Multiple sequence alignment - TraesCS6B01G229400

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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 TraesCS6B01G229400 chr6B 100.000 2855 0 0 1 2855 367348317 367351171 0.000000e+00 5273.0
1 TraesCS6B01G229400 chr6B 96.123 619 18 1 2243 2855 638231825 638232443 0.000000e+00 1005.0
2 TraesCS6B01G229400 chr6B 88.780 615 55 4 2249 2855 157198517 157197909 0.000000e+00 741.0
3 TraesCS6B01G229400 chr6B 90.737 529 42 6 946 1469 366167721 366167195 0.000000e+00 699.0
4 TraesCS6B01G229400 chr6B 93.304 224 10 4 1466 1688 366165238 366165019 2.740000e-85 326.0
5 TraesCS6B01G229400 chr6B 81.865 193 35 0 649 841 618094535 618094343 2.280000e-36 163.0
6 TraesCS6B01G229400 chr6B 81.188 202 33 3 650 847 48216714 48216914 1.060000e-34 158.0
7 TraesCS6B01G229400 chr6B 92.771 83 4 2 2152 2234 39190037 39190117 5.000000e-23 119.0
8 TraesCS6B01G229400 chr6A 97.010 1204 22 3 946 2149 313298713 313297524 0.000000e+00 2012.0
9 TraesCS6B01G229400 chr6A 92.453 53 4 0 892 944 313298813 313298761 3.050000e-10 76.8
10 TraesCS6B01G229400 chr6D 97.459 905 16 3 1248 2149 217759632 217758732 0.000000e+00 1537.0
11 TraesCS6B01G229400 chr6D 97.598 333 8 0 946 1278 217760182 217759850 3.190000e-159 571.0
12 TraesCS6B01G229400 chr6D 88.785 107 6 2 838 939 217760340 217760235 2.990000e-25 126.0
13 TraesCS6B01G229400 chr1B 95.285 615 22 2 2247 2855 186796197 186795584 0.000000e+00 968.0
14 TraesCS6B01G229400 chr7D 94.959 615 24 2 2247 2855 497007235 497006622 0.000000e+00 957.0
15 TraesCS6B01G229400 chr7D 93.827 81 4 1 2152 2232 402332407 402332328 1.390000e-23 121.0
16 TraesCS6B01G229400 chr7A 94.797 615 25 2 2246 2854 75025545 75026158 0.000000e+00 952.0
17 TraesCS6B01G229400 chr7A 82.698 341 38 13 1 337 539431608 539431285 1.670000e-72 283.0
18 TraesCS6B01G229400 chr7A 86.611 239 23 4 598 835 729715487 729715717 3.650000e-64 255.0
19 TraesCS6B01G229400 chr7A 91.411 163 13 1 1 162 729679609 729679771 3.700000e-54 222.0
20 TraesCS6B01G229400 chr7A 89.855 138 14 0 203 340 729688300 729688437 8.130000e-41 178.0
21 TraesCS6B01G229400 chr7A 89.051 137 15 0 204 340 729712052 729712188 1.360000e-38 171.0
22 TraesCS6B01G229400 chr3A 93.964 613 26 5 2249 2855 100034630 100035237 0.000000e+00 917.0
23 TraesCS6B01G229400 chr3A 81.714 350 42 16 1 345 606031048 606031380 3.620000e-69 272.0
24 TraesCS6B01G229400 chr3B 93.659 615 26 3 2247 2855 410612231 410611624 0.000000e+00 907.0
25 TraesCS6B01G229400 chr3B 91.566 166 12 1 100 263 795042837 795042672 7.960000e-56 228.0
26 TraesCS6B01G229400 chr3B 91.018 167 13 2 1 165 795043002 795042836 1.030000e-54 224.0
27 TraesCS6B01G229400 chr3B 77.451 204 28 8 651 841 664838299 664838101 3.890000e-19 106.0
28 TraesCS6B01G229400 chr5D 93.805 565 28 5 2239 2797 551868510 551867947 0.000000e+00 843.0
29 TraesCS6B01G229400 chr4B 90.113 617 52 4 2244 2853 672246637 672247251 0.000000e+00 793.0
30 TraesCS6B01G229400 chr4B 78.000 850 123 37 1 839 619358370 619359166 2.570000e-130 475.0
31 TraesCS6B01G229400 chr4D 82.192 365 46 11 12 373 414343289 414342941 2.150000e-76 296.0
32 TraesCS6B01G229400 chr4D 81.050 343 52 5 515 847 414342873 414342534 7.850000e-66 261.0
33 TraesCS6B01G229400 chr4D 79.024 205 33 4 646 841 444285887 444286090 6.420000e-27 132.0
34 TraesCS6B01G229400 chr7B 82.902 193 31 2 650 842 11170087 11170277 3.780000e-39 172.0
35 TraesCS6B01G229400 chr5B 79.167 264 38 13 460 716 515670218 515670471 1.760000e-37 167.0
