Multiple sequence alignment - TraesCS1D01G166700

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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 TraesCS1D01G166700 chr1D 100.000 3564 0 0 1 3564 238061889 238058326 0.000000e+00 6582
1 TraesCS1D01G166700 chr1B 95.112 2578 68 10 867 3434 336351087 336353616 0.000000e+00 4010
2 TraesCS1D01G166700 chr1B 88.150 692 70 9 27 711 399300475 399299789 0.000000e+00 813
3 TraesCS1D01G166700 chr1B 96.689 151 3 2 3415 3564 336353631 336353780 2.120000e-62 250
4 TraesCS1D01G166700 chr1A 96.610 1770 42 5 867 2624 301631670 301629907 0.000000e+00 2920
5 TraesCS1D01G166700 chr1A 92.737 950 37 9 2622 3564 301629794 301628870 0.000000e+00 1343
6 TraesCS1D01G166700 chr1A 88.028 710 38 12 20 708 186752144 186751461 0.000000e+00 797
7 TraesCS1D01G166700 chr1A 87.097 465 43 7 26 489 435393703 435393255 8.830000e-141 510
8 TraesCS1D01G166700 chr2D 91.000 700 52 6 22 712 229053339 229054036 0.000000e+00 933
9 TraesCS1D01G166700 chr3A 90.819 708 37 14 22 708 516837245 516837945 0.000000e+00 922
10 TraesCS1D01G166700 chr3A 86.107 619 62 11 21 620 624919611 624920224 0.000000e+00 645
11 TraesCS1D01G166700 chr5B 88.663 688 64 11 35 712 692353604 692354287 0.000000e+00 826
12 TraesCS1D01G166700 chr5B 80.053 757 88 30 13 715 600501210 600500463 1.480000e-138 503
13 TraesCS1D01G166700 chr5A 87.358 704 57 12 29 708 7834652 7833957 0.000000e+00 778
14 TraesCS1D01G166700 chr5A 84.422 398 40 10 22 402 79674279 79673887 4.350000e-99 372
15 TraesCS1D01G166700 chr5D 85.405 692 83 14 29 708 9945098 9944413 0.000000e+00 702
16 TraesCS1D01G166700 chr3B 80.828 725 98 24 21 708 545043742 545044462 6.770000e-147 531
17 TraesCS1D01G166700 chr3B 86.667 120 15 1 705 824 62211480 62211362 8.030000e-27 132
18 TraesCS1D01G166700 chr7A 80.357 728 101 27 18 708 572191207 572191929 6.820000e-142 514
19 TraesCS1D01G166700 chr7A 87.711 415 36 11 22 428 730913151 730912744 1.500000e-128 470
20 TraesCS1D01G166700 chr6B 80.563 710 97 27 38 710 352387221 352387926 3.170000e-140 508
21 TraesCS1D01G166700 chr2B 84.167 120 18 1 705 824 523252656 523252538 8.090000e-22 115


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 TraesCS1D01G166700 chr1D 238058326 238061889 3563 True 6582.0 6582 100.0000 1 3564 1 chr1D.!!$R1 3563
1 TraesCS1D01G166700 chr1B 336351087 336353780 2693 False 2130.0 4010 95.9005 867 3564 2 chr1B.!!$F1 2697
2 TraesCS1D01G166700 chr1B 399299789 399300475 686 True 813.0 813 88.1500 27 711 1 chr1B.!!$R1 684
3 TraesCS1D01G166700 chr1A 301628870 301631670 2800 True 2131.5 2920 94.6735 867 3564 2 chr1A.!!$R3 2697
4 TraesCS1D01G166700 chr1A 186751461 186752144 683 True 797.0 797 88.0280 20 708 1 chr1A.!!$R1 688
5 TraesCS1D01G166700 chr2D 229053339 229054036 697 False 933.0 933 91.0000 22 712 1 chr2D.!!$F1 690
6 TraesCS1D01G166700 chr3A 516837245 516837945 700 False 922.0 922 90.8190 22 708 1 chr3A.!!$F1 686
7 TraesCS1D01G166700 chr3A 624919611 624920224 613 False 645.0 645 86.1070 21 620 1 chr3A.!!$F2 599
8 TraesCS1D01G166700 chr5B 692353604 692354287 683 False 826.0 826 88.6630 35 712 1 chr5B.!!$F1 677
9 TraesCS1D01G166700 chr5B 600500463 600501210 747 True 503.0 503 80.0530 13 715 1 chr5B.!!$R1 702
10 TraesCS1D01G166700 chr5A 7833957 7834652 695 True 778.0 778 87.3580 29 708 1 chr5A.!!$R1 679
11 TraesCS1D01G166700 chr5D 9944413 9945098 685 True 702.0 702 85.4050 29 708 1 chr5D.!!$R1 679
