Multiple sequence alignment - TraesCS3B01G293200

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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 TraesCS3B01G293200 chr3B 100.000 3071 0 0 1 3071 472307984 472304914 0.000000e+00 5672.0
1 TraesCS3B01G293200 chr3B 91.577 1021 79 4 1315 2330 472586375 472587393 0.000000e+00 1402.0
2 TraesCS3B01G293200 chr3B 91.103 517 23 4 822 1315 472584790 472585306 0.000000e+00 678.0
3 TraesCS3B01G293200 chr3B 86.863 373 21 9 444 790 472584423 472584793 2.870000e-105 392.0
4 TraesCS3B01G293200 chr3D 92.688 2366 114 16 1 2330 362425689 362423347 0.000000e+00 3356.0
5 TraesCS3B01G293200 chr3D 90.562 1886 97 29 488 2330 362854910 362856757 0.000000e+00 2422.0
6 TraesCS3B01G293200 chr3A 90.188 2395 156 27 1 2330 482938117 482935737 0.000000e+00 3048.0
7 TraesCS3B01G293200 chr3A 91.101 1843 93 26 547 2330 482929320 482927490 0.000000e+00 2429.0
8 TraesCS3B01G293200 chr3A 90.769 65 3 2 469 530 482929424 482929360 1.960000e-12 84.2
9 TraesCS3B01G293200 chr5D 97.185 746 21 0 2326 3071 298795167 298795912 0.000000e+00 1262.0
10 TraesCS3B01G293200 chr5D 94.444 756 25 4 2326 3064 433930150 433930905 0.000000e+00 1147.0
11 TraesCS3B01G293200 chr2B 97.067 750 18 4 2324 3071 616480491 616481238 0.000000e+00 1260.0
12 TraesCS3B01G293200 chr2D 96.787 747 23 1 2326 3071 590375612 590376358 0.000000e+00 1245.0
13 TraesCS3B01G293200 chr2D 96.118 747 28 1 2326 3071 545604353 545603607 0.000000e+00 1218.0
14 TraesCS3B01G293200 chr2D 86.340 754 76 12 2326 3062 401954227 401953484 0.000000e+00 797.0
15 TraesCS3B01G293200 chr2D 80.021 941 153 26 1099 2029 637802164 637803079 0.000000e+00 664.0
16 TraesCS3B01G293200 chr6B 95.850 747 29 2 2326 3071 240431517 240432262 0.000000e+00 1206.0
17 TraesCS3B01G293200 chr7D 93.421 760 37 5 2325 3071 54052496 54051737 0.000000e+00 1114.0
18 TraesCS3B01G293200 chr5B 92.904 761 36 3 2326 3069 522136159 522135400 0.000000e+00 1090.0
19 TraesCS3B01G293200 chr1A 86.034 759 85 6 2326 3066 572710476 572711231 0.000000e+00 795.0
20 TraesCS3B01G293200 chr1A 82.036 167 30 0 1091 1257 441842041 441842207 3.190000e-30 143.0
21 TraesCS3B01G293200 chr7A 83.425 730 115 5 1298 2024 722767915 722768641 0.000000e+00 673.0
22 TraesCS3B01G293200 chr7B 82.574 746 122 7 1298 2039 727536981 727536240 0.000000e+00 651.0
23 TraesCS3B01G293200 chrUn 78.855 908 163 22 1127 2027 249446248 249447133 1.230000e-163 586.0
24 TraesCS3B01G293200 chr1D 81.437 167 31 0 1091 1257 342170302 342170468 1.490000e-28 137.0
