Multiple sequence alignment - TraesCS6D01G309200

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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 TraesCS6D01G309200 chr6D 100.000 3798 0 0 1 3798 419840789 419844586 0 7014
1 TraesCS6D01G309200 chr6D 98.761 1049 12 1 2751 3798 419860106 419861154 0 1864
2 TraesCS6D01G309200 chr6D 97.903 1049 21 1 2751 3798 207434572 207435620 0 1814
3 TraesCS6D01G309200 chr6D 97.235 1049 28 1 2751 3798 320426115 320427163 0 1775
4 TraesCS6D01G309200 chr3D 96.892 2767 79 7 1 2760 64822359 64819593 0 4626
5 TraesCS6D01G309200 chr3D 96.456 2765 91 7 1 2760 613553149 613555911 0 4556
6 TraesCS6D01G309200 chr4B 95.741 2747 110 7 18 2760 200734704 200731961 0 4418
7 TraesCS6D01G309200 chr2B 95.298 2765 122 8 1 2760 693491967 693494728 0 4379
8 TraesCS6D01G309200 chr2B 93.867 2772 150 16 1 2760 95264404 95261641 0 4159
9 TraesCS6D01G309200 chr2B 93.992 2763 134 21 1 2760 694895785 694898518 0 4154
10 TraesCS6D01G309200 chr7B 95.085 2767 110 20 1 2760 92647805 92650552 0 4333
11 TraesCS6D01G309200 chr6B 96.291 2615 89 6 1 2612 423064195 423061586 0 4285
12 TraesCS6D01G309200 chr1D 94.184 2768 146 10 1 2760 466346195 466343435 0 4205
13 TraesCS6D01G309200 chr1D 97.416 1045 23 4 2757 3798 476601285 476602328 0 1777
14 TraesCS6D01G309200 chr1D 97.411 1043 24 3 2757 3798 201135031 201133991 0 1773
15 TraesCS6D01G309200 chr1D 97.411 1043 24 3 2757 3798 201142585 201141545 0 1773
16 TraesCS6D01G309200 chr7D 97.608 1045 23 2 2755 3798 235563310 235562267 0 1790
17 TraesCS6D01G309200 chr7D 97.315 1043 25 3 2757 3798 70879782 70878742 0 1768
18 TraesCS6D01G309200 chr2D 97.230 1047 27 2 2753 3798 173866752 173865707 0 1772


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 TraesCS6D01G309200 chr6D 419840789 419844586 3797 False 7014 7014 100.000 1 3798 1 chr6D.!!$F3 3797
1 TraesCS6D01G309200 chr6D 419860106 419861154 1048 False 1864 1864 98.761 2751 3798 1 chr6D.!!$F4 1047
2 TraesCS6D01G309200 chr6D 207434572 207435620 1048 False 1814 1814 97.903 2751 3798 1 chr6D.!!$F1 1047
3 TraesCS6D01G309200 chr6D 320426115 320427163 1048 False 1775 1775 97.235 2751 3798 1 chr6D.!!$F2 1047
4 TraesCS6D01G309200 chr3D 64819593 64822359 2766 True 4626 4626 96.892 1 2760 1 chr3D.!!$R1 2759
5 TraesCS6D01G309200 chr3D 613553149 613555911 2762 False 4556 4556 96.456 1 2760 1 chr3D.!!$F1 2759
6 TraesCS6D01G309200 chr4B 200731961 200734704 2743 True 4418 4418 95.741 18 2760 1 chr4B.!!$R1 2742
7 TraesCS6D01G309200 chr2B 693491967 693494728 2761 False 4379 4379 95.298 1 2760 1 chr2B.!!$F1 2759
8 TraesCS6D01G309200 chr2B 95261641 95264404 2763 True 4159 4159 93.867 1 2760 1 chr2B.!!$R1 2759
9 TraesCS6D01G309200 chr2B 694895785 694898518 2733 False 4154 4154 93.992 1 2760 1 chr2B.!!$F2 2759
10 TraesCS6D01G309200 chr7B 92647805 92650552 2747 False 4333 4333 95.085 1 2760 1 chr7B.!!$F1 2759
11 TraesCS6D01G309200 chr6B 423061586 423064195 2609 True 4285 4285 96.291 1 2612 1 chr6B.!!$R1 2611
12 TraesCS6D01G309200 chr1D 466343435 466346195 2760 True 4205 4205 94.184 1 2760 1 chr1D.!!$R3 2759
13 TraesCS6D01G309200 chr1D 476601285 476602328 1043 False 1777 1777 97.416 2757 3798 1 chr1D.!!$F1 1041
14 TraesCS6D01G309200 chr1D 201133991 201135031 1040 True 1773 1773 97.411 2757 3798 1 chr1D.!!$R1 1041
15 TraesCS6D01G309200 chr1D 201141545 201142585 1040 True 1773 1773 97.411 2757 3798 1 chr1D.!!$R2 1041
16 TraesCS6D01G309200 chr7D 235562267 235563310 1043 True 1790 1790 97.608 2755 3798 1 chr7D.!!$R2 1043
17 TraesCS6D01G309200 chr7D 70878742 70879782 1040 True 1768 1768 97.315 2757 3798 1 chr7D.!!$R1 1041
18 TraesCS6D01G309200 chr2D 173865707 173866752 1045 True 1772 1772 97.230 2753 3798 1 chr2D.!!$R1 1045

