Multiple sequence alignment - TraesCS1B01G287600

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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 TraesCS1B01G287600 chr1B 100.000 2417 0 0 1 2417 499826020 499828436 0 4464
1 TraesCS1B01G287600 chrUn 96.328 2424 81 5 1 2417 221549587 221547165 0 3976
2 TraesCS1B01G287600 chrUn 96.246 2424 83 5 1 2417 186192585 186190163 0 3965
3 TraesCS1B01G287600 chr7B 96.000 2425 88 5 1 2417 743004893 743007316 0 3932
4 TraesCS1B01G287600 chr7B 94.261 2422 131 7 1 2417 247459879 247462297 0 3696
5 TraesCS1B01G287600 chr7A 95.704 2421 92 6 1 2417 120879287 120881699 0 3884
6 TraesCS1B01G287600 chr3A 95.468 2427 97 8 1 2417 51914989 51917412 0 3860
7 TraesCS1B01G287600 chr6A 94.513 2424 122 8 1 2417 79142508 79144927 0 3729
8 TraesCS1B01G287600 chr6D 96.110 2288 77 9 1 2279 458963780 458966064 0 3722
9 TraesCS1B01G287600 chr2B 93.155 2425 150 12 1 2417 343521092 343523508 0 3544
10 TraesCS1B01G287600 chr2B 91.162 1437 105 17 1 1419 357246209 357244777 0 1930


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 TraesCS1B01G287600 chr1B 499826020 499828436 2416 False 4464 4464 100.000 1 2417 1 chr1B.!!$F1 2416
1 TraesCS1B01G287600 chrUn 221547165 221549587 2422 True 3976 3976 96.328 1 2417 1 chrUn.!!$R2 2416
2 TraesCS1B01G287600 chrUn 186190163 186192585 2422 True 3965 3965 96.246 1 2417 1 chrUn.!!$R1 2416
3 TraesCS1B01G287600 chr7B 743004893 743007316 2423 False 3932 3932 96.000 1 2417 1 chr7B.!!$F2 2416
4 TraesCS1B01G287600 chr7B 247459879 247462297 2418 False 3696 3696 94.261 1 2417 1 chr7B.!!$F1 2416
5 TraesCS1B01G287600 chr7A 120879287 120881699 2412 False 3884 3884 95.704 1 2417 1 chr7A.!!$F1 2416
6 TraesCS1B01G287600 chr3A 51914989 51917412 2423 False 3860 3860 95.468 1 2417 1 chr3A.!!$F1 2416
7 TraesCS1B01G287600 chr6A 79142508 79144927 2419 False 3729 3729 94.513 1 2417 1 chr6A.!!$F1 2416
8 TraesCS1B01G287600 chr6D 458963780 458966064 2284 False 3722 3722 96.110 1 2279 1 chr6D.!!$F1 2278
9 TraesCS1B01G287600 chr2B 343521092 343523508 2416 False 3544 3544 93.155 1 2417 1 chr2B.!!$F1 2416
10 TraesCS1B01G287600 chr2B 357244777 357246209 1432 True 1930 1930 91.162 1 1419 1 chr2B.!!$R1 1418

