Multiple sequence alignment - TraesCS5B01G327900

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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 TraesCS5B01G327900 chr5B 100.000 2295 0 0 1 2295 511449597 511451891 0 4239
1 TraesCS5B01G327900 chr5B 96.167 2296 87 1 1 2295 538727047 538729342 0 3751
2 TraesCS5B01G327900 chr5B 95.470 2296 96 3 1 2295 427657201 427654913 0 3657
3 TraesCS5B01G327900 chr2B 95.862 2296 94 1 1 2295 215482696 215484991 0 3712
4 TraesCS5B01G327900 chr2B 95.468 2295 100 3 4 2295 152572079 152574372 0 3659
5 TraesCS5B01G327900 chr2B 94.707 2267 119 1 30 2295 2478750 2476484 0 3520
6 TraesCS5B01G327900 chr1B 95.399 2304 97 4 1 2295 331365114 331367417 0 3659
7 TraesCS5B01G327900 chr4B 95.035 2296 112 2 1 2295 68858487 68860781 0 3607
8 TraesCS5B01G327900 chr6B 94.993 2297 111 4 1 2295 624871095 624873389 0 3602
9 TraesCS5B01G327900 chr3B 94.599 2296 118 2 1 2295 786565130 786562840 0 3548


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 TraesCS5B01G327900 chr5B 511449597 511451891 2294 False 4239 4239 100.000 1 2295 1 chr5B.!!$F1 2294
1 TraesCS5B01G327900 chr5B 538727047 538729342 2295 False 3751 3751 96.167 1 2295 1 chr5B.!!$F2 2294
2 TraesCS5B01G327900 chr5B 427654913 427657201 2288 True 3657 3657 95.470 1 2295 1 chr5B.!!$R1 2294
3 TraesCS5B01G327900 chr2B 215482696 215484991 2295 False 3712 3712 95.862 1 2295 1 chr2B.!!$F2 2294
4 TraesCS5B01G327900 chr2B 152572079 152574372 2293 False 3659 3659 95.468 4 2295 1 chr2B.!!$F1 2291
5 TraesCS5B01G327900 chr2B 2476484 2478750 2266 True 3520 3520 94.707 30 2295 1 chr2B.!!$R1 2265
6 TraesCS5B01G327900 chr1B 331365114 331367417 2303 False 3659 3659 95.399 1 2295 1 chr1B.!!$F1 2294
7 TraesCS5B01G327900 chr4B 68858487 68860781 2294 False 3607 3607 95.035 1 2295 1 chr4B.!!$F1 2294
8 TraesCS5B01G327900 chr6B 624871095 624873389 2294 False 3602 3602 94.993 1 2295 1 chr6B.!!$F1 2294
9 TraesCS5B01G327900 chr3B 786562840 786565130 2290 True 3548 3548 94.599 1 2295 1 chr3B.!!$R1 2294

