Multiple sequence alignment - TraesCS2B01G314800

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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 TraesCS2B01G314800 chr2B 100.000 4260 0 0 1 4260 449939035 449934776 0.000000e+00 7867.0
1 TraesCS2B01G314800 chr2B 85.484 62 8 1 3465 3525 121483833 121483894 3.560000e-06 63.9
2 TraesCS2B01G314800 chr2D 93.859 1954 82 19 852 2768 378758320 378756368 0.000000e+00 2909.0
3 TraesCS2B01G314800 chr2D 92.203 1026 52 13 3248 4260 378739000 378737990 0.000000e+00 1426.0
4 TraesCS2B01G314800 chr2D 93.333 495 21 2 2771 3254 378751476 378750983 0.000000e+00 721.0
5 TraesCS2B01G314800 chr2D 79.231 130 23 4 3275 3402 11594440 11594567 2.110000e-13 87.9
6 TraesCS2B01G314800 chr2A 94.145 1503 72 10 819 2313 513824182 513822688 0.000000e+00 2274.0
7 TraesCS2B01G314800 chr2A 91.607 1120 63 13 3008 4101 513821654 513820540 0.000000e+00 1519.0
8 TraesCS2B01G314800 chr2A 98.376 739 12 0 1 739 553474995 553475733 0.000000e+00 1299.0
9 TraesCS2B01G314800 chr2A 96.119 438 15 2 2333 2768 513822519 513822082 0.000000e+00 713.0
10 TraesCS2B01G314800 chr2A 88.846 260 17 6 2768 3016 513821933 513821675 4.140000e-80 309.0
11 TraesCS2B01G314800 chr2A 92.903 155 11 0 4106 4260 513819758 513819604 4.290000e-55 226.0
12 TraesCS2B01G314800 chr2A 97.368 38 0 1 2296 2332 763140472 763140435 3.560000e-06 63.9
13 TraesCS2B01G314800 chr5B 98.241 739 13 0 1 739 92215273 92216011 0.000000e+00 1293.0
14 TraesCS2B01G314800 chr5B 97.970 739 15 0 1 739 71630621 71629883 0.000000e+00 1282.0
15 TraesCS2B01G314800 chr5B 92.135 623 47 2 1 622 635393861 635394482 0.000000e+00 878.0
16 TraesCS2B01G314800 chr5B 84.543 744 108 6 1 739 465992848 465993589 0.000000e+00 730.0
17 TraesCS2B01G314800 chr5B 88.889 72 5 3 3270 3339 83906474 83906544 7.590000e-13 86.1
18 TraesCS2B01G314800 chr5A 94.858 739 13 5 1 739 69837510 69838223 0.000000e+00 1131.0
19 TraesCS2B01G314800 chr5A 81.600 125 16 5 3420 3538 255350671 255350794 3.510000e-16 97.1
20 TraesCS2B01G314800 chr1B 91.984 736 58 1 4 738 514430513 514429778 0.000000e+00 1031.0
21 TraesCS2B01G314800 chr1B 96.970 33 0 1 2301 2332 525804125 525804093 2.000000e-03 54.7
22 TraesCS2B01G314800 chr7B 89.417 737 77 1 4 739 37585175 37584439 0.000000e+00 928.0
23 TraesCS2B01G314800 chr7B 91.935 62 4 1 2582 2642 524241135 524241196 7.590000e-13 86.1
24 TraesCS2B01G314800 chr7B 88.571 70 7 1 2582 2650 138742408 138742339 2.730000e-12 84.2
25 TraesCS2B01G314800 chr7B 88.462 52 3 3 2290 2339 639902136 639902186 4.600000e-05 60.2
26 TraesCS2B01G314800 chr1D 90.361 664 62 2 1 663 450024397 450025059 0.000000e+00 870.0
27 TraesCS2B01G314800 chr4D 78.319 226 45 4 3284 3508 63227349 63227571 4.440000e-30 143.0
28 TraesCS2B01G314800 chr4D 92.063 63 4 1 2582 2643 450203726 450203788 2.110000e-13 87.9
29 TraesCS2B01G314800 chr7D 91.176 68 5 1 2582 2648 119897012 119897079 1.630000e-14 91.6
30 TraesCS2B01G314800 chr7D 89.855 69 6 1 2582 2649 119897057 119896989 2.110000e-13 87.9
31 TraesCS2B01G314800 chr4A 90.909 66 5 1 2582 2646 16469388 16469323 2.110000e-13 87.9
32 TraesCS2B01G314800 chr6B 89.394 66 6 1 2582 2646 503544639 503544574 9.820000e-12 82.4
33 TraesCS2B01G314800 chr6B 87.500 48 5 1 3457 3504 61788855 61788809 2.000000e-03 54.7
34 TraesCS2B01G314800 chr4B 77.419 124 22 3 3278 3401 426146279 426146162 7.640000e-08 69.4
