Multiple sequence alignment - TraesCS6A01G370800

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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 TraesCS6A01G370800 chr6A 100.000 3365 0 0 1 3365 595497166 595500530 0.000000e+00 6215.0
1 TraesCS6A01G370800 chr6A 85.889 900 66 26 2489 3364 603371463 603370601 0.000000e+00 902.0
2 TraesCS6A01G370800 chr6A 83.878 490 58 10 2539 3011 616346937 616347422 6.620000e-122 448.0
3 TraesCS6A01G370800 chr6A 86.644 292 24 9 3081 3364 616347453 616347737 3.260000e-80 309.0
4 TraesCS6A01G370800 chr6D 94.358 1666 72 6 835 2488 449971479 449973134 0.000000e+00 2536.0
5 TraesCS6A01G370800 chr6D 87.590 1668 182 13 835 2487 449922005 449923662 0.000000e+00 1910.0
6 TraesCS6A01G370800 chr6D 84.580 1524 193 22 971 2487 449993960 449995448 0.000000e+00 1474.0
7 TraesCS6A01G370800 chr6B 92.746 1668 104 6 832 2488 682135925 682137586 0.000000e+00 2394.0
8 TraesCS6A01G370800 chr6B 92.646 1115 79 1 983 2094 682312818 682311704 0.000000e+00 1602.0
9 TraesCS6A01G370800 chr6B 89.082 806 54 15 2581 3365 492863393 492864185 0.000000e+00 970.0
10 TraesCS6A01G370800 chr6B 92.495 533 39 1 1957 2488 682310376 682309844 0.000000e+00 761.0
11 TraesCS6A01G370800 chr6B 86.525 141 6 3 832 962 682313447 682313310 3.500000e-30 143.0
12 TraesCS6A01G370800 chr2A 98.678 832 11 0 1 832 607190117 607190948 0.000000e+00 1476.0
13 TraesCS6A01G370800 chr2A 79.461 482 84 14 360 833 333798653 333799127 9.000000e-86 327.0
14 TraesCS6A01G370800 chr2A 85.079 315 42 5 520 832 677903269 677903580 1.950000e-82 316.0
15 TraesCS6A01G370800 chr2A 86.087 115 9 5 3255 3365 66314502 66314613 2.120000e-22 117.0
16 TraesCS6A01G370800 chr4D 89.093 871 62 15 2520 3365 418513706 418512844 0.000000e+00 1051.0
17 TraesCS6A01G370800 chr4D 86.967 867 73 21 2499 3338 298895921 298895068 0.000000e+00 939.0
18 TraesCS6A01G370800 chr4D 74.340 265 36 16 28 283 296587502 296587261 2.150000e-12 84.2
19 TraesCS6A01G370800 chr5D 87.377 911 75 26 2486 3364 371468135 371467233 0.000000e+00 1009.0
20 TraesCS6A01G370800 chr5D 77.419 465 57 29 2489 2917 59778999 59778547 2.020000e-57 233.0
21 TraesCS6A01G370800 chr2B 86.822 903 84 20 2492 3364 29759745 29758848 0.000000e+00 976.0
22 TraesCS6A01G370800 chr2B 83.596 317 47 5 518 832 732215062 732215375 3.280000e-75 292.0
23 TraesCS6A01G370800 chr2B 76.378 381 57 27 2795 3164 706696040 706695682 1.240000e-39 174.0
24 TraesCS6A01G370800 chr2D 86.082 776 74 18 2617 3364 516362255 516363024 0.000000e+00 804.0
