Multiple sequence alignment - TraesCS2D01G054300

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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 TraesCS2D01G054300 chr2D 100.000 2837 0 0 1 2837 21680319 21683155 0.000000e+00 5240.0
1 TraesCS2D01G054300 chr2D 95.656 2118 82 8 1 2112 21641505 21643618 0.000000e+00 3393.0
2 TraesCS2D01G054300 chr2D 100.000 1242 0 0 1 1242 21663904 21665145 0.000000e+00 2294.0
3 TraesCS2D01G054300 chr2D 93.998 1283 66 8 831 2112 21620839 21622111 0.000000e+00 1932.0
4 TraesCS2D01G054300 chr2D 100.000 462 0 0 2376 2837 21666076 21666537 0.000000e+00 854.0
5 TraesCS2D01G054300 chr2D 91.532 248 14 4 2440 2686 21622454 21622695 4.530000e-88 335.0
6 TraesCS2D01G054300 chr2D 92.766 235 10 4 2111 2344 21622148 21622376 1.630000e-87 333.0
7 TraesCS2D01G054300 chr2D 91.880 234 12 4 2111 2343 21643655 21643882 1.270000e-83 320.0
8 TraesCS2D01G054300 chr2D 91.667 168 9 2 2440 2607 21643961 21644123 7.910000e-56 228.0
9 TraesCS2D01G054300 chr2D 94.521 146 7 1 538 683 21619298 21619442 1.020000e-54 224.0
10 TraesCS2D01G054300 chr2D 90.141 142 14 0 2696 2837 21622744 21622885 4.830000e-43 185.0
11 TraesCS2D01G054300 chr2D 88.732 142 16 0 2696 2837 21644198 21644339 1.040000e-39 174.0
12 TraesCS2D01G054300 chr2D 92.174 115 9 0 727 841 21619518 21619632 2.260000e-36 163.0
13 TraesCS2D01G054300 chr2D 88.136 59 5 1 2383 2439 21622377 21622435 5.070000e-08 69.4
14 TraesCS2D01G054300 chr2D 86.441 59 6 1 2383 2439 21643884 21643942 2.360000e-06 63.9
15 TraesCS2D01G054300 chr2B 93.606 2127 113 12 1 2114 34865459 34863343 0.000000e+00 3153.0
16 TraesCS2D01G054300 chr2B 90.795 1673 133 16 454 2115 34890328 34888666 0.000000e+00 2217.0
17 TraesCS2D01G054300 chr2B 93.319 464 26 5 1 461 34952605 34952144 0.000000e+00 680.0
18 TraesCS2D01G054300 chr2B 85.329 593 54 16 2114 2686 34863305 34862726 1.460000e-162 582.0
19 TraesCS2D01G054300 chr2B 91.020 245 17 2 2113 2357 34888630 34888391 2.730000e-85 326.0
20 TraesCS2D01G054300 chr2B 91.667 132 11 0 2699 2830 34862680 34862549 1.740000e-42 183.0
21 TraesCS2D01G054300 chr2B 100.000 30 0 0 2519 2548 93442956 93442927 3.950000e-04 56.5
22 TraesCS2D01G054300 chr2A 93.661 1972 117 7 71 2040 23877926 23879891 0.000000e+00 2942.0
23 TraesCS2D01G054300 chr2A 91.230 1585 115 14 545 2112 23827985 23829562 0.000000e+00 2135.0
24 TraesCS2D01G054300 chr2A 91.069 683 28 8 2024 2686 23879910 23880579 0.000000e+00 893.0
25 TraesCS2D01G054300 chr2A 92.308 247 13 3 2111 2357 23829599 23829839 2.090000e-91 346.0
26 TraesCS2D01G054300 chr2A 95.070 142 6 1 2696 2837 23880628 23880768 3.680000e-54 222.0
27 TraesCS2D01G054300 chr2A 96.053 76 3 0 1 76 23866082 23866157 1.070000e-24 124.0
28 TraesCS2D01G054300 chr2A 97.778 45 0 1 704 748 23828187 23828230 3.030000e-10 76.8
29 TraesCS2D01G054300 chr6A 83.347 1231 138 36 776 1969 604573922 604572722 0.000000e+00 1075.0
30 TraesCS2D01G054300 chr6A 81.158 1295 178 38 703 1969 604456213 604454957 0.000000e+00 979.0
31 TraesCS2D01G054300 chr6D 82.982 1234 141 36 776 1969 457636689 457635485 0.000000e+00 1051.0
32 TraesCS2D01G054300 chr6D 80.635 1291 182 42 706 1969 457591155 457589906 0.000000e+00 937.0
33 TraesCS2D01G054300 chr6B 81.987 1238 146 38 776 1969 696100180 696098976 0.000000e+00 979.0
34 TraesCS2D01G054300 chr6B 84.750 859 100 15 774 1625 695947353 695948187 0.000000e+00 832.0
35 TraesCS2D01G054300 chr6B 87.088 364 32 11 148 496 68386153 68385790 5.690000e-107 398.0
36 TraesCS2D01G054300 chr6B 88.312 77 8 1 703 779 695947147 695947222 1.080000e-14 91.6
37 TraesCS2D01G054300 chr6B 93.617 47 2 1 2323 2368 695950172 695950218 5.070000e-08 69.4
38 TraesCS2D01G054300 chr3D 88.674 362 32 7 148 500 454744145 454744506 1.560000e-117 433.0
39 TraesCS2D01G054300 chr4D 87.744 359 36 7 146 496 391022701 391022343 2.030000e-111 412.0
40 TraesCS2D01G054300 chrUn 87.709 358 34 7 148 495 61736694 61736337 2.630000e-110 409.0
41 TraesCS2D01G054300 chrUn 90.000 70 7 0 2591 2660 455757067 455756998 1.080000e-14 91.6
42 TraesCS2D01G054300 chr3A 90.000 70 7 0 2591 2660 725161880 725161811 1.080000e-14 91.6
43 TraesCS2D01G054300 chr3A 90.000 70 7 0 2591 2660 725177273 725177204 1.080000e-14 91.6
44 TraesCS2D01G054300 chr3A 87.324 71 7 2 2591 2660 725108426 725108357 2.340000e-11 80.5
45 TraesCS2D01G054300 chr7B 90.769 65 6 0 2593 2657 600840648 600840712 1.400000e-13 87.9
46 TraesCS2D01G054300 chr7B 100.000 33 0 0 2516 2548 505470104 505470072 8.490000e-06 62.1


