Multiple sequence alignment - TraesCS5B01G272100

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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 TraesCS5B01G272100 chr5B 100.000 3726 0 0 1 3726 457391779 457388054 0.000000e+00 6881
1 TraesCS5B01G272100 chr5B 97.380 2214 57 1 386 2598 493911110 493913323 0.000000e+00 3766
2 TraesCS5B01G272100 chr5B 98.305 1298 20 2 2430 3726 48320123 48321419 0.000000e+00 2274
3 TraesCS5B01G272100 chr5B 99.742 388 1 0 1 388 48319685 48320072 0.000000e+00 712
4 TraesCS5B01G272100 chr4A 98.026 3343 62 4 386 3726 626535219 626531879 0.000000e+00 5805
5 TraesCS5B01G272100 chr4A 99.743 389 0 1 1 388 626535935 626535547 0.000000e+00 712
6 TraesCS5B01G272100 chr3B 97.995 3342 65 2 386 3726 784063793 784060453 0.000000e+00 5799
7 TraesCS5B01G272100 chr3B 98.980 392 0 2 1 388 784064512 784064121 0.000000e+00 699
8 TraesCS5B01G272100 chr7A 97.996 3344 60 6 386 3726 7421713 7425052 0.000000e+00 5797
9 TraesCS5B01G272100 chr7A 97.421 2288 58 1 484 2771 46729855 46727569 0.000000e+00 3897
10 TraesCS5B01G272100 chr7A 97.478 1467 37 0 386 1852 194167072 194168538 0.000000e+00 2505
11 TraesCS5B01G272100 chr7A 96.957 920 27 1 1838 2756 194170054 194170973 0.000000e+00 1543
12 TraesCS5B01G272100 chr7A 99.227 388 3 0 1 388 98750309 98750696 0.000000e+00 701
13 TraesCS5B01G272100 chr7A 99.227 388 3 0 1 388 194166357 194166744 0.000000e+00 701
14 TraesCS5B01G272100 chr7A 98.721 391 2 1 1 388 7420995 7421385 0.000000e+00 691
15 TraesCS5B01G272100 chr7A 85.410 329 36 8 2833 3153 680918614 680918290 7.710000e-87 331
16 TraesCS5B01G272100 chr1B 97.957 2545 50 2 386 2928 59040038 59042582 0.000000e+00 4410
17 TraesCS5B01G272100 chr1B 98.303 825 12 2 2903 3726 626237752 626236929 0.000000e+00 1445
18 TraesCS5B01G272100 chr1B 98.039 714 12 2 3013 3726 59042569 59043280 0.000000e+00 1240
19 TraesCS5B01G272100 chr1B 99.743 389 0 1 1 388 626238589 626238201 0.000000e+00 712
20 TraesCS5B01G272100 chr5A 97.277 2387 62 2 386 2771 41484987 41482603 0.000000e+00 4045
21 TraesCS5B01G272100 chr5A 98.977 391 1 1 1 388 41485705 41485315 0.000000e+00 697
22 TraesCS5B01G272100 chr7D 90.810 2394 182 29 386 2756 321475964 321478342 0.000000e+00 3168
23 TraesCS5B01G272100 chr7D 85.971 613 61 11 2928 3534 321478537 321479130 1.890000e-177 632
24 TraesCS5B01G272100 chr4B 97.585 1739 39 3 1990 3726 141440384 141438647 0.000000e+00 2976
25 TraesCS5B01G272100 chr4B 97.938 388 8 0 1 388 141453462 141453075 0.000000e+00 673
26 TraesCS5B01G272100 chr4B 98.496 266 4 0 3461 3726 17271443 17271178 1.570000e-128 470
27 TraesCS5B01G272100 chr5D 96.780 1056 28 5 2632 3686 500933949 500934999 0.000000e+00 1757
28 TraesCS5B01G272100 chr5D 100.000 58 0 0 3669 3726 500935152 500935209 1.420000e-19 108
29 TraesCS5B01G272100 chr1A 91.467 1043 81 8 940 1979 570926182 570927219 0.000000e+00 1426


