0.00 0.00 0.00 4.85
1293 1315 0.614697 CCCCATTCACCCCCTTCAAC 60.615 60.000 0.00 0.00 0.00 3.18
1470 1492 0.985490 AGGAGGAGAAGGCATCCACC 60.985 60.000 10.51 10.51 45.18 4.61
1475 1497 3.195698 GAAGGCATCCACCGTCGC 61.196 66.667 0.00 0.00 33.69 5.19
1628 1650 4.392921 TTCTCCAAGAGATTCCGTGATC 57.607 45.455 0.00 0.00 38.56 2.92
1670 1692 0.317020 GCCTTTTGATCATACCGCGC 60.317 55.000 0.00 0.00 0.00 6.86
1685 1709 6.427853 TCATACCGCGCTTAAGACTAGTAATA 59.572 38.462 6.67 0.00 0.00 0.98
1730 1754 5.733620 TCGAATATGGGGATGTTAGTACC 57.266 43.478 0.00 0.00 0.00 3.34
1780 1804 5.885912 TCTGATGGAAATGTAGGGTTTTAGC 59.114 40.000 0.00 0.00 0.00 3.09
1799 1823 1.673033 GCGGTTGAAGAGCTGCTAAGA 60.673 52.381 0.15 0.00 0.00 2.10
1801 1825 3.265791 CGGTTGAAGAGCTGCTAAGATT 58.734 45.455 0.15 0.00 0.00 2.40
1803 1827 4.201763 CGGTTGAAGAGCTGCTAAGATTTC 60.202 45.833 0.15 3.08 0.00 2.17
1804 1828 4.940654 GGTTGAAGAGCTGCTAAGATTTCT 59.059 41.667 0.15 0.00 0.00 2.52
1841 1867 0.463116 GACCGTGGCCGTGGAAATAT 60.463 55.000 19.24 0.00 0.00 1.28
1843 1869 0.462937 CCGTGGCCGTGGAAATATGA 60.463 55.000 7.28 0.00 0.00 2.15
1912 1938 1.894466 TCCATGCCTTTTGTCATGTGG 59.106 47.619 0.00 0.00 38.63 4.17
1917 1943 1.703411 CCTTTTGTCATGTGGGTGGT 58.297 50.000 0.00 0.00 0.00 4.16
1962 1988 2.357154 GGGTGTCCTCTGGCATAATGTT 60.357 50.000 0.00 0.00 0.00 2.71
1993 2019 5.643348 TCGCTCATTTTGCTTCTTTCATCTA 59.357 36.000 0.00 0.00 0.00 1.98
2031 2058 4.223700 TGTGCAGGAGAGATCACAGTAATT 59.776 41.667 0.00 0.00 34.87 1.40
2034 2061 4.813697 GCAGGAGAGATCACAGTAATTTCC 59.186 45.833 0.00 0.00 0.00 3.13
2035 2062 5.627735 GCAGGAGAGATCACAGTAATTTCCA 60.628 44.000 0.00 0.00 0.00 3.53
2038 2065 7.391554 CAGGAGAGATCACAGTAATTTCCAAAA 59.608 37.037 0.00 0.00 0.00 2.44
2073 2100 5.953183 TCATTTTGCTCAATGCTCGTAAAT 58.047 33.333 4.12 0.00 43.37 1.40
2076 2103 2.358957 TGCTCAATGCTCGTAAATGCT 58.641 42.857 0.00 0.00 43.37 3.79
2235 2264 1.525619 GCACCAACAACAGTACGAGTC 59.474 52.381 0.00 0.00 0.00 3.36
2262 2291 9.816354 TGAAAGAGAAACAAGGAAAATAAAAGG 57.184 29.630 0.00 0.00 0.00 3.11
2301 2330 7.029563 CAGCAGGATTTAAGTTTGTTCCATAC 58.970 38.462 0.00 0.00 0.00 2.39
2302 2331 6.948309 AGCAGGATTTAAGTTTGTTCCATACT 59.052 34.615 0.00 0.00 0.00 2.12
2325 2354 6.762187 ACTGTCATCTTGCAGAATTGATAGAG 59.238 38.462 16.13 7.12 36.62 2.43
2327 2356 6.537660 TGTCATCTTGCAGAATTGATAGAGTG 59.462 38.462 0.00 0.00 0.00 3.51
