Multiple sequence alignment - TraesCS4B01G121100

Loading Multiple Alignment...

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 TraesCS4B01G121100 chr4B 100.000 2561 0 0 1 2561 142696669 142699229 0 4730
1 TraesCS4B01G121100 chr4D 95.149 2556 102 11 1 2544 100482091 100484636 0 4013
2 TraesCS4B01G121100 chr4A 93.453 2566 137 18 1 2544 476067404 476064848 0 3779


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 TraesCS4B01G121100 chr4B 142696669 142699229 2560 False 4730 4730 100.000 1 2561 1 chr4B.!!$F1 2560
1 TraesCS4B01G121100 chr4D 100482091 100484636 2545 False 4013 4013 95.149 1 2544 1 chr4D.!!$F1 2543
2 TraesCS4B01G121100 chr4A 476064848 476067404 2556 True 3779 3779 93.453 1 2544 1 chr4A.!!$R1 2543

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
150 152 0.110486 ATCAGCTTGGGGTTCACGTT 59.89 50.0 0.0 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1762 1.269448 CCCAAAATGACAAGGACACGG 59.731 52.381 0.0 0.0 0.0 4.94 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
36 37 1.444895 GCTCCGCACAGCCAAATTG 60.445 57.895 0.00 0.00 32.76 2.32
80 81 9.362539 GTGCTCAATTTCACTAATCAAATGAAT 57.637 29.630 0.00 0.00 32.61 2.57
116 118 3.296854 TGACAGTAGCTCGGATGGTTAT 58.703 45.455 0.00 0.00 0.00 1.89
127 129 3.454447 TCGGATGGTTATGATCTTGTGGT 59.546 43.478 0.00 0.00 0.00 4.16
134 136 5.192927 GGTTATGATCTTGTGGTGGAATCA 58.807 41.667 0.00 0.00 0.00 2.57
135 137 5.297776 GGTTATGATCTTGTGGTGGAATCAG 59.702 44.000 0.00 0.00 0.00 2.90
137 139 2.306805 TGATCTTGTGGTGGAATCAGCT 59.693 45.455 0.00 0.00 41.59 4.24
139 141 2.507484 TCTTGTGGTGGAATCAGCTTG 58.493 47.619 0.00 0.00 41.59 4.01
150 152 0.110486 ATCAGCTTGGGGTTCACGTT 59.890 50.000 0.00 0.00 0.00 3.99
163 165 3.982058 GGTTCACGTTCTAGACTTGACAG 59.018 47.826 0.00 0.00 36.39 3.51
172 174 4.912586 TCTAGACTTGACAGTAGTGCTCT 58.087 43.478 0.00 0.00 31.22 4.09
212 214 7.894376 ATTTCATACTTTCTGGCAATGTTTG 57.106 32.000 0.00 0.00 0.00 2.93
229 231 6.712241 ATGTTTGTTTAGTGAGAGATGACG 57.288 37.500 0.00 0.00 0.00 4.35
236 238 8.277490 TGTTTAGTGAGAGATGACGTTACTAT 57.723 34.615 0.00 0.00 0.00 2.12
241 243 7.153315 AGTGAGAGATGACGTTACTATCGATA 58.847 38.462 4.78 4.78 0.00 2.92
252 254 8.340618 ACGTTACTATCGATAATAAGGCCTTA 57.659 34.615 27.11 27.11 0.00 2.69
256 258 9.524496 TTACTATCGATAATAAGGCCTTAGTGA 57.476 33.333 30.73 21.16 0.00 3.41
257 259 7.828712 ACTATCGATAATAAGGCCTTAGTGAC 58.171 38.462 30.73 22.44 0.00 3.67
