Multiple sequence alignment - TraesCS3D01G509300

Loading Multiple Alignment...

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 TraesCS3D01G509300 chr3D 100.000 2645 0 0 1 2645 594892048 594894692 0.000000e+00 4885.0
1 TraesCS3D01G509300 chr3D 92.264 349 27 0 1304 1652 594955602 594955950 1.830000e-136 496.0
2 TraesCS3D01G509300 chr3D 84.598 448 48 8 867 1302 594955062 594955500 2.430000e-115 425.0
3 TraesCS3D01G509300 chr3A 88.688 1715 83 41 749 2430 725842168 725843804 0.000000e+00 1989.0
4 TraesCS3D01G509300 chr3A 87.173 421 49 3 1067 1487 726716275 726715860 8.570000e-130 473.0
5 TraesCS3D01G509300 chr3A 82.780 482 49 22 1304 1771 725911624 725912085 1.470000e-107 399.0
6 TraesCS3D01G509300 chr3A 83.259 448 46 10 867 1302 725904435 725904865 4.130000e-103 385.0
7 TraesCS3D01G509300 chr3A 92.015 263 16 4 1 259 725841433 725841694 5.380000e-97 364.0
8 TraesCS3D01G509300 chr3A 82.353 425 42 22 332 740 725841715 725842122 3.260000e-89 339.0
9 TraesCS3D01G509300 chr3A 89.600 250 15 8 1478 1726 726714175 726713936 9.200000e-80 307.0
10 TraesCS3D01G509300 chr3A 87.600 250 17 8 1487 1726 725905324 725905569 7.210000e-71 278.0
11 TraesCS3D01G509300 chr3A 89.231 195 21 0 1304 1498 725904977 725905171 7.310000e-61 244.0
12 TraesCS3D01G509300 chr3A 86.555 119 12 4 1186 1302 725911405 725911521 7.680000e-26 128.0
13 TraesCS3D01G509300 chr3A 97.500 40 1 0 1882 1921 587393367 587393406 4.720000e-08 69.4
14 TraesCS3D01G509300 chr3B 90.184 1304 80 28 745 2027 798397023 798398299 0.000000e+00 1655.0
15 TraesCS3D01G509300 chr3B 85.424 542 49 11 1 541 798395788 798396300 1.080000e-148 536.0
16 TraesCS3D01G509300 chr3B 92.571 350 25 1 1304 1652 798404132 798404481 3.930000e-138 501.0
17 TraesCS3D01G509300 chr3B 87.054 448 37 12 867 1302 798403607 798404045 1.100000e-133 486.0
18 TraesCS3D01G509300 chr3B 83.953 430 31 18 2227 2645 798398430 798398832 6.910000e-101 377.0
19 TraesCS3D01G509300 chr3B 89.286 56 5 1 549 603 660327683 660327628 4.720000e-08 69.4
20 TraesCS3D01G509300 chr3B 89.286 56 5 1 2278 2332 798405339 798405394 4.720000e-08 69.4
21 TraesCS3D01G509300 chr7D 89.655 58 5 1 601 657 19311236 19311293 3.650000e-09 73.1
22 TraesCS3D01G509300 chr2A 93.478 46 2 1 1882 1927 13014867 13014911 1.700000e-07 67.6
23 TraesCS3D01G509300 chr5D 92.857 42 3 0 1885 1926 327480376 327480417 7.910000e-06 62.1
24 TraesCS3D01G509300 chr2B 92.857 42 3 0 1885 1926 45729753 45729712 7.910000e-06 62.1
25 TraesCS3D01G509300 chr7B 89.362 47 4 1 1878 1923 107645333 107645287 1.020000e-04 58.4
26 TraesCS3D01G509300 chr7A 91.111 45 1 2 1885 1926 730828938 730828894 1.020000e-04 58.4
27 TraesCS3D01G509300 chr4D 92.683 41 2 1 1882 1921 504595401 504595441 1.020000e-04 58.4


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 TraesCS3D01G509300 chr3D 594892048 594894692 2644 False 4885.000000 4885 100.000000 1 2645 1 chr3D.!!$F1 2644
1 TraesCS3D01G509300 chr3D 594955062 594955950 888 False 460.500000 496 88.431000 867 1652 2 chr3D.!!$F2 785
2 TraesCS3D01G509300 chr3A 725841433 725843804 2371 False 897.333333 1989 87.685333 1 2430 3 chr3A.!!$F2 2429
3 TraesCS3D01G509300 chr3A 726713936 726716275 2339 True 390.000000 473 88.386500 1067 1726 2 chr3A.!!$R1 659
