Multiple sequence alignment - TraesCS3A01G082400

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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 TraesCS3A01G082400 chr3A 100.000 2663 0 0 1 2663 53258332 53255670 0.000000e+00 4918
1 TraesCS3A01G082400 chr3A 92.308 78 4 2 2587 2663 641571336 641571260 2.800000e-20 110
2 TraesCS3A01G082400 chr3B 91.607 1120 50 18 782 1879 65269657 65268560 0.000000e+00 1507
3 TraesCS3A01G082400 chr3B 90.566 530 41 6 2081 2610 65241110 65240590 0.000000e+00 693
4 TraesCS3A01G082400 chr3B 91.667 204 12 5 1885 2085 65267803 65267602 7.260000e-71 278
5 TraesCS3A01G082400 chr3B 81.967 244 42 2 1 243 161685448 161685206 3.470000e-49 206
6 TraesCS3A01G082400 chr3B 94.203 69 4 0 2594 2662 705230159 705230091 3.630000e-19 106
7 TraesCS3A01G082400 chr3D 94.790 883 31 6 810 1691 41746819 41745951 0.000000e+00 1362
8 TraesCS3A01G082400 chr3D 90.899 934 56 9 1699 2610 41745898 41744972 0.000000e+00 1227
9 TraesCS3A01G082400 chr3D 77.147 652 124 13 1 629 110483825 110483176 3.260000e-94 355
10 TraesCS3A01G082400 chr3D 84.817 191 27 2 2009 2198 39532558 39532369 9.730000e-45 191
11 TraesCS3A01G082400 chr2B 90.164 671 62 3 998 1666 705348853 705348185 0.000000e+00 870
12 TraesCS3A01G082400 chr2B 88.262 673 71 7 998 1666 705357427 705358095 0.000000e+00 798
13 TraesCS3A01G082400 chr2A 90.149 670 60 5 998 1664 718965661 718964995 0.000000e+00 867
14 TraesCS3A01G082400 chr2A 88.889 675 72 3 994 1666 718975857 718976530 0.000000e+00 828
15 TraesCS3A01G082400 chr2A 95.714 70 0 3 2594 2663 355168092 355168026 2.800000e-20 110
16 TraesCS3A01G082400 chr2A 94.444 72 2 1 2592 2661 776010983 776010912 2.800000e-20 110
17 TraesCS3A01G082400 chr2A 86.957 92 7 5 2571 2662 607445255 607445169 6.070000e-17 99
18 TraesCS3A01G082400 chr2D 89.137 672 67 5 998 1666 584858568 584857900 0.000000e+00 832
19 TraesCS3A01G082400 chr2D 88.563 682 72 6 987 1664 584867298 584867977 0.000000e+00 822
20 TraesCS3A01G082400 chr2D 78.571 728 125 13 1 706 605296194 605296912 4.040000e-123 451
21 TraesCS3A01G082400 chr2D 80.978 184 28 6 1454 1635 568229377 568229555 3.570000e-29 139
22 TraesCS3A01G082400 chr2D 91.026 78 5 1 2586 2663 45588459 45588534 1.300000e-18 104
23 TraesCS3A01G082400 chr4D 80.110 729 111 12 1 706 480817287 480816570 1.830000e-141 512
24 TraesCS3A01G082400 chr4D 95.714 70 1 2 2596 2663 479284587 479284518 7.790000e-21 111
25 TraesCS3A01G082400 chr1D 78.022 728 128 21 1 706 435267327 435268044 1.890000e-116 429
26 TraesCS3A01G082400 chr1D 82.222 270 39 4 10 279 418650721 418650461 9.590000e-55 224
27 TraesCS3A01G082400 chr1D 83.444 151 24 1 2033 2182 156123362 156123212 3.570000e-29 139
28 TraesCS3A01G082400 chr1D 97.015 67 1 1 2597 2663 159236524 159236589 7.790000e-21 111
29 TraesCS3A01G082400 chr7A 78.809 571 98 6 158 706 547759899 547759330 1.950000e-96 363
30 TraesCS3A01G082400 chr7B 75.862 696 141 20 1 679 2734895 2735580 1.980000e-86 329
31 TraesCS3A01G082400 chr6A 76.804 582 120 11 145 715 4130384 4130961 1.990000e-81 313
32 TraesCS3A01G082400 chr6A 76.804 582 120 11 145 715 4230807 4231384 1.990000e-81 313
33 TraesCS3A01G082400 chr6A 76.632 582 121 11 145 715 4206010 4206587 9.260000e-80 307
34 TraesCS3A01G082400 chr1B 74.079 706 154 24 1 702 466941303 466940623 2.030000e-66 263
