Multiple sequence alignment - TraesCS5A01G150400

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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 TraesCS5A01G150400 chr5A 100.000 2428 0 0 1 2428 328007946 328010373 0.000000e+00 4484
1 TraesCS5A01G150400 chr5A 99.517 621 3 0 1808 2428 328015994 328016614 0.000000e+00 1131
2 TraesCS5A01G150400 chr5B 97.642 1739 41 0 1 1739 276959119 276960857 0.000000e+00 2985
3 TraesCS5A01G150400 chr5D 97.529 1740 43 0 1 1740 243833020 243834759 0.000000e+00 2976
4 TraesCS5A01G150400 chr1A 94.767 688 22 6 1753 2428 59586382 59587067 0.000000e+00 1059
5 TraesCS5A01G150400 chr7B 83.120 391 39 16 2038 2418 629786769 629787142 5.000000e-87 331
6 TraesCS5A01G150400 chr7D 84.536 291 20 7 2157 2423 572539879 572539590 5.150000e-67 265
7 TraesCS5A01G150400 chr7D 91.597 119 10 0 2038 2156 572540036 572539918 5.370000e-37 165
8 TraesCS5A01G150400 chr4A 87.156 218 28 0 1789 2006 434740684 434740901 5.180000e-62 248
9 TraesCS5A01G150400 chr7A 86.207 203 14 11 2232 2425 661577775 661577578 8.800000e-50 207


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 TraesCS5A01G150400 chr5A 328007946 328010373 2427 False 4484 4484 100.000 1 2428 1 chr5A.!!$F1 2427
1 TraesCS5A01G150400 chr5A 328015994 328016614 620 False 1131 1131 99.517 1808 2428 1 chr5A.!!$F2 620
2 TraesCS5A01G150400 chr5B 276959119 276960857 1738 False 2985 2985 97.642 1 1739 1 chr5B.!!$F1 1738
3 TraesCS5A01G150400 chr5D 243833020 243834759 1739 False 2976 2976 97.529 1 1740 1 chr5D.!!$F1 1739
4 TraesCS5A01G150400 chr1A 59586382 59587067 685 False 1059 1059 94.767 1753 2428 1 chr1A.!!$F1 675