4 TraesCS3D01G509300 chr3A 725904435 725905569 1134 False 302.333333 385 86.696667 867 1726 3 chr3A.!!$F3 859
5 TraesCS3D01G509300 chr3A 725911405 725912085 680 False 263.500000 399 84.667500 1186 1771 2 chr3A.!!$F4 585
6 TraesCS3D01G509300 chr3B 798395788 798398832 3044 False 856.000000 1655 86.520333 1 2645 3 chr3B.!!$F1 2644
7 TraesCS3D01G509300 chr3B 798403607 798405394 1787 False 352.133333 501 89.637000 867 2332 3 chr3B.!!$F2 1465

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
324 330 0.039618 ACCCACCATCAACCACCATC 59.96 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 4251 0.104855 TTCATCGCCTTGGATCCTCG 59.895 55.0 14.23 11.09 0.0 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
125 130 4.018415 AGCTATGGGGAAAAAGTTAGCAGA 60.018 41.667 0.00 0.00 0.00 4.26
177 182 3.510360 GCCTGACTGTCTCTTAACTACCA 59.490 47.826 9.51 0.00 0.00 3.25
186 191 6.822442 TGTCTCTTAACTACCATGTGTCAAA 58.178 36.000 0.00 0.00 0.00 2.69
189 194 7.225931 GTCTCTTAACTACCATGTGTCAAACAA 59.774 37.037 0.00 0.00 43.61 2.83
197 202 5.437060 ACCATGTGTCAAACAAGTTCTACT 58.563 37.500 0.00 0.00 43.61 2.57
252 257 6.712998 TCCAACATAATCTCTTTTTGACCGAA 59.287 34.615 0.00 0.00 0.00 4.30
271 276 3.486875 CGAAGGGATTTTGCGTGGAATAC 60.487 47.826 0.00 0.00 0.00 1.89
288 293 1.271856 TACGGCAGGAAATCTGGACA 58.728 50.000 0.00 0.00 43.54 4.02
292 297 0.807496 GCAGGAAATCTGGACAGTGC 59.193 55.000 0.00 0.00 43.54 4.40
313 319 3.490348 CTTTCAGTTCTTCACCCACCAT 58.510 45.455 0.00 0.00 0.00 3.55
314 320 2.859165 TCAGTTCTTCACCCACCATC 57.141 50.000 0.00 0.00 0.00 3.51
315 321 2.054021 TCAGTTCTTCACCCACCATCA 58.946 47.619 0.00 0.00 0.00 3.07
316 322 2.441375 TCAGTTCTTCACCCACCATCAA 59.559 45.455 0.00 0.00 0.00 2.57
317 323 2.554032 CAGTTCTTCACCCACCATCAAC 59.446 50.000 0.00 0.00 0.00 3.18
318 324 1.886542 GTTCTTCACCCACCATCAACC 59.113 52.381 0.00 0.00 0.00 3.77
319 325 1.144691 TCTTCACCCACCATCAACCA 58.855 50.000 0.00 0.00 0.00 3.67
320 326 1.202879 TCTTCACCCACCATCAACCAC 60.203 52.381 0.00 0.00 0.00 4.16
321 327 0.178975 TTCACCCACCATCAACCACC 60.179 55.000 0.00 0.00 0.00 4.61
322 328 1.152599 CACCCACCATCAACCACCA 59.847 57.895 0.00 0.00 0.00 4.17
323 329 0.251742 CACCCACCATCAACCACCAT 60.252 55.000 0.00 0.00 0.00 3.55
324 330 0.039618 ACCCACCATCAACCACCATC 59.960 55.000 0.00 0.00 0.00 3.51
325 331 1.031571 CCCACCATCAACCACCATCG 61.032 60.000 0.00 0.00 0.00 3.84
326 332 0.322456 CCACCATCAACCACCATCGT 60.322 55.000 0.00 0.00 0.00 3.73
327 333 1.533625 CACCATCAACCACCATCGTT 58.466 50.000 0.00 0.00 0.00 3.85
328 334 1.468520 CACCATCAACCACCATCGTTC 59.531 52.381 0.00 0.00 0.00 3.95
329 335 1.351017 ACCATCAACCACCATCGTTCT 59.649 47.619 0.00 0.00 0.00 3.01
330 336 2.224769 ACCATCAACCACCATCGTTCTT 60.225 45.455 0.00 0.00 0.00 2.52
335 341 4.963373 TCAACCACCATCGTTCTTTCTTA 58.037 39.130 0.00 0.00 0.00 2.10
366 375 3.586100 TCTAGTGTCACGCATTGCTAA 57.414 42.857 7.12 0.00 0.00 3.09
367 376 3.250744 TCTAGTGTCACGCATTGCTAAC 58.749 45.455 7.12 2.86 0.00 2.34
399 412 2.669364 ACTTTCTACACTACCAACGCG 58.331 47.619 3.53 3.53 0.00 6.01
440 453 3.084039 TGAATGAGCAGGATTGTTCCAC 58.916 45.455 0.00 0.00 45.30 4.02
489 503 3.199880 AGTATTGTGAGCATAGTGCCC 57.800 47.619 0.00 0.00 46.52 5.36
508 522 3.851098 CCCTTCTCTGTAACAGTAGTGC 58.149 50.000 0.00 0.00 32.61 4.40
