Multiple sequence alignment - TraesCS2B01G259200

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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 TraesCS2B01G259200 chr2B 100.000 3473 0 0 1 3473 320941291 320937819 0.000000e+00 6414
1 TraesCS2B01G259200 chr2B 93.616 2710 152 20 544 3243 386132462 386135160 0.000000e+00 4026
2 TraesCS2B01G259200 chr2B 95.710 2238 86 8 1 2232 115615670 115613437 0.000000e+00 3592
3 TraesCS2B01G259200 chr2B 96.032 378 12 3 3099 3473 386135098 386135475 2.290000e-171 612
4 TraesCS2B01G259200 chr2B 93.814 388 18 6 3090 3473 571080559 571080174 2.320000e-161 579
5 TraesCS2B01G259200 chr2B 94.430 377 18 3 3099 3473 571072158 571071783 8.360000e-161 577
6 TraesCS2B01G259200 chr4B 94.555 3012 126 25 480 3473 277835237 277832246 0.000000e+00 4619
7 TraesCS2B01G259200 chr4B 94.466 2783 124 26 479 3243 559209723 559206953 0.000000e+00 4259
8 TraesCS2B01G259200 chr6B 96.084 2809 102 7 669 3473 48901240 48904044 0.000000e+00 4571
9 TraesCS2B01G259200 chr6B 74.396 414 63 36 100 484 652698596 652698995 1.680000e-28 137
10 TraesCS2B01G259200 chr7B 95.158 2685 115 12 564 3243 393237311 393234637 0.000000e+00 4224
11 TraesCS2B01G259200 chr7B 92.377 2781 179 30 482 3243 319716347 319719113 0.000000e+00 3930
12 TraesCS2B01G259200 chr7B 95.299 2276 82 8 971 3243 240199659 240201912 0.000000e+00 3587
13 TraesCS2B01G259200 chr1B 94.723 2577 117 16 676 3243 60863658 60861092 0.000000e+00 3988
14 TraesCS2B01G259200 chr1B 92.849 2713 170 21 544 3243 348700009 348697308 0.000000e+00 3914
15 TraesCS2B01G259200 chr1B 96.277 376 12 2 3099 3473 348697370 348696996 1.770000e-172 616
16 TraesCS2B01G259200 chr1B 93.354 316 15 3 1 310 556069279 556068964 2.440000e-126 462
17 TraesCS2B01G259200 chr1B 91.104 326 13 3 1 310 556073942 556073617 8.910000e-116 427
18 TraesCS2B01G259200 chr1B 74.334 413 65 37 100 484 685388761 685388362 1.680000e-28 137
19 TraesCS2B01G259200 chr3A 91.766 838 46 10 1 819 364717926 364718759 0.000000e+00 1144
20 TraesCS2B01G259200 chr7A 91.155 814 58 9 1 806 396155665 396154858 0.000000e+00 1092
21 TraesCS2B01G259200 chr5D 93.400 697 23 6 1 688 506137625 506138307 0.000000e+00 1011
22 TraesCS2B01G259200 chr3B 94.845 388 14 5 3090 3473 413610743 413611128 4.960000e-168 601
23 TraesCS2B01G259200 chr3B 93.814 388 19 5 3090 3473 545288585 545288199 2.320000e-161 579
24 TraesCS2B01G259200 chr3B 92.573 377 25 3 3099 3473 668314713 668314338 3.940000e-149 538
25 TraesCS2B01G259200 chr6D 93.421 228 14 1 258 484 121109973 121109746 1.540000e-88 337