35 TraesCS2B01G314800 chr5D 82.895 76 9 3 3435 3507 312440484 312440410 9.890000e-07 65.8
36 TraesCS2B01G314800 chr5D 97.059 34 1 0 2324 2357 545993747 545993780 1.650000e-04 58.4
37 TraesCS2B01G314800 chr6A 92.308 39 3 0 2290 2328 563252501 563252463 5.950000e-04 56.5
38 TraesCS2B01G314800 chr6A 96.875 32 1 0 790 821 598319793 598319824 2.000000e-03 54.7
39 TraesCS2B01G314800 chr6A 96.875 32 1 0 790 821 598380276 598380307 2.000000e-03 54.7
40 TraesCS2B01G314800 chr6A 96.875 32 1 0 790 821 598453885 598453916 2.000000e-03 54.7
41 TraesCS2B01G314800 chr6A 96.875 32 1 0 790 821 598561592 598561623 2.000000e-03 54.7
42 TraesCS2B01G314800 chr3A 100.000 28 0 0 2328 2355 403412110 403412083 8.000000e-03 52.8


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 TraesCS2B01G314800 chr2B 449934776 449939035 4259 True 7867.0 7867 100.000 1 4260 1 chr2B.!!$R1 4259
1 TraesCS2B01G314800 chr2D 378756368 378758320 1952 True 2909.0 2909 93.859 852 2768 1 chr2D.!!$R3 1916
2 TraesCS2B01G314800 chr2D 378737990 378739000 1010 True 1426.0 1426 92.203 3248 4260 1 chr2D.!!$R1 1012
3 TraesCS2B01G314800 chr2A 553474995 553475733 738 False 1299.0 1299 98.376 1 739 1 chr2A.!!$F1 738
4 TraesCS2B01G314800 chr2A 513819604 513824182 4578 True 1008.2 2274 92.724 819 4260 5 chr2A.!!$R2 3441
5 TraesCS2B01G314800 chr5B 92215273 92216011 738 False 1293.0 1293 98.241 1 739 1 chr5B.!!$F2 738
6 TraesCS2B01G314800 chr5B 71629883 71630621 738 True 1282.0 1282 97.970 1 739 1 chr5B.!!$R1 738
7 TraesCS2B01G314800 chr5B 635393861 635394482 621 False 878.0 878 92.135 1 622 1 chr5B.!!$F4 621
8 TraesCS2B01G314800 chr5B 465992848 465993589 741 False 730.0 730 84.543 1 739 1 chr5B.!!$F3 738
9 TraesCS2B01G314800 chr5A 69837510 69838223 713 False 1131.0 1131 94.858 1 739 1 chr5A.!!$F1 738
10 TraesCS2B01G314800 chr1B 514429778 514430513 735 True 1031.0 1031 91.984 4 738 1 chr1B.!!$R1 734
11 TraesCS2B01G314800 chr7B 37584439 37585175 736 True 928.0 928 89.417 4 739 1 chr7B.!!$R1 735
12 TraesCS2B01G314800 chr1D 450024397 450025059 662 False 870.0 870 90.361 1 663 1 chr1D.!!$F1 662

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
800 805 0.320421 TGCTTTTTAGGAGCGCTCGT 60.320 50.0 32.39 32.39 43.02 4.18 F
1337 1358 0.543277 TTCATCTGCCAAGGATCGCT 59.457 50.0 0.00 0.00 0.00 4.93 F
2857 3183 0.036306 AACTCCAGCCTTTACGGTGG 59.964 55.0 0.35 0.35 36.11 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 1711 0.179048 TGAATAGGCAGCCGATGGTG 60.179 55.0 7.97 0.0 42.91 4.17 R
3237 3603 0.669619 CATCACACAGCAACAGCCAA 59.330 50.0 0.00 0.0 0.00 4.52 R
3701 4092 2.093288 GGTTGGATCAGAGAGCATCACA 60.093 50.0 0.00 0.0 37.82 3.58 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
106 107 2.832129 GCTCCGGGGTATCATGAATCTA 59.168 50.000 1.62 0.00 0.00 1.98
413 414 2.160417 GGACAGTTCTGCAATTTCCTCG 59.840 50.000 0.00 0.00 0.00 4.63
746 751 2.526873 CTAGGGTAGGGGGCGCAT 60.527 66.667 10.83 0.00 0.00 4.73
747 752 2.847234 TAGGGTAGGGGGCGCATG 60.847 66.667 10.83 0.00 0.00 4.06
760 765 3.792047 GCATGCACGCGAGCTTCA 61.792 61.111 27.94 9.80 34.99 3.02
761 766 2.398429 CATGCACGCGAGCTTCAG 59.602 61.111 27.94 11.99 34.99 3.02
762 767 3.494336 ATGCACGCGAGCTTCAGC 61.494 61.111 27.94 12.62 42.49 4.26
773 778 3.360886 GCTTCAGCTAGGAGCACTC 57.639 57.895 10.51 0.00 45.56 3.51
774 779 0.534412 GCTTCAGCTAGGAGCACTCA 59.466 55.000 10.51 0.00 45.56 3.41
775 780 1.471327 GCTTCAGCTAGGAGCACTCAG 60.471 57.143 10.51 0.00 45.56 3.35