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
47 50 1.412079 TTGTACCCCACGTGTACTGT 58.588 50.000 15.65 8.13 39.42 3.55 F
249 255 2.235898 TGAAATAAATGCAACCTGGCCC 59.764 45.455 0.00 0.00 0.00 5.80 F
1124 1146 3.427098 CGATCTGTTTACTACACGCAGGA 60.427 47.826 0.00 0.00 32.10 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1124 1146 1.134228 AGGGTTACCACCACGACTTT 58.866 50.000 2.98 0.0 46.43 2.66 R
1299 1322 1.882623 CCTTCTTCTCCTTGCACAACC 59.117 52.381 0.00 0.0 0.00 3.77 R
2943 2979 0.179004 TGCCACTTTGGGTTCACGAT 60.179 50.000 0.00 0.0 38.19 3.73 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
23 26 3.608073 GCATGCTAGCCAAAAGTAAAACG 59.392 43.478 13.29 0.00 0.00 3.60
47 50 1.412079 TTGTACCCCACGTGTACTGT 58.588 50.000 15.65 8.13 39.42 3.55
120 123 5.806654 ACATGTTTTCTGGCCAACTAAAT 57.193 34.783 7.01 0.00 0.00 1.40
249 255 2.235898 TGAAATAAATGCAACCTGGCCC 59.764 45.455 0.00 0.00 0.00 5.80
762 775 4.584874 TGCCAGCTATTTACTGCAAACTA 58.415 39.130 0.00 0.00 33.65 2.24
1124 1146 3.427098 CGATCTGTTTACTACACGCAGGA 60.427 47.826 0.00 0.00 32.10 3.86
1299 1322 2.203209 GCTGGGGCTATTGACGGG 60.203 66.667 0.00 0.00 35.22 5.28
1459 1482 0.824759 GAACACCTCTAGGCGGACAT 59.175 55.000 6.07 0.00 39.32 3.06
1496 1520 7.819900 TGTATTGGTAAAACAACAGTTTTGCTT 59.180 29.630 17.09 8.67 43.29 3.91
1724 1752 3.273434 TGTTGGTGAAGCTGATAGATGC 58.727 45.455 0.00 0.00 0.00 3.91
1829 1857 1.676746 CAAGGCATCTCACCTGATGG 58.323 55.000 6.62 0.00 42.82 3.51
1835 1863 2.295885 CATCTCACCTGATGGAAAGGC 58.704 52.381 0.00 0.00 39.91 4.35
1876 1904 3.560636 ACTGCAACTTGACTACAGGTT 57.439 42.857 0.00 0.00 44.92 3.50
1942 1974 5.230182 CAGTCTAGTGTGCAACTGTTATGA 58.770 41.667 5.91 0.00 40.26 2.15
2004 2036 3.153919 GTCCAACTTCCCATGCTGTTTA 58.846 45.455 0.00 0.00 0.00 2.01
2116 2150 0.764890 AAAGGTGCAGCTAGGTGTCA 59.235 50.000 20.51 17.10 0.00 3.58
2291 2327 1.595929 GTGCCGTTCGGACCAAAGA 60.596 57.895 15.69 0.00 0.00 2.52
2376 2412 3.127548 ACAATTGCGCACTTCAAGGATAG 59.872 43.478 11.12 0.00 0.00 2.08
2385 2421 5.179368 CGCACTTCAAGGATAGACAGAAAAA 59.821 40.000 0.00 0.00 0.00 1.94
2527 2563 4.801330 TGACACTACCTACATGACCAAG 57.199 45.455 0.00 0.00 0.00 3.61
2546 2582 6.530120 ACCAAGATGTATAATATGCCGTTCA 58.470 36.000 0.00 0.00 0.00 3.18
2587 2623 2.033801 CCGACATGGCCAATCTTTCATC 59.966 50.000 10.96 0.00 0.00 2.92
2682 2718 2.331265 GTGGCAAACCTCCTGACAC 58.669 57.895 0.00 0.00 45.16 3.67
2942 2978 4.530857 CCCGGGCCGACATGACTC 62.531 72.222 30.79 0.00 0.00 3.36
