Multiple sequence alignment - TraesCS4B01G277000

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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 TraesCS4B01G277000 chr4B 100.000 2436 0 0 1 2436 558726217 558723782 0.000000e+00 4499.0
1 TraesCS4B01G277000 chr4D 92.346 1215 61 13 701 1906 446650835 446649644 0.000000e+00 1700.0
2 TraesCS4B01G277000 chr4D 88.707 549 41 10 1907 2436 446649611 446649065 0.000000e+00 651.0
3 TraesCS4B01G277000 chr4D 88.321 548 45 8 1907 2436 446648246 446647700 7.340000e-180 640.0
4 TraesCS4B01G277000 chr4D 86.386 404 48 4 2036 2436 418386573 418386174 3.720000e-118 435.0
5 TraesCS4B01G277000 chr4D 92.657 286 9 5 1 282 446651862 446651585 3.770000e-108 401.0
6 TraesCS4B01G277000 chr4D 96.644 149 3 2 1759 1906 446648427 446648280 1.870000e-61 246.0
7 TraesCS4B01G277000 chr4D 93.750 48 3 0 323 370 446651573 446651526 3.360000e-09 73.1
8 TraesCS4B01G277000 chr4A 89.058 987 75 14 703 1669 21057724 21058697 0.000000e+00 1194.0
9 TraesCS4B01G277000 chr4A 85.854 410 54 4 2030 2436 597322191 597322599 1.340000e-117 433.0
10 TraesCS4B01G277000 chr4A 88.108 185 13 5 101 278 21053639 21053821 6.820000e-51 211.0
11 TraesCS4B01G277000 chr2D 86.683 413 48 4 2030 2435 366056411 366055999 3.690000e-123 451.0
12 TraesCS4B01G277000 chr1D 86.585 410 51 3 2030 2435 366007067 366007476 1.330000e-122 449.0
13 TraesCS4B01G277000 chr1D 93.023 43 2 1 405 446 302385476 302385518 7.270000e-06 62.1
14 TraesCS4B01G277000 chr3B 86.058 416 48 7 2030 2436 251785330 251784916 2.880000e-119 438.0
15 TraesCS4B01G277000 chr7D 85.888 411 54 3 2030 2436 84416396 84415986 3.720000e-118 435.0
16 TraesCS4B01G277000 chr7D 85.749 414 51 6 2030 2436 90038870 90039282 4.810000e-117 431.0
17 TraesCS4B01G277000 chr7D 97.368 38 1 0 401 438 245489304 245489341 5.620000e-07 65.8
18 TraesCS4B01G277000 chr6B 91.071 56 1 2 387 438 652982835 652982780 3.360000e-09 73.1
19 TraesCS4B01G277000 chr2A 93.478 46 1 2 398 442 86984298 86984342 1.560000e-07 67.6
20 TraesCS4B01G277000 chr2A 97.368 38 0 1 405 441 768258257 768258294 2.020000e-06 63.9
21 TraesCS4B01G277000 chr1B 89.286 56 3 3 387 442 389954959 389954907 1.560000e-07 67.6
22 TraesCS4B01G277000 chr7B 100.000 35 0 0 404 438 20063938 20063904 5.620000e-07 65.8
23 TraesCS4B01G277000 chr5B 90.909 44 3 1 402 445 687473405 687473447 9.410000e-05 58.4
24 TraesCS4B01G277000 chr2B 94.595 37 1 1 400 436 26893142 26893107 3.380000e-04 56.5


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 TraesCS4B01G277000 chr4B 558723782 558726217 2435 True 4499.000000 4499 100.000000 1 2436 1 chr4B.!!$R1 2435
1 TraesCS4B01G277000 chr4D 446647700 446651862 4162 True 618.516667 1700 92.070833 1 2436 6 chr4D.!!$R2 2435
2 TraesCS4B01G277000 chr4A 21053639 21058697 5058 False 702.500000 1194 88.583000 101 1669 2 chr4A.!!$F2 1568

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
513 3646 0.037303 AGGCACTCCAGGTTGATGTG 59.963 55.0 0.0 0.0 33.74 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 5811 0.324923 ACTGGTGTACGCATCCCCTA 60.325 55.0 8.97 0.0 0.0 3.53 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
95 97 6.558009 TGCTCATGAGAAAATTGCTTGATAC 58.442 36.000 27.04 3.05 0.00 2.24
96 98 6.376299 TGCTCATGAGAAAATTGCTTGATACT 59.624 34.615 27.04 0.00 0.00 2.12
97 99 6.691818 GCTCATGAGAAAATTGCTTGATACTG 59.308 38.462 27.04 0.00 0.00 2.74
98 100 7.627939 GCTCATGAGAAAATTGCTTGATACTGT 60.628 37.037 27.04 0.00 0.00 3.55
99 101 7.532571 TCATGAGAAAATTGCTTGATACTGTG 58.467 34.615 0.00 0.00 0.00 3.66
