Multiple sequence alignment - TraesCS4A01G175300

Loading Multiple Alignment...

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 TraesCS4A01G175300 chr4A 100.000 3567 0 0 1 3567 446472546 446476112 0 6588
1 TraesCS4A01G175300 chr4A 98.430 3567 49 2 1 3567 537233890 537230331 0 6270
2 TraesCS4A01G175300 chr4A 98.023 3540 63 4 34 3567 152579841 152583379 0 6143
3 TraesCS4A01G175300 chr2B 98.517 3573 45 5 1 3567 39425839 39429409 0 6298
4 TraesCS4A01G175300 chr3B 98.237 3573 54 6 1 3567 85118157 85114588 0 6240
5 TraesCS4A01G175300 chr7A 98.184 3580 49 7 3 3567 105263516 105259938 0 6237
6 TraesCS4A01G175300 chr6B 97.982 3568 58 6 1 3567 663847347 663850901 0 6178
7 TraesCS4A01G175300 chr2A 97.816 3571 49 5 1 3567 69201673 69198128 0 6135
8 TraesCS4A01G175300 chr2A 97.489 3584 62 6 2 3567 738201096 738197523 0 6095
9 TraesCS4A01G175300 chr1A 98.404 3446 48 6 1 3440 58179341 58182785 0 6052
10 TraesCS4A01G175300 chr7B 98.181 3189 57 1 34 3222 147534475 147537662 0 5566


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 TraesCS4A01G175300 chr4A 446472546 446476112 3566 False 6588 6588 100.000 1 3567 1 chr4A.!!$F2 3566
1 TraesCS4A01G175300 chr4A 537230331 537233890 3559 True 6270 6270 98.430 1 3567 1 chr4A.!!$R1 3566
2 TraesCS4A01G175300 chr4A 152579841 152583379 3538 False 6143 6143 98.023 34 3567 1 chr4A.!!$F1 3533
3 TraesCS4A01G175300 chr2B 39425839 39429409 3570 False 6298 6298 98.517 1 3567 1 chr2B.!!$F1 3566
4 TraesCS4A01G175300 chr3B 85114588 85118157 3569 True 6240 6240 98.237 1 3567 1 chr3B.!!$R1 3566
5 TraesCS4A01G175300 chr7A 105259938 105263516 3578 True 6237 6237 98.184 3 3567 1 chr7A.!!$R1 3564
6 TraesCS4A01G175300 chr6B 663847347 663850901 3554 False 6178 6178 97.982 1 3567 1 chr6B.!!$F1 3566
7 TraesCS4A01G175300 chr2A 69198128 69201673 3545 True 6135 6135 97.816 1 3567 1 chr2A.!!$R1 3566
8 TraesCS4A01G175300 chr2A 738197523 738201096 3573 True 6095 6095 97.489 2 3567 1 chr2A.!!$R2 3565
9 TraesCS4A01G175300 chr1A 58179341 58182785 3444 False 6052 6052 98.404 1 3440 1 chr1A.!!$F1 3439
10 TraesCS4A01G175300 chr7B 147534475 147537662 3187 False 5566 5566 98.181 34 3222 1 chr7B.!!$F1 3188