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
811 824 0.623324 TGGTTGCTAGTAGCCCCCAT 60.623 55.0 20.36 0.0 41.51 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2241 2256 2.317609 GCGCTTGTCGGAGAAAGCA 61.318 57.895 19.62 0.0 44.6 3.91 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
93 94 4.712337 TCCCTCAAGGTAATCTTCTCTGAC 59.288 45.833 0.00 0.00 36.75 3.51
104 105 2.639839 TCTTCTCTGACCCCCTTCTTTG 59.360 50.000 0.00 0.00 0.00 2.77
129 135 8.694540 TGGATCCAAGTAATGTTATCAAATTGG 58.305 33.333 13.46 0.00 37.80 3.16
226 232 7.953005 TGTTTGCCATTTTCCTATGATTAGA 57.047 32.000 0.00 0.00 0.00 2.10
301 307 3.267812 GGTTAGGTTTAGGGCTAGGGTTT 59.732 47.826 0.00 0.00 0.00 3.27
598 611 6.165742 TGGATGGACCCTAGTGATATCATA 57.834 41.667 9.02 2.19 38.00 2.15
599 612 5.958380 TGGATGGACCCTAGTGATATCATAC 59.042 44.000 9.02 0.00 38.00 2.39
646 659 1.902938 TTGGAATGCACATCCGTTGA 58.097 45.000 14.00 0.00 39.98 3.18
718 731 2.420129 GGTGGCCGAATCACTAGACAAT 60.420 50.000 0.00 0.00 35.61 2.71
810 823 0.842905 TTGGTTGCTAGTAGCCCCCA 60.843 55.000 20.36 20.36 41.51 4.96
811 824 0.623324 TGGTTGCTAGTAGCCCCCAT 60.623 55.000 20.36 0.00 41.51 4.00
832 846 5.163581 CCATCCTTGAAGCGAGATGAAATTT 60.164 40.000 10.29 0.00 0.00 1.82
861 875 4.455606 CTCTTTTGACCCAAGAAGTGAGT 58.544 43.478 0.00 0.00 29.74 3.41
913 927 1.242076 TGAAGCTTTGCAAGAGGAGC 58.758 50.000 12.02 12.02 35.42 4.70
981 995 3.273434 CAATGTGGGTGATCTCGACAAT 58.727 45.455 8.06 0.00 0.00 2.71
990 1004 7.441157 GTGGGTGATCTCGACAATTATCATTTA 59.559 37.037 0.00 0.00 31.49 1.40
1258 1273 3.610911 GGAGATGACAAGAACCGGATTT 58.389 45.455 9.46 0.00 0.00 2.17
1293 1308 9.496873 TCTAAGTTCGAAACATTCTTGGAATTA 57.503 29.630 0.00 0.00 0.00 1.40
1356 1371 1.003355 CAAGGTGGTGCACTCGGAT 60.003 57.895 17.98 0.00 34.40 4.18
1424 1439 1.209898 CGTGGATTGTGCGTGCAAT 59.790 52.632 0.00 6.34 41.28 3.56
1568 1583 1.731720 GCTTACAGGCTCTCCAACTG 58.268 55.000 0.00 0.00 38.19 3.16
1592 1607 6.891361 TGAATATCCACACTTCCAACAATGAT 59.109 34.615 0.00 0.00 0.00 2.45
1609 1624 5.163723 ACAATGATCGTCCAACATGTCATTC 60.164 40.000 0.00 0.00 34.96 2.67
1710 1725 1.972588 ATGGTACTTGGGAGGAAGCT 58.027 50.000 0.00 0.00 0.00 3.74
1737 1752 2.747446 CCGAATCCCTAGGTTGTTGTTG 59.253 50.000 8.29 0.00 0.00 3.33
1775 1790 2.894919 GGGCATGGTTCATGTGGC 59.105 61.111 9.28 0.00 43.10 5.01
1977 1992 3.258123 GTGATGCCAATAACCTGGTGTTT 59.742 43.478 0.00 0.00 38.86 2.83
1990 2005 3.496515 CCTGGTGTTTCCATTGGCATTTT 60.497 43.478 0.00 0.00 46.12 1.82
2093 2108 5.530915 GGGAAATTTGTGTCATATCGGATCA 59.469 40.000 0.00 0.00 0.00 2.92
2142 2157 2.440065 GACATTCCCGGGCATGCA 60.440 61.111 30.20 3.48 0.00 3.96
