Multiple sequence alignment - TraesCS5A01G124900

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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 TraesCS5A01G124900 chr5A 100.000 2874 0 0 1 2874 274989279 274992152 0.000000e+00 5308.0
1 TraesCS5A01G124900 chr5A 97.059 34 1 0 1126 1159 274990322 274990355 1.110000e-04 58.4
2 TraesCS5A01G124900 chr5A 97.059 34 1 0 1044 1077 274990404 274990437 1.110000e-04 58.4
3 TraesCS5A01G124900 chrUn 93.761 1731 83 11 1156 2864 152551062 152552789 0.000000e+00 2577.0
4 TraesCS5A01G124900 chrUn 93.945 1701 78 11 1186 2864 134953055 134954752 0.000000e+00 2549.0
5 TraesCS5A01G124900 chrUn 93.904 935 46 6 1156 2079 134957163 134958097 0.000000e+00 1400.0
6 TraesCS5A01G124900 chrUn 93.797 935 47 6 1156 2079 303761137 303762071 0.000000e+00 1395.0
7 TraesCS5A01G124900 chrUn 95.032 785 34 4 2082 2864 134959001 134959782 0.000000e+00 1229.0
8 TraesCS5A01G124900 chrUn 84.733 262 18 9 687 927 152550570 152550830 2.860000e-60 243.0
9 TraesCS5A01G124900 chrUn 84.733 262 18 9 687 927 303760645 303760905 2.860000e-60 243.0
10 TraesCS5A01G124900 chrUn 84.677 248 19 7 687 915 134956674 134956921 2.230000e-56 230.0
11 TraesCS5A01G124900 chrUn 92.405 158 11 1 966 1123 152550829 152550985 1.040000e-54 224.0
12 TraesCS5A01G124900 chrUn 92.405 158 11 1 966 1123 303760904 303761060 1.040000e-54 224.0
13 TraesCS5A01G124900 chrUn 91.772 158 12 1 966 1123 134956930 134957086 4.820000e-53 219.0
14 TraesCS5A01G124900 chrUn 92.405 79 3 3 1892 1967 202630599 202630521 3.030000e-20 110.0
15 TraesCS5A01G124900 chr6D 86.846 707 64 21 1 686 456832163 456831465 0.000000e+00 763.0
16 TraesCS5A01G124900 chr7D 86.448 701 66 21 1 687 134433984 134434669 0.000000e+00 741.0
17 TraesCS5A01G124900 chr7D 84.736 701 74 20 1 686 182331281 182330599 0.000000e+00 671.0
18 TraesCS5A01G124900 chr7D 82.374 278 31 9 2096 2369 196286445 196286708 2.880000e-55 226.0
19 TraesCS5A01G124900 chr2A 85.897 702 72 16 1 686 768684462 768685152 0.000000e+00 723.0
20 TraesCS5A01G124900 chr2A 86.074 675 64 23 1 656 706220602 706221265 0.000000e+00 699.0
21 TraesCS5A01G124900 chr2A 86.161 672 61 22 1 654 706224044 706224701 0.000000e+00 697.0
22 TraesCS5A01G124900 chr1A 85.756 688 73 18 12 686 391243421 391242746 0.000000e+00 704.0
23 TraesCS5A01G124900 chr1A 84.397 705 80 20 1 686 521563170 521562477 0.000000e+00 665.0
24 TraesCS5A01G124900 chr6B 84.397 705 75 22 1 685 583265612 583266301 0.000000e+00 660.0
25 TraesCS5A01G124900 chr3A 89.463 484 50 1 1405 1887 420837270 420836787 6.810000e-171 610.0
26 TraesCS5A01G124900 chr3A 80.989 647 93 22 2159 2790 569231417 569232048 1.200000e-133 486.0
27 TraesCS5A01G124900 chr3A 89.730 185 13 3 1156 1336 420837454 420837272 6.190000e-57 231.0
28 TraesCS5A01G124900 chr3A 94.643 112 5 1 1975 2086 420836773 420836663 3.810000e-39 172.0
29 TraesCS5A01G124900 chr3B 82.132 638 87 19 2164 2787 564024539 564025163 3.280000e-144 521.0
