Multiple sequence alignment - TraesCS2A01G161900

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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 TraesCS2A01G161900 chr2A 100.000 2822 0 0 1 2822 114324758 114321937 0.000000e+00 5212.0
1 TraesCS2A01G161900 chr2A 93.394 2089 90 12 757 2822 203540849 203538786 0.000000e+00 3049.0
2 TraesCS2A01G161900 chr2A 92.986 499 29 3 264 756 203541603 203541105 0.000000e+00 723.0
3 TraesCS2A01G161900 chr2A 93.704 270 15 2 1 269 203566297 203566029 1.220000e-108 403.0
4 TraesCS2A01G161900 chr2A 94.231 260 13 2 11 269 203543425 203543167 2.040000e-106 396.0
5 TraesCS2A01G161900 chr2A 83.881 335 39 8 1479 1806 1602227 1602553 3.530000e-79 305.0
6 TraesCS2A01G161900 chr2A 95.000 60 3 0 2563 2622 1603236 1603295 8.320000e-16 95.3
7 TraesCS2A01G161900 chr4A 95.597 2385 92 2 3 2375 407612326 407609943 0.000000e+00 3810.0
8 TraesCS2A01G161900 chr4A 96.431 1457 36 7 1 1444 712218406 712219859 0.000000e+00 2388.0
9 TraesCS2A01G161900 chr4A 97.073 410 12 0 2413 2822 407609975 407609566 0.000000e+00 691.0
10 TraesCS2A01G161900 chr7B 96.568 1457 35 6 1 1444 682905154 682906608 0.000000e+00 2399.0
11 TraesCS2A01G161900 chr6B 85.402 1007 104 23 526 1495 114458323 114457323 0.000000e+00 1005.0
12 TraesCS2A01G161900 chr6B 85.699 916 110 13 1310 2219 114457322 114456422 0.000000e+00 946.0
13 TraesCS2A01G161900 chr6B 83.465 635 79 14 1482 2105 80785819 80785200 4.080000e-158 568.0
14 TraesCS2A01G161900 chr6B 84.478 393 45 10 2178 2563 80785193 80784810 9.550000e-100 374.0
15 TraesCS2A01G161900 chr6B 83.914 373 46 7 2460 2822 114456331 114455963 7.480000e-91 344.0
16 TraesCS2A01G161900 chr6B 95.000 60 3 0 2563 2622 80784586 80784527 8.320000e-16 95.3
17 TraesCS2A01G161900 chr6A 85.371 998 115 15 523 1495 531462564 531461573 0.000000e+00 1005.0
18 TraesCS2A01G161900 chr6A 84.416 924 109 20 1310 2219 531461572 531460670 0.000000e+00 876.0
19 TraesCS2A01G161900 chr6A 84.873 747 84 9 1480 2217 557927421 557926695 0.000000e+00 726.0
20 TraesCS2A01G161900 chr6A 92.070 517 37 4 4 519 22162552 22162039 0.000000e+00 725.0
21 TraesCS2A01G161900 chr6A 85.540 491 54 5 1019 1493 557928906 557928417 5.430000e-137 497.0
22 TraesCS2A01G161900 chr6A 83.646 373 46 7 2460 2822 531460603 531460236 1.250000e-88 337.0
23 TraesCS2A01G161900 chr6A 84.000 200 25 5 2460 2655 557926626 557926430 4.800000e-43 185.0
24 TraesCS2A01G161900 chr3B 91.363 521 40 5 1 519 387428275 387428792 0.000000e+00 708.0
25 TraesCS2A01G161900 chr3B 83.810 630 83 10 2206 2822 799988482 799989105 5.240000e-162 580.0
26 TraesCS2A01G161900 chr3B 83.301 521 72 11 585 1095 536277567 536277052 1.530000e-127 466.0
27 TraesCS2A01G161900 chr1A 91.489 517 40 4 4 519 8010190 8009677 0.000000e+00 708.0
28 TraesCS2A01G161900 chr7A 91.085 516 44 2 4 519 675042115 675042628 0.000000e+00 697.0
29 TraesCS2A01G161900 chr4B 84.019 632 81 14 2206 2822 662532131 662532757 8.710000e-165 590.0
30 TraesCS2A01G161900 chr1B 87.978 183 20 2 1290 1470 400774736 400774554 6.120000e-52 215.0
31 TraesCS2A01G161900 chr3D 92.241 116 3 1 2713 2822 22075472 22075587 2.910000e-35 159.0
32 TraesCS2A01G161900 chr2D 91.379 116 4 1 2713 2822 33882858 33882743 1.350000e-33 154.0
33 TraesCS2A01G161900 chr1D 91.379 116 4 1 2713 2822 332606932 332607047 1.350000e-33 154.0
34 TraesCS2A01G161900 chr5D 83.226 155 25 1 2608 2761 390514026 390514180 1.050000e-29 141.0