12 TraesCS1D01G166700 chr3B 545043742 545044462 720 False 531.0 531 80.8280 21 708 1 chr3B.!!$F1 687
13 TraesCS1D01G166700 chr7A 572191207 572191929 722 False 514.0 514 80.3570 18 708 1 chr7A.!!$F1 690
14 TraesCS1D01G166700 chr6B 352387221 352387926 705 False 508.0 508 80.5630 38 710 1 chr6B.!!$F1 672

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
830 920 0.036010 CCACCAGGACAGTAGCCAAG 60.036 60.0 0.00 0.00 36.89 3.61 F
831 921 0.674895 CACCAGGACAGTAGCCAAGC 60.675 60.0 0.00 0.00 0.00 4.01 F
1995 2110 0.887387 TACAAGTCCAAAGTGCCGGC 60.887 55.0 22.73 22.73 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1934 2.045045 TGCCCGGCTTCCATGAAG 60.045 61.111 11.61 0.00 42.03 3.02 R
2025 2140 2.610833 TCATTCATCTTAAGCAGCGCAG 59.389 45.455 11.47 1.31 0.00 5.18 R
2868 3098 1.764723 TGATGTGGTAGATGGAGCCAG 59.235 52.381 0.00 0.00 32.31 4.85 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
24 25 5.497474 GAACCTGGGTATGTCTTGTGTATT 58.503 41.667 0.00 0.00 0.00 1.89
109 120 3.554129 CCACGACATGATTATTAGCCGGA 60.554 47.826 5.05 0.00 0.00 5.14
256 288 3.806949 TTCCCCTCTGTACAGCAAATT 57.193 42.857 18.45 0.00 0.00 1.82
257 289 3.806949 TCCCCTCTGTACAGCAAATTT 57.193 42.857 18.45 0.00 0.00 1.82
258 290 4.112634 TCCCCTCTGTACAGCAAATTTT 57.887 40.909 18.45 0.00 0.00 1.82
466 549 3.804518 TGTACGCATGCACTACAAAAG 57.195 42.857 19.57 0.00 0.00 2.27
712 802 2.420129 CCGTTTGGCCAGCTATAGTCTT 60.420 50.000 5.11 0.00 0.00 3.01
713 803 2.609459 CGTTTGGCCAGCTATAGTCTTG 59.391 50.000 5.11 0.00 0.00 3.02
714 804 3.610911 GTTTGGCCAGCTATAGTCTTGT 58.389 45.455 5.11 0.00 0.00 3.16
715 805 2.988010 TGGCCAGCTATAGTCTTGTG 57.012 50.000 0.00 0.00 0.00 3.33
716 806 2.187958 TGGCCAGCTATAGTCTTGTGT 58.812 47.619 0.00 0.00 0.00 3.72
717 807 2.168521 TGGCCAGCTATAGTCTTGTGTC 59.831 50.000 0.00 0.00 0.00 3.67
718 808 2.168521 GGCCAGCTATAGTCTTGTGTCA 59.831 50.000 0.00 0.00 0.00 3.58
719 809 3.190874 GCCAGCTATAGTCTTGTGTCAC 58.809 50.000 0.84 0.00 0.00 3.67
720 810 3.368427 GCCAGCTATAGTCTTGTGTCACA 60.368 47.826 0.18 0.18 0.00 3.58
721 811 4.177026 CCAGCTATAGTCTTGTGTCACAC 58.823 47.826 4.80 0.00 34.56 3.82
722 812 3.854240 CAGCTATAGTCTTGTGTCACACG 59.146 47.826 4.80 3.86 37.14 4.49
723 813 2.599082 GCTATAGTCTTGTGTCACACGC 59.401 50.000 4.80 0.78 37.14 5.34
724 814 3.673594 GCTATAGTCTTGTGTCACACGCT 60.674 47.826 4.80 8.16 37.14 5.07
725 815 2.417339 TAGTCTTGTGTCACACGCTC 57.583 50.000 4.80 1.24 37.14 5.03
726 816 0.595053 AGTCTTGTGTCACACGCTCG 60.595 55.000 4.80 0.00 37.14 5.03
727 817 1.949133 TCTTGTGTCACACGCTCGC 60.949 57.895 4.80 0.00 37.14 5.03
728 818 1.951130 CTTGTGTCACACGCTCGCT 60.951 57.895 4.80 0.00 37.14 4.93
729 819 1.880601 CTTGTGTCACACGCTCGCTC 61.881 60.000 4.80 0.00 37.14 5.03
730 820 2.354656 GTGTCACACGCTCGCTCA 60.355 61.111 0.00 0.00 0.00 4.26
731 821 1.734477 GTGTCACACGCTCGCTCAT 60.734 57.895 0.00 0.00 0.00 2.90
732 822 1.734117 TGTCACACGCTCGCTCATG 60.734 57.895 0.00 0.00 0.00 3.07
733 823 2.810887 TCACACGCTCGCTCATGC 60.811 61.111 0.00 0.00 0.00 4.06
734 824 3.857854 CACACGCTCGCTCATGCC 61.858 66.667 0.00 0.00 35.36 4.40
739 829 4.521062 GCTCGCTCATGCCGACCT 62.521 66.667 4.50 0.00 35.36 3.85
740 830 2.279120 CTCGCTCATGCCGACCTC 60.279 66.667 4.50 0.00 35.36 3.85
741 831 4.193334 TCGCTCATGCCGACCTCG 62.193 66.667 4.50 0.00 39.44 4.63
742 832 4.498520 CGCTCATGCCGACCTCGT 62.499 66.667 0.01 0.00 37.74 4.18
743 833 2.583593 GCTCATGCCGACCTCGTC 60.584 66.667 0.00 0.00 37.74 4.20
744 834 3.069980 GCTCATGCCGACCTCGTCT 62.070 63.158 0.00 0.00 37.74 4.18
