Multiple sequence alignment - TraesCS1B01G195500

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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 TraesCS1B01G195500 chr1B 100.000 2351 0 0 1 2351 350632254 350629904 0.000000e+00 4342
1 TraesCS1B01G195500 chr1B 89.737 419 34 7 1641 2056 669802665 669803077 5.750000e-146 527
2 TraesCS1B01G195500 chr1B 89.474 209 20 1 576 782 643042824 643043032 1.790000e-66 263
3 TraesCS1B01G195500 chr1B 88.517 209 21 3 576 782 593563261 593563468 1.390000e-62 250
4 TraesCS1B01G195500 chr1D 95.491 865 31 4 781 1639 261373340 261374202 0.000000e+00 1375
5 TraesCS1B01G195500 chr1D 89.952 418 36 4 1641 2056 458743046 458743459 3.440000e-148 534
6 TraesCS1B01G195500 chr1D 97.386 306 6 1 2047 2350 458744136 458744441 9.630000e-144 520
7 TraesCS1B01G195500 chr1D 93.510 339 9 3 1 336 261372822 261373150 2.100000e-135 492
8 TraesCS1B01G195500 chr1D 89.806 206 19 1 579 782 71764667 71764462 1.790000e-66 263
9 TraesCS1B01G195500 chr1D 89.552 201 19 2 378 577 261373148 261373347 1.080000e-63 254
10 TraesCS1B01G195500 chr1D 88.835 206 21 1 579 782 18864558 18864763 3.880000e-63 252
11 TraesCS1B01G195500 chr1D 88.462 130 14 1 575 703 486996012 486996141 3.130000e-34 156
12 TraesCS1B01G195500 chr1A 91.985 811 46 8 781 1578 338601039 338600235 0.000000e+00 1120
13 TraesCS1B01G195500 chr1A 90.777 206 17 1 579 782 566517100 566517305 8.280000e-70 274
14 TraesCS1B01G195500 chr1A 92.126 127 6 2 224 347 338601352 338601227 2.400000e-40 176
15 TraesCS1B01G195500 chr6D 90.670 418 32 5 1641 2056 148621808 148622220 1.230000e-152 549
16 TraesCS1B01G195500 chr6D 89.387 424 39 4 1635 2056 467362922 467363341 1.600000e-146 529
17 TraesCS1B01G195500 chr6D 97.394 307 6 1 2047 2351 310007841 310007535 2.680000e-144 521
18 TraesCS1B01G195500 chr6D 97.068 307 7 1 2047 2351 467364018 467364324 1.250000e-142 516
19 TraesCS1B01G195500 chr2D 90.670 418 32 5 1641 2056 527886473 527886885 1.230000e-152 549
20 TraesCS1B01G195500 chr2D 90.094 424 33 7 1636 2056 566728577 566728160 2.060000e-150 542
21 TraesCS1B01G195500 chr2D 97.068 307 7 1 2047 2351 618544866 618545172 1.250000e-142 516
22 TraesCS1B01G195500 chr2D 96.743 307 8 1 2047 2351 516844877 516845183 5.800000e-141 510
23 TraesCS1B01G195500 chr2D 96.743 307 8 1 2047 2351 565161138 565160832 5.800000e-141 510
24 TraesCS1B01G195500 chr3D 90.191 418 35 4 1641 2056 413947441 413947028 7.390000e-150 540
25 TraesCS1B01G195500 chr3D 89.524 420 36 6 1641 2058 92379868 92380281 2.070000e-145 525
26 TraesCS1B01G195500 chr3D 97.068 307 7 1 2047 2351 26669407 26669101 1.250000e-142 516
27 TraesCS1B01G195500 chr6B 89.362 423 38 5 1636 2056 572077086 572077503 2.070000e-145 525
28 TraesCS1B01G195500 chr6B 90.196 204 16 3 582 782 542504077 542503875 1.790000e-66 263
29 TraesCS1B01G195500 chr6B 88.626 211 21 2 575 782 87674524 87674314 1.080000e-63 254
30 TraesCS1B01G195500 chr4D 97.068 307 7 1 2047 2351 450521385 450521691 1.250000e-142 516
31 TraesCS1B01G195500 chr4D 96.743 307 8 1 2047 2351 508427857 508428163 5.800000e-141 510