35 TraesCS3A01G082400 chr1B 83.041 171 25 4 2033 2201 250414404 250414236 4.590000e-33 152
36 TraesCS3A01G082400 chr6B 77.162 451 89 10 1 450 213641216 213641653 1.580000e-62 250
37 TraesCS3A01G082400 chr7D 80.247 243 43 4 1999 2237 56512851 56512610 7.580000e-41 178
38 TraesCS3A01G082400 chr7D 80.889 225 39 3 1999 2220 56496508 56496285 9.800000e-40 174
39 TraesCS3A01G082400 chr7D 87.395 119 13 2 2015 2132 56588267 56588150 4.620000e-28 135
40 TraesCS3A01G082400 chr5B 76.797 306 53 8 1916 2206 356715670 356715972 3.550000e-34 156
41 TraesCS3A01G082400 chr5D 85.235 149 22 0 1 149 63093013 63092865 1.280000e-33 154
42 TraesCS3A01G082400 chr5D 81.208 149 25 3 1985 2132 333399608 333399462 1.670000e-22 117
43 TraesCS3A01G082400 chr1A 92.105 76 3 3 2586 2661 99960967 99960895 1.300000e-18 104


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 TraesCS3A01G082400 chr3A 53255670 53258332 2662 True 4918.0 4918 100.0000 1 2663 1 chr3A.!!$R1 2662
1 TraesCS3A01G082400 chr3B 65267602 65269657 2055 True 892.5 1507 91.6370 782 2085 2 chr3B.!!$R4 1303
2 TraesCS3A01G082400 chr3B 65240590 65241110 520 True 693.0 693 90.5660 2081 2610 1 chr3B.!!$R1 529
3 TraesCS3A01G082400 chr3D 41744972 41746819 1847 True 1294.5 1362 92.8445 810 2610 2 chr3D.!!$R3 1800
4 TraesCS3A01G082400 chr3D 110483176 110483825 649 True 355.0 355 77.1470 1 629 1 chr3D.!!$R2 628
5 TraesCS3A01G082400 chr2B 705348185 705348853 668 True 870.0 870 90.1640 998 1666 1 chr2B.!!$R1 668
6 TraesCS3A01G082400 chr2B 705357427 705358095 668 False 798.0 798 88.2620 998 1666 1 chr2B.!!$F1 668
7 TraesCS3A01G082400 chr2A 718964995 718965661 666 True 867.0 867 90.1490 998 1664 1 chr2A.!!$R3 666
8 TraesCS3A01G082400 chr2A 718975857 718976530 673 False 828.0 828 88.8890 994 1666 1 chr2A.!!$F1 672
9 TraesCS3A01G082400 chr2D 584857900 584858568 668 True 832.0 832 89.1370 998 1666 1 chr2D.!!$R1 668
10 TraesCS3A01G082400 chr2D 584867298 584867977 679 False 822.0 822 88.5630 987 1664 1 chr2D.!!$F3 677
11 TraesCS3A01G082400 chr2D 605296194 605296912 718 False 451.0 451 78.5710 1 706 1 chr2D.!!$F4 705
12 TraesCS3A01G082400 chr4D 480816570 480817287 717 True 512.0 512 80.1100 1 706 1 chr4D.!!$R2 705
13 TraesCS3A01G082400 chr1D 435267327 435268044 717 False 429.0 429 78.0220 1 706 1 chr1D.!!$F2 705
14 TraesCS3A01G082400 chr7A 547759330 547759899 569 True 363.0 363 78.8090 158 706 1 chr7A.!!$R1 548
15 TraesCS3A01G082400 chr7B 2734895 2735580 685 False 329.0 329 75.8620 1 679 1 chr7B.!!$F1 678
16 TraesCS3A01G082400 chr6A 4130384 4130961 577 False 313.0 313 76.8040 145 715 1 chr6A.!!$F1 570
17 TraesCS3A01G082400 chr6A 4230807 4231384 577 False 313.0 313 76.8040 145 715 1 chr6A.!!$F3 570
18 TraesCS3A01G082400 chr6A 4206010 4206587 577 False 307.0 307 76.6320 145 715 1 chr6A.!!$F2 570
19 TraesCS3A01G082400 chr1B 466940623 466941303 680 True 263.0 263 74.0790 1 702 1 chr1B.!!$R2 701

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
761 835 0.10104 TGCGCTGATGCATTTAAGGC 59.899 50.0 9.73 2.16 40.62 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2948 0.106268 TGGGCAGTGAAAGGCAAGAA 60.106 50.0 0.0 0.0 0.0 2.52 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
41 42 0.537188 AATGGGCGTCATCTTCGAGT 59.463 50.000 0.00 0.00 34.44 4.18
44 45 2.224885 GGCGTCATCTTCGAGTCGC 61.225 63.158 7.92 5.67 42.32 5.19