30 TraesCS5A01G124900 chr3B 81.211 644 94 19 2159 2790 564039472 564040100 7.150000e-136 494.0
31 TraesCS5A01G124900 chr3B 85.765 281 32 6 2221 2497 573469028 573469304 1.010000e-74 291.0
32 TraesCS5A01G124900 chr3B 90.588 85 5 3 1889 1970 11070080 11069996 3.030000e-20 110.0
33 TraesCS5A01G124900 chr3D 80.841 642 88 22 2159 2787 431833287 431833906 3.350000e-129 472.0
34 TraesCS5A01G124900 chr3D 81.522 276 31 10 2099 2369 200470842 200470582 2.900000e-50 209.0
35 TraesCS5A01G124900 chr4D 87.421 159 20 0 1723 1881 266700451 266700609 1.760000e-42 183.0
36 TraesCS5A01G124900 chr4D 92.391 92 7 0 1995 2086 276136978 276137069 6.460000e-27 132.0
37 TraesCS5A01G124900 chr4D 72.939 473 63 34 688 1123 276135104 276135548 1.410000e-18 104.0
38 TraesCS5A01G124900 chr5D 94.805 77 3 1 1884 1959 438782948 438782872 5.030000e-23 119.0
39 TraesCS5A01G124900 chr1B 89.773 88 6 3 1883 1967 661461649 661461736 3.030000e-20 110.0
40 TraesCS5A01G124900 chr7A 88.889 90 7 3 1881 1967 67016572 67016661 1.090000e-19 108.0


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 TraesCS5A01G124900 chr5A 274989279 274992152 2873 False 1808.266667 5308 98.039333 1 2874 3 chr5A.!!$F1 2873
1 TraesCS5A01G124900 chrUn 134953055 134959782 6727 False 1125.400000 2549 91.866000 687 2864 5 chrUn.!!$F1 2177
2 TraesCS5A01G124900 chrUn 152550570 152552789 2219 False 1014.666667 2577 90.299667 687 2864 3 chrUn.!!$F2 2177
3 TraesCS5A01G124900 chrUn 303760645 303762071 1426 False 620.666667 1395 90.311667 687 2079 3 chrUn.!!$F3 1392
4 TraesCS5A01G124900 chr6D 456831465 456832163 698 True 763.000000 763 86.846000 1 686 1 chr6D.!!$R1 685
5 TraesCS5A01G124900 chr7D 134433984 134434669 685 False 741.000000 741 86.448000 1 687 1 chr7D.!!$F1 686
6 TraesCS5A01G124900 chr7D 182330599 182331281 682 True 671.000000 671 84.736000 1 686 1 chr7D.!!$R1 685
7 TraesCS5A01G124900 chr2A 768684462 768685152 690 False 723.000000 723 85.897000 1 686 1 chr2A.!!$F1 685
8 TraesCS5A01G124900 chr2A 706220602 706224701 4099 False 698.000000 699 86.117500 1 656 2 chr2A.!!$F2 655
9 TraesCS5A01G124900 chr1A 391242746 391243421 675 True 704.000000 704 85.756000 12 686 1 chr1A.!!$R1 674
10 TraesCS5A01G124900 chr1A 521562477 521563170 693 True 665.000000 665 84.397000 1 686 1 chr1A.!!$R2 685
11 TraesCS5A01G124900 chr6B 583265612 583266301 689 False 660.000000 660 84.397000 1 685 1 chr6B.!!$F1 684
12 TraesCS5A01G124900 chr3A 569231417 569232048 631 False 486.000000 486 80.989000 2159 2790 1 chr3A.!!$F1 631
13 TraesCS5A01G124900 chr3A 420836663 420837454 791 True 337.666667 610 91.278667 1156 2086 3 chr3A.!!$R1 930
14 TraesCS5A01G124900 chr3B 564024539 564025163 624 False 521.000000 521 82.132000 2164 2787 1 chr3B.!!$F1 623
15 TraesCS5A01G124900 chr3B 564039472 564040100 628 False 494.000000 494 81.211000 2159 2790 1 chr3B.!!$F2 631
16 TraesCS5A01G124900 chr3D 431833287 431833906 619 False 472.000000 472 80.841000 2159 2787 1 chr3D.!!$F1 628

