Multiple sequence alignment - TraesCS2A01G309800

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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 TraesCS2A01G309800 chr2A 100.000 2527 0 0 1 2527 533181039 533178513 0.000000e+00 4667.0
1 TraesCS2A01G309800 chr5A 95.171 2547 95 12 1 2527 638638296 638640834 0.000000e+00 3997.0
2 TraesCS2A01G309800 chr7A 94.935 2547 103 13 1 2527 116057756 116055216 0.000000e+00 3965.0
3 TraesCS2A01G309800 chr7A 94.146 2101 96 13 447 2527 160993066 160990973 0.000000e+00 3173.0
4 TraesCS2A01G309800 chr7A 90.515 1845 159 12 691 2527 54862213 54860377 0.000000e+00 2423.0
5 TraesCS2A01G309800 chr7A 98.089 157 3 0 1 157 160993227 160993071 8.910000e-70 274.0
6 TraesCS2A01G309800 chr5B 90.688 1847 156 11 691 2527 523901449 523899609 0.000000e+00 2444.0
7 TraesCS2A01G309800 chr5B 94.340 53 3 0 592 644 703769192 703769140 5.790000e-12 82.4
8 TraesCS2A01G309800 chr5B 100.000 37 0 0 645 681 523904616 523904580 4.510000e-08 69.4
9 TraesCS2A01G309800 chr6A 90.352 1845 160 13 691 2527 577050676 577048842 0.000000e+00 2405.0
10 TraesCS2A01G309800 chr6A 89.066 1381 141 8 691 2068 46445426 46446799 0.000000e+00 1705.0
11 TraesCS2A01G309800 chr6A 100.000 36 0 0 646 681 46441948 46441983 1.620000e-07 67.6
12 TraesCS2A01G309800 chr6A 97.059 34 0 1 649 681 577054157 577054124 3.510000e-04 56.5
13 TraesCS2A01G309800 chr1B 93.709 1208 53 16 780 1984 18657455 18656268 0.000000e+00 1788.0
14 TraesCS2A01G309800 chr1B 95.005 921 38 5 1 918 18658370 18657455 0.000000e+00 1439.0
15 TraesCS2A01G309800 chr1B 100.000 32 0 0 645 676 12124820 12124789 2.710000e-05 60.2
16 TraesCS2A01G309800 chrUn 91.141 745 58 4 1791 2527 318613204 318613948 0.000000e+00 1003.0
17 TraesCS2A01G309800 chrUn 91.007 745 59 4 1791 2527 11852087 11852831 0.000000e+00 998.0
18 TraesCS2A01G309800 chrUn 90.872 745 60 5 1791 2527 385585134 385585878 0.000000e+00 992.0
19 TraesCS2A01G309800 chrUn 91.518 448 36 2 1347 1794 11851485 11851930 1.280000e-172 616.0
20 TraesCS2A01G309800 chrUn 90.657 396 30 5 691 1085 11851072 11851461 1.040000e-143 520.0
21 TraesCS2A01G309800 chr7B 83.461 393 46 14 1071 1448 107099346 107099734 5.170000e-92 348.0
22 TraesCS2A01G309800 chr3B 85.227 176 20 4 3 178 108285471 108285640 2.580000e-40 176.0
23 TraesCS2A01G309800 chr2B 85.311 177 18 6 3 178 2710360 2710529 2.580000e-40 176.0
24 TraesCS2A01G309800 chr4B 94.340 53 3 0 592 644 309437899 309437847 5.790000e-12 82.4
