Multiple sequence alignment - TraesCS5A01G436500

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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 TraesCS5A01G436500 chr5A 100.000 2216 0 0 1 2216 619266186 619263971 0.000000e+00 4093
1 TraesCS5A01G436500 chr5A 86.404 559 66 9 1663 2216 54800016 54800569 8.750000e-169 603
2 TraesCS5A01G436500 chrUn 97.989 1691 29 5 2 1690 93409817 93411504 0.000000e+00 2929
3 TraesCS5A01G436500 chrUn 97.993 1495 26 4 2 1494 216518788 216520280 0.000000e+00 2591
4 TraesCS5A01G436500 chr2D 97.753 1691 34 4 2 1690 272794079 272795767 0.000000e+00 2909
5 TraesCS5A01G436500 chr5D 97.751 1690 35 3 2 1690 503218032 503216345 0.000000e+00 2907
6 TraesCS5A01G436500 chr3B 97.457 1691 38 5 2 1690 201526838 201525151 0.000000e+00 2880
7 TraesCS5A01G436500 chr6D 97.456 1690 38 4 2 1690 168251352 168249667 0.000000e+00 2878
8 TraesCS5A01G436500 chr6D 97.926 1495 27 4 2 1494 168254740 168253248 0.000000e+00 2586
9 TraesCS5A01G436500 chr3A 96.984 1691 48 3 2 1690 672910193 672911882 0.000000e+00 2837
10 TraesCS5A01G436500 chr6A 96.517 1694 51 5 2 1690 260116466 260118156 0.000000e+00 2795
11 TraesCS5A01G436500 chr7A 98.859 526 6 0 1691 2216 421908818 421908293 0.000000e+00 939
12 TraesCS5A01G436500 chr7A 98.669 526 7 0 1691 2216 155279064 155278539 0.000000e+00 933
13 TraesCS5A01G436500 chr7A 98.669 526 7 0 1691 2216 191675195 191675720 0.000000e+00 933
14 TraesCS5A01G436500 chr7A 98.669 526 7 0 1691 2216 258787700 258788225 0.000000e+00 933
15 TraesCS5A01G436500 chr7A 98.669 526 7 0 1691 2216 527619027 527619552 0.000000e+00 933
16 TraesCS5A01G436500 chr7A 98.299 529 9 0 1688 2216 12851480 12850952 0.000000e+00 928
17 TraesCS5A01G436500 chr4A 98.669 526 7 0 1691 2216 395060761 395061286 0.000000e+00 933
18 TraesCS5A01G436500 chr2A 98.479 526 8 0 1691 2216 455754425 455754950 0.000000e+00 928
19 TraesCS5A01G436500 chr2A 94.709 567 22 8 1657 2216 672792159 672792724 0.000000e+00 874
20 TraesCS5A01G436500 chr4B 94.937 553 25 3 1664 2216 597755107 597754558 0.000000e+00 863
21 TraesCS5A01G436500 chr7D 90.647 556 49 3 1661 2216 486149361 486149913 0.000000e+00 736
22 TraesCS5A01G436500 chr2B 96.471 85 3 0 1597 1681 86511354 86511438 8.250000e-30 141


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 TraesCS5A01G436500 chr5A 619263971 619266186 2215 True 4093 4093 100.000 1 2216 1 chr5A.!!$R1 2215
1 TraesCS5A01G436500 chr5A 54800016 54800569 553 False 603 603 86.404 1663 2216 1 chr5A.!!$F1 553
2 TraesCS5A01G436500 chrUn 93409817 93411504 1687 False 2929 2929 97.989 2 1690 1 chrUn.!!$F1 1688
