Multiple sequence alignment - TraesCS1D01G430200

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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 TraesCS1D01G430200 chr1D 100.000 2270 0 0 1 2270 481380666 481382935 0.000000e+00 4193.0
1 TraesCS1D01G430200 chr1D 94.389 499 26 2 1 497 365276118 365275620 0.000000e+00 765.0
2 TraesCS1D01G430200 chr1D 94.188 499 27 2 1 497 329644651 329645149 0.000000e+00 760.0
3 TraesCS1D01G430200 chr1D 77.436 195 40 3 1790 1982 492780582 492780774 1.840000e-21 113.0
4 TraesCS1D01G430200 chr1A 90.150 1137 46 20 724 1835 577837849 577838944 0.000000e+00 1419.0
5 TraesCS1D01G430200 chr1A 89.327 431 23 5 1831 2260 577839133 577839541 9.290000e-144 520.0
6 TraesCS1D01G430200 chr1A 91.603 131 9 2 607 737 577837764 577837892 1.790000e-41 180.0
7 TraesCS1D01G430200 chr1B 87.691 1113 65 31 815 1896 669751213 669752284 0.000000e+00 1230.0
8 TraesCS1D01G430200 chr1B 85.915 213 23 5 498 706 669750977 669751186 1.060000e-53 220.0
9 TraesCS1D01G430200 chr1B 89.412 85 8 1 1342 1426 669753426 669753509 3.080000e-19 106.0
10 TraesCS1D01G430200 chr5D 94.188 499 27 2 1 497 268260729 268260231 0.000000e+00 760.0
11 TraesCS1D01G430200 chr5D 76.923 195 41 3 1790 1982 400991181 400991373 8.570000e-20 108.0
12 TraesCS1D01G430200 chr2D 94.188 499 27 2 1 497 559406460 559406958 0.000000e+00 760.0
13 TraesCS1D01G430200 chr2D 93.988 499 28 2 1 497 559418719 559419217 0.000000e+00 754.0
14 TraesCS1D01G430200 chr2D 93.812 501 29 2 1 499 78615708 78616208 0.000000e+00 752.0
15 TraesCS1D01G430200 chr2D 76.650 197 42 3 1788 1982 569552734 569552540 3.080000e-19 106.0
16 TraesCS1D01G430200 chr2D 100.000 40 0 0 1428 1467 634528509 634528548 8.700000e-10 75.0
17 TraesCS1D01G430200 chr3D 93.988 499 28 2 1 497 386518595 386519093 0.000000e+00 754.0
18 TraesCS1D01G430200 chr3D 93.825 502 28 3 1 499 411400893 411400392 0.000000e+00 752.0
19 TraesCS1D01G430200 chr3D 93.812 501 27 4 1 498 386585141 386585640 0.000000e+00 750.0
20 TraesCS1D01G430200 chr3D 100.000 40 0 0 1428 1467 39415283 39415322 8.700000e-10 75.0
21 TraesCS1D01G430200 chr7D 97.500 40 1 0 1428 1467 632967496 632967535 4.050000e-08 69.4
22 TraesCS1D01G430200 chr5B 97.500 40 1 0 1428 1467 515694497 515694536 4.050000e-08 69.4
23 TraesCS1D01G430200 chr6D 100.000 33 0 0 1435 1467 249348025 249348057 6.770000e-06 62.1
24 TraesCS1D01G430200 chr6D 94.286 35 1 1 904 937 288452580 288452614 4.000000e-03 52.8
25 TraesCS1D01G430200 chr4B 92.105 38 3 0 900 937 199136860 199136897 1.000000e-03 54.7
26 TraesCS1D01G430200 chr3A 94.286 35 1 1 904 937 257004302 257004336 4.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G430200 chr1D 481380666 481382935 2269 False 4193.000000 4193 100.000000 1 2270 1 chr1D.!!$F2 2269
1 TraesCS1D01G430200 chr1A 577837764 577839541 1777 False 706.333333 1419 90.360000 607 2260 3 chr1A.!!$F1 1653
2 TraesCS1D01G430200 chr1B 669750977 669753509 2532 False 518.666667 1230 87.672667 498 1896 3 chr1B.!!$F1 1398
3 TraesCS1D01G430200 chr2D 78615708 78616208 500 False 752.000000 752 93.812000 1 499 1 chr2D.!!$F1 498
4 TraesCS1D01G430200 chr3D 411400392 411400893 501 True 752.000000 752 93.825000 1 499 1 chr3D.!!$R1 498

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
