Multiple sequence alignment - TraesCS6B01G078000

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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 TraesCS6B01G078000 chr6B 100.000 2231 0 0 1 2231 54214319 54216549 0.000000e+00 4120
1 TraesCS6B01G078000 chr6B 97.359 2234 55 2 1 2231 426742334 426740102 0.000000e+00 3795
2 TraesCS6B01G078000 chr2A 89.450 2237 190 14 1 2231 717667474 717669670 0.000000e+00 2782
3 TraesCS6B01G078000 chr2A 88.043 92 11 0 1 92 723202725 723202816 2.340000e-20 110
4 TraesCS6B01G078000 chr2B 97.195 1640 41 3 596 2231 24829899 24831537 0.000000e+00 2769
5 TraesCS6B01G078000 chr2B 90.625 512 48 0 1720 2231 25811215 25811726 0.000000e+00 680
6 TraesCS6B01G078000 chr4A 89.053 2238 197 15 1 2231 96811159 96813355 0.000000e+00 2732
7 TraesCS6B01G078000 chr4A 95.430 1466 66 1 766 2231 720040489 720041953 0.000000e+00 2335
8 TraesCS6B01G078000 chr4A 93.182 264 15 1 16 276 720029922 720030185 3.480000e-103 385
9 TraesCS6B01G078000 chr7A 88.385 1300 101 15 1 1294 619594756 619596011 0.000000e+00 1519
10 TraesCS6B01G078000 chr7A 86.144 1097 130 10 512 1596 1324067 1325153 0.000000e+00 1164
11 TraesCS6B01G078000 chr7A 91.763 607 48 2 1627 2231 619596014 619596620 0.000000e+00 843
12 TraesCS6B01G078000 chr3A 89.059 1179 86 12 1 1173 453623729 453624870 0.000000e+00 1423
13 TraesCS6B01G078000 chr3A 90.875 1063 94 2 1169 2231 453626593 453627652 0.000000e+00 1423
14 TraesCS6B01G078000 chr6A 89.569 1045 66 11 4 1042 590206398 590205391 0.000000e+00 1286
15 TraesCS6B01G078000 chr6A 92.028 577 46 0 1655 2231 590196825 590196249 0.000000e+00 811
16 TraesCS6B01G078000 chr6A 87.664 535 63 2 1040 1574 590197379 590196848 8.750000e-174 619
17 TraesCS6B01G078000 chr3B 97.790 181 4 0 315 495 672704722 672704902 1.660000e-81 313


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 TraesCS6B01G078000 chr6B 54214319 54216549 2230 False 4120 4120 100.000 1 2231 1 chr6B.!!$F1 2230
1 TraesCS6B01G078000 chr6B 426740102 426742334 2232 True 3795 3795 97.359 1 2231 1 chr6B.!!$R1 2230
2 TraesCS6B01G078000 chr2A 717667474 717669670 2196 False 2782 2782 89.450 1 2231 1 chr2A.!!$F1 2230
3 TraesCS6B01G078000 chr2B 24829899 24831537 1638 False 2769 2769 97.195 596 2231 1 chr2B.!!$F1 1635
4 TraesCS6B01G078000 chr2B 25811215 25811726 511 False 680 680 90.625 1720 2231 1 chr2B.!!$F2 511
5 TraesCS6B01G078000 chr4A 96811159 96813355 2196 False 2732 2732 89.053 1 2231 1 chr4A.!!$F1 2230
6 TraesCS6B01G078000 chr4A 720040489 720041953 1464 False 2335 2335 95.430 766 2231 1 chr4A.!!$F3 1465
7 TraesCS6B01G078000 chr7A 619594756 619596620 1864 False 1181 1519 90.074 1 2231 2 chr7A.!!$F2 2230
8 TraesCS6B01G078000 chr7A 1324067 1325153 1086 False 1164 1164 86.144 512 1596 1 chr7A.!!$F1 1084
9 TraesCS6B01G078000 chr3A 453623729 453627652 3923 False 1423 1423 89.967 1 2231 2 chr3A.!!$F1 2230
10 TraesCS6B01G078000 chr6A 590205391 590206398 1007 True 1286 1286 89.569 4 1042 1 chr6A.!!$R1 1038
11 TraesCS6B01G078000 chr6A 590196249 590197379 1130 True 715 811 89.846 1040 2231 2 chr6A.!!$R2 1191

