Multiple sequence alignment - TraesCS6A01G302500

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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 TraesCS6A01G302500 chr6A 100.000 3595 0 0 1 3595 535992654 535989060 0.000000e+00 6639.0
1 TraesCS6A01G302500 chr6D 92.961 1520 65 26 826 2327 389598667 389597172 0.000000e+00 2176.0
2 TraesCS6A01G302500 chr6D 81.344 863 131 24 1 845 389600163 389599313 0.000000e+00 675.0
3 TraesCS6A01G302500 chr6D 89.567 393 25 8 2369 2758 389597174 389596795 5.400000e-133 484.0
4 TraesCS6A01G302500 chr6D 84.272 426 60 5 1 423 438516737 438516316 3.340000e-110 409.0
5 TraesCS6A01G302500 chr6D 89.726 292 29 1 2892 3182 389596661 389596370 4.380000e-99 372.0
6 TraesCS6A01G302500 chr6D 93.168 161 11 0 3241 3401 389596128 389595968 1.670000e-58 237.0
7 TraesCS6A01G302500 chr6B 89.556 1149 58 30 896 2017 583052477 583051364 0.000000e+00 1400.0
8 TraesCS6A01G302500 chr6B 91.789 341 20 5 2022 2354 583051202 583050862 5.430000e-128 468.0
9 TraesCS6A01G302500 chr6B 84.582 467 69 2 1 464 583053254 583052788 9.090000e-126 460.0
10 TraesCS6A01G302500 chr6B 88.796 357 37 2 3241 3595 583048821 583048466 5.510000e-118 435.0
11 TraesCS6A01G302500 chr6B 85.075 268 24 7 2474 2735 583050773 583050516 3.560000e-65 259.0
12 TraesCS6A01G302500 chr4D 83.333 444 70 3 1 441 408590705 408590263 1.200000e-109 407.0
13 TraesCS6A01G302500 chr4A 82.353 442 71 6 1 440 80160667 80160231 9.420000e-101 377.0
14 TraesCS6A01G302500 chr5D 82.009 428 70 6 6 429 34223620 34223196 1.230000e-94 357.0
15 TraesCS6A01G302500 chr7B 81.364 440 75 7 10 444 104256371 104255934 5.710000e-93 351.0
16 TraesCS6A01G302500 chr3B 81.647 425 71 4 1 423 229004549 229004130 2.660000e-91 346.0
17 TraesCS6A01G302500 chr3D 80.846 449 75 8 6 447 12219659 12219215 3.440000e-90 342.0
18 TraesCS6A01G302500 chr3D 82.857 70 10 2 796 864 555758655 555758723 1.080000e-05 62.1
19 TraesCS6A01G302500 chr1D 80.000 205 25 9 673 864 458672956 458673157 1.740000e-28 137.0
20 TraesCS6A01G302500 chr1B 78.000 200 30 10 673 864 629972045 629972238 2.930000e-21 113.0
21 TraesCS6A01G302500 chr2A 88.235 51 6 0 799 849 50428030 50427980 1.080000e-05 62.1
22 TraesCS6A01G302500 chr2A 100.000 29 0 0 2963 2991 32454110 32454082 2.000000e-03 54.7


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 TraesCS6A01G302500 chr6A 535989060 535992654 3594 True 6639.0 6639 100.0000 1 3595 1 chr6A.!!$R1 3594
1 TraesCS6A01G302500 chr6D 389595968 389600163 4195 True 788.8 2176 89.3532 1 3401 5 chr6D.!!$R2 3400
2 TraesCS6A01G302500 chr6B 583048466 583053254 4788 True 604.4 1400 87.9596 1 3595 5 chr6B.!!$R1 3594

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
76 77 0.026674 CGCTGCAATGATGTACCACG 59.973 55.0 0.0 0.0 0.00 4.94 F
1677 2388 0.038021 TTATTGCAGACAGGCAGGCA 59.962 50.0 0.0 0.0 45.88 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 2510 0.596577 GCAGTCTGACAGTACCGACA 59.403 55.0 10.88 0.0 0.00 4.35 R
2723 3627 0.031616 ACAAGGGCCCCTGACAAAAA 60.032 50.0 27.82 0.0 32.13 1.94 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
38 39 4.627035 TCATTCACTCAATGTTGCTCTACG 59.373 41.667 0.00 0.00 42.47 3.51
41 42 8.985839 CATTCACTCAATGTTGCTCTACGCAC 62.986 46.154 0.00 0.00 39.93 5.34
57 58 2.030562 ACTGTGCAGCCCGTACAC 59.969 61.111 0.00 0.00 35.03 2.90
64 65 4.308458 AGCCCGTACACGCTGCAA 62.308 61.111 14.19 0.00 37.82 4.08
76 77 0.026674 CGCTGCAATGATGTACCACG 59.973 55.000 0.00 0.00 0.00 4.94
