Multiple sequence alignment - TraesCS3A01G138300

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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 TraesCS3A01G138300 chr3A 100.000 5339 0 0 1 5339 115394275 115388937 0.000000e+00 9860.0
1 TraesCS3A01G138300 chr3A 98.728 5345 59 8 1 5339 115615740 115610399 0.000000e+00 9485.0
2 TraesCS3A01G138300 chr3A 97.428 5094 113 11 258 5339 115843633 115838546 0.000000e+00 8665.0
3 TraesCS3A01G138300 chr3A 95.959 3390 118 9 1956 5339 115164580 115161204 0.000000e+00 5483.0
4 TraesCS3A01G138300 chr3A 98.632 1973 25 2 1 1971 115167787 115165815 0.000000e+00 3493.0
5 TraesCS3A01G138300 chr3A 82.118 1756 260 27 2742 4480 116075556 116073838 0.000000e+00 1454.0
6 TraesCS3A01G138300 chr3A 82.426 1451 185 42 1118 2517 116077263 116075832 0.000000e+00 1203.0
7 TraesCS3A01G138300 chr3A 79.661 236 40 7 5 236 663450319 663450550 4.280000e-36 163.0
8 TraesCS3A01G138300 chr3A 95.238 63 3 0 1 63 115619929 115619867 3.400000e-17 100.0
9 TraesCS3A01G138300 chr3B 90.942 1645 114 16 795 2425 148547227 148545604 0.000000e+00 2180.0
10 TraesCS3A01G138300 chr3B 90.942 1645 114 16 795 2425 148583676 148582053 0.000000e+00 2180.0
11 TraesCS3A01G138300 chr3B 90.942 1645 114 16 795 2425 148625013 148623390 0.000000e+00 2180.0
12 TraesCS3A01G138300 chr3B 90.754 1644 117 17 795 2425 148660962 148659341 0.000000e+00 2161.0
13 TraesCS3A01G138300 chr3B 86.076 1185 149 10 3507 4678 148658232 148657051 0.000000e+00 1260.0
14 TraesCS3A01G138300 chr3B 86.912 871 98 9 3821 4678 148543747 148542880 0.000000e+00 963.0
15 TraesCS3A01G138300 chr3B 90.365 384 26 5 410 791 148584092 148583718 1.340000e-135 494.0
16 TraesCS3A01G138300 chr3B 90.365 384 26 5 410 791 148625429 148625055 1.340000e-135 494.0
17 TraesCS3A01G138300 chr3B 89.870 385 27 6 410 791 148547644 148547269 8.040000e-133 484.0
18 TraesCS3A01G138300 chr3B 89.896 386 26 7 410 791 148661380 148661004 8.040000e-133 484.0
19 TraesCS3A01G138300 chr3D 90.284 1657 129 15 795 2425 98150587 98148937 0.000000e+00 2139.0
20 TraesCS3A01G138300 chr3D 85.037 1223 150 20 3473 4678 98147857 98146651 0.000000e+00 1214.0
21 TraesCS3A01G138300 chr3D 90.851 470 39 3 222 688 98151877 98151409 1.260000e-175 627.0
22 TraesCS3A01G138300 chr3D 83.240 179 29 1 41 218 462818933 462819111 4.280000e-36 163.0
23 TraesCS3A01G138300 chr3D 92.982 57 4 0 742 798 98150676 98150620 3.430000e-12 84.2
24 TraesCS3A01G138300 chr7A 78.298 811 167 8 3537 4340 76355870 76355062 1.030000e-141 514.0
25 TraesCS3A01G138300 chr7A 78.079 812 169 8 3537 4341 76420077 76419268 6.170000e-139 505.0
26 TraesCS3A01G138300 chr6A 77.888 805 167 11 3545 4340 106737141 106737943 1.730000e-134 490.0
27 TraesCS3A01G138300 chr5B 85.047 428 58 5 4823 5245 507806142 507805716 1.060000e-116 431.0
28 TraesCS3A01G138300 chr5B 92.308 78 6 0 1333 1410 546522601 546522524 1.570000e-20 111.0
29 TraesCS3A01G138300 chr6D 84.352 409 58 5 4834 5237 294412511 294412918 3.880000e-106 396.0
30 TraesCS3A01G138300 chr6D 80.189 106 21 0 1168 1273 464011058 464010953 4.430000e-11 80.5
31 TraesCS3A01G138300 chr6B 85.488 379 45 9 4833 5206 688597563 688597190 2.330000e-103 387.0
32 TraesCS3A01G138300 chr5A 83.495 412 56 10 4830 5236 533345397 533345801 1.820000e-99 374.0
33 TraesCS3A01G138300 chr2D 83.374 409 60 6 4835 5237 24220925 24221331 6.530000e-99 372.0
34 TraesCS3A01G138300 chr4D 83.673 392 57 7 4849 5236 16717373 16716985 3.930000e-96 363.0
35 TraesCS3A01G138300 chr1D 84.234 222 32 1 1 222 196232535 196232753 4.190000e-51 213.0
36 TraesCS3A01G138300 chr7B 81.250 224 38 4 2 222 417834503 417834281 1.530000e-40 178.0
37 TraesCS3A01G138300 chr7B 85.549 173 22 3 1 171 440349845 440350016 1.530000e-40 178.0
38 TraesCS3A01G138300 chr1A 81.905 210 38 0 9 218 550833525 550833316 1.530000e-40 178.0
39 TraesCS3A01G138300 chr7D 81.308 214 34 4 6 216 583052852 583053062 9.200000e-38 169.0


