Multiple sequence alignment - TraesCS6A01G012300

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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 TraesCS6A01G012300 chr6A 100.000 4179 0 0 1 4179 5670616 5674794 0.000000e+00 7718.0
1 TraesCS6A01G012300 chr6A 98.708 4181 39 6 1 4179 5773255 5777422 0.000000e+00 7408.0
2 TraesCS6A01G012300 chr6A 97.052 2985 43 16 326 3297 5602244 5605196 0.000000e+00 4983.0
3 TraesCS6A01G012300 chr6A 98.414 883 14 0 3297 4179 5783570 5784452 0.000000e+00 1554.0
4 TraesCS6A01G012300 chr6A 98.817 338 2 2 1 338 5771162 5771497 5.980000e-168 601.0
5 TraesCS6A01G012300 chr6A 97.929 338 5 2 1 338 5769068 5769403 6.020000e-163 584.0
6 TraesCS6A01G012300 chr6A 93.949 314 18 1 1854 2167 129352667 129352979 1.360000e-129 473.0
7 TraesCS6A01G012300 chr6A 93.333 45 3 0 841 885 29651294 29651250 2.700000e-07 67.6
8 TraesCS6A01G012300 chr1B 98.754 883 11 0 3297 4179 380611200 380610318 0.000000e+00 1570.0
9 TraesCS6A01G012300 chr1B 98.414 883 14 0 3297 4179 553256348 553255466 0.000000e+00 1554.0
10 TraesCS6A01G012300 chr6B 98.641 883 12 0 3297 4179 62802661 62803543 0.000000e+00 1565.0
11 TraesCS6A01G012300 chr6B 91.558 995 82 2 2304 3297 11538723 11539716 0.000000e+00 1371.0
12 TraesCS6A01G012300 chr6B 88.282 1135 65 30 617 1699 11537523 11538641 0.000000e+00 1297.0
13 TraesCS6A01G012300 chr5B 98.526 882 13 0 3298 4179 372139207 372138326 0.000000e+00 1557.0
14 TraesCS6A01G012300 chr3A 98.526 882 13 0 3298 4179 82364125 82365006 0.000000e+00 1557.0
15 TraesCS6A01G012300 chr3A 93.519 324 20 1 1851 2174 9301039 9301361 8.130000e-132 481.0
16 TraesCS6A01G012300 chr2A 98.526 882 13 0 3298 4179 392698845 392699726 0.000000e+00 1557.0
17 TraesCS6A01G012300 chr7B 98.414 883 14 0 3297 4179 437449522 437448640 0.000000e+00 1554.0
18 TraesCS6A01G012300 chr6D 90.957 1139 90 12 2168 3297 6275115 6276249 0.000000e+00 1520.0
19 TraesCS6A01G012300 chr6D 90.165 1149 67 11 617 1736 6273943 6275074 0.000000e+00 1454.0
20 TraesCS6A01G012300 chr4A 94.062 320 19 0 1851 2170 613414526 613414207 1.750000e-133 486.0
21 TraesCS6A01G012300 chr5A 93.808 323 19 1 1847 2169 441172398 441172719 6.280000e-133 484.0
22 TraesCS6A01G012300 chr5A 93.168 322 21 1 1846 2167 228894947 228895267 4.890000e-129 472.0
23 TraesCS6A01G012300 chr7A 93.125 320 22 0 1850 2169 545042299 545041980 1.760000e-128 470.0
24 TraesCS6A01G012300 chr2D 93.103 319 22 0 1852 2170 36275112 36275430 6.330000e-128 468.0


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 TraesCS6A01G012300 chr6A 5670616 5674794 4178 False 7718.000000 7718 100.000000 1 4179 1 chr6A.!!$F2 4178
1 TraesCS6A01G012300 chr6A 5602244 5605196 2952 False 4983.000000 4983 97.052000 326 3297 1 chr6A.!!$F1 2971
2 TraesCS6A01G012300 chr6A 5769068 5777422 8354 False 2864.333333 7408 98.484667 1 4179 3 chr6A.!!$F5 4178
3 TraesCS6A01G012300 chr6A 5783570 5784452 882 False 1554.000000 1554 98.414000 3297 4179 1 chr6A.!!$F3 882
4 TraesCS6A01G012300 chr1B 380610318 380611200 882 True 1570.000000 1570 98.754000 3297 4179 1 chr1B.!!$R1 882
5 TraesCS6A01G012300 chr1B 553255466 553256348 882 True 1554.000000 1554 98.414000 3297 4179 1 chr1B.!!$R2 882
6 TraesCS6A01G012300 chr6B 62802661 62803543 882 False 1565.000000 1565 98.641000 3297 4179 1 chr6B.!!$F1 882
7 TraesCS6A01G012300 chr6B 11537523 11539716 2193 False 1334.000000 1371 89.920000 617 3297 2 chr6B.!!$F2 2680
8 TraesCS6A01G012300 chr5B 372138326 372139207 881 True 1557.000000 1557 98.526000 3298 4179 1 chr5B.!!$R1 881
9 TraesCS6A01G012300 chr3A 82364125 82365006 881 False 1557.000000 1557 98.526000 3298 4179 1 chr3A.!!$F2 881
10 TraesCS6A01G012300 chr2A 392698845 392699726 881 False 1557.000000 1557 98.526000 3298 4179 1 chr2A.!!$F1 881
11 TraesCS6A01G012300 chr7B 437448640 437449522 882 True 1554.000000 1554 98.414000 3297 4179 1 chr7B.!!$R1 882
12 TraesCS6A01G012300 chr6D 6273943 6276249 2306 False 1487.000000 1520 90.561000 617 3297 2 chr6D.!!$F1 2680

