Multiple sequence alignment - TraesCS6B01G272800

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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 TraesCS6B01G272800 chr6B 100.000 2701 0 0 1 2701 492220517 492217817 0.000000e+00 4988.0
1 TraesCS6B01G272800 chr6B 92.109 811 40 3 1 787 392484408 392485218 0.000000e+00 1122.0
2 TraesCS6B01G272800 chr6B 90.819 806 43 10 1 781 6885483 6884684 0.000000e+00 1050.0
3 TraesCS6B01G272800 chr6B 90.886 801 40 7 1 778 37233110 37232320 0.000000e+00 1044.0
4 TraesCS6B01G272800 chr6B 100.000 36 0 0 3003 3038 492217515 492217480 1.950000e-07 67.6
5 TraesCS6B01G272800 chr6A 95.522 1898 56 9 786 2682 467055678 467053809 0.000000e+00 3007.0
6 TraesCS6B01G272800 chr6A 89.791 813 40 19 1 787 76961803 76961008 0.000000e+00 1002.0
7 TraesCS6B01G272800 chr6A 96.154 78 2 1 2389 2466 467054169 467054093 3.180000e-25 126.0
8 TraesCS6B01G272800 chr6D 93.861 1629 45 15 786 2395 328342128 328340536 0.000000e+00 2403.0
9 TraesCS6B01G272800 chr6D 90.609 788 43 10 23 788 28873544 28874322 0.000000e+00 1016.0
10 TraesCS6B01G272800 chr6D 89.456 294 14 7 2389 2682 328340613 328340337 3.730000e-94 355.0
11 TraesCS6B01G272800 chr3D 91.895 802 39 5 1 778 565800612 565799813 0.000000e+00 1098.0
12 TraesCS6B01G272800 chr1B 92.820 766 25 4 1 738 520281910 520282673 0.000000e+00 1083.0
13 TraesCS6B01G272800 chr1B 91.375 800 25 2 1 778 520347621 520346844 0.000000e+00 1055.0
14 TraesCS6B01G272800 chr1B 90.446 785 39 12 23 778 586279774 586278997 0.000000e+00 1002.0
15 TraesCS6B01G272800 chr7D 91.120 777 40 6 23 778 27042610 27043378 0.000000e+00 1026.0
16 TraesCS6B01G272800 chr2D 89.889 811 49 8 1 785 104151383 104150580 0.000000e+00 1013.0
17 TraesCS6B01G272800 chr2D 90.921 771 39 7 23 771 521766614 521765853 0.000000e+00 1007.0
18 TraesCS6B01G272800 chr2D 90.525 781 45 5 23 781 457250777 457250004 0.000000e+00 1005.0
19 TraesCS6B01G272800 chr2B 90.018 561 24 11 1 537 794770429 794770981 0.000000e+00 697.0
20 TraesCS6B01G272800 chr3B 90.533 507 18 9 1 485 622758463 622758961 0.000000e+00 643.0


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 TraesCS6B01G272800 chr6B 492217480 492220517 3037 True 2527.8 4988 100.0000 1 3038 2 chr6B.!!$R3 3037
1 TraesCS6B01G272800 chr6B 392484408 392485218 810 False 1122.0 1122 92.1090 1 787 1 chr6B.!!$F1 786
2 TraesCS6B01G272800 chr6B 6884684 6885483 799 True 1050.0 1050 90.8190 1 781 1 chr6B.!!$R1 780
3 TraesCS6B01G272800 chr6B 37232320 37233110 790 True 1044.0 1044 90.8860 1 778 1 chr6B.!!$R2 777