25 TraesCS3B01G293200 chr2A 84.946 93 12 2 2303 2394 65952061 65951970 3.260000e-15 93.5
26 TraesCS3B01G293200 chr6A 91.111 45 1 2 638 679 599757461 599757505 1.190000e-04 58.4


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 TraesCS3B01G293200 chr3B 472304914 472307984 3070 True 5672.0 5672 100.000000 1 3071 1 chr3B.!!$R1 3070
1 TraesCS3B01G293200 chr3B 472584423 472587393 2970 False 824.0 1402 89.847667 444 2330 3 chr3B.!!$F1 1886
2 TraesCS3B01G293200 chr3D 362423347 362425689 2342 True 3356.0 3356 92.688000 1 2330 1 chr3D.!!$R1 2329
3 TraesCS3B01G293200 chr3D 362854910 362856757 1847 False 2422.0 2422 90.562000 488 2330 1 chr3D.!!$F1 1842
4 TraesCS3B01G293200 chr3A 482935737 482938117 2380 True 3048.0 3048 90.188000 1 2330 1 chr3A.!!$R1 2329
5 TraesCS3B01G293200 chr3A 482927490 482929424 1934 True 1256.6 2429 90.935000 469 2330 2 chr3A.!!$R2 1861
6 TraesCS3B01G293200 chr5D 298795167 298795912 745 False 1262.0 1262 97.185000 2326 3071 1 chr5D.!!$F1 745
7 TraesCS3B01G293200 chr5D 433930150 433930905 755 False 1147.0 1147 94.444000 2326 3064 1 chr5D.!!$F2 738
8 TraesCS3B01G293200 chr2B 616480491 616481238 747 False 1260.0 1260 97.067000 2324 3071 1 chr2B.!!$F1 747
9 TraesCS3B01G293200 chr2D 590375612 590376358 746 False 1245.0 1245 96.787000 2326 3071 1 chr2D.!!$F1 745
10 TraesCS3B01G293200 chr2D 545603607 545604353 746 True 1218.0 1218 96.118000 2326 3071 1 chr2D.!!$R2 745
11 TraesCS3B01G293200 chr2D 401953484 401954227 743 True 797.0 797 86.340000 2326 3062 1 chr2D.!!$R1 736
12 TraesCS3B01G293200 chr2D 637802164 637803079 915 False 664.0 664 80.021000 1099 2029 1 chr2D.!!$F2 930
13 TraesCS3B01G293200 chr6B 240431517 240432262 745 False 1206.0 1206 95.850000 2326 3071 1 chr6B.!!$F1 745
14 TraesCS3B01G293200 chr7D 54051737 54052496 759 True 1114.0 1114 93.421000 2325 3071 1 chr7D.!!$R1 746
15 TraesCS3B01G293200 chr5B 522135400 522136159 759 True 1090.0 1090 92.904000 2326 3069 1 chr5B.!!$R1 743
16 TraesCS3B01G293200 chr1A 572710476 572711231 755 False 795.0 795 86.034000 2326 3066 1 chr1A.!!$F2 740
17 TraesCS3B01G293200 chr7A 722767915 722768641 726 False 673.0 673 83.425000 1298 2024 1 chr7A.!!$F1 726
18 TraesCS3B01G293200 chr7B 727536240 727536981 741 True 651.0 651 82.574000 1298 2039 1 chr7B.!!$R1 741
19 TraesCS3B01G293200 chrUn 249446248 249447133 885 False 586.0 586 78.855000 1127 2027 1 chrUn.!!$F1 900

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
176 177 0.534412 AGGTGTCCAATCTGCTCTCG 59.466 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 3342 0.108329 TTCGCTTGTACTAGGCCAGC 60.108 55.0 5.01 1.39 0.0 4.85 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
