Multiple sequence alignment - TraesCS2B01G604400

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 TraesCS2B01G604400 chr2B 100.000 1772 0 0 1 1772 786049585 786051356 0.000000e+00 3273
1 TraesCS2B01G604400 chr2B 87.421 946 102 13 841 1772 646976916 646977858 0.000000e+00 1072
2 TraesCS2B01G604400 chr2B 100.000 395 0 0 2056 2450 786051640 786052034 0.000000e+00 730
3 TraesCS2B01G604400 chr2B 75.200 750 178 7 1013 1758 403549099 403549844 5.010000e-92 348
4 TraesCS2B01G604400 chr2B 90.698 129 8 2 2056 2180 171009294 171009166 4.190000e-38 169
5 TraesCS2B01G604400 chr4D 91.782 937 69 5 842 1772 386201848 386202782 0.000000e+00 1297
6 TraesCS2B01G604400 chr4D 86.284 401 46 5 2056 2450 386202873 386203270 6.260000e-116 427
7 TraesCS2B01G604400 chr6A 89.022 920 91 6 857 1772 475900547 475901460 0.000000e+00 1131
8 TraesCS2B01G604400 chrUn 94.009 701 42 0 7 707 23282643 23281943 0.000000e+00 1062
9 TraesCS2B01G604400 chr4A 93.191 705 40 5 7 708 695022626 695021927 0.000000e+00 1029
10 TraesCS2B01G604400 chr4A 86.403 934 106 9 841 1771 654800343 654801258 0.000000e+00 1002
11 TraesCS2B01G604400 chr4A 88.434 709 78 4 4 711 581185948 581186653 0.000000e+00 852
12 TraesCS2B01G604400 chr7A 87.931 870 101 2 903 1772 634456385 634457250 0.000000e+00 1022
13 TraesCS2B01G604400 chr7A 91.857 700 55 2 7 706 274578659 274579356 0.000000e+00 976
14 TraesCS2B01G604400 chr7A 91.311 702 60 1 7 707 664840543 664841244 0.000000e+00 957
15 TraesCS2B01G604400 chr7A 90.313 702 67 1 7 708 538864493 538865193 0.000000e+00 918
16 TraesCS2B01G604400 chr3D 91.880 702 52 5 7 708 444478134 444477438 0.000000e+00 976
17 TraesCS2B01G604400 chr3B 89.886 702 68 3 7 707 783710198 783710897 0.000000e+00 900
18 TraesCS2B01G604400 chr1A 87.784 704 85 1 4 707 563661107 563661809 0.000000e+00 822
19 TraesCS2B01G604400 chr5A 74.819 691 167 6 1076 1763 673647808 673647122 3.060000e-79 305
20 TraesCS2B01G604400 chr7B 75.079 630 150 6 1076 1702 611900705 611901330 1.110000e-73 287


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 TraesCS2B01G604400 chr2B 786049585 786052034 2449 False 2001.5 3273 100.000 1 2450 2 chr2B.!!$F3 2449
1 TraesCS2B01G604400 chr2B 646976916 646977858 942 False 1072.0 1072 87.421 841 1772 1 chr2B.!!$F2 931
2 TraesCS2B01G604400 chr2B 403549099 403549844 745 False 348.0 348 75.200 1013 1758 1 chr2B.!!$F1 745
3 TraesCS2B01G604400 chr4D 386201848 386203270 1422 False 862.0 1297 89.033 842 2450 2 chr4D.!!$F1 1608
4 TraesCS2B01G604400 chr6A 475900547 475901460 913 False 1131.0 1131 89.022 857 1772 1 chr6A.!!$F1 915
5 TraesCS2B01G604400 chrUn 23281943 23282643 700 True 1062.0 1062 94.009 7 707 1 chrUn.!!$R1 700
6 TraesCS2B01G604400 chr4A 695021927 695022626 699 True 1029.0 1029 93.191 7 708 1 chr4A.!!$R1 701
7 TraesCS2B01G604400 chr4A 654800343 654801258 915 False 1002.0 1002 86.403 841 1771 1 chr4A.!!$F2 930
8 TraesCS2B01G604400 chr4A 581185948 581186653 705 False 852.0 852 88.434 4 711 1 chr4A.!!$F1 707
9 TraesCS2B01G604400 chr7A 634456385 634457250 865 False 1022.0 1022 87.931 903 1772 1 chr7A.!!$F3 869
10 TraesCS2B01G604400 chr7A 274578659 274579356 697 False 976.0 976 91.857 7 706 1 chr7A.!!$F1 699
11 TraesCS2B01G604400 chr7A 664840543 664841244 701 False 957.0 957 91.311 7 707 1 chr7A.!!$F4 700
12 TraesCS2B01G604400 chr7A 538864493 538865193 700 False 918.0 918 90.313 7 708 1 chr7A.!!$F2 701