4 TraesCS6B01G272800 chr6A 467053809 467055678 1869 True 1566.5 3007 95.8380 786 2682 2 chr6A.!!$R2 1896
5 TraesCS6B01G272800 chr6A 76961008 76961803 795 True 1002.0 1002 89.7910 1 787 1 chr6A.!!$R1 786
6 TraesCS6B01G272800 chr6D 328340337 328342128 1791 True 1379.0 2403 91.6585 786 2682 2 chr6D.!!$R1 1896
7 TraesCS6B01G272800 chr6D 28873544 28874322 778 False 1016.0 1016 90.6090 23 788 1 chr6D.!!$F1 765
8 TraesCS6B01G272800 chr3D 565799813 565800612 799 True 1098.0 1098 91.8950 1 778 1 chr3D.!!$R1 777
9 TraesCS6B01G272800 chr1B 520281910 520282673 763 False 1083.0 1083 92.8200 1 738 1 chr1B.!!$F1 737
10 TraesCS6B01G272800 chr1B 520346844 520347621 777 True 1055.0 1055 91.3750 1 778 1 chr1B.!!$R1 777
11 TraesCS6B01G272800 chr1B 586278997 586279774 777 True 1002.0 1002 90.4460 23 778 1 chr1B.!!$R2 755
12 TraesCS6B01G272800 chr7D 27042610 27043378 768 False 1026.0 1026 91.1200 23 778 1 chr7D.!!$F1 755
13 TraesCS6B01G272800 chr2D 104150580 104151383 803 True 1013.0 1013 89.8890 1 785 1 chr2D.!!$R1 784
14 TraesCS6B01G272800 chr2D 521765853 521766614 761 True 1007.0 1007 90.9210 23 771 1 chr2D.!!$R3 748
15 TraesCS6B01G272800 chr2D 457250004 457250777 773 True 1005.0 1005 90.5250 23 781 1 chr2D.!!$R2 758
16 TraesCS6B01G272800 chr2B 794770429 794770981 552 False 697.0 697 90.0180 1 537 1 chr2B.!!$F1 536

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
839 885 0.031449 TTGACGACACTGCGTGATCA 59.969 50.0 14.18 11.24 45.72 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 2103 0.108992 CATGTCACCTGTGCCAATGC 60.109 55.0 0.0 0.0 38.26 3.56 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
274 301 1.197721 CCGCGAGAAAAGCTTCAACAT 59.802 47.619 8.23 0.00 33.64 2.71
426 453 4.966274 ACAGGGGGTGCCGGTGTA 62.966 66.667 1.90 0.00 0.00 2.90
485 513 2.750350 CTTTCTGCTGGACCGGGT 59.250 61.111 6.32 0.00 0.00 5.28
666 710 5.878406 AGAAGAGGAAGAAGAAGTCAACA 57.122 39.130 0.00 0.00 0.00 3.33
671 716 2.484947 GGAAGAAGAAGTCAACACGGGT 60.485 50.000 0.00 0.00 0.00 5.28
689 735 0.250513 GTGAAGGAGGCACGAGGAAT 59.749 55.000 0.00 0.00 0.00 3.01
839 885 0.031449 TTGACGACACTGCGTGATCA 59.969 50.000 14.18 11.24 45.72 2.92
932 978 1.569479 GGAAGTGCAGAACAGCGTCC 61.569 60.000 0.00 0.00 37.31 4.79
984 1031 2.225017 ACCACATCCGAACCCAAATCTT 60.225 45.455 0.00 0.00 0.00 2.40
1070 1117 2.178580 GCCATCCACCTCCAAATCAAA 58.821 47.619 0.00 0.00 0.00 2.69
1479 1529 3.532155 GCCGTCCTCGCAGGAGAT 61.532 66.667 5.28 0.00 46.90 2.75
1626 1676 2.943978 CGGCCAGTTCCTCGACCTT 61.944 63.158 2.24 0.00 0.00 3.50
1665 1715 1.741401 CGAAGCCGAGGTCATGCAA 60.741 57.895 0.00 0.00 38.22 4.08