3 TraesCS5A01G436500 chrUn 216518788 216520280 1492 False 2591 2591 97.993 2 1494 1 chrUn.!!$F2 1492
4 TraesCS5A01G436500 chr2D 272794079 272795767 1688 False 2909 2909 97.753 2 1690 1 chr2D.!!$F1 1688
5 TraesCS5A01G436500 chr5D 503216345 503218032 1687 True 2907 2907 97.751 2 1690 1 chr5D.!!$R1 1688
6 TraesCS5A01G436500 chr3B 201525151 201526838 1687 True 2880 2880 97.457 2 1690 1 chr3B.!!$R1 1688
7 TraesCS5A01G436500 chr6D 168249667 168254740 5073 True 2732 2878 97.691 2 1690 2 chr6D.!!$R1 1688
8 TraesCS5A01G436500 chr3A 672910193 672911882 1689 False 2837 2837 96.984 2 1690 1 chr3A.!!$F1 1688
9 TraesCS5A01G436500 chr6A 260116466 260118156 1690 False 2795 2795 96.517 2 1690 1 chr6A.!!$F1 1688
10 TraesCS5A01G436500 chr7A 421908293 421908818 525 True 939 939 98.859 1691 2216 1 chr7A.!!$R3 525
11 TraesCS5A01G436500 chr7A 155278539 155279064 525 True 933 933 98.669 1691 2216 1 chr7A.!!$R2 525
12 TraesCS5A01G436500 chr7A 191675195 191675720 525 False 933 933 98.669 1691 2216 1 chr7A.!!$F1 525
13 TraesCS5A01G436500 chr7A 258787700 258788225 525 False 933 933 98.669 1691 2216 1 chr7A.!!$F2 525
14 TraesCS5A01G436500 chr7A 527619027 527619552 525 False 933 933 98.669 1691 2216 1 chr7A.!!$F3 525
15 TraesCS5A01G436500 chr7A 12850952 12851480 528 True 928 928 98.299 1688 2216 1 chr7A.!!$R1 528
16 TraesCS5A01G436500 chr4A 395060761 395061286 525 False 933 933 98.669 1691 2216 1 chr4A.!!$F1 525
17 TraesCS5A01G436500 chr2A 455754425 455754950 525 False 928 928 98.479 1691 2216 1 chr2A.!!$F1 525
18 TraesCS5A01G436500 chr2A 672792159 672792724 565 False 874 874 94.709 1657 2216 1 chr2A.!!$F2 559
19 TraesCS5A01G436500 chr4B 597754558 597755107 549 True 863 863 94.937 1664 2216 1 chr4B.!!$R1 552
20 TraesCS5A01G436500 chr7D 486149361 486149913 552 False 736 736 90.647 1661 2216 1 chr7D.!!$F1 555

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
420 421 4.458989 CCCAAAACTGCTTAGCAATAGTCA 59.541 41.667 8.68 0.0 38.41 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2140 5536 0.671251 GATTCGTGCCAACCCAACAA 59.329 50.0 0.0 0.0 0.0 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
293 294 5.147330 ACATAGAAATCACACGTGGAAGA 57.853 39.130 21.57 14.78 0.00 2.87
415 416 5.264395 AGTATCCCAAAACTGCTTAGCAAT 58.736 37.500 8.68 0.00 38.41 3.56
420 421 4.458989 CCCAAAACTGCTTAGCAATAGTCA 59.541 41.667 8.68 0.00 38.41 3.41
900 905 5.934043 CGAGATATTGGACATAGAATGCCAA 59.066 40.000 14.05 14.05 44.45 4.52
975 980 6.690098 CGAATCCTTTTGTAGCTCATCATTTG 59.310 38.462 0.00 0.00 0.00 2.32
1028 1033 9.674068 GAAGGAGGAGAAAGAAACAATAGTAAT 57.326 33.333 0.00 0.00 0.00 1.89
1037 1042 6.134535 AGAAACAATAGTAATGTGGTCCCA 57.865 37.500 0.00 0.00 0.00 4.37
