Multiple sequence alignment - TraesCS6B01G010300

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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 TraesCS6B01G010300 chr6B 100.000 3458 0 0 1 3458 6214394 6210937 0.000000e+00 6386.0
1 TraesCS6B01G010300 chr6B 98.372 983 13 3 2476 3458 604690353 604691332 0.000000e+00 1724.0
2 TraesCS6B01G010300 chr6A 99.176 971 8 0 2488 3458 569701806 569700836 0.000000e+00 1749.0
3 TraesCS6B01G010300 chr3A 98.974 975 10 0 2484 3458 730996629 730997603 0.000000e+00 1746.0
4 TraesCS6B01G010300 chr3A 86.747 1494 158 19 988 2467 90293298 90294765 0.000000e+00 1626.0
5 TraesCS6B01G010300 chr3A 84.997 1433 179 17 1013 2427 90364105 90365519 0.000000e+00 1423.0
6 TraesCS6B01G010300 chr3A 82.322 758 108 23 44 783 315537387 315538136 4.870000e-178 634.0
7 TraesCS6B01G010300 chr3A 82.633 714 105 18 76 779 723716858 723716154 6.340000e-172 614.0
8 TraesCS6B01G010300 chr1B 98.872 975 11 0 2484 3458 60346201 60347175 0.000000e+00 1740.0
9 TraesCS6B01G010300 chr1B 98.768 974 12 0 2485 3458 22994767 22995740 0.000000e+00 1733.0
10 TraesCS6B01G010300 chr4A 98.970 971 10 0 2488 3458 441957506 441956536 0.000000e+00 1738.0
11 TraesCS6B01G010300 chr4A 84.417 738 91 23 55 779 465772678 465773404 0.000000e+00 704.0
12 TraesCS6B01G010300 chr2A 98.868 972 10 1 2487 3458 159203356 159202386 0.000000e+00 1733.0
13 TraesCS6B01G010300 chr2B 98.672 979 8 2 2484 3458 161707312 161706335 0.000000e+00 1731.0
14 TraesCS6B01G010300 chr7A 98.570 979 13 1 2481 3458 9721031 9722009 0.000000e+00 1729.0
15 TraesCS6B01G010300 chr3D 87.292 1503 152 21 983 2467 75946782 75948263 0.000000e+00 1681.0
16 TraesCS6B01G010300 chr3D 85.395 1431 173 18 1015 2427 75962120 75963532 0.000000e+00 1452.0
17 TraesCS6B01G010300 chr3D 83.445 749 96 26 43 779 36629865 36630597 0.000000e+00 671.0
18 TraesCS6B01G010300 chr3B 86.749 1449 164 15 1030 2467 122826299 122827730 0.000000e+00 1587.0
19 TraesCS6B01G010300 chr3B 85.177 1410 173 18 1030 2427 123033357 123034742 0.000000e+00 1413.0
20 TraesCS6B01G010300 chr3B 83.152 736 95 25 53 778 549433377 549434093 0.000000e+00 645.0
21 TraesCS6B01G010300 chr3B 83.516 91 11 4 2069 2157 39632907 39632819 7.950000e-12 82.4
22 TraesCS6B01G010300 chr3B 82.418 91 12 4 2069 2157 39570464 39570376 3.700000e-10 76.8
23 TraesCS6B01G010300 chr6D 95.390 911 25 5 1579 2487 3038420 3037525 0.000000e+00 1434.0
24 TraesCS6B01G010300 chr6D 94.622 688 15 5 901 1588 3040301 3039636 0.000000e+00 1046.0
25 TraesCS6B01G010300 chr6D 82.148 745 109 24 43 778 9539987 9540716 4.900000e-173 617.0
26 TraesCS6B01G010300 chr4D 85.014 734 92 17 55 779 111143863 111143139 0.000000e+00 730.0
27 TraesCS6B01G010300 chr1A 84.563 732 97 15 55 779 376143220 376143942 0.000000e+00 712.0
28 TraesCS6B01G010300 chr1A 83.287 712 93 22 83 779 261379604 261380304 1.750000e-177 632.0
29 TraesCS6B01G010300 chr1A 70.000 960 197 67 1033 1942 130149255 130150173 3.670000e-15 93.5
30 TraesCS6B01G010300 chr1D 71.429 483 86 40 1033 1477 118510524 118510992 2.860000e-11 80.5
31 TraesCS6B01G010300 chr2D 83.529 85 11 2 2097 2179 84744038 84744121 3.700000e-10 76.8