2048 2098 4.272100 GCTTTAAGCGTGGACGGA 57.728 55.556 0.00 0.00 40.23 4.69
2049 2099 1.785951 GCTTTAAGCGTGGACGGAC 59.214 57.895 0.00 0.00 40.23 4.79
2050 2100 1.952266 GCTTTAAGCGTGGACGGACG 61.952 60.000 0.00 0.00 42.42 4.79
2289 2339 1.878953 AGCTGACCCAAGTTTACACG 58.121 50.000 0.00 0.00 0.00 4.49
2335 2399 6.051646 TCGTTTGTAAGAAAGTTAACCTGC 57.948 37.500 0.88 0.00 0.00 4.85
2355 2419 0.375454 TGTGCTTGTTCGTCGTTTGG 59.625 50.000 0.00 0.00 0.00 3.28
2430 2494 1.326245 TGTGCTTGTTCGTCGTTTGAG 59.674 47.619 0.00 0.00 0.00 3.02
2497 2561 3.770933 AGGCCATCACAATGCTTTGTTAT 59.229 39.130 14.80 10.29 43.57 1.89
2499 2563 4.114794 GCCATCACAATGCTTTGTTATCC 58.885 43.478 14.80 3.88 43.57 2.59
2500 2564 4.381825 GCCATCACAATGCTTTGTTATCCA 60.382 41.667 14.80 0.00 43.57 3.41
2565 2629 1.978542 AAGCACGCGTCAACTAGTAG 58.021 50.000 9.86 0.00 0.00 2.57
2567 2631 1.135746 AGCACGCGTCAACTAGTAGTC 60.136 52.381 9.86 0.00 0.00 2.59
2642 2706 9.132923 TCTTGTCTAGGGAGTTAACACTATATG 57.867 37.037 8.61 0.00 31.22 1.78
2694 2758 9.635404 TCTAAAATTTTAGGAAAGAAGTCCACA 57.365 29.630 29.04 9.27 40.48 4.17
2698 2762 7.939784 ATTTTAGGAAAGAAGTCCACATACC 57.060 36.000 0.00 0.00 40.48 2.73
2699 2763 5.431179 TTAGGAAAGAAGTCCACATACCC 57.569 43.478 0.00 0.00 40.48 3.69
2700 2764 2.576648 AGGAAAGAAGTCCACATACCCC 59.423 50.000 0.00 0.00 40.48 4.95
3034 3098 5.506730 TGGACTATCCAATACCACACAAA 57.493 39.130 0.00 0.00 45.00 2.83
3035 3099 6.073447 TGGACTATCCAATACCACACAAAT 57.927 37.500 0.00 0.00 45.00 2.32
3036 3100 6.119536 TGGACTATCCAATACCACACAAATC 58.880 40.000 0.00 0.00 45.00 2.17
3037 3101 6.119536 GGACTATCCAATACCACACAAATCA 58.880 40.000 0.00 0.00 36.28 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 301 3.436704 CGGTTGAAGCTTTTCTCTATGCA 59.563 43.478 0.00 0.00 0.00 3.96
382 409 3.083349 ACCTAGCAGCCGCCATCA 61.083 61.111 0.00 0.00 39.83 3.07
426 453 0.889186 AAATGGCGCCGTCTTGAAGT 60.889 50.000 24.10 0.13 0.00 3.01
485 513 2.494445 CAGCATCCGTACTCGCCA 59.506 61.111 0.00 0.00 35.54 5.69
666 710 4.003788 CGTGCCTCCTTCACCCGT 62.004 66.667 0.00 0.00 0.00 5.28
671 716 1.757118 CTATTCCTCGTGCCTCCTTCA 59.243 52.381 0.00 0.00 0.00 3.02
689 735 0.179043 AGCTCGAGCCGTCAGATCTA 60.179 55.000 32.94 0.00 43.38 1.98
853 899 5.221322 CCCATTATCAGATCACGAGTTCTCA 60.221 44.000 0.00 0.00 0.00 3.27
1070 1117 1.833049 CGGATAGGGAGGAAGCGGT 60.833 63.158 0.00 0.00 0.00 5.68
1494 1544 1.153429 GATGACGTGGGTGTAGGCC 60.153 63.158 0.00 0.00 0.00 5.19
1647 1697 1.699656 CTTGCATGACCTCGGCTTCG 61.700 60.000 0.00 0.00 0.00 3.79
1665 1715 1.344763 CCGAACTTCTTGGTCAGGACT 59.655 52.381 0.00 0.00 31.03 3.85