36 TraesCS6B01G229400 chr2B 79.592 196 38 2 650 844 218403973 218403779 3.840000e-29 139.0
37 TraesCS6B01G229400 chr2B 77.232 224 36 6 635 845 43780299 43780078 1.800000e-22 117.0
38 TraesCS6B01G229400 chr1D 96.386 83 3 0 2152 2234 138495441 138495359 1.380000e-28 137.0
39 TraesCS6B01G229400 chr3D 84.783 92 4 3 2151 2234 80292967 80293056 1.820000e-12 84.2


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 TraesCS6B01G229400 chr6B 367348317 367351171 2854 False 5273.000000 5273 100.0000 1 2855 1 chr6B.!!$F3 2854
1 TraesCS6B01G229400 chr6B 638231825 638232443 618 False 1005.000000 1005 96.1230 2243 2855 1 chr6B.!!$F4 612
2 TraesCS6B01G229400 chr6B 157197909 157198517 608 True 741.000000 741 88.7800 2249 2855 1 chr6B.!!$R1 606
3 TraesCS6B01G229400 chr6B 366165019 366167721 2702 True 512.500000 699 92.0205 946 1688 2 chr6B.!!$R3 742
4 TraesCS6B01G229400 chr6A 313297524 313298813 1289 True 1044.400000 2012 94.7315 892 2149 2 chr6A.!!$R1 1257
5 TraesCS6B01G229400 chr6D 217758732 217760340 1608 True 744.666667 1537 94.6140 838 2149 3 chr6D.!!$R1 1311
6 TraesCS6B01G229400 chr1B 186795584 186796197 613 True 968.000000 968 95.2850 2247 2855 1 chr1B.!!$R1 608
7 TraesCS6B01G229400 chr7D 497006622 497007235 613 True 957.000000 957 94.9590 2247 2855 1 chr7D.!!$R2 608
8 TraesCS6B01G229400 chr7A 75025545 75026158 613 False 952.000000 952 94.7970 2246 2854 1 chr7A.!!$F1 608
9 TraesCS6B01G229400 chr7A 729712052 729715717 3665 False 213.000000 255 87.8310 204 835 2 chr7A.!!$F4 631
10 TraesCS6B01G229400 chr3A 100034630 100035237 607 False 917.000000 917 93.9640 2249 2855 1 chr3A.!!$F1 606
11 TraesCS6B01G229400 chr3B 410611624 410612231 607 True 907.000000 907 93.6590 2247 2855 1 chr3B.!!$R1 608
12 TraesCS6B01G229400 chr5D 551867947 551868510 563 True 843.000000 843 93.8050 2239 2797 1 chr5D.!!$R1 558
13 TraesCS6B01G229400 chr4B 672246637 672247251 614 False 793.000000 793 90.1130 2244 2853 1 chr4B.!!$F2 609
14 TraesCS6B01G229400 chr4B 619358370 619359166 796 False 475.000000 475 78.0000 1 839 1 chr4B.!!$F1 838
15 TraesCS6B01G229400 chr4D 414342534 414343289 755 True 278.500000 296 81.6210 12 847 2 chr4D.!!$R1 835

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
381 387 0.029567 GGATCTCGATCGAGCGTGTT 59.97 55.0 34.92 15.45 41.71 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 6843 0.181587 TGTTCAAGCCGGGTCTTTCA 59.818 50.0 6.62 1.78 0.0 2.69 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
21 25 2.836981 ACCTGACAGGGAAGAGATCAAG 59.163 50.000 25.34 0.00 40.58 3.02
24 28 4.163839 CCTGACAGGGAAGAGATCAAGAAT 59.836 45.833 14.26 0.00 0.00 2.40
28 32 2.768527 AGGGAAGAGATCAAGAATCGCA 59.231 45.455 0.00 0.00 39.55 5.10
57 61 1.450312 CTGATGGAACCACCGGCTC 60.450 63.158 0.00 0.00 42.61 4.70
58 62 1.903877 CTGATGGAACCACCGGCTCT 61.904 60.000 0.00 0.00 42.61 4.09
59 63 1.153349 GATGGAACCACCGGCTCTC 60.153 63.158 0.00 0.00 42.61 3.20
60 64 1.899437 GATGGAACCACCGGCTCTCA 61.899 60.000 0.00 0.00 42.61 3.27
61 65 2.047179 GGAACCACCGGCTCTCAC 60.047 66.667 0.00 0.00 0.00 3.51
62 66 2.741092 GAACCACCGGCTCTCACA 59.259 61.111 0.00 0.00 0.00 3.58
63 67 1.374758 GAACCACCGGCTCTCACAG 60.375 63.158 0.00 0.00 0.00 3.66
64 68 2.100879 GAACCACCGGCTCTCACAGT 62.101 60.000 0.00 0.00 0.00 3.55
65 69 2.100879 AACCACCGGCTCTCACAGTC 62.101 60.000 0.00 0.00 0.00 3.51
66 70 2.279069 CCACCGGCTCTCACAGTCT 61.279 63.158 0.00 0.00 0.00 3.24
67 71 1.668294 CACCGGCTCTCACAGTCTT 59.332 57.895 0.00 0.00 0.00 3.01
