Multiple sequence alignment - TraesCS1B01G385500

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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 TraesCS1B01G385500 chr1B 100.000 2273 0 0 1 2273 619184699 619186971 0 4198
1 TraesCS1B01G385500 chr2B 98.593 2274 31 1 1 2273 449208696 449210969 0 4021
2 TraesCS1B01G385500 chr2B 98.548 2273 33 0 1 2273 234530528 234532800 0 4015
3 TraesCS1B01G385500 chr7A 98.504 2273 34 0 1 2273 60220133 60222405 0 4010
4 TraesCS1B01G385500 chr3A 98.504 2273 34 0 1 2273 495091908 495094180 0 4010
5 TraesCS1B01G385500 chr3B 98.461 2274 34 1 1 2273 6000134 6002407 0 4004
6 TraesCS1B01G385500 chr4B 98.196 2273 41 0 1 2273 495577615 495579887 0 3971
7 TraesCS1B01G385500 chr6B 97.011 2275 65 2 1 2273 625612107 625614380 0 3821


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 TraesCS1B01G385500 chr1B 619184699 619186971 2272 False 4198 4198 100.000 1 2273 1 chr1B.!!$F1 2272
1 TraesCS1B01G385500 chr2B 449208696 449210969 2273 False 4021 4021 98.593 1 2273 1 chr2B.!!$F2 2272
2 TraesCS1B01G385500 chr2B 234530528 234532800 2272 False 4015 4015 98.548 1 2273 1 chr2B.!!$F1 2272
3 TraesCS1B01G385500 chr7A 60220133 60222405 2272 False 4010 4010 98.504 1 2273 1 chr7A.!!$F1 2272
4 TraesCS1B01G385500 chr3A 495091908 495094180 2272 False 4010 4010 98.504 1 2273 1 chr3A.!!$F1 2272
5 TraesCS1B01G385500 chr3B 6000134 6002407 2273 False 4004 4004 98.461 1 2273 1 chr3B.!!$F1 2272
6 TraesCS1B01G385500 chr4B 495577615 495579887 2272 False 3971 3971 98.196 1 2273 1 chr4B.!!$F1 2272
7 TraesCS1B01G385500 chr6B 625612107 625614380 2273 False 3821 3821 97.011 1 2273 1 chr6B.!!$F1 2272

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
555 556 1.272203 TGAAGAACGGAGAGGAGCTCT 60.272 52.381 14.64 0.0 44.28 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 1818 2.169769 CCCCATTCTTGCAATTGCTCAT 59.83 45.455 29.37 13.76 42.66 2.9 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
25 26 5.906113 TTTGGAGAGTTTGCTTTTACACA 57.094 34.783 0.00 0.00 0.00 3.72
197 198 6.810911 TGAATTTTTCGAATCTTGTTGGGAA 58.189 32.000 0.00 0.00 0.00 3.97
339 340 3.083349 CATCCCGGGAGCAGACCA 61.083 66.667 30.42 2.28 0.00 4.02
354 355 2.365105 CCACTCCCCCGGAAGCTA 60.365 66.667 0.73 0.00 0.00 3.32
555 556 1.272203 TGAAGAACGGAGAGGAGCTCT 60.272 52.381 14.64 0.00 44.28 4.09
570 571 5.022787 AGGAGCTCTGTGAAGAAGACTATT 58.977 41.667 14.64 0.00 0.00 1.73
660 661 2.943033 CTGAACAGACTCCAAAACGGTT 59.057 45.455 0.00 0.00 35.57 4.44
967 971 4.916041 TCTCTGACATTCCATGTTTCCT 57.084 40.909 0.00 0.00 45.03 3.36
1133 1137 5.047660 TGGTATTTTCCGTTTCTTTGGATGG 60.048 40.000 0.00 0.00 33.42 3.51
1149 1153 6.467490 TTGGATGGTATGATGGGTCAATAT 57.533 37.500 0.00 0.00 38.01 1.28
1347 1351 8.519799 TCTCTTCTTTCTTTTCTTTTTGCCTA 57.480 30.769 0.00 0.00 0.00 3.93
1496 1500 7.339466 GCATATGGTACCCAAATAAGAATAGGG 59.661 40.741 10.07 0.00 45.20 3.53
1643 1647 0.951558 GAATGTGCACGGTCTGGTTT 59.048 50.000 13.13 0.00 0.00 3.27
1814 1818 4.345257 CCTAGCAGCTAAAAGAGGGTATCA 59.655 45.833 3.09 0.00 0.00 2.15
1955 1959 4.402474 AGCACATAAGGGGTTATTTCTTGC 59.598 41.667 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.944349 GTTCGATAGGGTCTTCGTCTCT 59.056 50.000 0.00 0.00 36.74 3.10
123 124 8.568617 AGTATGAAGAAAAGACCTATATGGGT 57.431 34.615 11.08 11.08 43.07 4.51
339 340 1.766461 CCATAGCTTCCGGGGGAGT 60.766 63.158 0.00 0.00 31.21 3.85
354 355 1.078848 GCCGCTCTTGACTGACCAT 60.079 57.895 0.00 0.00 0.00 3.55
407 408 1.349357 GGAGGGTTCTGTTCTGCTTCT 59.651 52.381 0.00 0.00 0.00 2.85
472 473 1.530323 GCGGGCCTTTTGTAGAGAAA 58.470 50.000 0.84 0.00 0.00 2.52
555 556 4.350368 TGGTGCAATAGTCTTCTTCACA 57.650 40.909 0.00 0.00 0.00 3.58
660 661 1.347707 AGAAGTTTGAGATCGTGCCCA 59.652 47.619 0.00 0.00 0.00 5.36
1006 1010 6.661304 TCCCCGAATACCTAAAATAGAGAC 57.339 41.667 0.00 0.00 0.00 3.36
1133 1137 7.715657 TGAAGCAAAATATTGACCCATCATAC 58.284 34.615 0.00 0.00 38.94 2.39
1149 1153 6.272318 CACTGTTGGAACTAATGAAGCAAAA 58.728 36.000 0.00 0.00 0.00 2.44
1210 1214 5.185635 TCCCTCGGACTCGAAAAGTAATAAA 59.814 40.000 0.00 0.00 45.47 1.40
1347 1351 5.724328 TCGAAGCTATTTGATGTCTGACTT 58.276 37.500 9.51 2.27 0.00 3.01
1496 1500 6.341316 TCAGACCTGCTTTTGACATATCTAC 58.659 40.000 0.00 0.00 0.00 2.59
1643 1647 8.089625 TCAGATTCTAAGTTCATTCCATACCA 57.910 34.615 0.00 0.00 0.00 3.25
1814 1818 2.169769 CCCCATTCTTGCAATTGCTCAT 59.830 45.455 29.37 13.76 42.66 2.90
1955 1959 8.251750 TCAAGTTATTAATGACTGGACGAAAG 57.748 34.615 13.14 0.00 0.00 2.62
2156 2160 5.163353 TGCAGGATTATACACGAAAGATCCA 60.163 40.000 0.00 0.00 36.39 3.41


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

AutoCloner maintained by Alex Coulton.