152 154 4.668118 GGCGGGGAAACGTCGTGA 62.668 66.667 0.00 0.00 35.98 4.35
155 157 1.080366 CGGGGAAACGTCGTGATCA 60.080 57.895 0.00 0.00 0.00 2.92
205 207 2.844451 GCTCCAGCGCAAACCAACA 61.844 57.895 11.47 0.00 0.00 3.33
244 246 3.254654 CGCGTAGGCACACATCGG 61.255 66.667 8.32 0.00 39.92 4.18
263 265 1.079819 GCGCTGCTCCAGTGTAAGA 60.080 57.895 0.00 0.00 43.09 2.10
267 269 1.731720 CTGCTCCAGTGTAAGAAGCC 58.268 55.000 0.00 0.00 0.00 4.35
339 346 2.595095 GAATGGGGATCCGGTGCA 59.405 61.111 5.45 0.00 35.24 4.57
354 361 0.895100 GTGCAGGTCCAGATGCCAAA 60.895 55.000 0.00 0.00 41.85 3.28
355 362 0.178967 TGCAGGTCCAGATGCCAAAA 60.179 50.000 0.00 0.00 41.85 2.44
373 380 1.032014 AAGTGCGGCAACTTGACATT 58.968 45.000 3.23 0.00 38.95 2.71
388 395 2.575735 TGACATTTGGATACTGCAGGGA 59.424 45.455 19.93 5.78 37.61 4.20
402 409 3.001406 GGGACCGGTGGTACTGCT 61.001 66.667 14.63 0.00 36.61 4.24
481 497 2.882876 GCGTCTAGCCGGTGAAGA 59.117 61.111 1.90 0.24 40.81 2.87
489 514 1.302511 GCCGGTGAAGAAGGAAGCA 60.303 57.895 1.90 0.00 0.00 3.91
493 518 1.538047 GGTGAAGAAGGAAGCATGCA 58.462 50.000 21.98 0.00 0.00 3.96
505 530 1.153489 GCATGCAGGAAGAGCTCGA 60.153 57.895 14.21 0.00 0.00 4.04
521 546 1.081376 CGAGTCGACGCTGAACCTT 60.081 57.895 17.32 0.00 0.00 3.50
529 554 1.374947 CGCTGAACCTTCCCTTCCA 59.625 57.895 0.00 0.00 0.00 3.53
556 588 2.284190 GCTGAAGAAGTCCATGGCTAC 58.716 52.381 6.96 0.21 0.00 3.58
563 616 0.911525 AGTCCATGGCTACTGGCTGT 60.912 55.000 6.96 1.74 41.46 4.40
606 676 0.315568 GACGAGAGAGCAAGTGTGGT 59.684 55.000 0.00 0.00 38.47 4.16
607 677 0.753262 ACGAGAGAGCAAGTGTGGTT 59.247 50.000 0.00 0.00 35.00 3.67
618 688 3.738982 CAAGTGTGGTTAGATGTGGACA 58.261 45.455 0.00 0.00 0.00 4.02
630 701 1.741028 TGTGGACAGGGAGATGGAAA 58.259 50.000 0.00 0.00 0.00 3.13
645 716 2.516930 AAATGGATGAGGCCGGCG 60.517 61.111 22.54 0.00 0.00 6.46
680 754 4.447138 TCATTAAAAGGGACGGGCATAT 57.553 40.909 0.00 0.00 0.00 1.78
706 780 2.421314 CACACACTGTCAGGCGGA 59.579 61.111 4.53 0.00 0.00 5.54
714 788 4.268687 GTCAGGCGGACACTGAAG 57.731 61.111 13.03 0.00 45.66 3.02
715 789 1.374758 GTCAGGCGGACACTGAAGG 60.375 63.158 13.03 0.00 45.66 3.46
716 790 2.046892 CAGGCGGACACTGAAGGG 60.047 66.667 0.00 0.00 38.20 3.95
717 791 2.203788 AGGCGGACACTGAAGGGA 60.204 61.111 0.00 0.00 0.00 4.20
718 792 1.613630 AGGCGGACACTGAAGGGAT 60.614 57.895 0.00 0.00 0.00 3.85
719 793 0.325296 AGGCGGACACTGAAGGGATA 60.325 55.000 0.00 0.00 0.00 2.59
720 794 0.179081 GGCGGACACTGAAGGGATAC 60.179 60.000 0.00 0.00 0.00 2.24
721 795 0.527817 GCGGACACTGAAGGGATACG 60.528 60.000 0.00 0.00 37.60 3.06
722 796 0.527817 CGGACACTGAAGGGATACGC 60.528 60.000 0.00 0.00 37.60 4.42
723 797 0.527817 GGACACTGAAGGGATACGCG 60.528 60.000 3.53 3.53 37.60 6.01
724 798 0.454600 GACACTGAAGGGATACGCGA 59.545 55.000 15.93 0.00 37.60 5.87
725 799 0.172803 ACACTGAAGGGATACGCGAC 59.827 55.000 15.93 3.33 37.60 5.19
726 800 0.866061 CACTGAAGGGATACGCGACG 60.866 60.000 15.93 0.00 37.60 5.12
727 801 1.944676 CTGAAGGGATACGCGACGC 60.945 63.158 15.93 10.49 37.60 5.19
742 816 2.622085 CGCGTCCGTTTCGTGTTT 59.378 55.556 0.00 0.00 34.71 2.83
743 817 1.716378 CGCGTCCGTTTCGTGTTTG 60.716 57.895 0.00 0.00 34.71 2.93
744 818 2.001880 GCGTCCGTTTCGTGTTTGC 61.002 57.895 0.00 0.00 0.00 3.68
745 819 1.716378 CGTCCGTTTCGTGTTTGCG 60.716 57.895 0.00 0.00 0.00 4.85
746 820 2.001880 GTCCGTTTCGTGTTTGCGC 61.002 57.895 0.00 0.00 0.00 6.09