90 91 2.280552 CCACGGGAAAGAGGGACGA 61.281 63.158 0.00 0.00 0.00 4.20
94 95 1.597461 GGGAAAGAGGGACGACCAG 59.403 63.158 6.20 0.00 43.89 4.00
119 120 5.957771 AGGTACATACACTGTTGGATGAT 57.042 39.130 3.81 0.00 46.09 2.45
143 146 1.910580 AAGGGGCAGTATGTGGGACG 61.911 60.000 0.00 0.00 39.31 4.79
171 175 6.205784 TGATCCGTTCATGAAAAACTTGTTC 58.794 36.000 10.35 0.89 0.00 3.18
180 184 5.568685 TGAAAAACTTGTTCAACATCCGA 57.431 34.783 0.00 0.00 32.13 4.55
268 272 6.194796 TGTGCTATTTTCTATCCAAACTGC 57.805 37.500 0.00 0.00 0.00 4.40
283 287 4.437255 CCAAACTGCGATGAATTTCGATCA 60.437 41.667 3.75 0.00 41.62 2.92
302 306 4.159377 TCAGTTTGCATGAATTTCGTCC 57.841 40.909 0.00 0.00 0.00 4.79
304 308 2.811431 AGTTTGCATGAATTTCGTCCGA 59.189 40.909 0.00 0.00 0.00 4.55
311 315 5.198274 GCATGAATTTCGTCCGATTAGTTC 58.802 41.667 0.00 0.00 0.00 3.01
317 321 3.947910 TCGTCCGATTAGTTCAAAGGT 57.052 42.857 0.00 0.00 0.00 3.50
318 322 3.581755 TCGTCCGATTAGTTCAAAGGTG 58.418 45.455 0.00 0.00 0.00 4.00
335 339 6.783708 AAAGGTGGTTTGAACTGTATTTGA 57.216 33.333 0.00 0.00 0.00 2.69
336 340 6.391227 AAGGTGGTTTGAACTGTATTTGAG 57.609 37.500 0.00 0.00 0.00 3.02
340 344 6.485648 GGTGGTTTGAACTGTATTTGAGTAGT 59.514 38.462 0.00 0.00 0.00 2.73
341 345 7.658575 GGTGGTTTGAACTGTATTTGAGTAGTA 59.341 37.037 0.00 0.00 0.00 1.82
380 384 2.694829 ATTCGTATCCGCGGACTGGC 62.695 60.000 33.75 19.00 0.00 4.85
390 395 2.895424 CGGACTGGCCCCTTTGTCT 61.895 63.158 0.00 0.00 0.00 3.41
395 400 2.283173 GGCCCCTTTGTCTGTGGG 60.283 66.667 0.00 0.00 41.23 4.61
396 401 2.520968 GCCCCTTTGTCTGTGGGT 59.479 61.111 0.00 0.00 40.36 4.51
431 436 1.403814 TTTGCGGGTCAATGTTGGAA 58.596 45.000 0.00 0.00 34.12 3.53
468 473 6.201044 GGGTAGTTCACTCGATATTTGATGTG 59.799 42.308 0.00 0.00 0.00 3.21
471 476 7.672983 AGTTCACTCGATATTTGATGTGTTT 57.327 32.000 0.00 0.00 0.00 2.83
474 479 7.848223 TCACTCGATATTTGATGTGTTTCAT 57.152 32.000 0.00 0.00 39.77 2.57
494 499 1.134220 TGACACGGAGCTTTTGAACCT 60.134 47.619 0.00 0.00 0.00 3.50
497 502 1.532868 CACGGAGCTTTTGAACCTGAG 59.467 52.381 0.00 0.00 0.00 3.35
498 503 0.519077 CGGAGCTTTTGAACCTGAGC 59.481 55.000 0.00 0.00 35.42 4.26
505 510 5.994250 AGCTTTTGAACCTGAGCTCATATA 58.006 37.500 18.63 0.00 41.34 0.86
508 513 6.018343 GCTTTTGAACCTGAGCTCATATACTC 60.018 42.308 18.63 10.20 32.54 2.59
511 516 5.700183 TGAACCTGAGCTCATATACTCTCT 58.300 41.667 18.63 0.00 33.92 3.10
518 523 7.123098 CCTGAGCTCATATACTCTCTGATGAAT 59.877 40.741 18.63 0.00 33.92 2.57
522 527 8.959548 AGCTCATATACTCTCTGATGAATAGTG 58.040 37.037 0.00 0.00 0.00 2.74
601 606 3.082698 TGTCTCAACTGCATGCAAAAC 57.917 42.857 22.88 13.08 0.00 2.43
605 610 4.026310 GTCTCAACTGCATGCAAAACTTTG 60.026 41.667 22.88 17.77 41.03 2.77
606 611 3.859443 TCAACTGCATGCAAAACTTTGT 58.141 36.364 22.88 11.26 40.24 2.83
623 628 6.653526 ACTTTGTGATGAAATGACATCCAA 57.346 33.333 0.00 0.00 40.97 3.53
625 630 5.648178 TTGTGATGAAATGACATCCAAGG 57.352 39.130 0.00 0.00 40.97 3.61
650 655 4.754114 GGTTTGTGCCAATAAGCAAAATCA 59.246 37.500 0.00 0.00 46.19 2.57
658 663 6.709397 TGCCAATAAGCAAAATCAATGTTTCA 59.291 30.769 0.00 0.00 40.56 2.69
694 699 4.445052 TGTTGAAAGCATTTTGAAGCATCG 59.555 37.500 0.00 0.00 39.27 3.84
696 701 4.869215 TGAAAGCATTTTGAAGCATCGAA 58.131 34.783 0.00 0.00 39.27 3.71
700 705 5.773239 AGCATTTTGAAGCATCGAATTTG 57.227 34.783 0.00 0.00 0.00 2.32
723 728 4.280929 GGTTTTTGTTGCCTAGACTTCCAT 59.719 41.667 0.00 0.00 0.00 3.41
724 729 5.222631 GTTTTTGTTGCCTAGACTTCCATG 58.777 41.667 0.00 0.00 0.00 3.66