745 835 1.064946 CTCATGCCGACCTCGTCTC 59.935 63.158 0.00 0.00 37.74 3.36
746 836 1.378646 TCATGCCGACCTCGTCTCT 60.379 57.895 0.00 0.00 37.74 3.10
747 837 1.226802 CATGCCGACCTCGTCTCTG 60.227 63.158 0.00 0.00 37.74 3.35
748 838 1.378646 ATGCCGACCTCGTCTCTGA 60.379 57.895 0.00 0.00 37.74 3.27
749 839 0.965866 ATGCCGACCTCGTCTCTGAA 60.966 55.000 0.00 0.00 37.74 3.02
750 840 1.137825 GCCGACCTCGTCTCTGAAG 59.862 63.158 0.00 0.00 37.74 3.02
751 841 1.137825 CCGACCTCGTCTCTGAAGC 59.862 63.158 0.00 0.00 37.74 3.86
752 842 1.137825 CGACCTCGTCTCTGAAGCC 59.862 63.158 0.00 0.00 34.11 4.35
753 843 1.513622 GACCTCGTCTCTGAAGCCC 59.486 63.158 0.00 0.00 0.00 5.19
754 844 1.228894 ACCTCGTCTCTGAAGCCCA 60.229 57.895 0.00 0.00 0.00 5.36
755 845 1.216710 CCTCGTCTCTGAAGCCCAC 59.783 63.158 0.00 0.00 0.00 4.61
756 846 1.216710 CTCGTCTCTGAAGCCCACC 59.783 63.158 0.00 0.00 0.00 4.61
757 847 2.125912 CGTCTCTGAAGCCCACCG 60.126 66.667 0.00 0.00 0.00 4.94
758 848 2.636412 CGTCTCTGAAGCCCACCGA 61.636 63.158 0.00 0.00 0.00 4.69
759 849 1.901085 GTCTCTGAAGCCCACCGAT 59.099 57.895 0.00 0.00 0.00 4.18
760 850 0.460987 GTCTCTGAAGCCCACCGATG 60.461 60.000 0.00 0.00 0.00 3.84
761 851 1.817099 CTCTGAAGCCCACCGATGC 60.817 63.158 0.00 0.00 0.00 3.91
762 852 2.825836 CTGAAGCCCACCGATGCC 60.826 66.667 0.00 0.00 0.00 4.40
763 853 4.424711 TGAAGCCCACCGATGCCC 62.425 66.667 0.00 0.00 0.00 5.36
764 854 4.115199 GAAGCCCACCGATGCCCT 62.115 66.667 0.00 0.00 0.00 5.19
765 855 3.645268 GAAGCCCACCGATGCCCTT 62.645 63.158 0.00 0.00 0.00 3.95
766 856 2.265467 GAAGCCCACCGATGCCCTTA 62.265 60.000 0.00 0.00 0.00 2.69
767 857 1.858739 AAGCCCACCGATGCCCTTAA 61.859 55.000 0.00 0.00 0.00 1.85
768 858 1.823899 GCCCACCGATGCCCTTAAG 60.824 63.158 0.00 0.00 0.00 1.85
769 859 1.823899 CCCACCGATGCCCTTAAGC 60.824 63.158 0.00 0.00 0.00 3.09
770 860 1.823899 CCACCGATGCCCTTAAGCC 60.824 63.158 0.00 0.00 0.00 4.35
771 861 1.224592 CACCGATGCCCTTAAGCCT 59.775 57.895 0.00 0.00 0.00 4.58
772 862 1.097547 CACCGATGCCCTTAAGCCTG 61.098 60.000 0.00 0.00 0.00 4.85
773 863 1.224592 CCGATGCCCTTAAGCCTGT 59.775 57.895 0.00 0.00 0.00 4.00
774 864 0.815615 CCGATGCCCTTAAGCCTGTC 60.816 60.000 0.00 0.00 0.00 3.51
775 865 0.815615 CGATGCCCTTAAGCCTGTCC 60.816 60.000 0.00 0.00 0.00 4.02
776 866 0.466372 GATGCCCTTAAGCCTGTCCC 60.466 60.000 0.00 0.00 0.00 4.46
777 867 0.921256 ATGCCCTTAAGCCTGTCCCT 60.921 55.000 0.00 0.00 0.00 4.20
778 868 1.224870 GCCCTTAAGCCTGTCCCTC 59.775 63.158 0.00 0.00 0.00 4.30
779 869 1.275421 GCCCTTAAGCCTGTCCCTCT 61.275 60.000 0.00 0.00 0.00 3.69
780 870 0.833949 CCCTTAAGCCTGTCCCTCTC 59.166 60.000 0.00 0.00 0.00 3.20
781 871 1.623834 CCCTTAAGCCTGTCCCTCTCT 60.624 57.143 0.00 0.00 0.00 3.10
782 872 2.192263 CCTTAAGCCTGTCCCTCTCTT 58.808 52.381 0.00 0.00 0.00 2.85
783 873 2.573915 CCTTAAGCCTGTCCCTCTCTTT 59.426 50.000 0.00 0.00 0.00 2.52
784 874 3.775316 CCTTAAGCCTGTCCCTCTCTTTA 59.225 47.826 0.00 0.00 0.00 1.85
785 875 4.141824 CCTTAAGCCTGTCCCTCTCTTTAG 60.142 50.000 0.00 0.00 0.00 1.85
786 876 1.199615 AGCCTGTCCCTCTCTTTAGC 58.800 55.000 0.00 0.00 0.00 3.09
787 877 0.179234 GCCTGTCCCTCTCTTTAGCC 59.821 60.000 0.00 0.00 0.00 3.93
788 878 1.573108 CCTGTCCCTCTCTTTAGCCA 58.427 55.000 0.00 0.00 0.00 4.75
789 879 1.208293 CCTGTCCCTCTCTTTAGCCAC 59.792 57.143 0.00 0.00 0.00 5.01
790 880 1.208293 CTGTCCCTCTCTTTAGCCACC 59.792 57.143 0.00 0.00 0.00 4.61
791 881 1.203313 TGTCCCTCTCTTTAGCCACCT 60.203 52.381 0.00 0.00 0.00 4.00