797 800 0.106268 TCACTTTTTGCAGGAGGGCA 60.106 50.0 0.0 0.0 43.19 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1800 0.109597 GAACAACAGAAGCATGCCCG 60.11 55.0 15.66 2.67 0.0 6.13 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
19 20 1.874345 CGTCAGGGTGTAGCCGAGTT 61.874 60.000 0.00 0.00 38.44 3.01
32 33 0.179171 CCGAGTTGAGTCGCGTACAT 60.179 55.000 5.77 0.00 38.69 2.29
41 42 1.141019 TCGCGTACATTGCTCTCCC 59.859 57.895 5.77 0.00 0.00 4.30
248 250 4.776322 TGACCCGCGGCTGGATTG 62.776 66.667 22.85 6.71 0.00 2.67
253 255 3.630148 CGCGGCTGGATTGCGTAG 61.630 66.667 0.00 0.00 46.29 3.51
266 268 2.784596 CGTAGCACGCCATGGTTG 59.215 61.111 14.67 12.16 40.36 3.77
267 269 2.749865 CGTAGCACGCCATGGTTGG 61.750 63.158 14.67 5.82 46.66 3.77
285 287 4.463879 CGCTGGCCTGGTGAGGAG 62.464 72.222 12.06 0.00 42.93 3.69
286 288 4.106925 GCTGGCCTGGTGAGGAGG 62.107 72.222 12.06 0.00 42.93 4.30
291 293 4.730487 CCTGGTGAGGAGGCTTTG 57.270 61.111 0.00 0.00 42.93 2.77
292 294 1.001641 CCTGGTGAGGAGGCTTTGG 60.002 63.158 0.00 0.00 42.93 3.28
293 295 1.676967 CTGGTGAGGAGGCTTTGGC 60.677 63.158 0.00 0.00 37.82 4.52
316 318 2.093216 CCAGATTCGGCTGTCTTGC 58.907 57.895 0.00 0.00 34.06 4.01
317 319 1.699656 CCAGATTCGGCTGTCTTGCG 61.700 60.000 0.00 0.00 34.06 4.85
318 320 2.103042 AGATTCGGCTGTCTTGCGC 61.103 57.895 0.00 0.00 0.00 6.09
319 321 3.100862 GATTCGGCTGTCTTGCGCC 62.101 63.158 4.18 0.00 42.86 6.53
320 322 3.899981 ATTCGGCTGTCTTGCGCCA 62.900 57.895 4.18 0.00 46.62 5.69
323 325 2.980233 GGCTGTCTTGCGCCAGTT 60.980 61.111 4.18 0.00 45.59 3.16
324 326 2.253452 GCTGTCTTGCGCCAGTTG 59.747 61.111 4.18 0.00 0.00 3.16
325 327 2.546494 GCTGTCTTGCGCCAGTTGT 61.546 57.895 4.18 0.00 0.00 3.32
326 328 2.024918 CTGTCTTGCGCCAGTTGTT 58.975 52.632 4.18 0.00 0.00 2.83
327 329 0.317269 CTGTCTTGCGCCAGTTGTTG 60.317 55.000 4.18 0.00 0.00 3.33
335 337 2.672996 CCAGTTGTTGGGGCCGAG 60.673 66.667 0.00 0.00 43.75 4.63
336 338 2.113139 CAGTTGTTGGGGCCGAGT 59.887 61.111 0.00 0.00 0.00 4.18
337 339 1.966451 CAGTTGTTGGGGCCGAGTC 60.966 63.158 0.00 0.00 0.00 3.36
338 340 3.047877 GTTGTTGGGGCCGAGTCG 61.048 66.667 5.29 5.29 0.00 4.18
339 341 3.235481 TTGTTGGGGCCGAGTCGA 61.235 61.111 15.64 0.00 0.00 4.20
340 342 3.524648 TTGTTGGGGCCGAGTCGAC 62.525 63.158 15.64 7.70 0.00 4.20
345 347 4.773117 GGGCCGAGTCGACGTGTC 62.773 72.222 15.64 3.96 0.00 3.67
346 348 3.735029 GGCCGAGTCGACGTGTCT 61.735 66.667 15.64 0.00 0.00 3.41
347 349 2.254651 GCCGAGTCGACGTGTCTT 59.745 61.111 15.64 0.00 0.00 3.01
348 350 2.081212 GCCGAGTCGACGTGTCTTG 61.081 63.158 15.64 0.00 0.00 3.02
349 351 2.081212 CCGAGTCGACGTGTCTTGC 61.081 63.158 15.64 0.00 0.00 4.01
350 352 2.081212 CGAGTCGACGTGTCTTGCC 61.081 63.158 6.73 0.00 0.00 4.52
351 353 2.050351 AGTCGACGTGTCTTGCCG 60.050 61.111 10.46 0.00 0.00 5.69
352 354 3.103911 GTCGACGTGTCTTGCCGG 61.104 66.667 0.00 0.00 0.00 6.13
353 355 4.351938 TCGACGTGTCTTGCCGGG 62.352 66.667 2.18 0.00 0.00 5.73
354 356 4.657824 CGACGTGTCTTGCCGGGT 62.658 66.667 2.18 0.00 0.00 5.28
355 357 2.737376 GACGTGTCTTGCCGGGTC 60.737 66.667 2.18 0.00 0.00 4.46
356 358 4.657824 ACGTGTCTTGCCGGGTCG 62.658 66.667 2.18 0.00 0.00 4.79
366 368 2.421739 CCGGGTCGGCTAATCTGG 59.578 66.667 0.00 0.00 41.17 3.86
367 369 2.280186 CGGGTCGGCTAATCTGGC 60.280 66.667 0.00 0.00 0.00 4.85
368 370 2.111251 GGGTCGGCTAATCTGGCC 59.889 66.667 0.00 0.00 45.32 5.36
373 375 2.193248 GGCTAATCTGGCCGGCTT 59.807 61.111 28.56 15.48 40.19 4.35