68 72 0.668706 CACCGGCTCTCACAGTCTTG 60.669 60.000 0.00 0.00 0.00 3.02
69 73 1.115930 ACCGGCTCTCACAGTCTTGT 61.116 55.000 0.00 0.00 38.31 3.16
70 74 0.389166 CCGGCTCTCACAGTCTTGTC 60.389 60.000 0.00 0.00 34.62 3.18
71 75 0.600557 CGGCTCTCACAGTCTTGTCT 59.399 55.000 0.00 0.00 34.62 3.41
81 85 1.133407 CAGTCTTGTCTCCGTAGCCTC 59.867 57.143 0.00 0.00 0.00 4.70
86 90 0.541063 TGTCTCCGTAGCCTCCACAA 60.541 55.000 0.00 0.00 0.00 3.33
87 91 0.606604 GTCTCCGTAGCCTCCACAAA 59.393 55.000 0.00 0.00 0.00 2.83
95 99 5.048573 TCCGTAGCCTCCACAAAATTAAAAC 60.049 40.000 0.00 0.00 0.00 2.43
98 102 3.970640 AGCCTCCACAAAATTAAAACCCA 59.029 39.130 0.00 0.00 0.00 4.51
116 120 6.590234 AACCCAAAGAACAATCTAATGTCC 57.410 37.500 0.00 0.00 33.77 4.02
121 125 7.393234 CCCAAAGAACAATCTAATGTCCTAACA 59.607 37.037 0.00 0.00 35.64 2.41
157 161 1.221021 GTAGGTACACAGGGCTGCC 59.779 63.158 11.05 11.05 0.00 4.85
158 162 2.355986 TAGGTACACAGGGCTGCCG 61.356 63.158 13.40 1.87 0.00 5.69
159 163 4.778143 GGTACACAGGGCTGCCGG 62.778 72.222 13.40 10.03 0.00 6.13
160 164 3.702048 GTACACAGGGCTGCCGGA 61.702 66.667 13.40 0.00 0.00 5.14
161 165 2.925706 TACACAGGGCTGCCGGAA 60.926 61.111 13.40 0.00 0.00 4.30
173 177 1.452108 GCCGGAAGAACCATCTGGG 60.452 63.158 5.05 0.00 42.57 4.45
177 181 1.602237 GAAGAACCATCTGGGCGGA 59.398 57.895 0.54 0.00 42.05 5.54
180 184 1.201429 AGAACCATCTGGGCGGAAGT 61.201 55.000 0.54 0.00 42.05 3.01
189 193 0.613853 TGGGCGGAAGTAGTGCTAGT 60.614 55.000 0.00 0.00 0.00 2.57
273 278 4.056125 CTCTGCCAGGACACGCGA 62.056 66.667 15.93 0.00 0.00 5.87
275 280 2.664851 CTGCCAGGACACGCGAAA 60.665 61.111 15.93 0.00 0.00 3.46
293 298 3.369147 CGAAAAGCGAGATGAACAGACAT 59.631 43.478 0.00 0.00 44.57 3.06
296 301 6.237942 CGAAAAGCGAGATGAACAGACATAAT 60.238 38.462 0.00 0.00 44.57 1.28
301 306 5.107683 GCGAGATGAACAGACATAATAGTGC 60.108 44.000 0.00 0.00 0.00 4.40
308 313 2.365617 CAGACATAATAGTGCCCGGTCT 59.634 50.000 0.00 0.00 34.70 3.85
319 324 2.270205 CCGGTCTGCTGCTGGATT 59.730 61.111 6.69 0.00 34.35 3.01
325 330 2.355108 GGTCTGCTGCTGGATTGAAGTA 60.355 50.000 6.69 0.00 0.00 2.24
367 373 0.962356 CGGGTGCTTTGCTTGGATCT 60.962 55.000 0.00 0.00 0.00 2.75
370 376 1.442769 GTGCTTTGCTTGGATCTCGA 58.557 50.000 0.00 0.00 0.00 4.04
378 384 0.309302 CTTGGATCTCGATCGAGCGT 59.691 55.000 34.92 26.35 41.71 5.07
381 387 0.029567 GGATCTCGATCGAGCGTGTT 59.970 55.000 34.92 15.45 41.71 3.32
389 395 3.114616 CGAGCGTGTTGGCTGGAG 61.115 66.667 0.00 0.00 44.93 3.86
415 432 1.820906 CATCACGCCATCACCTGGG 60.821 63.158 0.00 0.00 46.06 4.45
422 439 1.224315 CCATCACCTGGGCGAATCA 59.776 57.895 0.00 0.00 41.82 2.57
432 449 2.890474 GCGAATCACCCGCGTCAT 60.890 61.111 4.92 0.00 43.28 3.06
434 451 2.576893 CGAATCACCCGCGTCATCG 61.577 63.158 4.92 2.43 40.37 3.84
458 475 3.470888 CTTCGCCCGGATCCCACT 61.471 66.667 0.73 0.00 0.00 4.00
459 476 3.447025 CTTCGCCCGGATCCCACTC 62.447 68.421 0.73 0.00 0.00 3.51
462 479 3.917760 GCCCGGATCCCACTCGAG 61.918 72.222 11.84 11.84 0.00 4.04
463 480 3.917760 CCCGGATCCCACTCGAGC 61.918 72.222 13.61 0.00 0.00 5.03
464 481 4.271816 CCGGATCCCACTCGAGCG 62.272 72.222 13.61 1.99 0.00 5.03
465 482 4.933064 CGGATCCCACTCGAGCGC 62.933 72.222 13.61 0.00 0.00 5.92
466 483 4.933064 GGATCCCACTCGAGCGCG 62.933 72.222 13.61 2.41 39.35 6.86
467 484 4.194720 GATCCCACTCGAGCGCGT 62.195 66.667 13.61 0.00 38.98 6.01
468 485 4.194720 ATCCCACTCGAGCGCGTC 62.195 66.667 13.61 3.06 38.98 5.19
565 594 0.827368 GATCCACCTCCTCTGTCCAC 59.173 60.000 0.00 0.00 0.00 4.02
