Multiple sequence alignment - TraesCS6A01G414100

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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 TraesCS6A01G414100 chr6A 100.000 3140 0 0 1 3140 614692157 614689018 0.000000e+00 5799.0
1 TraesCS6A01G414100 chrUn 99.431 2110 9 2 1 2110 297823975 297821869 0.000000e+00 3827.0
2 TraesCS6A01G414100 chrUn 95.520 1049 26 2 2112 3140 315496148 315495101 0.000000e+00 1657.0
3 TraesCS6A01G414100 chrUn 79.436 1843 344 26 98 1930 62091362 62093179 0.000000e+00 1271.0
4 TraesCS6A01G414100 chrUn 76.635 1254 267 25 164 1402 62149025 62150267 0.000000e+00 669.0
5 TraesCS6A01G414100 chr6B 87.734 2462 237 42 39 2472 715968107 715965683 0.000000e+00 2813.0
6 TraesCS6A01G414100 chr6B 81.568 2257 348 47 128 2353 716226286 716224067 0.000000e+00 1801.0
7 TraesCS6A01G414100 chr6B 81.239 2292 342 59 128 2389 715900311 715898078 0.000000e+00 1770.0
8 TraesCS6A01G414100 chr6B 77.874 1157 225 24 166 1306 715860638 715859497 0.000000e+00 689.0
9 TraesCS6A01G414100 chr6D 79.825 1829 337 22 110 1930 469790147 469788343 0.000000e+00 1304.0
10 TraesCS6A01G414100 chr6D 77.243 1226 247 26 164 1371 469917772 469918983 0.000000e+00 689.0
11 TraesCS6A01G414100 chr6D 87.805 82 9 1 2730 2810 469941418 469941337 9.270000e-16 95.3
12 TraesCS6A01G414100 chr7D 91.111 45 2 1 3096 3140 28547537 28547579 3.380000e-05 60.2
13 TraesCS6A01G414100 chr7A 91.111 45 2 2 3097 3140 186148501 186148458 3.380000e-05 60.2


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 TraesCS6A01G414100 chr6A 614689018 614692157 3139 True 5799 5799 100.000 1 3140 1 chr6A.!!$R1 3139
1 TraesCS6A01G414100 chrUn 297821869 297823975 2106 True 3827 3827 99.431 1 2110 1 chrUn.!!$R1 2109
2 TraesCS6A01G414100 chrUn 315495101 315496148 1047 True 1657 1657 95.520 2112 3140 1 chrUn.!!$R2 1028
3 TraesCS6A01G414100 chrUn 62091362 62093179 1817 False 1271 1271 79.436 98 1930 1 chrUn.!!$F1 1832
4 TraesCS6A01G414100 chrUn 62149025 62150267 1242 False 669 669 76.635 164 1402 1 chrUn.!!$F2 1238
5 TraesCS6A01G414100 chr6B 715965683 715968107 2424 True 2813 2813 87.734 39 2472 1 chr6B.!!$R3 2433
6 TraesCS6A01G414100 chr6B 716224067 716226286 2219 True 1801 1801 81.568 128 2353 1 chr6B.!!$R4 2225
7 TraesCS6A01G414100 chr6B 715898078 715900311 2233 True 1770 1770 81.239 128 2389 1 chr6B.!!$R2 2261
8 TraesCS6A01G414100 chr6B 715859497 715860638 1141 True 689 689 77.874 166 1306 1 chr6B.!!$R1 1140
9 TraesCS6A01G414100 chr6D 469788343 469790147 1804 True 1304 1304 79.825 110 1930 1 chr6D.!!$R1 1820
10 TraesCS6A01G414100 chr6D 469917772 469918983 1211 False 689 689 77.243 164 1371 1 chr6D.!!$F1 1207

