Multiple sequence alignment - TraesCS4B01G147100

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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 TraesCS4B01G147100 chr4B 100.000 2960 0 0 1 2960 209296795 209293836 0 5467
1 TraesCS4B01G147100 chr7B 98.178 2963 51 2 1 2960 716881821 716884783 0 5169
2 TraesCS4B01G147100 chr7A 98.144 2963 50 4 1 2960 60276273 60273313 0 5162
3 TraesCS4B01G147100 chr7A 97.941 2963 56 4 1 2960 120844192 120847152 0 5129
4 TraesCS4B01G147100 chr7D 97.941 2962 55 2 1 2960 381976796 381979753 0 5127
5 TraesCS4B01G147100 chr1B 97.873 2962 59 3 1 2960 672557173 672560132 0 5118


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 TraesCS4B01G147100 chr4B 209293836 209296795 2959 True 5467 5467 100.000 1 2960 1 chr4B.!!$R1 2959
1 TraesCS4B01G147100 chr7B 716881821 716884783 2962 False 5169 5169 98.178 1 2960 1 chr7B.!!$F1 2959
2 TraesCS4B01G147100 chr7A 60273313 60276273 2960 True 5162 5162 98.144 1 2960 1 chr7A.!!$R1 2959
3 TraesCS4B01G147100 chr7A 120844192 120847152 2960 False 5129 5129 97.941 1 2960 1 chr7A.!!$F1 2959
4 TraesCS4B01G147100 chr7D 381976796 381979753 2957 False 5127 5127 97.941 1 2960 1 chr7D.!!$F1 2959
5 TraesCS4B01G147100 chr1B 672557173 672560132 2959 False 5118 5118 97.873 1 2960 1 chr1B.!!$F1 2959