603 632 2.995574 CGGACGTTCCACCTCCCT 60.996 66.667 0.00 0.00 35.91 4.20
619 648 0.036010 CCCTTGTGGAGCGAGAACAT 60.036 55.000 0.00 0.00 35.39 2.71
624 657 4.437239 CTTGTGGAGCGAGAACATCTTAT 58.563 43.478 0.00 0.00 0.00 1.73
634 667 6.042093 AGCGAGAACATCTTATCTTAATGGGA 59.958 38.462 0.00 0.00 0.00 4.37
638 671 7.465116 AGAACATCTTATCTTAATGGGATGGG 58.535 38.462 0.00 0.00 36.05 4.00
639 672 5.574188 ACATCTTATCTTAATGGGATGGGC 58.426 41.667 0.00 0.00 36.05 5.36
642 675 2.986534 ATCTTAATGGGATGGGCTGG 57.013 50.000 0.00 0.00 0.00 4.85
643 676 0.852842 TCTTAATGGGATGGGCTGGG 59.147 55.000 0.00 0.00 0.00 4.45
664 697 0.325602 TAACCGGCCCAGTTTACCAG 59.674 55.000 10.85 0.00 0.00 4.00
683 716 2.830370 GGGCTTGGATTCGGCCTG 60.830 66.667 0.00 0.00 44.70 4.85
686 719 3.056313 GCTTGGATTCGGCCTGTGC 62.056 63.158 0.00 0.00 0.00 4.57
688 721 1.651240 CTTGGATTCGGCCTGTGCAG 61.651 60.000 0.00 0.00 40.13 4.41
689 722 3.512516 GGATTCGGCCTGTGCAGC 61.513 66.667 0.00 0.00 40.13 5.25
730 763 1.817099 CCAGTTGCGGGAGAGATGC 60.817 63.158 0.00 0.00 0.00 3.91
731 764 1.817099 CAGTTGCGGGAGAGATGCC 60.817 63.158 0.00 0.00 0.00 4.40
740 773 2.739932 CGGGAGAGATGCCTTTACACAG 60.740 54.545 0.00 0.00 0.00 3.66
741 774 2.420687 GGGAGAGATGCCTTTACACAGG 60.421 54.545 0.00 0.00 36.95 4.00
747 780 3.135530 AGATGCCTTTACACAGGAGATCC 59.864 47.826 0.00 0.00 35.71 3.36
754 787 2.043852 ACAGGAGATCCGACGGCT 60.044 61.111 9.66 0.00 42.08 5.52
763 796 1.331756 GATCCGACGGCTAGAAACGTA 59.668 52.381 9.66 0.00 44.24 3.57
770 803 4.084171 CGACGGCTAGAAACGTATAGATCA 60.084 45.833 7.40 0.00 44.24 2.92
771 804 5.390673 CGACGGCTAGAAACGTATAGATCAT 60.391 44.000 7.40 0.00 44.24 2.45
781 814 7.926555 AGAAACGTATAGATCATGAAAACGGAT 59.073 33.333 17.20 9.29 33.44 4.18
791 824 5.009631 TCATGAAAACGGATGGTCAGAAAT 58.990 37.500 0.00 0.00 0.00 2.17
792 825 4.764679 TGAAAACGGATGGTCAGAAATG 57.235 40.909 0.00 0.00 0.00 2.32
794 827 1.086696 AACGGATGGTCAGAAATGCG 58.913 50.000 6.69 6.69 42.51 4.73
797 830 1.328680 CGGATGGTCAGAAATGCGAAG 59.671 52.381 2.98 0.00 39.65 3.79
841 874 5.104652 AGGTGCGGTTATACTGTCCTTAATT 60.105 40.000 0.00 0.00 30.98 1.40
842 875 5.007332 GGTGCGGTTATACTGTCCTTAATTG 59.993 44.000 0.00 0.00 0.00 2.32
856 889 5.955959 GTCCTTAATTGGAAAGGGGTTATGT 59.044 40.000 5.79 0.00 43.20 2.29
941 979 1.035139 GCTATTTGGTCTGGCCCATG 58.965 55.000 0.00 0.00 33.60 3.66
962 1046 2.758423 GGCTATTCGAACCCCAAATTGT 59.242 45.455 0.00 0.00 0.00 2.71
963 1052 3.181490 GGCTATTCGAACCCCAAATTGTC 60.181 47.826 0.00 0.00 0.00 3.18
1455 4177 0.523966 CTATCCGCGTCATCCTCCTC 59.476 60.000 4.92 0.00 0.00 3.71
1634 6316 0.179012 GAGGGGAACACGGGAAACAA 60.179 55.000 0.00 0.00 0.00 2.83
1738 6420 1.904771 CGGGAGGTGGATAGCAACA 59.095 57.895 0.00 0.00 0.00 3.33
1930 6612 1.136891 TCGATCGAATGTGCATCTGGT 59.863 47.619 16.99 0.00 0.00 4.00
2106 6791 3.006430 CCAAGGCGGACAAAAATAGGTTT 59.994 43.478 0.00 0.00 36.56 3.27
2149 6834 8.695456 GGTTGAAATCAGGGTATTGATTATGTT 58.305 33.333 2.05 0.00 44.74 2.71
2174 6859 2.447630 TCTGAAAGACCCGGCTTGA 58.552 52.632 0.00 0.00 38.67 3.02
2175 6860 0.762418 TCTGAAAGACCCGGCTTGAA 59.238 50.000 0.00 0.00 38.67 2.69
2176 6861 0.875059 CTGAAAGACCCGGCTTGAAC 59.125 55.000 0.00 0.00 34.07 3.18
2177 6862 0.181587 TGAAAGACCCGGCTTGAACA 59.818 50.000 0.00 0.00 0.00 3.18
2178 6863 0.591659 GAAAGACCCGGCTTGAACAC 59.408 55.000 0.00 0.00 0.00 3.32
2179 6864 1.164041 AAAGACCCGGCTTGAACACG 61.164 55.000 0.00 0.00 0.00 4.49
2180 6865 3.047877 GACCCGGCTTGAACACGG 61.048 66.667 0.00 0.00 46.79 4.94