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 4248 0.386113 GCTTAGTAGTAGGCTGCGCT 59.614 55.0 9.73 2.46 32.36 5.92 F
1173 4722 0.110104 CCCAAGCCATGATCCTCTCC 59.890 60.0 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 5200 2.437359 GAATGAGCAGCGGCCACT 60.437 61.111 4.82 0.0 42.56 4.00 R
2795 7286 0.235665 GACATGCACACACAACGGAG 59.764 55.000 0.00 0.0 0.00 4.63 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
93 96 0.464036 AAGCACAACCGTGACTCTCA 59.536 50.000 0.00 0.00 46.80 3.27
208 327 2.849502 GCAAAACCGTGACTCGTGAAAG 60.850 50.000 0.00 0.00 37.94 2.62
227 3683 7.401860 GTGAAAGAAAGAAAACAGAAAATGCC 58.598 34.615 0.00 0.00 0.00 4.40
233 3689 6.682423 AAGAAAACAGAAAATGCCTTTTGG 57.318 33.333 4.31 0.02 44.18 3.28
239 3695 5.744171 ACAGAAAATGCCTTTTGGTTTTCT 58.256 33.333 4.31 6.22 46.72 2.52
391 3854 2.800544 GTGACTCTCGCTAAAGCACAAA 59.199 45.455 2.44 0.00 42.21 2.83
403 3866 3.244105 CACAAACGTGCCTCTCGG 58.756 61.111 0.00 0.00 0.00 4.63
427 3897 4.816277 AAAAACGTGACTTTCGCAAAAG 57.184 36.364 0.00 0.00 46.11 2.27
509 3985 2.559668 TCGAAAAGCTAAGGAAGACCGA 59.440 45.455 0.00 0.00 41.83 4.69
570 4049 3.002149 CGAAAACGCATGCGGAAAAATAG 60.002 43.478 39.95 20.56 44.69 1.73
596 4083 1.911057 TCTGAAGAGAGCGTCCAGAA 58.089 50.000 0.00 0.00 0.00 3.02
598 4085 1.270826 CTGAAGAGAGCGTCCAGAACA 59.729 52.381 0.00 0.00 0.00 3.18
618 4105 0.455464 CGACACGTGACGAATGGCTA 60.455 55.000 31.37 0.00 35.37 3.93
627 4114 1.878522 CGAATGGCTAAGAGCGCGT 60.879 57.895 8.43 0.00 43.62 6.01
654 4141 1.878775 GCAGATCGTTGCAAGGCTT 59.121 52.632 14.22 0.00 43.53 4.35
658 4145 1.298859 GATCGTTGCAAGGCTTCCGT 61.299 55.000 14.22 0.00 0.00 4.69
675 4162 1.192436 CGTAGGAGCGCTCGTTAACG 61.192 60.000 34.48 31.66 41.45 3.18
689 4176 3.320541 TCGTTAACGAGTTGGTCCCTTTA 59.679 43.478 26.00 0.00 44.22 1.85
695 4182 3.073356 ACGAGTTGGTCCCTTTATTTCCA 59.927 43.478 0.00 0.00 0.00 3.53
702 4189 7.778382 AGTTGGTCCCTTTATTTCCACATATAC 59.222 37.037 0.00 0.00 0.00 1.47
710 4197 7.649306 CCTTTATTTCCACATATACAGCAAAGC 59.351 37.037 0.00 0.00 0.00 3.51
729 4216 2.283676 GTCCACGGTCCCCTCTCA 60.284 66.667 0.00 0.00 0.00 3.27
758 4245 3.004944 CAGTAGGCTTAGTAGTAGGCTGC 59.995 52.174 11.10 7.65 46.62 5.25
759 4246 1.033574 AGGCTTAGTAGTAGGCTGCG 58.966 55.000 11.10 0.00 45.63 5.18
760 4247 0.597898 GGCTTAGTAGTAGGCTGCGC 60.598 60.000 11.10 0.00 35.48 6.09
761 4248 0.386113 GCTTAGTAGTAGGCTGCGCT 59.614 55.000 9.73 2.46 32.36 5.92
762 4249 1.607628 GCTTAGTAGTAGGCTGCGCTA 59.392 52.381 9.73 1.40 32.36 4.26
777 4274 3.141488 CTACGCAGTCCTCGCCCT 61.141 66.667 0.00 0.00 43.93 5.19
781 4278 3.450115 GCAGTCCTCGCCCTACGT 61.450 66.667 0.00 0.00 44.19 3.57
798 4295 1.367471 GTGCAAAGGTTCTTGGCCC 59.633 57.895 0.00 0.00 0.00 5.80
804 4301 2.368221 CAAAGGTTCTTGGCCCATGAAA 59.632 45.455 13.15 0.00 31.20 2.69
806 4303 1.428912 AGGTTCTTGGCCCATGAAAGA 59.571 47.619 13.15 0.00 31.20 2.52
818 4322 4.430007 CCCATGAAAGATACGAGACGAAA 58.570 43.478 0.00 0.00 0.00 3.46
835 4339 7.218204 CGAGACGAAAAATTCAGACTTGTTTTT 59.782 33.333 0.00 0.00 36.71 1.94