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 TraesCS5B01G272100 chr5B 457388054 457391779 3725 True 6881.0 6881 100.000000 1 3726 1 chr5B.!!$R1 3725
1 TraesCS5B01G272100 chr5B 493911110 493913323 2213 False 3766.0 3766 97.380000 386 2598 1 chr5B.!!$F1 2212
2 TraesCS5B01G272100 chr5B 48319685 48321419 1734 False 1493.0 2274 99.023500 1 3726 2 chr5B.!!$F2 3725
3 TraesCS5B01G272100 chr4A 626531879 626535935 4056 True 3258.5 5805 98.884500 1 3726 2 chr4A.!!$R1 3725
4 TraesCS5B01G272100 chr3B 784060453 784064512 4059 True 3249.0 5799 98.487500 1 3726 2 chr3B.!!$R1 3725
5 TraesCS5B01G272100 chr7A 46727569 46729855 2286 True 3897.0 3897 97.421000 484 2771 1 chr7A.!!$R1 2287
6 TraesCS5B01G272100 chr7A 7420995 7425052 4057 False 3244.0 5797 98.358500 1 3726 2 chr7A.!!$F2 3725
7 TraesCS5B01G272100 chr7A 194166357 194170973 4616 False 1583.0 2505 97.887333 1 2756 3 chr7A.!!$F3 2755
8 TraesCS5B01G272100 chr1B 59040038 59043280 3242 False 2825.0 4410 97.998000 386 3726 2 chr1B.!!$F1 3340
9 TraesCS5B01G272100 chr1B 626236929 626238589 1660 True 1078.5 1445 99.023000 1 3726 2 chr1B.!!$R1 3725
10 TraesCS5B01G272100 chr5A 41482603 41485705 3102 True 2371.0 4045 98.127000 1 2771 2 chr5A.!!$R1 2770
11 TraesCS5B01G272100 chr7D 321475964 321479130 3166 False 1900.0 3168 88.390500 386 3534 2 chr7D.!!$F1 3148
12 TraesCS5B01G272100 chr4B 141438647 141440384 1737 True 2976.0 2976 97.585000 1990 3726 1 chr4B.!!$R2 1736
13 TraesCS5B01G272100 chr5D 500933949 500935209 1260 False 932.5 1757 98.390000 2632 3726 2 chr5D.!!$F1 1094
14 TraesCS5B01G272100 chr1A 570926182 570927219 1037 False 1426.0 1426 91.467000 940 1979 1 chr1A.!!$F1 1039