539 553 2.844122 AACAGCGTTCAGAAAACCAC 57.156 45.000 0.00 0.00 0.00 4.16
578 641 4.766891 GCTAATAGCATATTTTCAGGGGCA 59.233 41.667 7.49 0.00 41.89 5.36
580 643 1.406903 AGCATATTTTCAGGGGCAGC 58.593 50.000 0.00 0.00 0.00 5.25
598 661 3.787826 CAGCGCTATTTTGTATAGCACG 58.212 45.455 10.99 3.42 45.32 5.34
599 662 2.221055 AGCGCTATTTTGTATAGCACGC 59.779 45.455 8.99 11.24 45.32 5.34
600 663 2.221055 GCGCTATTTTGTATAGCACGCT 59.779 45.455 14.90 0.00 45.32 5.07
601 664 3.427528 GCGCTATTTTGTATAGCACGCTA 59.572 43.478 14.90 0.39 45.32 4.26
602 665 4.091509 GCGCTATTTTGTATAGCACGCTAT 59.908 41.667 15.45 15.45 45.32 2.97
603 666 5.287752 GCGCTATTTTGTATAGCACGCTATA 59.712 40.000 13.51 13.51 45.32 1.31
604 667 6.506513 GCGCTATTTTGTATAGCACGCTATAG 60.507 42.308 17.07 8.27 45.32 1.31
605 668 6.506513 CGCTATTTTGTATAGCACGCTATAGC 60.507 42.308 17.07 15.09 45.32 2.97
606 669 6.310467 GCTATTTTGTATAGCACGCTATAGCA 59.690 38.462 23.99 14.68 44.64 3.49
607 670 7.010552 GCTATTTTGTATAGCACGCTATAGCAT 59.989 37.037 23.99 6.50 44.64 3.79
608 671 9.516314 CTATTTTGTATAGCACGCTATAGCATA 57.484 33.333 23.99 10.96 40.79 3.14
609 672 8.948631 ATTTTGTATAGCACGCTATAGCATAT 57.051 30.769 23.99 16.52 40.79 1.78
610 673 8.771920 TTTTGTATAGCACGCTATAGCATATT 57.228 30.769 23.99 9.36 40.79 1.28
611 674 9.863845 TTTTGTATAGCACGCTATAGCATATTA 57.136 29.630 23.99 11.12 40.79 0.98
612 675 9.863845 TTTGTATAGCACGCTATAGCATATTAA 57.136 29.630 23.99 10.21 40.79 1.40
616 679 8.749841 ATAGCACGCTATAGCATATTAATAGC 57.250 34.615 23.99 7.19 42.95 2.97
628 691 8.335532 AGCATATTAATAGCGCAATTTAAGGA 57.664 30.769 11.47 3.78 0.00 3.36
629 692 8.237267 AGCATATTAATAGCGCAATTTAAGGAC 58.763 33.333 11.47 2.76 0.00 3.85
630 693 7.216317 GCATATTAATAGCGCAATTTAAGGACG 59.784 37.037 11.47 2.85 0.00 4.79
631 694 3.963383 AATAGCGCAATTTAAGGACGG 57.037 42.857 11.47 0.00 0.00 4.79
632 695 2.389962 TAGCGCAATTTAAGGACGGT 57.610 45.000 11.47 0.00 38.17 4.83
633 696 0.802494 AGCGCAATTTAAGGACGGTG 59.198 50.000 11.47 0.00 32.66 4.94
634 697 0.796870 GCGCAATTTAAGGACGGTGC 60.797 55.000 0.30 0.00 0.00 5.01
635 698 0.802494 CGCAATTTAAGGACGGTGCT 59.198 50.000 0.00 0.00 0.00 4.40
636 699 2.004017 CGCAATTTAAGGACGGTGCTA 58.996 47.619 1.54 0.00 0.00 3.49
637 700 2.612212 CGCAATTTAAGGACGGTGCTAT 59.388 45.455 1.54 0.00 0.00 2.97
638 701 3.064820 CGCAATTTAAGGACGGTGCTATT 59.935 43.478 1.54 0.00 0.00 1.73
639 702 4.438200 CGCAATTTAAGGACGGTGCTATTT 60.438 41.667 1.54 0.00 0.00 1.40
640 703 5.407502 GCAATTTAAGGACGGTGCTATTTT 58.592 37.500 1.54 0.00 0.00 1.82
641 704 5.288472 GCAATTTAAGGACGGTGCTATTTTG 59.712 40.000 1.54 6.42 0.00 2.44
642 705 6.386654 CAATTTAAGGACGGTGCTATTTTGT 58.613 36.000 1.54 0.00 0.00 2.83
643 706 7.531716 CAATTTAAGGACGGTGCTATTTTGTA 58.468 34.615 1.54 0.00 0.00 2.41
644 707 7.875327 ATTTAAGGACGGTGCTATTTTGTAT 57.125 32.000 1.54 0.00 0.00 2.29
645 708 8.967664 ATTTAAGGACGGTGCTATTTTGTATA 57.032 30.769 1.54 0.00 0.00 1.47
646 709 8.428186 TTTAAGGACGGTGCTATTTTGTATAG 57.572 34.615 1.54 0.00 0.00 1.31
647 710 4.377897 AGGACGGTGCTATTTTGTATAGC 58.622 43.478 0.00 9.29 45.28 2.97
692 756 1.072331 ACCTACTCCCACACAAGCAAG 59.928 52.381 0.00 0.00 0.00 4.01
740 805 3.057946 ACAAATCTTCAAGGAAAGCGCTC 60.058 43.478 12.06 0.00 0.00 5.03