239 245 6.998074 TCTTTTTATACACAGGGCATATCTGG 59.002 38.462 0.00 0.00 36.62 3.86
282 291 8.594550 ACTCAGTGTAATTAGAAATGTAGTGGT 58.405 33.333 0.00 0.00 0.00 4.16
309 318 6.811253 AAAAATGTACTGGTTTATCTCGCA 57.189 33.333 0.00 0.00 0.00 5.10
310 319 6.811253 AAAATGTACTGGTTTATCTCGCAA 57.189 33.333 0.00 0.00 0.00 4.85
311 320 6.811253 AAATGTACTGGTTTATCTCGCAAA 57.189 33.333 0.00 0.00 0.00 3.68
312 321 6.422776 AATGTACTGGTTTATCTCGCAAAG 57.577 37.500 0.00 0.00 0.00 2.77
313 322 5.142061 TGTACTGGTTTATCTCGCAAAGA 57.858 39.130 0.00 0.00 38.72 2.52
314 323 5.543714 TGTACTGGTTTATCTCGCAAAGAA 58.456 37.500 0.00 0.00 37.61 2.52
315 324 5.992829 TGTACTGGTTTATCTCGCAAAGAAA 59.007 36.000 0.00 0.00 37.61 2.52
316 325 6.483974 TGTACTGGTTTATCTCGCAAAGAAAA 59.516 34.615 0.00 0.00 37.61 2.29
317 326 6.385649 ACTGGTTTATCTCGCAAAGAAAAA 57.614 33.333 0.00 0.00 37.61 1.94
357 366 0.519999 GCTCGCAATTTGCTCAGTCG 60.520 55.000 18.57 2.91 42.25 4.18
365 374 2.423926 TTTGCTCAGTCGAGACTCAC 57.576 50.000 2.29 0.44 42.34 3.51
370 379 2.608268 CTCAGTCGAGACTCACGAGTA 58.392 52.381 2.29 0.00 42.66 2.59
372 381 2.029200 TCAGTCGAGACTCACGAGTACT 60.029 50.000 2.29 0.00 42.66 2.73
374 383 4.114073 CAGTCGAGACTCACGAGTACTAT 58.886 47.826 2.29 0.00 42.66 2.12
375 384 4.567558 CAGTCGAGACTCACGAGTACTATT 59.432 45.833 2.29 0.00 42.66 1.73
376 385 4.805192 AGTCGAGACTCACGAGTACTATTC 59.195 45.833 4.59 0.00 42.66 1.75
378 387 3.248125 CGAGACTCACGAGTACTATTCCC 59.752 52.174 2.82 0.00 42.66 3.97
379 388 4.453751 GAGACTCACGAGTACTATTCCCT 58.546 47.826 0.00 0.00 42.66 4.20
380 389 4.453751 AGACTCACGAGTACTATTCCCTC 58.546 47.826 0.00 0.00 42.66 4.30
382 391 2.548904 CTCACGAGTACTATTCCCTCCG 59.451 54.545 0.00 0.00 0.00 4.63
383 392 2.092753 TCACGAGTACTATTCCCTCCGT 60.093 50.000 0.00 0.00 0.00 4.69
385 394 2.172293 ACGAGTACTATTCCCTCCGTCT 59.828 50.000 0.00 0.00 0.00 4.18
386 395 2.807392 CGAGTACTATTCCCTCCGTCTC 59.193 54.545 0.00 0.00 0.00 3.36
388 397 4.400120 GAGTACTATTCCCTCCGTCTCAT 58.600 47.826 0.00 0.00 0.00 2.90
389 398 4.805744 AGTACTATTCCCTCCGTCTCATT 58.194 43.478 0.00 0.00 0.00 2.57
390 399 5.950023 AGTACTATTCCCTCCGTCTCATTA 58.050 41.667 0.00 0.00 0.00 1.90
391 400 6.553857 AGTACTATTCCCTCCGTCTCATTAT 58.446 40.000 0.00 0.00 0.00 1.28
392 401 7.696981 AGTACTATTCCCTCCGTCTCATTATA 58.303 38.462 0.00 0.00 0.00 0.98
394 403 9.624373 GTACTATTCCCTCCGTCTCATTATATA 57.376 37.037 0.00 0.00 0.00 0.86
396 405 9.191479 ACTATTCCCTCCGTCTCATTATATAAG 57.809 37.037 1.02 0.00 0.00 1.73
397 406 9.409918 CTATTCCCTCCGTCTCATTATATAAGA 57.590 37.037 1.02 0.00 0.00 2.10
398 407 7.704578 TTCCCTCCGTCTCATTATATAAGAG 57.295 40.000 1.02 8.07 0.00 2.85
399 408 6.791371 TCCCTCCGTCTCATTATATAAGAGT 58.209 40.000 15.55 0.00 0.00 3.24
400 409 6.659668 TCCCTCCGTCTCATTATATAAGAGTG 59.340 42.308 15.55 5.48 0.00 3.51
401 410 6.434652 CCCTCCGTCTCATTATATAAGAGTGT 59.565 42.308 15.55 0.00 0.00 3.55
402 411 7.610692 CCCTCCGTCTCATTATATAAGAGTGTA 59.389 40.741 15.55 2.31 0.00 2.90
403 412 8.670135 CCTCCGTCTCATTATATAAGAGTGTAG 58.330 40.741 15.55 11.26 0.00 2.74
404 413 9.438228 CTCCGTCTCATTATATAAGAGTGTAGA 57.562 37.037 15.55 6.98 0.00 2.59
405 414 9.788889 TCCGTCTCATTATATAAGAGTGTAGAA 57.211 33.333 15.55 1.36 0.00 2.10
443 452 3.170717 TGAAACGGAGGGAGTACTCAAT 58.829 45.455 23.91 11.72 39.27 2.57
453 462 5.953571 AGGGAGTACTCAATTTGAACCTTT 58.046 37.500 23.91 0.00 0.00 3.11
455 464 6.940867 AGGGAGTACTCAATTTGAACCTTTAC 59.059 38.462 23.91 1.06 0.00 2.01
456 465 6.940867 GGGAGTACTCAATTTGAACCTTTACT 59.059 38.462 23.91 3.15 0.00 2.24