792 882 1.909986 GTCCCTCTCTTTAGCCACCTT 59.090 52.381 0.00 0.00 0.00 3.50
793 883 2.306219 GTCCCTCTCTTTAGCCACCTTT 59.694 50.000 0.00 0.00 0.00 3.11
794 884 2.986728 TCCCTCTCTTTAGCCACCTTTT 59.013 45.455 0.00 0.00 0.00 2.27
795 885 3.084786 CCCTCTCTTTAGCCACCTTTTG 58.915 50.000 0.00 0.00 0.00 2.44
803 893 4.679412 CCACCTTTTGGCATGTGC 57.321 55.556 0.00 0.00 45.59 4.57
814 904 4.424566 CATGTGCCTTGCGCCCAC 62.425 66.667 4.18 7.79 38.39 4.61
821 911 4.641645 CTTGCGCCCACCAGGACA 62.642 66.667 4.18 0.00 38.24 4.02
822 912 4.641645 TTGCGCCCACCAGGACAG 62.642 66.667 4.18 0.00 38.24 3.51
824 914 3.702048 GCGCCCACCAGGACAGTA 61.702 66.667 0.00 0.00 38.24 2.74
825 915 2.579201 CGCCCACCAGGACAGTAG 59.421 66.667 0.00 0.00 38.24 2.57
826 916 2.269241 GCCCACCAGGACAGTAGC 59.731 66.667 0.00 0.00 38.24 3.58
827 917 2.990479 CCCACCAGGACAGTAGCC 59.010 66.667 0.00 0.00 38.24 3.93
828 918 1.918293 CCCACCAGGACAGTAGCCA 60.918 63.158 0.00 0.00 38.24 4.75
829 919 1.488705 CCCACCAGGACAGTAGCCAA 61.489 60.000 0.00 0.00 38.24 4.52
830 920 0.036010 CCACCAGGACAGTAGCCAAG 60.036 60.000 0.00 0.00 36.89 3.61
831 921 0.674895 CACCAGGACAGTAGCCAAGC 60.675 60.000 0.00 0.00 0.00 4.01
832 922 1.078143 CCAGGACAGTAGCCAAGCC 60.078 63.158 0.00 0.00 0.00 4.35
833 923 1.078143 CAGGACAGTAGCCAAGCCC 60.078 63.158 0.00 0.00 0.00 5.19
834 924 2.125106 GGACAGTAGCCAAGCCCG 60.125 66.667 0.00 0.00 0.00 6.13
835 925 2.125106 GACAGTAGCCAAGCCCGG 60.125 66.667 0.00 0.00 0.00 5.73
836 926 3.682292 GACAGTAGCCAAGCCCGGG 62.682 68.421 19.09 19.09 0.00 5.73
837 927 3.717294 CAGTAGCCAAGCCCGGGT 61.717 66.667 24.63 5.98 40.65 5.28
838 928 3.400054 AGTAGCCAAGCCCGGGTC 61.400 66.667 24.63 14.90 37.99 4.46
839 929 4.484872 GTAGCCAAGCCCGGGTCC 62.485 72.222 24.63 6.10 37.99 4.46
840 930 4.733725 TAGCCAAGCCCGGGTCCT 62.734 66.667 24.63 8.89 37.99 3.85
841 931 3.320411 TAGCCAAGCCCGGGTCCTA 62.320 63.158 24.63 12.38 37.99 2.94
842 932 2.615191 TAGCCAAGCCCGGGTCCTAT 62.615 60.000 24.63 6.92 37.99 2.57
843 933 2.144738 GCCAAGCCCGGGTCCTATA 61.145 63.158 24.63 0.00 0.00 1.31
844 934 1.702022 GCCAAGCCCGGGTCCTATAA 61.702 60.000 24.63 0.00 0.00 0.98
845 935 1.064825 CCAAGCCCGGGTCCTATAAT 58.935 55.000 24.63 0.00 0.00 1.28
846 936 1.003233 CCAAGCCCGGGTCCTATAATC 59.997 57.143 24.63 0.79 0.00 1.75
847 937 1.978580 CAAGCCCGGGTCCTATAATCT 59.021 52.381 24.63 3.65 0.00 2.40
848 938 2.372172 CAAGCCCGGGTCCTATAATCTT 59.628 50.000 24.63 10.46 0.00 2.40
849 939 2.258109 AGCCCGGGTCCTATAATCTTC 58.742 52.381 24.63 0.00 0.00 2.87
850 940 2.158143 AGCCCGGGTCCTATAATCTTCT 60.158 50.000 24.63 1.94 0.00 2.85
851 941 2.028020 GCCCGGGTCCTATAATCTTCTG 60.028 54.545 24.63 0.00 0.00 3.02
852 942 2.567615 CCCGGGTCCTATAATCTTCTGG 59.432 54.545 14.18 0.00 0.00 3.86
853 943 3.507411 CCGGGTCCTATAATCTTCTGGA 58.493 50.000 0.00 0.00 0.00 3.86
854 944 3.511934 CCGGGTCCTATAATCTTCTGGAG 59.488 52.174 0.00 0.00 0.00 3.86
855 945 4.408276 CGGGTCCTATAATCTTCTGGAGA 58.592 47.826 0.00 0.00 39.13 3.71
856 946 4.833380 CGGGTCCTATAATCTTCTGGAGAA 59.167 45.833 0.00 0.00 38.06 2.87
857 947 5.482175 CGGGTCCTATAATCTTCTGGAGAAT 59.518 44.000 0.00 0.00 38.06 2.40
858 948 6.014156 CGGGTCCTATAATCTTCTGGAGAATT 60.014 42.308 0.00 0.00 38.06 2.17
859 949 7.473511 CGGGTCCTATAATCTTCTGGAGAATTT 60.474 40.741 0.00 0.00 38.06 1.82
860 950 8.881262 GGGTCCTATAATCTTCTGGAGAATTTA 58.119 37.037 0.00 0.00 38.06 1.40
1232 1347 1.089920 ATGTGCATCGTCAAGAAGCC 58.910 50.000 0.00 0.00 42.44 4.35