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 TraesCS2B01G259200 chr2B 320937819 320941291 3472 True 6414 6414 100.000 1 3473 1 chr2B.!!$R2 3472
1 TraesCS2B01G259200 chr2B 115613437 115615670 2233 True 3592 3592 95.710 1 2232 1 chr2B.!!$R1 2231
2 TraesCS2B01G259200 chr2B 386132462 386135475 3013 False 2319 4026 94.824 544 3473 2 chr2B.!!$F1 2929
3 TraesCS2B01G259200 chr4B 277832246 277835237 2991 True 4619 4619 94.555 480 3473 1 chr4B.!!$R1 2993
4 TraesCS2B01G259200 chr4B 559206953 559209723 2770 True 4259 4259 94.466 479 3243 1 chr4B.!!$R2 2764
5 TraesCS2B01G259200 chr6B 48901240 48904044 2804 False 4571 4571 96.084 669 3473 1 chr6B.!!$F1 2804
6 TraesCS2B01G259200 chr7B 393234637 393237311 2674 True 4224 4224 95.158 564 3243 1 chr7B.!!$R1 2679
7 TraesCS2B01G259200 chr7B 319716347 319719113 2766 False 3930 3930 92.377 482 3243 1 chr7B.!!$F2 2761
8 TraesCS2B01G259200 chr7B 240199659 240201912 2253 False 3587 3587 95.299 971 3243 1 chr7B.!!$F1 2272
9 TraesCS2B01G259200 chr1B 60861092 60863658 2566 True 3988 3988 94.723 676 3243 1 chr1B.!!$R1 2567
10 TraesCS2B01G259200 chr1B 348696996 348700009 3013 True 2265 3914 94.563 544 3473 2 chr1B.!!$R5 2929
11 TraesCS2B01G259200 chr3A 364717926 364718759 833 False 1144 1144 91.766 1 819 1 chr3A.!!$F1 818
12 TraesCS2B01G259200 chr7A 396154858 396155665 807 True 1092 1092 91.155 1 806 1 chr7A.!!$R1 805
13 TraesCS2B01G259200 chr5D 506137625 506138307 682 False 1011 1011 93.400 1 688 1 chr5D.!!$F1 687

