Multiple sequence alignment - TraesCS6B01G472000

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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 TraesCS6B01G472000 chr6B 100.000 2786 0 0 1 2786 719745157 719742372 0.000000e+00 5145.0
1 TraesCS6B01G472000 chr6B 97.529 2630 32 17 188 2786 719732780 719735407 0.000000e+00 4466.0
2 TraesCS6B01G472000 chr6B 78.932 1030 189 18 596 1604 719728985 719730007 0.000000e+00 675.0
3 TraesCS6B01G472000 chr6B 77.720 1149 218 26 481 1607 719910336 719909204 0.000000e+00 669.0
4 TraesCS6B01G472000 chr6B 92.105 38 3 0 1746 1783 719903398 719903361 1.000000e-03 54.7
5 TraesCS6B01G472000 chr6A 92.597 2418 118 23 312 2715 615781909 615779539 0.000000e+00 3417.0
6 TraesCS6B01G472000 chr6A 91.971 2105 87 30 142 2211 615791247 615793304 0.000000e+00 2876.0
7 TraesCS6B01G472000 chr6A 83.290 1155 150 29 237 1362 615947626 615948766 0.000000e+00 1024.0
8 TraesCS6B01G472000 chr6A 88.679 477 19 10 2320 2786 615793311 615793762 1.460000e-152 549.0
9 TraesCS6B01G472000 chr6A 86.325 117 12 4 1 116 615782238 615782125 1.050000e-24 124.0
10 TraesCS6B01G472000 chr6D 89.827 2251 120 38 1 2214 470975555 470977733 0.000000e+00 2787.0
11 TraesCS6B01G472000 chr6D 92.827 474 17 3 2320 2786 470977735 470978198 0.000000e+00 671.0
12 TraesCS6B01G472000 chr6D 81.780 708 115 12 589 1287 459382013 459382715 5.170000e-162 580.0
13 TraesCS6B01G472000 chr6D 82.736 307 31 15 408 702 471177510 471177214 1.280000e-63 254.0
14 TraesCS6B01G472000 chr6D 77.320 388 28 19 1 367 471178229 471177881 1.030000e-39 174.0
15 TraesCS6B01G472000 chr6D 89.474 95 5 2 1270 1364 459386719 459386808 6.310000e-22 115.0
16 TraesCS6B01G472000 chr6D 87.931 58 3 3 1715 1772 450861466 450861519 6.440000e-07 65.8
17 TraesCS6B01G472000 chr3A 80.164 610 85 20 1299 1895 574346236 574345650 9.220000e-115 424.0
18 TraesCS6B01G472000 chr3A 97.917 96 1 1 1270 1365 574344730 574344636 6.170000e-37 165.0


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 TraesCS6B01G472000 chr6B 719742372 719745157 2785 True 5145.0 5145 100.0000 1 2786 1 chr6B.!!$R1 2785
1 TraesCS6B01G472000 chr6B 719728985 719735407 6422 False 2570.5 4466 88.2305 188 2786 2 chr6B.!!$F1 2598
2 TraesCS6B01G472000 chr6B 719909204 719910336 1132 True 669.0 669 77.7200 481 1607 1 chr6B.!!$R3 1126
3 TraesCS6B01G472000 chr6A 615779539 615782238 2699 True 1770.5 3417 89.4610 1 2715 2 chr6A.!!$R1 2714
4 TraesCS6B01G472000 chr6A 615791247 615793762 2515 False 1712.5 2876 90.3250 142 2786 2 chr6A.!!$F2 2644
5 TraesCS6B01G472000 chr6A 615947626 615948766 1140 False 1024.0 1024 83.2900 237 1362 1 chr6A.!!$F1 1125