25 TraesCS2A01G309800 chr4B 93.750 48 3 0 597 644 328588484 328588531 3.490000e-09 73.1
26 TraesCS2A01G309800 chr1A 92.453 53 4 0 592 644 517449423 517449371 2.700000e-10 76.8
27 TraesCS2A01G309800 chr3A 97.368 38 1 0 592 629 560755323 560755360 5.840000e-07 65.8
28 TraesCS2A01G309800 chr6B 100.000 31 0 0 646 676 116091382 116091412 9.760000e-05 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 TraesCS2A01G309800 chr2A 533178513 533181039 2526 True 4667.000000 4667 100.000000 1 2527 1 chr2A.!!$R1 2526
1 TraesCS2A01G309800 chr5A 638638296 638640834 2538 False 3997.000000 3997 95.171000 1 2527 1 chr5A.!!$F1 2526
2 TraesCS2A01G309800 chr7A 116055216 116057756 2540 True 3965.000000 3965 94.935000 1 2527 1 chr7A.!!$R2 2526
3 TraesCS2A01G309800 chr7A 54860377 54862213 1836 True 2423.000000 2423 90.515000 691 2527 1 chr7A.!!$R1 1836
4 TraesCS2A01G309800 chr7A 160990973 160993227 2254 True 1723.500000 3173 96.117500 1 2527 2 chr7A.!!$R3 2526
5 TraesCS2A01G309800 chr5B 523899609 523904616 5007 True 1256.700000 2444 95.344000 645 2527 2 chr5B.!!$R2 1882
6 TraesCS2A01G309800 chr6A 577048842 577054157 5315 True 1230.750000 2405 93.705500 649 2527 2 chr6A.!!$R1 1878
7 TraesCS2A01G309800 chr6A 46441948 46446799 4851 False 886.300000 1705 94.533000 646 2068 2 chr6A.!!$F1 1422
8 TraesCS2A01G309800 chr1B 18656268 18658370 2102 True 1613.500000 1788 94.357000 1 1984 2 chr1B.!!$R2 1983
9 TraesCS2A01G309800 chrUn 318613204 318613948 744 False 1003.000000 1003 91.141000 1791 2527 1 chrUn.!!$F1 736
10 TraesCS2A01G309800 chrUn 385585134 385585878 744 False 992.000000 992 90.872000 1791 2527 1 chrUn.!!$F2 736
11 TraesCS2A01G309800 chrUn 11851072 11852831 1759 False 711.333333 998 91.060667 691 2527 3 chrUn.!!$F3 1836

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
731 4199 0.710588 TCTCACTTGGCCTCTCCCTA 59.289 55.0 3.32 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 6278 1.411246 CCGACCGACATAGATTTCCCA 59.589 52.381 0.0 0.0 0.0 4.37 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
216 217 4.010349 GGGTCATGGAGGAACAACTAAAG 58.990 47.826 0.00 0.00 0.00 1.85
470 472 4.280101 TCAACGTGTTAACACATGGTTG 57.720 40.909 31.32 31.32 46.75 3.77
520 522 5.237815 TGTATTGTTGAGAATGAGACGCTT 58.762 37.500 0.00 0.00 0.00 4.68
557 559 8.352201 GCATTTCAATACTATAGTCCAATTGCA 58.648 33.333 9.12 2.08 0.00 4.08
565 567 4.804868 ATAGTCCAATTGCATGCAACAA 57.195 36.364 34.10 14.55 38.88 2.83
731 4199 0.710588 TCTCACTTGGCCTCTCCCTA 59.289 55.000 3.32 0.00 0.00 3.53