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
127 128 1.411612 GATTCGGTATCACGGGGTCTT 59.588 52.381 0.0 0.0 33.21 3.01 F
133 134 1.553704 GTATCACGGGGTCTTTGGTCT 59.446 52.381 0.0 0.0 0.00 3.85 F
704 714 2.383527 GGGTTCAGCGACTCTTGCG 61.384 63.158 0.0 0.0 37.44 4.85 F
2160 2171 1.550130 GGGGGACGATGTGAGTTCCA 61.550 60.000 0.0 0.0 39.04 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 1462 1.202580 CCGTTGCCTTCTCCTATCCAG 60.203 57.143 0.0 0.0 0.00 3.86 R
2086 2097 1.834263 ACCTAGAGGCAGATGGTTCAC 59.166 52.381 0.0 0.0 39.32 3.18 R
2280 2291 3.531934 TGTCATCATCAAGCTCATCGT 57.468 42.857 0.0 0.0 0.00 3.73 R
3418 3475 0.546267 AGAGGCTTGGAGGAAGAGCA 60.546 55.000 0.0 0.0 38.14 4.26 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
127 128 1.411612 GATTCGGTATCACGGGGTCTT 59.588 52.381 0.00 0.00 33.21 3.01
133 134 1.553704 GTATCACGGGGTCTTTGGTCT 59.446 52.381 0.00 0.00 0.00 3.85
539 549 4.243008 TTTGCGACGTGCCCTCCA 62.243 61.111 0.00 0.00 45.60 3.86
704 714 2.383527 GGGTTCAGCGACTCTTGCG 61.384 63.158 0.00 0.00 37.44 4.85
811 821 9.844790 CATTGTTTTTCTTTCATATGTAGCTGA 57.155 29.630 1.90 0.00 0.00 4.26
879 889 8.198109 GGTAATCTGCTTCTACTTTCTGTATGA 58.802 37.037 0.00 0.00 0.00 2.15
990 1000 3.684413 CGTGGGCTTACAAGTGGGATATT 60.684 47.826 0.00 0.00 0.00 1.28
2056 2067 4.667519 AGAAGTTAAGGCGGTTATCGAT 57.332 40.909 2.16 2.16 42.43 3.59
2086 2097 2.549064 TGCCGTGATCCTGAATATGG 57.451 50.000 0.00 0.00 0.00 2.74
2160 2171 1.550130 GGGGGACGATGTGAGTTCCA 61.550 60.000 0.00 0.00 39.04 3.53
2280 2291 6.315144 CCATATTGTTTCGTTGTGTGATAGGA 59.685 38.462 0.00 0.00 0.00 2.94
2391 2402 2.356135 GCCCAACGACTATGACAACAT 58.644 47.619 0.00 0.00 40.16 2.71
2453 2464 0.755079 CTTGGATGATGAGGCGGAGA 59.245 55.000 0.00 0.00 0.00 3.71
2634 2687 7.985476 ACTTGTGAGGTTATGTTATATGTTGC 58.015 34.615 0.00 0.00 0.00 4.17
2653 2706 5.163447 TGTTGCTGAACTCTTACTAGTGTGT 60.163 40.000 5.39 0.00 32.79 3.72
2785 2838 7.437267 GTGAACTCTTACTAGTGCAGTTTACAA 59.563 37.037 21.16 2.60 35.63 2.41
2900 2957 0.532862 GCTGCACTGTACTGTGTGGT 60.533 55.000 27.27 1.64 39.89 4.16
3048 3105 4.633175 TGCAGCATCACAACAATTTGAAT 58.367 34.783 2.79 0.00 36.48 2.57
3049 3106 5.780984 TGCAGCATCACAACAATTTGAATA 58.219 33.333 2.79 0.00 36.48 1.75
3418 3475 2.091610 TCCATCCTCTCCTTCTGACGAT 60.092 50.000 0.00 0.00 0.00 3.73
3449 3506 2.484264 CCAAGCCTCTTCGAAACGATTT 59.516 45.455 0.00 0.00 35.23 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 4.521338 TCGTAAGGCATGGCAAGACCAA 62.521 50.000 22.64 3.42 46.91 3.67
133 134 1.667236 CTCATCGTAAGGCATGGCAA 58.333 50.000 22.64 6.11 38.47 4.52
337 338 1.721664 CCCGTCGATAGCAAGACCGA 61.722 60.000 0.00 0.00 34.10 4.69
539 549 4.135306 GGATCACATCATCAGTTGCATCT 58.865 43.478 0.00 0.00 0.00 2.90
704 714 4.479619 CAACTACCTGTCGGTACAAGTAC 58.520 47.826 1.77 1.77 43.29 2.73
879 889 4.400961 GGCAGACGCTCCCAGCTT 62.401 66.667 0.00 0.00 39.60 3.74
990 1000 1.267533 TCGTTCGTCATCTCGGAAACA 59.732 47.619 0.00 0.00 0.00 2.83
1452 1462 1.202580 CCGTTGCCTTCTCCTATCCAG 60.203 57.143 0.00 0.00 0.00 3.86
1738 1748 3.350219 AGTTAATCACCGGAACAGCAT 57.650 42.857 9.46 0.00 0.00 3.79
2086 2097 1.834263 ACCTAGAGGCAGATGGTTCAC 59.166 52.381 0.00 0.00 39.32 3.18
2160 2171 7.128418 ACCCTCATCATCCATATAAGCATATGT 59.872 37.037 4.29 0.00 41.68 2.29
2280 2291 3.531934 TGTCATCATCAAGCTCATCGT 57.468 42.857 0.00 0.00 0.00 3.73
2634 2687 9.477484 ACAAATAACACACTAGTAAGAGTTCAG 57.523 33.333 0.00 0.00 0.00 3.02
2653 2706 4.902443 TCAGGTTCGCAAACACAAATAA 57.098 36.364 0.00 0.00 37.10 1.40
2785 2838 7.864379 GCAGCAGCACTCACATAATAAAAATAT 59.136 33.333 0.00 0.00 41.58 1.28
2830 2887 5.920273 GCTATAAGCAAAACTGCAGAAACAA 59.080 36.000 23.35 0.00 41.89 2.83
3048 3105 8.505625 ACTCGTCGGCTTAAAATTTATGTTTTA 58.494 29.630 0.00 0.00 33.62 1.52
3049 3106 7.364970 ACTCGTCGGCTTAAAATTTATGTTTT 58.635 30.769 0.00 0.00 35.60 2.43
3104 3161 1.218875 TGTGTCGTGAACCATGTCGC 61.219 55.000 0.00 0.00 0.00 5.19
3418 3475 0.546267 AGAGGCTTGGAGGAAGAGCA 60.546 55.000 0.00 0.00 38.14 4.26


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

AutoCloner maintained by Alex Coulton.