747 821 2.174969 TCCGTTTCGTGTTTGCGCT 61.175 52.632 9.73 0.00 0.00 5.92
748 822 2.003443 CCGTTTCGTGTTTGCGCTG 61.003 57.895 9.73 0.00 0.00 5.18
749 823 1.011684 CGTTTCGTGTTTGCGCTGA 60.012 52.632 9.73 0.00 0.00 4.26
750 824 0.384230 CGTTTCGTGTTTGCGCTGAT 60.384 50.000 9.73 0.00 0.00 2.90
751 825 1.044725 GTTTCGTGTTTGCGCTGATG 58.955 50.000 9.73 0.00 0.00 3.07
752 826 0.660005 TTTCGTGTTTGCGCTGATGC 60.660 50.000 9.73 0.00 0.00 3.91
753 827 1.780025 TTCGTGTTTGCGCTGATGCA 61.780 50.000 9.73 0.00 44.61 3.96
754 828 1.154169 CGTGTTTGCGCTGATGCAT 60.154 52.632 9.73 0.00 45.78 3.96
755 829 0.730155 CGTGTTTGCGCTGATGCATT 60.730 50.000 9.73 0.00 45.78 3.56
756 830 1.421382 GTGTTTGCGCTGATGCATTT 58.579 45.000 9.73 0.00 45.78 2.32
757 831 2.594321 GTGTTTGCGCTGATGCATTTA 58.406 42.857 9.73 0.00 45.78 1.40
758 832 2.985809 GTGTTTGCGCTGATGCATTTAA 59.014 40.909 9.73 0.00 45.78 1.52
759 833 3.059834 GTGTTTGCGCTGATGCATTTAAG 59.940 43.478 9.73 0.32 45.78 1.85
760 834 2.565210 TTGCGCTGATGCATTTAAGG 57.435 45.000 9.73 0.00 45.78 2.69
761 835 0.101040 TGCGCTGATGCATTTAAGGC 59.899 50.000 9.73 2.16 40.62 4.35
762 836 0.595825 GCGCTGATGCATTTAAGGCC 60.596 55.000 0.00 0.00 39.64 5.19
763 837 1.027357 CGCTGATGCATTTAAGGCCT 58.973 50.000 0.00 0.00 39.64 5.19
764 838 2.221169 CGCTGATGCATTTAAGGCCTA 58.779 47.619 5.16 0.00 39.64 3.93
765 839 2.618241 CGCTGATGCATTTAAGGCCTAA 59.382 45.455 5.16 0.00 39.64 2.69
766 840 3.066621 CGCTGATGCATTTAAGGCCTAAA 59.933 43.478 5.16 7.79 39.64 1.85
767 841 4.261741 CGCTGATGCATTTAAGGCCTAAAT 60.262 41.667 5.16 9.90 40.24 1.40
768 842 5.604565 GCTGATGCATTTAAGGCCTAAATT 58.395 37.500 5.16 0.00 38.00 1.82
769 843 6.051074 GCTGATGCATTTAAGGCCTAAATTT 58.949 36.000 5.16 0.00 38.00 1.82
770 844 6.018507 GCTGATGCATTTAAGGCCTAAATTTG 60.019 38.462 5.16 1.60 38.00 2.32
771 845 6.347696 TGATGCATTTAAGGCCTAAATTTGG 58.652 36.000 5.16 0.00 38.00 3.28
772 846 5.096443 TGCATTTAAGGCCTAAATTTGGG 57.904 39.130 15.89 15.89 38.00 4.12
773 847 4.534103 TGCATTTAAGGCCTAAATTTGGGT 59.466 37.500 20.43 5.09 38.00 4.51
774 848 5.116180 GCATTTAAGGCCTAAATTTGGGTC 58.884 41.667 16.84 16.84 38.00 4.46
775 849 5.670485 CATTTAAGGCCTAAATTTGGGTCC 58.330 41.667 20.39 19.89 38.00 4.46
776 850 4.405756 TTAAGGCCTAAATTTGGGTCCA 57.594 40.909 25.07 12.71 33.34 4.02
777 851 3.268034 AAGGCCTAAATTTGGGTCCAA 57.732 42.857 25.07 0.00 33.34 3.53
790 864 1.173043 GGTCCAAAATGCATCGTCCA 58.827 50.000 0.00 0.00 0.00 4.02
791 865 1.133025 GGTCCAAAATGCATCGTCCAG 59.867 52.381 0.00 0.00 0.00 3.86
792 866 1.812571 GTCCAAAATGCATCGTCCAGT 59.187 47.619 0.00 0.00 0.00 4.00
806 880 1.078497 CCAGTCGTTGCTATGCCCA 60.078 57.895 0.00 0.00 0.00 5.36
807 881 1.091771 CCAGTCGTTGCTATGCCCAG 61.092 60.000 0.00 0.00 0.00 4.45
871 945 3.009115 TTCCCTTCCCTGCCCTCG 61.009 66.667 0.00 0.00 0.00 4.63
876 950 3.003173 TTCCCTGCCCTCGTCCAG 61.003 66.667 0.00 0.00 0.00 3.86
937 1012 2.034053 CGTAGCTAGCTTCTTCCTCCTG 59.966 54.545 24.88 0.00 0.00 3.86
995 1070 1.818642 CTCAAGAAACCAGGCTGAGG 58.181 55.000 17.94 1.96 0.00 3.86
996 1071 0.250901 TCAAGAAACCAGGCTGAGGC 60.251 55.000 17.94 0.00 37.82 4.70
1691 1767 8.674263 ATTTAGGAGTGACTGATTGATTGATC 57.326 34.615 0.00 0.00 0.00 2.92
1729 1855 9.797556 AGTTACTGTATTTCACTTTTTGTTTCC 57.202 29.630 0.00 0.00 0.00 3.13
1759 1885 3.911260 TGGTAGATTGTCCCCACTTTGTA 59.089 43.478 0.00 0.00 0.00 2.41
