Multiple sequence alignment - TraesCS6A01G247800

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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 TraesCS6A01G247800 chr6A 100.000 2624 0 0 1 2624 459850666 459848043 0.000000e+00 4846.0
1 TraesCS6A01G247800 chr6A 78.979 333 57 10 326 650 448362821 448362494 5.690000e-52 215.0
2 TraesCS6A01G247800 chr6B 90.749 2270 136 36 327 2570 501103680 501105901 0.000000e+00 2961.0
3 TraesCS6A01G247800 chr6B 91.165 249 21 1 1 248 501082291 501082539 1.160000e-88 337.0
4 TraesCS6A01G247800 chr6B 86.022 93 8 2 237 328 501103521 501103609 7.730000e-16 95.3
5 TraesCS6A01G247800 chr6B 100.000 41 0 0 2584 2624 501105896 501105936 2.800000e-10 76.8
6 TraesCS6A01G247800 chr6D 94.541 1832 79 9 799 2624 322461325 322459509 0.000000e+00 2809.0
7 TraesCS6A01G247800 chr6D 87.526 489 44 10 327 800 322461973 322461487 1.370000e-152 549.0
8 TraesCS6A01G247800 chr6D 91.765 340 16 3 1 328 322462384 322462045 1.840000e-126 462.0
9 TraesCS6A01G247800 chr6D 81.293 294 51 4 334 625 9974678 9974387 4.370000e-58 235.0
10 TraesCS6A01G247800 chr6D 94.643 56 3 0 1094 1149 339002698 339002643 1.290000e-13 87.9
11 TraesCS6A01G247800 chr4A 79.511 327 55 9 330 648 691156877 691156555 3.400000e-54 222.0
12 TraesCS6A01G247800 chr3A 80.471 297 52 6 331 625 171541164 171541456 3.400000e-54 222.0
13 TraesCS6A01G247800 chr7D 78.882 322 60 6 326 641 258233322 258233641 7.360000e-51 211.0
14 TraesCS6A01G247800 chr7A 78.738 301 60 4 327 625 280020041 280020339 5.730000e-47 198.0
15 TraesCS6A01G247800 chr1A 78.641 309 53 11 348 648 286011504 286011201 2.670000e-45 193.0
16 TraesCS6A01G247800 chr5B 96.429 56 2 0 1094 1149 677806399 677806344 2.780000e-15 93.5


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 TraesCS6A01G247800 chr6A 459848043 459850666 2623 True 4846.000000 4846 100.000000 1 2624 1 chr6A.!!$R2 2623
1 TraesCS6A01G247800 chr6B 501103521 501105936 2415 False 1044.366667 2961 92.257000 237 2624 3 chr6B.!!$F2 2387
2 TraesCS6A01G247800 chr6D 322459509 322462384 2875 True 1273.333333 2809 91.277333 1 2624 3 chr6D.!!$R3 2623

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
624 711 0.098376 AACGACGATGACTACGGCTC 59.902 55.0 0.0 0.0 36.56 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 2475 1.357137 TAACTGGATGACTGGTGCCA 58.643 50.0 0.0 0.0 0.0 4.92 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
51 53 2.159226 ACTCGACTGGAATTAGCCTTCG 60.159 50.000 0.00 0.00 36.26 3.79
61 63 5.885352 TGGAATTAGCCTTCGAAATGAATGA 59.115 36.000 0.00 0.00 35.63 2.57
68 70 7.664082 AGCCTTCGAAATGAATGATACATAG 57.336 36.000 0.00 0.00 35.63 2.23