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
806 846 1.536766 GCGTAAAAACCCCACTGTACC 59.463 52.381 0.0 0.0 0.00 3.34 F
834 876 1.876497 ATCATTTTGGCGCCGTTGCT 61.876 50.000 23.9 5.1 34.43 3.91 F
1425 1468 4.104102 AGGTACAATGAGGAGAACCACAAA 59.896 41.667 0.0 0.0 39.90 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2005 2.625737 TCATCTACAGCAGCTTCTTGC 58.374 47.619 0.00 0.0 44.41 4.01 R
2059 2102 6.623486 CAAAGAAATCACAAGGCATCATGTA 58.377 36.000 0.00 0.0 0.00 2.29 R
3300 3517 2.230130 TAAGCTGGGACCCCAAAATG 57.770 50.000 8.45 0.0 46.63 2.32 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
317 332 7.973388 GGATCTGACTAGTTGATGCATCTATAC 59.027 40.741 26.32 19.87 0.00 1.47
571 601 9.809096 TGTTTTCTTGTGTTAGCATTAAATTCA 57.191 25.926 0.00 0.00 0.00 2.57
806 846 1.536766 GCGTAAAAACCCCACTGTACC 59.463 52.381 0.00 0.00 0.00 3.34
810 850 4.262592 CGTAAAAACCCCACTGTACCTACT 60.263 45.833 0.00 0.00 0.00 2.57
834 876 1.876497 ATCATTTTGGCGCCGTTGCT 61.876 50.000 23.90 5.10 34.43 3.91
894 936 7.013369 AGACTAGGTTTAGCTTGTTTCCTTTTG 59.987 37.037 0.00 0.00 0.00 2.44
944 986 6.559429 TCTAACTCCTAACCCTTGTTCTAGT 58.441 40.000 0.00 0.00 35.87 2.57
948 990 7.809880 ACTCCTAACCCTTGTTCTAGTTTAT 57.190 36.000 0.00 0.00 35.87 1.40
950 992 8.666821 ACTCCTAACCCTTGTTCTAGTTTATTT 58.333 33.333 0.00 0.00 35.87 1.40
1122 1165 4.443266 GCTCGGCAGCGAGAGGTT 62.443 66.667 15.39 0.00 41.81 3.50
1425 1468 4.104102 AGGTACAATGAGGAGAACCACAAA 59.896 41.667 0.00 0.00 39.90 2.83
1695 1738 4.577875 AGATCAAGAGTGGAAAAGAGCTG 58.422 43.478 0.00 0.00 0.00 4.24
1962 2005 8.637099 TCATCATCTATTACTCCTGAAGAAGTG 58.363 37.037 0.00 0.00 0.00 3.16
2059 2102 6.881602 GTCAGGTTTACTCAATCCTCTTGATT 59.118 38.462 0.00 0.00 44.67 2.57
2114 2157 5.532032 CCTTGCATTACATGATACCATCACA 59.468 40.000 0.00 0.00 43.01 3.58
2881 2924 7.942894 TGGCACTTAAGTAGTAGCTATGATCTA 59.057 37.037 8.04 0.00 34.56 1.98
3058 3102 3.531538 GATCGGTGGCTTGTGAAATCTA 58.468 45.455 0.00 0.00 0.00 1.98
3330 3547 1.220493 TCCCAGCTTATCTCAGGGCTA 59.780 52.381 0.00 0.00 39.42 3.93
3362 3579 8.614469 GAGCCAGCTCTTGATTATTAGTATTT 57.386 34.615 12.42 0.00 39.80 1.40
3391 3608 3.094572 CTCAAGGCCATTGACTTGGAAT 58.905 45.455 12.24 0.00 43.09 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
424 440 9.075678 CTGAATATATTTCTGCAGAAAAGGGAT 57.924 33.333 37.81 28.71 45.81 3.85
571 601 7.581213 TTTGGCAATTTCCATATTACTCGAT 57.419 32.000 0.00 0.00 35.77 3.59
806 846 3.303132 GGCGCCAAAATGATCGTTAGTAG 60.303 47.826 24.80 0.00 0.00 2.57
810 850 0.375454 CGGCGCCAAAATGATCGTTA 59.625 50.000 28.98 0.00 0.00 3.18
834 876 3.138798 GCTCGACGCTAGTCCCCA 61.139 66.667 0.00 0.00 44.28 4.96
924 966 7.809880 ATAAACTAGAACAAGGGTTAGGAGT 57.190 36.000 0.00 0.00 37.36 3.85
926 968 9.511272 GAAAATAAACTAGAACAAGGGTTAGGA 57.489 33.333 0.00 0.00 37.36 2.94
927 969 9.516546 AGAAAATAAACTAGAACAAGGGTTAGG 57.483 33.333 0.00 0.00 37.36 2.69
950 992 8.503196 GCAAAAAGGAAAAGAAAACAAAGAGAA 58.497 29.630 0.00 0.00 0.00 2.87
954 996 7.022979 CCTGCAAAAAGGAAAAGAAAACAAAG 58.977 34.615 0.00 0.00 40.02 2.77
960 1002 7.176589 TCTAACCTGCAAAAAGGAAAAGAAA 57.823 32.000 0.00 0.00 40.02 2.52
1122 1165 3.523564 AGCTAGGCCTATCCTCAAAAACA 59.476 43.478 14.30 0.00 43.20 2.83
1425 1468 7.013655 GGTGAATAAATCTGTTGTGGAGCATAT 59.986 37.037 0.00 0.00 0.00 1.78
1695 1738 5.805728 TCAATCTTCCTTACTTCTTCCACC 58.194 41.667 0.00 0.00 0.00 4.61
1962 2005 2.625737 TCATCTACAGCAGCTTCTTGC 58.374 47.619 0.00 0.00 44.41 4.01
2059 2102 6.623486 CAAAGAAATCACAAGGCATCATGTA 58.377 36.000 0.00 0.00 0.00 2.29
2881 2924 8.103305 ACTGTTTTTCACATACTACAGATCCAT 58.897 33.333 0.00 0.00 37.15 3.41
3190 3323 5.163488 CGAGAACATGGTATACACCTGGTTA 60.163 44.000 5.01 0.00 45.98 2.85
3300 3517 2.230130 TAAGCTGGGACCCCAAAATG 57.770 50.000 8.45 0.00 46.63 2.32
3362 3579 4.072131 GTCAATGGCCTTGAGTCAAAGTA 58.928 43.478 15.31 0.00 44.44 2.24


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

AutoCloner maintained by Alex Coulton.