374 376 2.189499 GGCTAATCTGGCCGGCTTG 61.189 63.158 28.56 19.13 40.19 4.01
375 377 2.838974 GCTAATCTGGCCGGCTTGC 61.839 63.158 28.56 14.91 0.00 4.01
376 378 2.513666 TAATCTGGCCGGCTTGCG 60.514 61.111 28.56 12.25 0.00 4.85
406 408 4.373116 GTCGAGCGACCTGGCCAA 62.373 66.667 7.01 0.00 39.08 4.52
407 409 4.069232 TCGAGCGACCTGGCCAAG 62.069 66.667 7.01 2.23 0.00 3.61
430 432 4.929707 GCCGGTATTGAGGGGCGG 62.930 72.222 1.90 0.00 35.59 6.13
431 433 3.476419 CCGGTATTGAGGGGCGGT 61.476 66.667 0.00 0.00 0.00 5.68
432 434 2.203015 CGGTATTGAGGGGCGGTG 60.203 66.667 0.00 0.00 0.00 4.94
433 435 2.516225 GGTATTGAGGGGCGGTGC 60.516 66.667 0.00 0.00 0.00 5.01
445 447 4.954970 CGGTGCCAGCCCTGTTGT 62.955 66.667 0.00 0.00 0.00 3.32
446 448 2.521708 GGTGCCAGCCCTGTTGTT 60.522 61.111 0.00 0.00 0.00 2.83
447 449 2.133641 GGTGCCAGCCCTGTTGTTT 61.134 57.895 0.00 0.00 0.00 2.83
448 450 1.685355 GGTGCCAGCCCTGTTGTTTT 61.685 55.000 0.00 0.00 0.00 2.43
449 451 0.177836 GTGCCAGCCCTGTTGTTTTT 59.822 50.000 0.00 0.00 0.00 1.94
450 452 1.410882 GTGCCAGCCCTGTTGTTTTTA 59.589 47.619 0.00 0.00 0.00 1.52
451 453 2.111384 TGCCAGCCCTGTTGTTTTTAA 58.889 42.857 0.00 0.00 0.00 1.52
452 454 2.501723 TGCCAGCCCTGTTGTTTTTAAA 59.498 40.909 0.00 0.00 0.00 1.52
453 455 3.055094 TGCCAGCCCTGTTGTTTTTAAAA 60.055 39.130 0.00 0.00 0.00 1.52
454 456 3.942115 GCCAGCCCTGTTGTTTTTAAAAA 59.058 39.130 9.31 9.31 0.00 1.94
470 472 2.281539 AAAAAGATCCGGGTTCCGTT 57.718 45.000 0.00 0.00 46.80 4.44
471 473 1.530323 AAAAGATCCGGGTTCCGTTG 58.470 50.000 0.00 0.00 46.80 4.10
472 474 0.958876 AAAGATCCGGGTTCCGTTGC 60.959 55.000 0.00 0.00 46.80 4.17
473 475 3.192922 GATCCGGGTTCCGTTGCG 61.193 66.667 0.00 0.00 46.80 4.85
474 476 3.945304 GATCCGGGTTCCGTTGCGT 62.945 63.158 0.00 0.00 46.80 5.24
475 477 4.973055 TCCGGGTTCCGTTGCGTG 62.973 66.667 0.00 0.00 46.80 5.34
513 515 0.951558 ACAAGGTTGGTCAACGATGC 59.048 50.000 13.59 0.59 42.02 3.91
532 534 1.681264 GCCATTATACAACACCTGGGC 59.319 52.381 0.00 0.00 0.00 5.36
535 537 2.389962 TTATACAACACCTGGGCGAC 57.610 50.000 0.00 0.00 0.00 5.19
539 541 1.671054 CAACACCTGGGCGACGAAT 60.671 57.895 0.00 0.00 0.00 3.34
541 543 0.390735 AACACCTGGGCGACGAATAC 60.391 55.000 0.00 0.00 0.00 1.89
546 548 0.939577 CTGGGCGACGAATACGATGG 60.940 60.000 0.00 0.00 42.66 3.51
548 550 2.308039 GGCGACGAATACGATGGCC 61.308 63.158 0.00 0.00 42.66 5.36
549 551 2.645510 GCGACGAATACGATGGCCG 61.646 63.158 0.00 0.00 42.66 6.13
560 563 2.690173 CGATGGCCGTTGTTTTTGTA 57.310 45.000 0.00 0.00 0.00 2.41
564 567 6.050454 CGATGGCCGTTGTTTTTGTATATA 57.950 37.500 0.00 0.00 0.00 0.86
565 568 6.664515 CGATGGCCGTTGTTTTTGTATATAT 58.335 36.000 0.00 0.00 0.00 0.86
566 569 6.577055 CGATGGCCGTTGTTTTTGTATATATG 59.423 38.462 0.00 0.00 0.00 1.78
571 574 8.588789 GGCCGTTGTTTTTGTATATATGAAAAC 58.411 33.333 19.48 19.48 40.54 2.43
590 593 2.213310 ACCTCATCCTCTCTCTCTCCA 58.787 52.381 0.00 0.00 0.00 3.86
600 603 4.441913 CCTCTCTCTCTCCAGCATTTTCTC 60.442 50.000 0.00 0.00 0.00 2.87
601 604 4.092279 TCTCTCTCTCCAGCATTTTCTCA 58.908 43.478 0.00 0.00 0.00 3.27
615 618 6.602406 AGCATTTTCTCAAGCATTCTATGACT 59.398 34.615 0.00 0.00 0.00 3.41
617 620 6.748333 TTTTCTCAAGCATTCTATGACTGG 57.252 37.500 0.00 0.00 0.00 4.00
641 644 4.013728 TCCCCAAAATTAATCACCTCACG 58.986 43.478 0.00 0.00 0.00 4.35
711 714 9.406828 GAACACTGGGTATTACTCAAATTTTTC 57.593 33.333 0.00 0.00 0.00 2.29