89 92 7.770897 ACATAGGACTTCAAATGAATGGTACTC 59.229 37.037 4.15 0.00 29.55 2.59
156 169 5.309638 TCTATGTTTTTGGTCGTTGGATGA 58.690 37.500 0.00 0.00 0.00 2.92
198 211 4.620803 GCCGTCAGATCTTCCTCTAAACAA 60.621 45.833 0.00 0.00 0.00 2.83
219 232 8.865090 AAACAATAGTTTACCATGATTTGGTCA 58.135 29.630 0.00 0.00 46.84 4.02
317 330 8.915036 ACACTATAGTAACATTTCCTCCTGTAG 58.085 37.037 4.74 0.00 0.00 2.74
350 436 1.446272 CGGTTGCGGAGAGGAGAAC 60.446 63.158 0.00 0.00 0.00 3.01
355 441 2.362632 CGGAGAGGAGAACCCCGT 60.363 66.667 0.00 0.00 35.07 5.28
364 450 4.324991 GAACCCCGTTGCCTCCGT 62.325 66.667 0.00 0.00 0.00 4.69
425 511 3.243907 GCTGGTGTAATGCTAGGGTAGAG 60.244 52.174 0.00 0.00 0.00 2.43
428 514 3.321396 GGTGTAATGCTAGGGTAGAGGAC 59.679 52.174 0.00 0.00 0.00 3.85
430 516 1.705873 AATGCTAGGGTAGAGGACGG 58.294 55.000 0.00 0.00 0.00 4.79
454 540 4.319118 CGCTTCTTCTTGGAGTTTGTCTTC 60.319 45.833 0.00 0.00 0.00 2.87
476 562 1.313812 GGCTTCGACCCTTCTCGAGA 61.314 60.000 12.08 12.08 43.34 4.04
483 569 2.018515 GACCCTTCTCGAGATTCGTCT 58.981 52.381 17.44 0.00 41.35 4.18
488 574 4.142447 CCCTTCTCGAGATTCGTCTGTTTA 60.142 45.833 17.44 0.00 41.35 2.01
492 578 7.254829 CCTTCTCGAGATTCGTCTGTTTAGATA 60.255 40.741 17.44 0.00 41.35 1.98
506 592 6.482641 TCTGTTTAGATATAGTCGACGAGCTT 59.517 38.462 10.46 0.00 0.00 3.74
507 593 7.012138 TCTGTTTAGATATAGTCGACGAGCTTT 59.988 37.037 10.46 0.00 0.00 3.51
518 604 5.094134 GTCGACGAGCTTTAGTGTAGATTT 58.906 41.667 0.00 0.00 0.00 2.17
519 605 5.572126 GTCGACGAGCTTTAGTGTAGATTTT 59.428 40.000 0.00 0.00 0.00 1.82
524 610 5.106712 CGAGCTTTAGTGTAGATTTTTGCCA 60.107 40.000 0.00 0.00 0.00 4.92
525 611 6.403636 CGAGCTTTAGTGTAGATTTTTGCCAT 60.404 38.462 0.00 0.00 0.00 4.40
584 670 2.621338 GCGAGATTTGGTGTCAGATGA 58.379 47.619 0.00 0.00 0.00 2.92
621 708 1.909532 GTTCAACGACGATGACTACGG 59.090 52.381 7.37 0.00 34.93 4.02
624 711 0.098376 AACGACGATGACTACGGCTC 59.902 55.000 0.00 0.00 36.56 4.70
667 768 2.766263 TGGAACTATCATCGACAGGCTT 59.234 45.455 0.00 0.00 0.00 4.35
677 778 2.852075 ACAGGCTTCGGTGGGGAA 60.852 61.111 0.00 0.00 0.00 3.97
681 782 2.430367 GCTTCGGTGGGGAACAGT 59.570 61.111 0.00 0.00 0.00 3.55
689 790 0.886490 GTGGGGAACAGTGACAGCAG 60.886 60.000 0.00 0.00 0.00 4.24
691 792 1.227943 GGGAACAGTGACAGCAGCA 60.228 57.895 0.00 0.00 0.00 4.41
697 798 2.354656 GTGACAGCAGCACGTCGA 60.355 61.111 0.00 0.00 34.78 4.20
698 799 1.734477 GTGACAGCAGCACGTCGAT 60.734 57.895 0.00 0.00 34.78 3.59
719 820 0.525761 GCTTATTTTGGCGGCAGTGA 59.474 50.000 12.87 2.35 0.00 3.41
739 840 2.620112 GGTCGTTCGGTGGTCTCGA 61.620 63.158 0.00 0.00 34.62 4.04
784 885 5.649782 TGTTTAAGGTACCTCTTACTCCG 57.350 43.478 16.64 0.00 0.00 4.63