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 TraesCS2A01G161900 chr2A 114321937 114324758 2821 True 5212.000000 5212 100.000000 1 2822 1 chr2A.!!$R1 2821
1 TraesCS2A01G161900 chr2A 203538786 203543425 4639 True 1389.333333 3049 93.537000 11 2822 3 chr2A.!!$R3 2811
2 TraesCS2A01G161900 chr2A 1602227 1603295 1068 False 200.150000 305 89.440500 1479 2622 2 chr2A.!!$F1 1143
3 TraesCS2A01G161900 chr4A 712218406 712219859 1453 False 2388.000000 2388 96.431000 1 1444 1 chr4A.!!$F1 1443
4 TraesCS2A01G161900 chr4A 407609566 407612326 2760 True 2250.500000 3810 96.335000 3 2822 2 chr4A.!!$R1 2819
5 TraesCS2A01G161900 chr7B 682905154 682906608 1454 False 2399.000000 2399 96.568000 1 1444 1 chr7B.!!$F1 1443
6 TraesCS2A01G161900 chr6B 114455963 114458323 2360 True 765.000000 1005 85.005000 526 2822 3 chr6B.!!$R2 2296
7 TraesCS2A01G161900 chr6B 80784527 80785819 1292 True 345.766667 568 87.647667 1482 2622 3 chr6B.!!$R1 1140
8 TraesCS2A01G161900 chr6A 531460236 531462564 2328 True 739.333333 1005 84.477667 523 2822 3 chr6A.!!$R2 2299
9 TraesCS2A01G161900 chr6A 22162039 22162552 513 True 725.000000 725 92.070000 4 519 1 chr6A.!!$R1 515
10 TraesCS2A01G161900 chr6A 557926430 557928906 2476 True 469.333333 726 84.804333 1019 2655 3 chr6A.!!$R3 1636
11 TraesCS2A01G161900 chr3B 387428275 387428792 517 False 708.000000 708 91.363000 1 519 1 chr3B.!!$F1 518
12 TraesCS2A01G161900 chr3B 799988482 799989105 623 False 580.000000 580 83.810000 2206 2822 1 chr3B.!!$F2 616
13 TraesCS2A01G161900 chr3B 536277052 536277567 515 True 466.000000 466 83.301000 585 1095 1 chr3B.!!$R1 510
14 TraesCS2A01G161900 chr1A 8009677 8010190 513 True 708.000000 708 91.489000 4 519 1 chr1A.!!$R1 515
15 TraesCS2A01G161900 chr7A 675042115 675042628 513 False 697.000000 697 91.085000 4 519 1 chr7A.!!$F1 515
16 TraesCS2A01G161900 chr4B 662532131 662532757 626 False 590.000000 590 84.019000 2206 2822 1 chr4B.!!$F1 616

