Multiple sequence alignment - TraesCS2D01G051300

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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 TraesCS2D01G051300 chr2D 100.000 3303 0 0 1 3303 19545843 19542541 0.000000e+00 6100.0
1 TraesCS2D01G051300 chr2D 87.188 1483 156 22 952 2411 10310167 10311638 0.000000e+00 1655.0
2 TraesCS2D01G051300 chr2D 90.009 1141 105 5 1249 2382 19245524 19244386 0.000000e+00 1467.0
3 TraesCS2D01G051300 chr2D 90.272 514 42 4 697 1208 19246322 19245815 0.000000e+00 665.0
4 TraesCS2D01G051300 chr2D 86.667 75 7 1 177 251 19246866 19246795 2.730000e-11 80.5
5 TraesCS2D01G051300 chr3D 98.042 3167 22 4 154 3303 589695301 589698444 0.000000e+00 5469.0
6 TraesCS2D01G051300 chr3D 89.231 585 39 18 2739 3303 581826852 581826272 0.000000e+00 710.0
7 TraesCS2D01G051300 chr3D 85.256 468 34 17 2735 3186 438059517 438059965 1.810000e-122 449.0
8 TraesCS2D01G051300 chr3D 91.429 245 20 1 2460 2703 581828093 581827849 5.280000e-88 335.0
9 TraesCS2D01G051300 chr3D 95.882 170 2 2 1 166 589695117 589695285 1.510000e-68 270.0
10 TraesCS2D01G051300 chrUn 89.211 1826 138 34 658 2458 169570502 169572293 0.000000e+00 2226.0
11 TraesCS2D01G051300 chrUn 84.375 1024 148 6 1292 2303 150939697 150940720 0.000000e+00 994.0
12 TraesCS2D01G051300 chrUn 85.538 892 76 29 658 1528 391746266 391747125 0.000000e+00 883.0
13 TraesCS2D01G051300 chrUn 85.561 187 26 1 1019 1204 2685 2499 9.350000e-46 195.0
14 TraesCS2D01G051300 chr1B 89.211 1826 138 34 658 2458 44790418 44788627 0.000000e+00 2226.0
15 TraesCS2D01G051300 chr2A 87.059 1445 150 18 975 2393 10465043 10466476 0.000000e+00 1598.0
16 TraesCS2D01G051300 chr2B 87.034 1396 147 25 943 2326 38841490 38842863 0.000000e+00 1544.0
17 TraesCS2D01G051300 chr2B 86.338 1398 162 25 986 2369 4482064 4483446 0.000000e+00 1496.0
18 TraesCS2D01G051300 chr4D 88.926 596 35 14 2735 3303 437821415 437822006 0.000000e+00 706.0
19 TraesCS2D01G051300 chr4D 88.815 599 28 13 2735 3303 497693902 497693313 0.000000e+00 699.0
20 TraesCS2D01G051300 chr4D 91.393 244 15 4 2460 2703 497695152 497694915 2.460000e-86 329.0
21 TraesCS2D01G051300 chr4D 88.686 274 19 6 2460 2729 437820204 437820469 1.140000e-84 324.0
22 TraesCS2D01G051300 chr5B 88.660 582 46 13 2739 3303 686435718 686435140 0.000000e+00 691.0
23 TraesCS2D01G051300 chr5B 87.148 568 46 23 2735 3288 11304082 11304636 1.300000e-173 619.0
24 TraesCS2D01G051300 chr5B 84.016 244 21 3 2460 2703 686436965 686436740 5.550000e-53 219.0
25 TraesCS2D01G051300 chr3B 88.095 588 42 21 2739 3303 642470440 642469858 0.000000e+00 673.0
26 TraesCS2D01G051300 chr3B 86.239 436 22 13 2739 3137 25487933 25488367 3.910000e-119 438.0
27 TraesCS2D01G051300 chr1A 86.842 608 39 19 2735 3303 35134155 35134760 2.780000e-180 641.0
28 TraesCS2D01G051300 chr1A 90.265 113 10 1 2459 2571 559046021 559046132 2.660000e-31 147.0
29 TraesCS2D01G051300 chr6B 86.023 601 43 15 2741 3303 719333773 719333176 1.010000e-169 606.0
30 TraesCS2D01G051300 chr6B 85.492 579 47 24 2735 3293 413939240 413938679 1.330000e-158 569.0
31 TraesCS2D01G051300 chr7A 85.691 601 41 19 2735 3303 658925718 658925131 2.840000e-165 592.0
32 TraesCS2D01G051300 chr3A 85.439 570 56 21 2735 3288 549912259 549911701 4.780000e-158 568.0
33 TraesCS2D01G051300 chr1D 86.789 492 37 16 2735 3203 218326287 218326773 1.050000e-144 523.0
34 TraesCS2D01G051300 chr5D 90.476 273 19 4 2460 2728 542467694 542467425 1.460000e-93 353.0
35 TraesCS2D01G051300 chr6D 91.429 245 15 4 2460 2703 111019850 111020089 6.830000e-87 331.0
36 TraesCS2D01G051300 chr6D 81.951 205 24 10 2462 2655 308937545 308937343 9.490000e-36 161.0
37 TraesCS2D01G051300 chr6A 86.842 114 5 4 2624 2728 445616011 445615899 5.790000e-23 119.0


