Multiple sequence alignment - TraesCS5B01G476600

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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 TraesCS5B01G476600 chr5B 100.000 2720 0 0 1 2720 648997821 649000540 0 5024
1 TraesCS5B01G476600 chr5A 94.201 2742 111 19 1 2700 644103766 644106501 0 4139
2 TraesCS5B01G476600 chr5D 93.509 2773 105 22 1 2720 516638775 516641525 0 4054


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 TraesCS5B01G476600 chr5B 648997821 649000540 2719 False 5024 5024 100.000 1 2720 1 chr5B.!!$F1 2719
1 TraesCS5B01G476600 chr5A 644103766 644106501 2735 False 4139 4139 94.201 1 2700 1 chr5A.!!$F1 2699
2 TraesCS5B01G476600 chr5D 516638775 516641525 2750 False 4054 4054 93.509 1 2720 1 chr5D.!!$F1 2719

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
134 135 1.077501 GTATCCTTGCTGGCAGCCA 60.078 57.895 34.58 24.31 41.51 4.75 F
749 765 1.279271 GCTACTGAGGCTCCAAAGGAA 59.721 52.381 12.86 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 1117 0.462047 GGCGAGTGTTACCATGGAGG 60.462 60.0 21.47 0.0 45.67 4.30 R
2634 2701 0.039437 TCGTTCGCCTGAAGACTGAC 60.039 55.0 0.00 0.0 33.98 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
33 34 6.550843 CAGTTGACAATATGGCGTAAATTCA 58.449 36.000 0.00 0.00 0.00 2.57
134 135 1.077501 GTATCCTTGCTGGCAGCCA 60.078 57.895 34.58 24.31 41.51 4.75
298 301 7.807680 ACATCGATTTTCTCTTTTGTTAGACC 58.192 34.615 0.00 0.00 0.00 3.85
405 410 4.442706 TCGATCTCTTGCCAAAGGAATAC 58.557 43.478 0.00 0.00 33.90 1.89
601 607 4.624015 ACGTAAAGCAGTTGTTAGCACTA 58.376 39.130 0.00 0.00 0.00 2.74
605 611 4.884668 AAGCAGTTGTTAGCACTACCTA 57.115 40.909 0.00 0.00 29.60 3.08
649 665 4.001652 TGTGGCCAAAATTAACATGCATG 58.998 39.130 25.09 25.09 0.00 4.06
685 701 6.461640 TCTCTATGCATGATCATTGTAGGTG 58.538 40.000 10.16 0.00 0.00 4.00
692 708 6.153170 TGCATGATCATTGTAGGTGTCATTTT 59.847 34.615 5.16 0.00 0.00 1.82
709 725 5.532779 GTCATTTTGGGCTCCTCCTTATTAG 59.467 44.000 0.00 0.00 34.39 1.73
749 765 1.279271 GCTACTGAGGCTCCAAAGGAA 59.721 52.381 12.86 0.00 0.00 3.36
793 809 3.903530 AGAATGGAGGTTTGGTCCTTT 57.096 42.857 0.00 0.00 38.02 3.11
902 918 5.622233 GCTTTGGCAAAGTATACAAAGGGAG 60.622 44.000 33.45 10.91 45.95 4.30
1132 1148 4.810191 AACACTCGCCTCTCTAATTTCT 57.190 40.909 0.00 0.00 0.00 2.52
1141 1157 5.066634 CGCCTCTCTAATTTCTCACTAGACA 59.933 44.000 0.00 0.00 0.00 3.41
1245 1261 2.304470 TGTCAAGCCAGCCAACATACTA 59.696 45.455 0.00 0.00 0.00 1.82
1281 1297 5.151297 ACATGCCAAAAATCTCGGATTTT 57.849 34.783 14.87 14.87 33.12 1.82