776 781 1.824230 CTTCAGCTAGGAGCACTCAGT 59.176 52.381 0.64 0.00 45.56 3.41
777 782 2.808906 TCAGCTAGGAGCACTCAGTA 57.191 50.000 0.64 0.00 45.56 2.74
778 783 2.370349 TCAGCTAGGAGCACTCAGTAC 58.630 52.381 0.64 0.00 45.56 2.73
779 784 1.064803 CAGCTAGGAGCACTCAGTACG 59.935 57.143 0.64 0.00 45.56 3.67
780 785 1.065345 AGCTAGGAGCACTCAGTACGA 60.065 52.381 0.64 0.00 45.56 3.43
781 786 1.950909 GCTAGGAGCACTCAGTACGAT 59.049 52.381 0.00 0.00 41.89 3.73
782 787 2.287308 GCTAGGAGCACTCAGTACGATG 60.287 54.545 0.00 0.00 41.89 3.84
783 788 0.457851 AGGAGCACTCAGTACGATGC 59.542 55.000 0.00 5.80 38.39 3.91
786 791 2.751166 AGCACTCAGTACGATGCTTT 57.249 45.000 9.50 0.00 46.06 3.51
787 792 3.045601 AGCACTCAGTACGATGCTTTT 57.954 42.857 9.50 0.00 46.06 2.27
788 793 3.403038 AGCACTCAGTACGATGCTTTTT 58.597 40.909 9.50 0.00 46.06 1.94
789 794 4.566004 AGCACTCAGTACGATGCTTTTTA 58.434 39.130 9.50 0.00 46.06 1.52
790 795 4.627467 AGCACTCAGTACGATGCTTTTTAG 59.373 41.667 9.50 0.00 46.06 1.85
791 796 4.201724 GCACTCAGTACGATGCTTTTTAGG 60.202 45.833 0.00 0.00 35.16 2.69
792 797 5.168569 CACTCAGTACGATGCTTTTTAGGA 58.831 41.667 0.00 0.00 0.00 2.94
793 798 5.289675 CACTCAGTACGATGCTTTTTAGGAG 59.710 44.000 0.00 0.00 0.00 3.69
794 799 4.181578 TCAGTACGATGCTTTTTAGGAGC 58.818 43.478 0.00 0.00 40.53 4.70
795 800 3.000322 CAGTACGATGCTTTTTAGGAGCG 60.000 47.826 2.88 2.88 44.20 5.03
796 801 0.727398 ACGATGCTTTTTAGGAGCGC 59.273 50.000 0.00 0.00 42.49 5.92
797 802 1.009829 CGATGCTTTTTAGGAGCGCT 58.990 50.000 11.27 11.27 43.02 5.92
798 803 1.004504 CGATGCTTTTTAGGAGCGCTC 60.005 52.381 29.38 29.38 43.02 5.03
799 804 1.004504 GATGCTTTTTAGGAGCGCTCG 60.005 52.381 29.81 15.78 43.02 5.03
800 805 0.320421 TGCTTTTTAGGAGCGCTCGT 60.320 50.000 32.39 32.39 43.02 4.18
801 806 0.796927 GCTTTTTAGGAGCGCTCGTT 59.203 50.000 34.48 24.71 0.00 3.85
802 807 1.997606 GCTTTTTAGGAGCGCTCGTTA 59.002 47.619 34.48 24.55 0.00 3.18
803 808 2.414138 GCTTTTTAGGAGCGCTCGTTAA 59.586 45.455 34.48 28.43 0.00 2.01
804 809 3.724128 GCTTTTTAGGAGCGCTCGTTAAC 60.724 47.826 34.48 19.04 0.00 2.01
805 810 3.308438 TTTTAGGAGCGCTCGTTAACT 57.692 42.857 34.48 24.56 0.00 2.24
806 811 4.439305 TTTTAGGAGCGCTCGTTAACTA 57.561 40.909 34.48 23.56 0.00 2.24
807 812 4.439305 TTTAGGAGCGCTCGTTAACTAA 57.561 40.909 34.48 27.18 0.00 2.24
808 813 4.644103 TTAGGAGCGCTCGTTAACTAAT 57.356 40.909 34.48 12.58 0.00 1.73
809 814 3.521947 AGGAGCGCTCGTTAACTAATT 57.478 42.857 29.81 3.47 0.00 1.40
810 815 3.187700 AGGAGCGCTCGTTAACTAATTG 58.812 45.455 29.81 0.00 0.00 2.32
811 816 2.285660 GGAGCGCTCGTTAACTAATTGC 60.286 50.000 29.81 8.45 0.00 3.56
812 817 2.603560 GAGCGCTCGTTAACTAATTGCT 59.396 45.455 23.61 6.50 0.00 3.91
813 818 2.603560 AGCGCTCGTTAACTAATTGCTC 59.396 45.455 2.64 0.00 0.00 4.26
814 819 2.603560 GCGCTCGTTAACTAATTGCTCT 59.396 45.455 0.00 0.00 0.00 4.09
815 820 3.301899 GCGCTCGTTAACTAATTGCTCTC 60.302 47.826 0.00 0.00 0.00 3.20
816 821 3.243177 CGCTCGTTAACTAATTGCTCTCC 59.757 47.826 3.71 0.00 0.00 3.71
817 822 4.434520 GCTCGTTAACTAATTGCTCTCCT 58.565 43.478 3.71 0.00 0.00 3.69
829 834 5.903198 ATTGCTCTCCTTTTATAGAGGCT 57.097 39.130 0.00 0.00 39.73 4.58
835 840 7.236432 TGCTCTCCTTTTATAGAGGCTGATATT 59.764 37.037 0.00 0.00 39.73 1.28
836 841 7.548780 GCTCTCCTTTTATAGAGGCTGATATTG 59.451 40.741 0.00 0.00 39.73 1.90
838 843 8.589338 TCTCCTTTTATAGAGGCTGATATTGTC 58.411 37.037 0.00 0.00 34.17 3.18