32 TraesCS1B01G195500 chr4D 82.781 302 26 21 1026 1323 501234114 501233835 1.800000e-61 246
33 TraesCS1B01G195500 chr4D 90.419 167 15 1 1158 1323 501161638 501161472 3.930000e-53 219
34 TraesCS1B01G195500 chr5A 84.641 306 27 15 1022 1323 683125619 683125908 1.060000e-73 287
35 TraesCS1B01G195500 chr5A 88.479 217 22 1 576 789 560808246 560808462 2.320000e-65 259
36 TraesCS1B01G195500 chr3B 91.748 206 14 2 579 782 61546135 61546339 1.380000e-72 283
37 TraesCS1B01G195500 chr3B 90.291 206 18 1 579 782 62672649 62672444 3.850000e-68 268
38 TraesCS1B01G195500 chr7B 89.498 219 18 3 579 794 645396204 645395988 2.980000e-69 272
39 TraesCS1B01G195500 chr7B 90.047 211 19 1 574 782 714779749 714779959 2.980000e-69 272
40 TraesCS1B01G195500 chr5B 90.732 205 17 2 579 782 586274534 586274331 2.980000e-69 272
41 TraesCS1B01G195500 chr5B 89.320 206 19 2 579 782 387765921 387765717 3.000000e-64 255
42 TraesCS1B01G195500 chr2B 90.338 207 17 1 579 782 27548138 27547932 3.850000e-68 268
43 TraesCS1B01G195500 chrUn 89.524 210 18 3 576 782 74802855 74803063 1.790000e-66 263
44 TraesCS1B01G195500 chrUn 88.350 206 21 3 579 782 138415666 138415870 6.490000e-61 244
45 TraesCS1B01G195500 chrUn 87.923 207 21 3 579 782 138271934 138272139 8.400000e-60 241
46 TraesCS1B01G195500 chrUn 87.981 208 20 4 579 782 171112601 171112395 8.400000e-60 241
47 TraesCS1B01G195500 chrUn 87.864 206 22 3 579 782 138345952 138346156 3.020000e-59 239
48 TraesCS1B01G195500 chrUn 87.864 206 22 3 579 782 312018740 312018944 3.020000e-59 239
49 TraesCS1B01G195500 chrUn 87.379 206 24 1 579 782 73675783 73675578 3.910000e-58 235
50 TraesCS1B01G195500 chr4B 88.942 208 17 5 579 782 560238409 560238614 3.880000e-63 252
51 TraesCS1B01G195500 chr4B 82.353 306 31 16 1022 1323 645084442 645084156 6.490000e-61 244
52 TraesCS1B01G195500 chr6A 87.923 207 21 3 579 782 558457705 558457500 8.400000e-60 241
53 TraesCS1B01G195500 chr6A 87.923 207 21 3 579 782 558461025 558460820 8.400000e-60 241
54 TraesCS1B01G195500 chr4A 86.916 214 24 3 578 788 733355899 733355687 1.090000e-58 237


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 TraesCS1B01G195500 chr1B 350629904 350632254 2350 True 4342.0 4342 100.0000 1 2351 1 chr1B.!!$R1 2350
1 TraesCS1B01G195500 chr1D 261372822 261374202 1380 False 707.0 1375 92.8510 1 1639 3 chr1D.!!$F3 1638
2 TraesCS1B01G195500 chr1D 458743046 458744441 1395 False 527.0 534 93.6690 1641 2350 2 chr1D.!!$F4 709
3 TraesCS1B01G195500 chr1A 338600235 338601352 1117 True 648.0 1120 92.0555 224 1578 2 chr1A.!!$R1 1354
4 TraesCS1B01G195500 chr6D 467362922 467364324 1402 False 522.5 529 93.2275 1635 2351 2 chr6D.!!$F2 716
5 TraesCS1B01G195500 chr6A 558457500 558461025 3525 True 241.0 241 87.9230 579 782 2 chr6A.!!$R1 203


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
570 579 0.955428 TCTCGTGGCCACAAAGCATC 60.955 55.0 34.16 6.15 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1750 1807 0.109412 AATCGACGACTGGGACGAAC 60.109 55.0 0.0 0.0 38.22 3.95 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)



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AutoCloner maintained by Alex Coulton.