Multiple sequence alignment - TraesCS2D01G503600

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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 TraesCS2D01G503600 chr2D 100.000 3473 0 0 1 3473 598327725 598331197 0.000000e+00 6414.0
1 TraesCS2D01G503600 chr2D 97.584 3477 26 7 1 3473 642099318 642102740 0.000000e+00 5903.0
2 TraesCS2D01G503600 chr2D 84.052 464 43 14 2373 2811 642212778 642213235 5.360000e-113 418.0
3 TraesCS2D01G503600 chr2D 93.333 150 10 0 6 155 528992777 528992926 4.510000e-54 222.0
4 TraesCS2D01G503600 chr2D 90.303 165 13 3 4 168 270905437 270905276 2.720000e-51 213.0
5 TraesCS2D01G503600 chr2D 94.937 79 4 0 3388 3466 642213258 642213336 1.310000e-24 124.0
6 TraesCS2D01G503600 chr2A 91.980 2182 132 21 294 2445 767017286 767019454 0.000000e+00 3020.0
7 TraesCS2D01G503600 chr2A 91.179 1247 55 14 2238 3473 767147005 767145803 0.000000e+00 1642.0
8 TraesCS2D01G503600 chr2A 85.978 813 83 12 1633 2432 766981491 766982285 0.000000e+00 841.0
9 TraesCS2D01G503600 chr2A 94.262 244 12 2 966 1208 766981206 766981448 4.230000e-99 372.0
10 TraesCS2D01G503600 chr2A 86.905 336 28 12 2867 3190 110894267 110893936 2.550000e-96 363.0
11 TraesCS2D01G503600 chr2A 88.841 233 17 6 2505 2729 766982321 766982552 9.490000e-71 278.0
12 TraesCS2D01G503600 chr2A 89.147 129 5 6 1120 1240 767147315 767147188 6.000000e-33 152.0
13 TraesCS2D01G503600 chr2A 78.926 242 16 17 709 930 766980989 766981215 7.820000e-27 132.0
14 TraesCS2D01G503600 chr2B 88.728 1863 143 30 982 2811 799577195 799575367 0.000000e+00 2215.0
15 TraesCS2D01G503600 chr2B 93.782 579 17 4 384 943 799577773 799577195 0.000000e+00 852.0
16 TraesCS2D01G503600 chr2B 83.887 391 38 14 2813 3191 388944314 388944691 1.980000e-92 350.0
17 TraesCS2D01G503600 chr2B 86.186 333 29 12 2867 3190 789967528 789967204 9.230000e-91 344.0
18 TraesCS2D01G503600 chr2B 82.697 393 38 15 1237 1619 657085196 657085568 4.320000e-84 322.0
19 TraesCS2D01G503600 chr2B 94.819 193 8 2 192 382 799578051 799577859 2.030000e-77 300.0
20 TraesCS2D01G503600 chr2B 83.228 316 27 8 2521 2811 799595660 799595346 2.060000e-67 267.0
21 TraesCS2D01G503600 chr2B 89.423 208 21 1 3267 3473 799540712 799540505 9.560000e-66 261.0
22 TraesCS2D01G503600 chr2B 91.111 180 7 5 850 1025 799584207 799584033 5.800000e-58 235.0
23 TraesCS2D01G503600 chr2B 93.023 86 4 2 567 651 799584316 799584232 1.310000e-24 124.0
24 TraesCS2D01G503600 chr4B 85.859 396 32 16 2812 3190 115554271 115554659 1.940000e-107 399.0
25 TraesCS2D01G503600 chr4B 92.000 50 3 1 493 542 576192228 576192180 6.220000e-08 69.4
26 TraesCS2D01G503600 chr3B 84.810 395 42 12 2812 3194 65210367 65210755 7.030000e-102 381.0
