Multiple sequence alignment - TraesCS2B01G142300

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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 TraesCS2B01G142300 chr2B 100.000 2616 0 0 1 2616 109161176 109163791 0.000000e+00 4831.0
1 TraesCS2B01G142300 chr2B 97.427 2604 51 11 1 2594 109788743 109791340 0.000000e+00 4423.0
2 TraesCS2B01G142300 chr2B 95.556 1305 46 6 416 1711 109082333 109083634 0.000000e+00 2078.0
3 TraesCS2B01G142300 chr2B 90.099 909 64 13 1714 2616 716362605 716363493 0.000000e+00 1157.0
4 TraesCS2B01G142300 chr2B 94.866 409 14 1 1 409 109076271 109076672 1.320000e-177 632.0
5 TraesCS2B01G142300 chr2B 86.435 575 49 14 231 788 109356645 109357207 1.040000e-168 603.0
6 TraesCS2B01G142300 chr2B 89.159 452 44 5 1260 1711 109357666 109358112 2.270000e-155 558.0
7 TraesCS2B01G142300 chr2B 95.172 145 7 0 984 1128 109357463 109357607 2.030000e-56 230.0
8 TraesCS2B01G142300 chr2D 96.690 1420 31 3 307 1712 72651368 72652785 0.000000e+00 2348.0
9 TraesCS2B01G142300 chr2D 97.014 1306 28 3 411 1712 72371027 72372325 0.000000e+00 2185.0
10 TraesCS2B01G142300 chr2D 92.694 917 45 7 1713 2616 46164629 46163722 0.000000e+00 1303.0
11 TraesCS2B01G142300 chr2D 90.398 854 59 13 1780 2616 603706062 603706909 0.000000e+00 1101.0
12 TraesCS2B01G142300 chr2D 93.794 709 21 8 307 994 72627712 72628418 0.000000e+00 1044.0
13 TraesCS2B01G142300 chr2D 99.038 104 1 0 307 410 72370867 72370970 1.240000e-43 187.0
14 TraesCS2B01G142300 chr2A 96.894 1288 29 4 434 1712 71112250 71113535 0.000000e+00 2146.0
15 TraesCS2B01G142300 chr2A 91.247 457 40 0 717 1173 71073611 71074067 7.950000e-175 623.0
16 TraesCS2B01G142300 chr2A 94.413 358 18 1 40 395 71111516 71111873 1.370000e-152 549.0
17 TraesCS2B01G142300 chr2A 86.988 415 35 8 1961 2362 722211475 722211883 1.430000e-122 449.0
18 TraesCS2B01G142300 chr2A 90.179 336 23 5 132 460 71072523 71072855 1.860000e-116 429.0
19 TraesCS2B01G142300 chr2A 87.500 352 42 2 1359 1710 71078583 71078932 3.130000e-109 405.0
20 TraesCS2B01G142300 chr2A 97.183 142 4 0 450 591 71073466 71073607 9.360000e-60 241.0
21 TraesCS2B01G142300 chr2A 85.143 175 4 6 1199 1361 71074543 71074707 2.690000e-35 159.0
22 TraesCS2B01G142300 chr3D 93.566 917 35 9 1713 2616 465467544 465468449 0.000000e+00 1345.0
23 TraesCS2B01G142300 chr3A 92.942 921 43 6 1713 2616 524322950 524322035 0.000000e+00 1321.0
24 TraesCS2B01G142300 chr3A 89.255 940 73 11 1699 2616 600067974 600068907 0.000000e+00 1151.0
25 TraesCS2B01G142300 chr7A 90.497 926 53 14 1704 2616 158416612 158417515 0.000000e+00 1190.0
26 TraesCS2B01G142300 chr7A 92.649 721 37 3 1907 2616 34766712 34765997 0.000000e+00 1024.0
27 TraesCS2B01G142300 chr7A 89.062 64 6 1 45 107 695814895 695814832 7.760000e-11 78.7
28 TraesCS2B01G142300 chr7A 97.222 36 1 0 45 80 24340593 24340558 7.820000e-06 62.1
29 TraesCS2B01G142300 chr5A 93.481 721 30 3 1907 2616 465636442 465635728 0.000000e+00 1055.0
30 TraesCS2B01G142300 chr5A 85.567 97 12 2 11 106 412912240 412912335 1.660000e-17 100.0