13 TraesCS2B01G604400 chr3D 444477438 444478134 696 True 976.0 976 91.880 7 708 1 chr3D.!!$R1 701
14 TraesCS2B01G604400 chr3B 783710198 783710897 699 False 900.0 900 89.886 7 707 1 chr3B.!!$F1 700
15 TraesCS2B01G604400 chr1A 563661107 563661809 702 False 822.0 822 87.784 4 707 1 chr1A.!!$F1 703
16 TraesCS2B01G604400 chr5A 673647122 673647808 686 True 305.0 305 74.819 1076 1763 1 chr5A.!!$R1 687
17 TraesCS2B01G604400 chr7B 611900705 611901330 625 False 287.0 287 75.079 1076 1702 1 chr7B.!!$F1 626

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
828 834 0.034896 GAGGAGAACCACGAAGCCAA 59.965 55.0 0.0 0.0 38.94 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 2428 0.323629 TTCCCGGTCACATCCTTGTC 59.676 55.0 0.0 0.0 32.34 3.18 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
43 44 6.015603 TGCTAAAATCACAACAATCATGTGGA 60.016 34.615 6.80 0.00 46.37 4.02
147 148 0.615331 TTGCGCTCCTGAATCTTCCT 59.385 50.000 9.73 0.00 0.00 3.36
417 421 4.305539 TGTGATCATGGAAGTGGATTGT 57.694 40.909 0.00 0.00 0.00 2.71
445 449 1.425066 TGGTGATGCTCTGGAAAACCT 59.575 47.619 0.00 0.00 0.00 3.50
670 675 0.111446 TTGTCCGGGGAATGCTTTCA 59.889 50.000 13.72 0.00 33.23 2.69
722 728 3.870538 AAAAAGGGACCTTTCCTACGT 57.129 42.857 16.12 0.00 44.50 3.57
723 729 2.853235 AAAGGGACCTTTCCTACGTG 57.147 50.000 10.47 0.00 41.91 4.49
724 730 1.725803 AAGGGACCTTTCCTACGTGT 58.274 50.000 0.00 0.00 42.38 4.49
725 731 2.610438 AGGGACCTTTCCTACGTGTA 57.390 50.000 0.00 0.00 42.38 2.90
726 732 2.174360 AGGGACCTTTCCTACGTGTAC 58.826 52.381 0.00 0.00 42.38 2.90
727 733 2.174360 GGGACCTTTCCTACGTGTACT 58.826 52.381 0.00 0.00 42.38 2.73
728 734 2.094338 GGGACCTTTCCTACGTGTACTG 60.094 54.545 0.00 0.00 42.38 2.74
729 735 2.094338 GGACCTTTCCTACGTGTACTGG 60.094 54.545 0.00 0.00 39.13 4.00
730 736 2.560105 GACCTTTCCTACGTGTACTGGT 59.440 50.000 0.00 0.00 0.00 4.00
731 737 3.758554 GACCTTTCCTACGTGTACTGGTA 59.241 47.826 0.00 0.00 0.00 3.25
732 738 3.507622 ACCTTTCCTACGTGTACTGGTAC 59.492 47.826 0.00 4.15 36.63 3.34
733 739 3.426695 CCTTTCCTACGTGTACTGGTACG 60.427 52.174 0.00 2.25 45.19 3.67
737 743 4.874534 CGTGTACTGGTACGTGGG 57.125 61.111 0.00 0.00 38.85 4.61
738 744 1.444895 CGTGTACTGGTACGTGGGC 60.445 63.158 0.00 0.00 38.85 5.36
739 745 1.079612 GTGTACTGGTACGTGGGCC 60.080 63.158 0.00 0.00 38.85 5.80
740 746 1.228956 TGTACTGGTACGTGGGCCT 60.229 57.895 4.53 0.00 38.85 5.19
741 747 1.217244 GTACTGGTACGTGGGCCTG 59.783 63.158 4.53 4.71 0.00 4.85
742 748 2.652095 TACTGGTACGTGGGCCTGC 61.652 63.158 4.53 0.00 0.00 4.85
743 749 4.778143 CTGGTACGTGGGCCTGCC 62.778 72.222 4.53 0.00 0.00 4.85
745 751 4.778143 GGTACGTGGGCCTGCCAG 62.778 72.222 10.86 3.37 37.98 4.85
755 761 3.449227 CCTGCCAGCGGACTCGTA 61.449 66.667 0.00 0.00 38.89 3.43
756 762 2.202623 CTGCCAGCGGACTCGTAC 60.203 66.667 0.00 0.00 38.89 3.67
757 763 2.986979 TGCCAGCGGACTCGTACA 60.987 61.111 0.00 0.00 38.89 2.90
758 764 2.284798 CTGCCAGCGGACTCGTACAT 62.285 60.000 0.00 0.00 38.89 2.29
759 765 1.878522 GCCAGCGGACTCGTACATG 60.879 63.158 0.00 0.00 38.89 3.21
760 766 1.226974 CCAGCGGACTCGTACATGG 60.227 63.158 0.00 0.00 38.89 3.66
761 767 1.226974 CAGCGGACTCGTACATGGG 60.227 63.158 0.00 0.00 38.89 4.00
762 768 2.585247 GCGGACTCGTACATGGGC 60.585 66.667 0.00 0.00 38.89 5.36
763 769 2.106332 CGGACTCGTACATGGGCC 59.894 66.667 0.00 0.00 0.00 5.80
764 770 2.717044 CGGACTCGTACATGGGCCA 61.717 63.158 9.61 9.61 0.00 5.36