2368 2397 6.042437 TGACATGCACTATCTGAGGATGTAAT 59.958 38.462 0.00 0.00 44.92 1.89
2369 2398 7.233348 TGACATGCACTATCTGAGGATGTAATA 59.767 37.037 0.00 0.00 44.92 0.98
2370 2399 7.966812 ACATGCACTATCTGAGGATGTAATAA 58.033 34.615 0.00 0.00 43.67 1.40
2447 2476 1.457738 CGTACGCTGACTTCTCATCG 58.542 55.000 0.52 0.00 40.99 3.84
2496 2525 6.627087 TTAAGGTTCTCATGATCAGTTCCT 57.373 37.500 0.09 0.58 0.00 3.36
2603 2632 5.299782 GGATCAGGATGTCGTCTTACTTACT 59.700 44.000 0.00 0.00 37.40 2.24
2613 2642 9.924650 ATGTCGTCTTACTTACTAAGAAACAAT 57.075 29.630 2.65 0.00 42.15 2.71
2614 2643 9.754382 TGTCGTCTTACTTACTAAGAAACAATT 57.246 29.630 2.65 0.00 42.15 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 46 0.250770 GCCGTTCCCTTCTTGAAGGT 60.251 55.000 23.12 0.00 38.28 3.50
99 102 1.048601 AGGTGAAAACCTGCTCTCGA 58.951 50.000 0.00 0.00 38.98 4.04
118 122 4.141135 AGGGAGGATCTTCGAACAGATCTA 60.141 45.833 20.95 0.00 46.02 1.98
165 169 1.760875 GTCCCCGGCAGAGATGGTA 60.761 63.158 0.00 0.00 0.00 3.25
188 192 1.696097 GGCGGCCTAGATCCCTTTCA 61.696 60.000 12.87 0.00 0.00 2.69
275 279 3.009723 CAGTTCCGGTTTGCATCTACAT 58.990 45.455 0.00 0.00 0.00 2.29
539 547 1.378646 TCGTCGCCTGAGGTCTCAT 60.379 57.895 0.00 0.00 39.13 2.90
554 562 2.361357 CCTCCTCCGTCCTGTCGT 60.361 66.667 0.00 0.00 0.00 4.34
557 565 4.361971 TCGCCTCCTCCGTCCTGT 62.362 66.667 0.00 0.00 0.00 4.00
646 654 3.983821 ACTCCCTCTAGAAAATCCTCGT 58.016 45.455 0.00 0.00 0.00 4.18
649 657 4.228010 GCCTACTCCCTCTAGAAAATCCT 58.772 47.826 0.00 0.00 0.00 3.24
650 658 3.325425 GGCCTACTCCCTCTAGAAAATCC 59.675 52.174 0.00 0.00 0.00 3.01
651 659 3.006003 CGGCCTACTCCCTCTAGAAAATC 59.994 52.174 0.00 0.00 0.00 2.17
652 660 2.966516 CGGCCTACTCCCTCTAGAAAAT 59.033 50.000 0.00 0.00 0.00 1.82
653 661 2.292061 ACGGCCTACTCCCTCTAGAAAA 60.292 50.000 0.00 0.00 0.00 2.29
654 662 1.287146 ACGGCCTACTCCCTCTAGAAA 59.713 52.381 0.00 0.00 0.00 2.52
655 663 0.924823 ACGGCCTACTCCCTCTAGAA 59.075 55.000 0.00 0.00 0.00 2.10
656 664 0.924823 AACGGCCTACTCCCTCTAGA 59.075 55.000 0.00 0.00 0.00 2.43
657 665 1.133730 AGAACGGCCTACTCCCTCTAG 60.134 57.143 0.00 0.00 0.00 2.43
658 666 0.924823 AGAACGGCCTACTCCCTCTA 59.075 55.000 0.00 0.00 0.00 2.43
659 667 0.684805 CAGAACGGCCTACTCCCTCT 60.685 60.000 0.00 0.00 0.00 3.69
660 668 1.817209 CAGAACGGCCTACTCCCTC 59.183 63.158 0.00 0.00 0.00 4.30
