Multiple sequence alignment - TraesCS1B01G385800

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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 TraesCS1B01G385800 chr1B 100.000 2465 0 0 1 2465 619196408 619193944 0 4553
1 TraesCS1B01G385800 chr3B 98.095 2467 41 4 1 2465 92297808 92295346 0 4290
2 TraesCS1B01G385800 chr3B 97.890 2465 50 2 1 2465 6011842 6009380 0 4263
3 TraesCS1B01G385800 chr3A 98.093 2465 46 1 1 2465 495105836 495103373 0 4290
4 TraesCS1B01G385800 chr2B 98.012 2465 48 1 1 2465 234542236 234539773 0 4279
5 TraesCS1B01G385800 chrUn 97.890 2465 50 2 1 2465 217906592 217909054 0 4263
6 TraesCS1B01G385800 chr4A 97.809 2465 53 1 1 2465 67518422 67520885 0 4252
7 TraesCS1B01G385800 chr7A 97.769 2465 54 1 1 2465 563523174 563520711 0 4246
8 TraesCS1B01G385800 chr6D 97.567 2466 57 2 1 2465 108484132 108486595 0 4218


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 TraesCS1B01G385800 chr1B 619193944 619196408 2464 True 4553 4553 100.000 1 2465 1 chr1B.!!$R1 2464
1 TraesCS1B01G385800 chr3B 92295346 92297808 2462 True 4290 4290 98.095 1 2465 1 chr3B.!!$R2 2464
2 TraesCS1B01G385800 chr3B 6009380 6011842 2462 True 4263 4263 97.890 1 2465 1 chr3B.!!$R1 2464
3 TraesCS1B01G385800 chr3A 495103373 495105836 2463 True 4290 4290 98.093 1 2465 1 chr3A.!!$R1 2464
4 TraesCS1B01G385800 chr2B 234539773 234542236 2463 True 4279 4279 98.012 1 2465 1 chr2B.!!$R1 2464
5 TraesCS1B01G385800 chrUn 217906592 217909054 2462 False 4263 4263 97.890 1 2465 1 chrUn.!!$F1 2464
6 TraesCS1B01G385800 chr4A 67518422 67520885 2463 False 4252 4252 97.809 1 2465 1 chr4A.!!$F1 2464
7 TraesCS1B01G385800 chr7A 563520711 563523174 2463 True 4246 4246 97.769 1 2465 1 chr7A.!!$R1 2464
8 TraesCS1B01G385800 chr6D 108484132 108486595 2463 False 4218 4218 97.567 1 2465 1 chr6D.!!$F1 2464