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 TraesCS6B01G010300 chr6B 6210937 6214394 3457 True 6386 6386 100.000 1 3458 1 chr6B.!!$R1 3457
1 TraesCS6B01G010300 chr6B 604690353 604691332 979 False 1724 1724 98.372 2476 3458 1 chr6B.!!$F1 982
2 TraesCS6B01G010300 chr6A 569700836 569701806 970 True 1749 1749 99.176 2488 3458 1 chr6A.!!$R1 970
3 TraesCS6B01G010300 chr3A 730996629 730997603 974 False 1746 1746 98.974 2484 3458 1 chr3A.!!$F4 974
4 TraesCS6B01G010300 chr3A 90293298 90294765 1467 False 1626 1626 86.747 988 2467 1 chr3A.!!$F1 1479
5 TraesCS6B01G010300 chr3A 90364105 90365519 1414 False 1423 1423 84.997 1013 2427 1 chr3A.!!$F2 1414
6 TraesCS6B01G010300 chr3A 315537387 315538136 749 False 634 634 82.322 44 783 1 chr3A.!!$F3 739
7 TraesCS6B01G010300 chr3A 723716154 723716858 704 True 614 614 82.633 76 779 1 chr3A.!!$R1 703
8 TraesCS6B01G010300 chr1B 60346201 60347175 974 False 1740 1740 98.872 2484 3458 1 chr1B.!!$F2 974
9 TraesCS6B01G010300 chr1B 22994767 22995740 973 False 1733 1733 98.768 2485 3458 1 chr1B.!!$F1 973
10 TraesCS6B01G010300 chr4A 441956536 441957506 970 True 1738 1738 98.970 2488 3458 1 chr4A.!!$R1 970
11 TraesCS6B01G010300 chr4A 465772678 465773404 726 False 704 704 84.417 55 779 1 chr4A.!!$F1 724
12 TraesCS6B01G010300 chr2A 159202386 159203356 970 True 1733 1733 98.868 2487 3458 1 chr2A.!!$R1 971
13 TraesCS6B01G010300 chr2B 161706335 161707312 977 True 1731 1731 98.672 2484 3458 1 chr2B.!!$R1 974
14 TraesCS6B01G010300 chr7A 9721031 9722009 978 False 1729 1729 98.570 2481 3458 1 chr7A.!!$F1 977
15 TraesCS6B01G010300 chr3D 75946782 75948263 1481 False 1681 1681 87.292 983 2467 1 chr3D.!!$F2 1484
16 TraesCS6B01G010300 chr3D 75962120 75963532 1412 False 1452 1452 85.395 1015 2427 1 chr3D.!!$F3 1412
17 TraesCS6B01G010300 chr3D 36629865 36630597 732 False 671 671 83.445 43 779 1 chr3D.!!$F1 736
18 TraesCS6B01G010300 chr3B 122826299 122827730 1431 False 1587 1587 86.749 1030 2467 1 chr3B.!!$F1 1437
19 TraesCS6B01G010300 chr3B 123033357 123034742 1385 False 1413 1413 85.177 1030 2427 1 chr3B.!!$F2 1397
20 TraesCS6B01G010300 chr3B 549433377 549434093 716 False 645 645 83.152 53 778 1 chr3B.!!$F3 725
21 TraesCS6B01G010300 chr6D 3037525 3040301 2776 True 1240 1434 95.006 901 2487 2 chr6D.!!$R1 1586
22 TraesCS6B01G010300 chr6D 9539987 9540716 729 False 617 617 82.148 43 778 1 chr6D.!!$F1 735
23 TraesCS6B01G010300 chr4D 111143139 111143863 724 True 730 730 85.014 55 779 1 chr4D.!!$R1 724
24 TraesCS6B01G010300 chr1A 376143220 376143942 722 False 712 712 84.563 55 779 1 chr1A.!!$F3 724
25 TraesCS6B01G010300 chr1A 261379604 261380304 700 False 632 632 83.287 83 779 1 chr1A.!!$F2 696

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
776 807 0.169009 GCACGGGCTCTTTTTGCTAG 59.831 55.0 0.00 0.00 36.96 3.42 F
893 924 0.801251 GCAAGATATCTCGGCCATGC 59.199 55.0 15.14 12.04 0.00 4.06 F
981 1012 1.067295 AGCTCCACATTCCACTTCCA 58.933 50.0 0.00 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 3263 0.546122 TCAGCACCCACAAGAACTGT 59.454 50.0 0.00 0.0 39.56 3.55 R
2006 3283 0.669318 CTCGCTGCGGTTGTCCTTTA 60.669 55.0 23.03 0.0 0.00 1.85 R