396 398 4.271049 CACGATGATCAATTACTGGGTGAC 59.729 45.833 0.00 0.00 0.00 3.67
422 426 4.239495 ACCACACATCAAGCCCCTATATA 58.761 43.478 0.00 0.00 0.00 0.86
598 608 0.391130 AACACGCACGGCAGACATAT 60.391 50.000 0.00 0.00 0.00 1.78
599 609 0.458260 ACACGCACGGCAGACATATA 59.542 50.000 0.00 0.00 0.00 0.86
601 611 0.597637 ACGCACGGCAGACATATAGC 60.598 55.000 0.00 0.00 0.00 2.97
609 619 3.498397 CGGCAGACATATAGCGGAAAAAT 59.502 43.478 0.00 0.00 0.00 1.82
662 672 1.018226 TCGTCGAGTTCGGTCCTCTC 61.018 60.000 1.26 0.00 40.29 3.20
663 673 1.020333 CGTCGAGTTCGGTCCTCTCT 61.020 60.000 1.26 0.00 40.29 3.10
704 714 5.353956 GCAAAATCCAACAACAATATTCCCC 59.646 40.000 0.00 0.00 0.00 4.81
825 841 3.247648 ACACACGAATACACACAGCTTTC 59.752 43.478 0.00 0.00 0.00 2.62
826 842 3.247411 CACACGAATACACACAGCTTTCA 59.753 43.478 0.00 0.00 0.00 2.69
827 843 3.247648 ACACGAATACACACAGCTTTCAC 59.752 43.478 0.00 0.00 0.00 3.18
828 844 3.494626 CACGAATACACACAGCTTTCACT 59.505 43.478 0.00 0.00 0.00 3.41
829 845 4.024893 CACGAATACACACAGCTTTCACTT 60.025 41.667 0.00 0.00 0.00 3.16
830 846 4.574828 ACGAATACACACAGCTTTCACTTT 59.425 37.500 0.00 0.00 0.00 2.66
909 928 3.496331 TGCACTACTCGATCATATCCCA 58.504 45.455 0.00 0.00 0.00 4.37
950 969 2.341846 TCTTCCTGAAACCACCACAC 57.658 50.000 0.00 0.00 0.00 3.82
951 970 1.562008 TCTTCCTGAAACCACCACACA 59.438 47.619 0.00 0.00 0.00 3.72
994 1013 2.973899 CTCAGCTGGTACGCAGGT 59.026 61.111 15.13 9.41 0.00 4.00
1011 1030 4.402528 TACACCATGCGGCGGCTT 62.403 61.111 17.76 8.37 40.82 4.35
1140 1159 0.832626 ACATGGTGATCATCCTCGCA 59.167 50.000 2.86 0.00 32.92 5.10
1161 1180 3.352447 GCTGCTCTGCGTTCTCATA 57.648 52.632 0.00 0.00 0.00 2.15
1354 1373 4.324991 GGGCCAAGTCGTCCGGTT 62.325 66.667 4.39 0.00 0.00 4.44
1741 1762 1.405933 GGGCTTGATGCAAATGTTCCC 60.406 52.381 0.00 0.00 45.15 3.97
1776 1797 2.799126 TTGGGTTGGAGCATACGATT 57.201 45.000 0.00 0.00 0.00 3.34
1872 1893 5.515797 AGATGAGTAGTATTGCGCTGTTA 57.484 39.130 9.73 0.00 0.00 2.41
2143 2171 6.714810 TGTGTTCAAAGCATGGTATTTCTAGT 59.285 34.615 0.00 0.00 0.00 2.57
2168 2196 8.968242 GTGAACGAAAGAAAATAAGCAAAGAAT 58.032 29.630 0.00 0.00 0.00 2.40
2216 2245 2.988010 AGCTGTCATCGCCAATAAGA 57.012 45.000 0.00 0.00 0.00 2.10
2224 2253 7.308229 GCTGTCATCGCCAATAAGAATATCTTT 60.308 37.037 0.00 0.00 37.89 2.52
2271 2301 6.321690 GGCTTAGACTAACTCCAACAGATCTA 59.678 42.308 0.00 0.00 0.00 1.98