2943 2979 3.770040 CCGGGCCGACATGACTCA 61.770 66.667 30.79 0.00 0.00 3.41
3600 3638 4.209911 GGTAACAAGCTAAACGTCGAAGTT 59.790 41.667 11.11 11.11 35.59 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.553172 TGGGGTACAATGCACGTTTTAC 59.447 45.455 0.00 0.00 0.00 2.01
23 26 0.887387 ACACGTGGGGTACAATGCAC 60.887 55.000 21.57 0.00 0.00 4.57
120 123 2.896044 TCAGTTTTGGCCAACATGCATA 59.104 40.909 20.35 0.00 0.00 3.14
249 255 5.781210 TGGCTAGAATAGATGTCTCAGTG 57.219 43.478 0.00 0.00 42.77 3.66
474 482 2.795329 CTTTGCAATAGGTGTGGGACT 58.205 47.619 0.00 0.00 0.00 3.85
762 775 7.336679 TGCATAGAGTTGTTATGTTAGTTGCAT 59.663 33.333 0.00 0.00 32.38 3.96
1124 1146 1.134228 AGGGTTACCACCACGACTTT 58.866 50.000 2.98 0.00 46.43 2.66
1299 1322 1.882623 CCTTCTTCTCCTTGCACAACC 59.117 52.381 0.00 0.00 0.00 3.77
1347 1370 2.092212 CCTCATGCCAACATAGGGTTCT 60.092 50.000 0.00 0.00 37.72 3.01
1424 1447 5.684704 AGGTGTTCATCTTGACAGAGAAAA 58.315 37.500 0.00 0.00 30.36 2.29
1496 1520 3.011566 TGGGCTTCTTGAACTTGTTGA 57.988 42.857 0.00 0.00 0.00 3.18
1835 1863 5.002468 CAGTTATACAAGATGCGCAAAAACG 59.998 40.000 17.11 4.76 0.00 3.60
1942 1974 6.467677 AGTCATTTCAGTTGCACAGTAGTAT 58.532 36.000 0.00 0.00 0.00 2.12
2004 2036 7.315142 CACAACAAGCACCAAAAGTGATATAT 58.685 34.615 0.00 0.00 46.71 0.86
2116 2150 6.335777 GCACAGAAGATAATTGCAGGAAATT 58.664 36.000 0.00 0.00 34.24 1.82
2291 2327 9.296400 GAAACTTGTACACACATTTGTTATTGT 57.704 29.630 0.00 0.00 33.76 2.71
2376 2412 4.991687 AGAAGTCTGGATCGTTTTTCTGTC 59.008 41.667 0.00 0.00 0.00 3.51
2385 2421 6.130569 ACCTTATAGAAGAAGTCTGGATCGT 58.869 40.000 0.00 0.00 37.12 3.73
2450 2486 3.209410 CTTTTCGAGCTAAGCCATCCAT 58.791 45.455 0.00 0.00 0.00 3.41
2527 2563 5.121768 GGGTGTGAACGGCATATTATACATC 59.878 44.000 0.00 0.00 0.00 3.06
2546 2582 3.761752 CGGTTTATTCCAATGAAGGGTGT 59.238 43.478 0.00 0.00 33.05 4.16
2587 2623 1.010125 CACAAACGTGCAACCGAGG 60.010 57.895 3.48 0.00 0.00 4.63
2682 2718 4.512944 CACCATCTTGATCGGTTATGAAGG 59.487 45.833 0.00 0.00 30.43 3.46
2942 2978 0.240945 GCCACTTTGGGTTCACGATG 59.759 55.000 0.00 0.00 38.19 3.84
2943 2979 0.179004 TGCCACTTTGGGTTCACGAT 60.179 50.000 0.00 0.00 38.19 3.73
3132 3168 2.744202 GGCATGTGATTCACTTCGTTCT 59.256 45.455 17.26 0.00 35.11 3.01
3600 3638 1.020861 TCGCTAGTAGTTCCGCGTGA 61.021 55.000 4.92 0.00 45.25 4.35


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

AutoCloner maintained by Alex Coulton.