2659 3957 1.312815 GCCACAGTTTGAGACTTGCT 58.687 50.0 0.00 0.0 36.10 3.91 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 7.601705 AAAAATCCCTGTTTCTGAGAAATCA 57.398 32.000 11.20 9.82 0.00 2.57
25 26 7.601705 AAAATCCCTGTTTCTGAGAAATCAA 57.398 32.000 11.20 0.00 0.00 2.57
26 27 6.581171 AATCCCTGTTTCTGAGAAATCAAC 57.419 37.500 11.20 0.00 0.00 3.18
27 28 4.398319 TCCCTGTTTCTGAGAAATCAACC 58.602 43.478 11.20 0.00 0.00 3.77
28 29 3.507622 CCCTGTTTCTGAGAAATCAACCC 59.492 47.826 11.20 0.00 0.00 4.11
29 30 4.144297 CCTGTTTCTGAGAAATCAACCCA 58.856 43.478 11.20 2.49 0.00 4.51
30 31 4.022849 CCTGTTTCTGAGAAATCAACCCAC 60.023 45.833 11.20 0.00 0.00 4.61
31 32 4.531854 TGTTTCTGAGAAATCAACCCACA 58.468 39.130 11.20 0.00 0.00 4.17
32 33 4.580167 TGTTTCTGAGAAATCAACCCACAG 59.420 41.667 11.20 0.00 0.00 3.66
33 34 4.437682 TTCTGAGAAATCAACCCACAGT 57.562 40.909 0.00 0.00 0.00 3.55
34 35 4.008074 TCTGAGAAATCAACCCACAGTC 57.992 45.455 0.00 0.00 0.00 3.51
35 36 3.648067 TCTGAGAAATCAACCCACAGTCT 59.352 43.478 0.00 0.00 0.00 3.24
36 37 4.103153 TCTGAGAAATCAACCCACAGTCTT 59.897 41.667 0.00 0.00 0.00 3.01
37 38 5.306937 TCTGAGAAATCAACCCACAGTCTTA 59.693 40.000 0.00 0.00 0.00 2.10
38 39 5.935945 TGAGAAATCAACCCACAGTCTTAA 58.064 37.500 0.00 0.00 0.00 1.85
39 40 5.763204 TGAGAAATCAACCCACAGTCTTAAC 59.237 40.000 0.00 0.00 0.00 2.01
40 41 5.941788 AGAAATCAACCCACAGTCTTAACT 58.058 37.500 0.00 0.00 35.60 2.24
41 42 6.365520 AGAAATCAACCCACAGTCTTAACTT 58.634 36.000 0.00 0.00 31.71 2.66
51 52 6.037391 CCCACAGTCTTAACTTAAACGTTTCA 59.963 38.462 18.42 5.67 31.71 2.69
67 68 8.806177 AAACGTTTCACTTTTTGTAGAAAACT 57.194 26.923 7.96 0.00 32.16 2.66
111 113 6.708949 TCAACTGTGGTCCTATTTTAAGTGAC 59.291 38.462 0.00 0.00 0.00 3.67
129 132 6.635030 AGTGACAATAGAAAACCTTTCACC 57.365 37.500 2.25 0.00 34.01 4.02
160 167 6.590234 AGAAAACCCACTGATATTTTGGTC 57.410 37.500 0.00 0.00 0.00 4.02
175 182 3.420300 TTGGTCAATTAACCTGCCGTA 57.580 42.857 0.00 0.00 40.20 4.02
182 189 2.919666 TTAACCTGCCGTACGTCTAC 57.080 50.000 15.21 1.21 0.00 2.59
342 359 5.279056 CCCGTTAACCATTTTTAAAGGCTGA 60.279 40.000 0.00 0.00 38.53 4.26
349 366 8.422577 AACCATTTTTAAAGGCTGATTAGAGT 57.577 30.769 0.00 0.00 0.00 3.24
350 367 9.528489 AACCATTTTTAAAGGCTGATTAGAGTA 57.472 29.630 0.00 0.00 0.00 2.59
361 378 8.499403 AGGCTGATTAGAGTAAATTCAAACTC 57.501 34.615 7.23 7.23 42.02 3.01
526 550 6.039493 ACTTACTTAGTAGTGGACGATCCATG 59.961 42.308 9.47 0.00 41.53 3.66
537 561 4.023279 TGGACGATCCATGTTTCTTTTGTG 60.023 41.667 3.02 0.00 42.67 3.33
541 565 2.028130 TCCATGTTTCTTTTGTGCCGT 58.972 42.857 0.00 0.00 0.00 5.68
561 585 4.375908 CCGTTGCCGATTCAAATTGAAAAC 60.376 41.667 12.75 10.59 40.12 2.43
583 608 7.980742 AACGAACACCTTAGAAAAACAAATC 57.019 32.000 0.00 0.00 0.00 2.17
619 644 5.929697 AACATCTATAACCATGCATGTCG 57.070 39.130 24.58 13.14 0.00 4.35
649 675 5.480205 GAGAGTGGAAAGAAGGATAAACGT 58.520 41.667 0.00 0.00 0.00 3.99
684 710 7.093201 ACAAGATGCCATGTTGAAATAAAGGAT 60.093 33.333 20.13 0.00 37.04 3.24
721 749 4.250464 GGTTCGAGTCATGGTTATTGTGA 58.750 43.478 0.00 0.00 0.00 3.58
725 753 6.709018 TCGAGTCATGGTTATTGTGATAGA 57.291 37.500 0.00 0.00 0.00 1.98