778 781 8.034804 GCAAGGGTATTACTCAAATTGTTCAAT 58.965 33.333 0.00 0.00 0.00 2.57
795 798 2.892852 TCAATCACTTTTTGCAGGAGGG 59.107 45.455 0.00 0.00 0.00 4.30
796 799 1.260544 ATCACTTTTTGCAGGAGGGC 58.739 50.000 0.00 0.00 0.00 5.19
797 800 0.106268 TCACTTTTTGCAGGAGGGCA 60.106 50.000 0.00 0.00 43.19 5.36
825 829 4.373116 CAGCCCACGTACGTGCCT 62.373 66.667 36.76 30.14 44.16 4.75
966 985 4.308458 CGGCGACTCCACCACCAA 62.308 66.667 0.00 0.00 34.01 3.67
1273 1325 3.774959 CTCGCCCCGTTCTGATCGG 62.775 68.421 17.99 17.99 46.49 4.18
1315 1375 0.100861 GCTAGGGTTCGTTCGAGAGG 59.899 60.000 0.00 0.00 0.00 3.69
1324 1384 0.784778 CGTTCGAGAGGTGAAACAGC 59.215 55.000 0.00 0.00 39.98 4.40
1329 1389 1.517242 GAGAGGTGAAACAGCCAGTG 58.483 55.000 0.00 0.00 39.98 3.66
1357 1417 4.974275 CCGTGGTAGTTAGTTATGTCATCG 59.026 45.833 0.00 0.00 0.00 3.84
1393 1456 0.677731 TTATCTGTGCTGCACCTGCC 60.678 55.000 28.17 5.27 41.18 4.85
1490 1553 6.391537 TGATTTGGTGATGTGATTGTTGATG 58.608 36.000 0.00 0.00 0.00 3.07
1529 1592 0.916086 GTGATGTGGGGGTGTGGATA 59.084 55.000 0.00 0.00 0.00 2.59
1619 1689 3.187227 CAGGGATTTGTGTTCTCTGTTCG 59.813 47.826 0.00 0.00 37.01 3.95
1629 1699 3.863424 TGTTCTCTGTTCGTGTTCTTCAC 59.137 43.478 0.00 0.00 43.03 3.18
1668 1739 3.008704 TGGTGATATGATCTGGATGCCTG 59.991 47.826 0.00 0.00 0.00 4.85
1670 1741 4.506271 GGTGATATGATCTGGATGCCTGTT 60.506 45.833 0.00 0.00 0.00 3.16
1681 1752 2.484770 GGATGCCTGTTGGTAATCGCTA 60.485 50.000 0.00 0.00 32.69 4.26
1729 1800 7.652909 TGTCATCAATGATTTCAAAGTTTCACC 59.347 33.333 0.00 0.00 39.30 4.02
1757 1831 3.004002 TGCTTCTGTTGTTCTTGCATCTG 59.996 43.478 0.00 0.00 0.00 2.90
1762 1836 4.639755 TCTGTTGTTCTTGCATCTGTTCAA 59.360 37.500 0.00 0.00 0.00 2.69
1764 1838 3.607422 TGTTCTTGCATCTGTTCAACG 57.393 42.857 0.00 0.00 0.00 4.10
1791 1866 4.556233 GCTCACAGTGGGTAAAATTTTCC 58.444 43.478 6.72 8.54 0.00 3.13
1804 1879 7.094075 GGGTAAAATTTTCCGGTAGAATCACTT 60.094 37.037 6.72 0.00 33.44 3.16
1841 2109 5.666969 TTTAGGTTATGTGCATGCGTATC 57.333 39.130 14.09 4.21 0.00 2.24
1857 2125 3.205338 CGTATCTGGCATTGTTCATCCA 58.795 45.455 0.00 0.00 0.00 3.41
1861 2130 4.724074 TCTGGCATTGTTCATCCAATTC 57.276 40.909 0.00 0.00 32.81 2.17
1868 2137 5.278169 GCATTGTTCATCCAATTCGCTATCT 60.278 40.000 0.00 0.00 32.81 1.98
1886 2155 6.571344 CGCTATCTGTATATCCTTGAGCTTGT 60.571 42.308 0.00 0.00 0.00 3.16
1887 2156 6.589523 GCTATCTGTATATCCTTGAGCTTGTG 59.410 42.308 0.00 0.00 0.00 3.33
1888 2157 4.697514 TCTGTATATCCTTGAGCTTGTGC 58.302 43.478 0.00 0.00 40.05 4.57
1921 2190 8.076178 GTGCTTATGTGTCTTCACTTTTATGTT 58.924 33.333 0.00 0.00 44.14 2.71
1937 2206 7.803189 ACTTTTATGTTATCTTTGTTGTCGCTG 59.197 33.333 0.00 0.00 0.00 5.18
1939 2208 4.725556 TGTTATCTTTGTTGTCGCTGAC 57.274 40.909 2.32 2.32 0.00 3.51
1956 2225 3.244596 GCTGACCTTTTGAGGTTCCTACT 60.245 47.826 0.00 0.00 43.24 2.57
1958 2227 5.479124 TGACCTTTTGAGGTTCCTACTAC 57.521 43.478 0.00 0.00 43.24 2.73
1976 2245 2.685850 ACTACCACTGGTATTTCCGC 57.314 50.000 8.45 0.00 37.56 5.54
1983 2252 0.583438 CTGGTATTTCCGCGATGCTG 59.417 55.000 8.23 0.00 39.52 4.41
1986 2255 1.003866 GGTATTTCCGCGATGCTGTTC 60.004 52.381 8.23 0.00 0.00 3.18
1994 2263 0.175760 GCGATGCTGTTCTACTGGGA 59.824 55.000 0.00 0.00 0.00 4.37
2012 2281 6.969043 ACTGGGAAATCAATAATCTGTGGTA 58.031 36.000 0.00 0.00 0.00 3.25
2013 2282 7.586349 ACTGGGAAATCAATAATCTGTGGTAT 58.414 34.615 0.00 0.00 0.00 2.73