27 TraesCS2D01G503600 chr3B 85.000 320 42 5 1303 1619 829275160 829274844 1.560000e-83 320.0
28 TraesCS2D01G503600 chr3B 80.422 332 35 13 1308 1619 818341081 818341402 3.490000e-55 226.0
29 TraesCS2D01G503600 chr3B 83.333 102 16 1 335 435 702857818 702857717 3.690000e-15 93.5
30 TraesCS2D01G503600 chr7B 84.751 341 38 12 2867 3198 713675681 713676016 2.580000e-86 329.0
31 TraesCS2D01G503600 chr7B 82.353 102 17 1 335 435 594985061 594984960 1.720000e-13 87.9
32 TraesCS2D01G503600 chr1B 82.456 399 41 18 2812 3191 689825782 689826170 4.320000e-84 322.0
33 TraesCS2D01G503600 chr1B 82.524 103 17 1 334 435 683469668 683469566 4.770000e-14 89.8
34 TraesCS2D01G503600 chr1A 83.471 363 37 14 1278 1619 254185213 254184853 2.010000e-82 316.0
35 TraesCS2D01G503600 chr7A 83.056 360 39 13 1278 1617 639742328 639742685 1.210000e-79 307.0
36 TraesCS2D01G503600 chr7A 94.558 147 8 0 9 155 210688466 210688320 9.700000e-56 228.0
37 TraesCS2D01G503600 chr7A 83.810 105 16 1 332 435 10269117 10269221 7.930000e-17 99.0
38 TraesCS2D01G503600 chr4A 83.483 333 41 12 1297 1619 494621338 494621010 7.290000e-77 298.0
39 TraesCS2D01G503600 chrUn 81.667 360 46 12 1278 1626 70364200 70363850 7.340000e-72 281.0
40 TraesCS2D01G503600 chr7D 94.156 154 9 0 1 154 131313668 131313821 5.800000e-58 235.0
41 TraesCS2D01G503600 chr7D 83.495 103 16 1 334 435 579148700 579148802 1.030000e-15 95.3
42 TraesCS2D01G503600 chr7D 82.692 104 13 4 335 435 556642493 556642392 1.720000e-13 87.9
43 TraesCS2D01G503600 chr3D 93.878 147 9 0 9 155 480389254 480389108 4.510000e-54 222.0
44 TraesCS2D01G503600 chr3D 93.289 149 10 0 4 152 294348320 294348172 1.620000e-53 220.0
45 TraesCS2D01G503600 chr3D 92.157 51 3 1 493 542 524172625 524172575 1.730000e-08 71.3
46 TraesCS2D01G503600 chr4D 92.763 152 11 0 4 155 84781051 84780900 1.620000e-53 220.0
47 TraesCS2D01G503600 chr6D 92.715 151 11 0 4 154 162122759 162122609 5.840000e-53 219.0
48 TraesCS2D01G503600 chr6D 97.619 42 1 0 501 542 467043064 467043105 4.810000e-09 73.1
49 TraesCS2D01G503600 chr3A 77.285 361 36 20 1278 1619 624750593 624750260 1.660000e-38 171.0
50 TraesCS2D01G503600 chr3A 91.228 57 5 0 501 557 431125057 431125001 1.030000e-10 78.7
51 TraesCS2D01G503600 chr6A 90.909 66 5 1 492 556 573411223 573411158 1.720000e-13 87.9
52 TraesCS2D01G503600 chr5D 82.353 102 17 1 335 435 257163170 257163271 1.720000e-13 87.9
53 TraesCS2D01G503600 chr6B 88.060 67 7 1 500 565 203689381 203689315 1.030000e-10 78.7


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 TraesCS2D01G503600 chr2D 598327725 598331197 3472 False 6414.000000 6414 100.00000 1 3473 1 chr2D.!!$F2 3472