765 771 1.144057 GGACTCGTACATGGGCCAG 59.856 63.158 13.78 6.92 0.00 4.85
766 772 1.144057 GACTCGTACATGGGCCAGG 59.856 63.158 18.06 18.06 0.00 4.45
767 773 2.203070 CTCGTACATGGGCCAGGC 60.203 66.667 19.71 1.26 0.00 4.85
779 785 4.397348 CCAGGCCTGGTTGTACAC 57.603 61.111 39.52 0.00 45.53 2.90
789 795 2.989422 GGTTGTACACCATCAACTGC 57.011 50.000 0.00 0.00 46.42 4.40
790 796 2.504367 GGTTGTACACCATCAACTGCT 58.496 47.619 0.00 0.00 46.42 4.24
791 797 2.226437 GGTTGTACACCATCAACTGCTG 59.774 50.000 0.00 0.00 46.42 4.41
792 798 2.878406 GTTGTACACCATCAACTGCTGT 59.122 45.455 0.00 0.00 40.20 4.40
793 799 2.766313 TGTACACCATCAACTGCTGTC 58.234 47.619 0.00 0.00 0.00 3.51
794 800 1.726791 GTACACCATCAACTGCTGTCG 59.273 52.381 0.00 0.00 0.00 4.35
795 801 0.392706 ACACCATCAACTGCTGTCGA 59.607 50.000 0.00 0.00 0.00 4.20
796 802 0.792640 CACCATCAACTGCTGTCGAC 59.207 55.000 9.11 9.11 0.00 4.20
797 803 0.681733 ACCATCAACTGCTGTCGACT 59.318 50.000 17.92 0.00 0.00 4.18
798 804 1.893137 ACCATCAACTGCTGTCGACTA 59.107 47.619 17.92 2.26 0.00 2.59
799 805 2.094494 ACCATCAACTGCTGTCGACTAG 60.094 50.000 17.92 14.19 0.00 2.57
800 806 2.164422 CCATCAACTGCTGTCGACTAGA 59.836 50.000 17.92 4.58 0.00 2.43
801 807 3.367395 CCATCAACTGCTGTCGACTAGAA 60.367 47.826 17.92 6.33 0.00 2.10
802 808 3.560902 TCAACTGCTGTCGACTAGAAG 57.439 47.619 17.92 17.24 0.00 2.85
803 809 2.885266 TCAACTGCTGTCGACTAGAAGT 59.115 45.455 17.92 17.85 35.52 3.01
804 810 4.070009 TCAACTGCTGTCGACTAGAAGTA 58.930 43.478 21.58 9.36 32.80 2.24
805 811 4.083431 TCAACTGCTGTCGACTAGAAGTAC 60.083 45.833 21.58 6.08 32.80 2.73
806 812 2.415857 ACTGCTGTCGACTAGAAGTACG 59.584 50.000 20.53 6.70 32.18 3.67
807 813 2.415857 CTGCTGTCGACTAGAAGTACGT 59.584 50.000 17.92 0.00 0.00 3.57
808 814 3.588955 TGCTGTCGACTAGAAGTACGTA 58.411 45.455 17.92 0.00 0.00 3.57
809 815 3.615937 TGCTGTCGACTAGAAGTACGTAG 59.384 47.826 17.92 1.90 0.00 3.51
810 816 3.862267 GCTGTCGACTAGAAGTACGTAGA 59.138 47.826 17.92 0.00 0.00 2.59
811 817 4.026640 GCTGTCGACTAGAAGTACGTAGAG 60.027 50.000 17.92 1.23 0.00 2.43
812 818 4.428209 TGTCGACTAGAAGTACGTAGAGG 58.572 47.826 17.92 0.00 0.00 3.69
813 819 4.158579 TGTCGACTAGAAGTACGTAGAGGA 59.841 45.833 17.92 0.00 0.00 3.71
814 820 4.739716 GTCGACTAGAAGTACGTAGAGGAG 59.260 50.000 8.70 0.00 0.00 3.69
815 821 4.642437 TCGACTAGAAGTACGTAGAGGAGA 59.358 45.833 0.00 0.00 0.00 3.71
816 822 5.126222 TCGACTAGAAGTACGTAGAGGAGAA 59.874 44.000 0.00 0.00 0.00 2.87
817 823 5.231991 CGACTAGAAGTACGTAGAGGAGAAC 59.768 48.000 0.00 0.00 0.00 3.01
818 824 5.427378 ACTAGAAGTACGTAGAGGAGAACC 58.573 45.833 0.00 0.00 0.00 3.62
819 825 4.298103 AGAAGTACGTAGAGGAGAACCA 57.702 45.455 0.00 0.00 38.94 3.67
820 826 4.009002 AGAAGTACGTAGAGGAGAACCAC 58.991 47.826 0.00 0.00 38.94 4.16
821 827 2.354259 AGTACGTAGAGGAGAACCACG 58.646 52.381 0.00 0.00 38.49 4.94
822 828 2.027745 AGTACGTAGAGGAGAACCACGA 60.028 50.000 0.00 0.00 36.84 4.35
823 829 1.901591 ACGTAGAGGAGAACCACGAA 58.098 50.000 0.00 0.00 36.84 3.85
824 830 1.811359 ACGTAGAGGAGAACCACGAAG 59.189 52.381 0.00 0.00 36.84 3.79
825 831 1.467713 CGTAGAGGAGAACCACGAAGC 60.468 57.143 0.00 0.00 35.88 3.86
826 832 1.135053 GTAGAGGAGAACCACGAAGCC 60.135 57.143 0.00 0.00 38.94 4.35
827 833 0.832135 AGAGGAGAACCACGAAGCCA 60.832 55.000 0.00 0.00 38.94 4.75
828 834 0.034896 GAGGAGAACCACGAAGCCAA 59.965 55.000 0.00 0.00 38.94 4.52
829 835 0.250338 AGGAGAACCACGAAGCCAAC 60.250 55.000 0.00 0.00 38.94 3.77
