Multiple sequence alignment - TraesCS2A01G150500

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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 TraesCS2A01G150500 chr2A 100.000 3815 0 0 1 3815 98136097 98139911 0.000000e+00 7046
1 TraesCS2A01G150500 chr2B 94.376 3876 135 27 1 3815 150709716 150713569 0.000000e+00 5873
2 TraesCS2A01G150500 chr2D 94.865 2376 86 14 618 2960 99132257 99134629 0.000000e+00 3679
3 TraesCS2A01G150500 chr2D 94.988 858 21 10 2962 3815 99134721 99135560 0.000000e+00 1327
4 TraesCS2A01G150500 chr2D 91.159 328 23 5 238 561 99131542 99131867 1.260000e-119 440
5 TraesCS2A01G150500 chr2D 89.062 192 17 3 90 281 99131367 99131554 6.370000e-58 235
6 TraesCS2A01G150500 chr3D 93.289 894 23 20 1029 1922 284204420 284205276 0.000000e+00 1284
7 TraesCS2A01G150500 chr7B 91.723 894 37 19 1029 1922 29705080 29704224 0.000000e+00 1206
8 TraesCS2A01G150500 chr3B 93.986 582 21 11 1029 1610 245914013 245914580 0.000000e+00 869
9 TraesCS2A01G150500 chr3B 95.816 239 10 0 1684 1922 245921643 245921881 1.660000e-103 387
10 TraesCS2A01G150500 chr6A 98.837 172 2 0 636 807 24832593 24832422 1.330000e-79 307
11 TraesCS2A01G150500 chr6A 100.000 97 0 0 316 412 24832686 24832590 3.030000e-41 180


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 TraesCS2A01G150500 chr2A 98136097 98139911 3814 False 7046.00 7046 100.0000 1 3815 1 chr2A.!!$F1 3814
1 TraesCS2A01G150500 chr2B 150709716 150713569 3853 False 5873.00 5873 94.3760 1 3815 1 chr2B.!!$F1 3814
2 TraesCS2A01G150500 chr2D 99131367 99135560 4193 False 1420.25 3679 92.5185 90 3815 4 chr2D.!!$F1 3725
3 TraesCS2A01G150500 chr3D 284204420 284205276 856 False 1284.00 1284 93.2890 1029 1922 1 chr3D.!!$F1 893
4 TraesCS2A01G150500 chr7B 29704224 29705080 856 True 1206.00 1206 91.7230 1029 1922 1 chr7B.!!$R1 893
5 TraesCS2A01G150500 chr3B 245914013 245914580 567 False 869.00 869 93.9860 1029 1610 1 chr3B.!!$F1 581

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
631 999 0.111253 GCGGAATTGGGGAGATGGAT 59.889 55.000 0.00 0.0 0.00 3.41 F
831 1225 0.251474 AATGAAGCAGGAGCAGCCAA 60.251 50.000 0.00 0.0 45.49 4.52 F
2214 2623 1.138247 GAGCATGCCTTTTGAGCCG 59.862 57.895 15.66 0.0 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 2167 1.376424 CTCTGCGCCAATGGTCAGT 60.376 57.895 18.11 0.0 31.25 3.41 R
2367 2776 1.398692 TTTCTGCAACACCTTCCCAC 58.601 50.000 0.00 0.0 0.00 4.61 R
3050 3569 2.082140 ACCTGTTCTTTGTTTCCCCC 57.918 50.000 0.00 0.0 0.00 5.40 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