2014 2283 7.721399 ACTGGGAAATCAATAATCTGTGGTATC 59.279 37.037 0.00 0.00 0.00 2.24
2015 2284 6.710295 TGGGAAATCAATAATCTGTGGTATCG 59.290 38.462 0.00 0.00 0.00 2.92
2016 2285 6.348540 GGGAAATCAATAATCTGTGGTATCGC 60.349 42.308 0.00 0.00 0.00 4.58
2017 2286 6.204688 GGAAATCAATAATCTGTGGTATCGCA 59.795 38.462 0.00 0.00 0.00 5.10
2018 2287 7.094634 GGAAATCAATAATCTGTGGTATCGCAT 60.095 37.037 0.00 0.00 32.43 4.73
2019 2288 7.750229 AATCAATAATCTGTGGTATCGCATT 57.250 32.000 0.00 0.00 32.43 3.56
2020 2289 7.750229 ATCAATAATCTGTGGTATCGCATTT 57.250 32.000 0.00 0.00 32.43 2.32
2021 2290 7.189693 TCAATAATCTGTGGTATCGCATTTC 57.810 36.000 0.00 0.00 32.43 2.17
2022 2291 6.992123 TCAATAATCTGTGGTATCGCATTTCT 59.008 34.615 0.00 0.00 32.43 2.52
2046 2315 5.163602 TGTGTTGTTCATCCAAGTTGTTACC 60.164 40.000 1.45 0.00 0.00 2.85
2062 2331 1.414158 TACCTGTATGCCCTGAGCTC 58.586 55.000 6.82 6.82 44.23 4.09
2074 2343 1.667724 CCTGAGCTCGCTTTTATGTGG 59.332 52.381 9.64 0.00 0.00 4.17
2122 2391 2.096496 AGATTCGTACAATTGCTGCTGC 59.904 45.455 8.89 8.89 40.20 5.25
2158 2427 7.156876 TGCTGTTTTTACTGGGAATCAATAG 57.843 36.000 0.00 0.00 0.00 1.73
2260 2533 7.351981 CAACATGTGATCTTTTCAACTTCGTA 58.648 34.615 0.00 0.00 35.70 3.43
2261 2534 7.672983 ACATGTGATCTTTTCAACTTCGTAT 57.327 32.000 0.00 0.00 35.70 3.06
2262 2535 7.521529 ACATGTGATCTTTTCAACTTCGTATG 58.478 34.615 0.00 0.00 35.70 2.39
2263 2536 7.387673 ACATGTGATCTTTTCAACTTCGTATGA 59.612 33.333 0.00 0.00 35.70 2.15
2264 2537 7.722795 TGTGATCTTTTCAACTTCGTATGAA 57.277 32.000 0.00 0.00 35.70 2.57
2265 2538 8.148807 TGTGATCTTTTCAACTTCGTATGAAA 57.851 30.769 0.00 0.00 42.17 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.330372 TACGCGACTCAACTCGGCT 61.330 57.895 15.93 0.00 34.06 5.52
19 20 0.526211 AGAGCAATGTACGCGACTCA 59.474 50.000 15.93 9.22 0.00 3.41
32 33 1.376466 GGCAACTGAGGGAGAGCAA 59.624 57.895 0.00 0.00 0.00 3.91
133 135 0.179124 CCTCTAGTCAGCAGGAACGC 60.179 60.000 0.00 0.00 0.00 4.84
249 251 2.749865 CCAACCATGGCGTGCTACG 61.750 63.158 13.04 4.61 45.88 3.51
250 252 3.187058 CCAACCATGGCGTGCTAC 58.813 61.111 13.04 0.00 40.58 3.58
268 270 4.463879 CTCCTCACCAGGCCAGCG 62.464 72.222 5.01 0.00 40.12 5.18
269 271 4.106925 CCTCCTCACCAGGCCAGC 62.107 72.222 5.01 0.00 40.12 4.85
274 276 1.001641 CCAAAGCCTCCTCACCAGG 60.002 63.158 0.00 0.00 42.01 4.45
275 277 1.676967 GCCAAAGCCTCCTCACCAG 60.677 63.158 0.00 0.00 0.00 4.00
276 278 2.436109 GCCAAAGCCTCCTCACCA 59.564 61.111 0.00 0.00 0.00 4.17
298 300 1.699656 CGCAAGACAGCCGAATCTGG 61.700 60.000 4.75 0.00 38.36 3.86
299 301 1.712081 CGCAAGACAGCCGAATCTG 59.288 57.895 0.00 0.00 43.02 2.90
300 302 2.103042 GCGCAAGACAGCCGAATCT 61.103 57.895 0.30 0.00 43.02 2.40
301 303 2.401195 GCGCAAGACAGCCGAATC 59.599 61.111 0.30 0.00 43.02 2.52
311 313 2.192861 CCCAACAACTGGCGCAAGA 61.193 57.895 21.26 0.00 44.90 3.02
312 314 2.336088 CCCAACAACTGGCGCAAG 59.664 61.111 11.17 11.17 44.90 4.01
313 315 3.222855 CCCCAACAACTGGCGCAA 61.223 61.111 10.83 0.00 44.90 4.85
317 319 4.966787 TCGGCCCCAACAACTGGC 62.967 66.667 0.00 0.00 44.90 4.85
318 320 2.672996 CTCGGCCCCAACAACTGG 60.673 66.667 0.00 0.00 45.97 4.00
319 321 1.966451 GACTCGGCCCCAACAACTG 60.966 63.158 0.00 0.00 0.00 3.16
320 322 2.430367 GACTCGGCCCCAACAACT 59.570 61.111 0.00 0.00 0.00 3.16
321 323 3.047877 CGACTCGGCCCCAACAAC 61.048 66.667 0.00 0.00 0.00 3.32
