Multiple sequence alignment - TraesCS5D01G473200

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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 TraesCS5D01G473200 chr5D 100.000 3726 0 0 1 3726 513540904 513537179 0.000000e+00 6881
1 TraesCS5D01G473200 chr5B 97.173 2158 31 10 1585 3726 644448891 644446748 0.000000e+00 3620
2 TraesCS5D01G473200 chr5B 97.187 711 19 1 879 1589 644449756 644449047 0.000000e+00 1201
3 TraesCS5D01G473200 chr5B 95.685 394 11 1 422 809 644450172 644449779 2.440000e-176 628
4 TraesCS5D01G473200 chr5A 93.972 1576 68 15 1 1559 641223380 641221815 0.000000e+00 2359
5 TraesCS5D01G473200 chr5A 83.043 920 108 23 2339 3237 641220442 641219550 0.000000e+00 791
6 TraesCS5D01G473200 chr5A 89.525 611 51 3 1587 2197 641221734 641221137 0.000000e+00 761
7 TraesCS5D01G473200 chr5A 93.519 108 7 0 2224 2331 641220960 641220853 1.070000e-35 161
8 TraesCS5D01G473200 chrUn 78.699 1230 201 44 1005 2196 124690599 124689393 0.000000e+00 763
9 TraesCS5D01G473200 chr2D 77.708 1283 227 36 933 2202 640015309 640016545 0.000000e+00 730
10 TraesCS5D01G473200 chr2A 78.664 1153 192 35 965 2108 761519239 761520346 0.000000e+00 717
11 TraesCS5D01G473200 chr2A 76.194 1235 228 37 935 2141 761903227 761902031 3.200000e-165 592
12 TraesCS5D01G473200 chr2A 80.788 203 39 0 962 1164 762207054 762206852 3.850000e-35 159
13 TraesCS5D01G473200 chr2B 79.823 902 141 28 1317 2196 795576497 795577379 1.470000e-173 619
14 TraesCS5D01G473200 chr2B 76.108 406 67 19 2255 2631 796023572 796023976 6.350000e-43 185


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 TraesCS5D01G473200 chr5D 513537179 513540904 3725 True 6881.000000 6881 100.000000 1 3726 1 chr5D.!!$R1 3725
1 TraesCS5D01G473200 chr5B 644446748 644450172 3424 True 1816.333333 3620 96.681667 422 3726 3 chr5B.!!$R1 3304
2 TraesCS5D01G473200 chr5A 641219550 641223380 3830 True 1018.000000 2359 90.014750 1 3237 4 chr5A.!!$R1 3236
3 TraesCS5D01G473200 chrUn 124689393 124690599 1206 True 763.000000 763 78.699000 1005 2196 1 chrUn.!!$R1 1191
4 TraesCS5D01G473200 chr2D 640015309 640016545 1236 False 730.000000 730 77.708000 933 2202 1 chr2D.!!$F1 1269
5 TraesCS5D01G473200 chr2A 761519239 761520346 1107 False 717.000000 717 78.664000 965 2108 1 chr2A.!!$F1 1143
6 TraesCS5D01G473200 chr2A 761902031 761903227 1196 True 592.000000 592 76.194000 935 2141 1 chr2A.!!$R1 1206
7 TraesCS5D01G473200 chr2B 795576497 795577379 882 False 619.000000 619 79.823000 1317 2196 1 chr2B.!!$F1 879