1760 1886 4.538490 TGGTAGATTGTCCCCACTTTGTAT 59.462 41.667 0.00 0.00 0.00 2.29
1769 1895 3.964031 TCCCCACTTTGTATGTGCTTTTT 59.036 39.130 0.00 0.00 34.38 1.94
1780 1906 7.060600 TGTATGTGCTTTTTCACTTAGATCG 57.939 36.000 0.00 0.00 37.81 3.69
1818 1944 8.500837 TTTTCACTGTCGCATAAACTTTATTG 57.499 30.769 0.00 0.00 0.00 1.90
1823 1949 8.604035 CACTGTCGCATAAACTTTATTGTCTAT 58.396 33.333 0.00 0.00 0.00 1.98
1852 1978 4.174411 TGTGGACGACAAATCTCTACTG 57.826 45.455 0.00 0.00 0.00 2.74
1915 2793 8.445493 GCCCTTCATTCTTTGATTTATTTGTTG 58.555 33.333 0.00 0.00 33.34 3.33
1935 2813 8.974060 TTGTTGTTTTTCTAGTAATCTCACCT 57.026 30.769 0.00 0.00 0.00 4.00
2002 2880 9.308000 ACAATCTAAATCAATTTGGTACTTCCA 57.692 29.630 0.00 0.00 45.60 3.53
2012 2890 3.367646 TGGTACTTCCACAAAACCACA 57.632 42.857 0.00 0.00 41.93 4.17
2111 2989 7.567458 CCCATACCCAAATCAAATCAAATCTT 58.433 34.615 0.00 0.00 0.00 2.40
2151 3029 4.553330 TCGGAACTTTTATGCCTTCTCT 57.447 40.909 0.00 0.00 0.00 3.10
2208 3086 7.503566 CCAAATCTATAATGTGGTGGATGTCTT 59.496 37.037 0.00 0.00 0.00 3.01
2273 3151 3.406764 CCTCTAATCAAGCATGGTAGGC 58.593 50.000 0.00 0.00 0.00 3.93
2288 3166 1.931841 GTAGGCGCCTTAGTAAAGTGC 59.068 52.381 37.74 6.56 33.62 4.40
2289 3167 0.392595 AGGCGCCTTAGTAAAGTGCC 60.393 55.000 27.08 23.13 45.74 5.01
2409 3287 1.614903 ACGTCGTGGTACCTTGATTCA 59.385 47.619 14.36 0.00 0.00 2.57
2415 3293 4.283978 TCGTGGTACCTTGATTCAAACCTA 59.716 41.667 14.36 4.49 0.00 3.08
2497 3375 6.557633 ACCTCTCCGGTATCCTATAATGTTTT 59.442 38.462 0.00 0.00 46.73 2.43
2564 3442 3.356290 GTCCCAATTTGATGTGGCTACT 58.644 45.455 0.64 0.00 33.21 2.57
2569 3447 5.163513 CCAATTTGATGTGGCTACTTCAAC 58.836 41.667 24.84 4.04 45.21 3.18
2610 3488 1.580845 CTTCCTGCCGCAAGAACCTG 61.581 60.000 0.00 0.00 43.02 4.00
2611 3489 2.032528 CCTGCCGCAAGAACCTGA 59.967 61.111 0.00 0.00 43.02 3.86
2612 3490 1.600636 CCTGCCGCAAGAACCTGAA 60.601 57.895 0.00 0.00 43.02 3.02
2613 3491 1.580845 CCTGCCGCAAGAACCTGAAG 61.581 60.000 0.00 0.00 43.02 3.02
2614 3492 1.580845 CTGCCGCAAGAACCTGAAGG 61.581 60.000 0.00 0.00 43.02 3.46
2615 3493 1.302511 GCCGCAAGAACCTGAAGGA 60.303 57.895 2.62 0.00 43.02 3.36
2616 3494 0.889186 GCCGCAAGAACCTGAAGGAA 60.889 55.000 2.62 0.00 43.02 3.36
2617 3495 1.604604 CCGCAAGAACCTGAAGGAAA 58.395 50.000 2.62 0.00 43.02 3.13
2618 3496 2.162681 CCGCAAGAACCTGAAGGAAAT 58.837 47.619 2.62 0.00 43.02 2.17
2619 3497 3.343617 CCGCAAGAACCTGAAGGAAATA 58.656 45.455 2.62 0.00 43.02 1.40
2620 3498 3.947834 CCGCAAGAACCTGAAGGAAATAT 59.052 43.478 2.62 0.00 43.02 1.28
2621 3499 4.201950 CCGCAAGAACCTGAAGGAAATATG 60.202 45.833 2.62 0.00 43.02 1.78
2622 3500 4.676546 GCAAGAACCTGAAGGAAATATGC 58.323 43.478 2.62 3.65 38.94 3.14
2623 3501 4.440663 GCAAGAACCTGAAGGAAATATGCC 60.441 45.833 2.62 0.00 38.94 4.40
2624 3502 3.903467 AGAACCTGAAGGAAATATGCCC 58.097 45.455 2.62 0.00 38.94 5.36
2625 3503 3.529319 AGAACCTGAAGGAAATATGCCCT 59.471 43.478 2.62 0.00 38.94 5.19
2626 3504 4.726825 AGAACCTGAAGGAAATATGCCCTA 59.273 41.667 2.62 0.00 38.94 3.53
2627 3505 4.713792 ACCTGAAGGAAATATGCCCTAG 57.286 45.455 2.62 0.00 38.94 3.02
2628 3506 4.307259 ACCTGAAGGAAATATGCCCTAGA 58.693 43.478 2.62 0.00 38.94 2.43
2629 3507 4.349342 ACCTGAAGGAAATATGCCCTAGAG 59.651 45.833 2.62 0.00 38.94 2.43