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 TraesCS2D01G051300 chr2D 19542541 19545843 3302 True 6100.0 6100 100.000000 1 3303 1 chr2D.!!$R1 3302
1 TraesCS2D01G051300 chr2D 10310167 10311638 1471 False 1655.0 1655 87.188000 952 2411 1 chr2D.!!$F1 1459
2 TraesCS2D01G051300 chr2D 19244386 19246866 2480 True 737.5 1467 88.982667 177 2382 3 chr2D.!!$R2 2205
3 TraesCS2D01G051300 chr3D 589695117 589698444 3327 False 2869.5 5469 96.962000 1 3303 2 chr3D.!!$F2 3302
4 TraesCS2D01G051300 chr3D 581826272 581828093 1821 True 522.5 710 90.330000 2460 3303 2 chr3D.!!$R1 843
5 TraesCS2D01G051300 chrUn 169570502 169572293 1791 False 2226.0 2226 89.211000 658 2458 1 chrUn.!!$F2 1800
6 TraesCS2D01G051300 chrUn 150939697 150940720 1023 False 994.0 994 84.375000 1292 2303 1 chrUn.!!$F1 1011
7 TraesCS2D01G051300 chrUn 391746266 391747125 859 False 883.0 883 85.538000 658 1528 1 chrUn.!!$F3 870
8 TraesCS2D01G051300 chr1B 44788627 44790418 1791 True 2226.0 2226 89.211000 658 2458 1 chr1B.!!$R1 1800
9 TraesCS2D01G051300 chr2A 10465043 10466476 1433 False 1598.0 1598 87.059000 975 2393 1 chr2A.!!$F1 1418
10 TraesCS2D01G051300 chr2B 38841490 38842863 1373 False 1544.0 1544 87.034000 943 2326 1 chr2B.!!$F2 1383
11 TraesCS2D01G051300 chr2B 4482064 4483446 1382 False 1496.0 1496 86.338000 986 2369 1 chr2B.!!$F1 1383
12 TraesCS2D01G051300 chr4D 437820204 437822006 1802 False 515.0 706 88.806000 2460 3303 2 chr4D.!!$F1 843
13 TraesCS2D01G051300 chr4D 497693313 497695152 1839 True 514.0 699 90.104000 2460 3303 2 chr4D.!!$R1 843
14 TraesCS2D01G051300 chr5B 11304082 11304636 554 False 619.0 619 87.148000 2735 3288 1 chr5B.!!$F1 553
15 TraesCS2D01G051300 chr5B 686435140 686436965 1825 True 455.0 691 86.338000 2460 3303 2 chr5B.!!$R1 843
16 TraesCS2D01G051300 chr3B 642469858 642470440 582 True 673.0 673 88.095000 2739 3303 1 chr3B.!!$R1 564
17 TraesCS2D01G051300 chr1A 35134155 35134760 605 False 641.0 641 86.842000 2735 3303 1 chr1A.!!$F1 568
18 TraesCS2D01G051300 chr6B 719333176 719333773 597 True 606.0 606 86.023000 2741 3303 1 chr6B.!!$R2 562
19 TraesCS2D01G051300 chr6B 413938679 413939240 561 True 569.0 569 85.492000 2735 3293 1 chr6B.!!$R1 558
20 TraesCS2D01G051300 chr7A 658925131 658925718 587 True 592.0 592 85.691000 2735 3303 1 chr7A.!!$R1 568
21 TraesCS2D01G051300 chr3A 549911701 549912259 558 True 568.0 568 85.439000 2735 3288 1 chr3A.!!$R1 553

