Multiple sequence alignment - TraesCS7A01G080500

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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 TraesCS7A01G080500 chr7A 100.000 2360 0 0 1 2360 46394305 46391946 0 4359
1 TraesCS7A01G080500 chr7A 98.136 2360 44 0 1 2360 60120927 60118568 0 4115
2 TraesCS7A01G080500 chr7A 97.754 2360 52 1 1 2360 63429290 63431648 0 4063
3 TraesCS7A01G080500 chr7D 98.475 2360 35 1 1 2360 203518117 203520475 0 4157
4 TraesCS7A01G080500 chr7B 98.263 2360 41 0 1 2360 644470082 644472441 0 4132
5 TraesCS7A01G080500 chr3A 97.881 2360 48 1 1 2360 633113889 633116246 0 4080
6 TraesCS7A01G080500 chr3A 97.373 2360 62 0 1 2360 51869813 51872172 0 4015
7 TraesCS7A01G080500 chr1B 97.627 2360 56 0 1 2360 638698025 638695666 0 4048


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 TraesCS7A01G080500 chr7A 46391946 46394305 2359 True 4359 4359 100.000 1 2360 1 chr7A.!!$R1 2359
1 TraesCS7A01G080500 chr7A 60118568 60120927 2359 True 4115 4115 98.136 1 2360 1 chr7A.!!$R2 2359
2 TraesCS7A01G080500 chr7A 63429290 63431648 2358 False 4063 4063 97.754 1 2360 1 chr7A.!!$F1 2359
3 TraesCS7A01G080500 chr7D 203518117 203520475 2358 False 4157 4157 98.475 1 2360 1 chr7D.!!$F1 2359
4 TraesCS7A01G080500 chr7B 644470082 644472441 2359 False 4132 4132 98.263 1 2360 1 chr7B.!!$F1 2359
5 TraesCS7A01G080500 chr3A 633113889 633116246 2357 False 4080 4080 97.881 1 2360 1 chr3A.!!$F2 2359
6 TraesCS7A01G080500 chr3A 51869813 51872172 2359 False 4015 4015 97.373 1 2360 1 chr3A.!!$F1 2359
7 TraesCS7A01G080500 chr1B 638695666 638698025 2359 True 4048 4048 97.627 1 2360 1 chr1B.!!$R1 2359

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
866 867 0.172803 GGATTAGTGCGTGAGACCGT 59.827 55.0 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 2320 1.211212 GTAGCGGGGTTGGGAAAGTAT 59.789 52.381 0.0 0.0 0.0 2.12 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
29 30 1.995626 CCCATGGGTTCGAGGACCT 60.996 63.158 23.93 0.0 39.71 3.85
219 220 0.179034 GAGGTTGGCTGCCTATCCTG 60.179 60.000 25.40 0.0 36.29 3.86
281 282 8.391075 TGGTTTAGTATCAAGGTTCTTCTTTG 57.609 34.615 0.00 0.0 34.95 2.77
354 355 2.025793 TCAATTAATGGGACTTGGCCGA 60.026 45.455 0.00 0.0 0.00 5.54
629 630 2.756283 CCTCTCCTCCGGCGAACT 60.756 66.667 9.30 0.0 0.00 3.01
866 867 0.172803 GGATTAGTGCGTGAGACCGT 59.827 55.000 0.00 0.0 0.00 4.83
925 926 4.398319 TGAGAATGGAAGAAGGGAAACAC 58.602 43.478 0.00 0.0 0.00 3.32
927 928 4.803452 AGAATGGAAGAAGGGAAACACAA 58.197 39.130 0.00 0.0 0.00 3.33
940 941 4.351192 GGAAACACAACATGTCACAAGAC 58.649 43.478 0.00 0.0 42.31 3.01
1090 1091 3.968649 TGGAGTAAAGGGAAGTGTGTACA 59.031 43.478 0.00 0.0 0.00 2.90
1104 1105 2.703536 TGTGTACATTGTCACACTCCCT 59.296 45.455 20.26 0.0 44.30 4.20
1405 1410 5.981315 ACAACCTAACGATACATCCAATACG 59.019 40.000 0.00 0.0 0.00 3.06
1792 1797 6.504279 CCCAAGGAAGGGGTATACTATATTGT 59.496 42.308 2.25 0.0 45.60 2.71
1841 1846 2.067365 GGAACCCTGAACAACACCTT 57.933 50.000 0.00 0.0 0.00 3.50
2078 2083 6.500684 TGCTTGCTACTTTCTAAAATGGAG 57.499 37.500 0.00 0.0 0.00 3.86
2277 2282 6.085555 AGGAAGGAAAAAGGAATTCGAAAC 57.914 37.500 0.00 0.0 0.00 2.78
2315 2320 0.690192 TCATCGGGCTTGACTTTCCA 59.310 50.000 0.00 0.0 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.393646 CCCCTTTTCCTTTGACCAACA 58.606 47.619 0.00 0.00 0.00 3.33
219 220 4.860022 TCTTCTTGGAAATGGGAAGATCC 58.140 43.478 0.00 0.00 39.10 3.36
281 282 7.974501 CACGGACCCATATATATAGAAACAGAC 59.025 40.741 0.00 0.00 0.00 3.51
354 355 7.148171 GCTAATGATAGAGGCAAGAACACTTTT 60.148 37.037 0.00 0.00 0.00 2.27
629 630 0.806102 GTTAGAGGCAGCGATCGCAA 60.806 55.000 38.60 21.13 44.88 4.85
639 640 3.008375 AGTTGAGCATTCAGTTAGAGGCA 59.992 43.478 0.00 0.00 34.15 4.75
749 750 2.084546 GGCTCGGCTTCAAAACTGTAT 58.915 47.619 0.00 0.00 0.00 2.29
753 754 1.609072 GAAAGGCTCGGCTTCAAAACT 59.391 47.619 6.18 0.00 0.00 2.66
866 867 1.805943 CATGCGTCAGTTTGTGGATCA 59.194 47.619 0.00 0.00 0.00 2.92
925 926 1.800586 CCTCGGTCTTGTGACATGTTG 59.199 52.381 0.00 0.00 44.61 3.33
927 928 0.320771 GCCTCGGTCTTGTGACATGT 60.321 55.000 0.00 0.00 44.61 3.21
1090 1091 1.136329 AGGGCAGGGAGTGTGACAAT 61.136 55.000 0.00 0.00 0.00 2.71
1260 1261 3.750922 CGGGTACTATGGATCCTCTGACA 60.751 52.174 14.23 0.00 0.00 3.58
1326 1327 4.474651 TCCATTGCAGAAAAGAGATCCCTA 59.525 41.667 0.00 0.00 0.00 3.53
1364 1369 0.250252 TGTGCCGAGTCAAATCAGCA 60.250 50.000 0.00 0.00 0.00 4.41
1405 1410 2.890808 TCGGTAGGCACAGATCATTC 57.109 50.000 0.00 0.00 0.00 2.67
1789 1794 4.397103 TCAACATTTTGCATTTTGGCACAA 59.603 33.333 0.00 0.00 44.86 3.33
1792 1797 5.507482 CCATTCAACATTTTGCATTTTGGCA 60.507 36.000 0.00 0.00 43.19 4.92
1841 1846 2.029110 GCATGTAGCTTTGAAAAGGGCA 60.029 45.455 0.00 0.00 41.15 5.36
2277 2282 1.562672 ATTCTGTGGGAAGGGACGGG 61.563 60.000 0.00 0.00 37.36 5.28
2315 2320 1.211212 GTAGCGGGGTTGGGAAAGTAT 59.789 52.381 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.