2630 3508 4.263243 CCTGAAGGAAATATGCCCTAGAGG 60.263 50.000 0.00 0.00 37.39 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 98 4.467107 GGAGGAGGAGGCGGAGGT 62.467 72.222 0.00 0.00 0.00 3.85
244 246 2.047274 TTACACTGGAGCAGCGCC 60.047 61.111 8.52 8.52 34.37 6.53
257 259 1.736645 GCGTCGCAGGCTTCTTACA 60.737 57.895 13.44 0.00 0.00 2.41
339 346 1.915141 CACTTTTGGCATCTGGACCT 58.085 50.000 0.00 0.00 0.00 3.85
354 361 1.032014 AATGTCAAGTTGCCGCACTT 58.968 45.000 0.00 0.00 37.49 3.16
355 362 1.032014 AAATGTCAAGTTGCCGCACT 58.968 45.000 0.00 0.00 0.00 4.40
365 372 3.379372 CCCTGCAGTATCCAAATGTCAAG 59.621 47.826 13.81 0.00 0.00 3.02
373 380 1.622607 CCGGTCCCTGCAGTATCCAA 61.623 60.000 13.81 0.00 0.00 3.53
388 395 1.885163 GCACTAGCAGTACCACCGGT 61.885 60.000 0.00 0.00 41.58 5.28
425 432 1.400530 GGGAGCGGCTGTACATACCT 61.401 60.000 7.50 0.46 0.00 3.08
476 483 1.352017 TCCTGCATGCTTCCTTCTTCA 59.648 47.619 20.33 0.00 0.00 3.02
478 488 2.040813 TCTTCCTGCATGCTTCCTTCTT 59.959 45.455 20.33 0.00 0.00 2.52
481 497 1.954258 GCTCTTCCTGCATGCTTCCTT 60.954 52.381 20.33 0.00 0.00 3.36
489 514 0.459489 GACTCGAGCTCTTCCTGCAT 59.541 55.000 13.61 0.00 0.00 3.96
493 518 1.363145 CGTCGACTCGAGCTCTTCCT 61.363 60.000 13.61 0.00 36.23 3.36
505 530 1.289380 GGAAGGTTCAGCGTCGACT 59.711 57.895 14.70 0.00 0.00 4.18
521 546 2.203938 AGCGGGAAGTGGAAGGGA 60.204 61.111 0.00 0.00 0.00 4.20
556 588 1.557269 AACCCTAGCCAGACAGCCAG 61.557 60.000 0.00 0.00 0.00 4.85
563 616 1.628846 GACCAGAAAACCCTAGCCAGA 59.371 52.381 0.00 0.00 0.00 3.86
593 662 3.557898 CCACATCTAACCACACTTGCTCT 60.558 47.826 0.00 0.00 0.00 4.09
606 676 3.041211 CCATCTCCCTGTCCACATCTAA 58.959 50.000 0.00 0.00 0.00 2.10
607 677 2.247372 TCCATCTCCCTGTCCACATCTA 59.753 50.000 0.00 0.00 0.00 1.98
618 688 2.715336 CCTCATCCATTTCCATCTCCCT 59.285 50.000 0.00 0.00 0.00 4.20
653 725 2.515912 CGTCCCTTTTAATGAAAGCGC 58.484 47.619 0.00 0.00 42.79 5.92
680 754 0.396435 GACAGTGTGTGGATGGGTCA 59.604 55.000 0.00 0.00 0.00 4.02
686 760 1.004560 CGCCTGACAGTGTGTGGAT 60.005 57.895 0.00 0.00 0.00 3.41
706 780 0.172803 GTCGCGTATCCCTTCAGTGT 59.827 55.000 5.77 0.00 0.00 3.55
708 782 1.432251 CGTCGCGTATCCCTTCAGT 59.568 57.895 5.77 0.00 0.00 3.41
709 783 1.944676 GCGTCGCGTATCCCTTCAG 60.945 63.158 5.77 0.00 0.00 3.02
710 784 2.103538 GCGTCGCGTATCCCTTCA 59.896 61.111 5.77 0.00 0.00 3.02
722 796 4.099585 CACGAAACGGACGCGTCG 62.100 66.667 30.99 26.50 35.90 5.12
723 797 2.081276 AAACACGAAACGGACGCGTC 62.081 55.000 30.67 30.67 35.90 5.19
724 798 2.166579 AAACACGAAACGGACGCGT 61.167 52.632 13.85 13.85 39.04 6.01
725 799 1.716378 CAAACACGAAACGGACGCG 60.716 57.895 3.53 3.53 0.00 6.01
726 800 2.001880 GCAAACACGAAACGGACGC 61.002 57.895 0.00 0.00 0.00 5.19
727 801 1.716378 CGCAAACACGAAACGGACG 60.716 57.895 0.00 0.00 34.06 4.79
728 802 2.001880 GCGCAAACACGAAACGGAC 61.002 57.895 0.30 0.00 34.06 4.79
729 803 2.174969 AGCGCAAACACGAAACGGA 61.175 52.632 11.47 0.00 34.06 4.69
730 804 2.003443 CAGCGCAAACACGAAACGG 61.003 57.895 11.47 0.00 34.06 4.44
731 805 0.384230 ATCAGCGCAAACACGAAACG 60.384 50.000 11.47 0.00 34.06 3.60
732 806 1.044725 CATCAGCGCAAACACGAAAC 58.955 50.000 11.47 0.00 34.06 2.78
733 807 0.660005 GCATCAGCGCAAACACGAAA 60.660 50.000 11.47 0.00 34.06 3.46
734 808 1.082169 GCATCAGCGCAAACACGAA 60.082 52.632 11.47 0.00 34.06 3.85
735 809 1.576451 ATGCATCAGCGCAAACACGA 61.576 50.000 11.47 0.00 46.87 4.35
736 810 0.730155 AATGCATCAGCGCAAACACG 60.730 50.000 11.47 0.00 46.87 4.49