850 4459 4.289672 TGGAAATAGAGAAGCCCTTGAAGT 59.710 41.667 0.00 0.00 0.00 3.01
875 4484 4.510038 AAAGTTCTTTATGTGCAGCAGG 57.490 40.909 0.00 0.00 0.00 4.85
892 4501 6.376864 TGCAGCAGGTAATTAAGCTTCATTAA 59.623 34.615 13.36 0.00 34.61 1.40
894 4503 7.922811 GCAGCAGGTAATTAAGCTTCATTAATT 59.077 33.333 13.36 11.24 43.96 1.40
940 4549 5.827797 ACTTTCATGAACTGGTTACACATGT 59.172 36.000 7.89 0.00 39.18 3.21
941 4550 6.321181 ACTTTCATGAACTGGTTACACATGTT 59.679 34.615 7.89 0.00 39.18 2.71
1041 4651 0.874390 CATGGTGGACAAAGGTCACG 59.126 55.000 0.00 0.00 46.17 4.35
1077 4687 7.545265 TGGCTTCAAAGTTACATTCAAATATGC 59.455 33.333 0.00 0.00 0.00 3.14
1087 4697 6.212888 ACATTCAAATATGCCACTTCCTTC 57.787 37.500 0.00 0.00 0.00 3.46
1088 4698 5.716228 ACATTCAAATATGCCACTTCCTTCA 59.284 36.000 0.00 0.00 0.00 3.02
1105 4715 1.847328 TCACATTCGAGAGGTGGCTA 58.153 50.000 11.61 0.00 33.45 3.93
1140 4750 9.148104 GAATTTCTTTCTGCTGCATTTTCTAAT 57.852 29.630 1.31 0.00 0.00 1.73
1338 4955 6.476053 GGTGAAGTAACGATTGAAGGAGATAC 59.524 42.308 0.00 0.00 0.00 2.24
1476 5093 4.260253 GCAAATGCTTTCGCTACTACCTAC 60.260 45.833 0.00 0.00 38.21 3.18
1549 5166 1.053424 GCGTTATCCCCCATGTCCTA 58.947 55.000 0.00 0.00 0.00 2.94
1627 5245 7.675619 TCCTTTCATGTATCTCAGGATATAGCA 59.324 37.037 0.00 0.00 36.72 3.49
1686 5304 1.685180 GGTACCCCTTTTCCCATCAGC 60.685 57.143 0.00 0.00 0.00 4.26
1723 5341 9.077885 TCTCTTTAGTTGCTTTGGTATGAAATT 57.922 29.630 0.00 0.00 0.00 1.82
1724 5342 9.132521 CTCTTTAGTTGCTTTGGTATGAAATTG 57.867 33.333 0.00 0.00 0.00 2.32
1734 5352 8.250332 GCTTTGGTATGAAATTGTATTGAAGGA 58.750 33.333 0.00 0.00 0.00 3.36
1753 5371 9.911788 TTGAAGGAAGCTTAGAGAAAATATCAT 57.088 29.630 0.00 0.00 0.00 2.45
1794 5572 7.068470 GTGTGGAAATATTAACCGGGGATTTTA 59.932 37.037 6.32 0.00 0.00 1.52
1846 5624 8.041323 TGTTCTCCAATAAGATGTAGAAGGAAC 58.959 37.037 0.00 0.00 0.00 3.62
1932 5710 2.137177 TTGCCCACTACAAGGAGCCC 62.137 60.000 0.00 0.00 0.00 5.19
1957 5735 5.511234 GCAGATGATGTGCCTCTTAAAAT 57.489 39.130 2.74 0.00 34.67 1.82
2491 6278 3.399330 CATCACCAACAAGTAGTCGGTT 58.601 45.455 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
216 217 5.819379 GCCCACTACATACCTTTTTACTACC 59.181 44.000 0.00 0.00 0.00 3.18
370 372 6.037172 GTCAGCAGAAGTGTTTGTTTCTTCTA 59.963 38.462 6.38 0.00 43.71 2.10
493 495 7.023575 GCGTCTCATTCTCAACAATACAAATT 58.976 34.615 0.00 0.00 0.00 1.82
516 518 0.877071 AATGCCAACACAGAGAAGCG 59.123 50.000 0.00 0.00 0.00 4.68
