Multiple sequence alignment - TraesCS3B01G033600

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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 TraesCS3B01G033600 chr3B 100.000 2264 0 0 1 2264 16124437 16122174 0.000000e+00 4181
1 TraesCS3B01G033600 chr2B 97.572 2265 49 3 1 2264 563917141 563914882 0.000000e+00 3873
2 TraesCS3B01G033600 chr2B 89.139 488 45 7 1768 2248 798602683 798603169 3.220000e-168 601
3 TraesCS3B01G033600 chr2B 88.548 489 44 9 1767 2248 154583805 154583322 1.170000e-162 582
4 TraesCS3B01G033600 chr5B 97.923 2167 40 3 1 2166 464634105 464636267 0.000000e+00 3747
5 TraesCS3B01G033600 chr5B 94.079 2280 88 14 1 2264 530940832 530938584 0.000000e+00 3419
6 TraesCS3B01G033600 chr4A 94.190 2289 103 13 1 2264 712877477 712879760 0.000000e+00 3463
7 TraesCS3B01G033600 chr4A 86.364 176 11 5 1700 1875 664928786 664928624 1.790000e-41 180
8 TraesCS3B01G033600 chr7B 94.118 2278 92 10 1 2264 235458095 235455846 0.000000e+00 3426
9 TraesCS3B01G033600 chr7B 96.646 1968 41 10 1 1967 687040621 687042564 0.000000e+00 3245
10 TraesCS3B01G033600 chr4B 97.713 1968 44 1 1 1967 402787204 402785237 0.000000e+00 3384
11 TraesCS3B01G033600 chr4B 96.294 1781 56 5 1 1780 576450751 576452522 0.000000e+00 2915
12 TraesCS3B01G033600 chr1B 96.394 1969 45 5 1 1967 38183390 38185334 0.000000e+00 3219
13 TraesCS3B01G033600 chr1B 88.095 504 52 6 1768 2264 649299583 649299081 1.940000e-165 592
14 TraesCS3B01G033600 chr5A 88.911 505 46 9 1768 2264 591475463 591475965 4.130000e-172 614
15 TraesCS3B01G033600 chrUn 87.500 504 55 6 1768 2264 361056132 361055630 1.950000e-160 575
16 TraesCS3B01G033600 chr7A 87.500 504 55 6 1768 2264 497717793 497717291 1.950000e-160 575


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 TraesCS3B01G033600 chr3B 16122174 16124437 2263 True 4181 4181 100.000 1 2264 1 chr3B.!!$R1 2263
1 TraesCS3B01G033600 chr2B 563914882 563917141 2259 True 3873 3873 97.572 1 2264 1 chr2B.!!$R2 2263
2 TraesCS3B01G033600 chr5B 464634105 464636267 2162 False 3747 3747 97.923 1 2166 1 chr5B.!!$F1 2165
3 TraesCS3B01G033600 chr5B 530938584 530940832 2248 True 3419 3419 94.079 1 2264 1 chr5B.!!$R1 2263
4 TraesCS3B01G033600 chr4A 712877477 712879760 2283 False 3463 3463 94.190 1 2264 1 chr4A.!!$F1 2263
5 TraesCS3B01G033600 chr7B 235455846 235458095 2249 True 3426 3426 94.118 1 2264 1 chr7B.!!$R1 2263
6 TraesCS3B01G033600 chr7B 687040621 687042564 1943 False 3245 3245 96.646 1 1967 1 chr7B.!!$F1 1966
7 TraesCS3B01G033600 chr4B 402785237 402787204 1967 True 3384 3384 97.713 1 1967 1 chr4B.!!$R1 1966
8 TraesCS3B01G033600 chr4B 576450751 576452522 1771 False 2915 2915 96.294 1 1780 1 chr4B.!!$F1 1779
9 TraesCS3B01G033600 chr1B 38183390 38185334 1944 False 3219 3219 96.394 1 1967 1 chr1B.!!$F1 1966
10 TraesCS3B01G033600 chr1B 649299081 649299583 502 True 592 592 88.095 1768 2264 1 chr1B.!!$R1 496
11 TraesCS3B01G033600 chr5A 591475463 591475965 502 False 614 614 88.911 1768 2264 1 chr5A.!!$F1 496
12 TraesCS3B01G033600 chrUn 361055630 361056132 502 True 575 575 87.500 1768 2264 1 chrUn.!!$R1 496
13 TraesCS3B01G033600 chr7A 497717291 497717793 502 True 575 575 87.500 1768 2264 1 chr7A.!!$R1 496

