Multiple sequence alignment - TraesCS2B01G312800

Loading Multiple Alignment...

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 TraesCS2B01G312800 chr2B 100.000 2348 0 0 1 2348 448250688 448253035 0.000000e+00 4337
1 TraesCS2B01G312800 chr2A 95.138 2386 64 23 1 2348 510803644 510806015 0.000000e+00 3716
2 TraesCS2B01G312800 chr2D 95.086 2381 67 19 1 2348 376813653 376816016 0.000000e+00 3703
3 TraesCS2B01G312800 chr4B 97.547 2161 39 7 200 2348 640325454 640327612 0.000000e+00 3685
4 TraesCS2B01G312800 chr4B 97.561 205 4 1 1 205 640324534 640324737 1.340000e-92 350
5 TraesCS2B01G312800 chr4B 96.585 205 6 1 1 205 640329585 640329382 2.890000e-89 339
6 TraesCS2B01G312800 chr4B 97.674 43 1 0 200 242 640328690 640328648 9.000000e-10 75


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 TraesCS2B01G312800 chr2B 448250688 448253035 2347 False 4337.0 4337 100.0000 1 2348 1 chr2B.!!$F1 2347
1 TraesCS2B01G312800 chr2A 510803644 510806015 2371 False 3716.0 3716 95.1380 1 2348 1 chr2A.!!$F1 2347
2 TraesCS2B01G312800 chr2D 376813653 376816016 2363 False 3703.0 3703 95.0860 1 2348 1 chr2D.!!$F1 2347
3 TraesCS2B01G312800 chr4B 640324534 640327612 3078 False 2017.5 3685 97.5540 1 2348 2 chr4B.!!$F1 2347
4 TraesCS2B01G312800 chr4B 640328648 640329585 937 True 207.0 339 97.1295 1 242 2 chr4B.!!$R1 241