48 49 8.620416 TGATATCAACGATTTAATTGTGGAAGG 58.380 33.333 1.98 0.00 30.52 3.46
110 111 8.792830 TTCTAAAGCTCAGCAAGTACATTAAT 57.207 30.769 0.00 0.00 0.00 1.40
139 140 6.827251 ACATCTATGCTCATTTTGACATCAGT 59.173 34.615 0.00 0.00 0.00 3.41
184 185 6.895782 ACTAGCATGGTATAAAGGTTGCTTA 58.104 36.000 4.84 0.00 40.60 3.09
272 303 6.700960 TGAACAAGGAACATGCAAATAACAAG 59.299 34.615 0.00 0.00 0.00 3.16
293 324 3.984508 CATCATGATGCCTGAAGTTCC 57.015 47.619 22.20 0.00 31.39 3.62
301 332 1.239347 GCCTGAAGTTCCTTCACCAC 58.761 55.000 0.00 0.00 44.27 4.16
307 338 1.410004 AGTTCCTTCACCACGACTGA 58.590 50.000 0.00 0.00 0.00 3.41
335 369 3.250762 TGACCTGCTTGAATTTTGACTCG 59.749 43.478 0.00 0.00 0.00 4.18
352 386 0.176680 TCGGCTTGAGGCTTCTGATC 59.823 55.000 0.00 0.00 41.46 2.92
354 388 0.254178 GGCTTGAGGCTTCTGATCCA 59.746 55.000 0.00 0.00 41.46 3.41
407 441 4.344102 ACCATTCTTCTATACGCAGCCTTA 59.656 41.667 0.00 0.00 0.00 2.69
458 492 8.827832 ATATGAACTCAAATTTGGGAGATTGA 57.172 30.769 24.78 3.33 35.17 2.57
463 497 4.478203 TCAAATTTGGGAGATTGACACCA 58.522 39.130 17.90 0.00 0.00 4.17
470 504 3.181453 TGGGAGATTGACACCAACGTTTA 60.181 43.478 0.00 0.00 34.72 2.01
471 505 3.435671 GGGAGATTGACACCAACGTTTAG 59.564 47.826 0.00 0.00 34.72 1.85
489 523 4.519540 TTAGCCAAAATCCAGCAGAAAC 57.480 40.909 0.00 0.00 0.00 2.78
490 524 2.601905 AGCCAAAATCCAGCAGAAACT 58.398 42.857 0.00 0.00 0.00 2.66
510 544 1.338337 TGCTAGCAGATTAGCTCGTCC 59.662 52.381 14.93 0.00 45.26 4.79
526 560 0.802607 GTCCGAGCAAGAACTAGCCG 60.803 60.000 0.00 0.00 0.00 5.52
536 570 1.079503 GAACTAGCCGGACAAAGCTG 58.920 55.000 5.05 0.00 40.28 4.24
564 598 1.300465 CCTGAGATGATCCGCCGTG 60.300 63.158 0.00 0.00 0.00 4.94
585 619 0.321122 GATATTCGCAGGGGGAGCAG 60.321 60.000 0.00 0.00 0.00 4.24
586 620 2.403132 ATATTCGCAGGGGGAGCAGC 62.403 60.000 0.00 0.00 0.00 5.25
606 640 3.412408 GGCAGGGAGGAAGGGGTC 61.412 72.222 0.00 0.00 0.00 4.46
629 997 1.529244 GGCGGAATTGGGGAGATGG 60.529 63.158 0.00 0.00 0.00 3.51
630 998 1.531748 GCGGAATTGGGGAGATGGA 59.468 57.895 0.00 0.00 0.00 3.41
631 999 0.111253 GCGGAATTGGGGAGATGGAT 59.889 55.000 0.00 0.00 0.00 3.41
726 1101 0.321671 CTCCCTTTCTTCCTCGTGCA 59.678 55.000 0.00 0.00 0.00 4.57
730 1105 1.740025 CCTTTCTTCCTCGTGCAATCC 59.260 52.381 0.00 0.00 0.00 3.01
742 1117 2.414785 GCAATCCCGCCGGACAAAT 61.415 57.895 5.05 0.00 42.48 2.32
743 1118 1.727467 CAATCCCGCCGGACAAATC 59.273 57.895 5.05 0.00 42.48 2.17
831 1225 0.251474 AATGAAGCAGGAGCAGCCAA 60.251 50.000 0.00 0.00 45.49 4.52
851 1245 2.106683 GCCGCTCCACGTATTTGCT 61.107 57.895 0.00 0.00 41.42 3.91