733 761 3.802685 GGTTATTGTGATAGAGGCGTGTC 59.197 47.826 0.00 0.00 0.00 3.67
734 762 4.441634 GGTTATTGTGATAGAGGCGTGTCT 60.442 45.833 0.00 0.00 0.00 3.41
739 770 3.745975 TGTGATAGAGGCGTGTCTTTTTG 59.254 43.478 0.00 0.00 0.00 2.44
755 786 2.270352 TTTGTCTCTCCCGTTGCAAT 57.730 45.000 0.59 0.00 0.00 3.56
771 802 0.240945 CAATCGCACGGGCTCTTTTT 59.759 50.000 8.62 0.00 38.10 1.94
772 803 0.240945 AATCGCACGGGCTCTTTTTG 59.759 50.000 8.62 0.00 38.10 2.44
773 804 2.200170 ATCGCACGGGCTCTTTTTGC 62.200 55.000 8.62 0.00 38.10 3.68
774 805 2.908073 CGCACGGGCTCTTTTTGCT 61.908 57.895 8.62 0.00 38.10 3.91
775 806 1.573829 CGCACGGGCTCTTTTTGCTA 61.574 55.000 8.62 0.00 38.10 3.49
776 807 0.169009 GCACGGGCTCTTTTTGCTAG 59.831 55.000 0.00 0.00 36.96 3.42
777 808 1.523758 CACGGGCTCTTTTTGCTAGT 58.476 50.000 0.00 0.00 0.00 2.57
778 809 2.695359 CACGGGCTCTTTTTGCTAGTA 58.305 47.619 0.00 0.00 0.00 1.82
779 810 2.415512 CACGGGCTCTTTTTGCTAGTAC 59.584 50.000 0.00 0.00 0.00 2.73
780 811 2.302157 ACGGGCTCTTTTTGCTAGTACT 59.698 45.455 0.00 0.00 0.00 2.73
781 812 3.512724 ACGGGCTCTTTTTGCTAGTACTA 59.487 43.478 1.89 1.89 0.00 1.82
782 813 4.113354 CGGGCTCTTTTTGCTAGTACTAG 58.887 47.826 23.25 23.25 36.29 2.57
801 832 6.823678 ACTAGCTAAATACATGTACGTTGC 57.176 37.500 7.96 11.17 0.00 4.17
802 833 6.570692 ACTAGCTAAATACATGTACGTTGCT 58.429 36.000 21.62 21.62 0.00 3.91
803 834 7.709947 ACTAGCTAAATACATGTACGTTGCTA 58.290 34.615 21.56 21.56 0.00 3.49
804 835 8.358148 ACTAGCTAAATACATGTACGTTGCTAT 58.642 33.333 22.41 14.97 0.00 2.97
805 836 7.408132 AGCTAAATACATGTACGTTGCTATG 57.592 36.000 18.59 0.00 0.00 2.23
806 837 6.423905 AGCTAAATACATGTACGTTGCTATGG 59.576 38.462 18.59 0.00 0.00 2.74
807 838 6.347402 GCTAAATACATGTACGTTGCTATGGG 60.347 42.308 7.96 0.00 0.00 4.00
808 839 4.948341 ATACATGTACGTTGCTATGGGA 57.052 40.909 7.96 0.00 0.00 4.37
809 840 2.901249 ACATGTACGTTGCTATGGGAC 58.099 47.619 0.00 0.00 0.00 4.46
810 841 1.858458 CATGTACGTTGCTATGGGACG 59.142 52.381 0.00 0.00 42.13 4.79
811 842 1.175654 TGTACGTTGCTATGGGACGA 58.824 50.000 0.00 0.00 39.85 4.20
812 843 1.545136 TGTACGTTGCTATGGGACGAA 59.455 47.619 0.00 0.00 39.85 3.85
813 844 2.029200 TGTACGTTGCTATGGGACGAAA 60.029 45.455 0.00 0.00 39.85 3.46
814 845 2.396590 ACGTTGCTATGGGACGAAAT 57.603 45.000 1.90 0.00 39.85 2.17
815 846 3.530265 ACGTTGCTATGGGACGAAATA 57.470 42.857 1.90 0.00 39.85 1.40
816 847 3.864243 ACGTTGCTATGGGACGAAATAA 58.136 40.909 1.90 0.00 39.85 1.40
817 848 3.869246 ACGTTGCTATGGGACGAAATAAG 59.131 43.478 1.90 0.00 39.85 1.73
818 849 3.869246 CGTTGCTATGGGACGAAATAAGT 59.131 43.478 0.00 0.00 38.99 2.24
819 850 5.045215 CGTTGCTATGGGACGAAATAAGTA 58.955 41.667 0.00 0.00 38.99 2.24
820 851 5.521010 CGTTGCTATGGGACGAAATAAGTAA 59.479 40.000 0.00 0.00 38.99 2.24
821 852 6.202188 CGTTGCTATGGGACGAAATAAGTAAT 59.798 38.462 0.00 0.00 38.99 1.89
822 853 7.383029 CGTTGCTATGGGACGAAATAAGTAATA 59.617 37.037 0.00 0.00 38.99 0.98
823 854 9.216117 GTTGCTATGGGACGAAATAAGTAATAT 57.784 33.333 0.00 0.00 0.00 1.28
824 855 9.787435 TTGCTATGGGACGAAATAAGTAATATT 57.213 29.630 0.00 0.00 35.69 1.28
825 856 9.787435 TGCTATGGGACGAAATAAGTAATATTT 57.213 29.630 0.00 0.00 44.92 1.40