865 1130 9.426837 CAAATTCTTCTTTGAAAAGGATGCATA 57.573 29.630 0.00 0.00 38.17 3.14
868 1133 4.621068 TCTTTGAAAAGGATGCATAGCG 57.379 40.909 0.00 0.00 36.67 4.26
1320 1596 3.760035 AAGCTCATCGTCCGCCGT 61.760 61.111 0.00 0.00 37.94 5.68
1353 1629 2.171079 CAACGCCGCGGACATGTAT 61.171 57.895 33.48 3.47 0.00 2.29
1363 1639 3.642901 GACATGTATGTCGCCGTCT 57.357 52.632 9.04 0.00 46.46 4.18
1392 1668 4.974438 TGGTCCTTCCCCAGCGGT 62.974 66.667 0.00 0.00 34.77 5.68
1617 1893 1.234615 GCCGCACCAGCTTTCTTGTA 61.235 55.000 0.00 0.00 39.10 2.41
1644 1920 5.280654 AGTTCTTGCATGTTTTTGGTCAT 57.719 34.783 0.00 0.00 0.00 3.06
1651 1927 3.061161 GCATGTTTTTGGTCATTCGCATC 59.939 43.478 0.00 0.00 0.00 3.91
1734 2010 2.351111 GCTAGTGCTTGAACTGATGAGC 59.649 50.000 0.00 0.00 36.03 4.26
1881 2157 5.221880 TGCAAATGACAATTGACAACTAGC 58.778 37.500 13.59 14.75 0.00 3.42
1923 2199 7.856145 AACATGATTACTCTTCCTTCATCAC 57.144 36.000 0.00 0.00 0.00 3.06
1982 2258 5.192176 AGTGCATTGGAAACATTGGTTTTT 58.808 33.333 0.00 0.00 46.84 1.94
2004 2280 2.197465 GATCCCAGGTGTTCTTACCCT 58.803 52.381 0.00 0.00 41.83 4.34
2021 2297 2.402564 CCCTCATCATGGGTAGACAGT 58.597 52.381 0.00 0.00 39.82 3.55
2054 2330 5.565592 TGAATGTTCACATCATAGTTGCC 57.434 39.130 0.00 0.00 35.10 4.52
2060 2336 6.883744 TGTTCACATCATAGTTGCCTATACA 58.116 36.000 0.00 0.00 32.49 2.29
2061 2337 6.986231 TGTTCACATCATAGTTGCCTATACAG 59.014 38.462 0.00 0.00 32.49 2.74
2062 2338 6.731292 TCACATCATAGTTGCCTATACAGT 57.269 37.500 0.00 0.00 32.49 3.55
2064 2340 7.886338 TCACATCATAGTTGCCTATACAGTAG 58.114 38.462 0.00 0.00 32.49 2.57
2137 2413 6.870971 ATATTCCATGCCAATTTGATTTGC 57.129 33.333 0.00 0.00 0.00 3.68
2147 2423 4.690280 CCAATTTGATTTGCCAGGTTACAC 59.310 41.667 0.00 0.00 0.00 2.90
2149 2425 6.295011 CCAATTTGATTTGCCAGGTTACACTA 60.295 38.462 0.00 0.00 0.00 2.74
2184 2461 1.597578 GCTATCAGCTGCAGGAGGC 60.598 63.158 17.12 9.85 45.13 4.70
2198 2475 2.504996 CAGGAGGCTCCTCTCAGAAAAT 59.495 50.000 33.04 5.89 45.66 1.82
2205 2482 1.704628 TCCTCTCAGAAAATGGCACCA 59.295 47.619 0.00 0.00 0.00 4.17
2271 2549 5.777732 AGTCTTCTCAGAACTAGGATGTTGT 59.222 40.000 0.00 0.00 0.00 3.32
2294 2572 1.209990 CAGCTTGCTTCTGGGAGATCT 59.790 52.381 0.00 0.00 0.00 2.75
2298 2576 1.942776 TGCTTCTGGGAGATCTCACA 58.057 50.000 25.85 25.85 41.39 3.58
2347 2628 4.759693 TGTATCCAAATGTTGAAAGCGAGT 59.240 37.500 0.00 0.00 0.00 4.18
2459 2740 4.126437 GGCATTTTTGTACTGTTTTGCCT 58.874 39.130 17.07 0.00 43.86 4.75
2565 2847 0.731855 GTGGACGACGGTAGCTGAAC 60.732 60.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 4.876107 TCATTTCGAAGGCTAATTCCAGTC 59.124 41.667 0.00 0.00 0.00 3.51
61 63 9.561069 GTACCATTCATTTGAAGTCCTATGTAT 57.439 33.333 0.00 0.00 37.48 2.29