31 TraesCS2B01G142300 chr5D 87.764 899 76 13 1743 2616 45218682 45219571 0.000000e+00 1020.0
32 TraesCS2B01G142300 chr5D 89.985 679 49 9 1951 2616 54065390 54064718 0.000000e+00 859.0
33 TraesCS2B01G142300 chr7D 83.047 932 117 25 1713 2616 604700897 604699979 0.000000e+00 808.0
34 TraesCS2B01G142300 chr7D 96.203 79 3 0 1715 1793 591233436 591233358 2.110000e-26 130.0
35 TraesCS2B01G142300 chr6B 79.769 865 132 30 782 1619 176969891 176969043 2.900000e-164 588.0
36 TraesCS2B01G142300 chr6D 83.265 490 70 9 772 1258 95787880 95788360 8.590000e-120 440.0
37 TraesCS2B01G142300 chr6D 84.354 147 20 3 242 387 112914714 112914570 9.760000e-30 141.0
38 TraesCS2B01G142300 chr5B 86.649 367 40 6 1714 2077 565322694 565323054 5.250000e-107 398.0
39 TraesCS2B01G142300 chr7B 84.833 389 43 11 1943 2319 670183330 670183714 6.830000e-101 377.0
40 TraesCS2B01G142300 chr6A 96.053 76 3 0 1711 1786 48798485 48798410 9.830000e-25 124.0
41 TraesCS2B01G142300 chr1A 91.139 79 6 1 1713 1790 291965413 291965491 3.560000e-19 106.0
42 TraesCS2B01G142300 chr1D 92.754 69 5 0 35 103 315546767 315546835 1.660000e-17 100.0
43 TraesCS2B01G142300 chr4A 100.000 28 0 0 415 442 710415115 710415088 5.000000e-03 52.8


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 TraesCS2B01G142300 chr2B 109161176 109163791 2615 False 4831.000000 4831 100.000000 1 2616 1 chr2B.!!$F3 2615
1 TraesCS2B01G142300 chr2B 109788743 109791340 2597 False 4423.000000 4423 97.427000 1 2594 1 chr2B.!!$F4 2593
2 TraesCS2B01G142300 chr2B 109082333 109083634 1301 False 2078.000000 2078 95.556000 416 1711 1 chr2B.!!$F2 1295
3 TraesCS2B01G142300 chr2B 716362605 716363493 888 False 1157.000000 1157 90.099000 1714 2616 1 chr2B.!!$F5 902
4 TraesCS2B01G142300 chr2B 109356645 109358112 1467 False 463.666667 603 90.255333 231 1711 3 chr2B.!!$F6 1480
5 TraesCS2B01G142300 chr2D 72651368 72652785 1417 False 2348.000000 2348 96.690000 307 1712 1 chr2D.!!$F2 1405
6 TraesCS2B01G142300 chr2D 46163722 46164629 907 True 1303.000000 1303 92.694000 1713 2616 1 chr2D.!!$R1 903
7 TraesCS2B01G142300 chr2D 72370867 72372325 1458 False 1186.000000 2185 98.026000 307 1712 2 chr2D.!!$F4 1405
8 TraesCS2B01G142300 chr2D 603706062 603706909 847 False 1101.000000 1101 90.398000 1780 2616 1 chr2D.!!$F3 836
9 TraesCS2B01G142300 chr2D 72627712 72628418 706 False 1044.000000 1044 93.794000 307 994 1 chr2D.!!$F1 687
10 TraesCS2B01G142300 chr2A 71111516 71113535 2019 False 1347.500000 2146 95.653500 40 1712 2 chr2A.!!$F3 1672
11 TraesCS2B01G142300 chr2A 71072523 71078932 6409 False 371.400000 623 90.250400 132 1710 5 chr2A.!!$F2 1578
12 TraesCS2B01G142300 chr3D 465467544 465468449 905 False 1345.000000 1345 93.566000 1713 2616 1 chr3D.!!$F1 903
13 TraesCS2B01G142300 chr3A 524322035 524322950 915 True 1321.000000 1321 92.942000 1713 2616 1 chr3A.!!$R1 903
14 TraesCS2B01G142300 chr3A 600067974 600068907 933 False 1151.000000 1151 89.255000 1699 2616 1 chr3A.!!$F1 917