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
521 4710 5.047164 TGGTGTGTTTGGTAGATACGTACAT 60.047 40.000 0.0 0.0 0.00 2.29 F
1499 5764 0.909610 TTCCTGTTCTGGATCGGGCT 60.910 55.000 0.0 0.0 35.83 5.19 F
2460 6735 2.746277 GCCAAGATCAACGGCCGT 60.746 61.111 28.7 28.7 40.07 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 6229 0.326264 GGAAGGTGTGCTCAGGTGAT 59.674 55.0 0.00 0.0 0.00 3.06 R
2513 6788 0.678048 GGCGACCTTTTGCATCTCCT 60.678 55.0 0.00 0.0 33.08 3.69 R
3807 8090 1.635817 ATGCATTACCGAGTGGGCCT 61.636 55.0 4.53 0.0 40.62 5.19 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
458 4647 5.119588 GCATGCATACATAATGAAATGTGGC 59.880 40.000 14.21 4.62 40.29 5.01
521 4710 5.047164 TGGTGTGTTTGGTAGATACGTACAT 60.047 40.000 0.00 0.00 0.00 2.29
1499 5764 0.909610 TTCCTGTTCTGGATCGGGCT 60.910 55.000 0.00 0.00 35.83 5.19
1687 5952 3.376546 CCTTCCTGCTTTCAACTATGAGC 59.623 47.826 0.00 0.00 36.78 4.26
1864 6139 8.602472 ATTCAATAACATTAAGGGCCTGTTTA 57.398 30.769 6.92 0.75 35.00 2.01
1954 6229 8.282455 TGTTTGTTTGTCACCTGACTTATAAA 57.718 30.769 6.97 3.55 44.99 1.40
2132 6407 6.525280 GTCACTTTTTGCACTTTTCGACTTAA 59.475 34.615 0.00 0.00 0.00 1.85
2460 6735 2.746277 GCCAAGATCAACGGCCGT 60.746 61.111 28.70 28.70 40.07 5.68
4007 8290 1.139058 AGGGTTTGATCGAATCCTCGG 59.861 52.381 20.42 0.00 45.49 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
458 4647 3.947868 TCCTTGCTTCCATTTCTCTCTG 58.052 45.455 0.00 0.00 0.00 3.35
1499 5764 0.399091 AGAGAAGATGGCGGGGATCA 60.399 55.000 0.00 0.00 0.00 2.92
1556 5821 0.824109 CTTCTGATACAGGCCCGTCA 59.176 55.000 0.00 0.00 31.51 4.35
1687 5952 4.125703 GACCATGCTCTAACCTTGATCTG 58.874 47.826 0.00 0.00 0.00 2.90
1954 6229 0.326264 GGAAGGTGTGCTCAGGTGAT 59.674 55.000 0.00 0.00 0.00 3.06
2071 6346 7.793948 AACAGACCTAACTTATAAGTCACCT 57.206 36.000 18.28 5.74 38.57 4.00
2132 6407 7.176589 TGGTTTCAAATAAGTCACCAACTTT 57.823 32.000 0.00 0.00 46.26 2.66
2513 6788 0.678048 GGCGACCTTTTGCATCTCCT 60.678 55.000 0.00 0.00 33.08 3.69
3706 7989 5.105310 CCTGTAGTGCACCTTTATAGTCACT 60.105 44.000 14.63 0.00 38.24 3.41
3807 8090 1.635817 ATGCATTACCGAGTGGGCCT 61.636 55.000 4.53 0.00 40.62 5.19
4007 8290 2.466867 ATCGGTTGAACCACGATGC 58.533 52.632 15.58 0.00 44.66 3.91


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

AutoCloner maintained by Alex Coulton.