68 70 6.349363 GGTTGAGTACCATTCATTTGAAGTCC 60.349 42.308 0.00 0.00 46.92 3.85
89 92 4.461198 AGGCTATCCTAAAATTCCGGTTG 58.539 43.478 0.00 0.00 42.06 3.77
156 169 6.646240 TGACGGCTAGAAACTAATTAAAACGT 59.354 34.615 0.00 0.00 0.00 3.99
219 232 5.151454 AGTAGTGGCTCATTAGGATAAGCT 58.849 41.667 0.00 0.00 35.12 3.74
220 233 5.245075 AGAGTAGTGGCTCATTAGGATAAGC 59.755 44.000 0.00 0.00 37.94 3.09
224 237 5.777732 CCTTAGAGTAGTGGCTCATTAGGAT 59.222 44.000 0.00 0.00 37.94 3.24
304 317 2.021936 ACCTAGGGCTACAGGAGGAAAT 60.022 50.000 14.81 0.00 35.76 2.17
341 427 2.593956 GGCAACGGGGTTCTCCTCT 61.594 63.158 0.00 0.00 35.33 3.69
364 450 4.646492 CCTAGCCTAAACTACTAACCGGAA 59.354 45.833 9.46 0.00 0.00 4.30
395 481 2.571653 AGCATTACACCAGCAAGGACTA 59.428 45.455 1.83 0.00 41.22 2.59
402 488 1.285280 ACCCTAGCATTACACCAGCA 58.715 50.000 0.00 0.00 0.00 4.41
411 497 1.705873 CCGTCCTCTACCCTAGCATT 58.294 55.000 0.00 0.00 0.00 3.56
425 511 2.391389 CCAAGAAGAAGCGCCGTCC 61.391 63.158 2.29 0.00 0.00 4.79
428 514 0.951040 AACTCCAAGAAGAAGCGCCG 60.951 55.000 2.29 0.00 0.00 6.46
430 516 1.604278 ACAAACTCCAAGAAGAAGCGC 59.396 47.619 0.00 0.00 0.00 5.92
469 555 7.731882 ATATCTAAACAGACGAATCTCGAGA 57.268 36.000 19.19 19.19 43.74 4.04
483 569 6.615264 AAGCTCGTCGACTATATCTAAACA 57.385 37.500 14.70 0.00 0.00 2.83
488 574 5.759273 ACACTAAAGCTCGTCGACTATATCT 59.241 40.000 14.70 0.66 0.00 1.98
492 578 5.114780 TCTACACTAAAGCTCGTCGACTAT 58.885 41.667 14.70 0.00 0.00 2.12
506 592 6.721318 AGGAGATGGCAAAAATCTACACTAA 58.279 36.000 1.17 0.00 37.45 2.24
507 593 6.313519 AGGAGATGGCAAAAATCTACACTA 57.686 37.500 1.17 0.00 37.45 2.74
518 604 1.305213 GCCCCAAGGAGATGGCAAA 60.305 57.895 0.00 0.00 43.46 3.68
519 605 2.360191 GCCCCAAGGAGATGGCAA 59.640 61.111 0.00 0.00 43.46 4.52
524 610 2.610859 ACACCGCCCCAAGGAGAT 60.611 61.111 0.00 0.00 34.21 2.75
525 611 3.636231 CACACCGCCCCAAGGAGA 61.636 66.667 0.00 0.00 34.21 3.71
570 656 9.551734 CATAGATCTTAATCATCTGACACCAAA 57.448 33.333 0.00 0.00 34.07 3.28
584 670 6.992123 TCGTTGAACCATGCATAGATCTTAAT 59.008 34.615 0.00 0.00 0.00 1.40
621 708 0.815615 CCCTAAGGACCAATGCGAGC 60.816 60.000 0.00 0.00 33.47 5.03
667 768 1.754380 CTGTCACTGTTCCCCACCGA 61.754 60.000 0.00 0.00 0.00 4.69
677 778 1.592669 GACGTGCTGCTGTCACTGT 60.593 57.895 16.87 12.34 35.20 3.55
681 782 1.734117 CATCGACGTGCTGCTGTCA 60.734 57.895 20.02 11.03 34.78 3.58
689 790 2.440501 CAAAATAAGCCATCGACGTGC 58.559 47.619 0.00 0.00 0.00 5.34
691 792 1.400494 GCCAAAATAAGCCATCGACGT 59.600 47.619 0.00 0.00 0.00 4.34
697 798 0.461135 CTGCCGCCAAAATAAGCCAT 59.539 50.000 0.00 0.00 0.00 4.40
698 799 0.897863 ACTGCCGCCAAAATAAGCCA 60.898 50.000 0.00 0.00 0.00 4.75