737 811 1.421382 AAATGCATCAGCGCAAACAC 58.579 45.000 11.47 0.00 46.87 3.32
738 812 3.244156 CTTAAATGCATCAGCGCAAACA 58.756 40.909 11.47 0.00 46.87 2.83
739 813 2.599973 CCTTAAATGCATCAGCGCAAAC 59.400 45.455 11.47 0.00 46.87 2.93
740 814 2.878580 CCTTAAATGCATCAGCGCAAA 58.121 42.857 11.47 0.00 46.87 3.68
741 815 1.469595 GCCTTAAATGCATCAGCGCAA 60.470 47.619 11.47 0.00 46.87 4.85
743 817 0.595825 GGCCTTAAATGCATCAGCGC 60.596 55.000 0.00 0.00 46.23 5.92
744 818 1.027357 AGGCCTTAAATGCATCAGCG 58.973 50.000 0.00 0.00 46.23 5.18
745 819 4.654091 TTTAGGCCTTAAATGCATCAGC 57.346 40.909 12.58 0.00 42.57 4.26
746 820 6.480981 CCAAATTTAGGCCTTAAATGCATCAG 59.519 38.462 12.58 0.00 40.29 2.90
747 821 6.347696 CCAAATTTAGGCCTTAAATGCATCA 58.652 36.000 12.58 0.00 40.29 3.07
748 822 5.759763 CCCAAATTTAGGCCTTAAATGCATC 59.240 40.000 12.58 0.00 40.29 3.91
749 823 5.191522 ACCCAAATTTAGGCCTTAAATGCAT 59.808 36.000 12.58 0.00 40.29 3.96
750 824 4.534103 ACCCAAATTTAGGCCTTAAATGCA 59.466 37.500 12.58 0.00 40.29 3.96
751 825 5.097742 ACCCAAATTTAGGCCTTAAATGC 57.902 39.130 12.58 0.00 40.29 3.56
752 826 5.188751 TGGACCCAAATTTAGGCCTTAAATG 59.811 40.000 12.58 11.94 40.29 2.32
753 827 5.346270 TGGACCCAAATTTAGGCCTTAAAT 58.654 37.500 12.58 12.17 42.41 1.40
754 828 4.753186 TGGACCCAAATTTAGGCCTTAAA 58.247 39.130 12.58 10.22 35.79 1.52
755 829 4.405756 TGGACCCAAATTTAGGCCTTAA 57.594 40.909 12.58 9.22 0.00 1.85
756 830 4.405756 TTGGACCCAAATTTAGGCCTTA 57.594 40.909 12.58 0.00 32.44 2.69
757 831 3.268034 TTGGACCCAAATTTAGGCCTT 57.732 42.857 12.58 0.00 32.44 4.35
758 832 3.268034 TTTGGACCCAAATTTAGGCCT 57.732 42.857 11.78 11.78 40.51 5.19
759 833 4.260985 CATTTTGGACCCAAATTTAGGCC 58.739 43.478 14.26 4.01 44.14 5.19
760 834 3.689161 GCATTTTGGACCCAAATTTAGGC 59.311 43.478 14.26 9.65 44.14 3.93
761 835 4.904241 TGCATTTTGGACCCAAATTTAGG 58.096 39.130 14.26 0.60 44.14 2.69
762 836 5.291614 CGATGCATTTTGGACCCAAATTTAG 59.708 40.000 14.26 6.79 44.14 1.85
763 837 5.174395 CGATGCATTTTGGACCCAAATTTA 58.826 37.500 14.26 1.43 44.14 1.40
764 838 4.002316 CGATGCATTTTGGACCCAAATTT 58.998 39.130 14.26 3.85 44.14 1.82
765 839 3.007831 ACGATGCATTTTGGACCCAAATT 59.992 39.130 14.26 8.71 44.14 1.82
766 840 2.566724 ACGATGCATTTTGGACCCAAAT 59.433 40.909 14.26 6.46 44.14 2.32
767 841 1.967066 ACGATGCATTTTGGACCCAAA 59.033 42.857 9.96 9.96 43.23 3.28
768 842 1.543802 GACGATGCATTTTGGACCCAA 59.456 47.619 0.00 0.00 0.00 4.12
769 843 1.173043 GACGATGCATTTTGGACCCA 58.827 50.000 0.00 0.00 0.00 4.51
770 844 0.455815 GGACGATGCATTTTGGACCC 59.544 55.000 0.00 0.00 0.00 4.46
771 845 1.133025 CTGGACGATGCATTTTGGACC 59.867 52.381 0.00 1.86 0.00 4.46
772 846 1.812571 ACTGGACGATGCATTTTGGAC 59.187 47.619 0.00 0.00 0.00 4.02
773 847 2.083774 GACTGGACGATGCATTTTGGA 58.916 47.619 0.00 0.00 0.00 3.53
774 848 1.202065 CGACTGGACGATGCATTTTGG 60.202 52.381 0.00 0.00 35.09 3.28
775 849 1.464608 ACGACTGGACGATGCATTTTG 59.535 47.619 0.00 0.00 37.03 2.44
776 850 1.808411 ACGACTGGACGATGCATTTT 58.192 45.000 0.00 0.00 37.03 1.82
777 851 1.464608 CAACGACTGGACGATGCATTT 59.535 47.619 0.00 0.00 37.03 2.32
778 852 1.078709 CAACGACTGGACGATGCATT 58.921 50.000 0.00 0.00 37.03 3.56
779 853 2.754648 CAACGACTGGACGATGCAT 58.245 52.632 0.00 0.00 37.03 3.96
780 854 4.260194 CAACGACTGGACGATGCA 57.740 55.556 0.00 0.00 37.03 3.96