2184 6869 2.978010 CGGCTTGAACACGGGCTT 60.978 61.111 0.00 0.00 0.00 4.35
2185 6870 2.954611 GGCTTGAACACGGGCTTC 59.045 61.111 0.00 0.00 0.00 3.86
2186 6871 1.896660 GGCTTGAACACGGGCTTCA 60.897 57.895 0.00 0.00 0.00 3.02
2187 6872 1.244019 GGCTTGAACACGGGCTTCAT 61.244 55.000 3.99 0.00 0.00 2.57
2188 6873 0.598065 GCTTGAACACGGGCTTCATT 59.402 50.000 3.99 0.00 0.00 2.57
2189 6874 1.666888 GCTTGAACACGGGCTTCATTG 60.667 52.381 3.99 2.81 0.00 2.82
2190 6875 1.879380 CTTGAACACGGGCTTCATTGA 59.121 47.619 3.99 0.00 0.00 2.57
2191 6876 2.198827 TGAACACGGGCTTCATTGAT 57.801 45.000 0.00 0.00 0.00 2.57
2192 6877 2.513753 TGAACACGGGCTTCATTGATT 58.486 42.857 0.00 0.00 0.00 2.57
2193 6878 2.890311 TGAACACGGGCTTCATTGATTT 59.110 40.909 0.00 0.00 0.00 2.17
2194 6879 4.075682 TGAACACGGGCTTCATTGATTTA 58.924 39.130 0.00 0.00 0.00 1.40
2195 6880 4.155826 TGAACACGGGCTTCATTGATTTAG 59.844 41.667 0.00 0.00 0.00 1.85
2196 6881 2.423538 ACACGGGCTTCATTGATTTAGC 59.576 45.455 0.98 0.98 0.00 3.09
2197 6882 2.423185 CACGGGCTTCATTGATTTAGCA 59.577 45.455 10.21 0.00 35.36 3.49
2198 6883 2.684881 ACGGGCTTCATTGATTTAGCAG 59.315 45.455 10.21 6.59 35.36 4.24
2199 6884 2.945008 CGGGCTTCATTGATTTAGCAGA 59.055 45.455 10.21 0.00 35.36 4.26
2200 6885 3.378112 CGGGCTTCATTGATTTAGCAGAA 59.622 43.478 10.21 0.00 35.36 3.02
2201 6886 4.142403 CGGGCTTCATTGATTTAGCAGAAA 60.142 41.667 10.21 0.00 35.36 2.52
2202 6887 5.346522 GGGCTTCATTGATTTAGCAGAAAG 58.653 41.667 10.21 0.00 35.36 2.62
2203 6888 4.802563 GGCTTCATTGATTTAGCAGAAAGC 59.197 41.667 10.21 0.00 46.19 3.51
2230 6915 6.710278 TGGAAACATGTAGATCAAGTGATCA 58.290 36.000 20.52 0.00 44.08 2.92
2231 6916 7.167535 TGGAAACATGTAGATCAAGTGATCAA 58.832 34.615 20.52 8.43 44.08 2.57
2232 6917 7.665145 TGGAAACATGTAGATCAAGTGATCAAA 59.335 33.333 20.52 7.87 44.08 2.69
2599 7296 2.371658 ACTTGGGAGCAAAAGCTTCT 57.628 45.000 0.00 0.00 0.00 2.85
2656 7353 5.200483 CCATTTCCTCCAGCAATAAACCTA 58.800 41.667 0.00 0.00 0.00 3.08
2679 7376 1.901591 TTGTCGTCTCTTAGGACCGT 58.098 50.000 0.00 0.00 41.37 4.83
2724 7421 5.988310 TCATGGTCAAAAGAAGCATCAAT 57.012 34.783 0.00 0.00 32.78 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.935203 TGTTGCGATTCTTGATCTCTTCC 59.065 43.478 0.00 0.00 32.30 3.46
21 25 5.446473 CCATCAGTTAGAAGTGTTGCGATTC 60.446 44.000 0.00 0.00 31.02 2.52
24 28 3.006430 TCCATCAGTTAGAAGTGTTGCGA 59.994 43.478 0.00 1.34 31.02 5.10
28 32 5.063880 GTGGTTCCATCAGTTAGAAGTGTT 58.936 41.667 0.00 0.00 0.00 3.32
57 61 2.414824 GCTACGGAGACAAGACTGTGAG 60.415 54.545 0.00 0.00 35.30 3.51
58 62 1.540267 GCTACGGAGACAAGACTGTGA 59.460 52.381 0.00 0.00 35.30 3.58
59 63 1.402984 GGCTACGGAGACAAGACTGTG 60.403 57.143 0.00 0.00 35.30 3.66
60 64 0.889306 GGCTACGGAGACAAGACTGT 59.111 55.000 0.00 0.00 38.98 3.55
61 65 1.133407 GAGGCTACGGAGACAAGACTG 59.867 57.143 1.57 0.00 31.70 3.51
62 66 1.465794 GAGGCTACGGAGACAAGACT 58.534 55.000 1.57 0.00 34.15 3.24
63 67 0.456628 GGAGGCTACGGAGACAAGAC 59.543 60.000 1.57 0.00 30.20 3.01
64 68 0.039180 TGGAGGCTACGGAGACAAGA 59.961 55.000 1.57 0.00 30.20 3.02
65 69 0.173708 GTGGAGGCTACGGAGACAAG 59.826 60.000 1.57 0.00 30.20 3.16
66 70 0.541063 TGTGGAGGCTACGGAGACAA 60.541 55.000 1.57 0.00 30.20 3.18
67 71 0.541063 TTGTGGAGGCTACGGAGACA 60.541 55.000 1.57 0.00 30.20 3.41
68 72 0.606604 TTTGTGGAGGCTACGGAGAC 59.393 55.000 0.00 0.00 0.00 3.36
69 73 1.344065 TTTTGTGGAGGCTACGGAGA 58.656 50.000 0.00 0.00 0.00 3.71
70 74 2.403252 ATTTTGTGGAGGCTACGGAG 57.597 50.000 0.00 0.00 0.00 4.63