2241 2256 6.093219 CCGATGATCTTCAAGATTGTTGTCTT 59.907 38.462 0.16 0.00 34.53 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 1.359130 ACTTGGATCCAAAGAAGGGGG 59.641 52.381 26.87 15.25 35.33 5.40
104 105 8.695456 ACCAATTTGATAACATTACTTGGATCC 58.305 33.333 4.20 4.20 36.31 3.36
129 135 5.146010 TCCCCAAAATAGCAACAAATGAC 57.854 39.130 0.00 0.00 0.00 3.06
301 307 4.817286 ACCATAACCCTAACCAAAACCAA 58.183 39.130 0.00 0.00 0.00 3.67
503 516 5.012239 ACTATCAAACACCATGTCAAGCAT 58.988 37.500 0.00 0.00 38.60 3.79
504 517 4.397420 ACTATCAAACACCATGTCAAGCA 58.603 39.130 0.00 0.00 0.00 3.91
551 564 9.546428 CCAATTCAAATCTTTCCTAACTTGTTT 57.454 29.630 0.00 0.00 0.00 2.83
598 611 1.668826 TATGCCTTCCCTCCAACTGT 58.331 50.000 0.00 0.00 0.00 3.55
599 612 2.806945 TTATGCCTTCCCTCCAACTG 57.193 50.000 0.00 0.00 0.00 3.16
718 731 3.812609 TCGTTGCAAATAACTCAAGAGCA 59.187 39.130 0.00 0.00 0.00 4.26
810 823 6.521151 AAAATTTCATCTCGCTTCAAGGAT 57.479 33.333 0.00 0.00 0.00 3.24
811 824 5.964958 AAAATTTCATCTCGCTTCAAGGA 57.035 34.783 0.00 0.00 0.00 3.36
832 846 4.605183 TCTTGGGTCAAAAGAGGTTCAAA 58.395 39.130 0.00 0.00 0.00 2.69
861 875 3.772387 TGTAAATGGGCTCAATGTTGGA 58.228 40.909 0.00 0.00 0.00 3.53
913 927 4.385146 GTCATCGTCTGCATACTCATCATG 59.615 45.833 0.40 0.00 0.00 3.07
927 941 5.728471 AGATCAACTTCATTGTCATCGTCT 58.272 37.500 0.00 0.00 39.54 4.18
981 995 8.106462 TGGTCCATTGTCTCTTGTAAATGATAA 58.894 33.333 0.00 0.00 32.86 1.75
990 1004 3.690460 GGAATGGTCCATTGTCTCTTGT 58.310 45.455 22.12 0.00 44.26 3.16
1258 1273 5.430007 TGTTTCGAACTTAGACCCTTTTGA 58.570 37.500 0.00 0.00 0.00 2.69
1293 1308 2.550830 AGTTGTCGAGCCACATCTTT 57.449 45.000 0.00 0.00 0.00 2.52
1424 1439 1.203505 TGGGACCTCCTTTCCATGGTA 60.204 52.381 12.58 0.00 34.45 3.25
1568 1583 6.757897 TCATTGTTGGAAGTGTGGATATTC 57.242 37.500 0.00 0.00 0.00 1.75
1592 1607 2.038426 AGGTGAATGACATGTTGGACGA 59.962 45.455 0.00 0.00 0.00 4.20
1665 1680 3.056607 ACATCTTAAATGCGGCTTGCTTT 60.057 39.130 0.00 0.00 46.63 3.51
1977 1992 4.102210 TCAACCAAAGAAAATGCCAATGGA 59.898 37.500 2.05 0.00 0.00 3.41
1990 2005 2.507886 TGTTCTCCACCTCAACCAAAGA 59.492 45.455 0.00 0.00 0.00 2.52
2061 2076 3.149196 GACACAAATTTCCCTCTGAGCA 58.851 45.455 0.00 0.00 0.00 4.26
2093 2108 4.809426 CCGCGTTAAGAATACCTTGATTCT 59.191 41.667 4.92 0.00 46.02 2.40
2142 2157 3.752796 CCATCGATGGTGTAACGGT 57.247 52.632 32.39 0.00 43.05 4.83
2168 2183 7.040409 CCCTATAGAAGTTTGAACAAAAGTGCT 60.040 37.037 0.00 0.32 39.91 4.40
2241 2256 2.317609 GCGCTTGTCGGAGAAAGCA 61.318 57.895 19.62 0.00 44.60 3.91


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

AutoCloner maintained by Alex Coulton.