2275 2305 9.616156 TTAGACTAACTCCAACAGATCTAGTAG 57.384 37.037 0.00 0.00 0.00 2.57
2280 2310 7.540474 AACTCCAACAGATCTAGTAGAAACA 57.460 36.000 3.45 0.00 0.00 2.83
2338 2368 3.627395 TTGCCGGAATTGTCAGATAGT 57.373 42.857 5.05 0.00 0.00 2.12
2341 2371 5.290493 TGCCGGAATTGTCAGATAGTTAT 57.710 39.130 5.05 0.00 0.00 1.89
2356 2386 8.602424 TCAGATAGTTATTTTTCTCAGTTCCCA 58.398 33.333 0.00 0.00 0.00 4.37
2433 2464 2.124529 TGCAAGCCGGTGACACAA 60.125 55.556 8.08 0.00 0.00 3.33
2438 2469 1.027792 AAGCCGGTGACACAACGTTT 61.028 50.000 8.08 0.40 43.64 3.60
2544 2575 3.880846 GAAGCGAAGGCCGGCATG 61.881 66.667 30.85 11.99 41.24 4.06
2549 2580 4.424711 GAAGGCCGGCATGGTGGA 62.425 66.667 30.85 0.00 41.21 4.02
2550 2581 4.431131 AAGGCCGGCATGGTGGAG 62.431 66.667 30.85 0.00 41.21 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.414454 TGAGCACTTATCATTTTACCCACAC 59.586 40.000 0.00 0.00 0.00 3.82
80 81 7.097192 AGCTACTGTCAATTCGTCTATTTTCA 58.903 34.615 0.00 0.00 0.00 2.69
91 93 3.126831 CCATCCGAGCTACTGTCAATTC 58.873 50.000 0.00 0.00 0.00 2.17
99 101 4.411927 AGATCATAACCATCCGAGCTACT 58.588 43.478 0.00 0.00 0.00 2.57
116 118 2.306805 AGCTGATTCCACCACAAGATCA 59.693 45.455 0.00 0.00 0.00 2.92
127 129 0.776810 TGAACCCCAAGCTGATTCCA 59.223 50.000 0.00 0.00 0.00 3.53
134 136 1.002087 CTAGAACGTGAACCCCAAGCT 59.998 52.381 0.00 0.00 0.00 3.74
135 137 1.001633 TCTAGAACGTGAACCCCAAGC 59.998 52.381 0.00 0.00 0.00 4.01
137 139 2.322658 AGTCTAGAACGTGAACCCCAA 58.677 47.619 0.00 0.00 0.00 4.12
139 141 2.298163 TCAAGTCTAGAACGTGAACCCC 59.702 50.000 0.00 0.00 42.36 4.95
150 152 4.912586 AGAGCACTACTGTCAAGTCTAGA 58.087 43.478 0.00 0.00 37.88 2.43
163 165 9.757227 ATAAATTAAGAGACATGAGAGCACTAC 57.243 33.333 0.00 0.00 0.00 2.73
194 196 7.067615 TCACTAAACAAACATTGCCAGAAAGTA 59.932 33.333 0.00 0.00 0.00 2.24
212 214 7.583401 CGATAGTAACGTCATCTCTCACTAAAC 59.417 40.741 0.00 0.00 0.00 2.01
229 231 9.570488 CACTAAGGCCTTATTATCGATAGTAAC 57.430 37.037 25.37 7.67 37.40 2.50
236 238 4.823442 TCGTCACTAAGGCCTTATTATCGA 59.177 41.667 25.37 25.09 0.00 3.59
241 243 4.222145 TGAAGTCGTCACTAAGGCCTTATT 59.778 41.667 25.37 17.42 30.14 1.40
252 254 7.406031 TCTTAGGATTAATGAAGTCGTCACT 57.594 36.000 0.00 0.00 39.72 3.41
396 398 0.962356 GGGCTTGATGTGTGGTCCAG 60.962 60.000 0.00 0.00 0.00 3.86
422 426 3.077359 CAGAGAGCGAAAACCCTCATTT 58.923 45.455 0.00 0.00 0.00 2.32