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 TraesCS3A01G138300 chr3A 115388937 115394275 5338 True 9860.000000 9860 100.000000 1 5339 1 chr3A.!!$R1 5338
1 TraesCS3A01G138300 chr3A 115610399 115615740 5341 True 9485.000000 9485 98.728000 1 5339 1 chr3A.!!$R2 5338
2 TraesCS3A01G138300 chr3A 115838546 115843633 5087 True 8665.000000 8665 97.428000 258 5339 1 chr3A.!!$R4 5081
3 TraesCS3A01G138300 chr3A 115161204 115167787 6583 True 4488.000000 5483 97.295500 1 5339 2 chr3A.!!$R5 5338
4 TraesCS3A01G138300 chr3A 116073838 116077263 3425 True 1328.500000 1454 82.272000 1118 4480 2 chr3A.!!$R6 3362
5 TraesCS3A01G138300 chr3B 148582053 148584092 2039 True 1337.000000 2180 90.653500 410 2425 2 chr3B.!!$R2 2015
6 TraesCS3A01G138300 chr3B 148623390 148625429 2039 True 1337.000000 2180 90.653500 410 2425 2 chr3B.!!$R3 2015
7 TraesCS3A01G138300 chr3B 148657051 148661380 4329 True 1301.666667 2161 88.908667 410 4678 3 chr3B.!!$R4 4268
8 TraesCS3A01G138300 chr3B 148542880 148547644 4764 True 1209.000000 2180 89.241333 410 4678 3 chr3B.!!$R1 4268
9 TraesCS3A01G138300 chr3D 98146651 98151877 5226 True 1016.050000 2139 89.788500 222 4678 4 chr3D.!!$R1 4456
10 TraesCS3A01G138300 chr7A 76355062 76355870 808 True 514.000000 514 78.298000 3537 4340 1 chr7A.!!$R1 803
11 TraesCS3A01G138300 chr7A 76419268 76420077 809 True 505.000000 505 78.079000 3537 4341 1 chr7A.!!$R2 804
12 TraesCS3A01G138300 chr6A 106737141 106737943 802 False 490.000000 490 77.888000 3545 4340 1 chr6A.!!$F1 795