839 844 8.497910 TCCTTTTATAGAGGCTGATATTGTCT 57.502 34.615 0.00 0.00 34.17 3.41
840 845 8.938883 TCCTTTTATAGAGGCTGATATTGTCTT 58.061 33.333 0.00 0.00 34.17 3.01
841 846 9.566432 CCTTTTATAGAGGCTGATATTGTCTTT 57.434 33.333 0.00 0.00 0.00 2.52
844 849 9.770097 TTTATAGAGGCTGATATTGTCTTTCAG 57.230 33.333 0.00 0.00 39.87 3.02
846 851 6.305272 AGAGGCTGATATTGTCTTTCAGAA 57.695 37.500 0.00 0.00 39.36 3.02
848 853 7.170965 AGAGGCTGATATTGTCTTTCAGAAAA 58.829 34.615 0.00 0.00 39.36 2.29
849 854 7.667219 AGAGGCTGATATTGTCTTTCAGAAAAA 59.333 33.333 0.00 0.00 39.36 1.94
850 855 7.824672 AGGCTGATATTGTCTTTCAGAAAAAG 58.175 34.615 3.47 0.00 39.36 2.27
858 863 6.144078 TGTCTTTCAGAAAAAGTAAAGGCC 57.856 37.500 0.00 0.00 33.63 5.19
946 959 9.903682 GTAAATAAACCTACCTTTCCTCAAAAC 57.096 33.333 0.00 0.00 0.00 2.43
948 961 8.541899 AATAAACCTACCTTTCCTCAAAACAA 57.458 30.769 0.00 0.00 0.00 2.83
978 991 5.884232 GGGTAAAGAAACCTACCGATTCAAT 59.116 40.000 0.00 0.00 38.82 2.57
1011 1032 3.387091 ACGTCCATGGCCGCAGTA 61.387 61.111 16.40 0.00 0.00 2.74
1183 1204 1.403814 CATCTCCCGCTTCTACCTGA 58.596 55.000 0.00 0.00 0.00 3.86
1337 1358 0.543277 TTCATCTGCCAAGGATCGCT 59.457 50.000 0.00 0.00 0.00 4.93
1407 1428 2.740981 CTCTTTGCATCTTCGCTCTGTT 59.259 45.455 0.00 0.00 0.00 3.16
1430 1451 1.841302 ATCTTGTGCCGCCCTGAAGA 61.841 55.000 0.00 0.00 0.00 2.87
1440 1461 2.584791 CGCCCTGAAGAAAAATTCGTG 58.415 47.619 0.00 0.00 34.02 4.35
1441 1462 2.668279 CGCCCTGAAGAAAAATTCGTGG 60.668 50.000 0.00 0.00 34.02 4.94
1465 1486 1.577328 GCAGCTGCGCCTAAGTGAAA 61.577 55.000 25.23 0.00 0.00 2.69
1712 1733 1.162698 CATCGGCTGCCTATTCATGG 58.837 55.000 17.92 0.00 0.00 3.66
1740 1761 4.110493 GGTGCAGATCTACACCGC 57.890 61.111 25.87 11.71 46.32 5.68
1858 1879 3.985019 TGCTTCCTGGTACGGATTTTA 57.015 42.857 0.00 0.00 36.31 1.52
1866 1887 5.046159 TCCTGGTACGGATTTTATTGTCACT 60.046 40.000 0.00 0.00 36.31 3.41
1877 1898 7.489113 GGATTTTATTGTCACTTGCCATACTTG 59.511 37.037 0.00 0.00 0.00 3.16
1906 1927 0.987294 AGACATGGTGTGGGAAGAGG 59.013 55.000 0.00 0.00 0.00 3.69
1940 1961 6.434302 TCACATCTCATGAAATATGGGGTTT 58.566 36.000 12.32 0.00 0.00 3.27
1942 1963 5.532406 ACATCTCATGAAATATGGGGTTTCG 59.468 40.000 13.83 0.00 38.18 3.46
1988 2009 3.141398 TGATGTTTCCTCTTGTGAGTGC 58.859 45.455 0.00 0.00 38.61 4.40
2022 2043 7.445402 TCAAATGAGCTATACTTTCTATTGCCC 59.555 37.037 0.00 0.00 0.00 5.36
2063 2084 1.606668 TGACAAGGTTTCGGTGATTGC 59.393 47.619 0.00 0.00 0.00 3.56
2079 2100 6.701841 CGGTGATTGCTGTTGATACTATTACT 59.298 38.462 0.00 0.00 0.00 2.24
2086 2107 8.593492 TGCTGTTGATACTATTACTAAGCATG 57.407 34.615 0.00 0.00 32.39 4.06
2087 2108 8.204160 TGCTGTTGATACTATTACTAAGCATGT 58.796 33.333 0.00 0.00 32.39 3.21
2089 2110 9.750125 CTGTTGATACTATTACTAAGCATGTGA 57.250 33.333 0.00 0.00 0.00 3.58
2107 2128 6.910972 GCATGTGAAGATTCATCAGTACATTG 59.089 38.462 0.00 0.00 39.73 2.82
2162 2183 0.107848 ATGGTTAGGCGAAAGTCCCG 60.108 55.000 0.00 0.00 35.23 5.14
2185 2206 1.753903 TCTCCATCCCTTTGTTCCCA 58.246 50.000 0.00 0.00 0.00 4.37
2294 2318 8.529424 ACATAGTAGTATGTGGTAGCTGTTAA 57.471 34.615 20.15 0.00 46.31 2.01
2349 2522 8.903059 AGATCCTATATTAGTTTACAGAGGGG 57.097 38.462 0.00 0.00 0.00 4.79
2587 2761 4.163458 TCAACTGTTACTCCCTCAAGTGTT 59.837 41.667 0.00 0.00 0.00 3.32
2704 2881 6.098124 AGGACTCAAATTTGATGAAAACCACA 59.902 34.615 20.76 0.00 36.46 4.17
2778 3104 6.145535 GTCCTGTTTTCAACATTCTGATGAC 58.854 40.000 0.00 0.00 41.26 3.06