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
616 618 0.612453 GGCCCGGAAATACAACCCAA 60.612 55.0 0.73 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 2060 1.427895 GGGAGGGATAGGGGGAAAGC 61.428 65.0 0.0 0.0 0.0 3.51 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
77 78 2.042464 TGCCGAGAGATAGGAGCATTT 58.958 47.619 0.00 0.00 0.00 2.32
195 196 2.232298 GAACGGAGAGTGGGCAGAGG 62.232 65.000 0.00 0.00 0.00 3.69
255 256 1.000993 AGTGCGGGAGACTGGAGAT 59.999 57.895 0.00 0.00 37.94 2.75
273 274 3.442076 AGATTGGGTCGAGTAAACTCCT 58.558 45.455 4.58 0.00 39.79 3.69
279 280 3.513119 GGGTCGAGTAAACTCCTTTAGGT 59.487 47.826 4.58 0.00 39.79 3.08
526 527 3.972950 AACAGGTCGAGATAGATGACG 57.027 47.619 0.00 0.00 33.45 4.35
616 618 0.612453 GGCCCGGAAATACAACCCAA 60.612 55.000 0.73 0.00 0.00 4.12
668 670 1.301322 GCGGGATCCAGAGCTAAGC 60.301 63.158 16.86 2.85 0.00 3.09
782 784 2.426738 CTCATATTCAAAAGGCGCCCAA 59.573 45.455 26.15 8.90 0.00 4.12
923 925 4.934001 CAGAGAGCACTTGTGTATGTGATT 59.066 41.667 2.61 0.00 34.77 2.57
967 969 5.705902 AGCTGTCGTAAAGTTTTGTTGTTT 58.294 33.333 0.00 0.00 0.00 2.83
980 982 1.130749 TGTTGTTTGTTCCGTCGTTGG 59.869 47.619 0.00 0.00 0.00 3.77
1143 1145 6.758416 CACTTGCTTCAACTACTCATGCTATA 59.242 38.462 0.00 0.00 0.00 1.31
1186 1188 1.499007 TCCTTTGGGCTTTTGAGGAGT 59.501 47.619 0.00 0.00 32.91 3.85
1243 1247 2.056223 GCCAGGATGCATGCCAGTT 61.056 57.895 16.68 0.00 31.97 3.16
1244 1248 1.610554 GCCAGGATGCATGCCAGTTT 61.611 55.000 16.68 0.00 31.97 2.66
1580 1584 0.033504 GTGAAGCCTTGGAGACGACA 59.966 55.000 0.00 0.00 0.00 4.35
2056 2060 7.614192 ACCCTATTTATATGATTTTTAGGGCCG 59.386 37.037 11.18 0.00 45.49 6.13
2089 2093 4.363546 TCCCTCCCTTATGTTTAGGAGT 57.636 45.455 4.34 0.00 43.73 3.85
2130 2134 1.298667 GTGGTGGTACGGAAGGCAT 59.701 57.895 0.00 0.00 0.00 4.40
2246 2250 2.203337 TTCCTTGCTGTTGCGGCT 60.203 55.556 0.00 0.00 43.34 5.52
2299 2303 6.297582 CAGATCATAAGGAAAGATGCCTCTT 58.702 40.000 0.00 0.00 43.71 2.85
2440 2446 0.468029 AAAGTGAAGTGGTGGGCCTG 60.468 55.000 4.53 0.00 35.27 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.215014 TATGCTTCGGATGCTTCGCG 61.215 55.000 15.69 0.0 0.00 5.87
77 78 0.393820 GTAGTTCACCGGTTCCACCA 59.606 55.000 2.97 0.0 38.47 4.17
255 256 4.020839 CCTAAAGGAGTTTACTCGACCCAA 60.021 45.833 3.96 0.0 43.76 4.12
273 274 5.808540 CGTCTGTGATTTAATCGGACCTAAA 59.191 40.000 14.61 0.0 0.00 1.85
279 280 3.697542 TCCTCGTCTGTGATTTAATCGGA 59.302 43.478 0.23 0.0 0.00 4.55
358 359 5.662456 GCCTCTTCGAAGTATTTACCTCTT 58.338 41.667 23.85 0.0 0.00 2.85
526 527 3.969553 AGGAAGAGGATAAAAAGGTGCC 58.030 45.455 0.00 0.0 0.00 5.01
609 611 0.187361 TCAGAAAGGGGGTTGGGTTG 59.813 55.000 0.00 0.0 0.00 3.77
616 618 2.287584 TGAATGGATCAGAAAGGGGGT 58.712 47.619 0.00 0.0 33.04 4.95
923 925 4.492895 GCTTTTTCGTACACGTTCACTTGA 60.493 41.667 1.19 0.0 40.80 3.02
960 962 1.130749 CCAACGACGGAACAAACAACA 59.869 47.619 0.00 0.0 0.00 3.33
967 969 1.546589 ATAGGGCCAACGACGGAACA 61.547 55.000 6.18 0.0 0.00 3.18
980 982 5.411781 CCATCGTAGAAACATAGATAGGGC 58.588 45.833 0.00 0.0 43.58 5.19
1143 1145 2.706339 GAGTTGATGCTCCCACATCT 57.294 50.000 6.13 0.0 45.51 2.90
1186 1188 7.181361 TCATAGAATTCCAACAATTTCTCCCA 58.819 34.615 0.65 0.0 0.00 4.37
1243 1247 1.548719 CACTCCACCAGGTCGTATGAA 59.451 52.381 0.00 0.0 35.89 2.57
1244 1248 1.182667 CACTCCACCAGGTCGTATGA 58.817 55.000 0.00 0.0 35.89 2.15
2007 2011 6.262273 GGTTGTAGAAAGACCAGTTTCATTCA 59.738 38.462 0.00 0.0 38.66 2.57
2056 2060 1.427895 GGGAGGGATAGGGGGAAAGC 61.428 65.000 0.00 0.0 0.00 3.51
2299 2303 2.689471 CGAATCATTCTCAAATGCCCCA 59.311 45.455 0.00 0.0 41.76 4.96
2307 2311 2.672961 ACGGCTCGAATCATTCTCAA 57.327 45.000 0.00 0.0 0.00 3.02


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

AutoCloner maintained by Alex Coulton.