457 466 7.094762 GGGAGTACTCAATTTGAACCTTTACTG 60.095 40.741 23.91 0.00 0.00 2.74
509 3642 3.586470 TTTTTAGGCACTCCAGGTTGA 57.414 42.857 0.00 0.00 41.75 3.18
510 3643 3.806949 TTTTAGGCACTCCAGGTTGAT 57.193 42.857 0.00 0.00 41.75 2.57
511 3644 2.787473 TTAGGCACTCCAGGTTGATG 57.213 50.000 0.00 0.00 41.75 3.07
512 3645 1.656587 TAGGCACTCCAGGTTGATGT 58.343 50.000 0.00 0.00 41.75 3.06
513 3646 0.037303 AGGCACTCCAGGTTGATGTG 59.963 55.000 0.00 0.00 33.74 3.21
514 3647 1.878775 GCACTCCAGGTTGATGTGC 59.121 57.895 0.00 0.00 45.23 4.57
515 3648 3.327600 CACTCCAGGTTGATGTGCA 57.672 52.632 0.00 0.00 0.00 4.57
516 3649 1.830279 CACTCCAGGTTGATGTGCAT 58.170 50.000 0.00 0.00 0.00 3.96
517 3650 1.741706 CACTCCAGGTTGATGTGCATC 59.258 52.381 5.30 5.30 38.29 3.91
518 3651 1.632409 ACTCCAGGTTGATGTGCATCT 59.368 47.619 12.64 0.00 38.60 2.90
519 3652 2.286872 CTCCAGGTTGATGTGCATCTC 58.713 52.381 12.64 6.57 38.60 2.75
520 3653 1.065199 TCCAGGTTGATGTGCATCTCC 60.065 52.381 12.64 13.53 38.60 3.71
521 3654 1.012086 CAGGTTGATGTGCATCTCCG 58.988 55.000 12.64 8.22 38.60 4.63
522 3655 0.615331 AGGTTGATGTGCATCTCCGT 59.385 50.000 12.64 3.34 38.60 4.69
523 3656 0.729116 GGTTGATGTGCATCTCCGTG 59.271 55.000 12.64 0.00 38.60 4.94
567 3700 1.093972 TGTGGACAACAGCAACAGTG 58.906 50.000 0.00 0.00 33.78 3.66
578 3711 1.061411 CAACAGTGCGATGCGATGG 59.939 57.895 0.00 0.00 0.00 3.51
580 3713 3.945434 CAGTGCGATGCGATGGGC 61.945 66.667 0.00 0.00 43.96 5.36
600 3760 4.195334 GCGATGGGATGGGCCTGT 62.195 66.667 4.53 0.00 36.66 4.00
604 3764 1.067295 GATGGGATGGGCCTGTATCA 58.933 55.000 4.53 0.00 36.66 2.15
631 4217 0.324614 TCGTTGGTCCATGCATGTCT 59.675 50.000 24.58 0.00 0.00 3.41
640 4226 1.584175 CATGCATGTCTCTCTCCTGC 58.416 55.000 18.91 0.00 0.00 4.85
665 4254 2.819608 CCAAACACGGACCATCAAGATT 59.180 45.455 0.00 0.00 0.00 2.40
674 4263 4.201950 CGGACCATCAAGATTGCCTAAAAG 60.202 45.833 0.00 0.00 0.00 2.27
706 4319 1.470805 CGCACACGGTATCTCATCCAA 60.471 52.381 0.00 0.00 34.97 3.53
707 4320 2.627945 GCACACGGTATCTCATCCAAA 58.372 47.619 0.00 0.00 0.00 3.28
745 4768 3.623960 TGCGTATCCCTGTTTTATTTCGG 59.376 43.478 0.00 0.00 0.00 4.30
772 4795 6.964370 TCTTGATTTCAAATGTTAATACCGCG 59.036 34.615 0.00 0.00 35.15 6.46
786 4809 1.312371 ACCGCGCATTTAATGGTGCT 61.312 50.000 8.75 0.00 39.16 4.40
794 4817 6.565060 CGCGCATTTAATGGTGCTTAAGTATA 60.565 38.462 8.75 0.00 39.16 1.47
796 4819 7.271223 GCGCATTTAATGGTGCTTAAGTATATG 59.729 37.037 0.30 0.56 39.16 1.78
806 4829 5.061064 GTGCTTAAGTATATGAGATTCCGCG 59.939 44.000 0.00 0.00 0.00 6.46
834 4857 3.283751 TGGATTTGTTTATACGGGCTGG 58.716 45.455 0.00 0.00 0.00 4.85
854 4877 2.280797 GCTGACGGACACTTGCCA 60.281 61.111 0.00 0.00 0.00 4.92
856 4879 1.915614 GCTGACGGACACTTGCCATG 61.916 60.000 0.00 0.00 0.00 3.66
859 4882 2.741985 CGGACACTTGCCATGCGA 60.742 61.111 0.00 0.00 0.00 5.10
867 4890 1.721664 CTTGCCATGCGAGGTGGATG 61.722 60.000 5.48 0.00 45.29 3.51
875 4898 2.599597 GAGGTGGATGCCATGCCT 59.400 61.111 0.00 0.00 35.28 4.75
876 4899 1.826921 GAGGTGGATGCCATGCCTG 60.827 63.158 0.80 0.00 35.28 4.85
877 4900 2.274948 GAGGTGGATGCCATGCCTGA 62.275 60.000 0.80 0.00 35.28 3.86
878 4901 1.152610 GGTGGATGCCATGCCTGAT 60.153 57.895 0.00 0.00 35.28 2.90
879 4902 1.461091 GGTGGATGCCATGCCTGATG 61.461 60.000 0.00 0.00 35.28 3.07
880 4903 1.830847 TGGATGCCATGCCTGATGC 60.831 57.895 0.00 0.00 41.77 3.91
881 4904 2.571216 GGATGCCATGCCTGATGCC 61.571 63.158 0.00 0.00 40.16 4.40
882 4905 1.530891 GATGCCATGCCTGATGCCT 60.531 57.895 0.00 0.00 40.16 4.75
883 4906 1.524863 GATGCCATGCCTGATGCCTC 61.525 60.000 0.00 0.00 40.16 4.70