15 TraesCS2B01G142300 chr7A 158416612 158417515 903 False 1190.000000 1190 90.497000 1704 2616 1 chr7A.!!$F1 912
16 TraesCS2B01G142300 chr7A 34765997 34766712 715 True 1024.000000 1024 92.649000 1907 2616 1 chr7A.!!$R2 709
17 TraesCS2B01G142300 chr5A 465635728 465636442 714 True 1055.000000 1055 93.481000 1907 2616 1 chr5A.!!$R1 709
18 TraesCS2B01G142300 chr5D 45218682 45219571 889 False 1020.000000 1020 87.764000 1743 2616 1 chr5D.!!$F1 873
19 TraesCS2B01G142300 chr5D 54064718 54065390 672 True 859.000000 859 89.985000 1951 2616 1 chr5D.!!$R1 665
20 TraesCS2B01G142300 chr7D 604699979 604700897 918 True 808.000000 808 83.047000 1713 2616 1 chr7D.!!$R2 903
21 TraesCS2B01G142300 chr6B 176969043 176969891 848 True 588.000000 588 79.769000 782 1619 1 chr6B.!!$R1 837

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
900 1905 1.616865 ACTAAGTCTACCTTGTGCGCA 59.383 47.619 5.66 5.66 34.46 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 7393 2.04345 CGGAGAGAGAGCAGGGGT 60.043 66.667 0.0 0.0 0.0 4.95 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
40 41 2.445654 GGCAGAGGAGGGAGGAGG 60.446 72.222 0.00 0.00 0.00 4.30
43 44 1.945447 CAGAGGAGGGAGGAGGGAT 59.055 63.158 0.00 0.00 0.00 3.85
130 132 4.212913 GCGCGAGGAGGAGATGCA 62.213 66.667 12.10 0.00 0.00 3.96
204 206 6.316390 ACTTACAAGTAGCTAATTGGACATGC 59.684 38.462 30.88 1.08 37.52 4.06
900 1905 1.616865 ACTAAGTCTACCTTGTGCGCA 59.383 47.619 5.66 5.66 34.46 6.09
1373 6761 4.031201 CGCTTGTTATATTGTTTTTGGCGG 59.969 41.667 0.00 0.00 35.20 6.13
2276 7722 3.065648 TGCCGTAAGTTTTTGAACTGACC 59.934 43.478 2.10 0.00 31.69 4.02
2277 7723 3.549423 GCCGTAAGTTTTTGAACTGACCC 60.549 47.826 2.10 0.00 31.69 4.46
2278 7724 3.004002 CCGTAAGTTTTTGAACTGACCCC 59.996 47.826 2.10 0.00 31.69 4.95
2279 7725 3.004002 CGTAAGTTTTTGAACTGACCCCC 59.996 47.826 2.10 0.00 31.69 5.40
2365 7811 1.446516 CCATTCATGATTCGCCGCCA 61.447 55.000 0.00 0.00 0.00 5.69
2388 7834 4.776435 TGTCCTATGATGATTTCTGCCA 57.224 40.909 0.00 0.00 0.00 4.92
2487 7934 8.579850 TCTGTTTTATCATGCTCTTATGGTTT 57.420 30.769 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.059006 AGATCTGCCACCCCTCATCC 61.059 60.000 0.00 0.00 0.00 3.51
43 44 1.997311 CCAGATCTGCCACCCCTCA 60.997 63.158 17.76 0.00 0.00 3.86
130 132 0.673644 GTGTATGGAACCAGCGCAGT 60.674 55.000 11.47 3.05 0.00 4.40
204 206 1.133025 GTCCAACGCTTCATGGATTGG 59.867 52.381 0.00 0.00 46.78 3.16
592 1557 9.401058 GCTTATTAATAGGATGCCACATTAGAT 57.599 33.333 8.68 0.00 0.00 1.98
900 1905 6.088819 TGGGCTATTTATATACCAGGACACT 58.911 40.000 0.00 0.00 0.00 3.55
1373 6761 1.594862 GCACATACATCAGACGGCTTC 59.405 52.381 0.00 0.00 0.00 3.86
1612 7006 6.978659 TGATTAATCACAACGATGAGACCTAC 59.021 38.462 14.23 0.00 33.40 3.18
1966 7393 2.043450 CGGAGAGAGAGCAGGGGT 60.043 66.667 0.00 0.00 0.00 4.95
2365 7811 5.698104 TGGCAGAAATCATCATAGGACAAT 58.302 37.500 0.00 0.00 0.00 2.71
2388 7834 3.053917 ACCCTACCAGCGACCAAAATAAT 60.054 43.478 0.00 0.00 0.00 1.28
2487 7934 5.710099 GGTGGTAATTCAATTCCTTCACTGA 59.290 40.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.