881 1276 2.046507 CTCGCTGGCAGCTTCCTT 60.047 61.111 34.17 0.00 39.60 3.36
1507 1916 3.652539 TTCGACGGAATGCGGGACC 62.653 63.158 0.00 0.00 0.00 4.46
1935 2344 6.660521 TGCTTACTTGGAGTTCAATGATCATT 59.339 34.615 15.36 15.36 34.45 2.57
2133 2542 1.264749 TGCCAAGGGTCGAGCACTAT 61.265 55.000 17.59 0.00 0.00 2.12
2214 2623 1.138247 GAGCATGCCTTTTGAGCCG 59.862 57.895 15.66 0.00 0.00 5.52
2268 2677 4.631131 CCTGTCGCATCCATAAGAATGTA 58.369 43.478 0.00 0.00 0.00 2.29
2305 2714 5.582689 AGCTATGGCCAAATTGAAAGTAC 57.417 39.130 10.96 0.00 39.73 2.73
2394 2803 5.451798 GGAAGGTGTTGCAGAAATGAGAAAA 60.452 40.000 0.00 0.00 0.00 2.29
2463 2872 3.007940 TCGAATGGGAGAACACAGTTCAT 59.992 43.478 11.92 0.00 30.90 2.57
2472 2881 5.277538 GGAGAACACAGTTCATGAGTTTGTC 60.278 44.000 11.92 0.00 41.97 3.18
2475 2884 5.028549 ACACAGTTCATGAGTTTGTCTCT 57.971 39.130 0.00 0.00 43.13 3.10
2562 2971 4.576330 AATACAAGCAGGATATAGGCCC 57.424 45.455 0.00 0.00 0.00 5.80
2604 3013 7.049754 TGCAAGATATTGATGAGCAGTCTAAA 58.950 34.615 3.77 0.00 0.00 1.85
2634 3043 2.760634 TGGCTGAACATAGCGAGAAA 57.239 45.000 0.00 0.00 44.60 2.52
2749 3176 5.919755 TGGTATATGGTCGCAAGTTGATTA 58.080 37.500 7.16 0.00 39.48 1.75
2844 3271 7.544622 AGAACCTTTTGTACCAGAAAAAGTTC 58.455 34.615 16.31 16.31 40.30 3.01
2871 3298 3.217681 ACCAATTGTTTGTCCGTACCT 57.782 42.857 4.43 0.00 0.00 3.08
2878 3305 2.366266 TGTTTGTCCGTACCTTGCTAGT 59.634 45.455 0.00 0.00 0.00 2.57
2880 3307 4.039004 TGTTTGTCCGTACCTTGCTAGTAA 59.961 41.667 0.00 0.00 0.00 2.24
2923 3350 9.868277 GCTAGATATTCTTATACTTGAGCATGT 57.132 33.333 0.00 0.00 0.00 3.21
2989 3506 6.927294 ATATTCTTCCGAAAGTCATGGAAC 57.073 37.500 0.00 0.00 36.87 3.62
3050 3569 9.319143 CCTTCCAGTATACATCAAACTTAAGAG 57.681 37.037 10.09 0.00 0.00 2.85
3083 3602 8.612619 ACAAAGAACAGGTAATTCTTATATGCG 58.387 33.333 0.69 0.00 43.91 4.73
3108 3627 8.998989 CGCACTTCAACTGTTTACATAATATTG 58.001 33.333 0.00 0.00 0.00 1.90
3484 4003 0.109272 CACAGCTGCAGCAAGAATGG 60.109 55.000 38.24 20.06 45.16 3.16
3546 4066 8.236586 TGACCGAAATGATCAAGAAATAAACAG 58.763 33.333 0.00 0.00 0.00 3.16
3580 4100 2.615747 GGACTCAGCAAGGGAAGTAACC 60.616 54.545 0.00 0.00 0.00 2.85
3671 4191 4.163441 TCTCAAACACCTGGAATCACAA 57.837 40.909 0.00 0.00 0.00 3.33
3673 4193 3.625853 TCAAACACCTGGAATCACAACA 58.374 40.909 0.00 0.00 0.00 3.33
3693 4213 6.486657 ACAACACAACTATGTTAAGATGCAGT 59.513 34.615 0.00 0.00 40.89 4.40
3711 4234 5.237815 TGCAGTAATGTCTAACAGGAACAG 58.762 41.667 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.818921 TGCTAATTGCCCTTCCACAAT 58.181 42.857 0.00 0.00 42.00 2.71