1088 1093 4.996758 TGGCCATACAATCGTGATTCATAG 59.003 41.667 0.00 0.00 0.00 2.23
1153 1158 1.548269 GTCGCAAATTGGGGGAATTCA 59.452 47.619 10.15 0.00 32.76 2.57
1290 4681 2.435437 TGTAGGCGGGGAATAACCTTAC 59.565 50.000 0.00 0.00 38.98 2.34
1362 4753 3.876309 AAAGTGGGCTAAGGAAACTCA 57.124 42.857 0.00 0.00 42.68 3.41
1436 4827 4.393680 GCACAAAAACGTATCCCTATGTCA 59.606 41.667 0.00 0.00 0.00 3.58
1505 4896 8.743085 ACTACGAGGAAACTGTTATGATACTA 57.257 34.615 0.00 0.00 44.43 1.82
1509 4900 8.308931 ACGAGGAAACTGTTATGATACTAAACA 58.691 33.333 0.00 0.00 44.43 2.83
1522 4913 7.315066 TGATACTAAACATCATGCCCTATCA 57.685 36.000 0.00 0.00 0.00 2.15
1545 4936 7.000472 TCAAGCATCTTATCCCATCTTAAAGG 59.000 38.462 0.00 0.00 0.00 3.11
2051 5447 2.040813 ACCATGAGATTGTGCAACTCCT 59.959 45.455 0.00 0.00 38.04 3.69
2085 5481 2.445682 TACTTTGGGTGTGCCAAACT 57.554 45.000 0.00 0.00 34.15 2.66
2109 5505 2.006888 CAACGTAACTGGGTGGCTATG 58.993 52.381 0.00 0.00 0.00 2.23
2140 5536 4.771054 ACTACAGGTATCTCCGAAAGTGTT 59.229 41.667 0.00 0.00 41.99 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.759059 TCCATCATCTGGCTTATGTTCTTT 58.241 37.500 0.00 0.00 45.52 2.52
293 294 1.141858 GCTCTAGCTAATTGCCCACCT 59.858 52.381 0.00 0.00 44.23 4.00
324 325 5.392380 CCTCTTTTGCAATGAGTTTCGCTAT 60.392 40.000 21.02 0.00 32.43 2.97
415 416 5.512404 CCAACATTACCCACTTGTCTGACTA 60.512 44.000 9.51 0.09 0.00 2.59
420 421 2.225017 CCCCAACATTACCCACTTGTCT 60.225 50.000 0.00 0.00 0.00 3.41
454 455 1.807814 AGATCCGGCTCTACCCAAAT 58.192 50.000 5.89 0.00 33.26 2.32
949 954 4.832248 TGATGAGCTACAAAAGGATTCGT 58.168 39.130 0.00 0.00 0.00 3.85
975 980 5.705609 TGACCTTTTCTATCTTTGCCAAC 57.294 39.130 0.00 0.00 0.00 3.77
1028 1033 1.626356 GCTAGATGCCTGGGACCACA 61.626 60.000 0.00 0.00 35.15 4.17
1037 1042 2.370189 GTGGGTAGAATGCTAGATGCCT 59.630 50.000 0.00 0.00 42.00 4.75
1088 1093 9.841295 TGTAAATAGGTATATGTTCCTTTCCAC 57.159 33.333 0.00 0.00 35.51 4.02
1129 1134 0.923358 TCCCCCAATTTGCGACCTAT 59.077 50.000 0.00 0.00 0.00 2.57
1269 4660 1.587066 AAGGTTATTCCCCGCCTACA 58.413 50.000 0.00 0.00 36.75 2.74
1436 4827 6.272822 AGAACTCTTTGTGCTTTGAAAACT 57.727 33.333 0.00 0.00 27.44 2.66
1505 4896 3.634504 TGCTTGATAGGGCATGATGTTT 58.365 40.909 0.00 0.00 33.23 2.83
1522 4913 6.774656 CACCTTTAAGATGGGATAAGATGCTT 59.225 38.462 0.00 0.00 0.00 3.91
2051 5447 4.345837 CCCAAAGTATTCCTACGGTATCCA 59.654 45.833 0.00 0.00 32.82 3.41
2085 5481 1.956297 CCACCCAGTTACGTTGTGAA 58.044 50.000 0.00 0.00 0.00 3.18
2109 5505 4.275443 CGGAGATACCTGTAGTGTACCTTC 59.725 50.000 0.00 0.00 36.31 3.46
2140 5536 0.671251 GATTCGTGCCAACCCAACAA 59.329 50.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.