1240 1355 3.621805 TCAAGAAGCCCGTCCGCA 61.622 61.111 0.00 0.00 0.00 5.69
1251 1366 4.884257 GTCCGCATCCGCCGCTTA 62.884 66.667 0.00 0.00 33.11 3.09
1295 1410 3.053896 CCCAACCCCGAAGCGAAC 61.054 66.667 0.00 0.00 0.00 3.95
1303 1418 1.004918 CCGAAGCGAACACTCCCTT 60.005 57.895 0.00 0.00 0.00 3.95
1498 1613 2.301577 AGAACTCTCATTGCTACGGC 57.698 50.000 0.00 0.00 39.26 5.68
1819 1934 2.834968 GCCATTGTAGCCAGGGCC 60.835 66.667 6.70 0.00 43.17 5.80
1995 2110 0.887387 TACAAGTCCAAAGTGCCGGC 60.887 55.000 22.73 22.73 0.00 6.13
2025 2140 4.368315 TCGATGTACATGTGCAGGATAAC 58.632 43.478 21.32 3.58 0.00 1.89
2140 2255 7.228706 ACAAACTTACTGCTAAATGCTTACTGT 59.771 33.333 0.00 0.00 43.37 3.55
2227 2342 5.128919 CCTCACCGTAGTACTTGGTATAGT 58.871 45.833 16.55 0.00 33.82 2.12
2450 2565 5.185056 AGGGATGTTTACCACATTTTACTGC 59.815 40.000 0.00 0.00 46.96 4.40
2573 2688 5.453903 GGAATATGCCAGTAGATATCCGCAT 60.454 44.000 13.16 13.16 39.98 4.73
2611 2726 7.172654 AGCAATTTCGTTGGTTGTTTATTTC 57.827 32.000 0.00 0.00 45.78 2.17
2643 2873 5.104109 AGGTAGCTGCTAAACCATCCAATTA 60.104 40.000 20.57 0.00 35.64 1.40
2644 2874 5.770162 GGTAGCTGCTAAACCATCCAATTAT 59.230 40.000 11.57 0.00 33.28 1.28
2645 2875 6.265422 GGTAGCTGCTAAACCATCCAATTATT 59.735 38.462 11.57 0.00 33.28 1.40
2646 2876 7.447238 GGTAGCTGCTAAACCATCCAATTATTA 59.553 37.037 11.57 0.00 33.28 0.98
2868 3098 4.589908 TCAGTCTTTTAAGCCAATCTCCC 58.410 43.478 0.00 0.00 0.00 4.30
2907 3137 3.210227 TCAAATTCTTCCACTTGCGACA 58.790 40.909 0.00 0.00 0.00 4.35
2920 3150 2.010145 TGCGACATAACTGCTTCTCC 57.990 50.000 0.00 0.00 0.00 3.71
2935 3165 7.261325 ACTGCTTCTCCTTTTCTTTTCTTTTC 58.739 34.615 0.00 0.00 0.00 2.29
2971 3201 0.912487 TCCAAAGTCGCTATGGGGGT 60.912 55.000 0.00 0.00 34.89 4.95
2997 3227 1.415289 TGACATGAGCTGATAGCCTGG 59.585 52.381 0.00 0.00 43.77 4.45
3142 3373 8.706035 CATTTAGCTTTTGTTCTTCATTTGAGG 58.294 33.333 0.00 0.00 0.00 3.86
3199 3434 2.206322 TGCCTACAATATGGGAGGGT 57.794 50.000 10.68 0.00 0.00 4.34
3244 3479 3.056328 GCGGCAAGTTGTCCCTCC 61.056 66.667 0.97 0.00 0.00 4.30
3259 3494 1.758862 CCCTCCAATGGCCTGAATTTC 59.241 52.381 3.32 0.00 0.00 2.17
3305 3540 1.675641 GGCCTGGCATCAAACGAGT 60.676 57.895 22.05 0.00 0.00 4.18
3388 3623 1.200716 AGTTGCTGCACAAATGGATCG 59.799 47.619 0.00 0.00 40.82 3.69
3529 3804 4.336433 CACTTAATGTAGGGTGAGCCAATG 59.664 45.833 2.50 0.00 36.17 2.82
3534 3809 2.292267 GTAGGGTGAGCCAATGATGTG 58.708 52.381 2.50 0.00 36.17 3.21
3555 3831 7.859325 TGTGTTATAACTAGAATTGCCTTCC 57.141 36.000 16.33 0.00 34.11 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.289444 ACACAAGACATACCCAGGTTCG 60.289 50.000 0.00 0.00 0.00 3.95
2 3 5.497474 GAATACACAAGACATACCCAGGTT 58.503 41.667 0.00 0.00 0.00 3.50
6 7 4.080582 CCAGGAATACACAAGACATACCCA 60.081 45.833 0.00 0.00 0.00 4.51
7 8 4.451900 CCAGGAATACACAAGACATACCC 58.548 47.826 0.00 0.00 0.00 3.69
8 9 3.877508 GCCAGGAATACACAAGACATACC 59.122 47.826 0.00 0.00 0.00 2.73
9 10 3.877508 GGCCAGGAATACACAAGACATAC 59.122 47.826 0.00 0.00 0.00 2.39
10 11 3.521531 TGGCCAGGAATACACAAGACATA 59.478 43.478 0.00 0.00 0.00 2.29
11 12 2.308570 TGGCCAGGAATACACAAGACAT 59.691 45.455 0.00 0.00 0.00 3.06
12 13 1.702401 TGGCCAGGAATACACAAGACA 59.298 47.619 0.00 0.00 0.00 3.41
13 14 2.489938 TGGCCAGGAATACACAAGAC 57.510 50.000 0.00 0.00 0.00 3.01
14 15 3.153919 GTTTGGCCAGGAATACACAAGA 58.846 45.455 5.11 0.00 0.00 3.02
15 16 2.095263 CGTTTGGCCAGGAATACACAAG 60.095 50.000 5.11 0.00 0.00 3.16
16 17 1.883275 CGTTTGGCCAGGAATACACAA 59.117 47.619 5.11 0.00 0.00 3.33