25 TraesCS6A01G370800 chr2D 86.160 513 51 14 2840 3337 605620399 605619892 1.370000e-148 536.0
26 TraesCS6A01G370800 chr2D 85.067 375 30 14 2479 2841 605620922 605620562 3.190000e-95 359.0
27 TraesCS6A01G370800 chr2D 76.190 378 62 19 2795 3164 44344352 44343995 1.240000e-39 174.0
28 TraesCS6A01G370800 chr7A 82.538 922 86 30 2488 3365 728017469 728016579 0.000000e+00 741.0
29 TraesCS6A01G370800 chr7A 83.191 351 52 7 487 833 505392620 505392967 7.010000e-82 315.0
30 TraesCS6A01G370800 chr7B 89.183 416 35 2 417 832 687443924 687444329 8.330000e-141 510.0
31 TraesCS6A01G370800 chr7B 90.390 385 29 5 1 380 687443547 687443928 1.800000e-137 499.0
32 TraesCS6A01G370800 chr5A 82.403 466 72 9 375 833 417286426 417286888 6.770000e-107 398.0
33 TraesCS6A01G370800 chr5A 84.444 315 44 5 520 832 451785456 451785767 4.220000e-79 305.0
34 TraesCS6A01G370800 chr1A 80.045 446 74 12 391 832 222919420 222919854 1.950000e-82 316.0


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 TraesCS6A01G370800 chr6A 595497166 595500530 3364 False 6215.000000 6215 100.000000 1 3365 1 chr6A.!!$F1 3364
1 TraesCS6A01G370800 chr6A 603370601 603371463 862 True 902.000000 902 85.889000 2489 3364 1 chr6A.!!$R1 875
2 TraesCS6A01G370800 chr6A 616346937 616347737 800 False 378.500000 448 85.261000 2539 3364 2 chr6A.!!$F2 825
3 TraesCS6A01G370800 chr6D 449971479 449973134 1655 False 2536.000000 2536 94.358000 835 2488 1 chr6D.!!$F2 1653
4 TraesCS6A01G370800 chr6D 449922005 449923662 1657 False 1910.000000 1910 87.590000 835 2487 1 chr6D.!!$F1 1652
5 TraesCS6A01G370800 chr6D 449993960 449995448 1488 False 1474.000000 1474 84.580000 971 2487 1 chr6D.!!$F3 1516
6 TraesCS6A01G370800 chr6B 682135925 682137586 1661 False 2394.000000 2394 92.746000 832 2488 1 chr6B.!!$F2 1656
7 TraesCS6A01G370800 chr6B 492863393 492864185 792 False 970.000000 970 89.082000 2581 3365 1 chr6B.!!$F1 784
8 TraesCS6A01G370800 chr6B 682309844 682313447 3603 True 835.333333 1602 90.555333 832 2488 3 chr6B.!!$R1 1656
9 TraesCS6A01G370800 chr2A 607190117 607190948 831 False 1476.000000 1476 98.678000 1 832 1 chr2A.!!$F3 831
10 TraesCS6A01G370800 chr4D 418512844 418513706 862 True 1051.000000 1051 89.093000 2520 3365 1 chr4D.!!$R3 845
11 TraesCS6A01G370800 chr4D 298895068 298895921 853 True 939.000000 939 86.967000 2499 3338 1 chr4D.!!$R2 839
12 TraesCS6A01G370800 chr5D 371467233 371468135 902 True 1009.000000 1009 87.377000 2486 3364 1 chr5D.!!$R2 878
13 TraesCS6A01G370800 chr2B 29758848 29759745 897 True 976.000000 976 86.822000 2492 3364 1 chr2B.!!$R1 872