6 TraesCS6B01G472000 chr6D 470975555 470978198 2643 False 1729.0 2787 91.3270 1 2786 2 chr6D.!!$F4 2785
7 TraesCS6B01G472000 chr6D 459382013 459382715 702 False 580.0 580 81.7800 589 1287 1 chr6D.!!$F2 698
8 TraesCS6B01G472000 chr6D 471177214 471178229 1015 True 214.0 254 80.0280 1 702 2 chr6D.!!$R1 701
9 TraesCS6B01G472000 chr3A 574344636 574346236 1600 True 294.5 424 89.0405 1270 1895 2 chr3A.!!$R1 625

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
53 60 0.631753 TCAGGTTTGGTTTGTCCCCA 59.368 50.0 0.0 0.0 34.77 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 5839 0.820891 GGCAGGCACGGATCATTCAT 60.821 55.0 0.0 0.0 0.0 2.57 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
38 45 1.776662 TACTCTGACCCGGATTCAGG 58.223 55.000 24.76 19.21 40.87 3.86
53 60 0.631753 TCAGGTTTGGTTTGTCCCCA 59.368 50.000 0.00 0.00 34.77 4.96
90 97 4.079961 GCCCCCTCCCCTGCAATT 62.080 66.667 0.00 0.00 0.00 2.32
104 111 4.141574 CCCTGCAATTGAATGGAATGGAAT 60.142 41.667 10.34 0.00 0.00 3.01
119 126 9.807649 ATGGAATGGAATAAAGAAAGAAAATCG 57.192 29.630 0.00 0.00 0.00 3.34
120 127 7.759433 TGGAATGGAATAAAGAAAGAAAATCGC 59.241 33.333 0.00 0.00 0.00 4.58
121 128 7.759433 GGAATGGAATAAAGAAAGAAAATCGCA 59.241 33.333 0.00 0.00 0.00 5.10
179 212 2.029020 AGAGCAGCACTTGTCGATGTAA 60.029 45.455 0.00 0.00 0.00 2.41
185 218 4.389992 CAGCACTTGTCGATGTAAAGATGT 59.610 41.667 0.00 0.00 0.00 3.06
186 219 5.576774 CAGCACTTGTCGATGTAAAGATGTA 59.423 40.000 0.00 0.00 0.00 2.29
189 222 6.454318 GCACTTGTCGATGTAAAGATGTACAG 60.454 42.308 0.33 0.00 37.41 2.74
190 223 6.586463 CACTTGTCGATGTAAAGATGTACAGT 59.414 38.462 0.33 0.00 37.41 3.55
191 224 7.116376 CACTTGTCGATGTAAAGATGTACAGTT 59.884 37.037 0.33 0.00 37.41 3.16
192 225 6.944557 TGTCGATGTAAAGATGTACAGTTG 57.055 37.500 0.33 0.00 37.41 3.16
193 226 5.347635 TGTCGATGTAAAGATGTACAGTTGC 59.652 40.000 0.33 0.07 37.41 4.17
194 227 5.577164 GTCGATGTAAAGATGTACAGTTGCT 59.423 40.000 0.33 0.00 37.41 3.91
195 228 5.576774 TCGATGTAAAGATGTACAGTTGCTG 59.423 40.000 0.33 0.00 37.41 4.41
196 229 5.576774 CGATGTAAAGATGTACAGTTGCTGA 59.423 40.000 0.33 0.00 37.41 4.26
348 4006 3.118454 CACATGACGACCCACCGC 61.118 66.667 0.00 0.00 0.00 5.68
462 4464 3.817647 CCATGCTTCTTATTCCTGGTAGC 59.182 47.826 0.00 0.00 0.00 3.58
796 4819 4.033776 CCACATGCCCCTCGTGGT 62.034 66.667 2.33 0.00 44.27 4.16
1786 5839 2.115427 TCTACTCGGATGGCCAATGAA 58.885 47.619 10.96 0.00 0.00 2.57
1787 5840 2.705658 TCTACTCGGATGGCCAATGAAT 59.294 45.455 10.96 0.00 0.00 2.57
1788 5841 1.683943 ACTCGGATGGCCAATGAATG 58.316 50.000 10.96 1.03 0.00 2.67
1789 5842 1.212688 ACTCGGATGGCCAATGAATGA 59.787 47.619 10.96 1.08 0.00 2.57