598 608 3.189702 GCCGCCATATTATTTTTCCGCTA 59.810 43.478 0.00 0.00 0.00 4.26
599 609 2.030274 GCCGCCATATTATTTTTCCGCT 60.030 45.455 0.00 0.00 0.00 5.52
601 611 2.294791 TGGCCGCCATATTATTTTTCCG 59.705 45.455 8.43 0.00 0.00 4.30
609 619 0.037697 CGCTAGTGGCCGCCATATTA 60.038 55.000 16.96 8.09 35.28 0.98
662 672 9.780413 GGATTTTGCTTTTCTCTAGAAACATAG 57.220 33.333 4.66 2.19 43.01 2.23
663 673 9.295825 TGGATTTTGCTTTTCTCTAGAAACATA 57.704 29.630 4.66 0.00 43.01 2.29
704 714 5.072040 AGTCGGCAAATTTAGGAAATTGG 57.928 39.130 0.00 0.00 40.05 3.16
825 841 4.014847 TGCGAAAGTGAAAGTGAAAGTG 57.985 40.909 0.00 0.00 0.00 3.16
826 842 3.487544 GCTGCGAAAGTGAAAGTGAAAGT 60.488 43.478 0.00 0.00 0.00 2.66
827 843 3.038710 GCTGCGAAAGTGAAAGTGAAAG 58.961 45.455 0.00 0.00 0.00 2.62
828 844 2.682856 AGCTGCGAAAGTGAAAGTGAAA 59.317 40.909 0.00 0.00 0.00 2.69
829 845 2.032054 CAGCTGCGAAAGTGAAAGTGAA 59.968 45.455 0.00 0.00 0.00 3.18
830 846 1.599071 CAGCTGCGAAAGTGAAAGTGA 59.401 47.619 0.00 0.00 0.00 3.41
909 928 7.410120 AGAAATCAAGAGAGTGTTTTGGTTT 57.590 32.000 1.88 1.88 37.72 3.27
950 969 1.904852 GCTGCTGATGGACGTGTGTG 61.905 60.000 0.00 0.00 0.00 3.82
951 970 1.669115 GCTGCTGATGGACGTGTGT 60.669 57.895 0.00 0.00 0.00 3.72
994 1013 2.916502 CTAAGCCGCCGCATGGTGTA 62.917 60.000 0.00 0.00 44.67 2.90
1161 1180 4.451150 TTGAGCCCGAGCGCGAAT 62.451 61.111 12.10 0.00 46.67 3.34
1434 1453 3.599285 GAATCCGTGGTGGCACCGA 62.599 63.158 30.14 21.74 42.58 4.69
1491 1510 4.659172 CGGCAGTTGGGGCAGGAA 62.659 66.667 0.00 0.00 0.00 3.36
1741 1762 1.269448 CCCAAAATGACAAGGACACGG 59.731 52.381 0.00 0.00 0.00 4.94
2108 2136 6.312426 CCATGCTTTGAACACAAGTTAACAAA 59.688 34.615 8.61 0.00 38.30 2.83
2216 2245 3.279434 GTGACCGGCCAGAAAAGATATT 58.721 45.455 0.00 0.00 0.00 1.28
2224 2253 2.847234 AGTGGTGACCGGCCAGAA 60.847 61.111 0.00 0.00 36.57 3.02
2271 2301 6.485648 AGCACTTTTACGGAAATGTTTCTACT 59.514 34.615 8.84 0.64 37.35 2.57
2275 2305 6.822073 AAAGCACTTTTACGGAAATGTTTC 57.178 33.333 8.84 4.85 32.22 2.78
2341 2371 8.533569 AGAAGTTTTATGGGAACTGAGAAAAA 57.466 30.769 0.00 0.00 37.41 1.94
2433 2464 0.454196 GTTGCCACACTTCCAAACGT 59.546 50.000 0.00 0.00 0.00 3.99
2438 2469 0.813610 CGTCTGTTGCCACACTTCCA 60.814 55.000 0.00 0.00 0.00 3.53
2469 2500 3.936203 GCACCACCTCACCGGTCA 61.936 66.667 2.59 0.00 44.93 4.02


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

AutoCloner maintained by Alex Coulton.