830 836 1.235281 GGAGAACCACGAAGCCAACC 61.235 60.000 0.00 0.00 35.97 3.77
831 837 0.534203 GAGAACCACGAAGCCAACCA 60.534 55.000 0.00 0.00 0.00 3.67
832 838 0.535102 AGAACCACGAAGCCAACCAG 60.535 55.000 0.00 0.00 0.00 4.00
833 839 0.818040 GAACCACGAAGCCAACCAGT 60.818 55.000 0.00 0.00 0.00 4.00
834 840 0.470766 AACCACGAAGCCAACCAGTA 59.529 50.000 0.00 0.00 0.00 2.74
835 841 0.034896 ACCACGAAGCCAACCAGTAG 59.965 55.000 0.00 0.00 0.00 2.57
836 842 1.298859 CCACGAAGCCAACCAGTAGC 61.299 60.000 0.00 0.00 0.00 3.58
837 843 0.320771 CACGAAGCCAACCAGTAGCT 60.321 55.000 0.00 0.00 38.88 3.32
838 844 0.320771 ACGAAGCCAACCAGTAGCTG 60.321 55.000 0.00 0.00 36.84 4.24
855 861 0.680061 CTGGTCCCCTAGGCGATAAC 59.320 60.000 2.05 0.00 0.00 1.89
868 875 2.699321 GGCGATAACCTAGGGTTTCTCT 59.301 50.000 14.81 0.00 44.33 3.10
880 887 0.038526 GTTTCTCTGTCTTCCGGCGA 60.039 55.000 9.30 0.00 0.00 5.54
899 908 2.674177 CGATAGCCGCCGGAATTTATCT 60.674 50.000 7.68 0.00 0.00 1.98
912 922 1.487482 TTTATCTTCTGATCGGCGCG 58.513 50.000 0.00 0.00 34.32 6.86
982 997 2.552743 TCTCTGTTTTTCTCTCGCGAGA 59.447 45.455 34.65 34.65 44.32 4.04
1254 1273 4.723789 ACTGTGGTATGGAGGAAGATCAAT 59.276 41.667 0.00 0.00 0.00 2.57
1390 1409 0.179097 GAAGCCCGAGAGTGTCATCC 60.179 60.000 0.00 0.00 0.00 3.51
1392 1411 0.259065 AGCCCGAGAGTGTCATCCTA 59.741 55.000 0.00 0.00 0.00 2.94
1447 1483 7.229308 TCTGCTGCCAGATAATTTTCTGATAT 58.771 34.615 22.84 0.00 44.88 1.63
1451 1487 8.786898 GCTGCCAGATAATTTTCTGATATAACA 58.213 33.333 22.84 11.82 44.88 2.41
1524 1560 4.840005 CTCCCGGCGGGCTTCTTC 62.840 72.222 39.66 0.00 43.94 2.87
1658 1705 9.886132 GAAACTCCCAATCTTCTGTTATAACTA 57.114 33.333 16.33 2.49 0.00 2.24
1676 1723 2.303600 ACTACGGTGAATTTGGCCACTA 59.696 45.455 3.88 0.00 33.99 2.74
1693 1740 0.678395 CTAGCATGAGGAGTGCGGAT 59.322 55.000 0.00 0.00 46.86 4.18
1707 1754 2.802816 GTGCGGATATGGAGTTCATGAC 59.197 50.000 0.00 0.00 37.30 3.06
2078 2125 1.421382 GCGCTTCAATGCACAACAAT 58.579 45.000 0.00 0.00 0.00 2.71
2084 2131 4.622740 GCTTCAATGCACAACAATAGAACC 59.377 41.667 0.00 0.00 0.00 3.62
2091 2138 4.887071 TGCACAACAATAGAACCAGAACTT 59.113 37.500 0.00 0.00 0.00 2.66
2097 2144 4.278419 ACAATAGAACCAGAACTTTGCCAC 59.722 41.667 0.00 0.00 0.00 5.01
2110 2157 3.357079 GCCACGGCACCAACAGAG 61.357 66.667 2.36 0.00 41.49 3.35
2120 2167 2.917933 CACCAACAGAGGAAGTGACAA 58.082 47.619 0.00 0.00 0.00 3.18
2127 2174 1.578206 GAGGAAGTGACAAAGCCGGC 61.578 60.000 21.89 21.89 0.00 6.13
2145 2196 1.295792 GCAGTTCAGGTTGTGACGAA 58.704 50.000 0.00 0.00 33.71 3.85
2149 2200 3.621268 CAGTTCAGGTTGTGACGAAAAGA 59.379 43.478 0.00 0.00 33.71 2.52
2163 2214 3.181454 ACGAAAAGACCAGTGGTGATCTT 60.181 43.478 22.50 14.25 35.25 2.40
2171 2222 0.329596 AGTGGTGATCTTGAAGGGGC 59.670 55.000 0.00 0.00 0.00 5.80
2181 2232 2.312741 TCTTGAAGGGGCAGATGGAAAT 59.687 45.455 0.00 0.00 0.00 2.17
2183 2234 1.925255 TGAAGGGGCAGATGGAAATCT 59.075 47.619 0.00 0.00 0.00 2.40
2185 2236 3.723681 TGAAGGGGCAGATGGAAATCTAT 59.276 43.478 0.00 0.00 0.00 1.98
2193 2244 6.238869 GGGCAGATGGAAATCTATCAAAGAAC 60.239 42.308 9.11 0.00 37.89 3.01
2202 2253 3.664107 TCTATCAAAGAACAAGCGTGCT 58.336 40.909 0.00 0.00 29.15 4.40
2204 2255 2.755836 TCAAAGAACAAGCGTGCTTC 57.244 45.000 3.68 3.45 40.41 3.86
2206 2257 3.462982 TCAAAGAACAAGCGTGCTTCTA 58.537 40.909 3.68 1.95 40.41 2.10
2216 2267 5.682951 CAAGCGTGCTTCTATGGAACATCA 61.683 45.833 3.68 0.00 37.35 3.07