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
363 365 0.460987 AGTGCGGCTCAGTCATAAGC 60.461 55.000 0.0 0.0 37.8 3.09 F
570 572 2.070028 GGTTCTTCTCTTCCAGCGTTC 58.930 52.381 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1166 1192 1.068588 CCCGCGGATCTTGATAAGACA 59.931 52.381 30.73 0.0 41.01 3.41 R
2131 2166 1.276140 TAATTGCCCCCGCCAGTACT 61.276 55.000 0.00 0.0 0.00 2.73 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
104 105 1.405821 CATCCTACGCCGTCTCTCTTT 59.594 52.381 0.00 0.0 0.00 2.52
105 106 0.809385 TCCTACGCCGTCTCTCTTTG 59.191 55.000 0.00 0.0 0.00 2.77
122 123 7.244886 TCTCTTTGAGAACCTCACAATCATA 57.755 36.000 0.00 0.0 40.46 2.15
237 238 4.871822 TGATGAGGAGTGAGGTAGATTCA 58.128 43.478 0.00 0.0 0.00 2.57
319 321 0.826715 TGGCTAGTCTCAGGCATGAC 59.173 55.000 0.00 0.0 45.28 3.06
363 365 0.460987 AGTGCGGCTCAGTCATAAGC 60.461 55.000 0.00 0.0 37.80 3.09
398 400 2.629137 TGAAGTAAGTTGTCGGTAGCCA 59.371 45.455 0.00 0.0 0.00 4.75
399 401 3.069872 TGAAGTAAGTTGTCGGTAGCCAA 59.930 43.478 0.00 0.0 0.00 4.52
458 460 8.883302 TCCAGAAATATCATAGAATGGTGATCA 58.117 33.333 0.00 0.0 36.53 2.92
529 531 4.713792 ATCAAGTCACCAAGAAGTTCCT 57.286 40.909 0.00 0.0 0.00 3.36
570 572 2.070028 GGTTCTTCTCTTCCAGCGTTC 58.930 52.381 0.00 0.0 0.00 3.95
580 582 4.637276 TCTTCCAGCGTTCAGTATTCAAA 58.363 39.130 0.00 0.0 0.00 2.69
601 604 2.203938 TTCTCTTCCAGCCCCCGT 60.204 61.111 0.00 0.0 0.00 5.28
842 868 6.551975 GCCTACTTCCTTATTACTCTTCCTCT 59.448 42.308 0.00 0.0 0.00 3.69
1098 1124 2.369860 TCTACCGATCGAGCCCTACTTA 59.630 50.000 18.66 0.0 0.00 2.24
1156 1182 3.876914 TCACGCAACTGATTCTTTCACTT 59.123 39.130 0.00 0.0 0.00 3.16
1166 1192 6.830838 ACTGATTCTTTCACTTTTCTCCAAGT 59.169 34.615 0.00 0.0 37.49 3.16
1181 1207 6.227298 TCTCCAAGTGTCTTATCAAGATCC 57.773 41.667 0.00 0.0 40.18 3.36
1570 1604 8.466617 TCTTCTCTACTAACCACAAGGATATC 57.533 38.462 0.00 0.0 38.69 1.63
1687 1721 5.419788 TCAAATTCTTGGTGGGAATCATCAG 59.580 40.000 0.00 0.0 37.84 2.90
1697 1731 7.068702 TGGTGGGAATCATCAGCTTTATAATT 58.931 34.615 6.59 0.0 30.22 1.40
1851 1886 5.555966 TGTATCATTCTAGTTGTTGCCACA 58.444 37.500 0.00 0.0 0.00 4.17
1856 1891 6.058833 TCATTCTAGTTGTTGCCACAAAGTA 58.941 36.000 4.72 0.0 44.72 2.24
1867 1902 2.421424 GCCACAAAGTATCTTGCTCCTG 59.579 50.000 0.00 0.0 0.00 3.86
2283 2318 8.972127 GGTGTATATTCTCATTCTGCCTAGATA 58.028 37.037 0.00 0.0 31.81 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.264373 ACATTCTTTCCACAACAACTAGAAG 57.736 36.000 0.00 0.0 0.00 2.85
86 87 0.809385 CAAAGAGAGACGGCGTAGGA 59.191 55.000 14.74 0.0 0.00 2.94
104 105 6.014242 AGACACTTATGATTGTGAGGTTCTCA 60.014 38.462 5.51 0.0 38.25 3.27
105 106 6.312426 CAGACACTTATGATTGTGAGGTTCTC 59.688 42.308 5.51 0.0 37.59 2.87
122 123 7.756395 ATTCATCATGAAACTTCAGACACTT 57.244 32.000 3.63 0.0 40.12 3.16
203 204 8.206867 CCTCACTCCTCATCATAACTCAAATAA 58.793 37.037 0.00 0.0 0.00 1.40
