Multiple sequence alignment - TraesCS1D01G165900

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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 TraesCS1D01G165900 chr1D 100.000 2264 0 0 1 2264 236926713 236924450 0.000000e+00 4181.0
1 TraesCS1D01G165900 chr1D 83.584 731 96 21 102 818 25871572 25870852 0.000000e+00 664.0
2 TraesCS1D01G165900 chr1B 95.170 1884 75 7 86 1958 342332295 342330417 0.000000e+00 2961.0
3 TraesCS1D01G165900 chr1B 96.154 338 7 2 1932 2264 342330416 342330080 4.250000e-152 547.0
4 TraesCS1D01G165900 chr1B 94.595 37 1 1 36 72 677290754 677290789 3.140000e-04 56.5
5 TraesCS1D01G165900 chr1A 94.294 1437 59 5 839 2264 308786619 308788043 0.000000e+00 2178.0
6 TraesCS1D01G165900 chr1A 92.320 651 45 4 134 781 308785973 308786621 0.000000e+00 920.0
7 TraesCS1D01G165900 chr1A 88.000 75 3 2 5 73 308785900 308785974 1.440000e-12 84.2
8 TraesCS1D01G165900 chr4B 86.997 646 77 7 96 736 260074576 260075219 0.000000e+00 721.0
9 TraesCS1D01G165900 chr4B 87.304 638 72 8 97 728 359681965 359682599 0.000000e+00 721.0
10 TraesCS1D01G165900 chr4B 87.107 636 66 13 93 718 385567356 385566727 0.000000e+00 706.0
11 TraesCS1D01G165900 chr4B 84.783 92 11 1 5 96 606550537 606550449 3.100000e-14 89.8
12 TraesCS1D01G165900 chr5B 85.735 680 78 17 92 763 440209124 440208456 0.000000e+00 701.0
13 TraesCS1D01G165900 chr3D 86.719 640 73 10 96 729 386738316 386738949 0.000000e+00 701.0
14 TraesCS1D01G165900 chr3D 100.000 31 0 0 43 73 260997188 260997158 8.730000e-05 58.4
15 TraesCS1D01G165900 chr2D 86.646 644 73 13 92 728 130809380 130808743 0.000000e+00 701.0
16 TraesCS1D01G165900 chr6B 75.758 891 162 43 871 1727 41977927 41977057 1.260000e-107 399.0
17 TraesCS1D01G165900 chr4D 82.759 145 16 7 6 145 222015516 222015656 1.100000e-23 121.0
18 TraesCS1D01G165900 chr3A 88.406 69 6 1 5 73 508205392 508205458 5.180000e-12 82.4
19 TraesCS1D01G165900 chr3B 100.000 32 0 0 41 72 146977040 146977009 2.430000e-05 60.2
20 TraesCS1D01G165900 chr2B 97.143 35 0 1 38 72 58839822 58839855 8.730000e-05 58.4
21 TraesCS1D01G165900 chr2B 94.595 37 1 1 36 72 101119808 101119843 3.140000e-04 56.5


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 TraesCS1D01G165900 chr1D 236924450 236926713 2263 True 4181.000000 4181 100.000 1 2264 1 chr1D.!!$R2 2263
1 TraesCS1D01G165900 chr1D 25870852 25871572 720 True 664.000000 664 83.584 102 818 1 chr1D.!!$R1 716
2 TraesCS1D01G165900 chr1B 342330080 342332295 2215 True 1754.000000 2961 95.662 86 2264 2 chr1B.!!$R1 2178
3 TraesCS1D01G165900 chr1A 308785900 308788043 2143 False 1060.733333 2178 91.538 5 2264 3 chr1A.!!$F1 2259
4 TraesCS1D01G165900 chr4B 260074576 260075219 643 False 721.000000 721 86.997 96 736 1 chr4B.!!$F1 640
5 TraesCS1D01G165900 chr4B 359681965 359682599 634 False 721.000000 721 87.304 97 728 1 chr4B.!!$F2 631