2217 2268 7.099365 CAAGCGTGCTTCTATGGAACATCAA 62.099 44.000 3.68 0.00 37.35 2.57
2251 2302 1.064017 AGGAGAAACAAGTTGTGGGCA 60.064 47.619 9.79 0.00 0.00 5.36
2257 2308 3.525268 AACAAGTTGTGGGCAAGAAAG 57.475 42.857 9.79 0.00 34.94 2.62
2258 2309 2.456577 ACAAGTTGTGGGCAAGAAAGT 58.543 42.857 7.96 0.00 34.94 2.66
2260 2311 4.020543 ACAAGTTGTGGGCAAGAAAGTAA 58.979 39.130 7.96 0.00 34.94 2.24
2272 2323 6.446318 GGCAAGAAAGTAAATGATCACAACA 58.554 36.000 0.00 0.00 0.00 3.33
2274 2325 6.917477 GCAAGAAAGTAAATGATCACAACACA 59.083 34.615 0.00 0.00 0.00 3.72
2341 2392 1.542472 CCCCGGTTTATGTTTCACCAC 59.458 52.381 0.00 0.00 0.00 4.16
2346 2397 3.707793 GGTTTATGTTTCACCACGCAAA 58.292 40.909 0.00 0.00 0.00 3.68
2347 2398 3.487942 GGTTTATGTTTCACCACGCAAAC 59.512 43.478 0.00 0.00 33.78 2.93
2352 2403 2.094494 TGTTTCACCACGCAAACACATT 60.094 40.909 0.00 0.00 37.54 2.71
2361 2412 2.478894 ACGCAAACACATTAAGAGACCG 59.521 45.455 0.00 0.00 0.00 4.79
2367 2418 6.348540 GCAAACACATTAAGAGACCGAAGAAT 60.349 38.462 0.00 0.00 0.00 2.40
2373 2424 6.380274 ACATTAAGAGACCGAAGAATACTGGA 59.620 38.462 0.00 0.00 0.00 3.86
2375 2426 4.993029 AGAGACCGAAGAATACTGGAAG 57.007 45.455 0.00 0.00 42.29 3.46
2390 2441 3.070018 CTGGAAGTGACAAGGATGTGAC 58.930 50.000 0.00 0.00 43.12 3.67
2391 2442 2.224523 TGGAAGTGACAAGGATGTGACC 60.225 50.000 0.00 0.00 43.74 4.02
2393 2444 0.321671 AGTGACAAGGATGTGACCGG 59.678 55.000 0.00 0.00 43.74 5.28
2398 2449 0.613260 CAAGGATGTGACCGGGAAGA 59.387 55.000 6.32 0.00 34.73 2.87
2430 2481 5.221303 CCTCTCTTTTGAAAACATGGCTGAA 60.221 40.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.816204 AGCACGATCATCATCCAGAG 57.184 50.000 0.00 0.00 0.00 3.35
3 4 4.670896 TTTAGCACGATCATCATCCAGA 57.329 40.909 0.00 0.00 0.00 3.86
4 5 5.467735 TGATTTTAGCACGATCATCATCCAG 59.532 40.000 0.00 0.00 0.00 3.86
5 6 5.237127 GTGATTTTAGCACGATCATCATCCA 59.763 40.000 0.00 0.00 32.92 3.41
43 44 0.981183 TTACGGGAGTGCCAGATTGT 59.019 50.000 0.08 0.00 46.80 2.71
147 148 1.308069 GGATTGCAGCTGCCTTTCGA 61.308 55.000 34.64 13.43 41.18 3.71
417 421 4.142045 AGCATCACCAGCTCCAGA 57.858 55.556 0.00 0.00 38.01 3.86
445 449 2.254546 ACTGAACGAGAATTGTGGCA 57.745 45.000 0.00 0.00 29.05 4.92
670 675 7.263496 GGCAATTCAGAGAGCTTTATTCAAAT 58.737 34.615 0.00 0.00 0.00 2.32
709 715 2.560105 ACCAGTACACGTAGGAAAGGTC 59.440 50.000 0.00 0.00 0.00 3.85
710 716 2.601905 ACCAGTACACGTAGGAAAGGT 58.398 47.619 0.00 0.00 0.00 3.50
711 717 3.426695 CGTACCAGTACACGTAGGAAAGG 60.427 52.174 8.57 0.00 35.87 3.11
712 718 3.751621 CGTACCAGTACACGTAGGAAAG 58.248 50.000 8.57 0.00 35.87 2.62
713 719 3.829886 CGTACCAGTACACGTAGGAAA 57.170 47.619 8.57 0.00 35.87 3.13
720 726 1.444895 GCCCACGTACCAGTACACG 60.445 63.158 8.57 0.00 43.63 4.49
721 727 1.079612 GGCCCACGTACCAGTACAC 60.080 63.158 8.57 0.00 35.87 2.90
722 728 1.228956 AGGCCCACGTACCAGTACA 60.229 57.895 0.00 0.00 35.87 2.90
723 729 1.217244 CAGGCCCACGTACCAGTAC 59.783 63.158 0.00 0.00 0.00 2.73
724 730 2.652095 GCAGGCCCACGTACCAGTA 61.652 63.158 0.00 0.00 0.00 2.74
725 731 4.016706 GCAGGCCCACGTACCAGT 62.017 66.667 0.00 0.00 0.00 4.00
726 732 4.778143 GGCAGGCCCACGTACCAG 62.778 72.222 0.00 0.00 0.00 4.00
728 734 4.778143 CTGGCAGGCCCACGTACC 62.778 72.222 6.61 0.00 39.18 3.34
738 744 3.449227 TACGAGTCCGCTGGCAGG 61.449 66.667 17.64 6.32 39.95 4.85
739 745 2.202623 GTACGAGTCCGCTGGCAG 60.203 66.667 10.94 10.94 39.95 4.85
740 746 2.348104 ATGTACGAGTCCGCTGGCA 61.348 57.895 0.00 0.00 39.95 4.92