790 864 1.450312 GCTGGGCATAGCAACGACT 60.450 57.895 7.95 0.00 43.17 4.18
791 865 2.472909 GGCTGGGCATAGCAACGAC 61.473 63.158 13.78 0.00 45.46 4.34
792 866 2.124736 GGCTGGGCATAGCAACGA 60.125 61.111 13.78 0.00 45.46 3.85
896 970 4.436998 ACGTGAGGTAGCGGCAGC 62.437 66.667 0.00 0.00 45.58 5.25
897 971 2.202623 GACGTGAGGTAGCGGCAG 60.203 66.667 1.45 0.00 35.95 4.85
898 972 2.986979 TGACGTGAGGTAGCGGCA 60.987 61.111 1.45 0.00 44.50 5.69
899 973 2.506438 GTGACGTGAGGTAGCGGC 60.506 66.667 0.00 0.00 36.53 6.53
900 974 1.638388 TACGTGACGTGAGGTAGCGG 61.638 60.000 22.16 0.00 41.39 5.52
901 975 0.247576 CTACGTGACGTGAGGTAGCG 60.248 60.000 22.16 1.37 41.39 4.26
1225 1301 4.729856 GTAGGCGAACGCGGTGGT 62.730 66.667 12.47 0.00 43.06 4.16
1269 1345 2.879756 GCTCATGGCCCAGTTCTTGTTA 60.880 50.000 0.00 0.00 34.27 2.41
1340 1416 2.279784 GCCTGATCCGCTCGAAGG 60.280 66.667 0.40 0.40 0.00 3.46
1729 1855 4.526262 TGGGGACAATCTACCAACAATTTG 59.474 41.667 0.00 0.00 37.44 2.32
1759 1885 6.373779 CAACGATCTAAGTGAAAAAGCACAT 58.626 36.000 0.00 0.00 41.19 3.21
1760 1886 5.277779 CCAACGATCTAAGTGAAAAAGCACA 60.278 40.000 0.00 0.00 41.19 4.57
1769 1895 2.816411 ACTCCCCAACGATCTAAGTGA 58.184 47.619 0.00 0.00 0.00 3.41
1780 1906 2.031870 AGTGAAAAGCAACTCCCCAAC 58.968 47.619 0.00 0.00 0.00 3.77
1818 1944 9.909644 ATTTGTCGTCCACAACTATATATAGAC 57.090 33.333 23.70 10.97 45.12 2.59
1823 1949 8.234136 AGAGATTTGTCGTCCACAACTATATA 57.766 34.615 0.00 0.00 45.12 0.86
1837 1963 7.313646 TCTCCTTTAACAGTAGAGATTTGTCG 58.686 38.462 0.00 0.00 0.00 4.35
1845 1971 6.159988 CACCAACTCTCCTTTAACAGTAGAG 58.840 44.000 0.00 0.00 39.65 2.43
1852 1978 5.347907 CGTGATACACCAACTCTCCTTTAAC 59.652 44.000 0.00 0.00 0.00 2.01
1915 2793 8.202745 CCATCAGGTGAGATTACTAGAAAAAC 57.797 38.462 0.00 0.00 0.00 2.43
2002 2880 4.100808 AGTTAATGCATGGTGTGGTTTTGT 59.899 37.500 0.00 0.00 0.00 2.83
2012 2890 7.172868 TGATTTCATTGAGTTAATGCATGGT 57.827 32.000 0.00 0.00 44.69 3.55
2070 2948 0.106268 TGGGCAGTGAAAGGCAAGAA 60.106 50.000 0.00 0.00 0.00 2.52
2085 2963 4.751767 TTGATTTGATTTGGGTATGGGC 57.248 40.909 0.00 0.00 0.00 5.36
2111 2989 7.499895 AGTTCCGATTTAGTTGAGTTTTTGGTA 59.500 33.333 0.00 0.00 0.00 3.25
2127 3005 5.946377 AGAGAAGGCATAAAAGTTCCGATTT 59.054 36.000 0.00 0.00 0.00 2.17
2141 3019 6.753913 TTGAGTATGGATAAGAGAAGGCAT 57.246 37.500 0.00 0.00 0.00 4.40
2178 3056 7.401060 TCCACCACATTATAGATTTGGGTAT 57.599 36.000 0.00 0.00 0.00 2.73
2256 3134 1.593196 GCGCCTACCATGCTTGATTA 58.407 50.000 0.00 0.00 0.00 1.75
2273 3151 0.746923 GGGGGCACTTTACTAAGGCG 60.747 60.000 0.00 0.00 35.61 5.52
2295 3173 3.572255 CGAATAGAAGGGGAGAGAGAAGG 59.428 52.174 0.00 0.00 0.00 3.46
2296 3174 4.211920 ACGAATAGAAGGGGAGAGAGAAG 58.788 47.826 0.00 0.00 0.00 2.85
2297 3175 4.208746 GACGAATAGAAGGGGAGAGAGAA 58.791 47.826 0.00 0.00 0.00 2.87
2298 3176 3.202373 TGACGAATAGAAGGGGAGAGAGA 59.798 47.826 0.00 0.00 0.00 3.10
2409 3287 2.689983 CCGTCCACGTATAGGTAGGTTT 59.310 50.000 0.00 0.00 37.74 3.27
2415 3293 0.813184 CACACCGTCCACGTATAGGT 59.187 55.000 0.00 0.00 37.74 3.08
2497 3375 2.758327 AGGCTCGTGGTATCGCCA 60.758 61.111 0.00 0.00 46.95 5.69
2564 3442 3.496331 GAAGGATTCACCCAAGGTTGAA 58.504 45.455 1.41 1.41 46.62 2.69
2621 3499 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19


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

AutoCloner maintained by Alex Coulton.