1 TraesCS2D01G503600 chr2D 642099318 642102740 3422 False 5903.000000 5903 97.58400 1 3473 1 chr2D.!!$F3 3472
2 TraesCS2D01G503600 chr2D 642212778 642213336 558 False 271.000000 418 89.49450 2373 3466 2 chr2D.!!$F4 1093
3 TraesCS2D01G503600 chr2A 767017286 767019454 2168 False 3020.000000 3020 91.98000 294 2445 1 chr2A.!!$F1 2151
4 TraesCS2D01G503600 chr2A 767145803 767147315 1512 True 897.000000 1642 90.16300 1120 3473 2 chr2A.!!$R2 2353
5 TraesCS2D01G503600 chr2A 766980989 766982552 1563 False 405.750000 841 87.00175 709 2729 4 chr2A.!!$F2 2020
6 TraesCS2D01G503600 chr2B 799575367 799578051 2684 True 1122.333333 2215 92.44300 192 2811 3 chr2B.!!$R4 2619

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
33 34 0.759436 TTTGCCACGCCCCCTAAAAA 60.759 50.000 0.0 0.0 0.0 1.94 F
1242 1394 1.140852 TCCATTGGCGGTTCTATGAGG 59.859 52.381 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1974 0.903454 AGTAGGGCAGTACGTTGGCT 60.903 55.000 12.82 3.2 42.73 4.75 R
3326 3552 3.560636 AAAGTAGTGTTGTGAGGCTGT 57.439 42.857 0.00 0.0 0.00 4.40 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
33 34 0.759436 TTTGCCACGCCCCCTAAAAA 60.759 50.000 0.00 0.0 0.00 1.94
89 90 2.194889 GTTGGTTTTTCCGCCCCGA 61.195 57.895 0.00 0.0 39.52 5.14
120 121 1.639280 GCGGTTATTTTACGGGTCGA 58.361 50.000 0.00 0.0 0.00 4.20
356 359 5.450688 CGTACTCCCTCCTTAAGAATCACTG 60.451 48.000 3.36 0.0 0.00 3.66
1242 1394 1.140852 TCCATTGGCGGTTCTATGAGG 59.859 52.381 0.00 0.0 0.00 3.86
1640 1798 5.691896 TCGTGATTCTATACCTCTTCCTCA 58.308 41.667 0.00 0.0 0.00 3.86
1809 1974 1.422662 CGAGCGCACGTACACTCTA 59.577 57.895 19.34 0.0 0.00 2.43
3073 3298 5.111293 GGTGAAATTTCCCATGCATAACAG 58.889 41.667 15.48 0.0 0.00 3.16
3326 3552 1.798223 CAATTCGGCTTGTCTTGTCGA 59.202 47.619 0.00 0.0 39.87 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.705289 GCCCCGGCCTGCAAAAAT 61.705 61.111 0.00 0.00 34.56 1.82
58 59 0.840722 AACCAACCCGATCAGACCCT 60.841 55.000 0.00 0.00 0.00 4.34
103 104 1.935873 GCCTCGACCCGTAAAATAACC 59.064 52.381 0.00 0.00 0.00 2.85
356 359 1.202336 GCTACATGCATTGCTCCAACC 60.202 52.381 10.49 0.00 42.31 3.77
1242 1394 1.138247 CGGCTGCTGAAAATCCTGC 59.862 57.895 1.17 0.00 0.00 4.85
1276 1428 9.575868 TGAATTTACTGTTCATAAAGGGTGTAA 57.424 29.630 0.00 0.00 31.07 2.41
1332 1485 6.558771 AAAGTTCGATCATGTTTGATGTCA 57.441 33.333 0.00 0.00 42.73 3.58
1640 1798 4.653801 ACAAATTTTGGTTAGCAAGACCCT 59.346 37.500 13.42 0.00 36.30 4.34
1794 1959 1.872679 GGCTAGAGTGTACGTGCGC 60.873 63.158 9.34 9.34 0.00 6.09
1809 1974 0.903454 AGTAGGGCAGTACGTTGGCT 60.903 55.000 12.82 3.20 42.73 4.75
3326 3552 3.560636 AAAGTAGTGTTGTGAGGCTGT 57.439 42.857 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.