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
250 251 0.252696 AGTGGCCTGAGTACCATGGA 60.253 55.000 21.47 0.0 38.46 3.41 F
576 578 1.340405 GGTAGTGGTGGTCGTAGAGGA 60.340 57.143 0.00 0.0 36.95 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1220 1222 0.036765 TGCGTTAGTTGGCCTTCGAT 60.037 50.0 3.32 0.0 0.00 3.59 R
1605 1607 0.900182 GGGCCACTTTCCCTTCTTGG 60.900 60.0 4.39 0.0 40.66 3.61 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
89 90 5.716979 AGAGGCCTAGTAAGTATCATTGGA 58.283 41.667 4.42 0.00 0.00 3.53
108 109 3.884693 TGGACATGCTCGCATTTGATAAT 59.115 39.130 0.85 0.00 33.90 1.28
111 112 3.633525 ACATGCTCGCATTTGATAATGGT 59.366 39.130 0.85 0.00 41.21 3.55
153 154 2.815478 TGTTTGTGATGGAAAAACCGC 58.185 42.857 0.00 0.00 42.61 5.68
250 251 0.252696 AGTGGCCTGAGTACCATGGA 60.253 55.000 21.47 0.00 38.46 3.41
261 262 6.441924 CCTGAGTACCATGGACCTCATATTAT 59.558 42.308 26.97 3.96 33.77 1.28
293 294 2.287977 TCTGAAGGTGGAGACGAAGA 57.712 50.000 0.00 0.00 0.00 2.87
371 372 3.323115 TGGCATGAAACAATTTGGTAGCA 59.677 39.130 0.00 0.00 0.00 3.49
576 578 1.340405 GGTAGTGGTGGTCGTAGAGGA 60.340 57.143 0.00 0.00 36.95 3.71
867 869 2.294979 GGATCGGCCTTCGGTTATTTT 58.705 47.619 0.00 0.00 39.77 1.82
869 871 1.741528 TCGGCCTTCGGTTATTTTCC 58.258 50.000 0.00 0.00 39.77 3.13
1056 1058 1.685224 GGACCAAGAGGACATGCCA 59.315 57.895 8.58 0.00 40.02 4.92
1220 1222 3.054508 TGTCCCAACTATGCACATGATCA 60.055 43.478 0.00 0.00 0.00 2.92
1254 1256 2.543777 ACGCATATGACATACCACCC 57.456 50.000 6.97 0.00 0.00 4.61
1421 1423 3.259064 CAACATCGAGATTGGTTACGGT 58.741 45.455 3.97 0.00 0.00 4.83
1944 2008 1.360393 AACACCAGGTCCACACCCAT 61.360 55.000 0.00 0.00 45.12 4.00
2114 2179 2.581354 GCGCAGGAGACCAGACAT 59.419 61.111 0.30 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 3.633525 ACCATTATCAAATGCGAGCATGT 59.366 39.130 11.64 2.73 41.06 3.21
108 109 3.171828 TTTCTCGCCTTCGCCACCA 62.172 57.895 0.00 0.00 35.26 4.17
111 112 0.248012 TATGTTTCTCGCCTTCGCCA 59.752 50.000 0.00 0.00 35.26 5.69
153 154 1.091771 ATGGAACTCTTGCATCCGCG 61.092 55.000 0.00 0.00 37.06 6.46
250 251 3.584848 GAGGGTCTGGCATAATATGAGGT 59.415 47.826 4.14 0.00 0.00 3.85
261 262 0.979665 CTTCAGAAGAGGGTCTGGCA 59.020 55.000 3.82 0.00 44.40 4.92
293 294 6.553857 TGAACCTCTTAGTTCTCCTTCTACT 58.446 40.000 6.04 0.00 45.25 2.57
576 578 1.879796 GCACCTCTAGCACTTGTGCTT 60.880 52.381 29.37 15.68 46.56 3.91
867 869 7.878621 ATTAGATCAACCATCTGGATTAGGA 57.121 36.000 2.55 0.00 42.37 2.94
1056 1058 1.299976 GGCCTCCATCCACGTCTTT 59.700 57.895 0.00 0.00 0.00 2.52
1220 1222 0.036765 TGCGTTAGTTGGCCTTCGAT 60.037 50.000 3.32 0.00 0.00 3.59
1404 1406 1.472728 GCCACCGTAACCAATCTCGAT 60.473 52.381 0.00 0.00 0.00 3.59
1605 1607 0.900182 GGGCCACTTTCCCTTCTTGG 60.900 60.000 4.39 0.00 40.66 3.61
1626 1628 8.478877 CCTTTCCATTTGTCTACTGAGTAGTAT 58.521 37.037 18.33 6.52 38.65 2.12
2114 2179 1.751351 GATCAGACACATCAGACGGGA 59.249 52.381 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.