71 75 2.871096 AATTTTGTGGAGGCTACGGA 57.129 45.000 0.00 0.00 0.00 4.69
81 85 7.617041 TGTTCTTTGGGTTTTAATTTTGTGG 57.383 32.000 0.00 0.00 0.00 4.17
95 99 7.393234 TGTTAGGACATTAGATTGTTCTTTGGG 59.607 37.037 0.00 0.00 36.77 4.12
110 114 4.360951 TCCTCCGTTTTGTTAGGACATT 57.639 40.909 0.00 0.00 35.29 2.71
111 115 4.569719 ATCCTCCGTTTTGTTAGGACAT 57.430 40.909 0.00 0.00 40.83 3.06
116 120 5.240844 ACAGGAAAATCCTCCGTTTTGTTAG 59.759 40.000 0.00 0.00 45.66 2.34
121 125 4.202535 ACCTACAGGAAAATCCTCCGTTTT 60.203 41.667 1.29 0.00 45.66 2.43
123 127 2.910977 ACCTACAGGAAAATCCTCCGTT 59.089 45.455 1.29 0.00 45.66 4.44
125 129 3.449737 TGTACCTACAGGAAAATCCTCCG 59.550 47.826 1.29 0.00 45.66 4.63
148 152 2.747855 GTTCTTCCGGCAGCCCTG 60.748 66.667 5.63 0.00 0.00 4.45
152 156 1.078143 AGATGGTTCTTCCGGCAGC 60.078 57.895 0.00 0.00 39.52 5.25
153 157 0.745845 CCAGATGGTTCTTCCGGCAG 60.746 60.000 0.00 0.00 39.52 4.85
154 158 1.299648 CCAGATGGTTCTTCCGGCA 59.700 57.895 0.00 0.00 39.52 5.69
155 159 1.452108 CCCAGATGGTTCTTCCGGC 60.452 63.158 0.00 0.00 39.52 6.13
157 161 1.815421 CGCCCAGATGGTTCTTCCG 60.815 63.158 0.00 0.00 39.52 4.30
158 162 1.452108 CCGCCCAGATGGTTCTTCC 60.452 63.158 0.00 0.00 36.04 3.46
159 163 0.035439 TTCCGCCCAGATGGTTCTTC 60.035 55.000 0.00 0.00 36.04 2.87
160 164 0.035056 CTTCCGCCCAGATGGTTCTT 60.035 55.000 0.00 0.00 36.04 2.52
161 165 1.201429 ACTTCCGCCCAGATGGTTCT 61.201 55.000 0.00 0.00 36.04 3.01
173 177 0.806492 GCCACTAGCACTACTTCCGC 60.806 60.000 0.00 0.00 42.97 5.54
177 181 0.903454 ACCGGCCACTAGCACTACTT 60.903 55.000 0.00 0.00 46.50 2.24
180 184 0.686441 ATCACCGGCCACTAGCACTA 60.686 55.000 0.00 0.00 46.50 2.74
189 193 2.142356 ATGAATTCAATCACCGGCCA 57.858 45.000 13.09 0.00 30.82 5.36
273 278 6.992063 ATTATGTCTGTTCATCTCGCTTTT 57.008 33.333 0.00 0.00 0.00 2.27
275 280 6.699204 CACTATTATGTCTGTTCATCTCGCTT 59.301 38.462 0.00 0.00 0.00 4.68
293 298 0.464036 CAGCAGACCGGGCACTATTA 59.536 55.000 11.69 0.00 0.00 0.98
296 301 4.082523 GCAGCAGACCGGGCACTA 62.083 66.667 11.69 0.00 0.00 2.74
301 306 3.335356 AATCCAGCAGCAGACCGGG 62.335 63.158 6.32 0.00 0.00 5.73
308 313 2.675032 CGACTACTTCAATCCAGCAGCA 60.675 50.000 0.00 0.00 0.00 4.41
319 324 1.208358 CGCGACCACGACTACTTCA 59.792 57.895 0.00 0.00 42.66 3.02
350 356 0.449388 CGAGATCCAAGCAAAGCACC 59.551 55.000 0.00 0.00 0.00 5.01
352 358 2.283298 GATCGAGATCCAAGCAAAGCA 58.717 47.619 1.77 0.00 31.76 3.91
367 373 2.506217 GCCAACACGCTCGATCGA 60.506 61.111 18.32 18.32 0.00 3.59
370 376 2.434884 CCAGCCAACACGCTCGAT 60.435 61.111 0.00 0.00 36.82 3.59
378 384 2.280797 GCACGACTCCAGCCAACA 60.281 61.111 0.00 0.00 0.00 3.33
381 387 2.230994 GATGAGCACGACTCCAGCCA 62.231 60.000 7.56 0.00 45.61 4.75
406 423 1.224592 GGTGATTCGCCCAGGTGAT 59.775 57.895 4.83 0.00 34.40 3.06
441 458 3.447025 GAGTGGGATCCGGGCGAAG 62.447 68.421 5.45 0.00 0.00 3.79
442 459 3.467226 GAGTGGGATCCGGGCGAA 61.467 66.667 5.45 0.00 0.00 4.70
450 467 4.194720 ACGCGCTCGAGTGGGATC 62.195 66.667 39.30 18.29 40.38 3.36
451 468 4.194720 GACGCGCTCGAGTGGGAT 62.195 66.667 39.30 26.56 40.38 3.85
460 477 3.537297 GAAGCACTCGACGCGCTC 61.537 66.667 5.73 1.80 34.11 5.03
565 594 3.782244 GTTGTGCTCGCTGCTCGG 61.782 66.667 0.00 0.00 43.37 4.63
582 611 3.966026 GAGGTGGAACGTCCGCTCG 62.966 68.421 14.44 0.00 45.45 5.03
603 632 2.839486 AAGATGTTCTCGCTCCACAA 57.161 45.000 0.00 0.00 0.00 3.33
619 648 4.043310 CCAGCCCATCCCATTAAGATAAGA 59.957 45.833 0.00 0.00 0.00 2.10