730 735 4.574674 TGCCTAGACTTCCATGAATGTT 57.425 40.909 0.00 0.00 0.00 2.71
788 795 9.013490 GGATTCATCGATGTTTATCACAAAAAG 57.987 33.333 24.09 0.00 39.50 2.27
789 796 8.915871 ATTCATCGATGTTTATCACAAAAAGG 57.084 30.769 24.09 0.00 39.50 3.11
795 802 8.191446 TCGATGTTTATCACAAAAAGGTCAAAA 58.809 29.630 0.00 0.00 39.50 2.44
841 856 4.460382 ACTGTTTATCAAAGAGCATGTGGG 59.540 41.667 0.00 0.00 35.34 4.61
862 1519 2.704572 CTCGGGATCAAAGAGCACTTT 58.295 47.619 3.03 3.03 45.75 2.66
863 1520 2.675348 CTCGGGATCAAAGAGCACTTTC 59.325 50.000 6.13 0.00 43.41 2.62
923 1599 8.678199 AGAACTCTGTTCTGGTAAAAGAAAAAG 58.322 33.333 11.56 0.00 37.90 2.27
1022 1698 1.970114 CTTGCAGCCACAGTCTGGG 60.970 63.158 4.53 0.00 41.02 4.45
1502 2212 4.660105 TCAAGTTTTAACCCGTCGTTTTG 58.340 39.130 0.00 0.00 35.79 2.44
1503 2213 4.155644 TCAAGTTTTAACCCGTCGTTTTGT 59.844 37.500 0.00 0.00 35.79 2.83
1504 2214 4.277257 AGTTTTAACCCGTCGTTTTGTC 57.723 40.909 0.00 0.00 35.79 3.18
1624 2335 1.682005 GGCAAGGTGGGCAGCATTA 60.682 57.895 0.00 0.00 0.00 1.90
1677 2388 0.038021 TTATTGCAGACAGGCAGGCA 59.962 50.000 0.00 0.00 45.88 4.75
1681 2392 3.067091 CAGACAGGCAGGCAGAGT 58.933 61.111 0.00 0.00 0.00 3.24
1684 2395 0.475906 AGACAGGCAGGCAGAGTTTT 59.524 50.000 0.00 0.00 0.00 2.43
1685 2396 0.877743 GACAGGCAGGCAGAGTTTTC 59.122 55.000 0.00 0.00 0.00 2.29
1686 2397 0.475906 ACAGGCAGGCAGAGTTTTCT 59.524 50.000 0.00 0.00 0.00 2.52
1687 2398 1.163554 CAGGCAGGCAGAGTTTTCTC 58.836 55.000 0.00 0.00 46.50 2.87
1736 2448 8.191446 GCTTAAACCCTTCTATTTTCTTCCATC 58.809 37.037 0.00 0.00 0.00 3.51
1816 2528 2.922758 GCTTGTCGGTACTGTCAGACTG 60.923 54.545 6.91 5.91 34.58 3.51
1869 2581 4.441087 GCATTTCGTTCCAAACAAACTCTC 59.559 41.667 0.00 0.00 0.00 3.20
1877 2589 5.576447 TCCAAACAAACTCTCACCTTTTC 57.424 39.130 0.00 0.00 0.00 2.29
1894 2609 4.453819 CCTTTTCCTGAACTGTGATGTCTC 59.546 45.833 0.00 0.00 0.00 3.36
1987 2706 2.226674 GCTGCTTCTCAGGTACCAAAAC 59.773 50.000 15.94 0.00 43.06 2.43
2001 2721 6.038603 AGGTACCAAAACGAAAACCTAGTTTC 59.961 38.462 15.94 0.00 37.13 2.78
2013 2733 5.584551 AACCTAGTTTCCAGTTGAGGAAT 57.415 39.130 0.00 0.00 46.45 3.01
2014 2734 4.911390 ACCTAGTTTCCAGTTGAGGAATG 58.089 43.478 0.00 0.00 46.45 2.67
2015 2735 4.351111 ACCTAGTTTCCAGTTGAGGAATGT 59.649 41.667 0.00 0.00 46.45 2.71
2016 2736 5.546499 ACCTAGTTTCCAGTTGAGGAATGTA 59.454 40.000 0.00 0.00 46.45 2.29
2017 2737 6.215636 ACCTAGTTTCCAGTTGAGGAATGTAT 59.784 38.462 0.00 0.00 46.45 2.29
2018 2738 6.540189 CCTAGTTTCCAGTTGAGGAATGTATG 59.460 42.308 0.00 0.00 46.45 2.39
2019 2739 6.126863 AGTTTCCAGTTGAGGAATGTATGA 57.873 37.500 0.00 0.00 46.45 2.15
2020 2740 6.542821 AGTTTCCAGTTGAGGAATGTATGAA 58.457 36.000 0.00 0.00 46.45 2.57
2126 3006 2.297880 GCCCATGCATGCATATTCAGAA 59.702 45.455 31.73 1.39 37.47 3.02
2272 3160 3.492829 GCATAGGTCCAGTACAAGGTAGC 60.493 52.174 0.00 0.00 0.00 3.58
2277 3165 2.500098 GTCCAGTACAAGGTAGCATCCA 59.500 50.000 0.00 0.00 0.00 3.41
2278 3166 3.055385 GTCCAGTACAAGGTAGCATCCAA 60.055 47.826 0.00 0.00 0.00 3.53
2279 3167 3.197766 TCCAGTACAAGGTAGCATCCAAG 59.802 47.826 0.00 0.00 0.00 3.61
2280 3168 2.939103 CAGTACAAGGTAGCATCCAAGC 59.061 50.000 0.00 0.00 0.00 4.01
2281 3169 2.092914 AGTACAAGGTAGCATCCAAGCC 60.093 50.000 0.00 0.00 34.23 4.35
2285 3173 0.548510 AGGTAGCATCCAAGCCCTTC 59.451 55.000 0.00 0.00 34.23 3.46
2286 3174 0.255890 GGTAGCATCCAAGCCCTTCA 59.744 55.000 0.00 0.00 34.23 3.02