885 4908 2.203451 CCATGCCTGATGCCTCCC 60.203 66.667 0.00 0.00 40.16 4.30
887 4910 1.153061 CATGCCTGATGCCTCCCAT 59.847 57.895 0.00 0.00 40.16 4.00
893 4916 2.031768 GATGCCTCCCATCGAGCC 59.968 66.667 0.00 0.00 40.84 4.70
894 4917 3.873026 GATGCCTCCCATCGAGCCG 62.873 68.421 0.00 0.00 40.84 5.52
897 4920 3.854669 CCTCCCATCGAGCCGCTT 61.855 66.667 0.00 0.00 37.27 4.68
898 4921 2.587194 CTCCCATCGAGCCGCTTG 60.587 66.667 0.56 0.56 0.00 4.01
914 4937 1.003866 GCTTGTTATAAAGCGAGGGCG 60.004 52.381 0.00 0.00 42.86 6.13
954 4987 3.620427 TCTTGTGTGTGTGTTACCAGT 57.380 42.857 0.00 0.00 0.00 4.00
1029 5062 1.137614 CGCTCTCGTGCTGCTTCTA 59.862 57.895 0.00 0.00 0.00 2.10
1200 5245 5.739752 CAGTTGCTGGATCGATCATTTTA 57.260 39.130 25.93 6.24 0.00 1.52
1206 5251 8.345565 GTTGCTGGATCGATCATTTTACTTTAT 58.654 33.333 25.93 0.00 0.00 1.40
1230 5275 5.779529 AATATTCGCTTGATTTGATGGCT 57.220 34.783 0.00 0.00 0.00 4.75
1284 5329 2.153401 TGGTGAAGGTGGAGGTGGG 61.153 63.158 0.00 0.00 0.00 4.61
1393 5438 2.610859 ATCTGCACCTTCCCCGGT 60.611 61.111 0.00 0.00 37.93 5.28
1532 5581 1.895131 AGGGTGATGGAATGTTTGTGC 59.105 47.619 0.00 0.00 0.00 4.57
1581 5630 1.450025 GTGAGCGAGTAAAAAGGGGG 58.550 55.000 0.00 0.00 0.00 5.40
1630 5679 1.209747 GCCGGTAGATTTTGGTCTCCT 59.790 52.381 1.90 0.00 0.00 3.69
1675 5724 3.771160 CGCCGCACCCCTCTAGTT 61.771 66.667 0.00 0.00 0.00 2.24
1695 5744 4.638421 AGTTCACTGGAAACGAACAATTCA 59.362 37.500 0.00 0.00 41.17 2.57
1899 5948 4.963276 TGAACTCATATCCCGCAAAAAG 57.037 40.909 0.00 0.00 0.00 2.27
1947 6027 4.774200 TCATCTCATCCTCTTGAACTGACA 59.226 41.667 0.00 0.00 0.00 3.58
1958 6038 1.816863 GAACTGACACCTGCCGAGGA 61.817 60.000 0.00 0.00 42.93 3.71
1959 6039 2.100879 AACTGACACCTGCCGAGGAC 62.101 60.000 0.00 0.00 42.93 3.85
1960 6040 2.203640 TGACACCTGCCGAGGACT 60.204 61.111 0.00 0.00 42.93 3.85
1961 6041 2.219325 CTGACACCTGCCGAGGACTC 62.219 65.000 0.00 0.00 42.93 3.36
1970 6065 3.369471 CCTGCCGAGGACTCTATTTTTGA 60.369 47.826 0.00 0.00 42.93 2.69
1975 6070 5.048991 GCCGAGGACTCTATTTTTGACAAAA 60.049 40.000 9.30 9.30 36.30 2.44
2022 6117 1.644786 GACTTGTCAAATCCGGCCCG 61.645 60.000 0.00 0.00 0.00 6.13
2024 6119 1.644786 CTTGTCAAATCCGGCCCGTC 61.645 60.000 0.85 0.00 0.00 4.79
2028 6123 2.750237 AAATCCGGCCCGTCAAGC 60.750 61.111 0.85 0.00 0.00 4.01
2043 6138 4.196193 CGTCAAGCCACCCTTCATATTTA 58.804 43.478 0.00 0.00 0.00 1.40
2056 6151 9.965902 ACCCTTCATATTTATCATTCTACATCC 57.034 33.333 0.00 0.00 0.00 3.51
2065 6160 9.950496 ATTTATCATTCTACATCCGCTTATCTT 57.050 29.630 0.00 0.00 0.00 2.40
2075 6170 5.187772 ACATCCGCTTATCTTATATCTGGCA 59.812 40.000 0.00 0.00 0.00 4.92
2109 6204 2.235155 ACTACCCATGCACACGTTGATA 59.765 45.455 0.00 0.00 0.00 2.15
2117 6213 4.130286 TGCACACGTTGATATATCCACA 57.870 40.909 15.19 0.00 0.00 4.17
2135 6231 3.181507 CCACATGATCAAATGACGGACAC 60.182 47.826 0.00 0.00 0.00 3.67
2136 6232 3.436359 CACATGATCAAATGACGGACACA 59.564 43.478 0.00 0.00 0.00 3.72
2175 6271 3.120304 GGAACACAAGATCGGCTACAAAC 60.120 47.826 0.00 0.00 0.00 2.93
2177 6273 2.288579 ACACAAGATCGGCTACAAACGA 60.289 45.455 0.00 0.00 43.85 3.85
2196 6292 7.174253 ACAAACGAACATAACATACTTCACCAT 59.826 33.333 0.00 0.00 0.00 3.55
2199 6295 8.589335 ACGAACATAACATACTTCACCATATC 57.411 34.615 0.00 0.00 0.00 1.63
2208 6304 8.682936 ACATACTTCACCATATCCAAAAGATC 57.317 34.615 0.00 0.00 36.33 2.75
2222 6318 4.032900 CCAAAAGATCATAGTTCGTCCACG 59.967 45.833 0.00 0.00 41.45 4.94
2298 7761 0.246635 CGGAATCACCACTTCCTCGT 59.753 55.000 1.05 0.00 40.07 4.18
2320 7783 2.434331 CCTTTGCCCTTCCGGTCA 59.566 61.111 0.00 0.00 0.00 4.02