741 747 1.878522 CATGTACGAGTCCGCTGGC 60.879 63.158 0.00 0.00 39.95 4.85
742 748 1.226974 CCATGTACGAGTCCGCTGG 60.227 63.158 0.00 0.00 39.95 4.85
743 749 1.226974 CCCATGTACGAGTCCGCTG 60.227 63.158 0.00 0.00 39.95 5.18
744 750 3.077519 GCCCATGTACGAGTCCGCT 62.078 63.158 0.00 0.00 39.95 5.52
745 751 2.585247 GCCCATGTACGAGTCCGC 60.585 66.667 0.00 0.00 39.95 5.54
746 752 2.106332 GGCCCATGTACGAGTCCG 59.894 66.667 0.00 0.00 42.50 4.79
747 753 1.144057 CTGGCCCATGTACGAGTCC 59.856 63.158 0.00 0.00 0.00 3.85
748 754 1.144057 CCTGGCCCATGTACGAGTC 59.856 63.158 0.00 0.00 0.00 3.36
749 755 3.031417 GCCTGGCCCATGTACGAGT 62.031 63.158 7.66 0.00 0.00 4.18
750 756 2.203070 GCCTGGCCCATGTACGAG 60.203 66.667 7.66 0.00 0.00 4.18
751 757 3.792736 GGCCTGGCCCATGTACGA 61.793 66.667 27.77 0.00 44.06 3.43
778 784 0.681733 AGTCGACAGCAGTTGATGGT 59.318 50.000 19.50 0.00 40.21 3.55
779 785 2.164422 TCTAGTCGACAGCAGTTGATGG 59.836 50.000 19.50 0.00 40.21 3.51
780 786 3.494045 TCTAGTCGACAGCAGTTGATG 57.506 47.619 19.50 0.00 40.21 3.07
781 787 3.508012 ACTTCTAGTCGACAGCAGTTGAT 59.492 43.478 19.50 0.00 40.21 2.57
782 788 2.885266 ACTTCTAGTCGACAGCAGTTGA 59.115 45.455 19.50 0.00 35.78 3.18
783 789 3.290308 ACTTCTAGTCGACAGCAGTTG 57.710 47.619 19.50 10.60 0.00 3.16
784 790 3.120269 CGTACTTCTAGTCGACAGCAGTT 60.120 47.826 19.50 0.00 0.00 3.16
785 791 2.415857 CGTACTTCTAGTCGACAGCAGT 59.584 50.000 19.50 18.73 0.00 4.40
786 792 2.415857 ACGTACTTCTAGTCGACAGCAG 59.584 50.000 19.50 14.31 0.00 4.24
787 793 2.420642 ACGTACTTCTAGTCGACAGCA 58.579 47.619 19.50 2.92 0.00 4.41
788 794 3.862267 TCTACGTACTTCTAGTCGACAGC 59.138 47.826 19.50 0.00 0.00 4.40
789 795 4.503734 CCTCTACGTACTTCTAGTCGACAG 59.496 50.000 19.50 12.94 0.00 3.51
790 796 4.158579 TCCTCTACGTACTTCTAGTCGACA 59.841 45.833 19.50 2.84 0.00 4.35
791 797 4.677584 TCCTCTACGTACTTCTAGTCGAC 58.322 47.826 7.70 7.70 0.00 4.20
792 798 4.642437 TCTCCTCTACGTACTTCTAGTCGA 59.358 45.833 0.00 0.00 0.00 4.20
793 799 4.930963 TCTCCTCTACGTACTTCTAGTCG 58.069 47.826 0.00 0.00 0.00 4.18
794 800 5.523552 GGTTCTCCTCTACGTACTTCTAGTC 59.476 48.000 0.00 0.00 0.00 2.59
795 801 5.046014 TGGTTCTCCTCTACGTACTTCTAGT 60.046 44.000 0.00 0.00 34.23 2.57
796 802 5.294060 GTGGTTCTCCTCTACGTACTTCTAG 59.706 48.000 0.00 0.00 34.23 2.43
797 803 5.181748 GTGGTTCTCCTCTACGTACTTCTA 58.818 45.833 0.00 0.00 34.23 2.10
798 804 4.009002 GTGGTTCTCCTCTACGTACTTCT 58.991 47.826 0.00 0.00 34.23 2.85
799 805 3.181512 CGTGGTTCTCCTCTACGTACTTC 60.182 52.174 0.00 0.00 34.23 3.01
800 806 2.746362 CGTGGTTCTCCTCTACGTACTT 59.254 50.000 0.00 0.00 34.23 2.24
801 807 2.027745 TCGTGGTTCTCCTCTACGTACT 60.028 50.000 0.00 0.00 33.99 2.73
802 808 2.350522 TCGTGGTTCTCCTCTACGTAC 58.649 52.381 0.00 0.00 33.99 3.67
803 809 2.768253 TCGTGGTTCTCCTCTACGTA 57.232 50.000 0.00 0.00 33.99 3.57
804 810 1.811359 CTTCGTGGTTCTCCTCTACGT 59.189 52.381 0.00 0.00 33.99 3.57
805 811 1.467713 GCTTCGTGGTTCTCCTCTACG 60.468 57.143 0.00 0.00 33.72 3.51
806 812 1.135053 GGCTTCGTGGTTCTCCTCTAC 60.135 57.143 0.00 0.00 34.23 2.59
807 813 1.183549 GGCTTCGTGGTTCTCCTCTA 58.816 55.000 0.00 0.00 34.23 2.43
808 814 0.832135 TGGCTTCGTGGTTCTCCTCT 60.832 55.000 0.00 0.00 34.23 3.69
809 815 0.034896 TTGGCTTCGTGGTTCTCCTC 59.965 55.000 0.00 0.00 34.23 3.71
810 816 0.250338 GTTGGCTTCGTGGTTCTCCT 60.250 55.000 0.00 0.00 34.23 3.69
811 817 1.235281 GGTTGGCTTCGTGGTTCTCC 61.235 60.000 0.00 0.00 0.00 3.71