48 49 4.935352 TGGATTTACCATGCTAATTGCC 57.065 40.909 0.00 0.00 44.64 4.52
110 111 8.913487 ATGTCAAAATGAGCATAGATGTGATA 57.087 30.769 0.00 0.00 0.00 2.15
139 140 8.347771 GCTAGTTGCTCATTCATAATTGAATCA 58.652 33.333 0.00 0.00 43.09 2.57
161 162 7.801716 TTAAGCAACCTTTATACCATGCTAG 57.198 36.000 0.00 0.00 42.82 3.42
209 210 6.851222 CATGAAAGGCAATTAGACGAGTAT 57.149 37.500 0.00 0.00 0.00 2.12
293 324 3.056821 TCAGGTAATCAGTCGTGGTGAAG 60.057 47.826 0.00 0.00 0.00 3.02
301 332 1.478510 AGCAGGTCAGGTAATCAGTCG 59.521 52.381 0.00 0.00 0.00 4.18
307 338 5.774690 TCAAAATTCAAGCAGGTCAGGTAAT 59.225 36.000 0.00 0.00 0.00 1.89
335 369 0.254178 TGGATCAGAAGCCTCAAGCC 59.746 55.000 0.00 0.00 45.47 4.35
362 396 2.340443 GAGTCCCATCCCGATCGC 59.660 66.667 10.32 0.00 0.00 4.58
407 441 4.070716 CTCTGAATCTTCTGTTGCAGGTT 58.929 43.478 0.00 0.00 31.51 3.50
449 483 1.892209 AACGTTGGTGTCAATCTCCC 58.108 50.000 0.00 0.00 35.10 4.30
458 492 3.243602 GGATTTTGGCTAAACGTTGGTGT 60.244 43.478 0.00 0.00 0.00 4.16
463 497 2.625790 TGCTGGATTTTGGCTAAACGTT 59.374 40.909 0.00 0.00 0.00 3.99
470 504 2.298163 CAGTTTCTGCTGGATTTTGGCT 59.702 45.455 0.00 0.00 33.11 4.75
471 505 2.680577 CAGTTTCTGCTGGATTTTGGC 58.319 47.619 0.00 0.00 33.11 4.52
489 523 2.606795 GGACGAGCTAATCTGCTAGCAG 60.607 54.545 34.48 34.48 45.69 4.24
490 524 1.338337 GGACGAGCTAATCTGCTAGCA 59.662 52.381 18.22 18.22 45.69 3.49
495 529 3.171705 CTCGGACGAGCTAATCTGC 57.828 57.895 8.93 0.00 35.31 4.26
510 544 0.802607 GTCCGGCTAGTTCTTGCTCG 60.803 60.000 0.00 7.75 0.00 5.03
536 570 3.513515 GGATCATCTCAGGATGGTAGTCC 59.486 52.174 6.22 5.85 46.70 3.85
556 590 2.732016 CGAATATCCCACGGCGGA 59.268 61.111 13.24 0.00 36.56 5.54
561 595 1.301716 CCCCTGCGAATATCCCACG 60.302 63.158 0.00 0.00 0.00 4.94
564 598 1.679898 CTCCCCCTGCGAATATCCC 59.320 63.158 0.00 0.00 0.00 3.85
589 623 3.412408 GACCCCTTCCTCCCTGCC 61.412 72.222 0.00 0.00 0.00 4.85
590 624 3.787001 CGACCCCTTCCTCCCTGC 61.787 72.222 0.00 0.00 0.00 4.85
629 997 1.619332 GTCCCCTTCCGAGGTATCATC 59.381 57.143 0.00 0.00 41.85 2.92
630 998 1.718280 GTCCCCTTCCGAGGTATCAT 58.282 55.000 0.00 0.00 41.85 2.45
631 999 0.754217 CGTCCCCTTCCGAGGTATCA 60.754 60.000 0.00 0.00 41.85 2.15
726 1101 1.817941 CGATTTGTCCGGCGGGATT 60.818 57.895 27.98 8.90 46.14 3.01
814 1201 1.303074 CTTGGCTGCTCCTGCTTCA 60.303 57.895 0.00 0.00 40.48 3.02
831 1225 1.449601 CAAATACGTGGAGCGGCCT 60.450 57.895 0.00 0.00 46.52 5.19
881 1276 2.685017 AGGCTGGATCTGACGGCA 60.685 61.111 0.00 0.00 41.96 5.69