2335 7798 2.165301 GTCACCGGCGCAGATGTAC 61.165 63.158 10.83 0.00 0.00 2.90
2336 7799 2.125713 CACCGGCGCAGATGTACA 60.126 61.111 10.83 0.00 0.00 2.90
2369 7832 1.123077 TGGAGGATCTTGGTCATCGG 58.877 55.000 0.00 0.00 33.73 4.18
2371 7834 1.974236 GGAGGATCTTGGTCATCGGAT 59.026 52.381 0.00 0.00 33.73 4.18
2388 7851 0.607489 GATGACCACCTGCAGCTGTT 60.607 55.000 16.64 0.00 0.00 3.16
2390 7853 1.526917 GACCACCTGCAGCTGTTGT 60.527 57.895 16.64 3.74 0.00 3.32
2394 7857 3.730761 CCTGCAGCTGTTGTCGCC 61.731 66.667 16.64 0.00 0.00 5.54
2395 7858 2.974148 CTGCAGCTGTTGTCGCCA 60.974 61.111 16.64 1.46 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 87 2.299013 ACGAGACCACAGTATCAAGCAA 59.701 45.455 0.00 0.00 33.67 3.91
95 97 0.248907 ACACACGAACGAGACCACAG 60.249 55.000 0.14 0.00 0.00 3.66
96 98 0.526739 CACACACGAACGAGACCACA 60.527 55.000 0.14 0.00 0.00 4.17
97 99 0.526954 ACACACACGAACGAGACCAC 60.527 55.000 0.14 0.00 0.00 4.16
98 100 0.526739 CACACACACGAACGAGACCA 60.527 55.000 0.14 0.00 0.00 4.02
99 101 0.526954 ACACACACACGAACGAGACC 60.527 55.000 0.14 0.00 0.00 3.85
215 221 6.207417 CCCAGATATGCCCTGTGTATAAAAAG 59.793 42.308 0.00 0.00 0.00 2.27
226 232 1.701292 TCATGTCCCAGATATGCCCTG 59.299 52.381 0.00 0.00 32.47 4.45
239 245 2.688446 TGAGTACCTCGTCATCATGTCC 59.312 50.000 0.00 0.00 32.35 4.02
286 295 6.811253 TGCGAGATAAACCAGTACATTTTT 57.189 33.333 0.00 0.00 0.00 1.94
287 296 6.811253 TTGCGAGATAAACCAGTACATTTT 57.189 33.333 0.00 0.00 0.00 1.82
288 297 6.653320 TCTTTGCGAGATAAACCAGTACATTT 59.347 34.615 0.00 0.00 0.00 2.32
289 298 6.170506 TCTTTGCGAGATAAACCAGTACATT 58.829 36.000 0.00 0.00 0.00 2.71
290 299 5.730550 TCTTTGCGAGATAAACCAGTACAT 58.269 37.500 0.00 0.00 0.00 2.29
291 300 5.142061 TCTTTGCGAGATAAACCAGTACA 57.858 39.130 0.00 0.00 0.00 2.90
292 301 6.476243 TTTCTTTGCGAGATAAACCAGTAC 57.524 37.500 0.00 0.00 33.49 2.73
316 325 5.301805 AGCTTATTACACTGTGCCAGTTTTT 59.698 36.000 7.90 0.00 42.59 1.94
317 326 4.827284 AGCTTATTACACTGTGCCAGTTTT 59.173 37.500 7.90 0.00 42.59 2.43
318 327 4.398319 AGCTTATTACACTGTGCCAGTTT 58.602 39.130 7.90 2.83 42.59 2.66
319 328 4.003648 GAGCTTATTACACTGTGCCAGTT 58.996 43.478 7.90 0.00 42.59 3.16
320 329 3.600388 GAGCTTATTACACTGTGCCAGT 58.400 45.455 7.90 2.38 46.51 4.00
321 330 2.604914 CGAGCTTATTACACTGTGCCAG 59.395 50.000 7.90 1.16 37.52 4.85
357 366 4.453751 AGGGAATAGTACTCGTGAGTCTC 58.546 47.826 5.66 1.79 42.54 3.36
365 374 2.807392 GAGACGGAGGGAATAGTACTCG 59.193 54.545 0.00 0.00 32.11 4.18
370 379 9.191479 CTTATATAATGAGACGGAGGGAATAGT 57.809 37.037 0.00 0.00 0.00 2.12
372 381 9.409918 CTCTTATATAATGAGACGGAGGGAATA 57.590 37.037 12.80 0.00 0.00 1.75
374 383 7.176865 CACTCTTATATAATGAGACGGAGGGAA 59.823 40.741 19.93 0.00 0.00 3.97
375 384 6.659668 CACTCTTATATAATGAGACGGAGGGA 59.340 42.308 19.93 2.42 0.00 4.20
376 385 6.434652 ACACTCTTATATAATGAGACGGAGGG 59.565 42.308 19.93 13.79 0.00 4.30
378 387 9.438228 TCTACACTCTTATATAATGAGACGGAG 57.562 37.037 19.93 16.63 0.00 4.63
379 388 9.788889 TTCTACACTCTTATATAATGAGACGGA 57.211 33.333 19.93 11.30 0.00 4.69
410 419 9.117183 ACTCCCTCCGTTTCATAATATAAAAAC 57.883 33.333 0.00 0.00 0.00 2.43
412 421 9.768662 GTACTCCCTCCGTTTCATAATATAAAA 57.231 33.333 0.00 0.00 0.00 1.52
413 422 9.151177 AGTACTCCCTCCGTTTCATAATATAAA 57.849 33.333 0.00 0.00 0.00 1.40
414 423 8.716674 AGTACTCCCTCCGTTTCATAATATAA 57.283 34.615 0.00 0.00 0.00 0.98
415 424 7.946219 TGAGTACTCCCTCCGTTTCATAATATA 59.054 37.037 20.11 0.00 0.00 0.86
416 425 6.781014 TGAGTACTCCCTCCGTTTCATAATAT 59.219 38.462 20.11 0.00 0.00 1.28