17 18 1.529226 CGTTTGGCCAGGAATACACA 58.471 50.000 5.11 0.00 0.00 3.72
18 19 0.808755 CCGTTTGGCCAGGAATACAC 59.191 55.000 5.11 0.00 0.00 2.90
85 96 3.138304 GGCTAATAATCATGTCGTGGCA 58.862 45.455 0.00 0.00 0.00 4.92
162 173 2.044352 GTGCCGGCCCAAATAGGT 60.044 61.111 26.77 0.00 34.66 3.08
333 394 2.514803 AGGTTTTAATGAGGCAAGCGT 58.485 42.857 0.00 0.00 0.00 5.07
531 620 2.323213 CGGCACAACCCGTTTAACT 58.677 52.632 0.00 0.00 43.24 2.24
712 802 2.354656 GAGCGAGCGTGTGACACA 60.355 61.111 16.74 3.56 33.40 3.72
713 803 1.734477 ATGAGCGAGCGTGTGACAC 60.734 57.895 5.47 5.47 0.00 3.67
714 804 1.734117 CATGAGCGAGCGTGTGACA 60.734 57.895 0.00 0.00 0.00 3.58
715 805 3.075998 CATGAGCGAGCGTGTGAC 58.924 61.111 0.00 0.00 0.00 3.67
716 806 2.810887 GCATGAGCGAGCGTGTGA 60.811 61.111 0.00 0.00 0.00 3.58
717 807 3.857854 GGCATGAGCGAGCGTGTG 61.858 66.667 0.00 0.00 43.41 3.82
733 823 1.137825 GCTTCAGAGACGAGGTCGG 59.862 63.158 4.13 0.00 44.95 4.79
734 824 1.137825 GGCTTCAGAGACGAGGTCG 59.862 63.158 0.00 0.00 46.33 4.79
735 825 1.251527 TGGGCTTCAGAGACGAGGTC 61.252 60.000 0.00 0.00 0.00 3.85
736 826 1.228894 TGGGCTTCAGAGACGAGGT 60.229 57.895 0.00 0.00 0.00 3.85
737 827 1.216710 GTGGGCTTCAGAGACGAGG 59.783 63.158 0.00 0.00 0.00 4.63
738 828 1.216710 GGTGGGCTTCAGAGACGAG 59.783 63.158 0.00 0.00 0.00 4.18
739 829 2.636412 CGGTGGGCTTCAGAGACGA 61.636 63.158 0.00 0.00 0.00 4.20
740 830 1.949847 ATCGGTGGGCTTCAGAGACG 61.950 60.000 0.00 0.00 0.00 4.18
741 831 0.460987 CATCGGTGGGCTTCAGAGAC 60.461 60.000 0.00 0.00 0.00 3.36
742 832 1.900351 CATCGGTGGGCTTCAGAGA 59.100 57.895 0.00 0.00 0.00 3.10
743 833 1.817099 GCATCGGTGGGCTTCAGAG 60.817 63.158 0.00 0.00 0.00 3.35
744 834 2.268920 GCATCGGTGGGCTTCAGA 59.731 61.111 0.00 0.00 0.00 3.27
745 835 2.825836 GGCATCGGTGGGCTTCAG 60.826 66.667 0.00 0.00 0.00 3.02
746 836 4.424711 GGGCATCGGTGGGCTTCA 62.425 66.667 0.00 0.00 0.00 3.02
747 837 2.265467 TAAGGGCATCGGTGGGCTTC 62.265 60.000 0.00 0.00 0.00 3.86
748 838 1.858739 TTAAGGGCATCGGTGGGCTT 61.859 55.000 0.00 0.00 0.00 4.35
749 839 2.270874 CTTAAGGGCATCGGTGGGCT 62.271 60.000 0.00 0.00 0.00 5.19
750 840 1.823899 CTTAAGGGCATCGGTGGGC 60.824 63.158 0.00 0.00 0.00 5.36
751 841 1.823899 GCTTAAGGGCATCGGTGGG 60.824 63.158 4.29 0.00 0.00 4.61
752 842 1.823899 GGCTTAAGGGCATCGGTGG 60.824 63.158 4.29 0.00 40.53 4.61
753 843 1.097547 CAGGCTTAAGGGCATCGGTG 61.098 60.000 4.29 0.00 43.56 4.94
754 844 1.224592 CAGGCTTAAGGGCATCGGT 59.775 57.895 4.29 0.00 43.56 4.69
755 845 0.815615 GACAGGCTTAAGGGCATCGG 60.816 60.000 4.29 0.00 43.56 4.18
756 846 0.815615 GGACAGGCTTAAGGGCATCG 60.816 60.000 4.29 0.00 43.56 3.84
757 847 0.466372 GGGACAGGCTTAAGGGCATC 60.466 60.000 4.29 0.62 43.56 3.91
758 848 0.921256 AGGGACAGGCTTAAGGGCAT 60.921 55.000 4.29 0.00 43.56 4.40
759 849 1.541368 AGGGACAGGCTTAAGGGCA 60.541 57.895 4.29 0.00 43.56 5.36
760 850 1.224870 GAGGGACAGGCTTAAGGGC 59.775 63.158 4.29 0.00 41.20 5.19
761 851 0.833949 GAGAGGGACAGGCTTAAGGG 59.166 60.000 4.29 0.00 0.00 3.95
762 852 1.872773 AGAGAGGGACAGGCTTAAGG 58.127 55.000 4.29 0.00 0.00 2.69
763 853 3.990959 AAAGAGAGGGACAGGCTTAAG 57.009 47.619 0.00 0.00 0.00 1.85
764 854 3.197983 GCTAAAGAGAGGGACAGGCTTAA 59.802 47.826 0.00 0.00 0.00 1.85
765 855 2.766828 GCTAAAGAGAGGGACAGGCTTA 59.233 50.000 0.00 0.00 0.00 3.09
766 856 1.557371 GCTAAAGAGAGGGACAGGCTT 59.443 52.381 0.00 0.00 0.00 4.35
767 857 1.199615 GCTAAAGAGAGGGACAGGCT 58.800 55.000 0.00 0.00 0.00 4.58