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
545 553 0.044244 TCCCCTTCCCCTTCACTAGG 59.956 60.0 0.0 0.0 44.33 3.02 F
815 829 0.537371 AAGGGGAGCCAAAGTCAACG 60.537 55.0 0.0 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2186 2.645297 TGGCGCCAAATATCCCCTATAA 59.355 45.455 30.74 0.0 0.0 0.98 R
2791 3582 3.594134 GAAAGAGGGATGTGTGAGTCAG 58.406 50.000 0.00 0.0 0.0 3.51 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
22 23 3.899052 TCGGTACTATTTGACCCCTTG 57.101 47.619 0.00 0.00 31.50 3.61
32 33 3.611025 TTGACCCCTTGGAATGAGTTT 57.389 42.857 0.00 0.00 34.81 2.66
36 37 5.016173 TGACCCCTTGGAATGAGTTTATTG 58.984 41.667 0.00 0.00 34.81 1.90
44 45 7.148171 CCTTGGAATGAGTTTATTGAAGAGGTC 60.148 40.741 0.00 0.00 0.00 3.85
47 48 6.540551 GGAATGAGTTTATTGAAGAGGTCTCC 59.459 42.308 0.00 0.00 0.00 3.71
58 59 0.683504 GAGGTCTCCTCCCGCAGTTA 60.684 60.000 4.60 0.00 44.36 2.24
70 71 6.094881 TCCTCCCGCAGTTAAATAATGAAAAG 59.905 38.462 0.00 0.00 0.00 2.27
71 72 6.202516 TCCCGCAGTTAAATAATGAAAAGG 57.797 37.500 0.00 0.00 0.00 3.11
142 144 4.599047 AAATCTCTATCTGGAAGCTCGG 57.401 45.455 0.00 0.00 0.00 4.63
149 151 2.203788 TGGAAGCTCGGGGTGTCT 60.204 61.111 0.00 0.00 0.00 3.41
150 152 2.232298 CTGGAAGCTCGGGGTGTCTC 62.232 65.000 0.00 0.00 0.00 3.36
169 171 3.834813 TCTCTATTGGCTCGCTCCATATT 59.165 43.478 0.00 0.00 35.77 1.28
196 198 8.877779 CAATTCATATTCTGACCGATATTCTCC 58.122 37.037 0.00 0.00 32.17 3.71
208 210 1.953559 TATTCTCCGCATTGGCACTC 58.046 50.000 0.00 0.00 41.24 3.51
227 233 6.368791 GGCACTCTTGTTTGTTTCTTTCTTTT 59.631 34.615 0.00 0.00 0.00 2.27
229 235 8.921670 GCACTCTTGTTTGTTTCTTTCTTTTTA 58.078 29.630 0.00 0.00 0.00 1.52
265 271 2.949451 ACTCTGCATCGGTACTCAAG 57.051 50.000 0.00 0.00 0.00 3.02
290 296 9.372369 AGATCCGTGTTTGATTTTGTTTAAAAA 57.628 25.926 0.00 0.00 39.09 1.94
324 330 4.698201 TTAGGATATGGAATCCGCAACA 57.302 40.909 0.00 0.00 42.87 3.33
327 333 2.416547 GGATATGGAATCCGCAACATCG 59.583 50.000 0.00 0.00 0.00 3.84
545 553 0.044244 TCCCCTTCCCCTTCACTAGG 59.956 60.000 0.00 0.00 44.33 3.02
569 577 4.872691 CAGGTAAATCTGAAGCTCAATCGT 59.127 41.667 0.00 0.00 36.93 3.73
720 734 4.202172 TGCGGATTATCACTAATTGGTCGA 60.202 41.667 0.00 0.00 0.00 4.20
748 762 4.586618 CAGCTAGACTGCGCTGTT 57.413 55.556 21.36 13.09 46.38 3.16
815 829 0.537371 AAGGGGAGCCAAAGTCAACG 60.537 55.000 0.00 0.00 0.00 4.10
828 842 5.448632 CCAAAGTCAACGTTACTGCTTTCTT 60.449 40.000 0.00 0.00 0.00 2.52
980 998 5.650266 TCAGTTTGCTCTTGTTTTCAGGTTA 59.350 36.000 0.00 0.00 0.00 2.85
1210 1232 4.148891 GCTTGATTTGGTAACTCGAAACG 58.851 43.478 0.00 0.00 37.61 3.60
1237 1261 3.195610 CGATGATATGCTAACAGGGCCTA 59.804 47.826 5.28 0.00 0.00 3.93
1334 1358 5.639506 TGAAACAGAATTTCATCGAGAGGTC 59.360 40.000 0.00 0.00 33.90 3.85
1630 1851 3.581265 TTGTAAACCCGGTTTCTCCTT 57.419 42.857 19.02 0.00 37.01 3.36
2028 2252 0.508641 CACACAGCGCTGACTTGTAC 59.491 55.000 42.03 0.00 0.00 2.90
2197 2424 6.208402 TGTCCAGCTCATACTTTGCAAATTTA 59.792 34.615 13.23 7.67 0.00 1.40
2221 2598 9.783081 TTATGATGCAGACACAAATATACTCAT 57.217 29.630 0.00 0.00 0.00 2.90
2780 3571 5.304614 GCATGAGTCCCATAACTCTAGGTTA 59.695 44.000 0.00 6.36 44.90 2.85
2791 3582 9.530633 CCATAACTCTAGGTTATTTAGTCACAC 57.469 37.037 11.65 0.00 45.65 3.82
3160 3961 4.443063 TCGCCACGAAAAATATAGTGATCG 59.557 41.667 6.39 6.39 36.79 3.69