661 669 2.359967 GCAGAACGGCCTACTCCCT 61.360 63.158 0.00 0.00 0.00 4.20
662 670 2.187163 GCAGAACGGCCTACTCCC 59.813 66.667 0.00 0.00 0.00 4.30
663 671 2.202756 CGCAGAACGGCCTACTCC 60.203 66.667 0.00 0.00 38.44 3.85
672 680 2.270923 TGATTTCAGATCCGCAGAACG 58.729 47.619 0.00 0.00 43.15 3.95
673 681 3.436704 TGTTGATTTCAGATCCGCAGAAC 59.563 43.478 0.00 0.00 0.00 3.01
674 682 3.673902 TGTTGATTTCAGATCCGCAGAA 58.326 40.909 0.00 0.00 0.00 3.02
675 683 3.333029 TGTTGATTTCAGATCCGCAGA 57.667 42.857 0.00 0.00 0.00 4.26
676 684 4.627611 AATGTTGATTTCAGATCCGCAG 57.372 40.909 0.00 0.00 0.00 5.18
677 685 5.389859 AAAATGTTGATTTCAGATCCGCA 57.610 34.783 0.00 0.00 30.02 5.69
699 707 5.293560 CCTCGCTTTATGGTTTTGGAAAAA 58.706 37.500 0.00 0.00 0.00 1.94
700 708 4.262249 CCCTCGCTTTATGGTTTTGGAAAA 60.262 41.667 0.00 0.00 0.00 2.29
701 709 3.257127 CCCTCGCTTTATGGTTTTGGAAA 59.743 43.478 0.00 0.00 0.00 3.13
702 710 2.823154 CCCTCGCTTTATGGTTTTGGAA 59.177 45.455 0.00 0.00 0.00 3.53
703 711 2.224917 ACCCTCGCTTTATGGTTTTGGA 60.225 45.455 0.00 0.00 0.00 3.53
704 712 2.167662 ACCCTCGCTTTATGGTTTTGG 58.832 47.619 0.00 0.00 0.00 3.28
705 713 3.934457 AACCCTCGCTTTATGGTTTTG 57.066 42.857 0.00 0.00 37.84 2.44
706 714 6.436218 AGAAATAACCCTCGCTTTATGGTTTT 59.564 34.615 0.00 0.00 41.22 2.43
707 715 5.949952 AGAAATAACCCTCGCTTTATGGTTT 59.050 36.000 0.00 0.00 41.22 3.27
708 716 5.506708 AGAAATAACCCTCGCTTTATGGTT 58.493 37.500 0.00 0.00 43.28 3.67
709 717 5.112129 AGAAATAACCCTCGCTTTATGGT 57.888 39.130 0.00 0.00 0.00 3.55
710 718 6.053005 TGTAGAAATAACCCTCGCTTTATGG 58.947 40.000 0.00 0.00 0.00 2.74
711 719 6.984474 TCTGTAGAAATAACCCTCGCTTTATG 59.016 38.462 0.00 0.00 0.00 1.90
712 720 7.120923 TCTGTAGAAATAACCCTCGCTTTAT 57.879 36.000 0.00 0.00 0.00 1.40
713 721 6.534475 TCTGTAGAAATAACCCTCGCTTTA 57.466 37.500 0.00 0.00 0.00 1.85
714 722 5.416271 TCTGTAGAAATAACCCTCGCTTT 57.584 39.130 0.00 0.00 0.00 3.51
715 723 5.615925 ATCTGTAGAAATAACCCTCGCTT 57.384 39.130 0.00 0.00 0.00 4.68
716 724 5.244178 CCTATCTGTAGAAATAACCCTCGCT 59.756 44.000 0.00 0.00 0.00 4.93
717 725 5.243283 TCCTATCTGTAGAAATAACCCTCGC 59.757 44.000 0.00 0.00 0.00 5.03
718 726 6.570764 GCTCCTATCTGTAGAAATAACCCTCG 60.571 46.154 0.00 0.00 0.00 4.63
719 727 6.295405 GGCTCCTATCTGTAGAAATAACCCTC 60.295 46.154 0.00 0.00 0.00 4.30
720 728 5.544562 GGCTCCTATCTGTAGAAATAACCCT 59.455 44.000 0.00 0.00 0.00 4.34