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 TraesCS2D01G054300 chr2D 21680319 21683155 2836 False 5240.000000 5240 100.000000 1 2837 1 chr2D.!!$F1 2836
1 TraesCS2D01G054300 chr2D 21663904 21666537 2633 False 1574.000000 2294 100.000000 1 2837 2 chr2D.!!$F4 2836
2 TraesCS2D01G054300 chr2D 21641505 21644339 2834 False 835.780000 3393 90.875200 1 2837 5 chr2D.!!$F3 2836
3 TraesCS2D01G054300 chr2D 21619298 21622885 3587 False 463.057143 1932 91.895429 538 2837 7 chr2D.!!$F2 2299
4 TraesCS2D01G054300 chr2B 34862549 34865459 2910 True 1306.000000 3153 90.200667 1 2830 3 chr2B.!!$R3 2829
5 TraesCS2D01G054300 chr2B 34888391 34890328 1937 True 1271.500000 2217 90.907500 454 2357 2 chr2B.!!$R4 1903
6 TraesCS2D01G054300 chr2A 23877926 23880768 2842 False 1352.333333 2942 93.266667 71 2837 3 chr2A.!!$F3 2766
7 TraesCS2D01G054300 chr2A 23827985 23829839 1854 False 852.600000 2135 93.772000 545 2357 3 chr2A.!!$F2 1812
8 TraesCS2D01G054300 chr6A 604572722 604573922 1200 True 1075.000000 1075 83.347000 776 1969 1 chr6A.!!$R2 1193
9 TraesCS2D01G054300 chr6A 604454957 604456213 1256 True 979.000000 979 81.158000 703 1969 1 chr6A.!!$R1 1266
10 TraesCS2D01G054300 chr6D 457635485 457636689 1204 True 1051.000000 1051 82.982000 776 1969 1 chr6D.!!$R2 1193
11 TraesCS2D01G054300 chr6D 457589906 457591155 1249 True 937.000000 937 80.635000 706 1969 1 chr6D.!!$R1 1263
12 TraesCS2D01G054300 chr6B 696098976 696100180 1204 True 979.000000 979 81.987000 776 1969 1 chr6B.!!$R2 1193
13 TraesCS2D01G054300 chr6B 695947147 695950218 3071 False 331.000000 832 88.893000 703 2368 3 chr6B.!!$F1 1665