812 818 0.534203 TGGTTGGCTTCGTGGTTCTC 60.534 55.000 0.00 0.00 0.00 2.87
813 819 0.535102 CTGGTTGGCTTCGTGGTTCT 60.535 55.000 0.00 0.00 0.00 3.01
814 820 0.818040 ACTGGTTGGCTTCGTGGTTC 60.818 55.000 0.00 0.00 0.00 3.62
815 821 0.470766 TACTGGTTGGCTTCGTGGTT 59.529 50.000 0.00 0.00 0.00 3.67
816 822 0.034896 CTACTGGTTGGCTTCGTGGT 59.965 55.000 0.00 0.00 0.00 4.16
817 823 1.298859 GCTACTGGTTGGCTTCGTGG 61.299 60.000 0.00 0.00 0.00 4.94
818 824 0.320771 AGCTACTGGTTGGCTTCGTG 60.321 55.000 0.00 0.00 31.81 4.35
819 825 0.320771 CAGCTACTGGTTGGCTTCGT 60.321 55.000 0.00 0.00 33.74 3.85
820 826 1.021390 CCAGCTACTGGTTGGCTTCG 61.021 60.000 5.43 0.00 45.82 3.79
821 827 2.859992 CCAGCTACTGGTTGGCTTC 58.140 57.895 5.43 0.00 45.82 3.86
836 842 5.667556 TAGGTTATCGCCTAGGGGACCAG 62.668 56.522 29.21 0.80 45.98 4.00
837 843 3.843926 TAGGTTATCGCCTAGGGGACCA 61.844 54.545 29.21 17.72 45.98 4.02
838 844 1.203100 TAGGTTATCGCCTAGGGGACC 60.203 57.143 29.21 24.80 44.68 4.46
839 845 2.299326 TAGGTTATCGCCTAGGGGAC 57.701 55.000 29.21 17.59 39.84 4.46
855 861 2.166664 CGGAAGACAGAGAAACCCTAGG 59.833 54.545 0.06 0.06 0.00 3.02
880 887 3.008049 AGAAGATAAATTCCGGCGGCTAT 59.992 43.478 23.83 14.40 0.00 2.97
899 908 3.411418 GAGACCGCGCCGATCAGAA 62.411 63.158 0.00 0.00 0.00 3.02
949 962 0.394565 AACAGAGATAGCGATGGCCC 59.605 55.000 0.00 0.00 41.24 5.80
982 997 2.346529 CATCCCCAGATCCAATCTCCT 58.653 52.381 0.00 0.00 37.58 3.69
1067 1083 1.751924 CCTCCTCCTCCTGTAAGTTCG 59.248 57.143 0.00 0.00 0.00 3.95
1180 1196 0.464036 CCGTACAGAGCATTAGGGCA 59.536 55.000 0.00 0.00 35.83 5.36
1239 1258 7.986704 ACAGATTATCATTGATCTTCCTCCAT 58.013 34.615 1.55 0.00 30.43 3.41
1254 1273 5.241403 ACTGGGTTGTGAACAGATTATCA 57.759 39.130 0.00 0.00 36.17 2.15
1309 1328 1.427072 AACAACCAGGGTCCCTCCAG 61.427 60.000 7.76 2.18 38.11 3.86
1390 1409 2.352814 CCCAGACCGACAACTTGTCTAG 60.353 54.545 17.81 12.12 44.85 2.43
1392 1411 0.393077 CCCAGACCGACAACTTGTCT 59.607 55.000 17.81 2.31 44.85 3.41
1399 1418 1.533033 TCTGAGCCCAGACCGACAA 60.533 57.895 0.00 0.00 44.01 3.18
1447 1483 1.080638 AACCCCCTGATTGCCTGTTA 58.919 50.000 0.00 0.00 0.00 2.41
1451 1487 2.772924 CCAACCCCCTGATTGCCT 59.227 61.111 0.00 0.00 0.00 4.75
1456 1492 2.610859 AGACGCCAACCCCCTGAT 60.611 61.111 0.00 0.00 0.00 2.90
1658 1705 1.821216 CTAGTGGCCAAATTCACCGT 58.179 50.000 7.24 0.00 34.67 4.83
1676 1723 1.001746 CATATCCGCACTCCTCATGCT 59.998 52.381 0.00 0.00 41.10 3.79
1693 1740 3.130516 GTGGACTCGTCATGAACTCCATA 59.869 47.826 12.61 0.00 36.41 2.74
1707 1754 1.812571 CCCCATTCAAAAGTGGACTCG 59.187 52.381 0.00 0.00 37.72 4.18
2068 2115 4.460263 AGTTCTGGTTCTATTGTTGTGCA 58.540 39.130 0.00 0.00 0.00 4.57
2069 2116 5.438761 AAGTTCTGGTTCTATTGTTGTGC 57.561 39.130 0.00 0.00 0.00 4.57
2070 2117 5.687285 GCAAAGTTCTGGTTCTATTGTTGTG 59.313 40.000 0.00 0.00 0.00 3.33
2071 2118 5.221244 GGCAAAGTTCTGGTTCTATTGTTGT 60.221 40.000 0.00 0.00 0.00 3.32
2078 2125 2.489971 CGTGGCAAAGTTCTGGTTCTA 58.510 47.619 0.00 0.00 0.00 2.10
2097 2144 1.071471 ACTTCCTCTGTTGGTGCCG 59.929 57.895 0.00 0.00 0.00 5.69
2110 2157 1.856265 CTGCCGGCTTTGTCACTTCC 61.856 60.000 29.70 0.00 0.00 3.46
2120 2167 1.898574 CAACCTGAACTGCCGGCTT 60.899 57.895 29.70 15.25 0.00 4.35
2127 2174 3.621268 TCTTTTCGTCACAACCTGAACTG 59.379 43.478 0.00 0.00 0.00 3.16
2145 2196 4.392940 CTTCAAGATCACCACTGGTCTTT 58.607 43.478 0.00 0.00 44.24 2.52