721 729 5.544562 AGGCTCCTATCTGTAGAAATAACCC 59.455 44.000 0.00 0.00 0.00 4.11
722 730 6.673839 AGGCTCCTATCTGTAGAAATAACC 57.326 41.667 0.00 0.00 0.00 2.85
723 731 8.966069 AAAAGGCTCCTATCTGTAGAAATAAC 57.034 34.615 0.00 0.00 0.00 1.89
725 733 8.358148 CGTAAAAGGCTCCTATCTGTAGAAATA 58.642 37.037 0.00 0.00 0.00 1.40
726 734 7.069578 TCGTAAAAGGCTCCTATCTGTAGAAAT 59.930 37.037 0.00 0.00 0.00 2.17
727 735 6.379133 TCGTAAAAGGCTCCTATCTGTAGAAA 59.621 38.462 0.00 0.00 0.00 2.52
728 736 5.889853 TCGTAAAAGGCTCCTATCTGTAGAA 59.110 40.000 0.00 0.00 0.00 2.10
729 737 5.443283 TCGTAAAAGGCTCCTATCTGTAGA 58.557 41.667 0.00 0.00 0.00 2.59
730 738 5.278561 CCTCGTAAAAGGCTCCTATCTGTAG 60.279 48.000 0.00 0.00 0.00 2.74
731 739 4.583489 CCTCGTAAAAGGCTCCTATCTGTA 59.417 45.833 0.00 0.00 0.00 2.74
732 740 3.385111 CCTCGTAAAAGGCTCCTATCTGT 59.615 47.826 0.00 0.00 0.00 3.41
733 741 3.243907 CCCTCGTAAAAGGCTCCTATCTG 60.244 52.174 0.00 0.00 34.88 2.90
734 742 2.966516 CCCTCGTAAAAGGCTCCTATCT 59.033 50.000 0.00 0.00 34.88 1.98
735 743 2.963782 TCCCTCGTAAAAGGCTCCTATC 59.036 50.000 0.00 0.00 34.88 2.08
736 744 3.042059 TCCCTCGTAAAAGGCTCCTAT 57.958 47.619 0.00 0.00 34.88 2.57
737 745 2.537633 TCCCTCGTAAAAGGCTCCTA 57.462 50.000 0.00 0.00 34.88 2.94
738 746 1.763545 GATCCCTCGTAAAAGGCTCCT 59.236 52.381 0.00 0.00 34.88 3.69
739 747 1.202663 GGATCCCTCGTAAAAGGCTCC 60.203 57.143 0.00 0.00 34.88 4.70
740 748 1.538419 CGGATCCCTCGTAAAAGGCTC 60.538 57.143 6.06 0.00 34.88 4.70
741 749 0.464452 CGGATCCCTCGTAAAAGGCT 59.536 55.000 6.06 0.00 34.88 4.58
742 750 0.532196 CCGGATCCCTCGTAAAAGGC 60.532 60.000 6.06 0.00 34.88 4.35
743 751 0.532196 GCCGGATCCCTCGTAAAAGG 60.532 60.000 5.05 0.00 36.08 3.11
744 752 0.532196 GGCCGGATCCCTCGTAAAAG 60.532 60.000 5.05 0.00 0.00 2.27
745 753 1.523524 GGCCGGATCCCTCGTAAAA 59.476 57.895 5.05 0.00 0.00 1.52
746 754 2.788640 CGGCCGGATCCCTCGTAAA 61.789 63.158 20.10 0.00 0.00 2.01
747 755 3.221389 CGGCCGGATCCCTCGTAA 61.221 66.667 20.10 0.00 0.00 3.18
755 763 3.774599 AATCTTGCCCGGCCGGATC 62.775 63.158 45.44 33.26 37.50 3.36
756 764 3.358932 AAATCTTGCCCGGCCGGAT 62.359 57.895 45.44 27.28 37.50 4.18
757 765 4.041762 AAATCTTGCCCGGCCGGA 62.042 61.111 45.44 26.15 37.50 5.14
758 766 3.825611 CAAATCTTGCCCGGCCGG 61.826 66.667 37.99 37.99 0.00 6.13
759 767 1.309499 TAACAAATCTTGCCCGGCCG 61.309 55.000 21.04 21.04 0.00 6.13