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
166 199 0.544697 GTCCGGGAGAGAGAGAGAGT 59.455 60.000 0.0 0.0 0.00 3.24 F
860 1048 1.069296 TCGGTTGCTTTGCATCTTTCG 60.069 47.619 0.0 0.0 38.76 3.46 F
1201 1392 5.871396 ACAACTCAAGACCTTCTGTAAGA 57.129 39.130 0.0 0.0 44.68 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1392 9.277783 CCTACTACTATATTTGCATGCTTTCTT 57.722 33.333 20.33 3.82 0.00 2.52 R
2206 2679 0.473694 TCATCACACCCCACTCACCT 60.474 55.000 0.00 0.00 0.00 4.00 R
2393 2886 4.963318 TTATTGTGATGCCCTAGAGAGG 57.037 45.455 0.00 0.00 43.33 3.69 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
68 69 7.013750 TCCATGTTGAACAACTAGTTTATTGCA 59.986 33.333 5.07 2.01 41.51 4.08
150 151 4.873746 TCTCTATCGATTGGATTGGTCC 57.126 45.455 1.71 0.00 45.31 4.46
166 199 0.544697 GTCCGGGAGAGAGAGAGAGT 59.455 60.000 0.00 0.00 0.00 3.24
170 203 3.071892 TCCGGGAGAGAGAGAGAGTATTC 59.928 52.174 0.00 0.00 0.00 1.75
673 859 6.948886 GGTCTGTTCCCATCTATAGTCATCTA 59.051 42.308 0.00 0.00 0.00 1.98
860 1048 1.069296 TCGGTTGCTTTGCATCTTTCG 60.069 47.619 0.00 0.00 38.76 3.46
1201 1392 5.871396 ACAACTCAAGACCTTCTGTAAGA 57.129 39.130 0.00 0.00 44.68 2.10
2206 2679 2.124653 GAGGAGGACGGAGAGCGA 60.125 66.667 0.00 0.00 0.00 4.93
2393 2886 5.741982 ACAAGCGTTCAAATTGTACAACTTC 59.258 36.000 11.22 0.00 35.47 3.01
2483 2976 1.560923 CGACTGGACATCAATCGACC 58.439 55.000 0.00 0.00 46.61 4.79
2655 3149 4.398673 TGCTGTTTACAGATGCATGCATAA 59.601 37.500 32.27 20.00 46.59 1.90
2672 3166 4.756642 TGCATAAACAGAAGACAACTCCAG 59.243 41.667 0.00 0.00 0.00 3.86
3104 4676 6.515832 AGCAAAATACCCACAAAAGAAAGAG 58.484 36.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 0.324614 TCAGACCGCCACATGTCAAT 59.675 50.000 0.00 0.00 33.89 2.57
150 151 4.351874 AGAATACTCTCTCTCTCTCCCG 57.648 50.000 0.00 0.00 0.00 5.14
152 153 5.445964 ACCAAGAATACTCTCTCTCTCTCC 58.554 45.833 0.00 0.00 0.00 3.71
166 199 5.445964 GCATAAAAGGGAGGACCAAGAATA 58.554 41.667 0.00 0.00 43.89 1.75
170 203 2.291540 TGGCATAAAAGGGAGGACCAAG 60.292 50.000 0.00 0.00 43.89 3.61
494 540 9.410556 GTGAAGCATAATGTTCAACAATTTAGT 57.589 29.630 0.00 0.00 34.52 2.24
495 541 9.409312 TGTGAAGCATAATGTTCAACAATTTAG 57.591 29.630 0.00 0.00 34.52 1.85
496 542 9.926158 ATGTGAAGCATAATGTTCAACAATTTA 57.074 25.926 0.00 0.00 35.74 1.40
497 543 8.714179 CATGTGAAGCATAATGTTCAACAATTT 58.286 29.630 0.00 0.00 35.74 1.82
498 544 7.332430 CCATGTGAAGCATAATGTTCAACAATT 59.668 33.333 0.00 0.00 35.74 2.32
499 545 6.814644 CCATGTGAAGCATAATGTTCAACAAT 59.185 34.615 0.00 0.00 35.74 2.71
673 859 2.081425 GAGCCGATCGAGCAGGACAT 62.081 60.000 24.07 7.99 0.00 3.06
860 1048 8.049655 ACTAGGCTCATTTGAGAAAGAAAATC 57.950 34.615 11.70 0.00 44.74 2.17
1201 1392 9.277783 CCTACTACTATATTTGCATGCTTTCTT 57.722 33.333 20.33 3.82 0.00 2.52
2206 2679 0.473694 TCATCACACCCCACTCACCT 60.474 55.000 0.00 0.00 0.00 4.00
2393 2886 4.963318 TTATTGTGATGCCCTAGAGAGG 57.037 45.455 0.00 0.00 43.33 3.69
2483 2976 7.030165 AGTGACTGACTCAAGTATTATGTTCG 58.970 38.462 0.00 0.00 0.00 3.95
2655 3149 9.427821 AGTATATATCTGGAGTTGTCTTCTGTT 57.572 33.333 0.00 0.00 0.00 3.16
2672 3166 6.485984 ACATACGTCGATGGGGAGTATATATC 59.514 42.308 9.90 0.00 0.00 1.63
3104 4676 5.240844 GGTAATACCAATGCCACCTATTCAC 59.759 44.000 4.24 0.00 38.42 3.18


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

AutoCloner maintained by Alex Coulton.