69 70 1.338579 GGAAGAGGAGTTGGAGCACTG 60.339 57.143 0.00 0.00 0.00 3.66
72 73 1.152030 AGGAGTTGGAGCACTGGGA 60.152 57.895 0.00 0.00 0.00 4.37
86 87 2.196776 GGGATGCTCCACCCCATG 59.803 66.667 0.00 0.00 38.64 3.66
170 171 3.981071 TGAACCTAGGTGTCCAATCTG 57.019 47.619 17.14 0.00 0.00 2.90
176 177 0.534412 AGGTGTCCAATCTGCTCTCG 59.466 55.000 0.00 0.00 0.00 4.04
198 199 6.415702 TCGTGTGAAGTTTCGTGAAAAATAG 58.584 36.000 0.00 0.00 31.33 1.73
272 279 7.931578 AAAATACTGTTTGGATGGATCGTAA 57.068 32.000 0.00 0.00 0.00 3.18
290 297 1.168714 AAGCCGGACTGCATTTTCTC 58.831 50.000 5.05 0.00 0.00 2.87
296 303 1.464997 GGACTGCATTTTCTCCGACAC 59.535 52.381 0.00 0.00 0.00 3.67
333 340 7.687941 TGATATCTTTTCAGGAAACTTCACC 57.312 36.000 3.98 0.00 40.21 4.02
352 359 1.825474 CCCGTGAGTAGATTGGACACT 59.175 52.381 0.00 0.00 0.00 3.55
376 383 3.719871 GGTTTGATACCCCCAAATTCCT 58.280 45.455 0.00 0.00 41.43 3.36
377 384 4.101114 GGTTTGATACCCCCAAATTCCTT 58.899 43.478 0.00 0.00 41.43 3.36
452 478 2.457598 CACCCAGGAGCTCTAGTGTAA 58.542 52.381 14.64 0.00 0.00 2.41
456 482 4.536489 ACCCAGGAGCTCTAGTGTAATTTT 59.464 41.667 14.64 0.00 0.00 1.82
467 493 8.653338 GCTCTAGTGTAATTTTCGTTGTAATGA 58.347 33.333 0.00 0.00 0.00 2.57
810 926 5.344743 TTCCATTAGTGATCACTGACTCC 57.655 43.478 33.76 3.83 42.52 3.85
818 934 4.013728 GTGATCACTGACTCCTCTGTAGT 58.986 47.826 18.83 0.00 0.00 2.73
1014 1139 1.717791 CTGGCACACACACACCACTG 61.718 60.000 0.00 0.00 0.00 3.66
1406 2630 0.033781 ACAACTACGGCGCCTTTGTA 59.966 50.000 26.68 18.03 0.00 2.41
1817 3041 2.959372 TCGAGCCACGACGTGATT 59.041 55.556 28.83 15.92 46.45 2.57
2100 3334 7.604927 TCTCTAAATACTGTAACAATGGCGTTT 59.395 33.333 0.00 0.00 0.00 3.60
2248 3487 6.309494 GCCCGACTTTAAATTAATGAAACCAC 59.691 38.462 5.76 0.00 0.00 4.16
2268 3507 3.353370 CCAACCGGGTAGGATACAAAA 57.647 47.619 6.32 0.00 45.43 2.44
2277 3516 5.277974 CGGGTAGGATACAAAATGCAGATTG 60.278 44.000 11.53 11.53 45.43 2.67
2278 3517 5.827797 GGGTAGGATACAAAATGCAGATTGA 59.172 40.000 18.13 5.45 45.43 2.57
2287 3526 4.637483 AAATGCAGATTGATACAACGGG 57.363 40.909 0.00 0.00 0.00 5.28
2443 3684 5.642063 AGATAACACAAACACAATCGGGTAG 59.358 40.000 0.00 0.00 0.00 3.18
2684 3925 7.445402 ACCCATTCTGTACAAGCAATATATGTC 59.555 37.037 0.00 0.00 0.00 3.06
2809 4066 2.446435 CGGACACATCCCTTCCATTTT 58.554 47.619 0.00 0.00 42.83 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.716998 ACAGACATTTCACATGTTAAGAACTCT 59.283 33.333 0.00 0.00 31.52 3.24