760 768 0.172578 GTAACAAATCTTGCCCGGCC 59.827 55.000 7.03 0.00 0.00 6.13
761 769 0.885196 TGTAACAAATCTTGCCCGGC 59.115 50.000 1.04 1.04 0.00 6.13
762 770 2.161609 GTCTGTAACAAATCTTGCCCGG 59.838 50.000 0.00 0.00 0.00 5.73
763 771 2.159707 CGTCTGTAACAAATCTTGCCCG 60.160 50.000 0.00 0.00 0.00 6.13
764 772 3.071479 TCGTCTGTAACAAATCTTGCCC 58.929 45.455 0.00 0.00 0.00 5.36
765 773 3.746492 AGTCGTCTGTAACAAATCTTGCC 59.254 43.478 0.00 0.00 0.00 4.52
766 774 4.686554 AGAGTCGTCTGTAACAAATCTTGC 59.313 41.667 0.00 0.00 0.00 4.01
767 775 5.920840 TGAGAGTCGTCTGTAACAAATCTTG 59.079 40.000 0.00 0.00 30.97 3.02
768 776 6.085555 TGAGAGTCGTCTGTAACAAATCTT 57.914 37.500 0.00 0.00 30.97 2.40
769 777 5.241949 ACTGAGAGTCGTCTGTAACAAATCT 59.758 40.000 0.00 0.00 30.97 2.40
770 778 5.343593 CACTGAGAGTCGTCTGTAACAAATC 59.656 44.000 0.00 0.00 30.97 2.17
771 779 5.223382 CACTGAGAGTCGTCTGTAACAAAT 58.777 41.667 0.00 0.00 30.97 2.32
772 780 4.499188 CCACTGAGAGTCGTCTGTAACAAA 60.499 45.833 0.00 0.00 30.97 2.83
773 781 3.004419 CCACTGAGAGTCGTCTGTAACAA 59.996 47.826 0.00 0.00 30.97 2.83
774 782 2.552743 CCACTGAGAGTCGTCTGTAACA 59.447 50.000 0.00 0.00 30.97 2.41
775 783 2.553172 ACCACTGAGAGTCGTCTGTAAC 59.447 50.000 0.00 0.00 30.97 2.50
776 784 2.552743 CACCACTGAGAGTCGTCTGTAA 59.447 50.000 0.00 0.00 30.97 2.41
777 785 2.152016 CACCACTGAGAGTCGTCTGTA 58.848 52.381 0.00 0.00 30.97 2.74
778 786 0.955178 CACCACTGAGAGTCGTCTGT 59.045 55.000 0.00 0.00 30.97 3.41
779 787 0.242286 CCACCACTGAGAGTCGTCTG 59.758 60.000 0.00 0.00 30.97 3.51
780 788 1.528292 GCCACCACTGAGAGTCGTCT 61.528 60.000 0.00 0.00 34.86 4.18
781 789 1.080434 GCCACCACTGAGAGTCGTC 60.080 63.158 0.00 0.00 0.00 4.20
782 790 0.251209 TAGCCACCACTGAGAGTCGT 60.251 55.000 0.00 0.00 0.00 4.34
783 791 1.066303 GATAGCCACCACTGAGAGTCG 59.934 57.143 0.00 0.00 0.00 4.18
784 792 2.100584 CAGATAGCCACCACTGAGAGTC 59.899 54.545 0.00 0.00 32.90 3.36
785 793 2.106566 CAGATAGCCACCACTGAGAGT 58.893 52.381 0.00 0.00 32.90 3.24
786 794 1.411977 CCAGATAGCCACCACTGAGAG 59.588 57.143 0.00 0.00 32.90 3.20
787 795 1.007118 TCCAGATAGCCACCACTGAGA 59.993 52.381 0.00 0.00 32.90 3.27
788 796 1.489481 TCCAGATAGCCACCACTGAG 58.511 55.000 0.00 0.00 32.90 3.35
789 797 1.833630 CTTCCAGATAGCCACCACTGA 59.166 52.381 0.00 0.00 32.90 3.41
790 798 1.134280 CCTTCCAGATAGCCACCACTG 60.134 57.143 0.00 0.00 0.00 3.66