1326 1735 4.415332 GCGGTGCGGACGAAGAGA 62.415 66.667 0.00 0.00 0.00 3.10
1758 2167 1.376424 CTCTGCGCCAATGGTCAGT 60.376 57.895 18.11 0.00 31.25 3.41
1935 2344 2.220586 TCCGTGATTGGCCAGTCCA 61.221 57.895 24.09 12.17 44.85 4.02
2133 2542 2.684374 CAAAAGATCGACCATGCATCCA 59.316 45.455 0.00 0.00 0.00 3.41
2214 2623 6.212888 AGTGTTCTCCAAATAATTGCATCC 57.787 37.500 0.00 0.00 35.10 3.51
2268 2677 3.071312 CCATAGCTTCCTCTGCAATCTCT 59.929 47.826 0.00 0.00 0.00 3.10
2367 2776 1.398692 TTTCTGCAACACCTTCCCAC 58.601 50.000 0.00 0.00 0.00 4.61
2394 2803 4.020218 TGAATGTTCTCCCTCTTGATCGTT 60.020 41.667 0.00 0.00 0.00 3.85
2472 2881 2.415224 CGGATGCGATCTATCACCAGAG 60.415 54.545 0.00 0.00 0.00 3.35
2475 2884 1.541588 CTCGGATGCGATCTATCACCA 59.458 52.381 10.57 0.00 0.00 4.17
2562 2971 3.853831 TGCAATACCAAGCTTGTCATG 57.146 42.857 24.35 17.26 0.00 3.07
2604 3013 3.790416 TTCAGCCAGTGCCCGCTTT 62.790 57.895 0.00 0.00 38.69 3.51
2634 3043 2.060370 CCCAAAAGCAATGGCCAGT 58.940 52.632 13.05 5.37 42.56 4.00
2749 3176 4.056092 GGAAACGATTCCGGTCTCTAAT 57.944 45.455 8.86 0.00 45.44 1.73
2852 3279 3.855524 GCAAGGTACGGACAAACAATTGG 60.856 47.826 10.83 0.00 41.01 3.16
2871 3298 8.999431 CAACCTTAAACTTCAGATTACTAGCAA 58.001 33.333 0.00 0.00 0.00 3.91
2923 3350 7.468141 TCTTCTAGTGCAGTTCTTTCAGATA 57.532 36.000 0.00 0.00 0.00 1.98
2989 3506 6.596888 TGTCAATCCTTCAGCTTCTAAATGAG 59.403 38.462 0.00 0.00 0.00 2.90
3050 3569 2.082140 ACCTGTTCTTTGTTTCCCCC 57.918 50.000 0.00 0.00 0.00 5.40
3083 3602 8.798153 GCAATATTATGTAAACAGTTGAAGTGC 58.202 33.333 0.00 0.00 0.00 4.40
3108 3627 6.347240 GCAGATTTGCTACTGACTATGTATGC 60.347 42.308 0.00 0.00 46.95 3.14
3223 3742 9.983804 GTAAAACCAAGTTGTAGATATACAAGC 57.016 33.333 13.06 8.50 40.21 4.01
3316 3835 5.212745 AGCAAGAGAGCCTACTAGGTAAAT 58.787 41.667 3.95 0.00 37.80 1.40
3502 4021 3.243839 GGTCACAGCACAACATCCAAATT 60.244 43.478 0.00 0.00 0.00 1.82
3546 4066 6.967199 CCTTGCTGAGTCCGTTTTAAATAATC 59.033 38.462 0.00 0.00 0.00 1.75
3580 4100 3.158676 GCTCCCTATACAGACAGGTAGG 58.841 54.545 0.00 0.00 34.74 3.18
3671 4191 8.668353 CATTACTGCATCTTAACATAGTTGTGT 58.332 33.333 0.00 0.00 35.83 3.72
3673 4193 8.792830 ACATTACTGCATCTTAACATAGTTGT 57.207 30.769 0.00 0.00 37.82 3.32
3693 4213 6.371548 GTGCAATCTGTTCCTGTTAGACATTA 59.628 38.462 0.00 0.00 0.00 1.90
3738 4261 6.721571 TGCAAAAGAAGAAGTAACTATCCG 57.278 37.500 0.00 0.00 0.00 4.18
3779 4304 9.952030 TGAGGTACTTTTATCATATTGTCACAA 57.048 29.630 0.00 0.00 41.55 3.33


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

AutoCloner maintained by Alex Coulton.