6 TraesCS1D01G165900 chr4B 385566727 385567356 629 True 706.000000 706 87.107 93 718 1 chr4B.!!$R1 625
7 TraesCS1D01G165900 chr5B 440208456 440209124 668 True 701.000000 701 85.735 92 763 1 chr5B.!!$R1 671
8 TraesCS1D01G165900 chr3D 386738316 386738949 633 False 701.000000 701 86.719 96 729 1 chr3D.!!$F1 633
9 TraesCS1D01G165900 chr2D 130808743 130809380 637 True 701.000000 701 86.646 92 728 1 chr2D.!!$R1 636
10 TraesCS1D01G165900 chr6B 41977057 41977927 870 True 399.000000 399 75.758 871 1727 1 chr6B.!!$R1 856

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
818 970 0.523125 CCGCACGTGTGGCAAATATG 60.523 55.0 33.26 9.17 39.04 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2299 2.524394 ACCTCACTCGCCACCTGT 60.524 61.111 0.0 0.0 0.0 4.0 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
49 50 2.168326 GGGGGCAAAAAGTTGTCATG 57.832 50.000 0.00 0.00 41.39 3.07
50 51 1.691434 GGGGGCAAAAAGTTGTCATGA 59.309 47.619 0.00 0.00 41.39 3.07
51 52 2.302733 GGGGGCAAAAAGTTGTCATGAT 59.697 45.455 0.00 0.00 41.39 2.45
52 53 3.328505 GGGGCAAAAAGTTGTCATGATG 58.671 45.455 0.00 0.00 41.39 3.07
53 54 3.244181 GGGGCAAAAAGTTGTCATGATGT 60.244 43.478 0.00 0.00 41.39 3.06
54 55 4.379652 GGGCAAAAAGTTGTCATGATGTT 58.620 39.130 0.00 0.00 41.39 2.71
55 56 4.815846 GGGCAAAAAGTTGTCATGATGTTT 59.184 37.500 0.00 0.00 41.39 2.83
56 57 5.988561 GGGCAAAAAGTTGTCATGATGTTTA 59.011 36.000 0.00 0.00 41.39 2.01
57 58 6.073819 GGGCAAAAAGTTGTCATGATGTTTAC 60.074 38.462 0.00 0.00 41.39 2.01
58 59 6.478344 GGCAAAAAGTTGTCATGATGTTTACA 59.522 34.615 0.00 0.00 39.28 2.41
59 60 7.336975 GCAAAAAGTTGTCATGATGTTTACAC 58.663 34.615 0.00 0.00 37.06 2.90
60 61 7.222611 GCAAAAAGTTGTCATGATGTTTACACT 59.777 33.333 0.00 0.00 37.06 3.55
61 62 8.533965 CAAAAAGTTGTCATGATGTTTACACTG 58.466 33.333 0.00 0.00 0.00 3.66
62 63 7.566760 AAAGTTGTCATGATGTTTACACTGA 57.433 32.000 0.00 0.00 0.00 3.41
63 64 7.566760 AAGTTGTCATGATGTTTACACTGAA 57.433 32.000 0.00 0.00 0.00 3.02
64 65 7.194607 AGTTGTCATGATGTTTACACTGAAG 57.805 36.000 0.00 0.00 0.00 3.02
65 66 6.767902 AGTTGTCATGATGTTTACACTGAAGT 59.232 34.615 0.00 0.00 0.00 3.01
66 67 7.283127 AGTTGTCATGATGTTTACACTGAAGTT 59.717 33.333 0.00 0.00 0.00 2.66
67 68 6.958255 TGTCATGATGTTTACACTGAAGTTG 58.042 36.000 0.00 0.00 0.00 3.16
68 69 5.853282 GTCATGATGTTTACACTGAAGTTGC 59.147 40.000 0.00 0.00 0.00 4.17
69 70 4.829064 TGATGTTTACACTGAAGTTGCC 57.171 40.909 0.00 0.00 0.00 4.52
70 71 4.203226 TGATGTTTACACTGAAGTTGCCA 58.797 39.130 0.00 0.00 0.00 4.92
71 72 4.826733 TGATGTTTACACTGAAGTTGCCAT 59.173 37.500 0.00 0.00 0.00 4.40
72 73 6.000840 TGATGTTTACACTGAAGTTGCCATA 58.999 36.000 0.00 0.00 0.00 2.74
73 74 5.940192 TGTTTACACTGAAGTTGCCATAG 57.060 39.130 0.00 0.00 0.00 2.23
