Multiple sequence alignment - TraesCS2B01G132200

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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 TraesCS2B01G132200 chr2B 100.000 2333 0 0 1 2333 98449180 98446848 0.000000e+00 4309
1 TraesCS2B01G132200 chr2B 96.190 315 9 3 1 312 655681530 655681844 1.600000e-141 512
2 TraesCS2B01G132200 chr2B 95.873 315 10 3 1 312 717661563 717661877 7.440000e-140 507
3 TraesCS2B01G132200 chr2B 95.873 315 10 3 1 312 738160642 738160328 7.440000e-140 507
4 TraesCS2B01G132200 chr2B 95.192 312 13 2 3 312 655677325 655677014 2.080000e-135 492
5 TraesCS2B01G132200 chr7B 94.786 2244 83 16 106 2333 714383205 714385430 0.000000e+00 3465
6 TraesCS2B01G132200 chr7B 93.354 316 17 4 1 312 599848417 599848102 4.540000e-127 464
7 TraesCS2B01G132200 chr4B 92.466 2336 121 24 10 2333 75638959 75641251 0.000000e+00 3288
8 TraesCS2B01G132200 chr4B 90.625 320 18 7 1 312 603279128 603279443 4.640000e-112 414
9 TraesCS2B01G132200 chr1B 90.963 2346 154 32 1 2333 502077031 502074731 0.000000e+00 3105
10 TraesCS2B01G132200 chr3B 90.646 2352 175 35 1 2333 699175560 699173235 0.000000e+00 3083
11 TraesCS2B01G132200 chr3B 90.284 1760 123 38 608 2333 16320969 16319224 0.000000e+00 2259
12 TraesCS2B01G132200 chr3B 85.485 2060 206 50 349 2333 754470679 754468638 0.000000e+00 2061
13 TraesCS2B01G132200 chr3B 87.696 1406 126 33 969 2333 657800883 657799484 0.000000e+00 1594
14 TraesCS2B01G132200 chr3B 89.885 524 38 9 93 612 16322913 16322401 0.000000e+00 660
15 TraesCS2B01G132200 chr3B 96.178 314 10 2 1 312 60583194 60582881 1.600000e-141 512
16 TraesCS2B01G132200 chr3B 95.860 314 11 2 1 312 657802825 657802512 7.440000e-140 507
17 TraesCS2B01G132200 chr7D 90.593 2275 155 39 93 2333 560757706 560759955 0.000000e+00 2961
18 TraesCS2B01G132200 chr6D 88.669 2277 182 43 93 2333 356196854 356199090 0.000000e+00 2706
19 TraesCS2B01G132200 chr6B 91.203 2012 129 30 98 2085 470911386 470909399 0.000000e+00 2691
20 TraesCS2B01G132200 chr7A 88.351 2292 188 51 93 2333 635160794 635163057 0.000000e+00 2680
21 TraesCS2B01G132200 chr2D 88.949 2208 176 38 174 2333 87968452 87966265 0.000000e+00 2663
22 TraesCS2B01G132200 chr5D 88.145 2210 193 40 174 2333 36575169 36572979 0.000000e+00 2566
23 TraesCS2B01G132200 chr5B 94.070 1467 70 9 1 1461 684498909 684500364 0.000000e+00 2211
24 TraesCS2B01G132200 chr2A 89.058 1645 124 36 93 1723 130739129 130740731 0.000000e+00 1989


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 TraesCS2B01G132200 chr2B 98446848 98449180 2332 True 4309.0 4309 100.0000 1 2333 1 chr2B.!!$R1 2332
1 TraesCS2B01G132200 chr7B 714383205 714385430 2225 False 3465.0 3465 94.7860 106 2333 1 chr7B.!!$F1 2227
2 TraesCS2B01G132200 chr4B 75638959 75641251 2292 False 3288.0 3288 92.4660 10 2333 1 chr4B.!!$F1 2323
3 TraesCS2B01G132200 chr1B 502074731 502077031 2300 True 3105.0 3105 90.9630 1 2333 1 chr1B.!!$R1 2332
4 TraesCS2B01G132200 chr3B 699173235 699175560 2325 True 3083.0 3083 90.6460 1 2333 1 chr3B.!!$R2 2332
5 TraesCS2B01G132200 chr3B 754468638 754470679 2041 True 2061.0 2061 85.4850 349 2333 1 chr3B.!!$R3 1984
6 TraesCS2B01G132200 chr3B 16319224 16322913 3689 True 1459.5 2259 90.0845 93 2333 2 chr3B.!!$R4 2240
7 TraesCS2B01G132200 chr3B 657799484 657802825 3341 True 1050.5 1594 91.7780 1 2333 2 chr3B.!!$R5 2332
8 TraesCS2B01G132200 chr7D 560757706 560759955 2249 False 2961.0 2961 90.5930 93 2333 1 chr7D.!!$F1 2240
9 TraesCS2B01G132200 chr6D 356196854 356199090 2236 False 2706.0 2706 88.6690 93 2333 1 chr6D.!!$F1 2240
10 TraesCS2B01G132200 chr6B 470909399 470911386 1987 True 2691.0 2691 91.2030 98 2085 1 chr6B.!!$R1 1987
11 TraesCS2B01G132200 chr7A 635160794 635163057 2263 False 2680.0 2680 88.3510 93 2333 1 chr7A.!!$F1 2240
12 TraesCS2B01G132200 chr2D 87966265 87968452 2187 True 2663.0 2663 88.9490 174 2333 1 chr2D.!!$R1 2159
13 TraesCS2B01G132200 chr5D 36572979 36575169 2190 True 2566.0 2566 88.1450 174 2333 1 chr5D.!!$R1 2159
14 TraesCS2B01G132200 chr5B 684498909 684500364 1455 False 2211.0 2211 94.0700 1 1461 1 chr5B.!!$F1 1460
15 TraesCS2B01G132200 chr2A 130739129 130740731 1602 False 1989.0 1989 89.0580 93 1723 1 chr2A.!!$F1 1630