859 890 8.239038 GGATAGATCCGATGGTCTAAATATGA 57.761 38.462 0.00 0.00 37.19 2.15
860 891 8.865090 GGATAGATCCGATGGTCTAAATATGAT 58.135 37.037 0.00 0.00 37.19 2.45
861 892 9.689976 GATAGATCCGATGGTCTAAATATGATG 57.310 37.037 0.00 0.00 31.29 3.07
862 893 7.724490 AGATCCGATGGTCTAAATATGATGA 57.276 36.000 0.00 0.00 0.00 2.92
863 894 8.316497 AGATCCGATGGTCTAAATATGATGAT 57.684 34.615 0.00 0.00 0.00 2.45
864 895 8.766476 AGATCCGATGGTCTAAATATGATGATT 58.234 33.333 0.00 0.00 0.00 2.57
865 896 9.388506 GATCCGATGGTCTAAATATGATGATTT 57.611 33.333 0.00 0.00 33.60 2.17
887 918 9.604626 GATTTATTTTCTTGCAAGATATCTCGG 57.395 33.333 28.89 2.87 34.49 4.63
888 919 4.882671 TTTTCTTGCAAGATATCTCGGC 57.117 40.909 28.89 17.90 34.49 5.54
889 920 2.533266 TCTTGCAAGATATCTCGGCC 57.467 50.000 25.16 0.00 0.00 6.13
890 921 1.762370 TCTTGCAAGATATCTCGGCCA 59.238 47.619 25.16 12.47 0.00 5.36
891 922 2.369860 TCTTGCAAGATATCTCGGCCAT 59.630 45.455 25.16 0.00 0.00 4.40
892 923 2.174363 TGCAAGATATCTCGGCCATG 57.826 50.000 20.49 10.14 0.00 3.66
893 924 0.801251 GCAAGATATCTCGGCCATGC 59.199 55.000 15.14 12.04 0.00 4.06
894 925 1.446907 CAAGATATCTCGGCCATGCC 58.553 55.000 5.51 0.00 46.75 4.40
977 1008 1.209019 CAGCTAGCTCCACATTCCACT 59.791 52.381 16.15 0.00 0.00 4.00
978 1009 1.912043 AGCTAGCTCCACATTCCACTT 59.088 47.619 12.68 0.00 0.00 3.16
979 1010 2.093235 AGCTAGCTCCACATTCCACTTC 60.093 50.000 12.68 0.00 0.00 3.01
980 1011 2.911484 CTAGCTCCACATTCCACTTCC 58.089 52.381 0.00 0.00 0.00 3.46
981 1012 1.067295 AGCTCCACATTCCACTTCCA 58.933 50.000 0.00 0.00 0.00 3.53
986 1017 2.094675 CCACATTCCACTTCCACATCC 58.905 52.381 0.00 0.00 0.00 3.51
1286 1329 2.093658 GGGACATCACGGACTACATGTT 60.094 50.000 2.30 0.00 29.43 2.71
1477 1520 3.718210 CTCGCCGCCTACTTCCACC 62.718 68.421 0.00 0.00 0.00 4.61
1481 1524 1.817209 CCGCCTACTTCCACCTCTC 59.183 63.158 0.00 0.00 0.00 3.20
1654 2922 4.201679 TACCCGACATGCGCGAGG 62.202 66.667 12.10 10.92 39.11 4.63
1801 3069 3.068691 CCTTCCTGGACGCCTCGA 61.069 66.667 0.00 0.00 38.35 4.04
1837 3114 4.260375 GCAACAACAACAACAACAACAACA 60.260 37.500 0.00 0.00 0.00 3.33
1849 3126 4.279671 ACAACAACAACAACCTGTTCAAGA 59.720 37.500 0.00 0.00 38.77 3.02
2006 3283 1.143684 ACAGTTCTTGTGGGTGCTGAT 59.856 47.619 0.00 0.00 38.99 2.90
2007 3284 2.371841 ACAGTTCTTGTGGGTGCTGATA 59.628 45.455 0.00 0.00 38.99 2.15
2430 3724 2.357517 CTCAGGGCGTTCGTTGCT 60.358 61.111 0.00 0.00 0.00 3.91
2659 3957 0.618458 AGAAGGGTAAGATTGCGCCA 59.382 50.000 4.18 0.00 0.00 5.69
2964 4262 4.526262 CAGCCTTATACTCAGCCTCAGTAT 59.474 45.833 0.00 0.00 39.79 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.015095 GGTTGATTTCTCAGAAACAGGGATTT 60.015 38.462 0.68 0.00 31.68 2.17
4 5 5.012893 GGTTGATTTCTCAGAAACAGGGAT 58.987 41.667 0.68 0.00 31.68 3.85
5 6 4.398319 GGTTGATTTCTCAGAAACAGGGA 58.602 43.478 0.68 0.00 31.68 4.20
6 7 3.507622 GGGTTGATTTCTCAGAAACAGGG 59.492 47.826 0.68 0.00 31.68 4.45
7 8 4.022849 GTGGGTTGATTTCTCAGAAACAGG 60.023 45.833 0.68 0.00 31.68 4.00
8 9 4.580167 TGTGGGTTGATTTCTCAGAAACAG 59.420 41.667 0.68 0.00 31.68 3.16
9 10 4.531854 TGTGGGTTGATTTCTCAGAAACA 58.468 39.130 0.68 0.25 31.68 2.83