15 16 7.865707 ACAGACATTTCACATGTTAAGAACTC 58.134 34.615 0.00 0.00 31.52 3.01
25 26 6.094719 CCCATTACAACAGACATTTCACATG 58.905 40.000 0.00 0.00 0.00 3.21
35 36 3.263425 TCCTCTTCCCCATTACAACAGAC 59.737 47.826 0.00 0.00 0.00 3.51
37 38 3.264450 ACTCCTCTTCCCCATTACAACAG 59.736 47.826 0.00 0.00 0.00 3.16
72 73 1.422781 CTCATACATGGGGTGGAGCAT 59.577 52.381 0.00 0.00 0.00 3.79
142 143 3.974642 GGACACCTAGGTTCAATATCCCT 59.025 47.826 13.15 0.00 0.00 4.20
150 151 2.027192 GCAGATTGGACACCTAGGTTCA 60.027 50.000 13.15 8.47 0.00 3.18
151 152 2.237392 AGCAGATTGGACACCTAGGTTC 59.763 50.000 13.15 13.01 0.00 3.62
170 171 1.190323 CACGAAACTTCACACGAGAGC 59.810 52.381 0.00 0.00 0.00 4.09
176 177 5.968848 TGCTATTTTTCACGAAACTTCACAC 59.031 36.000 0.00 0.00 0.00 3.82
198 199 8.728088 TTTTTCTTCGAGAATACATTTTCTGC 57.272 30.769 0.00 0.00 36.10 4.26
272 279 0.678048 GGAGAAAATGCAGTCCGGCT 60.678 55.000 0.00 0.00 34.04 5.52
296 303 8.607441 TGAAAAGATATCAGGAAATGTATCCG 57.393 34.615 5.32 0.00 44.60 4.18
333 340 2.492088 TGAGTGTCCAATCTACTCACGG 59.508 50.000 0.00 0.00 44.10 4.94
436 462 5.411781 ACGAAAATTACACTAGAGCTCCTG 58.588 41.667 10.93 6.04 0.00 3.86
437 463 5.662674 ACGAAAATTACACTAGAGCTCCT 57.337 39.130 10.93 0.10 0.00 3.69
439 465 6.707599 ACAACGAAAATTACACTAGAGCTC 57.292 37.500 5.27 5.27 0.00 4.09
441 467 8.653338 TCATTACAACGAAAATTACACTAGAGC 58.347 33.333 0.00 0.00 0.00 4.09
452 478 7.925993 TGAACAGTCTTCATTACAACGAAAAT 58.074 30.769 0.00 0.00 0.00 1.82
456 482 7.817478 ACATATGAACAGTCTTCATTACAACGA 59.183 33.333 10.38 0.00 39.59 3.85
486 514 2.159382 CCGACCAGGCAAACTATGTTT 58.841 47.619 0.00 0.00 0.00 2.83
810 926 5.677612 CGATTCGTGTAAGCTAACTACAGAG 59.322 44.000 0.00 0.00 0.00 3.35
818 934 4.177165 TGTTCCGATTCGTGTAAGCTAA 57.823 40.909 5.20 0.00 0.00 3.09
2100 3334 2.105993 TGTACTAGGCCAGCTCTATCGA 59.894 50.000 5.01 0.00 0.00 3.59
2108 3342 0.108329 TTCGCTTGTACTAGGCCAGC 60.108 55.000 5.01 1.39 0.00 4.85
2111 3345 3.746492 CCATTATTCGCTTGTACTAGGCC 59.254 47.826 6.46 0.00 0.00 5.19
2149 3388 5.609696 GCATTATAATCGACTACACACGCAC 60.610 44.000 0.00 0.00 0.00 5.34
2248 3487 3.353370 TTTTGTATCCTACCCGGTTGG 57.647 47.619 11.56 11.56 41.37 3.77
2268 3507 2.945008 CACCCGTTGTATCAATCTGCAT 59.055 45.455 0.00 0.00 0.00 3.96
2277 3516 1.087202 TCATGCGCACCCGTTGTATC 61.087 55.000 14.90 0.00 36.67 2.24
2278 3517 1.078778 TCATGCGCACCCGTTGTAT 60.079 52.632 14.90 0.00 36.67 2.29
2640 3881 3.454812 TGGGTATAAGTCAAGGAAGAGGC 59.545 47.826 0.00 0.00 0.00 4.70
2684 3925 9.499585 CTTTGATGAGAAGTATTTGTGCTAATG 57.500 33.333 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.