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
603 610 0.178961 GGATCCCCAGGGGTTAATGC 60.179 60.0 25.52 12.43 44.74 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 3702 3.772387 TGGTGGAAATACAAATGAGCCA 58.228 40.909 0.0 0.0 0.0 4.75 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
31 32 3.609853 CGTCATTTCCCTCCTTGATTGA 58.390 45.455 0.00 0.00 0.00 2.57
110 114 2.568623 TCCTCTCCAAGAACAAAGGC 57.431 50.000 0.00 0.00 0.00 4.35
147 151 1.210155 GGGCATGCGTCAACTGAAC 59.790 57.895 12.44 0.00 0.00 3.18
159 163 2.543848 TCAACTGAACAAGTCGATGCAC 59.456 45.455 0.00 0.00 38.56 4.57
184 188 0.846693 ACACTTTGCTCCCTTGTCCT 59.153 50.000 0.00 0.00 0.00 3.85
198 202 4.412199 CCCTTGTCCTAATGACCCAAGATA 59.588 45.833 0.00 0.00 43.78 1.98
277 283 8.762481 TCTCTATGTAATAGTAGCTTGGACAA 57.238 34.615 0.00 0.00 46.98 3.18
330 336 8.620416 TGGAATAGTTCATATGTTTGCATACAC 58.380 33.333 12.37 0.00 40.05 2.90
338 344 2.766313 TGTTTGCATACACGAGAGCTT 58.234 42.857 5.83 0.00 0.00 3.74
479 486 8.186821 AGCATGAAAATTGTGCTCTTACTTATC 58.813 33.333 0.00 0.00 45.42 1.75
558 565 2.424234 CCCCACCAAAGAAGAGGTTGAA 60.424 50.000 0.00 0.00 35.52 2.69
603 610 0.178961 GGATCCCCAGGGGTTAATGC 60.179 60.000 25.52 12.43 44.74 3.56
622 629 1.871080 CCGTGTTATCTCAGGCATCC 58.129 55.000 0.00 0.00 0.00 3.51
905 914 5.499139 TGCAAGAGAGTTTTTGGTTGTAG 57.501 39.130 0.00 0.00 0.00 2.74
923 932 4.341487 TGTAGAAGAGCAGCTGGTACTAA 58.659 43.478 20.22 10.37 0.00 2.24
1033 1046 7.787028 ACCTGATCCAAATAGTCTAGAGAAAC 58.213 38.462 0.00 0.00 0.00 2.78
1081 1094 2.649312 TGGGAGTTGGTGAGGATGATTT 59.351 45.455 0.00 0.00 0.00 2.17
1146 1159 9.871238 GGATTTAGAAGATTTGTGTACAGTCTA 57.129 33.333 0.00 0.00 0.00 2.59
1224 2964 7.678837 TGCTATTTCATGAACAAAGGGAAAAT 58.321 30.769 7.89 0.00 31.98 1.82
1251 2991 7.476540 TTGAGAGGCTATACAGAACTTAACA 57.523 36.000 0.00 0.00 0.00 2.41
1391 3131 2.954753 GCGAGGCAGAAACACCACG 61.955 63.158 0.00 0.00 42.07 4.94
1518 3258 5.538118 TCGTGTGTGAAGTACATCAAATCT 58.462 37.500 1.69 0.00 42.24 2.40
1824 3574 2.598565 AGGAGAGCATTCACCGCTATA 58.401 47.619 0.00 0.00 40.63 1.31
1952 3702 7.365295 GGTGGTATCCGGTACATTATATCCAAT 60.365 40.741 0.00 0.00 34.87 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.912486 AAGGAGGGAAATGACGGAGG 59.088 55.000 0.00 0.00 0.00 4.30
14 15 4.021916 CAGCTTCAATCAAGGAGGGAAAT 58.978 43.478 0.00 0.00 31.94 2.17
31 32 2.321213 GGTGACGAAACAGCAGCTT 58.679 52.632 0.00 0.00 38.05 3.74
110 114 2.093869 CCCTTTGTTCTTGGATGCATGG 60.094 50.000 2.46 0.00 0.00 3.66
147 151 2.157668 GTGTTGTAGGTGCATCGACTTG 59.842 50.000 11.67 0.00 0.00 3.16
159 163 2.554032 CAAGGGAGCAAAGTGTTGTAGG 59.446 50.000 0.00 0.00 37.06 3.18
184 188 5.104527 CCTTGGTGAGTATCTTGGGTCATTA 60.105 44.000 0.00 0.00 34.92 1.90
277 283 4.709397 CACTATCTCAGTTCACCCTCTCTT 59.291 45.833 0.00 0.00 34.26 2.85
338 344 6.859112 ATAACTAGTCTCCAGCTTTTCTCA 57.141 37.500 0.00 0.00 0.00 3.27
479 486 7.656948 ACCTGTTTTCAATCACACAAATAATGG 59.343 33.333 0.00 0.00 0.00 3.16
603 610 1.541233 GGGATGCCTGAGATAACACGG 60.541 57.143 0.00 0.00 0.00 4.94
622 629 3.670625 TCGTTTCACACCTAATCTTGGG 58.329 45.455 0.00 0.00 34.56 4.12
693 700 8.462811 TGACATTAAAACTTAACATGTGTGTGT 58.537 29.630 0.00 0.00 38.92 3.72
905 914 4.392921 TGATTAGTACCAGCTGCTCTTC 57.607 45.455 8.66 2.12 0.00 2.87
990 999 1.002315 GGTTGTGGCATGGCTGATTTT 59.998 47.619 21.08 0.00 0.00 1.82
1033 1046 0.669077 CTCTCGGGGTCATAGTTCCG 59.331 60.000 0.00 0.00 43.42 4.30
1081 1094 6.349243 AGAGAATGGCAATTCATGAACAAA 57.651 33.333 16.24 0.00 44.05 2.83
1224 2964 9.216117 GTTAAGTTCTGTATAGCCTCTCAAAAA 57.784 33.333 0.00 0.00 0.00 1.94
1251 2991 2.416972 GGCGGTTAAAGAGACACGAGAT 60.417 50.000 0.00 0.00 0.00 2.75
1432 3172 5.309282 TCTTCTTTGGCAAACCCCAATATTT 59.691 36.000 8.93 0.00 43.91 1.40
1738 3488 4.332788 CGTGTGACAACGTCTAGAGATAC 58.667 47.826 0.00 0.00 38.74 2.24
1824 3574 5.767665 TGTATATGTTGTGTCCTGCAACTTT 59.232 36.000 9.16 1.22 44.54 2.66
1852 3602 7.522399 CGTTTCCCATTCAACATTTGTAGGTTA 60.522 37.037 0.00 0.00 0.00 2.85
1952 3702 3.772387 TGGTGGAAATACAAATGAGCCA 58.228 40.909 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.