768 858 0.179234 GGCTAAAGAGAGGGACAGGC 59.821 60.000 0.00 0.00 0.00 4.85
769 859 1.208293 GTGGCTAAAGAGAGGGACAGG 59.792 57.143 0.00 0.00 0.00 4.00
770 860 1.208293 GGTGGCTAAAGAGAGGGACAG 59.792 57.143 0.00 0.00 0.00 3.51
771 861 1.203313 AGGTGGCTAAAGAGAGGGACA 60.203 52.381 0.00 0.00 0.00 4.02
772 862 1.574263 AGGTGGCTAAAGAGAGGGAC 58.426 55.000 0.00 0.00 0.00 4.46
773 863 2.344093 AAGGTGGCTAAAGAGAGGGA 57.656 50.000 0.00 0.00 0.00 4.20
774 864 3.084786 CAAAAGGTGGCTAAAGAGAGGG 58.915 50.000 0.00 0.00 0.00 4.30
775 865 3.084786 CCAAAAGGTGGCTAAAGAGAGG 58.915 50.000 0.00 0.00 41.72 3.69
804 894 4.641645 TGTCCTGGTGGGCGCAAG 62.642 66.667 10.83 0.00 41.88 4.01
805 895 4.641645 CTGTCCTGGTGGGCGCAA 62.642 66.667 10.83 0.00 41.88 4.85
807 897 3.665675 CTACTGTCCTGGTGGGCGC 62.666 68.421 0.00 0.00 41.88 6.53
808 898 2.579201 CTACTGTCCTGGTGGGCG 59.421 66.667 0.00 0.00 41.88 6.13
809 899 2.269241 GCTACTGTCCTGGTGGGC 59.731 66.667 0.00 0.00 38.74 5.36
810 900 1.488705 TTGGCTACTGTCCTGGTGGG 61.489 60.000 0.00 0.00 0.00 4.61
811 901 0.036010 CTTGGCTACTGTCCTGGTGG 60.036 60.000 0.00 0.00 0.00 4.61
812 902 0.674895 GCTTGGCTACTGTCCTGGTG 60.675 60.000 0.00 0.00 0.00 4.17
813 903 1.679898 GCTTGGCTACTGTCCTGGT 59.320 57.895 0.00 0.00 0.00 4.00
814 904 1.078143 GGCTTGGCTACTGTCCTGG 60.078 63.158 0.00 0.00 0.00 4.45
815 905 1.078143 GGGCTTGGCTACTGTCCTG 60.078 63.158 0.00 0.00 0.00 3.86
816 906 2.660064 CGGGCTTGGCTACTGTCCT 61.660 63.158 0.00 0.00 0.00 3.85
817 907 2.125106 CGGGCTTGGCTACTGTCC 60.125 66.667 0.00 0.00 0.00 4.02
818 908 2.125106 CCGGGCTTGGCTACTGTC 60.125 66.667 0.00 0.00 0.00 3.51
819 909 3.717294 CCCGGGCTTGGCTACTGT 61.717 66.667 8.08 0.00 0.00 3.55
820 910 3.682292 GACCCGGGCTTGGCTACTG 62.682 68.421 24.08 0.00 0.00 2.74
821 911 3.400054 GACCCGGGCTTGGCTACT 61.400 66.667 24.08 0.00 0.00 2.57
822 912 4.484872 GGACCCGGGCTTGGCTAC 62.485 72.222 24.08 0.00 0.00 3.58
823 913 2.615191 ATAGGACCCGGGCTTGGCTA 62.615 60.000 24.08 10.33 0.00 3.93
824 914 2.615191 TATAGGACCCGGGCTTGGCT 62.615 60.000 24.08 0.00 0.00 4.75
825 915 1.702022 TTATAGGACCCGGGCTTGGC 61.702 60.000 24.08 4.72 0.00 4.52
826 916 1.003233 GATTATAGGACCCGGGCTTGG 59.997 57.143 24.08 0.00 0.00 3.61
827 917 1.978580 AGATTATAGGACCCGGGCTTG 59.021 52.381 24.08 0.00 0.00 4.01
828 918 2.417719 AGATTATAGGACCCGGGCTT 57.582 50.000 24.08 12.80 0.00 4.35
829 919 2.158143 AGAAGATTATAGGACCCGGGCT 60.158 50.000 24.08 13.80 0.00 5.19
830 920 2.028020 CAGAAGATTATAGGACCCGGGC 60.028 54.545 24.08 13.95 0.00 6.13
831 921 2.567615 CCAGAAGATTATAGGACCCGGG 59.432 54.545 22.25 22.25 0.00 5.73
832 922 3.507411 TCCAGAAGATTATAGGACCCGG 58.493 50.000 0.00 0.00 0.00 5.73
833 923 4.408276 TCTCCAGAAGATTATAGGACCCG 58.592 47.826 0.00 0.00 0.00 5.28
834 924 6.943899 ATTCTCCAGAAGATTATAGGACCC 57.056 41.667 0.00 0.00 37.48 4.46
842 932 9.218525 AGACAGGATAAATTCTCCAGAAGATTA 57.781 33.333 9.12 0.00 37.48 1.75
843 933 8.100135 AGACAGGATAAATTCTCCAGAAGATT 57.900 34.615 9.12 0.00 37.48 2.40
844 934 7.688918 AGACAGGATAAATTCTCCAGAAGAT 57.311 36.000 9.12 0.00 37.48 2.40
845 935 7.118496 GAGACAGGATAAATTCTCCAGAAGA 57.882 40.000 9.12 0.00 37.48 2.87
852 942 3.977326 AGGGGGAGACAGGATAAATTCTC 59.023 47.826 0.00 0.00 34.83 2.87
853 943 4.027782 AGGGGGAGACAGGATAAATTCT 57.972 45.455 0.00 0.00 0.00 2.40
854 944 4.446455 GGAAGGGGGAGACAGGATAAATTC 60.446 50.000 0.00 0.00 0.00 2.17
855 945 3.463704 GGAAGGGGGAGACAGGATAAATT 59.536 47.826 0.00 0.00 0.00 1.82
856 946 3.056832 GGAAGGGGGAGACAGGATAAAT 58.943 50.000 0.00 0.00 0.00 1.40