911 4417 3.279434 GGCCATTTCCACTCGTTTATCT 58.721 45.455 0.00 0.00 0.00 1.98
912 4418 3.312697 GGCCATTTCCACTCGTTTATCTC 59.687 47.826 0.00 0.00 0.00 2.75
913 4419 4.192317 GCCATTTCCACTCGTTTATCTCT 58.808 43.478 0.00 0.00 0.00 3.10
914 4420 4.271291 GCCATTTCCACTCGTTTATCTCTC 59.729 45.833 0.00 0.00 0.00 3.20
915 4421 5.665459 CCATTTCCACTCGTTTATCTCTCT 58.335 41.667 0.00 0.00 0.00 3.10
916 4422 5.751028 CCATTTCCACTCGTTTATCTCTCTC 59.249 44.000 0.00 0.00 0.00 3.20
917 4423 4.985538 TTCCACTCGTTTATCTCTCTCC 57.014 45.455 0.00 0.00 0.00 3.71
918 4424 4.237976 TCCACTCGTTTATCTCTCTCCT 57.762 45.455 0.00 0.00 0.00 3.69
919 4425 4.601084 TCCACTCGTTTATCTCTCTCCTT 58.399 43.478 0.00 0.00 0.00 3.36
920 4426 4.641094 TCCACTCGTTTATCTCTCTCCTTC 59.359 45.833 0.00 0.00 0.00 3.46
921 4427 4.642885 CCACTCGTTTATCTCTCTCCTTCT 59.357 45.833 0.00 0.00 0.00 2.85
922 4428 5.449862 CCACTCGTTTATCTCTCTCCTTCTG 60.450 48.000 0.00 0.00 0.00 3.02
923 4429 4.097286 ACTCGTTTATCTCTCTCCTTCTGC 59.903 45.833 0.00 0.00 0.00 4.26
924 4430 3.381908 TCGTTTATCTCTCTCCTTCTGCC 59.618 47.826 0.00 0.00 0.00 4.85
925 4431 3.131223 CGTTTATCTCTCTCCTTCTGCCA 59.869 47.826 0.00 0.00 0.00 4.92
926 4432 4.202202 CGTTTATCTCTCTCCTTCTGCCAT 60.202 45.833 0.00 0.00 0.00 4.40
927 4433 5.010112 CGTTTATCTCTCTCCTTCTGCCATA 59.990 44.000 0.00 0.00 0.00 2.74
928 4434 6.461648 CGTTTATCTCTCTCCTTCTGCCATAA 60.462 42.308 0.00 0.00 0.00 1.90
929 4435 7.275920 GTTTATCTCTCTCCTTCTGCCATAAA 58.724 38.462 0.00 0.00 0.00 1.40
930 4436 5.965033 ATCTCTCTCCTTCTGCCATAAAA 57.035 39.130 0.00 0.00 0.00 1.52
931 4437 5.762179 TCTCTCTCCTTCTGCCATAAAAA 57.238 39.130 0.00 0.00 0.00 1.94
953 4459 6.694445 AAAAATCTCTCTCCTTCTTCTCCA 57.306 37.500 0.00 0.00 0.00 3.86
954 4460 6.889595 AAAATCTCTCTCCTTCTTCTCCAT 57.110 37.500 0.00 0.00 0.00 3.41
955 4461 6.484364 AAATCTCTCTCCTTCTTCTCCATC 57.516 41.667 0.00 0.00 0.00 3.51
956 4462 3.909732 TCTCTCTCCTTCTTCTCCATCC 58.090 50.000 0.00 0.00 0.00 3.51
957 4463 2.965147 CTCTCTCCTTCTTCTCCATCCC 59.035 54.545 0.00 0.00 0.00 3.85
958 4464 1.686052 CTCTCCTTCTTCTCCATCCCG 59.314 57.143 0.00 0.00 0.00 5.14
959 4465 1.288037 TCTCCTTCTTCTCCATCCCGA 59.712 52.381 0.00 0.00 0.00 5.14
960 4466 2.091055 TCTCCTTCTTCTCCATCCCGAT 60.091 50.000 0.00 0.00 0.00 4.18
961 4467 2.298729 CTCCTTCTTCTCCATCCCGATC 59.701 54.545 0.00 0.00 0.00 3.69
962 4468 2.091055 TCCTTCTTCTCCATCCCGATCT 60.091 50.000 0.00 0.00 0.00 2.75
963 4469 3.140332 TCCTTCTTCTCCATCCCGATCTA 59.860 47.826 0.00 0.00 0.00 1.98
964 4470 3.509575 CCTTCTTCTCCATCCCGATCTAG 59.490 52.174 0.00 0.00 0.00 2.43
977 4483 3.828083 ATCTAGATCCCGCCGCCCA 62.828 63.158 0.00 0.00 0.00 5.36
979 4485 3.084646 TAGATCCCGCCGCCCAAA 61.085 61.111 0.00 0.00 0.00 3.28
981 4487 2.391724 TAGATCCCGCCGCCCAAATC 62.392 60.000 0.00 0.00 0.00 2.17
985 4491 4.489771 CCGCCGCCCAAATCCTCT 62.490 66.667 0.00 0.00 0.00 3.69
1118 4624 3.457234 CTGCACAAATACCAGCGAGATA 58.543 45.455 0.00 0.00 0.00 1.98