1371 1387 0.107081 ACCCGATGTTCCGTGAAACA 59.893 50.000 0.00 0.00 42.92 2.83
1471 1487 5.349817 GTGTATGATGGAAATCATAGGCTCG 59.650 44.000 8.34 0.00 42.30 5.03
1587 1603 0.322277 AGATTGGCAGACTGGCTGTG 60.322 55.000 27.23 0.00 46.62 3.66
1848 1874 3.751175 GTGCCATAAAGTCTGTTGCAGTA 59.249 43.478 0.00 0.00 32.61 2.74
1864 1890 9.760660 CTGTTGCAGTAAATAGTTATCAAACTC 57.239 33.333 0.00 0.00 42.42 3.01
1867 1893 8.840833 TGCAGTAAATAGTTATCAAACTCACA 57.159 30.769 0.00 0.00 42.42 3.58
1917 1943 6.961554 CCTTGTTCTTCGAAGTGTTAATATGC 59.038 38.462 23.85 1.23 0.00 3.14
1960 1987 2.169144 ACATTGAGATCGACATCTGCCA 59.831 45.455 0.00 0.00 39.71 4.92
1996 2023 5.864628 AATTCCTAGAGTTTTCTTGACGC 57.135 39.130 0.00 0.00 34.79 5.19
1999 2026 2.737252 CCTAGAGTTTTCTTGACGCCAC 59.263 50.000 0.00 0.00 34.79 5.01
2235 2287 7.041167 GCTGATGTTGGTGCTACAATATATCAA 60.041 37.037 3.90 0.00 33.19 2.57
2315 2372 7.334421 TGGAGACTACTGAATGCTAAAATGAAC 59.666 37.037 0.00 0.00 0.00 3.18
2629 2696 5.473846 TCTGAAGATCGACTGTAGAAGTGTT 59.526 40.000 0.00 0.00 40.07 3.32
2634 2701 7.022055 AGATCGACTGTAGAAGTGTTGATAG 57.978 40.000 0.00 0.00 40.07 2.08
2700 2769 5.008613 CAGCATCTCTCCAGTACTTCTACTC 59.991 48.000 0.00 0.00 30.03 2.59
2702 2771 5.238650 GCATCTCTCCAGTACTTCTACTCTC 59.761 48.000 0.00 0.00 30.03 3.20
2703 2772 5.013568 TCTCTCCAGTACTTCTACTCTCG 57.986 47.826 0.00 0.00 30.03 4.04
2714 2783 0.875040 CTACTCTCGCTCGACGGCTA 60.875 60.000 0.00 0.00 43.89 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.954318 GCCATATTGTCAACTGCTCCAT 59.046 45.455 0.00 0.00 0.00 3.41
33 34 4.367386 GTGTACACCACTAGTTATCGCT 57.633 45.455 15.42 0.00 41.11 4.93
127 128 1.789078 CGCACATATTCCTGGCTGCC 61.789 60.000 12.87 12.87 0.00 4.85
134 135 2.967362 TCGTTGTTCGCACATATTCCT 58.033 42.857 0.00 0.00 39.67 3.36
139 140 2.442212 TCCTTCGTTGTTCGCACATA 57.558 45.000 0.00 0.00 39.67 2.29
278 279 7.230712 TCCCTTGGTCTAACAAAAGAGAAAATC 59.769 37.037 0.00 0.00 0.00 2.17
279 280 7.066781 TCCCTTGGTCTAACAAAAGAGAAAAT 58.933 34.615 0.00 0.00 0.00 1.82
291 292 5.294552 CGAATGAAATCTCCCTTGGTCTAAC 59.705 44.000 0.00 0.00 0.00 2.34
293 294 4.469945 ACGAATGAAATCTCCCTTGGTCTA 59.530 41.667 0.00 0.00 0.00 2.59
294 295 3.264450 ACGAATGAAATCTCCCTTGGTCT 59.736 43.478 0.00 0.00 0.00 3.85
295 296 3.375299 CACGAATGAAATCTCCCTTGGTC 59.625 47.826 0.00 0.00 0.00 4.02
298 301 2.098117 GCCACGAATGAAATCTCCCTTG 59.902 50.000 0.00 0.00 0.00 3.61
336 339 6.043938 AGTCCCTTATTCCAGTTAGACACAAA 59.956 38.462 0.00 0.00 0.00 2.83