74 75 5.373222 TGTTTACACTGAAGTTGCCATAGT 58.627 37.500 0.00 0.00 0.00 2.12
75 76 5.238432 TGTTTACACTGAAGTTGCCATAGTG 59.762 40.000 0.00 0.00 43.20 2.74
76 77 3.769739 ACACTGAAGTTGCCATAGTGA 57.230 42.857 9.39 0.00 40.80 3.41
77 78 4.292186 ACACTGAAGTTGCCATAGTGAT 57.708 40.909 9.39 0.00 40.80 3.06
78 79 4.655963 ACACTGAAGTTGCCATAGTGATT 58.344 39.130 9.39 0.00 40.80 2.57
79 80 5.804639 ACACTGAAGTTGCCATAGTGATTA 58.195 37.500 9.39 0.00 40.80 1.75
80 81 5.643777 ACACTGAAGTTGCCATAGTGATTAC 59.356 40.000 9.39 0.00 40.80 1.89
81 82 5.643348 CACTGAAGTTGCCATAGTGATTACA 59.357 40.000 0.00 0.00 40.80 2.41
82 83 5.643777 ACTGAAGTTGCCATAGTGATTACAC 59.356 40.000 0.00 0.00 46.24 2.90
469 614 7.813148 GGCAAGTTTAGTTTCTTAATTCCCTTC 59.187 37.037 0.00 0.00 0.00 3.46
692 843 9.638239 TTTCAATCGGATTTTTCATTTAAGAGG 57.362 29.630 0.00 0.00 0.00 3.69
781 932 4.948608 TGTTGCTACAAGAACGTTTGAA 57.051 36.364 0.46 0.00 0.00 2.69
818 970 0.523125 CCGCACGTGTGGCAAATATG 60.523 55.000 33.26 9.17 39.04 1.78
821 973 1.468520 GCACGTGTGGCAAATATGAGT 59.531 47.619 18.38 0.00 0.00 3.41
836 988 7.328493 GCAAATATGAGTGTCCAAAAACTAACC 59.672 37.037 0.00 0.00 0.00 2.85
846 998 5.476945 GTCCAAAAACTAACCATGACAGGAT 59.523 40.000 0.00 0.00 0.00 3.24
860 1012 2.231478 GACAGGATGGTTCGTCTTCTCA 59.769 50.000 0.00 0.00 43.62 3.27
879 1031 1.731324 ATAGACTCCCTCCCTCCCGG 61.731 65.000 0.00 0.00 0.00 5.73
1238 1417 1.602851 CTACTACGACCGATCTGGGTG 59.397 57.143 8.20 3.22 44.64 4.61
1410 1601 4.793201 AGGTGTTCAAGAAATATAGCCCC 58.207 43.478 0.00 0.00 0.00 5.80
1549 1740 3.205784 TGGCATTGTTTTTCCAAAGGG 57.794 42.857 0.00 0.00 0.00 3.95
1622 1815 2.536066 TCTAACACTTAGCTGGAGCCA 58.464 47.619 0.00 0.00 43.38 4.75
1702 1896 3.681593 AGAAAATTGGCGCTGGTAGTTA 58.318 40.909 7.64 0.00 0.00 2.24
1760 1963 4.755123 GGCTGCAACTGTCTACTTCTTTTA 59.245 41.667 0.50 0.00 0.00 1.52
1844 2047 1.098869 TTTGTGCAGCACCTTTCGAA 58.901 45.000 23.06 6.35 32.73 3.71
2069 2299 8.996271 GTTGTGATGATTGAGAGCATATTATGA 58.004 33.333 7.87 0.00 30.70 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.889301 AGCCATCGAAACATATCAATCAAT 57.111 33.333 0.00 0.00 0.00 2.57
1 2 6.698008 AAGCCATCGAAACATATCAATCAA 57.302 33.333 0.00 0.00 0.00 2.57
35 36 8.533965 CAGTGTAAACATCATGACAACTTTTTG 58.466 33.333 0.00 0.00 38.83 2.44
36 37 8.465999 TCAGTGTAAACATCATGACAACTTTTT 58.534 29.630 0.00 0.00 0.00 1.94
38 39 7.566760 TCAGTGTAAACATCATGACAACTTT 57.433 32.000 0.00 0.00 0.00 2.66
39 40 7.283127 ACTTCAGTGTAAACATCATGACAACTT 59.717 33.333 0.00 0.00 0.00 2.66
41 42 6.959361 ACTTCAGTGTAAACATCATGACAAC 58.041 36.000 0.00 0.00 0.00 3.32
44 45 5.853282 GCAACTTCAGTGTAAACATCATGAC 59.147 40.000 0.00 0.00 0.00 3.06
45 46 5.048782 GGCAACTTCAGTGTAAACATCATGA 60.049 40.000 0.00 0.00 0.00 3.07
47 48 4.826733 TGGCAACTTCAGTGTAAACATCAT 59.173 37.500 0.00 0.00 37.61 2.45