1119 4625 3.194861 TGCACAAATACCAGCGAGATAC 58.805 45.455 0.00 0.00 0.00 2.24
1120 4626 3.118775 TGCACAAATACCAGCGAGATACT 60.119 43.478 0.00 0.00 0.00 2.12
1128 4634 0.872021 CAGCGAGATACTGGCGAACC 60.872 60.000 0.00 0.00 40.09 3.62
1129 4635 1.141019 GCGAGATACTGGCGAACCA 59.859 57.895 0.00 0.00 46.51 3.67
1137 4643 4.467084 TGGCGAACCATCTCCCGC 62.467 66.667 0.00 0.00 42.67 6.13
1140 4646 4.547367 CGAACCATCTCCCGCCCC 62.547 72.222 0.00 0.00 0.00 5.80
1141 4647 4.191015 GAACCATCTCCCGCCCCC 62.191 72.222 0.00 0.00 0.00 5.40
1173 4722 0.110104 CCCAAGCCATGATCCTCTCC 59.890 60.000 0.00 0.00 0.00 3.71
1179 4728 2.044469 GCCATGATCCTCTCCCCTCTT 61.044 57.143 0.00 0.00 0.00 2.85
1233 4782 1.736586 CCGTCGAGGGAGATCTTGG 59.263 63.158 19.44 0.00 35.97 3.61
1284 4835 1.066914 CTCAGCTCGTTCAAGTGCTC 58.933 55.000 0.00 0.00 38.70 4.26
1331 4885 0.539051 CCAGGGAGTCTGACATGGAC 59.461 60.000 10.88 0.00 46.18 4.02
1373 4927 3.836365 TGGAGATTCCGTCATGCATTA 57.164 42.857 0.00 0.00 40.17 1.90
1423 4977 4.054671 GACAACTGAGAAGGAAGTGTCAG 58.945 47.826 0.00 0.00 42.97 3.51
1474 5029 6.412362 TTCTTGGCCTTTAGTTTGCAAATA 57.588 33.333 16.21 6.23 0.00 1.40
1628 5183 1.702401 TGTTGTCTAACAGATGGGCCA 59.298 47.619 9.61 9.61 41.66 5.36
1643 5198 1.547675 GGGCCATGAGTTTGGACTTCA 60.548 52.381 4.39 0.00 44.91 3.02
1645 5200 2.229792 GCCATGAGTTTGGACTTCACA 58.770 47.619 0.00 0.00 39.25 3.58
1743 5298 2.045438 TGCGTCGGCATCCCATTT 60.045 55.556 0.00 0.00 46.21 2.32
2036 5598 1.070445 CTGGCGTGATCTCCATCCC 59.930 63.158 0.00 0.00 0.00 3.85
2037 5599 1.383109 TGGCGTGATCTCCATCCCT 60.383 57.895 0.00 0.00 0.00 4.20
2079 5641 8.584063 TTGAATTTCTGATTTGAGATGGATCA 57.416 30.769 0.00 0.00 0.00 2.92
2092 6555 5.221702 TGAGATGGATCATGGAATTTAGCGA 60.222 40.000 0.00 0.00 0.00 4.93
2115 6578 4.641396 TGTGAACTTGTATTAGCAGCACT 58.359 39.130 0.00 0.00 0.00 4.40
2117 6580 6.227522 TGTGAACTTGTATTAGCAGCACTTA 58.772 36.000 0.00 0.00 0.00 2.24
2222 6686 8.796475 AGCACAAAAGAGAATGAATAAAAGCTA 58.204 29.630 0.00 0.00 0.00 3.32
2590 7075 6.545666 TCGTGTTTGGAAATATCCTGCAATAT 59.454 34.615 0.00 0.00 46.70 1.28
2746 7237 5.672503 CATGGGAAATGCAAATGGTATGAA 58.327 37.500 0.00 0.00 0.00 2.57
2798 7289 4.449131 TGATCAGCTTCAATCACATCTCC 58.551 43.478 0.00 0.00 0.00 3.71
2810 7301 0.179059 ACATCTCCGTTGTGTGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
2812 7303 1.135888 CATCTCCGTTGTGTGTGCATG 60.136 52.381 0.00 0.00 0.00 4.06
2831 7322 7.148255 TGTGCATGTCTATTTGTCTTATGGTTC 60.148 37.037 0.00 0.00 0.00 3.62
2848 7339 5.092554 TGGTTCGCCTATGTTTCATTCTA 57.907 39.130 0.00 0.00 38.36 2.10
2849 7340 5.680619 TGGTTCGCCTATGTTTCATTCTAT 58.319 37.500 0.00 0.00 38.36 1.98
2850 7341 6.822442 TGGTTCGCCTATGTTTCATTCTATA 58.178 36.000 0.00 0.00 38.36 1.31
2866 7357 8.026341 TCATTCTATATGTTAGGTCGAGTACG 57.974 38.462 0.00 0.00 41.26 3.67
2867 7358 7.658982 TCATTCTATATGTTAGGTCGAGTACGT 59.341 37.037 0.00 0.00 40.69 3.57
2868 7359 7.792374 TTCTATATGTTAGGTCGAGTACGTT 57.208 36.000 0.00 0.00 40.69 3.99
