Multiple sequence alignment - TraesCS1B01G054800

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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 TraesCS1B01G054800 chr1B 100.000 5384 0 0 1 5384 36185535 36190918 0.000000e+00 9943
1 TraesCS1B01G054800 chr1B 94.792 2496 80 22 2376 4851 284046170 284043705 0.000000e+00 3843
2 TraesCS1B01G054800 chr1B 95.563 1555 64 5 3298 4850 595833848 595835399 0.000000e+00 2484
3 TraesCS1B01G054800 chr1B 93.606 1564 94 3 624 2187 595831219 595832776 0.000000e+00 2329
4 TraesCS1B01G054800 chr1B 93.478 1564 96 3 624 2187 595882633 595884190 0.000000e+00 2318
5 TraesCS1B01G054800 chr1B 95.445 1405 61 2 946 2349 284048246 284046844 0.000000e+00 2237
6 TraesCS1B01G054800 chr1B 95.521 960 40 3 2376 3335 595832967 595833923 0.000000e+00 1531
7 TraesCS1B01G054800 chr1B 95.521 960 39 4 2376 3335 595884381 595885336 0.000000e+00 1531
8 TraesCS1B01G054800 chr1B 94.190 327 17 2 624 950 284057459 284057135 1.040000e-136 497
9 TraesCS1B01G054800 chr1B 80.682 264 16 15 4619 4850 27132079 27131819 7.170000e-39 172
10 TraesCS1B01G054800 chrUn 99.322 4723 26 5 1 4721 155228558 155233276 0.000000e+00 8540
11 TraesCS1B01G054800 chrUn 95.563 1555 64 5 3298 4850 335149631 335151182 0.000000e+00 2484
12 TraesCS1B01G054800 chrUn 94.733 1291 37 8 4118 5382 352102546 352103831 0.000000e+00 1978
13 TraesCS1B01G054800 chrUn 94.630 1229 35 8 4180 5382 320661016 320662239 0.000000e+00 1875
14 TraesCS1B01G054800 chrUn 94.630 1229 35 8 4180 5382 343367998 343366775 0.000000e+00 1875
15 TraesCS1B01G054800 chrUn 94.630 1229 35 8 4180 5382 355314622 355315845 0.000000e+00 1875
16 TraesCS1B01G054800 chrUn 99.077 650 6 0 4735 5384 155233251 155233900 0.000000e+00 1168
17 TraesCS1B01G054800 chrUn 93.814 582 16 1 171 732 472899318 472898737 0.000000e+00 857
18 TraesCS1B01G054800 chrUn 100.000 390 0 0 4866 5255 480080604 480080993 0.000000e+00 721
19 TraesCS1B01G054800 chrUn 96.407 167 5 1 1 166 442090731 442090897 1.910000e-69 274
20 TraesCS1B01G054800 chrUn 96.407 167 5 1 1 166 442110076 442109910 1.910000e-69 274
21 TraesCS1B01G054800 chr7B 96.014 2484 88 9 2376 4850 144866776 144864295 0.000000e+00 4028
22 TraesCS1B01G054800 chr7B 95.161 2418 104 12 2376 4791 398612849 398615255 0.000000e+00 3805
23 TraesCS1B01G054800 chr7B 94.435 1743 81 4 624 2365 144868557 144866830 0.000000e+00 2667
24 TraesCS1B01G054800 chr7B 94.111 1749 99 2 618 2365 398611050 398612795 0.000000e+00 2656
25 TraesCS1B01G054800 chr6A 96.710 2401 75 4 2376 4775 557671287 557673684 0.000000e+00 3993
26 TraesCS1B01G054800 chr1D 94.011 2254 97 19 2376 4612 38868441 38870673 0.000000e+00 3380
27 TraesCS1B01G054800 chr1D 93.611 1346 73 4 1023 2365 38867052 38868387 0.000000e+00 1997
28 TraesCS1B01G054800 chr5A 96.680 1747 55 3 3030 4775 646961662 646963406 0.000000e+00 2902
29 TraesCS1B01G054800 chr5A 95.069 1744 71 4 624 2365 646954812 646956542 0.000000e+00 2730
30 TraesCS1B01G054800 chr6B 93.337 1741 112 3 626 2365 363476811 363478548 0.000000e+00 2569
31 TraesCS1B01G054800 chr1A 92.097 1569 112 4 624 2185 300543235 300541672 0.000000e+00 2200
32 TraesCS1B01G054800 chr3A 88.925 930 95 6 2409 3335 90484339 90483415 0.000000e+00 1140