742 807 2.254546 TCTTCAAGGAAAGCGCTCAA 57.745 45.000 12.06 0.00 0.00 3.02
743 808 2.571212 TCTTCAAGGAAAGCGCTCAAA 58.429 42.857 12.06 0.00 0.00 2.69
789 1510 3.741344 CCGTACTCAAACTGACCAAGAAG 59.259 47.826 0.00 0.00 0.00 2.85
810 1531 2.294512 GGAAACTCAAAAGGCAGAGGTG 59.705 50.000 0.00 0.00 36.20 4.00
835 1556 2.914379 GATTACGAATCCAGCCCGG 58.086 57.895 0.00 0.00 31.60 5.73
897 1618 2.283894 GGGACCCCAAAGCCCAAG 60.284 66.667 0.00 0.00 41.64 3.61
911 1636 0.745845 CCCAAGGCCTCATCAACTCG 60.746 60.000 5.23 0.00 0.00 4.18
1056 1800 4.254709 ACCTCACCGCAGCAGCAA 62.255 61.111 0.82 0.00 42.27 3.91
1061 1805 4.569180 ACCGCAGCAGCAACAGGT 62.569 61.111 0.82 0.00 42.27 4.00
1082 1829 1.887707 CGGCCGCCAAGAAGGATAC 60.888 63.158 14.67 0.00 41.22 2.24
1557 4136 1.607467 GATGGGCTTGCCAACCAGT 60.607 57.895 14.04 0.00 37.75 4.00
1608 4187 1.359168 AACTCAAGTCCCAGTACCCC 58.641 55.000 0.00 0.00 0.00 4.95
1652 4233 6.111382 TGAAGATGCCTTCTTAGATTGTCTG 58.889 40.000 6.71 0.00 44.88 3.51
1655 4251 6.112058 AGATGCCTTCTTAGATTGTCTGTTC 58.888 40.000 0.00 0.00 0.00 3.18
1677 4273 3.217626 GAGGATCCAAGGCGATGAATTT 58.782 45.455 15.82 0.00 0.00 1.82
1679 4275 4.990526 AGGATCCAAGGCGATGAATTTAT 58.009 39.130 15.82 0.00 0.00 1.40
1829 4496 6.019075 CGATGCTTCCGAAATATAAGTGAACA 60.019 38.462 0.00 0.00 0.00 3.18
1944 4616 2.559698 TCTTCCGTTTGGCTCATGAA 57.440 45.000 0.00 0.00 34.14 2.57
2002 4674 0.904649 AGCGAATCAGTGGGACATCA 59.095 50.000 0.00 0.00 44.52 3.07
2062 4735 4.810790 CAGGTTCTTGTCGACTGAATACT 58.189 43.478 17.92 17.40 0.00 2.12
2064 4737 5.696724 CAGGTTCTTGTCGACTGAATACTTT 59.303 40.000 17.92 4.57 0.00 2.66
2067 4740 7.039923 AGGTTCTTGTCGACTGAATACTTTCTA 60.040 37.037 17.92 0.00 32.78 2.10
2076 4749 8.963725 TCGACTGAATACTTTCTATCTAACCAA 58.036 33.333 0.00 0.00 32.78 3.67
2131 4864 2.365293 GTTTCAGATTTTGGTGGGTGCT 59.635 45.455 0.00 0.00 0.00 4.40
2133 4866 1.962807 TCAGATTTTGGTGGGTGCTTG 59.037 47.619 0.00 0.00 0.00 4.01
2134 4867 1.962807 CAGATTTTGGTGGGTGCTTGA 59.037 47.619 0.00 0.00 0.00 3.02
2135 4868 1.963515 AGATTTTGGTGGGTGCTTGAC 59.036 47.619 0.00 0.00 0.00 3.18
2173 4906 4.508861 GGCGATGCCGAACTTAATTACTAA 59.491 41.667 0.00 0.00 39.62 2.24
2179 4912 4.034858 GCCGAACTTAATTACTAACAGCCC 59.965 45.833 0.00 0.00 0.00 5.19
2204 4937 4.578516 ACCAAACGTCATGATGTCTTTGAA 59.421 37.500 24.57 0.00 0.00 2.69
2205 4938 5.067153 ACCAAACGTCATGATGTCTTTGAAA 59.933 36.000 24.57 0.00 0.00 2.69
2219 4952 6.959361 TGTCTTTGAAAACAGCTCTATTGAC 58.041 36.000 0.00 0.00 0.00 3.18
2315 5224 4.051237 TGCTGCTTCGATCATACACATAC 58.949 43.478 0.00 0.00 0.00 2.39
2366 5276 2.121291 TGGTTGCTGTTTCTGTGTGA 57.879 45.000 0.00 0.00 0.00 3.58
2388 5298 4.862371 ACCTTTGGAGTGTTTTTCCTACA 58.138 39.130 0.00 0.00 35.67 2.74
2389 5299 4.887655 ACCTTTGGAGTGTTTTTCCTACAG 59.112 41.667 0.00 0.00 35.67 2.74
2390 5300 5.130350 CCTTTGGAGTGTTTTTCCTACAGA 58.870 41.667 0.00 0.00 35.67 3.41
2457 5367 7.069578 ACTGATGTCCGGTAATTTACTAGTCAT 59.930 37.037 0.00 7.39 31.20 3.06
2461 5371 7.934457 TGTCCGGTAATTTACTAGTCATAGTC 58.066 38.462 0.00 0.00 41.46 2.59
2520 5434 7.581213 TTTTTCAGCAACTGGAGAATCTTAA 57.419 32.000 0.00 0.00 33.73 1.85
2521 5435 7.765695 TTTTCAGCAACTGGAGAATCTTAAT 57.234 32.000 0.00 0.00 33.73 1.40
2523 5437 5.809001 TCAGCAACTGGAGAATCTTAATGT 58.191 37.500 0.00 0.00 33.73 2.71