2287 3175 1.133668 GGTAGCATCCAAGCCCTTCAT 60.134 52.381 0.00 0.00 34.23 2.57
2288 3176 2.106511 GGTAGCATCCAAGCCCTTCATA 59.893 50.000 0.00 0.00 34.23 2.15
2289 3177 3.435026 GGTAGCATCCAAGCCCTTCATAA 60.435 47.826 0.00 0.00 34.23 1.90
2291 3179 3.026694 AGCATCCAAGCCCTTCATAAAC 58.973 45.455 0.00 0.00 34.23 2.01
2295 3185 5.569428 GCATCCAAGCCCTTCATAAACTTTT 60.569 40.000 0.00 0.00 0.00 2.27
2354 3244 3.430779 GCTCTGGCAGCCATTTTTC 57.569 52.632 16.64 0.00 43.17 2.29
2355 3245 0.604578 GCTCTGGCAGCCATTTTTCA 59.395 50.000 16.64 0.00 43.17 2.69
2356 3246 1.001181 GCTCTGGCAGCCATTTTTCAA 59.999 47.619 16.64 0.00 43.17 2.69
2363 3253 2.741612 CAGCCATTTTTCAAAGCACGA 58.258 42.857 0.00 0.00 0.00 4.35
2368 3265 2.079941 TTTTTCAAAGCACGACGTCG 57.920 45.000 34.58 34.58 46.33 5.12
2406 3303 3.311110 AGGCGGGCAGACGAAGAA 61.311 61.111 3.78 0.00 35.47 2.52
2415 3312 4.153475 CGGGCAGACGAAGAAAAAGATTTA 59.847 41.667 0.00 0.00 35.47 1.40
2416 3313 5.163754 CGGGCAGACGAAGAAAAAGATTTAT 60.164 40.000 0.00 0.00 35.47 1.40
2442 3340 1.402968 CTTCATTCATTCAGGTGGCGG 59.597 52.381 0.00 0.00 0.00 6.13
2449 3347 1.910580 ATTCAGGTGGCGGAATCGGT 61.911 55.000 0.00 0.00 36.79 4.69
2460 3358 2.125106 AATCGGTTGCTCTCCGGC 60.125 61.111 0.00 0.00 46.82 6.13
2512 3410 7.195646 GCAAGCAATCTGTACAAATAGCATTA 58.804 34.615 0.00 0.00 0.00 1.90
2552 3450 2.092838 GCATGTAAAGCGTCACTCTGTC 59.907 50.000 0.00 0.00 0.00 3.51
2589 3491 6.030548 AGTCGTGTTATATATGCTGCTGAT 57.969 37.500 0.00 0.00 0.00 2.90
2591 3493 6.587990 AGTCGTGTTATATATGCTGCTGATTC 59.412 38.462 0.00 0.00 0.00 2.52
2688 3592 2.092838 GCTCAGCTCACGTTTATGACAC 59.907 50.000 0.00 0.00 0.00 3.67
2723 3627 3.256631 GCACCCTCTTGTTGATCACATTT 59.743 43.478 0.00 0.00 34.43 2.32
2748 3652 2.100197 GTCAGGGGCCCTTGTTATTTC 58.900 52.381 31.34 13.25 0.00 2.17
2770 3687 2.815478 CTTACAGCGTCAGGGATTCTC 58.185 52.381 0.00 0.00 0.00 2.87
2778 3695 2.464865 GTCAGGGATTCTCGTTGATCG 58.535 52.381 0.00 0.00 41.41 3.69
2785 3702 1.614227 TTCTCGTTGATCGCACGTGC 61.614 55.000 30.42 30.42 39.67 5.34
2806 3723 2.361438 CGGTAGCCTGGAGTTTAGTAGG 59.639 54.545 0.00 0.00 0.00 3.18
2823 3740 4.371681 AGTAGGCTTTTATCCCTCCAAGA 58.628 43.478 0.00 0.00 32.65 3.02
2825 3742 4.888626 AGGCTTTTATCCCTCCAAGAAT 57.111 40.909 0.00 0.00 0.00 2.40
2826 3743 5.212472 AGGCTTTTATCCCTCCAAGAATT 57.788 39.130 0.00 0.00 0.00 2.17
2850 3767 2.287069 CCGTACCTGAGAACTAGATGCG 60.287 54.545 0.00 0.00 0.00 4.73
2861 3778 2.732366 ACTAGATGCGCAGTTATGACG 58.268 47.619 18.32 1.61 0.00 4.35
2862 3779 2.054363 CTAGATGCGCAGTTATGACGG 58.946 52.381 18.32 0.00 0.00 4.79
2863 3780 1.154205 AGATGCGCAGTTATGACGGC 61.154 55.000 18.32 2.59 42.55 5.68
2906 3857 0.762418 ACCAGACATGTTCGGGACAA 59.238 50.000 16.39 0.00 42.00 3.18
2913 3864 0.536460 ATGTTCGGGACAAAAGCCGT 60.536 50.000 0.00 0.00 42.62 5.68
2933 3885 0.995024 CTGTCCCCCTTTGTCCATCT 59.005 55.000 0.00 0.00 0.00 2.90
2943 3895 2.885135 TTGTCCATCTGAGCAACCAT 57.115 45.000 0.00 0.00 0.00 3.55
2960 3912 1.619654 CATGCCCCTCACACTGAAAA 58.380 50.000 0.00 0.00 0.00 2.29
2961 3913 1.270550 CATGCCCCTCACACTGAAAAC 59.729 52.381 0.00 0.00 0.00 2.43
2978 3930 8.090214 CACTGAAAACCTCAAATCCATACAAAT 58.910 33.333 0.00 0.00 32.17 2.32
3091 4979 4.616802 GCTACACAAATGAATGAAACACCG 59.383 41.667 0.00 0.00 0.00 4.94
3108 4996 1.247567 CCGTTGGTTTGCTCCTTGAT 58.752 50.000 0.00 0.00 0.00 2.57
3109 4997 2.224670 ACCGTTGGTTTGCTCCTTGATA 60.225 45.455 0.00 0.00 27.29 2.15
3165 5054 2.500098 TGTTATCCACGAGCCTAGCTTT 59.500 45.455 0.00 0.00 39.88 3.51