10 11 4.580580 ACTGTGGGTTGATTTCTCAGAAAC 59.419 41.667 0.68 0.00 31.68 2.78
11 12 4.792068 ACTGTGGGTTGATTTCTCAGAAA 58.208 39.130 1.30 1.30 31.68 2.52
12 13 4.103153 AGACTGTGGGTTGATTTCTCAGAA 59.897 41.667 0.00 0.00 31.68 3.02
13 14 3.648067 AGACTGTGGGTTGATTTCTCAGA 59.352 43.478 0.00 0.00 31.68 3.27
14 15 4.013267 AGACTGTGGGTTGATTTCTCAG 57.987 45.455 0.00 0.00 31.68 3.35
15 16 4.437682 AAGACTGTGGGTTGATTTCTCA 57.562 40.909 0.00 0.00 0.00 3.27
16 17 5.998363 AGTTAAGACTGTGGGTTGATTTCTC 59.002 40.000 0.00 0.00 33.99 2.87
17 18 5.941788 AGTTAAGACTGTGGGTTGATTTCT 58.058 37.500 0.00 0.00 33.99 2.52
18 19 6.635030 AAGTTAAGACTGTGGGTTGATTTC 57.365 37.500 0.00 0.00 35.91 2.17
19 20 8.410912 GTTTAAGTTAAGACTGTGGGTTGATTT 58.589 33.333 0.00 0.00 35.91 2.17
20 21 7.255001 CGTTTAAGTTAAGACTGTGGGTTGATT 60.255 37.037 0.00 0.00 35.91 2.57
21 22 6.204108 CGTTTAAGTTAAGACTGTGGGTTGAT 59.796 38.462 0.00 0.00 35.91 2.57
22 23 5.524646 CGTTTAAGTTAAGACTGTGGGTTGA 59.475 40.000 0.00 0.00 35.91 3.18
23 24 5.295045 ACGTTTAAGTTAAGACTGTGGGTTG 59.705 40.000 0.00 0.00 35.91 3.77
24 25 5.430886 ACGTTTAAGTTAAGACTGTGGGTT 58.569 37.500 0.00 0.00 35.91 4.11
25 26 5.027293 ACGTTTAAGTTAAGACTGTGGGT 57.973 39.130 0.00 0.00 35.91 4.51
26 27 5.996669 AACGTTTAAGTTAAGACTGTGGG 57.003 39.130 0.00 0.00 35.91 4.61
27 28 6.903479 GTGAAACGTTTAAGTTAAGACTGTGG 59.097 38.462 14.65 0.00 35.91 4.17
28 29 7.681903 AGTGAAACGTTTAAGTTAAGACTGTG 58.318 34.615 14.65 0.00 45.86 3.66
29 30 7.838771 AGTGAAACGTTTAAGTTAAGACTGT 57.161 32.000 14.65 0.00 45.86 3.55
30 31 9.550811 AAAAGTGAAACGTTTAAGTTAAGACTG 57.449 29.630 17.10 0.00 46.40 3.51
51 52 5.828328 CCTCTGGGAGTTTTCTACAAAAAGT 59.172 40.000 0.00 0.00 31.81 2.66
67 68 2.907696 TGATTAACCGAAACCTCTGGGA 59.092 45.455 0.00 0.00 36.25 4.37
151 158 4.767928 ACGGCAGGTTAATTGACCAAAATA 59.232 37.500 20.51 0.00 42.35 1.40
160 167 2.613691 AGACGTACGGCAGGTTAATTG 58.386 47.619 25.52 0.00 0.00 2.32
231 244 9.734620 GTTAAAACTGGAGTTACGGTTTAAAAT 57.265 29.630 1.85 0.00 46.27 1.82
337 354 8.499403 AGAGTTTGAATTTACTCTAATCAGCC 57.501 34.615 13.83 0.00 46.89 4.85
526 550 0.927537 GGCAACGGCACAAAAGAAAC 59.072 50.000 0.00 0.00 43.71 2.78
537 561 2.924454 TTCAATTTGAATCGGCAACGGC 60.924 45.455 7.74 0.00 46.25 5.68
541 565 4.611943 TCGTTTTCAATTTGAATCGGCAA 58.388 34.783 23.62 11.07 36.11 4.52
561 585 5.623673 CCGATTTGTTTTTCTAAGGTGTTCG 59.376 40.000 0.00 0.00 0.00 3.95
598 623 5.213891 TCGACATGCATGGTTATAGATGT 57.786 39.130 29.41 6.81 0.00 3.06
619 644 0.456221 TCTTTCCACTCTCGCGGATC 59.544 55.000 6.13 0.00 0.00 3.36
649 675 3.244665 ACATGGCATCTTGTCAGTCTTGA 60.245 43.478 0.00 0.00 34.38 3.02
659 685 6.632909 TCCTTTATTTCAACATGGCATCTTG 58.367 36.000 8.96 8.96 0.00 3.02
684 710 1.481871 GAACCCTCGATAGGTCCACA 58.518 55.000 7.67 0.00 41.89 4.17
701 729 7.107639 TCTATCACAATAACCATGACTCGAA 57.892 36.000 0.00 0.00 0.00 3.71
721 749 4.021016 AGAGACAAAAAGACACGCCTCTAT 60.021 41.667 0.00 0.00 0.00 1.98
725 753 2.484889 GAGAGACAAAAAGACACGCCT 58.515 47.619 0.00 0.00 0.00 5.52
733 761 1.946768 TGCAACGGGAGAGACAAAAAG 59.053 47.619 0.00 0.00 0.00 2.27
734 762 2.045561 TGCAACGGGAGAGACAAAAA 57.954 45.000 0.00 0.00 0.00 1.94