520 522 5.316167 AGTATTGAAATGCCAACACAGAGA 58.684 37.500 0.00 0.00 0.00 3.10
557 559 2.535331 GGTTTGACGTTGTTGTTGCAT 58.465 42.857 0.00 0.00 0.00 3.96
558 560 1.729472 CGGTTTGACGTTGTTGTTGCA 60.729 47.619 0.00 0.00 0.00 4.08
565 567 1.729284 AGAACACGGTTTGACGTTGT 58.271 45.000 0.00 0.00 46.25 3.32
698 4164 5.068987 GCCAAGTGAGAGAGTGAGATCTTAT 59.931 44.000 0.00 0.00 0.00 1.73
751 4222 5.356751 AGTTCAAATCTGCACACTACAACAA 59.643 36.000 0.00 0.00 0.00 2.83
754 4225 6.288294 ACTAGTTCAAATCTGCACACTACAA 58.712 36.000 0.00 0.00 0.00 2.41
809 4281 6.474140 TTTCCATGAATCAAAGCAGCATAT 57.526 33.333 0.00 0.00 0.00 1.78
850 4459 6.371548 CCTGCTGCACATAAAGAACTTTACTA 59.628 38.462 0.00 0.00 37.80 1.82
1014 4624 3.879295 CCTTTGTCCACCATGCTACTATG 59.121 47.826 0.00 0.00 0.00 2.23
1015 4625 3.523564 ACCTTTGTCCACCATGCTACTAT 59.476 43.478 0.00 0.00 0.00 2.12
1041 4651 5.444663 AACTTTGAAGCCAAGATCTGTTC 57.555 39.130 0.00 0.00 33.23 3.18
1077 4687 3.257393 CTCTCGAATGTGAAGGAAGTGG 58.743 50.000 0.00 0.00 0.00 4.00
1087 4697 2.868583 CAATAGCCACCTCTCGAATGTG 59.131 50.000 2.53 2.53 0.00 3.21
1088 4698 2.501723 ACAATAGCCACCTCTCGAATGT 59.498 45.455 0.00 0.00 0.00 2.71
1105 4715 8.742777 TGCAGCAGAAAGAAATTCTTATACAAT 58.257 29.630 8.83 0.00 46.39 2.71
1140 4750 3.762288 ACAATCAGTTCGCCTAGACACTA 59.238 43.478 0.00 0.00 0.00 2.74
1338 4955 8.693504 CACTTGCTATCACAAACAACAATTTAG 58.306 33.333 0.00 0.00 0.00 1.85
1417 5034 1.203364 CCTATGGGGATAGGTGGAGCT 60.203 57.143 0.00 0.00 39.03 4.09
1627 5245 5.146010 TGTGTTTCCTGCAACTTCTTTTT 57.854 34.783 0.00 0.00 0.00 1.94
1686 5304 9.994432 AAAGCAACTAAAGAGAATTCATTATCG 57.006 29.630 8.44 0.00 33.49 2.92
1734 5352 9.336171 GGAGAACATGATATTTTCTCTAAGCTT 57.664 33.333 17.62 3.48 43.24 3.74
1753 5371 4.698201 TCCACACAATAACTGGAGAACA 57.302 40.909 0.00 0.00 30.27 3.18
1767 5385 3.266254 TCCCCGGTTAATATTTCCACACA 59.734 43.478 0.00 0.00 0.00 3.72
1794 5572 5.993441 CCTCCAATTTGAAAATCTGCAAGTT 59.007 36.000 0.00 0.00 33.76 2.66
1846 5624 5.220043 CGTTCTAGTACTTGACATCAAAGCG 60.220 44.000 6.52 0.00 35.15 4.68
1957 5735 9.847224 ATCCCTCGCTTTATTTTCTAGAATTTA 57.153 29.630 5.89 0.00 0.00 1.40
2205 5988 3.775866 TCCTACCGACCAACATCCATTAA 59.224 43.478 0.00 0.00 0.00 1.40
2367 6154 1.516161 TCCCGACCGACTATCATACG 58.484 55.000 0.00 0.00 0.00 3.06
2407 6194 1.621814 CCTTTCCCGACCAACAGTCTA 59.378 52.381 0.00 0.00 43.91 2.59
2491 6278 1.411246 CCGACCGACATAGATTTCCCA 59.589 52.381 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.