2149 2200 1.352352 CCCTTCAAGATCACCACTGGT 59.648 52.381 0.00 0.00 35.62 4.00
2163 2214 1.925255 AGATTTCCATCTGCCCCTTCA 59.075 47.619 0.00 0.00 38.44 3.02
2171 2222 7.914346 GCTTGTTCTTTGATAGATTTCCATCTG 59.086 37.037 0.00 0.00 40.28 2.90
2181 2232 3.664107 AGCACGCTTGTTCTTTGATAGA 58.336 40.909 0.00 0.00 0.00 1.98
2183 2234 4.065088 AGAAGCACGCTTGTTCTTTGATA 58.935 39.130 9.42 0.00 36.26 2.15
2185 2236 2.288666 AGAAGCACGCTTGTTCTTTGA 58.711 42.857 9.42 0.00 36.26 2.69
2193 2244 2.076100 TGTTCCATAGAAGCACGCTTG 58.924 47.619 9.42 0.00 36.26 4.01
2202 2253 3.010027 TGCTGGGTTGATGTTCCATAGAA 59.990 43.478 0.00 0.00 0.00 2.10
2204 2255 3.003394 TGCTGGGTTGATGTTCCATAG 57.997 47.619 0.00 0.00 0.00 2.23
2206 2257 2.537633 ATGCTGGGTTGATGTTCCAT 57.462 45.000 0.00 0.00 0.00 3.41
2216 2267 3.051940 TCTCCTCTGATATGCTGGGTT 57.948 47.619 0.00 0.00 0.00 4.11
2217 2268 2.783379 TCTCCTCTGATATGCTGGGT 57.217 50.000 0.00 0.00 0.00 4.51
2220 2271 5.426504 ACTTGTTTCTCCTCTGATATGCTG 58.573 41.667 0.00 0.00 0.00 4.41
2225 2276 5.513094 CCCACAACTTGTTTCTCCTCTGATA 60.513 44.000 0.00 0.00 0.00 2.15
2226 2277 4.392940 CCACAACTTGTTTCTCCTCTGAT 58.607 43.478 0.00 0.00 0.00 2.90
2251 2302 7.255590 CCCTGTGTTGTGATCATTTACTTTCTT 60.256 37.037 0.00 0.00 0.00 2.52
2257 2308 3.119495 GCCCCTGTGTTGTGATCATTTAC 60.119 47.826 0.00 0.00 0.00 2.01
2258 2309 3.088532 GCCCCTGTGTTGTGATCATTTA 58.911 45.455 0.00 0.00 0.00 1.40
2260 2311 1.549203 GCCCCTGTGTTGTGATCATT 58.451 50.000 0.00 0.00 0.00 2.57
2272 2323 3.031417 GCACTATGACCGCCCCTGT 62.031 63.158 0.00 0.00 0.00 4.00
2274 2325 3.849951 CGCACTATGACCGCCCCT 61.850 66.667 0.00 0.00 0.00 4.79
2322 2373 1.198178 CGTGGTGAAACATAAACCGGG 59.802 52.381 6.32 0.00 39.98 5.73
2328 2379 3.128764 TGTGTTTGCGTGGTGAAACATAA 59.871 39.130 0.00 0.00 42.43 1.90
2341 2392 2.734606 TCGGTCTCTTAATGTGTTTGCG 59.265 45.455 0.00 0.00 0.00 4.85
2346 2397 7.036220 CAGTATTCTTCGGTCTCTTAATGTGT 58.964 38.462 0.00 0.00 0.00 3.72
2347 2398 6.477033 CCAGTATTCTTCGGTCTCTTAATGTG 59.523 42.308 0.00 0.00 0.00 3.21
2352 2403 5.950549 ACTTCCAGTATTCTTCGGTCTCTTA 59.049 40.000 0.00 0.00 0.00 2.10
2361 2412 5.794894 TCCTTGTCACTTCCAGTATTCTTC 58.205 41.667 0.00 0.00 0.00 2.87
2367 2418 3.901222 TCACATCCTTGTCACTTCCAGTA 59.099 43.478 0.00 0.00 32.34 2.74
2373 2424 1.270839 CCGGTCACATCCTTGTCACTT 60.271 52.381 0.00 0.00 32.34 3.16
2375 2426 0.673644 CCCGGTCACATCCTTGTCAC 60.674 60.000 0.00 0.00 32.34 3.67
2376 2427 0.834261 TCCCGGTCACATCCTTGTCA 60.834 55.000 0.00 0.00 32.34 3.58
2377 2428 0.323629 TTCCCGGTCACATCCTTGTC 59.676 55.000 0.00 0.00 32.34 3.18
2378 2429 0.324943 CTTCCCGGTCACATCCTTGT 59.675 55.000 0.00 0.00 36.15 3.16
2379 2430 0.613260 TCTTCCCGGTCACATCCTTG 59.387 55.000 0.00 0.00 0.00 3.61
2381 2432 0.978146 CCTCTTCCCGGTCACATCCT 60.978 60.000 0.00 0.00 0.00 3.24
2382 2433 1.522569 CCTCTTCCCGGTCACATCC 59.477 63.158 0.00 0.00 0.00 3.51
2383 2434 0.976073 TCCCTCTTCCCGGTCACATC 60.976 60.000 0.00 0.00 0.00 3.06
2384 2435 0.978146 CTCCCTCTTCCCGGTCACAT 60.978 60.000 0.00 0.00 0.00 3.21
2385 2436 1.609501 CTCCCTCTTCCCGGTCACA 60.610 63.158 0.00 0.00 0.00 3.58
2386 2437 1.605971 GACTCCCTCTTCCCGGTCAC 61.606 65.000 0.00 0.00 0.00 3.67
2390 2441 2.764547 GGGACTCCCTCTTCCCGG 60.765 72.222 6.90 0.00 42.35 5.73
2430 2481 1.846007 TGGTTGGTGTTGCTTCACTT 58.154 45.000 10.53 0.00 38.28 3.16


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

AutoCloner maintained by Alex Coulton.