739 770 1.696832 GCGATTGCAACGGGAGAGAC 61.697 60.000 18.46 2.08 42.15 3.36
755 786 2.903547 GCAAAAAGAGCCCGTGCGA 61.904 57.895 0.00 0.00 44.33 5.10
775 806 7.646922 GCAACGTACATGTATTTAGCTAGTACT 59.353 37.037 9.18 0.00 0.00 2.73
776 807 7.646922 AGCAACGTACATGTATTTAGCTAGTAC 59.353 37.037 18.26 10.03 0.00 2.73
777 808 7.709947 AGCAACGTACATGTATTTAGCTAGTA 58.290 34.615 18.26 0.00 0.00 1.82
778 809 6.570692 AGCAACGTACATGTATTTAGCTAGT 58.429 36.000 18.26 4.95 0.00 2.57
779 810 8.639428 CATAGCAACGTACATGTATTTAGCTAG 58.361 37.037 24.21 17.28 34.78 3.42
780 811 7.597369 CCATAGCAACGTACATGTATTTAGCTA 59.403 37.037 23.21 23.21 35.62 3.32
781 812 6.423905 CCATAGCAACGTACATGTATTTAGCT 59.576 38.462 21.35 21.35 0.00 3.32
782 813 6.347402 CCCATAGCAACGTACATGTATTTAGC 60.347 42.308 9.18 11.29 0.00 3.09
783 814 6.926826 TCCCATAGCAACGTACATGTATTTAG 59.073 38.462 9.18 4.20 0.00 1.85
784 815 6.702723 GTCCCATAGCAACGTACATGTATTTA 59.297 38.462 9.18 0.00 0.00 1.40
785 816 5.526111 GTCCCATAGCAACGTACATGTATTT 59.474 40.000 9.18 2.93 0.00 1.40
786 817 5.054477 GTCCCATAGCAACGTACATGTATT 58.946 41.667 9.18 0.00 0.00 1.89
787 818 4.628074 GTCCCATAGCAACGTACATGTAT 58.372 43.478 9.18 0.00 0.00 2.29
788 819 3.489568 CGTCCCATAGCAACGTACATGTA 60.490 47.826 0.08 0.08 0.00 2.29
789 820 2.737359 CGTCCCATAGCAACGTACATGT 60.737 50.000 2.69 2.69 0.00 3.21
790 821 1.858458 CGTCCCATAGCAACGTACATG 59.142 52.381 0.00 0.00 0.00 3.21
791 822 1.752498 TCGTCCCATAGCAACGTACAT 59.248 47.619 0.00 0.00 37.64 2.29
792 823 1.175654 TCGTCCCATAGCAACGTACA 58.824 50.000 0.00 0.00 37.64 2.90
793 824 2.282701 TTCGTCCCATAGCAACGTAC 57.717 50.000 0.00 0.00 37.64 3.67
794 825 3.530265 ATTTCGTCCCATAGCAACGTA 57.470 42.857 0.00 0.00 37.64 3.57
795 826 2.396590 ATTTCGTCCCATAGCAACGT 57.603 45.000 0.00 0.00 37.64 3.99
796 827 3.869246 ACTTATTTCGTCCCATAGCAACG 59.131 43.478 0.00 0.00 37.74 4.10
797 828 6.913873 TTACTTATTTCGTCCCATAGCAAC 57.086 37.500 0.00 0.00 0.00 4.17
798 829 9.787435 AATATTACTTATTTCGTCCCATAGCAA 57.213 29.630 0.00 0.00 0.00 3.91
799 830 9.787435 AAATATTACTTATTTCGTCCCATAGCA 57.213 29.630 0.00 0.00 36.00 3.49
834 865 8.239038 TCATATTTAGACCATCGGATCTATCC 57.761 38.462 0.00 0.00 43.65 2.59
835 866 9.689976 CATCATATTTAGACCATCGGATCTATC 57.310 37.037 0.00 0.00 0.00 2.08
836 867 9.426534 TCATCATATTTAGACCATCGGATCTAT 57.573 33.333 0.00 0.00 0.00 1.98
837 868 8.823220 TCATCATATTTAGACCATCGGATCTA 57.177 34.615 0.00 0.00 0.00 1.98
838 869 7.724490 TCATCATATTTAGACCATCGGATCT 57.276 36.000 0.00 0.00 0.00 2.75
839 870 8.954950 AATCATCATATTTAGACCATCGGATC 57.045 34.615 0.00 0.00 0.00 3.36
861 892 9.604626 CCGAGATATCTTGCAAGAAAATAAATC 57.395 33.333 31.55 23.06 38.77 2.17
862 893 8.078596 GCCGAGATATCTTGCAAGAAAATAAAT 58.921 33.333 31.55 16.39 38.77 1.40
863 894 7.417612 GCCGAGATATCTTGCAAGAAAATAAA 58.582 34.615 31.55 13.83 38.77 1.40
864 895 6.017109 GGCCGAGATATCTTGCAAGAAAATAA 60.017 38.462 31.55 15.47 38.77 1.40
865 896 5.470098 GGCCGAGATATCTTGCAAGAAAATA 59.530 40.000 31.55 20.06 38.77 1.40
866 897 4.276926 GGCCGAGATATCTTGCAAGAAAAT 59.723 41.667 31.55 25.76 38.77 1.82
867 898 3.627577 GGCCGAGATATCTTGCAAGAAAA 59.372 43.478 31.55 22.52 38.77 2.29