343 346 9.681062 TGAAAATAAGTCCCTTATTCCAGTTAG 57.319 33.333 9.09 0.00 43.27 2.34
453 459 6.252036 GCATTCGCAATGAAACTATTGAAG 57.748 37.500 11.52 0.00 41.46 3.02
479 485 6.313658 TGGTATATATGTGAATTGCGCATCTC 59.686 38.462 12.75 11.84 44.07 2.75
486 492 9.184062 CAAATGTGTGGTATATATGTGAATTGC 57.816 33.333 0.00 0.00 0.00 3.56
601 607 6.900194 ACATAGCAATACAAAGTGGATAGGT 58.100 36.000 0.00 0.00 0.00 3.08
605 611 7.315142 CACAAACATAGCAATACAAAGTGGAT 58.685 34.615 0.00 0.00 0.00 3.41
685 701 2.222227 AAGGAGGAGCCCAAAATGAC 57.778 50.000 0.00 0.00 37.37 3.06
692 708 3.460825 ACAACTAATAAGGAGGAGCCCA 58.539 45.455 0.00 0.00 37.37 5.36
709 725 2.409879 GCGTCGAAAGTAGAGCAACAAC 60.410 50.000 0.00 0.00 0.00 3.32
1101 1117 0.462047 GGCGAGTGTTACCATGGAGG 60.462 60.000 21.47 0.00 45.67 4.30
1132 1148 1.834188 TCCAGTCGCATGTCTAGTGA 58.166 50.000 0.00 0.00 0.00 3.41
1141 1157 3.884693 TCAATTGCAATATCCAGTCGCAT 59.115 39.130 13.39 0.00 31.67 4.73
1245 1261 9.729281 ATTTTTGGCATGTTCTTTTCATCTAAT 57.271 25.926 0.00 0.00 0.00 1.73
1281 1297 4.610605 TGTAAGAAACTTCGATGTCCCA 57.389 40.909 4.21 0.00 0.00 4.37
1371 1387 6.174720 TCACTCTTCTGTGTTAATTGTCCT 57.825 37.500 0.00 0.00 38.90 3.85
1471 1487 9.979270 CTGATAAACATCACAGAAATCAACTAC 57.021 33.333 0.00 0.00 32.90 2.73
1848 1874 8.893727 GCTACCATGTGAGTTTGATAACTATTT 58.106 33.333 0.00 0.00 44.51 1.40
1864 1890 2.622942 ACACCAACAAAGCTACCATGTG 59.377 45.455 0.00 0.00 0.00 3.21
1867 1893 6.542370 GTGATATACACCAACAAAGCTACCAT 59.458 38.462 0.00 0.00 43.05 3.55
1996 2023 6.387041 TCTAAGGTACTGAATATCACGTGG 57.613 41.667 17.00 0.00 40.86 4.94
1999 2026 7.039644 AGGGATTCTAAGGTACTGAATATCACG 60.040 40.741 0.00 0.00 40.86 4.35
2235 2287 5.909621 AGCAGCACATGTTATTTGATTCT 57.090 34.783 0.00 0.00 0.00 2.40
2315 2372 8.996651 AGGATGACCCTTAATTTATTGTTAGG 57.003 34.615 0.00 0.00 44.85 2.69
2341 2398 5.947663 TGAAACTTCCCCAGTTGAGAATAA 58.052 37.500 0.00 0.00 45.77 1.40
2351 2408 5.789643 TTCAATTTCTGAAACTTCCCCAG 57.210 39.130 4.73 0.00 41.21 4.45
2629 2696 2.723273 TCGCCTGAAGACTGACTATCA 58.277 47.619 0.00 0.00 0.00 2.15
2634 2701 0.039437 TCGTTCGCCTGAAGACTGAC 60.039 55.000 0.00 0.00 33.98 3.51
2678 2747 5.130350 AGAGTAGAAGTACTGGAGAGATGC 58.870 45.833 0.00 0.00 39.78 3.91
2680 2749 5.607477 CGAGAGTAGAAGTACTGGAGAGAT 58.393 45.833 0.00 0.00 39.78 2.75
2700 2769 0.658829 CATCTTAGCCGTCGAGCGAG 60.659 60.000 8.63 3.60 44.77 5.03
2702 2771 3.909312 CATCTTAGCCGTCGAGCG 58.091 61.111 0.00 0.00 38.01 5.03


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

AutoCloner maintained by Alex Coulton.