624 657 0.852842 CCCAGCCCATCCCATTAAGA 59.147 55.000 0.00 0.00 0.00 2.10
634 667 3.133365 GCCGGTTATCCCAGCCCAT 62.133 63.158 1.90 0.00 0.00 4.00
642 675 1.671979 GTAAACTGGGCCGGTTATCC 58.328 55.000 30.11 16.84 32.14 2.59
643 676 1.065272 TGGTAAACTGGGCCGGTTATC 60.065 52.381 30.11 23.24 32.14 1.75
664 697 2.517166 GGCCGAATCCAAGCCCTC 60.517 66.667 0.00 0.00 41.00 4.30
688 721 4.082523 TGTCCTACGGCCTGCTGC 62.083 66.667 0.00 0.00 40.16 5.25
689 722 2.185350 CTGTCCTACGGCCTGCTG 59.815 66.667 0.00 0.00 0.00 4.41
698 731 1.842381 AACTGGCCCAGCTGTCCTAC 61.842 60.000 11.63 0.00 34.37 3.18
730 763 2.479730 CGTCGGATCTCCTGTGTAAAGG 60.480 54.545 0.00 0.00 38.84 3.11
731 764 2.479730 CCGTCGGATCTCCTGTGTAAAG 60.480 54.545 4.91 0.00 0.00 1.85
740 773 1.030457 TTTCTAGCCGTCGGATCTCC 58.970 55.000 17.49 0.00 0.00 3.71
741 774 1.597445 CGTTTCTAGCCGTCGGATCTC 60.597 57.143 17.49 0.00 0.00 2.75
747 780 3.867055 TCTATACGTTTCTAGCCGTCG 57.133 47.619 0.00 1.23 38.43 5.12
754 787 8.407832 TCCGTTTTCATGATCTATACGTTTCTA 58.592 33.333 0.00 0.00 0.00 2.10
763 796 5.928976 TGACCATCCGTTTTCATGATCTAT 58.071 37.500 0.00 0.00 0.00 1.98
770 803 4.380867 GCATTTCTGACCATCCGTTTTCAT 60.381 41.667 0.00 0.00 0.00 2.57
771 804 3.057596 GCATTTCTGACCATCCGTTTTCA 60.058 43.478 0.00 0.00 0.00 2.69
781 814 2.161831 CGCTTCGCATTTCTGACCA 58.838 52.632 0.00 0.00 0.00 4.02
794 827 1.226547 CGAGTCTCCTCAGCGCTTC 60.227 63.158 7.50 0.00 37.59 3.86
820 853 5.104859 TCCAATTAAGGACAGTATAACCGCA 60.105 40.000 0.00 0.00 31.23 5.69
821 854 5.362263 TCCAATTAAGGACAGTATAACCGC 58.638 41.667 0.00 0.00 31.23 5.68
841 874 0.621609 CCGGACATAACCCCTTTCCA 59.378 55.000 0.00 0.00 0.00 3.53
842 875 0.622136 ACCGGACATAACCCCTTTCC 59.378 55.000 9.46 0.00 0.00 3.13
871 904 2.122768 CTCCCAGCAGATTCCCTAACT 58.877 52.381 0.00 0.00 0.00 2.24
872 905 1.141858 CCTCCCAGCAGATTCCCTAAC 59.858 57.143 0.00 0.00 0.00 2.34
880 913 4.390341 GGAGACCTCCCAGCAGAT 57.610 61.111 4.72 0.00 43.94 2.90
941 979 2.758423 ACAATTTGGGGTTCGAATAGCC 59.242 45.455 0.00 0.00 34.91 3.93
944 982 6.350612 GGATTTGACAATTTGGGGTTCGAATA 60.351 38.462 0.00 0.00 0.00 1.75
962 1046 1.064017 CCGAGGGATTTGGGGATTTGA 60.064 52.381 0.00 0.00 0.00 2.69
963 1052 1.402787 CCGAGGGATTTGGGGATTTG 58.597 55.000 0.00 0.00 0.00 2.32
1428 4150 4.853142 ACGCGGATAGGCAGGGGA 62.853 66.667 12.47 0.00 0.00 4.81
1738 6420 2.681778 CCTCCTCGCACTCCCACT 60.682 66.667 0.00 0.00 0.00 4.00
1858 6540 1.067142 TGACTGACATACAAGACCGCC 60.067 52.381 0.00 0.00 0.00 6.13
1895 6577 3.266964 CGAACAGGTCGTCGGGTA 58.733 61.111 0.00 0.00 45.09 3.69
2106 6791 0.466555 ACCACGCCCAGTAAAGCAAA 60.467 50.000 0.00 0.00 0.00 3.68
2152 6837 2.358322 AGCCGGGTCTTTCAGAAAAA 57.642 45.000 0.00 0.00 0.00 1.94
2153 6838 1.953686 CAAGCCGGGTCTTTCAGAAAA 59.046 47.619 6.62 0.00 0.00 2.29
2154 6839 1.142060 TCAAGCCGGGTCTTTCAGAAA 59.858 47.619 6.62 0.00 0.00 2.52
2155 6840 0.762418 TCAAGCCGGGTCTTTCAGAA 59.238 50.000 6.62 0.00 0.00 3.02
2156 6841 0.762418 TTCAAGCCGGGTCTTTCAGA 59.238 50.000 6.62 0.00 0.00 3.27
2157 6842 0.875059 GTTCAAGCCGGGTCTTTCAG 59.125 55.000 6.62 0.00 0.00 3.02
2158 6843 0.181587 TGTTCAAGCCGGGTCTTTCA 59.818 50.000 6.62 1.78 0.00 2.69
2159 6844 0.591659 GTGTTCAAGCCGGGTCTTTC 59.408 55.000 6.62 0.00 0.00 2.62
2160 6845 1.164041 CGTGTTCAAGCCGGGTCTTT 61.164 55.000 6.62 0.00 0.00 2.52
2161 6846 1.597027 CGTGTTCAAGCCGGGTCTT 60.597 57.895 6.62 0.00 0.00 3.01
2162 6847 2.030562 CGTGTTCAAGCCGGGTCT 59.969 61.111 6.62 0.00 0.00 3.85
2163 6848 3.047877 CCGTGTTCAAGCCGGGTC 61.048 66.667 6.62 0.00 38.09 4.46