417 426 6.131264 TGAGTACTCCCTCCGTTTCATAATA 58.869 40.000 20.11 0.00 0.00 0.98
418 427 4.960469 TGAGTACTCCCTCCGTTTCATAAT 59.040 41.667 20.11 0.00 0.00 1.28
419 428 4.346730 TGAGTACTCCCTCCGTTTCATAA 58.653 43.478 20.11 0.00 0.00 1.90
420 429 3.972133 TGAGTACTCCCTCCGTTTCATA 58.028 45.455 20.11 0.00 0.00 2.15
421 430 2.816411 TGAGTACTCCCTCCGTTTCAT 58.184 47.619 20.11 0.00 0.00 2.57
422 431 2.297698 TGAGTACTCCCTCCGTTTCA 57.702 50.000 20.11 0.00 0.00 2.69
423 432 3.889520 ATTGAGTACTCCCTCCGTTTC 57.110 47.619 20.11 0.00 0.00 2.78
424 433 4.041198 TCAAATTGAGTACTCCCTCCGTTT 59.959 41.667 20.11 8.85 0.00 3.60
425 434 3.581332 TCAAATTGAGTACTCCCTCCGTT 59.419 43.478 20.11 3.40 0.00 4.44
426 435 3.170717 TCAAATTGAGTACTCCCTCCGT 58.829 45.455 20.11 0.00 0.00 4.69
427 436 3.887621 TCAAATTGAGTACTCCCTCCG 57.112 47.619 20.11 6.42 0.00 4.63
428 437 4.019231 AGGTTCAAATTGAGTACTCCCTCC 60.019 45.833 20.11 10.53 0.00 4.30
429 438 5.167303 AGGTTCAAATTGAGTACTCCCTC 57.833 43.478 20.11 0.00 0.00 4.30
430 439 5.584551 AAGGTTCAAATTGAGTACTCCCT 57.415 39.130 20.11 12.95 0.00 4.20
431 440 6.940867 AGTAAAGGTTCAAATTGAGTACTCCC 59.059 38.462 20.11 10.92 0.00 4.30
432 441 7.444487 ACAGTAAAGGTTCAAATTGAGTACTCC 59.556 37.037 20.11 1.86 0.00 3.85
433 442 8.379457 ACAGTAAAGGTTCAAATTGAGTACTC 57.621 34.615 16.32 16.32 0.00 2.59
489 3622 3.586470 TCAACCTGGAGTGCCTAAAAA 57.414 42.857 0.00 0.00 34.31 1.94
490 3623 3.181434 ACATCAACCTGGAGTGCCTAAAA 60.181 43.478 0.00 0.00 34.31 1.52
491 3624 2.375174 ACATCAACCTGGAGTGCCTAAA 59.625 45.455 0.00 0.00 34.31 1.85
492 3625 1.985159 ACATCAACCTGGAGTGCCTAA 59.015 47.619 0.00 0.00 34.31 2.69
493 3626 1.278985 CACATCAACCTGGAGTGCCTA 59.721 52.381 0.00 0.00 34.31 3.93
494 3627 0.037303 CACATCAACCTGGAGTGCCT 59.963 55.000 0.00 0.00 34.31 4.75
495 3628 2.559785 CACATCAACCTGGAGTGCC 58.440 57.895 0.00 0.00 0.00 5.01
497 3630 1.741706 GATGCACATCAACCTGGAGTG 59.258 52.381 0.00 0.00 37.74 3.51
498 3631 1.632409 AGATGCACATCAACCTGGAGT 59.368 47.619 12.87 0.00 40.22 3.85
499 3632 2.286872 GAGATGCACATCAACCTGGAG 58.713 52.381 12.87 0.00 40.22 3.86
500 3633 1.065199 GGAGATGCACATCAACCTGGA 60.065 52.381 12.87 0.00 40.22 3.86
501 3634 1.386533 GGAGATGCACATCAACCTGG 58.613 55.000 12.87 0.00 40.22 4.45
502 3635 1.012086 CGGAGATGCACATCAACCTG 58.988 55.000 12.87 8.20 40.22 4.00
503 3636 0.615331 ACGGAGATGCACATCAACCT 59.385 50.000 12.87 4.12 40.22 3.50
504 3637 0.729116 CACGGAGATGCACATCAACC 59.271 55.000 12.87 13.14 40.22 3.77
505 3638 0.729116 CCACGGAGATGCACATCAAC 59.271 55.000 12.87 6.39 40.22 3.18
506 3639 0.324614 ACCACGGAGATGCACATCAA 59.675 50.000 12.87 0.00 40.22 2.57
507 3640 0.391528 CACCACGGAGATGCACATCA 60.392 55.000 12.87 0.00 40.22 3.07
508 3641 1.091771 CCACCACGGAGATGCACATC 61.092 60.000 2.28 2.28 36.56 3.06
509 3642 1.078214 CCACCACGGAGATGCACAT 60.078 57.895 0.00 0.00 36.56 3.21
510 3643 2.050836 AACCACCACGGAGATGCACA 62.051 55.000 0.00 0.00 38.63 4.57
511 3644 1.302511 AACCACCACGGAGATGCAC 60.303 57.895 0.00 0.00 38.63 4.57
512 3645 1.302431 CAACCACCACGGAGATGCA 60.302 57.895 0.00 0.00 38.63 3.96
513 3646 2.040544 CCAACCACCACGGAGATGC 61.041 63.158 0.00 0.00 38.63 3.91
514 3647 1.377202 CCCAACCACCACGGAGATG 60.377 63.158 0.00 0.00 38.63 2.90
515 3648 3.077907 CCCAACCACCACGGAGAT 58.922 61.111 0.00 0.00 38.63 2.75
516 3649 3.948719 GCCCAACCACCACGGAGA 61.949 66.667 0.00 0.00 38.63 3.71
539 3672 1.279840 GTTGTCCACAGCAACTCGC 59.720 57.895 0.00 0.00 41.94 5.03
560 3693 1.061411 CCATCGCATCGCACTGTTG 59.939 57.895 0.00 0.00 0.00 3.33
561 3694 2.108514 CCCATCGCATCGCACTGTT 61.109 57.895 0.00 0.00 0.00 3.16