2525 5439 6.716628 TCAGCAACTGGAGAATCTTAATGTTT 59.283 34.615 0.00 0.00 33.73 2.83
2526 5440 7.882791 TCAGCAACTGGAGAATCTTAATGTTTA 59.117 33.333 0.00 0.00 33.73 2.01
2527 5441 7.965107 CAGCAACTGGAGAATCTTAATGTTTAC 59.035 37.037 0.00 0.00 33.73 2.01
2528 5442 7.665559 AGCAACTGGAGAATCTTAATGTTTACA 59.334 33.333 0.00 0.00 33.73 2.41
2529 5443 7.965107 GCAACTGGAGAATCTTAATGTTTACAG 59.035 37.037 0.00 0.00 33.73 2.74
2530 5444 8.454106 CAACTGGAGAATCTTAATGTTTACAGG 58.546 37.037 0.00 0.00 33.73 4.00
2531 5445 7.112779 ACTGGAGAATCTTAATGTTTACAGGG 58.887 38.462 0.00 0.00 33.73 4.45
2532 5446 7.037586 ACTGGAGAATCTTAATGTTTACAGGGA 60.038 37.037 0.00 0.00 33.73 4.20
2533 5447 7.872138 TGGAGAATCTTAATGTTTACAGGGAT 58.128 34.615 0.00 0.00 33.73 3.85
2534 5448 8.998814 TGGAGAATCTTAATGTTTACAGGGATA 58.001 33.333 0.00 0.00 33.73 2.59
2535 5449 9.274206 GGAGAATCTTAATGTTTACAGGGATAC 57.726 37.037 0.00 0.00 33.73 2.24
2536 5450 9.832445 GAGAATCTTAATGTTTACAGGGATACA 57.168 33.333 0.00 0.00 39.74 2.29
2539 5453 9.975218 AATCTTAATGTTTACAGGGATACAAGT 57.025 29.630 0.00 0.00 39.74 3.16
2549 5463 5.789535 ACAGGGATACAAGTATAACCCTCT 58.210 41.667 13.74 3.72 44.77 3.69
2551 5465 5.012148 CAGGGATACAAGTATAACCCTCTGG 59.988 48.000 13.74 3.72 44.77 3.86
2553 5467 7.266224 GGGATACAAGTATAACCCTCTGGGC 62.266 52.000 1.99 0.00 43.75 5.36
2569 5483 0.865111 GGGCGAACCAAAATGCAAAC 59.135 50.000 0.00 0.00 39.85 2.93
2582 5503 5.543507 AAATGCAAACTACCCACATCAAA 57.456 34.783 0.00 0.00 0.00 2.69
2597 5518 2.584835 TCAAATACAGTGGCTGCCTT 57.415 45.000 21.03 5.28 34.37 4.35
2604 5525 6.494666 AATACAGTGGCTGCCTTAACTATA 57.505 37.500 21.03 9.09 34.37 1.31
2605 5526 6.688073 ATACAGTGGCTGCCTTAACTATAT 57.312 37.500 21.03 11.04 34.37 0.86
2612 5533 4.640647 GGCTGCCTTAACTATATTATGGGC 59.359 45.833 12.43 0.00 38.87 5.36
2613 5534 5.253330 GCTGCCTTAACTATATTATGGGCA 58.747 41.667 0.00 0.00 44.75 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.103398 ACAACTGCTCAAGTGCCCAC 61.103 55.000 0.00 0.00 39.81 4.61
125 130 5.244626 ACAAGCCAGCTCTTCAATACATTTT 59.755 36.000 0.00 0.00 0.00 1.82
177 182 8.500753 TGTTAAGTAGAACTTGTTTGACACAT 57.499 30.769 2.59 0.00 39.11 3.21
245 250 0.250553 ACGCAAAATCCCTTCGGTCA 60.251 50.000 0.00 0.00 0.00 4.02
252 257 2.014128 CGTATTCCACGCAAAATCCCT 58.986 47.619 0.00 0.00 45.03 4.20
262 267 4.832576 CAGATTTCCTGCCGTATTCCACG 61.833 52.174 0.00 0.00 41.14 4.94
264 269 2.421388 CCAGATTTCCTGCCGTATTCCA 60.421 50.000 0.00 0.00 41.57 3.53
271 276 0.036010 ACTGTCCAGATTTCCTGCCG 60.036 55.000 0.40 0.00 41.57 5.69
274 279 2.486472 AGCACTGTCCAGATTTCCTG 57.514 50.000 0.40 0.00 42.55 3.86
275 280 3.181440 TGAAAGCACTGTCCAGATTTCCT 60.181 43.478 0.40 0.00 32.96 3.36
288 293 2.092429 TGGGTGAAGAACTGAAAGCACT 60.092 45.455 0.00 0.00 37.60 4.40
292 297 2.930950 TGGTGGGTGAAGAACTGAAAG 58.069 47.619 0.00 0.00 42.29 2.62
313 319 3.485463 AGAAAGAACGATGGTGGTTGA 57.515 42.857 0.00 0.00 0.00 3.18
314 320 4.755123 AGTAAGAAAGAACGATGGTGGTTG 59.245 41.667 0.00 0.00 0.00 3.77
315 321 4.969484 AGTAAGAAAGAACGATGGTGGTT 58.031 39.130 0.00 0.00 0.00 3.67
316 322 4.618920 AGTAAGAAAGAACGATGGTGGT 57.381 40.909 0.00 0.00 0.00 4.16
317 323 5.701290 AGAAAGTAAGAAAGAACGATGGTGG 59.299 40.000 0.00 0.00 0.00 4.61