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
944 2787 1.202989 TGGCAATGTTGGGCAAGAGTA 60.203 47.619 0.0 0.0 37.93 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 4809 3.385193 TGCTCTTGATGTCTTGAACGA 57.615 42.857 0.0 0.0 0.0 3.85 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
37 38 2.169144 CTCATGCAGGAGGACATGTACA 59.831 50.000 20.50 0.00 43.34 2.90
359 1930 1.665679 GCATCACGGTGAACATGGTAG 59.334 52.381 15.72 0.00 0.00 3.18
563 2135 7.305474 CCATTAATGGGATATCACTTAAACGC 58.695 38.462 24.61 0.00 44.31 4.84
738 2321 7.591426 GTCCTGTGTTTGTGAGTTCATATTTTC 59.409 37.037 0.00 0.00 0.00 2.29
741 2325 6.261158 TGTGTTTGTGAGTTCATATTTTCCGA 59.739 34.615 0.00 0.00 0.00 4.55
944 2787 1.202989 TGGCAATGTTGGGCAAGAGTA 60.203 47.619 0.00 0.00 37.93 2.59
1166 3019 7.907389 TCCATAGGAGTATTTCGATTAGCAAT 58.093 34.615 0.00 0.00 0.00 3.56
1191 3045 7.448748 AGTTCCGTGCAATTAAGAAAATAGT 57.551 32.000 0.00 0.00 0.00 2.12
1281 3136 4.583907 TGAGAAAATCTGGTTGCACAATCA 59.416 37.500 0.00 0.00 0.00 2.57
1382 3249 6.831664 ATGATTAGATGTTTCCACCCTAGT 57.168 37.500 0.00 0.00 0.00 2.57
1639 4532 6.447162 AGAAAAAGGAAGGTTAGATTTTGCG 58.553 36.000 0.00 0.00 0.00 4.85
1741 4636 5.102953 TGCAGATCAAGTAGGTATGCTTT 57.897 39.130 0.00 0.00 33.47 3.51
1907 4809 0.846693 AGAAGGCAAGAAGGTGGTGT 59.153 50.000 0.00 0.00 0.00 4.16
2004 4907 7.339721 AGAACCGAAGATCTCTTACACAATAGA 59.660 37.037 0.00 0.00 36.11 1.98
2077 4989 8.123639 AGCTTGAAACAAGTAGACTACTATCA 57.876 34.615 15.51 13.73 38.26 2.15
2426 5353 6.633500 TGTGAGGTCAGTTTTATTTCCAAG 57.367 37.500 0.00 0.00 0.00 3.61
2458 5409 5.298989 AGTACCATGAATATTAACGGCCA 57.701 39.130 2.24 0.00 0.00 5.36
2507 5459 3.915073 TGGAGGTAGATCCGGTATAGAGT 59.085 47.826 0.00 0.00 42.77 3.24
2685 5865 2.573462 TGCTAGAGCTTGGAATGAAGGT 59.427 45.455 2.72 0.00 42.66 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.183014 CCTCCTGCATGAGGCTCAAT 59.817 55.000 22.97 7.45 45.13 2.57
335 1906 1.805943 CATGTTCACCGTGATGCTTCA 59.194 47.619 1.09 0.00 31.20 3.02
359 1930 1.537202 GCTCCATCAACAACCTGACAC 59.463 52.381 0.00 0.00 0.00 3.67
436 2008 6.697892 GTCTGCATAACATCAGTACCTCTTAC 59.302 42.308 0.00 0.00 0.00 2.34
563 2135 1.089920 CTTTGATCCAGCAACGAGGG 58.910 55.000 0.00 0.00 0.00 4.30
738 2321 2.099141 TGCTCAATTCAACTCCTCGG 57.901 50.000 0.00 0.00 0.00 4.63
741 2325 5.351458 GTTTGTTTGCTCAATTCAACTCCT 58.649 37.500 0.00 0.00 0.00 3.69
944 2787 2.259818 CTCGAAGACTGCCTGCGT 59.740 61.111 0.00 0.00 44.39 5.24
1166 3019 8.556213 ACTATTTTCTTAATTGCACGGAACTA 57.444 30.769 0.00 0.00 0.00 2.24
1409 3464 8.548025 TCTTTCCTATTCATTCCATGTTACTGA 58.452 33.333 0.00 0.00 0.00 3.41
1540 4428 4.080582 TGGTAGCCTACAAGTGCATGTTAT 60.081 41.667 3.95 0.00 34.75 1.89
1639 4532 8.077991 TGAAAAATATGCTTGCATGCTACTATC 58.922 33.333 23.31 13.57 0.00 2.08
1741 4636 5.298989 TCTTTAGTCCACTGCCACTTTAA 57.701 39.130 0.00 0.00 0.00 1.52
1907 4809 3.385193 TGCTCTTGATGTCTTGAACGA 57.615 42.857 0.00 0.00 0.00 3.85
2077 4989 8.402798 TGTTATAACACAAATCAAGGTCATGT 57.597 30.769 14.35 0.00 33.17 3.21
2458 5409 7.448469 ACTTTGTTGTGGTCTTCAATATAAGCT 59.552 33.333 0.00 0.00 0.00 3.74
2685 5865 4.141574 CCCCTCGTTCTATATTGGACCAAA 60.142 45.833 11.82 1.24 0.00 3.28


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

AutoCloner maintained by Alex Coulton.