Multiple sequence alignment - TraesCS2B01G146800

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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 TraesCS2B01G146800 chr2B 100.000 2646 0 0 1 2646 112847905 112845260 0.000000e+00 4887
1 TraesCS2B01G146800 chr2B 97.924 2649 52 2 1 2646 391167714 391165066 0.000000e+00 4584
2 TraesCS2B01G146800 chr2B 97.088 2610 72 3 1 2606 357518483 357521092 0.000000e+00 4396
3 TraesCS2B01G146800 chr2B 96.897 580 16 2 1961 2539 129614688 129614110 0.000000e+00 970
4 TraesCS2B01G146800 chr2B 97.183 568 15 1 2079 2645 357208141 357208708 0.000000e+00 959
5 TraesCS2B01G146800 chr2B 97.250 509 14 0 1 509 357293286 357293794 0.000000e+00 863
6 TraesCS2B01G146800 chr2B 96.673 511 17 0 1 511 357650923 357651433 0.000000e+00 850
7 TraesCS2B01G146800 chr2B 98.540 137 2 0 1272 1408 357496641 357496505 2.630000e-60 243
8 TraesCS2B01G146800 chr2B 96.667 60 2 0 1130 1189 121199132 121199191 1.680000e-17 100
9 TraesCS2B01G146800 chrUn 98.414 2649 39 2 1 2646 186201715 186204363 0.000000e+00 4656
10 TraesCS2B01G146800 chr7B 98.377 2649 40 2 1 2646 742996151 742993503 0.000000e+00 4650
11 TraesCS2B01G146800 chr7B 98.226 2649 43 3 1 2646 716872076 716874723 0.000000e+00 4628
12 TraesCS2B01G146800 chr1A 98.339 2649 38 4 1 2646 498684525 498687170 0.000000e+00 4643
13 TraesCS2B01G146800 chr5A 97.961 2649 51 2 1 2646 492862433 492859785 0.000000e+00 4590


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 TraesCS2B01G146800 chr2B 112845260 112847905 2645 True 4887 4887 100.000 1 2646 1 chr2B.!!$R1 2645
1 TraesCS2B01G146800 chr2B 391165066 391167714 2648 True 4584 4584 97.924 1 2646 1 chr2B.!!$R4 2645
2 TraesCS2B01G146800 chr2B 357518483 357521092 2609 False 4396 4396 97.088 1 2606 1 chr2B.!!$F4 2605
3 TraesCS2B01G146800 chr2B 129614110 129614688 578 True 970 970 96.897 1961 2539 1 chr2B.!!$R2 578
4 TraesCS2B01G146800 chr2B 357208141 357208708 567 False 959 959 97.183 2079 2645 1 chr2B.!!$F2 566
5 TraesCS2B01G146800 chr2B 357293286 357293794 508 False 863 863 97.250 1 509 1 chr2B.!!$F3 508
6 TraesCS2B01G146800 chr2B 357650923 357651433 510 False 850 850 96.673 1 511 1 chr2B.!!$F5 510
7 TraesCS2B01G146800 chrUn 186201715 186204363 2648 False 4656 4656 98.414 1 2646 1 chrUn.!!$F1 2645
8 TraesCS2B01G146800 chr7B 742993503 742996151 2648 True 4650 4650 98.377 1 2646 1 chr7B.!!$R1 2645
9 TraesCS2B01G146800 chr7B 716872076 716874723 2647 False 4628 4628 98.226 1 2646 1 chr7B.!!$F1 2645
10 TraesCS2B01G146800 chr1A 498684525 498687170 2645 False 4643 4643 98.339 1 2646 1 chr1A.!!$F1 2645
11 TraesCS2B01G146800 chr5A 492859785 492862433 2648 True 4590 4590 97.961 1 2646 1 chr5A.!!$R1 2645

