Multiple sequence alignment - TraesCS1A01G111500

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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 TraesCS1A01G111500 chr1A 100.000 2513 0 0 1 2513 112926811 112929323 0.000000e+00 4641
1 TraesCS1A01G111500 chr1D 97.662 1540 30 3 974 2513 109454916 109456449 0.000000e+00 2639
2 TraesCS1A01G111500 chr1D 96.416 586 11 3 379 962 109454281 109454858 0.000000e+00 957
3 TraesCS1A01G111500 chr1D 91.899 395 29 3 1 395 109453862 109454253 1.310000e-152 549
4 TraesCS1A01G111500 chr1B 97.497 1518 33 4 996 2513 165064663 165066175 0.000000e+00 2588
5 TraesCS1A01G111500 chr1B 92.550 698 28 11 1 691 165063582 165064262 0.000000e+00 979
6 TraesCS1A01G111500 chr1B 95.380 303 5 3 687 980 165064318 165064620 8.140000e-130 473


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 TraesCS1A01G111500 chr1A 112926811 112929323 2512 False 4641.000000 4641 100.000000 1 2513 1 chr1A.!!$F1 2512
1 TraesCS1A01G111500 chr1D 109453862 109456449 2587 False 1381.666667 2639 95.325667 1 2513 3 chr1D.!!$F1 2512
2 TraesCS1A01G111500 chr1B 165063582 165066175 2593 False 1346.666667 2588 95.142333 1 2513 3 chr1B.!!$F1 2512