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
632 968 2.581354 GTCTGCCTCAGATGCCGT 59.419 61.111 0.0 0.0 42.73 5.68 F
1797 2170 0.798776 GATCAACACCACGCCTGAAG 59.201 55.000 0.0 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 3943 1.680735 TGCTACCTGTTTTTGTGCCAG 59.319 47.619 0.0 0.0 0.00 4.85 R
2726 4635 2.162408 GGAGCACAGACAATACCTTTGC 59.838 50.000 0.0 0.0 37.54 3.68 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
632 968 2.581354 GTCTGCCTCAGATGCCGT 59.419 61.111 0.00 0.0 42.73 5.68
822 1158 6.359804 AGAACTATTCAATCTAAGGCATGCA 58.640 36.000 21.36 0.0 0.00 3.96
1105 1441 6.011981 TCAAAGGGACCTTGGTAATTCTATGT 60.012 38.462 4.03 0.0 36.26 2.29
1432 1805 6.664515 TCTTAATGTGACGTTGGATTTTCAC 58.335 36.000 0.00 0.0 39.09 3.18
1612 1985 1.360852 TGGCCAAAATGGGTGGACTAT 59.639 47.619 0.61 0.0 45.35 2.12
1662 2035 8.772250 AGGAACTGAACAATTTATATCCAGAGA 58.228 33.333 0.00 0.0 37.18 3.10
1797 2170 0.798776 GATCAACACCACGCCTGAAG 59.201 55.000 0.00 0.0 0.00 3.02
2035 3941 1.280133 CTCACATCAAGGAAGCCTCCA 59.720 52.381 3.68 0.0 45.24 3.86
2037 3943 1.815003 CACATCAAGGAAGCCTCCAAC 59.185 52.381 3.68 0.0 45.24 3.77
2644 4553 6.546428 TCTTCTCCCCACTAAAGATAAGTG 57.454 41.667 0.00 0.0 43.26 3.16
2663 4572 3.071023 AGTGTGTAAGGCTTAGTTGAGCA 59.929 43.478 7.33 0.0 44.49 4.26
2682 4591 2.489329 GCAAGTATTCCTTTGCAGCTCA 59.511 45.455 4.48 0.0 31.55 4.26
2726 4635 3.870274 TCAATCAATCTGGTGCTCTGAG 58.130 45.455 0.00 0.0 0.00 3.35
2894 4900 4.160252 ACCTGTGTTGAGAACTTGCAATTT 59.840 37.500 0.00 0.0 0.00 1.82
2898 4904 6.162079 TGTGTTGAGAACTTGCAATTTTTGA 58.838 32.000 0.00 0.0 0.00 2.69
2951 4957 3.099905 ACCTGCTGCTGTCTAGAACATA 58.900 45.455 0.00 0.0 37.23 2.29
3436 5447 7.172868 ACTATGTTCAAATGGATGATTGCAA 57.827 32.000 0.00 0.0 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
390 726 9.915564 AGGGAGGATATAAATTCCTAAAGTACT 57.084 33.333 0.00 0.0 43.75 2.73
443 779 4.935352 AGGCAGTTCTGCATTAAACAAA 57.065 36.364 23.23 0.0 36.33 2.83
550 886 2.687370 GCAGGCGACCATCAAATTTTT 58.313 42.857 0.00 0.0 0.00 1.94
632 968 9.208022 CCGATTGAATAGCAGATTTCAATACTA 57.792 33.333 10.01 0.0 46.94 1.82
782 1118 4.199002 AGTTCTTTGGGGTTCTTTGGAT 57.801 40.909 0.00 0.0 0.00 3.41
822 1158 3.501445 GCTCTATATGGTTCCGTAGACGT 59.499 47.826 0.85 0.0 37.74 4.34
1105 1441 3.765381 TCCTGTTGGCAATTTCATCTCA 58.235 40.909 1.92 0.0 0.00 3.27
1419 1759 7.410728 GCAACATAAGAATGTGAAAATCCAACG 60.411 37.037 0.00 0.0 45.79 4.10
1432 1805 9.447040 CTGATCACATTAAGCAACATAAGAATG 57.553 33.333 0.00 0.0 39.17 2.67
1612 1985 4.253685 GACAACTTGATTCCATCCTTCGA 58.746 43.478 0.00 0.0 0.00 3.71
1662 2035 3.397955 ACCTGATCCTTGGTAAACCTTGT 59.602 43.478 0.02 0.0 34.36 3.16
1797 2170 4.205587 ACTGCAATGATCTCTTCCCATTC 58.794 43.478 0.00 0.0 0.00 2.67
2035 3941 2.100749 GCTACCTGTTTTTGTGCCAGTT 59.899 45.455 0.00 0.0 0.00 3.16
2037 3943 1.680735 TGCTACCTGTTTTTGTGCCAG 59.319 47.619 0.00 0.0 0.00 4.85
2644 4553 4.065789 ACTTGCTCAACTAAGCCTTACAC 58.934 43.478 0.00 0.0 41.77 2.90
2663 4572 4.026356 ACTGAGCTGCAAAGGAATACTT 57.974 40.909 1.02 0.0 42.52 2.24
2682 4591 3.054361 AGGAATACCGCCAGATGAAAACT 60.054 43.478 0.00 0.0 41.83 2.66
2726 4635 2.162408 GGAGCACAGACAATACCTTTGC 59.838 50.000 0.00 0.0 37.54 3.68
2894 4900 8.604640 TTGAATGCAAAAATGATAGCTTCAAA 57.395 26.923 0.00 0.0 38.03 2.69
3489 5502 5.565592 TTGCACAGGTATAAAATGAGCTG 57.434 39.130 0.00 0.0 44.80 4.24
3547 5560 6.860023 ACAGACTTTCTAATACACACGTACAC 59.140 38.462 0.00 0.0 0.00 2.90


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

AutoCloner maintained by Alex Coulton.