791 799 1.207791 CCTTCCAGATAGCCACCACT 58.792 55.000 0.00 0.00 0.00 4.00
792 800 0.181350 CCCTTCCAGATAGCCACCAC 59.819 60.000 0.00 0.00 0.00 4.16
793 801 0.044092 TCCCTTCCAGATAGCCACCA 59.956 55.000 0.00 0.00 0.00 4.17
794 802 0.470341 GTCCCTTCCAGATAGCCACC 59.530 60.000 0.00 0.00 0.00 4.61
795 803 1.414550 GAGTCCCTTCCAGATAGCCAC 59.585 57.143 0.00 0.00 0.00 5.01
796 804 1.794714 GAGTCCCTTCCAGATAGCCA 58.205 55.000 0.00 0.00 0.00 4.75
797 805 0.676736 CGAGTCCCTTCCAGATAGCC 59.323 60.000 0.00 0.00 0.00 3.93
798 806 1.693627 TCGAGTCCCTTCCAGATAGC 58.306 55.000 0.00 0.00 0.00 2.97
799 807 3.954904 TCTTTCGAGTCCCTTCCAGATAG 59.045 47.826 0.00 0.00 0.00 2.08
800 808 3.977312 TCTTTCGAGTCCCTTCCAGATA 58.023 45.455 0.00 0.00 0.00 1.98
801 809 2.821437 TCTTTCGAGTCCCTTCCAGAT 58.179 47.619 0.00 0.00 0.00 2.90
802 810 2.304221 TCTTTCGAGTCCCTTCCAGA 57.696 50.000 0.00 0.00 0.00 3.86
803 811 2.300437 ACTTCTTTCGAGTCCCTTCCAG 59.700 50.000 0.00 0.00 0.00 3.86
804 812 2.299297 GACTTCTTTCGAGTCCCTTCCA 59.701 50.000 0.00 0.00 38.02 3.53
805 813 2.299297 TGACTTCTTTCGAGTCCCTTCC 59.701 50.000 2.20 0.00 42.20 3.46
806 814 3.662247 TGACTTCTTTCGAGTCCCTTC 57.338 47.619 2.20 0.00 42.20 3.46
807 815 3.134081 TGTTGACTTCTTTCGAGTCCCTT 59.866 43.478 2.20 0.00 42.20 3.95
808 816 2.698797 TGTTGACTTCTTTCGAGTCCCT 59.301 45.455 2.20 0.00 42.20 4.20
809 817 3.107642 TGTTGACTTCTTTCGAGTCCC 57.892 47.619 2.20 0.00 42.20 4.46
810 818 5.479716 TTTTGTTGACTTCTTTCGAGTCC 57.520 39.130 2.20 0.00 42.20 3.85
811 819 7.971004 AAATTTTGTTGACTTCTTTCGAGTC 57.029 32.000 0.00 0.00 42.98 3.36
851 859 9.751542 CAGATTCAACTCTTTAATACTCCGTAT 57.248 33.333 0.00 0.00 0.00 3.06
852 860 8.195436 CCAGATTCAACTCTTTAATACTCCGTA 58.805 37.037 0.00 0.00 0.00 4.02
853 861 7.042335 CCAGATTCAACTCTTTAATACTCCGT 58.958 38.462 0.00 0.00 0.00 4.69
854 862 7.265673 TCCAGATTCAACTCTTTAATACTCCG 58.734 38.462 0.00 0.00 0.00 4.63
882 890 5.770162 AGTTTACTCCCTCCAACATTTCAAG 59.230 40.000 0.00 0.00 0.00 3.02
899 907 8.000127 TGGGTAAATGGTACTTTTCAGTTTACT 59.000 33.333 0.00 0.00 34.06 2.24
917 925 4.067192 GGATAATAACGCCGTGGGTAAAT 58.933 43.478 0.00 0.00 0.00 1.40
1422 1444 3.578968 TTCCTCCTCCGCCTCGACA 62.579 63.158 0.00 0.00 0.00 4.35
1470 1492 3.093278 GCCTTGAGATTGGCGACG 58.907 61.111 0.00 0.00 39.71 5.12
1475 1497 0.179062 CTCTCCGGCCTTGAGATTGG 60.179 60.000 18.85 7.22 38.16 3.16