14 TraesCS6A01G370800 chr2D 516362255 516363024 769 False 804.000000 804 86.082000 2617 3364 1 chr2D.!!$F1 747
15 TraesCS6A01G370800 chr2D 605619892 605620922 1030 True 447.500000 536 85.613500 2479 3337 2 chr2D.!!$R2 858
16 TraesCS6A01G370800 chr7A 728016579 728017469 890 True 741.000000 741 82.538000 2488 3365 1 chr7A.!!$R1 877
17 TraesCS6A01G370800 chr7B 687443547 687444329 782 False 504.500000 510 89.786500 1 832 2 chr7B.!!$F1 831

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
659 665 0.106918 GCCGGGAAATACATGGGTCA 60.107 55.0 2.18 0.0 0.00 4.02 F
1642 2140 0.037326 GCAGATCAAGGACCGTGTCA 60.037 55.0 7.33 0.0 33.68 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 4252 0.617413 CACAGCTCTCTGGGTGGATT 59.383 55.000 0.0 0.0 44.54 3.01 R
2648 4617 2.711542 GCTTCAGCCTGCTAAGGTTTA 58.288 47.619 0.0 0.0 46.43 2.01 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
206 207 4.235079 TGTTGAACCTGGAGATATTGGG 57.765 45.455 0.00 0.00 0.00 4.12
584 590 3.489059 CCATATTTGTGCCGGCAGTTTAG 60.489 47.826 33.73 16.33 0.00 1.85
659 665 0.106918 GCCGGGAAATACATGGGTCA 60.107 55.000 2.18 0.00 0.00 4.02
669 675 1.219773 ACATGGGTCATGGCAGAGAT 58.780 50.000 11.85 0.00 45.16 2.75
843 849 5.744171 TGTGGTGTAGTGATATGCAAATCT 58.256 37.500 0.00 0.00 0.00 2.40
847 853 6.037062 TGGTGTAGTGATATGCAAATCTTTCG 59.963 38.462 0.00 0.00 0.00 3.46
992 1482 2.360350 CAGCCACGGCAACCAGAT 60.360 61.111 11.35 0.00 44.88 2.90
1011 1501 6.327365 ACCAGATACATAACATGGAGATCACA 59.673 38.462 0.00 0.00 34.99 3.58
1013 1503 7.440198 CAGATACATAACATGGAGATCACAGT 58.560 38.462 0.00 0.00 33.60 3.55
1064 1554 1.974236 GCTAGTCCATGTCCTGCCTAT 59.026 52.381 0.00 0.00 0.00 2.57
1272 1765 1.483415 GGTACCCATTTCCTCGTGCTA 59.517 52.381 0.00 0.00 0.00 3.49
1427 1920 3.657350 CAACCCCATCCACCCCGT 61.657 66.667 0.00 0.00 0.00 5.28
1492 1986 2.431771 TCGGCGTCGACACCATTG 60.432 61.111 21.81 6.54 40.88 2.82
1642 2140 0.037326 GCAGATCAAGGACCGTGTCA 60.037 55.000 7.33 0.00 33.68 3.58
2160 4123 1.078848 CTCCCGGCACCTCTTCTTG 60.079 63.158 0.00 0.00 0.00 3.02
2289 4252 1.228521 CAGGGCCAACACCATCACA 60.229 57.895 6.18 0.00 0.00 3.58
2477 4442 2.532250 TCATGCACAGTCTCCTCCTA 57.468 50.000 0.00 0.00 0.00 2.94
2497 4462 9.010029 CCTCCTATTTTTAGTTTCACTTTAGCA 57.990 33.333 0.00 0.00 0.00 3.49
2648 4617 0.395173 ACCAGTGTTTTGGGCGAGTT 60.395 50.000 0.00 0.00 42.76 3.01
2792 4788 9.989394 GACGTCTTTAGAATTTTATTTTGTTGC 57.011 29.630 8.70 0.00 0.00 4.17
2920 5082 5.727249 GCAATTTTAGTGCAAAGTTGTGTC 58.273 37.500 6.69 0.00 42.68 3.67