237 238 5.499139 TTCTTCGCTTTCTTCAACAATGT 57.501 34.783 0.00 0.0 0.00 2.71
319 321 7.306205 TGCTTTCCAAAAGAAATTGAAACTG 57.694 32.000 3.68 0.0 43.50 3.16
363 365 9.084164 ACAACTTACTTCATGCTATTACTAACG 57.916 33.333 0.00 0.0 0.00 3.18
398 400 8.478775 AGAAGCTTTTCCTTTTACCTAATGTT 57.521 30.769 0.00 0.0 0.00 2.71
399 401 7.724061 TGAGAAGCTTTTCCTTTTACCTAATGT 59.276 33.333 13.97 0.0 0.00 2.71
458 460 2.571653 TGATTCCCGTCAAGGTGATCTT 59.428 45.455 0.00 0.0 38.74 2.40
469 471 1.750193 TGCAAAGGATGATTCCCGTC 58.250 50.000 0.00 0.0 43.76 4.79
529 531 9.856162 AGAACCTTAATACTAAACCAAGTTTCA 57.144 29.630 0.00 0.0 37.01 2.69
570 572 7.414984 GGCTGGAAGAGAAGAATTTGAATACTG 60.415 40.741 0.00 0.0 34.07 2.74
580 582 0.922626 GGGGGCTGGAAGAGAAGAAT 59.077 55.000 0.00 0.0 34.07 2.40
601 604 5.860648 AACTTTCCTTATCAAAGAGGGGA 57.139 39.130 0.00 0.0 35.24 4.81
650 653 1.066573 AGAAGAGCCATCGAACCACAG 60.067 52.381 0.00 0.0 0.00 3.66
652 655 1.646189 GAGAAGAGCCATCGAACCAC 58.354 55.000 0.00 0.0 0.00 4.16
695 698 8.642908 AGGAAACTTAATACAAAAGTGCAAAC 57.357 30.769 0.00 0.0 37.44 2.93
798 809 7.840931 AGTAGGCTCCAAAAGGATTAAAAATG 58.159 34.615 0.00 0.0 0.00 2.32
804 815 4.788617 AGGAAGTAGGCTCCAAAAGGATTA 59.211 41.667 0.00 0.0 0.00 1.75
809 820 7.339482 AGTAATAAGGAAGTAGGCTCCAAAAG 58.661 38.462 0.00 0.0 0.00 2.27
821 847 8.783903 TCTCTAGAGGAAGAGTAATAAGGAAGT 58.216 37.037 19.67 0.0 43.02 3.01
842 868 2.975489 GCTTGGGGATCCTGAATCTCTA 59.025 50.000 12.58 0.0 34.99 2.43
878 904 4.589374 GGCTCAGATAGAAGTTTAGCCCTA 59.411 45.833 0.00 0.0 41.73 3.53
1098 1124 0.388649 AACGAAGCGCTTCATCGACT 60.389 50.000 40.22 22.0 38.06 4.18
1156 1182 7.106239 GGATCTTGATAAGACACTTGGAGAAA 58.894 38.462 0.00 0.0 41.01 2.52
1166 1192 1.068588 CCCGCGGATCTTGATAAGACA 59.931 52.381 30.73 0.0 41.01 3.41
1181 1207 2.419198 CTCCCTCATTCTCCCGCG 59.581 66.667 0.00 0.0 0.00 6.46
1260 1286 2.416107 CTTCCAGGCACCTCCTTGCA 62.416 60.000 0.00 0.0 44.75 4.08
1481 1514 5.600669 AACTTTCCTTATCAAAGAGGGGT 57.399 39.130 0.00 0.0 35.24 4.95
1523 1557 4.776349 AGCCATCGTACCATATTTGTCAA 58.224 39.130 0.00 0.0 0.00 3.18
1537 1571 3.633065 GGTTAGTAGAGAAGAGCCATCGT 59.367 47.826 0.00 0.0 0.00 3.73
1570 1604 4.541779 CGAAGATGAAATAGAGAGTCCCG 58.458 47.826 0.00 0.0 0.00 5.14
1697 1731 7.954788 AAAAAGCATGAGCCGTTATTAAAAA 57.045 28.000 0.00 0.0 43.56 1.94
1851 1886 5.810095 AGCTTAACAGGAGCAAGATACTTT 58.190 37.500 0.00 0.0 42.56 2.66
1856 1891 3.871485 CTGAGCTTAACAGGAGCAAGAT 58.129 45.455 0.00 0.0 42.56 2.40
1867 1902 5.808030 CACTTCTACTAAGGCTGAGCTTAAC 59.192 44.000 3.72 0.0 0.00 2.01
2093 2128 8.974060 AAAAGTAGGAATGTTGTCACTAGAAA 57.026 30.769 0.00 0.0 0.00 2.52
2131 2166 1.276140 TAATTGCCCCCGCCAGTACT 61.276 55.000 0.00 0.0 0.00 2.73
2302 2337 5.049954 CGGTTTTCTTGAAAAGGTCGATACA 60.050 40.000 8.57 0.0 46.24 2.29


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

AutoCloner maintained by Alex Coulton.