1628 1650 2.744202 CAACCTTTCTTCTCACCCATCG 59.256 50.000 0.00 0.00 0.00 3.84
1699 1723 4.345859 TCCCCATATTCGAACCATGTAC 57.654 45.455 16.34 0.00 0.00 2.90
1702 1726 3.754965 ACATCCCCATATTCGAACCATG 58.245 45.455 0.00 7.30 0.00 3.66
1730 1754 4.891277 AAACCAAAGTACGACGATTACG 57.109 40.909 0.00 0.00 45.75 3.18
1780 1804 2.370281 TCTTAGCAGCTCTTCAACCG 57.630 50.000 0.00 0.00 0.00 4.44
1799 1823 4.271049 CACGATGATTAAGGACGCAGAAAT 59.729 41.667 0.00 0.00 0.00 2.17
1801 1825 3.119280 TCACGATGATTAAGGACGCAGAA 60.119 43.478 0.00 0.00 0.00 3.02
1803 1827 2.535984 GTCACGATGATTAAGGACGCAG 59.464 50.000 0.00 0.00 0.00 5.18
1804 1828 2.536365 GTCACGATGATTAAGGACGCA 58.464 47.619 0.00 0.00 0.00 5.24
1841 1867 1.969923 CCCAAAAGGAGCCACATTTCA 59.030 47.619 0.00 0.00 38.24 2.69
1843 1869 1.693606 CACCCAAAAGGAGCCACATTT 59.306 47.619 0.00 0.00 39.89 2.32
1912 1938 9.376075 CATATCATCAGATTAATACAGACCACC 57.624 37.037 0.00 0.00 35.67 4.61
1917 1943 8.262933 CCCTGCATATCATCAGATTAATACAGA 58.737 37.037 0.00 0.00 35.67 3.41
1962 1988 5.363101 AGAAGCAAAATGAGCGAGATATCA 58.637 37.500 5.32 0.00 37.01 2.15
1993 2019 1.625315 TGCACAAGAGAGCACATACCT 59.375 47.619 0.00 0.00 36.40 3.08
2043 2070 5.616488 GCATTGAGCAAAATGAAAATGGT 57.384 34.783 13.77 0.00 44.79 3.55
2076 2103 2.793288 TGAGAGCAATCCAGCATCAA 57.207 45.000 0.00 0.00 36.85 2.57
2113 2142 9.927668 CTAAATTCAATTCAAGGTATTGGTGTT 57.072 29.630 0.00 0.00 37.02 3.32
2172 2201 9.651913 GGTGAATGCCTATTTTGAGATTAAAAA 57.348 29.630 0.00 0.00 33.67 1.94
2173 2202 8.257306 GGGTGAATGCCTATTTTGAGATTAAAA 58.743 33.333 0.00 0.00 34.39 1.52
2174 2203 7.147742 GGGGTGAATGCCTATTTTGAGATTAAA 60.148 37.037 0.00 0.00 0.00 1.52
2175 2204 6.323739 GGGGTGAATGCCTATTTTGAGATTAA 59.676 38.462 0.00 0.00 0.00 1.40
2176 2205 5.833131 GGGGTGAATGCCTATTTTGAGATTA 59.167 40.000 0.00 0.00 0.00 1.75
2177 2206 4.651045 GGGGTGAATGCCTATTTTGAGATT 59.349 41.667 0.00 0.00 0.00 2.40
2301 2330 6.762187 ACTCTATCAATTCTGCAAGATGACAG 59.238 38.462 0.00 0.00 46.36 3.51
2302 2331 6.537660 CACTCTATCAATTCTGCAAGATGACA 59.462 38.462 0.00 0.00 46.36 3.58
2325 2354 9.949174 TGCATGTCAATATATCACAAATTACAC 57.051 29.630 0.00 0.00 0.00 2.90
2447 2476 0.031994 AAACCTTGCAACATCCACGC 59.968 50.000 0.00 0.00 0.00 5.34
2580 2609 6.380095 AGTAAGTAAGACGACATCCTGATC 57.620 41.667 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.