2869 7360 7.792374 TCTATATGTTAGGTCGAGTACGTTT 57.208 36.000 0.00 0.00 40.69 3.60
2870 7361 8.213518 TCTATATGTTAGGTCGAGTACGTTTT 57.786 34.615 0.00 0.00 40.69 2.43
2871 7362 8.338259 TCTATATGTTAGGTCGAGTACGTTTTC 58.662 37.037 0.00 0.00 40.69 2.29
2872 7363 4.566545 TGTTAGGTCGAGTACGTTTTCA 57.433 40.909 0.00 0.00 40.69 2.69
2873 7364 4.930963 TGTTAGGTCGAGTACGTTTTCAA 58.069 39.130 0.00 0.00 40.69 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 82 3.653344 TCTTTCATGAGAGTCACGGTTG 58.347 45.455 12.62 0.00 0.00 3.77
128 134 1.557269 GCCCTGCCTCTCAGAAAGGA 61.557 60.000 0.00 0.00 45.72 3.36
208 327 7.148255 ACCAAAAGGCATTTTCTGTTTTCTTTC 60.148 33.333 6.03 0.00 36.47 2.62
286 3742 1.837538 CGGTTTTGCTTCCGCGAGAA 61.838 55.000 8.23 8.88 40.28 2.87
481 3957 7.242079 GTCTTCCTTAGCTTTTCGATAAAACC 58.758 38.462 0.00 0.00 31.37 3.27
482 3958 7.242079 GGTCTTCCTTAGCTTTTCGATAAAAC 58.758 38.462 0.00 0.00 31.37 2.43
509 3985 1.026584 CGACGTTTTGGTTTTCCCCT 58.973 50.000 0.00 0.00 39.73 4.79
546 4025 2.465097 TTTCCGCATGCGTTTTCGGG 62.465 55.000 35.55 20.00 44.29 5.14
584 4070 1.286260 GTCGTGTTCTGGACGCTCT 59.714 57.895 0.00 0.00 36.75 4.09
598 4085 2.019951 GCCATTCGTCACGTGTCGT 61.020 57.895 28.92 12.81 42.36 4.34
618 4105 3.044305 GCCACTTGACGCGCTCTT 61.044 61.111 5.73 0.00 0.00 2.85
627 4114 1.005037 AACGATCTGCGCCACTTGA 60.005 52.632 4.18 0.00 46.04 3.02
638 4125 1.021390 CGGAAGCCTTGCAACGATCT 61.021 55.000 0.00 0.00 0.00 2.75
654 4141 1.026182 TTAACGAGCGCTCCTACGGA 61.026 55.000 30.66 10.09 0.00 4.69
658 4145 2.470156 TCGTTAACGAGCGCTCCTA 58.530 52.632 30.66 19.29 44.22 2.94
675 4162 4.403734 TGTGGAAATAAAGGGACCAACTC 58.596 43.478 0.00 0.00 32.32 3.01
681 4168 6.770785 TGCTGTATATGTGGAAATAAAGGGAC 59.229 38.462 0.00 0.00 0.00 4.46
689 4176 4.036734 CCGCTTTGCTGTATATGTGGAAAT 59.963 41.667 0.00 0.00 0.00 2.17
695 4182 2.093181 TGGACCGCTTTGCTGTATATGT 60.093 45.455 0.00 0.00 0.00 2.29
702 4189 3.726517 CCGTGGACCGCTTTGCTG 61.727 66.667 3.03 0.00 34.38 4.41
760 4247 1.822613 TAGGGCGAGGACTGCGTAG 60.823 63.158 0.00 0.00 0.00 3.51
761 4248 2.117156 GTAGGGCGAGGACTGCGTA 61.117 63.158 0.00 0.00 0.00 4.42
762 4249 3.450115 GTAGGGCGAGGACTGCGT 61.450 66.667 0.00 0.00 0.00 5.24
774 4271 1.535462 CAAGAACCTTTGCACGTAGGG 59.465 52.381 7.02 0.00 35.79 3.53
777 4274 0.948678 GCCAAGAACCTTTGCACGTA 59.051 50.000 0.00 0.00 0.00 3.57
781 4278 0.471591 ATGGGCCAAGAACCTTTGCA 60.472 50.000 11.89 0.00 0.00 4.08
798 4295 8.168626 TGAATTTTTCGTCTCGTATCTTTCATG 58.831 33.333 0.00 0.00 0.00 3.07
804 4301 6.622549 AGTCTGAATTTTTCGTCTCGTATCT 58.377 36.000 0.00 0.00 0.00 1.98
806 4303 6.645415 ACAAGTCTGAATTTTTCGTCTCGTAT 59.355 34.615 0.00 0.00 0.00 3.06
861 4366 1.745087 ACCATGAGCATAAAACGGCTG 59.255 47.619 0.00 0.00 41.22 4.85
862 4367 1.745087 CACCATGAGCATAAAACGGCT 59.255 47.619 0.00 0.00 44.48 5.52
863 4368 1.472480 ACACCATGAGCATAAAACGGC 59.528 47.619 0.00 0.00 0.00 5.68
864 4369 2.159393 CCACACCATGAGCATAAAACGG 60.159 50.000 0.00 0.00 0.00 4.44