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 TraesCS1B01G054800 chr1B 36185535 36190918 5383 False 9943.000000 9943 100.000000 1 5384 1 chr1B.!!$F1 5383
1 TraesCS1B01G054800 chr1B 284043705 284048246 4541 True 3040.000000 3843 95.118500 946 4851 2 chr1B.!!$R3 3905
2 TraesCS1B01G054800 chr1B 595831219 595835399 4180 False 2114.666667 2484 94.896667 624 4850 3 chr1B.!!$F2 4226
3 TraesCS1B01G054800 chr1B 595882633 595885336 2703 False 1924.500000 2318 94.499500 624 3335 2 chr1B.!!$F3 2711
4 TraesCS1B01G054800 chrUn 155228558 155233900 5342 False 4854.000000 8540 99.199500 1 5384 2 chrUn.!!$F7 5383
5 TraesCS1B01G054800 chrUn 335149631 335151182 1551 False 2484.000000 2484 95.563000 3298 4850 1 chrUn.!!$F2 1552
6 TraesCS1B01G054800 chrUn 352102546 352103831 1285 False 1978.000000 1978 94.733000 4118 5382 1 chrUn.!!$F3 1264
7 TraesCS1B01G054800 chrUn 320661016 320662239 1223 False 1875.000000 1875 94.630000 4180 5382 1 chrUn.!!$F1 1202
8 TraesCS1B01G054800 chrUn 343366775 343367998 1223 True 1875.000000 1875 94.630000 4180 5382 1 chrUn.!!$R1 1202
9 TraesCS1B01G054800 chrUn 355314622 355315845 1223 False 1875.000000 1875 94.630000 4180 5382 1 chrUn.!!$F4 1202
10 TraesCS1B01G054800 chrUn 472898737 472899318 581 True 857.000000 857 93.814000 171 732 1 chrUn.!!$R3 561
11 TraesCS1B01G054800 chr7B 144864295 144868557 4262 True 3347.500000 4028 95.224500 624 4850 2 chr7B.!!$R1 4226
12 TraesCS1B01G054800 chr7B 398611050 398615255 4205 False 3230.500000 3805 94.636000 618 4791 2 chr7B.!!$F1 4173
13 TraesCS1B01G054800 chr6A 557671287 557673684 2397 False 3993.000000 3993 96.710000 2376 4775 1 chr6A.!!$F1 2399
14 TraesCS1B01G054800 chr1D 38867052 38870673 3621 False 2688.500000 3380 93.811000 1023 4612 2 chr1D.!!$F1 3589
15 TraesCS1B01G054800 chr5A 646961662 646963406 1744 False 2902.000000 2902 96.680000 3030 4775 1 chr5A.!!$F2 1745
16 TraesCS1B01G054800 chr5A 646954812 646956542 1730 False 2730.000000 2730 95.069000 624 2365 1 chr5A.!!$F1 1741
17 TraesCS1B01G054800 chr6B 363476811 363478548 1737 False 2569.000000 2569 93.337000 626 2365 1 chr6B.!!$F1 1739
18 TraesCS1B01G054800 chr1A 300541672 300543235 1563 True 2200.000000 2200 92.097000 624 2185 1 chr1A.!!$R1 1561
19 TraesCS1B01G054800 chr3A 90483415 90484339 924 True 1140.000000 1140 88.925000 2409 3335 1 chr3A.!!$R1 926