2922 5084 6.508404 GCAATTTTAGTGCAAAGTTGTGTCTG 60.508 38.462 6.69 0.00 42.68 3.51
2923 5085 5.637006 TTTTAGTGCAAAGTTGTGTCTGT 57.363 34.783 0.00 0.00 0.00 3.41
2938 5100 9.353999 AGTTGTGTCTGTGTTTTTCTTAATTTC 57.646 29.630 0.00 0.00 0.00 2.17
3229 5429 9.669353 CAATGCCACTAGTTTATTCATCATTAC 57.331 33.333 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 8.434733 TGCAACAGATCAAAAATTCAAAATGA 57.565 26.923 0.00 0.00 0.00 2.57
206 207 5.859824 AAACAAAATGAGCGTAAAACGTC 57.140 34.783 1.07 0.00 44.73 4.34
584 590 1.356938 GAACTACAGTTACCGGCAGC 58.643 55.000 0.00 0.00 38.56 5.25
669 675 4.097286 GCAGATAAATTTTTCCCGGCAGTA 59.903 41.667 0.00 0.00 0.00 2.74
843 849 6.368779 AATTAGTATATAGCCAGGCCGAAA 57.631 37.500 8.22 0.00 0.00 3.46
847 853 9.462606 ACAAATTAATTAGTATATAGCCAGGCC 57.537 33.333 8.22 0.00 0.00 5.19
992 1482 7.043961 GAGACTGTGATCTCCATGTTATGTA 57.956 40.000 0.00 0.00 39.46 2.29
1011 1501 2.919856 AGCAGCACGGTGGAGACT 60.920 61.111 10.60 0.00 0.00 3.24
1013 1503 4.687215 GCAGCAGCACGGTGGAGA 62.687 66.667 10.60 0.00 43.61 3.71
1405 1898 4.360405 GTGGATGGGGTTGGGCGT 62.360 66.667 0.00 0.00 0.00 5.68
1427 1920 2.765250 GAAGGAGCACTTGTCGCCGA 62.765 60.000 0.00 0.00 40.21 5.54
1491 1985 1.348064 AAGTCGGATCACCCAGAACA 58.652 50.000 0.00 0.00 34.14 3.18
1492 1986 2.076863 CAAAGTCGGATCACCCAGAAC 58.923 52.381 0.00 0.00 34.14 3.01
1609 2103 3.590714 TGATCTGCATGATAAGGGAGGA 58.409 45.455 0.00 0.00 35.14 3.71
1642 2140 1.305381 AGTAGGAGAAGCGCCAGGT 60.305 57.895 2.29 0.00 0.00 4.00
2160 4123 1.947456 ACCTGCTCGTTTTCAACCTTC 59.053 47.619 0.00 0.00 0.00 3.46
2234 4197 1.779025 CGTATCCACCTGCTGCATGC 61.779 60.000 11.82 11.82 43.25 4.06
2289 4252 0.617413 CACAGCTCTCTGGGTGGATT 59.383 55.000 0.00 0.00 44.54 3.01
2585 4551 5.295431 TCAGAAACAACACACAACAGAAG 57.705 39.130 0.00 0.00 0.00 2.85
2602 4570 2.925966 ATTCCCAGCCCAAATCAGAA 57.074 45.000 0.00 0.00 0.00 3.02
2648 4617 2.711542 GCTTCAGCCTGCTAAGGTTTA 58.288 47.619 0.00 0.00 46.43 2.01
2790 4786 5.186797 CCCACCAAACATCCTAAAAATAGCA 59.813 40.000 0.00 0.00 0.00 3.49
2792 4788 6.210584 ACACCCACCAAACATCCTAAAAATAG 59.789 38.462 0.00 0.00 0.00 1.73
2943 5105 9.547279 AGTGAATTCCTATTACCCTTTGAAAAT 57.453 29.630 2.27 0.00 0.00 1.82
3030 5196 7.309805 GCATTGGTGTTACCCTTAAAGAAGAAT 60.310 37.037 0.00 0.00 37.50 2.40
3283 5483 4.881157 ATGGCTTTGGTATTACCCTCTT 57.119 40.909 10.37 0.00 37.50 2.85
3285 5485 7.286775 TGAATTAATGGCTTTGGTATTACCCTC 59.713 37.037 10.37 0.00 37.50 4.30


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

AutoCloner maintained by Alex Coulton.