569 3702 4.916293 TCGCAGGCCCATCGCATC 62.916 66.667 0.00 0.00 40.31 3.91
570 3703 4.260609 ATCGCAGGCCCATCGCAT 62.261 61.111 0.00 0.00 40.31 4.73
574 3707 3.201707 ATCCCATCGCAGGCCCATC 62.202 63.158 0.00 0.00 0.00 3.51
575 3708 3.180799 ATCCCATCGCAGGCCCAT 61.181 61.111 0.00 0.00 0.00 4.00
578 3711 4.962836 CCCATCCCATCGCAGGCC 62.963 72.222 0.00 0.00 0.00 5.19
580 3713 4.962836 GGCCCATCCCATCGCAGG 62.963 72.222 0.00 0.00 0.00 4.85
589 3749 4.074970 CAGTTAATGATACAGGCCCATCC 58.925 47.826 0.00 0.00 0.00 3.51
600 3760 5.408880 TGGACCAACGACAGTTAATGATA 57.591 39.130 0.00 0.00 38.79 2.15
604 3764 2.747446 GCATGGACCAACGACAGTTAAT 59.253 45.455 0.00 0.00 38.79 1.40
631 4217 2.927856 TTTGGCGGGCAGGAGAGA 60.928 61.111 3.91 0.00 0.00 3.10
655 4241 6.587608 GTGTTTCTTTTAGGCAATCTTGATGG 59.412 38.462 0.00 0.00 0.00 3.51
665 4254 2.223618 GGCAACGTGTTTCTTTTAGGCA 60.224 45.455 0.00 0.00 0.00 4.75
706 4319 2.562298 ACGCATCATTTGTTCCCATGTT 59.438 40.909 0.00 0.00 0.00 2.71
707 4320 2.170166 ACGCATCATTTGTTCCCATGT 58.830 42.857 0.00 0.00 0.00 3.21
745 4768 7.044052 GCGGTATTAACATTTGAAATCAAGAGC 60.044 37.037 0.00 0.00 37.15 4.09
772 4795 9.831737 CTCATATACTTAAGCACCATTAAATGC 57.168 33.333 1.29 2.37 42.39 3.56
786 4809 7.599171 TGATTCGCGGAATCTCATATACTTAA 58.401 34.615 22.67 1.27 45.92 1.85
794 4817 2.810274 CCATTGATTCGCGGAATCTCAT 59.190 45.455 22.67 15.54 45.92 2.90
796 4819 2.483876 TCCATTGATTCGCGGAATCTC 58.516 47.619 22.67 6.26 45.92 2.75
806 4829 6.640907 GCCCGTATAAACAAATCCATTGATTC 59.359 38.462 0.00 0.00 40.34 2.52
854 4877 1.527611 CATGGCATCCACCTCGCAT 60.528 57.895 0.00 0.00 35.80 4.73
856 4879 3.589881 GCATGGCATCCACCTCGC 61.590 66.667 0.00 0.00 35.80 5.03
859 4882 1.652187 ATCAGGCATGGCATCCACCT 61.652 55.000 22.64 11.63 35.80 4.00
875 4898 2.824546 GCTCGATGGGAGGCATCA 59.175 61.111 0.00 0.00 43.36 3.07
880 4903 3.854669 AAGCGGCTCGATGGGAGG 61.855 66.667 1.45 0.00 43.36 4.30
881 4904 2.587194 CAAGCGGCTCGATGGGAG 60.587 66.667 1.45 0.00 46.06 4.30
882 4905 1.609635 TAACAAGCGGCTCGATGGGA 61.610 55.000 1.45 0.00 0.00 4.37
883 4906 0.532862 ATAACAAGCGGCTCGATGGG 60.533 55.000 1.45 0.00 0.00 4.00
885 4908 3.604772 GCTTTATAACAAGCGGCTCGATG 60.605 47.826 1.45 0.00 39.92 3.84
887 4910 1.931172 GCTTTATAACAAGCGGCTCGA 59.069 47.619 1.45 0.00 39.92 4.04
894 4917 1.003866 CGCCCTCGCTTTATAACAAGC 60.004 52.381 0.00 0.00 45.01 4.01
895 4918 2.277084 ACGCCCTCGCTTTATAACAAG 58.723 47.619 0.00 0.00 39.84 3.16
896 4919 2.093869 AGACGCCCTCGCTTTATAACAA 60.094 45.455 0.00 0.00 39.84 2.83
897 4920 1.479323 AGACGCCCTCGCTTTATAACA 59.521 47.619 0.00 0.00 39.84 2.41
898 4921 1.859080 CAGACGCCCTCGCTTTATAAC 59.141 52.381 0.00 0.00 39.84 1.89
914 4937 0.389426 ACAATGCCGTACGTCCAGAC 60.389 55.000 15.21 0.00 0.00 3.51
954 4987 0.677288 ATCGACAGTCCGGTTCACAA 59.323 50.000 0.00 0.00 0.00 3.33
1206 5251 7.275888 AGCCATCAAATCAAGCGAATATTAA 57.724 32.000 0.00 0.00 0.00 1.40
1216 5261 7.988737 TGAACACTAATAGCCATCAAATCAAG 58.011 34.615 0.00 0.00 0.00 3.02
1230 5275 5.393787 CCAGGCTCGTACTTGAACACTAATA 60.394 44.000 0.00 0.00 0.00 0.98
1284 5329 1.369091 CTTGCACTCCATGTACCCGC 61.369 60.000 0.00 0.00 0.00 6.13
1342 5387 2.792947 GCCGGGCATCTCGAAGGTA 61.793 63.158 15.62 0.00 0.00 3.08
1393 5438 1.078918 CATGCCCTTCTCGCAGTGA 60.079 57.895 0.00 0.00 40.15 3.41
1426 5471 3.574396 TCAGTCAATTCCGCTATCTAGGG 59.426 47.826 0.00 0.00 36.17 3.53
1436 5481 7.011773 CGCTATTTATCAATCAGTCAATTCCG 58.988 38.462 0.00 0.00 0.00 4.30
1437 5482 6.798959 GCGCTATTTATCAATCAGTCAATTCC 59.201 38.462 0.00 0.00 0.00 3.01
