Multiple sequence alignment - TraesCS5A01G333100

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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 TraesCS5A01G333100 chr5A 100.000 3497 0 0 1 3497 541980600 541984096 0 6458
1 TraesCS5A01G333100 chr5A 97.202 3502 91 5 1 3497 465657818 465661317 0 5917
2 TraesCS5A01G333100 chr5A 97.144 3502 95 3 1 3497 34939664 34936163 0 5908
3 TraesCS5A01G333100 chr6A 97.599 3499 78 2 1 3497 158979764 158976270 0 5991
4 TraesCS5A01G333100 chr2A 97.571 3500 82 2 1 3497 685100616 685097117 0 5989
5 TraesCS5A01G333100 chr2A 97.401 3502 83 7 1 3497 284803616 284807114 0 5956
6 TraesCS5A01G333100 chr1A 97.400 3500 85 4 1 3497 70942064 70938568 0 5954
7 TraesCS5A01G333100 chr7A 96.973 3502 97 8 1 3497 245432354 245428857 0 5871
8 TraesCS5A01G333100 chr3A 96.517 3503 114 6 1 3497 554831139 554834639 0 5786
9 TraesCS5A01G333100 chr3A 96.234 3505 97 9 1 3497 662006703 662003226 0 5709


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 TraesCS5A01G333100 chr5A 541980600 541984096 3496 False 6458 6458 100.000 1 3497 1 chr5A.!!$F2 3496
1 TraesCS5A01G333100 chr5A 465657818 465661317 3499 False 5917 5917 97.202 1 3497 1 chr5A.!!$F1 3496
2 TraesCS5A01G333100 chr5A 34936163 34939664 3501 True 5908 5908 97.144 1 3497 1 chr5A.!!$R1 3496
3 TraesCS5A01G333100 chr6A 158976270 158979764 3494 True 5991 5991 97.599 1 3497 1 chr6A.!!$R1 3496
4 TraesCS5A01G333100 chr2A 685097117 685100616 3499 True 5989 5989 97.571 1 3497 1 chr2A.!!$R1 3496
5 TraesCS5A01G333100 chr2A 284803616 284807114 3498 False 5956 5956 97.401 1 3497 1 chr2A.!!$F1 3496
6 TraesCS5A01G333100 chr1A 70938568 70942064 3496 True 5954 5954 97.400 1 3497 1 chr1A.!!$R1 3496
7 TraesCS5A01G333100 chr7A 245428857 245432354 3497 True 5871 5871 96.973 1 3497 1 chr7A.!!$R1 3496
8 TraesCS5A01G333100 chr3A 554831139 554834639 3500 False 5786 5786 96.517 1 3497 1 chr3A.!!$F1 3496
9 TraesCS5A01G333100 chr3A 662003226 662006703 3477 True 5709 5709 96.234 1 3497 1 chr3A.!!$R1 3496