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
431 482 0.252513 AAAACCCATACCCCAAGGCC 60.253 55.0 0.0 0.0 36.11 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2333 1.746991 GCTGCTTGCTAGGGTGTCC 60.747 63.158 0.0 0.0 38.95 4.02 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
137 138 9.628500 TCTAAACACTATCTCATAGCTGTTCTA 57.372 33.333 0.00 0.0 36.75 2.10
221 224 8.537049 TTTTGAAAAATATCATTCCAGTGCTG 57.463 30.769 0.00 0.0 0.00 4.41
237 240 4.756642 CAGTGCTGGATGTTTCTTCTAACA 59.243 41.667 0.00 0.0 41.81 2.41
374 381 8.641499 TTCTTCGTAATTCTTTGTGCATTTTT 57.359 26.923 0.00 0.0 0.00 1.94
393 444 4.685169 TTTTGCGGATCTCATTTGTCTC 57.315 40.909 0.00 0.0 0.00 3.36
404 455 7.384660 GGATCTCATTTGTCTCTACAATAGCAG 59.615 40.741 0.00 0.0 44.85 4.24
429 480 0.901827 GCAAAACCCATACCCCAAGG 59.098 55.000 0.00 0.0 40.04 3.61
430 481 0.901827 CAAAACCCATACCCCAAGGC 59.098 55.000 0.00 0.0 36.11 4.35
431 482 0.252513 AAAACCCATACCCCAAGGCC 60.253 55.000 0.00 0.0 36.11 5.19
432 483 2.176202 AAACCCATACCCCAAGGCCC 62.176 60.000 0.00 0.0 36.11 5.80
433 484 3.026847 CCCATACCCCAAGGCCCA 61.027 66.667 0.00 0.0 36.11 5.36
434 485 2.631525 CCCATACCCCAAGGCCCAA 61.632 63.158 0.00 0.0 36.11 4.12
435 486 1.076044 CCATACCCCAAGGCCCAAG 60.076 63.158 0.00 0.0 36.11 3.61
570 622 6.044287 TGGGAATAATTGAGGCAAGCTAGATA 59.956 38.462 0.00 0.0 0.00 1.98
596 648 6.207509 AGGGAGAGAACATACATAGCTAGA 57.792 41.667 0.00 0.0 0.00 2.43
644 696 2.350895 CTGAACGTGCATGGGGGA 59.649 61.111 11.36 0.0 0.00 4.81
851 963 4.050553 CAACGCAAAGACCATGACAAAAT 58.949 39.130 0.00 0.0 0.00 1.82
918 1036 2.837031 ATTGGTCACCCCACGATGCC 62.837 60.000 0.00 0.0 45.19 4.40
968 1092 1.314730 GAGAGACATCCTCGACCTCC 58.685 60.000 0.00 0.0 46.49 4.30
1080 1246 0.039764 TCAGGATCGTCCACCTCAGT 59.960 55.000 6.78 0.0 39.61 3.41
1131 1297 2.909965 GCCGGCGAGATCCTCTCT 60.910 66.667 12.58 0.0 41.26 3.10
1391 1557 1.806461 AAGAGCAAGCCGTCGTCAGA 61.806 55.000 0.00 0.0 0.00 3.27
1432 1598 2.490685 GGTCCGAGAAGAGGTCGC 59.509 66.667 0.00 0.0 36.06 5.19
1766 1932 2.173519 TGTTCCGTTCTATCCTCCGTT 58.826 47.619 0.00 0.0 0.00 4.44
1836 2005 3.775261 AATGGGCATGTGCTTCTTTTT 57.225 38.095 4.84 0.0 41.70 1.94
1945 2114 7.200434 ACTAGTGGTAATGTCAATCAATCCT 57.800 36.000 0.00 0.0 0.00 3.24
2164 2333 4.916983 TTCATGTGGAGGTTGACAAAAG 57.083 40.909 0.00 0.0 0.00 2.27
2368 2537 8.475639 TCATCCAACTAGAGAACAATTACCTAC 58.524 37.037 0.00 0.0 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.177608 TCATCCACCAAATAGTTCATCTTAAAG 57.822 33.333 0.00 0.00 0.00 1.85
275 278 4.989279 ATTGCTCAAAGATACCGCAATT 57.011 36.364 0.00 0.00 45.81 2.32
281 288 3.193267 TGTGGCAATTGCTCAAAGATACC 59.807 43.478 28.42 9.43 41.70 2.73
374 381 3.616956 AGAGACAAATGAGATCCGCAA 57.383 42.857 0.00 0.00 0.00 4.85
404 455 2.956333 GGGGTATGGGTTTTGCATAGTC 59.044 50.000 0.00 0.00 0.00 2.59
429 480 0.324645 ATGGGTGTTGATCCTTGGGC 60.325 55.000 0.00 0.00 0.00 5.36
430 481 1.285962 AGATGGGTGTTGATCCTTGGG 59.714 52.381 0.00 0.00 0.00 4.12
431 482 2.814805 AGATGGGTGTTGATCCTTGG 57.185 50.000 0.00 0.00 0.00 3.61
432 483 3.941483 GTGTAGATGGGTGTTGATCCTTG 59.059 47.826 0.00 0.00 0.00 3.61
433 484 3.846588 AGTGTAGATGGGTGTTGATCCTT 59.153 43.478 0.00 0.00 0.00 3.36
434 485 3.198635 CAGTGTAGATGGGTGTTGATCCT 59.801 47.826 0.00 0.00 0.00 3.24
435 486 3.535561 CAGTGTAGATGGGTGTTGATCC 58.464 50.000 0.00 0.00 0.00 3.36
570 622 4.140805 AGCTATGTATGTTCTCTCCCTCCT 60.141 45.833 0.00 0.00 0.00 3.69
596 648 8.712228 TTTATGGGGGCAATTTGTTTATTTTT 57.288 26.923 0.00 0.00 0.00 1.94
644 696 7.067251 GGCAGTAGAACACTACTAGAACTACAT 59.933 40.741 9.15 0.00 43.08 2.29
851 963 9.283768 CATATGTCCAAGGTAGCATACAATTTA 57.716 33.333 0.00 0.00 45.43 1.40
918 1036 2.110011 TCCTTTTCCTTTCCCTCCCTTG 59.890 50.000 0.00 0.00 0.00 3.61
968 1092 9.195411 GATACTATGAATCTTTCTCTCTGCTTG 57.805 37.037 0.00 0.00 0.00 4.01
1131 1297 4.178169 ACGTGGTTCGGGTTGGCA 62.178 61.111 0.00 0.00 44.69 4.92
1415 1581 2.047443 AGCGACCTCTTCTCGGACC 61.047 63.158 0.00 0.00 0.00 4.46
1766 1932 6.047870 CCAATCAAACACTCATCCACAAAAA 58.952 36.000 0.00 0.00 0.00 1.94
1885 2054 5.651139 AGGATGAACAGATTGAAACTCCATG 59.349 40.000 0.00 0.00 0.00 3.66
1945 2114 6.480763 TGGATTATTTGAAGGTAAGCAGTGA 58.519 36.000 0.00 0.00 0.00 3.41
2164 2333 1.746991 GCTGCTTGCTAGGGTGTCC 60.747 63.158 0.00 0.00 38.95 4.02
2368 2537 7.224362 TGTGTCATTTTCCTTTGCACATTTAAG 59.776 33.333 0.00 0.00 31.57 1.85
2375 2544 6.646240 ACATTATGTGTCATTTTCCTTTGCAC 59.354 34.615 0.00 0.00 35.77 4.57


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

AutoCloner maintained by Alex Coulton.