322 324 3.235481 TCGACTCGGCCCCAACAA 61.235 61.111 0.00 0.00 0.00 2.83
323 325 3.998672 GTCGACTCGGCCCCAACA 61.999 66.667 8.70 0.00 0.00 3.33
328 330 4.773117 GACACGTCGACTCGGCCC 62.773 72.222 14.70 0.00 34.94 5.80
329 331 3.264866 AAGACACGTCGACTCGGCC 62.265 63.158 14.70 0.00 34.94 6.13
330 332 2.081212 CAAGACACGTCGACTCGGC 61.081 63.158 14.70 6.40 34.94 5.54
331 333 2.081212 GCAAGACACGTCGACTCGG 61.081 63.158 14.70 5.24 34.94 4.63
332 334 2.081212 GGCAAGACACGTCGACTCG 61.081 63.158 14.70 6.77 34.09 4.18
333 335 2.081212 CGGCAAGACACGTCGACTC 61.081 63.158 14.70 4.49 34.09 3.36
334 336 2.050351 CGGCAAGACACGTCGACT 60.050 61.111 14.70 0.00 34.09 4.18
335 337 3.103911 CCGGCAAGACACGTCGAC 61.104 66.667 5.18 5.18 34.09 4.20
336 338 4.351938 CCCGGCAAGACACGTCGA 62.352 66.667 0.00 0.00 34.09 4.20
337 339 4.657824 ACCCGGCAAGACACGTCG 62.658 66.667 0.00 0.00 34.09 5.12
338 340 2.737376 GACCCGGCAAGACACGTC 60.737 66.667 0.00 0.00 0.00 4.34
339 341 4.657824 CGACCCGGCAAGACACGT 62.658 66.667 0.00 0.00 0.00 4.49
350 352 2.280186 GCCAGATTAGCCGACCCG 60.280 66.667 0.00 0.00 0.00 5.28
351 353 2.111251 GGCCAGATTAGCCGACCC 59.889 66.667 0.00 0.00 41.41 4.46
357 359 2.838974 GCAAGCCGGCCAGATTAGC 61.839 63.158 26.15 13.04 0.00 3.09
358 360 2.537560 CGCAAGCCGGCCAGATTAG 61.538 63.158 26.15 6.39 0.00 1.73
359 361 2.513666 CGCAAGCCGGCCAGATTA 60.514 61.111 26.15 0.00 0.00 1.75
389 391 4.373116 TTGGCCAGGTCGCTCGAC 62.373 66.667 5.11 13.45 43.87 4.20
390 392 4.069232 CTTGGCCAGGTCGCTCGA 62.069 66.667 5.11 0.00 0.00 4.04
413 415 4.929707 CCGCCCCTCAATACCGGC 62.930 72.222 0.00 0.00 38.07 6.13
414 416 3.476419 ACCGCCCCTCAATACCGG 61.476 66.667 0.00 0.00 44.19 5.28
415 417 2.203015 CACCGCCCCTCAATACCG 60.203 66.667 0.00 0.00 0.00 4.02
416 418 2.516225 GCACCGCCCCTCAATACC 60.516 66.667 0.00 0.00 0.00 2.73
417 419 2.516225 GGCACCGCCCCTCAATAC 60.516 66.667 0.00 0.00 44.06 1.89
428 430 4.954970 ACAACAGGGCTGGCACCG 62.955 66.667 2.88 0.00 34.19 4.94
429 431 1.685355 AAAACAACAGGGCTGGCACC 61.685 55.000 2.88 0.00 34.19 5.01
430 432 0.177836 AAAAACAACAGGGCTGGCAC 59.822 50.000 2.88 0.00 34.19 5.01
431 433 1.781786 TAAAAACAACAGGGCTGGCA 58.218 45.000 2.88 0.00 34.19 4.92
432 434 2.900716 TTAAAAACAACAGGGCTGGC 57.099 45.000 0.00 0.00 34.19 4.85
481 483 2.590092 CTTGTCGGGGGATGGACC 59.410 66.667 0.00 0.00 38.08 4.46
482 484 1.848886 AACCTTGTCGGGGGATGGAC 61.849 60.000 0.00 0.00 36.97 4.02
483 485 1.540367 AACCTTGTCGGGGGATGGA 60.540 57.895 0.00 0.00 36.97 3.41
484 486 1.378514 CAACCTTGTCGGGGGATGG 60.379 63.158 0.00 0.00 36.97 3.51
485 487 1.378514 CCAACCTTGTCGGGGGATG 60.379 63.158 0.00 0.00 36.97 3.51
486 488 1.848886 GACCAACCTTGTCGGGGGAT 61.849 60.000 0.00 0.00 35.81 3.85
487 489 2.448931 ACCAACCTTGTCGGGGGA 60.449 61.111 0.00 0.00 35.81 4.81
488 490 2.033602 GACCAACCTTGTCGGGGG 59.966 66.667 0.00 0.00 37.37 5.40
489 491 1.149627 TTGACCAACCTTGTCGGGG 59.850 57.895 0.00 0.00 36.97 5.73
490 492 1.503818 CGTTGACCAACCTTGTCGGG 61.504 60.000 7.24 0.00 38.03 5.14
491 493 0.531090 TCGTTGACCAACCTTGTCGG 60.531 55.000 7.24 0.00 38.03 4.79
492 494 1.194547 CATCGTTGACCAACCTTGTCG 59.805 52.381 7.24 0.00 38.03 4.35
493 495 1.069227 GCATCGTTGACCAACCTTGTC 60.069 52.381 7.24 0.00 38.03 3.18
494 496 0.951558 GCATCGTTGACCAACCTTGT 59.048 50.000 7.24 0.00 38.03 3.16
495 497 0.240945 GGCATCGTTGACCAACCTTG 59.759 55.000 7.24 6.39 38.03 3.61