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
233 234 1.523711 GCGATTCCTCATCCGCCAA 60.524 57.895 0.0 0.0 0.0 4.52 F
1065 1088 1.597854 CCCACGATGCACACACACT 60.598 57.895 0.0 0.0 0.0 3.55 F
1231 1261 1.043116 CCCGCTCACCATCTCCACTA 61.043 60.000 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1231 1261 1.677637 GGCGAGGAGAGAAACCGGAT 61.678 60.000 9.46 0.0 0.00 4.18 R
2992 3694 4.801891 TGCATAACGGGAGTATATTCGAC 58.198 43.478 0.00 0.0 46.69 4.20 R
4709 5464 2.032681 GGCTGACGGCAAAGGAGT 59.967 61.111 8.86 0.0 44.01 3.85 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
233 234 1.523711 GCGATTCCTCATCCGCCAA 60.524 57.895 0.00 0.00 0.00 4.52
723 744 3.276882 GCTTACAAAAAGCTAACGGCA 57.723 42.857 2.55 0.00 44.79 5.69
724 745 3.634283 GCTTACAAAAAGCTAACGGCAA 58.366 40.909 2.55 0.00 44.79 4.52
836 857 1.602237 GGACGGCAAAGAGGATGGA 59.398 57.895 0.00 0.00 0.00 3.41
1065 1088 1.597854 CCCACGATGCACACACACT 60.598 57.895 0.00 0.00 0.00 3.55
1231 1261 1.043116 CCCGCTCACCATCTCCACTA 61.043 60.000 0.00 0.00 0.00 2.74
1343 1373 2.280592 GGGCACAAAGACGTCGGT 60.281 61.111 10.46 7.32 0.00 4.69
1365 1395 2.685017 TCAGGATGGTCGCAGCCT 60.685 61.111 0.00 0.00 36.16 4.58
1912 1954 6.040616 CCTCTTTCCCATCGTGTAGTATAGTT 59.959 42.308 0.00 0.00 0.00 2.24
2600 3292 8.125448 GCATTTTGATGACATACCTTCTTCTAC 58.875 37.037 0.00 0.00 0.00 2.59
2992 3694 7.413644 TGTACATTTAATTATGGTGCATGTCG 58.586 34.615 0.00 0.00 0.00 4.35
3118 3822 3.314307 TGACTATACACTAGCCTGGCT 57.686 47.619 26.52 26.52 43.41 4.75
4157 4863 0.743688 GTTGTGGTGGTTGCATCACA 59.256 50.000 18.36 11.34 43.62 3.58
4429 5158 7.614124 TGATATTTGTGATATATGCATGCGT 57.386 32.000 18.07 18.07 0.00 5.24
4809 5609 1.597989 GCCATTCATGCCTTTGCCA 59.402 52.632 0.00 0.00 36.33 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 234 0.537371 CGGGAAGTGGCCTGAAGTTT 60.537 55.000 3.32 0.00 36.35 2.66
836 857 0.108329 CGTTCTCGTTAGTGGGCCAT 60.108 55.000 10.70 1.02 0.00 4.40
1231 1261 1.677637 GGCGAGGAGAGAAACCGGAT 61.678 60.000 9.46 0.00 0.00 4.18
1343 1373 2.171209 CTGCGACCATCCTGACCACA 62.171 60.000 0.00 0.00 0.00 4.17
1365 1395 2.164219 GCCGCCATTGAGAATCTTGAAA 59.836 45.455 0.00 0.00 34.92 2.69
1517 1547 2.674754 GGATGGGGTTCGCCTTGA 59.325 61.111 7.39 0.00 37.45 3.02
1912 1954 5.213891 TCATGTTTGACTGACTTGCTAGA 57.786 39.130 1.04 0.00 0.00 2.43
2527 3219 5.176406 CGTGACATTGGTGCTAGATAGATTG 59.824 44.000 0.00 0.00 0.00 2.67
2600 3292 6.917533 ACTGATTGCAACCAAAGATTCTAAG 58.082 36.000 0.00 0.00 34.05 2.18
2992 3694 4.801891 TGCATAACGGGAGTATATTCGAC 58.198 43.478 0.00 0.00 46.69 4.20
4709 5464 2.032681 GGCTGACGGCAAAGGAGT 59.967 61.111 8.86 0.00 44.01 3.85


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

AutoCloner maintained by Alex Coulton.