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
297 300 2.296190 GCTCTGGTAGGTTTTTGGGTTG 59.704 50.000 0.00 0.0 0.00 3.77 F
729 1437 2.438434 CAGCCCCCACGGTTGATC 60.438 66.667 0.00 0.0 45.48 2.92 F
2697 4854 0.371989 CGTGCGCCGAAACATAATCA 59.628 50.000 4.18 0.0 39.56 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 4413 2.815211 CTGTCGTGACCCATGGCG 60.815 66.667 6.09 4.48 0.00 5.69 R
2697 4854 9.358406 TCAAGAATGTTCAATGAATGCCTATAT 57.642 29.630 0.00 0.00 0.00 0.86 R
4586 7297 1.134491 GGGGTTGACGGAATACTCTGG 60.134 57.143 0.00 0.00 31.52 3.86 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
143 144 3.791320 TGAGAGGTCTGGTTAGGTCAAT 58.209 45.455 0.00 0.00 0.00 2.57
297 300 2.296190 GCTCTGGTAGGTTTTTGGGTTG 59.704 50.000 0.00 0.00 0.00 3.77
362 365 5.406175 GCGTAGTTTTACATGTACACTGGAA 59.594 40.000 20.37 4.68 0.00 3.53
729 1437 2.438434 CAGCCCCCACGGTTGATC 60.438 66.667 0.00 0.00 45.48 2.92
2697 4854 0.371989 CGTGCGCCGAAACATAATCA 59.628 50.000 4.18 0.00 39.56 2.57
2809 5047 2.877168 ACTCTACTCTGAACAACGACGT 59.123 45.455 0.00 0.00 0.00 4.34
2926 5164 4.739195 TCAGTTTAAAACTTTTGCGCAGT 58.261 34.783 11.31 1.68 40.46 4.40
3886 6576 1.104577 TTTCGACTTTGGTGGTGGCC 61.105 55.000 0.00 0.00 0.00 5.36
3887 6577 2.203280 CGACTTTGGTGGTGGCCA 60.203 61.111 0.00 0.00 36.62 5.36
5061 7775 5.277825 TCGAATTGTTCACGCTTGATTTTT 58.722 33.333 0.00 0.00 0.00 1.94
5228 7943 2.529389 AGTCCGGGCTCTGGGTTT 60.529 61.111 0.35 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
844 1595 2.492088 ACGTGATCGAGGAGAACAATCA 59.508 45.455 0.00 0.00 40.62 2.57
2331 4413 2.815211 CTGTCGTGACCCATGGCG 60.815 66.667 6.09 4.48 0.00 5.69
2465 4564 9.647918 TGTATTTGGGTGCATTTTCCTATATAA 57.352 29.630 0.00 0.00 0.00 0.98
2697 4854 9.358406 TCAAGAATGTTCAATGAATGCCTATAT 57.642 29.630 0.00 0.00 0.00 0.86
2736 4974 9.784531 TTAAGATCAAAGACAAATGAGAGAGTT 57.215 29.630 0.00 0.00 0.00 3.01
2809 5047 3.436704 CGCATGAACAAGCTCCTTAAAGA 59.563 43.478 0.00 0.00 0.00 2.52
2926 5164 0.320374 CTAACCACTCCTCCGTGCAA 59.680 55.000 0.00 0.00 33.60 4.08
3140 5378 3.106672 GTGCGATTTCGTAGTCTACCAG 58.893 50.000 4.39 0.00 42.22 4.00
3195 5433 2.383527 CCAGGCAACGCGACTTCTC 61.384 63.158 15.93 0.00 46.39 2.87
3886 6576 1.137872 GGCTCTGTCTGGGTCTATGTG 59.862 57.143 0.00 0.00 0.00 3.21
3887 6577 1.273267 TGGCTCTGTCTGGGTCTATGT 60.273 52.381 0.00 0.00 0.00 2.29
3967 6659 4.499696 GCAACCATGTAACAATCCTATGGC 60.500 45.833 0.00 0.00 41.50 4.40
4586 7297 1.134491 GGGGTTGACGGAATACTCTGG 60.134 57.143 0.00 0.00 31.52 3.86
5228 7943 8.792633 CAATTCCAGGGAAAATAGCGATAATTA 58.207 33.333 4.63 0.00 37.69 1.40


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

AutoCloner maintained by Alex Coulton.