496 498 0.179004 TGGCATCGTTGACCAACCTT 60.179 50.000 7.24 0.00 38.03 3.50
513 515 1.946768 CGCCCAGGTGTTGTATAATGG 59.053 52.381 0.00 0.00 0.00 3.16
532 534 3.522568 CGGCCATCGTATTCGTCG 58.477 61.111 2.24 0.00 38.33 5.12
541 543 2.690173 TACAAAAACAACGGCCATCG 57.310 45.000 2.24 0.00 45.88 3.84
546 548 8.588789 GGTTTTCATATATACAAAAACAACGGC 58.411 33.333 23.06 11.02 41.25 5.68
560 563 8.971032 AGAGAGAGGATGAGGTTTTCATATAT 57.029 34.615 0.00 0.00 46.51 0.86
565 568 4.682563 AGAGAGAGAGGATGAGGTTTTCA 58.317 43.478 0.00 0.00 40.85 2.69
566 569 4.099419 GGAGAGAGAGAGGATGAGGTTTTC 59.901 50.000 0.00 0.00 0.00 2.29
571 574 2.867624 CTGGAGAGAGAGAGGATGAGG 58.132 57.143 0.00 0.00 0.00 3.86
580 583 4.468765 TGAGAAAATGCTGGAGAGAGAG 57.531 45.455 0.00 0.00 0.00 3.20
581 584 4.829968 CTTGAGAAAATGCTGGAGAGAGA 58.170 43.478 0.00 0.00 0.00 3.10
590 593 6.602406 AGTCATAGAATGCTTGAGAAAATGCT 59.398 34.615 0.00 0.00 0.00 3.79
600 603 2.877168 GGAGCCAGTCATAGAATGCTTG 59.123 50.000 0.00 0.00 0.00 4.01
601 604 2.158696 GGGAGCCAGTCATAGAATGCTT 60.159 50.000 0.00 0.00 0.00 3.91
615 618 3.103742 GGTGATTAATTTTGGGGAGCCA 58.896 45.455 0.00 0.00 0.00 4.75
617 620 4.023291 TGAGGTGATTAATTTTGGGGAGC 58.977 43.478 0.00 0.00 0.00 4.70
641 644 8.073768 TGAGGTGATTAATTTCACTCGAAAAAC 58.926 33.333 9.54 0.00 44.12 2.43
682 685 4.713824 TGAGTAATACCCAGTGTTCGAG 57.286 45.455 0.00 0.00 0.00 4.04
685 688 9.406828 GAAAAATTTGAGTAATACCCAGTGTTC 57.593 33.333 0.00 0.00 0.00 3.18
744 747 5.636123 TGAGTAATACCCTTGCCTCAAAAA 58.364 37.500 0.00 0.00 0.00 1.94
745 748 5.249780 TGAGTAATACCCTTGCCTCAAAA 57.750 39.130 0.00 0.00 0.00 2.44
746 749 4.919774 TGAGTAATACCCTTGCCTCAAA 57.080 40.909 0.00 0.00 0.00 2.69
747 750 4.919774 TTGAGTAATACCCTTGCCTCAA 57.080 40.909 0.00 0.00 36.79 3.02
748 751 4.919774 TTTGAGTAATACCCTTGCCTCA 57.080 40.909 0.00 0.00 0.00 3.86
749 752 5.652452 ACAATTTGAGTAATACCCTTGCCTC 59.348 40.000 2.79 0.00 0.00 4.70
750 753 5.580022 ACAATTTGAGTAATACCCTTGCCT 58.420 37.500 2.79 0.00 0.00 4.75
751 754 5.914898 ACAATTTGAGTAATACCCTTGCC 57.085 39.130 2.79 0.00 0.00 4.52
752 755 6.919721 TGAACAATTTGAGTAATACCCTTGC 58.080 36.000 2.79 0.00 0.00 4.01
778 781 0.106268 TGCCCTCCTGCAAAAAGTGA 60.106 50.000 0.00 0.00 38.56 3.41
795 798 1.081442 GGGCTGCTGTACGTTTTGC 60.081 57.895 0.00 0.00 0.00 3.68
796 799 0.040425 GTGGGCTGCTGTACGTTTTG 60.040 55.000 0.00 0.00 0.00 2.44
797 800 1.503818 CGTGGGCTGCTGTACGTTTT 61.504 55.000 0.00 0.00 0.00 2.43
801 804 1.804326 GTACGTGGGCTGCTGTACG 60.804 63.158 17.27 17.27 41.86 3.67
802 805 1.804326 CGTACGTGGGCTGCTGTAC 60.804 63.158 7.22 7.19 35.11 2.90
966 985 4.694233 CTCGCCTGGTGCTGCTGT 62.694 66.667 1.39 0.00 38.05 4.40
1315 1375 0.663153 GACACCACTGGCTGTTTCAC 59.337 55.000 0.00 0.00 0.00 3.18
1324 1384 1.292223 CTACCACGGACACCACTGG 59.708 63.158 0.00 0.00 0.00 4.00
1329 1389 4.082026 ACATAACTAACTACCACGGACACC 60.082 45.833 0.00 0.00 0.00 4.16
1357 1417 7.910683 GCACAGATAATTCTAGCAAGTTTTACC 59.089 37.037 0.00 0.00 34.21 2.85
1393 1456 5.830000 TCAATTTGATCCAGAGCAGAATG 57.170 39.130 0.00 0.00 40.87 2.67
1468 1531 6.349243 ACATCAACAATCACATCACCAAAT 57.651 33.333 0.00 0.00 0.00 2.32
1471 1534 3.758023 GGACATCAACAATCACATCACCA 59.242 43.478 0.00 0.00 0.00 4.17
1473 1536 3.436704 ACGGACATCAACAATCACATCAC 59.563 43.478 0.00 0.00 0.00 3.06
1490 1553 0.608640 AGTCCAGAATCCACACGGAC 59.391 55.000 0.00 0.00 46.79 4.79