1439 5484 6.202762 TCGCGCTATTTATCAATCAGTCAATT 59.797 34.615 5.56 0.00 0.00 2.32
1532 5581 1.157870 AAGAACAACCAGGACGTGCG 61.158 55.000 0.00 0.00 0.00 5.34
1581 5630 2.032178 GGCGCAAAATCTAGTGTCATCC 59.968 50.000 10.83 0.00 0.00 3.51
1582 5631 2.677836 TGGCGCAAAATCTAGTGTCATC 59.322 45.455 10.83 0.00 0.00 2.92
1583 5632 2.710377 TGGCGCAAAATCTAGTGTCAT 58.290 42.857 10.83 0.00 0.00 3.06
1584 5633 2.177394 TGGCGCAAAATCTAGTGTCA 57.823 45.000 10.83 0.00 0.00 3.58
1586 5635 2.017049 GGATGGCGCAAAATCTAGTGT 58.983 47.619 10.83 0.00 0.00 3.55
1587 5636 1.334869 GGGATGGCGCAAAATCTAGTG 59.665 52.381 10.83 0.00 0.00 2.74
1630 5679 2.616256 GGTGGAATCAGCAGACATGACA 60.616 50.000 0.00 0.00 40.79 3.58
1673 5722 4.915704 TGAATTGTTCGTTTCCAGTGAAC 58.084 39.130 0.00 0.00 41.75 3.18
1675 5724 4.497340 GCTTGAATTGTTCGTTTCCAGTGA 60.497 41.667 0.00 0.00 0.00 3.41
1695 5744 2.084546 GCTGGATTGTTAGGAACGCTT 58.915 47.619 0.00 0.00 0.00 4.68
1762 5811 0.324923 ACTGGTGTACGCATCCCCTA 60.325 55.000 8.97 0.00 0.00 3.53
1905 5954 6.083383 AGATGAGGTCACTTCCAGATATGAT 58.917 40.000 0.00 0.00 0.00 2.45
1947 6027 1.867363 AAATAGAGTCCTCGGCAGGT 58.133 50.000 3.45 0.00 41.28 4.00
1997 6092 2.354704 CCGGATTTGACAAGTCCAGCTA 60.355 50.000 24.57 0.00 32.23 3.32
2001 6096 0.608035 GGCCGGATTTGACAAGTCCA 60.608 55.000 24.57 0.00 32.23 4.02
2003 6098 1.644786 CGGGCCGGATTTGACAAGTC 61.645 60.000 20.56 2.19 0.00 3.01
2022 6117 5.827797 TGATAAATATGAAGGGTGGCTTGAC 59.172 40.000 0.00 0.00 0.00 3.18
2024 6119 6.906157 ATGATAAATATGAAGGGTGGCTTG 57.094 37.500 0.00 0.00 0.00 4.01
2028 6123 9.745018 ATGTAGAATGATAAATATGAAGGGTGG 57.255 33.333 0.00 0.00 0.00 4.61
2034 6129 9.725019 AAGCGGATGTAGAATGATAAATATGAA 57.275 29.630 0.00 0.00 0.00 2.57
2056 6151 5.078411 AGGTGCCAGATATAAGATAAGCG 57.922 43.478 0.00 0.00 0.00 4.68
2071 6166 4.842380 GGGTAGTAAGGATATAAGGTGCCA 59.158 45.833 0.00 0.00 0.00 4.92
2075 6170 6.013639 GTGCATGGGTAGTAAGGATATAAGGT 60.014 42.308 0.00 0.00 0.00 3.50
2085 6180 2.380084 ACGTGTGCATGGGTAGTAAG 57.620 50.000 0.00 0.00 0.00 2.34
2086 6181 2.037381 TCAACGTGTGCATGGGTAGTAA 59.963 45.455 0.00 0.00 0.00 2.24
2109 6204 5.702670 GTCCGTCATTTGATCATGTGGATAT 59.297 40.000 12.79 0.00 36.00 1.63
2117 6213 5.703978 TTTTGTGTCCGTCATTTGATCAT 57.296 34.783 0.00 0.00 0.00 2.45
2135 6231 4.571580 TGTTCCTTTGCAGCTCAATTTTTG 59.428 37.500 0.00 0.00 34.12 2.44
2136 6232 4.571984 GTGTTCCTTTGCAGCTCAATTTTT 59.428 37.500 0.00 0.00 34.12 1.94
2175 6271 7.655732 TGGATATGGTGAAGTATGTTATGTTCG 59.344 37.037 0.00 0.00 0.00 3.95
2177 6273 9.693739 TTTGGATATGGTGAAGTATGTTATGTT 57.306 29.630 0.00 0.00 0.00 2.71
2196 6292 6.984474 GTGGACGAACTATGATCTTTTGGATA 59.016 38.462 0.00 0.00 34.33 2.59
2199 6295 4.032900 CGTGGACGAACTATGATCTTTTGG 59.967 45.833 0.00 0.00 43.02 3.28
2277 6375 3.905249 GGAAGTGGTGATTCCGGC 58.095 61.111 0.00 0.00 37.10 6.13
2320 7783 2.125673 GTGTACATCTGCGCCGGT 60.126 61.111 4.18 0.00 0.00 5.28
2345 7808 1.280457 GACCAAGATCCTCCACCAGT 58.720 55.000 0.00 0.00 0.00 4.00
2369 7832 0.607489 AACAGCTGCAGGTGGTCATC 60.607 55.000 40.06 12.67 46.90 2.92
2371 7834 1.526686 CAACAGCTGCAGGTGGTCA 60.527 57.895 40.06 0.00 42.19 4.02
2377 7840 3.730761 GGCGACAACAGCTGCAGG 61.731 66.667 17.12 5.93 34.52 4.85
2390 7853 1.377366 GACTCCGACTCAGATGGCGA 61.377 60.000 0.00 0.00 0.00 5.54
2394 7857 1.313772 ATCCGACTCCGACTCAGATG 58.686 55.000 0.00 0.00 38.22 2.90
2395 7858 2.551287 CCTATCCGACTCCGACTCAGAT 60.551 54.545 0.00 0.00 38.22 2.90


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

AutoCloner maintained by Alex Coulton.