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
1545 3076 3.23463 CTTCCCGGACGCCAACAGA 62.235 63.158 0.73 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2373 5381 2.334307 GCATTCACACTGCCACACT 58.666 52.632 0.0 0.0 33.44 3.55 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
1545 3076 3.234630 CTTCCCGGACGCCAACAGA 62.235 63.158 0.73 0.0 0.00 3.41
1609 3140 1.581934 TCTGTCCAGCTTTGTGTTCG 58.418 50.000 0.00 0.0 0.00 3.95
1674 4394 1.608717 CTCCTCCCCAGAAGGTCGTG 61.609 65.000 0.00 0.0 0.00 4.35
1890 4628 7.173218 ACTTTGTGAAGTATACATGTTCAGTGG 59.827 37.037 2.30 0.0 44.13 4.00
1942 4683 8.693542 AAATATTTTATGTCAGAAGCAAGTGC 57.306 30.769 0.00 0.0 42.49 4.40
2012 4790 6.512297 TGTTCTTATTTGTTCCTTTTGAGCC 58.488 36.000 0.00 0.0 0.00 4.70
2248 5099 3.747976 GCACCGAATGCGCCCTTT 61.748 61.111 4.18 0.0 46.55 3.11
2299 5150 6.094048 ACATTTGATAGACGCTAAAGCACAAT 59.906 34.615 2.44 0.0 42.21 2.71
2300 5151 6.494893 TTTGATAGACGCTAAAGCACAATT 57.505 33.333 2.44 0.0 42.21 2.32
2301 5152 7.603963 TTTGATAGACGCTAAAGCACAATTA 57.396 32.000 2.44 0.0 42.21 1.40
2302 5153 7.603963 TTGATAGACGCTAAAGCACAATTAA 57.396 32.000 2.44 0.0 42.21 1.40
2364 5372 4.196193 TCTTGATCGGAAAAATATGGCGT 58.804 39.130 0.00 0.0 0.00 5.68
2365 5373 3.961477 TGATCGGAAAAATATGGCGTG 57.039 42.857 0.00 0.0 0.00 5.34
2370 5378 4.505808 TCGGAAAAATATGGCGTGAACTA 58.494 39.130 0.00 0.0 0.00 2.24
2373 5381 6.762187 TCGGAAAAATATGGCGTGAACTATTA 59.238 34.615 0.00 0.0 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1545 3076 0.106708 TGAGCAGCTCTTCGGTGTTT 59.893 50.000 23.15 0.00 42.99 2.83
1609 3140 1.065126 CCTCTTGGTGGGGAAGATGAC 60.065 57.143 0.00 0.00 0.00 3.06
1890 4628 1.533625 TACAAGACAACCATGGCAGC 58.466 50.000 13.04 0.00 36.86 5.25
1932 4673 6.308766 CACCTACATAATTTTGCACTTGCTTC 59.691 38.462 2.33 0.00 42.66 3.86
1942 4683 3.434637 GCACGGCACCTACATAATTTTG 58.565 45.455 0.00 0.00 0.00 2.44
2003 4781 6.967199 GTCCTTGTATTATTTCGGCTCAAAAG 59.033 38.462 0.00 0.00 0.00 2.27
2248 5099 2.289444 ACCTCTTTCCGATTCGAGCAAA 60.289 45.455 7.83 3.04 0.00 3.68
2302 5153 9.482627 TCCGTTGCAAAAAGAAATAAATAACAT 57.517 25.926 0.00 0.00 0.00 2.71
2364 5372 4.039852 TCACACTGCCACACTAATAGTTCA 59.960 41.667 0.00 0.00 0.00 3.18
2365 5373 4.566004 TCACACTGCCACACTAATAGTTC 58.434 43.478 0.00 0.00 0.00 3.01
2370 5378 2.489329 GCATTCACACTGCCACACTAAT 59.511 45.455 0.00 0.00 33.44 1.73
2373 5381 2.334307 GCATTCACACTGCCACACT 58.666 52.632 0.00 0.00 33.44 3.55


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

AutoCloner maintained by Alex Coulton.