2782 3108 7.115805 CCTGTTTTCAACATTCTGATGACAATG 59.884 37.037 0.00 0.00 41.26 2.82
2792 3118 5.725325 TCTGATGACAATGCCAAAATCAA 57.275 34.783 0.00 0.00 0.00 2.57
2853 3179 1.606668 TGCAAAACTCCAGCCTTTACG 59.393 47.619 0.00 0.00 0.00 3.18
2857 3183 0.036306 AACTCCAGCCTTTACGGTGG 59.964 55.000 0.35 0.35 36.11 4.61
2906 3243 3.370840 TGGCAACATCTCCAATTAGCT 57.629 42.857 0.00 0.00 46.17 3.32
2909 3246 3.065925 GGCAACATCTCCAATTAGCTGAC 59.934 47.826 0.00 0.00 0.00 3.51
2921 3258 2.649331 TAGCTGACGGTAGTTTCTGC 57.351 50.000 0.00 0.00 37.06 4.26
2931 3268 7.145985 TGACGGTAGTTTCTGCATAGAATATC 58.854 38.462 0.00 0.00 42.25 1.63
2964 3301 4.302067 ACCTCCATATGTCATTCCAGAGT 58.698 43.478 1.24 0.00 0.00 3.24
2966 3303 5.905331 ACCTCCATATGTCATTCCAGAGTAA 59.095 40.000 1.24 0.00 0.00 2.24
2968 3305 6.425210 TCCATATGTCATTCCAGAGTAAGG 57.575 41.667 1.24 0.00 0.00 2.69
2971 3308 6.484643 CCATATGTCATTCCAGAGTAAGGTTG 59.515 42.308 1.24 0.00 0.00 3.77
2972 3309 4.974645 TGTCATTCCAGAGTAAGGTTGT 57.025 40.909 0.00 0.00 0.00 3.32
3051 3417 2.623416 AGGAACCTTTTGCTGTAGTTGC 59.377 45.455 0.00 0.00 30.98 4.17
3198 3564 5.584649 TCAAGTTAAGGTGTGTTGAAGACTG 59.415 40.000 0.00 0.00 0.00 3.51
3214 3580 2.143122 GACTGCCAAGACGAATTGACA 58.857 47.619 6.03 0.66 31.55 3.58
3237 3603 1.131638 TCAAGCAACCAGGTCTCTGT 58.868 50.000 0.00 0.00 39.31 3.41
3272 3638 7.201794 GCTGTGTGATGTAGGAGTGTATTAGTA 60.202 40.741 0.00 0.00 0.00 1.82
3350 3718 2.170187 AGACTTGACATGGATGCTCTCC 59.830 50.000 0.00 0.00 45.19 3.71
3372 3740 7.350921 TCTCCTATTCCTGGATTAATTTCAGGT 59.649 37.037 25.25 16.27 45.97 4.00
3413 3781 2.901042 GGAGACGATGTCCCCCAC 59.099 66.667 0.00 0.00 32.18 4.61
3414 3782 2.732619 GGAGACGATGTCCCCCACC 61.733 68.421 0.00 0.00 32.18 4.61
3416 3784 1.537889 AGACGATGTCCCCCACCAA 60.538 57.895 0.00 0.00 32.18 3.67
3417 3785 1.131303 AGACGATGTCCCCCACCAAA 61.131 55.000 0.00 0.00 32.18 3.28
3447 3819 1.267806 CCTGCAGCGACTTTGTCAATT 59.732 47.619 8.66 0.00 32.09 2.32
3458 3830 6.575132 CGACTTTGTCAATTTCAAGATTTGC 58.425 36.000 0.00 0.00 32.09 3.68
3538 3928 5.551233 AGGTGGTGTACATGCATGTATATC 58.449 41.667 35.33 32.40 44.25 1.63
3567 3957 7.328737 AGTGTCTACTTTTGTACTGTGTTTCT 58.671 34.615 0.00 0.00 31.66 2.52
3571 3961 8.114905 GTCTACTTTTGTACTGTGTTTCTCAAC 58.885 37.037 0.00 0.00 0.00 3.18
3572 3962 6.811253 ACTTTTGTACTGTGTTTCTCAACA 57.189 33.333 0.00 0.00 40.82 3.33
3576 3966 8.873215 TTTTGTACTGTGTTTCTCAACAAAAA 57.127 26.923 10.04 0.00 44.72 1.94
3663 4054 1.133325 TGCCAGGTTATGTGGGTGTTT 60.133 47.619 0.00 0.00 35.39 2.83
3753 4144 4.335037 GGATGGCTCTGTTTCTGAGATTTC 59.665 45.833 7.61 1.78 32.36 2.17
3820 4211 7.559335 AATGTAGCAGAGATCCCAATACATA 57.441 36.000 7.98 0.00 32.71 2.29
3822 4213 8.844865 ATGTAGCAGAGATCCCAATACATATA 57.155 34.615 6.47 0.00 32.25 0.86
3823 4214 8.067751 TGTAGCAGAGATCCCAATACATATAC 57.932 38.462 0.00 0.00 0.00 1.47
4027 4419 7.748691 TCTGCACATTGTATGTTATATGCAT 57.251 32.000 3.79 3.79 42.70 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.093341 GCGTGGAGATAAACCCTAACCA 60.093 50.000 0.00 0.00 0.00 3.67
17 18 1.751351 CAGGTGAAGAGCGTGGAGATA 59.249 52.381 0.00 0.00 0.00 1.98
743 748 3.713615 CTGAAGCTCGCGTGCATGC 62.714 63.158 31.73 21.27 34.99 4.06
744 749 2.398429 CTGAAGCTCGCGTGCATG 59.602 61.111 31.73 15.87 34.99 4.06
745 750 3.494336 GCTGAAGCTCGCGTGCAT 61.494 61.111 31.73 22.53 38.21 3.96
755 760 0.534412 TGAGTGCTCCTAGCTGAAGC 59.466 55.000 0.00 2.92 42.97 3.86