866 4371 2.417243 GCCCACACCATGAGCATAAAAC 60.417 50.000 0.00 0.00 0.00 2.43
867 4372 1.824230 GCCCACACCATGAGCATAAAA 59.176 47.619 0.00 0.00 0.00 1.52
869 4374 0.625316 AGCCCACACCATGAGCATAA 59.375 50.000 0.00 0.00 0.00 1.90
930 4436 6.694445 TGGAGAAGAAGGAGAGAGATTTTT 57.306 37.500 0.00 0.00 0.00 1.94
931 4437 6.126796 GGATGGAGAAGAAGGAGAGAGATTTT 60.127 42.308 0.00 0.00 0.00 1.82
932 4438 5.366477 GGATGGAGAAGAAGGAGAGAGATTT 59.634 44.000 0.00 0.00 0.00 2.17
933 4439 4.901250 GGATGGAGAAGAAGGAGAGAGATT 59.099 45.833 0.00 0.00 0.00 2.40
934 4440 4.482990 GGATGGAGAAGAAGGAGAGAGAT 58.517 47.826 0.00 0.00 0.00 2.75
939 4445 1.288037 TCGGGATGGAGAAGAAGGAGA 59.712 52.381 0.00 0.00 0.00 3.71
948 4454 2.024846 GGGATCTAGATCGGGATGGAGA 60.025 54.545 23.30 0.00 38.69 3.71
950 4456 1.341089 CGGGATCTAGATCGGGATGGA 60.341 57.143 23.30 0.00 38.69 3.41
951 4457 1.107114 CGGGATCTAGATCGGGATGG 58.893 60.000 23.30 7.53 38.69 3.51
952 4458 0.457851 GCGGGATCTAGATCGGGATG 59.542 60.000 23.30 13.16 38.69 3.51
953 4459 0.684805 GGCGGGATCTAGATCGGGAT 60.685 60.000 23.30 3.70 38.69 3.85
954 4460 1.304217 GGCGGGATCTAGATCGGGA 60.304 63.158 23.30 0.00 38.69 5.14
955 4461 2.701780 CGGCGGGATCTAGATCGGG 61.702 68.421 23.30 18.40 38.69 5.14
956 4462 2.878429 CGGCGGGATCTAGATCGG 59.122 66.667 23.30 18.71 38.69 4.18
957 4463 2.179517 GCGGCGGGATCTAGATCG 59.820 66.667 23.30 16.11 38.69 3.69
958 4464 2.574399 GGCGGCGGGATCTAGATC 59.426 66.667 22.41 22.41 37.11 2.75
959 4465 2.997897 GGGCGGCGGGATCTAGAT 60.998 66.667 9.78 4.47 0.00 1.98
960 4466 4.533124 TGGGCGGCGGGATCTAGA 62.533 66.667 9.78 0.00 0.00 2.43
961 4467 2.397413 ATTTGGGCGGCGGGATCTAG 62.397 60.000 9.78 0.00 0.00 2.43
962 4468 2.391724 GATTTGGGCGGCGGGATCTA 62.392 60.000 9.78 0.00 0.00 1.98
963 4469 3.774599 GATTTGGGCGGCGGGATCT 62.775 63.158 9.78 0.00 0.00 2.75
964 4470 3.287520 GATTTGGGCGGCGGGATC 61.288 66.667 9.78 2.06 0.00 3.36
977 4483 1.006227 GGGGGAGGGGAGAGGATTT 59.994 63.158 0.00 0.00 0.00 2.17
1005 4511 2.273776 GAAAGGGGGAGCTGGCTC 59.726 66.667 13.56 13.56 42.04 4.70
1006 4512 3.342477 GGAAAGGGGGAGCTGGCT 61.342 66.667 0.00 0.00 0.00 4.75
1009 4515 2.679716 CTGGGAAAGGGGGAGCTG 59.320 66.667 0.00 0.00 0.00 4.24
1040 4546 2.303282 GGGGCGGGAGAGGGTTTTA 61.303 63.158 0.00 0.00 0.00 1.52
1041 4547 3.658422 GGGGCGGGAGAGGGTTTT 61.658 66.667 0.00 0.00 0.00 2.43
1123 4629 4.547367 GGGGCGGGAGATGGTTCG 62.547 72.222 0.00 0.00 0.00 3.95
1128 4634 4.320456 CGATGGGGGCGGGAGATG 62.320 72.222 0.00 0.00 0.00 2.90
1129 4635 4.880426 ACGATGGGGGCGGGAGAT 62.880 66.667 0.00 0.00 0.00 2.75
1137 4643 4.489771 GGAGCACCACGATGGGGG 62.490 72.222 8.13 0.00 42.59 5.40
1139 4645 4.489771 GGGGAGCACCACGATGGG 62.490 72.222 1.58 0.64 43.37 4.00
1140 4646 3.266686 TTGGGGAGCACCACGATGG 62.267 63.158 1.58 0.00 43.75 3.51
1141 4647 1.746615 CTTGGGGAGCACCACGATG 60.747 63.158 1.58 0.00 43.75 3.84
1150 4656 3.876161 GAGGATCATGGCTTGGGGAGC 62.876 61.905 0.09 0.00 42.90 4.70
1151 4657 0.110104 GAGGATCATGGCTTGGGGAG 59.890 60.000 0.09 0.00 33.17 4.30