318 324 6.787085 AGAAAGTAAGAAAGAACGATGGTG 57.213 37.500 0.00 0.00 0.00 4.17
319 325 7.929785 TGTAAGAAAGTAAGAAAGAACGATGGT 59.070 33.333 0.00 0.00 0.00 3.55
320 326 8.306680 TGTAAGAAAGTAAGAAAGAACGATGG 57.693 34.615 0.00 0.00 0.00 3.51
321 327 9.959775 GATGTAAGAAAGTAAGAAAGAACGATG 57.040 33.333 0.00 0.00 0.00 3.84
322 328 9.930693 AGATGTAAGAAAGTAAGAAAGAACGAT 57.069 29.630 0.00 0.00 0.00 3.73
330 336 9.909644 GTGACACTAGATGTAAGAAAGTAAGAA 57.090 33.333 0.00 0.00 43.56 2.52
335 341 5.162075 GCGTGACACTAGATGTAAGAAAGT 58.838 41.667 3.68 0.00 43.56 2.66
355 364 3.976169 ACATTTGTTGTTAGCAATGCGT 58.024 36.364 0.00 0.00 33.74 5.24
367 376 9.659830 GGTAGTGTAGAAAGTAAACATTTGTTG 57.340 33.333 0.00 0.00 38.44 3.33
383 396 1.402968 GGATCGCGTTGGTAGTGTAGA 59.597 52.381 5.77 0.00 0.00 2.59
388 401 0.968901 TGGAGGATCGCGTTGGTAGT 60.969 55.000 5.77 0.00 34.37 2.73
399 412 0.464373 TGCTTGCCGAATGGAGGATC 60.464 55.000 0.00 0.00 37.49 3.36
489 503 2.917971 GCGCACTACTGTTACAGAGAAG 59.082 50.000 20.07 14.38 35.18 2.85
520 534 2.097466 CAGTGGTTTTCTGAACGCTGTT 59.903 45.455 10.29 0.00 35.20 3.16
549 563 7.097192 CCTGAAAATATGCTATTAGCGTCCTA 58.903 38.462 13.58 0.00 46.26 2.94
551 565 5.122396 CCCTGAAAATATGCTATTAGCGTCC 59.878 44.000 13.58 1.65 46.26 4.79
552 566 5.122396 CCCCTGAAAATATGCTATTAGCGTC 59.878 44.000 13.58 0.71 46.26 5.19
553 567 5.003804 CCCCTGAAAATATGCTATTAGCGT 58.996 41.667 14.53 14.53 46.26 5.07
567 630 0.323360 AATAGCGCTGCCCCTGAAAA 60.323 50.000 22.90 0.00 0.00 2.29
569 632 0.323360 AAAATAGCGCTGCCCCTGAA 60.323 50.000 22.90 0.00 0.00 3.02
580 643 8.775273 TGCTATAGCGTGCTATACAAAATAGCG 61.775 40.741 19.55 6.19 45.51 4.26
602 665 9.443323 TCCTTAAATTGCGCTATTAATATGCTA 57.557 29.630 17.22 11.57 0.00 3.49
603 666 8.237267 GTCCTTAAATTGCGCTATTAATATGCT 58.763 33.333 17.22 2.99 0.00 3.79
604 667 7.216317 CGTCCTTAAATTGCGCTATTAATATGC 59.784 37.037 17.22 11.14 0.00 3.14
605 668 7.692291 CCGTCCTTAAATTGCGCTATTAATATG 59.308 37.037 17.22 9.15 0.00 1.78
606 669 7.389607 ACCGTCCTTAAATTGCGCTATTAATAT 59.610 33.333 17.22 4.75 0.00 1.28
607 670 6.707161 ACCGTCCTTAAATTGCGCTATTAATA 59.293 34.615 17.22 4.83 0.00 0.98
608 671 5.529800 ACCGTCCTTAAATTGCGCTATTAAT 59.470 36.000 17.22 5.81 0.00 1.40
609 672 4.877251 ACCGTCCTTAAATTGCGCTATTAA 59.123 37.500 17.22 13.41 0.00 1.40
610 673 4.271533 CACCGTCCTTAAATTGCGCTATTA 59.728 41.667 17.22 6.75 0.00 0.98
611 674 3.064820 CACCGTCCTTAAATTGCGCTATT 59.935 43.478 11.38 11.38 0.00 1.73
612 675 2.612212 CACCGTCCTTAAATTGCGCTAT 59.388 45.455 9.73 2.86 0.00 2.97
613 676 2.004017 CACCGTCCTTAAATTGCGCTA 58.996 47.619 9.73 0.00 0.00 4.26
614 677 0.802494 CACCGTCCTTAAATTGCGCT 59.198 50.000 9.73 0.00 0.00 5.92
615 678 0.796870 GCACCGTCCTTAAATTGCGC 60.797 55.000 0.00 0.00 0.00 6.09
616 679 0.802494 AGCACCGTCCTTAAATTGCG 59.198 50.000 0.00 0.00 35.10 4.85
617 680 4.632538 AATAGCACCGTCCTTAAATTGC 57.367 40.909 0.00 0.00 0.00 3.56
618 681 6.386654 ACAAAATAGCACCGTCCTTAAATTG 58.613 36.000 0.00 0.00 0.00 2.32
619 682 6.584185 ACAAAATAGCACCGTCCTTAAATT 57.416 33.333 0.00 0.00 0.00 1.82
620 683 7.875327 ATACAAAATAGCACCGTCCTTAAAT 57.125 32.000 0.00 0.00 0.00 1.40
621 684 7.011669 GCTATACAAAATAGCACCGTCCTTAAA 59.988 37.037 11.21 0.00 44.64 1.52
622 685 6.480981 GCTATACAAAATAGCACCGTCCTTAA 59.519 38.462 11.21 0.00 44.64 1.85