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
959 972 0.03582 AGTTCGTCGGCTCTCTCTCT 60.036 55.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 2369 1.347707 TGTCGCCTTGTCTCCTCAAAT 59.652 47.619 0.0 0.0 0.0 2.32 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
958 971 0.806241 AAGTTCGTCGGCTCTCTCTC 59.194 55.000 0.00 0.0 0.00 3.20
959 972 0.035820 AGTTCGTCGGCTCTCTCTCT 60.036 55.000 0.00 0.0 0.00 3.10
2214 2261 6.145696 ACCTTTCTCTTAATTTCGTTGACTCG 59.854 38.462 0.00 0.0 0.00 4.18
2219 2266 6.252869 TCTCTTAATTTCGTTGACTCGTATGC 59.747 38.462 0.00 0.0 0.00 3.14
2242 2289 5.126061 GCTCATGTTTCCTTCCATGTACAAT 59.874 40.000 0.00 0.0 39.53 2.71
2254 2309 6.154203 TCCATGTACAATCTCAAGCTAGAG 57.846 41.667 0.00 0.0 36.97 2.43
2298 2353 5.297776 CAGGAAGGGACTAATTATTGCACTG 59.702 44.000 0.00 0.0 38.49 3.66
2313 2369 0.904865 CACTGTCAGCTCCCCACCTA 60.905 60.000 0.00 0.0 0.00 3.08
2476 2532 1.296755 ACATGAGAGTTGCTGCTGCG 61.297 55.000 11.21 0.0 43.34 5.18
2479 2535 0.033366 TGAGAGTTGCTGCTGCGTTA 59.967 50.000 11.21 0.0 43.34 3.18
2480 2536 1.338105 TGAGAGTTGCTGCTGCGTTAT 60.338 47.619 11.21 0.0 43.34 1.89
2501 2557 8.285394 CGTTATTCCCTTTGATGATACATTCTG 58.715 37.037 0.00 0.0 0.00 3.02
2509 2565 3.118445 TGATGATACATTCTGTTCCCGCA 60.118 43.478 0.00 0.0 0.00 5.69
2593 2669 3.137360 ACTCCTTAATTGGCTCATCTCCC 59.863 47.826 0.00 0.0 0.00 4.30
2753 2829 3.975035 GTCGGTTCTCAAATTCAAACAGC 59.025 43.478 0.00 0.0 0.00 4.40
2771 2847 7.884354 TCAAACAGCATCTGGATATATTGCATA 59.116 33.333 8.61 0.0 35.51 3.14
2794 2870 9.978044 CATACTTCTCTGTTCTATGATTCATCA 57.022 33.333 1.55 0.0 41.70 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
871 881 6.093495 TGACAAAGTTCACTTCGATTGACTTT 59.907 34.615 13.40 13.40 34.61 2.66
958 971 3.988976 TCCTTCCTCATCAACTTGGAG 57.011 47.619 0.00 0.00 0.00 3.86
959 972 4.722526 TTTCCTTCCTCATCAACTTGGA 57.277 40.909 0.00 0.00 0.00 3.53
1260 1276 6.370442 CGAGGTTCACAATAGTTGATGGTAAA 59.630 38.462 0.00 0.00 0.00 2.01
1681 1706 0.798776 CGCAACAGCTGGAGGTTTAG 59.201 55.000 19.93 0.00 0.00 1.85
2186 2230 7.171678 AGTCAACGAAATTAAGAGAAAGGTCAG 59.828 37.037 0.00 0.00 0.00 3.51
2190 2234 6.145696 ACGAGTCAACGAAATTAAGAGAAAGG 59.854 38.462 0.00 0.00 37.03 3.11
2214 2261 4.641989 ACATGGAAGGAAACATGAGCATAC 59.358 41.667 11.17 0.00 45.55 2.39
2219 2266 6.600822 AGATTGTACATGGAAGGAAACATGAG 59.399 38.462 11.17 0.00 45.55 2.90
2242 2289 7.094248 GCATAGATGATCTTCTCTAGCTTGAGA 60.094 40.741 21.78 21.78 40.87 3.27
2298 2353 1.559682 TCAAATAGGTGGGGAGCTGAC 59.440 52.381 0.00 0.00 0.00 3.51
2313 2369 1.347707 TGTCGCCTTGTCTCCTCAAAT 59.652 47.619 0.00 0.00 0.00 2.32
2509 2565 2.028567 GCTAGCTAGAAATGCCGAGGAT 60.029 50.000 25.15 0.00 0.00 3.24
2753 2829 9.315525 CAGAGAAGTATGCAATATATCCAGATG 57.684 37.037 0.00 0.00 0.00 2.90
2771 2847 9.327628 CATTGATGAATCATAGAACAGAGAAGT 57.672 33.333 0.00 0.00 36.56 3.01


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

AutoCloner maintained by Alex Coulton.