1152 4658 0.327867 AGAGGATCATGGCTTGGGGA 60.328 55.000 0.09 0.00 37.82 4.81
1163 4712 1.207791 GCAAAGAGGGGAGAGGATCA 58.792 55.000 0.00 0.00 37.82 2.92
1173 4722 0.250553 TTACACCACGGCAAAGAGGG 60.251 55.000 0.00 0.00 0.00 4.30
1179 4728 0.816018 CACCACTTACACCACGGCAA 60.816 55.000 0.00 0.00 0.00 4.52
1233 4782 1.510844 CCAAATGGCACCTTACGGC 59.489 57.895 0.00 0.00 0.00 5.68
1284 4835 4.333649 TGCATCTCTAGCTTTTCAAATCGG 59.666 41.667 0.00 0.00 0.00 4.18
1331 4885 1.404583 GGCCCATTGCTTGCAGTAAAG 60.405 52.381 0.00 0.00 40.92 1.85
1446 5001 5.070313 TGCAAACTAAAGGCCAAGAAAGAAT 59.930 36.000 5.01 0.00 0.00 2.40
1474 5029 7.065085 GTGCATTCTGTATCTCAACAATAGTGT 59.935 37.037 0.00 0.00 40.75 3.55
1567 5122 8.800370 TTTGAAAAGGGAAAGCAAACTAAATT 57.200 26.923 0.00 0.00 0.00 1.82
1590 5145 6.978080 AGACAACAAAATTACGTGCAAGATTT 59.022 30.769 6.65 0.00 0.00 2.17
1628 5183 3.480470 CCACTGTGAAGTCCAAACTCAT 58.520 45.455 9.86 0.00 33.48 2.90
1643 5198 3.557903 AATGAGCAGCGGCCACTGT 62.558 57.895 21.51 8.89 42.56 3.55
1645 5200 2.437359 GAATGAGCAGCGGCCACT 60.437 61.111 4.82 0.00 42.56 4.00
1713 5268 4.908687 ACGCAGCGCAGGACACAA 62.909 61.111 16.61 0.00 0.00 3.33
1868 5423 5.648092 AGGGAATACTTGTGAACACTTATGC 59.352 40.000 6.51 0.55 0.00 3.14
1872 5427 4.351111 AGGAGGGAATACTTGTGAACACTT 59.649 41.667 6.51 0.00 0.00 3.16
1958 5518 9.756571 CCTAAATCATACTAGTAGTACTCCCAT 57.243 37.037 12.25 0.00 32.84 4.00
1959 5519 8.730948 ACCTAAATCATACTAGTAGTACTCCCA 58.269 37.037 12.25 0.00 32.84 4.37
1978 5540 3.005791 GGAGCAGCAACAACAACCTAAAT 59.994 43.478 0.00 0.00 0.00 1.40
2036 5598 6.764308 ATTCAAATGTACATTCCTGGTCAG 57.236 37.500 21.02 5.12 0.00 3.51
2037 5599 7.451255 AGAAATTCAAATGTACATTCCTGGTCA 59.549 33.333 21.02 6.02 0.00 4.02
2079 5641 5.415701 ACAAGTTCACATCGCTAAATTCCAT 59.584 36.000 0.00 0.00 0.00 3.41
2092 6555 5.248640 AGTGCTGCTAATACAAGTTCACAT 58.751 37.500 0.00 0.00 0.00 3.21
2249 6714 4.632153 GCTTCACTCACACTCCTTTTCTA 58.368 43.478 0.00 0.00 0.00 2.10
2566 7051 4.433186 TTGCAGGATATTTCCAAACACG 57.567 40.909 4.92 0.00 45.30 4.49
2709 7200 6.238703 GCATTTCCCATGCTTCAAAAGAAAAA 60.239 34.615 0.00 0.00 41.52 1.94
2746 7237 5.488262 AAGGCCTTTTAACTTCATGCATT 57.512 34.783 13.78 0.00 0.00 3.56
2795 7286 0.235665 GACATGCACACACAACGGAG 59.764 55.000 0.00 0.00 0.00 4.63
2798 7289 3.811722 AATAGACATGCACACACAACG 57.188 42.857 0.00 0.00 0.00 4.10
2810 7301 5.527582 GGCGAACCATAAGACAAATAGACAT 59.472 40.000 0.00 0.00 35.26 3.06
2812 7303 5.116882 AGGCGAACCATAAGACAAATAGAC 58.883 41.667 0.00 0.00 39.06 2.59
2831 7322 8.873830 CCTAACATATAGAATGAAACATAGGCG 58.126 37.037 0.00 0.00 0.00 5.52
2848 7339 6.855836 TGAAAACGTACTCGACCTAACATAT 58.144 36.000 0.00 0.00 40.62 1.78
2849 7340 6.252967 TGAAAACGTACTCGACCTAACATA 57.747 37.500 0.00 0.00 40.62 2.29
2850 7341 5.125100 TGAAAACGTACTCGACCTAACAT 57.875 39.130 0.00 0.00 40.62 2.71


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

AutoCloner maintained by Alex Coulton.