3183 5072 0.174845 TTGGCTAACACGATCCTCGG 59.825 55.000 1.29 0.00 45.59 4.63
3190 5079 3.532155 ACGATCCTCGGCTCCTGC 61.532 66.667 1.29 0.00 45.59 4.85
3226 5225 4.346418 AGCCTCACTTTCTCTTTCTCAAGA 59.654 41.667 0.00 0.00 36.62 3.02
3239 5467 7.601886 TCTCTTTCTCAAGATCAATTGTCTCAC 59.398 37.037 5.13 0.00 38.42 3.51
3261 5489 2.965671 ATAGGATCCATGCTTGTGGG 57.034 50.000 15.82 0.00 39.80 4.61
3262 5490 0.846015 TAGGATCCATGCTTGTGGGG 59.154 55.000 15.82 0.00 39.80 4.96
3269 5497 2.112998 CCATGCTTGTGGGGAATGAAT 58.887 47.619 0.00 0.00 35.55 2.57
3409 5639 2.604046 AATTCGGAGGATCTTGACCG 57.396 50.000 0.00 0.00 45.61 4.79
3430 5660 7.048629 ACCGTCATCTATCATATCCATCATC 57.951 40.000 0.00 0.00 0.00 2.92
3456 5686 5.941733 TGAGTCATAAACATGCATCACAAC 58.058 37.500 0.00 0.00 0.00 3.32
3482 5712 7.431084 CGAAATTACCATCTTAAAATTGGTCCG 59.569 37.037 6.85 3.02 42.65 4.79
3498 5728 3.419759 CGCGCCCGCTAAAGTTGT 61.420 61.111 11.12 0.00 39.32 3.32
3500 5730 2.867472 CGCCCGCTAAAGTTGTGG 59.133 61.111 0.00 0.00 35.05 4.17
3554 5784 2.027285 TCTCCAACATGAAGGCATTCGA 60.027 45.455 6.62 0.00 38.34 3.71
3556 5786 2.027285 TCCAACATGAAGGCATTCGAGA 60.027 45.455 6.62 0.00 38.34 4.04
3559 5789 3.272574 ACATGAAGGCATTCGAGATGT 57.727 42.857 6.62 8.04 38.34 3.06
3578 5808 2.179018 CGACCATTGCAAAGCCGG 59.821 61.111 1.71 0.00 0.00 6.13
3580 5810 1.508088 GACCATTGCAAAGCCGGAG 59.492 57.895 5.05 0.00 0.00 4.63
3583 5813 1.153901 CATTGCAAAGCCGGAGCAG 60.154 57.895 5.05 0.00 43.56 4.24
3585 5815 4.953010 TGCAAAGCCGGAGCAGCA 62.953 61.111 5.05 6.83 43.56 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.183360 CGTAGAGCAACATTGAGTGAATGAAT 60.183 38.462 9.45 0.00 43.87 2.57
38 39 3.423154 GTACGGGCTGCACAGTGC 61.423 66.667 19.37 19.37 45.29 4.40
41 42 3.112075 CGTGTACGGGCTGCACAG 61.112 66.667 1.50 0.00 35.28 3.66
57 58 0.026674 CGTGGTACATCATTGCAGCG 59.973 55.000 0.00 0.00 44.52 5.18
59 60 1.016627 CCCGTGGTACATCATTGCAG 58.983 55.000 0.00 0.00 44.52 4.41
63 64 3.370527 CCTCTTTCCCGTGGTACATCATT 60.371 47.826 0.00 0.00 44.52 2.57
64 65 2.170607 CCTCTTTCCCGTGGTACATCAT 59.829 50.000 0.00 0.00 44.52 2.45
76 77 1.192803 ACTGGTCGTCCCTCTTTCCC 61.193 60.000 0.00 0.00 0.00 3.97
94 95 6.636705 TCATCCAACAGTGTATGTACCTAAC 58.363 40.000 0.00 0.00 43.00 2.34
119 120 0.035152 CACATACTGCCCCTTCAGCA 60.035 55.000 0.00 0.00 37.59 4.41
171 175 4.051237 TCAGCGAGATTAATCGGATGTTG 58.949 43.478 19.92 14.28 42.94 3.33
180 184 9.941664 CAATAGTTCAAATTCAGCGAGATTAAT 57.058 29.630 0.00 0.00 0.00 1.40
215 219 8.949177 CATCCATACATAGCATGCAAATAAGTA 58.051 33.333 21.98 11.24 0.00 2.24
268 272 4.650985 TGCAAACTGATCGAAATTCATCG 58.349 39.130 0.00 0.00 44.04 3.84
283 287 2.811431 TCGGACGAAATTCATGCAAACT 59.189 40.909 0.00 0.00 0.00 2.66
302 306 5.682943 TCAAACCACCTTTGAACTAATCG 57.317 39.130 0.00 0.00 44.42 3.34
311 315 6.568869 TCAAATACAGTTCAAACCACCTTTG 58.431 36.000 0.00 0.00 40.76 2.77
317 321 9.787435 AATACTACTCAAATACAGTTCAAACCA 57.213 29.630 0.00 0.00 0.00 3.67
326 330 9.613957 CGACTATCCAATACTACTCAAATACAG 57.386 37.037 0.00 0.00 0.00 2.74
332 336 5.138276 AGCCGACTATCCAATACTACTCAA 58.862 41.667 0.00 0.00 0.00 3.02
333 337 4.726583 AGCCGACTATCCAATACTACTCA 58.273 43.478 0.00 0.00 0.00 3.41
335 339 4.080687 GGAGCCGACTATCCAATACTACT 58.919 47.826 0.00 0.00 35.54 2.57
336 340 3.193056 GGGAGCCGACTATCCAATACTAC 59.807 52.174 0.00 0.00 37.33 2.73
384 389 0.888736 CGCATCCACCCACAGACAAA 60.889 55.000 0.00 0.00 0.00 2.83