1710 1760 2.345244 CCTAGCATAGCCCCGCAG 59.655 66.667 0.00 0.00 37.37 5.18
1884 1934 3.815569 GAGCTCCTCGACGATGCCG 62.816 68.421 0.87 0.00 42.50 5.69
2040 2090 2.742372 AATGCTGCGTCCGTCCAC 60.742 61.111 0.00 0.00 0.00 4.02
2041 2091 2.741985 CAATGCTGCGTCCGTCCA 60.742 61.111 0.00 0.00 0.00 4.02
2042 2092 3.499737 CCAATGCTGCGTCCGTCC 61.500 66.667 0.00 0.00 0.00 4.79
2043 2093 4.166011 GCCAATGCTGCGTCCGTC 62.166 66.667 0.00 0.00 33.53 4.79
2045 2095 4.465512 GTGCCAATGCTGCGTCCG 62.466 66.667 0.00 0.00 38.71 4.79
2046 2096 3.332493 CTGTGCCAATGCTGCGTCC 62.332 63.158 0.00 0.00 38.71 4.79
2047 2097 2.177531 CTGTGCCAATGCTGCGTC 59.822 61.111 0.00 0.00 38.71 5.19
2048 2098 3.367743 CCTGTGCCAATGCTGCGT 61.368 61.111 0.00 0.00 38.71 5.24
2049 2099 3.367743 ACCTGTGCCAATGCTGCG 61.368 61.111 0.00 0.00 38.71 5.18
2050 2100 2.260434 CACCTGTGCCAATGCTGC 59.740 61.111 0.00 0.00 38.71 5.25
2051 2101 1.174078 TGTCACCTGTGCCAATGCTG 61.174 55.000 0.00 0.00 38.71 4.41
2052 2102 0.251474 ATGTCACCTGTGCCAATGCT 60.251 50.000 0.00 0.00 38.71 3.79
2053 2103 0.108992 CATGTCACCTGTGCCAATGC 60.109 55.000 0.00 0.00 38.26 3.56
2054 2104 1.250328 ACATGTCACCTGTGCCAATG 58.750 50.000 0.00 0.00 0.00 2.82
2230 2280 7.653767 AGGAACTCGAAAATTGTTAGTACAG 57.346 36.000 0.00 0.00 35.28 2.74
2232 2282 8.645487 CAGTAGGAACTCGAAAATTGTTAGTAC 58.355 37.037 0.00 0.00 41.75 2.73
2239 2289 5.327091 CATGCAGTAGGAACTCGAAAATTG 58.673 41.667 0.00 0.00 41.75 2.32
2246 2296 0.824109 TCCCATGCAGTAGGAACTCG 59.176 55.000 4.33 0.00 41.75 4.18
2289 2339 4.798574 ACAATTCGAAAGCTCCAAACATC 58.201 39.130 0.00 0.00 0.00 3.06
2329 2393 0.748005 ACGAACAAGCACAGCAGGTT 60.748 50.000 0.00 0.00 31.78 3.50
2335 2399 1.594518 CCAAACGACGAACAAGCACAG 60.595 52.381 0.00 0.00 0.00 3.66
2397 2461 3.361786 ACAAGCACACCAGGTAAACTTT 58.638 40.909 0.00 0.00 0.00 2.66
2447 2511 5.467035 ACCTGAAATGTTTTACCACCATG 57.533 39.130 0.00 0.00 0.00 3.66
2528 2592 6.602179 CGTGCTTTCTCATTTTCAATGTCTA 58.398 36.000 0.00 0.00 0.00 2.59
2565 2629 3.800531 AGACCTAGAGACGCTCTTAGAC 58.199 50.000 13.34 7.19 41.50 2.59
2567 2631 3.562557 GGAAGACCTAGAGACGCTCTTAG 59.437 52.174 13.34 8.70 41.50 2.18
2606 2670 6.468543 ACTCCCTAGACAAGAATCAAGAAAC 58.531 40.000 0.00 0.00 0.00 2.78
2668 2732 9.635404 TGTGGACTTCTTTCCTAAAATTTTAGA 57.365 29.630 30.86 18.07 42.05 2.10
3012 3076 5.506730 TTTGTGTGGTATTGGATAGTCCA 57.493 39.130 0.00 0.00 46.61 4.02
3013 3077 6.119536 TGATTTGTGTGGTATTGGATAGTCC 58.880 40.000 0.00 0.00 36.96 3.85


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

AutoCloner maintained by Alex Coulton.