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
332 334 0.107831 ACCTGACACCGCTTTGCTAA 59.892 50.0 0.0 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2081 2.359354 CACGAAACATCGGCCCCA 60.359 61.111 0.0 0.0 37.45 4.96 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
67 68 4.697352 GCACTACATGAACAAGAAGGACAT 59.303 41.667 0.00 0.0 0.00 3.06
142 144 0.730840 GTTCGATAGGGGGCAAAACG 59.269 55.000 0.00 0.0 0.00 3.60
176 178 7.233553 TCCTAATAGAAGTTCATGTCGATCCAT 59.766 37.037 5.50 0.0 0.00 3.41
183 185 1.764723 TCATGTCGATCCATCCAAGCT 59.235 47.619 0.00 0.0 0.00 3.74
332 334 0.107831 ACCTGACACCGCTTTGCTAA 59.892 50.000 0.00 0.0 0.00 3.09
411 413 5.654650 ACTCCAATGGCATTTTCGGTAAATA 59.345 36.000 10.65 0.0 34.69 1.40
1086 1088 3.077484 CCAGAGATGGCTTTCTTTCCA 57.923 47.619 0.00 0.0 36.70 3.53
1469 1472 9.606631 ACAGAAATACTTATAGCCAGAAAAGAG 57.393 33.333 0.00 0.0 0.00 2.85
1585 1588 1.148310 CATTCTGGCACTTCGTTCGT 58.852 50.000 0.00 0.0 0.00 3.85
1617 1620 4.907879 AAGGACTTGCTTGTCTTTTGAG 57.092 40.909 8.96 0.0 33.41 3.02
1824 1827 1.732259 AGAACACATTAGGAAAGCGCG 59.268 47.619 0.00 0.0 0.00 6.86
1906 1911 6.432162 GCTAATTCAAATCCTATGCTCCATGA 59.568 38.462 0.00 0.0 0.00 3.07
1911 1916 7.320384 TCAAATCCTATGCTCCATGATCTTA 57.680 36.000 0.00 0.0 0.00 2.10
1920 1925 3.873910 CTCCATGATCTTACGGGTTTGT 58.126 45.455 0.00 0.0 0.00 2.83
2070 2075 2.896854 GGATGATCGGCAAGCGCA 60.897 61.111 11.47 0.0 41.24 6.09
2076 2081 4.961511 TCGGCAAGCGCAACGAGT 62.962 61.111 11.47 0.0 41.24 4.18
2119 2124 1.173043 GTGGCCATCGGATTGTTCAA 58.827 50.000 9.72 0.0 0.00 2.69
2268 2275 5.474578 ACGTCATGCTAGGAATGTATCAT 57.525 39.130 0.00 0.0 0.00 2.45
2294 2301 2.224354 CCATGCAAACCAAAGGAAAGCT 60.224 45.455 0.00 0.0 0.00 3.74
2362 2369 2.291605 GGGAGTGGGCTTCCTTTGTAAT 60.292 50.000 3.89 0.0 37.41 1.89
2375 2382 7.928706 GCTTCCTTTGTAATAGCTCTATTCTGA 59.071 37.037 5.49 0.0 37.07 3.27
2529 2537 7.404671 AAAAAGGAGAGCTCTAAAAACAACA 57.595 32.000 18.25 0.0 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.322456 TCCTTCCCGCACTTGATTGG 60.322 55.000 0.00 0.00 0.00 3.16
67 68 6.040878 GCAGCCGACTTCTAATTCTAGTTAA 58.959 40.000 0.00 0.00 0.00 2.01
142 144 5.488341 TGAACTTCTATTAGGACAGCAACC 58.512 41.667 0.00 0.00 0.00 3.77
176 178 3.711190 TCTAATGATGGCACTAGCTTGGA 59.289 43.478 0.00 0.00 41.70 3.53
183 185 4.442893 CCGGACTTTCTAATGATGGCACTA 60.443 45.833 0.00 0.00 0.00 2.74
332 334 6.293680 GCAACTTCTCTTCCTCTTTCGAAAAT 60.294 38.462 12.41 0.00 0.00 1.82
1086 1088 5.280727 GGCAAGGAAGGCTACCTATTGATAT 60.281 44.000 9.22 0.00 36.67 1.63
1469 1472 6.183360 TGGAGTTGTTTTCGTTCTCTTGTTAC 60.183 38.462 0.00 0.00 0.00 2.50
1585 1588 4.150897 AGCAAGTCCTTTGAGTACACAA 57.849 40.909 1.22 1.22 39.21 3.33
1824 1827 5.051374 CGAGCGAACTCCAAATAGAAATCTC 60.051 44.000 0.00 0.00 40.03 2.75
1920 1925 4.097741 CAGTGTGGACAAGTTCAAATGGAA 59.902 41.667 0.00 0.00 0.00 3.53
2070 2075 2.406002 AAACATCGGCCCCACTCGTT 62.406 55.000 0.00 0.00 0.00 3.85
2076 2081 2.359354 CACGAAACATCGGCCCCA 60.359 61.111 0.00 0.00 37.45 4.96
2119 2124 4.856801 GGATCCGCATGGGCACGT 62.857 66.667 3.80 0.00 41.24 4.49
2294 2301 9.298250 GGACTAGGATCTGTAATAGTTGTATCA 57.702 37.037 0.00 0.00 0.00 2.15
2362 2369 3.491342 AGCCACGATCAGAATAGAGCTA 58.509 45.455 0.00 0.00 0.00 3.32
2375 2382 1.593787 CAGTGAGGTGAGCCACGAT 59.406 57.895 0.00 0.00 38.26 3.73
2529 2537 5.373812 AAATCACATTCTCCCCGTAGAAT 57.626 39.130 0.00 0.00 45.07 2.40


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

AutoCloner maintained by Alex Coulton.