623 686 5.987347 GCTATACAAAATAGCACCGTCCTTA 59.013 40.000 11.21 0.00 44.64 2.69
624 687 4.814771 GCTATACAAAATAGCACCGTCCTT 59.185 41.667 11.21 0.00 44.64 3.36
625 688 4.377897 GCTATACAAAATAGCACCGTCCT 58.622 43.478 11.21 0.00 44.64 3.85
626 689 4.727235 GCTATACAAAATAGCACCGTCC 57.273 45.455 11.21 0.00 44.64 4.79
633 696 8.782533 AAAAATAGCGTGCTATACAAAATAGC 57.217 30.769 14.33 9.54 45.28 2.97
661 724 1.405661 GGGAGTAGGTTTCTGCGAAGG 60.406 57.143 0.00 0.00 0.00 3.46
663 726 1.001633 GTGGGAGTAGGTTTCTGCGAA 59.998 52.381 0.00 0.00 0.00 4.70
665 728 0.320374 TGTGGGAGTAGGTTTCTGCG 59.680 55.000 0.00 0.00 0.00 5.18
692 756 3.305608 CCCATGAAGTTTCTTGTGAAGGC 60.306 47.826 0.00 0.00 33.28 4.35
789 1510 2.294512 CACCTCTGCCTTTTGAGTTTCC 59.705 50.000 0.00 0.00 0.00 3.13
865 1586 4.828387 TGGGGTCCCGTTTATTTATATTGC 59.172 41.667 0.48 0.00 39.42 3.56
897 1618 1.086634 GCAGACGAGTTGATGAGGCC 61.087 60.000 0.00 0.00 0.00 5.19
911 1636 1.079405 TGGGGTTTCGATCGCAGAC 60.079 57.895 11.09 8.41 42.51 3.51
952 1678 0.901580 AGGGTTTCGGTCGGCTTCTA 60.902 55.000 0.00 0.00 0.00 2.10
1362 2233 0.894835 TGAGCAGTATGGACAGCGAA 59.105 50.000 0.00 0.00 42.60 4.70
1431 2302 2.278206 CGCTGGGTGTCGATCTCG 60.278 66.667 0.00 0.00 41.45 4.04
1551 4130 1.649321 TCTGCATCTCCTCACTGGTT 58.351 50.000 0.00 0.00 37.07 3.67
1557 4136 0.907486 CCTGGTTCTGCATCTCCTCA 59.093 55.000 0.00 0.00 0.00 3.86
1608 4187 1.141881 CCCGGAGAAGTCCATGTCG 59.858 63.158 0.73 0.00 44.18 4.35
1652 4233 0.105039 ATCGCCTTGGATCCTCGAAC 59.895 55.000 14.23 0.00 32.74 3.95
1655 4251 0.104855 TTCATCGCCTTGGATCCTCG 59.895 55.000 14.23 11.09 0.00 4.63
1701 4298 9.793252 CGAGTACTAATTAAGGTAGTAAAAGCA 57.207 33.333 0.00 0.00 36.16 3.91
1702 4299 9.794685 ACGAGTACTAATTAAGGTAGTAAAAGC 57.205 33.333 0.00 0.95 36.16 3.51
1789 4456 1.588932 ATCGCGCATACTGTGACCG 60.589 57.895 8.75 0.00 0.00 4.79
1841 4508 4.811557 AGAACCAAGAAAGTCGACAAGAAG 59.188 41.667 19.50 2.70 0.00 2.85
1921 4591 4.584874 TCATGAGCCAAACGGAAGATAAA 58.415 39.130 0.00 0.00 0.00 1.40
1944 4616 5.104900 ACGAAGGCCTAATTTCTCATACACT 60.105 40.000 5.16 0.00 0.00 3.55
1982 4654 1.278985 TGATGTCCCACTGATTCGCTT 59.721 47.619 0.00 0.00 0.00 4.68
1986 4658 4.774124 TGAGATTGATGTCCCACTGATTC 58.226 43.478 0.00 0.00 0.00 2.52
2002 4674 4.768968 CCCAATGTCTGAACCTTTGAGATT 59.231 41.667 0.00 0.00 0.00 2.40
2062 4735 8.946085 CAGTGCATAGTTTTGGTTAGATAGAAA 58.054 33.333 0.00 0.00 0.00 2.52
2064 4737 7.047891 CCAGTGCATAGTTTTGGTTAGATAGA 58.952 38.462 0.00 0.00 0.00 1.98
2067 4740 5.570320 ACCAGTGCATAGTTTTGGTTAGAT 58.430 37.500 0.00 0.00 38.98 1.98
2076 4749 6.205464 GTGCATATCATACCAGTGCATAGTTT 59.795 38.462 1.48 0.00 46.08 2.66
2131 4864 3.214328 GCCAACTTCAGGAAAGAGTCAA 58.786 45.455 0.00 0.00 38.44 3.18
2133 4866 1.801178 CGCCAACTTCAGGAAAGAGTC 59.199 52.381 0.00 0.00 38.44 3.36
2134 4867 1.416401 TCGCCAACTTCAGGAAAGAGT 59.584 47.619 0.00 0.00 38.44 3.24
2135 4868 2.169832 TCGCCAACTTCAGGAAAGAG 57.830 50.000 0.00 0.00 38.44 2.85
2166 4899 3.340928 GTTTGGTCGGGCTGTTAGTAAT 58.659 45.455 0.00 0.00 0.00 1.89
2167 4900 2.769893 GTTTGGTCGGGCTGTTAGTAA 58.230 47.619 0.00 0.00 0.00 2.24
2168 4901 1.337074 CGTTTGGTCGGGCTGTTAGTA 60.337 52.381 0.00 0.00 0.00 1.82