385 390 1.302431 CGCATCCACCCACAGACAA 60.302 57.895 0.00 0.00 0.00 3.18
387 392 2.436646 CCGCATCCACCCACAGAC 60.437 66.667 0.00 0.00 0.00 3.51
390 395 3.716195 CTCCCGCATCCACCCACA 61.716 66.667 0.00 0.00 0.00 4.17
416 421 2.094752 GGACATTTCCAACATTGACCCG 60.095 50.000 0.00 0.00 42.30 5.28
417 422 3.165071 AGGACATTTCCAACATTGACCC 58.835 45.455 0.00 0.00 45.72 4.46
431 436 5.342866 AGTGAACTACCCTCTAAGGACATT 58.657 41.667 0.00 0.00 37.67 2.71
468 473 3.003275 TCAAAAGCTCCGTGTCATGAAAC 59.997 43.478 5.89 5.89 0.00 2.78
471 476 2.542020 TCAAAAGCTCCGTGTCATGA 57.458 45.000 0.00 0.00 0.00 3.07
474 479 1.134220 AGGTTCAAAAGCTCCGTGTCA 60.134 47.619 0.00 0.00 33.03 3.58
479 484 0.519077 GCTCAGGTTCAAAAGCTCCG 59.481 55.000 0.00 0.00 37.06 4.63
494 499 9.176460 CTATTCATCAGAGAGTATATGAGCTCA 57.824 37.037 20.79 20.79 31.36 4.26
497 502 8.955388 TCACTATTCATCAGAGAGTATATGAGC 58.045 37.037 0.00 0.00 31.36 4.26
563 568 8.651588 GTTGAGACATCCATCGATATTTATCAC 58.348 37.037 0.00 0.00 32.98 3.06
571 576 3.384467 TGCAGTTGAGACATCCATCGATA 59.616 43.478 0.00 0.00 0.00 2.92
574 579 2.014335 TGCAGTTGAGACATCCATCG 57.986 50.000 0.00 0.00 0.00 3.84
579 584 3.564235 TTTGCATGCAGTTGAGACATC 57.436 42.857 21.50 0.00 0.00 3.06
584 589 3.866910 ACAAAGTTTTGCATGCAGTTGAG 59.133 39.130 21.50 11.15 41.79 3.02
601 606 6.071784 TCCTTGGATGTCATTTCATCACAAAG 60.072 38.462 8.56 8.23 44.00 2.77
605 610 4.337555 CCTCCTTGGATGTCATTTCATCAC 59.662 45.833 8.56 0.54 44.00 3.06
606 611 4.018141 ACCTCCTTGGATGTCATTTCATCA 60.018 41.667 8.56 0.00 44.00 3.07
665 670 8.838365 TGCTTCAAAATGCTTTCAACAATAATT 58.162 25.926 0.00 0.00 0.00 1.40
666 671 8.380743 TGCTTCAAAATGCTTTCAACAATAAT 57.619 26.923 0.00 0.00 0.00 1.28
668 673 7.148771 CGATGCTTCAAAATGCTTTCAACAATA 60.149 33.333 0.08 0.00 0.00 1.90
669 674 6.347079 CGATGCTTCAAAATGCTTTCAACAAT 60.347 34.615 0.08 0.00 0.00 2.71
687 692 5.503846 GCAACAAAAACCAAATTCGATGCTT 60.504 36.000 0.00 0.00 0.00 3.91
694 699 6.280643 AGTCTAGGCAACAAAAACCAAATTC 58.719 36.000 0.00 0.00 41.41 2.17
696 701 5.869649 AGTCTAGGCAACAAAAACCAAAT 57.130 34.783 0.00 0.00 41.41 2.32
700 705 3.634910 TGGAAGTCTAGGCAACAAAAACC 59.365 43.478 0.00 0.00 41.41 3.27
750 755 8.147642 ACATCGATGAATCCTTTAAACTCATC 57.852 34.615 31.33 11.40 39.23 2.92
762 767 8.909708 TTTTTGTGATAAACATCGATGAATCC 57.090 30.769 31.33 20.03 38.99 3.01
845 860 1.740025 CGGAAAGTGCTCTTTGATCCC 59.260 52.381 17.92 11.52 42.99 3.85
847 862 2.079925 AGCGGAAAGTGCTCTTTGATC 58.920 47.619 17.92 4.51 42.99 2.92
862 1519 1.732941 ACATTTTGCGATACAGCGGA 58.267 45.000 0.00 0.00 40.67 5.54
863 1520 2.542766 AACATTTTGCGATACAGCGG 57.457 45.000 0.00 0.00 40.67 5.52
894 1570 9.675464 TTTCTTTTACCAGAACAGAGTTCTTTA 57.325 29.630 9.53 2.59 32.28 1.85
895 1571 8.575649 TTTCTTTTACCAGAACAGAGTTCTTT 57.424 30.769 9.53 3.45 32.28 2.52
923 1599 0.727398 CGGTGGGCTCTCGAAAATTC 59.273 55.000 0.00 0.00 0.00 2.17
964 1640 1.332028 GGATGCTCGTTTTACGCGATG 60.332 52.381 15.93 0.00 42.21 3.84
1022 1698 2.012673 GAGGCGGCATGATGATTATCC 58.987 52.381 13.08 0.00 32.09 2.59
1353 2029 2.623173 GACTTCGACGTCGCAGTAC 58.377 57.895 36.27 26.12 45.08 2.73
1502 2212 2.230508 TGTATCTGACAACCACCGAGAC 59.769 50.000 0.00 0.00 34.15 3.36
1503 2213 2.230508 GTGTATCTGACAACCACCGAGA 59.769 50.000 0.00 0.00 40.66 4.04
1504 2214 2.231478 AGTGTATCTGACAACCACCGAG 59.769 50.000 0.00 0.00 40.66 4.63
1624 2335 3.969287 TGCATCTTTCAGTAGTGAGCT 57.031 42.857 9.39 0.00 32.98 4.09