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
575 576 0.250234 CTCGACAAGCATCCTCCCAA 59.75 55.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 2353 1.81806 TGGATGCATAGCGCTTTGTTT 59.182 42.857 25.42 15.04 43.06 2.83 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 2.364002 TGAGTTCCACATGACTTCGTCA 59.636 45.455 0.00 0.00 46.90 4.35
215 216 5.750547 GCAATACAGATCGATGACTGAAGAA 59.249 40.000 18.18 4.25 37.54 2.52
461 462 5.809562 ACTCTTGCTAGTGATCATCGAAAAG 59.190 40.000 0.00 1.57 0.00 2.27
503 504 1.808512 CGCCCACAGTTTGAGTACACA 60.809 52.381 0.00 0.00 0.00 3.72
575 576 0.250234 CTCGACAAGCATCCTCCCAA 59.750 55.000 0.00 0.00 0.00 4.12
608 609 5.728637 TTGAGTAGAAGTCAATGAGAGCA 57.271 39.130 0.00 0.00 32.96 4.26
765 766 4.269183 TGACCGCATCATCCTTACAAAAT 58.731 39.130 0.00 0.00 29.99 1.82
998 999 2.104792 ACACTTGCAGTACATGTCCACT 59.895 45.455 0.00 0.00 34.59 4.00
1121 1122 1.333619 ACAACCGTAGCAAGCACAAAG 59.666 47.619 0.00 0.00 0.00 2.77
1189 1190 4.518211 ACCAATCTCTCTGAACAAAGCAAG 59.482 41.667 0.00 0.00 0.00 4.01
1316 1317 2.672908 CCTGCAGAGACCATGCCA 59.327 61.111 17.39 0.00 43.18 4.92
1443 1444 1.902508 TGTAGGAGAAGCAGTTCCTGG 59.097 52.381 11.79 0.00 43.54 4.45
1625 1626 2.041762 AGGAGCTGGATGGAGCCA 59.958 61.111 0.00 0.00 40.08 4.75
1722 1723 2.341846 TTTGGACTGTTGGACTCACC 57.658 50.000 0.00 0.00 39.54 4.02
1740 1741 1.071699 ACCGGTGTGCTGTACAAATCT 59.928 47.619 6.12 0.00 41.89 2.40
1741 1742 2.151202 CCGGTGTGCTGTACAAATCTT 58.849 47.619 0.00 0.00 41.89 2.40
1742 1743 3.244284 ACCGGTGTGCTGTACAAATCTTA 60.244 43.478 6.12 0.00 41.89 2.10
1743 1744 3.124636 CCGGTGTGCTGTACAAATCTTAC 59.875 47.826 0.00 0.00 41.89 2.34
1744 1745 3.743911 CGGTGTGCTGTACAAATCTTACA 59.256 43.478 0.00 0.00 41.89 2.41
1745 1746 4.391830 CGGTGTGCTGTACAAATCTTACAT 59.608 41.667 0.00 0.00 41.89 2.29
1746 1747 5.106712 CGGTGTGCTGTACAAATCTTACATT 60.107 40.000 0.00 0.00 41.89 2.71
1747 1748 6.314784 GGTGTGCTGTACAAATCTTACATTC 58.685 40.000 0.00 0.00 41.89 2.67
1748 1749 6.149474 GGTGTGCTGTACAAATCTTACATTCT 59.851 38.462 0.00 0.00 41.89 2.40
1749 1750 7.308589 GGTGTGCTGTACAAATCTTACATTCTT 60.309 37.037 0.00 0.00 41.89 2.52
1750 1751 7.746475 GTGTGCTGTACAAATCTTACATTCTTC 59.254 37.037 0.00 0.00 41.89 2.87
1751 1752 7.661437 TGTGCTGTACAAATCTTACATTCTTCT 59.339 33.333 0.00 0.00 36.06 2.85
1795 1796 2.165319 GGAAGTCCTACAACTTGCGT 57.835 50.000 0.00 0.00 39.55 5.24
1955 1956 1.506025 TTTTGCAAAGAGGCCCCTTT 58.494 45.000 12.41 6.40 36.87 3.11
2340 2353 4.892934 ACAAACCAGATCAGCTAAAAACCA 59.107 37.500 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 4.487714 TTTCGATGGAATAGACAAGCCT 57.512 40.909 0.00 0.00 30.88 4.58
215 216 2.613977 GCAGTCTGACCATGTTGTAGCT 60.614 50.000 3.32 0.00 0.00 3.32
461 462 4.364860 GGATAGAAGAGGCGAAAAGAGTC 58.635 47.826 0.00 0.00 0.00 3.36
503 504 4.157289 GTGGTGCTCAATTCAATGATCACT 59.843 41.667 0.00 0.00 42.91 3.41
575 576 4.401925 ACTTCTACTCAAAATGCAGCCTT 58.598 39.130 0.00 0.00 0.00 4.35
608 609 4.334759 GTCAATGACATGATAGCAGCAAGT 59.665 41.667 8.74 0.00 32.09 3.16
877 878 1.645034 CTATGCTTCACGTGGACAGG 58.355 55.000 17.00 0.00 0.00 4.00
998 999 1.874231 TCGGTTTTGAGTTGCGCATTA 59.126 42.857 12.75 0.00 0.00 1.90
1121 1122 1.493950 CCTCGCCGTGCAATGATCTC 61.494 60.000 0.00 0.00 0.00 2.75
1316 1317 0.036952 CCTGGAACGCAGTGATCACT 60.037 55.000 22.89 22.89 45.00 3.41
1443 1444 2.097728 GTTCGACGAAATGCCCGC 59.902 61.111 12.67 0.00 0.00 6.13
1654 1655 4.033776 CCCATGCCCCACGTCAGT 62.034 66.667 0.00 0.00 0.00 3.41
1689 1690 3.547468 CAGTCCAAAAACTTCGCACTTTG 59.453 43.478 0.00 0.00 0.00 2.77
1722 1723 3.743911 TGTAAGATTTGTACAGCACACCG 59.256 43.478 0.00 0.00 36.69 4.94
1751 1752 9.321562 CCGGTGCTTTTATAACTCTTCTTATAA 57.678 33.333 0.00 0.00 30.13 0.98
1754 1755 6.938507 TCCGGTGCTTTTATAACTCTTCTTA 58.061 36.000 0.00 0.00 0.00 2.10
1757 1758 5.642491 ACTTCCGGTGCTTTTATAACTCTTC 59.358 40.000 0.00 0.00 0.00 2.87
1764 1765 4.467082 TGTAGGACTTCCGGTGCTTTTATA 59.533 41.667 0.00 0.00 44.21 0.98
1765 1766 3.262405 TGTAGGACTTCCGGTGCTTTTAT 59.738 43.478 0.00 0.00 44.21 1.40
1795 1796 6.303054 TCTAGAACCAAACCATCACATTCAA 58.697 36.000 0.00 0.00 0.00 2.69
1955 1956 3.078837 GCGGGTAGATTCAAACCAAAGA 58.921 45.455 9.61 0.00 37.51 2.52
2073 2074 2.735823 CATTGCTCTGTCGATCGATCA 58.264 47.619 22.50 18.53 0.00 2.92
2340 2353 1.818060 TGGATGCATAGCGCTTTGTTT 59.182 42.857 25.42 15.04 43.06 2.83


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

AutoCloner maintained by Alex Coulton.