1508 1571 1.303561 CCACACCCCCACATCACAG 60.304 63.158 0.00 0.00 0.00 3.66
1595 1665 1.466167 CAGAGAACACAAATCCCTGCG 59.534 52.381 0.00 0.00 0.00 5.18
1619 1689 4.536065 TGATGATTTTGCGTGAAGAACAC 58.464 39.130 0.00 0.00 45.11 3.32
1629 1699 2.086869 ACCACCTCTGATGATTTTGCG 58.913 47.619 0.00 0.00 0.00 4.85
1635 1705 6.024247 AGATCATATCACCACCTCTGATGAT 58.976 40.000 0.00 0.00 35.91 2.45
1668 1739 5.310451 TCCCCAATTATAGCGATTACCAAC 58.690 41.667 0.00 0.00 0.00 3.77
1670 1741 5.570205 TTCCCCAATTATAGCGATTACCA 57.430 39.130 0.00 0.00 0.00 3.25
1681 1752 7.079451 ACAAGACGAGATATTCCCCAATTAT 57.921 36.000 0.00 0.00 0.00 1.28
1729 1800 0.109597 GAACAACAGAAGCATGCCCG 60.110 55.000 15.66 2.67 0.00 6.13
1757 1831 0.798776 CTGTGAGCCCATCGTTGAAC 59.201 55.000 0.00 0.00 0.00 3.18
1762 1836 2.665000 CCACTGTGAGCCCATCGT 59.335 61.111 9.86 0.00 0.00 3.73
1764 1838 0.618458 TTACCCACTGTGAGCCCATC 59.382 55.000 9.86 0.00 0.00 3.51
1841 2109 3.441163 CGAATTGGATGAACAATGCCAG 58.559 45.455 0.00 0.00 40.71 4.85
1857 2125 7.038659 GCTCAAGGATATACAGATAGCGAATT 58.961 38.462 0.00 0.00 0.00 2.17
1861 2130 5.574891 AGCTCAAGGATATACAGATAGCG 57.425 43.478 0.00 0.00 32.82 4.26
1886 2155 4.578871 AGACACATAAGCACACATAAGCA 58.421 39.130 0.00 0.00 0.00 3.91
1887 2156 5.122239 TGAAGACACATAAGCACACATAAGC 59.878 40.000 0.00 0.00 0.00 3.09
1888 2157 6.537566 GTGAAGACACATAAGCACACATAAG 58.462 40.000 0.00 0.00 45.32 1.73
1889 2158 6.480524 GTGAAGACACATAAGCACACATAA 57.519 37.500 0.00 0.00 45.32 1.90
1921 2190 3.678056 AGGTCAGCGACAACAAAGATA 57.322 42.857 10.14 0.00 33.68 1.98
1956 2225 2.099592 CGCGGAAATACCAGTGGTAGTA 59.900 50.000 25.67 6.95 41.83 1.82
1958 2227 1.135527 TCGCGGAAATACCAGTGGTAG 59.864 52.381 25.67 13.61 41.83 3.18
1976 2245 2.672961 TTCCCAGTAGAACAGCATCG 57.327 50.000 0.00 0.00 0.00 3.84
1983 2252 8.616076 CACAGATTATTGATTTCCCAGTAGAAC 58.384 37.037 0.00 0.00 0.00 3.01
1986 2255 7.056635 ACCACAGATTATTGATTTCCCAGTAG 58.943 38.462 0.00 0.00 0.00 2.57
1994 2263 7.750229 ATGCGATACCACAGATTATTGATTT 57.250 32.000 0.00 0.00 0.00 2.17
2012 2281 4.379813 GGATGAACAACACAGAAATGCGAT 60.380 41.667 0.00 0.00 0.00 4.58
2013 2282 3.058293 GGATGAACAACACAGAAATGCGA 60.058 43.478 0.00 0.00 0.00 5.10
2014 2283 3.236816 GGATGAACAACACAGAAATGCG 58.763 45.455 0.00 0.00 0.00 4.73
2015 2284 4.241590 TGGATGAACAACACAGAAATGC 57.758 40.909 0.00 0.00 0.00 3.56
2016 2285 5.835257 ACTTGGATGAACAACACAGAAATG 58.165 37.500 0.00 0.00 0.00 2.32
2017 2286 6.127366 ACAACTTGGATGAACAACACAGAAAT 60.127 34.615 0.00 0.00 0.00 2.17
2018 2287 5.184864 ACAACTTGGATGAACAACACAGAAA 59.815 36.000 0.00 0.00 0.00 2.52
2019 2288 4.704540 ACAACTTGGATGAACAACACAGAA 59.295 37.500 0.00 0.00 0.00 3.02
2020 2289 4.269183 ACAACTTGGATGAACAACACAGA 58.731 39.130 0.00 0.00 0.00 3.41
2021 2290 4.637483 ACAACTTGGATGAACAACACAG 57.363 40.909 0.00 0.00 0.00 3.66
2022 2291 5.163602 GGTAACAACTTGGATGAACAACACA 60.164 40.000 0.00 0.00 0.00 3.72
2046 2315 1.593750 GCGAGCTCAGGGCATACAG 60.594 63.158 15.40 0.00 44.79 2.74
2062 2331 6.183359 GCAATAACAAAGACCACATAAAAGCG 60.183 38.462 0.00 0.00 0.00 4.68
2074 2343 2.164422 GAGGGCTGGCAATAACAAAGAC 59.836 50.000 2.88 0.00 0.00 3.01
2122 2391 8.011106 CCAGTAAAAACAGCATTGCAAAAATAG 58.989 33.333 11.91 0.00 0.00 1.73
2158 2427 4.533919 ACAGATATGAGATACCAGCAGC 57.466 45.455 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.