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
453 1211 3.961408 CTGTAACTACATACCCAGCCTCT 59.039 47.826 0.0 0.0 35.36 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2879 0.251916 ATTAGGTTGCTGGCGTGCTA 59.748 50.0 4.08 0.0 0.0 3.49 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
27 28 4.641541 TGCTAGCAGTATGATGTGCATTTT 59.358 37.500 14.93 0.00 39.50 1.82
141 147 6.058183 GCAATTAGGACAGGTATTGATGAGT 58.942 40.000 0.00 0.00 31.29 3.41
176 182 9.398538 TCAACTACACACCCAATAATAATAACC 57.601 33.333 0.00 0.00 0.00 2.85
399 1147 7.414266 AGCTTTCATTAGGGTAAAGAGGAAAT 58.586 34.615 0.00 0.00 33.05 2.17
453 1211 3.961408 CTGTAACTACATACCCAGCCTCT 59.039 47.826 0.00 0.00 35.36 3.69
1233 1999 0.616395 TCTACGTCATGCTCCCCCAA 60.616 55.000 0.00 0.00 0.00 4.12
1417 2183 6.481434 AGCGTTTATATGAAGTCCTAGGTT 57.519 37.500 9.08 0.00 0.00 3.50
1584 2352 4.210746 GTGTTCTTCTTCGGTGGTTCTAAC 59.789 45.833 0.00 0.00 0.00 2.34
1610 2378 5.128991 GGAGTAGTTTGTTAGGCATAGGACT 59.871 44.000 0.00 0.00 35.57 3.85
1807 2586 4.096984 ACAAAGTGGAGAAAGTGCAAGAAG 59.903 41.667 0.00 0.00 0.00 2.85
1808 2587 3.845781 AGTGGAGAAAGTGCAAGAAGA 57.154 42.857 0.00 0.00 0.00 2.87
1809 2588 4.156455 AGTGGAGAAAGTGCAAGAAGAA 57.844 40.909 0.00 0.00 0.00 2.52
2085 2865 9.458727 CTTGCCATTATACTTCCATCTGAATAT 57.541 33.333 0.00 0.00 31.06 1.28
2088 2868 9.890629 GCCATTATACTTCCATCTGAATATGTA 57.109 33.333 0.00 0.00 31.06 2.29
2097 2877 9.112725 CTTCCATCTGAATATGTACATTGTGAA 57.887 33.333 14.77 8.76 31.06 3.18
2099 2879 8.267183 TCCATCTGAATATGTACATTGTGAAGT 58.733 33.333 14.77 0.00 0.00 3.01
2250 3031 4.942761 ACTTGTTGGCTTGAATCACATT 57.057 36.364 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.177394 TTATTTGGCACAGCGTCTCA 57.823 45.000 0.00 0.00 42.39 3.27
113 116 6.061022 TCAATACCTGTCCTAATTGCTTCA 57.939 37.500 0.00 0.00 30.99 3.02
141 147 5.010933 TGGGTGTGTAGTTGAAAGTTGAAA 58.989 37.500 0.00 0.00 0.00 2.69
176 182 9.684448 AGATAGACACATCTTGTAATTATGACG 57.316 33.333 0.00 0.00 39.17 4.35
399 1147 6.974932 TTGACATGTTTTGCTTTGCTTTTA 57.025 29.167 0.00 0.00 0.00 1.52
942 1708 3.885724 TGAACTGTCGGATTAGCATCA 57.114 42.857 0.00 0.00 0.00 3.07
943 1709 3.000322 CGTTGAACTGTCGGATTAGCATC 60.000 47.826 0.00 0.00 0.00 3.91
1417 2183 6.745116 TGATCAAACGAAAGAGAACTACTGA 58.255 36.000 0.00 0.00 0.00 3.41
1584 2352 5.128827 TCCTATGCCTAACAAACTACTCCAG 59.871 44.000 0.00 0.00 0.00 3.86
1610 2378 9.357161 AGTAAGAAACAGAAGAGAAGAAGTCTA 57.643 33.333 0.00 0.00 36.41 2.59
1707 2475 5.296780 TCATGGTGTGAAGTCTTTTCTTGTC 59.703 40.000 0.00 0.00 32.78 3.18
1708 2476 5.192927 TCATGGTGTGAAGTCTTTTCTTGT 58.807 37.500 0.00 0.00 32.78 3.16
1709 2477 5.756195 TCATGGTGTGAAGTCTTTTCTTG 57.244 39.130 0.00 0.00 32.78 3.02
1710 2478 5.652014 TGTTCATGGTGTGAAGTCTTTTCTT 59.348 36.000 0.00 0.00 46.99 2.52
1714 2482 4.526970 AGTGTTCATGGTGTGAAGTCTTT 58.473 39.130 0.00 0.00 46.99 2.52
1807 2586 2.558359 CCATTTCTGGGGTTGACTGTTC 59.442 50.000 0.00 0.00 39.04 3.18
1808 2587 2.176798 TCCATTTCTGGGGTTGACTGTT 59.823 45.455 0.00 0.00 43.34 3.16
1809 2588 1.780309 TCCATTTCTGGGGTTGACTGT 59.220 47.619 0.00 0.00 43.34 3.55
2029 2808 4.453751 TGATGGATGCTGAAATCAATCGA 58.546 39.130 0.00 0.00 39.13 3.59
2085 2865 2.734606 GCGTGCTACTTCACAATGTACA 59.265 45.455 0.00 0.00 36.80 2.90
2088 2868 1.156736 GGCGTGCTACTTCACAATGT 58.843 50.000 0.00 0.00 36.80 2.71
2097 2877 1.541310 TAGGTTGCTGGCGTGCTACT 61.541 55.000 13.84 7.58 38.40 2.57
2099 2879 0.251916 ATTAGGTTGCTGGCGTGCTA 59.748 50.000 4.08 0.00 0.00 3.49
2250 3031 8.466798 CCTGTCTGTTTTTCTTTTCCTTTTCTA 58.533 33.333 0.00 0.00 0.00 2.10
2320 3101 2.006888 ACGTGCTTACCATTCCAATCG 58.993 47.619 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.