2167 6852 2.966309 GAAGCCCGTGTTCAAGCCG 61.966 63.158 0.00 0.00 0.00 5.52
2168 6853 1.244019 ATGAAGCCCGTGTTCAAGCC 61.244 55.000 0.00 0.00 37.46 4.35
2169 6854 0.598065 AATGAAGCCCGTGTTCAAGC 59.402 50.000 0.00 0.00 37.46 4.01
2170 6855 1.879380 TCAATGAAGCCCGTGTTCAAG 59.121 47.619 0.00 0.00 37.46 3.02
2171 6856 1.974265 TCAATGAAGCCCGTGTTCAA 58.026 45.000 0.00 0.00 37.46 2.69
2172 6857 2.198827 ATCAATGAAGCCCGTGTTCA 57.801 45.000 0.00 0.00 38.28 3.18
2173 6858 3.575965 AAATCAATGAAGCCCGTGTTC 57.424 42.857 0.00 0.00 0.00 3.18
2174 6859 3.119495 GCTAAATCAATGAAGCCCGTGTT 60.119 43.478 0.00 0.00 0.00 3.32
2175 6860 2.423538 GCTAAATCAATGAAGCCCGTGT 59.576 45.455 0.00 0.00 0.00 4.49
2176 6861 2.423185 TGCTAAATCAATGAAGCCCGTG 59.577 45.455 3.30 0.00 33.99 4.94
2177 6862 2.684881 CTGCTAAATCAATGAAGCCCGT 59.315 45.455 3.30 0.00 33.99 5.28
2178 6863 2.945008 TCTGCTAAATCAATGAAGCCCG 59.055 45.455 3.30 0.00 33.99 6.13
2179 6864 4.989279 TTCTGCTAAATCAATGAAGCCC 57.011 40.909 3.30 0.00 33.99 5.19
2180 6865 4.802563 GCTTTCTGCTAAATCAATGAAGCC 59.197 41.667 3.30 0.00 38.95 4.35
2181 6866 5.404946 TGCTTTCTGCTAAATCAATGAAGC 58.595 37.500 0.00 0.00 43.37 3.86
2182 6867 7.010183 CCATTGCTTTCTGCTAAATCAATGAAG 59.990 37.037 26.00 15.62 40.75 3.02
2183 6868 6.814644 CCATTGCTTTCTGCTAAATCAATGAA 59.185 34.615 26.00 3.51 40.75 2.57
2184 6869 6.153170 TCCATTGCTTTCTGCTAAATCAATGA 59.847 34.615 26.00 16.84 40.75 2.57
2185 6870 6.334989 TCCATTGCTTTCTGCTAAATCAATG 58.665 36.000 21.74 21.74 43.37 2.82
2186 6871 6.534475 TCCATTGCTTTCTGCTAAATCAAT 57.466 33.333 7.78 7.78 43.37 2.57
2187 6872 5.981088 TCCATTGCTTTCTGCTAAATCAA 57.019 34.783 4.60 4.60 43.37 2.57
2188 6873 5.981088 TTCCATTGCTTTCTGCTAAATCA 57.019 34.783 0.00 0.00 43.37 2.57
2189 6874 6.158598 TGTTTCCATTGCTTTCTGCTAAATC 58.841 36.000 0.00 0.00 43.37 2.17
2190 6875 6.100404 TGTTTCCATTGCTTTCTGCTAAAT 57.900 33.333 0.00 0.00 43.37 1.40
2191 6876 5.528043 TGTTTCCATTGCTTTCTGCTAAA 57.472 34.783 0.00 0.00 43.37 1.85
2192 6877 5.010922 ACATGTTTCCATTGCTTTCTGCTAA 59.989 36.000 0.00 0.00 43.37 3.09
2193 6878 4.523943 ACATGTTTCCATTGCTTTCTGCTA 59.476 37.500 0.00 0.00 43.37 3.49
2194 6879 3.322828 ACATGTTTCCATTGCTTTCTGCT 59.677 39.130 0.00 0.00 43.37 4.24
2195 6880 3.656559 ACATGTTTCCATTGCTTTCTGC 58.343 40.909 0.00 0.00 43.25 4.26
2196 6881 6.258230 TCTACATGTTTCCATTGCTTTCTG 57.742 37.500 2.30 0.00 0.00 3.02
2197 6882 6.660521 TGATCTACATGTTTCCATTGCTTTCT 59.339 34.615 2.30 0.00 0.00 2.52
2198 6883 6.855836 TGATCTACATGTTTCCATTGCTTTC 58.144 36.000 2.30 0.00 0.00 2.62
2199 6884 6.839124 TGATCTACATGTTTCCATTGCTTT 57.161 33.333 2.30 0.00 0.00 3.51
2200 6885 6.435277 ACTTGATCTACATGTTTCCATTGCTT 59.565 34.615 2.30 0.00 33.99 3.91
2201 6886 5.948162 ACTTGATCTACATGTTTCCATTGCT 59.052 36.000 2.30 0.00 33.99 3.91
2202 6887 6.032094 CACTTGATCTACATGTTTCCATTGC 58.968 40.000 2.30 0.00 35.22 3.56
2203 6888 7.381766 TCACTTGATCTACATGTTTCCATTG 57.618 36.000 2.30 0.00 35.22 2.82
2204 6889 8.218338 GATCACTTGATCTACATGTTTCCATT 57.782 34.615 2.30 0.00 45.60 3.16
2205 6890 7.798596 GATCACTTGATCTACATGTTTCCAT 57.201 36.000 2.30 0.00 45.60 3.41
2298 6983 7.567458 TGAGATTGTAATGATCCTCATGAACA 58.433 34.615 0.00 0.00 37.15 3.18
2426 7117 8.858003 TGTTTTCATTACGCTTGTGATTTTAA 57.142 26.923 0.00 0.00 0.00 1.52
2656 7353 2.561858 GGTCCTAAGAGACGACAAAGGT 59.438 50.000 0.00 0.00 37.66 3.50
2679 7376 1.342672 GCTTAGGGGAACGATGGGGA 61.343 60.000 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.