756 761 1.824230 ACTGAGTGCTCCTAGCTGAAG 59.176 52.381 0.00 0.00 42.97 3.02
757 762 1.930251 ACTGAGTGCTCCTAGCTGAA 58.070 50.000 0.00 0.00 42.97 3.02
758 763 2.370349 GTACTGAGTGCTCCTAGCTGA 58.630 52.381 0.00 0.00 42.97 4.26
759 764 1.064803 CGTACTGAGTGCTCCTAGCTG 59.935 57.143 0.00 0.00 42.97 4.24
760 765 1.065345 TCGTACTGAGTGCTCCTAGCT 60.065 52.381 0.00 0.00 42.97 3.32
761 766 1.380524 TCGTACTGAGTGCTCCTAGC 58.619 55.000 0.00 0.00 42.82 3.42
762 767 2.287308 GCATCGTACTGAGTGCTCCTAG 60.287 54.545 0.00 0.00 34.85 3.02
763 768 1.676529 GCATCGTACTGAGTGCTCCTA 59.323 52.381 0.00 0.00 34.85 2.94
764 769 0.457851 GCATCGTACTGAGTGCTCCT 59.542 55.000 0.00 0.00 34.85 3.69
765 770 0.457851 AGCATCGTACTGAGTGCTCC 59.542 55.000 0.00 0.00 43.97 4.70
766 771 2.285827 AAGCATCGTACTGAGTGCTC 57.714 50.000 16.41 0.00 46.37 4.26
768 773 3.813529 AAAAAGCATCGTACTGAGTGC 57.186 42.857 0.00 0.00 37.84 4.40
769 774 5.168569 TCCTAAAAAGCATCGTACTGAGTG 58.831 41.667 0.00 0.00 0.00 3.51
770 775 5.401531 TCCTAAAAAGCATCGTACTGAGT 57.598 39.130 0.00 0.00 0.00 3.41
771 776 4.268884 GCTCCTAAAAAGCATCGTACTGAG 59.731 45.833 0.00 0.00 39.61 3.35
772 777 4.181578 GCTCCTAAAAAGCATCGTACTGA 58.818 43.478 0.00 0.00 39.61 3.41
773 778 3.000322 CGCTCCTAAAAAGCATCGTACTG 60.000 47.826 0.00 0.00 39.81 2.74
774 779 3.187700 CGCTCCTAAAAAGCATCGTACT 58.812 45.455 0.00 0.00 39.81 2.73
775 780 2.285660 GCGCTCCTAAAAAGCATCGTAC 60.286 50.000 0.00 0.00 39.81 3.67
776 781 1.931172 GCGCTCCTAAAAAGCATCGTA 59.069 47.619 0.00 0.00 39.81 3.43
777 782 0.727398 GCGCTCCTAAAAAGCATCGT 59.273 50.000 0.00 0.00 39.81 3.73
778 783 1.004504 GAGCGCTCCTAAAAAGCATCG 60.005 52.381 27.22 0.00 39.81 3.84
779 784 1.004504 CGAGCGCTCCTAAAAAGCATC 60.005 52.381 30.66 2.96 39.81 3.91
780 785 1.009829 CGAGCGCTCCTAAAAAGCAT 58.990 50.000 30.66 0.00 39.81 3.79
781 786 0.320421 ACGAGCGCTCCTAAAAAGCA 60.320 50.000 30.66 0.00 39.81 3.91
782 787 0.796927 AACGAGCGCTCCTAAAAAGC 59.203 50.000 30.66 4.24 36.38 3.51
783 788 3.678548 AGTTAACGAGCGCTCCTAAAAAG 59.321 43.478 30.66 17.26 0.00 2.27
784 789 3.656559 AGTTAACGAGCGCTCCTAAAAA 58.343 40.909 30.66 15.17 0.00 1.94
785 790 3.308438 AGTTAACGAGCGCTCCTAAAA 57.692 42.857 30.66 16.87 0.00 1.52
786 791 4.439305 TTAGTTAACGAGCGCTCCTAAA 57.561 40.909 30.66 18.60 0.00 1.85
787 792 4.644103 ATTAGTTAACGAGCGCTCCTAA 57.356 40.909 30.66 27.45 0.00 2.69
788 793 4.357142 CAATTAGTTAACGAGCGCTCCTA 58.643 43.478 30.66 21.50 0.00 2.94
789 794 3.187700 CAATTAGTTAACGAGCGCTCCT 58.812 45.455 30.66 22.52 0.00 3.69
790 795 2.285660 GCAATTAGTTAACGAGCGCTCC 60.286 50.000 30.66 16.60 0.00 4.70
791 796 2.603560 AGCAATTAGTTAACGAGCGCTC 59.396 45.455 27.64 27.64 0.00 5.03
792 797 2.603560 GAGCAATTAGTTAACGAGCGCT 59.396 45.455 11.27 11.27 0.00 5.92
793 798 2.603560 AGAGCAATTAGTTAACGAGCGC 59.396 45.455 0.00 0.00 0.00 5.92
794 799 3.243177 GGAGAGCAATTAGTTAACGAGCG 59.757 47.826 0.00 0.00 0.00 5.03
795 800 4.434520 AGGAGAGCAATTAGTTAACGAGC 58.565 43.478 0.00 1.72 0.00 5.03
796 801 6.969828 AAAGGAGAGCAATTAGTTAACGAG 57.030 37.500 0.00 0.00 0.00 4.18
802 807 7.717436 GCCTCTATAAAAGGAGAGCAATTAGTT 59.283 37.037 5.23 0.00 38.31 2.24
803 808 7.071824 AGCCTCTATAAAAGGAGAGCAATTAGT 59.928 37.037 5.23 0.00 38.31 2.24
804 809 7.387397 CAGCCTCTATAAAAGGAGAGCAATTAG 59.613 40.741 5.23 0.00 38.31 1.73
805 810 7.071196 TCAGCCTCTATAAAAGGAGAGCAATTA 59.929 37.037 5.23 0.00 38.31 1.40
806 811 6.060788 CAGCCTCTATAAAAGGAGAGCAATT 58.939 40.000 5.23 0.00 38.31 2.32