3253 4054 3.243643 GCAATTCAGTTTGAACAGTGTGC 59.756 43.478 0.00 0.00 39.45 4.57
3508 4310 7.925483 TCATCATTTCTTTTCGGATTTTGTTGT 59.075 29.630 0.00 0.00 0.00 3.32
3674 4481 1.089920 GCAGTCACATAGCCCAACAG 58.910 55.000 0.00 0.00 0.00 3.16
3707 4524 0.038892 GTCAGCAAGCATGTGTTGGG 60.039 55.000 10.73 0.00 31.24 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.261216 TCAATAAACTCATTCCAAGGGGTC 58.739 41.667 0.00 0.0 34.93 4.46
22 23 6.540551 GGAGACCTCTTCAATAAACTCATTCC 59.459 42.308 0.00 0.0 0.00 3.01
47 48 6.094881 TCCTTTTCATTATTTAACTGCGGGAG 59.905 38.462 0.00 0.0 0.00 4.30
70 71 0.179081 GTCGCCACCAGGAAGTATCC 60.179 60.000 0.00 0.0 46.98 2.59
71 72 0.535335 TGTCGCCACCAGGAAGTATC 59.465 55.000 0.00 0.0 36.89 2.24
128 130 0.325296 ACACCCCGAGCTTCCAGATA 60.325 55.000 0.00 0.0 0.00 1.98
130 132 2.203788 ACACCCCGAGCTTCCAGA 60.204 61.111 0.00 0.0 0.00 3.86
131 133 2.232298 GAGACACCCCGAGCTTCCAG 62.232 65.000 0.00 0.0 0.00 3.86
142 144 0.530870 GCGAGCCAATAGAGACACCC 60.531 60.000 0.00 0.0 0.00 4.61
149 151 3.578282 TGAATATGGAGCGAGCCAATAGA 59.422 43.478 0.62 0.0 42.16 1.98
150 152 3.930336 TGAATATGGAGCGAGCCAATAG 58.070 45.455 0.62 0.0 42.16 1.73
169 171 9.645059 GAGAATATCGGTCAGAATATGAATTGA 57.355 33.333 0.00 0.0 40.43 2.57
196 198 1.269206 ACAAACAAGAGTGCCAATGCG 60.269 47.619 0.00 0.0 41.78 4.73
235 241 3.250762 CCGATGCAGAGTTCTGACAAAAA 59.749 43.478 13.13 0.0 46.59 1.94
293 299 9.367444 CGGATTCCATATCCTAAACAATAGTAC 57.633 37.037 3.09 0.0 36.07 2.73
297 303 6.774673 TGCGGATTCCATATCCTAAACAATA 58.225 36.000 3.09 0.0 36.07 1.90
298 304 5.630121 TGCGGATTCCATATCCTAAACAAT 58.370 37.500 3.09 0.0 36.07 2.71
299 305 5.042463 TGCGGATTCCATATCCTAAACAA 57.958 39.130 3.09 0.0 36.07 2.83
545 553 4.260538 CGATTGAGCTTCAGATTTACCTGC 60.261 45.833 0.00 0.0 34.28 4.85
569 577 0.907486 ATGCTGCTGCCTAGTGAAGA 59.093 50.000 13.47 0.0 38.71 2.87
720 734 2.094078 CAGTCTAGCTGCAAGAGAGCTT 60.094 50.000 1.02 0.0 44.65 3.74
772 786 0.710567 CGTTTACTGCTGCGACTCAG 59.289 55.000 0.00 0.0 45.62 3.35
828 842 8.978874 ATCACTCACCTGTATATTATGCAAAA 57.021 30.769 0.00 0.0 0.00 2.44
980 998 5.010922 TCCATTTGCAGTCAGTAAGCAATTT 59.989 36.000 0.00 0.0 46.32 1.82
1039 1058 2.540101 CGGTTTCATCGGCTAACATCTC 59.460 50.000 0.00 0.0 0.00 2.75
1210 1232 4.452455 CCCTGTTAGCATATCATCGGTTTC 59.548 45.833 0.00 0.0 0.00 2.78
1334 1358 2.440796 ACCCGCATCAGGCATTGG 60.441 61.111 0.00 0.0 45.17 3.16
1630 1851 5.584649 CACGACTTGCATCTATAAAGGGAAA 59.415 40.000 0.00 0.0 0.00 3.13
1727 1948 3.129988 GGCTGGTTTCAGATCCAAATGAG 59.870 47.826 0.00 0.0 43.49 2.90
1962 2186 2.645297 TGGCGCCAAATATCCCCTATAA 59.355 45.455 30.74 0.0 0.00 0.98
2028 2252 4.939439 TCAATGATGATCACACCAAGACTG 59.061 41.667 0.00 0.0 0.00 3.51
2040 2264 6.293845 GCCCAGTCAGTATTTCAATGATGATC 60.294 42.308 0.00 0.0 34.96 2.92
2197 2424 7.718314 ACATGAGTATATTTGTGTCTGCATCAT 59.282 33.333 0.00 0.0 0.00 2.45
2221 2598 6.816136 TCCTTCTCGCAAATGATAAGATACA 58.184 36.000 0.00 0.0 0.00 2.29
2791 3582 3.594134 GAAAGAGGGATGTGTGAGTCAG 58.406 50.000 0.00 0.0 0.00 3.51
3421 4223 9.584839 GACAATTTATTTGAAACTTGACAATGC 57.415 29.630 0.00 0.0 38.76 3.56
3496 4298 5.416326 TGAATAGGGGTAACAACAAAATCCG 59.584 40.000 0.00 0.0 39.74 4.18
3653 4460 1.078497 TTGGGCTATGTGACTGCGG 60.078 57.895 0.00 0.0 0.00 5.69


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

AutoCloner maintained by Alex Coulton.