868 899 3.206150 GGCCGAGATATCTTGCAAGAAA 58.794 45.455 31.55 11.88 38.77 2.52
869 900 2.170397 TGGCCGAGATATCTTGCAAGAA 59.830 45.455 31.55 20.53 38.77 2.52
870 901 1.762370 TGGCCGAGATATCTTGCAAGA 59.238 47.619 30.23 30.23 39.78 3.02
871 902 2.245159 TGGCCGAGATATCTTGCAAG 57.755 50.000 20.81 20.81 0.00 4.01
872 903 2.497138 CATGGCCGAGATATCTTGCAA 58.503 47.619 22.31 15.61 0.00 4.08
873 904 1.879372 GCATGGCCGAGATATCTTGCA 60.879 52.381 22.31 13.80 32.72 4.08
874 905 0.801251 GCATGGCCGAGATATCTTGC 59.199 55.000 13.85 15.07 0.00 4.01
875 906 1.446907 GGCATGGCCGAGATATCTTG 58.553 55.000 8.35 12.50 39.62 3.02
876 907 3.944476 GGCATGGCCGAGATATCTT 57.056 52.632 8.35 0.00 39.62 2.40
886 917 0.796312 CGATGTATTACGGCATGGCC 59.204 55.000 14.46 0.00 46.75 5.36
887 918 0.165944 GCGATGTATTACGGCATGGC 59.834 55.000 9.69 9.69 39.02 4.40
888 919 1.726791 GAGCGATGTATTACGGCATGG 59.273 52.381 0.00 0.00 0.00 3.66
889 920 2.155732 GTGAGCGATGTATTACGGCATG 59.844 50.000 0.00 0.00 0.00 4.06
890 921 2.035961 AGTGAGCGATGTATTACGGCAT 59.964 45.455 0.00 0.00 0.00 4.40
891 922 1.407618 AGTGAGCGATGTATTACGGCA 59.592 47.619 0.00 0.00 0.00 5.69
892 923 2.052157 GAGTGAGCGATGTATTACGGC 58.948 52.381 0.00 0.00 0.00 5.68
893 924 2.307929 CGAGTGAGCGATGTATTACGG 58.692 52.381 0.00 0.00 0.00 4.02
894 925 1.709203 GCGAGTGAGCGATGTATTACG 59.291 52.381 0.00 0.00 0.00 3.18
895 926 2.052157 GGCGAGTGAGCGATGTATTAC 58.948 52.381 0.00 0.00 38.18 1.89
896 927 1.334689 CGGCGAGTGAGCGATGTATTA 60.335 52.381 0.00 0.00 38.18 0.98
897 928 0.595053 CGGCGAGTGAGCGATGTATT 60.595 55.000 0.00 0.00 38.18 1.89
898 929 1.008424 CGGCGAGTGAGCGATGTAT 60.008 57.895 0.00 0.00 38.18 2.29
899 930 2.407616 CGGCGAGTGAGCGATGTA 59.592 61.111 0.00 0.00 38.18 2.29
977 1008 2.358125 CGTGCGTGGGATGTGGAA 60.358 61.111 0.00 0.00 0.00 3.53
980 1011 3.792047 CTGCGTGCGTGGGATGTG 61.792 66.667 0.00 0.00 0.00 3.21
986 1017 4.764336 CCATTGCTGCGTGCGTGG 62.764 66.667 9.89 9.89 46.63 4.94
1063 1097 2.675242 CCGGGTTGATGTGGCCCTA 61.675 63.158 0.00 0.00 40.22 3.53
1223 1257 1.001764 TCGGAGAAGGGCACGTAGA 60.002 57.895 0.00 0.00 0.00 2.59
1815 3092 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
1816 3093 5.220681 GGTTGTTGTTGTTGTTGTTGTTGTT 60.221 36.000 0.00 0.00 0.00 2.83
1817 3094 4.271291 GGTTGTTGTTGTTGTTGTTGTTGT 59.729 37.500 0.00 0.00 0.00 3.32
1837 3114 1.882352 GCCGTCCATCTTGAACAGGTT 60.882 52.381 0.00 0.00 0.00 3.50
1849 3126 2.676265 GGTACCCCTTGCCGTCCAT 61.676 63.158 0.00 0.00 0.00 3.41
1986 3263 0.546122 TCAGCACCCACAAGAACTGT 59.454 50.000 0.00 0.00 39.56 3.55
1988 3265 3.788227 TTATCAGCACCCACAAGAACT 57.212 42.857 0.00 0.00 0.00 3.01
2006 3283 0.669318 CTCGCTGCGGTTGTCCTTTA 60.669 55.000 23.03 0.00 0.00 1.85
2007 3284 1.961277 CTCGCTGCGGTTGTCCTTT 60.961 57.895 23.03 0.00 0.00 3.11
2073 3362 4.394712 CCTGGTCGCACCACTCCC 62.395 72.222 4.16 0.00 44.79 4.30
2606 3904 3.121929 AGTGGCTAAGATTGAGGGAGA 57.878 47.619 0.00 0.00 0.00 3.71
2659 3957 1.312815 GCCACAGTTTGAGACTTGCT 58.687 50.000 0.00 0.00 36.10 3.91
3051 4349 1.031571 GCTGGCAATCCGGATGACAA 61.032 55.000 19.95 5.75 41.45 3.18


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

AutoCloner maintained by Alex Coulton.