807 812 5.367937 TCAGCCTCTATAAAAGGAGAGCAAT 59.632 40.000 5.23 0.00 38.31 3.56
808 813 4.716784 TCAGCCTCTATAAAAGGAGAGCAA 59.283 41.667 5.23 0.00 38.31 3.91
809 814 4.290093 TCAGCCTCTATAAAAGGAGAGCA 58.710 43.478 5.23 0.00 38.31 4.26
810 815 4.946478 TCAGCCTCTATAAAAGGAGAGC 57.054 45.455 5.23 0.00 38.31 4.09
811 816 8.592809 ACAATATCAGCCTCTATAAAAGGAGAG 58.407 37.037 5.23 0.00 39.18 3.20
812 817 8.497910 ACAATATCAGCCTCTATAAAAGGAGA 57.502 34.615 5.23 3.08 35.83 3.71
813 818 8.592809 AGACAATATCAGCCTCTATAAAAGGAG 58.407 37.037 5.23 0.00 35.83 3.69
814 819 8.497910 AGACAATATCAGCCTCTATAAAAGGA 57.502 34.615 5.23 0.00 35.83 3.36
815 820 9.566432 AAAGACAATATCAGCCTCTATAAAAGG 57.434 33.333 0.00 0.00 36.95 3.11
838 843 5.432885 TCGGCCTTTACTTTTTCTGAAAG 57.567 39.130 0.00 0.00 0.00 2.62
839 844 7.362574 CCATATCGGCCTTTACTTTTTCTGAAA 60.363 37.037 0.00 0.00 0.00 2.69
840 845 6.094881 CCATATCGGCCTTTACTTTTTCTGAA 59.905 38.462 0.00 0.00 0.00 3.02
841 846 5.588648 CCATATCGGCCTTTACTTTTTCTGA 59.411 40.000 0.00 0.00 0.00 3.27
842 847 5.221048 CCCATATCGGCCTTTACTTTTTCTG 60.221 44.000 0.00 0.00 0.00 3.02
844 849 4.499188 GCCCATATCGGCCTTTACTTTTTC 60.499 45.833 0.00 0.00 43.66 2.29
846 851 2.956333 GCCCATATCGGCCTTTACTTTT 59.044 45.455 0.00 0.00 43.66 2.27
848 853 2.271944 GCCCATATCGGCCTTTACTT 57.728 50.000 0.00 0.00 43.66 2.24
903 908 3.854669 CCTAGCAGACCTGGCGGG 61.855 72.222 11.83 11.83 41.89 6.13
978 991 3.253921 TGGACGTGAAGATCGTTTGACTA 59.746 43.478 0.00 0.00 41.64 2.59
1010 1031 4.831913 GAGCATCATCCACTCCATGGGTA 61.832 52.174 13.02 0.00 41.38 3.69
1011 1032 4.146137 GAGCATCATCCACTCCATGGGT 62.146 54.545 13.02 5.94 45.92 4.51
1174 1195 1.550130 CCCGGCCACTTCAGGTAGAA 61.550 60.000 2.24 0.00 34.41 2.10
1430 1451 0.318614 CTGCGCCACCACGAATTTTT 60.319 50.000 4.18 0.00 34.06 1.94
1690 1711 0.179048 TGAATAGGCAGCCGATGGTG 60.179 55.000 7.97 0.00 42.91 4.17
1798 1819 0.923358 TCCTCCGGGGCAACATTAAT 59.077 50.000 0.00 0.00 39.74 1.40
1877 1898 1.072331 ACACCATGTCTTGTGTCCTCC 59.928 52.381 0.21 0.00 41.70 4.30
1906 1927 1.629013 TGAGATGTGATGACGAACGC 58.371 50.000 0.00 0.00 0.00 4.84
1940 1961 3.214696 TGTATGAGAGAGAGGCATCGA 57.785 47.619 0.00 0.00 0.00 3.59
1942 1963 3.995705 GCATTGTATGAGAGAGAGGCATC 59.004 47.826 0.00 0.00 0.00 3.91
1988 2009 1.737838 TAGCTCATTTGACTTGGCCG 58.262 50.000 0.00 0.00 0.00 6.13
2022 2043 2.815647 GCACGCTCCCCTTTCTCG 60.816 66.667 0.00 0.00 0.00 4.04
2063 2084 9.750125 TCACATGCTTAGTAATAGTATCAACAG 57.250 33.333 0.00 0.00 0.00 3.16
2079 2100 7.330262 TGTACTGATGAATCTTCACATGCTTA 58.670 34.615 0.00 0.00 40.49 3.09
2086 2107 7.550551 TCCTTCAATGTACTGATGAATCTTCAC 59.449 37.037 8.35 0.00 40.49 3.18
2087 2108 7.623630 TCCTTCAATGTACTGATGAATCTTCA 58.376 34.615 8.35 0.00 42.14 3.02
2089 2110 7.855375 TCTCCTTCAATGTACTGATGAATCTT 58.145 34.615 8.35 0.00 33.03 2.40
2162 2183 3.348119 GGAACAAAGGGATGGAGAAGAC 58.652 50.000 0.00 0.00 0.00 3.01
2185 2206 3.380320 CAGAAAAACTTTGGGAACTCGGT 59.620 43.478 0.00 0.00 0.00 4.69
2294 2318 9.900112 AGACCTTATATTAGTTTACAGAGGGAT 57.100 33.333 0.00 0.00 0.00 3.85
2331 2504 8.634188 AAAGTACCCCCTCTGTAAACTAATAT 57.366 34.615 0.00 0.00 0.00 1.28
2360 2533 4.806330 TGAGAAGCTTAGTACAAAGACCG 58.194 43.478 0.00 0.00 0.00 4.79
2510 2684 8.103305 GGTGATCATTACCACTACCATCATAAT 58.897 37.037 0.00 0.00 38.12 1.28
2587 2761 9.575868 TTAGTTGATATTTGGACTAAAACCACA 57.424 29.630 0.00 0.00 37.13 4.17