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
915 3406 4.467769 CATCCCCTGCAAGTATCTTCAAT 58.532 43.478 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 4538 1.001068 TCCATTTGTGTGCATGGCAAG 59.999 47.619 0.0 0.0 41.47 4.01 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
866 3357 5.715434 TTTTCTAATCCTTTTGTTCCCCG 57.285 39.130 0.00 0.00 0.00 5.73
915 3406 4.467769 CATCCCCTGCAAGTATCTTCAAT 58.532 43.478 0.00 0.00 0.00 2.57
921 3412 6.127253 CCCCTGCAAGTATCTTCAATTTGAAT 60.127 38.462 12.04 1.81 35.59 2.57
936 3427 6.210584 TCAATTTGAATAAGGACTTGGTTCCC 59.789 38.462 0.00 0.00 36.12 3.97
1089 3580 2.996742 AGAAAGGGGGAAGATTCCTGTT 59.003 45.455 11.28 0.69 46.72 3.16
1114 3605 2.883574 CCGCAAGTGTTCGTAGGATAA 58.116 47.619 0.00 0.00 0.00 1.75
1339 3831 8.384718 TGCCCCTTCAACTAGTTTAAGTATTTA 58.615 33.333 22.10 7.38 0.00 1.40
1356 3848 7.978099 AGTATTTATCCAAAAAGCTTCCCAT 57.022 32.000 0.00 0.00 0.00 4.00
1388 3935 5.357032 GGATGTCAATGGAATAACGGAAACT 59.643 40.000 0.00 0.00 0.00 2.66
1632 4212 5.508567 TCTTTGGATGTTGATGAGCCAATA 58.491 37.500 0.00 0.00 38.32 1.90
1917 4538 4.035208 TCAGTCTTCTTCGAACCTTTTTGC 59.965 41.667 0.00 0.00 0.00 3.68
1933 4554 0.177373 TTGCTTGCCATGCACACAAA 59.823 45.000 4.56 0.00 38.71 2.83
2145 4821 7.097192 CACTAATAGTAGCAACAGGAAAGTGA 58.903 38.462 0.00 0.00 33.09 3.41
2242 4930 7.439655 GGAGTACCAGAATTATTGTCACTCATC 59.560 40.741 15.24 0.00 33.26 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
381 1385 7.557719 CCTATTTTGACTTATGACTTGTCCCAT 59.442 37.037 0.00 0.00 0.00 4.00
416 1420 2.292267 GTCGTCATGGCTTGATCCATT 58.708 47.619 6.35 0.00 44.04 3.16
778 3235 1.446907 CTGGGCAACTGCTTAGTGAG 58.553 55.000 1.06 0.00 41.70 3.51
847 3319 3.073356 ACACGGGGAACAAAAGGATTAGA 59.927 43.478 0.00 0.00 0.00 2.10
859 3350 3.273434 GACCCTATTAAACACGGGGAAC 58.727 50.000 3.15 0.00 41.11 3.62
866 3357 5.723295 TGTTCCTACGACCCTATTAAACAC 58.277 41.667 0.00 0.00 0.00 3.32
906 3397 9.753674 ACCAAGTCCTTATTCAAATTGAAGATA 57.246 29.630 14.10 0.09 40.05 1.98
907 3398 8.655935 ACCAAGTCCTTATTCAAATTGAAGAT 57.344 30.769 14.10 1.05 40.05 2.40
1089 3580 0.319986 TACGAACACTTGCGGCATCA 60.320 50.000 2.28 0.00 0.00 3.07
1114 3605 0.042581 CCCCTATTTGGCAAACCCCT 59.957 55.000 16.00 1.57 33.59 4.79
1260 3751 4.111198 CACGGAGAAAGTCATCATCAGAG 58.889 47.826 0.00 0.00 0.00 3.35
1262 3753 2.606725 GCACGGAGAAAGTCATCATCAG 59.393 50.000 0.00 0.00 0.00 2.90
1303 3795 1.228552 GAAGGGGCAAGGAAGCACA 60.229 57.895 0.00 0.00 40.53 4.57
1339 3831 2.102578 CCGATGGGAAGCTTTTTGGAT 58.897 47.619 0.00 0.00 34.06 3.41
1356 3848 1.836802 TCCATTGACATCCATGACCGA 59.163 47.619 0.00 0.00 0.00 4.69
1578 4152 3.253188 ACAACAGCTGCGTAATGACAAAT 59.747 39.130 15.27 0.00 0.00 2.32
1771 4374 8.588290 ATGGTAGTGTTGCCTGAAAATAATAA 57.412 30.769 0.00 0.00 0.00 1.40
1917 4538 1.001068 TCCATTTGTGTGCATGGCAAG 59.999 47.619 0.00 0.00 41.47 4.01
1933 4554 7.054124 ACAATCCTTCGTGTACAAATATCCAT 58.946 34.615 0.00 0.00 0.00 3.41
1999 4655 6.098679 ACATGTAAAATGCACGCACAATAAT 58.901 32.000 0.00 0.00 0.00 1.28
2145 4821 7.008332 TCTGAAAATTCCTGCATCCATGATAT 58.992 34.615 0.00 0.00 0.00 1.63
2221 4904 5.734720 ACGATGAGTGACAATAATTCTGGT 58.265 37.500 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.