48 49 4.203226 TGGCAACTTCAGTGTAAACATCA 58.797 39.130 0.00 0.00 37.61 3.07
49 50 4.829064 TGGCAACTTCAGTGTAAACATC 57.171 40.909 0.00 0.00 37.61 3.06
50 51 6.003950 ACTATGGCAACTTCAGTGTAAACAT 58.996 36.000 0.00 0.00 37.61 2.71
51 52 5.238432 CACTATGGCAACTTCAGTGTAAACA 59.762 40.000 0.00 0.00 33.53 2.83
52 53 5.468746 TCACTATGGCAACTTCAGTGTAAAC 59.531 40.000 12.89 0.00 38.20 2.01
53 54 5.616270 TCACTATGGCAACTTCAGTGTAAA 58.384 37.500 12.89 0.00 38.20 2.01
54 55 5.222079 TCACTATGGCAACTTCAGTGTAA 57.778 39.130 12.89 0.00 38.20 2.41
55 56 4.882842 TCACTATGGCAACTTCAGTGTA 57.117 40.909 12.89 0.00 38.20 2.90
56 57 3.769739 TCACTATGGCAACTTCAGTGT 57.230 42.857 12.89 0.00 38.20 3.55
57 58 5.643348 TGTAATCACTATGGCAACTTCAGTG 59.357 40.000 0.00 0.70 38.34 3.66
58 59 5.643777 GTGTAATCACTATGGCAACTTCAGT 59.356 40.000 0.00 0.00 40.98 3.41
59 60 6.111768 GTGTAATCACTATGGCAACTTCAG 57.888 41.667 0.00 0.00 40.98 3.02
67 68 8.754461 TGGCAACTTTAGTGTAATCACTATGGC 61.754 40.741 17.86 17.86 46.77 4.40
68 69 6.597672 TGGCAACTTTAGTGTAATCACTATGG 59.402 38.462 8.56 7.41 45.84 2.74
69 70 7.609760 TGGCAACTTTAGTGTAATCACTATG 57.390 36.000 8.56 5.88 45.84 2.23
70 71 7.201732 GCATGGCAACTTTAGTGTAATCACTAT 60.202 37.037 8.56 0.00 45.84 2.12
71 72 6.093495 GCATGGCAACTTTAGTGTAATCACTA 59.907 38.462 0.00 4.29 45.28 2.74
72 73 7.468636 TGCATGGCAACTTTAGTGTAATCACT 61.469 38.462 6.16 6.16 45.49 3.41
73 74 5.095490 GCATGGCAACTTTAGTGTAATCAC 58.905 41.667 0.00 0.00 40.49 3.06
74 75 4.764308 TGCATGGCAACTTTAGTGTAATCA 59.236 37.500 0.00 0.00 34.76 2.57
75 76 5.309323 TGCATGGCAACTTTAGTGTAATC 57.691 39.130 0.00 0.00 34.76 1.75
76 77 5.720371 TTGCATGGCAACTTTAGTGTAAT 57.280 34.783 0.00 0.00 43.99 1.89
636 787 1.864711 CACCATTAAATCCGTCGCGAT 59.135 47.619 14.06 0.00 0.00 4.58
781 932 2.348998 CAGCAAGGAGGAAGGCGT 59.651 61.111 0.00 0.00 0.00 5.68
818 970 5.298276 TGTCATGGTTAGTTTTTGGACACTC 59.702 40.000 0.00 0.00 0.00 3.51
821 973 4.582656 CCTGTCATGGTTAGTTTTTGGACA 59.417 41.667 0.00 0.00 33.48 4.02
836 988 2.680312 AGACGAACCATCCTGTCATG 57.320 50.000 0.00 0.00 33.83 3.07
860 1012 1.854874 CGGGAGGGAGGGAGTCTAT 59.145 63.158 0.00 0.00 0.00 1.98
1212 1391 4.366586 CAGATCGGTCGTAGTAGTACTCA 58.633 47.826 5.96 0.00 0.00 3.41
1549 1740 1.755179 ACATGTGCATTAGCTCCACC 58.245 50.000 0.00 0.00 42.74 4.61
1702 1896 6.771267 GGGGAATAAACTTGAGATACGGAAAT 59.229 38.462 0.00 0.00 0.00 2.17
1745 1948 9.706691 TGTAAGGTTGATAAAAGAAGTAGACAG 57.293 33.333 0.00 0.00 0.00 3.51
1760 1963 8.153550 TGCAAATTTACCAAATGTAAGGTTGAT 58.846 29.630 11.09 0.00 40.42 2.57
2069 2299 2.524394 ACCTCACTCGCCACCTGT 60.524 61.111 0.00 0.00 0.00 4.00
2111 2346 5.803461 AGTCGTCAATCGTCAAAATTCGATA 59.197 36.000 0.77 0.00 44.29 2.92


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

AutoCloner maintained by Alex Coulton.