2704 2881 5.796424 ATGGAGAAGCTCAAATTTGTGTT 57.204 34.783 17.47 10.60 31.08 3.32
2778 3104 4.214545 AGCACATTGTTGATTTTGGCATTG 59.785 37.500 0.00 0.00 0.00 2.82
2782 3108 7.775397 ATAATAGCACATTGTTGATTTTGGC 57.225 32.000 0.00 0.00 0.00 4.52
2817 3143 4.591321 TTTGCAGGGACATAGAAGGAAT 57.409 40.909 0.00 0.00 0.00 3.01
2824 3150 3.012518 CTGGAGTTTTGCAGGGACATAG 58.987 50.000 0.00 0.00 38.94 2.23
2853 3179 4.850680 TGTGTTATTCCAGAATACCCACC 58.149 43.478 17.98 8.16 36.04 4.61
2857 3183 7.257722 CACCATTTGTGTTATTCCAGAATACC 58.742 38.462 0.00 0.00 40.26 2.73
2886 3212 3.018856 CAGCTAATTGGAGATGTTGCCA 58.981 45.455 0.00 0.00 0.00 4.92
2887 3213 3.065925 GTCAGCTAATTGGAGATGTTGCC 59.934 47.826 0.00 0.00 34.41 4.52
2888 3214 3.242543 CGTCAGCTAATTGGAGATGTTGC 60.243 47.826 0.00 0.00 34.41 4.17
2906 3243 4.794278 TTCTATGCAGAAACTACCGTCA 57.206 40.909 0.00 0.00 37.85 4.35
2909 3246 6.150318 ACGATATTCTATGCAGAAACTACCG 58.850 40.000 0.00 0.00 43.89 4.02
2921 3258 8.926710 GGAGGTATGAAACAACGATATTCTATG 58.073 37.037 0.00 0.00 0.00 2.23
2931 3268 5.815222 TGACATATGGAGGTATGAAACAACG 59.185 40.000 7.80 0.00 35.96 4.10
2964 3301 8.485578 AATTGGAGATGGTAAAAACAACCTTA 57.514 30.769 0.00 0.00 37.91 2.69
2966 3303 6.994421 AATTGGAGATGGTAAAAACAACCT 57.006 33.333 0.00 0.00 37.91 3.50
2968 3305 6.073276 GCCAAATTGGAGATGGTAAAAACAAC 60.073 38.462 17.47 0.00 40.96 3.32
2971 3308 5.546526 TGCCAAATTGGAGATGGTAAAAAC 58.453 37.500 17.47 0.00 40.96 2.43
2972 3309 5.815233 TGCCAAATTGGAGATGGTAAAAA 57.185 34.783 17.47 0.00 40.96 1.94
3003 3340 2.050144 GGATAGATTGTCTGGCAGGGA 58.950 52.381 15.73 1.04 0.00 4.20
3034 3400 0.951558 CGGCAACTACAGCAAAAGGT 59.048 50.000 0.00 0.00 0.00 3.50
3051 3417 4.404098 GGCACACTACCCCACCGG 62.404 72.222 0.00 0.00 37.81 5.28
3163 3529 5.189736 ACACCTTAACTTGAGCCATGAGATA 59.810 40.000 0.00 0.00 0.00 1.98
3198 3564 4.545610 TGATTTTGTCAATTCGTCTTGGC 58.454 39.130 0.00 0.00 32.78 4.52
3214 3580 3.571401 CAGAGACCTGGTTGCTTGATTTT 59.429 43.478 0.00 0.00 36.77 1.82
3237 3603 0.669619 CATCACACAGCAACAGCCAA 59.330 50.000 0.00 0.00 0.00 4.52
3412 3780 0.676782 GCAGGCACCTCGTATTTGGT 60.677 55.000 0.00 0.00 36.96 3.67
3413 3781 0.676466 TGCAGGCACCTCGTATTTGG 60.676 55.000 0.00 0.00 0.00 3.28
3414 3782 0.729116 CTGCAGGCACCTCGTATTTG 59.271 55.000 5.57 0.00 0.00 2.32
3416 3784 1.450312 GCTGCAGGCACCTCGTATT 60.450 57.895 17.12 0.00 41.35 1.89
3417 3785 2.187946 GCTGCAGGCACCTCGTAT 59.812 61.111 17.12 0.00 41.35 3.06
3447 3819 1.305219 CGAGGCCGGCAAATCTTGAA 61.305 55.000 30.85 0.00 0.00 2.69
3473 3845 2.388735 CTACACCTATGAGCACCTCCA 58.611 52.381 0.00 0.00 0.00 3.86
3538 3928 6.701841 ACACAGTACAAAAGTAGACACTCATG 59.298 38.462 0.00 0.00 32.29 3.07
3551 3941 8.873215 TTTTTGTTGAGAAACACAGTACAAAA 57.127 26.923 0.00 0.00 40.28 2.44
3577 3967 5.416326 CCCAAATCCATCAATGCATGTTTTT 59.584 36.000 0.00 0.00 0.00 1.94
3578 3968 4.944930 CCCAAATCCATCAATGCATGTTTT 59.055 37.500 0.00 0.00 0.00 2.43
3579 3969 4.019141 ACCCAAATCCATCAATGCATGTTT 60.019 37.500 0.00 0.00 0.00 2.83
3588 3978 7.493499 ACAATTCAATACCCAAATCCATCAA 57.507 32.000 0.00 0.00 0.00 2.57
3701 4092 2.093288 GGTTGGATCAGAGAGCATCACA 60.093 50.000 0.00 0.00 37.82 3.58
3820 4211 4.279671 TGCCAAACAGAAAAACGATGGTAT 59.720 37.500 0.00 0.00 0.00 2.73
3822 4213 2.428890 TGCCAAACAGAAAAACGATGGT 59.571 40.909 0.00 0.00 0.00 3.55
3823 4214 3.090952 TGCCAAACAGAAAAACGATGG 57.909 42.857 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.