2169 4902 0.601841 CGTTTGGTCGGGCTGTTAGT 60.602 55.000 0.00 0.00 0.00 2.24
2173 4906 2.280592 GACGTTTGGTCGGGCTGT 60.281 61.111 0.00 0.00 35.61 4.40
2204 4937 7.393216 AGAATTCAGAGTCAATAGAGCTGTTT 58.607 34.615 8.44 0.00 32.24 2.83
2205 4938 6.945218 AGAATTCAGAGTCAATAGAGCTGTT 58.055 36.000 8.44 0.00 32.24 3.16
2219 4952 7.035004 CAGAGACCACTTAAGAGAATTCAGAG 58.965 42.308 10.09 0.68 0.00 3.35
2366 5276 4.862371 TGTAGGAAAAACACTCCAAAGGT 58.138 39.130 0.00 0.00 35.20 3.50
2388 5298 2.101582 CTGCGCACCTAGGTTTCTATCT 59.898 50.000 13.15 0.00 0.00 1.98
2389 5299 2.100916 TCTGCGCACCTAGGTTTCTATC 59.899 50.000 13.15 0.00 0.00 2.08
2390 5300 2.108168 TCTGCGCACCTAGGTTTCTAT 58.892 47.619 13.15 0.00 0.00 1.98
2430 5340 7.093640 TGACTAGTAAATTACCGGACATCAGTT 60.094 37.037 9.46 0.00 0.00 3.16
2431 5341 6.379133 TGACTAGTAAATTACCGGACATCAGT 59.621 38.462 9.46 0.00 0.00 3.41
2439 5349 9.813446 AAAAGACTATGACTAGTAAATTACCGG 57.187 33.333 0.00 0.00 38.33 5.28
2469 5380 2.694397 AGCAGGGACTAATGGATGCTA 58.306 47.619 0.00 0.00 41.90 3.49
2475 5386 3.356529 AAGTGAAGCAGGGACTAATGG 57.643 47.619 0.00 0.00 36.02 3.16
2501 5415 6.506500 AACATTAAGATTCTCCAGTTGCTG 57.493 37.500 0.00 0.00 0.00 4.41
2519 5433 9.623000 GGTTATACTTGTATCCCTGTAAACATT 57.377 33.333 0.00 0.00 0.00 2.71
2520 5434 8.215736 GGGTTATACTTGTATCCCTGTAAACAT 58.784 37.037 9.18 0.00 32.87 2.71
2521 5435 7.403813 AGGGTTATACTTGTATCCCTGTAAACA 59.596 37.037 15.26 0.00 40.72 2.83
2523 5437 7.847848 AGAGGGTTATACTTGTATCCCTGTAAA 59.152 37.037 18.92 0.00 41.77 2.01
2525 5439 6.781014 CAGAGGGTTATACTTGTATCCCTGTA 59.219 42.308 18.92 0.00 41.77 2.74
2526 5440 5.602978 CAGAGGGTTATACTTGTATCCCTGT 59.397 44.000 18.92 14.35 41.77 4.00
2527 5441 5.012148 CCAGAGGGTTATACTTGTATCCCTG 59.988 48.000 18.92 12.53 41.77 4.45
2528 5442 5.155905 CCAGAGGGTTATACTTGTATCCCT 58.844 45.833 15.71 15.71 43.50 4.20
2529 5443 4.286291 CCCAGAGGGTTATACTTGTATCCC 59.714 50.000 8.64 8.64 38.25 3.85
2530 5444 4.262938 GCCCAGAGGGTTATACTTGTATCC 60.263 50.000 3.68 0.00 46.51 2.59
2531 5445 4.560919 CGCCCAGAGGGTTATACTTGTATC 60.561 50.000 3.68 0.00 46.51 2.24
2532 5446 3.323979 CGCCCAGAGGGTTATACTTGTAT 59.676 47.826 3.68 0.00 46.51 2.29
2533 5447 2.696707 CGCCCAGAGGGTTATACTTGTA 59.303 50.000 3.68 0.00 46.51 2.41
2534 5448 1.485066 CGCCCAGAGGGTTATACTTGT 59.515 52.381 3.68 0.00 46.51 3.16
2535 5449 1.760613 TCGCCCAGAGGGTTATACTTG 59.239 52.381 3.68 0.00 46.51 3.16
2536 5450 2.169978 GTTCGCCCAGAGGGTTATACTT 59.830 50.000 3.68 0.00 46.51 2.24
2537 5451 1.761198 GTTCGCCCAGAGGGTTATACT 59.239 52.381 3.68 0.00 46.51 2.12
2538 5452 1.202615 GGTTCGCCCAGAGGGTTATAC 60.203 57.143 3.68 0.00 46.51 1.47
2539 5453 1.125633 GGTTCGCCCAGAGGGTTATA 58.874 55.000 3.68 0.00 46.51 0.98
2540 5454 0.912487 TGGTTCGCCCAGAGGGTTAT 60.912 55.000 3.68 0.00 46.51 1.89
2549 5463 0.465705 TTTGCATTTTGGTTCGCCCA 59.534 45.000 0.00 0.00 43.27 5.36
2551 5465 1.864565 AGTTTGCATTTTGGTTCGCC 58.135 45.000 0.00 0.00 37.92 5.54
2553 5467 3.243569 TGGGTAGTTTGCATTTTGGTTCG 60.244 43.478 0.00 0.00 0.00 3.95
2556 5470 3.034635 TGTGGGTAGTTTGCATTTTGGT 58.965 40.909 0.00 0.00 0.00 3.67
2582 5503 6.688073 ATATAGTTAAGGCAGCCACTGTAT 57.312 37.500 15.80 13.24 33.43 2.29


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

AutoCloner maintained by Alex Coulton.