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
442 443 1.125021 CACTCCGCAAATATCGATCGC 59.875 52.381 11.09 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2275 0.606401 TAGCCTGCTGCACCTGTTTC 60.606 55.0 0.0 0.0 44.83 2.78 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
30 31 6.078664 CCCTGGACTAGACCTATGTAGATTT 58.921 44.000 12.54 0.00 0.00 2.17
52 53 3.181479 TGGAATTATCTGTCGCTACGCTT 60.181 43.478 0.00 0.00 0.00 4.68
250 251 4.637534 CGGATGATTGATGGAAGAAACACT 59.362 41.667 0.00 0.00 0.00 3.55
329 330 4.400251 ACCGGAGATATTCGTGTTACTTCA 59.600 41.667 9.46 0.00 0.00 3.02
404 405 8.538409 AATTATGGACAACTTCAAATCTTTGC 57.462 30.769 0.00 0.00 38.05 3.68
442 443 1.125021 CACTCCGCAAATATCGATCGC 59.875 52.381 11.09 0.00 0.00 4.58
514 515 6.710744 GGAAATGGGTAGTCAGTATTGGTATG 59.289 42.308 0.00 0.00 0.00 2.39
548 549 6.014669 TCCCATGTTCCGATCTTTTCATTTTT 60.015 34.615 0.00 0.00 0.00 1.94
737 738 3.511934 GGAGAGGCAGAAGTGAAAGACTA 59.488 47.826 0.00 0.00 33.09 2.59
764 769 6.029346 ACCAATAAAGATCCAAAACTGCAG 57.971 37.500 13.48 13.48 0.00 4.41
891 896 5.733620 TCGCTCGGGGAAAAGTATTATAT 57.266 39.130 0.00 0.00 0.00 0.86
1024 1029 7.716799 ATGCAGGTTCTATTTTATTGTTCCA 57.283 32.000 0.00 0.00 0.00 3.53
1290 1296 9.868277 ATGAAGTTCGATGAGGATAATCTATTC 57.132 33.333 0.00 0.00 0.00 1.75
1385 1391 4.355549 TGCCTACCAAGTAGCTTACCTAA 58.644 43.478 0.00 0.00 35.06 2.69
1495 1501 7.309621 CCGTAGTTAGGGCAGCTAGATTTATAA 60.310 40.741 0.00 0.00 0.00 0.98
1944 1950 3.606687 AGGAGGTTACTTATGCAAACCG 58.393 45.455 10.78 0.00 45.93 4.44
1970 1976 5.246203 CGGGGGATATCTAGAATCACTTTCA 59.754 44.000 13.43 0.00 36.75 2.69
2427 2434 5.288232 TGAGCGTGATTTGTCAAAAAGTTTG 59.712 36.000 1.31 0.00 0.00 2.93
2602 2610 5.465390 CAGACTGAAATGTTTACTTCGGACA 59.535 40.000 0.00 0.00 33.08 4.02
2624 2632 7.201635 GGACAAAAGTTTCATTCAATTTGCTGT 60.202 33.333 0.00 0.00 32.49 4.40
2668 2677 7.781324 TTTTTCATAGCCAAGATCCTTTCTT 57.219 32.000 0.00 0.00 45.83 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.756434 CGATTTTGCTAGTCCTTGGGAAA 59.244 43.478 0.00 0.00 31.38 3.13
250 251 5.571285 AGCGAGAAGTATGGGATATGTCTA 58.429 41.667 0.00 0.00 0.00 2.59
329 330 3.462982 TCGTGTACAAACAAGTGCAGAT 58.537 40.909 0.00 0.00 37.36 2.90
404 405 2.697751 AGTGGATCATCCCTCTCGAAAG 59.302 50.000 0.00 0.00 35.03 2.62
514 515 4.873746 TCGGAACATGGGAATAGATCTC 57.126 45.455 0.00 0.00 0.00 2.75
578 579 6.575162 AACCAATCCATTTTCCGATATAGC 57.425 37.500 0.00 0.00 0.00 2.97
737 738 6.127619 GCAGTTTTGGATCTTTATTGGTAGCT 60.128 38.462 0.00 0.00 0.00 3.32
764 769 9.431887 TGGATACATAACTCTAAAAAGTGTGTC 57.568 33.333 0.00 0.00 46.17 3.67
891 896 9.815306 AGGATCAGAATAAGTACTAATGCTCTA 57.185 33.333 0.00 0.00 0.00 2.43
981 986 8.110908 ACCTGCATACTTTTATTTGTTACCCTA 58.889 33.333 0.00 0.00 0.00 3.53
1024 1029 9.961264 ATTCTCAATGCTATCATCATATGTCTT 57.039 29.630 1.90 0.00 31.27 3.01
1074 1079 8.438676 AATCGTTCCAGAACTCCTTAATAATG 57.561 34.615 8.77 0.00 39.08 1.90
1194 1199 6.920758 CGGAAAACACACCATTTTGATTCTTA 59.079 34.615 0.00 0.00 29.44 2.10
1385 1391 7.599245 GCGTATAGATACCAAACATCTTAAGCT 59.401 37.037 0.00 0.00 34.58 3.74
1478 1484 7.751768 AGTTGATTTATAAATCTAGCTGCCC 57.248 36.000 29.37 14.78 43.97 5.36
1495 1501 8.827177 TCTCGTACAGTTGAATTAAGTTGATT 57.173 30.769 0.00 0.00 0.00 2.57
1825 1831 5.643421 AGATTGAGTTTGATAGGGAGCAT 57.357 39.130 0.00 0.00 0.00 3.79
1944 1950 4.345854 AGTGATTCTAGATATCCCCCGTC 58.654 47.826 0.00 0.00 0.00 4.79
1970 1976 8.914011 GGTTTAAGTCATGGGAAATTAATAGCT 58.086 33.333 0.00 0.00 0.00 3.32
1979 1985 5.701224 AGAAGTGGTTTAAGTCATGGGAAA 58.299 37.500 0.00 0.00 0.00 3.13
2268 2275 0.606401 TAGCCTGCTGCACCTGTTTC 60.606 55.000 0.00 0.00 44.83 2.78
2427 2434 4.271291 GGATGATCGGCAGAAAAGAGTAAC 59.729 45.833 0.00 0.00 0.00 2.50
2519 2527 8.530269 GTTCGAGAACTTTGGATACTTAAAGA 57.470 34.615 8.58 0.00 37.35 2.52
2602 2610 6.093771 TGCACAGCAAATTGAATGAAACTTTT 59.906 30.769 0.00 0.00 34.76 2.27
2668 2677 9.607333 ATGATAATTACTCACTCCTTCATCCTA 57.393 33.333 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.