1992 6072 4.989044 AGTTTTAACTTTTGTGGTGTCGG 58.011 39.130 0.00 0.00 35.21 4.79
1993 6073 3.423996 TTTAACTTTTGTGGTGTCGGC 57.576 42.857 0.00 0.00 0.00 5.54
1994 6074 2.039818 TAACTTTTGTGGTGTCGGCA 57.960 45.000 0.00 0.00 0.00 5.69
1995 6075 0.454196 AACTTTTGTGGTGTCGGCAC 59.546 50.000 12.83 12.83 44.53 5.01
1996 6076 0.393808 ACTTTTGTGGTGTCGGCACT 60.394 50.000 21.13 0.00 44.65 4.40
1997 6077 1.134340 ACTTTTGTGGTGTCGGCACTA 60.134 47.619 21.13 12.00 44.65 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 45 3.055747 TCAAAACTGGGGACAAACCAAAC 60.056 43.478 0.00 0.00 42.06 2.93
53 60 1.126846 CGCTCGAATTCGCTCAAAACT 59.873 47.619 22.90 0.00 39.60 2.66
104 111 6.038825 TGTTGAGGTGCGATTTTCTTTCTTTA 59.961 34.615 0.00 0.00 0.00 1.85
116 123 5.446143 TTAAAATGTTGTTGAGGTGCGAT 57.554 34.783 0.00 0.00 0.00 4.58
118 125 4.981674 ACATTAAAATGTTGTTGAGGTGCG 59.018 37.500 2.47 0.00 46.95 5.34
179 212 5.065914 ACACATTCAGCAACTGTACATCTT 58.934 37.500 0.00 0.00 32.61 2.40
185 218 5.208463 TCTGTACACATTCAGCAACTGTA 57.792 39.130 0.00 0.00 32.61 2.74
186 219 4.071961 TCTGTACACATTCAGCAACTGT 57.928 40.909 0.00 0.00 32.61 3.55
189 222 5.639506 ACTACATCTGTACACATTCAGCAAC 59.360 40.000 0.00 0.00 0.00 4.17
190 223 5.793817 ACTACATCTGTACACATTCAGCAA 58.206 37.500 0.00 0.00 0.00 3.91
191 224 5.405935 ACTACATCTGTACACATTCAGCA 57.594 39.130 0.00 0.00 0.00 4.41
192 225 8.353684 AGTATACTACATCTGTACACATTCAGC 58.646 37.037 2.75 0.00 0.00 4.26
193 226 9.670719 CAGTATACTACATCTGTACACATTCAG 57.329 37.037 4.74 0.00 0.00 3.02
194 227 8.135529 GCAGTATACTACATCTGTACACATTCA 58.864 37.037 4.74 0.00 0.00 2.57
195 228 8.353684 AGCAGTATACTACATCTGTACACATTC 58.646 37.037 4.74 0.00 0.00 2.67
196 229 8.239038 AGCAGTATACTACATCTGTACACATT 57.761 34.615 4.74 0.00 0.00 2.71
348 4006 8.964420 ACAACAGTTTAATCGGATTACATTTG 57.036 30.769 9.88 11.04 0.00 2.32
462 4464 7.584108 TGTGTATCAAAGAAACTTGCTATGTG 58.416 34.615 0.00 0.00 0.00 3.21
796 4819 0.898326 TACGAGGAGAAGGCAGCACA 60.898 55.000 0.00 0.00 0.00 4.57
1786 5839 0.820891 GGCAGGCACGGATCATTCAT 60.821 55.000 0.00 0.00 0.00 2.57
1787 5840 1.451927 GGCAGGCACGGATCATTCA 60.452 57.895 0.00 0.00 0.00 2.57
1788 5841 1.442526 CTGGCAGGCACGGATCATTC 61.443 60.000 6.61 0.00 0.00 2.67
1789 5842 1.452651 CTGGCAGGCACGGATCATT 60.453 57.895 6.61 0.00 0.00 2.57
2318 6700 2.226912 GAGACGAGGCGCAGAACTATAT 59.773 50.000 10.83 0.00 0.00 0.86
2319 6701 1.602851 GAGACGAGGCGCAGAACTATA 59.397 52.381 10.83 0.00 0.00 1.31
2320 6702 0.382515 GAGACGAGGCGCAGAACTAT 59.617 55.000 10.83 0.00 0.00 2.12
2321 6703 0.958876 TGAGACGAGGCGCAGAACTA 60.959 55.000 10.83 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.