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
830 835 1.292223 CCCCACGACCACTACACAG 59.708 63.158 0.0 0.0 0.0 3.66 F
1185 1191 0.738975 CAGACAAGGCCGACGAGATA 59.261 55.000 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 2354 0.321919 GATGAGGTTGTCTGGCAGCA 60.322 55.0 10.34 8.61 0.0 4.41 R
2941 2964 2.496899 ATGTTGTCCTCGGCTGAAAT 57.503 45.0 0.00 0.00 0.0 2.17 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
234 236 2.270352 ATGTCCACACCACAACGAAT 57.730 45.000 0.00 0.00 0.00 3.34
354 357 4.007644 TCAGGCCACTCGCACCAG 62.008 66.667 5.01 0.00 40.31 4.00
380 383 5.990996 GTGACATCAAATTTCAAACCCATGT 59.009 36.000 0.00 0.00 0.00 3.21
752 757 5.534207 TTTGTCTTGGACGGTTAGTTCTA 57.466 39.130 0.00 0.00 34.95 2.10
830 835 1.292223 CCCCACGACCACTACACAG 59.708 63.158 0.00 0.00 0.00 3.66
847 852 3.745803 GACGCCCTCGACGAACCT 61.746 66.667 0.00 0.00 39.41 3.50
943 949 2.181975 CCATTGCCACTTCCATTTCCT 58.818 47.619 0.00 0.00 0.00 3.36
1185 1191 0.738975 CAGACAAGGCCGACGAGATA 59.261 55.000 0.00 0.00 0.00 1.98
1234 1240 2.483714 GGCTTGTATCCGAGCTTCATCA 60.484 50.000 0.00 0.00 45.90 3.07
1310 1317 1.660575 AGTTGTGCGTCGAGGAACG 60.661 57.895 9.75 0.00 45.31 3.95
1311 1318 1.947642 GTTGTGCGTCGAGGAACGT 60.948 57.895 9.75 0.00 44.38 3.99
1372 1381 7.773690 GGTAACCCATACTACTGTTCATTCATT 59.226 37.037 0.00 0.00 34.74 2.57
1382 1391 6.084326 ACTGTTCATTCATTTGTTGTACCC 57.916 37.500 0.00 0.00 0.00 3.69
1400 1409 7.466746 TGTACCCGTACTAGTCACTAAAAAT 57.533 36.000 0.00 0.00 37.00 1.82
1957 1970 4.567959 TGAACTACATTCATGCATGACTCG 59.432 41.667 28.72 20.53 42.62 4.18
2063 2078 3.716872 CCTATAAATGTGTGTCTCCCCCT 59.283 47.826 0.00 0.00 0.00 4.79
2194 2209 3.304911 TCAACCCCAACAACTTCATCA 57.695 42.857 0.00 0.00 0.00 3.07
2240 2255 7.995488 AGATCCAAAGACCAGAAAATACTATGG 59.005 37.037 0.00 0.00 38.83 2.74
2339 2354 1.005924 CAAACTGTGGGGGAATAGCCT 59.994 52.381 0.00 0.00 36.66 4.58
2402 2417 1.390123 CGCAACGTACAAGTCATGGAG 59.610 52.381 0.00 0.00 0.00 3.86
2595 2610 4.902443 TGCTTTCGTTATGTTGAACCAA 57.098 36.364 0.00 0.00 0.00 3.67
2941 2964 8.706492 TTCAGACGAACACTAAAAAGACTAAA 57.294 30.769 0.00 0.00 0.00 1.85
3166 3190 5.992829 TCAGTTCGCATTCCTTAAAACAGTA 59.007 36.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 133 9.607988 TGAATTTTAGTAGTTGAACTTGTCAGA 57.392 29.630 1.97 0.00 37.61 3.27
234 236 7.224753 GGTTGAGATTATTTTACGAGCAGATCA 59.775 37.037 0.00 0.00 0.00 2.92
354 357 5.355596 TGGGTTTGAAATTTGATGTCACAC 58.644 37.500 0.00 0.00 0.00 3.82
380 383 7.978414 TGAACTGAATTGTAATTTCAAACAGCA 59.022 29.630 22.30 15.62 38.25 4.41
830 835 3.680338 GAGGTTCGTCGAGGGCGTC 62.680 68.421 5.12 6.44 38.98 5.19
847 852 3.238497 CGGTGGTGTGTGGGAGGA 61.238 66.667 0.00 0.00 0.00 3.71
931 937 2.158623 TGTGTGCAGAGGAAATGGAAGT 60.159 45.455 0.00 0.00 0.00 3.01
943 949 0.819259 GCTGGAGGTTTGTGTGCAGA 60.819 55.000 0.00 0.00 34.22 4.26
1091 1097 0.520404 GAGCGTTCTGGTGTACTCGA 59.480 55.000 0.00 0.00 0.00 4.04
1234 1240 2.231478 CGGTGTACTCCACATCAACTCT 59.769 50.000 14.09 0.00 46.44 3.24
1372 1381 4.144297 AGTGACTAGTACGGGTACAACAA 58.856 43.478 11.23 0.00 38.48 2.83
1915 1928 7.772332 AGTTCAGAAACTAGTACACAAAGTG 57.228 36.000 0.00 0.00 43.98 3.16
2041 2056 3.716872 AGGGGGAGACACACATTTATAGG 59.283 47.826 0.00 0.00 32.66 2.57
2194 2209 1.454572 TTCCACTTGCGCTGCATGTT 61.455 50.000 9.73 3.81 42.78 2.71
2240 2255 3.056313 GCAACATCGGCCAAGGAGC 62.056 63.158 2.24 0.00 0.00 4.70
2271 2286 1.271856 TGCCTTCGTAGAATGGGTGA 58.728 50.000 0.00 0.00 45.90 4.02
2339 2354 0.321919 GATGAGGTTGTCTGGCAGCA 60.322 55.000 10.34 8.61 0.00 4.41
2425 2440 5.309323 TGCTCTTTTGAAATATCCCAACG 57.691 39.130 0.00 0.00 0.00 4.10
2595 2610 5.163405 CCTGACACACATAGCATAAGGTAGT 60.163 44.000 0.00 0.00 0.00 2.73
2941 2964 2.496899 ATGTTGTCCTCGGCTGAAAT 57.503 45.000 0.00 0.00 0.00 2.17
3115 3139 9.856162 AGCTTCCCGTTCCTTTTTATATATTTA 57.144 29.630 0.00 0.00 0.00 1.40
3166 3190 8.630054 TTGCCACTGTTAATTCTTAGTATGTT 57.370 30.769 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.