1677 2388 5.053145 CACACACTGCTAAGAGAAAACTCT 58.947 41.667 0.00 0.00 34.76 3.24
1681 2392 4.686091 CGATCACACACTGCTAAGAGAAAA 59.314 41.667 0.00 0.00 0.00 2.29
1684 2395 2.820197 ACGATCACACACTGCTAAGAGA 59.180 45.455 0.00 0.00 0.00 3.10
1685 2396 3.119673 AGACGATCACACACTGCTAAGAG 60.120 47.826 0.00 0.00 0.00 2.85
1686 2397 2.820197 AGACGATCACACACTGCTAAGA 59.180 45.455 0.00 0.00 0.00 2.10
1687 2398 2.919859 CAGACGATCACACACTGCTAAG 59.080 50.000 0.00 0.00 0.00 2.18
1688 2399 2.352715 CCAGACGATCACACACTGCTAA 60.353 50.000 0.00 0.00 0.00 3.09
1724 2435 5.126699 AGGATCTGCAGATGGAAGAAAAT 57.873 39.130 33.33 6.37 34.37 1.82
1729 2441 1.270199 CGGAGGATCTGCAGATGGAAG 60.270 57.143 33.33 15.97 32.86 3.46
1736 2448 3.136750 CCCTCGGAGGATCTGCAG 58.863 66.667 25.60 7.63 42.67 4.41
1798 2510 0.596577 GCAGTCTGACAGTACCGACA 59.403 55.000 10.88 0.00 0.00 4.35
1816 2528 1.386533 AATGTACAGATGGCTGCTGC 58.613 50.000 7.10 7.10 46.26 5.25
1869 2581 3.885297 ACATCACAGTTCAGGAAAAGGTG 59.115 43.478 0.00 0.00 0.00 4.00
1877 2589 3.303881 TTCGAGACATCACAGTTCAGG 57.696 47.619 0.00 0.00 0.00 3.86
1894 2609 1.156736 CCCACCTGTTAGCAGTTTCG 58.843 55.000 5.81 0.00 41.02 3.46
1987 2706 4.213482 CCTCAACTGGAAACTAGGTTTTCG 59.787 45.833 0.00 0.00 35.77 3.46
2001 2721 8.727910 CATCATATTCATACATTCCTCAACTGG 58.272 37.037 0.00 0.00 0.00 4.00
2013 2733 6.051074 GGGATCGATGCATCATATTCATACA 58.949 40.000 25.70 0.00 0.00 2.29
2014 2734 5.468072 GGGGATCGATGCATCATATTCATAC 59.532 44.000 25.70 8.14 0.00 2.39
2015 2735 5.614308 GGGGATCGATGCATCATATTCATA 58.386 41.667 25.70 1.61 0.00 2.15
2016 2736 4.458397 GGGGATCGATGCATCATATTCAT 58.542 43.478 25.70 7.58 0.00 2.57
2017 2737 3.679639 CGGGGATCGATGCATCATATTCA 60.680 47.826 25.70 3.04 42.43 2.57
2018 2738 2.868583 CGGGGATCGATGCATCATATTC 59.131 50.000 25.70 16.27 42.43 1.75
2019 2739 2.910199 CGGGGATCGATGCATCATATT 58.090 47.619 25.70 7.38 42.43 1.28
2020 2740 1.473965 GCGGGGATCGATGCATCATAT 60.474 52.381 25.70 17.77 42.43 1.78
2076 2956 1.202927 TCAGGGGAGAAAACAAGCCAG 60.203 52.381 0.00 0.00 0.00 4.85
2126 3006 6.260936 CCCTGTCAACGATTGATATAAGCTTT 59.739 38.462 3.20 0.00 42.47 3.51
2272 3160 5.665916 AAAGTTTATGAAGGGCTTGGATG 57.334 39.130 0.00 0.00 0.00 3.51
2295 3185 1.338105 CCACTGACGAGCATGGAGAAA 60.338 52.381 0.00 0.00 33.80 2.52
2349 3239 1.852861 GCGACGTCGTGCTTTGAAAAA 60.853 47.619 35.48 0.00 42.22 1.94
2354 3244 2.128128 GTGCGACGTCGTGCTTTG 60.128 61.111 35.48 9.81 42.22 2.77
2355 3245 3.688330 CGTGCGACGTCGTGCTTT 61.688 61.111 35.48 0.00 42.22 3.51
2363 3253 1.588824 TTCAGTATCCCGTGCGACGT 61.589 55.000 0.00 0.00 40.58 4.34
2368 3265 4.547532 CTGTATAGTTCAGTATCCCGTGC 58.452 47.826 0.00 0.00 0.00 5.34
2376 3273 1.684983 GCCCGCCTGTATAGTTCAGTA 59.315 52.381 0.00 0.00 0.00 2.74
2415 3312 6.096001 GCCACCTGAATGAATGAAGAACTAAT 59.904 38.462 0.00 0.00 0.00 1.73
2416 3313 5.415701 GCCACCTGAATGAATGAAGAACTAA 59.584 40.000 0.00 0.00 0.00 2.24
2426 3324 2.301346 GATTCCGCCACCTGAATGAAT 58.699 47.619 0.00 0.00 31.56 2.57
2427 3325 1.750193 GATTCCGCCACCTGAATGAA 58.250 50.000 0.00 0.00 31.56 2.57
2428 3326 0.461870 CGATTCCGCCACCTGAATGA 60.462 55.000 0.00 0.00 31.56 2.57
2429 3327 1.439353 CCGATTCCGCCACCTGAATG 61.439 60.000 0.00 0.00 31.56 2.67
2430 3328 1.153168 CCGATTCCGCCACCTGAAT 60.153 57.895 0.00 0.00 34.02 2.57
2431 3329 2.119484 AACCGATTCCGCCACCTGAA 62.119 55.000 0.00 0.00 0.00 3.02
2432 3330 2.589157 AACCGATTCCGCCACCTGA 61.589 57.895 0.00 0.00 0.00 3.86