719 820 1.664306 GAGACCACCGAACGACCTT 59.336 57.895 0.00 0.00 0.00 3.50
767 868 2.732763 GTCCGGAGTAAGAGGTACCTT 58.267 52.381 17.53 3.18 32.58 3.50
770 871 2.029838 TCGTCCGGAGTAAGAGGTAC 57.970 55.000 3.06 0.00 0.00 3.34
774 875 4.373348 AAAGATTCGTCCGGAGTAAGAG 57.627 45.455 3.06 0.00 0.00 2.85
776 877 8.813643 ATTATAAAAGATTCGTCCGGAGTAAG 57.186 34.615 3.06 0.00 0.00 2.34
803 1067 9.312904 TCCAGTTTTCTTTGAAAGGATCATATT 57.687 29.630 4.94 0.00 38.03 1.28
857 1122 0.041839 CGCTTTGACGCTATGCATCC 60.042 55.000 0.19 0.00 0.00 3.51
861 1126 2.023320 GCCGCTTTGACGCTATGC 59.977 61.111 0.00 0.00 0.00 3.14
865 1130 2.741486 TTAAGGGCCGCTTTGACGCT 62.741 55.000 11.15 0.00 0.00 5.07
868 1133 3.630312 TGAATATTAAGGGCCGCTTTGAC 59.370 43.478 11.15 0.00 0.00 3.18
1459 1735 2.435586 CGCCCAGAGGAACAGCAG 60.436 66.667 0.00 0.00 33.47 4.24
1604 1880 5.181748 AGAACTAGCATACAAGAAAGCTGG 58.818 41.667 0.00 0.00 40.80 4.85
1644 1920 1.866601 CTTGTGTGACAGTGATGCGAA 59.133 47.619 0.00 0.00 0.00 4.70
1651 1927 3.425577 AAATGCACTTGTGTGACAGTG 57.574 42.857 0.00 0.00 46.55 3.66
1811 2087 4.706476 CCATCCACCAACAATTGTACTCAT 59.294 41.667 12.39 0.00 0.00 2.90
1812 2088 4.078537 CCATCCACCAACAATTGTACTCA 58.921 43.478 12.39 0.00 0.00 3.41
1881 2157 4.456280 TGTTAGGACATCAGTACTGCTG 57.544 45.455 22.04 22.04 39.92 4.41
1982 2258 3.013648 AGGGTAAGAACACCTGGGATCTA 59.986 47.826 0.00 0.00 38.73 1.98
2004 2280 5.026121 AGAAGAACTGTCTACCCATGATGA 58.974 41.667 0.00 0.00 32.16 2.92
2112 2388 8.556213 GCAAATCAAATTGGCATGGAATATAT 57.444 30.769 0.00 0.00 39.06 0.86
2113 2389 7.966246 GCAAATCAAATTGGCATGGAATATA 57.034 32.000 0.00 0.00 39.06 0.86
2137 2413 6.436532 TCTTAAACCTCTCTAGTGTAACCTGG 59.563 42.308 0.00 0.00 37.80 4.45
2147 2423 8.001881 TGATAGCACTTCTTAAACCTCTCTAG 57.998 38.462 0.00 0.00 0.00 2.43
2149 2425 6.629291 GCTGATAGCACTTCTTAAACCTCTCT 60.629 42.308 0.00 0.00 41.89 3.10
2184 2461 2.290514 TGGTGCCATTTTCTGAGAGGAG 60.291 50.000 0.00 0.00 0.00 3.69
2198 2475 1.357137 TAACTGGATGACTGGTGCCA 58.643 50.000 0.00 0.00 0.00 4.92
2205 2482 8.643324 GGAACAGACTAATATAACTGGATGACT 58.357 37.037 0.00 0.00 35.08 3.41
2271 2549 1.421268 TCTCCCAGAAGCAAGCTGAAA 59.579 47.619 0.00 0.00 35.39 2.69
2294 2572 4.870426 GCCATCGATTACTTTCTTCTGTGA 59.130 41.667 0.00 0.00 0.00 3.58
2298 2576 4.080863 ACCTGCCATCGATTACTTTCTTCT 60.081 41.667 0.00 0.00 0.00 2.85
2299 2577 4.034510 CACCTGCCATCGATTACTTTCTTC 59.965 45.833 0.00 0.00 0.00 2.87
2300 2578 3.941483 CACCTGCCATCGATTACTTTCTT 59.059 43.478 0.00 0.00 0.00 2.52
2459 2740 6.489700 TGTTGCTGAAATATCAAAGGTCTTGA 59.510 34.615 0.00 0.00 34.49 3.02


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

AutoCloner maintained by Alex Coulton.