857 947 2.047296 AGGAAGGGGGAGACAGGATAAA 59.953 50.000 0.00 0.00 0.00 1.40
858 948 1.657162 AGGAAGGGGGAGACAGGATAA 59.343 52.381 0.00 0.00 0.00 1.75
859 949 1.330155 AGGAAGGGGGAGACAGGATA 58.670 55.000 0.00 0.00 0.00 2.59
860 950 0.423544 AAGGAAGGGGGAGACAGGAT 59.576 55.000 0.00 0.00 0.00 3.24
861 951 0.196118 AAAGGAAGGGGGAGACAGGA 59.804 55.000 0.00 0.00 0.00 3.86
862 952 0.621082 GAAAGGAAGGGGGAGACAGG 59.379 60.000 0.00 0.00 0.00 4.00
863 953 0.250513 CGAAAGGAAGGGGGAGACAG 59.749 60.000 0.00 0.00 0.00 3.51
864 954 0.178915 TCGAAAGGAAGGGGGAGACA 60.179 55.000 0.00 0.00 0.00 3.41
865 955 1.205055 ATCGAAAGGAAGGGGGAGAC 58.795 55.000 0.00 0.00 0.00 3.36
870 960 5.763698 GGTTAATCTAATCGAAAGGAAGGGG 59.236 44.000 0.00 0.00 0.00 4.79
1007 1113 4.824515 CGCGAGGAGGGAGGAGGT 62.825 72.222 0.00 0.00 34.27 3.85
1240 1355 2.426023 GTGGGATAAGCGGCGGAT 59.574 61.111 9.78 0.00 0.00 4.18
1295 1410 4.389576 GTGCGCGCAAAGGGAGTG 62.390 66.667 38.24 0.00 34.27 3.51
1345 1460 1.674519 CGGTCGGTCATCCACATTGAA 60.675 52.381 0.00 0.00 0.00 2.69
1434 1549 0.456312 GTAGTTCACGGCACTCTCGG 60.456 60.000 0.00 0.00 0.00 4.63
1498 1613 2.502295 GCATAGCATTTCAGGAGGGAG 58.498 52.381 0.00 0.00 0.00 4.30
1534 1649 1.079750 GAGCTTTTCGGCCTCGTCT 60.080 57.895 0.00 0.00 37.69 4.18
1819 1934 2.045045 TGCCCGGCTTCCATGAAG 60.045 61.111 11.61 0.00 42.03 3.02
1995 2110 3.786489 GCACATGTACATCGAGTTGCATG 60.786 47.826 19.24 19.24 42.71 4.06
2025 2140 2.610833 TCATTCATCTTAAGCAGCGCAG 59.389 45.455 11.47 1.31 0.00 5.18
2028 2143 4.808077 ATGTCATTCATCTTAAGCAGCG 57.192 40.909 0.00 0.00 29.76 5.18
2072 2187 4.031611 ACATACCTACTTTCCCACTCTCC 58.968 47.826 0.00 0.00 0.00 3.71
2140 2255 3.308402 CCTTCTCCATAAGACCTTTGGCA 60.308 47.826 0.00 0.00 32.27 4.92
2213 2328 6.127140 CCACTAGCCAAACTATACCAAGTACT 60.127 42.308 0.00 0.00 0.00 2.73
2227 2342 3.831911 CCTGGAAAAATCCACTAGCCAAA 59.168 43.478 0.00 0.00 35.63 3.28
2450 2565 4.193865 TGTCCTGCATGAACATATGTCTG 58.806 43.478 9.23 8.52 0.00 3.51
2573 2688 6.640518 ACGAAATTGCTTAGTGATAGGAAGA 58.359 36.000 0.00 0.00 0.00 2.87
2643 2873 9.014297 CAGTGGAAGGAAGTCAAACTAATTAAT 57.986 33.333 0.00 0.00 0.00 1.40
2644 2874 7.040686 GCAGTGGAAGGAAGTCAAACTAATTAA 60.041 37.037 0.00 0.00 0.00 1.40
2645 2875 6.430000 GCAGTGGAAGGAAGTCAAACTAATTA 59.570 38.462 0.00 0.00 0.00 1.40
2646 2876 5.241728 GCAGTGGAAGGAAGTCAAACTAATT 59.758 40.000 0.00 0.00 0.00 1.40
2868 3098 1.764723 TGATGTGGTAGATGGAGCCAG 59.235 52.381 0.00 0.00 32.31 4.85
2907 3137 8.470657 AAGAAAAGAAAAGGAGAAGCAGTTAT 57.529 30.769 0.00 0.00 0.00 1.89
2935 3165 4.524316 TTGGATGCCATGAAAACAGAAG 57.476 40.909 0.00 0.00 31.53 2.85
2971 3201 4.021632 GGCTATCAGCTCATGTCAGACATA 60.022 45.833 15.98 0.00 41.99 2.29
2997 3227 9.880157 TCTCTGGTTTATTACACAAGGTATTAC 57.120 33.333 0.00 0.00 0.00 1.89
3098 3328 9.672673 AGCTAAATGTGAATGTACTTCAGTAAT 57.327 29.630 7.68 2.13 44.44 1.89
3199 3434 2.655090 TCCAGCATTCTCACAACCAA 57.345 45.000 0.00 0.00 0.00 3.67
3244 3479 2.827322 TCCACAGAAATTCAGGCCATTG 59.173 45.455 5.01 0.00 0.00 2.82
3305 3540 2.841266 TCTGAACCATTATTCCACCCGA 59.159 45.455 0.00 0.00 0.00 5.14
3388 3623 5.186198 AGCCATACTGAAATACTTCACCAC 58.814 41.667 0.00 0.00 36.62 4.16
3529 3804 8.560374 GGAAGGCAATTCTAGTTATAACACATC 58.440 37.037 17.65 0.00 38.07 3.06
3534 3809 5.986936 GCGGAAGGCAATTCTAGTTATAAC 58.013 41.667 7.57 7.57 42.87 1.89


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

AutoCloner maintained by Alex Coulton.