2433 3331 2.046314 AACCGATTCCGCCACCTG 60.046 61.111 0.00 0.00 0.00 4.00
2552 3450 3.822996 ACACGACTCGACTTTACAGATG 58.177 45.455 5.20 0.00 0.00 2.90
2589 3491 1.878102 GCAAAGACGGCTTCAGGAGAA 60.878 52.381 2.63 0.00 31.82 2.87
2591 3493 0.321122 AGCAAAGACGGCTTCAGGAG 60.321 55.000 2.63 0.00 38.81 3.69
2723 3627 0.031616 ACAAGGGCCCCTGACAAAAA 60.032 50.000 27.82 0.00 32.13 1.94
2758 3675 2.464865 CGATCAACGAGAATCCCTGAC 58.535 52.381 0.00 0.00 45.77 3.51
2760 3677 1.212616 GCGATCAACGAGAATCCCTG 58.787 55.000 0.00 0.00 45.77 4.45
2785 3702 2.361438 CCTACTAAACTCCAGGCTACCG 59.639 54.545 0.00 0.00 0.00 4.02
2823 3740 1.628846 AGTTCTCAGGTACGGCCAATT 59.371 47.619 2.24 0.00 40.61 2.32
2825 3742 1.822990 CTAGTTCTCAGGTACGGCCAA 59.177 52.381 2.24 0.00 40.61 4.52
2826 3743 1.005097 TCTAGTTCTCAGGTACGGCCA 59.995 52.381 2.24 0.00 40.61 5.36
2833 3750 1.135915 CTGCGCATCTAGTTCTCAGGT 59.864 52.381 12.24 0.00 0.00 4.00
2850 3767 1.726853 AGAACAGCCGTCATAACTGC 58.273 50.000 0.00 0.00 36.01 4.40
2861 3778 4.512484 AGATGCTCTAGAAAAGAACAGCC 58.488 43.478 0.00 0.00 37.41 4.85
2862 3779 5.641209 TGAAGATGCTCTAGAAAAGAACAGC 59.359 40.000 0.00 0.00 37.05 4.40
2863 3780 7.360776 GGTTGAAGATGCTCTAGAAAAGAACAG 60.361 40.741 0.00 0.00 33.89 3.16
2906 3857 1.716028 AAAGGGGGACAGACGGCTTT 61.716 55.000 0.00 0.00 0.00 3.51
2913 3864 0.991920 GATGGACAAAGGGGGACAGA 59.008 55.000 0.00 0.00 0.00 3.41
2919 3870 0.329261 TGCTCAGATGGACAAAGGGG 59.671 55.000 0.00 0.00 0.00 4.79
2943 3895 0.467290 GGTTTTCAGTGTGAGGGGCA 60.467 55.000 0.00 0.00 0.00 5.36
2960 3912 6.154877 TGCATGAATTTGTATGGATTTGAGGT 59.845 34.615 0.00 0.00 0.00 3.85
2961 3913 6.477688 GTGCATGAATTTGTATGGATTTGAGG 59.522 38.462 0.00 0.00 0.00 3.86
2978 3930 3.780902 ACGAATCATCTACGTGCATGAA 58.219 40.909 14.17 0.00 38.79 2.57
3051 4939 4.771127 CGCCCCGCTTATGTACAT 57.229 55.556 13.93 13.93 0.00 2.29
3091 4979 5.904362 AGAATATCAAGGAGCAAACCAAC 57.096 39.130 0.00 0.00 0.00 3.77
3183 5072 3.145551 CAAGGGCCATGCAGGAGC 61.146 66.667 6.18 0.99 41.22 4.70
3226 5225 8.211030 TGGATCCTATATGTGAGACAATTGAT 57.789 34.615 13.59 0.00 0.00 2.57
3239 5467 4.267536 CCCACAAGCATGGATCCTATATG 58.732 47.826 14.23 9.68 43.02 1.78
3261 5489 4.081697 CCTTGGGGTGTAAACATTCATTCC 60.082 45.833 0.00 0.00 0.00 3.01
3262 5490 4.620567 GCCTTGGGGTGTAAACATTCATTC 60.621 45.833 0.00 0.00 34.45 2.67
3269 5497 1.427368 AGATGCCTTGGGGTGTAAACA 59.573 47.619 0.00 0.00 34.45 2.83
3394 5624 0.747255 ATGACGGTCAAGATCCTCCG 59.253 55.000 15.72 11.88 46.98 4.63
3430 5660 6.557110 TGTGATGCATGTTTATGACTCATTG 58.443 36.000 2.46 0.00 36.36 2.82
3482 5712 2.175811 CACAACTTTAGCGGGCGC 59.824 61.111 0.00 0.00 42.33 6.53
3491 5721 3.192466 GTGTACGAGTCACCACAACTTT 58.808 45.455 0.00 0.00 0.00 2.66
3492 5722 2.817901 GTGTACGAGTCACCACAACTT 58.182 47.619 0.00 0.00 0.00 2.66
3531 5761 2.885135 ATGCCTTCATGTTGGAGACA 57.115 45.000 10.16 1.06 43.71 3.41
3532 5762 2.096496 CGAATGCCTTCATGTTGGAGAC 59.904 50.000 10.16 0.00 32.23 3.36
3538 5768 3.614092 ACATCTCGAATGCCTTCATGTT 58.386 40.909 2.57 0.00 32.23 2.71
3539 5769 3.201290 GACATCTCGAATGCCTTCATGT 58.799 45.455 6.06 6.06 31.68 3.21
3547 5777 0.179111 TGGTCGGACATCTCGAATGC 60.179 55.000 10.76 0.00 38.42 3.56
3554 5784 2.086869 CTTTGCAATGGTCGGACATCT 58.913 47.619 10.76 0.00 0.00 2.90
3556 5786 0.527565 GCTTTGCAATGGTCGGACAT 59.472 50.000 13.62 0.00 0.00 3.06
3559 5789 2.331893 CGGCTTTGCAATGGTCGGA 61.332 57.895 15.86 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.